1 microbial ecology microbial ecology the interactions of m.o. with the biotic and abiotic...
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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
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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
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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The role of microorganisms ?
producers consumers
decomposers
- 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
Help in
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• 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.
CO2 CH4 CO2
Anaerobic
Aerobic
CO2 fixation
CO2 fixation
Respiration
Anaerobic respiration and fermentation
Org.cpd.
Methanogenic
procaryotes
Methane-oxidizing
procaryotes
(phototrophic bacteria) (anaerobic m.o.)
(cyanobacteria, algae, plants, and chemoautotrophic procaryotes)
(animals, plants, and m.o.)
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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
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
CO2
4+ H2
CH4
+ 2 H2
O
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Nitrification
Organic nitrogen NH3
Anaerobic
Aerobic
Nitrogen fixation
Denitrification
NO2-
N2
NO3-
NO2-
N2O
N2
Nitrogen fixation
Assimilation Ammonification
(Pseudomonas)
(Klebsiella)
(Nitrosococcus)
(Rhizobium)
(Nitrococcus)
Assimilation
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Siklus Nitrogen
• Fiksasi NitrogenKonversi nitrogen
atmosfer menjadi amoniak
• AmonifikasiAsam amino menjadi
amonia
• NitrifikasiKonversi amonia menjadi
nitrat
• DenitrifikasiReduksi 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
Heterotrof AerobBeijerinckia indica
Derxia gummosa
Cyanobacteria Fotosintetik
Clostridium sp Heterotrof
Anaerob
Desulvovibrio spp.
Chromatium vinosum
Fotosintetik
Chlorobium
Rhodospirillum rubrum
Rhodomicrobium vanielli
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Higher plant
Precipitated inorg.-P
Dissolved org.-P
zooplanktonphytoplankton
bacteria
Dissolved org.ortho-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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R-SH H2S SO42- R-SH
So
Dissimilatory sulfate reduction
SoS2O3
2-
R-SH
sulfateassimilation
sulfateassimilation
desulfurylation
Anaerobic
Aerobic
Chromatium
Chlorobium Chromatium
Chlorobium
Beggiatoa
Thiothrix
Thiobacillus(some procaryotes)
Desulfovibrio
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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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• they are responsible for many of the
biochemical changes in soil
• the most common soil bacteria : Arthrobacter,
Bacillus, Pseudomonas, Agrobacterium, Alcal
igenes, Flavobacterium, Streptomyces, and N
ocardia (Actinomyces)
Bacteria are the dominant m.o. in soil
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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 fungiRole 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 algaeRole 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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• are found in greatest abundance near the soil
surface (104 -105 cells)• why ?
Protozoa
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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• 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
Virus
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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 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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MycorrhizaMycorrhizacertain 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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• are typically found in trees and shrubs,
particularly in temperate forests
• the plant roots are surrounded but not penetrated by fungal hyphae
Ectomycorrhiza
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Microbial Leac Microbial Leachinghing
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- SO4
2-
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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BenefitBenefit : 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+ 8 Fe3+ + 4 H2O
CuS + 8 Fe3+ + 4 H2O Cu2++ 8 Fe2++ SO42-+ 8 H+
T. ferrooxidans
• microbial leaching of low-grade copper ores
is important in the mining industry
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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 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 bact
eria and agricultural chemicals through surfac
e runoff water
• Rivers can be polluted with sewage bacteria
esp. E. coli, Enterococcus faecalis, Proteus v
ulgaris, Clostridium sp., and other intestinal b
acteria
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Littoral zone
Limnetic zone
profundal zone
LakesLakes are relatively stagnant bodies of water
that can be divided into
- zone of light penetration
- temperature
epilimnion
hypolimnion
The microflora of a lake is determined by lake’s 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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QualityQuality of Water 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
Inorg. : metals (Fe, Cd, Hg, Cu)
Org. : pesticides, petroleum wastes, detergents, etc.
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biological contbiological contaminantaminant
Microbes (bacteria and virus
es)
• 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 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 Detection for presence and quantity
of coliformsof coliforms
- The most probable number (MPN)
- The membrane filtration (MF)
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Biological Wastewater Treatme Biological Wastewater Treatmentnt
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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
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Tertiaryadditional 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, anaer obic digestion, UA
SB
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CHONPS + O2
CO2
+ H2
O
m.o.
Oxidation pond
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Activated sludge
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Wastewater treatment plant
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CHONPS org. acids CO2
H+2
S
H H+3
+ CH4
m.o. m.o.
Septic tankSeptic tank
63Anaerobic digestionAnaerobic 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
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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