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Microbial Ecology Biogeochemical Cycling

Microbial Ecology the interactions of m.o.
with the biotic and abiotic components of the The cycling of nutrients through
environment ecosystems via food chains and
food webs,, includingg the exchange
g
The iimportance
Th t off th
these iinteractions
t ti and
d th
their
i
effects on the environment of nutrients between the biosphere
and the hydrosphere, atmosphere
Biogeochemical Cycles : describe the movement and geosphere (e.g., soils and
of chemical elements through the biological and sediments)
geological component of the world

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Key Elements of Biogeochemical Cycles

producers consumers

The role of microorganisms ?

decomposers
Help in

- the decomposition of pollutants and toxic wastes

- the efficient utilization of limited natural resources
a. Where do the nutrients that ecosystems use come from?
b. What happens to the nutrients within the ecosystem itself? - transformations of chemical substances that can
c. What happens to the nutrients once they leave the ecosystem?
be used by other organisms
d. Once nutrients are cycled through an ecosystem, how do they get back?
e. What are the rates of exchange of nutrients between the different pools?
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Siklus Karbon

• critically important to all form of life

closely linked with the flow of energy
• the
th ultimate
lti t source off allll carbon
b iis CO2
- raw material for photosynthesis
- major waste product of respiration and
combustion
• Fiksasi Karbondioksida
• Degradasi selulosa/karbohidrat
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•Ecosystems produce and process energy

primarily through the production and exchange
CO2 fixation
Org.cpd. Anaerobic of carbohydrates which depends on the carbon
cycle.
respiration and
(phototrophic fermentation •Once energy is used, it is lost to the ecosystem
bacteria) (anaerobic m.o.) through generation of heat
•Carbon is passed through the food chain
Methanogenic through herbivory, predation, and
Anaerobic procaryotes decomposition, it is eventually lost to the
atmosphere through decomposition in the form
CO2 CH4 CO2 of CO2 and CH4 . It is then re-introduced into
Aerobic Methane-oxidizing the ecosystem via photosynthesis.
procaryotes •However, the amount of carbon present in a
CO2 fixation system is not only related to the amount of
Respiration (cyanobacteria, primary production, as well herbivory and
algae, plants, and predation (e.g., secondary production), it is also
(animals, plants, driven by the rates of decomposition by micro-
chemoautotrophic
and m.o.) organisms
Org.cpd. procaryotes)
•Atmospheric carbon is rarely limiting to plant
growth
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• Contoh dekomposisi
komponen substrat
daun pohon Oak

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Methanogens (Methanobacterium, Methanococcus)

can anaerobically reduce CO2 to CH4
N2 O
Denitrification
CO2 + 4H2 CH4 + 2H2O N2
(Pseudomonas)
Nitrogen fixation
NO2
(Klebsiella)
Methanogens are found in anaerobic habitats -
Anaerobic
rich in organic matter e.g. swamps, marine Assimilation
Organic nitrogen NH3
sediments, intestinal tract and rumens of animals) Aerobic
Assimilation Ammonification Nitrogen fixation
the amount of CO2 fixed by heterotrophs and NO3
(Rhizobium)
-
methanogens is quite small compare to
photoautotrophs N2
(Nitrococcus) Nitrification
NO2 (Nitrosococcus)
-
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Siklus Nitrogen • Nitrogenase

Fiksasi Nitrogen
• Fiksasi nitrogen
• Fiksasi Nitrogen 1.Simbiotik :Rhizobium
Konversi nitrogen atmosfer 2. Non simbiotik : mikroorganisme bebas dan
independen
menjadi amoniak
Genus/Species Karakteristik Fisiologi
• Amonifikasi Azotobacter chroococcum
Asam amino menjadi Beijerinckia indica
amonia Derxia gummosa Heterotrof Aerob

• Nitrifikasi Cyanobacteria Fotosintetik

Clostridium sp Heterotrof
Konversi amonia menjadi Desulvovibrio spp.
nitrat Chromatium vinosum Anaerob

• Denitrifikasi Chlorobium
Rhodospirillum rubrum
Reduksi nitrat menjadi gas Rhodomicrobium vanielli
Fotosintetik

nitrogen
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•When we look at other nutrients, a somewhat different picture emerges than with the energy
cycle – e.g., phosphorous in a food chain within a small pond.
•Algae remove dissolved phosphorous from the water
•The phosphorous is then passed through different trophic levels through herbivory and
predation.
Higher phytoplankton •At each level there is some mortality, and then the phosphorous is passed to decomposers
bacteria zooplankton
plant •These organisms release phosphorous into the water where it is again taken up by primary
producers and the whole cycle starts up again

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

Sediment

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

sulfate
y
desulfurylation Aerobic assimilation
R-SH H2S SO4 2- R-SH
Anaerobic
•Example of changes in the amounts of tracer phosphorous being exchanged within an
aquatic food web Chromatium Dissimilatory
sulfate reduction Chromatium
•The values themselves represent changes in the pool levels, where each one of the Chlorobium
Desulfovibrio
lines represents a different pool Chlorobium
S2O3 2-
•Understanding the feeding relationship allows us to build a nutrient cycle model for So
this ecosystem
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Siklus Sulfur Human impact on the sulfur cycle is primarily in

the production of sulfur dioxide (SO2) from
industry (e.g. burning coal) and the internal
combustion engine. Sulfur dioxide can
precipitate onto surfaces where it can be
oxidized to sulfate in the soil (it is also toxic to
some plants), reduced to sulfide in the
atmosphere, or oxidized to sulfate in the
atmosphere as sulfuric acid, a principal
1.Sulfur dalam bentuk unsur tidak dapat digunakan oleh tanaman.Oksidasi
component of acid rain.
menjadi sulfat
2. Tanaman gunakan sulfur dalam sulfat untuk membentuk asam amino
dan protein
3. Sulfat dapat direduksi menjadi hidrogen sulfida oleh beberapa mikroba
tanah
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4. Beberapa bakteri fototrof hijau dan ungu dapat mengoksidasi hidrogen 20
sulfida

Microbes and Soil • many kinds of bacteria, fungi, algae, and

protozoa are found in soil
• soil consists of organic and
mineral matter and capable of
supporting life
• soil characteristics depend on
1. Climate and availability
of water
2. Geologic age (young-old)
3. Biological inhabitants

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Bacteria are the dominant m.o. in soil • obligate anaerobes such as Clostridium and
Desulfovibrio are also found in soil
• they are responsible for many of the
• soil bacteria are especially noted for their
biochemical changes in soil diverse metabolisms because the organic
• the most common soil bacteria : Arthrobacter, nutrients in soil vary
Bacillus, Pseudomonas, Agrobacterium,
Pseudomonas Different types
Alcaligenes, Flavobacterium, Streptomyces,
of CHO
and Nocardia (Actinomyces)
Bacillus Starch, cellulose, gelatin
Arthrobacter Pesticides, caffeine, phenol
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Fungi Role and activity of fungi

• degrade organic matters
• account for a large part of microbial • control growth of other organisms e.g.
population in well-aerated, cultivated soil
Predator protozoa, nematode
• make up a significant part of total biomass
• humus formation
because of their large size and extensive
• improve soil aggregation
network of filaments
• help in the nutrient adsorption
• most common fungi isolated from soil :
of plant root e.g. mycorrhiza
Penicillium and Aspergillus
• cause disease in human, plants, and animals
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Role and activity of algae

Algae
increase organic carbon in soil
• eucaryotic algae and cyanobacteria are found CO2 org.-C
in the upper layers of soil
soil corrosion (from respiration product)
• algae do not require a source of organic
CO2 + H2O H2CO3
carbon because …????…
prevent soil erosion and improve soil
• light accessibility, N, and P are the limiting
aggregation
factor in the distribution of algae
nitrogen fixation blue-green algae

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Protozoa Virus
• are found in greatest abundance near the soil • different types of viruses persist in soil
surface (104 -105 cells) - Bacteriophages of soil bacteria
• why ? adequate food supply - viruses that cause human, animal, and
water availability and plant dieases ee.g.
g hepatitis virus
virus, tobacco
organic matter mosaic virus
• flagellated protozoa (e.g. Allantion, Bodo) - are of agricultural and public health
importance
dominate the flora of terrestrial habitats
• soil can also be a reservoir for pathogenic - the detection and monitoring of such
protozoa such as Entamoeba histolytica viruses in soil is important
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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 5-10 times more nitrogen is fixed
symbiotically than nonsymbiotically in free-
living bacteria
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the mutualistic association between rhizobia

Mycorrhiza
and legumes is highly specific certain types of soil fungi are closely
The plant benefits from the bacterial conversion associated with the roots of vascular plants
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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Endomycorrhiza
they significantly increase the absorption
area of the roots for minerals and water
Mycorrhizae are especially important in
nutrient-poor and water-limited environments
the fungus benefits from the carbohydrates
• the more common type and occur in approx.
made available to it by plant 80% of all vascular plant
the plants benefit from the increased • the fungal hyphae penetrate the cortical
absorption area provided by the fungus cells of the plant root and extend into the
surrounding soil
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Ectomycorrhiza Microbial Leaching

• are typically found in trees and shrubs,
particularly in temperate forests
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

• the plant roots are surrounded but not they obtain carbon from CO2 and energy
penetrated by fungal hyphae for growth from the oxidation of either iron
or sulfur
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Fe2+ Fe3+ Benefit : Microbial leaching in Copper mining

So S2- S2O32- SO42- • low grade Cu ores contain <0.5% Cu in the

form of chalcocite (Cu2S) or covellite (CuS)
Acid mine drainage serious problem
T.
8 Fe2+ + 2 O2 +8 H+ ferrooxid 8 Fe3+ + 4 H2O
FeS2 + H2SO4 + 1/2 O2 FeSO4 + 2 So + H2O ans2+
CuS + 8 Fe3+ + 4 H2O Cu + 8 Fe2++ SO42-+ 8
2 So + 2 H2O + 3 O2 2 H2SO4 H+
• microbial leaching of low-grade copper ores

Acidification of water is important in the mining industry

and surrounding soil
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• 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
i carbon
b
• 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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Lakes are relatively stagnant bodies of water

• Rivers also receive high concentration of
bacteria and agricultural chemicals through that can be divided into
Littoral zone

surface runoff water - zone of light penetration

Limnetic zone
• Rivers can be polluted with sewage bacteria
- temperature
p
esp E.
esp. E coli
coli, Enterococcus faecalis
faecalis, Proteus profundal zone

vulgaris, Clostridium sp., and other intestinal

epilimnion hypolimnion
bacteria

The microflora of a lake is determined by

lake’s nutrient content, thermal stratification,
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and light compensation level 46

Cyanobacteria and algae are abundant in the Quality of Water

littoral and limnetic zones
• less than 2 % of the world water is potable
Photoautotrophic bacteria (Clorobium,
Rhodopeudomonas, and Chromatium ---- use • fresh water is a precious resource that must
be conserved and closely monitored
reduced org. and inorg. substanses as
• Chemical
C e ca a anddbbiological
o og ca co
contaminants
a a sa affect
ec
e donors) are found at lower depths
e-donors)
the quality of water
Chemolithotrophic bacteria (Nitrosomonas,
Org. : pesticides, petroleum
Nitrobacter, and Thiobacillus) are also found
wastes, detergents, etc.
in freshwater bodies Chemical
contaminant
The m.o in water frequently are the beginning Inorg. : metals (Fe, Cd,
of food chain in aquatic environment Hg, Cu)
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Microbes
biological
(bacteria and
contaminant indicator organisms are frequently used to
viruses)
monitor bacterial contamination of water

• physical properties such as pH, temperature, those generally used are associated with the
gastrointestinal tract, since many waterborne
di
dissolved
l d oxygen, and
d salinity
li it also
l affect
ff t th
the pathogens are also found in the gastro-
quality of biological life in water intestinal tract and cause gastrointestinal
diseases
• Biochemical Oxygen Demand (BOD) is one
the most common group of indicator organisms
method to monitor water quality are the Coliforms G-ve, aerobic or
facultative anaerobic, nonspore-
49 forming rods, 50

ferment lactose with gas production within

48 hours at 35oC
they are in the family Enterobacteriaceae ;
E. coli, Enterobacter aerogenes, and
Klebsiella pneumoniae

Detection for presence and quantity

of coliforms

- The most probable number (MPN)

- The membrane filtration (MF)

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Biological Wastewater Treatment

The objective of wastewater treatment are
1. Remove organic matter and pathogenic
microorganisms
2. Remove toxic chemicals
wastewater treatment is classified as primary
primary,
secondary, or tertiary.
Primary involves the removal of
suspended solid and floating material
secondary microbes are used to further
purified the wastewater
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Tertiary additional purification, either m.o.

CHONPS + O2 CO2 + H2O
through filtration or chlorination
in 2nd treatment, organic matter in the
wastewater is oxidized by m.o.

O id ti pond,
Oxidation d
Aerobic process
activated sludge,
trickling filter

septic tank,
Anaerobic process
anaerobic
digestion, UASB Oxidation pond
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Activated sludge
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m.o. m.o.
CHONPS org. acids CO2 + H2S

+ NH3 + CH4

Wastewater treatment plant Septic tank

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Anaerobic digestion
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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
t h i pressures
m.o. are frequently found in the lower
portion of the troposphere (8-12 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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