toxics

Review
Recent Strategies for Bioremediation of Emerging Pollutants:
A Review for a Green and Sustainable Environment
Saroj Bala 1,† , Diksha Garg 1,† , Banjagere Veerabhadrappa Thirumalesh 2,† , Minaxi Sharma 3 ,
Kandi Sridhar 4 , Baskaran Stephen Inbaraj 5, * and Manikant Tripathi 6, *

1 Department of Microbiology, Punjab Agriculture University, Ludhiana 141001, India

2 Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and
Technology, Thiruvananthapuram 695019, India
3 Laboratoire de Chimie Verte et Produits Biobasés, Département Agro Bioscience et Chimie, Haute Ecole
Provinciale de Hainaut-Condorcet, 11 Rue de la Sucrerie, 7800 Ath, Belgium
4 UMR1253, Science et Technologie du Lait et de l’œuf, INRAE, L’Institut Agro Rennes-Angers,
65 Rue de Saint Brieuc, F-35042 Rennes, France
5 Department of Food Science, Fu Jen Catholic University, New Taipei City 24205, Taiwan
6 Biotechnology Program, Dr. Rammanohar Lohia Avadh University, Ayodhya 224001, India
* Correspondence: [email protected] (B.S.I.); [email protected] (M.T.)
† These authors contributed equally to this work.

Abstract: Environmental pollution brought on by xenobiotics and other related recalcitrant com-
pounds have recently been identified as a major risk to both human health and the natural envi-
ronment. Due to their toxicity and non-biodegradability, a wide range of pollutants, such as heavy
metals, polychlorinated biphenyls, plastics, and various agrochemicals are present in the environ-
ment. Bioremediation is an effective cleaning technique for removing toxic waste from polluted
environments that is gaining popularity. Various microorganisms, including aerobes and anaerobes,
are used in bioremediation to treat contaminated sites. Microorganisms play a major role in bioreme-
Citation: Bala, S.; Garg, D.; diation, given that it is a process in which hazardous wastes and pollutants are eliminated, degraded,
Thirumalesh, B.V.; Sharma, M.; detoxified, and immobilized. Pollutants are degraded and converted to less toxic forms, which is a
Sridhar, K.; Inbaraj, B.S.; Tripathi, M. primary goal of bioremediation. Ex situ or in situ bioremediation can be used, depending on a variety
Recent Strategies for Bioremediation of of factors, such as cost, pollutant types, and concentration. As a result, a suitable bioremediation
Emerging Pollutants: A Review for a method has been chosen. This review focuses on the most recent developments in bioremediation
Green and Sustainable Environment. techniques, how microorganisms break down different pollutants, and what the future holds for
Toxics 2022, 10, 484. https://
bioremediation in order to reduce the amount of pollution in the world.
doi.org/10.3390/toxics10080484

Academic Editor: Mariusz Cycoń Keywords: bioremediation; microbes; pollutants; environment; sustainable technologies

Received: 17 July 2022

Accepted: 17 August 2022
Published: 19 August 2022
1. Introduction
Publisher’s Note: MDPI stays neutral
Pollution of the environment, freshwater, and topsoil has evolved from global in-
with regard to jurisdictional claims in
dustrialization. Water quality has worsened as a result of human activity, such as due to
published maps and institutional affil-
mining and ultimate removal of toxic metal effluents from steel mills, battery companies,
iations.
and electricity generation, posing major environmental concerns. Effluents like petroleum,
polythenes, and trace metals harm the environment. Heavy metals are pollutants that exist
in nature in the Earth’s crust and are difficult to decompose. They exist as ores in rocks
Copyright: © 2022 by the authors.
and are recovered as minerals. High-level exposures can release heavy metals into the
Licensee MDPI, Basel, Switzerland. environment. Once in the environment, they remain toxic for much longer [1]. Many of
This article is an open access article these pollutants are mutagenic to both humans along with their surroundings. Absorbing
distributed under the terms and heavy metals accumulates in the brain, liver, and kidney. Other effects on animals include
conditions of the Creative Commons cancer, nervous system damage, stunted growth, and even death [2]. Heavy metals in
Attribution (CC BY) license (https:// soils reduce food quality and quantity by inhibiting nutrient absorption, plant growth, and
creativecommons.org/licenses/by/ physiological metabolic processes. Metal-contaminated soils are being remedied using
4.0/). chemical, biological, and physical methods. However, physicochemical methods produce a

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Toxics 2022, 10, 484 2 of 24

lot of waste and pollution, so they are not valued [3]. Bioremediation is a cost-effective and
practical solution for removing environmental contaminants [4]. Plant growth promotion,
insect control, soil conservation, nutrient recycling, and pollutant reduction are all key
functions of soil microorganisms [5]. Bioremediation has come a long way in terms of
efficiency, cost, and social acceptability [6]. Bioremediation research has largely focused on
bacterial processes, which have numerous applications. Archaea are known to play a role in
bioremediation in many applications where bacteria are involved. Many hostile situations
have degraded, requiring bioremediation. Microbes can also assist in the elimination of
pollutants from hyperthermal, acidic, hypersaline, or basic industrial waste [7,8]. Recent
research suggests that using more than one living organism will improve the efficiency
and results, and allow for greater microbial diversity in bioremediation [8,9]. Many re-
searchers employed bioremediation technology for the removal of organic and inorganic
pollutants [10–12]. In a study, bioremediation technology was used for the treatment of
various pollutants, including organophosphate pesticides such as chlorpyrifos, methyl
parathion, and profenofos, by Aspergillus sydowii, and chloramphenicol by endophytic
fungi, respectively [13,14]. In another study, Cymbella sp. has been shown to detoxify
naproxen-polluted water with an efficiency of 97.1% [15].
A bioremediation approach requires the use of microbial enzymes to break down
hydrocarbons into less harmful compounds. The widespread use of genetically-modified
microorganisms that can also help to eliminate petroleum, naphthalene, toluene, benzene,
and other xenobiotic chemicals is now being studied [16]. Several factors, such as tem-
perature of the surrounding environment, aerobic or anaerobic conditions, and nutrient
availability, all influence bioremediation for better outcomes. Emerging environmental pol-
lutants, such as persistent organic compounds, heavy metals, toxins, and air pollutants that
are of synthetic or natural origin, reach ecosystems mainly through anthropogenic activities
and pose adverse threats to lifeforms like plants, animals, and humans [17]. One of the most
economical and environmentally favorable biotechnological innovations is bioremediation.
Waste management mainly relies on bioremediation. It can remove persistent organic
pollutants, which are hard to breakdown and are thought to be heterologous biological
substances. This review addresses the recent approaches and updated information of
bioremediation strategies for eco-friendly detoxification and the effective degradation of
various organic and inorganic contaminants to control environmental pollution.

2. Microorganisms Used in Bioremediation

Biological equilibrium is maintained in part by the contribution of microorganisms
to nutritional chains. Bioremediation is the process of using bacteria, algae, fungi, and
yeast to remove contaminated materials from the environment [18]. In the presence of
hazardous compounds or any waste stream, microbes can grow at temperatures as low as
−196 degrees Fahrenheit and as high as 1200 degrees Fahrenheit. The adaptability and
biological systems of microbes make them an ideal choice for remediation [19]. Carbon is
the most important nutrient for microorganisms. Microbes from a variety of environments
were used to perform bioremediation. Achromobacter, Alcaligenes, Xanthobacter, Arthrobacter,
Pseudomonas, Bacillus, Mycobacterium, Corynebacterium, Flavobacterium, Nitrosomonas, and
other microorganisms [9] are examples of microbes.

2.1. Aerobic
Several microorganisms have the ability to bioremediate different types of environmental
pollutants under aerobic conditions. Bacillus, Pseudomonas, Sphingomonas, Flavobacterium, Nocar-
dia, Rhodococcus, and Mycobacterium are aerobic bacteria that can degrade a variety of complex
organic compounds [20]. Pesticides, alkane hydrocarbons, and polyaromatic compounds have
been shown to be degraded by these microbes. Several of these microorganisms make use
of these contaminants as a source of carbon and energy [21]. In the aerobic bioremediation
process, oxygen is the limiting factor for the growth of microorganisms.
Toxics 2022, 10, 484 3 of 24

2.2. Anaerobic
Amphibious bacteria that degrade and convert pollutants to fewer toxic forms are be-
coming increasingly popular for the bioremediation of polychlorinated biphenyls, chlorine
compounds, and the chlorinated solvents, trichlorethylene and chloroform [22]. Several
bacteria, such as Pseudomonas, Aeromonas, and sulfate-reducing bacteria, have been used in
the bioremediation process under anaerobic conditions. Garg and Tripathi [23] reported
microbial discoloration of azo dyes under different environmental situations. Azo dyes
can decompose anaerobically through reduction reactions using electrons produced by the
oxidation of the organic substrate(s). Due to such controlled dye decolorization events,
microbe electrochemical properties would have a major impact on the effectiveness of
color removal. Dyes were anaerobically decolored for industrial activities to progressively
acquire such time-variant decolorized-metabolites (DMs). However, external augmentation
of DMs gathered under certain conditions was carried out for improved research so that a
precise system can be used [24].

3. Factors Affecting Microbial Bioremediation

Bioremediation is the process of using microorganisms such as bacteria, algae, fungi,
and plants to break down, change, remove, immobilize, or detoxify various physical
and chemical pollutants in the environment. Microorganisms’ enzymatic metabolic path-
ways speed up biochemical reactions that break down pollutants [25,26]. In order for
microorganisms to combat pollutants, they must come into contact with compounds that
provide them with the energy and nutrients they need to multiply. There are several
factors such as physical, chemical, biological, soil-type, carbon and nitrogen source, type
of microorganisms—i.e., single or consortium—and others that affect the process of biore-
mediation [27]. Microbial consortiums often have both multifunctionality and resistance
because different species work together to use all substrates in the best way possible,
thereby increasing the bioremediation efficiency compared to single microorganism [28]. In
a study, carbon is one of the most important nutrients that help in situ bioremediation by
increasing the metabolic activity of natural microbial communities and speeding up the
bioremediation process to break down existing pollutants. Bioremediation may use organic
carbon more than any other additive. In an anaerobic environment, many microorganisms
can ferment organic carbon and make hydrogen gas [29]. In a study, bioremediation was
found to be significantly affected by soil types, and the removal efficiency of pollutants var-
ied in sandy soil and clay soil, respectively [30]. For bioremediation to be a success, it must
be able to access existing microorganisms as well as the environment’s physicochemical
characteristics (Table 1). The microbial population responsible for degrading pollutants,
the accessibility of contaminants, and the following factors are taken into consideration.

Table 1. Critical factors for microbial bioremediation.

Factors Remarks References

Soil microorganisms compete for carbon sources, or bacteriophages
and protozoa prey on each other, all of which can affect organic
compound degradation. Derivatization rates are influenced by
contaminants and catalyst levels. Expressed enzymes can speed up or
Biological factors [31,32]
slow contaminant degradation. Enzymes must also be involved in
contaminant metabolism to have an affinity for the contaminant and
availability. The major biological factors: interaction (competition,
predation, and succession), population size, and composition.
Biodegradation rates can be improved by using organisms that don’t
require oxygen. Anaerobic decomposition occurs as most living
Oxygen [33]
organisms need oxygen to survive. In most cases, hydrocarbon
metabolism can be boosted by the addition of oxygen.
Toxics 2022, 10, 484 4 of 24

Table 1. Cont.

Factors Remarks References

Microorganisms require a sufficient amount of water to achieve their
Moisture content growth goals. When the soil is too wet, the biodegradation agents [34]
don’t work as well.
Nutrients can influence microbial growth and reproduction, as well
as biodegradation rate and effectiveness. Optimizing the bacterial
C:N:P ratio can improve biodegradation efficiency, especially when
essential nutrients like N and P are supplied. Carbon, phosphorous,
and nitrogen are just a few of the nutrients microorganisms need to
Nutrients survive. In low concentrations, hydrocarbon degradation is also [35,36]
limited. Adding nutrients to cold environments can increase
microorganisms’ metabolic activity and thus the biodegradation rate.
Aquatic biodegradation is limited by nutrient availability. Oil-eating
microbes require nutrients to thrive. These essential nutrients are
found in small amounts in nature.
The most important physical factor influencing microorganism
survival and hydrocarbon composition is temperature. In cold
climates like the Arctic, natural oil degradation is slow, putting more
pressure on microbes to clean up spilled oil. Here, the sub-zero water
freezes the microbial transport channels, rendering them unable to
perform their metabolic functions.Temperature affects the metabolic
Temperature [37,38]
turnover of enzymes involved in degradation. Also, each
compound’s degradation requires a specific temperature.
Temperature affects microbial physiological properties and thus
speeds up or slows down bioremediation. Increased microbial
activity occurs at higher temperatures. It started to drop suddenly as
the temperature increased or decreased, and theneventually stopped.
A compound’s acidity, alkalinity, and basicity affect microbial
metabolism and the removal process. Microbial growth can be
pH [39]
predicted by the soil’s pH. Even minor pH shifts have a significant
impact on metabolic processes.
Before proposing a bioremediation remedy, it is necessary to conduct
adequate remedial investigation work to characterize the extent of
Sitecharacterization and the contamination. Site selection procedures include determining the
[40]
selection horizontal and vertical extent of contamination, defining parameters
and sampling locations, and describing sampling and analysis
methods.
Metals are essential for bacteria and fungi, but excessive amounts
Metal ions inhibit cell metabolism. Degradation rates are influenced by metal [41]
compounds on both a direct and indirect basis.
High concentrations of some toxic compounds can harm
Microorganisms microorganisms and slow decontamination process. Toxicity varies [42]
with the toxicant, concentration, and microorganisms exposed.

4. Principle of Bioremediation
When organic wastes are biologically degraded under controlled conditions, “biore-
mediation” is the term used to describe this process. Using bioremediation, harmful
substances can be degraded or detoxified by providing the organisms with the nutrients
and other chemicals they need to function optimally. Enzymes play a critical role in every
stage of the metabolic process [24,43]. It is part of the family of oxidoreductases, lyases,
transferases, and hydrolases. Non-specific and specific substrate affinities allow many
enzymes to degrade a wide range of substrates. There must be enzymatic action on the
pollutants in order for bioremediation to be successful. In order to speed up microbial
growth and degradation, environmental parameters must often be manipulated during
Toxics 2022, 10, 484 5 of 24

bioremediation [38,43]. This is because bioremediation only works when the environment
is right for microbes to grow and move around.
Living organisms and fertilizers can aid in the process of bioremediation, which
occurs naturally and is encouraged. Biodegradation is a key component of bioremediation
technology. It’s the process of converting harmful organic pollutants like carbon dioxide
and water into non-toxic or naturally-occurring inorganic compounds that are safe for use
by humans, plants, animals, and aquatic life [44].

5. Types of Bioremediations
Bioremediation can be used in a plethora of ways, and some of the most commonly
used methods are presented here (Figure 1).

Figure 1. Diverse bioremediation techniques.

5.1. Biopile
In bioremediation, aeration and nutrient supplementation are used to enhance micro-
bial metabolic activities in the piled-up polluted soil above ground. Aeration, nutrients,
irrigation, leachate collection, and treatment bed systems are all included in this procedure.
When it comes to ex situ biodegradation, this method is becoming increasingly popular
because of its cost-effectiveness and useful features, such as pH and nutrient control. Us-
ing the biopile to clean up polluted cold environments and treat low-molecular-weight
volatile pollutants is an option [15,45]. The biopile’s adaptability allows for a reduction in
remediation time by increasing microbial activity and contaminant availability while also
increasing biodegradation rate. When warm air is introduced into the biopile system to
provide air and heat simultaneously, bioremediation is improved. The biopile’s remediation
process has been helped by the addition of bulking agents like straw, sawdust, or wood
chips. To replenish the air supply to polluted piled soil in biopiles, ex situ bioremediation
techniques such as land farming, biosparging, and bioventing can be applied [46]. How-
ever, these techniques are expensive to implement and require a power supply at remote
locations. Bioremediation may be slowed down by extreme air temperatures that dry soil
and make it more likely to be vaporized than to be broken down by living organisms [47].
Bio-available organic carbon (BOC) plays an important role in bioremediation through the
biopile method. Petroleum contaminated soil has been bioremediated using mesophillic
conditions (30 ◦ C–40 ◦ C) and a low aeration rate for the removal of total petroleum hydro-
carbon (TPH) using alpha, beta, and gamma proteobacteria [48]. Biopile systems have also
Toxics 2022, 10, 484 6 of 24

been utilized for treating the diesel contaminated soil of the sub-Antarctic region. A total
of 93% of the total petroleum hydrocarbon (TPH) was removed using the biopile system
within one year [49].

5.2. Windrows
Windrows boosts bioremediation by enhancing the biodegradation processes of native
and transitory hydrocarbon plastic found in the contaminated soils when spinning the
heaped contaminated soils. The aeration, mineralization, and biotransformation of toxic
soil can be performed through acclimation, biological treatment, and mineralization [50],
can speed up bioremediation. The biopile approach can remove more hydrocarbons from
soil than windrow treatment [15,51], which was more efficient in terms of hydrocarbon
removal. The periodic rotation connected with windrow remediation is not a better selection
approach for the bioremediation of soil affected by harmful volatile chemicals. Windrow
treatment is a source of greenhouse gas (CH4 ) due to the anaerobic system generated
inside the heaped contaminated soil [52]. The windrow method of has been applied for
the bioremediation of the Gurugram–Faridabad dumpsite in Bandhwari, India by forming
terraces and windrows and utilizing bio-culture, and the results showed a decrease in the
garbage [53].

5.3. Land Farming

Land farming is the most significant and simple bioremediation method because of its
low operating costs and lack of specialized equipment [54]. Ex situ bioremediation is the
most common method, but it can also occur with in situ bioremediation. The reason for this
is the location of the treatment. It is common practice in land farming to remove and till
polluted soils on a regular basis, and the location of treatment dictates the type of bioreme-
diation. On-site treatment is classified as in situ, whereas ex situ bioremediation approaches
are used for the treatment of the contaminated soil [55]. Extracted contaminated soils are
usually placed on a permanent layer of substrate well above Earth’s surface to permit
native microorganisms to aerobically degrade contaminants [56]. Land bioremediation of
polluted soil using land farming bioremediation technology is a reasonably simple process
that takes little capital, has little ecological footprint, and uses very little energy [57].

5.4. Bioreactor
Following a series of biological reactions, bioreactors transform raw materials into
specific products. Bioremediation thrives in a bioreactor, which provides the ideal con-
ditions for growth [58]. The remediation samples are placed in a bioreactor. There are a
number of advantages to using a bioreactor to treat contaminated soil as opposed to ex
situ bioremediation methods. An efficient bioremediation process based on bioreactors
that can precisely regulate pH, agitation, temperature, aeration, substrate concentration,
and inoculum concentration significantly reduce the time required for bioremediation [59].
Biological reactions can take place when the bioreactor can be controlled and manipulated.
Given their adaptability, bioreactor designs are able to maximize microbial degradation
while abiotic losses are kept to a minimum.

In Situ Bioremediation Techniques

These methods entail cleaning up polluted substances right where they were cre-
ated. It does not necessitate any digging or disturbance of the surrounding soil. These
techniques ought to be more cost-effective in comparison to the ex situ bioremediation
techniques. Bioventing, phytoremediation, and biosparging are examples of in situ biore-
mediation techniques that can be improved, while intrinsic bioremediation and natural
attenuation are examples of in situ bioremediation techniques that cannot be improved [60].
In situ bioremediation approaches have effectively treated chlorine, paints, toxic metals,
and hydrocarbon-contaminated areas [61]. The practice of in situ bioremediation can be
categorized into two distinct types: intrinsic and engineered.
Toxics 2022, 10, 484 7 of 24

(a) Intrinsic in situ bioremediation:

Natural reduction is another term for in situ bioremediation. Intrinsic bioremediation
utilizes polluted sites in a non-invasive manner (human intervention) [62]. The goal of
this procedure is to stimulate an already existing microbial population. The biodegrada-
tion of polluting constituents, including those that are recalcitrant, is based on aerobic
and anaerobic processes in microorganisms. It costs less because there isn’t a lot of force
behind this technique [63]. Intrinsic in situ bioremediation can be performed using anaer-
obic reductive dechlorination, aerobic treatment, amendment delivery, biosparging, and
bioslurping [64]. Using a stimulation–optimization approach that is powered by machine
learning and particle swarm optimization (ELM–PSO) techniques, in situ bioremediation
has been used as a method for the biological treatment of clogged groundwater [65]. This
technique was implemented through the use of in situ bioremediation. This results in
cheaper technology for the pumping system and requires less capital for the whole process.
The concentration of contaminants was reduced from 40 ppm to 5 ppm (within permissible
range) in 3 years using in situ bioremediation. In situ remediation has also been explored
for the decontamination of Cr (VI) found in shallow unsaturated soil. Microorganisms
possess the capability to survive under high concentrations of Cr (VI) in the soil and their
sub-cellular machinery was utilized to interact with heavy metals. Microbial inoculants
can be utilized for the in situ treatment of heavy metals [66]. Cr (VI) interacts with Fe (II)
ions also through the redox reactions, and the release of iron in soluble forms promotes the
reductive reactions [67].
(b) Engineered in-situ bioremediation
In the second method, a specific microorganism is brought into the area of contamina-
tion to clean it up. In situ bioremediation is a technique that employs microorganisms that
have undergone genetic engineering in order to hasten the decomposition process. This
is accomplished by enhancing the physicochemical conditions that foster the growth of
microorganisms [68].

5.5. Bioventing
Bioventing is a technique that uses controlled airflow to increase the activity of in-
digenous microbes for bioremediation by delivering oxygen to the unsaturated zone. The
bioremediation process is aided by the addition of nutrients and moisture during the
bioventing process. This will lead to the microbial transformation of pollutants into harm-
less substances. Other in situ bioremediation methods have flocked to this one in recent
years [69]. Bioventing is a technique that helps in stimulating the indigenous microflora
through ample amounts of aeration to enhance the biodegradation ability of the various
microbes and promote decontamination of the heavy metal pollutants by precipitation [70].

5.6. Bioslurping
A direct oxygen supply and stimulation of contaminant biodegradation are used
in conjunction with vacuum-assisted pumping, bioventing, and soil vapour extraction
(SVE) in order to reach soil and groundwater levels for restoration [71]. This approach can
be used to recover unsaturated and saturated zones as well as light non-aqueous phase
liquids (LNAPLs). This technology can be used to remediate soils contaminated with
flammable and moderately-flammable organic substances. Liquid is drawn from the free
product layer by means of a “slurp” that spreads into the layer. LNAPLs are lifted to the
surface by the pumping machine, where they are separated from the surrounding air and
water [72]. To reduce microbial activity, soil moisture is used in this technique to reduce air
permeability and oxygen transfer rate. Given that it uses less groundwater, this method
saves money on storage, disposal, and treatment, even though it’s not ideal for remediation
in low-permeable soils. Bioslurping requires 25 feet of digging below the ground surface
and then the contaminants floating on the water can be removed. It combines both the
approaches of bioventing, which utilize aerobic bioremediation of contaminated soil in
situ. Free product is recovered by a vacuum-enhanced system that utilizes LNAPLs from
Toxics 2022, 10, 484 8 of 24

the capillary fringe [73]. Free product is “slurped” up the bioslurping tube into a trap or
oil–water separator for further treatment after the bioslurping tube is vacuumed. When the
LNAPL is removed, the height of the LNAPL drops, which encourages the flow of LNAPL
from distant locations into the bioslurping well. The bioslurping tube starts to remove
vapours from the unsaturated zone when the fluid level in the bioslurping well decreases
as a result of the vacuum extraction of LNAPL. This vapour extraction encourages soil gas
movement, which in turn boosts aerobic biodegradation and aeration [74].

5.7. Biosparging
Air is introduced into the soil’s core, just like bioventing, to encourage microbiolog-
ical activity, which in turn removes pollutants from polluted sites. As an alternative to
conventional biodegradation methods, bioventing involves injecting air into a saturated
zone in order to encourage the movement of flammable organic chemicals upward to an
unsaturated zone nearby [75]. The success of biosparging is dependent on soil porosity
and contaminant biodegradability. When it comes to bioventing and soil vapour extrac-
tion (SVE), in situ air sparging (IAS) uses high air-flow rates to volatilize contaminants,
while biosparging encourages microbial degradation [76]. It is common practice to use
biosparging to remove diesel and kerosene from water supplies. In order to hasten the
biodegradation processes, oxygen is supplied into microorganisms during enhanced biore-
mediation [77]. The removal of organic pollutants (BTEX) can be accomplished using a
variety of technologies, including adsorption, microbial degradation, biosparging, PRBs,
and the use of modified or synthesized zeolites. However, there aren’t many investigations
on readily available, inexpensive materials like natural zeolite for BTEX adsorption [78].

5.8. Phytoremediation
Contaminated soils can be cleaned up using phytoremediation. In contaminated areas,
this method uses plant interactions at the physical, biological, chemical, biochemical, and
microbiological levels to reduce pollutant toxicity. Depending on the quantity and form of
the pollutant, phytoremediation employs a variety of processes [79]. Extraction, sequestra-
tion, and transformation are common methods for removing pollutants like heavy metals.
When using plants like willow or alfalfa, the decay, immobilization, rhizoremediation, and
evaporation of organic contaminants such as oils and chloro-compounds is feasible [80].
Tap root system or fibrous root system, penetration, toxicity levels, adaptability to the harsh
environmental conditions of the contaminants, plant annual growth, supervision, and,
notably, the time needed to reach standard of cleanliness are all important factors in plants
that serve as phytoremediators. The plant must also be disease and insect resistant [81]. An
important part of phytoremediation is removing pollutants from the roots and shoots. The
movement of water and nutrients is also dependent on transpiration and partitioning [82].
When it comes to contaminants and plant nature, it is possible to alter this process. Phy-
toremediation can be accomplished with the help of the majority of the plants present at
a polluted site. In polluted environments, native plants can be bioaugmented by natural
or anthropogenic plants, or a combination of both. Phytomining, the process of extracting
precious metals from polluted sites with plants, is one of them [83].
Numerous plants (over 300) are better candidates for phytoremediation because they
ideally absorb Cu, Zn, and Ni. Phytostabilization, sometimes referred to as in situ in-
activation or immobilisation of heavy metals, reduces their bioavailability and prevents
their off-site transfer. At the plant roots, it absorbs metals and restores them. Several
species, notably Acanthus ilicifolius and Virola surinamensis, are capable of Cd photostability.
Cinnamomum camphora, Osmanthus fragrans, Euonymus japonicus, Ligustrum vicaryi, and
Loropetalum chinense are five decorative plants chosen for their capacity to phytostabilize
Cd [84]. Water from various places that has been contaminated with metal can be success-
fully treated using bacterially-aided phytoremediation. The phytoremediation method
of metal reduction in wastewater utilising plants can be used by coalitions of growth-
Toxics 2022, 10, 484 9 of 24

promoting rhizobacteria, degrading bacteria, as well as endophytic bacteria [85]. There are
a few limitations to bioremediation techniques, as presented in Table 2.

Table 2. Limitations of various bioremediation techniques.

Methods Limitation Reference

The extent of weathering can change the chemical make-up by making the
Biopile materials more hydrophobic, which limits the potential of the biopiling [86]
method for biodegradation.
The major limitation in studying windrows in situ is probably knowing
where and when they will emerge. Although it is possible to forecast some
Windrows sub-mesoscale convergences, it is still difficult to predict where and when [87]
litter windrows would form because of the additional uncertainty brought
on by the dependency on litter loading.
This method has the drawback that the objectives specified in the
constraint set must be strictly upheld; if they are not, the issue will appear
to be insurmountable. Fresh organic waste can be troublesome since it can
Land Farming [88]
occasionally lead to anoxic conditions, which are hazardous to plant
development. To preserve the quality of pre-existing soils, it is advisable to
refrain from adding more organic material over years.
The primary limitation to employing membrane bioreactors (MBR) at such
high concentrations of mixed liquid suspended solids (MLSS) appears to
be very low to zero oxygen transfer efficiency reported when using
traditional diffused aeration systems (such as fine and coarse bubble
Bioreactor [89]
diffusers). This suggests that a deeper understanding is required of the
constraints imposed by traditional bubble diffusers (measured in terms of
the alpha factor) under that specific combination of operational parameters
(high MLSS).
Intrinsic in situ The site has to have very permeable soil for in situ bioremediation, which is
[90]
bioremediation the main limitation of in situ bioremediation.
This technique’s disadvantage is that it only works at the deepest levels of
Bioventing [91]
the contaminated soil ecosystem.
Phytoremediation, such as phytoextraction and rhizodegradation, is used
to remediate the polluted soil in the superficial layers of the soil. This
Phytoremediation [85]
approach could be time-consuming and may not be able to eliminate all
the contaminants.

6. Bioremediation of Various Pollutants

6.1. Bioremediation for Organic Pollutants
Organic compounds (OCs) such as biocides and flame retardants have been widely
used and are now considered a threat to nearly all forms of life on the planet because
of the widespread and massive use of these chemicals in the environment. Most OCs,
such as polychlorinated biphenyls (PCBs), polybrominated biphenyl ethers (PBEs), and
polycyclic aromatic hydrocarbons (PAHs), can be degraded in the environment by microbes.
Biodegradation is the process by which microbes break down organic compounds into less
toxic or entirely non-toxic residues [91]. In order to obtain organic carbons and energy,
the microbes consume the organic substrate. Isolated from other microbes, an individual
microbial species usually does not degrade any organic substrate [92] and does well in a
community. As a result of community microbe interactions, resistance, chemical-degrading
ability, and tolerance are all conferred by the exchange of genetic information among
microbial species. Many OC-degrading microorganisms are misidentified due to a lack of
internationally agreed-upon methods and protocols for microbial identification [93]. This
underlines the significance of studies into microbial consortiums using metagenomics tools
and conventional genetic engineering protocols. Bacteria and other microorganisms have
the ability to degrade a wide range of organic compounds, depending on the chromosomal
Toxics 2022, 10, 484 10 of 24

genes, as well as the extracellular enzymatic activity (in the case of bacteria) (fungal
degradation process). The varying environmental conditions that affect the microbe growth
pattern further complicate these processes [94].
A successfully bioengineered microbe requires the identification of the relevant species
and strains for each substrate. A viable alternative to the recombinant degradation of
resistant organic compounds is biodegradation by microbes using readily-available organic
carbon and energy sources in the surrounding environment. Microbes use the fluctuation
in chemical gradients in their environment to determine the most favourable conditions for
growth. This allows them to thrive in an optimal environment [95]. Microbial consortia and
microbial fuel cells (MFCs and bioreactors) are two new developments in microbiological
bioremediation that are being used to degrade recalcitrant organic compounds. Toxic
organics can be remedied more effectively using fungi rather than bacteria because the
latter cannot grow at high concentrations of toxic organics [96]. For example, the enzymes,
laccase (LAC), lignin peroxidase (Lip), and manganese decarboxylase (MDA), are active
in the metabolism of lignocellulosic compounds by the white rot fungus Phanerochaete
chrysosporium [97].

6.2. Bioremediation for Inorganic Pollutants

Toxic heavy metals and their compounds resulting from mining, power plants, met-
allurgy, and chemical manufacturing processes are among the most common inorganic
contaminants [98]. One of the main concerns of environmentalists is toxic elemental pol-
lution because the disposal of toxic metals to soils and waters on or below the surface
causes unacceptable health risks [99]. Microbes cannot degrade metal ions; it is essential
to know that they are only capable of changing the oxidation states of the metals to sta-
bilize them [100]. They can metabolize and detoxify metals like any other nutrient in the
cells. Several microorganisms have been reported for the bioremediation of organic and
inorganic pollutants (Table 3). Microbes that release chelating agents and acids, as well as
those that alter physicochemical properties such as redox potential in their environment
can cause significant changes in the environment by increasing the bioavailability of metal
ions [101]. Physical adsorption, biosorption, and ion complexation are the first steps in the
interaction between metals and microbial cells [102]. Enzymes for oxidation, methylation,
reduction, precipitation, and dealkylation are involved in the biochemical transformation of
metal ions by microorganisms. The adaptability of microbes to heavy metals, such as iron,
zinc, chrome, magnesium, mercury, and barium in textile waste, was demonstrated in the
multidrug-resistant Pseudomonas aeruginosa T-3 isolate from tannery effluent [67,83]. This
shows that microbes can adapt to changing environmental conditions. A plasmid-encoded
copper and cadmium metal resistance gene in the bacteria, Pseudomonas putida PhCN,
has also been discovered [103]. Plasmid-encoded biochemical information and genetic
engineering techniques were used to create recombinant Escherichia coli that expresses
the metallothionein gene (Neurospora crasa) for Cd uptake, resulting in significantly faster
Cd uptake than the donor microbe [104]. A poly-histidyl peptide was introduced into
Staphylococcus xylosus and Staphylococcus carnosus that encoded genes that allowed these
microbes to bind nickel [105].
Toxics 2022, 10, 484 11 of 24

Table 3. Potentially hazardous organic and inorganic pollutants and their degrading microbes
(bacteria, fungi, and algae).

Substrate Compound Microorganisms References

Chlorobenzenes P. putida (GJ31) [106]
N, N-dimethyl-
Klebsiella pneumonia (RS-13) [107]
pphenylenediamine
Polycyclic aromatic
Burkholderia sp., Myceliophthorathermophila [108]
hydrocarbons
Remazol Black B Kluyveromyces marxianus (IMB3) [109]
Sulfonate benzene A. radiobacter (S2) [110]
4,4 dibromodiphenyl ether Phanerochaete chrysosporium [111]
Acinetobacter sp., Microbacterium sp., Pseudomonas sp.
Aromatic hydrocarbons [112]
and Ralstonia sp.
Alcaligenes odorans, Corynebacterium propinquum, B.
Phenol [113]
subtilis, and P. aeruginosa
Organic substrate
Toluene and its derivatives P. putida (F1), Penicillium chrysogenum [114]
Methyl parathion and Acinetobactor sp., Pseudomonas sp., Enterobacter sp. and
[115]
chlorpyrifos Photobacterium sp.
Endosulfan Bacillus, Staphylococcus [116]
Exiguobacterium indicum, B. cereus, E. aurantiacums and
Azo dyes effluents [117]
A. baumanii
B. firmus, Staphylococcus aureus, B. macerans, and K.
Vat dyes [118]
oxytoca
Oil-based based paints B. subtilis strain NAP1, NAP2, NAP4 [119]
Aspergillus niger, Candida krusei, C. glabrata, and
Crude oil [120]
Saccharomyces cerevisiae
P. cepacia, B. coagulans, B. cereus, B. cereus A and
Diesel oil [121]
Serratia ficaria
Alcaligenes odorans, Corynebacterium propinquum, P.
Oils [122]
aeruginosa and Fusarium sp.
Heavy metals, mercury nickel
Saccharomyces cerevisiae and, Cunninghamella elegans [123]
and lead
Cr6+ Pseudomonas putida [124]
Cobalt, chromium, copper,
Lysinibacillus sphaericus CBAM5 [125]
and lead
A. versicolor, Paecilomyces sp., A. fumigatus,
Cadmium [126]
Paecilomyces sp., Terichoderma sp. and Cladosporium sp.
Uranium, copper, nickel,
P. aeruginosa, Aeromonas sp. [127]
Inorganic substrate chromium
Lead, chromium, and
Aerococcus sp., Rhodopseudomonas palustris [128]
cadmium
Cyclotella cryptica, Chlamydomonas reinhardtii,
Hg2+ [129]
Pseudochlorococcum typicum, Spirogyra hyaline
Cr2 O7 22 Chlorella spp. Spirulina sp. (HD-104) [130]
Cr51 Spirulina sp., Ulothrix tenuissima and C. reinhardtii [131]
Oscillatoria laete-virens, Arthrospira platensis,
Pb21 [132]
Pseudochlorococcum typicum and Spirogyra insignis
Toxics 2022, 10, 484 12 of 24

7. Recent Advancement and Challenges in Bioremediation

7.1. Bioinformatics Approaches in Bioremediation
When it comes to waste management, bioremediation is a useful technique that can
be used to remove waste from contaminated areas and sites. It is particularly concerned
with the utilization of organisms to consume or neutralize pollutants [20]. Using data from
various biological databases, such as databases of chemical structure and composition,
RNA/protein expression, organic compounds, catalytic enzymes, microbial degradation
pathways, and comparative genomics to interpret the underlying degradation mechanism
carried out by a particular organism for a specific pollutant is the goal of bioremedia-
tion [133]. A variety of bioinformatics tools are used to interpret all of these sources in order
to study bioremediation in order to develop more effective environmental cleaning technol-
ogy. There has been a scarcity of data on the factors that control the growth and metabolism
of microbes with bioremediation potential, which has resulted in a limited number of
bioremediation applications [134]. These microorganisms with bioremediation capabilities
have been profiled and their mineralization pathways and mechanisms have been mapped
out using bioinformatics [135]. The use of proteomic approaches such as two-dimensional
polyacrylamide gel electrophoresis, microarrays, and mass spectrometry is also critical in
the investigation of bioremediation methods and technologies. It significantly improves
the structural characterization of microbial proteins that have contaminant-degradable
properties, according to the researchers [135]. The structural characterization of microbial
proteins capable of degrading contaminants has greatly improved. Research in this field
crosses the boundaries between computer science and biology. For example, computers are
used to store, manipulate, and retrieve information linked to the DNA, RNA, and proteins
of the genome [133,135].

7.1.1. Bioremediation Tools Based on Omics

Bioremediation studies can benefit from the use of genomics, transcriptomics, metabolomics,
and proteomics. Given its ability to correlate DNA sequences with the abundance of metabo-
lites, proteins, and mRNA, this technology aids in the in situ bioremediation process’s evalua-
tion [136,137].

7.1.2. Genomics
There is a new field in genomics for the study of bioremediation microbes. This
strategy is based on microbes’ ability to fully analyze their genetic information within the
cell. Bioremediation uses a wide variety of microorganisms [138]. To better understand the
biodegradation process, genomic tools such as PCR, analysis of isotope distribution, DNA
hybridization, molecular connectivity, metabolic footprinting, and metabolic engineering
are used. For genotypic fingerprinting, a variety of PCR-based techniques are available,
including amplified fragment length polymorphisms (AFLP), amplified ribosomal DNA
restriction analysis (ARDRA), automated ribosomal intergenic spacer analysis (ARISA),
terminal-restriction fragment length polymorphism (T-RFLP), randomly amplified poly-
morphic DNA analysis (RAPD), single strand conformation polymorphism (SSCP), and
length heterogeneity [139]. When it comes to studying soil microbial communities, RAPD
can be utilized for assessing inherently related bacterial species, constructing functional
structural models, and generating genetic fingerprints [140]. In microbial communities,
LH-PCR may be used to detect natural length variations of various SSU rRNA genes.
Multiple taxonomic groups of microbes can be profiled simultaneously using T-RFLP [141].
Research into how soil microbes interact with natural factors can also make use of a combi-
nation of molecular tools, such as genetic fingerprinting, microradiography, FISH, stable
isotope probing, and quantitative PCR. A PCR-based quantitative analysis of soil microbial
communities can be used to determine the abundance and appearance of taxonomic and
operational gene markers in the soil. Techniques for analysing a person’s DNA use ampli-
fied PCR products as a starting point for the direct analysis of specific molecular biomarker
genes [142]. In order to better understand the relationship between diverse microbial com-
Toxics 2022, 10, 484 13 of 24

munities, cluster-assisted analysis, which compares fingerprints from different samples,

could be used.

7.1.3. Transcriptomics and Metatranscriptomics

The transcriptome is a crucial link between cellular phenotype, interactome, genome,
and proteome because it represents the set of genes that are being transcribed at a specific
time and condition. The ability to control gene expression is critical to adapting to changes
in the environment and thus ensuring survival. Transcriptomics provides a comprehensive
view of this process across the entire human genome. In transcriptomics, DNA microarray
analysis is a powerful tool for determining mRNA expression levels [143]. To perform
a transcriptomic analysis, one must first isolate and enrich the total mRNA, then syn-
thesize cDNA, and then sequence the cDNA transcriptome. Using a DNA microarray
as a transcriptomics tool, almost every gene in an organism’s mRNA expression can be
examined and studied [144]. The study of transcriptional mRNA profiles, also known
as transcriptomics or metatranscriptomics, is critical for gaining functional insights into
the activities of environmental microbial communities [145]. Syntrophism between mi-
crobes and complementary metabolic pathways can be discovered using metagenomics
and genome binning as well as metatranscriptomics during the entire biodegradation
process [146]. Metatranscriptomics is a way to look at gene expression that can be used by
researchers [147].

7.1.4. Proteomics and Metabolomics

In contrast to metabolomics, which focuses on the total metabolites produced by an
organism in a given period of time or environment, proteomics focuses on the total proteins
expressed in a cell at a given location and time [148]. The analysis of protein abundance
and changes in composition, as well as the identification of key microbe-related proteins,
has been accomplished using proteomics [149]. In comparison to genomics, the functional
analysis of microbial communities is more useful and holds more promise. There are two
primary ways in which metabolomics studies can be used to analyze biological systems. It
is not necessary to have any prior knowledge of the metabolic pathways of the biological
system in order to conduct the first type of study. By employing this strategy, there are
numerous metabolites in the sample that can be identified and recovered, which generates
enormous amounts of data that can be used to establish the interconnectedness of various
samples in metabolic pathways. Another option is to conduct a targeted study to iden-
tify specific metabolic pathways or metabolites based on prior research [150]. Metabolite
profiling, foot printing, and target analysis are just some of the many tools in the tool-
box of microbial metabolomics that can be used to identify and quantify the myriad of
cellular byproducts present in living organisms [151]. Data from both the proteome and
metabolome will be useful for cell-free bioremediation.

7.2. Bioremediation Using Nanotechnological Methods

A nanometer is the smallest unit of measurement used in nanotechnology. Many
toxic substances can be removed with their help because of their unique abilities against
various recalcitrant contaminants. Technology such as water treatment has been given a
new perspective by nanotechnology. Techniques that are good for the environment can
now be categorized as nanofiltration [151].

7.2.1. Microbe and Nanotechnology

When using effective microbes (EM) technology, wastewater can be treated with
effective microbes, and the water can then be used for irrigation [152]. For water purifica-
tion, nanotechnology and EM technology can be helpful. Innumerable and all-pervasive
environmental issues arise from the presence of recalcitrant organic pollutants like poly-
cyclic aromatic hydrocarbons (PAHs) with multiple benzene rings. Polycyclic aromatic
hydrocarbons (PAHs) are mutagenic and non-biodegradable [153]. In a study, Ramos
Toxics 2022, 10, 484 14 of 24

et al. [154] synthesized silver nanoparticles using whole cells of the fungi Trichoderma spp.
for its application.

7.2.2. Engineered Polymeric Nanoparticles for Hydrophobic Contaminant Bioremediation

Soil sorption of organic pollutants, such as petroleum hydrocarbons and PAHs, re-
duces their solubility and mobility, which in turn reduces their environmental impact.
The phenanthrene solubility and phenanthrene release from contaminated aquifer mate-
rial are both improved by polymeric nano-network particles [155]. Precursor chains of
poly-(ethylene) glycol-modified urethane acrylate (PMUA) are used to create polymeric
nanoparticles. PMUA nanoparticles are designed to maintain their properties in the pres-
ence of a diverse range of bacterial populations [156].

7.3. Genetic and Metabolic Engineering

“Gene editing” refers to scientific technical developments that enable rational genetically-
created fragments at genome level to provide exact addition, deletion, or substitution of pieces
of DNA molecules. Transcription activators are utilized in a variety of gene editing methods,
including TALENs, ZFNs, and CRISPRs, which are widely used in research. CRISPR-Cas
has been dubbed the most efficient and straightforward gene editing tool [157]. A DNA-
binding element in TALEN is complementary to the sequence of the host DNA. When TALEN
attaches to DNA and exposes sticky ends for stabilization, it creates double-stranded breaks
(DSBs). ZFNs also have a DNA-binding domain made up of 30 amino acids. At the target
location of the host DNA, the Fok1 cleavage domain causes DSBs. A novel perspective
on composite endonuclease comprising TALENs and ZFN nucleases was required to solve
molecular problems [158,159]. Two of the CRISPR-Cas system’s unique properties are sequence
similarity complementarity and simultaneous gene editing [160,161]. The bacteria, Streptococcus
pyogenes, provides this unique ability as a sort of virus resistance. In the CRISPR-Cas system,
guide RNA connects crisper-derived RNA (crRNA) and trans-acting antisense RNA (trcRNA).
The Cas9 enzyme is able to carry out the requisite DSB when gRNA recognizes the target
DNA sequence. These gene editing tools’ knock-in and knock-out effects are being analyzed
for usage in bioremediation investigations [161]. In model organisms like Pseudomonas and
Escherichia coli, the CRISPR-Cas system has been widely accepted by researchers [138]. In
non-model species (such as Rhodococcus ruber TH, Achromobacter sp. HZ01, and Comamonas
testosteroni), the area of bioremediation is also exploring new insights into CRISPR toolkits and
the synthesis of gRNA for the production of remediation-specific genes [162].
Pollutant-tolerant bacteria are the greatest choices for genetic manipulation and bio-
chemical pathways since they are accustomed to tolerating and storing a variety of toxic,
refractory, and non-degradable xenobiotic compounds under harsh circumstances. Fur-
thermore, recognizing biochemical functions is critical for analyzing microbiological biore-
mediation, such as the bioremediation of harmful pollutants through the production of
haloalkane dehalogenases and the disposal of pyrethrins from land through the anaerobic
decomposition pathway of fenpropathrin studied in Bacillus sp. DG-02 [163]. The biore-
mediation process can be improved by metabolic engineering, which alters the existing
pathway. The likelihood of obtaining recombinant enzymes increases significantly when
using a genetic approach. Some extracellular enzymes have been found to play a role
in enzymatic bioremediation, according to some studies. PAHs are degraded by LiPs
((lignin peroxidase) from P. chrysosporium that encode hemoproteins [164]. Even though
contaminants can be consumed by microbes as substrates or intermediates in biological
pathways, incomplete or partial degradation leads to simpler, non-toxic degradable com-
pounds [136]. For example, LiP can degrade benzopyrene into three quinine compounds,
namely 1,6-quinol, 3,6-quinine, and 6,12-quinine [165]. MnP (Mn (II) peroxidase) can also
oxidise organic compounds in the presence of MnP (Manganese peroxidase) [166]. As well,
laccase, glutathione S transferase, and cytochrome P450 are involved in the biodegradation
of recalcitrant compounds [167]. It has been shown that the immobilization of enzymes
significantly increases enzyme stability, activity, and stability. Enzymatic bioremediation is
Toxics 2022, 10, 484 15 of 24

a simple, environmentally-friendly, and fast method for removing and degrading persistent
xenobiotic compounds by microorganisms [134,145]. Enzyme-producing microorganisms
have been isolated and characterized with the limitation of low productivity. Insecti-
cides’ main ingredients, organophosphates (OP) and organochlorines (OC), are found in
agricultural soil and run-off into waterways.
Genetically-engineered microorganisms have demonstrated successful bioremediation
of hexachlorocyclohexane and methyl parathion [135,146]. Genetically-modified P. putida
KT2440 was used in organophosphate and pyrethroid bioremediation experiments [168].
The degradation and catabolism of a variety of persistent compounds has been documented
since the advent of metabolic engineering. Sphingobium japonicum and Pseudomonas sp.
WBC-3 showed bioremediation of methyl parathion and -hexachlorocyclohexane degrada-
tion pathways [169]. When three enzymes from two different microorganisms are combined
in E. coli, a persistent fumigant called 1-, 2-, 3-trichloropropane is released into the envi-
ronment via heterologous catabolism [137,148]. To do this, microbes can be used to turn
persistent compounds into minerals [49].

7.4. Designing the Synthetic Microbial Communities

Synthetic biology advancements have had a significant impact on environmental
issues in recent years. Toxic compounds, pesticides, and xenobiotics can be removed from
the environment by using genetically-modified organisms (GMOs). Natural microbial
communities must be understood in order to create a synthetic one [170]. Identifying which
species are participating in bioremediation is difficult in a natural community. Through
the use of a synthetic microbial community, the development of an artificial microbiome
with functionally specific species is possible. Model systems for studying functional and
structural characteristics can be found in these communities. Synthetic communities were
formed by the co-culturing of two distinct microorganisms under precisely defined con-
ditions, which were based on their interactions and functions [171]. The community’s
dynamics and structure are determined by these variables; it is based on the discovery
of bacterial processes and behaviors. Metabolism drives these patterns of microbial inter-
action, which in turn facilitates communication within communities [172]. Interactions
between two microbial populations are social in nature (such as mutualism, competition,
and cooperation). Cooperation is said to be a key factor in community structure and
operation. Cooperation in community dynamics is influenced by the creation of synthetic
communities [173] and it was found that modifying environmental conditions, such as
deleting genes, could be used to engineer cooperation between two microbial strains. In ad-
dition to this, the synthetic community’s engineered microbial species have been examined
for other patterns of interaction. Bioremediation strategies frequently make use of this type
of engineered interaction [174]. It is possible to sustain the existence of microorganisms in
a large population by using synthetic biology.

8. Advantages and Disadvantages

Due to the harm that pollutants exert on both humans and other living things, en-
vironmental pollution is a serious public health problem. The complete elimination of
contaminants via chemical and physical methods of remediation is costly [175]. Addi-
tionally, both approaches may result in increased pollution and site disruption, which
could have a detrimental effect on nearby humans and other biota. As a result, remedia-
tion techniques using chemicals and physical means are not regarded as eco-sustainable.
Contrary to these techniques, bioremediation is the suggested solution to remove various
persistent contaminants by relying on biological processes (mediated by various types of
living organisms). However, all bioremediation techniques have their own advantages and
disadvantages (Figure 2) because they have their own specific applications [176,177].
Toxics 2022, 10, 484 16 of 24

Figure 2. Advantages and disadvantages of bioremediation.

9. Future Perspectives and Conclusions

Omics has gained prominence in the field of microbial remediation of the pulp and
paper industry, textile industry, food industry, dairy industry, wood industry, fisheries,
water and soil treatment industry, solid waste remediation, heavy metal pollution remedia-
tion, and hydrocarbon remediation. In order to better understand degradative pathways,
bioremediation data must be mined, and new algorithms can be used to fit these data into
simulation and numerical modeling with ease along with data assemblage, reposition-
ing, exploration, and transmission, which necessitate standard protocols. Bioremediation
processes may be better understood if new biomarkers are studied. Combining all the
omics data with genetically-engineered tools could provide a comprehensive picture of the
microbial remediation process. The role of phytoremediation in reducing environmental
pollution can also be studied. The phytoremediation process has a number of advantages
over other remediation strategies, including lower costs, greater public acceptance, and
increased pollution degradation capacity [178]. Groundwater and air pollution, along with
toxic waste generation as a by-product of semiconductor manufacturing, are problems for
the environment; some examples include glycol ethers, hydrochloric acid (HCl), xylene, hy-
drogen fluoride (HF), and methanol [179]. In the case of pharmaceuticals that are designed
to be long-lasting or even non-degradable, they pose a unique threat to the environment.
The pharmaceutical pollutants are environmentally persistent substances. Trace amounts
of pharmaceutical ingredients, such as birth control pills, anti-epileptics, pain relievers,
and antidepressant medications, are found in many urban and rural sources of groundwa-
ter [180]. While operating, solar power generation facilities produce less greenhouse gas
emissions, including air pollutants such as carbon monoxide, volatile organic compounds,
nitrogen oxides, and carbon dioxide, than conventional fossil fuel-based power generation
facilities [181]. Genetically-engineered plants can be able to bioremediate specific pollutants
through discovered metabolic processes, enzymes, genes, or operons [182]. Although ge-
nomics, metabolomics, and proteomics in bioremediation aid in the exploration of possible
solutions to specific pollutants, identifying and comparing gene and protein sequences
that are effective at removing contaminants is the next step in bioremediation research.
GMOs can clean up a wide range of waste effluents and polluted land [183]. When used
in conjunction with other physical and chemical methods, bioremediation can provide
a comprehensive approach toward removing pollution from the environment. Since it
appears to be a long-term solution, there is a need for additional research in this area.
Toxics 2022, 10, 484 17 of 24

Author Contributions: Conceptualization, M.T., M.S., K.S. and B.S.I.; Writing—original draft prepara-
tion, S.B., D.G. and B.V.T.; Writing—review and editing, M.S., M.T., K.S. and B.V.T.; visualization, S.B.
and D.G.; supervision, M.T., M.S., K.S. and B.S.I. All authors have read and agreed to the published
version of the manuscript.
Funding: This research received no external funding.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: Data that support these findings available within the article.
Acknowledgments: The author M.T. grateful to the Biotechnology Program, Department of Biochem-
istry, Dr. Rammanohar Lohia Avadh University, Ayodhya, India, for providing us with the research
environment.
Conflicts of Interest: The authors declare no conflict of interest.

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