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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