Division of Microbiology

DEPARTMENT OF BIOLOGY
BOGOR AGRICULTURAL UNIVERSITY
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Microbial Ecology the interactions of m.o.
with the biotic and abiotic components of the
environment

The importance of these interactions and their

effects on the environment

Biogeochemical Cycles describe the movement

of chemical elements through the biological and
geological component of the world

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 producers consumers

The role of microorganisms ?

decomposers
Help in

- the decomposition of pollutants and toxic wastes

- the efficient utilization of limited natural resources
- transformations of chemical substances that can
be used by other organisms

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Carbon Cycle
critically important to all form of life
closely linked with the flow of energy
the ultimate source of all carbon is CO
- raw material for photosynthesis
- major waste product of respiration and
combustion

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 CO fixation
Org. C Anaerobic
respiration and
(phototrophic fermentation
bacteria) (anaerobic m.o.)

Methanogenic
Anaerobic procaryotes
CO CH CO
Aerobic Methane-oxidizing
procaryotes
CO fixation
Respiration (cyanobacteria,
algae, plants, and
(animals, plants,
chemoautotrophic
and m.o.)
Org. C procaryotes)

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 Nitrogen Cycle
NO
Denitrification
N
(Pseudomonas)
Nitrogen fixation
NO Anammox (Klebsiella)
-
Anaerobic Brocardia
Assimilation
Organic nitrogen NH
Aerobic
Assimilation Ammonification Nitrogen fixation
NO
(Rhizobium)
-

N
(Nitrococcus) Nitrification
NO (Nitrosococcus)
-

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Phosphorus Cycle
Higher phytoplankton
bacteria zooplankton
plant

Dissolved
org.ortho-P
Precipitated
Dissolved
inorg.-P
org.-P

Sediment

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 Sulfur Cycle
Beggiatoa
sulfate
assimilation R-SH Thiothrix
So Thiobacillus
(some procaryotes)

desulfurylation sulfate
Aerobic assimilation
R-SH HS SO - R-SH
Anaerobic

Chromatium Dissimilatory
sulfate reduction Chromatium
Chlorobium
Desulfovibrio
Chlorobium
SO -
So

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 Photoautotroph
Use light as E-source for CO fixation
Photosynthetic bacteria fix CO by a reversal of
the TCA cycle
was discovered in in Chlorobium
thiosulfatophilum green sulfur bact., anoxygenic)
requires ATP, NADH + H , reduced flavin, and
reduced ferredoxin
ferredoxin is reduced in a light-dependent
reaction coupled with the oxidation of H S
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 reduced ferredoxin serves as an electron donor
for the reduction of CO
this cycle probably occurs as a sole pathway
for CO fixation or in association with the
Calvin cycle
photoorganotrops or photoheterotrophs use
light as an E-source and organic compound as
C-source e.g. Rhodospirillaceae (purple non-
sulfur bact.)
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Chemoautotroph
Use chemical compounds (NH , NO -, CH , H S,
H ) as E-source for CO fixation
are widely distributed in the natural environment
e.g. freshwater ponds and springs Nitrifying
soil bacteria

acid drainage water Sulfur-oxidizing bacteria

Thiobacillus thiooxidans
Thiobacillus ferrooxidans
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 Heterotrophic CO fixation is a important
way for m.o. to synthesize intermediates of
TCA cycle from other chemical compounds

Phosphoenolpyruvate + CO oxaloacetate + Pi

ATP + pyruvate + CO oxaloacetate + ADP + Pi

Oxaloacetate formed by either type of

mechanism is used to keep the TCA cycle
functioning
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Methanogens (Methanobacterium, Methanococcus)
can anaerobically reduce CO to CH

CO + H CH + H O

Methanogens are found in anaerobic habitats

rich in organic matter e.g. swamps, marine
sediments, intestinal tract and rumens of animals)
the amount of CO fixed by heterotrophs and
methanogens is quite small compare to
photoautotrophs

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 Mineral Soils: the weathering of rock,
Organic Soils: Sedimentation in bogs
and marshes

Soils are microbial habitats, water

availability limits microbial activity

A soil aggregate composed of mineral

and organic components

Profile of a mature soil

Bacteria are the dominant m.o. in soil
they are responsible for many of the
biochemical changes in soil
the most common soil bacteria : Arthrobacter,
Bacillus, Pseudomonas, Agrobacterium,
Alcaligenes, Flavobacterium, Streptomyces,
and Nocardia (Actinomyces)

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 obligate anaerobes such as Clostridium and
Desulfovibrio are also found in soil
soil bacteria are especially noted for their
diverse metabolisms because the organic
nutrients in soil vary

Pseudomonas Different types

of CHO
Bacillus Starch, cellulose, gelatin
Arthrobacter Pesticides, caffeine, phenol

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 Fungi

account for a large part of microbial

population in well-aerated, cultivated soil
make up a significant part of total biomass
because of their large size and extensive
network of filaments
most common fungi isolated from soil :
Penicillium and Aspergillus

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Role and activity of fungi
degrade organic matters
control growth of other organisms e.g.
Predator protozoa, nematode
humus formation
improve soil aggregation
help in the nutrient adsorption
of plant root e.g. mycorrhiza
cause disease in human, plants, and animals
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 eucaryotic algae and cyanobacteria are found
in the upper layers of soil
algae do not require a source of organic

carbon because ????

light accessibility, N, and P are the limiting

factor in the distribution of algae

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Role and activity of algae

increase organic carbon in soil

CO org.-C
soil corrosion (from respiration product)
CO + H O H CO
prevent soil erosion and improve soil
aggregation
nitrogen fixation blue-green algae

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 are found in greatest abundance near the soil
surface ( - cells)
why ?
adequate food supply
water availability and
organic matter

flagellated protozoa (e.g. Allantion Bodo

dominate the flora of terrestrial habitats
soil can also be a reservoir for pathogenic
protozoa such as Entamoeba histolytica
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 Virus
different types of viruses persist in soil
- Bacteriophages of soil bacteria
- viruses that cause human, animal, and
plant dieases e.g. hepatitis virus, tobacco
mosaic virus
- are of agricultural and public health
importance
- the detection and monitoring of such
viruses in soil is important

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Nitrogen Fixation
Symbiotic: Rhizobium, Bradyrhizobium
Non-Symbiotic/free-living: Azospirillum, Azotobacter,
Rhodospirillum, Rhodobacter, Clorobium
rhizosphere = the region of soil closely
surrounding the roots
rhizosphere effect = a consequence of the
excretion of organic matter by plant roots to
attract and stimulate the growth of soil
bacteria
an estimated - times more nitrogen is fixed
symbiotically than nonsymbiotically in free-
living bacteria
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N2+8H++8e-+16MgATP 2NH3+H2+16 MgADP+16Pi
Nitrogenase

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the mutualistic association between rhizobia
(Rhizobium or Bradyrhizobium) and legumes is
highly specific
The plant benefits from the bacterial conversion
of gaseous N into a usable combined form
the plant provides the bacterium with nutrient
for growth and metabolism
N-fixation occurs only if a legume is infected by
a specific rhizobial species
the roots of leguminous plant secrete flavonoid
compounds that attract rhizobia to rhizosphere
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Leaching : is commercially used for the
extraction of Cu, Pb, Zn, and Ur from
sulfide-containing ores
Thiobacillus thiooxidans and Thiobacillus
ferrooxidans are acidophilic and generally
found in acid environments e.g. hot
springs and sulfide ore deposits
they obtain carbon from CO and energy
for growth from the oxidation of either iron
or sulfur
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 Fe Fe

So S - SO - SO -

Acid mine drainage serious problem

FeS + H SO + / O FeSO + So + H O
So + H O+ O H SO

Acidification of water
and surrounding soil
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 Benefit : Microbial leaching in Copper mining
low grade Cu ores contain < . % Cu in the
form of chalcocite (Cu S) or covellite (CuS)

T. ferrooxidans
8 Fe + O + H Fe + HO

CuS + Fe + HO Cu + Fe + SO -+
H
microbial leaching of low-grade copper ores
is important in the mining industry

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Microbes and Water

typical aquatic environments are the oceans,

estuaries, salt marshes, lakes, ponds, rivers,
and springs
because aquatic environments differ considerably
in chemical and physical properties, so their
microbial species compositions also differ

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 saltwater organisms differ from freshwater
organisms based upon osmotic properties

Algae (phytoplankton) are common in

marine habitats and provide significant
organic carbon

the bacterial population in estuaries

consists of Pseudomonas, Flavobacterium,
and Vibrio, as well as enteric organisms

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 the numbers and types of bacteria in water
depend on the physical parameter of
water -- salinity, temperature, dissolved
oxygen, and pH
freshwater habitats contain a wide variety of
microorganisms
Rivers may contain large numbers
of soil bacteria (Bacillus, Actinomyces), fungi
Penicillium, Aspergillus), and algae
Microcystis, Nostoc
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 Rivers also receive high concentration of
bacteria and agricultural chemicals through
surface runoff water
Rivers can be polluted with sewage bacteria
esp. E. coli, Enterococcus faecalis, Proteus
vulgaris, Clostridium sp., and other intestinal
bacteria

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Lakes are relatively stagnant bodies of water

that can be divided into Littoral zone

- zone of light penetration

Limnetic zone

- temperature profundal zone

epilimnion hypolimnion

The microflora of a lake is determined by

lakes nutrient content, thermal stratification,
and light compensation level
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Cyanobacteria and algae are abundant in the
littoral and limnetic zones
Photoautotrophic bacteria (Clorobium,
Rhodopeudomonas, and Chromatium ---- use
reduced org. and inorg. substanses as
e-donors) are found at lower depths
Chemolithotrophic bacteria (Nitrosomonas,
Nitrobacter, and Thiobacillus) are also found
in freshwater bodies
The m.o in water frequently are the beginning
of food chain in aquatic environment
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Microbes and The Air
Microorganisms are not found in the upper
regions of the atmosphere because of the
temp. extremes, available oxygen, absence
of nutrients and moisture, and low
atmospheric pressures
m.o. are frequently found in the lower
portion of the troposphere ( - km from
earth)
most of them are either spore formers or
microbes that are easily dispersed in the air
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Ex. : Cladosporium, Alternaria, Penicillium,
Actinomyces, Aspergillus, Bacillus, Sarcina,
Corynebacterium, Achromobacter
the relative low humidity in the atmosphere
and UV rays from the sun limit the types
and number of m.o. in the air
Nevertheless, the atmosphere serves as an
important medium for dispersing many
types of microbes to new environment
many microbial diseases are transmitted
through the air during sneezing, coughing,
or even normal breathing
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