Microbial Ecology

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Microbial Ecology
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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Biogeochemical Cycling
The cycling of nutrients through ecosystems via
food chains and food webs, including the exchange
of nutrients between the biosphere and the
hydrosphere, atmosphere and geosphere (e.g.,
soils and sediments)
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Key Elements of Biogeochemical Cycles

1. Where do the nutrients that ecosystems use come
   from?
2. What happens to the nutrients within the
   ecosystem itself?
3. What happens to the nutrients once they leave the
   ecosystem?
4. Once nutrients are cycled through an ecosystem,
   how do they get back?
5. What are the rates of exchange of nutrients
   between the different pools?

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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 CO2
• - raw material for photosynthesis
• - major waste product of respiration and
• combustion

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Siklus Karbon

• Fiksasi Karbondioksida
• Degradasi selulosa/karbohidrat

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Org.cpd.
Anaerobic respiration and fermentation
CO2 fixation
(phototrophic bacteria)
(anaerobic m.o.)
Methanogenic procaryotes
Anaerobic
CO2 CH4
CO2
Aerobic
Methane-oxidizing procaryotes
CO2 fixation
Respiration
(cyanobacteria, algae, plants, and
chemoautotrophic procaryotes)
(animals, plants, and m.o.)
Org.cpd.
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• Ecosystems produce and process energy primarily
  through the production and exchange of
  carbohydrates which depends on the carbon cycle.
• Once energy is used, it is lost to the ecosystem
  through generation of heat
• Carbon is passed through the food chain through
  herbivory, predation, and decomposition, it is
  eventually lost to the atmosphere through
  decomposition in the form of CO2 and CH4 . It is
  then re-introduced into the ecosystem via
  photosynthesis.
• However, the amount of carbon present in a system
  is not only related to the amount of primary
  production, as well herbivory and predation
  (e.g., secondary production), it is also driven
  by the rates of decomposition by micro-organisms
• 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
CO2 4H2 CH4 2H2O
Methanogens are found in anaerobic habitats rich
in organic matter e.g. swamps, marine sediments,
intestinal tract and rumens of animals) the
amount of CO2 fixed by heterotrophs and
methanogens is quite small compare to
photoautotrophs
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Nitrogen Cycle
N2O
Denitrification
N2
(Pseudomonas)
Nitrogen fixation
NO2-
(Klebsiella)
Anaerobic
Assimilation
Organic nitrogen
NH3
Aerobic
Assimilation
Ammonification
Nitrogen fixation
NO3-
(Rhizobium)
N2
Nitrification
(Nitrococcus)
NO2-
(Nitrosococcus)
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Siklus Nitrogen

• Fiksasi Nitrogen
• Konversi nitrogen atmosfer menjadi amoniak
• Amonifikasi
• Asam amino menjadi amonia
• Nitrifikasi
• Konversi amonia menjadi nitrat
• Denitrifikasi
• Reduksi nitrat menjadi gas nitrogen

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Fiksasi Nitrogen

• Nitrogenase
• Fiksasi nitrogen
• 1.Simbiotik Rhizobium
• 2. Non simbiotik mikroorganisme bebas dan
  independen

Genus/Species Karakteristik Fisiologi Karakteristik Fisiologi
Azotobacter chroococcum Heterotrof Aerob
Beijerinckia indica Heterotrof Aerob
Derxia gummosa Heterotrof Aerob
Cyanobacteria Fotosintetik Aerob
Clostridium sp Heterotrof Anaerob
Desulvovibrio spp. Heterotrof Anaerob
Chromatium vinosum Fotosintetik Anaerob
Chlorobium Fotosintetik Anaerob
Rhodospirillum rubrum Fotosintetik Anaerob
Rhodomicrobium vanielli Fotosintetik Anaerob
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Phosphorus Cycle
phytoplankton
Higher plant
bacteria
zooplankton
Dissolved org.ortho-P
Precipitated inorg.-P
Dissolved org.-P
Sediment
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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.
• At each level there is some mortality, and then
  the phosphorous is passed to decomposers
• These organisms release phosphorous into the
  water where it is again taken up by primary
  producers and the whole cycle starts up again

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• Example of changes in the amounts of tracer
  phosphorous being exchanged within an aquatic
  food web
• The values themselves represent changes in the
  pool levels, where each one of the lines
  represents a different pool
• Understanding the feeding relationship allows us
  to build a nutrient cycle model for this ecosystem

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Sulfur Cycle
Beggiatoa Thiothrix Thiobacillus
sulfate assimilation
R-SH
So
(some procaryotes)
sulfate assimilation
desulfurylation
Aerobic
R-SH H2S
SO42- R-SH
Anaerobic
Dissimilatory sulfate reduction
Chromatium Chlorobium
Chromatium Chlorobium
Desulfovibrio
S2O32-
So
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Siklus Sulfur
1.Sulfur dalam bentuk unsur tidak dapat digunakan
oleh tanaman.Oksidasi 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 4. Beberapa bakteri fototrof hijau dan ungu
dapat mengoksidasi hidrogen sulfida
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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 component of acid rain.
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Microbes and 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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• many kinds of bacteria, fungi, algae, and
• protozoa are found in soil

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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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Algae

• 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 CO2 org.-C soi
l corrosion (from respiration product) CO2
H2O H2CO3 prevent soil erosion and improve
soil aggregation nitrogen fixation blue-green
algae
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Protozoa

• are found in greatest abundance near the soil
• surface (104 -105 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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Symbiotic Nitrogen Fixation
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 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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Mycorrhiza
certain types of soil fungi are closely
associated with the roots of vascular plants
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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 made available to it by
plant the plants benefit from the increased
absorption area provided by the fungus
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Endomycorrhiza

• the more common type and occur in approx.
• 80 of all vascular plant
• the fungal hyphae penetrate the cortical
• cells of the plant root and extend into the
• surrounding soil

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Ectomycorrhiza

• are typically found in trees and shrubs,
• particularly in temperate forests
• the plant roots are surrounded but not
• penetrated by fungal hyphae

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Microbial Leaching
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 CO2 and energy for growth from the
oxidation of either iron or sulfur
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Fe2 Fe3 So S2- S2O32- SO42-
Acid mine drainage serious problem
FeS2 H2SO4 1/2 O2 FeSO4 2 So H2O 2 So
2 H2O 3 O2 2 H2SO4
Acidification of water and surrounding soil
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• Benefit Microbial leaching in Copper mining
• low grade Cu ores contain lt0.5 Cu in the
• form of chalcocite (Cu2S) or covellite (CuS)

T. ferrooxidans
8 Fe2 2 O2 8 H 8 Fe3 4
H2O CuS 8 Fe3 4 H2O Cu2 8 Fe2
SO42- 8 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 - zone of light
penetration - temperature
Littoral zone
Limnetic zone
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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Quality of Water

• less than 2 of the world water is potable
• fresh water is a precious resource that must be
  conserved and closely monitored
• Chemical and biological contaminants affect the
  quality of water

Org. pesticides, petroleum wastes, detergents,
etc.
Chemical contaminant
Inorg. metals (Fe, Cd, Hg, Cu)
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Microbes (bacteria and viruses)
biological contaminant

• physical properties such as pH, temperature,
• dissolved oxygen, and salinity also affect the
• quality of biological life in water
• Biochemical Oxygen Demand (BOD) is one
• method to monitor water quality

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Indicator organisms
indicator organisms are frequently used to
monitor bacterial contamination of water those
generally used are associated with the
gastrointestinal tract, since many waterborne
pathogens are also found in the gastro-
intestinal tract and cause gastrointestinal
diseases the most common group of indicator
organisms are the Coliforms G-ve, aerobic or
facultative anaerobic, nonspore- forming rods,
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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
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The objective of wastewater treatment are 1.
Remove organic matter and pathogenic
microorganisms 2. Remove toxic chemicals wastewate
r treatment is classified as 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 through
filtration or chlorination in 2nd treatment,
organic matter in the wastewater is oxidized by
m.o.
Oxidation pond, activated sludge, trickling filter
Aerobic process
septic tank, anaerobic digestion, UASB
Anaerobic process
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m.o.
CHONPS O2 CO2 H2O
Oxidation pond
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Activated sludge
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Trickling filter
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Wastewater treatment plant
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m.o.
m.o.
CHONPS org. acids CO2 H2S
NH3 CH4
Septic tank
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Anaerobic digestion
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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 (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