THE LIFE OF MICROORGANISMS IN AIR, SPRINGS, RIVERS, LAKES AND SEAS.

AIR-MICROBIOLOGY
Like the soil and other environments, micro-organisms are represent in the air and because of
their role in the transmission of some air-borne infectious diseases and the dispersal of
microorganisms, the study of aeromicroorganisms has been receiving attention from
microbiologists and scientists generally. Human being inhales air every moment. Although most
of the microorganisms present in air are harmless but still less than 1% of the airborne bacteria
are pathogens. The components of the aerial environment are varied and mostly include pollen
grains, dust particles, fungal spores, bacterial spores, fungal hyphal fragments, actinomycetes,
spores of bryophytes and pteridophytes e.t.c
Aerosol: an aerosol represents a collection of particles in air that remain suspended for
appreciable time period. It is not indefinitely stable and its particle measure less than
100micrometer in diameter. Human health hazards due to air-borne microorganisms are usually
through aerosols. Human activities like coughing, sneezing, eating, talking, laughing etc usually
generate aerosols.
Bioaerosols are airborne particles of biological origin. Their composition depends on several
factors including the type of microbe, type of particles they are associated with (as mist or dust),
and the gases in which the bioaerosol is suspended. In general, bioaerosols range from less than
0.01 um to more than 100 um in diameter and are classified into different modes as follows:
Classification criteria
Examples
Biological Composition Bacteria, fungi, viruses, pollen, algae
Origin Natural (pollen, soil particles),
Anthropogenic (agriculture, waste disposal)
Size Inhalable (>10 µm), Thoracic (3-10 µm), Respirable (<3 µm)
Health Impact Allergenic (pollen, spores), Pathogenic (bacteria, viruses),
Toxic (mycotoxins)
Environmental Role Primary (direct release), Secondary (transformation)

Aeromicrobiology deals with the different aspects of microorganisms present in the

artmosphere. The vegetation and human activities determine the air microflora of that
environment
Aeromicrobiological studies are divided into
1. Intramural (indoor): places like warehouses, animal farms, storehouses, hospitals, etc.
Aeroflora of storehouses mainly contains storage fungi involved in the spoilage of stored food.
The hospital aero microflora is important in nosocomial infections.
2. Extramural (outdoor): places like crop fields, towns, cities, forests, grasslands etc. The
aeroflora of crop field varies according to the crop type which mostly include pathogenic fungal
spores. Outdoor air mostly does not contain disease causing pathogen whereas indoor air has
more pathogenic organisms especially in large gatherings like theaters and schools.
Air-borne Microorganisms
1. Bacteria: this comprise a heterogeneous group varying in size from 0.3 to 15 um and those
bacteria that are capable of withstanding prolonged desiccation only can persist in air for long
periods. Fortunately, such forms are saprophytic. Among these are sporulating species of bacilli,
cocci like Sarcina, and non-sporulating rods like Serratia. However, it is common to find throat
and mouth inhabiting bacteria examplified by Streptococcus, Staphylococcus, Pneumococcus,
etc. in air. Without any active dispersal mechanism the bacteria are carried in air via mechanical
disturbances of particulate matter, and on clothing and surgical dressings, etc. Minute droplets are
continuously thrown into air by rain splashes, breakers or sea sprays, sneezing or coughing.
Indoor source of airborne bacteria are mainly man and animals.
2. Protozoa. Most of the protozoans are transported as cysts; the cysts range from 2-50 um in
diameter. When protozoa are not in cyst condition, they vary in shape from irregular, plasmodial
to rigid flattened or ovoid.
3. Microalgae. Some common airborne microalgae are Chlamydomonas, Chlorococcum,
Gongrosira, Phormidium, Protococcus, Diatoms, Spirogyra, Oscillatoria, Chlorella, Amphora.
Some cyanobacteria (former blue green algae) like Aulosira, Lyngbya, Nostoc have also been
reported in air. The microalgae are airborne mainly due to air currents even in the absence of
adaptation for take off into air. A regular constituent of airborne microalgae comprises of algal
cysts or other resting stages. The microalgae in the range of 1-90 um are significant in respiratory
diseases and allergies as these are retained by the mucous membrane of respiratory tract.
4. Microfungi. Fungal spores are the propagative phase of microfungi and many of which are
adapted to air transport. The density of fungal spores in still air is approximately 1.0. However,
they are able to remain suspended in the atmosphere and become disseminated through the action
of turbulent air movement even though they are subjected to gravity. Hyphal Fragments of
microfungi constitute a significant population of air spora; these are primarily the conidiophores
of asexual forms. Culturing of these hyphal fragments revealed that they mostly belong to
Cladosporium, Alternaria, and Penicillium. These usually inhabit leaves of many plants and are
dispersed due to scrubbing action of the infected plants which occurs during air currents. Hyphal
fragments constitute an important airborne microflora.

The air of populated area generally contains cells or spores of Bacillus, Clostridium, ascospores
of yeasts, fragment of hyphae (Alternaria), conidia of Aspergillus, Penicillium etc. Few more
resistant non-spore forming bacteria such as Micrococcus, Corynebacterium, Coliform bacteria,
and some virus particles are also found in these areas.
Usually, micro-organisms in the air are in a state of suspended animation. Many of them are
easily killed by desiccation, ultra violent rays and other unfavorable conditions. Therefore the
living micro-organisms are either usually resistant or have been in the air for some time.
Resistant spores are capable of producing pigments and other means of adaptations.
The dispersal of airborne particles involves 3 stages
 Liberation and take off into the air
 Dispersion in air current
 Deposition on surfaces at the end of the journey before germination and growth.

LIBERATION:- Before a particle becomes airborne, a number of problems have to be

overcome. Example, energy is required to over come the adhesive forces attaching the particles to
the surface of substrates; also the particle has to be of a size that will be airborne. The degree of
adaptation to air borne dispersal varies greatly between different groups of micro-organisms and
this is reflected in their relative abundance in the air.
Viruses and bacteria are poorly adapted while fungi have developed many adaptation mechanism
to enable their spores become readily air-borne. While some have long sporophores (stalk) which
lift their spores well into the air, some others have ways of forcefully ejecting their spores into
the air. Some others rely on passive means. Rain splash, mechanical disturbance and other
physical adaptations help a lot in spore liberation into the air.

DISPERSION:- The dispersion of air-borne micro-organisms can be considered at two levels.

The individual spores and the behavior of groups or cloud of spores. These aspects are related
and depend on the physical characteristics of the spores and that of the atmosphere. The
important characteristics of spores in this respect are size, shape, degree of surface roughness,
density and electrostatic charges; while those of the environment include wind movements,
turbulences, layering convention, wind gradient near the ground and the pattern of atmospheric
circulation. Because they are heavier than air, spores tend to settle under gravity but because they
are also blown by air, they are affected by electrostatic charges. The distance traveled by a spore
depends on the interrelationship of the various factors mentioned.

DEPOSITION:- The final stage of airborne dispersal of microorganisms is deposition. The

microbes are returned to the surface layer of plants, animals or soil so that they can no longer be
blown by normal wind, though they may still be washed off. Deposition may occur in
precipitation or from dry air by several different methods such as sedimentation, rain washing
and so on.

The microbes released in the air are in three forms depending on the size and moisture content.
These three forms are:

1. Droplets

2. Droplets Nuclei

3. Infectious dust

Droplets: These droplets are water droplets that carry micro-organisms if a diseased person
released them. These droplets contain saliva and mucus. They are >5 μm in diameter that fall
rapidly to the ground under gravity, and therefore are transmitted only over a limited distance
<1m. Millions of Droplets are released when we sneeze, and mucus is expelled at about 200
miles away. The microorganisms they carry are mostly of respiratory tract. The size of droplet
determines for how long micro-organisms stay on the droplets. Droplets of large size settle in the
air rapidly. Diseases transmitted via droplets typically require close contact or direct exposure,
such as the flu, common cold

Droplets Nuclei: Particles of liquid, <5 micrograms in diameter that can remain suspended in air
for significant periods of time, allowing them to be transmitted over distances >1m. These result
from the evaporation of larger droplets. Droplet nuclei are considered to be the raw material for
the respiratory disorders. It contains saliva and mucus on its surface. They are primarily inhaled
into the respiratory system. Due to their small size they suspend in the air for a longer period of
time. Droplet nuclei are considered to be the constant source of bacterial infections if the bacteria
present on its surface remains viable. The viability of bacteria depends on the physical factors i.e.
humidity, sunlight, moisture and the size of droplets as well. Diseases like tuberculosis,
chickenpox, and measles are often transmitted via droplet nuclei, which can remain in the air for
hours and pose a risk to individuals even after the infected person has left the area.
Infected dust particles: this refers to dust particles that may contain pathogens. These dust
particles introduced in the air by bed making, handling a hand kerchief, dealing with a patient
having dried secretion, digging and ploughing. Microorganisms stick to the surface of these
droplets and get dried then they suspended by the methods given above. Dust particles laden with
microbes are larger in size and they settle in the air.

FACTORS AFFECTING CONCENTRATION OF MICROORGANISMS IN THE

ATMOSPHERE.
A number of factors can directly or indirectly affect the amount of micro-organisms and their
survival structures in air. Such factors may include wind speed, rain, temperature, pigmentation,
humidity, vegetation and human activities.
Wind Speed. Fast moving air blows force with it and so readily provides energy for detachment
of spores from their vegetative structure and other surfaces. Usually, it is difficult for spores to be
deposited at a spot except where there is an obstacle or a wind breaker along the wind course.

Rain Splashes. Rain washes air-borne spores to the soils and as such the amount of rain received
by an area may have some influence on the number of air-borne spores and microorganisms.
Where an area has a clearly defined raining and dry seasons, the amount of dust particles and
spores in the air may vary with the seasons of the year. Rain might reduce the levels of dust,
pollen, and some airborne bacteria, it doesn’t remove all microorganisms. Additionally, rainwater
can contain bacteria, viruses, and even pathogens that are present in the atmosphere or on
surfaces.

Temperature. During the dry season, those air-borne spores that are thin walled are easily
dehydrated to the advantage of those with thick warty walls which are more adapted to survive
high temperatures. There is also a relationship between temperature and humidity, then
temperature and wind movement. Many microorganisms, including bacteria, fungi, and viruses,
tend to be less active or dormant in cooler conditions. Higher temperatures typically promote the
growth and reproduction of many microorganisms. However, very high temperatures can be
lethal to microorganisms.
At higher temperatures, the rate of evaporation of water droplets (which might contain microbes)
increases, potentially forming droplet nuclei that stay suspended in the air longer. In cooler
conditions, larger droplets tend to fall to the ground more quickly, which reduces the chances of
airborne microbes traveling longer distances.
Humidity. The water amount in the air is usually referred to in terms of relative humidity that is
the ratio of the actual vapour pressure when the air is saturated with water at the same
temperature. Vapour pressure varies greatly with temperature and thus relative humidity is low
when temperature is high and vice visa. Relative humidity is a good indicator of the drying effect
air on micro-organisms. A wide range of relative humidity may be founds in the atmosphere from
10- 20% in desert regions to saturation or super saturation where cloud formation occurs at
ground level resulting in dews or frost. Different micro-organisms have different relative
humidity requirements for their survival in the air. The lower limit of relative humidity for fungal
growth is about 65%, while bacterial species require more.

Pigmentation and ultra-violent rays. Ultra violent radiation in the air originate from the sun
much of which is reflected or absorbed before reaching the earth’s surface. Micro-organisms
carried into the higher regions of the atmosphere may be exposed to the damaging doses of U.V
radiation. Though ultra-violent radiation of about 265mm is most lethal, other short waves
radiation even within the visible region can also be damaging. Pigmented spores especially those
of dermatophytes can resist strong ultra- violent rays from the sun. Generally speaking, radiation,
desiccation and temperature all interact to affect the survival of micro-organisms in the air. The
manner of interaction is not well understood but desiccation and freezing may protect micro-
organisms against radiation damage.

Vegetation: This can affect spores in air in two different ways. Leaves can trap spores when
washed down by the rain. Some may germinate when conditions are suitable. On the other hand,
when the leaves dry off the spores can be blown back into the atmosphere and thus increasing the
number of air-borne spores.

Man’s Activities: As a result of poor drainage systems of rubbish dumps and so on, micro-
organisms in rubbish dumps and dry faecal materials are blown up into air. Also during activation
and soil digging, soil-borne spores are released into the atmosphere. This maybe used to explain
why some farmers in some parts of the world suffer from an infection of the lungs and pulmonary
tracts caused by Aspergillus species, and the disease is called aspergillosis.

MICROORGANISNS IN WATER

Just like any other habitat, important special habitats can befound in aquatic environments and
the micro-organism inhabiting such habitats have special features of survival in such areas. Such
feature may be structural or physiological. One of such habitats in any water body is found in
sediments and particulate matter.
Physical and Chemical Factors in aquatic environments

Light: is a critical factors in determining the amount of carbon fixed into an inorganic compound
through photosynthesis. Much of the sun‟s radiation does not reaches the earth’s surface since it
is absorbed and scattered by atmosphere and
cloud cover. Some of the radiation which reach the water surface is reflected back to atmosphere.

Temperature: The amount of heat entering a body of water through insulation depends primarily
on the latitude and the water conditions; while the distribution of heat within the water body is
dependent on it morphological characteristics

and mixing by wind turbulence. In shallow waters such as streams and ponds, there may be large
temperature changes. In most case, it is the surface water that is temporarily variable, while
deeper waters show alternations seasonally. Such differential heating often can lead to thermal
stratification e.g. in a deep lakes, two stratified layers can be recognized viz:

The warm (upper) layer called epilimnion The cool (deeper) layer called hypolimnion.

However, in shallow lakes there is no stratification because there is a steady mixing of the water.
Where as in deeper waters, temperature remains fairly constant at a few degrees above freezing
point.

In the oceans and inland waters in cold climate areas where predominant water temperatures are
less than 5oc, the resident bacterial are mainly psychrophiles and they can grow event at 0 oc. In
warmer inland waters, mesophilic bacteria and fungi are the predominant species. Usually if
temperature is more than that required for the organisms, the cell components are destroyed or
denatured and this results in death. Whereas dropping in temperature below the normal range
may not necessarily kill the organisms, it slows down metabolic activity. Within a given range,
bacterial metabolism increases with increase in temperature and so there is increase growth with
increase temperature, but at temperatures higher than the optimum, growth rate is reduced.
Temperature has a profound effect on enzymatic activity.

PRESSURE: Hydrostatic pressure is not an important factor in inland waters but can be of
considerable importance in oceans at great depths. The pressure requirements of organisms differ
greatly even among the species. The term barophilic is used to describe bacteria which grow
preferably or exclusively at high pressures; While those which survive at high pressures without
injury but are normally active at atmospheric pressure condition are called barotolerant or
baroduric.

Dissolved Gases: The two most important dissolved gases in aquatic environments are oxygen
and carbon dioxide. Oxygen is impotent because of its importance in aerobic bioprocesses and in
relation to oxidation – reduction potentials; while carbondioxide is important for photosynthesis
and pH equilibrium. The concentration of oxygen in water is dependent on the water temperature,
partial pressure, salinity and biological activities. In water, an equilibrium is established between
carbondioxide (CO2), carbonic acid (H2CO3) and bicarbonate ions (HCO3)
Hydrogen Ion Concentration (PH): The optimum pH for most aquatic bacteria is between
pH6.5-8.5 and this corresponds with the PH of most large water bodies. The approximate PH of
sea water usually lies below PH 8-8.3 while those of lakes is approximately pH7; although
considerable fluctuations may occur. There are usually proportionally more fungal species in acid
waters compared with neutral and alkaline waters. The effect of pH is also related to enzymatic
activities, and drops in pH beyond the organism‟s normal range can affect its physiology, and
when extreme, can lead to death. Morphological changes can also occur such as enlargement of
cells and irregular swelling and branching. Photosynthesis is affected by pH through its influence
on carbon dioxide and carbonic acid equilibrium.

Salinity: Though salinity is not itself a physical factor, changes in salinity can have profound
osmotic effect which sometimes can be lethal and can also be toxic through denaturation of
cellular components. Most marine bacteria are halophilic and some have specific requirements
for sodium ions and some will not tolerate too high salt concentrations. Moderate changes in
salinity may have morphological and physiological effects e.g. rod-shaped bacteria may form
filaments with an increase in salinity and the microbial oxidation of organic acids and sugars are
affected

A planktonic environment refers to the habitat or ecological setting in which plankton exist.
Plankton are small, often microscopic organisms that drift in water bodies like oceans, lakes, and
rivers, typically floating or swimming passively with the currents.

There are three main types of plankton:

Phytoplankton: These are tiny, plant-like organisms that carry out photosynthesis. They
form the base of the aquatic food chain and are responsible for a large portion of Earth's
oxygen production. Phytoplankton include algae, diatoms, and cyanobacteria.

Zooplankton: These are animal-like organisms, ranging from tiny protozoa to larger
organisms like krill or jellyfish larvae. Zooplankton primarily feed on phytoplankton or
smaller zooplankton.

Bacterioplankton refers to the group of bacteria that exist as part of the plankton in
aquatic environments. These are microscopic, free-floating bacteria found in oceans,
freshwater bodies, and even in some land-based environments. They could be
Heterotrophic Bacterioplankton which consume organic matter in the water, such as dead
 plankton, plant material eg Caulobacter, or organic waste or Autotrophic
Bacterioplankton which are capable of photosynthesis (like phytoplankton) or
chemosynthesis (synthesizing food from inorganic substances like sulfur or methane) eg.
cyanobacteria

In a planktonic environment, conditions such as light availability, temperature, nutrient levels,

and water currents play key roles in shaping the distribution and productivity of plankton. This
environment is crucial for marine and freshwater ecosystems as plankton support many higher
trophic levels, such as fish, whales, and even some bird species.

MICROBES IN SPRING

Spring supplies are a source of groundwater, which in most instances has fewer micro-organisms
(e.g. coliform bacteria and protozoa such as Giardia and Cryptosporidium) and chemical
contaminants than a supply from surface water. The point at which the groundwater reaches the
surface is prone to contamination, so must be protected using a structure called a spring box. This
is often surrounded by a fence to keep animals out, with other common features being a ditch on
the uphill side, an overflow pipe and a well fitting lid. Spring water contains bacteria, algae,
fungi, protozoa, and viruses.

MICROBES IN LAKES

Lakes are divided into distinct zones based on their physical, chemical, and biological
characteristics. The four main zones are the littoral zone, limnetic zone, profundal zone, and
benthic zone. Factors affecting zonation include light penetration, temperature, dissolved
oxygen level, nutrient availability,
Littoral zone

 The littoral zone is the shallow, near-shore area of a lake where light penetrates to the
bottom
 Characterized by the presence of rooted aquatic plants (macrophytes) such as reeds,
rushes, and water lilies
 Provides diverse habitats for a wide range of aquatic organisms, including fish,
invertebrates, and amphibians
 Plays a crucial role in nutrient cycling and primary production
Organisms in this zone include: Phytoplankton: Algae and cyanobacteria such as Chlorella,
Spirogyra, and Anabaena. Bacteria: which helps in the decomposition and nutrient cycling (e.g.,
Pseudomonas, Aquaspirillum). Protozoa: Amoebae, ciliates, and flagellates like Paramecium
and Euglena that feed on bacteria and smaller algae. Fungi: Decomposers like Aspergillus and
Penicillium in the sediment and decaying plant matter.

Limnetic zone
 The limnetic zone, also known as the pelagic zone, is the open water area of a lake
away from the shore
  Extends from the surface to the depth where light penetrates sufficiently for
photosynthesis (photic zone)
 There are two main sources of oxygen to the photic zone: atmospheric mixing
and photosynthesis. Oxygen is dissolved when air interacts with water on the surface, and
is increased with wave and wind action. zone is the layer that receives sufficient sunlight,
allowing for photosynthesis. For this reason, it is often simply referred to as the photic
zone. The limnetic zone is the most photosynthetically-active zone of a lake since it is the
primary habitat for planktonic species.
 Dominated by phytoplankton, which are the primary producers in this zone
 Supports a diverse community of zooplankton and fish that feed on the phytoplankton
eg Chlorophyta, Anabaena, and Nostoc

Profundal zone

 The profundal zone is the deep, dark region of a lake below the limnetic zone
 Receives little to no sunlight (aphotic zone), limiting photosynthesis and primary
production
 Characterized by low oxygen levels due to the decomposition of organic matter settling
from above
 Plays a vital role in nutrient recycling, as bacteria and other microorganisms break
down dead organisms and detritus. The bacteria are anaerobic in nature, they inckude
Clostridium (fermenting bacteria) and sulfur-reducing bacteria (Desulfovibrio), Archaea
that produce methane, such as Methanococcus and Methanobacterium, Sulfate-reducing
bacteria eg, Desulfobacter and Desulfovibrio.
Benthic zone

 The benthic zone encompasses the lake bottom and the sediments that accumulate there
 Inhabited by a diverse community of microorganisms, including bacteria, fungi, and
protozoans
 Serves as a habitat for benthic invertebrates such as insect larvae, worms, and mollusks
 Plays a crucial role in decomposition and nutrient cycling, as organic matter settles and
is processed by the benthic community.
They also include Sulfate-reducing bacteria Desulfobacter, Methanogens, Nitrifying Bacteria
like Nitrosomonas and Nitrobacter, Fungi: e.g., Mucor and Rhizopus), Protozoa: Paramecium
MICROBES IN RIVER

Microorganisms in rivers which include bacteria, archaea, protozoa, fungi, and algae, are
involved in various biological processes that support the overall functioning of freshwater
environments.they help in nutrient cycling, water quality (by breaking down toxins like heavy
metals or organic contaminant), Ecosystem Health (by maintaining the health of river ecosystems
by supporting biodiversity)

MICROBES IN SEAS

The zones in seas include;

Epipelagic zone (Sunlight Zone): 0-200m. organisms include cyanobacteria (eg

Prochlorococcus) , Pseudomonas.

Mesopelagic Zone (Twilight Zone): 200–1000 meters. It is defined by light that begins at the
depth where only 1% of incident light reaches and ends where there is no light. Microorganisms
include Pseudomonas, Bacillus, Crenarchaeota and Euryarchaeota, fungi.

Bathypelagic Zone (Midnight Zone): Depth of between 1000–4000 meters. It is characterized by

complete darkness, with temperatures near freezing and extremely high pressure. There is little to
no light penetration, and the ecosystem relies heavily on the downward drift of organic matter
from the upper layers. Species of bacteria are adapted to high-pressure, low-nutrient
environments. Some are chemosynthetic, using chemicals like sulfur or methane instead of
sunlight for energy, eg, Alteromonas, Psychrobacter, Moritella, Alcanivorax, and members of the
Proteobacteria, Bacteroidetes.

Archaea are prominent in this zone, where they often play a role in methane production and
consumption. viruses are abundant and interact with both plankton and bacteria.

Abyssopelagic zone, also known as the abyssal zone, is the deepest part of the ocean, where
there is no sunlight. It is located between 4,000 and 6,000 meters below the ocean's
surface. Many of the bacteria in this zone are psychrophiles,Species of Pseudomonas, Vibrio,
and Shewanella have been found in deep-sea environments, including the abyssopelagic zone,
where they can break down organic matter or interact with other organisms. Fungi are less
commonly found compared to bacteria and archaea. Deep-sea viruses infect microorganisms like
bacteria (bacteriophages), archaea, and even other eukaryotic organisms, contributing to the
microbial dynamics of the environment

Brackish water, sometimes termed brack water, is water occurring in a natural environment
that has more salinity than freshwater, but not as much as seawater. It may result from mixing
seawater (salt water) and fresh water together, as in estuaries, or it may occur in brackish fossil
aquifers. various types of bacteria (like Vibrio, Pseudomonas, Bacillus), cyanobacteria (e.g.,
Microcystis), diatoms (Phaeodactylum, Thalassiosira), protozoa, and fungi.

BIOFILMS

Biofilm is an aggregate of microorganisms in which cells adhere to each other on a surface.

These cells are frequently embedded within a self-produced matrix of extracellular polymeric
substance (EPS). Biofilm EPS, also referred to as slime, is a polymeric conglomeration composed
of extracellular DNA, proteins, and polysaccharides. It can form on almost any surface, such as
pipes, medical devices, natural surfaces, or teeth (as dental plaque). Biofilms are typically
multilayered but relatively thin (micrometers to millimeters in thickness), and the
microorganisms are embedded in a matrix of extracellular polymeric substances (EPS)

Formation of a biofilm begins with the attachment of free-floating microorganisms to a surface.

These first colonists initially form a weak, reversible adhesion to the surface via van der Waals
forces. If the colonists are not immediately separated from the surface, they can anchor
themselves more permanently using cell adhesion structures such as pili. Some species are not
able to attach to a surface on their own but are able to anchor themselves to the matrix or directly
to earlier colonists. It is during this colonization that the cells are able to communicate via
quorum sensing.

the five stages of biofilm development are as follows:

 1. Initial attachment
2. Irreversible attachment
3. Maturation I
4. Maturation II
5. Dispersion
1. Initial attachment: This attachment is primarily driven by weak forces like van der Waals
forces and electrostatic interactions. The microbes often come from a surrounding fluid (e.g.,
water, blood) and will attach to almost any surface.

2. Irreversible Attachment: Over time, the microbial cells begin to produce adhesive
molecules (e.g., pili, adhesins) that help them irreversibly attach to the surface. The biofilm
formation process becomes more stable as the microorganisms anchor themselves more firmly.
3. Maturation I (Microcolony Formation): At this stage, the microbes start to divide and
form microcolonies. These are small clusters of microbial cells that grow and develop three-
dimensional structures. Cells communicate through chemical signals in a process called quorum
sensing, where the population density of microbes triggers changes in gene expression. The
microbial community also begins producing extracellular polymeric substances (EPS), which are
sticky, protective compounds that help the cells stay together and adhere to the surface more
firmly.
4. Maturation II (Biofilm Development): During this stage, the biofilm grows and
becomes more organized. The microcolonies expand and form larger, more complex structures.
The EPS matrix thickens and includes a variety of substances, such as polysaccharides, proteins,
and DNA, which protect the biofilm community from environmental stresses (e.g., antibiotics,
immune system attacks).
5. Dispersion: In the final stage, some cells in the biofilm are released or “dispersed” back
into the surrounding environment. This dispersion occurs in response to environmental signals
(such as nutrient depletion or the presence of antibiotics) and is crucial for the spread of the
biofilm to new surfaces.

Microbial mat

microbial mat is a firm structure of layered microorganisms with complementary physiological

activities that can develop on surfaces in aquatic environments. A microbial mat is a multi-
layered sheet or biofilm of microbial colonies, composed of mainly bacteria and/or archaea.
Microbial mats grow at interfaces between different types of material, mostly on submerged or
moist surfaces, but a few survive in deserts.

CYCLING OF ELEMENTS IN WATER AND SEDIMENTS

This refers to the continuous movement and transformation of chemical elements between the
water column and the sediment layer on the bottom of a body of water, involving biological,
chemical, and geological processes. The elements are absorbed, released, and transported through
various forms within the ecosystem, often driven by organisms and environmental factors like
temperature and oxygen levels.

Elements cycling through water and sediments are Phosphorus, nitrogen, iron, carbon, sulphur,
oxygen, heavy metals.
The nutrient cycles, also known as biogeochemical cycle, describe the movement of chemical
elements through different media, such as the atmosphere, soil, rocks, bodies of water, and
organisms. It keep essential elements available to plants and other organisms.
CARBON CYCLE
The carbon cycle is a natural carbon recycling process where carbon continuously moves
between biotic (living) and abiotic (non-living) systems in the ocean, Earth, and atmosphere. If
the carbon cycle is out of balance, biotic and abiotic systems become disrupted, as in what is
happening with global warming.
Carbon primarily exists as dissolved CO₂, bicarbonate (HCO₃⁻), or carbonate (CO₃² ⁻) in water.
Carbondioxide functions as a planetary temperature regulator. It is a greenhouse gas that absorbs
heat to keep the planet warm so it can sustain life. If there is too little CO2 in the atmosphere, the
planet excessively cools and falls into an ice age, and if too much, it causes the planet to
excessively warm and overheat. Phytoplankton and aquatic plants take up CO₂ during
photosynthesis, converting it into organic carbon. Some of this organic carbon is passed up the
food chain, while other portions may settle to the bottom as dead organic matter, contributing to
sediment. The ocean is a major player in the carbon cycle because it naturally absorbs a large
amount of CO2 from the atmosphere. When CO2 enters the ocean, it undergoes chemical
reactions with seawater, transforming into charged bicarbonate ions and hydrogen ions.
Excessive hydrogen ions decrease ocean pH, making seawater more acidic.
In Sediments, ie. anoxic (low-oxygen) environments, microbes break down organic carbon
through anaerobic respiration, producing methane (CH₄) or CO₂. Over time, carbon can become
sequestered in the sediment as carbonates or organic matter, contributing to long-term storage.
NITROGEN CYCLE
The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple
chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The
conversion of nitrogen can be carried out through both biological and physical processes.
Important processes in the nitrogen cycle include Nitrogen
fixation, ammonification, assimilation, nitrification, and denitrification.

Nitrogen fixation

It is the initial step of the nitrogen cycle. Here, Atmospheric nitrogen (N2) which is primarily
available in an inert form, is converted into the usable form -ammonia (NH3).

During the process of Nitrogen fixation, the inert form of nitrogen gas is deposited into soils from
the atmosphere and surface waters, mainly through precipitation.

The entire process of Nitrogen fixation is completed by symbiotic bacteria, which are known as
Diazotrophs. Azotobacter and Rhizobium also have a major role in this process. These bacteria
consist of a nitrogenase enzyme, which has the capability to combine gaseous nitrogen with
hydrogen to form ammonia.

Nitrogen fixation can occur either by atmospheric fixation- which involves lightening, or
industrial fixation by manufacturing ammonia under high temperature and pressure
conditions. This can also be fixed through man-made processes, primarily industrial processes
that create ammonia and nitrogen-rich fertilizers.
Types of Nitrogen Fixation

1. Atmospheric fixation: A natural phenomenon where the energy of lightning breaks the
nitrogen into nitrogen oxides, which are then used by plants.
2. Industrial nitrogen fixation: It is a man-made alternative that aids in nitrogen fixation
by the use of ammonia. Ammonia is produced by the direct combination of nitrogen and
hydrogen. Later, it is converted into various fertilizers such as urea.
3. Biological nitrogen fixation: We already know that nitrogen is not used directly from the
air by plants and animals. Bacteria like Rhizobium and blue-green algae transform the
unusable form of nitrogen into other compounds that are more readily usable. These
nitrogen compounds get fixed in the soil by these microbes.

Nitrification
In this process, the ammonia is converted into nitrate by the presence of bacteria in the
soil. Nitrites are formed by the oxidation of ammonia with the help of Nitrosomonas bacteria
species. Later, the produced nitrites are converted into nitrates by Nitrobacter. This conversion is
very important as ammonia gas is toxic for plants.
The reaction involved in the process of Nitrification is as follows:
2NH3 + 3O2 → 2NO2– + 2H+ + 2H2O
2NO2– + O2 → 2NO3–

Assimilation

Primary producers – plants take in the nitrogen compounds from the soil with the help of their
roots, which are available in the form of ammonia, nitrite ions, nitrate ions or ammonium ions
and are used in the formation of the plant and animal proteins. This way, it enters the food
web when the primary consumers eat the plants. HNO3 + 8H+ → NH3 + 3H2O

Ammonification

When plants or animals die, the nitrogen present in the organic matter is released back into the
soil. The decomposers, namely bacteria or fungi present in the soil, convert the organic matter
back into ammonium. This process of decomposition produces ammonia, which is further used
for other biological processes.

Denitrification

Denitrification is the process in which the nitrogen compounds make their way back into the
atmosphere by converting nitrate (NO3-) into gaseous nitrogen (N). This process of the nitrogen
cycle is the final stage and occurs in the absence of oxygen (sediment). Denitrification is carried
out by the denitrifying bacterial species- Clostridium and Pseudomonas, which will process
nitrate to gain oxygen and gives out free nitrogen gas as a byproduct.

2NO3− + 10 e− + 12 H+ → N2 + 6 H2O
Nitrogen Cycle in Marine Ecosystem
The process of the nitrogen cycle occurs in the same manner in the marine ecosystem as in the
terrestrial ecosystem. The only difference is that it is carried out by marine bacteria.

The nitrogen-containing compounds fall into the ocean as sediments get compressed over long
periods and form sedimentary rock.

Importance of Nitrogen Cycle

The importance of the nitrogen cycle are as follows:

1. Helps plants to synthesise chlorophyll from the nitrogen compounds.

2. Helps in converting inert nitrogen gas into a usable form for the plants through the
biochemical process.
3. In the process of ammonification, the bacteria help in decomposing the animal and plant
matter, which indirectly helps to clean up the environment.
4. Nitrates and nitrites are released into the soil, which helps in enriching the soil with the
necessary nutrients required for cultivation.
5. Nitrogen is an integral component of the cell and it forms many crucial compounds and
important biomolecules.
Nitrogen is also cycled by human activities such as the combustion of fuels and the use of
nitrogen fertilisers. These processes increase the levels of nitrogen-containing compounds in the
atmosphere. The fertilisers containing nitrogen are washed away in lakes, rivers and result in
eutrophication.

PHOSPHORUS CYCLE
Circulation of phosphorus in various forms through nature. Of all the elements recycled in
the biosphere, phosphorus is the scarcest and therefore the one most limiting in any given
ecological system. It is indispensable to life, being intimately involved in energy transfer and in
the passage of genetic information in the deoxyribonucleic acid (DNA) of all cells.

Much of the phosphorus on Earth is tied up in rock and sedimentary deposits, from which it is
released by weathering, leaching, and mining. Some of it passes through freshwater and
terrestrial ecosystems via plants, grazers, predators, and parasites, to be returned to those
ecosystems by death and decay. Much of it, however, is deposited in the sea, in shallow
sediments, where it circulates readily, or in ocean deeps, whence it wells up only occasionally.
Phosphorus is brought back to the land through fish harvests and through collection of guano
deposited by seabirds. Although there are seasonal pulses of availability, there appears to be a
steady loss of phosphorus to the ocean deeps.

Because of its high reactivity, phosphorus exists in combined form with other elements.
Microorganisms produce acids that form soluble phosphate from insoluble
phosphorus compounds. The phosphates are utilized by algae and terrestrial green plants, which
in turn pass into the bodies of animal consumers. Upon death and decay of organisms, phosphates
are released for recycling.
SULFUR CYCLE

The sulfur cycle describes the movement of sulfur through the atmosphere, mineral forms, and
through living things. Although sulfur is primarily found in sedimentary rocks or sea water, it is
particularly important to living things because it is a component of many proteins.

Sulfur is released from geologic sources through the weathering of rocks. Once sulfur is exposed
to the air, it combines with oxygen, and becomes sulfate SO 4. Plants and microbes assimilate
sulfate and convert it into organic forms. As animals consume plants, the sulfur is moved through
the food chain and released when organisms die and decompose.

Some bacteria like Proteus, Campylobacter, Pseudomonas and Salmonella – have the ability to
reduce sulfur, but can also use oxygen and other terminal electron acceptors. Others, such as
Desulfuromonas, use only sulfur. These bacteria get their energy by reducing elemental sulfur to
hydrogen sulfide. They may combine this reaction with the oxidation of acetate, succinate, or
other organic compounds.

The most well known sulfur reducing bacteria are those in the domain Archea, which are some of
the oldest forms of life on Earth. They are often extremophiles, living in hot springs and thermal
vents where other organisms cannot live. Lots of bacteria reduce small amounts of sulfates to
synthesize sulfur-containing cell components; this is known as assimilatory sulfate reduction. By
contrast, the sulfate-reducing bacteria considered here reduce sulfate in large amounts to obtain
energy and expel the resulting sulfide as waste. This process is known as dissimilatory sulfate
reduction. In a sense, they breathe sulfate.

Sulfur metabolic pathways for bacteria have important medical implications. For example,
Mycobacterium tuberculosis (the bacteria causing tuberculosis) and Mycobacterium leprae
(which causes leoprosy) both utilize sulfur, so the sulfur pathway is a target of drug development
to control these bacteria.
THE IRON CYCLE

The iron cycle (Fe) is the biogeochemical cycle of iron through

the atmosphere, hydrosphere, biosphere and lithosphere. While Fe is highly abundant in the
Earth's crust, it is less common in oxygenated surface waters. Iron is a
key micronutrient in primary productivity. The cycling of iron between its +2 and +3 oxidation
states is referred to as the iron cycle. This process can be entirely abiotic or facilitated
by microorganisms, especially iron-oxidizing bacteria. The abiotic processes include
the rusting of iron-bearing metals, where Fe2+ is abiotically oxidized to Fe3+ in the presence of
oxygen, and the reduction of Fe3+ to Fe2+ by iron-sulfide minerals. The biological cycling of
Fe2+ is done by iron oxidizing and reducing microbes.

Unlike terrestrial and sediment environments, iron is considered a limiting nutrient in the modern
marine environment. The largest flux of iron entering the oceans is fluvial in nature, meaning that
it enters as suspended particles or dissolved iron carried by rivers, or is associated with glacial
sediments. For the most part, this iron is deposited in the sediments of near coastal areas, and
does not reach the open ocean. Therefore, in the open ocean, the major pathway of iron entry is
eolian (entry through wind action), or as dust that is carried through the atmosphere mainly from
desert and other arid environment land surfaces.

Iron Oxidation

 Chemoautotrophs: Under aerobic conditions, ferrous iron tends to oxidize to the ferric form.
Ferrous iron will autoxidize or spontaneously oxidize under aerobic condition. Reduced iron
is an important source of energy for several specialized genera of chemoautotrophic bacteria,
the iron-oxidizers.
 Photoautotrophs: some members of the purple and green bacteria can use Fe21 as an electron
donor to carry out anaerobic photosynthesis coupled to photoautotrophic growth (i.e., growth
involving photosynthesis and oxidation). Phototrophic iron oxidation is a photoautotrophic,
anaerobic process that is limited to purple and green sulfur bacteria.

Iron Reduction

Iron is microbially reduced for two purposes, assimilation and energy generation. Assimilatory
iron reduction is the reduction of Fe3+ for uptake and incorporation into cell constituents. This
usually involves the release of siderophores, which complex Fe 3+ in the environment exterior to
the cell. The ironsiderophore complex then delivers the Fe 3+ to the cell, which is reduced to Fe 2+
as it is taken up. Dissimilatory iron reduction or iron respiration is the use of Fe 3+ as a terminal
electron acceptor for the purpose of energy generation during anaerobic respiration.

Due to its abundance in Earth’s crust, Fe 3+ found in iron oxides and oxyhydroxides serves as an
important terminal electron acceptor for anaerobic heterotrophic bacteria.
Because iron respiration has been an important activity during the evolution of Earth, there is
wide diversity among the bacteria and archaeans capable of carrying out this activity. The
problem for the iron-reducers is that most of the iron in environment is relatively unavailable. So,
microorganisms have developed some very interesting strategies to solve this problem.

The first is to make direct contact with an iron oxide surface. In this case, the iron reductase is a
membrane-bound enzyme allowing direct access of the enzyme with the substrate. A second
strategy is to use an electron shuttle that can act as an intermediate in transferring electrons from
the cell to the iron oxide surface.