Beneficial microbiomes for bioremediation of diverse contaminated environments for environmental sustainability: present status and future challenges

Abstract

Over the past few decades, the rapid development of agriculture and industries has resulted in contamination of the environment by diverse pollutants, including heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals. Their presence in the environment is of great concern due to their toxicity and non-biodegradable nature. Their interaction with each other and coexistence in the environment greatly influence and threaten the ecological environment and human health. Furthermore, the presence of these pollutants affects the soil quality and fertility. Physicochemical techniques are used to remediate such environments, but they are less effective and demand high costs of operation. Bioremediation is an efficient, widespread, cost-effective, and eco-friendly cleanup tool. The use of microorganisms has received significant attention as an efficient biotechnological strategy to decontaminate the environment. Bioremediation through microorganisms appears to be an economically viable and efficient approach because it poses the lowest risk to the environment. This technique utilizes the metabolic potential of microorganisms to clean up contaminated environments. Many microbial genera have been known to be involved in bioremediation, including Alcaligenes, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Mucor, Penicillium, Pseudomonas, Stenotrophomonas, Talaromyces, and Trichoderma. Archaea, including Natrialba and Haloferax, from extreme environments have also been reported as potent bioresources for biological remediation. Thus, utilizing microbes for managing environmental pollution is promising technology, and, in fact, the microbes provide a useful podium that can be used for an enhanced bioremediation model of diverse environmental pollutants.

Full text

REVIEW ARTICLE
Beneficial microbiomes for bioremediation of diverse contaminated
environments for environmental sustainability: present status
and future challenges
Divjot Kour
1
&Tanvir Kaur
1
&Rubee Devi
1
&Ashok Yadav
2
&Manali Singh
3
&Divya Joshi
4
&Jyoti Singh
5
&
Deep Chandra Suyal
6
&Ajay Kumar
7
&Vishnu D. Rajput
8
&Ajar Nath Yadav
1
&Karan Singh
9
&Joginder Singh
10
&
Riyaz Z. Sayyed
11
&Naveen Kumar Arora
12
&Anil Kumar Saxena
13
Received: 27 December 2020 /Accepted: 28 February 2021
#The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2021
Abstract
Over the past few decades, the rapid development of agriculture and industries has resulted in contamination of the environment by
diverse pollutants, including heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals. Their presence in the
environment is of great concern due to their toxicity and non-biodegradable nature. Their interaction with each other and coexistence
in the environment greatly influence and threaten the ecological environment and human health. Furthermore, the presence of these
pollutants affects the soil quality and fertility. Physicochemical techniques are used to remediate such environments, but they are less
effective and demand high costs of operation. Bioremediation is an efficient, widespread, cost-effective, and eco-friendly cleanup
tool. The use of microorganisms has received significant attention as an efficient biotechnological strategy to decontaminate the
environment. Bioremediation through microorganisms appears to be an economically viable and efficient approach because it poses
the lowest risk to the environment. This technique utilizes the metabolic potential of microorganisms to clean up contaminated
environments. Many microbial genera have been known to be involved in bioremediation, including Alcaligenes, Arthrobacter,
Aspergillus, Bacillus, Burkholderia, Mucor, Penicillium, Pseudomonas, Stenotrophomonas, Talaromyces,andTrichoderma.
Archaea, including Natrialba and Haloferax, from extreme environments have also been reported as potent bioresources for
biological remediation. Thus, utilizing microbes for managing environmental pollution is promising technology, and, in fact, the
microbes provide a useful podium that can be used for an enhanced bioremediation model of diverse environmental pollutants.
Keywords Bioremediation .Mechanisms .Microbes .Processes .Technologies
Responsible Editor: Diane Purchase
*Ajar Nath Yadav
ajar@eternaluniversity.edu.in; ajarbiotech@gmail.com
1
Microbial Biotechnology Laboratory, Department of Biotechnology,
Dr. Khem Singh Gill Akal College of Agriculture, Eternal
University, Baru Sahib, Himachal Pradesh 173101 Sirmour, India
2
Department of Botany, Banaras Hindu University, Varanasi, Uttar
Pradesh 221005, India
3
Invertis Institute of Engineering and Technology (IIET), Invertis
University, Bareilly, Uttar Pradesh, India
4
Uttarakhand Pollution Control Board, Regional Office, Kashipur,
Dehradun, Uttarakhand, India
5
Department of Microbiology, G. B. Pant University of Agriculture
and Technology, Pantnagar, Uttarakhand, India
6
Department of Microbiology, Akal College of Basic Sciences,
Eternal University, Baru Sahib, Sirmour, Himachal Pradesh 173101,
India
7
School of Bioengineering and Biosciences, Lovely Professional
University, Phagwara, Punjab 144411, India
8
Southern Federal University, Rostov-on-Don, Russia
9
Department of Chemistry, Indira Gandhi University, Haryana,
122502 Meerpur, Rewari, India
10
Department of Biotechnology, Lovely Professional University,
Phagwara, Punjab, India
11
Department of Microbiology, PSGVP Mandal’s Arts, Science and
Commerce College, Shahada, Maharashtra, India
12
Department of Environmental Science, Babasaheb Bhimrao
Ambedkar University (A Central University), Rae Bareli Road, Uttar
Pradesh 226025 Lucknow, India
13
ICAR-National Bureau of Agriculturally Important Microorganisms,
Kusmaur, Mau 275103, India
https://doi.org/10.1007/s11356-021-13252-7
/ Published online: 25 March 2021
Environmental Science and Pollution Research (2021) 28:24917–24939

Introduction
The worldwide increase of industrialization in the past de-
cades has led to different types of environmental pollution
such as air, water, and soil. Anthropogenic activities such as
mining, ultimate disposal of effluents containing toxic metals
as well as metal chelates from steel plants, battery industries,
and thermal power plants has resulted in the deterioration of
water quality rendering serious environmental problems.
Many types of pollutants such as hydrocarbons, heavy metals,
and polythenes have contaminated the environment. Heavy
metals are among the major contaminants of chief concern.
Heavy metals occur as natural constituents of the Earth’scrust
and are persistent contaminants because they cannot be de-
graded easily. In rocks, they exist as their ores from which
they are recovered as minerals. These ores include sulfides of
arsenic, cobalt, iron, lead, nickel, and silver; oxides such as
aluminum, antimony, gold, manganese, and selenium. Heavy
metals can enter the environment either by single high-level or
repeated low-level and high-level exposures. Once these enter
the environment, they stay in their toxic form for a much
longer time period (Das and Osborne 2018). Many of these
environmental contaminants pose mutagenic effects on the
health of humans and the environment. As the heavy metals
are absorbed by the body, they are accumulated in the brain,
liver and kidneys. Other effects on animals includediminished
growth and development, nervous system damage, cancer,
and in some cases, it may lead to death (Singh et al.
2018;Yadav 2021b). The abundance of heavy metals in soils
also leads to a reduction in the quality and quantity of food,
which prevents plant growth, the absorption of nutrients and
metabolic and physiological processes. Different biological,
chemical, and physical methods are being used for the reme-
diation of metals contaminated soils. However, physicochem-
ical methods result in enormous generation of sludge and
more contamination and thus are not appreciated (Ahluwalia
and Goyal 2007).
Bioremediation technology is an effective solution for the
removal of environmental contaminants, as this is a cost-
effective and practical solution. Soil is one of the largest de-
posits of genes from algae, bacteria, fungi, invertebrates, and
protozoa. The indigenous microbial population of soil often
plays major roles in plant growth regulation, plant pest con-
trol, maintenance of soil structure, recycling of nutrients and
transformation of contaminants (Kour et al. 2019b; Yadav
et al. 2017; Ite and Ibok 2019). Rapid progress has been made
in developing effective, economical, and socially viable bio-
remediation processes (Sharma et al. 2018). The research in
the bioremediation field has greatly focused on processes ma-
jorly from the bacterial domain, which possess diverse appli-
cations of bioremediation. In many applications where bacte-
ria are known tobe key players in bioremediation, archaea are
also known to be involved as well. Archaeal processes are
important for bioremediation as many extreme environments
have been contaminated and remediation is a major need.
Furthermore, wastewater generated by the many industries is
hyperthermal, hypersaline, acidic or alkaline pH, where ar-
chaea can help in the removal of contaminants (Shukla et al.
2016; Yadav and Saxena 2018; Krzmarzick et al. 2018).
Recent studies suggest that using more than one living organ-
ism will surely provide more efficient and improved results
and will open paths for exploring more microbial diversity to
achieve the best results in bioremediation (Saxena et al. 2016;
Yadav et al. 2020b; Yadav et al. 2019b). The present review
describes diverse groups of microbiomes involved in biore-
mediation, their biodiversity, and the recent advancements
and scientific knowledge on utilization of these microbiomes
as efficient bioresources for decontaminating the
environments.
Biotechnological applications of microbes
for bioremediation
Bioremediation of oily sludge-contaminated soil
Large scale contamination of soil with derivatives of oil has
become a global concern, primarily in countries that explore,
refine, transfer and consume crude oil, which has an undeni-
able impact on the health of soil (Haroni et al. 2019). The oil
leakage from pipelines, industry, and tanks in the form of oil
sludge can generate foremost health and environmental haz-
ard. This contaminant of soil is a viscous mixture of water, oil,
hydrocarbon, sediments (aromatics, alkanes, polycyclic,
asphaltenes, resin) and non-hydrocarbon compounds (sulfur,
nitrogen, and trace metals, particularly nickel, iron, and cop-
per) (Afzal et al. 2019). Oil sludge can hold up to 40% solids
and 80% oil. On account of their structural complexity, high
hydrophobicity and recalcitrant nature, several hydrocarbons
and their by-products can accumulate in the environment for a
long time and can easily enter into the food chain, thereby
posing a continuous threat to public health and the environ-
ment (Belal 2013). Severe diseases related to skin, including
erythema and cancers suchas gastrointestinal and bladder, can
occur when humans are exposed to high oil sludge concentra-
tions. In addition, these compounds diffuse in the soil and
adversely affects the ecosystems by changing parameters such
as pH, moisture, and aeration level of soil (Ma et al. 2018).
The rate of recycling and recovery may be improved, but the
amount of actual oil sludge contamination remains generally
the same and may add to the existing waste (Barnes et al.
2009). Hence, these compounds, due to their non-
biodegradable nature, producing various toxins, unfamiliar
environmental conditions, causing an array of healthproblems
in human beings, require priority treatment for sustainable
24918 Environ Sci Pollut Res (2021) 28:24917–24939

management to improve sludge disposal processes (Singh
et al. 2020).
The petroleum hydrocarbon in sludge and soil can be de-
termined using gas chromatography equipped with a flame
ionization detector as reported by Sarkar et al. (2016). The
percentage of total petroleum hydrocarbon (TPH) reduction
can be estimated by the following equation.
%reduction:of :TPH ¼Initial:TPH−Final:TPH
Initial:TPH 100
There are numerous physicochemical techniques for re-
moval of oil sludge contamination (i.e., chemical method,
dig and dump method, separation, stabilization techniques,
and thermal treatment), but those methods are expensive,
non-eco-friendly, and lead to soil fertility destruction. To con-
quer these limitations, bioremediation is a promising, cheaper,
eco-friendly, and reliable technology for removal of oil sludge
waste in a less destructive manner (Johnson et al. 2018). The
technology is generally classified in number of different
methods such as of ex situ and in situ, which include bioaug-
mentation, biostimulation, bioreactors, composting,
landfilling and landfarming.
Bioaugmentation and biostimulation
Bioaugmentation involves microorganisms that have the apti-
tude to degrade recalcitrant oily sludge waste from the pollut-
ed environment. Utilizing soil bacteria that have the ability to
remove the oil hydrocarbons can help in the degradation of
this contaminant from the soil. Because oil sludge components
are composed of diverse compounds, their deprivation usually
needs more than a single species of microbes. In many cases,
the action of bacteria or microbes is better in the case of con-
sortium than a single strain as the end product of the metabo-
lism of one of the microbe isutilized as a substrate by the other
bacteria in the consortium (Heinaru et al. 2005). The employ-
ment of genetically modified microorganisms (GMM) is a
further approach to ameliorate bioaugmentation practice.
The GMM are transfected with genes that code for catabolic
enzymes associated with pollutant biodegradation, hence es-
calating the efficiency of microorganism for oil sludge reme-
diation. For example, Pseudomonas putida and Pseudomonas
sp. have been genetically engineered with plasmids enclosing
genes that codes for catabolic enzymes, which are associated
with degradation of monoaromatic compounds
(chlorobenzoate, ethyl benzoate and methyl benzoate) (Nzila
et al. 2016;Kouretal.2019a; Rastegari et al. 2019;Yadav
et al. 2019a).
Biostimulation involves the natural environment manage-
ment by supplementing limited nutrients to support and mon-
itor the microbial population activity and growth (Crivelaro
et al. 2010). Microbial activity and growth can be inhibited
under the water and soil conditions. According to Crivelaro
et al. (2010), low degradation potential monitored with the
treatments of oil sludge assorted with soil (composting and
landfarming) is a consequence of the imbalanced nutritional
amendments. Biostimulation is one among the possibilities to
deal with this kind of problem since oil sludge has restricted
amounts of nutrients. This may be because in oil sludge, some
nutrients are not available as they are components of complex
structures and comparatively not accessible to the degrading
microbial population. In previous literature, vinasse, a
byproduct, has been utilized from processed sugarcane that
contains adequate amounts of nutrients such as nitrogen, phos-
phorus, and potassium (Baez-Smith 2006) utilized for oil
sludge biodegradation to mineralization level (Devi et al.
2020). The bioreactor procedure can be employed as a fer-
mentation technique for remediation of oil sludge waste into
non-hazardous effluents. This process utilizes a naturally se-
lected and adapted indigenous bacterial strain supplemented
with designed nutrient media containing vital surfactant and
minerals for degradation. The process operating parameters of
the technique promote the highly active microbial population
growth that quickly converts the components of oil sludge to
CO
2
and H
2
O(Ururahy2002). Several oil-degrading mi-
crobes such as Acinetobacter, Alcaligenes Pseudomonas,
and Rhodococcus are reported by Singh et al. (2001). This
method can be applied in the process recuperation of recycla-
ble oil, oil sludge biodegradation, and treated oil sludge dis-
posal (Ururahy 2002).
Composting and landfarming
Composting is a biological method that involves both
mesophilic and thermophilic microbial activities.
Composting generally relies on the mixing of prime ingredi-
ents of compost with oil sludge contaminants. This mixture
pertains to only organic waste (agricultural remains, animal
manures, municipal refuse, and sludge), which are in solid or
semi-solid form (Milne et al. 1998). As the compost matures,
the active microflora within the mixture degrades the present
pollutants. Performances of oil sludge degrading microorgan-
isms are affected by pH and nutrients composition. The pre-
liminary hydrocarbon degradation in oil sludge may probably
be catalyzed via mono and dioxygenase enzymes (Singer and
Finnerty 1984). These enzymes steadily oxidize the hydrocar-
bons in the presences of oxygen to form alcohol and alde-
hydes that lastly produce CO
2
and H
2
Obyfollowingameta-
bolic pathway (Britton 1984). When the total amount of hy-
drocarbons in composte undergoes degradation, there is de-
toxification of the toxic and substance mass. One of the lim-
iting steps of this technology of bioremediation is the
maintainance of humidity in the pile, conditions of the
24919Environ Sci Pollut Res (2021) 28:24917–24939

compost, microbial communities, and time (Fountoulakis
et al. 2009).
This process involves the optimum implication of oil
sludge on soil surface. This method involves the addition of
H
2
O, desired nutrient, and topsoil tilling (for undemanding
mixture with oil sludge). Tilling aids aeration, proper mixing
of sludge and nutrients, and makes the sludge bio-accessible
for microbial degradation. This method has the least impact on
the environment because it is inexpensive, odorless, and gen-
erates minimal residues that do not present disposal problems
(Ubani et al. 2013).
Another xenobiotic that pollutes the environment is oil mix-
ture or crude soil. This type of xenobiotic also causes serious
environmental damage when oil waste is released into the en-
vironment. Bioremediation of this xenobiotic through mi-
crobes, including Aspergillus terreus, A. sulphureus,
Nocardia spp., Pseudomonas spp., Rhodococcus rhodochrous,
and Streptomyces sp. (Sorkhoh et al. 1990), Acinetobacter
calcoaceticum, Flavobacterium sp., and Pseudomonas
aeruginosa (Mandri and Lin 2007), Bacillus cereus (Kebria
et al. 2009), Bacillus sp., and Enterobacter sp. (Zhang et al.
2010), Micrococcus sp. Pseudomonas sp. (Nikhil et al. 2013),
Achromobacter xylosoxidans, Bacillus licheniformis,
Micrococcus kristinae, Proteus mirabilis, Proteus vulgaris,
Sphingomonas paucimobilis,andSerratia marcescens
(Ibrahim et al. 2013), Bacillus sp., and Pseudomonas sp.
(Ahmad et al. 2015), Bacillus subtilis (Jalilzadeh et al. 2014),
Acinetobacter sp. (Ahmad et al. 2015), and Penicillium sp. (Al-
Hawash et al. 2018),hasalsobeenreported.
Bioremediation of xenobiotics
Xenobiotics are the foreign compounds produced by certain
human activities, including use of chemicals in agriculture and
toxic waste generation from industries such as paint, pharma-
ceuticals, plastics, and textile (Gursahani and Gupta 2011).
Chemical compounds such as drugs, oil mixtures, synthetic
azo dyes, antibiotics, alkanes, pesticides, polycyclic hydrocar-
bons (PAH’s), polyaromatic, fuels, chlorinated, and nitro aro-
matic compounds are the different types of xenobiotics found in
the environment (Sinha et al. 2009). DDT is the one of the major
xenobiotics that adversely affects the environment. Xenobiotics
in the environment pose some deleterious effects on the biota. In
human beings these hazardous compounds can cause diseases
related to skin and can also cause cancer on prolonged exposure.
Bioaccumulation of xenobiotics in the environment can lead to
them entering the food chain and can increase with the increas-
ing tropical level of the ecosystem (Bharadwaj 2018).
The effects of xenobiotics are an intense dilemma, and their
removal is necessary due to wide distribution in modern socie-
ty. However, the degradation of such compounds is not easy
because of their recalcitrant nature (Yadav 2021c). The com-
pounds that contain groups such as halogen, nitro, and sulfonyl
are not broken down into simple inorganic matter through
chemical processes. Therefore, bioremediation through micro-
bial is an efficient technique to remove or break down certain
chemicals in the environment. The use of minute organisms that
cover half of our planet’s biomass is the best tool for bioreme-
diation because they can easily grow and multiply on a huge
scale in very little time and are also cost-effective. Microbes can
degrade such hazardous compounds using certain enzymes that
break down xenobiotic compounds into harmless end products
(Bharadwaj 2018) (Supplementary Table 1).
Azo dyes, one of the major xenobiotics, are used for col-
oring various material such as plastics, cosmetics, leather, tex-
tile, and food. Currently, more than 2000 azo dyes are being
used in various industries, whereas textile coloration indus-
tries are the largest user. It has been estimated that when azo
dyes are used in industries, only 10% of the dye binds to the
material, and the rest of the dye is released into the sewage
treatment system or water bodies (Amoozegar et al. 2011).
When these dyes are released into the water they become
major pollutants and affect the transparency and visibility of
water that ultimately affects the aquatic life. Therefore, remov-
ing these dyes requires treatment, and several microbes have
been reported for degrading such dyes from the environment,
including Acinetobacter junii,Aeromonas sp., Alcaligenes
sp., Bacillus fusiformis,Bacillus sp., Brevibacillus sp.,
Candida tropicalis,Clostridium bufermentans, Enterococcus
faecalis, Halomonas sp., Marinobacterium sp., Micrococcus
luteus, Oceanimonas smirnovii, Paenibacillus polymyxa,
Pichia occidentalis,Pseudomonas sp., Rheinheimera sp.,
Schizophyllum sp., Shewanella indica, Shewanella
putrefaciens, Sphingomonas paucimobilis,Streptomyces sp.,
and Zobellella (Yadav and Yadav 2019).
Chemical fertilizers and pesticides have been used widely
during the green revolution in order to enhance the grain pro-
ductivity for the increasing population. Along with the in-
creasing productivity, the use of these chemicals lead to sev-
eral environmental problems such as loss of soil fertility and
biodiversity, increase of acidification of soil, nitrate leaching,
and weed species resistance. These chemicals pollute the air,
ground, and water bodies (Verma et al. 2013). If these
chemicals remain in the environment for extended periods,
they can also enter the food chain and affect the whole eco-
system. Therefore, many studies have been conducted to re-
move these xenobiotics using various microbial cultures.
Various microbes have been reported for degrading pesticides
such as chlorpyrifos, DDT, profenofos, phenylurea, endosul-
fan, parathion, atrazine, alachlor, mefenacet, methyl parathi-
on, fenpropathrin, and paichongding (Kumar et al. 2021).
Alcaligenes faecalis (Yang et al. 2005), Bacillus licheniformis
(Zhu et al. 2010), Acremonium sp. (Kulshrestha and Kumari
2011), and Bacillus thuringiensis (Wu et al. 2015)havebeen
widely reported for degrading the popular termite controller
insecticide named chlorpyrifos.
24920 Environ Sci Pollut Res (2021) 28:24917–24939

The most used pesticide in 1940s was DDT (Bajaj et al.
2014). Several studies showed its adverse effects to environ-
ment and non-target organisms such as fish and birds. Its accu-
mulation in adipose tissues and its estrogenic properties raised
concern about its possible long-term adverse effects. In addition
to its carcinogenic effect, it has also been reported to affect
neurobehavioral functions and to be associated with premature
births. On the basis of ecologic considerations, Sweden was the
first country to ban the use of DDT beginning in January 1970.
In 1981, the USSR banned the production and use of DDT. In
March 1989, DDT was also banned for medical-disinfecting
purposes. In other countries, by 1972 or shortly thereafter, most
uses of DDT were banned because of its negative impact on
wildlife (Turusov et al. 2002). Several legislative decrees were
even ratified in Europe to regulate its use. In 1978, its use in
agriculturewasbannedinItaly (Binelli and Provini 2003). This
recalcitrant pesticide takes 3 to 30 years for degradation and
thus remains for an extended period in the environment and
effects the surrounding. Many microbes such as
Sphingobacterium sp. (Fang et al. 2010), Alcaligenes sp. (Xie
et al. 2011; Gao et al. 2011), Stenotrophomonas sp. (Pan et al.
2016), and Ochrobactrum sp. (Pan et al. 2017) have been found
efficient in degrading this hazardous pesticide. Another insec-
ticide extensively used worldwide (after DDT was banned) for
controlling Colarodo potato beetle, cabbage worms, and peach
tree borer was endosulfan, and its degradation has been reported
by Mycobacterium (Sutherland et al. 2002), Bacillus subtilis
(Kumar et al. 2014). Some other microbes such as
Arthrobacter globiformis (Turnbull et al. 2001), Nocardioides
sp., Rhodococcus rhodochrous, Stenotrophomonas sp. (Harada
et al. 2006), Alcaligenes xylosoxydans, A. xylosoxydan,
Pseudomonas putida, P. marginalis, and Providencia
rustigianii (Chirnside et al. 2007) have been reported for
degrading different herbicides.
Nitro-aromatic compounds are a type of xenobiotic pro-
duced by incomplete combustion of fossil fuels. These xeno-
biotics are largely released into the environment through an-
thropogenic sources. Numerous microbes identified as
Rhodococcus wratislaviensis (Navrátilová et al. 2005),
Arthrobacter ureafaciens (Qiu et al. 2009), Streptomyces
mirabils (Xie et al. 2010), and Shewanella oneidensis
(Wang et al. 2020) have been reported for degrading these
compounds. Additionally, microbes have also been reported
for the bioremediation of chlorinated hydrocarbons that are
produced after the manufacturing of herbicides, dyes, drugs,
and some other chemicals. Microbes such as Paenibacillus sp.
(Sakai et al. 2005), Rhodococcus erythropolis (Yun et al.
2007), Xanthomonas sp., Rhizobium sp., Pseudomonas sp.
(Rayu et al. 2017), and Cupriavidus sp. (Min et al. 2017)have
been reported for degrading chlorinated hydrocarbons.
Di-(2-ethylhexyl) phthalate (DEHP), which is known to be
an endocrine disrupting chemical, is a widely used plasticizer.
The study of (Yuan et al. 2010) showed degradation of DEHP
through Bacillus sp. in mangrove sediments. The study ob-
served that under aerobic conditions, members of the
Actinomycetales were dominant degraders, while
Acidobacteria, Bacteroidetes, Gemmatimonadetes,and
Proteobacteria were involved under anaerobic conditions.
Furthermore, approximately 50% of esterase/lipase/cyto-
chrome P450 genes enriched by DEHP under aerobic condi-
tions were from Nocardioides. In one of the investigations,
Zhang et al. (2020) proposed modified models of Gompertz
and a first order decay model to simulate the DEHP degrada-
tion kinetics by the Gordonia terrae RL-JC02 strain using
sterilized and non-sterilized soil.
S¼S0−A:exp −exp Vm:e
A:L−tðÞþ1

S¼S0þAexp −
t
t1

where S represents the substrate concentration;S
0
is the fitted
initial concentration; A is the biodegradation potential; V
m
represents the maximum biodegradation rate; and L is the
lag phase.
Bioremediation of toxic and heavy metal
Heavy metals (HM) are a naturally occurring unique group of
compounds that are released anthropogeniccally or by natural
processes into the environment. These metals and metalloids
are recognized as having densities >5 g cm
−3
and atomic weight
greaterthanthatofiron(SinghandSingh2017; Kumar et al.
2019). These metals have been used from the beginning of
ancient human civilization and are constantly being supple-
mented to soil, water, and eventually to the biosphere through
rapid industrialization around the globe via the smelting of the
metalliferous surface finishing industry, combustion of fossils,
electroplating, photography, electrical devices, manufacturing,
aerospace, waste incineration, transportation, mining,
and agricultural applications. The noxious heavy metals within
different oxidation states include of Zn, As, Cr, Cd, Hg, Cu, Ni,
and Pb; the other radioactive compounds may be U, Sr in ad-
dition to organic compound such as trinitrotoluene, 1,3,5-
trinitro-1,3,5-hexahydrotriazine; petroleum hydrocarbons, in-
cluding benzene, toluene, xylene, and so on. The HM present
in soil can be presented by the following mass balance equation
as given by Lombi and Gerzabek (1998).
MTotal ¼MPþMAþMFþMAG þMOW þMIP
ðÞ−MCR−ML
ðÞ
Where M is the heavy metal, P is the parent material, A is
atmospheric deposition, F is fertilizer source, AG is agro-
chemical source, OW is organic waste source, IP is inorganic
24921Environ Sci Pollut Res (2021) 28:24917–24939

pollutant, CR is crop removal, and L is losses by leaching,
volatilization, and other processes.
Owing to their non-biodegradable nature, these metals are
difficult to eliminate fromthe environment and become acute-
ly toxic if their concentration exceeds a certain threshold.
However, there is a way to maximize the success chances of
bioremediation by exploiting metal resistant microorganisms.
Microbes augment the potential for plants that sequester heavy
metals, recycle various nutrients, detoxify chemicals, and de-
crease metal toxicity by altering their bioavailability within
plants (Singh and Singh 2017).
Metal microbe-interactions
Metals play a vital function in the life cycle of microorgan-
isms. Under heavy metal stress, soil microbiota adapt several
types of strategies that help reduce the lethal effects that are
generated by HM, including metal species exclusion outside
the microbial cell surface, bioaccumulation of metal ions in
the cell and biotransformation of toxic metals into less toxic
compounds, and metal adsorption on the cell wall (Ahemad
2014). These metal substances detoxify merely via formation
of complex or an effectual barrier around the cell (Rajkumar
et al. 2010).
The microbial biomass bioaccumulative capacity for a tar-
get HM is a measure of accumulation of μmolormgofheavy
metals being adsorbed or absorbed per gram dry weight of the
microbial biomass (Diep et al. 2018) and commonly reported
as μmol
x
or mg
x
per g
dry weight
, where x is the heavy metals
such as cadmium (Cd), cobalt (Co), copper (Cu), mercury
(Hg), metalloid arsenic (As
3+
,As
4+
), nickel (Ni), and uranium
(U). The amount of microbial biomass (biosorbent) and
biosorption bounded HM ions can be efficiently calculated
by the following equation as investigated by several re-
searchers (Farhan and Khadom 2015;Ovesetal.2013).
Q¼Ci−Cf

MV
E¼Ci−Cf

Ci
100
where Q = metal ion uptake capacity (mg g
−1
), C
i
=initial
concentration of metal in solution before the sorption
analysis (mg g
−1
), C
f
= final concentration of metal in
solution after the sorption analysis (mg g
−1
), M=dry
weight of biosorbent (g,), V= solution volume (l), E =
biosorption efficiency.
Langmuir and Freundlich model are used to describe the
biosorption isotherms of heavy metals
Q¼QmaxbC f
1þbC f
where Q
max
and bare the Langmuir constants.
The Freundlich equation of adsorption isotherm is given by
the following equation
Q¼KC
f

1=n
where Qis the amount adsorbed per unit mass of adsorbent
while K and n are Freundlich equilibrium constants indicative
of adsorption capacity and adsorption intensity, respectively.
Biosorption mechanism
The heavy metals uptake by bacterial strains via the
biosorption method can be categorized into two categories
1Metabolism-independent biosorption (occurs on the cells
exterior) and
2Metabolism-dependent bioaccumulation (sequestration,
redox reaction, and species-transformation).
Biosorption can be accomplished by living or dead bio-
mass as passive uptake through surface complexation on sur-
face layers and cell wall. Bioaccumulation relies on an array of
biological, chemical, and physicalprocesses, and these param-
eters are intra and extracellular procedures, where biosorption
has a limited and uncertain role (Igiri et al. 2018).
Intracellular sequestration refers to metal ions complexa-
tion through several cytoplasmic compounds. The interaction
of metal ions with exterior surface ligands of bacterial cells
can result in slow transport and accumulation of metal ions
into bacterial cells. The capability of microbial cells to accrue
metals intracellularly has been put into practices. Cd tolerant
Pseudomonas putida possessed the intracellular sequestration
capability of Zn, and Cd, Cu ions with the assistance of Cys
rich proteins having low molecular weight (Ayangbenro and
Babalola 2017). Furthermore, intracellular confiscation of Cd
ions by glutathione was observed in Rhizobium
leguminosarum cells. Fungi can remediate metal ions through
extra and intracellular precipitation, energetic uptake, and va-
lence conversion by holding metals to their mycelium and
spores (Yadav 2018). The fungal cell wall surface utilizes
ligand in support of metal ions labeling and enables inorganic
metals elimination (Gupta et al. 2015).
Extracellular sequestration is the accrual of metal ions
through periplasm cellular components. Under anaerobic con-
ditions the Klebsiella planticola strain converts S
2
O
3
into H
2
S
and precipitates Cd ions as insoluble sulfides. Cu inducible
periplasmic proteins (CopA and CopB) and outer membrane
protein (CopC) are produced by Cu resistant Pseudomonas
syringae that bind Cu ions. Geobacter and Desulfuromonas
24922 Environ Sci Pollut Res (2021) 28:24917–24939

spp. are proficient in transforming toxic metals to nontoxic or
less toxic metals. A strict anaerobe, G. metallireducens,is
proficient in bio remediating metals such as manganese
(Mn) and poisonous uranium (U), from lethal Mn (IV) to
Mn (II), and U (VI) to U (IV), respectively (Bruschi and
Goulhen 2007).
Bioremediation of polycyclic aromatic compounds in
contaminated sewage sludge and soil
Polycyclic aromatic compounds are the one of the harmful
hydrophobic chemicals that cause environmental damage.
These compounds are introduced in the environment through
the incomplete combustion of fossil fuels, coke, organic or
petroleum (Hajslova et al. 1999;Harvey1996). PAH can also
reach the water through numerous sources such as industries
waste and domestic waste as well as urban runoff and from
vehicles (Rogers 1996). The removal of this particular con-
taminant of the environment has gained attention because it
causes damage ranging from humans to the environment, ma-
rine and land animals and agricultural soil. PAH degradation
difficult as it has low biodegradability and high lipophilicity
(Villar et al. 2006). Its removal from the different environ-
ments can be done by saponification of the sample matrix
interferences and analytes extraction in hexane (Teresa Pena
et al. 2007). The other methods of treating this contaminant
are use of fertilizer that has some risks such as pollution to
plant and animals pastures (Bright and Healey 2003;Mangas
et al. 1998;Moredaetal.1998).
The developed procedure allows 16 PAHs extraction from
sewage sludge and soil samples by simultaneous saponifica-
tion. In agriculture, this sludge can be beneficial to the soil as
they help the modification of soil structure and also help in
providing the organic matter and nutrients that improves crops
production. In addition to the benefits, it usage has some risks
such as accumulation of pollutants in soil, animals pastures
and plants, and with such activity it also enters into the food
chain, leading to an increase in PAHs content (McGowin et al.
2001;Pinoetal.2000; Shu et al. 2000). The increase in the
PAHs content in soil leads to several harmful effects such as
biotic degradation, vitalization and transboundary transfer
through crops (Moreda et al. 1998) that can create a potential
problem through human food chain contamination.
According to a study by Shrivastava and Banerjee (2004),
the deployment of sewage sludge in urban areas deserves at-
tention where plant grows at a satisfactory level after gradual
nutrient release such as phosphorus, nitrogen, carbon and
some other macro and microelements. These released ele-
ments contribute to the soil quality and plant growth improve-
ment (Singh and Agrawal 2008). However, as noted by
Andrés et al. (2011), although plants and soil showed a posi-
tive effect regarding sewage sludge, it may adversely affect
soil biota. Owing to their toxic material, such as PAHs, PCB,
and heavy metals, these wastes can serve as secondary con-
taminants in the environment (Hillman et al. 2003;
Wlodarczyk-Makula 2005). Microbes play a major role in
the removal of PAHs from the environment. The different
pathways used by diverse microbes for biodegradation of dif-
ferent PAHs have been depicted in Figs. 1,2,3,and4.
Bioremediation of pentachlorophenol-contaminated
soil
Pentachlorophenol (PCP), an artificial semi volatile
organchlorine compound, is one the most dangerous pollut-
ants, with low chemical stability, biodegradability, but high
toxicity. Owing to its toxic nature, it has lethal effects on
humans as well as on the environment. In humans it affects
the kidney, liver, central nervous, and pulmonary system. This
compound is abundantly used as algaecides, bactericides, her-
bicide, insecticides, pesticide, biocide, and wood preserva-
tives in agriculture and industries (Bécaert et al. 2000;
Cortés et al. 2002; Fukushima and Tatsumi 2007). In a review,
it was found that wood preservative, bleaching of paper and
tissue, and biocide are the main cause of PCP in the environ-
ment (Bosso and Cristinzio 2014). Although, this hazardous
pollutant PCP has been banned worldwide, but it remains in
the soil and affects the soil quality. To degrade the PCP, the
most prominent method is bioaugmentation, where depletion
of PCP is achieved using microbes (Field and Sierra-Alvarez
2008;Juwarkaretal.2010).
Bioaugmentation is a low cost and environmentally friend-
ly technique that efficiently works in the case of recalcitrant
chemicals. Degradation of PCP through microbes occurs in
three different ways, such as hydroxylation, oxygenolysis or
reductive dehalogenation (Field and Sierra-Alvarez 2008). In
the process of hydroxylation, PCP is converted into
tetrachlorohydroquinone by replacing the chlorine atom with
the hydroxide group that forms an intermediate products for
further degradation (Xun et al. 2010). In oxygenolysis, one or
two atoms of oxygen from diatomic O
2
is incorporated into
the contaminant’s structure. This oxygenase process is per-
formed by various bacteria and fungi in the aerobic condition
that destroys the aromatic ring structure of PCP (Reddy and
Gold 2000). The reductive dehalogenation process is the only
process that occurs in the anaerobic conditions where mi-
crobes sequentially replace the chlorine atoms by the atoms
of hydrogen until the compound has been transformed into the
products such as acetate, benzoate, carbon dioxide, methane,
and phenol (Mohn and Tiedje 1992).
Bioremediation of PCP through bioaugmentation isa wide-
ly researched area and many different microbes in the category
of fungi and bacteria isolated from soil, plants, humans, water,
and animals have been reported so far. Numerous species
belonging to various genera such as Acinetobacter,Bacillus,
Desulfitobacterium,Flavobacterium,Kokuria,
24923Environ Sci Pollut Res (2021) 28:24917–24939

Mycobacterium,Novosphingobium,Nocardioides,
Pseudomonas,Sphingomonas,andSerratia sp. have been re-
ported for degrading the soil contaminated with PCP (Bosso
and Cristinzio 2014). On the other hand, fungi has also gained
some consideration for the bioremediation of PCP containing
soil. Various fungi sorted under the Ascomycetes,
Fig. 1 The three main pathways
for polycyclic aromatic
hydrocarbon degradation by fungi
and bacteria
Fig. 2 The main pathways in the
aerobic degradation of
naphthalene by bacteria
24924 Environ Sci Pollut Res (2021) 28:24917–24939

Basidiomycetes, Deuteromycetes, and Zygomycetes have
been reported for degrading the most dangerous environmen-
tal pollutants (Singh 2006; Yadav et al. 2020a).
Bioremediation of paper and pulp mill effluents in
irrigated soil
Paper and pulp mills are listed as the fifth largest contributors
to environmental contamination because they release 100 mil-
lion kg of toxic pollutants in every state, i.e., gaseous, liquid,
and solid (Singhal and Thakur 2009). They produce varieties
of pollution depending on the type of pulping process such as
dibenzofuran and dibenzo-p-dioxin (Thakur 1996). Effluents
from paper and pulp mill pollute soil, water, and air, posing
environmental threats (Barapatre and Jha 2016). Waste and
wastewater are produced from both bleaching and pulp pro-
cesses. The wastewater generated through such processes has
high organic content, adsorbable organic halide, toxic pollut-
ants, and coloration due to toxic dyes such as bleaching agent,
acids, salts, and alkalis, which pose major problems to the
environment. Along with the toxic pollutants and organic mat-
ter, the effluent of paper and pulp mill also releases heavy
metals such as Cd, Zn, Cu, and Cr, which adversely affect
aquatic life (Dey et al. 2013; Zahrim et al. 2007).
The untreated pulp and paper mill effluents discharged into
water bodies damage the quality of the water. The undiluted
effluent is toxic to aquatic organisms and is strongly mutagen-
ic. There have been several techniques assayed by numerous
researchers worldwide for the removal of color from the ef-
fluent of paper and pulp mills, several physical, chemical, and
biological methods are used (Singh and Singh 2004).
Biological treatment to remove the contaminant is the best
and most efficient known method for the reduction of toxic
effects of effluent from Kraft mills (Thakur 2004), while the
chemical and physical methods are on treatment track, due to
cost inefficiency and residual effects. Biological treatment
method involves the use of microbes such as algae, bacteria,
fungi, and enzymes (Bajpai and Bajpai 1994) as a single step
treatment or in the combination with chemical and physical
approaches (Afzal et al. 2008;Balcıoğlu et al. 2007;Pedroza
et al. 2007).
The microbes mainly treat the effluents through two pro-
cesses: enzyme action and biosorption (Park et al. 2007).
Enzymes such as lactase, lignin peroxidase, and manganese
peroxidase are involved in the treatment of effluent releases
from pulp and paper mills (Malaviya and Rathore 2007).
White rot fungi such as Corius versicolor, Phanerochaete
chrysosporium, and Trametes versicolor have been known
to be involved in the decolorization of effluent released by
paper and pulp mills. A saprophytic soil fungus named
Gliocladium virens is also known for the decolorization of
effluents by 42% by releasing enzymes such as hemicellulase,
managanese peroxidase, laccase, and lignin peroxidase.
Bacteria have been stated to possess the ability to degrade
the effluent compounds significantly as well as reduce the
toxicity effectively (Eriksson and Kolar 1985). Further bacte-
rial consortia may be more efficient in degrading than individ-
ual microbial species (Neilson et al. 1990). Paper is composed
of fiber containing cellulose and lignin that are derived from
various sources such as as crop residues, linen rags, trees, and
cotton. Fungi could use lignin and cellulose for their growth
and contribute to the environmental remediation of industrial
paper and cardboard wastes (Kulshreshtha et al. 2013).
Barapatre and Jha (2016) reported lignin-degrading
Aspergillus flavus for the removal of pulp and paper mill ef-
fluent. Thisfungus reduced the color and lignin content effec-
tively. In another investigation (Chuphal et al. 2005)reported
both fungi and bacteria Paecilomyces sp. and Pseudomonas
Fig. 3 Proposed pathway for the
degradation of phenanthrene by
the ligninolytic fungus Pleurotus
ostreatus
24925Environ Sci Pollut Res (2021) 28:24917–24939

syringae pv myricae for the treatment of effluent. Chandra and
Singh (2012) reported three different bacterial species
Providencia rettgeri, Pseudochrobactrum glaciale,and
Pantoea sp. from a polluted site of pulp paper mill effluent
and found them to detoxify and decolorize the effluent. In
another report, Bacillus cereus and Serratia marcescens bac-
terial species were found positive for the treatment of paper
andpulpmilleffluent(Chandraetal.2009).
The lateral filtration of industrial paper and pulp effluent
into agricultural land improved soil pH and electrical conduc-
tivity. The imaginative emission of the effluent increases ex-
tractable Ni, Pb, Mn, Fe, Zn, S, and exchangeable K, Na in
soil at the shorter distances from point sources. The content of
P, K, micronutrients, Pb, and Ni in wheat plant increased as
effluent washed into nearby agricultural field near the point
source (Giri et al. 2014).
Bioremediation technologies and its
limitations
Bioremediation is highly accepted technology for decontami-
nation of the environment because it is ecofriendly, non-haz-
ardous, safe, and cost-effective. The modern approaches in-
cluding technologies in bioremediation are available and high-
ly accepted nowadays. Bioremediation techniques can be
Fig. 4 The pathway of fluorene
degradation by Terrabacter sp.
strain DBF63
24926 Environ Sci Pollut Res (2021) 28:24917–24939

classified as: ex situ or in situ. There are some criteria to be
considered while choosing a bioremediation technique, in-
cluding pollutant nature, depth, degree of pollutant, location,
cost, and environmental policies.
Ex situ bioremediation techniques
In this technology, the pollutants are recovered from the site
that has been polluted and are transferred to a new location for
their treatment. These techniques rely on the expenses for
treatment, area of pollution, category of contaminant, degree
of pollutant,geology of site, geographical location of contam-
inated site, which determines the choice of ex situ bioremedi-
ation method (Philp and Atlas 2005). This method is some-
what complicated. Plants remediate the pollutants without
causing any damage to top soil and moderate the soil fertility.
Generally, this process is applied for remediation of soil due to
its suitable usage in the environment with consent of the gov-
ernmental protocols. This technology also has certain disad-
vantages such as health risks because of the exchange of the
contaminated sites (Kumar 2019)(Fig.5).
Windrows
This ex situ technique involves periodic turning of polluted
soil to improve bioremediation by more degradation activities
of microbes present in soil. The periodic turning of soil by
mixing water brings more about aeration, equal distribution
of pollutants, microbial and nutrient degradation, thus improv-
ing the bioremediation rate, which can be achieved through
assimilation, mineralization, and biotransformation.
Windrows showed a higher rate of removal of hydrocarbon
due to the soil type. For removal of toxic volatile substances,
this periodic turning of soil is not suitable and cannot be
adopted. This windrow treatment includes the release of
CH
4
gas because of the anaerobic zone leading to reduced
aeration (Azubuike et al. 2016;Hobsonetal.2005).
Biopile
This technique involves bioremediation by above ground re-
moval of layers of polluted soil, followed by increasing
microbial activities, degradation, nutrient alteration, and aera-
tion. This procedure takes a few weeks to several months to
degrade the soil pollutants. This procedure relies on several
aspects such as pH, oxygen, temperature, nutrients, and the
moisture content. These techniques include the following
components: hydration, air circulation, leachate, nutrient
collecting system and treatment bed. The biopiling procedure
comprises various systems that help in the treatment of con-
taminated soil such as an air circulation system, nutrient sys-
tem, and leachate collection system. Biopile is highly accepted
due to its constructive features such as cost effectiveness and
sustainability (Lors et al. 2012;Yadav2021a), which enhance
biodegradation on the condition that air circulation, hydration,
and nutrients can be abundantly controlled. The time required
for remediation in this procedure is less due to their high
adaptability and high degradation rate with a heating system
incorporated that raises the microbial activity. The addition of
wooden bark, sawdust, and straw stimulate the remediation
method. The application of this ex situ treatment can help in
limitation of vaporization and can effectively be used in ex-
treme environments such as very cold regions to remove pol-
lutants (Dias et al. 2015; Gomez and Sartaj 2014; Whelan
et al. 2015).
Bioreactor
Bioreactors are used for the protected and quick process of
bioremediation (Pino-Herrera et al. 2017). In a bioreactor,
raw materials are renewed into products by chemical reac-
tion in a vessel. In this method, a series of biological mech-
anisms converts the pollutants into specific products by
using a bioreactor. In a bioreactor, a continuous bioremedi-
ation of pollutants or contamination can be achieved by
regulating the factors such as temperature, moisture, nutri-
ents, pH, and level of oxygen (Athar and Sirajuddin 2019).
Many bioreactor operating modes are available such as
batch, continuous, fed batch, multistage, and sequencing
batch. As the bio-chemical reaction taking place in the bio-
reactor can be controlled and enhanced within less time.
Decontamination using bioreactors is an effective process
and yields of over 90% could be easily achieved (Cristorean
et al. 2016).
Fig. 5 Diagrammatic
representation of different types
of techniques for bioremediation
24927Environ Sci Pollut Res (2021) 28:24917–24939

In situ bioremediation techniques
The in situ technique treats polluted substances at their origi-
nal site of pollution without any excavation. It does not disturb
the soil structure, and also it is less expensive then ex situ
techniques of bioremediation, as in this method there is no
extra cost required for excavation processes. Along with this
advantage, this method also avoids the circulation of pollut-
ants from one place to another. In situ bioremediation also
brings out the activities between the pollutants and biomass
and upgrades the microbial degradation in the toxic polluted
soil (Sharaff et al. 2020; Singh et al. 2020). Biosparging,
bioventing can be enhanced. Chlorinated solvents, dyes,
heavy metals, and hydrocarbons polluted sites have been suc-
cessfully treated by this technique of bioremediation (Folch
et al. 2013; Frascari et al. 2015; Kim et al. 2014; Roy et al.
2015).
Bioventing
In this technique, oxygen is delivered to unsaturated zones,
increasing the indigenous microbe’s activities for increased
bioremediation. In bioventing, moisture and nutrients are be-
ingprovidedtoincreasebioremediation (Philp and Atlas
2005). Bioventing has come into consideration for areas con-
taminated with petroleum products (Sharma et al. 2019). It is
employed on a large scale due to its compatibility. In order to
increase the rate of pollutants degradation, this method joins
with the process of physical venting.
Bioslurping
Bioslurping combines the approaches of vacuum and
bioventing to enhance the recovery of free product to address
two separate pollutant medium. This technique effectively
treats contamination from petroleum hydrocarbons and is also
cost effective, remediates soil, and removes LNAPLs in the
vadose zone, i.e., unsaturated zone. This procedure suffers
from a drawback, i.e., the movement of microbial mass is
low due to the low rate of oxygen exchange. The microbial
activity is enormously affected by the humidity that restricts
the permeability into the soil.
Biosparging
Bioasparging is the same as bioventing in which air is sup-
plied into soil surfaces to raise microbial activity to enhance
removal of contaminants from contaminated sites. The effi-
ciency of biosparging relies on two key factors, namely soil
absorptiveness and contaminant biodegradability (Philp and
Atlas 2005). In this technique, the concentrations of ground-
water oxygen are increased by air supply through pressure by
which the process of biodegradation increases through
microbes that are present naturally in the soil (Singh and
Yadav 2020). It just enhances the interaction between soil
and water. The installation of small air injectors provides the
advantages of cost effectiveness and easy operation (Kumar
et al. 2018).
Microbial enzymes in bioremediation
Microbial dioxygenases
These are composite enzyme systems that raise molecular
oxygen into their substrate. Aromatic hydrocarbon
dioxygenases belong to a big family of Rieske non-haem iron
oxygenases. They mainly oxidize aromatic compounds and
therefore have application in environmental remediation.
Microbial peroxidases
Peroxidases are oxidoreductases that are produced by a
range of plants and microbes. Peroxidases require H
2
for
their catalytic activities. These are prevalent enzymes that
catalyze the lignin and phenolic compounds oxidation at the
outlay of hydrogen peroxide (H
2
O
2
) depending on the avail-
ability of mediator. They are involved in the biological pro-
cesses such as hormone regulation and immune responses in
the mammals. In plants, they help in the metabolism of
auxin and lignin, elongation of cells, defense against path-
ogen, and also cross linking if cell walls. The well-known
enzymes of this group include lignin peroxidases (LiP) and
manganese peroxidases (MnP) (Saglam et al. 2018). MnP
are enzymes of the heme group that are produced by a ba-
sidiomycetes group of fungus extracellularly and are re-
sponsible for the lignin degradation that oxidizes Mn
2+
to
Mn
3+
in a multistep manner. Ceriporiopsis subvermispora
was used for the MnP production that was genetically ma-
nipulated to increase the stability at acidic pH. An
engineered enzyme was found to oxidize veratryl alcohol
and Reactive Black 5 (Fernández-Fueyo et al. 2014). MnP
and LiP were reported for the recalcitrant toxic compounds
degradation by the group of basidiomycetes fungi and
white-rot fungi. Another important enzyme of this group is
versatile, which are specific a broad range of substrates, i.e.,
peroxidases. These enzymes carry out the phenolic and non-
phenolic compounds oxidation and bioremediate them
(Karigar and Rao 2011). They are known to oxidize sub-
strates in the absence of manganese when compared with
other groups of peroxidases. A highly efficient versatile
peroxidase production system in excess was formulated
for different applications in removal of xenobiotic com-
pounds and industries (Tsukihara et al. 2006; Yadav et al.
2019).
24928 Environ Sci Pollut Res (2021) 28:24917–24939

Bioinformatics approaches in bioremediation
The arena of bioremediation provides many undiscovered and
appealing alternatives from the bioinformatics perspective that
require an enormous amount of data from distinct sources, i.e.
sequence, biology and physiology of protein (enzymes), com-
parative genomics, chemical structure, reactivity of organic
compounds, and environmental biology. It is a cross-
disciplinary area of research at the boundary between comput-
er science and biological science. Bioinformatics utilizes com-
puters for storage, manipulation, recovery, and allocation of
information linked to DNA, RNA, and proteins.
Omics-based tools in bioremediation
Omics based tools such as genomics, transcriptomics,
interactomics, proteomics, and metabolomics can help in
studying bioremediation. This technology assists in correlat-
ing DNA sequences with mRNA, protein and metabolite
abundance, thereby giving a clear and truer picture of the in
situ bioremediation.
Genomics
Genomics is an emerging field for the study of microbial
strains involved in bioremediation. This approach is a con-
cept that relies on the complete genetic information analysis
in the cell of microbes. A wide range of microorganisms
have been reported for bioremediation (Khardenavis et al.
2007; Qureshi et al. 2007). Here genomic tools are used to
explain the biodegradation pathways using PCR,
microassay analysis, DNA hybridization, analysis of iso-
tope distribution, molecular connectivity, and the improve-
ment of the biodegradation process by metabolic engineer-
ing and metabolic foot printing.
A number of genotypic fingerprinting techniques based on
the PCR, including amplified fragment length polymorphisms
(AFLP), automated ribosomal intergenic spacer analysis
(ARISA), amplified ribosomal DNA restriction analysis
(ARDRA) terminal-restriction fragment length polymorphism
(T-RFLP), single strand conformation polymorphism (SSCP),
randomly amplified polymorphic DNA analysis (RAPD), and
length heterogeneity PCR (LH-PCR), are available for micro-
bial communities screening and effectiveness of bioremedia-
tion processes (Desai et al. 2010). RAPD could be used for
assessing inherently allied bacterial species, structural and
functional interpretation of the soil microbial communities,
and genetic fingerprinting (Gupta et al. 2020). LH-PCR could
be used to detect natural lengths variations of different SSU
rRNA genes within microbial communities. T-RFLP is useful
for simultaneous multiple taxonomic groups profiling of mi-
crobes within an ecosystem (Singh et al. 2006).
Further, the amalgamation of specific molecular tools, in-
cluding genetic fingerprinting, FISH, microradiography, sta-
ble isotope probing, and quantitative PCR, may also be used
for studying microbial interactions with natural factors in the
soil microenvironment. Quantitative PCR determines the
abundance and manifestation of taxonomic and operative
gene markers in the exploration of soil microbial communities
(Bustin et al. 2005). Genetic fingerprinting techniques per-
form specific molecular biomarker genes direct analysis using
amplified PCR products. The relationship between diverse
microbial communities could be studied using cluster-
assisted analysis, which compares fingerprints from various
samples.
Transcriptomics and metatranscriptomics
The set of genes transcribed in a given condition and time is
known as a transcriptome, which is an important link be-
tween cellular phenotype, genome, interactome, and prote-
ome. The gene expression control is a key processes for
adapting the changes in environmental conditions and thus
for survival. Transcriptomics interpret this process in a ge-
nome wide range. For determination of mRNA expression
level, DNA microassay analysisisanimmenselypowerful
tool in transcriptomics (Díaz 2004). Transcriptomics anal-
ysis involves extraction and enrichment of the total mRNA,
cDNA synthesis followed by either sequencing of the com-
plete cDNA transcriptome or microarray hybridization of
cDNA. DNA microarray is an effective transcriptomics tool
that helps to analyze and study the expression of the mRNA
of almost every gene present in an organism (Pandey et al.
2019).
Transcriptomics or metatranscriptomics are important to
gain functional insights into the environmental microbial
communities activities by studying the profiles transcrip-
tional mRNA (McGrath et al. 2008). It has been revealed
that metatranscriptomics along with metagenomics and ge-
nome binning can provide insights regarding microbiota
relationships, syntrophism, and complementary metabolic
pathways during the whole biodegradation process (Ishii
et al. 2015). Metatranscriptomics is a useful tool for quan-
titative and qualitative data about gene expression
(Giovanella et al. 2020).
Proteomics and metabolomics
Proteomics allows the study of the total number of proteins
expressed in a cell at a given location and time, whereas
metabolomics revolves around the total metabolites quanti-
fication and the characterization generated by an organism
in a given time or conditions (Rawat and Rangarajan 2019).
Proteomics based investigations have been useful in deter-
mining abundance of proteins and changes in the
24929Environ Sci Pollut Res (2021) 28:24917–24939

composition, as well as in identification of key proteins
involved in the physiological response of microbes when
exposed to anthropogenic pollutants (Desai et al. 2010).
The functional analysis of microbial communities is more
useful and has greater potential compared with genomics.
The studies through metabolomics employ two primary
strategies for analyzing biological systems. The first takes
into consideration global untargeted study in which no prior
knowledge of the biological system metabolic pathways is
required. This strategy helps in identification and recovery
of an extensive range of metabolites present in the sample,
generating a tremendous amount of information that could
then be correlated among diverse samples to establish their
interconnectivity in metabolic pathways. The second strat-
egy is a targeted study to identify specific metabolic path-
ways or metabolites based on previous knowledge (Hussain
et al. 2009). The microbial metabolomics toolbox includes
numerous methodologies such as foot printing and metabol-
ic fingerprinting, target analysis and metabolite profiling for
identification and quantification of a wide range of cellular
metabolites. The combination of proteome and metabolome
data will help in identification of the active molecules es-
sential for cell-free bioremediation. The schematic repre-
sentation showing different approaches for bioremediation
is shown in Fig. 6.
Nanotechnological approaches in bioremediation
The term nanotechnology was proposed by Norio Taniguchi
professor of Tokyo university of science in 1974 (Taniguchi
1974). Nanotechnology deals with the objects on the order of a
nanometer in size. Owing to their distinctive activity toward
various recalcitrant contaminants, they are under fast recogni-
tion for removal of various toxic compounds. Nanotechnology
has given a new perspective to technology such as treatment,
especially in the field of water. It is now possible to collect
techniques that are environmentally friendly under the titles of
photocatalysis and nanofiltration (Prasad 2017).
Effective microbes technology and nanotechnology
Effective microbes (EM) technology is a technique in which
effective microbes are used to treat waste water, and it is
recycled afterwards for irrigation (Leahy and Colwell 1990).
Nanotechnology and EM technology are helpful in the reduc-
tion of water impurities (Shrivastava et al. 2007). The sites
contaminated with recalcitrant organic pollutants, such as
PAHs (polycyclic aromatic hydrocarbons) with multiple ben-
zene rings, are immense and pose ubiquitous environmental
problems. PAHs are relatively non-biodegradable and
mutagenic.
Fig. 6. Schematic representation showing different approaches for bioremediation
24930 Environ Sci Pollut Res (2021) 28:24917–24939

Engineered polymeric nanoparticles for bioremediation
of hydrophobic contaminants
Sorption of organic pollutants, such as PAHs and petroleum
hydrocarbons, to soil restricts their rate of solubility and mo-
bility. Polymeric nano-network particles increase the solubil-
ity of phenanthrene and enhance the phenanthrene release
from contaminated aquifer material. Polymeric nanoparticles
are made from a poly(ethylene)glycol modified urethane ac-
rylate (PMUA) precursor chain. The properties of PMUA
nanoparticles are meant to be stable in the availability of a
heterogenous active bacterial population (Bhandari 2018).
Enhanced degradation for hazardous waste treatment using
cell immobilization technique
Immobilized cells are effectively used for bioremediation of
numerous toxic chemicals. Lee and Lee (2004) studied degra-
dation of chlorophenols using cells immobilized in Ca-
alginate gel beads and free cells. They found that immobilized
cells degraded chlorophenols much faster than free cells and
reduced the lag phase for the extraction of chlorophenols.
Monitoring of bioremediation processes
The success of bioremediation technology lies in its efficacy,
predictability, and reliability. These parameters need to be mon-
itored on a regular basis so that it can be adopted on a larger
scale. The monitoring protocols must be treatment specific and
statistically sound. Moreover, proper sampling, replication, and
data analysis are the important aspect for monitoring. A number
of analytical and biological methods are available nowadays
that can be employed for bioremediation monitoring.
Analytical methods
The analytical methods are at the heart of bioremediation tech-
nology, and without them, it is impossible to analyze it.
Electrochemical electrodes are the most preferred method for
in situ monitoring of the bioremediation, especially under an-
oxic environments. They are found very effective against
heavy metals. They can measure a wide range of the cations
(Ag
+
,Cd
2+,
Cu
2+
,H
+
,K
+
,Na
+
,NH
4+
and Pb
2+
)aswellas
anions (Br
−
,Cl
−
,ClO
4
−
,CN
−
,F
−
,I
−
,NO
3
−
and S
2
−
)(Bustos
López 2020). However, this technique was found less effec-
tive regarding hydrophobic organic compounds, viz. polycy-
clic aromatic hydrocarbons (Yan and Reible 2015).
Further, quantification of the contaminants, their interme-
diates and the final products is another way to monitor the
bioremediation process that can be achieved by various chro-
matographic, spectroscopic, and spectrometry techniques.
These involve detailed physical and chemical characterization
of the targeted compounds as well as their degraded products
with high reproducibility, sensitivity, and reliability
(Supplementary Table 2). Among the chromatographic
methods, gas chromatography (GC), high performance liquid
chromatography (HPLC), and thin layer chromatography
(TLC) are being used frequently to monitor the bioremedia-
tion of oily sludge (Jasmine and Mukherji 2019), petroleum
products (Viesser et al. 2020), hydrocarbons (Liu et al. 2020),
heavy metals (Prusty et al. 2019), and pesticides (Giri et al.
2017). Gas chromatography coupled with mass spectrometry
provides the excellent way to characterize the contaminants
and their intermediates. Similarly, several spectroscopy tech-
niques are available, viz. nuclear magnetic resonance (NMR),
fourier transform infrared spectroscopy (FTIR), X-ray diffrac-
tion (XRD), Raman spectroscopy, 3D fluorescence spectros-
copy, and atomic absorption spectroscopy (AAS). These tech-
niques have been reported for the degradation analysis of
cyhalothrin (Palmer-Brown et al. 2019), cyanate (Feng et al.
2019), palm oil mill effluent (Ganapathy et al. 2019), uranium
(Manobala et al. 2019), heavy metals (Sher et al. 2020), paper
mill effluent (Shankar et al. 2020), polyhydroxybutyrate
(Debbarma et al. 2017), and hydrocarbons (Innemanová and
Cajthaml 2020). Among them, FTIR and AAS are cost effec-
tive, sensitive, and reliable methods. Thermal analysis is an-
other way to characterize the contaminants. It employs the
changes in physical and chemical properties of the contami-
nants under thermal treatment. Derivative thermogravimetry
(DTG) analysis, thermogravimetric analysis (TGA), and dif-
ferential thermal analysis (DTA) can be used to monitor the
bioremediation process by comparing the thermal behavior of
the contaminants, their intermediates, and the products.
Gimžauskaitėet al. (2020) have used these techniques for
the analysisof diesel-contaminated soils. Moreover, they have
also been employed for monitoring the chromium removal
(Ren et al. 2020), waste water treatment (Ferreira et al.
2020), and petroleum sludge (Ziglio et al. 2019). Further,
mass spectrometry is another technique that characterizes the
sample on the basis of charge to mass ratio of the respective
ions. It is mostly used in association with the chromatographic
techniques.
Recently, Reddy et al. (2020) used this technique along
with GC in the bioremediation studies of hexanoic acid and
phenanthrene within oil sands. Moreover, Kang et al. (2020)
have used MS coupled with 2D-gel electrophoresis and
MALDI-TOF/TOF to characterize the bioremediation poten-
tial of Acinetobacter calcoaceticus. Moreover, solid-phase
microextraction (SPME)can also be used for the environmen-
tal monitoring of the PAH and products of petroleum
(Kuppusamy et al. 2020). Bragança et al. (2019) have devel-
oped a method for the determination of 3-phenoxybenzoic
acid that is a metabolite of many synthetic pyrethroid pesti-
cides, by using solid-phase extraction and GC/MS. Inaddition
to these, nowadays, the quantitative structure–activity
24931Environ Sci Pollut Res (2021) 28:24917–24939

relationship (QSAR) and quantitative structure biodegradabil-
ity relationships (QSBR) are also being used to predict the
biodegradability of the particular pollutant. Recently, Hassen
et al. (2018) used this approach to assess the bioremediation
potential of pseudomonads toward the pesticides, while Nolte
et al. (2020) employed this technique to monitor waste water
treatment. Nevertheless, Funar-Timofei and Ilia (2020) de-
scribed it for the ecotoxicological perspective.
Biological methods
Biological or molecular methods besides evaluating the per-
formance of the microorganisms offer an excellent way for
microbial identification. These methods also provide an idea
about the substrate concentration and their fate. They mainly
rely on the abundance and metabolic activities of the micro-
organisms associated with the bioremediation. For this, two
different type of approaches, viz. culture dependent and cul-
ture independent can be used (Supplementary Table 2).
Culture dependent approaches rely on the microbial cultiva-
tion and consist of both conventional, viz. plate count, most
probable number (MPN), carbon source utilization tests/
BIOLOG, and modern techniques, viz. immunochemical
methods, flow cytometry, mass spectrometry, proteomics,
and transcriptomics (Daverey et al. 2019; Fakhech et al.
2019). Among the immunochemical methods, enzyme-
linked immunosorbent assay (ELISA) is the commonly used
technique for monitoring the bioremediation process. Ko et al.
(2019) used it for bioremediation studies of eutrophic water,
especially for analyzing microcystin, a toxin produced by the
cyanobacteria. Unfortunately, only approximately 1% of the
total microorganisms are culturable; therefore, culture depen-
dent techniques cannot be utilized for whole community anal-
ysis. Thus, to complement the traditional identification
methods, a new approach is employed known as the culture
independent approach. These fingerprinting techniques pro-
vide a complete profile of the microbial communities and do
not rely on their culturing. These methods are high through-
put, accurate, and reproducible.
Metagenomics deals with the study of DNA extracted
directly from the environment through denaturing gradient
gel electrophoresis (DGGE), qRT-PCR, DNA:DNA hy-
bridization, microarray, and other techniques (Jadeja
et al. 2019; Shekhar et al. 2020). Moreover, several other
molecular biology techniques, viz. polymerase chain reac-
tion (PCR), repetitive sequence-based PCR (rep-PCR),
multiple locus variable number tandem repeat analysis
(MLVA), single strand conformation polymorphism
(SSCP), multilocus sequence typing (MLST), amplified
fragment length polymorphism (AFLP), restriction frag-
ment length polymorphism (RFLP), and random amplifi-
cation of polymorphic DNA (RAPD) can also be explored
for characterizing the bioremediation associated
microorganisms. In addition to these, phospholipid fatty
acid analysis (PLFA), respirometry, fluorescence in situ
hybridization (FISH), and reverse sample genome probing
(RSGP) are also being used frequently in bioremediation
studies (Srivastava et al. 2019). Enrichment of the meta-
bolically active cells is an alternative approach to monitor
the bioremediation, which attempts to link microbial
structure with function. The bromodeoxyuridine (BrdU)
method and stable isotope probing are two major enrich-
ment methods. The principle underlying (BrdU) enrich-
ment is that active organisms metabolically will incorpo-
rate a labeled nucleotide (BrdU) into their DNA, which
can be isolated on the basis of the incorporated label
(Salmonová and Bunešová 2017). This strategy could be
used for the enrichment of microbes grown on xenobiotics
compounds. Another enrichment method is stable-isotope
probing, which involves soil bacteria providing a
13
C-la-
beled substrate. The bacteria that can use the substrate
incorporate the
13
C into their DNA, making it denser than
normal DNA containing
12
C, thereby providing a way to
identify the metabolically active cells. The table isotope
probing (SIP) technique can also be used to monitor the
bioremediation. Kasanke et al. (2019) have employed this
technique successfully for the identification and character-
ization of sulfolane-degrading Rhodoferax sp.
Microbial fuel cells and microbial biosensors seem very
useful in the bioremediation technology. Recently, the signifi-
cance of microbial fuel cells for waste water treatment and
electricity generation has been reviewed. The microbial fuel
cells can also be used to develop the microbial sensors (Xu
et al. 2019). Several bacterial biosensors have been reported
in the literature, which are reported for the monitoring of the
bioremediation process (Elcin and Öktem 2020; Shin 2011;
Wang et al. 2019). Wang et al. (2019)usedEscherichia coli
cells for detection and bioremediation of copper ions in the
water samples. Ravikumar et al. (2017) developed a microbial
biosensor based on bacterial two-component systems.
Moreover, Tang et al. (2008) developed a laccase enzyme
based biosensor for the monitoring of catechol bioremediation.
Recently, Jin et al. (2020) developed a novel microbial-
electrochemical technology to monitor in situ microbial activi-
ties in the soil by assessing the electron flow associated with the
biodegradation.
Conclusion and future prospects
The major problem of the twenty-first century is environmen-
tal pollution, and research communities are devoting a great
deal of attention to this issue. Bioremediation through mi-
crobes is a potent technique for cleaning up pollution by en-
hancing the natural biodegradation processes as microbes
adapt quickly to changing and noxious environments. The
24932 Environ Sci Pollut Res (2021) 28:24917–24939

complete understanding of the microbial communities and
how they respond to the natural environment and in the pres-
ence of the pollutants is very important for development of
ecologically stable, novel, and potential bioremediation ap-
proaches. The amazing role of extremophiles in bioremedia-
tion reveals the need for deeper studies so that novel species
could be identified and the mechanisms they use in such ex-
treme environments could be studied.
The studies incorporating multi-omics remain inadequate
and could be explored more to fill gaps in understanding the
ecology, gene expression, and metabolism of the microbes
involved in bioremediation. Several microbes contain key
metabolic genes that could be incorporated into other organ-
isms. Genetically modified microbes with increased capabili-
ties for degrading pollutants will surely have an important
future in this field. Expanding the knowledge of microbial
genetics to increase the abilities to degrade pollutants and
conducting field experiments will surely pave the way for
advances in this field. Furthermore, it would also be interest-
ing if products of bioremediation are developed for large-scale
application.
Supplementary Information The online version contains supplementary
material available at https://doi.org/10.1007/s11356-021-13252-7.
Acknowledgments The authors are grateful to the Department of
Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture,
Eternal University, Baru Sahib and Department of Environment,
Science & Technology (DEST), Shimla, HP funded project
“Development of microbial consortium as bio-inoculants for drought
and low temperature growing crops for organic farming in Himachal
Pradesh”for providing the facilities and financial support to undertake
the investigations.
Authors’contributions Divjot Kour, Tanvir Kaur, Rubee Devi, Ashok
Yadav, Manali Singh, Divya Joshi, Jyoti Singh, Deep Chandra Suyal
helped in compiling the manuscript and Ajay Kumar, Vishnu D.
Rajput, Ajar Nath Yadav, Karan Singh, Joginder Singh, Riyaz Z.
Sayyed, Naveen Kumar Arora, Anil Kumar Saxena helped in reviewing
the manuscript.
Funding Department of Environment, Science & Technology (DEST),
Shimla, HP funded project “Development of microbial consortium as bio-
inoculants for drought and low temperature growing crops for organic
farming in Himachal Pradesh.”
Availability of data and materials Not applicable.
Declarations
Ethics approval and consent to participate Not applicable.
Competing interests The authors declare that they have no conflicts of
interest.
References
Afzal M, Rehman K, Shabir G, Tahseen R, Ijaz A, Hashmat AJ, Brix H
(2019) Large-scale remediation of oil-contaminated water using
floating treatment wetlands. Npj Clean Water 2:1–10
Afzal M, Shabir G, Hussain I, Khalid ZM (2008) Paper and board mill
effluent treatment with the combined biological–coagulation–filtra-
tion pilot scale reactor. Bioresour Technol 99:7383–7387
Ahemad M (2014) Remediation of metalliferous soils through the heavy
metal resistant plant growth promoting bacteria: paradigms and
prospects. Arab J Chem 12:1365–1377
Ahluwalia SS, Goyal D (2007) Microbial and plant derived biomass for
removal of heavy metals from wastewater. Bioresour Technol 98:
2243–2257
Ahmad M, Sajjad W, Rehman ZU, Hayat M, Khan I (2015) Identification
and characterization of intrinsic petrophillic bacteria from oil con-
taminated soil and water. Int J Curr Microbiol App Sci 4:338–346
Al-Hawash AB, Alkooranee JT, Abbood HA, Zhang J, Sun J, Zhang X,
Ma F (2018) Isolation and characterization of two crude oil-
degrading fungi strains from Rumaila oil field, Iraq. Biotechnol
Rep 17:104–109
Amoozegar MA, Hajighasemi M, Hamedi J, Asad S, Ventosa A (2011)
Azo dye decolorization by halophilic and halotolerant microorgan-
isms. Ann Microbiol 61:217–230
Andrés P, Mateos E, Tarrasón D, Cabrera C, Figuerola B (2011) Effects
of digested, composted, and thermally dried sewage sludge on soil
microbiota and mesofauna. Appl Soil Ecol 48:236–242
Athar H, Sirajuddin A (eds) (2019) Advanced Treatment Techniques for
Industrial Wastewater. IGI Global HersheyPA USA. https://doi.org/
10.4018/978-1-5225-5754-8
Ayangbenro AS, Babalola OO (2017) A new strategy for heavy metal
polluted environments: a review of microbial biosorbents. Int J
Environ Res Public Health 14:94
Azubuike CC, Chikere CB, Okpokwasili GC (2016) Bioremediation
techniques–classification based on site of application: principles,
advantages, limitations and prospects. World J Microbiol
Biotechnol 32:180
Baez-Smith C (2006) Anaerobic digestion of vinasse for the production
of methane in the sugar cane distillery. SPRI Conference on Sugar
Processing, Loxahatchee, pp 268–287
Bajaj A, Mayilraj S, Mudiam MKR, Patel DK, Manickam N (2014)
Isolation and functional analysis of a glycolipid producing
Rhodococcus sp. strain IITR03 with potential for degradation of 1,
1, 1-trichloro-2, 2-bis (4-chlorophenyl) ethane (DDT). Bioresour
Technol 167:398–406
Bajpai P, Bajpai PK (1994) Biological color removal of pulp and paper
mill wastewaters. J Biotechnol 33:211–220
Balcıoğlu IA, Tarlan E, Kıvılcımdan C, Saçan MT (2007) Merits of
ozonation and catalytic ozonation pre-treatment in the algal treat-
ment of pulp and paper mill effluents. J Environ Manag 85:918–926
Barapatre A, Jha H (2016) Decolourization and biological treatment of
pulp and paper mill effluent by lignin-degrading fungus Aspergillus
flavus strain F10. Int J Curr Microbiol App Sci 5:19–32
Barnes DK, Galgani F, Thompson RC, Barlaz M (2009) Accumulation
and fragmentation of plastic debris in global environments. Philos
Trans Royal Soc B: Biol Sci 364:1985–1998
Bécaert V, Deschênes L, Samson R (2000) A simple method to evaluate
the concentration of pentachlorophenol degraders in contaminated
soils. FEMS Microbiol Lett 184:261–264
Belal EB (2013) Biodegradation of aliphatic-aromatic coplyester under
thermophilic conditions. Res J Environ Earth Sci 5:677–690
Bhandari G (2018) Environmental nanotechnology: applicationsof nano-
particles for bioremediation. In: Approaches in bioremediation.
Springer, Singapore, pp 301–315
24933Environ Sci Pollut Res (2021) 28:24917–24939

Bharadwaj A (2018) Bioremediation of xenobiotics: an eco-friendly
cleanup approach. In: Green chemistry in environmental sustainabil-
ity and chemical education. Springer, Singapore, pp 1–13
Binelli A, Provini A (2003) DDT is still a problem in developed coun-
tries: the heavy pollution of Lake Maggiore. Chemosphere 52:717–
723 Bioremediation. American Society of Microbiology Press,
Washington, D.C, pp. 139–236
Bosso L, Cristinzio G (2014) A comprehensive overview of bacteria and
fungi used for pentachlorophenol biodegradation. Rev Environ Sci
Bio/Technol 13:387–427
Bragança I, Lemos PC, Delerue-Matos C, Domingues VF (2019)
Pyrethroid pesticide metabolite, 3-PBA, in soils: method develop-
ment and application to real agricultural soils. Environ Sci Poll Res
26:2987–2997
Bright D, Healey N (2003) Contaminant risks from biosolids land appli-
cation: contemporary organic contaminant levels in digested sewage
sludge from five treatment plants in Greater Vancouver, British
Columbia. Environ Poll 126:39–49
Britton LN (1984) Microbial degradation of aliphatic hydrocarbons. In:
Microbial degradation of organic compounds. Dekker, New York,
pp 89–129
Bruschi M, Goulhen F (2007) New bioremediation technologies to re-
move heavy metals and radionuclides using Fe (III)-, sulfate-and
sulfur-reducing bacteria. In: Environmental bioremediation technol-
ogies. Springer, Berlin, pp 35–55
Bustin S, Benes V, Nolan T, Pfaffl M (2005) Quantitative real-time RT-
PCR–a perspective. J Mol Endocrinol 34:597–601
Bustos López ON (2020) Role of modern innovative techniques for
assessing and monitoring environmental pollution. In: Hakeem
KR, Bhat RA, Qadri H (eds) Bioremediation and biotechnology:
sustainable approaches to pollution degradation. Springer, Cham,
pp 75–91. https://doi.org/10.1007/978-3-030-35691-0_4
Chandra R, Raj A, Yadav S, Patel DK (2009) Reduction of pollutants in
pulp paper mill effluent treated by PCP-degrading bacterial strains.
Environ Monit Assess 155:1
Chandra R, Singh R (2012) Decolourisation and detoxification of rayon
grade pulp paper mill effluent by mixed bacterial culture isolated
from pulp paper mill effluent polluted site. Biochem Eng J 61:49–58
Chirnside AE, Ritter WF, Radosevich M (2007) Isolation of a selected
microbial consortium from a pesticide-contaminated mix-load site
soil capable of degrading the herbicides atrazine and alachlor. Soil
Biol Biochem 39:3056–3065
Chuphal Y, Kumar V, Thakur IS (2005) Biodegradation and decoloriza-
tion of pulp and paper mill effluent by anaerobic and aerobic micro-
organisms in a sequential bioreactor. World J Microbiol Biotechnol
21:1439–1445
Cortés D, Barrios-González J, Tomasini A (2002) Pentachlorophenol
tolerance and removal by Rhizopus nigricans in solid-state culture.
Process Biochem 37:881–884
Cristorean C, Micle V, Sur IM (2016) A critical analysis of ex-situ bio-
remediation technologies of hydrocarbon polluted soils
ECOTERRA. J Environ Res Prot 13:17–29
Crivelaro SHR, Mariano AP, Furlan LT, Gonçalves RA, Seabra PN,
DdFd A (2010) Evaluation of the use of vinasse as a biostimulation
agent for the biodegradation of oily sludge in soil. Braz Arch Biol
Technol 53:1217–1224
Das A, Osborne JW (2018) Bioremediation of Heavy Metals. In:
Gothandam KM, Ranjan S, Dasgupta N, Ramalingam C,
Lichtfouse E (eds) Nanotechnology, food security and water treat-
ment. Springer, Cham, pp 277–311. https://doi.org/10.1007/978-3-
319-70166-0_9
Daverey A, Dutta K, Sarkar A (2019) An overview of analytical meth-
odologies for environmental monitoring. In: Kaur Brar S, Hegde K,
Pachapur VL (eds) Tools, techniques and protocols for monitoring
environmental contaminants. Elsevier, Amsterdam, pp 3–17. https://
doi.org/10.1016/B978-0-12-814679-8.00001-7
Debbarma P, Raghuwanshi S, Singh J, Suyal DC, Zaidi M, Goel R (2017)
Comparative in situ biodegradation studies of polyhydroxybutyrate
film composites. 3. Biotech 7:178
Desai C, Pathak H, Madamwar D (2010) Advances in molecular and “-
omics”technologies to gauge microbial communities and bioreme-
diation at xenobiotic/anthropogen contaminated sites. Bioresour
Technol 101:1558–1569
Devi R, KaurT, Guleria G,Rana K, Kour D,Yadav N et al (2020) Fungal
secondary metabolites and their biotechnological application for hu-
man health. In: Rastegari AA, Yadav AN, Yadav N (eds) Trends of
microbial biotechnology for sustainable agriculture and biomedicine
systems: perspectives for human health. Elsevier, Amsterdam, pp
147–161. https://doi.org/10.1016/B978-0-12-820528-0.00010-7
DiasRL,RubertoL,CalabróA,BalboAL,DelPannoMT,Mac
Cormack WP (2015) Hydrocarbon removal and bacterial communi-
ty structure in on-site biostimulated biopile systems designed for
bioremediation of diesel-contaminated Antarctic soil. Polar Biol
38:677–687
Diep P, Mahadevan R, Yakunin AF (2018) Heavy metal removal by
bioaccumulation using genetically engineered microorganisms.
FrontBioengBiotechnol6:1–39
Elcin E, Öktem HA (2020) Immobilization of fluorescent bacterial
bioreporter for arsenic detection. J Environ Health Sci Eng 18:
137–148
Eriksson KE, Kolar MC (1985) Microbial degradation of chlorolignins.
Environ Sci Technol 19:1086–1089
Fakhech A, Ouahmane L, Hafidi M (2019) Analysis of symbiotic micro-
bial status of Atlantic sand dunes forest and its effects on Acacia
gummifera and Retama monosperma (Fabaceae) to be used in refor-
estation. J For Res 31:1309–1317
Fang H, Dong B, Yan H, Tang F, Yu Y (2010) Characterization of a
bacterial strain capable of degrading DDT congeners and its use in
bioremediation of contaminated soil. J Hazard Mater 184:281–289
Farhan SN, Khadom AA (2015) Biosorption of heavy metals from aque-
ous solutions by Saccharomyces cerevisiae. Int J Ind Chem 6:119–
130
Feng J, Zhong J, Tang X (2019) Selective and sensitive detection of
cyanate using 3-amino-2-naphthoic acid-based turn-on fluorescence
probe. Anal Bioanal Chem 411:3613–3619
Fernández-Fueyo E, Ruiz-Dueñas FJ, Martínez AT (2014) Engineering a
fungal peroxidase that degrades lignin at very acidic pH. Biotechnol
Biofuel 7:1–12
Ferreira AF, Ferreira A, Dias APS, Gouveia L (2020) Pyrolysis of
Scenedesmus obliquus biomass following the treatment of different
wastewaters. BioEnergy Res 13:896–906
Field JA, Sierra-Alvarez R (2008) Microbial degradation of chlorinated
phenols. Rev Environ Sci Biotechnol 7:211–241
Folch A, Vilaplana M, Amado L, Vicent T, Caminal G (2013) Fungal
permeable reactive barrier to remediate groundwater in an artificial
aquifer. J Hazard Mater 262:554–560
Fountoulakis M, Terzakis S, Georgaki E, Drakopoulou S, Sabathianakis
I, Kouzoulakis M, Manios T (2009) Oil refinery sludge and green
waste simulated windrow composting. Biodegradation 20:177–189
Frascari D, Zanaroli G, Danko AS (2015) In situ aerobic cometabolism of
chlorinated solvents: a review. J Hazard Mater 283:382–399
Fukushima M, Tatsumi K (2007) Degradation of pentachlorophenol in
contaminated soil suspensions by potassium monopersulfate cata-
lyzed oxidation by a supramolecular complex between tetra (p-
sulfophenyl) porphineiron (III) and hydroxypropyl-β-cyclodextrin.
J Hazard Mater 144:222–228
Funar-Timofei S, Ilia G (2020) QSAR modeling of dye ecotoxicity. In:
Roy K (ed) Ecotoxicological QSARs. Springer, New York, pp 405–
436. https://doi.org/10.1007/978-1-0716-0150-1_18
Ganapathy B, Yahya A, Ibrahim N (2019) Bioremediation of palm oil
mill effluent (POME) using indigenous Meyerozyma guilliermondii.
Environ Sci Pollut Res 26:11113–11,125
24934 Environ Sci Pollut Res (2021) 28:24917–24939

Gao B, Liu W-B, Jia L-Y, Xu L, Xie J (2011) Isolation and characteriza-
tion of an Alcaligenes sp. strain DG-5 capable of degrading DDTs
under aerobic conditions. J Environ Sci Health-Part B 46:257–263
GimžauskaitėD, Tamošiūnas A, TučkutėS, SnapkauskienėV, Aikas M,
Uscila R (2020) Treatment of diesel-contaminated soil using thermal
water vapor arc plasma. Environ Sci Pollut Res 27:43–54
Giovanella P, Vieira GA, Otero IVR, Pellizzer EP, de Jesus Fontes B,
Sette LD (2020) Metal and organic pollutants bioremediation by
extremophile microorganisms. J Hazard Mater 382:121024
Giri J, Srivastva A, Pachauri S, Srivastva P (2014) Effluents from paper
and pulp industries and their impact on soil properties and chemical
composition of plants in Uttarakhand, India. J Environ. Waste
Manag 1:26–32
Giri K, Rai J, Pandey S, Mishra G, Kumar R, Suyal DC (2017)
Performance evaluation of isoproturon-degrading indigenous bacte-
rial isolates in soil microcosm. Chem Ecol 33:817–825
Gomez F, Sartaj M (2014) Optimization of field scale biopiles for biore-
mediation of petroleum hydrocarbon contaminated soil at low tem-
perature conditions by response surface methodology (RSM). Int
Biodeterior Biodegrad 89:103–109
Gupta K, Biswas R, Sarkar A (2020) Advancement of omics: prospects
for bioremediation of contaminated soils. In: Shah MP (ed)
Microbial bioremediation & biodegradation. Springer, Singapore,
pp 113–142. https://doi.org/10.1007/978-981-15-1812-6_5
Gupta VK, Nayak A, Agarwal S (2015) Bioadsorbents for remediation of
heavy metals: current status and their future prospects. Environ Eng
Res 20:1–18
Gursahani Y, Gupta S (2011) Decolourization of textile effluent by a
thermophilic bacteria Anoxybacillus rupiensis. J Pet Environ
Biotechnol 2:1–4
Hajslova J, Moffat C, Whittle K (1999) Environmental contaminants in
food (Sheffield Food Technology, Vol 4). CRC, Boca Raton
Harada N, Takagi K, Harazono A, Fujii K, Iwasaki A (2006) Isolation
and characterization of microorganisms capable of hydrolysing the
herbicide mefenacet. Soil Biol Biochem 38:173–179
Haroni NN, Badehian Z, Zarafshar M, Bazot S (2019) The effect of oil
sludge contamination on morphological and physiological charac-
teristics of some tree species. Ecotoxicology 28:507–519
Harvey RG (1996) Mechanisms of carcinogenesis of polycyclic aromatic
hydrocarbons. Polycycl Aromat Compd 9:1–23
Hassen W et al (2018) Assessment of genetic diversity and bioremedia-
tion potential of pseudomonads isolated from pesticide-
contaminated artichoke farm soils. 3 Biotech 8:263
Heinaru E, Merimaa M, Viggor S, Lehiste M, Leito I, Truu J, Heinaru A
(2005) Biodegradation efficiency of functionally important popula-
tions selected for bioaugmentation in phenol-and oil-polluted area.
FEMS Microbiol Ecol 51:363–373
Hillman J, Hill J, Morgan J, Wilkinson J (2003) Recycling of sewage
sludge to grassland: a review of the legislation to control of the
localization and accumulation of potential toxic metals in grazing
systems. Grass Forage Sci 58:101–111
Hobson A, Frederickson J, Dise N (2005) CH
4
and N
2
O from mechani-
cally turned windrow and vermicomposting systems following in-
vessel pre-treatment. Waste Manag 25:345–352
Hussain S, Siddique T, Saleem M, Arshad M, Khalid A (2009) Impact of
pesticides on soil microbial diversity, enzymes, and biochemical
reactions. Adv Agron 102:159–200
Ibrahim M, Ijah U, Manga S, Bilbis L, Umar S (2013) Production and
partial characterization of biosurfactant produced by crude oil
degrading bacteria. Int Biodeterior Biodegrad 81:28–34
Igiri BE, Okoduwa SIR, Idoko GO, Akabuogu EP, Adeyi AO, Ejiogu IK
(2018) Toxicity and bioremediation of heavy metals contaminated
ecosystem from tannery wastewater. A Rev J Toxicol 2018:
2568038. https://doi.org/10.1155/2018/2568038
Innemanová P, Cajthaml T (2020) Field study IX: pilot-scale composting
of PAH-contaminated materials: two different approaches. In: Filip
J, Cajthaml T, Najmanová P, Černík M, Zbořil R (eds) Advanced
nano-bio technologies for water and soil treatment. Springer, Cham,
pp 527–534. https://doi.org/10.1007/978-3-030-29840-1_25
Si I, Suzuki S, Tenney A, Norden-Krichmar TM, Nealson KH,
Bretschger O (2015) Microbial metabolic networks in a complex
electrogenic biofilm recovered from a stimulus-induced
metatranscriptomics approach. Sci Rep 5:14840
Ite AE, Ibok UJ (2019) Role of plants and microbes in bioremediation of
petroleum hydrocarbons contaminated soils. Int J Environ
Bioremediat Biodegrad 7:1–19
Jadeja NB, Purohit HJ, Kapley A (2019) Decoding microbial community
intelligence through metagenomics for efficient wastewater treat-
ment. Funct Integr Genomic 19:839–851
Jalilzadeh YR, Sekhavatjou M, Maktabi P, Arbab SN, Khadivi S,
Pourjafarian V (2014) The biodegradation of crude oil by Bacillus
subtilis isolated from contaminated soil in hot weather areas. Int J
Environ Res 8:509–514
Jasmine J, Mukherji S (2019) Impact of bioremediation strategies on
slurry phase treatment of aged oily sludge from a refinery. J
Environ Manag 246:625–635
Jin KS, Fallgren PH, Santiago NA, Ren ZJ, Li Y, Jin S(2020) Monitoring
in situ microbial activities in wet or clayey soils by a novel
microbial-electrochemical technology. Environ Technol Innov 18:
1–6
Johnson OA, Affam AC, Johnson OA, Affam AC (2018) Petroleum
sludge treatment and disposal: A review. Environ Eng Res 24:
191–201
Juwarkar AA, Singh SK, Mudhoo A (2010) A comprehensive overview
of elements in bioremediation. Rev Environ Sci Biotechnol 9:215–
288
Kang W, Zheng J, Bao J, Wang Z, Zheng Y, He J-Z, Hu H-W (2020)
Characterization of the copper resistance mechanism and bioreme-
diation potential of an Acinetobacter calcoaceticus strain isolated
from copper mine sludge. Environ Sci Pollut Res 27:7922–7933
Karigar CS, Rao SS (2011) Role of microbial enzymes in the bioremedi-
ation of pollutants: a review. Enzyme Res 2011:805187
Kasanke CP, Collins RE, Leigh MB (2019) Identification and character-
ization of a dominant sulfolane-degrading Rhodoferax sp. via stable
isotope probing combined with metagenomics. Sci Rep 9:1–9
Kebria DY, Khodadadi A, Ganjidoust H, Badkoubi A, Amoozegar M
(2009) Isolation and characterization of a novel native Bacillus
strain capable of degrading diesel fuel. Int J Environ Sci Technol
6:435–442
Khardenavis AA, Kapley A, Purohit HJ (2007) Simultaneous nitrification
and denitrification by diverse Diaphorobacter sp. Appl Microbiol
Biotechnol 77:403–409
Kim S, Krajmalnik-Brown R, Kim J-O, Chung J (2014) Remediation of
petroleum hydrocarbon-contaminated sites by DNA diagnosis-
based bioslurping technology. Sci Total Environ 497:250–259
Ko S-R, Srivastava A, Lee N, Jin L, Oh H-M, Ahn C-Y (2019)
Bioremediation of eutrophic water and control of cyanobacterial
bloom by attached periphyton. Int J Environ Sci Technol 16:
4173–4180
Kour D, Rana KL, Kumar R, Yadav N, Rastegari AA, Yadav AN et al
(2019a) Gene manipulation and regulation of catabolic genes for
biodegradation of biphenyl compounds. In: Singh HB, Gupta VK,
Jogaiah S (eds) New and future developments in microbial biotech-
nology and bioengineering. Elsevier, Amsterdam, pp 1–23. https://
doi.org/10.1016/B978-0-444-63503-7.00001-2
Kour D, Rana KL, Yadav N, Yadav AN, Singh J, Rastegari AA et al
(2019b) Agriculturally and industrially important fungi: current de-
velopments and potential biotechnological applications. In: Yadav
AN, Singh S, Mishra S, Gupta A (eds) Recent advancement in white
biotechnology through fungi, volume 2: perspective for value-added
products and environments. Springer, Cham, pp 1–64. https://doi.
org/10.1007/978-3-030-14846-1_1
24935Environ Sci Pollut Res (2021) 28:24917–24939

Krzmarzick MJ, Taylor DK, Fu X, McCutchan AL (2018) Diversity and
niche of Archaea in bioremediation. Archaea 3:194108. https://doi.
org/10.1155/2018/3194108
Kulshreshtha S, Mathur N, Bhatnagar P (2013) Mycoremediation of pa-
per, pulp and cardboard industrial wastes and pollutants. In:
Goltapeh EM, Danesh YR, Varma A (eds) Fungi as bioremediators.
Springer, Berlin, pp 77–116. https://doi.org/10.1007/978-3-642-
33,811-3_4
Kulshrestha G, Kumari A (2011) Fungal degradation of chlorpyrifos by
Acremonium sp. strain (GFRC-1) isolated from a laboratory-
enriched red agricultural soil. Biol Fert Soil 47:219–225
Kumar A, Bhoot N, Soni I, John P (2014) Isolation and characterization
of a Bacillus subtilis strain that degrades endosulfan and endosulfan
sulfate. 3 Biotech 4:467–475
Kumar A, Chaturvedi AK, Yadav K, Arunkumar KP, Malyan SK, Raja P
et al (2019) Fungal phytoremediation of heavy metal-contaminated
resources: Current scenario and future prospects. In: Yadav AN,
Singh S, Mishra S, Gupta A (eds) Recent advancement in white
biotechnology through fungi, volume 3: perspective for sustainable
environments. Springer, Cham, pp 437–461. https://doi.org/10.
1007/978-3-030-25506-0_18
Kumar A, Devi S, Singh D (2018) Significance and approaches of mi-
crobial bioremediation in sustainable development. In: Singh J,
Sharma D, Kumar G, Sharma NR (eds) Microbial bioprospecting
for sustainable development. Springer, Singapore, pp 93–114.
https://doi.org/10.1007/978-981-13-0053-0_5
Kumar M, Yadav AN, Saxena R, Paul D, Tomar RS (2021) Biodiversity
of pesticides degrading microbial communities and their environ-
mental impact. Biocatal Agric Biotechnol 31:101883. https://doi.
org/10.1016/j.bcab.2020.101883
Kumar PS (2019) Soil Bioremediation Techniques. In: Advanced
Treatment Techniques for Industrial Wastewater. IGI Global, pp.
35–50, https://doi.org/10.4018/978-1-5225-5754-8.ch003
Kuppusamy S, Maddela NR, Megharaj M, Venkateswarlu K (2020)
Methodologies for analysis and identification of total petroleum hy-
drocarbons. In: Total petroleum hydrocarbons: environmental fate,
toxicity, and remediation. Springer, Cham, pp 29–55. https://doi.
org/10.1007/978-3-030-24,035-6_2
Leahy JG, Colwell RR (1990) Microbial degradation of hydrocarbons in
the environment. Microbiol Mol Biol Rev. 54:305–315
Lee W-C, Lee KH (2004) Applications of affinity chromatography in
proteomics. Anal Biochem 324:1–10
Liu H, Gao H, Wu M, Ma C, Wu J, Ye X (2020) Distribution character-
istics of bacterial communities and hydrocarbon degradation dy-
namics during the remediation of petroleum-contaminated soil by
enhancing moisture content. Microb Ecol 80:202–211
Lombi E, Gerzabek MH (1998) Determination of mobile heavy metal
fraction in soil: results of a pot experiment with sewage sludge.
Commun Soil Sci Plant Anal 29:2545–2556
Lors C, Damidot D, Ponge J-F, Périé F (2012) Comparison of a biore-
mediationprocess of PAHs in a PAH-contaminated soil at field and
laboratory scales. Environ Pollut 165:11–17
Ma H et al (2018) Compared the physiological response of two
petroleum-tolerant contrasting plants to petroleum stress. Int J
Phytoremediation 20:1043–1048
Malaviya P, Rathore V (2007) Bioremediation of pulp and paper mill
effluent by a novel fungal consortium isolated from polluted soil.
Bioresour Technol 98:3647–3651
Mandri T, Lin J (2007) Isolation and characterization of engine oil
degrading indigenous microrganisms in Kwazulu-Natal. South
Africa. Afr J Biotechnol 6:23–27
Mangas E, Vaquero M, Comellas L, Broto-Puig F (1998) Analysis and
fate of aliphatic hydrocarbons, linear alkylbenzenes, polychlorinated
biphenyls and polycyclic aromatic hydrocarbons in sewage sludge-
amended soils. Chemosphere 36:61–72
Manobala T, Shukla SK, Rao TS, Kumar MD (2019) A new uranium
bioremediation approach using radio-tolerant Deinococcus
radiodurans biofilm. J Biosci 44:1–24
McGowin AE, Adom KK, Obubuafo AK (2001) Screening of compost
for PAHs and pesticides using static subcritical water extraction.
Chemosphere 45:857–864
McGrath KC, Thomas-Hall SR, Cheng CT, Leo L, Alexa A, Schmidt S,
Schenk PM (2008) Isolation and analysis of mRNA from environ-
mental microbial communities. J Microbiol Method 75:172–176
Milne B, Baheri H, Hill G (1998) Composting of a heavy oil refinery
sludge. Environmental Progress 17:24–27
Min J, Chen W, Wang J, Hu X (2017) Genetic and biochemical charac-
terization of 2-chloro-5-nitrophenol degradation in a newly isolated
bacterium, Cupriavidus sp. strain CNP-8. Front Microbiol 8:1778
Mohn WW, Tiedje JM (1992) Microbial reductive dehalogenation.
Microbiol Mol Biol Rev 56:482–507
Moreda J, Arranz A, De Betoño SF, Cid A, Arranz J (1998)
Chromatographic determination of aliphatic hydrocarbons and
polyaromatic hydrocarbons (PAHs) in a sewage sludge. Sci Total
Environ 220:33–43
Navrátilová J, Tvrzová L, Durnová E, Spröer C, Sedláček I, NečaJ,
Němec M (2005) Characterization of Rhodococcus wratislaviensis
strain J3 that degrades 4-nitrocatechol and other nitroaromatic com-
pounds. Antonie Van Leeuwenhoek 87:149–153
Neilson A, Allard A, Hynning P, Remberger M, Viktor T (1990) The
environmental fate of chlorophenolic constituents of bleachery ef-
fluents. Tappi, J 73:239–247
Nikhil T, Deepa V, Rohan G, Satish B (2013) Isolation, characterization
and identification of diesel engine oil degrading bacteria from ga-
rage soil and comparison of their bioremediation potential. Int. Res J
Environ Sci 2:48–52
Nolte TM, Chen G, van Schayk CS, Pinto-Gil K, Hendriks AJ,
Peijnenburg WJ, Ragas AM (2020) Disentanglement of the chemi-
cal, physical, and biological processes aids the development of
quantitative structure-biodegradation relationships for aerobic
wastewater treatment. Sci Total Environ 708:133863
Nzila A, Razzak SA, Zhu J (2016) Bioaugmentation: an emerging strat-
egy of industrial wastewater treatment for reuse and discharge. Int J
Environ Res Public Health 13:1–20
Oves M, Khan MS, Zaidi A (2013) Biosorption of heavy metals by
Bacillus thuringiensis strain OSM29 originating from industrial ef-
fluent contaminated north Indian soil. Saudi J Biol Sci 20:121–129
Palmer-Brown W, de Melo Souza PL, Murphy CD (2019) Cyhalothrin
biodegradation in Cunninghamella elegans.EnvironSciPollutRes
26:1414–1421
Pan X et al (2016) Biodegradation of DDT by Stenotrophomonas sp.
DDT-1: characterization and genome functional analysis. Sci Rep
6:21332
Pan X, Xu T, Xu H, Fang H, Yu Y (2017) Characterization and genome
functional analysis of the DDT-degrading bacterium Ochrobactrum
sp. DDT-2. Sci Total Environ 592:593–599
Pandey A, Tripathi PH, Tripathi AH, Pandey SC, Gangola S (2019)
Omics technology to study bioremediation and respective enzymes.
In: Bhatt P (ed) Smart Bioremediation Technologies. Academic
Press, Cambridge, pp 23–43. https://doi.org/10.1016/B978-0-12-
818307-6.00002-0
Park C, Lee M, Lee B, Kim S-W, Chase HA, Lee J, Kim S (2007)
Biodegradation and biosorption for decolorization of synthetic dyes
by Funalia trogii. Biochem Eng J 36:59–65
Pedroza AM, MosquedaR, Alonso-Vante N, Rodriguez-Vazquez R (eds)
(2007) Sequential treatment via Trametes versicolor and UV/TiO2/
RuxSey to reduce contaminants in waste water resulting from the
bleaching process during paper production. Chemosphere 67:793–
801
Philp J, Atlas R (2005) Bioremediationof contaminated soil and aquifers.
In: Atlas RM, Jim CP (eds) Bioremediation: applied microbial
24936 Environ Sci Pollut Res (2021) 28:24917–24939

solution for real-world environmental clean up. ASM Press,
Washington, DC, p 139
Pino V, Ayala JH, Afonso AM, González V (2000) Determination of
polycyclic aromatic hydrocarbons in marine sediments by high-
performance liquid chromatography after microwave-assisted ex-
traction with micellar media. J Chromatogr A 869:515–522
Pino-Herrera DO, Pechaud Y, Huguenot D, Esposito G, VanHullebusch
ED, Oturan MA(2017) Removal mechanisms in aerobic slurry bio-
reactors for remediation of soils andsediments polluted with hydro-
phobic organic compounds: An overview. J Hazard Mater 339:427–
449
Prasad R (2017) Mycoremediation and environmental sustainability.
Springer, Cham
Prusty JS, Rath BP, Thatoi H (2019) Production optimization and appli-
cation of extracellular chromate reductase from Bacillus sp. for bio-
remediation of hexavalent chromium. In: Kundu R, Narula R, Paul
R, Mukherjee S (eds) Environmental biotechnology for soil and
wastewater implications on ecosystems. Springer, Singapore, pp
103–108. https://doi.org/10.1007/978-981-13-6846-2_13
Qiu X, Wu P, Zhang H, Li M, Yan Z (2009) Isolation and characterization
of Arthrobacter sp. HY2 capable of degrading a high concentration
of p-nitrophenol. Bioresour Technol 100:5243–5248
Qureshi A, Verma V, Kapley A, Purohit HJ (2007) Degradation of 4-
nitroaniline by Stenotrophomonas strain HPC 135. Int Biodeterior
Biodegrad 60:215–218
Rajkumar M, Ae N, Prasad MNV, Freitas H (2010) Potential of
siderophore-producing bacteria for improving heavy metal
phytoextraction. Trends Biotechnol 28:142–149
Rastegari AA, Yadav AN, Yadav N (2019) Genetic manipulation of
secondary metabolites producers. In: Gupta VK, Pandey A (eds)
New and future developments in microbial biotechnology and bio-
engineering. Elsevier, Amsterdam, pp 13–29. https://doi.org/10.
1016/B978-0-444-63,504-4.00002-5
RavikumarS, Baylon MG, Park SJ, Choi J-i (2017) Engineered microbial
biosensors based on bacterial two-component systems as synthetic
biotechnology platforms in bioremediation and biorefinery. Microb
Cell Fact 16:1–10
Rawat M, Rangarajan S (2019) Chapter 11 - Omics approaches for elu-
cidating molecular mechanisms of microbial bioremediation. In:
Bhatt P (ed) Smart bioremediation technologies. Academic,
Cambridge, pp 191–203. https://doi.org/10.1016/B978-0-12-818,
307-6.00011-1
Rayu S, Nielsen UN, Nazaries L, Singh BK (2017) Isolation and molec-
ular characterization of novel chlorpyrifos and 3, 5, 6-trichloro-2-
pyridinol-degrading bacteria from sugarcane farm soils. Front
Microbiol 8:1–16
Reddy DO, Milliken CE, Foreman K, Fox J, Simpson W, Brigmon RL
(2020) Bioremediation of hexanoic acid and phenanthrene in oil
sands tailings by the microbial consortium BioTiger™.Bull
Environ Contam Toxicol 104:253–258
Reddy GVB, Gold MH (2000) Degradation of pentachlorophenol by
Phanerochaete chrysosporium: intermediates and reactions in-
volved. Microbiol 146:405–413
Ren L et al (2020) Hydrothermal synthesis of chemically stable cross-
linked poly-Schiff base for efficient Cr (VI) removal. J Mat Sci 55:
3259–3278
Rogers HR (1996) Sources, behavior and fate of organic contaminants
during sewage treatment and in sewage sludges. Sci Total Environ
185:3–26
Roy M, Giri AK, Dutta S, Mukherjee P (2015) Integrated phytobial
remediation for sustainable management of arsenic in soil and water.
Environ Int 75:180–198
Saglam N, Yesilada O, Saglam S, Apohan E, Sam M, Ilk S et al (2018)
Bioremediation applications with fungi. In: Prasad R (ed)
Mycoremediation and environmental sustainability: vol 2.
Springer, Cham, pp 1–37. https://doi.org/10.1007/978-3-319-
77386-5_1
Sakai M, Ezaki S, Suzuki N, Kurane R (2005) Isolation and characteri-
zation of a novel polychlorinated biphenyl-degrading bacterium,
Paenibacillus sp.KBC101. Appl Microbiol Biotechnol 68:111–116
Salmonová H, Bunešová V (2017) Methods of studying diversity of
bacterial comunities: a review. Sci Agric Bohemica 48:154–165
Sarkar J et al (2016) Biostimulation of indigenous microbial community
for bioremediation of petroleum refinery sludge. Front Microbiol 7:
1–20
Saxena AK, Yadav AN, Rajawat M, Kaushik R, Kumar R, Kumar M et al
(2016) Microbial diversity of extreme regions: An unseen heritage
and wealth. Indian J Plant Genet Resour 29:246–248
Shankar S, Shikha RA, Singh S, Rawat S (2020) Environmental contam-
ination, toxicity profile, and bioremediation approaches for detoxi-
fication of paper mill wastewater. In: Saxena G, Bharagava RN (eds)
Bioremediation of industrial waste for environmental safety, vol i:
industrial waste and its management. Springer, Singapore, pp 181–
206. https://doi.org/10.1007/978-981-13-1891-7_9
Sharaff MS, Subrahmanyam G, Kumar A, Yadav AN (2020) Mechanistic
understanding of root-microbiome interaction for sustainable agri-
culture in polluted soils. In: Rastegari AA, Yadav AN, Yadav N
(eds) Trends of microbial biotechnology for sustainable agriculture
and biomedicine systems: diversity and functional perspectives.
Elsevier, Amsterdam, pp 61–84. https://doi.org/10.1016/B978-0-
12-820,526-6.00005-1
Sharma JK, Gautam RK, Nanekar SV, Weber R, Singh BK, Singh SK,
Juwarkar AA (2018) Advances and perspective in bioremediation of
polychlorinated biphenyl-contaminated soils. Environ Sci Pollut
Res 25:16355–16,375
Sharma S, Kour D, Rana KL, Dhiman A, Thakur S, Thakur P et al (2019)
Trichoderma: biodiversity, ecological significances, and industrial
applications. In: Yadav AN, Mishra S, Singh S, Gupta A (eds)
Recent advancement in white biotechnology through fungi: volume
1: diversity and enzymes perspectives. Springer, Cham, pp 85–120.
https://doi.org/10.1007/978-3-030-10480-1_3
Shekhar SK, Godheja J, Modi DR (2020) Molecular technologies for
assessment of bioremediation and characterization of microbial
communities at pollutant-contaminated sites. In: Bharagava RN,
Saxena G (eds) Bioremediation of industrial waste for environmen-
tal safety, vol ii: biological agents and methods for industrial waste
management. Springer, Singapore, pp 437–474. https://doi.org/10.
1007/978-981-13-3426-9_18
Sher S, Hussain SZ, Rehman A (2020) Phenotypic and genomic analysis
of multiple heavy metal–resistant Micrococcus luteus strain AS2
isolated from industrial waste water and its potential use in arsenic
bioremediation. Appl Microbiol Biotechnol 104:2243–2254
Shin HJ (2011) Genetically engineered microbial biosensors for in situ
monitoring of environmental pollution. Appl Microbiol Biotechnol
89:867–877
Shrivastava S, Bera T, Roy A, Singh G, Ramachandrarao P, Dash D
(2007) Characterization of enhanced antibacterial effects of novel
silver nanoparticles. Nanotechnology 18:225103
Shrivastava SK, Banerjee DK (2004) Speciation of metals in sewage
sludge and sludge-amended soils. Water Air Soil Pollut 152:219–
232
Shu YY, Lao RC, Chiu CH, Turle R (2000) Analysis of polycyclic aro-
matic hydrocarbons in sediment reference materials by microwave-
assisted extraction. Chemosphere 41:1709–1716
Shukla L, Suman A, Yadav AN, Verma P, Saxena AK (2016) Syntrophic
microbial system for ex-situ degradation ofpaddy straw at low tem-
perature under controlled and natural environment. J Appl Biol
Biotechnol 4:30–37
Singer ME, Finnerty WR (1984) Microbial metabolism of straight-chain
and branched alkanes. In: Atlas RM (ed) Microbial metabolism of
24937Environ Sci Pollut Res (2021) 28:24917–24939

straight-chain and branched alkanes. Macmillan, New York, pp 1–
60
Singh A, Mullin B, Ward O (2001) Reactor-based process for the biolog-
ical treatment of petroleum wastes. In: Proceedings of the Middle
East Petrotech 2001 Conference. Petrotech, Bahrain, pp 1–13
Singh BK, Nazaries L, Munro S, Anderson IC, Campbell CD (2006)Use
of multiplex terminal restriction fragment length polymorphism for
rapid and simultaneous analysis of different components of the soil
microbial community. Appl Environ Microbiol 72:7278–7285
Singh C, Tiwari S, Singh JS, Yadav AN (2020) Microbes in agriculture
and environmental development. CRC, Boca Raton
Singh H (2006) Mycoremediation: fungal bioremediation. Wiley,
Hoboken
Singh J, Singh AV (2017) Microbial strategies for enhanced
phytoremediation of heavy metal-contaminated soils. In:
Bharagava RN (ed) Environmental pollutants and their bioremedia-
tion approaches. CRC, Boca Raton,pp 257–272
Singh J, Yadav AN (2020) Natural bioactive products in sustainable
agriculture. Springer, Singapore
Singh P, Singh A (2004) Physico-chemical characteristics of distillery
effluent and its chemical treatment Nature. Environ Pollut Technol
3:205–208
Singh R, Agrawal M (2008) Potential benefits and risks of land applica-
tion of sewage sludge. Waste Manag 28:347–358
Singh R, Ahirwar NK, Tiwari J, Pathak J (2018) Review on sources and
effect of heavy metal in soil: Its bioremediation. Int J Res Appl Nat
Soc Sci 2018:1–22
Singhal A, Thakur IS (2009) Decolourization and detoxification of pulp
and paper mill effluent by Cryptococcus sp. Biochem Eng J 46:21–
27
Sinha S, Chattopadhyay P, Pan L, Chatterjee S, Chanda P,
Bandyopadhyay D et al (2009) Microbial transformation of xenobi-
otics for environmental bioremediation. Afr J Biotechnol 8:6016–
6027
Sorkhoh N, Ghannoum M, Ibrahim A, Stretton R, Radwan S (1990)
Crude oil and hydrocarbon-degrading strains of Rhodococcus
rhodochrous isolated from soil and marine environments in
Kuwait. Environ Pollut 65:1–17
Srivastava N, Gupta B, Gupta S, Danquah MK, Sarethy IP (2019)
Analyzing functional microbial diversity: an overview of tech-
niques. In: Das S, Dash HR (eds) Microbial diversity in the genomic
era. Academic, Cambridge, pp 79–102. https://doi.org/10.1016/
B978-0-12-814849-5.00006-X
Sutherland T, Horne I, Harcourt R, Russell R, Oakeshott J (2002)
Isolation and characterization of a Mycobacterium strain that metab-
olizes the insecticide endosulfan. J Appl Microbiol 93:380–389
Tang L, Zeng G, Liu J, Xu Z, Zhang Y, Shen G et al (2008) Catechol
determination in compost bioremediation using a laccase sensor and
artificial neural networks. Anal Bioanal Chem 391:679–685
Taniguchi N (1974) On the basic concept of nanotechnology. Proceeding
of the ICPE, Tokyo
Teresa PenaM, Pensado L, Carmen CasaisM (2007) Sample preparation
of sewage sludge and soil samples for the determination of polycy-
clic aromatic hydrocarbons based on one-pot microwave-assisted
saponification and extraction. Anal Bioanal Chem 387:2559
Thakur I (1996) Use of monoclonal antibodies against dibenzo-p-dioxin
degrading Sphingomonas sp. strain RW1. Lett Appl Microbiol 22:
141–144
Thakur IS (2004) Screening and identification of microbial strains for
removal of color and adsorbable organic halogens in pulp and paper
mill effluent. Process Biochem 39:1693–1699
Tsukihara T, Honda Y, Sakai R, Watanabe T, Watanabe T (2006)
Exclusive overproduction of recombinant versatile peroxidase
MnP2 by genetically modified white rot fungus, Pleurotus
ostreatus. J Biotechnol 126:431–439
Turnbull GA, Ousley M, Walker A, Shaw E, Morgan JAW (2001)
Degradation of substituted Phenylurea herbicides by Arthrobacter
globiformis strain D47 and characterization of a plasmid-associated
hydrolase gene, puhA. Appl Environ Microbiol 67:2270–2275
Turusov V, Rakitsky V, Tomatis L (2002)
Dichlorodiphenyltrichloroethane (DDT): ubiquity, persistence. and
risks Environmental health perspectives 110:125–128
Ubani O, Atagana H, Thantsha MS (2013) Biological degradation of oil
sludge: a review of the current state of development. Afr J
Biotechnol 12:6544–6567
Ururahy A (2002) Oily sludge biotreatment. In: Proceedings of the 9th
Annual International Petroleum Environmental Conference. 22–25
October 2002, Albuquerque
Verma P, Verma P, Sagar R (2013) Variations in N mineralization and
herbaceous species diversity due to sites, seasons, and N treatments
in a seasonally dry tropical environment of India. Forest Ecol Manag
297:15–26
Viesser JA, Sugai-Guerios MH, Malucelli LC, Pincerati MR, Karp SG,
Maranho LT (2020) petroleum-tolerant rhizospheric bacteria: isola-
tion, characterization and bioremediation potential. Sci Rep 10:1–11
Villar P, Callejon M, Alonso E, Jiménez J, Guiraum A (2006) Temporal
evolution of polycyclic aromatic hydrocarbons (PAHs) in sludge
from wastewater treatment plants: Comparison between PAHs and
heavy metals. Chemosphere 64:535–541
Wang H, Zhao H-P, Zhu L (2020) Structures of nitroaromatic compounds
induce Shewanella oneidensis MR-1 to adopt different electron
transport pathways to reduce the contaminants. J Hazard Mater
384:121495
Wang W, Jiang F, Wu F, Li J, Ge R, Li J et al (2019) Biodetection and
bioremediation of copper ions in environmental water samples using
a temperature-controlled, dual-functional Escherichia coli cell. Appl
Microbiol Biotechnol 103:6797–6807
Whelan M, Coulon F, Hince G, Rayner J, McWatters R, Spedding T,
Snape I (2015) Fate and transport of petroleum hydrocarbons in
engineered biopiles in polar regions. Chemosphere 131:232–240
Wlodarczyk-Makula M (2005) The loads of PAHs in wastewater and
sewage sludge of municipal treatment plant. Polycycl Aromat
Compd 25:183–194
Wu SPY, Huang Z, Huang Z, Xu L, Ivan G et al (2015) Isolation and
characterization of a novel native Bacillus thuringiensis strain BRC-
HZM2 capable of degrading chlorpyrifos. J Basic Microbiol 55:
389–397
Xie B, Yang J, Yang Q (2010) Isolation and characterization of an effi-
cient nitro-reducing bacterium, Streptomyces mirabils DUT001,
from soil. World J Microbiol Biotechnol 26:855–862
Xie H, Zhu L, Xu Q, Wang J, Liu W, Jiang J, Meng Y (2011) Isolation
and degradation ability of the DDT-degrading bacterial strain KK.
Environ Earth Sci 62:93–99
Xu P, Xiao E, Zeng L, He F, Wu Z (2019) Enhanced degradation of
pyrene and phenanthrene in sediments through synergistic interac-
tions between microbial fuel cells and submerged macrophyte
Vallisneria spiralis. J Soils Sediments 19:2634–2649
Xun L et al (2010) S-Glutathionyl-(chloro) hydroquinone reductases: a
novel class of glutathione transferases. Biochem J 428:419–427
Yadav AN (2018) Biodiversity and biotechnological applications of host-
specific endophytic fungi for sustainable agriculture and allied sec-
tors. Acta Sci Microbiol 1:01–05
Yadav AN (2021a) Beneficial plant-microbe interactions for agricultural
sustainability. J Appl Biol Biotechnol 9:1–4. https://doi.org/10.
7324/JABB.2021.91ed
Yadav AN (2021b) Soil microbiomes for sustainable agriculture- func-
tional annotation. Springer, Cham
Yadav AN (2021c) Microbial biotechnology for bio-prospecting of mi-
crobial bioactive compounds and secondary metabolites. J Appl
Biol Biotechnol 9:1-6 doi:10.7324/JABB.2021.92ed
24938 Environ Sci Pollut Res (2021) 28:24917–24939

Yadav AN, Kour D, Rana KL, Yadav N, Singh B, Chauhan VS et al
(2019a) Metabolic engineering to synthetic biology of secondary
metabolites production. In: Gupta VK, Pandey A (eds) New and
future developments in microbial biotechnology and bioengineer-
ing. Elsevier, Amsterdam, pp 279–320. https://doi.org/10.1016/
B978-0-444-63504-4.00020-7
Yadav AN, Kumar R, Kumar S, Kumar V, Sugitha T, Singh B et al
(2017) Beneficial microbiomes: biodiversity and potential biotech-
nological applications for sustainable agriculture and human health.
JApplBiolBiotechnol5:45–57
Yadav AN, Rastegari AA, Gupta VK, Yadav N (2020a) Microbial
Biotechnology Approaches to Monuments of Cultural Heritage.
Springer, Singapore
Yadav AN, Rastegari AA, Yadav N (2020b) Microbiomes of Extreme
Environments, Volume 1: Biodiversity and Biotechnological
Applications. CRC, Boca Raton
Yadav AN, Saxena AK (2018) Biodiversity and biotechnological appli-
cations of halophilic microbes for sustainable agriculture. J Appl
Biol Biotechnol 6:48–55
Yadav AN, Singh S, Mishra S, Gupta A (2019) Recent advancement in
white biotechnology through fungi. Volume 3: perspective for sus-
tainable environments. Springer, Cham
Yadav AN, Yadav N, Sachan SG, Saxena AK (2019b) Biodiversity of
psychrotrophic microbes and their biotechnological applications. J
Appl Biol Biotechnol 7:99–108
Yadav N, Yadav AN (2019) Biodegradation of biphenyl compounds by
soil microbiomes. Biodivers Int J 3:37–40
Yan F, Reible D (2015)Electro-bioremediation of contaminated sediment
by electrode enhanced capping. J Environ Manag 155:154–161
Yang L, Y-h Z, B-x Z, Yang C-H, Zhang X (2005) Isolation and charac-
terization of a chlorpyrifos and 3, 5, 6-trichloro-2-pyridinol
degrading bacterium. FEMS Microbiol Lett 251:67–73
Yuan S-Y, Huang I-C, Chang B-V (2010) Biodegradation of dibutyl
phthalate and di-(2-ethylhexyl) phthalate and microbial community
changes in mangrove sediment. J Hazard Mater 184:826–831
Yun Q, Lin Z, Ojekunle ZO, Xin T (2007) Isolation and preliminary
characterization of a 3-chlorobenzoate degrading bacteria. J
Environ Sci 19:332–337
Zhang H, Lin Z, Liu B, Wang G, Weng L, Zhou J et al (2020)
Bioremediation of di-(2-ethylhexyl) phthalate contaminated red soil
by Gordonia terrae RL-JC02: characterization, metabolic pathway
and kinetics. Sci Total Environ 73:1–13
Zhang Z, Gai L, Hou Z, Yang C, Ma C, Wang Z et al (2010)
Characterization and biotechnological potential of petroleum-
degrading bacteria isolated from oil-contaminated soils. Bioresour
Technol 101:8452–8456
Zhu J, Zhao Y, Qiu J (2010) Isolation and application of a chlorpyrifos-
degrading Bacillus licheniformis ZHU-1. Afr J Microbiol Res 4:
2716–2719
Ziglio MF, de Melo Azevedo É, Dweck J (2019) Study of treatments to
remove water from petroleum sludge and evaluation of kinetic pa-
rameters by thermal analysis using isoconversional methods. J
Therm Anal Calorim 138:3603–3618
Publisher’snote Springer Nature remains neutral with regard to jurisdic-
tional claims in published maps and institutional affiliations.
24939Environ Sci Pollut Res (2021) 28:24917–24939