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1. 10. Environmental microbiology
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2. Learning objectives
At the end of this unit you must be able to
• To list microbes that are found in different waters
• To describe methods used in the determination of
bacteriological quality of water
• To describe steps in the purification of water
• To describe steps in sewage treatment
• To explain why water purification and sewage treatment is
necessary
• List the different groups of microbes found in the soil
• Discuss the role of microbes in the soil
• Describe/draw the carbon, nitrogen and sulfur cycles.
• Define mineralization and decomposition
• Distinguish between nitrogen fixation, nitrification,
denitrification and amonification 2

3. 10.1.Microbial Diversity
• Microorganisms live in a wide variety of habitats because
of their metabolic diversity and their ability to use a
variety of carbon and energy sources and to grow under
different physical conditions.
• Microbes that live in extreme conditions of temperature,
acidity, alkalinity, or salinity are called extremophiles.
• Most are members of the Archaea.
• The enzymes (extremozymes) produced by extremophiles
can tolerate extremes of temperature, salinity, and pH that
would inactivate other enzymes.
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4. 10.2. Soil microbiology and
biogeochemical cycles
Soil microbes and their roles
• Soil microbiology studies about soil
microorganisms and their roles.
• Soil microorganisms include bacteria, fungi,
actinonmycetes, protozoa, algae and
cyanobacteria
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5. Microorganism Number of cells/g of soil
Bacteria 106-109
Yeasts 103
Molds 10-102
Protozoa 104-106
Algae 102-104
Table 10.1. Relative abundance of different groups of microbes
in the soil
• Fungi occur as free living or associated with plant root.
• The most common soil fungi are fungi imperfecti, but
numerous ascomycetes and basidiomycetes also occur.
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6. • Microbes in the soil are important for
biodegradation and mineral cycling.
• Bacteria, fungi and actinomycetes are decomposers
and mineralizers in the biogeochemical cycles.
• They degrade important polymers such as cellulose
and lignin.
• Protozoa function as predators and they control
bacterial growth.
• The soil also contains pathogenic microorganisms.
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7. • Essential elements such as carbon, nitrogen, sulfur,
phosphorus, oxygen, and iron are recharged through
biological, geologic, and chemical mechanisms called
biogeochemical cycles.
• All elements ultimately originate from a nonliving, long-term
reservoir in the atmosphere, the lithosphere, or the
hydrosphere.
• Elements such as C, N, S, P, etc., are recycled between the
abiotic environment and the biotic environment.
• Recycling maintains a necessary balance of nutrients in the
biosphere so that they do not build up or become unavailable.
Microbial biogeochemical cycling
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8. Carbon cycle
• Carbon is actively cycled between inorganic CO2
and the variety of organic compounds that
compose living organisms and their dead
organic matter.
• This cycle primarily involves the transfer of CO2
and organic carbon between the atmosphere,
and the hydrosphere and lithosphere (Figure 1).
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9. 9

10. • Chemolithotrophs and photolithotrophs are
responsible for primary production i.e. conversion of
CO2 to organic carbon.
• Once carbon is fixed (reduced) into organic
compounds it will be available for heterotrophs.
• Respiration and degradation of soil organic matter
brings CO2 back to the atmosphere.
• Soil microbes convert organic matter to various
nutrients. This is called mineralization.
• Microbes decompose complex organic substances
such as cellulose, hemicellulose and pectin into
simple sugars. 10

11. Nitrogen cycle
• Nitrogen cycling involves nitrogen fixation, ammonification,
nitrification and denitrification (Figure 2).
• Nitrogen cycling is largely dependent on microbes.
Nitrogen fixation
• Nitrogen fixation, the conversion of N2 to ammonia or organic
nitrogen, is restricted to prokaryotes only.
• Ammonia is assimilated into amino acids and subsequently
synthesized into proteins and nucleic acids.
• In soil, microbial fixation of N2 is carried out by free-living
bacteria (asymbiotic) and those in symbiotic association with
plants (symbiotic).
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12. • In agricultural soils nitrogen fixation by Rhizobium and
Bradyrhizobium is most important, where these bacteria live
with legume crops only.
• In forests, other symbiotic N-fixing bacteria including
actinomycetes live in association with various trees
(nonleguminous plants).
• The Free-living N-fixing bacteria Azotobacter, Azomonas and
Derxia are common in temperate regions in neutral or alkaline
soils.
• In tropics, Beijerinkia, more acid tolerant, are prevalent in soil.
• In aquatic habitats, cyanobacteria, such as Nostoc and
Anabaena are important N-fixers.
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13. Ammonification
• Many microbes (bacteria & fungi) as well as plants
and animals are able to convert organic nitrogen
compounds such as amino acids, urea, etc to
ammonia i.e. ammonification.
• Ammonia is then returned to the atmosphere or it is
converted to NH4
+ in moist soil and is used by
bacteria & plants for amino acid synthesis.
Nitrification
• In this process, ammonium ions are initially oxidized
to nitrite ions and subsequently to nitrate ions.
• The two steps are carried out by nitrifying bacteria,
which are aerobic.. 13

14. • Nitrifying bacteria include:
a. Ammonia-oxidizing bacteria
• E.g. Nitrosomonas (dominant in the soil,) Nitrosospora,
nitrosococcus and Nitrosolobus.
b. Nitrite-oxidizing bacteria
• E.g. Nitrobacter, Nitrospora and Nitrococcus.
• Nitrification is an aerobic process.
Denitrification
• Is the conversion of toxic forms of nitrogen to
molecular nitrogen
• is anaerobic process carried out by Pseudomonas,
Moraxella, Spirillum, Thiobacillus and Bacillus. 14

15. 15

16. Sulfur cycle
• Microbes are able to remove sulfur from organic
compounds.
• Under aerobic conditions, the removal of sulfur results in
the formation of sulphate, whereas under anaerobic
conditions H2S is formed.
• H2S may also be produced by sulfate-reducing bacteria. In
anaerobic sulphate-rich marine sediments H2S is
generated by reducers like Desulfovibrio (Figure 3).
• Beggiatoa and Thiothrix are heterotrophs that oxidize H2S
to generate ATP.
• Thiobacillus species, which are found in acidic habitats
oxidize H2S and generate ATP that is used for CO2 fixation.
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17. Figure 3. Sulfur cycle
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18. 10.3. Aquatic microbiology and sewage treatment
• Aquatic microbiology is the study of microorganisms and
their activities in natural waters, such as lakes, ponds,
streams, rivers, estuaries, and oceans.
Aquatic Microorganisms
• Large numbers of microorganisms in a body of water
generally indicate high nutrient levels in the water.
• Water contaminated by inflows from sewage systems or from
biodegradable industrial organic wastes is relatively high in
bacterial numbers.
• Ocean estuaries (fed by rivers) have higher nutrient levels and
therefore larger microbial populations than other shoreline
waters. 18

19. Freshwater Microbiota
• Microbial populations of freshwater bodies
tend to be affected mainly by the availability
of oxygen and light.
• Photosynthetic algae are the primary
producers of a lake that support a population
of bacteria, protozoa, fish, and other aquatic
life.
• They are located in the limnetic zone.
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20. • Microorganisms growing on nutrients in stagnant water
quickly use up the dissolved oxygen in the water.
• In the oxygenless water, fish die, and anaerobic activity
produces odors.
• Wave action in shallow layers, or water movement in
rivers, tends to increase the amount of oxygen throughout
the water and aid in the growth of aerobic bacteria.
• Deeper waters of the profundal and benthic zones have
low oxygen concentrations and less light.
• Purple and green sulfur bacteria are found in the
profundal zone.
• These bacteria are anaerobic photosynthetic organisms
that metabolize H2S to sulfur. 20

21. • The sediment in the benthic zone includes
bacteria such as Desulfovibrio that use sulfate
(SO42-) as an electron acceptor and reduce it
to H2S.
• Methane-producing bacteria are also part of
these anaerobic benthic populations.
• In swamps, marshes, or bottom sediments,
they produce methane gas.
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22. Figure. Distribution of life in a freshwater lake 22

23. Seawater Microbiota
• Photosynthetic cyanobacteria fill the upper 100 meters of
ocean.
• They fix carbon dioxide to form organic matter that is
eventually released as dissolved organic matter and is used by
the ocean’s heterotrophic bacteria.
• Photosynthetic bacteria form the basis of the oceanic food
chain.
• Phytoplankton are the primary producers of the open ocean.
• Cyanobacteria fixes nitrogen and helps replenish the nitrogen
that is lost as organisms sink to oceanic depths.
• Archaea predominate below 100 m.
• Seafloor sediments bacteria are mostly Archaea. 23

24. Microbial pollution of water and water borne diseases
• Water that moves below the ground’s surface undergoes a
filtering that removes most microorganisms.
• For this reason, water from springs and deep wells is
generally of good quality.
• The most dangerous form of water pollution occurs when
feces enter the water supply.
• The contaminants include coliform bacteria such as E.coli,
Salmonella, faecal streptococci, cholera bacteria,
protozoan cysts, enteric viruses, etc.
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25. • Water can be a vehicle for the transfer of a wide
range microbial diseases, including typhoid fever,
cholera and bacterial dysentery.
• Viral diseases transmitted by water are virus A
hepatitis and polio.
• Protozoan diseases such as amoebiasis,
giardiasis, etc, are also transmitted through
water.
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26. Water treatment
• Water may contain pathogenic microorganisms.
– Must be purified
Steps in water purification:
Sedimentation
• Removes bulky objects such as leaves, sand and gravel
particles. Microbes are also removed.
Filtration
• passing water through fine sand or coal; microorganisms
adsorb to sand particles
• removes the remaining microbes from the water.
Disinfection
– Chlorination: chlorine gas is added to the water. Chlorine reacts
with organic matter in the water.
– Ozonation
– UV- radiation 26

27. Sewage treatment
• Domestic water is called sewage.
• It includes housed hold water, toilet wastes,
industrial wastes, and rainwater.
• Since sewage contains biological and chemical
contaminants, it has to undergo treatments
which remove or reduce the contaminants.
• Steps in sewage treatment: primary,
secondary and tertiary treatments.
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28. Primary sewage treatment
• It is the removal of solid matter (that collects at the
bottom) called sludges (by sedimentation).
• Sludge collects in sedimentation tanks
• It removes 25–35% of Biochemical oxygen demand
(BOD).
BOD
– the measure of the biodegradable organic matter in
water
– Determined by the amount of oxygen required by
bacteria to metabolize organic matter
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29. • Secondary sewage treatment
– the biological (microbial) degradation of organic matter in
sewage aerobically and anaerobically
– Degradation by aerobic microbes is done in two ways:
• Activated sludge system
– Air passes through the effluent from primary
treatment
– Contains aerobic sewage-metabolizing microbes
– Removes 75–95% of BOD
• Trickling filters
– Sewage sprayed over rocks or plastic, forming biofilm
of aerobic microbes
– Removes 80–85% of BOD
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30. • Degradation by anaerobic microbes occurs in
anaerobic sludge digesters.
– Sludge from primary treatment is placed in anaerobic sludge
digester and anaerobic bacteria degrade organic solids into
methane and carbon dioxide.
• Tertiary sewage treatment
– Removal of remaining BOD, nitrogen, and phosphorus
• N2 and NH3 evaporate and PO4 precipitated
– Physical and chemical treatment
• Filters of fine sands and activated charcoal remove small particulate
matter and dissolved chemicals.
• Chlorination
– Water is drinkable after treatment
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