Environmental

Biotechnology
(BBT427)

Spring 2020

Lecture 03
Prepared by Dr. Ishrat Jabeen
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 Role of Microbes in Biogeochemical Cycling
• Microorganisms play a primary role in regulating biogeochemical systems in virtually all of
our planet ‘s environments.

Figure: The Water Cycle:

Water is recycled in an
ecosystem through the water
cycle.

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The Carbon Cycle: •Carbon is critical for life
because it is the essential
building block of all
organic compounds.
•Plants and animals utilize
carbon to produce
carbohydrates, fats, and
proteins, which can then
be used to build their
internal structures or to
obtain energy.
Figure: Cyanobacteria: Cyanobacteria, also
known as blue-green bacteria, blue-green algae,
and Cyanophyta, is a phylum of bacteria that
obtain their energy through photosynthesis

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Aquatic microorganisms
• Freshwater microbiota: microbiota found in the
various zones of a typical lake or pond.
The littoral zone: along shore, rooted vegetation.
The limnetic zone: surface of the open water area
away from the shore.
The profundal zone: deeper water under the
limnetic zone.
The benthic zone: Bottom sediment.
• Seawater microbiota: Seafloor sediments have
been found to have large populations of bacteria.
Divides into zones based on light and O2 availability.
Includes abyssal zones dominated by archae.

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 Freshwater microbiota
• Low oxygen concentrations and less light in deeper water of the profundal and
benthic zones.
• Purple and green sulphur bacteria are found in the profundal zone which are
anaerobic photosynthetic organisms that metabolize H2S to sulphur and sulphate
in the bottom sediments of benthic zone.
• The sediment in the benthic zone includes Desulfovibrio that use sulphate as an
electron acceptor and reduce it to H2S.
• Methane producing bacteria are also part of these anaerobic benthic population
which produces methane in swamps, marshes or in bottom sediments.
• Clostridium species are also common in bottom sediments and may include
botulism organisms (those causing outbreaks of botulism in waterfowl).

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Freshwater microbiota

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Seawater microbiota
• Phytoplankton in top 100 m Luminous organ • Phytoplankton below ~ 100 m:
Photosynthetic cyanobacteria fix Members of Archaea dominate the
carbon microbial life
Prochlorococcus  Well adapted to the cool
Synechococcus temperatures and low O2 levels
 Fix nitrogen Crenarchaeota
Trichodesmium  Luminescent
• Decomposed by Have luciferase enzyme
Pelagibacter ubique Photoblepharon palpebratus-the
deep-sea flashlight fish

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Role of microorganisms in water quality
Microbes include microalgae, bacteria, fungi and virus
• Microalgae: Its mainly photosynthesize to absorb CO2 and to supply oxygen in
aquatic animal.
• Bacteria and fungi: To decompose organic matter and keep the water clean.
Microbes are the predominant photosynthetic organism in most aquatic
environment
• In aerobic condition, algae, diatoms and cyanobacteria predominant.
• In anaerobic conditions, other photosynthetic bacteria are dominant.

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 Pathogens and Parasites in Water and Waste
Water
• Waterborne pathogens can occur in all types of water sources and are
particularly rampant in areas where there are large amounts of untreated
wastewater.
• Wastewater is defined as any water that has been used, such as for domestic or
industrial use and contains waste products. These waste products are most often
liquid or solids and they can be biological, chemical or radioactive.
• Heavy, slow-moving, degraded water, filled with an excess of contaminants can
also create a sludge, which may contain pathogens such as fungi, worms and
toxins. Sludge can also contain fecal bacteria and bloodborne viruses.
• The commonly found viruses in wastewater are Hepatitis and Norwalk virus and a
common fungus is Candida.

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 Pathogens and Parasites in Water and Waste Water-
contd..

• Common bacteria, such as Salmonella can cause food poisoning where as Vibrio
cholerae is the pathogen that causes cholera.
• Parasites such as Cryptosporidium and Schistomsoma can cause diarrhoea, and
just about all wastewater pathogens can lead to serious gastrointestinal illness in
addition to other, more specific implications, which is significant cause of death
worldwide. (Source: 2005, Wastewater Pathogens by Michael H. Gerardi and Mel
C. Zimmerman and Rehydration Project: Focus on Diarrhoea, Dehydration and
Rehydration)
• Even water that looks clear can contain pathogens, as raw waste and pollutants
are sometimes discharged into relatively pristine waterways from point and non-
point sources.

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Adverse effects of pathogens and parasites in water and waste water

• Having adverse health implications.

• Wastewater contamination can also have natural and ecological affects. These
may include the degradation of ecosystems such as a decrease in important
aquatic plants that help preserve the condition of waterways or biodiversity loss
such as loss of aquatic life like fish and crustaceans that are an important part of
both animal and human diet.
• Excessive nutrients can hasten algae growth which then leads to a decrease in
dissolved oxygen. This overgrowth of algae clouds the water and prevents
sunlight from permeating, leading to the destruction of important organisms,
plant and animal life.

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Biosensors- Recent development in biosensors in
environment pollution detection

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 Indicator Organisms and Disinfections

Faecal indicator: Coliforms, thermotolerant coliforms,

Faecal streptococci, Enterococci, Sulphite-reducing
clostridia, Clostridium perfringens

Index and model organisms

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Limitations of pathogens

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Limitations of pathogens

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Water treatment
• Coagulation and filtration
• Disinfection

Sewage (Wastewater treatment)

• Primary sewage treatment
• Biological Oxygen Demand (BOD)
• Secondary sewage treatment
• Sludge digestion
• Septic tanks
• Oxidation ponds
• Tertiary sewage treatment

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 Use of commercial blend of microorganisms and
enzymes in waste water treatment
(i) Bioaugmentation (Use of Blends of Microorganism):
• Acceleration of biodegradation of specific compounds by inoculating bacterial
cells is called bioaugmentation.
• Bacterial cells contain specific plasmid which encodes enzymes for degradation of
those, compounds.
• A variety of plasmids have been reported from Alcaligenes, Acinetobacter,
Arthrobacter, Beijerinkia, Klebsiella, Flavobacterium and Pseudomonas.
• Several genetically engineered strains have been developed exploiting
Pseudomonas.

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Application of bio
augmentation includes:
(a) The increased BOD removal in
wastewater treatment plants,
(b) Reduction of sludge volume by
about 30% after addition of selected
microorganisms,
(c) Use of mixed cultures in sludge
digestion,
(d) Biotreatment of hydrocarbon
waste, and
(e) Biotreatment of hazardous wastes.

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(ii) Use of Enzymes in Wastewater Treatment:
• Several enzymes have been detected in wastewaters such as catalase,
phosphate esterases and aminopeptidases.
• These enzymes can be added to freshwater to improve
biodegradation of xenobiotic compounds.
• For example parathion hydrolases (isolated from Pseudomonas and
Flavobacterium) have been used to clean up the containers of
parathion and detoxification of wastes containing high concentration
of organophosphates.

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 Use of Commercial Blends of
Microorganisms/Enzymes in Wastewater Treatment
(a) Removal of brown lignin compounds:
Brown lignin compounds are found in paper mill effluents. Immobilised
white-rot fungus (Coriolus versicolor) can be used to remove this
compounds.
(b) Biodegradation of phenolic compounds:
• Much information is available on degradation of phenolic compounds
by using bacteria.
• Immobilised cells of Pseudomonas, Arthrobacter and Alcaligens
degrade chlorinated phenols.
• Bioreactors containing Flavobacterium immobilised in calcium alginate
can degrade pentachorophenol at maximum rate (i.e 0.85 mg/g beads/
hours).

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• Immobilised tyrosinase can remove rapidly phenol, chlorophenol,
methoxylphenol and cresols from fresh water.
• A polycation derived from chitin (chitosan) can remove efficiently the
coloured products from the effluents.
(c) Methane production by Immobilised methanogens:
Anaerobic waste treatment can be enhanced using immobilised
methanogens in two-staged bioreactors.
(d) Dehalogenation of chloroaromatics:
Immobilised cells of Pseudomonas sp. removes chlorides linked to aromatic
compounds.
(e) Immobilised activated sludge microorganisms:
A high treatment efficiency was achieved with a two step process consisting
a reactor containing immobilised activated sludge microorganisms followed
by a biofilm reactor.

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(f) Use of immobilised algae to remove micronutrients from
wastewater effluent:
Immobilised Phormidium or Scenedesmus removes nitrogen and
phosphorus from wastewater effluents.
(g) Use of immobilised cells/enzymes in biosensor technology:
• Biological sensing elements are immobilised microorganisms,
enzymes, nucleic acids or antibody which interacts with an analyze
and produce a signal.
• This signal is transmitted to transducer which converts it into an
electrical signal.
• Different types of biosensors have been developed for its use in food,
clinical, pharmaceutical and wastewater treatment. 

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 Potential applications of recombinant DNA
technology in waste treatment

Recombinant DNA technol­ogy is involved in

two steps:
(a) Searching out of micro­organisms of desired func­
tion, and
(b) Transfer of char­acter of desired function to the
other microbes relevant to environment.

Such mi­crobe is called genetically engineered

microorganism (GEM).

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 Stoichiometry and Kinetics
• Stoichiometry measures these quantitative relationships, and is used to
determine the amount of products and reactants that are produced or needed in
a given reaction. In Greek, stoikhein means element and metron means measure,
so stoichiometry literally translated means the measure of elements.
• A kinetic expression can be presented to describe the acetate-uptake rate of
phosphorus accumulating organisms (PAOs)-which are enriched in wastewater
treatment systems (when the biomass is continuously recirculated between
anaerobic and aerobic environments and when all of the influent is directed to
the anaerobic portion of the system).

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