Chapter 5
Contents
Role of microbes in degradation
Xenobiotics Biodegradation and
Bioremediation
Pesticide Catabolism and Dechlorination
Degradation of Stored Hydrocarbons
Biosorption/bioaccumulation of heavy metals
Xenobiotics
Greek ‘xenos’ meaning foreign
Xenobiotics are compounds which are not produced by a
biological procedure and for which no equivalent exists in
nature
• Can be degraded by MOs
E .g. Pseudomonads seem to have the most highly developed
ability to adapt quickly to new carbon sources
Xenobiotics Biodegradation and Bioremediation
A xenobiotic is a synthetic chemical not produced by organisms in
nature
Pesticides , herbicides, etc.
Xenobiotics are Polychlorinated biphenyls (PCBs)
include such as: Dyes & munitions
Chlorinated solvents
Some xenobiotics differ chemically in such major ways from
anything organisms have experienced in nature that they
biodegrade extremely slowly, if at all
Xenobiotics Biodegradation and Bioremediation
Other xenobiotics are structurally related to one or more natural
compounds and can sometimes be degraded slowly by enzymes
that normally degrade the structurally related natural
compounds
Phanerochaete
able to degrade xenobiotics
chrysosporium
Burkholderia dechlorinates the pesticide
2,4,5-T aerobically, releasing chloride ion
(Cl-) in the process this reaction is
catalyzed by oxygenase enzymes
Pesticide Catabolism
Over 1000 pesticides have been marketed worldwide for pest
control
Pesticides include herbicides, insecticides, and fungicides
Pesticides display a wide variety of chemistries such as
chlorinated, aromatic, and nitrogen- and phosphorus containing
compounds (Figure 2)
Some of these substances can be used as carbon and energy sources
by microorganisms, whereas others are utilized only poorly or not
at all
Highly chlorinated compounds are typically the pesticides most
resistant to microbial attack
DDT, dichlorodiphenyltrichloroethane
(an organochlorine)
Malathion, mercaptosuccinic
acid diethyl ester (an
organophosphate)
Trichloroethylene
2,4-D, 2,4-dichlorophenoxyacetic
acid
Atrazine, 2-chloro-4-ethylamino
-6-isopropylaminotriazine
Chlorinated biphenyl (PCB),
shown is 2,3,4,2’,4’,5’-
hexachlorobiphenyl
Figure 2: Examples of xenobiotic compounds. Although none of these compounds exist
naturally, microorganisms exist that can break them down.
Pesticide Catabolism
However, related compounds may differ remarkably in their
degradability
For example, chlorinated compounds such as DDT persist relatively
unaltered for years in soils, whereas chlorinated compounds such as
2,4-D are significantly degraded in just a few weeks
Environmental factors, such as temperature, pH, aeration, and
organic content of the soil, influence the rate of pesticide
decomposition
Some pesticides can disappear from soils non-biologically by
volatilization, leaching, or spontaneous chemical breakdown
Pesticide Catabolism
In addition, some pesticides are degraded only when other
organic material is present that can be used as the primary
energy source, a phenomenon called cometabolism
In most cases, pesticides that are cometabolized are only
partially degraded, generating new xenobiotic compounds that
may be even more toxic or difficult to degrade than the original
compound
Thus, from an environmental standpoint, cometabolism of a
pesticide is not always good
Dechlorination
Many xenobiotics are chlorinated compounds and their
degradation proceeds through dechlorination
For example, the bacterium Burkholderia dechlorinates the
pesticide 2,4,5-T aerobically, releasing chloride ion (Cl-) in the
process (Figure 3)
this reaction is catalyzed by oxygenase enzymes
Following dechlorination, a dioxygenase enzyme breaks the
aromatic ring to yield compounds that can enter the citric acid
cycle and yield energy
Figure 3: Biodegradation of the herbicide 2,4,5-T. Pathway of
aerobic 2,4,5-T biodegradation; note the importance of oxygenase
enzymes in the degradation process.
Dechlorination
Although the aerobic breakdown of chlorinated xenobiotics is
ecologically important, reductive dechlorination is probably more
due to anoxic conditions developed in microbial habitats polluted
with chlorinated compounds
Reductive dechlorination is due to anaerobic respiration in which
chlorinated organic compounds such as chlorobenzoate
(C7H4O2Cl-) used as a terminal electron acceptors
Many compounds can be reductively dechlorinated (dichloro-,
trichloro-, and tetrachloro- (perchloro-) ethylene, chloroform,
dichloromethane, and polychlorinated biphenyls)
Dechlorination
In addition, several brominated and fluorinated organic
compounds can be dehalogenated in analogous fashion
Many of these chlorinated or halogenated compounds are highly
toxic and some have been linked to cancer (e.g. trichloroethylene)
Some of these compounds, such as polychlorinated biphenyls
(PCBs), have been widely used as insulators in electrical
transformers and enter anoxic environments from slow leakage
of the transformer or from leaking storage containers
Dechlorination
Eventually these compounds end up in groundwater, where they
are the most common groundwater contaminants detected in the
United States
There is therefore great interest in reductive dechlorination as a
bioremediation strategy for their removal from anoxic
environments
Bioaccumulation of heavy metals / Biosorption
The most common treatment for metal-contaminated waters is
with microbial biofilms
Microorganisms can also increase metal solubility for recovery
through the production of surfactants
Because of their small size, biosurfactants are a potentially
powerful tool in metal remediation
Bacterial surfactants are water soluble, low-molecular-weight
molecules (<1500) that can move relatively freely through soil
pores
Bioaccumulation of heavy metals / Biosorption
In addition to their small size, biosurfactants have a high
affinity for metals so that, once complexed, contaminating
metals can be removed from the soil by soil flushing
Some surfactants, such as the rhamnolipid Lead
produced by Pseudomonas aeruginosa, show
Cadmium
specificity for certain metals such as:
Bioaccumulation of heavy metals / Biosorption
Biosurfactant specificity allows the optimization of removal of a
particular metal
Related to biosurfactants, the higher molecular weight ( ͌ 106)
bioemulsifiers such as emulsan
produced by Acinetobacter calcoaceticus
Emulsan
can also aid in metal removal and hence as a
potential application for metal recovery
Bioaccumulation of heavy metals / Biosorption
Microbial biofilms :
Many microorganisms, including Pseudomonas, Arthrobacter,
Bacillus, Citrobacter, Streptomyces and the yeasts Saccharomyces
and Candida, produce exopolymers as part of their growth regime.
Metals have high affinities for these anionic exopolymers
Microbial biofilms may be viable or nonviable when used in
remediation
In general, the biofilm is immobilized on a support as
contaminated water is passed through the support
Bioaccumulation of heavy metals / Biosorption
Microbial biofilms :
Often, a mixture of biofilm-producing organisms grows on these
supports (Figure 4), providing a constant supply of fresh biofilm
For example, live Citrobacter spp. biofilms are used to remove
uranium from contaminated water
Both Arthrobacter spp. biofilms and biomass (non-living) are used
in recovery of cadmium, chromium, copper, lead and zinc from
wastewaters
Non-living Bacillus spp. Biomass preparations effectively bind
cadmium, chromium, copper, mercury and nickel, among other
metals
Bioaccumulation of heavy metals / Biosorption
Microbial biofilms :
The success of microbial biomass in metal recovery from
contaminated waters has led to the commercial sale of several
biomass products
For example, Amtbioclaim (Bacillus biomass) and AlgaSORB
(Chlorella vulgaris) are commercially available immobilized, non-
living preparations for treating metal contaminated water
Interestingly, microbial biofilms are also used in the treatment of
metal-contaminated marine waters
However, marine bacteria such as Deleya venustas and Moraxella
sp. are used
Figure 4 Schematic demonstrating how microbial biofilms are used in removing metals
from contaminated waste streams. The biofilm located on the rotating drum accumulates
metals as the water passes through the drum. The treated water can be safely released.
The biofilm may either be viable or nonviable. When viable, the biofilm rarely needs to
be replaced; however, non-living biofilms need to be replaced periodically because their
metal removal efficiency will decrease with time.
Bioaccumulation of heavy metals / Biosorption
Microbial biofilms :
Microbial biofilms are likewise used in the removal of metals
from domestic wastewater
In domestic waste treatment, the important biofilm-producing
organisms include Zoogloea, Klebsiella and Pseudomonas spp.
Complexed metals are removed from the wastewater via
sedimentation before release from the sewage treatment plant
Bioaccumulation of heavy metals / Biosorption
Biosorption :
It is a processes of heavy metal absorption
Biosorption of heavy metals has been studied on metal ions like
Cr3+, Cd2+, Cu2+
Metal biosorption by bacteria comprises two steps
Passive biosorption Active biosorption
Biosorption of metals by living and referring to the uptake of metals
dead/inactive cells that essentially take (transport into cells)
place in the cell wall due to a number of It only occurs in living cells through a
metabolism-independent processes slower active metabolism-dependent
In this process, metal ions are sorbed transport of metals into bacterial cells
rapidly to the cell surface by reactions Once the metals are inside living cells,
between metals and functional groups on they may be bound, precipitated,
the cell surface, such as hydroxyl, accumulated, sequestered within specific
carbonyl, carboxyl, sulfhydryl, thioether, intracellular organelles, or translocated
sulfonate, amine, amide, and phosphonate to specific structures, depending upon the
organism and element concerned
Bioaccumulation of heavy metals / Biosorption
Biosorption (Cr Phytoremediation with Fungi):
The fungal species that have active Cr biosorption mechanisms are
Rhizomucor miehei , Candida tropicalis, Mucor hiemalis,
Aspergillus carbonarius, Penicillium chrysogenum , and
Saccharomyces cerevisiae
Degradation of Stored Hydrocarbons
o Interfaces where oil and water meet often form on a large scale
o Besides water that separates from crude petroleum during storage
and transport, moisture can be condensed inside bulk fuel storage
tanks (Figure 1) where there are leaks
o This water eventually accumulates in a layer beneath the
petroleum------ >result in pollution
o Gasoline and crude oil storage tanks are thus potential habitats
for hydrocarbon oxidizing microorganisms
Figure 1: Bulk petroleum storage tanks. Fuel tanks often support
microbial growth at oil-water interfaces
Degradation of Stored Hydrocarbons
o If sufficient sulfate (SO42-) is present in the oil, as it often in crude
oils, sulfate-reducing bacteria can grow in the tanks, consuming
hydrocarbons under anoxic conditions
o The sulfide (H2S) produced is highly corrosive and causes pitting
and subsequent leakage of the tanks along with souring of the
fuel
o Aerobic degradation of fuel components is less of a problem
because the storage tanks are sealed and the fuel itself contains
little dissolved O2
