ROLE OF MICROORGANISMS IN

THE ABATEMENT OF POLLUTANTS

by Azis Kemal Fauzie
Department of Studies in Environmental Science
University of Mysore
December 2016

BIODEGRADABLE POLLUTANTS
Hydrocarbons, Polycyclic Aromatic Hydrocarbons (PAHs)
Polychlorinated Biphenyls (PCBs), Pesticides, Plastics, Dyes
Heavy Metals, Radionuclides

HCs, PAHs

Dyes, PCBs

Pesticides

Plastics, Metals

HYDROCARBONS
SATURATES:
(a) Aliphatic/Paraffins:

(b) Cyclic/Naphthenes:

Cyclopentane

Methylcyclohexane

CH3

CH3

Methylcyclopentane
Methylcyclohexane

ASPHALTENES:

Benzaldehyde

(Mono-) AROMATICS:

RESINS:

Benzoate

Polycyclic Aromatic Hydrocarbons (PAHs)

PAHs are the class of hydrocarbons containing two or more fused
benzene rings and/or pentacyclic molecules. PAHs originate from fossil
fuels and industrial processes during coke production. PAHs are toxic
(carcinogenic, mutagenic and teratogenic) to human and animals.

PESTICIDES
ORGANOCHLORINES:

ORGANOPHOSPHOROUS:

PYRETHRINS/PYRETHROIDS:

CARBAMATES:

Fate of Pesticide in the Environment

Polychlorinated Biphenyls (PCBs)

PCBs are organic chemicals synthesized by catalytic chlorination of biphenyls.
First manufactured in 1929 by Monsanto. Manufacture, use, importation and
distribution of PCBs was banned in Sweden (1970), Japan (1972) and US (1976).
Trademark: Aroclor (US), Kaneclor (Japan), Fenclor (Italy), Pyralene (France),
Clophen (Germany).
Applications:
fluid in electrical (transformers, capacitors), heat transfer and hydraulic equipment
plasticizers in paints, plastics and rubber products
pigments, adhesives, pesticides, inks, dyes, waxes and carbonless copy paper
lubricants for turbines and pumps

Toxicity:
Reproductive disabilities in animals and human
Nervous system and liver damage
Hepatitis, skin diseases and endocrine disrupters
Carcinogenic and allow bioaccumulation

PLASTICS
Biodegradable:

Non-biodegradable:

petroleum-based

petroleum-based

Polycaprolctone (PCL)

Polybutylene succinate (PBS)

Polypropylene (PP)
Polyvinyl chloride (PVC)
Polystyrene (PS)

Polyethylene
succinate (PES)

biomass-based

Polyethylene terephtalate (PET)

biomass-based
Polyethylene (PE)

Polyhydroxy butyrate (PHB)

Nylon 11

Starch

Polylactic acid (PLA)

Acetyl cellulose
(AcC)

DYES
TRIPHENYLMETHANE:

AZO:
Congo Red

Methyl Orange
Bismark Brown Y
Brilliant Green

Allura
Red

Sunset
Yellow
FCF

Methyl
Violet

Fast Green FCF

Crystal
Violet

Oil Red O
PHENOXAZINE:

PHENOTHIAZINE:

XANTHENE:

Giemsa Stain
Brilliant Cresyl Blue
Darrow Red

Erythrosin
Methylene Violet

Cresyl Violet Acetate

Methylene Blue

Eosin Y

Rose Bengal

Rhodamine 123

OTHER CLASSES:
Phenazine, Cyanine
Phenanthridine
Acridine, Coumarin
Anthraquinone
Quinoline, Oxonol
Tetrazolium salt
Benzofuran, Indole
Benzodiazole, Styryl
Nitro, Nitroso, Indigo
Diphenylmethane
Heterocycle, etc.

HEAVY METALS

RADIONUCLIDES

BACTERIAL DEGRADATION
for Hydrocarbons, PAHs, PCBs, Pesticides, Plastics, Dyes
Heavy Metals, and Radionuclides

CO2
H2O

Hydrocarbon-degrading Bacteria
Hydrocarbon
s
Petroleum
hydrocarbons

Bacteria

Bacillus, Corynebacterium, Staphylococcus,

Streptococcus, Shigella, Alcaligenes, Klebsiella,
Acinetobacter, Escherichia, Enterobacter, Vibrio,
Pseudomonas, Brevibacillus, Micrococcus, Nocardia,
Achromobacter, Arthrobacter, Flavobacterium,
Oceanobacter kriegii
Crude oil
P. aeruginosa, Bacillus subtilis, Acinetobacter lwoffi,
Micrococcus roseus
Alkanes
Pseudomonas, Bacillus, Micrococcus, Acinetobacter
calcoaceticus, A. venetianus, Nocardia erythroplis,
Ochrobactrum, Alcaligenes sodorans, Serratia
marcescens, Arthrobacter, Rhodococcus, Marinobacter
hydrocarbanoclasticus, Alcanivorax borkumensis
Alkanes,
Methylococcus, Methylosinus, Methylocystis,
alkenes,
Methylomonas, Methylocella, Methylobacter,
cycloalkanes
Mycobacterium vaccae
Alkyl
Arthrobacter, Burkholderia, Pseudomonas,
benzenes,
Sphingomonas, Rhodococcus, Mycobacterium,
Ref:
Joutey,
2013; Pandey,
2016; Kothari;
Ghazali, 2014; Al-Wasify, 2014; Koch, 1993
alkanes,
fatty
Acinetobacter,
Caulobacter

PAH-degrading Bacteria
PAHs
PAHs

PAHs,
naphthalene,
phenanthrene,
pyrene
Naphthalene
Phenanthrene

Bacteria
Rhodococcus, Corynebacterium,
Achromobacter, Aeromonas, Alcaligenes
odorans, Sphingomonas paucimobilis,
Bacillus, Pseudomonas, Nocardia,
Mycobacterium flavescens, Burkholderia
cepacia, Arthrobacter, Xanthomonas
Marinobacter vinifirmus, M.alkaliphilus,
Stappia aggregate, Pseudoalteromonas
ganghwensis, Thalassospira lucentensis,
Kaistia adipata
Pseudomonas fluorescens, Rhodococcus
Marinobacter, Pseudoalteromonas,
Cycloclasticus, Marinomonas,
Halomonas, Brevibacterium, Vibrio,
Pseudomonas migulae, Sphingomonas
yanoikuyae

Phenanthrene,
Exiguobacterium, Shewanella,
bromodeoxyurid Methylomonas, Pseudomonas,

References
Mrozik,
2003; Kelley,
1990;
Bamforth &
Singleton,
2005
Cui et al.,
2008

Bamforth,
2005
Melcher,
2002;
Samanta,
1999;
Haritash,
2009
Edlund, 2008

PCB-degrading Bacteria
PCBs

Bacteria

References

PCBs

Pseudomonas, Burkholderia, Ralstonia,

Alcaligenes, Achromobacter,
Sphingomonas, Comamonas,
Rhodococcus, Janibacter, Paenibacillus,
Bacillus, Microbacterium, Acinetobacter,
Corynebacterium,
Arthrobacter, Moraxella, Variovorax,
Chloroflexi

Seeger,
Unterman,
Furukawa,
Bedard,
Abramowicz,
Petric, Abraham

Aroclor 1242

Alcaligenes odorans, A. denitrificans,

Janibacter, Acinetobacter

Clark, Sierra,
Brunner

Aroclor 1260

Dehalococcoides, Thermotogales,
Cytophagales

Tracey, Watts

Kaneclor

Rhodococcus sp., Acinetobacter sp.

Seeger,
Furukawa

Biphenyl,
Chlorobiphen
yl

Pseudomonas pseudoalcaligenes,
Micrococcus, Achromobacter,
Acinetobacter, Arthrobacter, Nocardia,
Alcaligenes, Burkholderia xenovorans,
Bacillus brevis, Ralstonia eutrophus

Furukawa,
Ahmed,
Benvinakatti,
Focht,
Mondello,

Pesticide-degrading Bacteria
Pesticides
Glyphosate

Bacteria

Pseudomonas, Alcaligenes, Bacillus megaterium, Rhizobium,

Arthrobacter atrocyaneus, Geobacillus caldoxylosilyticus,
Agrobacterium, Flavobacterium
DDT
Bacillus, Staphylococcus, Stenotrophomonas , P. fluorescens,
P. aeruginosa
Endosulphan Mycobacterium, Arthrobacter
Parathion
Pseudomonas sp, P. diminuta, P. stutzeri, Agrobacterium
radiobacter, Bacillus, Arthrobacter, Flavobacterium,
Xanthomonas
Met.
Bacillus, Plesimonas, Pseudomonas sp, P. putida,
parathion
Flavobacterium balustinum
Chlorpyrifos Providencia stuartii, Enterobacter, Micrococcus,
Flavobacterium, P. diminuta
Coumaphos Nocardiodes simplex, Agrobacterium radiobacter,
Pseudomonas monteilli, P. diminuta, Nocardia,
Flavobacterium
Monocrotoph Pseudomonas mendocina, P. aeruginosa, Bacillus
os
megaterium, Arthrobacter atrocyaneus, Clavibacter
michiganens
Ref: Singh & Walker,
2006; Hernndez et al., Joutey et al.

Plastic-degrading Bacteria
Plastics
Polyethylene
(PE)

Bacteria

Brevibacillus borstelensis, Rhodococcus rubber,

Sphingomonas, Pseudomonas chlororaphis, P.
fluorescens, Comamonas acidovorans
Polylactic Acid
Amycolatopsis, Saccharrotrix, Kibdelosporangium,
(PLA)
Streptoalloteichus
Polycaprolacton Bacillus brevis, B. pumilus, Amycolatopsis, Clostridium,
e
Paenibacillus
Polypropiolacto Bacillus, Acidovorax, Variovorax paradoxus,S.
ne
paucimobilis
Polyhydroxybuti Schlegelella thermodepolymerans, Pseudomonas,
rate (PHB)
Ralstonia piketti, Acidovorax faecalis, Alcaligens
faecalis, Illyobacter delafieldi, Comamonas, Bacillus,
Streptomyces, Caenibacterium thermophilum
Polycarbonates Amycolatopsis sp, Pseudomonas sp, Roseateles
(PHC, PBC)
depolymerans, Chromobacterium viscosus
Polyurethane
Comamonas acidovorans
(PU)
PHB, PES, PCL
Actinomadura, Microbispora, Streptomyces,
Ref: Tokiwa, 2009; Garrison,
2016; Leja & Lewandowicz,
2009
Thermoactinomyces,
Saccharomonospora

Dye-degrading Bacteria
Bacteria
Aeromonas
hydrophila

Dyes
Crystal violet, Basic fuchsine, Brilliant green, Great red,
Malachite green, Acid amaranth, Reactive red, Reactive
brilliant blue
Citrobacter
Crystal violet, Gentian violet, Methyl red, Congo red,
Malachite green, Brilliant green, Basic fuchsine
Enterobacter
Reactive black, Reactive red, Acid yellow, Acid orange,
cloacae
Disperse yellow
Pseudomonas
Crystal violet, Reactive red, Reactive orange, Reactive
sp, P. putida, P.
blue, Direct red, Direct orange, Acid yellow, Acid blue,
aeruginosa, P.
Acid black, Acid orange, Blue RR, Black B, Navy blue,
fluorescence, P.
Disperse yellow, Acid red, Malachite green, Fast green,
nitroreducens
Orange II, Reactive black, Acid orange, Methyl red
Morganella
Acid yellow, Acid orange, Reactive orange, Direct red,
Acid blue
Shewanella
Crystal violet, Reactive black, Direct red, Acid red,
Disperse orange
Bacillus sp, B.
Navy blue, Red RR, Yellow RR, Remazol black B, Acid
subtilis
red, Indigo blue
Clostridium
Reactive
red, Reactive
black,
yellow,
Ref: Ali, 2010; Barragn
et al., 2007;
Shah, 2013,
2014;Reactive
Bagewadi,
2011 Indigo

Metal-degrading Bacteria
Heavy
metals
As, Cd, Cu,
Co, Zn
Cu, Zn

Bacteria
Acidithiobacillus ferrooxidans
Bacillus spp, Pseudomonas aeruginosa

References
White, 1998

Philip,
Gunasekaran
Cd
Alcaligenes, Psedomonas, Moraxella,
Springael,
Bacillus cereus
Gazs
Ag, Hg
P. aeruginosa, Citrobacter freundii, C.
Lima e Silva,
youngae, Serratia, Klebsiella pneumoniae, 2012
Enterobacter
agglomerans, Chryseobacterium
Ag
P. stutzeri, Streptomyces noursei,
Lima e Silva,
Stenotrophomonas maltophilia,
2012;
Thiobacillus ferrooxidans, Acinetobacter
Mattuschka,
Gazs
Hg(II)
Alcaligenes faecalis, Bacillus pumilus, P.
Jaysankar,
aeruginosa, Brevibacterium iodinum,
2008; Brim,
Deinococcus radiodurans
2000
Fe, Cu, Mn, Ni Bacillus subtilis, Bacillus licheniformis
Beveridge,

Radionuclide-degrading Bacteria
Radionuc
lide

Bacteria

Technetiu
E. coli, Desulfovibrio desulfuricans, D. fructosovorans, D.
m, 99Tc(VII) vulgaris, Thiobacillus ferroxidans, T. thiooxidans, Geobacter
sulfurreducens, G. metallireducens
Neptuniu
Shewanella putrefaciens, Citrobacter, Pseudomonas
m,
fluorescens, P. aeruginosa, Micrococcus luteus, Streptomyces
237
Np(V)
viridochromogenes
Plutonium, Microbacterium flavescens, Bacillus sphaericus, B. subtilis, B.
239
Pu,
circulans, B. polymyxa, E. coli, Shewanella oneidensis, S. alga,
240
Pu,
G. metallireducens, Clostridium, Aeromonas hydrophila
Pu(V),
Pu(VI)
Cesium,
Rhodococcus erythropolis, E. coli, P. fluorescens, P. aeruginosa,
137
Cs
Deinococcus radiodurans, Arthrobacter, Nocardia
Thorium,
P. aeruginosa, Mycobacterium smegmatis
Th
Uranium,
Arthrobacter, Acinetobacter, Anaeromyxobacter, Bacillus,
235
U(VI)
Citrobacter, Geothrix, Cellulomonas, Clostridium, Deinococcus,
Desulfovibrio, Desulfosporosinus, Desulfitobacterium, E. coli,
Ref: Lloyd, 2005;
Newsome,Pseudomonas,
2014; Williams, 2013;
www.biorad.igib.res.in
Geobacter,
Paenibacillus,
Ralstonia, Rahnella,

Streptococcus

Bacillus
Corynebacterium
Staphylococcus

Shigella

Alcaligenes faecalis

Pseudomonas aeruginosa
Escherichia coli
Acinetobacter

Actinomycetes

Klebsiella pneumoniae

Enterobacter cloacae
Mycobacterium

Serratia marcescens

Enterococcus

Aeromonas hydrophila

Ralstonia

Achromobacter

Shewanella

Providencia
paradoxus

Variovorax

Burkholderia

Streptomyces

Rhodococcus

Clostridia

Deinococcus radiodurans

Proteus

OTHER MICROBIAL DEGRADATION

PGPR & PGPB, Microfungi & Mycorrhiza, Algae & Protozoa,
Genetically Engineered Microorganisms (GEMS)

Bacteria

Fungi

Algae

Protozoa

Degradation by PGPR & PGPB

Plant Growth Promoting Rhizobacteria (PGPR), or rhizospheric bacteria,
are naturally occurring soil bacteria that aggressively colonize plant
roots and benefit plants by providing growth promotion. The technique
to apply this in soil biodegradation is called rhizoremediation.
Plant Growth Promoting Bacteria (PGPB), or endophytic bacteria, are
non-pathogenic bacteria that occur naturally in plants as adjuncts in
phytoremediation. They can significantly facilitate the growth of plants
in the presence of high levels of pollutants, including metals.
Pollutants

Microorganisms

References

Hydrocarbo
ns

Pseudomonas putida

Hontzeas et al.,
2004

PAHs

Lysini bacillus

Ma et al., 2010

PCBs

Rhodococcus, Luteibacter,
Williamsia

Leigh et al., 2006

Degradation by Microfungi & Mycorrhiza

Microfungi are described as a group of eukaryotic organisms that are
important part of degrading microbiota. Like prokaryotic bacteria,
they metabolize organic matter and responsible for the
decomposition of carbon in the biosphere. But fungi, unlike
bacteria, can grow in low moisture areas and in low pH solutions.
Fungi species are ranging from unicellular yeasts to extensively
filamentous fungi or mycelial molds. Fungal metabolism can be nonligninolytic or ligninolytic (also known as white-rot fungi).
Mycorrhiza is a symbiotic association between fungus and the roots
of vascular plant. It is important for mycorrhizoremediation.
In a mycorrhizal association, the fungi colonizes the host plant's
roots, either intracellularly as in arbuscular mycorrhizal fungi (AMF),
or extracellularly as in ectomycorrhizal fungi.

Degradation by Yeasts
Pollutants

Yeasts

References

Aliphatic/petrole
um
hydrocarbons

Candida lipolytica, C. tropicalis, C.

apicola, Rhodoturula rubra, R.
mucilaginosa, Geotrichum,
Aureobasidium pullulans, Trichosporon
mucoides
Rhodotorula aurantiaca, Candida
ernobii
Candida maltose, C. tropicalis, Yarrowia
lipolytica
Trichosporon cutaneum

Bartha, 1986;
Scheuer, 1998;
Was, 2001

Diesel oil
Alkane, fatty
acids
Phenol
PCBs
Linuron,
metroburon
Aniline
Reactive black
PEA, PC, PLA

T. mucoides, Candida boidinii, C.

lipolytica
Botrytis cinerea
Candida methanosorbosa
Candida krusei, Pseudozyma rugulosa
Candida cylindracea, Tritirachium

de Cssia,
2007
Iida, 2000
Mrtberg,
1985
Sasek,
Sietman
Bordjiba, 2001
Mucha, 2010
Yu & Wen,
2005
Tokiwa, 2009

YEASTS

Rhodoturula
Candida tropicalis
Hansenula polymorpha

Aureobasidium pullulans
Saccharomyces cerevisiae
Schizosaccharomyces pombe

Botrytis cinerea

Geotrichum

Degradation by Filamentous Fungi

Pollutants
Aliphatic &
aromatic HCs
Toluene
PAHs

Hydrocarbons,
pesticide,
gelatin
Chlorpyrifos
Glyphosate
Malachite
green

Fungi

Referenc
es

Amorphoteca, Neosartorya, Talaromyces,

Aspergillus, Cunninghamella, Penicillium,
Fusarium, Cephalosporium
Cladophialophora, Exophiala, Leptodontium,
Pseudeurotium zonatum
Pleurotus ostreatus, Cunninghamella elegans,
Chrysosporium pannorum, Aspergillus niger,
Phanerochaete chrysosporium, Antrodia
vaillantii
Cladosporium cladosporioides

Chaillan,
Singh,
Steliga
Francesc,
2001
Okparanm
a, 2011;
Maigari,
2015
Steliga,
Chen,
Abruscia
Singh &
Walker,
2006

P. chrysosporium, Hypholama, Coriolus,

Trichoderma
Penicillium, Trichoderma, A. niger, Alternaria
alternata
Acremonium kiliense, Aspergillus flavus, A.
solani

Youssef, Ali

Alternaria alternata
Fusarium
Penicillium chrysogenum
Trichoderma

Pleurotus ostreatus
cladosporioides

Exophiala

Cladosporium

Rhizopus

Aspergillus niger

Aspergillus ustus

Aspergillus nidulans

Aspergillus

Degradation by Algae & Protozoa

Reports of algae and protozoa in biodegradation are scanty.
However, a number of cyanobacteria, green algae, brown algae,
red algae, and diatoms could oxidize naphthalene. Some studies
also reported degradation of dyes, pesticides and heavy metals.
Protozoa are main grazer on the degrading bacteria. Protozoa help
on regulating growth of bacteria and algae populations, reducing
competition, improving turnover of nutrients, increasing space
and oxygen content, releasing excess nitrogen and special enzyme
required for biodegradation, and stimulating decomposition rates.
For example, protozoa infusorians can accelerate biodegradation
of PAH. The degrading rate of bacteria has improved 8.5 times on
benzene and methylbenzene, and 4 times on naphthalene by the
influence of grazing bacteria of protozoa flagellate.

Degradation by Algae & Protozoa

Pollutants
Hydrocarbons

Microorganisms
Prototheca zopfii

PAHs, pyrene,
fluoranthene

Chlorella vulgaris, Scenedesmus

platydiscus, S. quadricauda, Selenastrum
capricornutum
Monocrotophos Aulosira fertilissima, Nostoc muscorum
Azo dyes
Methyl red,
orange II, GRed, basic
cationic, b.
fuchsin
Amido Black
Sky Blue, Acid
Red
Heavy metals

C. vulgaris, C. pyrenoidosa
C. vulgaris, Lyngbyala gerlerimi, Nostoc
lincki, Oscillatoria rubescens, Elkatothrix
viridis, Volvox aureus

Chroococcus minutus
Gloeocapsa pleurocapsoides, Phormidium
ceylanicum
Chlorella, Anabaena inacqualis,
Westiellopsis prolifica, Stigeoclonium
lenue, Synechococcus sp.

References
Walker,
1975
Wang, 2007;
Ueno, 2008
Megharaj,
1987
Jinqi, 1992
El-Sheekh,
2009

Parikh, 2005

Dwivedi,
2012

ALGAE

Chlorella

Scenedesmus quadricauda
Oscillatoria

Volvox aureus

Nostoc

Synechococcus

Stigeoclonium

Prototheca

Anabaena

PROTOZOA

Ciliate protozoa
surrounding
bacteria

Genetically Engineered Microorganisms

(GEMs)
Genetically Engineered Microorganisms (GEMs) or Genetically
Modified Organisms (GMOs) are microorganisms whose genetic
material have been altered using genetic engineering techniques
(known as recombinant DNA technology) inspired by natural
genetic exchange between microorganisms and have potential
capabilities of degrading chemical contaminants useful for
bioremediation.
In 1979, Dr. Anand Mohan Chakrabarty has engineered strain of
Pseudomonas putida (called as superbug or oil eating bug) that
contains hybrid plasmids capable of degrading different
compounds i.e. CAM (camphor), OCT (octane), XYL (xylene), and
NAH (naphthalene). This superbug was used by the US Govt. in
1990 for cleaning up oil spill in Texas.

Degradation by GEMs
Pollutants
Aliphatic,
aromatic,
terpenic, PAHs,
PCBs
TCE, BTEX,
salicylate,
naphthalene,
benzoate
BTEX,
naphthalene,
anthracene
TCE, toluene,
benzene
Chlorobiphenyls
Chromium, PCBs,
narcotics
2,4-D
Toluene, mercury

GEMs

References

Pseudomonas

Markandey,
2004;
Erickson, 1993

Pseudomonas putida TOL, RA500,

pAC25, pKF439, KT2442, TVA8

Sayler, 00;
Panke, 98;
Applegate, 98

Pseudomonas fluorescens HK44,

10586s/pUCD607

Sayler, 2000;
Sousa, 1997

P. pseudoalcaligenes KF707-D2

Suyama, 1996

Comamonas testosteroni VP44

Alcaligenes eutrophus
AE104/pEBZ141, H850Lr, 2050
Bacillus cepacia BRI6001L, A.
paradoxus
Deinococcus radiodurans

Hrywna, 1999
Srivastava,
Dyke, Layton,
Masson, 2002
Brim, 2000

BIOREMEDIATION & BIODEGRADATION

The principles, methods, strategies, mechanisms,
and limiting factors

Bioremediation & Biodegradation

Biodegradation is the process by which organic substances are broken
down into smaller compounds by living organisms.
Bioremediation is the process of utilizing microorganisms to degrade
environmental pollutants by transforming them into less toxic form.
Methods of bioremediation strategies could be:
in-situ (at the site) or ex-situ (away from the site)
aerobic (in presence of oxygen) or anaerobic (in absence of oxygen)
enhanced by enzymes or biosurfactants

Biodegradation can be mediated by:

Bacteria (bioremediation)
Fungi (mycoremediation)
Algae
Protozoa
Plants (phytoremediation)

In-situ Bioremediation
Natural Attenuation, Biostimulation, Bioaugmentation
Natural attenuation or bioattenuation is the reduction of contaminant
concentrations in the environment through biological processes (microbial
Indigenous
& exogenous plant and animal uptake), physical phenomena (advection,
biodegradation,
microorganisms
dispersion, dilution, diffusion, volatilization, sorption/desorption), and
chemical reactions (ion exchange, complexation, abiotic transformation).
Biostimulation is the addition of soil nutrients, trace minerals, electron
acceptors, or electron donors to enhance the biotransformation of soil
contaminants by indigenous microorganisms. It includes also bioventing and
biosparging.
Bioaugmentation is the technique for improving the capacity of a
contaminated biotope to remove pollution by the introduction of specific
competent strains of exogenous microorganisms or genetically engineered
microorganisms (GEMs).

Ex-situ Bioremediation

Composting, Land farming, Biopile, Bioreactor

Composting is a technique that involves combining contaminated soil

with non-hazardous organic amendants such as manure or agricultural
wastes.
Land farming is a simple technique in which contaminated soil is
excavated and spread over a prepared bed and periodically tilled until
pollutants are degraded.
Biopile is a hybrid of land farming and composting constructed as
aerated composted piles to control physical losses of the contaminants
by leaching and volatilization.
Bioreactor or slurry reactor is a containment vessel used to create a
three-phase (solid, liquid, gas) mixing condition to increase the
bioremediation rate of soil-bound and water-soluble pollutants as a
water slurry of the contaminated soil and biomass (microorganisms)
capable of degrading target contaminants.

Role of Enzymes in Biodegradation

The degradation of pollutants can be mediated or catalyzed by specific
enzymes secreted by the microorganisms like (mono- or di-) oxygenases,
peroxidases, oxidoreductases, hydrolases, hydroxylases, dehalogenase,
dehydrogenases, esterases, phosphotriesterases, etc.

Biosurfactants
Biosurfactants or bioemulsifiers are biological surface-active agents that
have both hydrophilic and hydrophobic moieties. Biosurfactants are
produced by either degrading or non-degrading microorganisms to help
on metabolizing carbon and energy source.

Biosurfactants can act by:

- forming micelles or microdroplets of pollutants
- reducing surface tension in chemical compounds
- increasing surface area of hydrophobic substrates
- increasing mixing of aqueous and non-aqueous fluid phases
- increasing rate of transfer into or through aqueous media
- increasing bioavailability of the compounds.
Low molecular weight biosurfactants include:
glycolipids (rhamnolipid, trehalose lipids, and sophorolipids)
or lipopeptides (surfactin, gramicidin S, and polymyxin).
High molecular weight biosurfactants include:
polysaccharides, proteins, lipopolysaccharides, lipoproteins
or complex mixtures of these biopolymers.

Aerobic Degradation:
R

R
NADH

O2

H OH
C

NAD+

NAD+

C
H OH

E1

Alkylbenzene

E2

OH

E3

O2

2,3-Dihydroxyalkylbenzene

Dihydrodiol

O
COOH

OH

NADH

RCOOH

COOH
E4

OH
Ring fission
product

O
2-Oxopenta4-enoate

E1 = Alkylbenzene dioxygenase
E2 = cis-alkylbenzene glycol dehydrogenase
E3 = 2,3-dihydroxyalkylbenzene 1,2-dioxygenase

Smith & Ratledge 1989

E4 = ring fission product-hydrolysing enzyme

CoA

Anaerobic Degradation:

Heider et al. 1999

H2 C

CH3

H
C

CH3

2[H]

CH2

Acetophenone
Carboxylase

Acetophenone

1-Phenylethanol

2[H]

CH3

1-Phenylethanol
Dehydrogenase

Ethylbenzene
Dehydrogenase

H2O

O
CoA

HO

Ethylbenzene

CoASH

CH2

Benzoylacetyl-CoA
forming enzyme

Benzoylacetate

CO2

Benzoylacetyl-CoA
CoA thiolase

Benzoylacetate-CoA

CoASH

Benzoyl-CoA

Acetyl-CoA

Pathway for Degradation of Aliphatic Compounds

degradation of a straight chain hydrocarbon:

E1

Bacteria involved:
Pseudomonas putida
Fungi (yeast) involved:
Candida maltosa, Candida tropicalis,
Candida apicola
e degradation of a cyclic hydrocarbon:

(Harayama et al. 1999)

E2

E3

Enzymes involved:
E1 = alkane monooxygenase
E2 = fatty alcohol
dehydrogenase
E3 = fatty aldehyde
dehydrogenase,

Pathway for Degradation of Aromatic Compounds

Benzene

Arene oxide

Bacteria involved:
Pseudomonas, Rhodococcus,
Mycobacterium
Fungi (yeast) involved:
Pleurotus ostreatus

cis/trans-dihydrodiol

Naphthalene

cis-1,2-naphthalene 1,2-dihydroxynaphthalene
dihydrodiol

he microbial degradation of catechol

Salicylic acid

Cathecol

Pathway for Degradation of PCBs

Organisms involved:
Dehalococcoides,
Thermotogales,
Chloroflexi

Pathway for anaerobic dechlorination of a highly chlorinated congener (Fish & Principe, 1994).

Organisms
involved:
Achromobacter,
Beijerinckia,
Pseudomonas
putida

Pathway for aerobic degradation of PCBs into chlorobenzoates (Sylvestre & Sandossi, 1994).

Mechanism in Plastic Degradation

Mechanism in Heavy Metal Degradation

Mechanisms of heavy metal bioremediation by
microorganisms include bioleaching, biomineralization,
biosorption, bioaccumulation, and biotransformation.

- Bioleaching: heavy metal mobilization through methylation reactions or

excretion of organic acids.
e.g. Acidithiobacillus ferrooxidans,Leptospirillum ferriphilum
- Biomineralization: heavy metal immobilization through formation of
insoluble sulfides, phosphates, carbonates, hydroxides or polymeric
complexes in response to localised alkaline conditions at cell surface.
e.g. Serratia, Citrobacter
- Biosorption: passive uptake of metals to the surface of living or dead
microbial cells by physico-chemical mechanisms including absorption,
adsorption, ion exchange, surface complexation and precipitation.
e.g. Bacillus subtilis, Rhizopus arrhizus
- Bioaccumulation: active uptake of essential elements (particularly heavy
metals) within the cell of microorganisms.
e.g. Pseudomonas, Arthrobacter
- Biotransformation: metabolic activity of microorganisms on metal ions
through enzyme-catalyzed redox reactions.

Mechanism in Radionuclide Degradation

Mechanisms of radionuclide bioremediation by microorganisms include bioreduction, biomineralisation,
bioaccumulation, and biosorption.

Factors affecting microbial degradation

Biological factors
competition between organisms for limited carbon sources
antagonistic interactions between microorganisms
predation of microbes by protozoa and bacteriophage

Physical factors
temperature
pH
moisture

Environmental factors
soil type and porosity
soil organic matter
soil oxidation-reduction potential

Temp.

(Bodishbaugh, 2006)

pH

References
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Das & Chandran, Microbial Degradation of Petroleum Hydrocarbon Contaminants: An
Overview, 2011.
Maigari & Maigari, Microbial Metabolism of PAHs: A Review, 2015.
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the Process, 2013.
Borja et al., Polychlorinated Biphenyls & Their Biodegradation, 2005.
Furukawa & Fujihara, Microbial Degradation of PCBs: Biochemical & Molecular Features,
2008.
Tokiwa et al., Biodegradability of Plastics, 2009.
Leja & Lewandowicz, Polymer Biodegradation & Biodegradable Polymers A Review, 2010.
Ali, Biodegradation of Synthetic Dyes - A Review, 2010.

Meenambigai et al., Biodegradation of Heavy Metals A Review, 2016.

Girma, Microbial Bioremediation of Some Heavy Metals in Soils: An Updated Review, 2015.
Newsome et al., The Biogeochemistry & Bioremediation of Uranium & Other Priority

References
Vidali, Bioremediation: An Overview, 2001.
Kothari et al., Microbial Degradation of Hydrocarbons.
Pandey et al., Microbial Ecology of Hydrocarbon Degradation in the Soil: A Review, 2016.
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