SCHOOL OF BIO AND CHEMICAL ENGINEERING

DEPARTMENT OF BIOTECHNOLOGY

UNIT – I – MICROBIAL ECOLOGY – SMB2101

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 UNIT:1

MICROBIAL HABITATS

Microbial ecology or environmental microbiology is

the ecology of microorganisms: their relationship with one another and with
their environment. It concerns the three major domains of life—
Eukaryota, Archaea, and Bacteria—as well as viruses.

Microbial Habitats

• Microbes are present in every kind of habitat.

• Microbes are incredibly diverse thriving in environments from the very

cold to the extremely hot.

• They are also tolerant of many other conditions such as limited water
availability, high salt content and low oxygen levels.

• Not every microbe can survive in all habitats.

Terrestrial Microbial Habitats: Microbes lives in/on soil.

• Only one percent of microbes that live in soil have been identified.

• These organisms take part in the formation of soil and are essential
components of their ecosystems.

• Bacteria and fungi that live in soil feed mostly on organic matter such as
other plants and animals.

• These microbes are very sensitive to their local environment.

• Factors such as the levels of carbon dioxide, oxygen, pH, moisture and
temperature all affect the growth of microbes in the soil.

Microbial Habitats in Other Organisms

• Microbes also live on other organisms.

• As with the ones found on people these microbes can be harmful or

beneficial to the host.

Example:
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 • Bacteria grow in nodules on the roots of pea and bean plants.

• These microbes convert nitrogen from the air into a form that the plants
can use.

• In many ways animals and plants have evolved as habitats for the
millions of microbes that call them home.

Extreme Microbial Environments

• The microbes living in extreme conditions are called extremophiles.

• This literally means that they love the extreme conditions of their habitat.

• The extremophiles are so well adapted to their own environment.

• Some like the ones in hot springs need extreme temperatures to grow.

ROLE OF MICROBES IN BIOGEOCHEMICAL CYCLE

Nutrients move through the ecosystem in biogeochemical cycles.

• A biogeochemical cycle is a pathway by which a chemical element (such

as carbon or nitrogen) circulates through the biotic (living) and the abiotic
(non-living) factors of an ecosystem.

• The elements that move through the factors of an ecosystem are not lost
but are instead recycled or accumulated in places called reservoirs (or
“sinks”) where they can be held for a long period of time.

• Elements, chemical compounds, and other forms of matter are passed

from one organism to another and from one part of the biosphere to
another through these biogeochemical cycles.

• Microorganisms play a primary role in regulating biogeochemical

systems in virtually all of our planet’s environments. This includes
extreme environments such as acid lakes and hydrothermal vents, and
even includes living systems such as the human gut.

• The key collective metabolic processes of microbes (including nitrogen

fixation, carbon fixation, methane metabolism, and sulfur metabolism)
effectively control global biogeochemical cycling.

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 • Incredibly, production by microbes is so immense that global
biogeochemistry would likely not change even if eukaryotic life were
totally absent!

• Microbes comprise the backbone of every ecological system, particularly

those in which there is no light (i.e. systems in which energy cannot be
collected through photosynthesis )

MICROBIAL SUCESSION

• Ecological succession is the process of change in the species structure of

an ecological community over time. The time scale can be decades (for
example, after a wildfire), or even millions of years after a mass
extinction

• Succession of micro-organisms including fungi and bacteria occurring

within a microhabitat is known as microsuccession or serule.

• Like in plants, microbial succession can occur in newly available habitats

(primary succession) such as surfaces of plant leaves, recently exposed
rock surfaces (i.e., glacial till) or animal infant guts,

• Growth on disturbed communities (secondary succession) like those

growing in recently dead trees or animal droppings.

• Microbial communities may also change due to products secreted by the

bacteria present. Changes of pH in a habitat could provide ideal
conditions for a new species to inhabit the area.

Membrane biofouling in waste water reactor: An example for microbial

succession

• In Phase I (0–2 days), small sludge flocs in the bulk liquid were
selectively attached on membrane surfaces, leading to the formation of
similar extracellular polymeric substances (EPS) and microbial
community composition as the early biofilms.

• Dominant populations in small flocs, e.g., Nitrosomonas, Nitrobacter,

and Acinetobacter spp., were also the major initial colonizers on
membranes.

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 • In Phase II (2–4 d), fouling layer structure, EPS composition, and
bacterial community went through significant changes. Initial colonizers
were replaced by fast-growing and metabolically
versatile heterotrophs (e.g., unclassified Sphingobacteria).

• The declining EPS polysaccharide to protein (PS:PN) ratios could be

correlated well with the increase in microbial community diversity.

• In Phase III (5–14 d), heterotrophs comprised over 90% of the

community, whereas biofilm structure and EPS composition remained
relatively stable.

• The overall microbial succession pattern from autotrophic colonization to

heterotrophic domination implied that MBR biofouling

• In some cases the new species may outcompete the present ones for
nutrients leading to the primary species demise. Changes can also occur
by microbial succession with variations in water availability and
temperature.

SOIL MICROFLORA

• Microflora means, bacteria and microscopic algae and fungi, living in a

particular site or habitat.

• 1 g of soil contain

• 100,000,000 bacterial cells

• 11,000 species of bacteria

• Also fungi and larger animals

Types of Microbes in Soil

• Prokaryotic Bacteria, Actinomycetes

• Fungi

• Algae

• Protozoa

• Viruses

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BACTERIA

• Tiny 1µm width, one celled

• Single cell division

• 1can produce 5 billion in 12 hours in lab

• (in environment limited by predators, water and food availability)

• Abundant in rhizosphere

• Zone surrounding root –dead root cells and exudate stimulate microbial
growth

MAIN TYPES OF SOIL BACTERIA

• Agarobacterium, Alcaligenes

• igenes, Bacillus

• Arthrobacter, Cellulomonas

Corynebacterium

• Caulobacter, Micrococcus

• Clostridum, Pseudomonas

• Flavobacterium, Achromobacter

• Methanobacterium

• Chromobacterium

• Agarobacterium, Alcaligenes

• igenes, Bacillus

• Arthrobacter, Cellulomonas

Corynebacterium

• Caulobacter, Micrococcus

• Clostridum, Pseudomonas

• Flavobacterium, Achromobacter

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 • Methanobacterium

• Chromobacterium

SOIL BACTERIA-ROLE IN SOIL

• Degrade organic matter

• Fix N2-and other steps of N cycle

• Rhizobium-nitrogen fixation

• Nitrification-Nitrosomonas, Nitrobacter

• Organisms involved with vital functions may be in lower aboundance

• Organisms present will depend on many factors-Nutrients, O2, Moisture,

pH.

SOIL ACTIOMYCETES

• Degrade organic matter

• Fix N2-and other steps of N cycle

• Rhizobium-nitrogen fixation

• Nitrification-Nitrosomonas, Nitrobacter

• Organisms involved with vital functions may be in lower aboundance

• Organisms present will depend on many factors-Nutrients, O2, Moisture,

pH.

• Actinomycetes are slow growing compared to bacteria and fungi

• Streptomyces may be up to 65% of soil population

• Nocardia and Micromonospora upto 35% of population

• Other common genera

• Streptosporangium

• Actinoplanes

• Thermoactinomyces

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• Thermomonospora

• Role of Actinomycetes in soil1. Organic matter decomposition

• Starch, cellulose, hemicellulose, lignin, humus

2. Antibiotic production

• Streptomycin, tetracycline, chloramphenicol

• 3. Maintain Microbial equillibrium in soil

• Control pathogenic organisms

• Produce proteases lyse cells of pathogens

• Fungi Grow as long threads (hyphe)

• Push through soil particles, roots, rocks

• Often group into masses called mycelium (look like roots)

• Higher fungi have basidium: club shaped structure

• Bearing fruiting body

PREDOMINANT FUNGI IN SOILFUNGI IMPERFECTI: MOST

PREDOMINANT GROUP IN SOIL

• Cephalosporium

• Verticillium

• Monilia

• Trichoderma

• Fusarium

• Cladosporium

• Gliocladium

• Role of fungi in soil Organic matter degradation: Degrade starch,

hemicellulose, cellulose, lignin,

• Ammonification: degrade proteins, nucleicacids and release NH3

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• Control of other organisms: some fungi kill nematodes

• Pathogenicity: Many fungi associated with plant disease-ythium,

Sclerotinia, Puccinia

• Formation of mycorrhizae, symbiotic relationship with plant root.

• AlgaeFilamentous, colonial, unicellular

• Photsynthetic

• Most in blue –green group, but also yellow-green, diatoms, green algae

• Form carbonic acid (weathering)

• Add OM(Organic matter) to soil, bind particles

• Aeration

• Some fix nitrogen

• Algal groups in soilChlorophyaceae-Green algae

• Cyabophyaceae-Bluegreen algae

• Bacillariophyaceae: Diatoms

• Xanthophyaceae-Yellow green algae

• Importance of algae in soilProvide organic matter

• Many algae produce polysaccharides, improve soil structure

• Produce oxygen, provide oxygen to rice plants

• Fix nitrogen and provide to rice plants after decomptosition

STRATIFICATION OF FRESHWATER

• Freshwater are areas which having low salt concentration approximately

less than 1%, and organisms that can not survive in other regions that
have high salt concentration such as sea and oceans.

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 Types

1. Ponds and lakes

2. Streams and rivers

• Freshwater are areas which having low salt concentration approximately

less than 1%, and organisms that cannot survive in other regions that have
high salt concentration such as sea and oceans.

• Few square meters to thousands of square kilometers.

• Many ponds are seasonal, lasting for a few months, while lakes may
exist for hundreds of years.

• Ponds and lakes may have limited species diversity, except ponds and
lakes that connected to other water sources such as river and ocean.

Lakes and ponds are divided into three different zones according to their
depth and distance from the shoreline

1- littoral zone

near of the shore either lakes or

ponds, also it is the warmest zone

because of high absorbance to the sun’s heat.

 it’s contain several species of

algae (like diatoms), rooted and

floating aquatic plants, grazing

snails, clams, insects, crustaceans, and fishes.

 only the egg and larvae stages are found in this zone.

 The vegetation and animals living in the littoral zone are food for other
creatures such as turtles, snakes, and ducks.

 2- limnetic zone

 the near surface after littoral zone, well lighted, and has a large amount
of phytoplankton and zooplankton.

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3- profundal zone

This zone is much colder, also there is a Little light penetrates into this zone.

 zone’s organisms are heterotrophs, , meaning that they eat dead

organisms and use oxygen for cellular respiration.

 For example, dead plankton that fall down from limnetic zone.

 During the summer,

the temperature can range from 4° C near the bottom to 22° C at the top.

 During the winter,

the temperature at the bottom can be 4° C while the top is 0° C (ice).

 In between the two layers, there is a narrow zone called the

thermocline where the temperature of the water changes rapidly.

 During the spring and fall seasons,

there is a mixing of the top and bottom layers, usually due to winds, which
results in a uniform water temperature of around 4° C and 10 °C.

 This mixing also circulates oxygen throughout the lake or ponds.

 new study showed that ,Microorganisms were more active at low

temperatures, low dissolved oxygen concentrations and high TN/TP
ratios.

 During stratification, the metalimnion (which is a layer of thermal

stratification) was observed from 2 to 10 m in spring and then dropped
to 16 m to 21 m in summer, and then appeared between 24 and 26 m
depths in fall.

 Also, during stratification, temperature, and pH were significantly higher

in the epilimnion and rapidly dropping down in the hypolimnion.

 The nutrient concentrations were stable in the water column, except for
total phosphorus.

 Specifically, the TN/TP mass ratio was significantly lower in

epilimnion

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 STREAMS AND RIVER

These are bodies of flowing water moving in one direction.

 they get their starts at headwaters, which may be springs, snowmelt or

even lakes, and then travel all the way to their mouths .e.g. ocean.

 The temperature is cooler at the source than it is at the mouth.

 the water has high oxygen levels, and freshwater fish such as trout
and heterotrophs can be found there

 The middle part of the stream/river, the width increases, as does

species diversity, also numerous aquatic green plants and algae can be
found.

 The mouth of the river/stream, the water becomes murky from all the
sediments that it has picked up upstream, decreasing the amount of light
that can penetrate through the water.

 Because of the lower oxygen levels in mouth, fish that require less
oxygen, such as catfish and carp, can be found. However, Since there is
less light, there is less diversity of flora.

• Microbial Flora in Fresh water

1. Neuston layer is the collective term for the organisms that float on the
top of water or live right under the surface.

• Uppermost layer / surface microlayer of the hydrosphere

• Is the interface between the atmosphere and the hydrosphere

• An extreme environment

• Many adverse factors (i.e. exposure to radiation, temperature

fluctuations) can occur

• Insoluble and less dense organic material accumulates in this layer and as
a result, is aligned with non-polar organic materials

• Therefore, is a thin gel-like structure where microbes can live

• is the collective term for the organisms that float on the top of water or
live right under the surface.

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 • Uppermost layer / surface microlayer of the hydrosphere

• Is the interface between the atmosphere and the hydrosphere

• An extreme environment

• Many adverse factors (i.e. exposure to radiation, temperature

fluctuations) can occur

• Insoluble and less dense organic material accumulates in this layer and as
a result, is aligned with non-polar organic materials

• Therefore, is a thin gel-like structure where microbes can live

Fresh water microbial communities

Depending on composition, organization and functioning as communities,

fresh water microbial communities can be divided as follows;

• Planktonic community

• Sediment community

• Microbial mats

• Biofilms

Planktonic community

• Organisms that have little or no control over where they go – Plankton

• Plankton are not essentially needed to be microscopic. But mostly, they

are..

• Fish are not plankton, they are nekton.

• Plankton can be;

• Plant-type : Phytoplankton

• Bacteria type: Bacterio-plankton

• Animal type: Zooplankton

• Zoo plankton can be divided in to;

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 Permanent zoo plankton Temporary zoo plankton

(Example: Barnacle larvae: nauplii)

• Temporary zoo plankton are rare in fresh water ecosystems

• Phytoplankton and Primary production

Are producers and base of many food webs

• Are very productive

• The principle component is the diatom, a form of single celled alga

• These diatoms have diurnal rhythm in a water column

• And can quickly reproduce and are highly productive

Phytoplanktonic primary production

• Many phytoplankton are single-celled algae.

• Fix dissolved carbon dioxide and produce various organic compounds

• Primary production is dependent upon;

• Availability of essential nutrients

• Water temperature

• pH of the water

• Organic matter produced can be divided as;

• Particulate Organic Matter (POM)

• Dissolved Organic Matter (DOM)

Diatoms

• Principle component of phytoplankton community

• A form of single-celled algae with an outer wall made out of silica

• Have a diurnal rhythm in water columns

• At nights, sink to lower levels

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 • At day moves to upper levels to obtain solar energy

Detritus

• All dead organic matter distinguishable from living matter

• POM is about 10%, DOM is about 90%

• Includes bodies and body fragments of dead organisms as well as excreta

and fecal material

Microbial Mats

• Together with biofilms, are defined as surface associated layers of

microbial cells embedded in Extracellular Polymeric Substances (EPS)

• Microbial mats are, multi-layered sheets of microorganisms that are

mainly formed by bacteria and archaea

Habitats??

• Mainly grow on submerged or moist surfaces

• Few can survive in deserts

• Few are endosymbionts

• Can colonize environments at -40 to 120 Celsius

• Usually held together by slimy Matrix substances created by inhabitant

microbes

• Some inhabitants form tangled web of filaments which makes the mat

tougher

• Mats are usually vertically stratified. Aerobic zone on the top is separated
from bottom anaerobic zone by a layer of oxidized iron

• Mats can grow to few cm of thickness at most. But still, creates a several
layers of different internal chemical environments

• Each layer is composed of microorganisms of the same or closely related

species that can tolerate or feed on dominant chemicals at their level

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• In each layer, dominant microbes are decided upon their comparative
advantage

or the ability o out perform other microbes to live and survive in that
layer

• It is dependent upon their metabolic capabilities and conditions

they can tolerate

• As metabolic capabilities decided by the phylogeny, several closely

related microbes can inhabit the same layer

• However, ecological relationship between microorganisms within the

same mat is a combination of both competition and cooperation.

• Hence, different layers are divided based on their individual metabolic

contribution to the microbial community within and also by their
phylogenetic relationships.

• A microbial mat generally forms its’ own food chain where;

• By-products of one group serve as ‘food’ for another group of

microbes within the mat

• One or two groups may remain on top of the food chain as their by-
products are not

utilized by others

Biofilms

• An aggregate of microbes in which cells that are frequently embedded

within a self-produced matrix of EPS, adhere to each other and/or to a
surface.

• Biofilm EPS is a polymeric conglomeration and may contain;

• Extracellular DNA

• Polysaccharides

• proteins

Habitats;

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 • Found commonly on submerged solid substrates or substrates
exposed to an aqueous solution.

• On mats floating on liquid surfaces

• On surfaces of leaves in high humidity

• A biofilm may contain many different types of microbes each of which

perform specialized metabolic function within the mat

• Some species are capable of forming single-species biofilms under

certain

conditions

• Social structure within a particular biofilm (i.e. interactions within

organisms present such as competition and cooperation) is highly
dependent on types of organisms present

• However, microbial cells growing in a biofilm are physiologically distinct

from planktonic cells of the same organism

• A biofilm may grow very quickly, from microscopic to macroscopic

when sufficient resources are available

Life cycle of a biofilm

• Biofilm lifecycle can be summarized in to three important steps;

1. Attachment

2. Growth and development

3. Detachment

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Step 1: Attachment

• Initial attachment of a free floating microbe to a surface is reversible

• Occur using weak Van Der Waal bonds

• Secondly it attaches more permanently using;

• Cell adhesion structures like pili

• Cell adhesion molecules such as extracellular proteins

• Hydrophobicity

• When considered, hydrophobicity is the most important of the above

three

• Initial attachment of a free floating microbe to a surface is reversible

• Occur using weak Van Der Waal bonds

• Secondly it attaches more permanently using;

• Cell adhesion structures like pili

• Cell adhesion molecules such as extracellular proteins

• Hydrophobicity

• When considered, hydrophobicity is the most important of the above

three

• Hydrophobicity determines the ability of microbes to form biofilms

• Increased hydrophobicity means less repulsion between the EPS

matrix and the bacterium

• Bacteria pioneers who initially attaches to the surface starts building the
EPS matrix that holds the biofilm together

• In addition to matrix substances and bacterial cells, EPS matrix

may also contain materials from environment such as minerals,
soil particles etc.

• This facilitate the arrival of other biofilm bacteria by providing more

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adhesion sites

• If there are species that are unable to attach to a surface on their

own, they are often able to anchor the matrix directly to earlier
colonists

• When a single bacterium joins a biofilm,

• Expression of approximately 800 genes have reported to be altered

and differentially regulated

• As a result, cell undergoes a phenotypic shift in behavior

• This impart different physiological characteristics to the joined

bacterium than its planktonic members

• During colonization cells within the biofilm are able to communicate via
Quorum Sensing

Step 2: Growth and Development

• Growth of a biofilm occurs through a combination of

• Division of existing cells

• Recruitment of new cells

• The next sub-step; is the development of the biofilm.

• At the development state;

• Biofilm gets well established

• May only change in size and shape

• Once the biofilm has fully formed,

• It contains channels in which nutrients and also, signaling molecules

involved in Quorum sensing can circulate.

• Cells in different regions exhibit different patterns of gene expression

• As a result of above, biofilms often develop their own metabolism

• Once the biofilm has fully formed,

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 • It contains channels in which nutrients and also, signaling molecules
involved in Quorum sensing can circulate.

• Cells in different regions exhibit different patterns of gene expression

• As a result of above, biofilms often develop their own metabolism

OCEAN ZONES

• The four major zones are :

• Intertidal Zone

• Neritic Zone

• Oceanic Zone

• Benthic Zone

Intertidal ZoneIntertidal Zone

Intertidal Zone

• Area between high tide line and low tide line

• Organisms adapted to harsh, changing environments

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• intertidal area (also called the littoral zone) is where the land and sea
meet, between the high and low tide zones. This complex marine
ecosystem is found along coastlines worldwide. It is rich in nutrients and
oxygen and is home to a

Neritic Zone

• Area over the continental shelf

• Area of greatest density and diversity of marine life

• Neritic Zone is located above the contiental shelf which extends along
the coastline of the major land masses of the world

• Producers

Primary producers are organisms that convert inorganic carbon in carbon

dioxide into organic carbon by autotrophs. There are two types of primary
producers. They are phytoplankton, or autotrophic producers, and
zooplankton, or heterotrophic producers.

• Consumers

The main pelagic consumers that live along the continental shelf include
herring, mackerel, Bluefin Tuna, capelin, and some smaller species which
feed on zooplankton and smaller fish. Sea Birds also feed on the fish
within the Neritic Zone because it is close to shore.

Oceanic Zones

Epipelagic Zone

• Photic Zone or Sunlight Zone, Enough sunlight for photosynthesis.

Primary area of food production. From surface down to about 200
meters

Mesopelagic Zone

• Disphotic Zone or Twilight Zone. From about 200 m down to 1,000 m

• Animals that live in the disphotic zone, like many types of squid, are
adapted to life in near darkness, cold water, and high pressure.

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 Bathypelagic Zone

• Aphotic zone or Midnight Zone. Animals that thrive in the aphotic zone
are used to living without light!

• No sunlight

• From 1,000 m down to 4,000 m

• Low density and diversity of marine life

Abyssopelagic Zone

• Aphotic Zone or Midnight Zone

• No sunlight

• From 4,000 m down to 6,000 m

• Low density and diversity of marine life

Hadopelagic Zone

• Aphotic Zone or Midnight Zone

• No sunlight

• From 6,000 m down to ocean floor, or around 11,000 m

• Low density and diversity of marine life

Benthic Zone

The benthic zone is home to many different creatures and dead

organisms. This zone begins at the end of the intertidal zone through the
dark abyss of the deep ocean. In the Benthic Zone there are few different
types of environments.

• 2 Basic Types:

• Sessile - Live attached to the bottom

• Vagrant - Able to move about

• Sessile:

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 • Barnacles

• Sponges

• Corals

• Sea Anemones

• Oysters

• Clams

• Marine microbial diversity

• In the marine environment, 90% of bacteria are Gram-negative with

different characteristics

• and the Gram-negative cell wall is better adapted

• for survival in the marine environment.

• Three domains of Bacterial life exist: Archaea, Bacteria and Eucarya.

• Archaea includes unusual microorganisms which grow under extreme

environments and differs from Bacteria due to lack of peptidoglycan.

• Both these domains collectively play a significant role in the marine

environment.

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•
ROLE OF BACTERIA IN THE MARINE ENVIRONMENT:

The marine environment is characterized by parameters such as high

pressure, salinity, low, temperature, absence of light, etc.

Marine heterotrophic bacteria have adapted themselves to survive in this

environment:

 They require Na+ for growth because it is essential to maintain the

osmotic environment for protection of cellular integrity.

 Oligotrophy is also one more adaptation because of the small amount of

available nutrient.

 Heterotrophic bacterial action promotes organic degradation,

decomposition and mineralization processes in sediments and in the
overlying water, and releases dissolved organic and inorganic substances.

 By mineralization of organic matter, are again available for primary

producers.

 These heterotrophic bacteria comprise the bulk of microbial populations

inhabiting the water column of oceans and are responsible for much of

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 the biological transformation of organic matter and production of carbon
dioxide.

 Decomposition of protein takes place by proteolytic bacteria, e.g.

Pseudomonas and other eubacteria.

 Cellulose is decomposed by cellulolytic bacteria, e.g. Cytophaga,

Sporocytophaga.

 Chitin, which is synthesized by several marine organisms as extracellular

material from algae, cell walls of some chlorophytes, exoskeletons,
including molts from cope pods and other marine invertebrates is a
structural polysaccharide. biopolymer is degraded by chitinolytic or
chitinoclastic bacteria, e.g. Bacillus, Pseudomonas and Vibrio, by their
exoenzyme chitinase.

 Pectins are also decomposed by numerous bacteria in anaerobic

condition, e.g. Clostridium, pectinovorum and the end-products are pectic
acid and methanol.

 Cyanobacteria (blue-green bacteria)

 Photosynthetic bacteria which are found in environments high in

dissolved oxygen, and produce free oxygen

 Store excess photosynthetic products as cyanophycean starch and

oils

 Primary photosynthetic pigments are chlorophyll a and chlorophyll

b

 Accessory pigments include carotenoids and phycobilins

Nutritional Types

• Cyanobacteria (con’t)

• Chromatic adaptation—response of pigment composition to the

quality of light in the sea

• May exist as single cells or form dense mats held together by

mucilage

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 • form associates called stromatolites—a coral-like mound of
microbes that trap sediment and precipitate minerals in
shallow tropical seas.

• Other photosynthetic bacteria

• Anaerobic green sulfur and purple sulfur and non-sulfur bacteria do

not produce oxygen

• The primary photosynthetic pigments are bacteriochlorophylls

• Sulfur bacteria are obligate anaerobes (tolerating no oxygen)

• Non-sulfur bacteria are facultative anaerobes (respiring when in

low oxygen or in the dark and photosynthesizing anaerobically
when in the presence of light)

• Chemosynthetic bacteria

• Use energy derived from chemical reactions that involve

substances such as ammonium ion, sulfides and elemental sulfur,
nitrites, hydrogen, and ferrous ion

• Chemosynthesis is less efficient than photosynthesis, so rates of

cell growth and division are slower

• Found around hydrothermal vents and some shallower habitats

where needed materials are available in abundance

• Heterotrophic bacteria

• Decomposers that obtain energy and materials from organic matter

in their surroundings

• Return many chemicals to the marine environment through

respiration and fermentation

• Populate the surface of organic particles suspended in the water by

secreting mucilage (glue-like substance)

• Heterotrophic bacteria

• Decomposers that obtain energy and materials from organic matter

in their surroundings

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 • Return many chemicals to the marine environment through
respiration and fermentation

• Populate the surface of organic particles suspended in the water by

secreting mucilage (glue-like substance)

• Heterotrophic bacteria

• Association of heterotrophic bacteria with particles in the water

column aids with:

• Consolidation: adjacent particles adhere

• Lithification: formation of mineral cement between particles

• Sedimentation: settling of particles

• Marine snow: large, cobweb-like drifting structures formed by

mucus secreted by many kinds of plankton, where particles may
accumulate

NITROGEN FIXATION AND NITRIFICATION

• Nitrogen fixation: process that converts molecular nitrogen dissolved in

seawater to ammonium ion

• Major process that adds new usable nitrogen to the sea

• Only some cyanobacteria and a few archaeons with nitrogenase

(enzyme) are capable of fixing nitrogen

• Nitrification: process of bacterial conversion of ammonium (NH4+) to

nitrite (NO2-) and nitrate (NO3-) ions

• Bacterial nitrification converts ammonium into a form of nitrogen

usable by other primary producers (autotrophs)

SYMBIOTIC BACTERIA

• Many bacteria have evolved symbiotic relationships with a variety of

marine organisms

• Endosymbiotic theory

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 • Mitochondria, plastids & hydrogenosomes evolved as symbionts
within other cells.

• Chemosynthetic bacteria live within tube worms and clams

• Some deep-sea or nocturnal animals host helpful bioluminescent bacteria

• Photophores

• Embedded in the ink sacs of squid

ARCHAEA

• General characteristics

• Small (0.1 to 15 micrometers)

• Prokaryotic

• Adapted to extreme environmental conditions: high and low

temperatures, high salinities, low pH, and high pressure

• Formerly considered bacteria

• Differences from bacteria

• Cell walls lack special sugar-amino acid compounds in

bacterial cell walls

• Cell membranes contain different lipids, which help stabilize

them under extreme conditions

NUTRITIONAL TYPES

• Archaea includes photosynthesizers, chemosynthesizers and

heterotrophs

• Most are methanogens: anaerobic organisms that metabolize

organic matter for energy, producing methane as a waste product

• Halobacteria (photosynthetic), thrive at high salinities, trap light

using bacteriorhodopsins, purple proteins

• Hyperthermophiles

28
 • organisms that can survive at temperatures exceeding 100o C, such
as near deep-sea vents

• Potential for biomedical and industrial application

EUKARYA

• Eukarya includes all organisms with eukaryotic cells

• Examples:

• plants

• animals

• fungi

• algae

• single-celled animal-like protozoa

FUNGI

• History of marine mycology

• Marine fungi first discovered in 1849

• Marine fungi’s ecological role is difficult to evaluate; biomass

needs to be quantified

• Important in marine ecosystems as decomposers, prey, pathogens

and symbionts

• General features of fungi (con’t)

• Store energy as glycogen

• kingdom Fungi is divided into 4 phyla:

• Chytridiomycota (motile cells)

• Zygomycota (e.g. black bread mold)

• Basidiomycota (club fungi, e.g. mushrooms)

• Ascomycota (sac fungi)

29
 • In the sea, ascomycotes are the most diverse and abundant fungi

• Ecology and physiology of marine fungi

• Can be either obligately marine, requiring ocean or brakish water

or facultatively marine (primarily of terrestrial or fresh water
origin)

• Salinity is toxic to fungi, so they must apply energy to removing

sodium

• Most marine fungi live on wood from land

• Some live on grass in salt marshes

• Others live on algae, mangroves or sand

• Fungi decompose the chitinous remains of dead crustaceans in

open sea plankton communities

• Marine yeasts reproduce asexually by budding—mitosis that produces

daughter cells of unequal size

• Filamentous marine ascomycotes can reproduce sexually by forming a

fruiting body called an ascocarp, a structure which produces ascospores

• Lichens: mutualistic associations between a fungus and an alga

• fungi are usually ascomycotes

• algae are usually green or blue-green bacteria

• The fungus provides attachment, general structure, minerals, moisture

• The alga produces organic matter through photosynthesis.

Stratification of Atmosphere

• Earth's atmosphere can be divided (called atmospheric stratification) into

five main layers.

• Exosphere: 700 to 10,000 km (440 to 6,200 miles)

• Thermosphere: 80 to 700 km (50 to 440 miles)

30
• Mesosphere: 50 to 80 km (31 to 50 miles)

• Stratosphere: 12 to 50 km (7 to 31 miles)

• Troposphere: 0 to 12 km (0 to 7 miles)

Exosphere

• The exosphere is the outermost layer of Earth's atmosphere.

• Exosphere—contains few particles that move into and from space.

• This layer is mainly composed of extremely low densities of hydrogen,

helium and several heavier molecules including nitrogen, oxygen and
carbon dioxide closer to the exobase. The atoms and molecules are so far
apart that they can travel hundreds of kilometers without colliding with
one another.

• Exobase—the lower boundary of the exosphere.

Thermosphere

• The thermosphere is the second-highest layer of Earth's atmosphere. This

layer is completely cloudless and free of water vapor.

• Temperature increases with height. The temperatures can rise to 1,500

degrees Celsius, but it would not feel warm because of the low air
pressure in this layer.

• The International Space Station orbits Earth in this layer.

• Mesopause—the boundary between the mesosphere and

the thermosphere; the coldest place on Earth.

Mesosphere

• The mesosphere is the third highest layer of Earth's atmosphere,

occupying the region above the stratosphere and below the thermosphere.

• The layer in which most meteors burn up after entering Earth’s

atmosphere and before reaching Earth’s surface.

31
• Stratopause—the boundary between the mesophere and the stratosphere.

Stratosphere

• The stratosphere is the second-lowest layer of Earth's atmosphere.

• Contains the ozone layer; the layer where volcanic gases can affect the
climate.

• Tropopause—the boundary between the stratosphere and troposphere.

Troposphere

• The layer closest to Earth’s surface in which all weather occurs. It

contains 75% of the atmosphere's mass and 99% of the total mass
of water vapour and aerosols.

Microflora of atmosphere

• Microbes normally found in atmosphere within 300-10000 feet above

from the land.

• Fungal spores which are found in air consist of Alternaria,

Cladosporium, Penecillium and Aspergillus found above 4000 feet from
the land, found in both polar and non polar air masses.

• Organisms found below 500 feet is mainly in overpopulated area, these

include spores of Bacillus and Clostridium, ascospores of yeast and
fragments of mycelium, mould, streptomycetaceae, pollen, protozoan
cysts, algae, Micrococcus and corynebacterium.

• Air found in school and hospital or living places of the person suffered
from infectious disease usually found microbes like tubercle bacilli,
streptococci and pneumococci.

• Many different microorganisms can be in aerosol form in the atmosphere,

including viruses, bacteria, fungi, yeasts and protozoans. In order to
survive in the atmosphere, it is important that these microbes adapt to
some of the harsh climatic characteristics of the exterior world, including
temperature, gasses and humidity. Many of the microbes that are capable
of surviving harsh conditions can readily form endospores, which can
withstand extreme conditions.

32
• Many of these microorganisms can be associated with specific and
commonly known diseases.

Airborne Plant pathogens and Diseases

• Microorganisms Resist atmospheric stress:

Bacterial

• One such bacterial microorganism that can resist environmental stresses

is Bacillus anthracis. It is a gram positive rod shaped bacteria that utilizes
spore formation to resist environmental stresses. The spore is a
dehydrated cell with extremely thick cell walls which can remain inactive
for many years.

• This spore makes Bacillus anthracis a highly resilient bacteria, allowing

it can survive extreme temperatures, chemical contamination, and low
nutrient environments (Gatchalian 2010). This bacteria is associated
with Anthrax, which is a severe respiratory disease that infects humans.

33
• The characteristics of atmosphere as a habitat include extreme
temperature variations, light, temperature, low amount of available water
and organic water.

• All these characters make the atmosphere unsuitable for growth of micro
organisms. Usually most of the organisms are found in the lower region
of atmosphere.

• The air in the atmosphere is often exposed to sunlight thus it contains less
moisture and higher temperature.

• Thus if the micro organisms are not protected from desiccation, almost
most of the organisms will die.

• The origin of the micro organisms takes place through various ways. Soil
is one of the source to transfer micro organisms to the air. Whenever the
wind blows it disturbs the micro organisms and liberate them into the air
and these micro organisms remains suspended in the air for long time.

• Another way of transferring micro organisms to the air is by manmade

actions like plugging and digging.

DISPERSAL OF AIR MICROBES

• Though there are significantly less atmospheric microorganisms than

there are in oceans and in soil, there is still a large enough number that
they can affect the atmosphere (Amato, 2012).

• Once suspended in the air column, these microbes have the opportunity to
travel long distances with the help of wind and precipitation, increasing
the occurrence of widespread disease by these microorganisms.

• These aerosols are ecologically significant because they can be

associated with disease in humans, animals and plants.

Airborne microbial pathogen transmission

1. Airborne droplet nuclei (small particles of 5 mm or smaller in size).

• Airborne droplet nuclei develop when the fluid of pathogenic droplets (1-
5 µm in size. They are so small and light they may remain suspended in
the air for several hours. Thus, they may also infect persons entering a
room which has been left by a patient long ago. Also, airborne droplet
34
 nuclei can be widely dispersed by air currents. Tuberculosis, chickenpox,
measles and possibly also influenza may be transmitted this way.

2. Dust particles containing infectious agents

• Microoganisms carried in this manner remain suspended in the air for

long periods of time and can be dispersed widely by air currents. Because
of this, there is risk that all the air in a room may be contaminated. Some
examples of microorganisms that are transmitted by the airborne route are
Transmission occurs when droplets containing microorganisms
generated during coughing, sneezing and talking are propelled through
the air.

• These microorganisms land on another person, entering that new person’s

system through contact with his/her conjunctivae, nasal mucosa or mouth.

• These microorganisms are relatively large and travel only short distances
(up to 6 feet/2 metres).

• M. tuberculosis, rubeola, varicella and hantaviruses

• However these infected droplets may linger on surfaces for long periods
of time, so these surfaces (within the range of the coughing/sneezing
person) will need additional cleaning.

• For this reason there may be both Droplet and Contact Precautions
required at the same time. Examples of microorganisms that are spread by
droplet transmission are: influenza, colds, respiratory syncytial virus
(RSV) and some organisms causing pneumonia.

EXTREMOPHILES

 Organisms found living in extreme harsh environments.

 Word originated from Greek- Extremus + Philia which

means extreme loving.

 Most members of this group comes under the domain Archae.

35
 These include thermophiles, hyperthermophiles, thermoacidophiles,
alkaliphiles, psychrophiles, halophiles, barophiles, radiation
resistant bacteria and endoliths.

 Organisms lives in physically/geochemically extreme conditions that

are mostly detrimental for other forms of life.

 In other words, an extremophile is a microorganism,

mostly an Achaeon that lives in conditions of
extreme acidity, alkalinity, temperature, salinity, pressure, nutrient
scarcities etc.

HOW DO THEY LIVE SO?

 Extremozymes- specialized enzymes that are highly stable.

 Can tolerate extremes of temperature, pH, salinity that would

inactivate other enzymes.

 Important in industries because of this property.

EXTREME CONDITIONS

 Temperature

 pH

 Salinity

 Nutritional scarcities

 Absence of oxygen

 Radiation

 Pressure

36
TYPES

Psychrophiles

 Temperatue range is -15 to 150C

 Also known as cryophiles.

 Have an optimum temperature of 150C or lower

 Isolated from Arctic and Antarctic habitats (90% of the ocean is 50C
or colder)

 Also found in ice bergs, glaciers, snowfields etc

 Metabolism is quite normal at colder temperatures.

 Cell membranes-high levels of fatty acids which remain fluid at colder

temperatures.

 Proteinaceous antifreeze mechanism to protect the cell and DNA

37
 Some of them cause spoilage in refrigerated food materials.

 Eg: Arthrobacter spp, Psychrobacter spp, Halomonas spp,

Pseudomonas, sphingomonas

FIRMICUTES

 Gram positive, spore forming bacterial family that can survive

desiccation and can survive extreme conditions.

 This group also is an example for extremophilic true bacteria

(eubacteria).

 Plays an important role in the spoilage of beer, wine and cider.

 Eg: Helicobacterium spp, Mycoplasma, Clostridium spp.

 Many members of the Family Firmicutes are also thermophiles.

 Eg: Bacillus stearothermophilus

 Recently, a DNA polymerase derived from these bacteria, Bst

polymerase has become important in biotechnology.

 Bst polymerase- helicase like activity (making it able to unwind DNA

strands.

 Optimum functional temperature is 60-650C and get inactivated at

temperatures above 800C

THERMOPHILES

 Greek- thermotita (heat) and philia (love)

 Temperature loving organisms.

 Most members are Archae

 Grows in a temperature range of 55-1130C

 Mostly found in geothermally heated regions on

earth viz., hot springs, hydrothermal vents etc.

 As they need extreme temperature, its very hard to study

them under laboratory conditions.

38
 Also that some members can produce heaty by themselves
(compost and garbage landfills).

 Eg : Cyanidium caldarium, Chaetomium thermophile

 Deinococcus-thermus is a small group of eubacteria which can thrive

environmental hazards.

 Stains Gram positive (thick cell wall) but possesses an

outer membrane, similar to the Gram negative cell wall.

 Several thermophilic bacteria comes under this group.

 It is the source of heat resistant enzyme- taq polymerase, which is well

used in PCR.

 The enzyme is isolated from Thermus aquaticus.

CLASSIFICATION OF THERMOPHILES

1. Obligate thermophiles

 Also known as extreme thermophiles.

 Temperature range is 80-1220C.

 Membranes and proteins are unusually stable at these extreme

temperatures.

 For this reason, most biological processes utilize thermophilic enzymes

because of their ability to withstand intense heat.

 Many of this group can resist radiation too.

 Eg: Methanopyrus kandleri, can survive and reproduce at 1220C,

Sulfolobus spp , Pyrococcus spp, Pyrodictium spp (optimum of 1130C)

39
 Most of the members require elemental sulfur for growth.

 Anaerobic members use sulfur as electron acceptor

instead of oxygen in cellular respiration.

 Some are lithotrophs that oxidizes sulfur to sulfururic acid as an energy

source.

 Such organisms require a very low pH and hence

known as thermoacidophiles.

 Inhabits regions associated with volcanic eruption viz; hot, sulfur rich,
acidic regions such as hot springs, natural geysers, fumaroles etc .

Thermoacidophiles

 Requires both high temperature and highly acidic environment for

optimum growth.

 Preferred temperature range is 70-800C and have an optimum

pH range of 2-3.

 All the organisms discovered belongs to the Domain Archae,

so far.

 They can thrive in acidous and sulfur rich environments.

 Instead of cell wall, possesses a unique membrane composed of

tetraether lipoglycan, which gives the unusual stability for the bacteria.

 Eg: Thermoplasma acidophilum and T.volcanium

Facultative Thermophiles

 Rare group of organisms that can live both in higher temperature and
normal temperature are referred to as facultative thermophiles.

 These organisms can live at 200C, and have an optimum of 500C.

Maximum temperature that they can survive is 600C.

 Eg: Bacillus flavothermus

ACIDOPHILES
40
  Microorganisms that lives in highly acidic

environments are called as acidophiles.

 The pH range is 1-5.

 Some members that mainly found in the drainage of coal mines are able
to oxidize sulfur into sulfuric acid.

 Mechanism of action is that they have a proton pump machinery to

eliminate protons from the cytoplasm of the cell to maintain low pH.

 Eg: Pyrodictium, Picrophilus, Ferroplasma, Sulfolobus

ALKALIPHILES

 These are extremophilic microorganisms which thrives in roughly

alkaline environments (8-11), and have an optimum of pH around 10.

 Organisms which needs high pH to survive are called as obligate

alkaliphiles.

 There are facultative alkaliphiles and haloalkaliphiles

(needs salty environment as well).

 Most of the alkaliphiles possess a bacillus morphology.

 Eg: Bacillus halodurans C125, Bacillus firmus OF4

 Two methods for surviving

 The cell will be having a unique cellular machinery that works

best in alkaline range of pH.

 The cell will have to acidify the cytosol to nullify the effect of the
high pH outside the cell.

 Experimental studies revealed that the cytosolic enzymes of alkaliphiles

functions best in a neutral pH range (7.5-8.5).

 This shows that for surviving in highly alkaline pH, the cell must have
some pH regulatory mechanism to protect the plasma membrane.

41
  The mechanism is that the cell wall contains acidic polymers composed
of residues such as galacturonic acid, gluconic acid, glutamic acid,
aspartic acid, and phosphoric acid.

 This protects the PM by preventing the entry of hydroxide ions and

allowing the entry of sodium (Na+) and hydronium ions(H+)

XEROPHILES

An extremophilic organism that can grow and reproduce in conditions with a

low availability of water.

 Water activity (aw) is a measure of the amount of water within a

substrate an organism can use to support sexual growth.

 Xerophiles are often said to be "xerotolerant", meaning tolerant of dry

conditions. They can survive in environments with water activity below
0.8.

 Endoliths and halophiles are often xerotolerant.

 Eg: many molds and yeast,

Trichosporonoides nigrescens

HALOPHILES

 This group comprises microorganisms that can thrive in high salty

environments such as The Great Salt Lake and Dead Sea.

 Most of the halophiles belong to the Domain Archae.

 Eg: Salinibacter ruber

 There are eukaryotic halophiles such as Dunaliella salina (algae) and

Wallemia icthyophaga (fungus).

 Extreme halophiles/obligate halophiles-adapted to

survive high salt concentrations

42
 Organisms from Dead Sea often requires nearly 33% salt (sea water has
only 3%), and the inoculating loop must be dipped in a saturated salt
solution to isolate them.

 Microorganisms live in such high salinity are termed as extreme

halophiles

Mechanism

Mainly employ two mechanism to prevent desiccation through

osmosis.

Both strategies work by increasing the osmotic

concentration of the cell.

1.In first method (followed my most halophiles including bacteria,

archae etc) organic compounds are accumulated in the cytoplasm.

 They are known as osmoprotectants or compatible solutes.

 It include sugars, aminoacids, polyols, betaines etc.

These compounds can be synthesised or accumulated from the

environment.

 Eg: Ectothiorhodospira halochloris

2. The second is the selective influx of potassium ions (K+) into

the cytoplasm.

 This adaptation is restricted to moderately halophilic organisms.

 The entire intracellular machinery (enzymes, structural proteins etc) is

highly adapted to withstand the high saline environment.

 Eg: Bacteria comes under the Family

Halobacteriaceae

 The 16S rRNA studies opens a broad range of information on the field
of evolution.

ENDOLITHS

43
 Endolith is an organism (archae, bacterium, fungus, lichen or algae) that
lives in nutritionally poor environments such as inside a rock or
something.

 Particularly interesting in the area of astrobiology (exobiology).

 These organisms opens a clue for life beyond earth. There are chances of
having life on endolithic environments such as mars and other planets.

Characteristics

 Endoliths have been found in rocks down to the depth of 3 km.

 It is not known that whether this is the limit since digging to the deep is
highly expensive.

 The major threats to live in such depth is the high temperature.

 Recently discovered strains can reproduce at 1210C.

 All the discovered organisms are autotrophs.

 Some utilize gas or dissolved nutrients from water moving through

fractured rocks

 Others may incorporate inorganic compounds found in their rock

substrate (possibly by excreting acids to dissolve the rock).

Endoliths can be classified into

 Chasmoendoliths

Colonizes fissures and cracks in the rock (chasmo- cleft)

 Cryptoendolith

Colonizes structural cavities within porous rocks, including spaces

produced and vacated by euendoliths (crypto = hidden)

 Euendolith

Penetrates actively into the interior of rocks forming tunnels that

conform with the shape of its body(eu = good, true).

Obligate Anaerobes

44
 Microorganisms which grow strictly in the absence of molecular oxygen
are called as obligate anaerobes.

 For these, oxygen is a toxin

 For energy generation, they must employ fermentation or anaerobic

respiration pathways.

 The toxic forms of oxygen are Singlet Oxygen(O2), Superoxide

 radicals (O -), peroxide anion (O 2-), and hydroxyl radical (OH).

 Some obligate anaerobes are Clostridium spp, Methanococcus and

Methanopyrus

 Microorganisms which can live both in the presence and absence of

oxygen are known as Facultative Anaerobes.

 They can utilize oxygen if available or, continue their growth by

fermentation and anaerobic respiration.

 Eg: Bacillus anthracis, Escherichia coli

 To routinely grow and maintain in pure cultures, reducing media which

stored in ordinary, tightly packed tubes is been used.( media containing
thioglycollate or cystein)

 For culturing in petriplates, sealed boxes and jars in which oxygen

removed completely is been used.

 Sometimes, certain chemicals which can produce hydrogen and carbon

di oxide will be added and the so formed hydrogen will be incorporated
with the oxygen present in the container to yield water

 This water can be utilized by the microorganisms.

 The most advanced system is that the media used for culture will be
containing an enzyme- oxyrase which will bind with oxygen and
eliminate as water. No addition of extra chemicals or hydrogen is
needed.

Radiation

45
 Although most living things are sensitive to radiation, there are some
microorganisms which can resist high levels of radiation.

 Deinococcus radiodurans is the radioresistant organism discovered so

far which is a eubacteria.

 Their ability to withstand radiation is more than that of

endospores.

 They can survive exposure to radiation doses as high as 15,000 Grays.

This much radiation is 1500 times the dosage that would kill a human.

 The mechanism for this extraordinary resistance lies in a unique

arrangement of its DNA that facilitates a rapid repair of radiation
damage.

 It is similarly resistant to many mutagenic chemicals.

Barophiles

 Microorganisms that can survive under immense hydrostatic pressure.

 Generally found in ocean floors where pressure exceeds

300 m (38 MPa).

 Some have been found at the bottom of the Pacific Ocean (Mariana
Trench-10500 m) where pressure often exceeds 117 MPa.

 These organisms cannot grow in pressure below 400-500atm

 True obligate barophiles also comprises bacteria which present in the gut
of holothurians and amphipods (crustaceans).

 Eg: Photobacterium, Shewanella, Colwellia

 Some thermophilc archae such as Pyrococcus spp.,

Methanococcus jannaschii are barophiles too.

SOME INTERESTING FACTS

 Halomonas titanicae- the bacterium which is responsible for

rusting of RMS Titanic.

46
 Pseudomonas putida (super bug) is a genetically
engineeredbacteria which literally “eats” petroleum products.
These are very much useful in oil spills.

 GFAJ-1 is a strain of rod shaped bacteria in the

family Halomonadaceae which is anextremophile,

highly resistant to the dangerous poison-Arsenic.

 There are chances of life forms beyond earth and the

field of study is known as astrobiology.

47
 SCHOOL OF BIO AND CHEMICAL ENGINEERING
DEPARTMENT OF BIOTECHNOLOGY

UNIT – II – MICROBIAL ECOLOGY – SMB2101

1
 UNIT: II

BIOGEOCHEMICAL CYCLES

The term biogeochemical tells us that Biological, Geological & Chemical

factors are involved. In earth science, a biogeochemical cycle is a pathway by
which a chemical substances moves through both Biotic(Biosphere) &
Abiotic(Lithosphere, Atmosphere & Hydrosphere) compartments of earth. A
cycle is a series of change which comes back to the starting point & which can
be repeated.

“ More or less circular pathways, through which the chemical elements,

including all the essential elements of the protoplasm, circulate in the
biosphere from environment to organisms and back to the environment, are
known as the Biogeochemical cycle”.

 Biogeochemical cycles always involve Hot equilibrium states: A balance

in the cycling of the elements between compartments.

 As biogeochemical cycles describe the movements of substances on the

entire globe, the study of these is inherently multidisciplinary.

CYCLINIG ELEMENTS

Macronutrients

Macronutrients are required in relatively large amounts

 Big six": Carbon , Hydrogen , Oxygen , Nitrogen, Phosphorous.

 other Macronutrients:

 Sulfur, Potassium , Calcium , Iron , Magnesium

2
 Micronutrients

Micronutrients are required in very small amounts, (but still necessary)

 Boron Copper Molybdenum

TYPES OF BIOGEOCHEMICAL CYCLES

Biogeochemical cycles can be classed as;

GASEOUS CYCLE
The term gaseous cycle refers to the transformation of gases between
various biogeochemical reservoirs; Hydrosphere, Atmosphere &
Biosphere Important gaseous cycles are;

 NITROGEN CYCLE

 OXYGEN CYCLE

 CARBON CYCLE

 WATER CYCLE

SEDIMENTARY CYCLE:

Leaching of minerals & salt’s from the earth’s crust, which the settle as
sediment or rock before the cycle repeats. Sedimentary cycle includes;

 PHOSPHORUS CYCLE

 SULFUR CYCLE

 IRON CYCLE

 CALCIUM CYCLE

 Sedimentary cycles vary from one elements to another, but each cycle
consist fundamentally of a solution phase & a sediment phase.

CARBON CYCLE

 Carbon is virtually important molecule in the carbon cycle.

 Proteins, nucleic acids, lipids, carbohydrates, and other molecules

essential to life contain carbon.
3
  Carbon is present in the atmosphere as the gas carbon dioxide (CO2),
which makes up approximately 0.04% of the atmosphere.

 It is also present in the ocean and fresh water as dissolved carbon

dioxide. Carbons are also present in rocks such as limestone (CaCO3).

 The global movement of carbon between the abiotic environment,

including the atmosphere and ocean, and organisms is known as the
CARBON CYCLE.

Step 1: PHOTOSYNTHESIS

 During photosynthesis, plants, algae, and cyanobacteria remove Carbon

dioxide from the air and fix, or incorporate it into complex organic
compounds such as glucose.

 Photosynthesis incorporates carbon from the abiotic into the

biological compounds of producers.

Step 2: DECOMPOSITION, ANIMAL & PLANT RESPIRATION, SOIL

MICROORGANISM RESPIRATION.

4
  Many of the compounds are used as fuel for cellular respiration by the
producer that made them, by a consumer that eats producer, or by a
decomposer that breaks down the remains of the producer or consumer.

 The process of a cellular respiration returns CO2 to the

atmosphere. A similar carbon cycle occurs in aquatic ecosystems
between aquatic organisms and dissolved CO2 in water.

 The process of photosynthesis incorporates the carbon atoms from

carbon dioxide into sugars.

 Animals eat the plants and use the carbon to build their own
tissues.

 Carnivores eat these animals and then use the carbon for their own needs.

 These animals return carbon dioxide into the air when they breathe, and
when they die,the carbon is returned to the soil during decomposition.

 Step 3: PARTLY DECOMPOSED PLANT REMAINS (COAL)

 Millions of years ago vast coal beds formed from the bodies of ancient
trees that were buried and subjected to anaerobic conditions before they
had fully decayed.

Step 4: MARINE PLANKTON REMAINS

 The oils of unicellular marine organisms probably gave rise to the

underground deposits of oil and natural gas that accumulated in the
geologic past.

 Coal, oil, and natural gas, called fossil fuels because they
formed from the remains of ancient organisms. Fossil fuels are
non- renewable resources. The Earth has a finite or limited supply
of these resources.

Step 5: COMBUSTION (HUMAN & NATURAL)

 The process of burning or combustion, may return the carbon in oil,

coal, natural gas, and wood to the atmosphere.

5
  In combustion, organic molecules are rapidly oxidized (combined
with oxygen) and converted to carbon dioxide and water with release of
light and heat.

Step 6: BURIAL AND COMPACTION TO FORM ROCK

(LIMESTONE)

 An even greater amount of carbon that is stored for millions of years is

incorporated into the shells of marine organisms.

 When these organisms die, their shells sink to the ocean floor and
sediments cover them forming cemented together to form limestone.

Step 7: EROSION OF LIMESTONE TO FORM DISSOLVED CO2

 When the process of geologic uplift expose limestone, chemical and

physical weathering processes slowly erode it away.

 This returns carbon to the water and atmosphere where it is available to

participate in the carbon cycle once again.

6
  Thus, photosynthesis removes carbon from the abiotic environment and
incorporate it into biological molecules.

 While, Cellular respiration, combustion, and erosion of limestone return

carbon to the water and atmosphere of the abiotic environment.

Why carbon cycle is important?

 Many elements have cycle, but the cycling of carbon atoms is

particularly important because:-

 Through photosynthesis and respiration, it is the way the earth produces

food and other renewal resources.

 CO2 plays a key role in trapping heat in the atmosphere - one of the
basic mechanisms behind the greenhouse effect.

 Carbon plays a central role in combustion.

 Through decomposition, it serves as the earth's waste disposal system.

 In addition, the carbon cycle is important because carbon-

containing gases in the atmosphere affect the earth's climate.

 Increased CO2 in the atmosphere has been responsible for more than
half of the climate warming observed in recent decades.

NITROGEN CYCLE

 The majority of earth’s atmosphere is Nitrogen(78%). However,

Atmospheric N2 has limited availability for biological use, and this form
is relatively nonreactive and unusable by plants.

 Nitrogen availability can affect the rate of key ecosystem processes

including primary production and decomposition

 The Nitrogen(N2) cycle is the process by which N2 is converted

between its various chemical forms.

 This transformation can be carried out through both biological &

physical processes.

PROCESS OF NITROGEN CYCLE

7
 Nitrogen is present in the environment in a wide variety of chemical
forms including

 Organic nitrogen,

 Ammonium(NH4+),

 Nitrite(NO -),

 Nitrate(NO _),

 Nitrous oxide(N2O),

 Nitric oxide (NO)

 Inorganic nitrogen gas.

 Organic nitrogen may be in the form of a living organism, humus or in

the intermediate products of organic matter decomposition.

 The process of N2-cycle transform nitrogen from one form to another.

Many of those processes are carried by microbes.

8
 NITROGEN FIXATION

Atmospheric nitrogen must be fixed in a usable form to be taken up by

the plants mostly fixation is done by free living (eg.Azotobacter and
Closteridium or symbiotic (Rhizobium) known as Diazotrophs.

symbiotic nitrogen fixing bacteria such as Rhizobium usually live in the

roots noodules of legumes. here they form a mutualistic relationship with
the plant, producing ammonia in exchange for carbohydrates. today
about 30% of the total fixed N2 is produced industrially using the Haber-
Bosh process which uses high temperature and pressure to convert
nitrogen gas and a hydrogen source in to ammonia. biological nitrogen
fixation can be represented by following equation.

N2 + 8H+8e-+16ATP= 2NH2+H2+16ADP

NITRIFICAITON

 The conversion of ammonia to nitrate is performed primarily by soil

living bacteria & other nitrifying bacteria.

 In the primary stage of nitrification the oxidation of ammonium is

performed by bacteria such as the Nitrosomonas species, which convert
ammonia to nitrites.

 Other bacterial species such as Nitrobacter are responsible for the

oxidation of the nitrite into nitrates.

 It is important for the ammonia to be converted to nitrates or nitrites

because ammonia gas is toxic to plants.

9
 ASSIMILATION

 Plant take nitrogen from soil by absorption through their roots

as Amino acids, Nitrate ions, Nitrite ions, or Ammonium ions.

 Plants can absorb nitrate or ammonium from the soil via their root hairs.
If nitrate is absorbed, it is first reduced to nitrite ions and then
ammonium ions for incorporated into amino acids, nucleic acids &
chlorophylls.

 In plants that have a symbiotic relationship with Rhizobia, some N2 is

assimilated in the form of ammonium ions directly from the nodules.

10
AMMONIFICATION

 When a plant or animal dies or an animal expels waste, the initial forms
of N2 is organic.

 Bacteria or fungi convert the organic N2 within the remains back to

ammonium, a process called Ammonification or Mineralization

 Enzymes are involved are; GS : Gln synthetase, GOGAT : Glu-2-

oxoglutarate GDH : Glu-dehydrogenase

11
DENITRIFICATION

 Denitrification is the reduction of nitrates back into the largely inert N2

gas, completing the N2-cycle.

 This process is performed by bacterial species such as Pseudomonas &

Clostridium in anaerobic conditions.

 They use the nitrate as an electron accepter in the place of oxygen during
respiration.

 Denitrification happens in anaerobic conditions eg. Waterlogged soils.

12
13
 NITROGEN CYCLE

ECOLOGICAL FUNCTIONS

 Nitrogen is necessary for all known forms of life on earth.

 It is a component in all amino acids as it is incorporated into proteins and

is present in the bases that make up nucleic acids such as RNA & DNA.

 Chemical processing or natural fixation are necessary to convert

gaseous nitrogen into compounds, such as nitrate or ammonia which can
be used by plants.

USES OF NITROGEN

 Nitrogen is important to the chemical industry, It is used to make

Fertilizers, Nitric acid, Nylon, Dyes & Explosives.

 Nitrogen is present in virtually all pharmacological drugs & In the form

of nitrous oxide it is used as anesthetic.

 The CPUs in computers use the N2-gas to keep them from heating up. X-
ray detectors also rely on this element.

14
 Cryopreservation also used N2 to conserves blood and other biological
specimens.

PHOSPHOROUS CYCLE

The phosphorus cycle is the slowest Biogeochemical cycle that

describes the movements of phosphorus(P) through the Lithosphere,
Hydrosphere & Biosphere.

Unlike many other biogeochemical cycles, the atmosphere dose not play
a significant role in the movement of P because phosphorus and P based
compounds are usually solids at the typical ranges of temperature &
pressure found on earth.Low conc. of P in soils reduces plant growth &
slows soil microbial growth.

Unlike other cycles P cannot be found in the air as a gas, it only occurs
under highly reducing conditions as the gas Phosphine. Initially ,
phosphate weathers from rocks and minerals, the most common mineral
being Apatite .

Overall small losses occurs in terrestrial environment by leaching

erosion, through the action of rain. Weathering of rocks & minerals
release phosphorus in a soluble form , where it is taken up by plants & it
is transformed into organic compounds.

The plants may then be consumed by herbivores and the phosphorus is

either incorporated into their tissues or excreted. After death of animal or
plant decays then phosphorus is returned to the soil where a large part of
the P is transformed into insoluble compounds. Runoff may carry a small
part of the P back to the ocean.

15


16
 ECOLOGICAL FUNCTIONS

P is an important nutrient for plants and animals, P is also limiting

nutrient for aquatic organisms.

 P does not enter the atmosphere, remaining mostly on land, in rock &
soil minerals.

 80% of the mined P is used to make fertilizers. P from fertilizers, sewage

can cause pollution in lakes & streams.

 P normally occurs in nature as part of a phosphate ion (PO4) -,The

most

abundant forms is Orthophosphate

17
 
IMPORTANCE OF PHOSPHOROUS

BIOLOGICAL FUNCTIONS

The primary biological importance of Phosphates is as a

component of nucleotides,

which serves as energy storage within cells (ATP) or when linked together
form the nucleic acids DNA & RNA.

 The double helix of two strands of DNA is only possible because of

phosphate ester bridge that binds the helix.

 Besides making biomoleculs, P is also found in bone & enamel of

mammalian teeth, whose strength is derived from calcium phosphate in
the form of Hydroxyl apatite.

 It is also found in the exoskeloton of insects & phospholipids.

OTHER USES

 Phosphorus catches fire readily, Red phosphorus is used in all matches.

 White phosphorus and zinc used as a poison for rats.

18
  It is used in making incendiary (fire causing) bombs, tracer bullets and
for producing smoke screen.

 Many soluble phosphates are used to remove unwanted metal salts from
the water.

THE SULFUR CYCLE

The sulfur cycle is the collection of processes by which sulfur moves to and
from minerals (including the waterways) and living systems. Such
biogeochemical cycles are important in geology because they affect many
minerals.

 Found in rocks or buried deep in the ocean in oceanic sediments.

 found in the atmosphere.( enter through both natural and human
sources.)
- occurs in combination with several metals such as, PbS and
HgS.
- a brittle yellow, tasteless and odorless non-metallic element.
 10th most abundant element in the universe,
 At room temp. it is a solid
 Present in proteins, amino acids, vitamins, and enzymes, necessary
for plants and animals

19
—
—

— USES OF SULFUR

 Important elements of industrial processes

 Sulfur dioxide (SO2) is a bleaching agent and is used to bleach wood
pulp
 Sulfur dioxide kills molds and bacteria. (preserve)
 Sulfur is found in every living cell (amino acids)
 Long used as a medicine ( Brimstone in the old days)
 Before the advent of antibiotics in the 1940s, sulfur-containing drugs-
sulfa drugs-were commonly used to treat infectious diseases.
 Component of penicillin-class antibiotics
 Medications for dandruff, and warts have this ingredient. Combining
alcohol and sulfur can be used to treat acne and other skin disorders.

SULPHUR CYCLE MICROORGANISMS CONTRIBUTE

GREATLY TO THE SULFUR CYCLE.

20
 Photosynthetic microorganisms transform sulfur by using sulfide as an
electron source, allowing Thiobacillus and similar
chemolithoautotrophic genera. In contrast, when sulfate diffuses into
reduced habitats, it provides an opportunity for different groups of
microorganisms to carry out sulfate reduction.

For example, when a usable organic reductant is present, Desulfovibrio

uses sulfate as an oxidant. This use of sulfate as an external electron
acceptor to form sulfide, which accumulates in the environment, is an
example of a dissimilatory reduction process and anaerobic
respiration.

In comparison, the reduction of sulfate for use in amino acid and protein
biosynthesis. Other microorganisms have been found to carry out
dissimilatory elemental sulfur reduction.

These include Desulfuromonas, thermophilic archaea and

also

cyanobacteria in hypersaline sediments. Sulfite is another critical intermediate

that can be reduced to sulfide by a wide variety of microorganisms, including
Alteromonas and Clostridium, as well as Desulfovibrio and Desulfotomaculum.

In addition to the very important photolithotrophic sulfur oxidizers such

as Chromatium and Chlorobium, which function under strict anaerobic
conditions in deep water columns, a large and varied group of bacteria
carry out aerobic anoxygenic photosynthesis. These aerobic
anoxygenic phototrophs use bacteriochlorophyll a and carotenoid
pigments and are found in marine and freshwater environments; they are
often components of microbial mat communities.

Important genera include Erythromonas, Roseococcus, Porphyrobacter,

and Roseobacter.

“Minor” compounds in the sulfur cycle play major roles in biology.

An excellent example is dimethylsulfoniopropionate

(DMSP),which is used by bacterioplankton (floating bacteria) as a
sulfur source for protein synthesis, and which is
transformed to dimethylsulfide (DMS), a volatile
sulfur form that can affect atmospheric processes.

21
 When pH and oxidation-reduction conditions are
favorable,

several key transformations in the sulfur cycle also occur as the result of
chemical reactions in the absence of microorganisms. An important example of
such an abiotic process is the oxidation of sulfide to elemental sulfur.

This takes place rapidly at a neutral pH, with a

half-life of approximately 10 minutes for sulfide at room
temperature.

USES:

It is also use to make cements, matches, fireworks, dyes, fungicides.

Powdered sulfur is found in lotions and skin cream ingredients.

The elements involved in sulfur cycles includes

22
— S is for sulfur

— SO4-2 is for sulfate

— SO2 is for Sulfur dioxide ,

— H2S for Hydrogen sulfide

It includes both atmospheric and terrestrial processes

 Hydrogen Sulfide (H2S) is released into the atmosphere (volcanic

eruptions, fossil fuel burning, and the anaerobic decay of sulfur- containg
biological material in swamps, bogs)

 Certain marine algae à dimethyl sufide Sulfur dioxide.

 Volcanic eruptions à Sulfur dioxide

 Burning of fossil fuels à Sulfur dioxide

 Sulfur dioxide + Oxygen = Sulfur trioxide, then reacts with tiny water
droplets = Sulfuric Acid

 Sulfur Oxides reacts with Ammonia = tiny particles of

ammonium salts.

23
  Wind carries Sulfuric acid and ammonium salts which falls to earth in
form of Precipitation.

 Plants get sulfur by taking up ions of sulfate salt from the soil.

 Animals get sulfur by eating plants and all living things release sulfur

 compounds when they decay.

 Decomposition releases sulfate salts (SO4 2-), which can be taken up by

plants as well as gaseous hydrogen sulfide.

 Some hydrogen sulfide enters the atmosphere. But when decay occurs in
an oxygem-free environment, anaerobic bacteria break down hydrogen
sulfide and release sulfur gas (H2)

 Oxygen-requiring bacteria can incorporate sulfure into sulfate salts

which can be taken up by plants and enter the food chain once again.

 The remaining sulfur is lost into the oceans depth combining with iron to
form Ferrous Sulfide which is responsible for the black color of most
marine sediments.

 We burn sulfur containing coal and oil to produce electricity. We refine

sulfur containing petroleum.

 Acid rain is corrosive rain caused by rainwater falling to the ground

through sulfur dioxide gas, turning it into weak sulfuric acid, which
causes damage to ecosystems.

 Transportation - cars are a major contributor to acid rain pollution,

 Alternative fuels - switch over to renewable sources of energy, (solar,

wind and water energy)

THE ROLE OF MICRO-ORGANISMS IN THE DECOMPOSITION OF

ORGANIC MATTER AND THE MICROBIAL COMMUNIITY
SUCCESSION

Two Components of Decomposition Decomposition is described as having two

components; autolysis and putrefaction.

24
 • Autolysis refers to the situation where the body’s own enzymes are
acting on itself, causing cellular and tissue destruction.

• Putrefaction refers to the situation where microorganisms (especially

bacteria and fungi) feed on and break down the tissues of the dead body.

Process of Decomposition by Microorganisms

• Within a very short time period microorganisms can breakdown and

digest a large amount of soft tissue, resulting in a large production of gas
and ‘decomposition fluid’

• As decomposition proceeds, the skin begins to darken to various shades

of green and brown. This is usually first seen within the right lower
abdominal quadrant (image below)

• The body becomes somewhat bloated due to the decomposition gases

produced, and the decomposition fluid is frequently expelled from the
mouth, nose or other opening in the presence of a red-brown fluid

• Bacteria and fungi contribute to the decay of the body.

Other decomposers

• Insects are not the only organisms involved in decomposition of a body.

• Bacteria also plays a major role.

• Those found in the gut invade the dead tissues after death of a body as
well as other fungi and bacteria from surroundings colonising the corpse.

• This in turn leads to decay.

• There is no set succession on the particular sequence of succession

however genera often found on corpses include Bacillus, Candida and
Argobacterium.

• These are collectively known as decomposers.

Microorganisms Found on Corpses

Early Stages of decomposition:

• Bacillus

25
 • Staphylococcus

• Candida

• Streptococcus

Followed by:

• Salmonella

• Cytophaga

• Agrobacterium

Microorganisms are Collectively known as Decomposers

• Decomposers obtain a great source of energy from the body such as

proteins, fats, organic carbohydrates and nucleic acids which are used as
a food source.

• This energy is then released through aerobic/anaerobic respiration.

• This energy allows rapid multiplication which leads to more

decomposition.

DECOMPOSITION OF OM

• Definition:

 Breakdown of dead plant and animal material and

release of inorganic nutrients

 Decomposition is a biological breakdown and biochemical

transformation of complex organic molecules of dead material into
simpler organic and inorganic molecules (Juma, 1998).

Decomposition (and respiration)

26
SOURCE OF ORGANIC MATTER

• Plant remains

• Animal tissue and excretory products

• Cells of microorganisms

• However, plant is the main contribution to OM.

ORGANIC CONSTITUENTS OF PLANTS

1) Cellulose most abundant 15 to 60% of dry weight.

2) Hemicellulose, 10 to 30 %

3) Lignin, 5 to 30%

4) Water soluble fraction include simple sugar, amino acids, aliphatic acids,
5 to 30 % of tissue weight

27
 5) Ether and alcohol-soluble constituents; fats, oils,waxes, resins and a
number of pigments.

6) Proteins

WHY ORGANISMS DECOMPOSE OM?

• Supplying energy for growth

• Supplying carbon for new cell synthesis

• The cells of most microorganisms commonly contain approximately 50

% carbon. This is derived mainly from the substrates.

WHY DO WE CARE ABOUT DECOMPOSITION?

Decomposition is important in releasing nutrients tied up in dead organic matter

and return it back to the soil.

A. SOIL FAUNA

 earthworms, arthropods

28
  Fragmentation (cominution) increases surface area.

 Distributes OM within soil profile

B. SOIL MICROORGANISM

 Heterotrophic bacteria, fungi

 Derive energy, carbon and nutrients from dead OM in

the process they release CO2 through respiration.

DECOMPOSITION PROCESS

• THREE MAIN PROCESSES:

1) ASSIMILATION

 Conversion of substrates materials into protoplasmic

materials

 E.g. OM carbon to microbial carbon

29
  E.g. protein to microbial protein

2) MINERALIZATION

 Conversion of organic substance to inorganic form.

 E.g. protein from OM will be converted to inorganic nitrogen

in the soil.

3) IMMOBILIZATION

 Conversion of inorganic form into organic.

 E.g. inorganic nitrogen from the soil converted into microbial protein.

FACTORS AFFECTING RATE OF DECOMPOSITION

TEMPERTURE

• Microbial activity responds exponentially to increased temperature until

enzymes denature, etc.

30
 MOISTURE

• Microbial activity has optimum moisture

• Low moisture = dessication, slow diffusion

• High moisture = low O2 availability; no lignin degradation

pH

• Most microbes exhibit optimum activity near pH 7.

• Fungi most active in acid soil and bacteria in

moderate soil pH.

31
 SCHOOL OF BIO AND CHEMICAL ENGINEERING

DEPARTMENT OF BIOTECHNOLOGY

UNIT – III – MICROBIAL ECOLOGY – SMB2101

1
 UNIT: III

MICROBIAL INTERACTIONS

The inter- and intra-relationships between various microorganisms which can

include both positive (like SYMBIOSIS) and negative (like ANTIBIOSIS)
interactions. Examples include virus - bacteria and bacteria - bacteria.

The consortium may be in intermitent,cyclic or permanent. These are

ubiquitous, diverse and critically important in the function of any biological
community.

These includes-

 Neutralism
 Mutualism
 Commensalism
 Parasitism
 Cooperation
 Predation
 Amensalism
 Competition
 Synergism

PARTNERS INVOLVED

 MICROBE-MICROBE INTERACTION.

 MICROBE-PLANT INTERACTION.

 MICROBE-ANIMAL INTERACTION.

 MICROBE-HUMAN INTERACTIONS.

 MICROBE-ENVIRONMENT INTERACTIONS AND DISEASES.

2
NEUTRALISM

Neutralism describes the relationship between two species (interspecific) which

interact but do not affect each other. Microorganisms have no effect on each
other. Observed in natural communities if-

 Culture density is low.

 Nutrient level is high.

 Each culture has distinct requirements.

 It describes interactions where the fitness of one species has absolutely no

effect whatsoever on that of the other.

 True neutralism is extremely unlikely or even impossible to prove. When

dealing with the complex networks of interactions presented
by ecosystems, one cannot assert positively that there is absolutely no
competition between or benefit to either species.

3
  Since true neutralism is rare or nonexistent, its usage is often extended to
situations where interactions are merely insignificant or negligible.

Examples of true neutralism are virtually impossible to prove; the term is

in practice used to describe situations where interactions are negligible or
insignificant

 Neutralism (no interaction)

 implies lack of interaction

 populations have very different metabolic capabilities

 cannot happen between populations having the same or overlapping

functional role very difficult to demonstrate experimentally (hard to
prove a negative) occurs between populations that are spatially distant
from each other

MUTUALISM

In which individuals interact physically or even live within the body of the other
mutualist. Frequently the relationship is essential for the survival of at least on
member.

eg. Lichens are a fungal-algal symbiosis (that frequently includes a third

member, a cyanobacterium). the mass of fungal hyphae provides a protected
habitat for the algae and gathers mineral nutrients from rain water and from
dissolving the rock underneath. In return the algae and cyanobacteria provides
cabohydrates as a sources of energy for the fungus.

• The cyanobacteria (Nostoc, Calothrix), and diatoms (Epithemia,

Rhopalodia) containing cyanobacterial endosymbionts.

In these associations the symbiont supplies fixed nitrogen and/or, more rarely,
fixed carbon to the host, and the host provides habitat (i.e., optimal oxygen,
nutritional, and pH conditions, and optimal oxidation/reduction gradients) for
localized growth of the symbiont. A certain kind of bacteria lives in the
intestines of humans and many other animals. The human cannot digest all of
the food that its eats. The bacteria eat the food that the human cannot digest and
partially digest it, allowing the human to finish the job.

4
DEGREE OF DEPENDENCE

OBLIGATE: At least one species could not grow and reproduce without the
other. The species involved are in close proximity and interdependent with one
another in a way that one cannot survive without the other.

FACULTATIVE: Mutualisms are not essential for the survival of either

species. Individuals of each species engage in mutualism when the other species
is present. Both organisms do better with their mutualist, but can survive and
reproduce without it.

COOPERATION

Cooperation is a mutually beneficial relationship, similar to that which occurs in

mutualism, but in cooperation, this relationship is not obligatory:beneficial
complementary resources are provided by each of the paired microorganisms.
The organisms involved in this type of relationship can be separated, and if the
resources provided by the complementary microorganism are supplied in the
growth environment, each microorganism will function independently.

 Positive but not obligatery symbiosis

 Can be separated from one another.

 For eg-Desulfovibrio & Chromatium,Cellulomonas & Azotobactor.

Eg: 1Desulfovibrio and Chromatium (figure 28.9a), in which the carbon and
sulfur cycles are linked.

5
(a) The organic matter (OM) and sulfate required by Desulfovibrio are produced
by the Chromatium in its photosynthesis-driven reduction of CO2 to organic
matter and oxidation of sulfide to sulfate.

Eg: 2 The interaction of a nitrogen-fixing microorganism with a cellulolytic

organism such as Cellulomonas (figure 28.9b). Here the cellulose-degrading
microorganism liberates glucose from the cellulose, which can be used by
nitrogen-fixing microbes.

Cellulose degrader (Cellulomonas)

Nitrogen fixer (Azotobacter)

6
Azotobacter uses glucose provided by a cellulose-degrading microorganism
such as Cellulomonas, which uses the nitrogen fixed by Azotobacter.

COMMENSALISM

Commensalistic relationships between microorganisms include situations in

which the waste product of one microorganism is the substrate for another
species.One partner(commensal) benefits. while other(host) remains unaffected.

 – Common among organisms, not obligatory

 – Unidirectional

 – Usually, unaffected population modifies the environment in a way that

other population benefits.

 An example is nitrification, the oxidation of ammonium ion to nitrite by

microorganisms such as Nitrosomonas, and the subsequent oxidation of
the nitrite to nitrate by Nitrobacter and similar bacteria.

 Nitrobacter benefits from its association with Nitrosomonas because it

uses nitrite to obtain energy for growth.

 Commensalistic associations also occur when one microbial group

modifies the environment to make it more suited for another organism.

 For example, in the intestine the common, non-pathogenic strain of

Escherichia coli lives in the human colon, but also grows quite well
outside the host, and thus is a typical commensal.

 When oxygen is used up by the facultatively anaerobic E. coli, obligate

anaerobes such as Bacteroides are able to grow in the colon.

 The anaerobes benefit from their association with the host and E. coli,
but E. coli derives no obvious benefit from the anaerobes.

 In this case the commensal E. coli contributes to the welfare of other

symbionts.

 Commensalism can involve other environmental modifications.

7
  The synthesis of acidic waste products during fermentation stimulate the
proliferation of more acid-tolerant microorganisms, which are only a
minor part of the microbial community at neutral pHs.

PARASITISM

One speices is dependent on a another for nutrition and growth. oIn it, one
organism is benefitted and other is harmed. Closly related to predation.
oCoexistence between host and parasite.

For eg-Viruses are the highly specialized intracellular parasites,generally kill

the host.

Microbial parasite may kill the host or can have stable relationship without
killing the host.(lysogeny provirus is carried on host chromosome). Pathogenic
parasite may attack and kill the plant or animal host.

Obligate parasite Treponema pallidum(syphilis),Rickettsia(Rockey mountain

fever) can’t grow without an appropriate host.

 Some bacterial viruses can establish a lysogenic relationship with their

hosts, and the viruses, in their prophage state, can confer positive new
attributes on the host bacteria, as occurs with toxin production by
Corynebacterium diphtheriae.

 Parasitic fungi include Rhizophydium sphaero-carpum with the alga

Spyrogyra.

 Also, Rhizoctonia solani is a parasite of Mucor and Pythium, which is

important in biocontrol processes, the use of one microorganism to
control another. Human diseases caused by viruses, bacteria, fungi, and
protozoa.

 Myxobacteria are predators that actively kill bacteria of other species to

consume their biomass.

 Myxobacterium Myxococcus xanthus, which can access nutrients from a

broad spectrum of microorganisms.

 M. xanthus displays an epibiotic predation strategy, i.e., it induces prey

lysis from the outside and feeds on the released biomass.

8
  This predatory behavior encompasses various processes: Gliding motility
and induced cell reversals allow M. xanthus to encounter prey and to
remain within the area to sweep up its biomass, which causes the
characteristic “rippling” of preying populations.

 Antibiotics and secreted bacteriolytic enzymes appear to be important

predation factors, which are possibly targeted to prey cells with the aid of
outer membrane vesicles.

PREDATION

It involves predator species which target other microbe for material to survive.

 Predator attacks and kills its prey.

 They can be obligate or facultative.

 Members of predatory bacteria are known as ‘Bdellovibrio and like

organisms’(BALO).They can be epibiotic,periplasmic,cytoplasmic.

 For eg- Bdellovibrio-E.coli interaction (Vampirococcus,Daptobacter

both attack Chromatium.

 Predation is a widespread phenomenon where the predator engulfs or

attacks the prey,

 They can be obligate or facultative

 The prey can be larger or smaller than the predator, and this normally
results in the death of the prey.

 An interesting array of predatory bacteria are active in nature. Several of

the best examples including Bdellovibrio, Vampirococcus, and
Daptobacter.

 Each of these has a unique mode of attack against a susceptible

bacterium.

 Bdellovib-rio penetrates the cell wall and multiplies between the wall and
the

9
 
Bdellovibrio, a periplasmic predator that penetrates the cell wall and
grows outside the plasma membrane,

 plasma membrane, a periplasmic mode of attack, followed by lysis of the

prey and release of progeny

 Vampirococcus with its unique epibiotic mode of attacking a prey

bacterium

 Vampirococcus attaches to the surface of the prey (an epibiotic

relationship) and then secretes enzymes to release the cell contents.

 Daptobacter showing its cytoplasmic location as it attacks a susceptible

bacterium.

 Daptobacter penetrates a susceptible host and uses the cytoplasmic

contents as a nutrient source.

AMMENSALISM

 Focuses on exclusion of an organism from growing on a specific site to

prevent the utilization of limiting nutrients.

 Unidirectional process based on the release of a specific compound by

one organism that has negative effect on another.

 Product of one impact another i.e one species remains uneffected while
other is harmed.

 For eg- microbial production of antibiotics that

10
can inhibits or kill another.penicillin by fungi inhibit a type of cell wall found

 Amensalism (from the Latin for not at the same table) describes the
negative effect that one organism has on another organism as shown in
figure 28.1.

 This is a unidirectional process based on the release of a specific

compound by one organism which has a negative effect on another
organism.

 A classic example of amensalism is the production of antibiotics that can

inhibit or kill a susceptible microorganism (figure 28.16a).

 The attine ant-fungal mutualistic relationship is promoted by antibiotic-

producing bacteria that are maintained in the fungal garden system (figure
28.16b).

 In this case a streptomycete produces an antibiotic that controls

Escovopsis, a persistent parasitic fungus that can destroy the ant's fungal
garden. This unique amensalis-tic process appears to have evolved 50
million years ago in South America.

 Other important amensalistic relationships involve microbial production

of specific organic compounds that disrupt cell wall or plasma membrane
integrity. These include the bacteriocins.

 These substances are of increasing interest as food additives for

controlling growth of undesired pathogens .

 Antibacterial peptides can be released by the host and microorganisms in

the intestine. These molecules, called ce-cropins in insects and defensins
in mammals, recently have been recognized as effector molecules that
play significant roles in innate immunity.

 In animals these molecules are released by phagocytes and intestinal

cells, and are as powerful as tetracyclines.

 Finally, metabolic products, such as organic acids formed in

fermentation, can produce amensalistic effects. These compounds inhibit
growth by changing the environmental pH, for example, during natural
milk spoilage

11
Penicillin Antibiotic production by pencillium against Staphylococcus

COMPETITION

It arises when different organisms within population try to acquire same

resources. Both the species are harmed. Competiton within the species or
among different species can be attributed to availibility of Nitrogen
source,carbon source,electron donors,electron accepter,vitamins,light,water.

 Competition may result in exclusion of other species or the establishment

of a steady state where multiple species coexist.

 Eg- In aquatic environment where extensive phototrophic activity

results in blooms of single species of diatoms or cyanobacteria.

 Thermophilic springs chemolithotrophic organisms are dominated.

 Lactic acid fermentation of food.

 Large intestine of animals,a single species doesn’t dominate but a mixed

population coexist.

SYNTROPISM

Two species are required for growth on a specific electron donor that is not
metabolized by either organism alone or one of the organisms remove end
products of metabolism from other,which enables both the organisms to grow.

 Both the species are benefited.

 This relationship was discovered by Meyer Wolin and colleagues,when

fermentation of propionic acid occurred when there was a coculture.

 Synophobacter produces H during fermentation and accumulation of

H makes the reaction thermodynamically unstable.

 Pesence of methanogen,Methanospirillum makes the oxidation

favourable by consuming the H.’

12
MICROBE PLANT INTERACTIONS

Different interactions between microorganisms and plants have been identified

and the most obvious environment for such interactions is soil.

 Microbe-plant association can be mutulistic(a highly specialized

interaction where there is considerable specificity found in mutulistic

13
 activities)or it can be commensilistic(secretions from plants benefit
bacteria and fungi but no apparent benefit to plant.

SYMBIOSIS WITH CYANOBACTERIA

Beneficial aspects of plant-microbe symbiosis are,plants provide c-material to

support growth of microbes and microbes promote plant growth by supplying
minerals or N2.

 Eg.Azolla(fresh water aquatic fern)lives in symbiotic association with

Anabena azollae ,where cyanobacteria fixes atmospheric N2and Azolla
provides carbohydrates.cyanobacteria are present in trichomes and
nutrient exchange occurs through tiny fibres extending from plant to
cavity.

INTERACTIONS IN RHIZOSPHERE AND SYMBIOTIC SYSTEMS

Fungus-Root system

 Mucilage,organic acids(rhizodepozition),dead root cells(nucleic

acid,complex carb.,proteins)released by root tip act as c-source for
microbes.

 Microorganisms enhance the cycling of c and N compounds,consume

rhizospheric O and lower the redox potential of rhizosphere.

 Eg.Mycorrhizae-mutulistic relationship between fungus and

plantroot,growth on exterior of the root is the characteristic of
ectomycorrhiza while growth inside the root is attributed to
endomycorrhiza.

 Plants with mycorrhiza-

 can grow in low nutrient soil.

 display greater growth rates.

 more disease resistent.

 Boletus elegans and larix sp.

 Gigaspora margarita and cotton.

14
15
BACTERIA ROOT NODULE SYSTEM

 Enzyme system for N2 fixation is present only in prokaryotes and

nodules are associated with roots of Leguminous
plants,bacteria(rhizobia) are specific for a legume species.

 Assciation is beneficial for both,plant provide c and energy source to

bacteria and bacteria fix N2 and provide amino acid to plant.

 Rhizobium leguminosarum sp.and pea, beans tropical(root nodules).

 Azorhizobium caulinodan and Aquatic tropical legume(stem nodule).

 MICROBE ANIMAL INTERACTIONS Bacteria and fungi interact with

humans and other animals and this interaction can be symbiotic,
commensalistic or parasitic.

 Symbiotic relationships are widespread and has evolved new metabolic

capabilities and cellular structures.(symbiogenesis).

16
 Evolutionary benefits in a symbiotic relationship are;-provision of
dietary needs that their hosts lack including essential amino
acids,cofactors,metabolic factors etc.

 N storage and recycling.

 Large alterations in genome of symbionts and adaptations by host to

favour the symbiosis occur during long association which can be in form
of genome size reduction or increase in AT content in genome.since
endosymbionts protect their hosts from pathogens,this may have
influenced the evolution of sociality in animals to acquire the
endosymbiont through horizontal and vertical transmission.


Primary symbionts are tranmitted through vertical transmission and
secondary symbionts through horizontal transmission in addition to
maternal transmission.

 Buchnera aphidicola and Wiglesworthia glossinidia (Bacteria) are

examples of primary symbionts showing marked genome reduction and
resultant genome is the commitment to a symbiotic lifestyle.

17
  Secondary symbionts may have negative or positive effect on host and
are generally facultative and their genomes indicate that they are
adapting themselves to an obligate mutulism.

MICROBE ANIMAL MUTUALISM

 In vertebrates gut microbial community produce vitamins needed by

host,help digetion and colonization resistence.

 Termite(Reticulitermis speratus) gut community(symbioses within

symbiosis) responsible for cellulose degradation include
bacteria(spirochaetes,TG1,2,3,bacteroidetes,firmicutes) which provideN-
comp. by fixing N2 and nutrients to host and protists with their bacterial
and archeal ecto and endosymbionts degrade cellulose,provide a.acid and
cofactors to protists.

 Ambrosia beetle carries fungus to a new environment where fungus

flourishes beetle uses fungus as food.

18
MICROBE ANIMAL PARASITISM

One fascinating parasitic interaction involves

nematod(Heterorhabditisbacteriophora harboring a bacterial endosymbiont
Photorhabdus luminescens) and parasitize insects and humans.

The beneficial nematodes can be used to control a broad range of soil

inhabiting insects and above ground insects in their soil inhabiting stage of life.
White grubs, Beetle grubs, Japanese beetle

This nematod arrest their development in a phase called infective juvinile larval
stage at which it is infected by endosymbiont and when it infects the
insect,nematod further development is induced by insects hemolymph.

19
Endosymbiont secretes proteases supressing insects immune system and
damage the insect and nematod parasite feeds on endosymbiont and the insect
as well.

Photorhabdus fluorescent bacteria within a Heterorhabditis nematode

20
21
22
23
24
Bioluminescent bacteria

• Bioluminescent bacteria are light-producing bacteria that are

predominantly present in sea water, marine sediments, the surface of
decomposing fish and in the gut of marine animals. While not as
common, bacterial bioluminescence is also found in terrestrial and
freshwater bacteria.

• These bacteria may be free living (such as Vibrio harveyi) or in symbiosis

with animals such as the Hawaiian Bobtail squid (Aliivibrio fischeri) or
terrestrial nematodes (Photorhabdus luminescens).

• The host organisms provide these bacteria a safe home and sufficient
nutrition. In exchange, the hosts use the light produced by the bacteria for
concealment, prey and/or mate attraction. Bioluminescent bacteria have
evolved symbiotic relationships with other organisms in which both
participants benefit close to equally.

25
Mechanism

• All bacterial luciferases are approximately 80 KDa heterodimers

containing two subunits: α and β. The α subunit is responsible for light
emission.

• The luxA and luxB genes encode for the α and β subunits, respectively. In
most bioluminescent bacteria, the luxA and luxB genes are flanked
upstream by luxC and luxD and downstream by luxE.

• The bioluminescent reaction is as follows:

• FMNH2 + O2 + R-CHO -> FMN + H2O + R-COOH + Light (~ 495 nm)

• Molecular oxygen reacts with FMNH2 (reduced flavin mononucleotide)

and a long-chain aldehyde to produce FMN (flavin mononucleotide),
water and a corresponding fatty acid. The blue-green light emission of
bioluminescence, such as that produced by Photobacterium
phosphoreum and Vibro harveyi, results from this reaction.

• Because light emission involves expending six ATP molecules for each
photon, it is an energetically expensive process. For this reason, light
emission is not constitutively expressed in bioluminescent bacteria; it is
expressed only when physiologically necessary.

• The symbiotic relationship between the Hawaiian bobtail

squid Euprymna scolopes and the marine gram-negative
bacterium Aliivibrio fischeri has been well studied.

• The two organisms exhibit a mutualistic relationship in which

bioluminescence produced by A. fischeri helps to attract pray to the squid
host, which provides nutrient-rich tissues and a protected environment
forA. fischeri.

• Euprymna scolopes lives in a symbiotic relationship with

the bioluminescent bacteria Aliivibrio fischeri, which inhabits a special
light organ in the squid's mantle.

• The bacteria are fed a sugar and amino acid solution by the squid and in
return hide the squid's silhouette when viewed from below by matching
the amount of light hitting the top of the mantle (counter-illumination)

26
 • Bioluminescence provided by A. fischeri also aids in the defense of the
squid E. scolopes by providing camouflage during its nighttime foraging
activity.

• Following bacterial colonization, the specialized organs of the squid

undergo developmental changes and a relationship becomes established.
The squid expels 90% of the bacterial population each morning, because
it no longer needs to produce bioluminescence in the daylight

• This expulsion benefits the bacteria by aiding in their dissemination. A

single expulsion by one bobtail squid produces enough bacterial
symbionts to fill 10,000m3 of seawater at a concentration that is
comparable to what is found in coastal waters..

• Thus, in at least some habitats, the symbiotic relationship between A.

fischeri and E. scolopes plays a key role in determining the abundance
and distribution of E. scolopes. There is a higher abundance of A.
fischeri in the vicinity of a population of E. scolopes and this abundance
markedly decreases with increasing distance from the host's habitat.

• Bioluminescent Photobacterium species also engage in mutually

beneficial associations with fish and squid.

• Dense populations of P. kishitanii, P. leiogathi, and P.

mandapamensis can live in the light organs of marine fish and squid, and
are provided with nutrients and oxygen for reproduction in return for
providing bioluminescence to their hosts, which can aid in sex-specific
signaling, predator avoidance, locating or attracting prey, and schooling.

NEMATOPHAGUS FUNGI

Some fungi prey on nematodes as a source of nutrients .

By parmer 1964, Nordbring-Hertz and Jansson 1984, Barron 1992

Common Genera of nematode-trapping fungi are:-

1. Arthrobotrys

2. Dactylaria

3. Dactylella

27
4. Trichothecium

Mechanisms by which the fungi capture nematode prey:-

1. Production of networks of adhesive branches

2. Stalked adhesive knobs

3. Adhesive rings

4. Constrictive rings

MECHANISM

When a nematode prey attempts to move past an adhesive hyphal structure, it is

sticks to it and is trapped. When it tries to pass through a constricting ring, a
fungal ring contracts by a sudden osmotic swelling and traps the nematode.

Voilent movements and attempts by nematodes to escape generally fails. The

fungal hyphae penetrates into nematode which is then enzymatically degraded.

When growing in the absence of nematode appears to induce the formation of

morphological structure that traps the nematodes. This is a unique relationship
in which presence of prey induces the formation of fungal structures that result
in its capture and consumption. When a nematode prey attempts to move past an
adhesive hyphal structure, it is sticks to it and is trapped.

When it tries to pass through a constricting ring, a fungal ring contracts by a

sudden osmotic swelling and traps the nematode. Voilent movements and
attempts by nematodes to escape generally fails.

The fungal hyphae penetrates into nematode which is then enzymatically

degraded. When growing in the absence of nematode appears to induce the
formation of morphological structure that traps the nematodes.

This is a unique relationship in which presence of prey induces the formation of

fungal structures that result in its capture and consumption.

MOSTLY DEUTEROMYCOTA ARE FEW BASIDOMYCOTA

EXAMPLE

28
Hohenbuehelia and Resupinatus- capture nematode by means of adhesive
knobs. Pleurotus ostreatus (edible oyster mushroom) & Pleurotus sp. Form no
trap structure. By mean of toxin they paralyze nematodes. The described
Basidiomycota often grow on decaying wood, a nitrogen poor substrate.It is
suggest by Thorn and Barron in 1984 that captured nematodes are source of
supplemental nitrogen for fungi.

Infective larvae captured by nematophagus fungi

29
 SCHOOL OF BIO AND CHEMICAL ENGINEERING
DEPARTMENT OF BIOTECHNOLOGY

UNIT – IV – MICROBIAL ECOLOGY – SMB2101

1
 UNIT: IV

MECHANISMS OF BACTERIAL PATHOGENESIS

Introduction

A pathogen is a microorganism that is able to cause disease in a plant, animal

or insect. Pathogenicity is the ability to produce disease in a host organism.
Microbes express their pathogenicity by means of their virulence, a term which
refers to the degree of pathogenicity of the microbe. Hence, the determinants
of virulence of a pathogen are any of its genetic or biochemical or structural
features that enable it to produce disease in a host.

Staphylococcus aureus, arguably the most prevalent pathogen of humans,

may cause up to one third of all bacterial diseases ranging from boils and
pimples to food poisoning, to septicemia and toxic shock.

The Underlying Mechanisms of Bacterial Pathogenesis

Two broad qualities of pathogenic bacteria underlie the means by which they
cause disease:

1. Exposure to the host

2. Attachment to the host

3. Colonization in the site of attachment and cause localized infection or

follow Invasiveness.

Invasiveness is the ability to invade tissues. It encompasses mechanisms for

colonization (adherence and initial multiplication), production of

2
extracellular substances which facilitate invasion (invasins) and ability to
bypass or overcome host defense mechanisms.

4.Establishment of disease in specific site by production of toxin or enzymes.

1. Bacterial Adherence to Mucosal Surfaces. In its simplest form, bacterial

adherence or attachment to a eucaryotic cell or tissue surface requires the
participation of two factors: a receptor and an ligand. The receptors so far
defined are usually specific carbohydrate or peptide residues on the eucaryotic
cell surface. The bacterial ligand, called an adhesin, is typically a
macromolecular component of the bacterial cell surface which interacts with the
host cell receptor. Adhesins and receptors usually interact in a complementary
and specific fashion. Table 1 is a list of terms that are used in medical
microbiology to refer to microbial adherence to surfaces or tissues.

TABLE 1. TERMS USED TO DESCRIBE ADHERENCE FACTORS

IN HOST-PARASITE INTERACTIONS
ADHERENCE
DESCRIPTION
FACTOR
A surface structure or macromolecule that binds a
Adhesin
bacterium to a specific surface
A complementary macromolecular binding site on a
Receptor (eucaryotic) surface that binds specific adhesins or
ligands
Lectin Any protein that binds to a carbohydrate
A surface molecule that exhibits specific binding to a
Ligand
receptor molecule on another surface
The mucopolysaccharide layer of glucosaminoglycans
Mucous
covering animal cell mucosal surfaces
Filamentous proteins on the surface of bacterial cells that
Fimbriae
may behave as adhesins for specific adherence
Common pili Same as fimbriae
A specialized pilus that binds mating procaryotes
Sex pilus
together for the purpose of DNA transfer
Fimbriae in Enterobacteriaceae which bind specifically
Type 1 fimbriae to mannose terminated glycoproteins on eucaryotic cell
surfaces
Type 4 pili Pili in certain Gram-positive and Gram-negative
bacteria. In Pseudomonas, thought to play a role in
adherence and biofilm formation

3
 Proteins that form the outermost cell envelope
S-layer component of a broad spectrum of bacteria, enabling
them to adhere to host cell membranes and
environmental surfaces in order to colonize.
A layer of exopolysaccharide fibers on the surface of
Glycocalyx bacterial cells which may be involved in adherence to a
surface. Sometimes a general term for a capsule.
A detectable layer of polysaccharide (rarely polypeptide)
Capsule on the surface of a bacterial cell which may mediate
specific or nonspecific attachment
A distinct cell wall component of the outer membrane of
Lipopolysaccharide Gram-negative bacteria with the potential structural
(LPS) diversity to mediate specific adherence. Probably
functions as an adhesion
Teichoic acids and
Cell wall components of Gram-positive bacteria that may
lipoteichoic acids
be involved in nonspecific or specific adherence
(LTA)

Specific Adherence of Bacteria to Cell and Tissue Surfaces

Several types of observations provide indirect evidence for specificity of

adherence of bacteria to host cells or tissues:

1. Tissue tropism: particular bacteria are known to have an apparent preference

for certain tissues over others, e.g. S. mutans is abundant in dental plaque but
does not occur on epithelial surfaces of the tongue; the reverse is true for S.
salivarius which is attached in high numbers to epithelial cells of the tongue but
is absent in dental plaque.

2. Species specificity: certain pathogenic bacteria infect only certain species of

animals, e.g. N. gonorrhoeae infections are limited to humans;
Enteropathogenic E. coli K-88 infections are limited to pigs; E. coli CFA I and
CFA II infect humans; E. coli K-99 strain infects calves.; Group A streptococcal
infections occur only in humans.

3. Genetic specificity within a species: certain strains or races within a species

are genetically immune to a pathogen , e.g. Certain pigs are not susceptible to E.
coli K-88 infections; Susceptibility to Plasmodium vivax infection (malaria) is
dependent on the presence of the Duffy antigens on the host's redblood cells.

Although other explanations are possible, the above observations might be

explained by the existence of specific interactions between microorganisms and

4
eucaryotic tissue surfaces which allow microorganisms to become established
on the surface.

Mechanisms of Adherence to Cell or Tissue Surfaces

The mechanisms for adherence may involve two steps:

1. nonspecific adherence: reversible attachment of the bacterium to the

eucaryotic surface (sometimes called "docking")

2. specific adherence: reversible permanent attachment of the

microorganism to the surface (sometimes called "anchoring").

The usual situation is that reversible attachment precedes irreversible

attachment but in some cases, the opposite situation occurs or specific
adherence may never occur.

Nonspecific adherence involves nonspecific attractive forces which allow

approach of the bacterium to the eucaryotic cell surface. Possible interactions
and forces involved are:

1. hydrophobic interactions

2. electrostatic attractions

3. atomic and molecular vibrations resulting from fluctuating dipoles of similar

frequencies

4. Brownian movement

5. recruitment and trapping by biofilm polymers interacting with the bacterial

glycocalyx (capsule)

Specific adherence involves permanent formation of many specific lock-and-

key bonds between complementary molecules on each cell surface.
Complementary receptor and adhesin molecules must be accessible and
arranged in such a way that many bonds form over the area of contact between
the two cells. Once the bonds are formed, attachment under physiological
conditions becomes virtually irreversible.

5
Specific adherence involves complementary chemical interactions between
the host cell or tissue surface and the bacterial surface. In the language of
medical microbiologist, a bacterial "adhesin" attaches covalently to a host
"receptor" so that the bacterium "docks" itself on the host surface. The
adhesins of bacterial cells are chemical components of capsules, cell walls,
pili or fimbriae. The host receptors are usually glycoproteins located on the
cell membrane or tissue surface.

Some Specific Bacterial Adhesins and their Receptors

The adhesins of E. coli are their common pili or fimbriae. A single strain of E.
coli is known to be able to express several distinct types of fimbriae encoded by
distinct regions of the chromosome or plasmids. This genetic diversity permits
an organism to adapt to its changing environment and exploit new opportunities
presented by different host surfaces. Many of the adhesive fimbriae of E. coli
have probably evolved from fimbrial ancestors resembling Type-I and Type IV
fimbriae.

Type-I fimbriae enable E. coli to bind to D-mannose residues on eucaryotic cell

surfaces. Type-I fimbriae are said to be "mannose-sensitive" since exogenous
mannose blocks binding to receptors on red blood cells. Although the primary
17kDa fimbrial subunit is the major protein component of Type-1 fimbriae, the
mannose-binding site is not located here, but resides in a minor protein (28-
31kDa) located at the tips or inserted along the length of the fimbriae. By
genetically varying the minor "tip protein" adhesin, the organisms can gain
ability to adhere to different receptors. For example, tip proteins on
pyelonephritis-associated (pap) pili recognize a galactose-galactose
disaccharide, while tip proteins on S-fimbriae recognize sialic acid.

Pseudomonas, Vibrio and Neisseria possess Type IV pili that contain protein
subunit with a methylated amino acid, often phenylalanine, at or near its amino
terminus. These "N-methylphenylalanine pili" have been established as
virulence determinants in pathogenesis of Pseudomonas aeruginosa lung
infection in cystic fibrosis patients. These type of fimbriae occur in Neisseria
gonorrhoeae and their receptor is thought to be an oligosaccharide. Type IV pili

6
are the tcp (toxin coregulated pili) fimbriae used in attachment of Vibrio
cholerae to the gastrointestinal epithelium.

Gram stain of Neisseria gonorrhoeae, the agent of the STD gonorrhea. The
bacteria are seen as pairs of cocci (diplococci) in association with host
pmn's (polymorphonuclear leukocytes). Gonorrhea is the second most
prevalent STD in the U.S. behind chlamydia. The bacterium has multiple
determinants of virulence including the ability to attach to and enter host
cells, resist phagocytic killing and produce endotoxins which eventually
lead to an intense inflammatory response. CDC.

The adhesins of Streptococcus pyogenes are controversial. In 1972, Gibbons

and his colleagues demonstrated that attachment of streptococci to the oral
mucosa of mice is dependent on M protein. Olfek and Beachey argued that
lipoteichoic acid (LTA), rather than M protein, was responsible for
streptococcal adherence to buccal epithelial cells. In 1996, Hasty and Courtney
proposed a two-step model of attachment that involved both M protein and
teichoic acids. They suggested that LTA loosely tethers streptococci to
epithelial cells, and then M protein secures a firmer, irreversible association. In
1992, protein F was discovered and found to be a fibronectin binding protein.

7
More recently, in 1998, M proteins M1 and M3 were also found to bind to
fibronectin. Apparently, S. pyogenes produces multiple adhesins with varied
specificities.

Electron micrograph of Streptococcus pyogenes (Group A strep) by Maria

Fazio and Vincent A. Fischetti, Ph.D. with permission. The Laboratory of
Bacterial Pathogenesis and Immunology, Rockefeller University. The cell
surface fibrils, that consist primarily of M protein, are clearly evident. The
M protein has several possible roles in virulence: it is involved in
adherence, resistance to phagocytosis, and in antigenic variation of the
pathogen.

Staphylococcus aureus also binds to the amino terminus of fibronectin by

means of a fibronectin-binding protein which occurs on the bacterial surface.
Apparently S. aureus and Group A streptococci use different mechanisms but
adhere to the same receptor on epithelial surfaces.

Treponema pallidum has three related surface adhesins (P1, P2 and P3) which
bind to a four-amino acid sequence (Arg-Gly-Asp-Ser) of the cell-binding
domain of fibronectin. It is not clear if T. pallidum uses fibronectin to attach to
host surfaces or coats itself with fibronectin to avoid host defenses (phagocytes
and immune responses).

8
**
Treponema pallidum, the spirochete that causes syphilis. Silver stain. CDC.

TABLE 2. EXAMPLES OF SPECIFIC ATTACHMENTS OF BACTERIA

TO HOST CELL OR TISSUE SURFACES

Attachment
Bacterium Adhesin Receptor Disease
site
Amino
Streptococcus Pharyngeal
Protein F terminus of Sore throat
pyogenes epithelium
fibronectin
Streptococcus Glycosyl Salivary Pellicle of
Dental caries
mutans transferase glycoprotein tooth
Buccal
Streptococcus Lipoteichoic
Unknown epithelium None
salivarius acid
of tongue
N-acetylhexos-
Streptococcus Cell-bound Mucosal
amine-galactose Pneumonia
pneumoniae protein epithelium
disaccharide
Amino
Staphylococcus Cell-bound Mucosal
terminus of Various
aureus protein epithelium
fibronectin
Type IV pili
Glucosamine- Urethral/
Neisseria (N-
galactose cervical Gonorrhea
gonorrhoeae methylphenyl-
carbohydrate epithelium
alanine pili)
Enterotoxigenic Species-specific Intestinal
Type-I fimbriae Diarrhea
E. coli carbohydrate(s) epithelium

9
Uropathogenic Complex Urethral
Type I fimbriae Urethritis
E. coli carbohydrate epithelium
Globobiose
Uropathogenic Upper
P-pili (pap) linked to Pyelonephritis
E. coli urinary tract
ceramide lipid
Fimbriae Galactose on
Bordetella Respiratory Whooping
("filamentous sulfated
pertussis epithelium cough
hemagglutinin") glycolipids
N- Fucose and
Intestinal
Vibrio cholerae methylphenyl- mannose Cholera
epithelium
alanine pili carbohydrate
Treponema Peptide in outer Surface protein Mucosal
Syphilis
pallidum membrane (fibronectin) epithelium
Membrane Respiratory
Mycoplasma Sialic acid Pneumonia
protein epithelium
Conjunctival
Conjunctivitis
Chlamydia Unknown Sialic acid or urethral
or urethritis
epithelium

COLONIZATION

Colonization: the establishment of the pathogen at the appropriate portal of

entry. Pathogens usually colonize host tissues that are in contact with the
external environment. Sites of entry in human hosts include the urogenital tract,
the digestive tract, the respiratory tract and the conjunctiva. Organisms that
infect these regions have usually developed tissue adherence mechanisms and
some ability to overcome or withstand the constant pressure of the host defenses
at the surface.

INVASION

The invasion of a host by a pathogen may be aided by the production of

bacterial extracellular substances which act against the host by breaking down
primary or secondary defenses of the body. Medical microbiologists have long
referred to these substances as invasins. Most invasins are proteins (enzymes)
that act locally to damage host cells and/or have the immediate effect of
facilitating the growth and spread of the pathogen. The damage to the host as a
result of this invasive activity may become part of the pathology of an
infectious disease.

10
The extracellular proteins produced by bacteria which promote their invasion
are not clearly distinguished from some extracellular protein toxins
("exotoxins") which also damage the host. Invasins usually act at a short range
(in the immediate vicinity of bacterial growth) and may not actually kill cells as
part of their range of activity; exotoxins are often cytotoxic and may act at
remote sites (removed from the site of bacterial growth). Also, exotoxins
typically are more specific and more potent in their activity than invasins. Even
so, some classic exotoxins (e.g. diphtheria toxin, anthrax toxin) may play some
role in colonization or invasion in the early stages of an infection, and some
invasins (e.g. staphylococcal leukocidin) have a relatively specific cytopathic
effect.

A Survey of Bacterial Invasins

Spreading Factors

"Spreading Factors" is a descriptive term for a family of bacterial enzymes that

affect the physical properties of tissue matrices and intercellular spaces, thereby
promoting the spread of the pathogen.

Hyaluronidase. is the original spreading factor. It is produced by streptococci.

staphylococci, and clostridia. The enzyme attacks the interstitial cement
("ground substance") of connective tissue by depolymerizing hyaluronic acid.

Collagenase is produced by Clostridium histolyticum and Clostridium

perfringens. It breaks down collagen, the framework of muscles, which
facilitates gas gangrene due to these organisms.

Neuraminidase is produced by intestinal pathogens such as Vibrio cholerae

and Shigella dysenteriae. It degrades neuraminic acid (also called sialic acid),
an intercellular cement of the epithelial cells of the intestinal mucosa.

Streptokinase and staphylokinase are produced by streptococci and

staphylococci, respectively. Kinase enzymes convert inactive plasminogen to
plasmin which digests fibrin and prevents clotting of the blood. The relative
absence of fibrin in spreading bacterial lesions allows more rapid diffusion of
the infectious bacteria.

Enzymes that Cause Hemolysis and/or Leucolysis

These enzymes usually act on the animal cell membrane by insertion into the
membrane (forming a pore that results in cell lysis), or by enzymatic attack on
phospholipids, which destabilizes the membrane. They may be referred to as
lecithinases or phospholipases, and if they lyse red blood cells they are

11
sometimes called hemolysins. Leukocidins, produced by staphylococci and
streptolysin produced by streptococci specifically lyse phagocytes and their
granules. These latter two enzymes are also considered to be bacterial
exotoxins.

Phospholipases, produced by Clostridium perfringens (i.e., alpha toxin),

hydrolyze phospholipids in cell membranes by removal of polar head groups.

Lecithinases, also produced by Clostridium perfringens, destroy lecithin

(phosphatidylcholine) in cell membranes.

Hemolysins, notably produced by staphylococci (i.e., alpha toxin), streptococci

(i.e., streptolysin) and various clostridia, may be channel-forming proteins or
phospholipases or lecithinases that destroy red blood cells and other cells (i.e.,
phagocytes) by lysis.

Beta-hemolytic Streptococcus. This is the characteristic appearance of a

blood agar plate culture of the bacterium. Note the translucency around
the bacterial colonies, representing hemolysis of the red cells in the culture
medium due to production of a diffusible hemolysin (streptolysin).

Staphylococcal coagulase

Coagulase, formed by Staphylococcus aureus, is a cell-associated and diffusible

enzyme that converts fibrinogen to fibrin which causes clotting. Coagulase
activity is almost always associated with pathogenic S. aureus and almost never
associated with nonpathogenic S. epidermidis, which has led to much
speculation as to its role as a determinant of virulence. Possibly, cell bound

12
coagulase could provide an antigenic disguise if it clotted fibrin on the cell
surface. Or a staphylococcal lesion encased in fibrin (e.g. a boil or pimple)
could make the bacterial cells resistant to phagocytes or tissue bactericides or
even drugs which might be unable to diffuse to their bacterial target.

Extracellular Digestive Enzymes

Heterotrophic bacteria, in general, produce a wide variety of extracellular

enzymes including proteases, lipases, glycohydrolases, nucleases, etc., which
are not clearly shown to have a direct role in invasion or pathogenesis. These
enzymes presumably have other functions related to bacterial nutrition or
metabolism, but may aid in invasion either directly or indirectly.

Toxins With Short-Range Effects Related to Invasion

Bacterial protein toxins which have adenylate cyclase activity, are thought to
have immediate effects on host cells that promote bacterial invasion. One
component of the anthrax toxin (EF or Edema Factor) is an adenylate cyclase
that acts on nearby cells to cause increased levels of cyclic AMP and disruption
of cell permeability. One of the toxins of Bordetella pertussis, the agent of
whooping cough, has a similar effect. These toxins may contribute to invasion
through their effects on macrophages or lymphocytes in the vicinity which are
playing an essential role to contain the infection. For example, since they use
ATP as a substrate, they may deplete phagocyte reserves of energy needed for
ingestion. Edema is seen as a pathology because the increase in cAMP in
affected cells disrupts equilibrium.

13
Gelatinous edema seen in a cutaneous anthrax lesion. CDC.

The following table summarizes the activities of many bacterial proteins that are
noted for their contribution to bacterial invasion of tissues.

TABLE 3. SOME EXTRACELLULAR

BACTERIAL PROTEINS THAT ARE
CONSIDERED INVASINS
Bacteria
Invasin Activity
Involved
Degrades
Streptococci,
hyaluronic of
Hyaluronidase staphylococci
connective
and clostridia
tissue
Collagenase Clostridium Dissolves

14
 species collagen
framework of
muscles
Degrades
Vibrio
neuraminic
cholerae and
Neuraminidase acid of
Shigella
intestinal
dysenteriae
mucosa
Converts
Staphylococcus fibrinogen to
Coagulase
aureus fibrin which
causes clotting
Converts
Staphylococci
plasminogen to
Kinases and
plasmin which
streptococci
digests fibrin
Disrupts
neutrophil
membranes
Staphylococcus
Leukocidin and causes
aureus
discharge of
lysosomal
granules
Repels
phagocytes
and disrupts
phagocyte
Streptococcus
Streptolysin membrane and
pyogenes
causes
discharge of
lysosomal
granules
Phospholipases
or lecithinases
Streptococci,
that destroy
Hemolysins staphylococci
red blood cells
and clostridia
(and other
cells) by lysis
Destroy
Clostridium
Lecithinases lecithin in cell
perfringens
membranes

15
 Destroy
Clostridium phospholipids
Phospholipases
perfringens in cell
membrane
One
component
(EF) is an
adenylate
Bacillus cyclase which
Anthrax EF
anthracis causes
increased
levels of
intracellular
cyclic AMP
One toxin
component is
an adenylate
cyclase that
Bordetella
Pertussis AC acts locally
pertussis
producing an
increase in
intracellular
cyclic AMP

EVASION OF HOST DEFENSES

Some pathogenic bacteria are inherently able to resist the bactericidal

components of host tissues. For example,

1.The poly-D-glutamate capsule of Bacillus anthracis protects the organisms

against cell lysis by cationic proteins in sera or in phagocytes.

2. The outer membrane of Gram-negative bacteria is a formidable permeability

barrier that is not easily penetrated by hydrophobic compounds such as bile salts
which are harmful to the bacteria.

3. Pathogenic mycobacteria have a waxy cell wall that resists attack or digestion
by most tissue bactericides.

4. And intact lipopolysaccharides (LPS) of Gram-negative pathogens may

protect the cells from complement-mediated lysis or the action of lysozyme.

16
Most successful pathogens, however, possess additional structural or
biochemical features which allow them to resist the main lines of host internal
defense against them, i.e., the phagocytic and immune responses of the host.

Overcoming Host Phagocytic Defenses

Microorganisms invading tissues are first and foremost exposed to phagocytes.

Bacteria that readily attract phagocytes, and that are easily ingested and killed,
are generally unsuccessful as parasites. In contrast, most bacteria that are
successful as parasites interfere to some extent with the activities of phagocytes
or in some way avoid their attention.

Microbial strategies to avoid phagocytic killing are numerous and diverse, but
are usually aimed at blocking one or of more steps in the phagocytic process.
Recall the steps in phagocytosis:

1. Contact between phagocyte and microbial cell

2. Engulfment

3. Phagosome formation

4. Phagosome-lysosome fusion

5. Killing and digestion

Avoiding Contact with Phagocytes

Bacteria can avoid the attention of phagocytes in a number of ways.

1. Invade or remain confined in regions inaccessible to phagocytes. Certain

internal tissues (e.g. the lumen of glands) and surface tissues (e.g. the skin) are
not patrolled by phagocytes.

2. Avoid provoking an overwhelming inflammatory response. Some pathogens

induce minimal or no inflammation required to focus the phagocytic defenses.

3. Inhibit phagocyte chemotaxis. e.g. Streptococcal streptolysin (which also

kills phagocytes) suppresses neutrophil chemotaxis, even in very low
concentrations. Fractions of Mycobacterium tuberculosis are known to inhibit
leukocyte migration. Clostridium ø toxin inhibits neutrophil chemotaxis.

4. Hide the antigenic surface of the bacterial cell. Some pathogens can cover the
surface of the bacterial cell with a component which is seen as "self" by the host
phagocytes and immune system. Phagocytes cannot recognize bacteria upon

17
contact and the possibility of opsonization by antibodies to enhance
phagocytosis is minimized. For example, pathogenic Staphylococcus aureus
produces cell-bound coagulase which clots fibrin on the bacterial surface.
Treponema pallidum binds fibronectin to its surface. Group A streptococci are
able to synthesize a capsule composed of hyaluronic acid.

Inhibition of Phagocytic Engulfment

Some bacteria employ strategies to avoid engulfment (ingestion) if phagocytes

do make contact with them. Many important pathogenic bacteria bear on their
surfaces substances that inhibit phagocytic adsorption or engulfment. Clearly it
is the bacterial surface that matters. Resistance to phagocytic ingestion is
usually due to a component of the bacterial cell wall, or fimbriae, or a capsule
enclosing the bacterial wall. Classical examples of antiphagocytic substances on
the bacterial surface include:

Polysaccharide capsules of S. pneumoniae, Haemophilus influenzae, Treponema

pallidum and Klebsiella pneumoniae

M protein and fimbriae of Group A streptococci

Surface slime (polysaccharide) produced by Pseudo monas aeruginosa

O antigen associated with LPS of E. coli

K antigen of E. coli or the analogous Vi antigen of Salmonella typhi

Cell-bound or soluble Protein A produced by Staphylococcus aureus

18
Streptococcus pneumoniae, FA stain showing its antphagocytic capsule
(CDC). S. pneumoniae cells that possess a capsule are virulent;
nonencapsulated strains are avirulent. Although S. pneumoniae strains
possess a variety of determinants of virulence, this illustrates the essential
role of their capsule in ability to resist phagocytosis by alveolar
macrophages in order to initiate disease.

Survival Inside of Phagocytes

Some bacteria survive inside of phagocytic cells, in either neutrophils or

macrophages. Bacteria that can resist killing and survive or multiply inside of
phagocytes are considered intracellular parasites. The environment of the
phagocyte may be a protective one, protecting the bacteria during the early
stages of infection or until they develop a full complement of virulence factors.
The intracellular environment guards the bacteria against the activities of
extracellular bactericides, antibodies, drugs, etc.

Most intracellular parasites have special (genetically-encoded) mechanisms to

get themselves into their host cell as well as special mechanisms to survive once

19
they are inside. Intracellular parasites usually survive by virtue of mechanisms
which interfere with the bactericidal activities of the host cell. Some of these
bacterial mechanisms include:

1. Inhibition of phagosome-lysosome fusion. The bacteria survive inside of

phagosomes because they prevent the discharge of lysosomal contents into the
phagosome environment. Specifically, phagolysosome formation is inhibited in
the phagocyte. This is the strategy employed by Salmonella, M. tuberculosis,
Legionella and the Chlamydiae.

Intracellular Mycobacterium tuberculosis in lung. Ziehl-Neelsen acid fast

stain (CDC).

2. Survival inside the phagolysosome. With some intracellular parasites,

phagosome-lysosome fusion occurs but the bacteria are resistant to inhibition
and killing by the lysosomal constituents. Also, some extracellular pathogens
can resist killing in phagocytes utilizing similar resistance mechanisms. Little is
known of how bacteria can resist phagocytic killing within the phagocytic
vacuole, but it may be due to the surface components of the bacteria or due to
extracellular substances that they produce which interfere with the mechanisms
of phagocytic killing. Bacillus anthracis, Mycobacterium tuberculosis and
Staphylococcus aureus all possess mechanisms to survive intracellular killing in
macrophages.

3. Escape from the phagosome. Early escape from the phagosome vacuole is
essential for growth and virulence of some intracellular pathogens. This is a
very clever strategy employed by the Rickettsias which produce a

20
phospholipase enzyme that lyses the phagosome membrane within thirty
seconds of after ingestion.

Products of Bacteria that Kill or Damage Phagocytes

One obvious strategy in defense against phagocytosis is direct attack by the

bacteria upon the professional phagocytes. Any of the substances that pathogens
produce that cause damage to phagocytes have been referred to as "aggressins".
Most of these are actually extracellular enzymes or toxins that kill phagocytes.
Phagocytes may be killed by a pathogen before or after ingestion.

Killing phagocytes before ingestion. Many Gram-positive pathogens,

particularly the pyogenic cocci, secrete extracellular enzymes which kill
phagocytes. Many of these enzymes are called "hemolysins" because their
activity in the presence of red blood cells results in the lysis of the rbcs.

Pathogenic streptococci produce streptolysin. Streptolysin O binds to

cholesterol in membranes. The effect on neutrophils is to cause lysosomal
granules to explode, releasing their contents into the cell cytoplasm.

Pathogenic staphylococci produce leukocidin, which also acts on the neutrophil

membrane and causes discharge of lysosomal granules.

Other examples of bacterial extracellular proteins that inhibit phagocytosis

include the Exotoxin A of Pseudomonas aeruginosa which kills macrophages,
and the bacterial exotoxins that are adenylate cyclases (e.g. anthrax toxin EF
and pertussis AC) which decrease phagocytic activity.

Gram stain of a pustular exudate from a mixed bacterial infection. Pus is

the usual outcome of the battle between phagocytes and bacterial strategies
to kill them.

Killing phagocytes after ingestion. Some bacteria exert their toxic action on
the phagocyte after ingestion has taken place. They may grow in the phagosome
and release substances which can pass through the phagosome membrane and
cause discharge of lysosomal granules, or they may grow in the phagolysosome

21
and release toxic substances which pass through the phagolysosome membrane
to other target sites in the cell. Many bacteria which are the intracellular
parasites of macrophages (e.g. Mycobacteria, Brucella, Listeria) usually destroy
macrophages in the end, but the mechanisms are not understood.

Evading Complement

Antibodies that are bound to bacterial surfaces will activate complement by the
classical pathway and bacterial polysaccharides activate complement by the
alternative pathway. Bacteria in serum and other tissues, especially Gram-
negative bacteria, need protection from the antimicrobial effects of complement
before and during an immunological response.

One role of capsules in bacterial virulence is to protect the bacteria from

complement activation and the ensuing inflammatory response. Polysaccharide
capsules can hide bacterial components such as LPS or peptidoglycan which
can induce the alternate complement pathway. Some bacterial capsules are able
to inhibit formation of the C3b complex on their surfaces, thus avoiding C3b
opsonization and subsequent formation of C5b and the membrane attack
complex (MAC) on the bacterial cell surface. Capsules that contain sialic acid (a
common component of host cell glycoproteins), such as found in Neisseria
meningitidis, have this effect.

One of the principal targets of complement on Gram-negative bacteria is LPS. It

serves as the attachment site for C3b and triggers the alternative pathway of
activation. It also binds C5b.

LPS can be modified by pathogens in two ways that affects its interaction with
complement. First, by attachment of sialic acid residues to the LPS O antigen, a
bacterium can prevent the formation of C3 convertase just as capsules that
contain sialic acid can do so. Both Neisseria meningitidis and Haemophilus
influenzae, which cause bacterial meningitis, are able to covalently attach sialic
acid residues to their O antigens resulting in resistance to MAC. Second, LPS
with long, intact O antigen side-chains can prevent effective MAC killing.
Apparently the MAC complex is held too far from the vulnerable outer
membrane to be effective.

Avoiding Host Immunological Responses

On epithelial surfaces the main antibacterial immune defense of the host is the
protection afforded by secretory antibody (IgA). Once the epithelial surfaces
have been penetrated, however, the major host defenses of inflammation,
complement, phagocytosis, Antibody-mediated Immunity (AMI), and Cell-
mediated Immunity (CMI) are encountered. If there is a way for a pathogen to

22
successfully bypass or overcome these host defenses, then some bacterial
pathogen has probably discovered it. Bacteria evolve very rapidly in relation to
their host, so that most of the feasible anti-host strategies are likely to have been
tried out and exploited. Ability to defeat the immune defenses may play a major
role in the virulence of a bacterium and in the pathology of disease. Several
strategic bacterial defenses are described below.

Immunological Tolerance to a Bacterial Antigen

Tolerance is a property of the host in which there is an immunologically-

specific reduction in the immune response to a given Ag. Tolerance to a
bacterial Ag does not involve a general failure in the immune response but a
particular deficiency in relation to the specific antigen(s) of a given bacterium.
If there is a depressed immune response to relevant antigens of a parasite, the
process of infection is facilitated. Tolerance can involve either AMI or CMI or
both arms of the immunological response.

Tolerance to an Ag can arise in a number of ways, but three are possibly

relevant to bacterial infections.

1. Fetal exposure to Ag

2. High persistent doses of circulating Ag

3. Molecular mimicry. If a bacterial Ag is very similar to normal host

"antigens", the immune responses to this Ag may be weak giving a degree of
tolerance. Resemblance between bacterial Ag and host Ag is referred to as
molecular mimicry. In this case the antigenic determinants of the bacterium are
so closely related chemically to host "self" components that the immunological
cells cannot distinguish between the two and an immune response cannot be
raised. Some bacterial capsules are composed of polysaccharides (hyaluronic
acid, sialic acid) so similar to host tissue polysaccharides that they are not
immunogenic.

Antigenic Disguise

Bacteria may be able to coat themselves with host proteins (fibrin, fibronectin,
antibody molecules) or with host polysaccharides (sialic acid, hyaluronic acid)
so that they are able to hide their own antigenic surface components from the
immunological system.

Immunosuppression

23
Some pathogens (mainly viruses and protozoa, rarely bacteria) cause
immunosuppression in the infected host. This means that the host shows
depressed immune responses to antigens in general, including those of the
infecting pathogen. Suppressed immune responses are occasionally observed
during chronic bacterial infections such as leprosy and tuberculosis.

Persistence of a Pathogen at Bodily Sites Inaccessible to the Immune

Response

Some pathogens can avoid exposing themselves to immune forces.

Intracellular pathogens can evade host immune responses as long as they stay
inside of infected cells and they do not allow microbial Ag to form on the cell
surface. Macrophages support the growth of the bacteria and at the same time
give them protection from immune responses.

Some pathogens persist on the luminal surfaces of the GI tract, oral cavity and
the urinary tract, or the lumen of the salivary gland, mammary gland or the
kidney tubule.

Induction of Ineffective Antibody

Many types of antibody are formed against a given Ag, and some bacterial
components may display various antigenic determinants. Antibodies tend to
range in their capacity to react with Ag (the ability of specific Ab to bind to an
Ag is called avidity). If Abs formed against a bacterial Ag are of low avidity, or
if they are directed against unimportant antigenic determinants, they may have
only weak antibacterial action. Such "ineffective" (non-neutralizing) Abs might
even aid a pathogen by combining with a surface Ag and blocking the
attachment of any functional Abs that might be present.

Antibodies Absorbed by Soluble Bacterial Antigens

Some bacteria can liberate antigenic surface components in a soluble form into
the tissue fluids. These soluble antigens are able to combine with and
"neutralize" antibodies before they reach the bacterial cells. For example, small
amounts of endotoxin (LPS) may be released into surrounding fluids by Gram-
negative bacteria.

Antigenic Variation

One way bacteria can avoid forces of the immune response is by periodically
changing antigens, i.e., undergoing antigenic variation. Some bacteria avoid the

24
host antibody response by changing from one type of fimbriae to another, by
switching fimbrial tips. This makes the original AMI response obsolete by using
new fimbriae that do not bind the previous antibodies. Pathogenic bacteria can
vary (change) other surface proteins that are the targets of antibodies. Antigenic
variation is prevalent among pathogenic viruses as well.

Changing antigens during the course of an infection

Antigens may vary or change within the host during the course of an infection,
or alternatively antigens may vary among multiple strains (antigenic types) of a
parasite in the population. Antigenic variation is an important mechanism used
by pathogenic microorganisms for escaping the neutralizing activities of
antibodies. Antigenic variation usually results from site-specific inversions or
gene conversions or gene rearrangements in the DNA of the microorganisms.

Changing antigens between infections

Many pathogenic bacteria exist in nature as multiple antigenic types or

serotypes, meaning that they are variant strains of the same pathogenic species.
For example, there are multiple serotypes of Salmonella typhimurium based on
differences in cell wall (O) antigens or flagellar (H) antigens. There are 80
different antigenic types of Streptococcus pyogenes based on M-proteins on the
cell surface. There are over one hundred strains of Streptococcus pneumoniae
depending on their capsular polysaccharide antigens. Based on minor
differences in surface structure chemistry there are multiple serotypes of Vibrio
cholerae, Staphylococcus aureus, Escherichia coli, Neisseria gonorrhoeae and
an assortment of other bacterial pathogens.

TOXIGENESIS

Two types of bacterial toxins

At a chemical level there are two types of bacterial toxins:

lipopolysaccharides, which are associated with the cell walls of Gram-negative

bacteria.

proteins, which may be released into the extracellular environment of

pathogenic bacteria.

The lipopolysaccharide (LPS) component of the Gram-negative bacterial outer

membrane bears the name endotoxin because of its association with the cell
wall of bacteria.

25
Most of the protein toxins are thought of as exotoxins, since they are "released"
from the bacteria and act on host cells at a distance.

BACTERIAL PROTEIN TOXINS

The protein toxins are typically soluble proteins secreted by living bacteria
during exponential growth. The production of protein toxins is generally
specific to a particular bacterial species (e.g. only Clostridium tetani produces
tetanus toxin; only Corynebacterium diphtheriae produces the diphtheria toxin).
Usually, virulent strains of the bacterium produce the toxin (or range of toxins)
while nonvirulent strains do not, such that the toxin is the major determinant of
virulence. Both Gram-positive and Gram-negative bacteria produce soluble
protein toxins. Bacterial protein toxins are the most potent poisons known and
may show activity at very high dilutions.

The protein toxins resemble enzymes in a number of ways. Like enzymes,

bacterial exotoxins:

are proteins

are denatured by heat, acid, proteolytic enzymes

have a high biological activity (most act catalytically)

exhibit specificity of action

As enzymes attack specific substrates, so bacterial protein toxins are highly

specific in the substrate utilized and in their mode of action. The substrate (in
the host) may be a component of tissue cells, organs, or body fluid. Usually the
site of damage caused by the toxin indicates the location of the substrate for that
toxin. Terms such as "enterotoxin", "neurotoxin", "leukocidin" or "hemolysin"
are sometimes used to indicate the target site of some well-defined protein
toxins.

Certain protein toxins have very specific cytotoxic activity (i.e., they attack
specific cells, for example, tetanus or botulinum toxins), but some (as produced
by staphylococci, streptococci, clostridia, etc.) have fairly broad cytotoxic
activity and cause nonspecific death of tissues (necrosis). Toxins that are
phospholipases may be relatively nonspecific in their cytotoxicity because they
cleave phospholipids which are components of host cell membranes resulting in
the death of the cell by leakage of cellular contents. This is also true of pore-
forming "hemolysins" and "leukocidins".

26
A few protein toxins obviously bring about the death of the host and are known
as "lethal toxins", and even though the tissues affected and the target sites may
be known, the precise mechanism by which death occurs is not understood (e.g.
anthrax toxin).

Protein toxins are inherently unstable: in time they lose their toxic properties but
retain their antigenic ones. This was first discovered by Ehrlich and he coined
the term toxoid for this product. Toxoids are detoxified toxins which retain their
antigenicity and their immunizing capacity. The formation of toxoids can be
accelerated by treating toxins with a variety of reagents including formalin,
iodine, pepsin, ascorbic acid, ketones, etc. The mixture is maintained at 37 o at
pH range 6 to 9 for several weeks. The resulting toxoids can be use for artificial
immunization against diseases caused by pathogens where the primary
determinant of bacterial virulence is toxin production. Toxoids are the
immunizing agents against diphtheria and tetanus that are part of the DPT
vaccine.

A + B Subunit Arrangement of Protein Toxins

Many protein toxins, notably those that act intracellularly (with regard to host
cells), consist of two components: one component (subunit A) is responsible for
the enzymatic activity of the toxin; the other component (subunit B) is
concerned with binding to a specific receptor on the host cell membrane and
transferring the enzyme across the membrane. The enzymatic component is not
active until it is released from the native toxin. Isolated A subunits are
enzymatically active and but lack binding and cell entry capability. Isolated B
subunits may bind to target cells (and even block the binding of the native A+B

27
toxin), but they are nontoxic.

Tertiary structure of the pertussis toxin produced by Bordetella pertussis.

Pertussis toxin is a member of the A-B bacterial toxin superfamily. It is a
hexameric protein comprising five distinct subunits, designated S1-S5. S2,
S3, S4 and S5 comprise the B oligomer, responsible for binding the toxin to
the cell surface. Each subunit is translated separately with an amino-
terminal signal sequence which is cleaved during transport to the
periplasm. S2 and S3 function as adhesins, S2 binds specifically to a
glycolipid called lactosylceramide, which is found primarily on the ciliated
epithelial cells. S3 binds to a glycoprotein found mainly on phagocytic cells.

Attachment and Entry of Toxins

There are at least two mechanisms of toxin entry into target cells. In one
mechanism called direct entry, the B subunit of the native toxin (A+B) binds to
a specific receptor on the target cell and induces the formation of a pore in the
membrane through which the A subunit is transferred into the cell cytoplasm. In
an alternative mechanism, the native toxin binds to the target cell and the A+B
structure is taken into the cell by the process of receptor-mediated endocytosis

28
(RME). The toxin is internalized in the cell in a membrane-enclosed vesicle
called an endosome. H+ ions enter the endosome lowering the internal pH which
causes the A+B subunits to separate. Somehow, the B subunit affects the release
of the A subunit from the endosome so that it will reach its target in the cell
cytoplasm. The B subunit remains in the endosome and is recycled to the cell
surface. In both cases, a large protein molecule must insert into and cross a
membrane lipid bilayer. This activity is reflected in the ability of most A/B
native toxins, or their B components, to insert into artificial lipid bilayers,
creating ion permeable pathways.

Table 4. SOURCES AND ACTIVITIES OF BACTERIAL

TOXINS
NAME OF BACTERIUM
ACTIVITY
TOXIN INVOLVED
Edema Factor (EF) is an adenylate
cyclase that causes increased levels
Anthrax toxin Bacillus in intracellular cyclic AMP in
(EF) anthracis phagocytes and formation of ion-
permeable pores in membranes
(hemolysis)
Acts locally to increase levels of
Adenylate Bordetella cyclic AMP in phagocytes and
cyclase toxin pertussis formation of ion-permeable pores
in membranes (hemolysis)
ADP ribosylation of G proteins
stimulates adenylate cyclase and
Cholera
Vibrio cholerae increases cAMP in cells of the GI
enterotoxin
tract, causing secretion of water
and electrolytes
E. coli LT
Escherichia coli Similar to cholera toxin
toxin
Enzymatically cleaves rRNA
Shigella
Shiga toxin resulting in inhibition of protein
dysenteriae
synthesis in susceptible cells
Zn++ dependent protease that
Botulinum Clostridium inhibits neurotransmission at
toxin botulinum neuromuscular synapses resulting
in flaccid paralysis
Tetanus toxin Clostridium Zn++ dependent protease that

29
 tetani inhibits neurotransmission at
inhibitory synapses resulting in
spastic paralysis
ADP ribosylation of elongation
Diphtheria Corynebacterium
factor 2 leads to inhibition of
toxin diphtheriae
protein synthesis in target cells
ADP ribosylation of G proteins
Bordetella
Pertussis toxin blocks inhibition of adenylate
pertussis
cyclase in susceptible cells
Massive activation of the immune
Staphylococcus Staphylococcus system, including lymphocytes and
enterotoxins* aureus macrophages, leads to emesis
(vomiting)
Toxic shock Acts on the vascular system
Staphylococcus
syndrome toxin causing inflammation, fever and
aureus
(TSST-1)* shock
Pyrogenic
exotoxins
(SPE) e.g. Streptococcus Causes localized erythematous
Erythrogenic pyogenes reactions
toxin (scarlet
fever toxin)*

Superantigens: The "pyrogenic exotoxins" produced by Staphylococcus aureus

and Streptococcus pyogenes have been designated as superantigens. They
represent a family of molecules with the ability to elicit massive activation of
the immune system. These proteins share the ability to stimulate T cell
proliferation by interaction with Class II MHC molecules on APCs and specific
V beta chains of the T cell receptor. The important feature of this interaction is
the resultant production of IL-1, TNF, and other lymphokines which appear to
be the principal mediators of disease processes associated with these toxins.

VIRAL VIRULENCE FACTOR

Although viral pathogens are not similar to bacterial pathogens in terms of
structure, some of the properties that contribute to their virulence are similar.
Virus virulence factors allow it to replicate, modify host defences, and spread
within the host, and they are toxic to the host.

1. REPLICASES:
The replicases of viruses like Human immunodeficiency virus 1 and Human
immunodeficiency virus 2 (HIV-1 and HIV-2, respectively) are called

30
 reverse transcriptases since they can make DNA copies using a genomic
RNA molecule as a template.
In most RNA viruses, the replicase is an RNA-dependent RNA polymerase,
or RdRp (RNA --> RNA). In the case of retroviruses (Family Retroviridae)
like HIV (genus Lentivirus), however, the replicase is an RNA-dependent
DNA polymerase (RNA --> DNA); that is, the said reverse transcriptase.
The enzymes are encoded and used by viruses that use reverse transcription
as a step in the process of replication. Reverse-transcribing RNA viruses,
such as retroviruses, use the enzyme to reverse-transcribe their RNA
genomes into DNA, which is then integrated into the host genome and
replicated along with it. Reverse-transcribing DNA viruses, such as the
hepadnaviruses, can allow RNA to serve as a template in assembling and
making DNA strands. HIV infects humans with the use of this enzyme.
Without reverse transcriptase, the viral genome would not be able to
incorporate into the host cell, resulting in failure to replicate.

2. VIRAL ADHESINS OR COAT PROTEIN

Viruses use adhesins to facilitate adhesion to host cells, and certain

enveloped viruses rely on antigenic variation to avoid the host immune
defenses. These virulence factors are discussed in more detail in the
following sections.

One of the first steps in any viral infection is adhesion of the virus to
specific receptors on the surface of cells. This process is mediated by
adhesins that are part of the viral capsid or membrane envelope. The
interaction of viral adhesins with specific cell receptors defines the tropism
(preferential targeting) of viruses for specific cells, tissues, and organs in
the body. The spike protein hemagglutinin found on Influenzavirus is an
example of a viral adhesin; it allows the virus to bind to the sialic acid on the
membrane of host respiratory and intestinal cells. Another viral adhesin is the
glycoprotein gp20, found on HIV. For HIV to infect cells of the immune
system, it must interact with two receptors on the surface of cells. The first
interaction involves binding between gp120 and the CD4 cellular marker
that is found on some essential immune system cells. However, before viral
entry into the cell can occur, a second interaction between gp120 and one of
two chemokine receptors (CCR5 and CXCR4) must occur. Table 6 lists
the adhesins for some common viral pathogens and the specific sites to which
these adhesins allow viruses to attach.

Table 6. Some Viral Adhesins and Their Host Attachment Sites

31
Pathogen Disease Adhesin Attachment Site

Sialic acid of
Influenzavirus Influenza Hemagglutinin respiratory and
intestinal cells

Heparan sulfate on
Oral herpes,
Herpes simplex Glycoproteins mucosal surfaces
genital
virus I or II gB, gC, gD of the mouth and
herpes
genitals

Human CD4 and CCR5 or

Glycoprotein
immunodeficiency HIV/AIDS CXCR4 of immune
gp120
virus system cells

3. ANTIGENIC VARIATION IN VIRUSES

Antigenic variation also occurs in certain types of enveloped viruses, including

influenza viruses, which exhibit two forms of antigenic variation: antigenic drift
and antigenic shift (Figure 9). Antigenic drift is the result of point mutations
causing slight changes in the spike proteins hemagglutinin (H) and
neuraminidase (N). On the other hand, antigenic shift is a major change in spike
proteins due to gene reassortment. This reassortment for antigenic shift occurs
typically when two different influenza viruses infect the same host.

The rate of antigenic variation in influenza viruses is very high, making it

difficult for the immune system to recognize the many different strains of
Influenzavirus. Although the body may develop immunity to one strain through
natural exposure or vaccination, antigenic variation results in the continual
emergence of new strains that the immune system will not recognize. This is the
main reason that vaccines against Influenzavirus must be given annually. Each
year’s influenza vaccine provides protection against the most prevalent strains
for that year, but new or different strains may be more prevalent the following
year.

32
Figure 9. Antigenic drift and antigenic shift in influenza viruses. (a) In
antigenic drift, mutations in the genes for the surface proteins
neuraminidase and/or hemagglutinin result in small antigenic changes over
time. (b) In antigenic shift, simultaneous infection of a cell with two
different influenza viruses results in mixing of the genes. The resultant
virus possesses a mixture of the proteins of the original viruses. Influenza
pandemics can often be traced to antigenic shifts.

4. SILENCING SUPPRESSORS

SUPPRESSORS ACTION OF HOST AGAINST VIRUSES

1. INTERFERON:

Interferons are naturally occurring proteins secreted by cells in

response to virus infections. When a cell is infected with a
virus, it releases interferon which diffuses to the surrounding
cells. After binding to the receptors present on the adjacent or
surrounding cells; interferon stimulates the production of
antiviral proteins in the cells.

33
Figure 2.5. Activation of interferon following virus infection:

Interferons are of two types

Type I (interferon α and β) and type II (interferon γ).
Interferon α is produced by lymphocyte, β by fibroblast, and γ
by T lymphocytes upon viral infection. The type of interferon
are less or more potent against the class of virus species, for
example, interferon α and β inhibits the vesicular stomatitis
and encephalomyocarditis viruses better than interferon γ
while interferon γ works better in case of vaccinia and reovirus
infection.

Many genes are transcriptionally regulated by interferons

following virus infection. Among all, three members have
been studied extensively for their antiviral activities.

1) dsRNA activated protein kinase (PKR)

2) 2’,5’- oligoadenylate synthetase (OAS)
3) Mx proteins

34
 Figure 2.7.Schematic representation of interferon signaling
for the activation of antiviral gene

1. dsRNA activated protein kinase (PKR) – During dsRNA virus infection PKR
forms the dimer, and is activated following phosphorylation. Eukaryotic
translation initiation factor (EIF-2α) is the most important substrate
phosphorylated by PKR. EIF-2α gets inactivated following its phosphorylation
leading to inhibition of viral protein synthesis. This way PKR exhibits antiviral
activity.
2. 2’, 5’- oligoadenylate synthetase (OAS) - Interferon inducible OAS is also
activated by dsRNA formed during viral infection. It binds to RNase L
triggering its dimerization and activation. Activated RNase L degrades the
mRNA leading to inhibition of protein synthesis
3. Mx proteins - Interferon induced Mx protein have antiviral activity against
several RNA viruses. Mice expressing Mx proteins are more resistant to many
virus infections e.g. influenza.

35
Apoptosis
Apoptosis (programmed cell death) is an interesting way explored by the host
cell in order to prevent virus infection. In apoptosis cell must die before virus
starts its replication. During apoptosis, cellular DNA undergo fragmentation and
apoptotic bodies are formed which are then engulfed by macrophages and other
cells of the immune system. Activation of apoptotic cycle involves release of
“cytochrome C” from mitochondria and downstream activation of caspases
(cysteine-aspartic proteases) cascade.

Role of the immune system against virus attack

Natural killer cells and cytotoxic T cells are the major type of immune cells
involved against virus infection in the host. Natural killer cells are activated
immediately upon virus infection and produce the cytokines such as tumor
necrosis factor (TNF) and interferon γ. They also cause the direct cytotoxicity of
the virus infected cells. In later stages of virus infection, the virus surface
antigens are presented over the major histocompatibility antigens class I (MHC-
I) molecules and activates the cytotoxic T lymphocytes (CTLs). CTLs exert
antiviral state by secreting cytokines and apoptosis. Sometime the level of
MHC-I gets downregulated in the virus infected cells, in that condition natural
killer cells comes at the site of rescue to take over the task and kills the virus
infected cells.

EVASION OF INTERFERON SYSTEM BY VIRUSES

Interferons are well studied and established defense system against virus
infection. Nevertheless, cohabitation between the host and viruses resulted in
the procurement of mechanism to inhibit interferon system by most of the
viruses. Viruses inhibit the interferon activation by blocking the different steps
involved in the interferon signaling cascade. Some of the unique strategies used
by the viruses to decoy the interferon system are enlisted below

Inhibition of protein synthesis

Many viruses hijack the host protein synthesis machinery for their own benefits.
This leads to inhibition of cellular protein synthesis and upregulation of viral
protein synthesis. As the interferons are also proteins, viral mediated inhibition
of host protein synthesis can assist to the inhibition of interferons. Translation
inhibition by phosphorylation of eIF2α is a host mediated antiviral mechanism,

36
many viruses evolved in a way to carryout eIF2α independent translation in
order to escape the immune surveillance.

Inhibition of interferon production

Type-I interferon production is activated by dsRNA formed during virus
infections. Many viruses encode dsRNA-binding proteins that inhibit the
enzymes protein kinases and 2’-5’ oligoadenylate synthetase. The sigma
protein of reoviruses, and the non structural protein of rotavirus and
influenza viruses are some examples of dsRNA- binding proteins.

37
Inhibition of interferon signaling
Herpes virus and papillomavirus blocks the interferon production by
inhibiting the downstream signaling pathway. Adenoviruses, measles virus,
and hepatitis viruses were also shown to inhibit the interferon production.
All the essential components of interferon signaling pathways, i.e.
interferon receptors, JAK/STAT and IRFs have been shown to be involved
in virus mediated inhibition.

Despite the identification of the various strategies by which virus interfere

with interferon action, little is known on the precise mechanism that exists
between viruses and the interferon pathways, and its possible implications
on viral pathogenicity, clearance, and viral immunity.

Virus response against apoptosis

Virus inhibits the apoptosis by interrupting the various stages of

transcription and translation. Herpes and poxviruses are evolved in a way
to modulate the apoptosis by blocking the activation of caspases. SV40 T
antigen and E1 protein of adenovirus are known to bind with p53 and
target it for proteasomal degradation. Although many viruses prevent
apoptosis, herpes virus can selectively cause apoptosis in the lymphocytes
in order to delay their removal from the host cell.

Virus response against host immune system

Many viruses come up with a system to reduce the expression of MHC-I

molecules over the virus infected host cell surface. This explains the
important role of MHC-I towards viral invasion into the susceptible host
cells.

HIV, adenovirus, and herpesvirus inhibits the translocation of peptide

within the endoplasmic reticulum, which is a necessary step for the loading
and trafficking of the peptide over the MHC-I molecules. Cytomegalovirus
produces a homologues of MHC-I molecule to decoy the host immune
system.Herpes simplex virus express a “glycoprotein E” that binds to the
immunoglobulin molecules and prevents the activation of antibody
mediated immune response.

38
EFFECTS OF PATHOGENS ON PLANT PHYSIOLOGICAL
FUNCTIONS

Plant pathogens: Organisms which cause diseases in plants called

plant pathogens. Pathogens interfere with the different
physiological function(s) (photosynthesis, translocation of water,
organic compounds, inorganic minerals, transpiration, respiration
etc) of the plant and lead to the development of different

symptoms (necrosis, chrorosis, stunted growth, no flower, no

fruit, no seed).

Eg: 1. Thus a pathogen that infects and kills the flowers of a

plant interferes with the ability of the plant to produce seed and
multiply.

Eg: 2. A pathogen that injects and kills part or cell of the roots
of a plant reduces the ability of the plant to absorb water and
nutrients and results in its wilting and death.

2.1 eg: The photosynthetic efficiency of bean leaves with rust,

angular leaf spot and anthrachose was found that these
diseases assess for the crop damage.

Similarly, a pathogen that infects and kills parts of the leaves or

destroys their chlorophyll leads to reduced photosynthesis,
growth and yield of the plant and so forth.

39
In most cases the relationship between the symptoms of the
plant and the physiological functions affected is obvious end
understandable.

Effect of pathogens on photosynthesis

Photosynthesis is the basic function of green plants. It enables them to

transform light energy into chemical energy, which they can utilize in all
cell activity. Photosynthesis is the ultimate source of nearly all energy used
in all living cells.

In view of the fundamental position of photosynthesis in the life of plants,

it is apparent that any interference by pathogens with photosynthesis results
in a diseased condition in the plant.
That pathogens do interfere with photosynthesis is obvious from the
chlorosis (chlorosis is a condition in which leaves produce insufficient
chlorophyll).

The infected plant produces neurotic lesions or large necrotic areas on green
plants parts, that leads to reduced growth and amounts of fruits produced by
many infected plants.

40
 Chlorosis in leaves
Diseases affect the photosynthesis: the leaf spots, blight and other kinds of
diseases in which there is destruction of leaf tissue. The diseases like cereal
rusts and fungal leaf spots, bacteial leaf spots, viral mosoics and yellowing
and stunting diseases or in defoliations, photosynthesis is reduced because
the photosynthetic surface of the plant is declined.

The effects of rust and anthrac nose (Anthracnose Disease Info Anthracnose is
a fungal disease that tends to attack plants in the spring when the weather is
cool and wet, primarily on leaves and twigs.) on the photosynthetic
competence of diseased bean leaves was reported. The overall chlorophyll
content of leaves in many fungal and bacterial diseases is reduced, but the
photosynthetic activity of the remaining chlorophyll seems to remain
unaffected.

41
 Leafy spot

Blight disease

Effect of Aschochyta blight on the decrease in

photosynthesizing leaf area and the reduction of
photosynthetic efficiency by green leaf area of dried-pea was
observed.

Accounting for photosynthetic efficiency of bean leaves with

rust, angular leaf spot and anthracnose was reported to
asses crop damage.

42
In some fungal and bacterial diseases, photosynthesis is
reduced because the toxins such as tentoxin and tabtoxin
produced by these pathogens inhibit some of the enzymes
that are involved directly or indirectly in photosynthesis:

In plants infected by many vascular pathogens, tomato

remain partially closed, chlorophyll is reduced and
photosynthesis stops, even before the plant eventually wilts.

Due to leaf blast of rice, ratio between virtual and visual

lesion size as a measure to describe reduction in leaf
photosynthesis was reported.

Most virus, mollicute (Mollicutes are a class of bacteria with no

bacterial cell wall) and nematode diseases also induce varying

degrees of Chlorosis and stunting. In the majority of such

diseases, the photosynthesis of infected plants is reduced

greatly. In advanced stages of disease, the rate of

photosynthesis is no more than one forth of normal rate.

Effect of pathogens on translocation of water and

nutrients in the host plant

All living plant cells require an abundance of water and an

adequate amount of organic and inorganic nutrients in order

to live and to carry out their physiological functions. Plants

absorb water and inorganic (mineral) nutrients from the soil

43
through their root system. Effect of potassium on growth,

water relations, the inorganic and organic solute contents for

two maize cultivers grown under saline conditions had been

reported. These substances are generally translocated upward

through the xylem vessels of the stem and into the vascular

bundles of the petioles and leaf veins, from which they enter

the leaf cells. All organic nutrients of plants are produced in the

leaf cells, following photosynthesis and are translocated down

ward and distributed to all the living plant cells passing, for the

most part, through the phloem tissues.

A calcium regulated gatekeeper in phloem sieve tube is found.

When a pathogen interferes with the upward movement of

inorganic nutrients and water or with the downward movement

of organic substances diseased conditions results in the parts

of plants denied these materials. The comparative

physiology of salt and water stress shows that the diseased

parts, in turn, will be unable to cary out their own

functions and will deny the rest of the plant their services

or their products, thus causing disease of the entire plant. Soil

water accumulation under different precipitation potential

evaporation and straw mulch conditions show reduction in the

yield crop.

For e.g. if water movement to the leaves is inhibited, the

leaves cannot function properly photosynthesis is reduced

44
or stopped and few or no nutrients are available to move up to
the roots, which in turn become starred and diseased and may
die.

Photosynthesis, transpiration and carbohydrate content of

apple leaves infected by Podosphaera leucotricha (fungi).
Interference with upward translocation of water and inorganic

Many plant pathogens interfere in one or more ways with the

translocation of water and inorganic nutrients through plants.
Some pathogen affect the integrity or function of the roots,
causing them to absorb less water; other pathogens, by growing
in the xylem vessels or by other means, interfere with
translocation of water through the stem; and in some diseases
pathogens interfere with the water economy of the plant by causing
excessive transpiration through their effects on leaves and
stomata.

Effect on translocation of water through the xylem

Fungal and bacterial pathogens that cause damping off, stem rots,
and cankers may reach the xylem vessels in the area of the
infection and if the affected plants and collapse. Canters is
older plants, particularly older trees, may cause some reduction in
the translocation of water, but generally do not kill plants unless
the cankers are big or numerous enough to encircle the plant.

45
In vascular wilts, however reduction in water translocation may
vary from little to complete. In many cases, affected vessels may
be filled with the bodies of the pathogen and with the substances
secreted by the pathogen or by the host in response to the
pathogen and may become clogged.

Certain pathogens, such as the crown gall bacterium, the club root
protozoa on the foot knot nematode induce gall formation in the
stem, roots or both. The enlarged and proliforating cells near or
around the xylem exert pressure on the xylem vessels, which may
be crushed and dislocated, there by becoming less efficient in
transporting water.

The most typical and complete dysfunction of xylem in

translocating water, however, is observed in the vascular wilts,

caused by the fungi cersatocystis, ophiostoma, fusarium and

verticillium and bacteria such as Pseudomonas, Ralstonia and

Erwinia. These pathogens invade the xylem of roots and stems

and produce diseases primarily by interfering with the upward

movement of water through the xylem.

In host combinations with the fastidious bacterium Xylella

fastidiosa growth, multiplication and spread of bacteria in xylem
vessels are clower and instead of causing wilting and rapid
death of the plant, a scorching of the margins of the leaves and
several other symptoms occur, but rarely does the plant die
quickly. In all cases, however in infected hosts the flow of water
is reduced through reduction in the size or collapse of vessels due

46
to infection, development of tyloses in the vessels, release of
large molecules compounds in the vessel as a result of cell wall
break down by pathogenic enzymes and reduced water tension
in the vessels due to pathogen induced alteration in foliar
transpiration.

Effect on transpiration

Stomatal transpiration

Lenticular transpiration

Cuticular transpiration

In plant diseases in which the pathogen infects the leaves,

transpiration is usually increased.

This is the result of destruction of at least part of the protection

afforded the leaf by the cuticle, an increase in the permeability
of leaf cells, and the dysfunction of stomata.

 In diseases such as rusts, in which numerous pustules form

and break up the epidermis.

47
Rust disease
 In most leaf spots; in which the cuticle epidermis and
all the other tissue, inducing xylem may be destroyed in the
infected areas

 In the powdery mildews, in which a large proportion of

the epidermal cells are invaded by the fungus,

Powdery mildew on leaves

 In apple scab, in which the fungus grows between the
cuticle and epidermis

 In all these examples, the destruction of a considerable

portion of cuticle and epidermis results in an uncontrolled loss
of water from the affected areas.

48
 If water absorption and translocation cannot keep up with
the excessive loss of water, loss of turgor, and wilting of
leaves follow.

 The suction forces of excessively transpiring leaves are

increased abnormally and may lead to collapse or dysfuction
of underlying vessels through the production of tyloses
(balloon like outgrowth of parenchymatous cells to the lumen
of tracheids or vessels of the secondary xylem) and gums.

Interference with translocation of organic nutrients through

the phloem

Organic nutrients produced in leaf cells through photosynthesis move

through plasmodesmeta into adjoining phloem elements. Plant
pathogens may interfere with the movement of organic nutrients
from the leaf cells to the phloem, with their translocation through
the phloem elements, or possibly, with their movement from
phloem into the cells that will utilize them.

Obligate fungal parasites, such as rust and mildew fungi, cause

an accumulation of photosynthetic product as well as inorganic

nutrients in the areas invaded by the pathogen. In these

diseases, the infected areas are characterized by reduced

photosynthesis and increased respiration.

In stem diseases of woody plants in which cankers develop, the

pathogen attacks and remains confined to the bark for a considerable

49
time. In diseases caused by phytoplasmas, as well as in diseases
caused by phloem-limited fastidious bacteria, bacteria exist and
reproduce in the phloem sieve tubes thereby interfering with the
downward translocation of nutrients.

Cankers

In several plants propagated by grafting a variety scion onto a

rootstock, infection of the combination with a virus e.g. infection of
an apple or stone-fruit root stock with (tomato ringspot virus)
leads to formation of a necrotic plate at the points of contact of
hypersensitive scion variety with the root stock, which leads to
the death of scion.

50
In some viral diseases, particularly the leaf curling type and

some yellows diseases, starch accumulation in the leaves, as

the result of degeneration (nacrosis) of the phloem of infected

plants, which is one of the first symptoms.

It is also possible however at least in some virus diseases, that

the interference with translocation of starch stems from

inhibition by the virus of the enzymes that break down starch

into smaller transposable molecules.

This is suggested by the observation that is some mosaic

diseases, in which there is no phloem necrosis, infected

discolored areas of leaves contain less starch than ‘healthy’,

greener areas at the end of the day, a period favorable for

photosynthesis, but the same leaf areas contain more starch

than the ‘healthy’ areas of the a period of dark, which favors

starch hydrolysis add translocation.

This suggests not only that virus infected areas synthesis less
starch than healthy ones, but also that starch is not degraded
and translocated easily from virus-infected areas, although no
damage to the phloem is present.

Effect of pathogens on host plant respiration

51
Respiration is the process by which cells, through the
enzymatically controlled oxidation (burning) of the energy rich
carbohydrates and fatty acids, liberate energy in a form that can
be utilized for the performance of various cellular processes.

The energy produced through respiration is utilized by the plant

for all types of cellular work, such as accumulation and
mobilization of compounds, synthesis of proteins, activation of
enzymes, cell growth and division, defense reactions, and a
host of other processes.

 The respiration is a complex process

 Number of enzymes involved

 Respiration occurs in every single cell

 It affects the functions and existence of the cell

From this we can understand that the respiration of plant tissues

is one of the first functions to be affected when plants are
infected by pathogens.

Respiration in diseased plants

When plants are infected by pathogen, the rate of respiration

generally increases. This means that affected tissues use up their
reserve carbohydrates faster than healthy tissues.
 The increased rate of respiration appears shortly after
infection certainly by the time of appearance of visible

52
symptoms and continues to rise during the multiplication and
sporulation of the pathogen.
 Stimulation of respiration in Ulva /eciuca by high
concentration of cadmium and zinc evidence for an alternative
respiratory pathway.
 In susceptible varieties, in which no defense mechanisms can
be mobilized quickly against a particular pathogen, respiration
increases slowly after inoculation, but continues to rise and
remains at a high level for much longer periods.

 The effect of Pb2 and Cd2 on respiration and mitochondrial

electron transport chain in germinating pea seed .

The increased respiration of diseased plants can also be

explained as the result of increased metabolism.

 In many plants diseases, growth is at first stimulated

protoplasmic streaming increases and materials are

synthesized translocated and accumulated in the diseased

area.

 It is also possible that the plant because of the

infection, utilizes ATP energy less efficiently than a healthy

plants.

 A number of chemicals was also found that affects the

respiration rates in the diseased plants e.g.- effects of

cadmimum on germination, amylasss and rate of respiration

on germinating peaseeds was observed by some workers.

53
 The cations play very prominent role in the regulation of

electron transport chain.

 The mechanism of the stimulation of state-4 respiration by

cadmium in potato tuber mitochondria become the cause of

diseases in potato plants.

Effect of pathogen on permeability of cell membrane

Cell membrane consist of a double layer of lipid molecules in

which many kinds of protein molecules are embedded; parts of
which usually protrude on one or both sides of the lipid
bilayer.

 The lipid bilayer is impermeable to most biological

molecules changes in all membrane permeability are often the
first detectable responses of cells to infection by pathogens,

 They allow most host specific and several non-specific

toxins, to certain pathogen enzymes and certain toxic
chemicals, such as air pollutants.

 The most commonly observed effect of changes in cell

membrane permeability is the loss of electrolytes i.e. of small
water soluble ions and molecules from the cell.

 Electrolyte leakage occurs much sooner and at a greater

rate when the host pathogen interaction is incompatible and
the host remains more resistant than when the host is
susceptible and develops extensive symptoms.

54
 If pathogens cause death by affecting cell membrane
permeability directly. It is by stimulating certain membrane
bound enzymes, such as ATP ase. Which are involved in the
pumping of H* in and K' out through the cell membrane, by
interfering with processes required for the maintenance and
repair of the fluid film making up the membrane or by
degrading the lipid or protein components of the membrane by
pathogen produced enzymes.

Effect of pathogens on plant growth

Pathogens that destroy part of the roots of a plant or clog the

xylem or phloem elements, thereby severely interfering with the
translocation of water and of inorganic or organic nutrients in
these plants, often cause a reduction in size and yields by these
plants and some times, their death.

In many plant diseases, however, infected tissues or entire plants

increase or reduce abnormally in size without a clear-cut
explanation of how those changes are brought about.

 The effects of beet yellow virus on the growth and

physiology of sugar beet (Beta vulgaris) was reported by Clo'ver,
ct al. (1999). It is apparent that growth regulators affecting plant
cell division and enlargement are involved, but very little is
known about the specific compounds and mechanisms involved
on the genes that controlled there events.

55
 Some of the most common diseases in which pathogens use
obvious abnormal growth of their host organs and tissues include
clubroot of crecifers caused by the plasmodiophoro mycete

 Plasmodiophora brassicae alfalfa wart caused by the fungus

Physoderma alfalfae,

 potato wart caused by the fungus Spongospora

subterranea,

 Peach leaf curl and plum pockets caused by the fungus

Taphrina sps.,

 Black knot canker on chery caused by Dibotryon morbosum

 Sphaeropsis gall stone fruits caused by Sphaeropsis sps;

 corn smut caused by Ustilago maydis,

 dwarf bunt of wheat caused by Tilletia contraversa,

 leaf gall of azalea caused by Exobacidism azoleae

 Several rusts of pine trees caused by Cronaritism sps.

 Some bacterial pathogens also cause abnormal growths such

as crown gall of many hosts and hairy root of apple caused
by Agrobacterium tumefaciens and A. rhizogenes respectively,

 olive knot and oleander gall caused by Pseudomonas

sarastanoi and leafy gall of several host caused by Rhodococcus
sps.

 Some phytoplasma-infected plants produce shoots that are

yellowish, short and bushy and are known as witches brooms.

56
 The most frequent and unusual effects on plant growth are
those caused by viruses and virioids. Many viruses cause stunting

57
or dwarfing of infected plants. Whereas others cause rolling

or curling of leaves, abnormally shaped fruits. Some

viruses cause plants to produce galls on their root stems or

leaves. Some induce pitting on the roots or stems of infected

plants. How the various viruses bring about these effects on

their respective hosts is not known.

Bostock, ei a/. (1999) studied in spite of growth of the plants

pathogen some substances secreted by host plant diminishes
the growth of pathogen e.g.- suppression of Monilinia
facticola cutinose production by peach fruit surface.

Effects of pathogens on plant reproduction

Pathogens that attack various organs and tissues of plants

weaker and often kill these organs or tissues, there by
weakening the plants; As a result such plants remain smaller
in size, may produce fewer flowers and may set fewer fruit
and seeds; the latter may be inferior vigor and vitality and
therefore, if planted they may produce fewer and weaker new
plants. In addition to these indirect effects on pathogens on
plant reproduction, many pathogens have a direct adverse
effect on plant reproduction because they attack and kill the
flowers, fruit or seed directly or interfere and inhibit their

58
production or the pathogen interfere directly or indirectly
with the propagation of their host plants,

59
50

Cao, H. et al. (2001) reported one of the most common ways

by which pathogens interfere with the reproduction of their host
is by infecting and killing the flowers of the host; as happens for
example with the brown rot of stone fruits caused by the fungus
Monilinia spp. the bacterial canker and gummosis of stone
fruit trees caused by Pseudotnonas syringae and the fire blight
disease of pears and apples caused by the bacterium Erwinia
amylovara reported by Chen, Z. et al., (2000), Prusky et al
(2001).

In some diseases e.g. in the boost bloom fruit drop of citrus, the
fruit after set, drops prematurely as a result of infection by
anthracnose fungus Colletotrlchum acutatutn.

In several plant diseases, especially in grain crops, the pathogen

interferes directly with the reproduction of the plant host by
killing the embryo, that would have produced the seed and
replacing the contents of the seed with its own fruiting structure
or its own spores.

Mareell, ct al. (2002) & Gold, S.E. (2003) Examples of such

diseases are ergot of grains caused by the fuagus Claviceps
purpurea core smut and the covered and loose smuts of the
60
various cereals caused by Tilletia and Utilago sps.
respectively.

Finally, in some diseases caused by viruses, phytoplasmas or

plasma-limited bacteria, no flowers are produced or those

produced are sterile and therefore few or no fruits and seedes

are reproduced.

61
62
 SCHOOL OF BIO AND CHEMICAL ENGINEERING
DEPARTMENT OF BIOTECHNOLOGY

UNIT – V – MICROBIAL ECOLOGY – SMB2101

1
 UNIT: V

PRINCIPLES OF PLANT PATHOLOGY

Introduction to plant pathology

Physiological activities of a healthy plant

1. Normal cell division, differentiation and development.
2. Uptake of water and nutrients from the soil.
3. Synthesis of food from sunlight by photosynthesis.
4. Translocation of water and food to the sites of necessity
through xylem and phloem.
5. Metabolism of synthesized material
6. Reproduction
A diseased plant fails to perform one or more of these functions.
The effect of a disease on functioning of an organ depends on
which cells or tissues were first attacked by the pathogen.
For example, rotting of root tissues will affect the absorption of
water and minerals from soil and if vascular tissues have been
affected, the translocation of water and photosynthesis will be
stopped or reduced.
If leaf tissues are attacked by a pathogen, photosynthesis is
affected and plant suffers from deficiency of carbohydrates
essential for supplying energy for other activities. Thus, disease can
be defined as malfunctioning process that is caused by continuous
irritation by a pathogen (Dimond, 1959).

Definitions:
Disease: Any malfunctioning of host cells and tissues that result
from continuous irritation by a pathogenic agent or
environmental factor and leads to development of symptoms
(G.N.Agrios, 1997).

Pathogens bring about these irritating processes through

different but inter-related pathways
1. by utilizing the host cell contents,
2. by causing death of cells or by interfering with their
metabolic activities through their enzymes, toxins and
growth regulators,
3. by weakening of tissues due to continuous loss of nutrients, and
4. by interfering with translocation of food, minerals and water.

OBJECTIVES OF PLANT PATHOLOGY:

The science of plant pathology has four main objectives:
1. to study the living, non-living and environmental causes of plant
diseases,
2. to study the mechanisms of disease development by pathogens,
3. to study the interactions between the plants and the pathogen, and
4. to develop the methods of controlling the diseases and
reducing the losses caused by them.

TERMS AND CONCEPTS USED IN PLANT PATHOLOGY

2
Disease: Any malfunctioning of host cells and tissues that result
from continuous irritation by a pathogenic agent or environmental
factor and leads to development of symptoms (G.N.Agrios, 1997).

Disorder: Non-infectious plant diseases due to abiotic causes such

as adverse soil and environmental conditions are termed disorders.
The common characteristic of non- infectious diseases of plants is
that they are caused by the lack or excess of something
(temperature, soil moisture, soil nutrients, light, air and soil
pollutants, air humidity, soil structure and pH) that supports life.
Non-infectious plant diseases occur in the absence of pathogens,
and cannot, therefore, be transmitted from diseased to healthy
plants.

Pathogen: An entity, usually a micro-organism that can incite

disease. In a literal sense a pathogen is any agent that causes pathos
(ailment, suffering) or damage. However, the term is generally used
to denote living organisms (Fungi, bacteria, MLO’s, nematodes
etc.,) and viruses but not nutritional deficiencies.

Parasite: Organisms which derive the materials they need for

growth from living plants (host or suscept) are called parasites.

Pathogenicity is the ability of the pathogen to cause disease

Pathogenesis is the chain of events that lead to development of

disease in the host (or) sequence of progress in disease
development from the initial contact between the pathogen and its
host to the completion of the syndrome

Sign: The pathogen or its parts or products seen on a host plant.

Symptom: The external or internal reactions or alterations of a

plant as a result of a disease.

Syndrome: The set of varying symptoms characterizing a disease

are collectively called a syndrome.

Biotroph: An organism that can live and multiply only on another

living organism. They always obtain their food from living tissues
on which they complete their life cycle.
Ex: Rust, smut and powdery mildew fungi.

Hemibiotroph (Facultative Saprophyte): The parasites which

attack living tissues in the same way as biotrophs but will continue
to grow and reproduce after the tissue is dead called as facultative
saprophytes.

Perthotrophs or perthophytes (Necrotroph): A parasite is a

necrotroph when it kills the host tissues in advance of penetration
and then lives saprophytically
Ex: Sclerotium rolfsii.

3
Inoculum: It is the part of the pathogen which on contact with
susceptible host plant causes infection (or) the infective propagules
which on coming in contact with the host plant causes an infection
are known as inoculum

Inoculum potential: The energy of growth of a parasite available

for infection of a host at the surface of the host organ to be infected
(or) The resultant of the action of environment, the vigour of the
pathogen to establish an infection, the susceptibility of the host and
the amount of inoculum present

Incubation period: The period of time (or time lapse) between

penetration of a host by a pathogen and the first appearance of
symptoms on the host. It varies with pathogens, hosts and
environmental conditions.
Predisposition: It is the action of set of environments, prior to
penetration and infection, which makes the plant vulnerable to
attack by the pathogen. It is related to the effect of environments on
the host, not on the pathogen, just before actual penetration occurs

Hypersensitivity: Excessive sensitivity of plant tissues to certain

pathogens. Affected cells are killed quickly, blocking the advance
of obligate parasites.

Infection is the establishment of parasitic relationship between two

organisms, following entry or penetration (or) the establishment of
a parasite within a host plant.

Systemic infection: The growth of pathogen from the point of

entry to varying extents without showing adverse effect on tissues
through which it passes.

Epidemic or Epiphytotic disease: A disease usually occurs widely

but periodically in a destructive form is referred as epidemic or
Epiphytotic disease.
Ex: Late blight of potato – Irish famine (1845)

Endemic: Constantly present in a moderate to severe form and is

confined to a particular country or district.
Ex: Club root of cabbage in Nilgiris
Black wart of potato – Synchytrium endobioticum
Onion smut – Urocystis cepulae

Sporadic disease: Occur at very irregular intervals and locations

and in relatively fewer instances. Ex: Udbatta disease of rice,
Angular leaf spot of cucumber – Pseudomonas lachrymans

SURVIVAL OF PLANT PATHOGENS

sources of survival of pathogens:

4
1) Infected host as reservoir of inoculum (or) survival in vital
association with living plants.
2) Survival as saprophytes outside the host.
3) Survival by means of specialized resting structures in or on the host or
outside the host.
4) Survival in association with insects, nematodes and fungi.

1) Infected host as reservoir of inoculum:

a) Seed: Seed may be externally or internally infected by plant

pathogens during the course of development and maturation in
fruit or pod.
b) Collateral hosts / Alternative hosts (wild hosts of same
families): Collateral hosts are weeds those which are susceptible
to the plant pathogens of crop plants and provide adequate
facilities for their growth and reproduction of these pathogens
during off- season.
Ex: The fungal pathogen for blast disease of rice, Pyricularia
grisea (Teleomorph: Magnaporthe grisea) can infect the grass
weeds like Brachiaria mutica.

c) Alternate hosts (Wild hosts of other families): These alternate

hosts are very important for the completion of the life cycle of
heteroecious rust pathogens.
The role of alternate hosts is not as important as of collateral
hosts. For example in temperate regions the alternate host of
Puccinia graminis tritici (black or stem rust pathogen of wheat),
the barberry bush (Berberis vulgaris) grows side by side with
the cultivated host. In such areas this wild host belonging to a
different family is important for survival of the fungus.
d) Self sown crops: Self sown crops, voluntary crops and early
sown crops are reservoirs of many plant pathogens. Ex: Self
sown rice plants harbour the pathogen (Rice tungro virus) as
well as vector (Nephottetix virescens).

e) Ratoon crops: Sometimes ratoon crops also harbour

the plant pathogens. Ex: Sugarcane mosaic.

f) Survival by latent infection: Latent infection refers to the

conditions in which the plant pathogens may survive for a long
time in plant tissue without development of visual symptoms.
Ex: Xylella fastidiosa, the causal agent of pierce’s disease of
grapevine infect different weeds without developing visible
symptoms.

2) Saprophytic survival outside the host:

Many plant pathogens survive in or on the soil in the absence of
growing susceptible plants. Waksman (1971) distinguished
between soil inhabitants and soil invaders; the former comprise
the basic fungal flora of the soil, whereas the later are short
lived exotics.
In the absence of the cultivated host plant, fungi are capable of
surviving as saprophytes and can be studied under three

5
 categories:
1) Soil inhabitants: Those organisms which survive
indefinitely in the soil as saprophytes in the absence of the
host plant. Ex: Species of Pythium, Rhizoctonia and
Sclerotium
2) Root inhabitants: These are more specialized parasites that
survive in soils in close association with their hosts. The
active saprophytic phase remains as long as the host tissue in
which they are living as parasites is not completely
decomposed. Ex: Species of Fusarium, Verticillium (vascular
wilt causing fungi) and root rot of cotton (Phymatotrichum
omnivorum)
3) Rhizosphere colonizers: Those organisms which colonize
the dead substrates in the root region and continue to live
like that for a longer period which are more tolerant to soil
antagonism. Ex: Leaf mold in tomato: Cladosporium fulvum

Differentiate Soil inhabitants and soil invaders:

Soil inhabitants Soil invaders / Root inhabiting

fungi

1. These are unspecialized parasites 1. These are more

specialized parasites that with a wide host range that are able
survive in soils in close association with to survive indefinitely
in the soil as their hosts.
saprophytes.

2. Soil inhabitants include obligate 2. Soil invaders include

facultative saprophytes and facultative parasites saprophytes
which are endo-pathogens they are exo-pathogens
(root infecting fungi).

3. Soil and plant debris serve as media 3. The active

saprophytic phase remains as for their saprophytic survival.
long as the host tissue in which they were
living as parasites is not
completely decom- posed.

4. They have high competitive saprophy- 4. They have low

competitive saprophytic tic survival ability. survival ability.

5. Species of Pythium, Rhizoctonia, 5. Most plant pathogenic

fungi and bacteria Sclerotium, etc., survive as soil inhabi-are soil
invaders. Many tants for considerable length of
time in vascular wilt causing species of
Fusarium,
absence of the host. Verticillium, etc., are soil invaders.

3) Survival as dormant spores or specialized resting structures:

Plant viruses have no resting stage and are transmitted through a

continuous infection chain.

6
Phytopathogenic bacteria: The plant bacteria also do not produce
resting spores or similar structures. They continuously live in their
active parasitic stage in the living host or as active saprophytes on
dead plant debris.
Nematodes: They survive in the form of active parasitic phase on a
living host and also survive through dormant structures, i.e., eggs,
cysts, galls, formed in host tissues. These structures may be present
in soil or in seed lots
Phanerogamic parasites: They survive in dormant state for many
years through seeds. Ex; Seeds of Orobanchae survive in soil for
more than 7 years.

Among plant pathogens, fungi are the only organisms that produce
spores, analogous to eggs of nematodes, and other resting structures
for their inactive survival. These dormant structures of survival can
be classified in the following categories.
1) Soil borne fungi:
a) Dormant spores {Conidia (Peach leaf curl pathogen,
Taphrina deformans), Chlamydospores (Wilt pathogen,
Fusarium sp.), oospores (Downy mildew fungi), perithecia
(Apple scab pathogen, Venturia inaequalis) etc.}.

Oospore Chlamydospores Perithecium

b) Other dormant structures such as thickened hypha, sclerotia

(Cottony rot fungus, Sclerotinia sclerotiorum),
microsclerotia (Verticillium), Rhizomorphs (Armillaria
mellea), etc.

Thickened hyphae Sclerotia Rhizomorphs

Microsclerotia

c) Factors affecting the survival of pathogen in the soil are a)

physical factors (high temperature, irradiation, dessication
and anaerobiosis), b) chemical factors (antibiotics,
antagonistic chemicals produced by other microbes) and c)
biotic factors (parasitism, predation by microflora and
microfauna).

7
2) Seed borne fungi:
a) Externally seed borne: Dormant spores on seed coat Ex:
Covered smut of barley, grain smut of jowar, bunt of wheat,
etc.
b) Internally seed borne: Dormant mycelium under the seed
coat or in the embryo Ex: Loose smut of wheat (Ustilago
nuda tritici)
c) Factors affecting the survival of the pathogen on/in the seed
are temperature and moisture.

3) Dormant fungal structures on dormant or active host Ex: In

downy mildew of grapevine, powdery mildew of grapevine,
apple etc., The fungus mycelium may be present in dormant
state in the affected twigs or its oospores or perithecia may be
embedded in the tissues of the affected organs.
Parasitic phanerogams survive in the form of seeds, and in plant
parasitic nematodes eggs, cysts and larvae serve as over
seasoning structures.

4) Survival in association with insects, nematodes and fungi

Several important plant pathogens may survive within the insect
body and over winter therein. The corn flea beetle,
Cheatocnema pulicaria carries inside its body, the corn wilt
pathogen, Xanthomonas stewartii and thus helps in over
wintering.
Plant viruses like wheat mosaic, tobacco necrosis, tobacco rattle
and tobacco ringspot viruses survive with nematodes or fungi
found in the soil between crop seasons. Tobacco ringspot is
associated with the nematode Xiphinema americana. The fungi,
Polymyxa graminis (Wheat soil borne mosaic & Barley yellow
mosaic) and Spongospora subterranea (Potato mop top virus)
carry the viruses internally and transmit them through the
resting spore.

DISPERSAL OF PLANT PATHOGENS

The second link in infection chain is the dissemination of plant

pathogens. Transport of spores or infectious bodies, acting as
inoculum, from one host to another host at various distances
resulting in the spread of the disease, is called dispersal,
dissemination or transmission of plant pathogens.

In fungi, productions of asexual and sexual spores follow the active

vegetative growth of the fungus in or on the host tissues and are
dispersed mechanically in time and space by various means. In
bacterial diseases, the bacterial cells come out on the host surface
as ooze or the tissues may be disintegrated so that the bacterial
mass is exposed and then dispersed by various physical and
biological agencies.

The dispersal of infectious plant pathogens in space occurs through two

ways:
1. Autonomous or direct or active dispersal.

8
 2. Indirect or passive dispersal.

I) Autonomous or direct or active dispersal:

In this method the dispersal of plant pathogens takes place through
soil, seed and planting material during normal agronomic
operations. There is no major role of external agencies like insects,
wind, water, etc. in this type of dispersal.

1) Seed as the source of autonomous dispersal:

1. The dormant structures of the pathogen (Ex: seeds of Cuscuta,
Sclerotia of ergot fungus, smut sori, etc.) are found mixed with
seed lots and they are dispersed as seed contaminants.
2. The bacterial cells or spores of fungi present on the seed coat
(such as in smuts of barley, sorghum, etc.) are transported to
long distances.
3. Dormant mycelium of many fungi present in the seed is
transmitted to long distances.

There are three types of dispersal by seed, viz.,

i. contamination of the seed
ii. externally seed borne
iii. internally seed borne.

i. Contamination of the seed: Seed borne pathogens move in seed

lot as separate contaminants without being in intimate
contact with the viable crop seeds. The seeds of the pathogen
or parasite and the host are mixed during harvest of the crop.
In many cases, the identity of the seeds of the two entities
(host and the pathogens) is difficult to separate.
Ex: Smut of pearlmillet and ergot of rye. Smut sori and ergots mix
easily with the seed lots during harvest and threshing.

ii. Externally seed borne: Close contact between structure of the

pathogen and seeds is established where the pathogen gets
lodged in the form of dormant spores or bacteria on the seed
coat during growth of the crop or at the time of harvest and
threshing.
Ex: Short smut of sorghum, bacterial blight of cotton, loose
smut of barley etc.
In many pathogens the externally seed borne structures such as smut spores
can persist for many years due to their inherent capacity for long survival.
Ex: The spores of Tilletia caries (Stinking smut of wheat) remain viable
even after 18 years and those of Ustilago avenae (Oat smut) for 13 years.
iii. Internally seed borne: The pathogen may penetrate into the
ovary and cause infection of the embryo while it is
developing. They become internally seed borne. Ex: Loose
smut of wheat.

Differentiate Seed infection and infestation

Seed infection: The seed in infected only when the pathogen has
grown in or on it for sometime and established its relationship with
the seed tissues. Ex: Loose smut of wheat, where the fungus grows

9
in the embryonic tissues and becomes dormant when the seed
enters dormancy.

Seed infestation: When the fungus or the pathogen is present on

the seed coat and in the seed lot, it is only transport of the
pathogen and the seed is infested.

2) Soil as a means of autonomous dispersal: Soil borne facultative

saprophytes or facultative parasites may survive through soil. The
dispersal may be by movement of pathogen in the soil or by its
growth in soil or by movement of the soil containing the pathogen.
The former is known as dispersal in soil while the later is called
dispersal by soil.
a) Dispersal in soil: The following are the three stages of dispersal in soil
i) Contamination of soil: Contamination of the soil takes place by
gradual spread of the pathogen from an infested area to a new area.

ii) Growth and spread of a pathogen in soil: Once the pathogen has
reached the soil it can grow and spread based on its ability to
multiply and spread. Among characters of the pathogen its
adaptability to soil environment including its saprophytic survival
ability are most important. The survival ability of the pathogen is
governed by high growth rate, rapid spore germination, better
enzymatic activity, capability to produce antibiotics and tolerance
to antibiotics produced by other soil-microorganisms.

iii) Persistence of the pathogen in soil: The pathogens persist in the

soil as dormant structures like oospores (Pythium, Phytophthora,
Sclerospora etc.), Chlamydospores (Fusarium), smut spores
(Ustilago) and sclerotia (Rhizoctonia, Sclerotium).

b) Dispersal by the soil: The pathogen is dispersed by the soil

during cultural operations through the agricultural implements,
irrigation water, workers feet etc. Propagules of fungi and the plant
debris containing the fungal and bacterial pathogens thus spread
through out the field. The transfer of soil from one place to another
along with propagating materials is the most important method of
dispersal of pathogen.

For example transfer of papaya seedlings from a nursery infested

with Pythium aphanidermatum (causal agent of stem or foot rot of
papaya) can introduce the pathogen in new pits for transplanting
the seedlings. Similarly grafts of fruit trees transported with soil
around their roots can transmit pathogens present in the nursery to
the orchards.

3) The plant and the plant organs as a means of autonomous dispersal:

The plants, plant parts other than seed that are used for vegetative
propagation, raw field produce and plant debris that accumulates
during the course of cropping constitute the third method of
autonomous dispersal. Ex: Late blight of potato was introduced in
North America and in Europe through seed tubers brought from the
native source of the in South America. Citrus canker was

10
introduced into California from Asia. The climatic conditions
favoured its epidemic in California.

II) Passive or Indirect dispersal:

Passive dispersal of plant pathogens happens through animate and

inanimate agents.

1) Animate agents:
a) Insects: Insects carry plant pathogens either externally (epizoic)
or internally (endozoic). They can disseminate bacteria, fungi,
viruses, mycoplasmas, spiroplasmas, rickettsia, etc.

S.No. Vecto Viru

r s
1. Aphid transmitted viruses
Myzus persicae Beet mosaic, Lettuce mosaic,
Potato virus Y, Turnip mosaic,
Beet yellows
Acyrthosiphon pisum Bean common mosaic, Bean
yellow mosaic, Soybean mosaic,
Pea enation
Mosaic
Toxoptera citricidus Citrus tristeza
2. Leaf hopper transmitted
viruses
Nephotettix impicticeps, N. Rice tungro virus
nigropictus,
N. virescens
Nephotettix cincticeps, N. Rice dwarf virus
nigropictus
Circulifer tenellus Beet curly top
Agallia contricta Potato yellow dwarf
Graminella nigrifrons Maize chlorotic dwarf
3. Tree hopper transmitted
viruses
Micrutalis malleifera Tomato-pseudo curly top
4. Plant hopper transmitted
viruses
Perigrinus maidis Maize mosaic
Sogatodes oryzicola Rice hoja blanca
5. Whitefly transmitted viruses
Bamesia tabaci Bhendi yellow vein mosaic,
Bhendi leaf curl, Chilli leaf curl,
Cotton leaf curl, Papaya leaf curl,
Mungbean yellow mosaic
6. Thrips transmitted viruses
Thrips tabaci, Frankliniella Tomato spotted wilt virus
schultzei, Scirtothrips dorsalis
7. Mealy bugs transmitted
viruses
Planococcoides njalensis Cocoa swollen shoot
Pseudococcus saccharifolii Sugarcane spike (Phytoplasma)
8. Grass hoppers transmitted
viruses
Melanophus differentialis Potato virus X, Tobacco mosaic
virus (Mechanical transmission)
9. Lace bugs transmitted

11
 viruses
Piesma quadratum Beet leaf curl virus
Stephanites typicus Root (wilt) disease of
coconut
(Phytoplasma)
10. Beetle transmitted viruses
Ceratoma trifurcate Cowpea mosaic
Acalymma trivitata Squash mosaic
Diabrotica longicornis Brome mosaic

Mycoplasma diseases: Plant MLO’s are phloem inhabitants and

those insects which are feeding on phloem of plants transfer the
MLO’s. Mycoplasmal diseases are mostly transmitted by leaf
hoppers. Ex: Sesamum phyllody (Orosious albicinctus) and little
leaf of brinjal (Hishimonas phycitis)

b) Mites: Mites belonging to the families Eryophyiidae

(eryophyiid mite) and Tetranychidae (spider mite) of class
Arachnida transmit plant viruses. The genera Abacarus, Aceria,
Eriophyes and Brevipalpus are important.
Ex: Aceria cajani transmits Pigeonpea sterility mosaic virus
Aceria tulipae transmits wheat streak mosaic

c) Fungi: Some soil borne fungal plant pathogens carry plant

viruses in or on their resting spores and zoospores, and transmit
them to susceptible hosts during the infection process. Tobacco
necrosis virus and Cucumber mosaic virus are carried outside the
fungi, while lettuce big vein virus is carried inside the zoospores.
Many soil borne viruses are transmitted by the members of
Chytridiales and Plasmodiophorales.

Fungal transmitted viruses

S.No. Fungal vector Disease
1. Olpidium brassicae Tobacco necrosis, Tobacco
stunt, Lettuce big vein
2. Olpidium cucurbitacearum Cucumber necrosis
3. Polymyxa graminis Barley yellow dwarf mosaic,
Wheat
soil borne mosaic, Peanut clump
4. Polymyxa betae Beet necrotic yellow vein
5. Spongospora subterranean Potato mop top
6. Synchytrium endobioticum Potato virus X

d) Nematodes: Several nematodes act as vectors for transmission of

fungi, bacteria and viruses.

Nematode transmitted viruses:

S.No. Nematode vector Virus Virus group
1. Paratrichodorus sp. & Pea early NETU group
Trichodorus sp. browning,
Tobacco rattle
2. Xiphenema index Grapevine fan leaf NEPO virus
3. Xiphenema americanum Tobacco ringspot, NEPO virus
Tomato ringspot
4. Longidorous elongatus Raspberry ringspot NEPO virus

12
e) Human beings: Human beings role in dissemination of plant
pathogens is more direct than indirect. The ways and means in
which human beings help in dispersal are as follows.

 Transportation of seeds (seed trade): The import and export

of contaminated seeds without proper precautions lead to
movement of pathogens from one country to another or from
one continent to another. The diseases which are amenable to
such transmission are mainly those that are carried in or on the
propagative parts and seed. Ex: Late blight of potato, Downy
mildew of grapevine, Citrus canker, Fusarium wilt of banana,
etc.

 Planting diseased seed materials: Planting diseased bulbs,

bulbils, corms, tubers, rhizomes, cuttings, etc., of vegetatively
propagated plants such as potato, sweet potato, cassava,
sugarcane, banana, many ornamentals and fruit trees etc., help
in dispersal of pathogens from field to field, orchard to
orchard, locality to locality or from one country to another.

 During adoption of normal farming practices: Human

beings engaged in preparatory cultivation, planting, irrigation,
weeding, pruning etc., help in dispersal of plant pathogens.
Spores and other external structures of fungi can be carried by
workers clothing’s, shoes, and hands etc., from plant to plant
and from field to field.

 By use of contaminated implements: Pathogens are

transferred from one area to another through implements used
in various cultural operations (weeding, thinning, hoeing etc.)
in the field. Ex: Soil borne diseases such as root rot, wilt etc.
Cutting knives and pruning knives also help in dispersal from
one plant to another. Ex: Bunchy top of banana.

 By use of diseased grafting and budding material: Grafting

and budding between healthy and diseased plants is the most
effective method of distribution of pathogens of horticultural
crops.

f) Dispersal by phanerogamic parasites: Phanerogamic

parasites transmit the viruses by acting as a bridge between the
diseased and healthy plants. Ex: Dodder (Cuscuta California,
C. campesris, C. subinclusa etc.)
Cuscuta subinclusa – Cucumber mosaic virus
Cuscuta california – Tobacco mosaic virus
Tobacco
rattle virus
Tomato
spotted wilt
virus
Cuscuta campestris - Tomato bushy stunt virus

g) Dispersal by birds: This mode of dispersal is important in

13
 dissemination of seeds of flowering parasites and certain
fungi. In tropics, crows feeding on the fleshy, sticky and
gelatinous berries of gaint mistletoe (Dendrophthoe sp.)
deposit the seeds on the other trees with excreta. Seeds of
Loranthus are disseminated by birds by sticking on their beaks
and also through excreta. Stem segments of dodder are carried
by birds for preparing their nests and thus get transported to
new areas. Moreover, spores of chestnut blight fungus,
Endothea parasitica are disseminated by more than 18 species
of birds. Cleistothecia of many powdery mildew fungi are
carried by feathers of birds.

h) Farm and wild animals: Farm animals (cattle) while feeding

on diseased fodder ingest the viable fungal propagules (spores
or oospores or sclerotia) and pass out as such in the dung. This
dung when used as manure spread in the field and act as
source of inoculum. Further, soil inhabiting fungi especially
sclerotia adhere to the hoofs and legs of animals and get
transported to other places.

2) Inanimate agents:
a) Wind: The dispersal of pathogens by wind is known as
anemochory. Wind transmission involves the upward air currents,
velocity and the downward movements of the wind. Wind acts as a
potent carrier of propagules of fungi, bacteria and viruses.

Fungi: Usually the fungal pathogens are light in weight and are
well adapted to wind dispersal. The adaptations for wind
dispersal in fungal pathogens include production of numerous
spores and conidia, discharge of spores with sufficient force,
production of very small and light spores so that they can move to
long distances. Ex: Powdery mildew, downy mildew, rusts, smuts
etc.

Both short and long distance dissemination is possible by means of wind.

i) Spores adopted for short distance dissemination- sporangia of
downy mildew fungi, conidia of powdery mildew fungi and
basidiospores of rust fungi. In the plains of northern India the
annual recurrence of cereal rusts is solely due to uredospores
brought by wind from the source of survival in the hills in the far
north (Himalayas) and south (Nilgiris).

ii) Spores adapted to long distance dispersal – uredospores of rust

fungi, Chlamydospores of smut fungi and conidia of Alternaria,
Helminthosporium and Pyricularia

Uredial stages of the rust fungi travel long distances through air
currents and thus are responsible for destructive epidemics over
wide areas. Ex: The uredospores of Puccinia graminis var. tritici
have been detected as high as 14000 feet above infected wheat
fields (Stackman and Christensen). Similarly, Alternaria spores at
8000 feet, Puccinia recondita and Cronartium ribicola spores at
12500 feet were reported.

14
Dispersal distance: In USA, uredospores of this fungus are blown
from the far south (Mexico) into Dakota and Minnesota (far north)
travelling more than 1000 miles in about two days without losing
their viability. If the uredospores reach an altitude of 5000 feet,
their distance dispersal in a 30 mile per hour wind could be about
1100 miles, without loosing viability.

Nematodes: In addition to fungi, it also helps in the dissemination

of the cysts of nematodes and also the seeds of phanerogamic
parasites. Ex: Cysts of the nematode Heterodera major, which
causes molya disease of wheat and barley, are carried by dust
storms from Rajasthan to Haryana

Bacteria: Some pathogenic bacteria are carried along with the

infected material to short distances by wind. Ex: Erwinia
amylovora, the causal agent of fire blight of apple and pear,
produces fine strands of dried bacterial exudates which may be
broken off and are transmitted by wind.
Viruses and phytoplasmas are not directly transmitted by wind,
but the insect and mite vectors that carry the viruses move to
different directions and distances based on the direction and speed
of the air.

b) Water: Transmission of plant pathogens by water is called as

hydrochory. Water is less important than air in long distance
transport of pathogens, but it is more efficient as the pathogens land
on the wet surface and can germinate immediately. Water
dissemination occurs mainly through surface running water and
rain splash.

The surface flow of water after heavy rains or during irrigation

from canals and wells carries the pathogens to short distances. Ex:
The mycelial fragments, spores or sclerotia of fungi,
Colletotrichum falcatum (red rot of sugaecane), Fusarium,
Ganoderma, Macrophomina, Pythium, Phytophthora, Sclerotium,
etc., are transmitted through rain or irrigation water. Long distance
dispersal is also possible by water only when the floods cover
larger areas or when the water flows from the sources of survival of
pathogens to longer distances.

Dissemination by rain splash is also called as splash dispersal. It is

one of the efficient methods of dispersal of bacterial plant
pathogens. Rain drops falling with force on sori, pustules, cankers
or even soil surface may splash the propagules in small droplets
and enable them to land on neighbouring healthy susceptible
surfaces or the water droplets may be carried to long distances by
air. Ex: Bacterial leaf spot of rice (Xanthomonas campestris pv.
oryzae), Bacterial leaf streak of rice (Xanthomonas campestris pv.
oryzicola), Green ear of bajra (Sclerospora graminicola).

Fungal spores and bacteria present in the air or plant surface are
washed downward by rain splash or drops from overhead irrigation

15
and are deposited on susceptible healthy plants. Water not only
plays an important role in the dissemination of plant pathogens, but
also helps in the growth and spore discharge of many fungi. It also
helps in the spore germination and infection process.

Phenomenon of infection/ infection process

It is the third link in the infection chain after survival and dispersal
of inoculum. Infection process means establishment of pathogen in
the host plant. Entry and colonization of pathogen in the host
tissues is known as establishment and the infective propagules
coming in contact with the host are known as inoculum.

Inoculum potential: It is the inoculum needed for successful infection. It is

a function of
inoculum density and their capacity.

In case of specialized pathogens as rusts and powdery mildews,

very few or even one spore is capable of causing infection
successfully. In case of non-specialized pathogens such as Pythium,
Phytophthora, Rhizoctonia and Sclerotium require high density of
inoculum on the surface of susceptible host for successful infection.

The success of process of infection depends on

1. Host factors

 Susceptibility of host: It is genetically controlled by DNA and it

is an inheritable character which is transmitted from parents to
off springs.
 Disease proneness of the host: It is decided by the external
factors such as host nutrition, i.e., more nitrogen application
makes the host more susceptible and more potash application
leads to less susceptibility.

2. Pathogen factors

 Virulence / aggressiveness of the pathogen: It is determined by

genetic material which is inheritable.
 High multiplication rate of the pathogen: Chances of infection
increases with high rate of multiplication. High birth rate and
low death rate is highly essential for successful infection.
 Proper inoculum potential: In case of specialized pathogens very
few or even one spore is capable of causing infection
successfully, whereas, non-specialized pathogens require high
density of inoculum on the surface of susceptible host for
successful infection.

3. Environmental factors: Environmental conditions such as

temperature, relative humidity, moisture, etc., are very important
for survival, dissemination and infection process.

16
Process of infection can be grouped into three stages, i.e., pre-
penetration, penetration and post-penetration.

17
 Stages in the development of infection or disease cycle

1. PRE-PENETRATION: Depending upon the plant pathogen activity, the

plant pathogens are classified in to 2 categories

1. Active invaders and 2.Passive invaders

Active Invaders Passive Invaders
1. Pathogens which make an 1. No aggressive effort
aggressive effort to gain entry into
intact host cells. 2. Require help of external agencies
2. They do not require help of any like insect vectors or wounds caused
external agency to gain entry into by agricultural implements.
host cells. 3. Eg. Plant viruses
Phyto-pathogenic bacteria
3. Eg. Phyto-pathogenic
fungi Phanerogamic
parasites

Plant viruses are particulate in nature and they do not have any capacity to
enter the host cell so they do not make any aggressive effort for entry, but
depend on different insect vectors for their entry into host cell. Bacteria have
no dormant structures; hence no pre- penetration activity except for
multiplication in infection drops on the natural openings. However,
nematodes show some orientation towards root surface before actual
penetration.

In fungal pathogens, pre-penetration includes spore germination and growth

of the resulting germ tube on the surface of the host plant. Germination is
essentially the change from low metabolic rate to a high metabolic rate and
involves a change from near dormancy to intense activity; for this an energy
source is needed such as a carbohydrate or fat reserve in the propagule.
Fungal invasion is chiefly by germ tubes or structures derived from them. In
some fungi like Rhizoctonia solani and Armillariella mellea, the hypha act in
a concerted way to achieve the penetration. In Rhizoctonia solani, the
fungus on coming in contact with root surface, first forms infection cushions
and appressoria and from these multiple infections takes place by means of
infection pegs. In Armillariella mellea, the fungus hyphae form the
rhizomorphs (aggregation of hyphae into rope like strands) and only these
can cause infection.

18
 Rhizomorphs Appressorium

2. PENETRATION: Pathogens penetrate plant surfaces by direct

penetration or indirectly through wounds or natural openings. Bacteria enter
plants mostly through wounds and less frequently through natural openings.
Viruses, viroids, mollicutes, fastidious bacteria enter through wounds made
by vectors. Fungi, nematodes and parasitic higher plants enter through direct
penetration and less frequently through natural openings and wounds.

19
A. Indirect Penetration
1. Wounds: Wounds caused by farm operations, hail storms, or insect
punctures, etc., will help in the entry of different plant pathogens into the
host cells. Organisms which cause storage diseases and ripe rots will enter
through the wounds caused by farm operations.
Ex. Rhizopus, Gloeosporium, Aspergillus, Penicilium, Colletotrichum,
Diplodia, etc. Weak parasites enter through the wounds caused by hail
storms and freezing
Ex. Macrophomina phaseolina

Pathogen causing brown rot of fruits (Sclerotinia fructicola) enters through

the wounds caused by insect punctures. Similarly, causal organism of Dutch
elm disease (Ceratostomella ulmi) enters through the wounds caused by elm
bark beetle.

2. Natural openings
a) Stomata: There is variation in the behaviour of germ tube at the time of
penetration through the stomata. In Puccinia graminis tritici, the uredospore
germinates and forms a germ tube which on approaching stoma swells at the
tip to form an appressorium in the stomatal aperture. From the appressorium
a blade like wedge grows through the stomatal slits and swells inside to form
a sub-stomatal vesicle from which the haustoria penetrating the cells are
produced.

In Peronospora destructor infecting onion leaves, the germ tube continues to

grow after the formation of first appressorium. In Pseudoperonospora
cubensis, the hyphae penetrate the stomatal aperture and swell to form a sub-
stomatal vesicle from which in turn other hyphae grow to form haustoria in
the adjacent cells of the leaves. Mycosphaerella musicola forms a small
structure called stomatopodium over the pore of the stoma after growing for
few days on the surface of the leaf. A hypha then arises from it which grows
into the sub-stomatal chamber and swells to form a vesicle, which in turn
gives rise to hyphae which invade palaside tissues.

Other examples: Xanthomonas campestris pv. malvacearum (Black arm of

cotton), Xanthomonas phaseoli (Bacterial leaf spot of green gram),
Phytophthora infestans (Late blight of potato), Albugo candida (White rust
of crucifers) and uredospores of Puccinia graminis tritici (Black stem rust of
wheat).

b) Lenticels: Sclerotinia fructicola (Brown rot of fruits), Streptomyces

scabies (Scab of potato), Phytophthora arecae (Mahali disease of arecanut)

c) Hydathodes: Xanthomonas campestris pv. campestris (Black rot of crucifers)

B) Direct penetration: Most fungi, nematodes and parasitic higher plants

are capable of penetrating the host surface directly. However, the plants are
provided with different mechanisms of defense which include structural
features of the host, presence of chemical coverings on the cell walls, and
anti-infection biochemical nature of the protoplasm. Hence, the pathogen
should have mechanisms to overcome these barriers for direct penetration.

a) Breakdown of physical barriers. Viruses have no physical force or

enzyme system of their own to overcome structural or chemical barriers of
20
the host and therefore come in contact with the host protoplasm only through
wounds. Bacteria are mostly weak parasites and cannot employ force to
effect penetration. Fungi and nematodes are the only group of plant
pathogens that employ force for direct penetration of the host. Fungi
penetrate host plants directly through a fine hypha produced directly by the
spore or mycelium or through a penetration peg produced by an
appressorium. These structures exert pressure on the surface which results in
stretching of the epidermis which becomes thin. Then the infection peg
punctures it and effects its entry.

b) Breakdown of chemical barriers: the host is provided with defense

mechanisms against invasion which include i) presence of cuticular layer on
the epidermis, ii) lack of suitable nutrients for the pathogen in the host cells,
iii) presence of inhibitory or toxic substances in the host cells, iv) exudation
of substances toxic to pathogen or stimulatory

21
to antagonists of the pathogen. Ex: The glands in leaf hairs of begalgram
contain maleic acidwhich is antifungal and provide resistance to infection by
the rust fungus (Uromyces ciceris arietini). Similarly, protocatecheuic acid
and catechol in the red scales of onion provide resistance to onion smudge
pathogen, Colletotrichum circinans. To overcome these physical and
chemical barriers, the fungi produce various enzymes, toxins organic acids
and growth regulators.

Through non-cutinized surfaces:

a) Seedlings: Grain smut of jowar (Sphacelotheca sorghi), Loose smut of
jowar (Sphacelotheca cruenta), Downy mildew of jowar and bajra
(Sclerospora graminicola), Wheat bunt disease (Tilletia caries, Tilletia
foetida)

b) Root hairs: Wilt causing fungi (Fusarium sp.), Club root of cabbage
(Plasmodiophora brassicae), Root rot of cotton (Phymatotrichum
omnivorum)

c) Buds: Pea rust fungi (Uromyces pisi), Witches broom of cherries (Taphrina cerasi)

d) Flowers: Loose smut of wheat (Ustilago nuda tritici), Long smut of

jowar (Tolyposporium ehrenbergi), Bunt of rice (Neovossia horrida), Ergot
of rye (Claviceps purpurea)

e) Leaves: Basidiospores of white pine blister rust fungus (Cronartium

ribicola) germinate and grow down into branches and leaves, where aecia
are produced.

d) Nectaries: Fire blight of apple (Erwinia amylovora)

e) Stalk ends: Penicillium italicum, Theilaviopsis paradoxa (Post harvest disease

fungi)

Through cutinized surfaces:

a) Cuticle: Leaf spot of spinach (Cercospora beticola), early blight of

solanaceous plants (Alternaria solani), Tikka disease of groundnut
(Cercospora personata)

3. POST PENETRATION
Invasion and colonization: Infection is the process by which pathogens
establish contact with the susceptible cells or tissues of the host and derive
nutrients from them. A parasitic relationship is formed between host
cytoplasm and parasite cytoplasm. During infection, pathogens grow and
multiply within the plant tissues. Invasion of plant tissues by the pathogen,
and growth and reproduction of the pathogen (colonization) are two
concurrent stages of disease development.

Fungi spread into all parts of host organs, either by growing directly through
the cells as an intracellular mycelium or by growing between the cells as an
intercellular mycelium. During establishment, pathogen produces different
substances which include enzymes, toxins, growth hormones and
polysaccharides which will help in colonization of the host.
22
In ectoparasites the main body of the pathogen lies on the surface of the
host with only feeding organs (haustoria) penetrating the tissues Ex: Most of
the powdery mildew fungi. Some fungal parasites develop both external and
internal mycelium Ex: Rhizoctonia solani. The endophytic parasites or
endoparasites grow subcuticularly (Diplocarpon rosae, black spot of rose),
in parenchyma tissues (most fungal and bacterial pathogens as well as many
nematodes) or in vascular tissues (vascular wilt parasites). Some pathogens
are endobiotic, i.e., mycelium is not produced and the thallus is entirely
present within a host cell Ex: Synchytrium endobioticum.

Bacteria invade tissues intercellularly, but also grow intracellularly when

parts of the cell walls dissolve. Viruses, viroids, mollicutes and fastidious
bacteria invade tissues by moving from cell to cell intracellularly.

23
Infection caused by microbes may be local (involve single cells or few cells
or small area) or systemic (pathogen spreads and invades most or all
susceptible cells and tissues throughout the plant Ex: Sclerospora
graminicola). The time interval between inoculation and appearance of
disease symptoms is called the incubation period.

Exit of the pathogen

After invasion and colonization of the host, the pathogens come out of the
host to maintain the continuity of the infection chain or disease cycle and
escape death due to overcrowding. Once the pathogens exit from the host,
they survive and are disseminated to other hosts and continue the infection
cycle.

Viruses can exist only with the living protoplasm and hence disseminated
through their animate vectors like insects, fungi, nematodes, etc. The
bacteria ooze out in the form of slime on the host surface from where they
can be disseminated through water and insects. However, the fungi have the
most elaborate system of exit. Most plant pathogenic fungi grow out on the
host surface and produce repeating spores (secondary inoculum), usually
asexually, under favourable conditions. The spores thus formed are
disseminated through wind, water, soil, seed, vegetative propagating
material, agricultural implements, etc.

ROLE OF ENZYMES IN
PATHOGENESIS

Enzymes are large protein molecules which catalyze all inter-related

reactions in the living cell. Most pathogens derive energy principally from
enzymatic break down of food materials from host tissue.

Composition of the cell wall: Functionally cell wall is divided into 3

regions, viz., middle lamella (made of pectins), primary wall (cellulose,
pectic substances) and secondary cell wall (entirely cellulose).

Middle lamella acts as intercellular cement which binds the cells together in
tissue system. Pectin or pectic substances are major chemical constituents of
wall layers and entire middle lamella, where as in other layers, cellulose is
found in good amounts.
Besides these two major components, other components such as
hemicelluloses, lignin and some amount of protein is also present. Main
components of cell wall are pectic substances, cellulose, hemicelluloses,
lignin and small quantity of protein.
24
The epidermis of plants is covered by cuticle, whose major chemical
substance is cutin in addition to cuticular wax.

Cuticular wax: Plant waxes are found as granular or rod like projections or
as a continuous layer outside / within the cuticle. Wax formation is a
continuous process and it is not a terminal phase in the development of leaf.
Cuticular waxes are made up of long chain molecules of paraffin,
hydrocarbons, alcohols, ketones and acids. Most of the fungi and parasitic
higher plants penetrate wax layers by means of mechanical force alone.

Cutin: It is an insoluble polyester of unbranched derivatives of C16 and C18

hydroxy fatty acids. Cutin is admixed with waxes on upper side and with
pectin and cellulose on the lower side. Cutinases break cutin molecules and
release monomers as well as oligomers from insoluble cutin polymer.
Cutinases reaches its highest concentration at penetrating point of the germ
tube and at infection peg of appressorium forming fungi
Ex: Colletotrichum gloeosporioides, Sphaerotheca pannosa, Venturia
inaequalis, Helminthosporium victoriae.

Pectic substances: These are major components of middle lamella

(intercellular cement that holds in place the cells of plant tissues). They also
make up a large portion of primary cell wall in which they form an
amorphous gel filling the spaces between cellulose microfibrils. Pectic
substances are polysaccharides consisting mostly of d- galactouronic acid
units with α-1,4-glycosidic bonds. These chains are esterified with methyl
groups or linked with other carboxyl groups in calcium and magnesium salt
bridges.
Pectic substances are of three types, namely, pectic acid (non methylated
units), pectinic acid (<75% methylated galacturonan units) and pectin
(>75% methylated units). Term protopectin is used to denote substances
which are soluble in water and upon restricted hydrolysis yields pectinic
acid.

25
The enzymes that degrade pectic substances are known as pectinases or
pectolytic enzymes. Pectinases and pectolytic enzymes are pectin methyl
esterases (PME’s), polygalactouronases (PG’s) and pectin lyases (PL’s).

1. Pectin methyl esterases: Breaks ester bonds and removes methyl groups
from pectin leading to the formation of pectic acid and methanol (CH3OH).

2. Polygalacturonases: Split pectin chain by adding a molecule of water and

breaks the linkage between two galacturonan units. These enzymes catalyze
reactions that break α- 1,4-glycosidic bonds.

3. Pectin lyases: Split pectin chain by removing a molecule of water from

the linkage, thereby breaking it and releasing products with unsaturated
double bonds.

These pectin enzymes can be exopectinases (break only terminal linkage) or

endopectinases (break pectin chain to random sites). Pectin degradation
results in liquefaction of the pectic substances and weakening of cell walls,
leading to tissue maceration
Ex: Soft rot bacterium, Erwinia caratovora subsp. caratovora and other fungi like
Botrytis cinerea, Sclerotium rolfsii, etc.

Cellulose: Cellulose is a polysaccharide, made of chains of β-D-

glucopyranose units (where C1 is linked to C4). Glucose chains are held by
hydrogen bonds. Cellulose occurs in all higher plants as the skeletal
substance of cell walls in the form of microfibrils. Primary and secondary
wall consists of a matrix in which a large number of microfibrils are
embedded. These microfibrils are like bundles of iron bars in a reinforced
concrete building. In some parts of microfibrils the chains are arranged in an
orderly fashion attaining crystalline form, when arranged in less orderly
fashion, it attains amorphous form. If the proportion of crystalline portion is
more, the resistance of the host to pathogen is more. The space between
microfibrils and between micelles or cellulose chains is filled with pectins,
hemicelluloses and also lignin at maturity.

Cellulose is insoluble in crystalline form (native form), and soluble in

amorphous form (modified cellulose). The enzymatic breakdown of
cellulose results in final production of glucose molecules.
Cellulose is degraded by cellulases. Cellulase one (C1) attacks native
cellulose by cleaving cross-linkages between chains. A second cellulase (C2)
also attacks native cellulose and breaks into shorter chains. These shorter
chains are then attacked by Cx enzyme, which degrade them into
disaccharide, cellobiose. Finally cellobiose is degraded by the enzyme, β-
glucosidase into glucose.

26
Cellulase degrading enzymes play a role in softening and degradation of cell
wall material and facilitate easy penetration and spread of pathogen in the
host.
Ex: Basidiomycetes fungi
Hemicellulose: These are the major constituents of primary cell wall and
also seen in middle lamella and secondary cell wall. The hemicellulose
polymers include primarily xyloglucan but also glucomannans,
galactomannans, arabinogalactans, etc. Hemicelluloses link the ends of
pectic polysaccharides and various points of the cellulose microfibrils.
Hemicellulases degrade hemicelluloses and depending on the monomer
released from polymer on which they act, they are termed as xylanase,
galactanase, glucanase, arabinase, mannose, and so on. Ex: Sclerotinia
sclerotiorum, Sclerotinia fructigena.

Lignin: Lignin is found in the middle lamella, as well as in the secondary

cell wall of xylem vessels and the fibres that strengthen plants. It is an
amorphous, three-dimensional polymer made up of basic structural unit,
phenylpropanoid. Lignin forms by oxidative condensation (C-C and C-O
bond formation) between phenylpropanoid units or substituted cinnamyl
alcohols (p-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol). White
rot fungi (Basidiomecetes) secrete one or more ligninases which enable
them to utilize lignin. Ex: Xylaria, Chaetomium, Alternaria,
Cephalosporium, etc.

Cell wall proteins: Cell wall proteins are similar to other proteins, except
that they are rich in aminoacid, hydroxy proline. Five classes of structural
proteins are found in cell walls: extensins, proline-rich proteins (PRP’s),
glycine-rich proteins (GRP’s), Solanaceous lectins and arabinogalactan
proteins (AGP’s). Proteins are degraded by means of enzymes, proteases or
proteinases or peptidases.

Lipids: Various types of lipids occur in all plant cells. The most important
ones are phospholipids and glycolipids. These lipids contain fatty acids,
which may be saturated or unsaturated. Lipolytic enzymes, called lipases
(phospholipases, glycolipases) hydrolyze lipids and release fatty acids.

Starch: Starch is the main reserve polysaccharide found in plant cells. It is a

glucose polymer and exists in two forms: amylose, a linear molecule, and
amylopectin, a highly branched molecule. Starch is degraded by enzyme,
27
amylases.

ROLE OF TOXINS IN PLANT PATHOGENESIS

Def: Toxin can be defined as a microbial metabolite excreted (exotoxin) or

released by lysed cells (endotoxin) which in very low concentration is
directly toxic to the cells of the suscept (host).

The term toxin is used for a product of the pathogen, its host, or pathogen
host interaction which even at very low concentration directly acts on living
host protoplasm to influence disease development or symptom expression.

Toxins are different from enzymes in that they do not attack structural
integrity of host tissues but affect the metabolism of the host because the
toxins will act on protoplast of the cell.

Toxin hypothesis (Luke and Wheeler, 1955):

1. A toxin should produce all symptoms characteristic of the disease
2. Sensitivity to toxin will be correlated with susceptibility to pathogen
3. Toxin production by the pathogen will be directly related to its ability to
cause disease. Except, victorin, the toxic metabolite of Cochliobolus
victoriae, the vast majority of toxins associated with plant diseases fail to
exhibit all the above characters.

Classification of toxins (Wheeler and Luke, 1963)

According to the source of origin, toxins are divided into 3 broad classes namely,
pathotoxins, vivotoxins and phytotoxins.

1. Pathotoxins: These are the toxins which play a major role in disease
production and produce all or most of the symptoms characteristic of the
disease in susceptible plants. Most of these toxins are produced by pathogens
during pathogenesis.
Ex: Victorin: Cochliobolus victoriae (Helminthosporium victoriae), the
causal agent of Victoria blight of oats. This is a host specific toxin.

2) Phytotoxins: These are the substances produced in the host plant due to
host-pathogen interactions for which a causal role in disease is merely
suspected rather than established. These are the products of parasites which
induce few or none of the symptoms caused by the living pathogen. They are
non-specific and there is no relationship between toxin production and
pathogenicity of disease causing agent.
Ex: Alternaric acid – Alternaria solani

3) Vivotoxins: These are the substances produced in the infected host by the
pathogen and / or its host which functions in the production of the disease,
but is not itself the initial inciting agent of the disease.
Fusaric acid – Wilt causing Fusarium sp.
Lycomarasmin – Fusarium oxysporum f.sp. lycopersici
Piricularin – Pyricularia oryzae

Classification based on specificity of toxins

1. Host specific / Host selective toxins: These are the metabolic products of
the pathogens which are selectively toxic only to the susceptible host of the
28
pathogen
Ex: Victorin, T-toxin, Phyto-alternarin, Amylovorin

2. Non-specific / Non-selective toxins

These are the metabolic products of the pathogen, but do not have host
specificity and affect the protoplasm of many unrelated plant species that are
normally not infected by the pathogen
Ex: Ten-toxin, Tab-toxin, Fusaric acid, Piricularin, Lycomarasmin and Alternaric
acid
Differentiate host – specific and non-host
specific toxins Host specific Non-host specific
1. Selectively toxic only to susceptible 1. No host specificity and can
also affect host of the pathogen the physiology of those plants that are
normally not infected by the pathogen

2. Primary determinants of disease 2. Secondary determinants of disease

3. Produce all the essential symptoms 3. Produce few or none of the

symptoms of of the disease the disease

4. Ex: Victorin, T- toxin 4. Ex: Tentoxin, Tabtoxin

Effect of toxins on host tissues

A) Changes in cell permeability: Toxins kill plant cells by altering the
permeability of plasma membrane, thus permitting loss of water and
electrolytes and also unrestricted entry of substances including toxins.
Cellular transport system, especially, H+ / K+ exchange at the cell membrane
is affected.

B) Disruption of normal metabolic processes

 Increase in respiration due to disturbed salt balance
 Malfunctioning of enzyme system Ex: Piricularin inhibits polyphenol oxidase
 Uncoupling of oxidative phosphorylation

C) Interfere with the growth regulatory system of host plant Ex: Restricted
development of roots induced by Fusarium moniliforme

ROLE OF GROWTH REGULATORS IN PLANT PATHOGENESIS

Growth regulators
Growth regulators are of two types
1. Growth promoting substances and 2. Growth inhibiting substances
Auxins, gibberellins and cytokinins are growth promoting substances,
whereas, dormin, ethylene and abscissic acid are growth inhibiting
substances.

The imbalance in growth promoting and growth inhibiting substances causes

hypertrophy (excessive increase in cell size) and atrophy (decrease in cell
size). Symptoms may appear as tumors, galls, knots, witches broom,
stunting, excessive root branching, defoliation and suppression of bud
growth.

1. Growth promoting substances:

29
a) Auxins: Indole-3-acetic acid (IAA) is the naturally occurring auxin. It is
continuously produced in young meristematic tissue and moves rapidly to
older tissues. If auxin concentration is more, its concentration is reduced by
the enzyme, IAA oxidase.

Functions: IAA regulates cell elongation and differentiation, also affects

permeability of the membrane, increases respiration, and promotes synthesis
of mRNA.

How disease is induced?

Increased IAA results in hypertrophy and decreased IAA results in
atrophy. Increased IAA may be due to inhibition of IAA oxidase.
Ex: Ralstonia solanacearum (Pseudomonas solanacearum), the causal agent
of wilt of Solanaceous plants, induces a 100 fold increase in IAA level in
diseased plants. Increased plasticity of cell walls as a result of high IAA
levels renders the pectin, cellulose and protein components of the cell wall
more accessible to pathogen degradation. Increase in IAA levels may also
inhibit lignifications of tissues.

b) Gibberellins: First isolated from Gibberella fujikuroi (Conidial stage:

Fusarium moniliforme), the causal agent of bakanae or foolish seedling
disease of rice. Infected seedlings show abnormal elongation due to
excessive elongation of internodes. Best known gibberellin is Gibberellic
acid.

Functions: Cell elongation, stem and root elongation, promote flowering and
growth of fruits. It also induces IAA synthesis. IAA and GA act
synergistically. Ex: Sclerospora sacchari, the causal agent of downy mildew
of sugarcane induces GA production.

c) Cytokinins: Are necessary for cell growth and differentiation. It inhibits

breakdown of proteins and aminoacids and thereby inhibit senescence and
they have the capacity to direct the flow of aminoacids and other nutrients
towards high cytokinin concentration. Cytokinin activity increases in club
root, in crown galls and in rust infected bean leaves.

Growth inhibiting substances

a) Ethylene (CH2=CH2): Ethylene exerts a variety of effects on plants, viz.,
chlorosis, leaf abscission, epinasty, stimulation of adventitious roots, fruit
ripening and increased permeability of cell membranes.
Ex: Ethylene is involved in premature ripening of fingers in banana infected
by Pseudomonas solanacearum, the causal agent of moko disease of banana.
Ethylene was also detected in leaf epinasty symptom of the vascular wilt
syndrome. Ex: Fusarium oxysporum f.sp. lycopersici (Wilt in tomato).

b) Abscissic acid: It exerts dormancy in seeds, closure of stomata, inhibition

of seed germination and growth and stimulated germination of fungal spores.
It is one of the factors involved in stunting of plants.

c) Dormin / Abscissin II: Dormin induces dormancy by converting

developing leaf primordia of a bud into bud scales. It acts as an antagonist of
gibberellins and masks the effect of IAA. However, the exact role of dormin
is not known.

30
 Role of polysaccharides in pathogenesis

Polysaccharides: Fungi, bacteria and nematodes release varying amounts of

mucilaginous substances that coat their bodies and provide interface between
the outer surface of the micro-organism and its environment. The role of
slimy polysaccharides is of utmost importance in wilt diseases. In the
vascular wilts, large polysaccharide molecules released by the pathogen in
the xylem causes mechanical blockage of vascular bundles and initiate
wilting.
Ex: Ralstonia solanacearum (Bacterial wilt of Solanaceous plants)

Defense mechanism in plants

In general plants defend themselves against pathogens by two ways

i. Structural or morphological characteristics that act as physical
barriers
ii. Biochemical reactions that take place in cells and tissues that
are either toxic to the pathogen or create conditions that
inhibit the growth of the pathogen in the plant.

I. Structural defense mechanisms: These may be pre-existing, which exist

in the plant even before the pathogen comes in contact with the plant or
induced, i.e, even after the pathogen has penetrated the preformed defense
structures, one or more type of structures are formed to protect the plant
from further pathogen invasion.

A) Pre-existing structural defense structures

These include the amount and quality of wax and cuticle that cover the
epidermal cells and the size, location and shapes of natural openings
(stomata and lenticels) and presence of thick walled cells in the tissues of the
plant that hinder the advance of the pathogen.

i) Waxes: Waxes on leaf and fruit surfaces form a hydrophobic or water

repellent surface preventing the germination of fungi and multiplication of
bacteria.

ii) Cuticle and epidermal cells: A thick cuticle and tough outer wall of
epidermal cells may increase resistance to infection in diseases in which the
pathogen enters its host only through direct penetration. Ex: Disease
resistance in Barbery species infected with Puccinia graminis tritici has been
attributed to the tough outer epidermal cells with a thick cuticle.

iii) Sclerenchyma cells: The sclerenchyma cells in stems and leaf veins
effectively blocks the spread of some fungal and bacterial pathogens that
cause angular leaf spots.

iv) Structure of natural openings:

a) Stomata: Most of the pathogens enter plants through natural openings.
Some pathogens like stem rust of wheat can enter its host only when the
stomata are open. The wheat varieties (Cultivar, Hope) in which stomata
open late in the day are resistant as the germ tubes of the spores germinating
in the night dew desiccate owing to evaporation of the dew before stomata
begin to open. This can also be called as functional resistance. The structure
31
of stomata provides resistance to penetration by certain plant pathogenic
bacteria.

b) Lenticels: The shape and internal structure of lenticels can increase or

decrease the incidence of fruit diseases. Small and suberised lenticels will
offer resistance to potato scab pathogen, Streptomyces scabies.

B) Post-infectional structural defense mechanisms/Induced structural

barriers: These may be regarded as histological defense barriers (cork layer,
abscission layers and tyloses) and cellular defense structures (hyphal
sheathing).

i) Histological defense structures

a) Cork layer: Infection by fungi, bacteria, some viruses and nematodes
induce plants to form several layers of cork cells beyond the point of
infection and inhibits the further invasion by the pathogen beyond the initial
lesion and also blocks the spread of toxin substances secreted by the
pathogen. Furthermore, cork layers stop the flow of nutrients and water from
the healthy to the infected area and deprive the pathogen of nourishment. Ex:
Potato tubers infected by Rhizoctonia; Prunus domestica leaves attacked by
Coccomyces pruniphorae.

32
b) Abscission layers
An abscission layer consists of a gap formed between infected and
healthy cells of a leaf surrounding the locus of infection due to the
disintegration of the middle lamella of parenchymatous tissue.

Gradually, infected area shrivels, dies, and sloughs off, carrying with it the
pathogen. Abscission layers are formed on young active leaves of stone
fruits infected by fungi, bacteria or viruses.
Ex: Xanthomonas pruni, and Closterosporium carpophylum on peach leaves

c) Tyloses
Tyloses are the overgrowths of the protoplast of adjacent living
parenchymatous cells, which protrude into xylem vessels through pits.
Tyloses have cellulosic walls and are formed quickly ahead of the pathogen
and may clog the xylem vessels completely blocking the further advance of
the pathogen in resistant varieties. In susceptible varieties, few or no tyloses
are formed ahead of pathogen invasion.
Ex: Tyloses form in xylem vessels of most plants under invasion by most of
the vascular wilt pathogens.

ii) Cellular defense structures:

Hyphal sheathing: When a hyphae penetrating the cell wall and growing
into the cell lumen are enveloped by a cellulosic sheath (callose) formed by
extension of cell wall, which become infused with phenolic substances and
prevents further spread of the pathogen.
Ex: Hyphal sheathing is observed in flax infected with Fusarium oxysporum f.sp. lini.

33
II) Biochemical defense mechanisms: These can be classified as pre-
existing and induced biochemical defenses.

1) Pre-existing chemical defenses:

a) Inhibitors released by the plant in its environment:
Plants exude a variety of leaf and root exudates which contain aminoacids,
sugars, glycosides, organic acids, enzymes, alkaloids, flavones, toxic
materials, inorganic ions and also certain growth factors. The inhibitory
substances directly affect micro-organisms or encourage certain groups to
dominate the environment which may act as antagonists to pathogen.
 Ex 1: Tomato leaves secrete exudates which are inhibitory to Botrytis cinerea
 Ex 2: Red scales of red onion contain the phenolic compounds,

b) Inhibitors present in plant cells before infection:

 Antimicrobial substances pre-existing in plant cells include unsaturated
lactones, cyanogenic glycosides, Sulphur containing compounds, phenols,
phenolic glycosides and saponins
 Several phenolic compounds, tannins, and some fatty acid like
compounds such as dienes, which are present in high concentrations in
cells of young fruits, leaves or seeds are responsible for the resistance of
young tissues to Botrytis. These compounds are potent inhibitors of many
hydrolytic enzymes.
 Saponins have antifungal membranolytic activity which excludes fungal
pathogens that lack saponinases. Ex: Tomatine in tomato and Avenacin
in oats
 Similarly, lectins, which are proteins that bind specifically to certain
sugars and occur in large concentrations in many types of seeds, cause
lysis and growth inhibition of many fungi.
 Plant surface cells also contain variable amounts of hydrolytic enzymes such as
glucanases and chitinases which may cause breakdown of pathogen cell wall.

2) Post inflectional or induced defense mechanisms:

a) Phytoalexins (Phyton = plant; alexin = to ward off)
 Muller and Borger (1940) first used the term phytoalexins for fungistatic
compounds produced by plants in response to injury (mechanical or
chemical) or infection.
 Phytoalexins are toxic antimicrobial substances produced in appreciable
amounts in plants only after stimulation by phytopathogenic micro-
organisms or by chemical or mechanical injury.

34
 Phytoalexins are not produced by uninfected healthy plants, but produced
by healthy cells adjacent to localized damaged or necrotic cells in
response to materials diffusing from the infected cells. These are not
produced during compatible biotrophic infections.
 Phytoalexins accumulate around both resistant and susceptible necrotic
tissues. However, resistance occurs when one or more phytoalexins reach
a concentration sufficient to restrict pathogen development.

Characteristics of phytoalexins
1. Fungitoxic and bacteriostatic at low concentrations.
2. Produced in host plants in response to stimulus (elicitors) and metabolic products.
3. Absent in healthy plants
4. Remain close to the site of infection.
5. Produced in quantities proportionate to the size of inoculum.
6. Produced in response to the weak or non-pathogens than pathogens
7. Produced within 12-14 hours reaching peak around 24 hours after inoculation.
8. Host specific rather than pathogen specific.
Synthesis and accumulation of phytoalexins are shown in diversified
families, viz., Leguminosae, Solanaceae, Malvaceae, Chenopodiaceae,
Convolvulaceae, Compositae and Graminaceae.

S.No. Phtoalexin Host Pathogen

1 Pisatin Pea Monilinia fructicola
2 Phaseolin French bean Sclerotinia fructigena
3 Rishitin Potato Phytophthora infestans
4 Gossypol Cotton Verticillium alboatrum
5 Cicerin Bengalgram Ascochyta rabiei
6 Ipomeamarone Sweet potato Ceratocystis fimbriata
7 Capsidol Pepper Colletotrichum capsici

b) Hypersensitive response (HR)

 The term hypersensitivity was first used by Stakman (1915) in wheat

infected by rust fungus, Puccinia graminis.
 The hypersensitive response is a localized induced cell death in the host
plant at the site of infection by a pathogen, thus limiting the growth of
pathogen. In the infected plant part, HR is seen as water soaked large
sectors which subsequently become necrotic and collapsed.
 HR occurs only in incompatible host-pathogen combinations. HR may
occur whenever virulent strains or races of pathogens are injected into
non-host plants or into resistant varieties, and when avirulent strains or
races of pathogens are injected into susceptible cultivars.
 HR is initiated by the recognition of specific pathogen-produced signal
molecules, known as elicitors. Recognition of the elicitors by the host
results in altered cell functions leading to the production of defense
related compounds.

The most common new cell functions and compounds include:

 A rapid burst of oxidative reactions
+ +
 Increased ion movement, especially of K and H through cell membrane
 Disruption of membranes and loss of cell compartmentalization
 Cross-linking of phenolics with cell wall components and strengthening of
plant cell wall
 Production of antimicrobial substances such as phytoalexins and
pathogenesis-related proteins (such as chitinases)

35
Cellular responses during HR
 In many host-pathogen combinations, as soon as the pathogen establishes
contact with the cell, the nucleus moves toward the invading pathogen and
soon disintegrates.
 Brown resin like granules form in the cytoplasm, first around the point of
penetration of pathogen and then throughout the cytoplasm
 As the browning discolouration of the cytoplasm continues and death sets
in, the invading hypha begins to degenerate and further invasion is
stopped.

36
 PRINCIPLES OF PLANT DISEASE MANAGEMENT

Management: It is based not only on the principle of eradication of the

pathogen but mainly on the principle of minimizing the damage or loss
below economic injury level.

Importance: Plant diseases are important because of the losses (qualitative

and quantitative) they cause. Loss may occur at any time between sowing of
the crop and consumption of the produce. The management practices
includes
 Measures taken to prevent the incidence of the disease,
 Reduce the amount of inoculum that initiates and spreads the disease
 And finally minimize the loss caused by the disease

Essential considerations in plant disease Management:

1. Benefit-cost ratio
2. Procedures for disease control should fit into general schedule of
operations of crop production
3. Control measures should be adopted on a co-operative basis over large
adjoining areas. This reduces frequency of applications, cost of control and
increases chances of success of control measures
4. Knowledge aspects of disease development is essential for effective
economical control. Information is needed on the following aspects
a. Cause of a disease
b. Mode of survival and dissemination of the pathogen
c. Host parasite relationship
d. Effect of environment on pathogenesis in the plant or spread in plant population
5. Prevention of disease depends on management of primary inoculum
6. Integration of different approaches of disease management is always recommended

General principles of plant disease management

1. Avoidance: Avoiding disease by planting at times when, or in areas
where, inoculum is ineffective due to environmental conditions, or is rare or
absent
2. Exclusion of inoculum: Preventing the inoculum from entering or
establishing in the field or area where it does not exist
3. Eradication: Reducing, inactivating, eliminating or destroying inoculum
at the source, either from a region or from an individual plant in which it is
already established
4. Protection: Preventing infection by creating a chemical toxic barrier
between the plant surface and the pathogen
37
5. Disease resistance (Immunization): Preventing infection or reducing
effect of infection by managing the host through improvement of resistance
in it by genetic manipulation or by chemical therapy.

I. Avoidance of the pathogen: These methods aim at avoiding the contact

between the pathogen and susceptible stage of the crop. This is achieved by
a. Proper selection of geographical area
b. Proper selection of the field
c. Adjusting time of sowing
d. Disease escaping varieties
e. Proper selection of seed and planting material
II. Exclusion of the pathogen: These measures aim at preventing the
inoculum from entering or establishing in the field or area where it does not
exist. Different methods of exclusion are seed treatment, seed inspection &
certification, and plant quarantine regulation.

a) Seed inspection and certification: Crops grown for seed purpose are
inspected periodically for the presence of diseases that are disseminated by
seed. Necessary precautions are to be taken to remove the diseased plants in
early stages, and then the crop is certified as disease free. This practice will
help in the prevention of inter and intra regional spread of seed borne
diseases.

b) Plant quarantine regulation: Plant quarantine is defined as “ a legal

restriction on the movement of agricultural commodities for the purpose of
exclusion, prevention or delaying the spread of the plant pests and diseases
in uninfected areas”.

Plant quarantine measures are of 3 types.

1. Domestic quarantine: Rules and regulations issued prohibiting the
movement of insects and diseases and their hosts from one state to another
state in India is called domestic quarantine. Domestic quarantine in India
exists for two pests (Rooted scale and Sanjose scale) and three diseases
(Bunchy top of banana, banana mosaic and wart of potato).
Bunchy top of banana: It is present in Kerala, Assam, Bihar, West Begal
and Orissa. Transport of any part of Musa species excluding the fruit is
prohibited from these states to other states in India.
Banana mosaic: It is present in Maharashtra and Gujarat. Transport of any part of
Musa
species excluding the fruit is prohibited from these states to other states in India.
Wart of potato: It is endemic in Darjeeling area of West Bengal, therefore
seed tubers are not to be imported from West Bengal to other states.

2. Foreign quarantine: Rules and regulations issued prohibiting the import

of plants, plant materials, insects and fungi into India from foreign countries
by air, sea and land. Foreign quarantine rules may be general or specific.
General rules aim at prevention of introduction of pests and diseases into a
country, where as the specific rules aim at specific diseases and insect pests.
The plant materials are to be imported only through the prescribed ports of
entry.

Phytosanitary certificate: It is an official certificate from the country of

origin, which should accompany the consignment without which the material
may be refused from entry.
38
Plant diseases introduced into India before/after enforcement of plant quarantine
laws:
S.No. Disease Year Introduced into From
1 Late blight of potato 1883 India Europe
2 Coffee rust 1879 India Srilanka
3 Flag smut of wheat 1906 India Australia
4 Downy mildew of grapes 1910 India Europe
5 Bacterial blight of rice 1964 India Phillippines
6 Rice blast 1918 India (Madras) South East Asia
7 Downy mildew of maize 1912 India (Madras) Java
8 Ergot of bajra 1957 India (Bombay) Africa
9 Panama wilt of banana 1920 India Panama canal
10 Bunchy top of banana 1940 India Srilanka
11 Wart of potato 1953 India Netherlands
12 Golden cyst nematode of 1961 India Europe
potato

Diseases not entered into India: Swollen shoot of cocoa, leaf blight of
rubber and many viral diseases.
III. Eradication: These methods aim at breaking the infection chain by
removing the foci of infection and starvation of the pathogen (i.e.,
elimination of the pathogen from the area by destruction of sources of
primary and secondary inoculum). It is achieved by

a) Rouging: Removal of diseased plants or their affected organs from field,

which prevent the dissemination of plant pathogens.
Ex: Loose smut of wheat and barley, whip smut of sugarcane, red rot of
sugarcane, ergot of bajra, yellow vein mosaic of bhendi,

b) Eradication of alternate and collateral hosts: Eradication of alternate

hosts will help in management of many plant diseases.
Ex: Barbery eradication programme in France and USA reduced the
severity of black stem rust of wheat
Ex: Eradication of Thalictrum species in USA to manage leaf rust of wheat
caused by Puccinia recondita.
Eradication of collateral hosts, such as Panicum repens, Digitaria marginata
will help in the management of rice blast disease (Pyricularia oryzae)

c) Crop rotation: Continuous cultivation of the same crop in the same field
helps in the perpetuation of the pathogen in the soil. Soils which are
saturated by the pathogen are often referred as sick soils. To reduce the
incidence and severity of many soil borne diseases, crop rotation is adopted.
Crop rotation is applicable to only root inhabitants and facultative
saprophytes, and may not work with soil inhabitants.
Ex: Panama wilt of banana (long crop rotation), wheat soil borne mosaic (6
yrs) and club root of cabbage (6-10 yrs), etc.

d) Crop sanitation: Collection and destruction of plant debris from soil will
help in the management of soil borne facultative saprophytes as most of
these survive in plant debris. Collection and destruction of plant debris is an
important method to reduce the primary inoculum.

e) Manures and fertilizers: The deficiency or excess of a nutrient may

predispose a plant to some diseases. Excessive nitrogen application
aggravates diseases like stem rot, bacterial leaf blight and blast of rice.
39
Nitrate form of nitrogen increases many diseases, whereas, phosphorous and
potash application increases the resistance of the host. Addition of farm yard
manure or organic manures such as green manure, 60-100 t/ha, helps to
manage the diseases like cotton wilt, Ganoderma root rot of citrus, coconut,
etc.

f) Mixed cropping: Root rot of cotton (Phymatotrichum omnivorum) is

reduced when cotton is grown along with sorghum. Intercropping sorghum
in cluster bean reduces the incidence of root rot and wilt (Rhizoctonia solani)

g) Summer ploughing: Ploughing the soil during summer months expose

soil to hot weather which will eradicate heat sensitive soil borne pathogens.

h) Soil amendments: Application of organic amendments like saw dust,

straw, oil cake, etc., will effectively manage the diseases caused by Pythium,
Phytophthora, Verticillium, Macrophomina, Phymatotrichum and
Aphanomyces. Beneficial micro-organisms increases in soil and helps in
suppression of pathogenic microbes.
Ex: Application of lime (2500 Kg/ha) reduces the club root of cabbage by
increasing soil pH to 8.5
Ex: Application of Sulphur (900 Kg/ha) to soil brings the soil pH to 5.2 and
reduces the incidence of common scab of potato (Streptomyces scabies).
ij) Changing time of sowing: Pathogens are able to infect susceptible plants
under certain environmental conditions. Alternation in date of sowing can
help avoidance of favourable conditions for the pathogens.
Ex: Rice blast can be managed by changing planting season from June to
September/October.

j) Seed rate and plant density: Close spacing raises atmospheric humidity
and favours sporulation by many pathogenic fungi. A spacing of 8’X8’
instead of 7’X7’ reduces sigatoka disease of banana due to better ventilation
and reduced humidity. High density planting in chillies leads to high
incidence of damping off in nurseries.

k) Irrigation and drainage: The amount, frequency and method of irrigation

may affect the dissemination of certain plant pathogens. Many pathogens,
including, Pseudomonas solanacearum, X. campestris pv. oryzae and
Colletotrichum falcatum are readily disseminated through irrigation water.
High soil moisture favours root knot and other nematodes and the root rots
caused by species of Sclerotium, Rhizoctonia, Pythium, Phytophthora,
Phymatotrichum, etc.

40
PHYSICAL METHODS: Physical methods include soil solarization and
hot water treatments.

i. Soil solarization: Soil solarization or slow soil pasteurization is the

hydro/thermal soil heating accomplished by covering moist soil with
polyethylene sheets as soil mulch during summer months for 4-6 weeks. Soil
solarization was developed for the first time in Israel (Egley and Katan) for
the management of plant pathogenic pests, diseases and weeds.

ii. Soil sterilization: Soil can be sterilized in green houses and sometimes in
seed beds by aerated steam or hot water. At about 500C, nematodes, some
oomycetous fungi and other water molds are killed. At about 60 and 72 0C,
most of the plant pathogenic fungi and bacteria are killed. At about 82 0C,
most weeds, plant pathogenic bacteria and insects are killed. Heat tolerant
weed seeds and some plant viruses, such as TMV are killed at or near the
boiling point (95-1000C).

iii. Hot water or Hot air treatment: Hot water treatment or hat air
treatment will prevent the seed borne and soil borne infectious diseases. Hot
water treatment of certain seeds, bulbs and nursery stock is done to kill many
pathogens present in or on the seed and other propagating materials. Hot
water treatment is used for controlling sett borne diseases of sugarcane
[whip smut, grassy shoot and red rot of sugarcane (520C for 30 min)] and
loose smut of wheat (520C for 10 min).

Biological methods:
Def: Biological control of plant disease is a condition or practice whereby
survival or activity of a pathogen is reduced through the agency of any other
living organism (except human beings), with the result that there is reduction
in incidence of the disease caused by the pathogen (Garett, 1965).

Def: Biological control is the reduction of inoculum density or disease

producing activity of a pathogen or a parasite in its active or dormant state
by one or more organisms accomplished naturally or through manipulation
of the environment of host or antagonist by mass introduction of one or more
antagonists (Baker and Cook, 1974)

Mechanisms of biological control

1. Competition: Most of the biocontrol agents are fast growing and they
compete with plant pathogens for space, organic nutrients and minerals.
Most aerobic and facultative anaerobic micro-organisms respond to low iron
stress by producing extracellular, low molecular weight (500-1000 daltons)
iron transport agents, designated as Siderophores, which selectively make
complex with iron (Fe3+) with very high affinity. Siderophore producing
strains are able to utilize Fe3+ - Siderophore complex and restrict the growth
of deleterious micro-organisms mostly at the plant roots. Iron starvation
prevents the germination of spores of fungal pathogens in rhizosphere as
well as rhizoplane. Siderophores produced by
Pseudomonas fluorescens (known as pseudobactins or pyoveridins) helps
in the control of soft rot bacterium, Erwinia caratovora.

2. Antibiosis: Antagonism mediated by specific or non-specific metabolites

of microbial origin, by lytic agents, enzymes, volatile compounds or other

41
toxic substances is known as antibiosis.

a. Antibiotics: Antibiotics are generally considered to be organic

compounds of low molecular weight produced by microbes. At low
concentrations, antibiotics are deleterious to the growth or metabolic
activities of other micro-organisms.
Ex: Gliocladium virens produces gliotoxin that was responsible for the death of
Rhizoctonia solani on potato tubers.
Ex: Colonization of pea seeds by Trichoderma viride resulted in the
accumulation of significant amount of the antibiotic viridin in the seeds,
thus controlling Pythium ultimum.

42
Ex: Some strains of Pseudomonas fluorescens produce a range of
compounds, viz., 2,4- diacetyl phloroglucinol (DAPG), phenazines,
pyocyanin, which have broad spectrum activity against many plant
pathogenic bacteria and fungi

b. Bacteriocins: These are antibiotic like compounds with bactericidal

specificity closely related to the bacteriocin producer. Ex: The control of
crown gall (caused by Agrobacterium tumefaciens) by the related
Agrobacterium radiobacter strain K 84 is by the production of bacteriocin,
Agrocin K84.

c. Volatile compounds: Antibiosis mediated by volatile compounds has

been observed in the management of soil borne pathogens, viz., Pythium
ultimum, Rhizoctonia solani and Verticillium dahlia, by Enterobacter
cloacae. The volatile fraction responsible for inhibition was identified as
ammonia.

3. Hyperparasitism: Direct parasitism or lysis and death of the pathogen by

another micro-organism when the pathogen is in parasitic phase is known as
hyperparasitism.
Ex: T. harzianum parasitize and lyse the mycelia of Rhizoctonia and Sclerotium.

Biocontrol agents for the management of plant

pathogens Biocontrol agent
Pathogen/disea
se
1. Ampelomyces quisqualis Powdery mildew fungi
2. Darluca filum, Verticillium lecanii Rust fungi
3. Pichia gulliermondii Botrytis, Penicillium

Biocontrol agent Nematode

1. Pasteuria penetrans (Bacteria) Juvenile parasite of root knot nematode
2. Paecilomyces lilacinus (Fungus) Egg parasite of Meloidogyne incognita

Important fungal biocontrol agents:

Most of the species of Trichoderma, viz., T. harzianum, T. viride, T. virens
(Gliocladium virens) are used as biocontrol agents against soil borne
diseases, such as, root rots, seedling rots, collar rots, damping off and wilts
caused by the species of Pythium, Fusarium, Rhizoctonia, Macrophomina,
Sclerotium, Verticillium, etc.

Formulations of biocontrol agents available: T. viride (Ecofit, Bioderma in

India), G. virens (GlioGard in USA), T. harzianum (F-Stop in USA) and T.
polysporum (BINAB- T)

Important bacterial biocontrol agents:

1. Pseudomonas fluorescens (Dagger-G against damping off of cotton seedlings in
USA)
2. Bacillus subtilis (Kodiak against damping off and soft rot in USA)
3. Agrobacterium radiobacter K-84 (Gallex or Galltrol against crown gall of
stone fruits caused by Agrobacterium tumefaciens)

Plant growth promoting Rhizobacteria (PGPR):

Rhizosphere bacteria that favourably affect plant growth and yield of
commercially important crops are designated as plant growth promoting
43
rhizobacteria. The growth promoting ability of PGPR is due to their ability
to produce phytohormones, Siderophores, Hydrogen cyanide (HCN),
chitinases, volatile compounds or antibiotics which will reduce infection of
host through phyto-pathogenic micro-organisms.
Many bacterial species, viz., Bacillus subtilis, Pseudomonas fluorescens,
etc., are usually used for the management of plant pathogenic microbes.
Bacillus has ecological advantages as it produces endospores that are
tolerant to extreme environmental conditions. Pseudomonas fluorescens
have been extensively used to manage soil borne plant pathogenic fungi due
to their ability to use many carbon sources that exude from the roots and to
compete with microflora by the production of antibiotics, HCN and
Siderophores that suppress plant root pathogens.

44
PROTECTION: Use of chemicals for the control of plant diseases is
generally referred to as protection or therapy.

Protection: The prevention of the pathogen from entering the host or

checking the further development in already infected plants by the
application of chemicals is called protection and the chemicals used are
called protectants.

Therapy means cure of a disease, in which fungicide is applied after the

pathogen is in contact with the host. Chemicals used are called
therapeutants.
Fungicide: Any agent (chemical) that kills the fungus

Fungistat: Some chemicals which do not kill fungi, but simply inhibit the
fungus growth temporarily.

Antisporulant: The chemical which inhibits spore production without

affecting vegetative growth of the fungus.

Fungicides are classified into three categories: Protectants, eradicants and

therapeutants.
1. Protectants: These are the chemicals which are effective only when used
before infection (prophylactic in behavior). Contact fungicides which kill the
pathogen present on the host surface when it comes in contact with the host
are called protectants. These are applied to seeds, plant surfaces or soil.
These are non-systemic in action (i.e, they cannot penetrate plant tissues).
Ex: Zineb,sulphur, captan, Thiram, etc.

2. Eradicants: Those chemicals which eradicate the dormant or active

pathogen from the host. They can remain on/in the host for some time. Ex:
Lime sulphur, Dodine.

3. Therapeutants: These are the agents that inhibit the development of a

disease syndrome in a plant when applied after infection by a pathogen.
Therapy can be by physical means (solar and hot water treatment) and
chemical means (by use of systemic fungicides, i.e., chemotherapy).

CLASSIFICATION OF FUNGICIDES BASED ON METHOD OF

APPLICATION
The fungicides can also be classified based on the nature of their use in
managing the diseases.
1. Seed protectants: Ex. Captan, thiram, carbendazim, carboxin etc.
2. Soil fungicides (preplant): Ex. Bordeaux mixture, copper oxy chloride,
Chloropicrin, Formaldehyde, Vapam, etc.
3. Soil fungicides: Ex. Bordeaux mixture, copper oxy chloride, Captan,
PCNB, thiram etc.
4. Foliage and blossom: Ex. Capton, ferbam, zineb, mancozeb, chlorothalonil etc.
5. Fruit protectants: Eg. Captan, maneb, carbendazim, mancozeb etc.
6. Eradicants: EX. Lime sulphur
7. Tree wound dressers: Ex. Boreaux paste, chaubattia paste, etc.
8. General purpose sprays and dust formulations.

HOST PLANT RESISTANCE (IMMUNIZATION)

45
Disease resistance: It is the ability of a plant to overcome completely or in
some degree the effect of a pathogen or damaging factor.

Susceptibility: The inability of a plant to resist the effect of a pathogen or

other damaging factor.

Types of resistance:
1. Vertical resistance: When a variety is more resistant to some races of the
pathogen than others, the resistance is called vertical resistance (race-
specific resistance, qualitative resistance, discriminatory resistance). Vertical
resistance is usually governed by single gene and is unstable.

2. Horizontal resistance: When the resistance is uniformly spread against all

the races of a pathogen, then it is called horizontal/generalized/non-
specific/field/qualitative resistance. Horizontal resistance is usually governed
by several genes and is more stable.

3. Monogenic resistance: When the defense mechanism is controlled by a

single gene pair, it is called monogenic resistance.

4. Oligogenic resistance: when the defense mechanism is governed by a few

gene pairs, it is called oligogenic resistance.

5. Polygenic resistance: When the defense mechanism is controlled by

many genes or more groups of supplementary genes, it is called polygenic
resistance.

Cross protection: The phenomenon in which plant tissues infected with

mild strain of a virus are protected from infection by other severe strains of
the same virus. This strategy is used in the management of severe strains of
Citrus Tristeza virus

46