Download Microbial Ecology

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
1
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)
2
Key Elements of Biogeochemical Cycles
a.
Where do the nutrients that ecosystems use come from?
b.
What happens to the nutrients within the ecosystem itself?
c.
What happens to the nutrients once they leave the ecosystem?
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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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
4
• 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
5
Siklus Karbon
•
•
Fiksasi Karbondioksida
Degradasi selulosa/karbohidrat
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Org.cpd.
CO2 fixation
Anaerobic
respiration and
fermentation
(anaerobic m.o.)
(phototrophic
bacteria)
Methanogenic
Anaerobic
procaryotes
CO2
Aerobic
CH4
CO2
Methane-oxidizing
procaryotes
Respiration
(animals, plants,
and m.o.)
Org.cpd.
CO2 fixation
(cyanobacteria,
algae, plants, and
chemoautotrophic
procaryotes)
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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 microorganisms
•Atmospheric carbon is rarely limiting to plant
growth
8
9
• 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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N2O
Denitrification
N2
(Pseudomonas)
Nitrogen fixation
NO2
(Klebsiella)
-
Anaerobic
Assimilation
Organic nitrogen
NH3
Aerobic
Assimilation
NO3
Ammonification
-
(Nitrococcus)
Nitrification
NO2
-
Nitrogen fixation
(Rhizobium)
N2
(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
Azotobacter chroococcum
Beijerinckia indica
Derxia gummosa
Heterotrof
Cyanobacteria
Fotosintetik
Clostridium sp
Heterotrof
Aerob
Desulvovibrio spp.
Anaerob
Chromatium vinosum
Chlorobium
Rhodospirillum rubrum
Rhodomicrobium vanielli
Fotosintetik
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Higher
plant
bacteria
phytoplankton
Dissolved
org.ortho-P
Dissolved
org.-P
zooplankton
Precipitated
inorg.-P
Sediment
15
•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
16
•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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Beggiatoa
sulfate
assimilation R-SH
(some procaryotes)
So
desulfurylation
R-SH
Thiothrix
Thiobacillus
sulfate
assimilation
Aerobic
SO42-
H2S
R-SH
Anaerobic
Chromatium
Chlorobium
Dissimilatory
sulfate reduction
Desulfovibrio
So
Chromatium
S2O3
2-
Chlorobium
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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
22
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)
23
• 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
Bacillus
Arthrobacter
Different types
of CHO
Starch, cellulose, gelatin
Pesticides, caffeine, phenol
24
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
soil 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)
adequate food supply
• why ?
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
29
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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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 freeliving bacteria
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32
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
37
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+
So
Fe3+
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
39
Benefit : Microbial leaching in Copper mining
• low grade Cu ores contain <0.5% Cu in the
form of chalcocite (Cu2S) or covellite (CuS)
8 Fe2+ + 2 O2 +8 H+
CuS + 8 Fe3+ + 4 H2O
T. ferrooxidans
8 Fe3+ + 4 H2O
Cu2++ 8 Fe2++ SO42-+ 8 H+
• microbial leaching of low-grade copper ores
is important in the mining industry
40
• 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
42
• 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
43
• 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)
44
• 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
45
Lakes are relatively stagnant bodies of water
that can be divided into
Littoral zone
- zone of light penetration
Limnetic zone
- temperature
epilimnion
profundal zone
hypolimnion
The microflora of a lake is determined by
lake’s nutrient content, thermal stratification,
and light compensation level
46
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
47
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
Chemical
contaminant
Org. : pesticides, petroleum
wastes, detergents, etc.
Inorg. : metals (Fe, Cd,
Hg, Cu)
48
biological
contaminant
Microbes
(bacteria and
viruses)
• 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
49
indicator organisms are frequently used to
monitor bacterial contamination of water
those generally used
gastrointestinal tract,
pathogens are also
intestinal tract and
diseases
are associated with the
since many waterborne
found in the gastrocause gastrointestinal
the most common group of indicator organisms
are the Coliforms
G-ve, aerobic or
facultative anaerobic, nonsporeforming 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
55
The objective of wastewater treatment are
1. Remove organic matter and pathogenic
microorganisms
2. Remove toxic chemicals
wastewater 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
56
Tertiary
additional purification, either
through filtration or chlorination
in 2nd treatment, organic matter in the
wastewater is oxidized by m.o.
Aerobic process
Anaerobic process
Oxidation pond,
activated sludge,
trickling filter
septic tank,
anaerobic
digestion, UASB
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CHONPS + O2
m.o.
Oxidation pond
CO2 + H2O
58
Activated sludge
59
Trickling filter
60
Wastewater treatment plant
61
m.o.
CHONPS
org. acids
m.o.
CO2 + H2S
+ NH3 + CH4
Septic tank
62
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 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
66
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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