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AN HND SEMINAR REPORT ON

MICROBES MEDIATED BIOREMEDIATION: CURRENT RESEARCH AND FUTURE

CHALLENGE

BY

ORIPOTA ELIZABETH OMOWUMI

MATRIC NO: S04/SLT/2018/3231

SUBMITTED TO

DEPARTMENT OF SCIENCE LABORATORY TECHNOLOGY, FACULTY OF

APPLIED SCIENCE,

RUFUS GIWA POLYTECHNIC, OWO, ONDO STATE, NIGERIA,

MR. ADELUWOYRE-AJAYI O.A (SEMINAR SUPERVISOR)

MRS. AKOMOLAFE O.Y (SEMINAR COORDINATOR)

DR. O.E SEYIFUNMI (HEAD OF DEPARTMENT)

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 ABSTRACT

The rise in environmental pollution over the past few decades due to rapid industrialization and
unsafe agricultural practices has become a major challenge. The presence of toxic pollutants such
as nuclear wastes, heavy metals, pesticides, and hydrocarbons has been languishing the
environment as well as the human health. Bioremediation using microbial communities is
emerging as an incredible, eco-friendly, and cost-effective approach to ameliorate the adverse
effects of toxic pollutants. Microbes possess astonishing metabolic capabilities to alter most
forms of organic material and can survive in extreme environmental conditions which make
them attractive candidate for the bioremediation. Microbes are the treasure houses for
environmental cleaning and recovering of contaminated soil and they have been reported from
diverse environmental conditions including hot, cold, drought, and saline. Different groups of
bioremediating microbes have reported from diverse conditions, that is, bacteria, fungi including
yeast, and algae. Microbes belonging to genera Alcaligenes, Aspergillus, Bacillus,
Flavobacterium, Ganoderma, Methosinus, Nocardia, Phormidium, Pseudomonas, Rhizopus,
Rhodococcus, and Stereum have been reported as potential and efficient bioremediators for the
degradation of different pollutants of the environment such as xenobiotics, heavy metals,
hydrocarbons, and paper and pulp effluent. The present review focuses on microbial diversity in
bioremediation, techniques applied in bioremediation, bioremediation of different environmental
pollutants, and how bioremediation processes could be monitored.

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 CHAPTER ONE

1.0 INTRODUCTION

The quality of life on Earth is linked inextricably to the overall quality of the environment. The
increasing civilization, urbanization, and advancements in the industrial sector have resulted in
generation of wastes and their dumping in the environment. It has been estimated that about 1000
new chemicals are synthesized annually. More than 450 million kilograms of toxins are released
globally into air and water in accordance to the third world network reports. The pulp and paper
industry is known to be the sixth largest polluter of the environment. Heavy metal pollution is
another significant threat to the public and environmental health for its toxicity, non-
biodegradability, and bio-accumulation. Polyaromatic hydrocarbons (PAHs) are known for their
mutagenic and carcinogenic properties. The toxic contaminants leading to ecological imbalance
are of global concern. Microbial biotechnology is a rapidly growing and emerging field with
diverse applications in dealing with the environmental issues. The application of the microbes for
bioremediation is a versatile technology with high stability, economical, eco-friendly, lack of
interference with the ecology of the ecosystem, and more public acceptance. Environmental
cleaning through bioremediation is a apt substitute to the physicochemical approaches, which are
rather environmentally disparaging and can be the cause of the secondary pollution.

Bioremediation could be utilized in cleanup of contaminated sites such as water, soils, sludge,
and waste streams. Bioremediation has been even approved by the US Environmental Protection
Agency (USEPA) as an effective environmentally sound technique for revitalization of the
contaminated environment and promotion of sustainable development. Microbes belonging to
genera Alcaligenes, Aspergillus, Bacillus, Flavobacterium, Ganoderma, Methosinus, Nocardia,
Phormidium, Pseudomonas, Rhizopus, Rhodococcus, and Stereum have been reported to have a
potential role in bioremediation. Bioremediation is not new to human race but surely the new
approaches that stem from advances in molecular biology and process engineering are emerging.

With the advancements of genetic engineering techniques, genetically modified organisms can
be generated and utilized to reduce the burden of toxic compounds from the environment. Thus,
implanting these methods and increasing their efficiency will lead to economic as well as social
benefits with reduced risks of diseases and costs being spent on management of these wastes, and
achievement of more ecological stability and greener environment

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 CHAPTER TWO

2.0 BIODIVERSITY OF BIOREMEDIATING MICROBES

The enticing process, bioremediation is one of the processes that help in detoxify environmental
pollutants using diverse group of microbes including fungi, yeast, and bacteria. Microorganisms
are considered as to be the outstanding creatures for the detoxification of pollutants as it is cheap,
simple, and eco-friendly clean-up method. To hold the assurance for detoxification of
environmental contaminants, diverse group of microbes are explored around the globe from
different locations and environmental conditions. In a report, phenol degrading yeasts, namely,
Candida boidinii, Pichia holstii, P. membranifaciens, and Saccharomyces cerevisiae, were
isolated from the olive mill wastewaters.

Zhang et al. [2019] reported petroleum degrading bacterium Bacillus sp. from the oil
contaminated soil. In another report, white rot fungi, Trametes versicolor was reported as a
bioremediating agent of polycyclic aromatic hydrocarbons.

In a report by Janbandhu, Fulekar [2021], three bacterial species, namely, Achromobacter

insolitus, Bacillus cereus, and Sphingobacterium sp., isolated from petrochemical refinery field
were reported for remediating PAHs. In a report, diversity of bioremediating bacterial isolates,
that is, Bacillus megaterium, B. cibi, B. cereus, Pseudomonas aeruginosa, and Stenotrophomonas
acidaminiphila from oily sludge contaminated soil was reported. These strains were reported for
having capability of degrading aliphatic and aromatic compounds.

Syakti et al. [2023] reported bioremediating potential bacterial isolated from the mangroves
growing in hydrocarbons contaminated soil and they were identified as Bacillus aquimaris, B.
megaterium, and B. pumilus, Flexibacteraceae bacterium, Halobacillus trueperi, and
Rhodobacteraceae bacterium. In another report, crude oil degrading microbes were reported and
they were reported for belonging to genera Achromobacter, Alcaligenes, acillus, Brevibacillus,
Delftia, Lysinibacillus, Paenibacillus, Pseudomonas, and Stenotrophomonas.

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 CHAPTER THREE

3.0 BIOREMEDIATION OF DIVERSE CONTAMINANTS

3.1. Bioremediation of Paper and Pulp Effluent

Pulp and paper industry is one of the important industrial sectors simultaneously being the source
of the toxic pollutants. The toxic effluent released from the paper and pulp industries has adverse
environmental impact as it contains high content of BOD (biological oxygen demand) and COD
(chemical oxygen demand), total dissolved solids, suspended solids, color, organic acids,
phosphorus, sulfur compounds, and toxic chlorophenols. This environmental pollutant also
affects the health of the humans working in the paper and pulp industries as it may cause
headache, vomiting, nausea, diarrhea, and eye irritation. In addition, flora and fauna of land as
well as aquatic are also affected by the pollutant. Moreover, the effluent has also declined the
quantity and quality of the water. To cope with this effluent problem, in the past decade, several
projects and technologies have been implemented and upgraded, respectively. Over the many
years, the wastewater generated from the industry was treated with physical methods such as
adsorption, microfiltration, and photoionization; and chemical methods such as coagulation,
oxidation, ozonation, and sedimentation. The physical and chemical methods of the treatment of
the effluent have shown to improve the quality of the effluent by enables to treat it completely.

3.2 Bioremediation of Heavy Metals

Heavy metals, the elements having greater density, are widespread environmental pollution
which has generated hype in recent years due to associated health risks. The major cause of this
widespread pollutant is industries including iron and steel, electroplating, electrolysis, energy
and fuel, fertilizer, and pesticides producing industries. These industries release of heavy metals
such as uranium, mercury, lead, chromium, cadmium, and arsenic that are poisonous to land as
well asaquatic flora and fauna. Heavy metals are also known to threaten the life of humans by
causing skin irritation, breathing problem, weakness, abdominal cramps, headache, diarrhea,
anemia, and permanent damage of kidney and brain. The metal cadmium toxicity could also
induce DNA breakage. To remove the heavy metals from the environment, conventional
methods such as chemical precipitation, electrochemical treatment, and ion exchange were being
used but these methods expensive and even remove the heavy metal at very low concentration.

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Microbial mediated bioremediation is one of the appropriates the method for the removal of
heavy metal accumulated into the environment.

3.3 Bioremediation of Polyaromatic Hydrocarbons

PAHs, a class of toxic-fused ring aromatic compounds, are widespread organic pollutants
accumulated in the environment either due to anthropogenic or natural activities. These
compounds have a high molecular weight and can persist for years. They are mostly produced
from incomplete combustion of fossil fuels, petroleum products, and industrial activities. The
natural calamities such as forest fires and volcanic eruptions also contribute to their
accumulation in the environment. PAHs exist as a complex mixture in many different petroleum-
based products. Soils and waters surrounding gas plants, soil refineries, air bases, petrol stations,
and chemical industrial sites are common sources of contamination. PAHs have been shown to
be carcinogenic and mutagenic to human and animal health, and as a result, the US EPA has
classified them as priority pollutants. PAHs can enter the human body through a variety of
pathways, including air, food, soil, water, and occupational exposure. PAH can also enter the
water supply through a variety of sources, including industrial and home waste, as well as urban
runoff and automobile emissions.

The removal of these specific contaminants of the atmosphere has extended attention because it
caused damage ranging from human to the environment, marine and land animals, and
agricultural soil. PAHs are challenging to remove from soil due to their insolubility in water and
degrade slowly.

3.4 TECHNIQUES FOR BIOREMEDIATION

The development of eco-friendly, cost-effective, and reliable clean-up technology is a priority to

decontaminate the environment. Microbes are the readily available and omnipresent bioresources
which can utilize these noxious elements as their source of nutrition.

 In situ Bioremediation

The technique involves the application of a biological treatment for cleaning up of hazardous
compounds and has been commonly applied for degradation of contaminants in saturated soils
and groundwater. It relies on the microbial activities for destruction and detoxification of

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contaminants present in a place. On the contrary, the capability of the microbes to convert the
toxic contaminants into less toxic or non-toxic forms is completely dependent on availability of
the nutrients and electron acceptorsand donors.

 Biosparging

This approach involves the injection of the air under pressure below the water table. This, in
turn, increases oxygen concentrations of groundwater and rate of biodegradation by naturally
occurring bacterial species. Biosparging finds major applications in the treatment of aquifers
polluted with kerosene and diesel, which have good biodegradation of the BTEX group and
naphthalene [130]. The effectiveness of biosparging depends on soil permeability as well as the
pollutant biodegradability.

 Bioventing

Bioventing is a potential technology that stimulates the natural in situ biodegradation of

compounds that can be degraded aerobically by existing soil microbial communities. The
technique involves controlled stimulation of the air flow, providing oxygen in sufficient levels to
sustain activities of the microbes thereby enhancing the process of bioremediation. The levels of
nutrients and humidity are maintained to achieve transformation of pollutants. This technique has
been successfully used in the remediation of soils polluted by oil products.

 Bioaugmentation and biostimulation

In bioaugmentation, the autochthonous microflora of the polluted site is enriched by adding

previously selected indigenous or genetically modified species of microbes to enhance the
process of remediation. Bioaugmentation is used for the soils and groundwater contaminated
with tetrachloroethylene and trichloroethylene where the approach ensures that the in situ
microbes degrade these contaminants to non-toxic compounds such as ethylene and chlorides.

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 CHAPTER FOUR

4.0 BIOTECHNOLOGICAL APPLICATIONS

Microbes, including bacteria, archaea, fungi, and algae through their enzymatic activity, can
degrade, transform, or neutralize toxic and hazardous pollutants. The identification of enriched
microbes at polluted sites has been accelerated by the growth and accessibilityof DNA
sequencing technology. The polluted sites are often allowed to naturally remediate in a process
called natural attenuation which is largely dependent on microbial activity. The growth and
activity of the indigenous microbes could be enhanced by supplementing the soil with nutrients
such as plant or animal waste, a process known as biostimulation. Alternatively, pollutant
degradation could b accelerated by bioaugmentation, which involves introduction of new wild
type or genetically engineered microbes that specialize in the degradation of toxic compounds
into the contaminated site.

Bioremediation through microbes has found practical applications as an economical tool in the
treatment of pollution in agricultural settings as well as in other environments.

4.1. Environmental Applications

The environment could be polluted by various sources ranging from industrial emissions and
effluents to incineration, fossil fuel combustion and automobile exhausts, chemical spills, and
landfills. Gaseous pollutants could be removed by passing industrial gases through a
microbiological filter surface in a process called biofiltration before being released into the
environment. Sewage treatment conducted worldwide to remediate water is a largely microbe-
driven process.

4.2. Agricultural Applications

Due to the increase in modern agriculture worldwide, there has been dramatic contamination of
produce, soil, groundwater, and the surrounding environment by agricultural pollutants and
toxins from fertilizers and heavy metals to pesticides. By exposure to agricultural fields and
through consumption of agricultural products, this pollution also impacts the safety of the
consumer. A key aspect of agricultural pollution stems from the usage of polluting inorganic

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fertilizers, especially those containing nitrogen, phosphorus, and potassium (N, P, and K). Over-
fertilized fields and those applying animal waste can be bioremediated using microbes.
Ammonia and nitrogen oxides emanating from nitrogen based fertilizers could be released into
the atmosphere aggravating the greenhouse effect, create ground-level smog, could contaminate
waterways and affect aquatic organisms, as well as pose harm to livestock and humans.
Nitrogenous compounds such as nitrates and nitrites released in agriculture could result in
respiratory distress, heart, or kidney diseases. Bacterial bioremediation can remove compounds
like nitrate in runoff through assimilatory nitrate reduction.

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 CHAPTER FIVE

5.0 CONCLUSION

There is a growing public concern for removal of the toxic pollutants introduced into the
environment by diverse human activities. Bioremediation through biological systems is a novel
technology and receiving immense credibility in the field of the pollution management.
Bioremediation is a viable and economical approach for waste disposal as compared to various
physiochemical methods. The continuous search for novel bioresources is still required for
successful implementation of this technology and safeguard nature and environment. Studying
the effect of microbes singly or in combination on diverse range of the pollutants is the need of
the hour. The application of genetically engineered microbes with potential to degrade a wider
range of pollutants could be a step forward. The enzymes involved in the process of
bioremediation could be over expressed, purified, and utilized. The understanding of the
mechanisms of microbial mediated bioremediation could be studied. Awareness and education
among the people about the role of the microbial communities in environmental cleaning is
either important.

5.1 RECOMMENDATION

The understanding of the mechanisms of microbial mediated bioremediation could be studied.

Awareness and education among the people about the role of the microbial communities in
environmental cleaning is either important. Field trials for demonstrating the efficiency of the
bioremediation technology will prove important. Further, metagenomics could be a useful
approach to study the microbial communities within polluted sites and genes could be identified
to improve the degradation abilities of the microbial strains. Thus, there is a great potential for
the development of the process for bioremediation using the microbes.

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 REFERENCE

ingh S, Tiwari G. Application of bioremediation on solid waste management: A review. J

Bioremed Biodegr 2014;5:19424.
Hossain K, Ismail N. Bioremediation and detoxification of pulp and paper mill effluent: A
review.
Res J Environ Toxicol 2015;9:113.
Guo H, Luo S, Chen L, Xiao X, Xi Q, Wei W, et al. Bioremediation of heavy metals by growing
hyperaccumulaor endophytic bacterium Bacillus sp. L14. Bioresour Technol
2010;101:8599-
605.
Balaji V, Arulazhagan P, Ebenezer P. Enzymatic bioremediation of polyaromatic hydrocarbons
by
fungal consortia enriched from petroleum contaminated soil and oil seeds. J Environ Biol
2014;35:521-9.
Kour D, Kaur T, Devi R, Yadav A, Singh M, Joshi D, et al. Beneficial microbiomes for
bioremediation of diverse contaminated environments for environmental sustainability:
Present status and future challenges. Environ Sci Poll Res 2021;28:24917-39.
Singh C, Tiwari S, Singh JS, Yadav AN. Microbes in Agriculture and nvironmental
Development.

Boca Raton: CRC Press; 2020.

Boopathy R. Factors limiting bioremediation technologies. Bioresour Technol 2000;74:63-7.

Kaur T, Devi R, Kour D, Yadav A, Yadav AN, Dikilitas M, et al. Plant growth promoting soil

microbiomes and their potential implications for agricultural and environmental

sustainability. Biologia 2021;76:2687-709.

Bharagava RN, Saxena G, Mulla SI. Introduction to industrial wastes containing organic and

inorganic pollutants and bioremediation approaches for environmental management. In:

Saxena G, Bharagava RN, editors. Bioremediation of Industrial Waste for Environmental Safety.

12
 Berlin: Springer; 2020. p. 1-18.
Verma S, Kuila A. Bioremediation of heavy metals by microbial process. Environ Technol Innov
2019;14:100369.
Yadav AN, Rastegari AA, Yadav N, Kour D. Advances in Plant Microbiome and Sustainable
Agriculture: Diversity and Biotechnological Applications. Singapore: Springer; 2020.
Kumar A, Yadav AN, Mondal R, Kour D, Subrahmanyam G, Shabnam AA, et al. Myco
remediation: A mechanistic understanding of contaminants alleviation from natural
environment and future prospect. Chemosphere 2021;284:131325.
Nduka J, Umeh L, Okerulu I, Umedum L, Okoye H. Utilization of different microbes in
bioremediation of hydrocarbon contaminated soils stimulated with inorganic and organic
fertilizers. J Pet Environ Biotechnol 2012;3:1-9.

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