MICROORGANISMS AS
XENOBIOTICS DEGRADERS
EKOLOGI MIKROORGANISME 2020
OUTLINE
➢ Definition of Xenobiotics.
➢ Properties and sources of xenobiotic compounds.
➢ Bioremediation approach:
1. Biodegradation and roles of microbial enzymes.
2. Biomineralization.
3. Cometabolism.
➢ Metal interaction with microorganisms.
XENOBIOTICS
➢ Xenos (Greek) meaning strange.
XENOBIOTICS: foreign chemicals which are synthesized within
the body.
➢ Examples:
Xenobiotics may be naturally occurring chemicals produced by
plants, animals, or microorganisms.
➢ Xenobiotics: synthetic chemicals produced by humans.
➢ Poisons are xenobiotics, but not all xenobiotics are poisonous.
Other definition:
➢ A chemical that is foreign to the biosphere, i.e. not produced
by natural biological or abiotic source.
➢ Also called anthropogenic, man-made, synthetic, pollutant,
contaminant, recalcitrant, persistent, and toxicant.
PROPERTIES OF XENOBIOTIC COMPOUNDS
RECALCITRANT XENOBIOTICS (resist biodegradation and
persist in environment):
➢ Non-recognizable as a substrate by microbes to act upon and
degrade it (not recognized as substrates by the existing
degradative enzymes).
➢ Highly stable, chemically and biologically inert.
➢ Insoluble in water/adsorbed to soil.
➢ Highly toxic.
➢ Large molecular nature makes it difficult to enter microbial cell
(large molecular weight prevents entry into microbial cell).
SOURCES OF XENOBIOTIC COMPOUNDS
Xenobiotic compounds
Biodegradable Non-Biodegradable
Hydrocarbons Synthetic polymers Oil mixtures Polychlorinated
biphenyls
PETROCHEMICAL INDUSTRY
➢ Oil/gas industry, refineries, and the production of basic
chemicals e.g. vinyl chloride, benzene.
PLASTIC INDUSTRY
➢ Closely related to the petrochemical industry.
➢ Uses a number of complex organic compounds such as anti-
oxidants, plasticizers, cross-linking agents.
Fresh water receive a vast variety of industrial pollutants.
HYDROCARBONS SUSCEPTIBILITY TO BIODEGRADATION
MICROBIAL PROPERTIES ENVIRONMENTAL PROPERTIES
➢ Gene regulation ➢ Electron acceptors
➢ Surface hydrophobicity ➢ Nutrients
➢ Metabolic flexibility ➢ Temperature
➢ Uptake mechanisms ➢ Salinity
➢ Tolerance to toxicity ➢ pH
HYDROCARBON PROPERTIES
➢ Bioavailability
➢ Molecular structure
➢ Toxicity
➢ Physical state
➢ Interactions
BIOREMEDIATION
DEFINITION
➢ The use of living organisms to transform, destroy or
immobilize contaminants.
➢ The use of biological systems for the reduction of pollution
from air, aquatic or terrestrial systems.
PROCESS
➢ Involves aerobic or anaerobic microorganisms that results in
degraded products (i.e. other compounds, H2O and CO2).
➢ Relies largely on the enzymatic activities of living organisms,
usually microorganisms, to catalyse the destruction of
pollutants or their transformation to less harmful forms.
GOAL
➢ Detoxification of the parent compound(s) and conversion to
products that are no longer hazardous to human health and
the environment.
➢ Create an optimal environment for the microorganisms to
degrade pollutants.
SCOPE OF BIOREMEDIATION
➢ To decrease the concentration of organic pollutants at
undetectable levels or, if measurable, lower than the limits
established as safe or tolerable by regulatory systems.
Bioremediation Approach (Strategy)
Bioremediation strategy uses microorganisms, plants or microbial
or plant enzymes to detoxify contaminants. The strategy:
➢ Biodegradation.
➢ Biomineralization.
➢ Cometabolism.
MICROORGANISMS
Pollution
(Air, Water, Soil)
Degraded
Products
Complete Incomplete
Eco-friendly Hazardous
(detoxification)
1. BIODEGRADATION AND ROLES OF ENZYMES
➢ BIODEGRADATION is the breakdown of organic
compounds that occur due to microbial activity.
➢ Biodegradation is a series of biological degradation steps or a
pathway that ultimately results in the oxidation of the parent
compound.
➢ Complete biodegradation or mineralization involves oxidation
of the parent compound to form carbon dioxide and energy
for growth, a process that provides both carbon and
reproduction of cells.
➢ Each degradation step in the pathway is catalyzed by a specific
enzyme made by the degrading cell. Extracellular enzymes are
important in the degradation of macromolecules.
➢ Sources of waste products have been both industrial and
agricultural. These contaminants can be considered as the
microbial food source or substrate.
➢ Contaminant compounds that have structures similar to those of
natural substrates are normally easily degraded.
→ the microorganisms have appropriate biodegrading enzymes.
➢ Contaminant compounds that are quite dissimilar to natural
substrates are often degraded slowly or not at all.
→ the compounds have unusual chemical structures that
existing enzymes do not recognize; the reason for persistence of
organic contaminants.
Principle diagram for degradation of a xenobiotic compound
Example: Oil, Fat, Grease
➢ Lipase enzyme removes oil/fatty deposits.
PHA: polyhydroxyalkanoates
(biodegradable, biocompatible
thermoplastics)
2. BIOMINERALIZATION
When a compound is biodegradable, it means that it
can be mineralized.
➢ A term related to BIODEGRADATION is BIOMINERALIZATION,
in which organic matter is converted into minerals (total
biodegradation) by the activities of organisms.
➢ MINERALIZATION is complete degradation to the end
products of CO2, water, and other inorganic compounds.
Mitchell & Gu, 2010
Example: Metal carbonate
Biomineralization of Metal Carbonates by Neurospora crassa
➢ The urease-positive fungus Neurospora crassa induced the
precipitation of metal carbonates (i.e. calcite and otavite) →
Biomineralization.
➢ Neurospora crassa play a potential role in the synthesis of
novel biominerals and in metal bioremediation or
biorecovery.
Li et al., 2014
Li et al., 2014
3. COMETABOLISM
COMETABOLISM
Transformation of an organic compound by a
microorganism that is unable to use the substrate as a
source of energy.
➢ Metabolites or transformation products from cometabolism
by one organism can be used as an energy source by another.
➢ Partial or incomplete degradation can also result in
polymerization or synthesis of compounds more complex and
stable than the parent compound.
Example: Trichloro-ethylene (TCE)
➢ The first step in the oxidation of methane by methanotrophic
bacteria is catalyzed by the enzyme methane mono-
oxygenase.
➢ This enzyme is nonspecific that it can also cometabolicaly
catalyze the first step in the oxidation of TCE (the industrial
solvent trichloro-ethylene) when both methane and TCE are
present.
➢ The bacteria receive no energy benefit from this cometabolic
degradation step.
➢ The subsequent degradation steps may be catalyzed
spontaneously, by other bacteria, or in some cases by the
methanotroph.
METAL INTERACTION WITH MICROORGANISMS
Metal uptake by organisms:
The biochemical processes occurring inside the microorganisms.
Geobacter metallireducens munching uranium
Mechanisms of Heavy Metal Removal
➢ Microorganims are potent bioremediators, removing metals
via passive or active uptake mechanisms.
➢ The uptake of metals by microorganism’s biomasses can take
place by:
✓ PASSIVE MODE (sorption and/or complexation)
termed as BIOSORPTION.
✓ ACTIVE MODE (dependent on the metabolic
activity) termed as BIOACCUMULATION.
Bahafid et al. 2017
Metal-microorganism
interactions
1. PASSIVE MODE
➢ BIOSORPTION involves the microbial cell wall, and extracellular
polymers.
➢ Binding is attributed to ion-exchange, adsorption,
complexation, precipitation and crystallization within the
multilaminate, microfibrillar cell wall structure.
➢ Large amounts of metals can remain associated with the cell
wall.
➢ Saccharomyces cerevisiae cells were constructed to display a
chain of hexa-histidine residues (His) as metal ion-adsorbents.
➢ This histidine-repeat is known to have high chelating activity
against metal ion Ni2+ and Cu2+.
Data on the biosorption of dyes by various yeasts
Yeast Biosorption of dye (primarily the azo (-N=N-) class
Candida spp., C. lipolytica, C. membranifaciens, C. Remazol Blue
guilliermondii, C. tropicalis, C. utilis
Candida rugosa, Cryptococcus heveanensis, Dekkera Reactive Blue 19, Reactive Black 5, Sulfur Black 1
bruxellensis, Kluyveromyces waltii, Pichia carsonii
Saccharomyces cerevisiae Remazol Blue, Reactive Blue 19
Kluyveromyces marxianus Remazol Black B, Remazol Blue, Remazol Turqoise Blue,
Remazol Red, Remazol Golden Yellow, Cibacron Orange
Schizosaccharomyces pombe Remazol Blue
2. ACTIVE MODE
➢ BIOACCUMULATION is a metabolism-dependent step.
➢ Suggested mechanisms for transport of metal ions into
microbial cells include lipid peroxidation, complex permeation,
carrier mediation, ion channels/pumps and endocytosis.
➢ Most mechanisms of metal transport rely on the
electrochemical proton gradient across the cell membrane.
➢ Metallotionein are low-molecular-weight Cys-rich proteins that
bind metal ions.
BIOSENSOR: an analytical device, used for the detection of
an analyte, that combines a biological component with a
physicochemical detector.
Potential Use of Yeast as Biosensor
Next Week: Individual Assignment
