J.Mycopathol.Res. 62(2) : 231-240, 2024, ISSN : 0971-3719 (Print), 2583-6315 (Online)© Indian Mycological Society, Department of Botany,
University of Calcutta, Kolkata 700 019, India

10.57023/JMycR.62.2.2024.231

REVIEW

An assessment of degradation of xenobiotic compounds by soil borne
bacteria and their adaptation to organic xenobiotic compounds: A
reviewJYOTI, HIMANI TOMAR, ABHIT SHARMA, SAURABH GULERI, NAVEEN GAURAV AND ARUN KUMAR*
School of Basic and Applied Sciences, Shri Guru Ram Rai University, Pathribagh,
Dehradun-248001, Uttarakhand
Received : 02.11.2023

Accepted : 21.03.2024

Published : 24.06.2024

Global environmental pollution caused by the complex mixture of xenobiotic drugs and toxic chemicals has
become a major environmental problem worldwide. Many such type of xenobiotic compounds effect theenvironment due to their high toxicity, persistence and low biodegradability. Microbial-assisted degradation ofxenobiotic compounds is considered the most efficient and effective method. Bacteria have significant
catabolic potential for biodegradation processes and involve different catabolic genes, enzymes to various
degradation pathways. Microorganisms can detoxify and use pollutants for their growth and metabolic
activities. However, different microbial groups survive in highly polluted environments and have significant
biodegradation capabilities that can break down and transform pollutants into less harmful chemicals so
present study, specifically defined the effects of xenobiotic compounds in soil, water, plants, human health,environment and role of bacterial originated enzymes involved in degradation of these xenobiotic chemicals.
Keywords: Enzymes, biodegradation, microbial-assisted degradation, xenobiotic compounds.

INTRODUCTION
Xenobiotic compounds can be defined in a strict
or broader sense. Consequently, “anycompounds that are released in any compartmentof the environment by the action of man andthereby occur in a concentration that is higher
than natural” are included in a larger definition ofxenobiotics. Heavy metals, polycyclic aromatichydrocarbons (PAHs), and oil derivatives liketoluene are also included in this broader category.
We will only address bacterial adaptation toorganic xenobiotics as described by Leisinger inthis review, and we’ll just call them xenobiotics or
xenobiotic substances (Top and Springael, 2003).
Environment is everything that is around us all
the time and affects our daily life in the world. A
safe and healthy environment is essential tosurvive in this world. However, a variety of humanactivities, including exposure to environmental
xenobiotics, constitute the primary cause ofpollution and harm in the era of industrialization
and urbanisation. Xenobiotics are substances that
*Correspondence:dean.sbas@sgrru.ac.in

are not found or expected to be found in livingorganisms.
The term “xenobiotics” is often used in the context
of environmental pollution and refers to synthetic
substances widely produced for commercial,
agricultural, and domestic use (Mishra andSrinivasan, 2001). There is increasing publicconcern about the intentional or unintentional
introduction into the environment of various
xenobiotics that pose high risks to humans andanimals (Godheja et al. 2016). Environmental
xenobiotics include pesticides, polycyclicaromatic hydrocarbons (PAHs), pharmaceutically
active compounds (PhACs), personal careproducts (PCPs), phenolic resins, chlorinatedcompounds, and other chemicals.
Microbial communities can adapt to the presenceof xenobiotics in the environment through various
mechanisms or combinations. First, by inducing
the necessary genes, the large population ofbacteria that can tolerate and even degrade thecompound will increase. Secondly, cells can be
modified by a variety of changes, such as232

A review on Degradation of xenobiotic compounds by soil borne bacteria

nucleotide changes or DNA rearrangements thatlead to degradation of compounds and they canobtain background information of relevant
individuals or different groups in society throughhorizontal gene transfer (HGT). Finally, single
cells that can best maintain or reduce thexenobiotic will be selected and screened throughthe population until they form a greater proportionof the microbial community than before theremoval of the xenobiotic.In response toenvironmental stress, microbes have evolved avariety of defence mechanisms, including
mutation, DNA recombination, and horizontal genetransfer. Horizontal transfer of genes plays animportant role in the transfer of catabolic genes
and thus enables the transfer of organisms topolluted areas.
In many artificially produced chlorinatedchemicals, the breaking of carbon-halogen bonds
is catalysed by bacterial de-halogenases. This isa critical phase in the process of detoxifying
common organic contaminants. Catabolic
pathways to form new compounds some appear
to have evolved through the accumulation ofhorizontally transmitted genes and subsequent
mutations and genetic modifications. Recent
studies have demonstrated the existence of novel
exogenous catabolic mobile genetic elements,
such as catabolic genomic islands, that integrate
into the chromosome after mutation. The
significance of the combination of horizontal genetransfer and patchwork is still unclear, but recent
reports suggest that this process occurs in theinfected area. Global pollution from exogenous
compounds has become a matter of concern.
Many xenobiotic compounds aff ect theenvironment due to their high toxicity, persistence
and low biodegradability. Microbial-assisted
degradation of xenobiotic compounds is
considered as the most efficient and effective
method. Significant catabolic potential exists inbacteria, and genes, enzymes, and degradation
pathways are involved in biodegradation
processes. Numerous microorganisms, including
Streptomyces, Rhodococcus, Kojima,
Penicillium, Aeromonas, Alcaligenes,
Microbacteria, Micrococci, Methanospirillum,
Candida, and Chrysos is involved in this process.
Microorganisms can use exhaust gases ascarbon or nitrogen to control their growth and[J.Mycopathol.Res :metabolic activity (Miglani et al., 2022). Different
microbial groups survive in highly polluted
environments and have significant biodegradation
capabilities that can break down and transformpollutants. However, investigating thesexenobiotics diseases necessitates the use of anincreasing number of techniques. To characterizehazardous bacteria, their metabolic processes,
new proteins, and catabolic genes involved in the
degradation process, diverse approaches suchas metagenomics, proteomics, transcriptomics,
and metabolomics are now applied. This method
is effective for learning about organisms’ genetic
diversity and community structure.
Advanced molecular methods to characterize
complex microbial communities can provide
insight into their structure and function and help
to resolve questions regarding the biodegradation
potential of bacteria. This review article
discusses the biodegradation potential of
microorganisms and provides insight into recent
advances and omics approaches for the uniquecharacterization of xenobiotic biodegradative
microorganisms in the environment. Microbial
remediation of xenobiotic compounds is
considered one of the most effective, efficient andeconomical methods that can consumes organic
solvents such as oxygen, carbon or nitrogen
added to control their growth (Embrandiri et al.
2016). There are diverse microbial communities
that thrive in toxic and highly stressf ulenvironments, including soil, water, humanintestines, hydrothermal vents, acid mine runoff,and oil reservoirs (Dhakal et. al, 2018). Due totheir genetic and functional diversity, microbial
populations have the potential to improve theenvironment (Baun et al. 2012). Therefore,
examining the microbial species present in thecontaminated environment provides important
information about the specif ic microbial
characteristics that increase the rate ofdegradation. However, the effective use of
microbial purification strategies requires atechnological process that leads to a deeper
understanding of microbial activity and survival
under environmental stress.
The development of molecular, biotechnological,
bioinformatics and systems biology tools relevant
to bioremediation problems has provided gene-62(2) June, 2024]

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level mechanisms for bioremediation (Maurya,
2016). In addition, the direct study of infectious
diseases, including all microbial diseases,
presents new challenges to the scientificcommunity in sharing information about the world
without microbial diseases (Derby et al. 2021).
The development of advanced molecular tools
and a better understanding of microbial
metabolism and genetic structure and function
have accelerated the development of newtechnologies to enhance bioremediation toeliminate environmental pollution (Zhou et al.
2022). Soil is an ideal environment for a wide
variety of microbial communities. It is estimatedthat one gram of soil contains approximately 109
bacteria, but only less than 1% of these can be
sampled in the laboratory (Elekwachi et al. 2014).
Culture-based identification of distinct microbial
populations in different areas is a difficult task
limited by the rapid growth of microbial diversity(Liu et al. 2019).Therefore, it is possible touncover the diversity and functional dynamics ofthe microbial community in contaminatedenvironments using contemporary cultureindependent molecular approaches. Additionally,
recent advances in molecular tools andtechnologies have provided new insights in thefield of bioremediation and transformed traditional
research (Bhandari et al., 2021). Omics
technology is the result of advanced moleculartechnology and directly characterizes microbial
genome structure without the need for culture.
Therefore, the use of modern technologies suchas metagenomics, transcriptomics, andproteomics has produced important information
about the gene and protein expression levels of
all microbial communities in the environment inorder to reveal the mechanisms of microbial
degradation and bioremediation (Perelo, 2010).
Omic method is efficient, fast and accurate
molecular method. It investigates advanced
microbial degradation processes, metabolic
activities, genetic control and molecular biology
aspects of xenobiotics (Azubuike et al. 2016).
The application of bacteria to remove exogenous
substances from soil, water or sediments by
conversion or mineralization into harmlessproducts such as CO2 and H2O is the main ideaof bioremediation strategies (Stefnac et al. 2021).
Idium and Exophiala have been reported to play233

a role in the efficient biodegradation of xenobiotic
compounds in soil/water environment due to their
excellent bioremediation potential (Saraswat,2014). The biodegradation ability of bacteria is
generally affected by soil, salinity, temperature,
carbon source, moisture content, pH, nitrogensource, amount of inoculum (Sikandar et al.
2013). Microorganisms have significant catabolic
capacity, genes, enzymes and degradation
pathways involved in the bioremediation processthat may be responsible for the transformation of
new properties and characteristics (Fent et. al.
2006). Additionally, microbial plasmids are thought
to be responsible for further amplification,transformation and delivery of new biodegradable
genes or enzymes (Faroon and Ruiz, 2016).
These new genes or enzymes, due to horizontal
gene transfers, endow microorganisms with thebiodegradation ability to remove or eliminate mostenvironmental contaminants (Yadav, 2020). The
treatment process for diseases can be further
improved by the successful application of genome
editing and biochemical technologies, which alter
existing bacteria and lead to the development ofgenetically, modified organisms capable ofdegrading many xenobiotics simultaneously.
Advances in genetic control techniques provide
more accurate information and explore the futureof xenobiotic bioremediation by intelligent
organisms (Piers and Joshi, 2005). The mostcommon type of xenobiotics are synthetic
pesticides, particularly the organochlorine
pesticides (OCPs), which have been used for avery long time in both agriculture and insect
control programs all over the world. Due to their
durability and bioaccumulative nature, a numberof OCPs, including benzene hexachloride (BHC),
dieldrin, aldrin, dichloro diphenyl trichloro ethane(DDT), and hexachlorocyclohexane, areextremely dangerous in the environment. One of
the most toxic organochlorine xenobiotic
compoundsislindane(ãhexachlorocyclohexane), which has beenthoroughly researched for its microbial
biodegradation through physical interactions (soilstructure, carbon and oxygen gradients, pH, andtemperature) and chemical interactions(dechlorination, dehydroxylation, anddehydrogenation) (Moore, 2008). Increased
lindane residues in the environment caused
serious harm to humans and other organisms,

234

A review on Degradation of xenobiotic compounds by soil borne bacteriasuch as carcinogenesis, mutagenicity, endocrine
disruption, and immune system disorders (Mishra
et al. 2021).
Bacterial strain genera including Burkholderia,
Bacillus, Pseudomonas, Kocuria, Archromobacter, Sphingomonas, and Chromohalobacter have all been shown to biodegradelindane under both axenic and anoxic conditions.
This process involves dehydrogenation,
dehydrochlorination, and hydroxylation, andultimately leads to complete degradation ormineralization. Pyrethroids are general
insecticides used to control agricultural anddomestic pests. Cypermethrin, cyhalothrin,deltamethrin, cyfluthrin and bifenthrin are
examples of synthetic pyrethroids (Wang et al.
2022). These pesticides are toxic and persistentand can cause molecular toxicity, neurotoxicity,and reproductive toxicity (Sall et al. 2022). Oneof these pyrethroids, cypermethrin, can cross the
blood-brain barrier and harm the body andimmune system. The persistence of pesticides
in the environment poses a threat to humans andother non-native species on land and in water(Juliano and Magrini, 2017). It has been reported
that microbial species of the genera
Acinetobacter, Trichoderma, Luteiella, Pseudomonas, Cunninghamia, and Bacillus candegrade common insecticides such as
cypermethrin and other pyrethroid insecticides via
pyrethroid hydrolases (Priyanka et al., 2022).
Degradation method
Nowadays, various methods, including
metagenomics, proteomics, transcriptomics, andmetabolomics, are used to characterize harmful
bacteria, their metabolic processes, novel
proteins, and catabolic genes involved in the
degradation process. This technique is very
effective in gaining information about the genetic
diversity and community structure of organisms.
Advanced molecular methods to characterize
complex microbial communities can provide
insight into their structure and function and helps
to solve questions regarding the biodegradation
potential of bacteria. Xenobiotics can be classified
according to different criteria, including its
properties, areas of use, physical properties andpatho-physiological effects. The effects on people[J.Mycopathol.Res :and the environment cannot be ignored. Chronic
exposure even to low levels can cause toxic,
mutagenic or teratogenic effects. Wastewater
treatment plant that cannot effectively reduce therelease of xenobiotics are one of the main
products of xenobiotics in the environment i.e.,
xenobiotics reach the environment and affecthumans and animals. To reduce the negative
impact, many laws and regulations have been
implemented in the EU and around the world
aimed at removing xenobiotics from industry, theenvironment and the social environment andpreventing them from polluting the environment(Godheja et al. 2016).
Parameters influencing bioavailability and therate of biodegradation
The extent of biodegradation and the rate at which
it occurs depend on the chemical structure andconcentration of the compound being degraded,
the type and number of microorganisms present,
and the physicochemical properties of theenvironment. In laboratory as well as
environmental systems, only the fraction of thexenobiotic pollutant that is dissolved in the
aqueous phase is generally assumed to beavailable to the microorganisms for degradation.
Bioavailability is controlled by parameters suchas the physical state of the pollutant compound(solid, liquid, gaseous), its solubility in water, andits tendency to adsorb or bind to soil or sedimentparticles. In soil aggregates or other solids,
microbes may be excluded from entering thesmaller micropores. Xenobiotics present in the
micropores are thus unavailable to themicroorganisms and must diffuse through porewater to the grain surface in order to be degraded.
However, diffusion in soil systems may be limited
by adsorption. In fact, adsorption, immobilizationand confinement of micropores are the main
reasons for the persistence of many impurities.
Aging, which is the contamination of soil orsediment by organisms over a long period of time,
also affects bioavailability: pollutants can affectsoil and sediment products, allowing bacteria to
become active over time. Many xenobiotics, suchas polycyclic aromatic hydrocarbons andpolychlorinated biphenyls, poorly soluble in waterand are mostly adsorbed and fixed by the soil
matrix and sediments (Baun et al. 2012). As

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mentioned above, the molecular structure ofxenobiotics is characterized by “non-physical”
changes and stable chemical properties that canhinder or prevent biodegradation. Unfavourable
concentrations of the xenobiotic compound also
affect biodegradation. In high concentrations,many xenobiotics are toxic to organisms,
including the degradative bacteria. On the other
hand, there may be a minimum concentration
below which a compound is not degraded any
more. Synthesis of catabolic enzymes may notoccur when the concentration of a chemical is
below a level that is effective for induction of thecorresponding catabolic genes. Besides, theminimal threshold concentration depends mainlyon the kinetic parameters of growth andmetabolism, but also on the thermodynamics ofthe overall transformation reaction. In fact,
constant substrate affinity is the most importantfactor for the biodegradation of pollutants to low
concentrations (Godheja et al. 2016). In aerobic
systems, minimum substrate concentrations canrange from 0.1 to 1.0 mg L-1, but in environmental
systems the final concentrations required are
generally 1 ìg L-1 or less (Fetzner, 2002). Other
factors that affect biodegradation include
environmental factors such as temperature, pH,moisture content and salinity, the presence ofinterfering chemicals, the availability of energy
and nutrients, and the presence of oxygen or otherenergy sources. For instance, the availability ofoxygen in soil is often the limiting factor for aerobic
biodegradation processes. Additionally, thepresence of competing organisms or predatorsin the microbial community can also affectbiodegradation (Derby et al. 2021). W hen
determining the rate of biodegradation it isimportant to remember that the visible xenobiotic“disappears” from the body. The ecosystem does
not necessarily mean that it is biodegraded, as
bio-transformation, leaching or chemical changeviz., polymerization, modification, decompositionas part of the degradation can also cause loss.
Monitoring a chemical’s environmental destiny
requires keeping an eye on its byproducts as wellas the parent compound’s disappearance (Zhouet al. 2022). The rates of xenobiotic
biodegradation in the environment may range
from days and weeks to years and decades. The
organophosphate insecticide malathion
disappears from soil within approximately one

235

week, and the herbicide 2, 4-D (2,4dichlorophenoxyacetic acid) is degraded withinfour to six weeks in soil. Modern herbicides aredesigned to undergo biodegradation within one
cropping season. On the other hand, there arerecalcitrant xenobiotics that persist in theenvironment for many years. Simple structuralchanges of a molecule, such as the addition of achlorine substituent, can convert a readily
biodegradable compound such as 2,4-D into a
more persistent substance such as 2,4,5-T(2,4,5-trichlorophenoxyacetic acid) (Elekwachi,2014).
Effects of Xenobiotic compounds
Microbial consortia have the potential to improvebiodegradation processes in xenobioticcontaminated soil/water environments. However,many of the important organisms involved inbioremediation are still unidentified because not
all organisms in nature can be introduced in-vitro
but exist in a viable but non-cultural (VBNC)
environment. Therefore, there is a great need for
new applications and modern technologies tounderstand the genetics and molecular biology
of organisms to discover the hidden knowledgeof these VBNC diseases. New molecular design
techniques offer promising avenues for deep
understanding of microbial communities, frommolecules to genes. New Omics technologies
such as metagenomics, transcriptomics, andproteomics provide information about nucleic
acids, enzymes, catabolic genes, plasmids, andmetabolic machinery and metabolites produced
during the biodegradation process. The
collaboration of many omics studies introduces
the perspective of systems biology to provide a
better understanding of the whole. The
relationship between genes, proteins and theenvironment in the process of microbial
degradation provides a gene therapy tool thatenables the development of various newtechnologies such as genome editing and nextgeneration tools CRISPR-Cas9, TALEN and ZFN.
It contains genes for specific degradation
activities and provides unique insights into
microbial remediation. Additionally, the successof omics technology is not possible without theuse of bioinformatics tools. Bioinformatics has
revolutionized the creation of genomic and236

A review on Degradation of xenobiotic compounds by soil borne bacteria

proteomic databases, facilitating information on
the cellular and metabolic processes ofenvironmental contaminants. The application ofthis technique in biological research paves thepath for further investigation into the possibilities
of microbial bioremediation and its capacity toeradicate external problems (Mishra andSrinivasan, 2001).
Effects of exogenous chemicals in the soil
Exogenous chemicals such as dioxins, 1,1,1trichloro-2,2-bis (4-chlorophenyl) ethane (DDT),
polychlorinated bis Benzene (PCB), chlordane,
polycyclic aromatic hydrocarbons (PAHs) andnitroaromatic compounds pose a major threat tosoil ecosystems in developing countries.
However, there are reports that some othercompounds such as benzene, nitrobenzene,
toluene, xylene, aniline, ethylbenzene,
trinitrotoluene/dibenzofuran and chlorinatedsolvents may be xenobiotic, especially in the soil
ecosystem (Godheja et al., 2016). Due to one ormore aromatic rings and azo linkages, cosmetics
and personal care items also contribute as
xenobiotic pollutants, particularly parabens in soil
and air and azodyes in soil. The use of pesticides,
fertilizers, military operations, industrial
processes, fuel burning, and soil alterations inhigh-yield agricultural techniques are examples
of anthropogenic activities that increase theconcentration of these chemical compounds insoil and have negative consequences (Miglani etal. 2022). The chemical properties and locationsof xenobiotics affect their bioavailability anddistribution in soil; Soil organic matter (SOM)
plays an important role. Pesticides (pesticides,
insecticides, fungicides, algicides, fungicides,etc.) are chemicals used in plant protection andmanagement and have been the most widely usedchemicals in the environment in the past year.
Millions of tons of pesticides are produced anddistributed worldwide each year. Environmental
factors such as temperature, soil pH and moistureaffect the behavior of persistent pollutants (POPs)in soil. One possible strategy is to mix thematerial with soil organic matter (SOM). A lot ofxenobiotics and their broken down derivatives arecommonly employed in humification because they
resemble humic precursors. It was suggested that
this resulting process could be used to reduce[J.Mycopathol.Res :environmental pollution in soil. Inorganic minerals
interact well with exogenous substances and play
an important role in the transformation ofexogenous substances (Embrandiri et al. 2016).
Impact of exogenous chemicals in water
Diffuse contribution and point contribution of urban
industrial development, transportation,
construction and other human activities such as
residential pollution to urban surface water andgroundwater. The presence of chemicals andsigns of human activity in urban sewers has been
the subject of many studies. Certain popularxenobiotic sensors need to be treated withmunicipal wastewater at sewage treatment plants
before they may be released into waterways.
Various types of metals, xenobiotics and synthetic
products such as polycyclic aromatichydrocarbons, phthalates and pesticides are also
found in different waters. Foreign substances canenter water from many sources include air
emissions; water runoff from roads and land;renewable products from industry, sewage andfossil fuel products; incineration waste.
Additionally, xenobiotics enter the water tablethrough leaching, which compromises theecological stability of aquatic ecosystems. The
presence of exogenous pollutants can cause
oxidative stress in aquatic organisms (Dhakal etal. 2018). A recent study found increased oxidative
stress in fish in an artificial lake in Eleyele, Nigeria.
Another study shows that exogenous compounds
alter the homeostasis of fish and cause oxidative
stress by increasing the amount of reactive
oxygen species and inhibiting antioxidant
systems.
Effects of exogenous substances on plants
Xenobiotics have a variety of effects on thephysiological and morphological traits of plants.
For example, particulate matter from theautomotive industry alters the proteins, cysteine
concentrations, photosynthetic pigments, leafarea, and foliar surface of plants. Various
xenobiotics with dif ferent structure andcomposition can cause changes in gene
expression, regulation and signaling in higher
plants. Xenobiotics, such as phytohormone
analogs, interact with phytohormone receptors
and signaling pathways. Metals that are necessary
for plant growth, such Cu, Zn, Fe, and Mo, are62(2) June, 2024]

Jyoti and othersharmful at high concentrations; however, nonnecessary metals, including Pb, Cd, Hg, and As,
are harmful even at low concentrations in plant
growth. The effects are negative. Concentrations
are lower during plant growth. Xenobiotics candamage plant DNA due to the production ofreactive oxygen species and oxidative stress. Dueto the toxicity of xenobiotics in plants, signaling
pathways are affected by interfering with various
signaling receptors (such as G protein-coupled
receptors and receptor tyrosine kinases)(Embrandiri et al. 2016).
Effects of Xenobiotics on human health
Xenobiotics pollute the environment and therefore
their assimilation by existing animals has
increased significantly in recent years. The
introduction of these chemicals into ecosystems
will cause allergic reactions, death of biologicalorganisms, genetic changes, and decline oforganisms, metabolic diseases and effects ofecosystem processes. Humans are exposed toa variety of xenobiotics (both medical and nonessential xenobiotics) throughout their lives
through ingestion, inhalation, dermal or othersystemic exposure, which may pose risks tohuman health. Xenobiotics can alter the humangut microbiota and cause dysbiosis, which is
directly associated with many diseases. The
continuous process of biotransformation always
attempts to balance the metabolic activity ofxenobiotics with the elimination of their mutagenic
metabolites as they are transformed into theenvironment and remove invading substancesfrom the body. When this balance is disrupted,
chronic diseases and DNA damage occur in the
body. The toxicity of xenobiotics varies greatly
between individuals. These oscillations arecaused by the body’s sensitivity and intraspecificvariation. There are many things that are foreign
to the human body. These drugs directly andindirectly cause problems and irritation in manyorgans and systems of the human body.
Xenobiotic degradative enzymes related to
Bacteria
Bacteria are known for their extraordinary ability
to rapidly multiply, grow, and withstand harshenvironments. Recent genome studies of237

organisms that digest xenobiotics suggest thatthey evolved by incorporating genes that destroy
xenobiotics. Pseudomonas, Escherichia,
Sphingobacterium, Pandora, Rhodococcus,
Bacillus, Bacillus, Moraxella, Micrococcus(aerobic bacteria), Pelatomaculum, Desulfotomaculum, Syntropicobacter, Syntropus,
Desulfovibrio, Methanopicilla were isolated fromsoil and characterized for the biodegradation
potential of xenobiotic compounds (DDT, lindane,
PCB, TNT and crystal violet (Malla et al. 2018).
The human gut microbiota has direct xenobiotic
metabolic capacity, but also influences hostmetabolic gene expression and host enzyme
activity (Miglani et al. 2022). Strain 1D ofthermotolerant bacteria isolated from oilcontaminated soil at a refinery was identified as
Gordonia species by the analysis of 16S rRNAand gyrB gene sequences. It was determined that
aromatic compounds (xenobiotics) act aselectron-free substrates in the absence of oxygen(anaerobic conditions), and bacteria grow byoxidizing substances in the presence of electron
acceptors (Mishra and Srinivasan, 2001).The firststep in enzymatic biodegradation is choosing an
enzyme for a bioremediation application; thisenzyme has to be able to break down the intended
contaminants into less harmful compounds.
Many types of bacteria can convert harmful
foreign substances into toxic or non-toxic
substances with the help of special enzymes
contained within them. Due to structural changes
at the molecular level in xenobiotic compounds,
diff erent enzymes are needed for thebiodegradation of different hydrocarbon species.
Degradation of aliphatic hydrocarbons occurs
through mono-oxygenases (addition of oxygen
molecule to the terminal methyl functionality) or
di-oxygenases (addition of two oxygen atoms,
resulting in peroxide formation and conversion to
fatty acids).The oxidized fatty acid molecule forms
intermediates in the TCA cycle, which
subsequently metabolize to produce CO2 andH2O. Aromatic hydrocarbons degrade slowly due
to lack of solubility, formation of toxic metabolites,
and metabolite inhibition. First, these compounds
are converted to cis-dihydrodiols and degradedby dioxygenases via the ortho or meta-cleavage
method. Cleavage of the aromatic ring thenoccurs between the hydroxyl group in the orthocleavage pathway and the adjacent hydroxyl group

238

A review on Degradation of xenobiotic compounds by soil borne bacteria[J.Mycopathol.Res :Table 1: Microorganisms and microbial communities using transcriptomic and meta transcriptomic approaches in biodegradation.

Microorganisms/ microbialcommunities

Isolation/ culturesourceXenobiotics/
pollutants

Comments/result

Dehalococcoides mccartyi(within trichloroethenedechlorinating community)

Dechlorinatedenrichment culture

Trichloro-ethane(TCE)

Transcriptomic approach identified genes encoding for
rRNA, and reductive dehalogenases tceAand vcrAas
the most expressed genes for TCE-dechlorinating
community, while in D. mccartyi , hydrogenases hup
and vhu were identified.

Rhodococcus sp. CS-1

Drinking-water
treatment plant

PhenolTranscriptomic analysis showed that Rhodococcussp.
CS-1 was capable of phenol degradation via
ketoadipate pathway.

Rhodococcus erythropolis
D310-1

Activated-sludge
sampleChlorimuron-ethyl

RNA-seq results suggested that cyt P450
carboxylesterase and glycosyltransferase genes are
key genes expressing degradation of chlorimuron
ethyl.

Burkholderia zhejiangensis
CEIB S4-3

Pesticide

Methyl parathione

Transcriptomic analysis of CEIB S4 -3 strain showedtranscriptional changes occurred in response to methyl
parathion, and identified expressed genes related to its
biodegradation.

Sphingomonas
haloaromaticamans P3

Wastewaterdisposal site soil

Polyphenol

Transcriptomics analysis of strain P3 revealed
expression patterns of catabolic genes of ortho-phenyl
phenol degradation pathway

Novos phingobium
sp. LH128

Contaminated soil

Phenanthrene

Transcriptomics analysis showed remarkably higher
expression of phenanthrene degradation.

Fig.1: Microbial enzymes in xenobiotic management. The figure summarizes a few representative enzymes and their corresponding
microbial sources involved in xenobiotic detoxification (Miglani et al. 2022).

in the Meta cleavage pathway, eventually forming
the middle of the intermediate pathway (Miglani
et al. 2022).
Effects of xenobiotics on the Environment
Environmental pollution caused by xenobiotic isa worldwide problem resulting from humanactivities such as urbanization and population
growth. Many harmful compounds are released
into the environment, causing pollution of theecosystem.Soil, sediment, and water include
notable materials such pesticides, fertilizers,
heavy metal ions, oil derivatives, and polycyclicaromatic hydrocarbons (PAHs). In a time of62(2) June, 2024]

Jyoti and others

change, science and technology has become thecentre of human exploitation of resources,
destroying many ecosystems (Liu et al. 2019).
Unreasonable usage of pharmaceutical waste,human, and veterinary medications is anotherwell-known source of environmental pollution. In
contrast to other chemicals, medications may
have an effect on aquatic life. However, it isthought that there is very little chance of acuteenvironmental damage from medications. The
situation may be different with long-term effects;
However, evidence regarding its long-term effects
and toxicity is insufficient. Additionally, althoughmany aquatic organisms are exposed to toxicity
throughout their lives, there is little or no evidenceof effects across many generations of life
(Bhandari et al. 2021). Major xenobiotic areharmful to the environment, plants, animals andhumans.
CONCLUSION
The omics approach is a good way to understandenvironmental toxicology and its remediation byusing hybrid or combination methods todetermine the various effects of xenobiotics andother pollutants on animals and plants, including
various ecosystems. Advantages include a better
understanding of catabolic genes, degradative
enzymes, and other metabolic pathways. In soil/
water ecosystems contaminated withxenobiotics, the microbial community appears toplay an important role in the successf ulbiodegradation process. Multi-moleculartechniques have the capacity to perform in-depth
analysis of microbial communities at all levels,from genes to molecules and from organisms toecosystems. Many organisms with strong
catabolic potential have been identified anddescribed.Numerous enzymes, particularly thosemade by unculturable microorganisms, havebeen discovered due to the omics method. This
new step led to the discovery of many organic
biocatalysts suitable for commercial use. This
review discusses several articles that used single
isolated or mixed microbial organisms for thebiotransformation of xenobiotics in diseased
areas. Practical considerations must be madewhile evaluating resistant microbial technology,
yet there is still debate on their field applicability.
To achieve remarkable breakthroughs in239

bioremediation, however, further research isneeded to create innovative geneticallyengineered strains with strong catabolizing genesthat can create ecosystems free of xenobiotics.
Furthermore, to tackle xenobiotic contamination,
careful consideration must be given to the
combined strategy of green nanotechnology andmicrobe-mediated bioremediation.
DECLARATIONSConflict of interest: Author declares no conflict ofinterest.
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