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Review
The accumulation of recalcitrant xenobiotic compounds is due to continuous efflux from population
and industrial inputs that have created a serious impact on the pristine nature of our environment.
Apart from this, these compounds are mostly carcinogenic, posing health hazards which persist over a
long period of time. Metabolic pathways and specific operon systems have been found in diverse but
limited groups of microbes that are responsible for the transformation of xenobiotic compounds.
Distinct catabolic genes are either present on mobile genetic elements, such as transposons and
plasmids, or the chromosome itself that facilitates horizontal gene transfer and enhances the rapid
microbial transformation of toxic xenobiotic compounds. Biotransformation of xenobiotic compounds
in natural environment has been studied to understand the microbial ecology, physiology and evolution
for their potential in bioremediation. Recent advance in the molecular techniques including DNA
fingerprinting, microarrays and metagenomics is being used to augment the transformation of
xenobiotic compounds. The present day understandings of aerobic, anaerobic and reductive
biotransformation by co-metabolic processes and an overview of latest developments in monitoring the
catabolic genes of xenobiotic-degrading bacteria are discussed elaborately in this work. Till date,
several reviews have come up, highlighting the problem of xenobiotic pollution, yet a comprehensive
understanding of the microbial biodegradation of xenobiotics and its application is in nascent stage.
Therefore, this is an attempt to understand the microbial role in biotransformation of xenobiotic
compounds in context to the modern day biotechnology.
Key words: Xenobiotics, degradation, bioremediation, co-metabolism, catabolic genes, plasmid, transposon,
horizontal gene transfer.
INTRODUCTION
Both natural and anthropogenic activities result in accu- aromatic compounds. The main concern with xenobiotic
mulation of wide ranges of toxic xenobiotic compounds in compounds is the toxicity threat they pose to public
the environment, and thus cause a global concern health. It is quite shocking that some xenobiotic com-
(Gienfrada and Rao, 2008). Primarily, xenobiotics are pounds (phenols, biphenyl compounds, phthalates, etc.)
those compounds that are alien to a living individual and act as endocrine disruptors (Nagao, 1998; Borgeest et
have a propensity to accumulate in the environment. al., 2002).
Principal xenobiotics include pesticides, fuels, solvents, Biodegradation is one of the natural processes that
alkanes, polycyclic hydrocarbons (PAHs), antibiotics, help to remove xenobiotic chemicals from the environ-
synthetic azo dyes, pollutants (dioxins and polychlori- ment by microorganisms. This is primarily a strategy for
nated biphenyls), polyaromatic, chlorinated and nitro- the survival of the microorganisms (Singh, 2008). It is one
of the most cost-effective methods amongst remedial
approaches. Several excellent reviews have been pub-
lished on the biodegradation or bioremediation, both
*Corresponding author. E-mail: sksenvb@rediffmail.com. generally (Prescott et al., 2008; Chatterjee et al., 2008)
Sinha et al. 6017
or specifically, of xenobiotic compounds (Austin et al., undergo bio-fix, a wide range of xenobiotic chemicals
1977; Chaudhry and Chapalamadugu, 1991; Zhang and include both aerobic e.g. Pseudomonas, Escherichia,
Bennet, 2005; Chauhan et al., 2008; Chowdhury et al., Sphingobium, Pandoraea, Rhodococcus, Gordonia,
2008). Although most organisms have detoxifying abilities Bacillus, Moraxella, Micrococcus and anaerobic types
(that is, mineralization, transformation and or immobi- e.g. Pelatomaculum, Desulfotomaculum, Syntropho-
lization of pollutants), microorganisms, particularly bac- bacter, Syntrophus, Desulphovibrio, Methanospirillum,
teria, play a crucial role in biogeochemical cycles for Methanosaeta (Chowdhury et al., 2008). It is found that
sustainable development of the biosphere (Tropel and Pseudomonas BCb12/1 and BCb12/3 are of excellent
Van der Meer, 2004). Horizontal gene transfer, high degradation capabilities of low ethoxylated NPnEO (Non
growth rates and metabolic versatility make them to phenol Polyethoxylates), maintaining high cell vitality
evolve quickly and to adapt themselves to changing (DiGioia et al., 2008). Several other bacterial genera that
conditions of environment, even at extreme environment help in the degradation of toxic and recalcitrant xenobiotic
that does not permit the proliferation of other living compounds are listed in Table 1.
organisms (Timmis and Pieper, 1999; Diaz and Prieto, Since bacterial genera aid efficiently in biotrans-
2000; Kim and Crowley, 2007). A large number of formation processes, evaluation of the xenobiotic con-
microbial communities have been characterized with their taminated areas is quite essential and involves the
responses to pollutants, in order to identify the potential enumeration and detection techniques of the xenobiotic
bacterial degrader that can adapt to use these chemicals degraders that generate quick and safe consequences.
as their novel growth and energy substrates (Janssen et The enumeration as well as monitoring of xenobiotic-
al., 1985). degrading bacterial populations in contaminated environ-
Microbial degradation of petroleum and other hydro- ment with traditional microbiological methods can acquire
carbons is incredibly an intricate course of action that an inordinate length of time (Lloyd-Jones et al., 1999). To
mainly depends on the composition of community and its meet this challenge, currently molecular approaches are
adaptive response to the presence of these compounds. practiced to exemplify the nucleic acids of micro-
Such degradation of petroleum in marine sites is organisms contained in the microbial community from
restricted principally by the availability of phosphorus and environmental samples (Widada et al., 2002). In spite of
nitrogen. Apart from this pH, moisture, oxygen and this, when molecular techniques are combined with basic
temperature are prime factors influencing the degradation microbiological methods, a comprehensive interpretation
rate (Leahy and Colwell, 1990). The biological treatment of the in situ microbial community along with its response
of xenobiotic wastes in the conventional activated sludge to both engineered bioremediation and natural attenua-
process varies under different conditions (Widada et al., tion processes is attained (Brockman, 1995).
2002). Relevance of current progress in molecular techni- The in-situ bioremediation process consists of three
ques has to be identified for isolation of plasmid DNA, fundamental steps (Madsen, 1991):
construction of DNA probes in recent perspective to
explore the efficient genes implicated in catabolism of (i) Bioattenuation: monitoring natural progress of degra-
xenobiotics and to study the genetic diversity of dation to ensure that contaminant decreases with time of
environmentally significant microbes. sampling.
The intent of the present review paper is to present a (ii) Biostimulation: intentional stimulation of resident xeno-
broad and updated overview of current understanding of biotic-degrading bacteria by electron acceptors, water,
the physiological, genetical and the molecular approa- nutrient addition, or electron donors.
ches for biodegradation of certain xenobiotic compounds (iii) Bioaugmentation: addition of laboratory grown bac-
by microorganisms. teria that have appropriate degradative abilities.
Figure 1. Interactions within ecosystem where microbes, environment and xenobiotic compounds are three limiting factors.
used to oxidize aromatic compounds (Zhang and Bennet, ethylene or perchloroethylene (PCE) to ethene, shown in
2005; Chauhan et al., 2008). Xenobiotic compounds are Figure 2a, is obtained from an anaerobic microbial
oxidized and mineralized under anaerobic conditions if enrichment culture containing Dehalococcoides etheno-
they are able to serve as electron donating substrates of genes 195 (Magnuson et al., 2000).
primary metabolism. Phenols, phthalates and hydro- The use of trinitrotoluene (TNT) as a terminal electron
carbons including benzene-toluene-ethyl benzene-xylene acceptor linked to growth has also been claimed (Esteve-
(BTEX) fall into this category (Reuter et al., 1994). Nunez et al., 2000). Anaerobic transformation of TNT at
Several xenobiotic compounds themselves act as termi- low redox potential minimizes oxidative polymerization
nal electron acceptors (TEA), supporting growth of micro- and releases toxic azoxy compounds that form readily in
organisms by gaining energy from the oxidation of simple the presence of oxygen. However, the enzymes have not
substrates (e.g. H2). been characterized completely (Mishra et al., 2001;
Pesticides, during anaerobic degradation, undergo Esteve-Nunez et al., 2001). Xenobiotics with electron-
dechlorination, hydrolysis, nitro reduction and withdrawing substituents as azo dyes, cyclotrimethyle-
dealkylation, which generally has a metabolic shift from netrinitramine (RDX) and carbon tetrachloride are readily
one pathway to another. Reductive dechlorination is biotransformed by cometabolic reduction processes
common to all halogenated pesticides including aliphatic, (Janssen et al., 2005). Benzoyl coenzyme-A (CoA)
cyclic aliphatic, aromatic, aniline-based phenoxy- pathway is one of the centralized pathways in majority of
alkanotes and cyclodiene types as the terminal electron denitrifying anaerobes where key enzyme is benzoate
accepting the process. This metabolism is referred to as coenzyme A ligase which attaches the coenzyme to the
halorespiration or dehalorespiration (Cutter et al., 2001). carboxy group and activates the benzoate for
Reductive dehalogenases constitute a novel pathway metabolism. Oxygen is incorporated and a subsequent
intended for complete dechlorination of tetrachloro- hydratase breaks the ring open. Thereafter, a series of
Sinha et al. 6021
reaction steps precede chopping away at simple aliphatic 1963). Though co-metabolism entails the parallel
acids until acetyl-CoA is formed (Schink et al., 2000). A oxidation of a non-growth substrate during growth of bac-
large majority of monocyclic aromatic compounds funnel teria on a compatible carbon and energy source, it also
into the benzoyl-CoA pathway as shown in Figure 2b. describes oxidation of non-utilizable substrates by resting
Phthalate compound degradation is mainly carried out cell suspensions grown at the disbursement of sub-
by anaerobic methanogens (Methanospirillum hungatei, stances that are capable of supporting microbial growth.
Methanosaeta concilii, Syntrophobacter fumaroxidens), Consequently, practice of co-metabolism refers to
producing acetate and methane as end products by oxidation of substances without utilization of the energy
decarboxylation initially, then reduction followed by ring derived from the oxidation to support microbial growth
cleave and ultimately pave to the -oxidation pathway and does not infer presence or absence of growth sub-
(Qiu et al., 2004; Zhang and Bennet, 2005). BTEX strate during the oxidation. So, it is a technique generally
compounds act as carbon and energy sources for diverse employed for the biochemical study of microbial aromatic
anaerobic bacteria under nitrate-reducing, Fe (III) metabolism (Horvath, 1972).
reducing, sulphate-reducing and methanogenic condi- Due to rapid decomposition of the herbicide, dalapon is
tions. Methyl tert-butyl ether (MTBE), a parallel conta- observed without an increase in bacterial numbers in soil
minant with BTEX and PAHs in petroleum-contaminated (Burge, 1969). Expression of the action of catechol-1,6-
sites, prone to aerobic degradation generally, and also on dioxygenase, a metacleaving enzyme possessed by
the anaerobic metabolism of MTBE, has been reported Achromobacter, has been accomplished by using the
(Kolhatkar et al., 2002). Truly with an anaerobe, the technique of co-metabolism (Horvath and Alexander,
cleavage involves methyl transferases with tetrahydro- 1970). Co-metabolism is especially important for the
folate for the degradation of lignin and hydroxyl group degradation of mixtures of polycyclic aromatic hydro-
addition during fermentation of polyethylene glycols but carbons (Chauhan et al., 2008). Strains that exhibit the
with an aerobic, bacteria degradation occurs with mono phenomenon of co-metabolism in a well organized
oxygenase (Zhang and Bennet, 2005). manner include Nocardia, Pseudomonas, Xanthomonas,
The biotransformation of pyrene and benzo[a]pyrene Bacillus, Brevibacterium, Flavobacterium, Aspergillus,
(BaP) is well studied in different bacterial species such as Azotobacter, Trichoderma, Vibrio, Achromobacter,
Mycobacterium vanbaalenii PYR-1, M. flavescens PYR- Arthrobacter, Hydrogenomonas, Microbacterium, Micro-
GCK, Mycobacterium RJGII-135, Mycobacterium KR2 coccus and Streptomyces (Beam and Perry, 1973).
and MycobacteriumAP1. Different pathways have been
anticipated. Mycobacterium KMS has been used to study
the metabolites produced during pyrene transformation. CATABOLIC GENE ORGANIZATION
First pathway indicates that pyrene hydroxylation takes
place at the 1,2 positions, leading to the formation of 4- Degradation of xenobiotic compounds is frequently inter-
hydroxy-perinaphthenone which is the ultimate product fered by a network of enzymes, present in the bacterial
so far found only in M. vanbaalenii PYR-1 cultures (Khan system. This brings about constraints in the completion of
et al., 2001). Another pathway involves the accumulation the process. The manipulation of the catabolic genes
of 6,6 -dihydroxy-2,2 -biphenyl-dicarboxylic acid in Myco- from degradative enzymes could solve the problem and
bacterium sp. strain AP1. Several key metabolites, boost up the process. For instance, degradation of
including pyrene-4,5-dione, cis-4,5-pyrene-dihydrodiol, xenobiotic compounds such as atrazine and nitrotoluene
phenanthrene-4,5-dicarboxylic acid, and 4-phenanthroic is occasionally mediated through a permutation of
acid are obtained. Pyrene-4,5-dione accumulates as a bacterial strains, which carry assorted genes responsible
final product in some gram-negative bacteria, and is for various fractions of the pathway (De Souza et al.,
further utilized followed by biotransformation (Liang et al., 1998). The degradation mainly depends upon the adap-
2006). The generalized pathway of biodegradation of ting response of the microbial communities which include
pyrene and BaP is presented in Figure 2c. Pyrene-4,5- both selective enrichment (resulting in amplification of
dione can be formed following the auto oxidation of 4,5- genes) and genetic changes (mainly includes gene
dihydroxy-pyrene and is also a pyrene transformation transfer or mutation). With the mobilization of silent
metabolite in several bacteria as in Sphingomonas sequences into the functional catabolic routes and advan-
yanoikuyae R1 (Khan et al., 2001). cement of substrate range by gradual or spontaneous
mutations, the recalcitrance of several toxic synthetic
pollutants would certainly decrease.
Co-metabolic pathway Recently, approaches have been made to assemble
data with reference to adaptation in bacterial populations
The oxidation of ethane to acetic acid, propane to propa- to specific xenobiotic compounds by gene transfer and to
noic acid and butane to butanoic acid and methyl ethyl characterize and compare the genes involved in
ketone during growth of Pseudomonas methanica on degradation of identical or similar xenobiotic compounds
methane initiated the concept of co-metabolism (Jensen, in nearly diverse or more isolated bacterial genera from
6022 Afr. J. Biotechnol.
a b
C
Figure 2. Pathway of degradation of different xenobiotic compounds. a. Aliphatic compound; b. Aromatic monocyclic
compound; c. Aromatic polycyclic compound.
Sinha et al. 6023
Mobile genetic elements support horizontal gene trans- appropriate genes and to enhance the process of degra-
fer more accurately via conjugation or transformation that dation through improved constructed strains, a proper
can impart novel phenotypes or may modify existing management is required. And for the same, degradation
genes through mutational processes. Typical catabolic technology is spanning the spectrum from environmental
plasmids are TOL, OCT, CAM, NAH etc. (Mishra et al., monitoring ultimately to biodegradation as well as
2001). Studies have confirmed that horizontal transfer of bioremediation (Eyers et al., 2004). Currently, molecular
catabolic genes, mostly by means of plasmid-mediated approaches are being used to characterize the nucleic
conjugation, happens in soil microcosms, bioreactors and acids of various bacteria from environmental samples
so on after inoculation of a donor strain containing natural (Hurt et al., 2001). Comparing with standard micro-
catabolic genes (Fulthorpe and Wyndham, 1992). The biological methods, the molecular techniques provide us
catabolism of benzoate and phthalate suggests high with a more comprehensive interpretation of the in situ
degree of redundancy, as RhodocccusRHA1 has three microbial community and its response to both engineered
linear plasmids (1,1,0.45 and 0.33 Mb). The smallest one bioremediation and natural attenuation processes
has 300 putative genes and performs one fourth of the (Brockman, 1995).
catabolic reactions, encoding 2,3-dihydroxybiphenyl 1,2- PCR amplification, subsequent analysis of bacterial
dioxygenase. This suggests that it has potential to rRNA genes by sequencing, preparing metagenomic
degrade various PCB congeners (Larkin et al., 2005). libraries, RFLP, dot-blot, southern blot, denaturing gra-
Toluene degrading plasmid (TOL) is also one of the best dient gel electrophoresis (DGGE), microarrays are
studied catabolic plasmids, as it bears degradative genes several techniques which are applied for degradation.
for xylene, toluene, benzoate, salicylate, catechol, phenol The gene encoding TCE-RDase required for PCE
and several other complex compounds (Lloyd et al., biotransformation, tceA has been cloned and sequenced
1999). by an inverse PCR approach. Sequence comparisons of
Generally, the mechanism of gene action for degra- tceA to proteins in the public databases revealed weak
dation varies from organism to organism, depending on sequence similarity confined to the C-terminal region,
the entire organization as seen below. which contains the eight-iron ferredoxin cluster binding
motif (Magnuson et al., 2000). Direct DNA hybridization
(i) In the first category, genes are organized on single techniques have been made to monitor TOL and naph-
operon system e.g. phenol (Khan et al., 2001). Here the thalene degrading plasmid (NAH) (Sayler and Layton,
genes may be characterized by the plasmid genome or 1990). Polychlorinated biphenyl (PCB) catabolic genes
may be present separately on the chromosome. have been used to measure the level of PCB-degrading
(ii) In the second group, genes are organized on two organisms in soil microbial communities with the help of
operon systems e.g. polychlorinated biphenyls etc. Here dot-blot technique (Walia et al., 1990). To quantify the
the genes are characterized by plasmid genome (Shimizu degradation of 2,4-dichlorophenoxyacetic acid (2, 4-D),
et al., 2001). tfdA and tfdB gene probes have been used and identified
(iii) In the third group, genes are organized on more than with the help of southern hybridization technique (Holben
two operon systems e.g. 2,4-dichlorophenoxyaceticacid et al., 1992).
etc. Here, the genes are characterized by plasmid Another powerful molecular technique known as meta-
genome and the capability or incapability of bacteria to do genomic libraries has been flourished for the identification
the entire degradation depends on the existence of the of the desired catabolic genes. Basically, metagenomic is
complementary enzymes encoded by genes of the a culture dependent genomic analysis; it is either function
chromosome (Don and Pemberton, 1981). driven approach or sequence driven approach, of total
(iv) In another group, the genes are organized on trans- microbial communities, which provides access to retrieve
posons, e.g. 2,4,5-trichlorophenoxyacetate (2,4,5-T is a unknown sequences (Schloss and Handelsman, 2003).
herbicide). Pseudomonas AC1100 contains two insertion Though the technique is applicable, yet contains certain
elements, RS110 selected as IS931 and IS932; they play drawbacks. One of the major drawbacks is less recovery
a significant role in degradation of 2,4,5-T (Chaudhry and of desired clones that however can be overcome. The
Chapalamadugu, 1991). metagenomic libraries are particularly promising for
The expression of catabolic genes is in total when locating denitrifying genes (Eyers et al., 2004). The
enzymes (peripheral and ring cleavages), substrate, sequence-driven approach which is primarily based on
metabolites and structure of respective genes all are in a conserved regions in bacterial genes has also been
synchronized manner (Whyte et al., 2002). studied. It is reported that certain hybridization probes
(screen out clone libraries for specific DNA sequences)
may identify the required genes for degradation. For
MOLECULAR APPROACHES example, in the denitration of 2,4,6-trinitrophenol, the
ndpG and ndpI genes were identified in Rhodococcus
Most of the xenobiotic degrading bacteria harbor plasmids erythropolis HL-PMI (Heiss et al., 2003).
which code for catabolic genes. To characterize the In order to search out diverse degrading genes in
Sinha et al. 6025
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