Microbial Ecology Biogeochemical...

12
5/15/2009 1 Microbial Ecology Microbial Ecology Microbial Ecology the interactions of m.o. with the biotic and abiotic components of the environment Th i t f th it ti dth i 1 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 Biogeochemical Cycling The cycling of nutrients through ecosystems via food chains and food webs, including the exchange 2 of nutrients between the biosphere and the hydrosphere, atmosphere and geosphere (e.g., soils and sediments) Key Elements of Biogeochemical Cycles 3 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? The role of microorganisms ? producers consumers decomposers Help in 4 - 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 • critically important to all form of life closely linked with the flow of energy th lti t f ll b i CO 5 the ultimate source of all carbon is CO 2 - raw material for photosynthesis - major waste product of respiration and combustion Siklus Karbon 6 Fiksasi Karbondioksida Degradasi selulosa/karbohidrat

Transcript of Microbial Ecology Biogeochemical...

Page 1: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

1

Microbial EcologyMicrobial EcologyMicrobial Ecology the interactions of m.o. with the biotic and abiotic components of the environment

Th i t f th i t ti d th i

1

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

Biogeochemical Cycling

The cycling of nutrients through ecosystems via food chains and food webs, including the exchange

2

, g gof nutrients between the biosphere and the hydrosphere, atmosphere and geosphere (e.g., soils and sediments)

Key Elements of Biogeochemical Cycles

3

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?

The role of microorganisms ?

producers consumers

decomposers

Help in

4

- 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

• critically important to all form of life

closely linked with the flow of energy

th lti t f ll b i CO

5

• the ultimate source of all carbon is CO2

- raw material for photosynthesis

- major waste product of respiration and

combustion

Siklus Karbon

6

• Fiksasi Karbondioksida• Degradasi selulosa/karbohidrat

Page 2: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

2

CO2 CH4 CO2

Anaerobic

CO2 fixation Anaerobic respiration and fermentation

Org.cpd.

Methanogenicprocaryotes

(phototrophic bacteria) (anaerobic m.o.)

7

Org.cpd.

CO2 CH4 CO2Aerobic

CO2 fixationRespiration

Methane-oxidizingprocaryotes

(cyanobacteria, algae, plants, and chemoautotrophic procaryotes)

(animals, plants, and m.o.)

•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

8

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

9

• Contoh dekomposisi komponen substrat daun pohon Oak

10

Methanogens (Methanobacterium, Methanococcus) can anaerobically reduce CO2 to CH4

Methanogens are found in anaerobic habitats

CO2 + 4H2 CH4 + 2H2O

11

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

Anaerobic

Denitrification

NO2-

N2O

N2Nitrogen fixation

(Pseudomonas)

(Klebsiella)

12

Nitrification

Organic nitrogen NH3

Anaerobic

Aerobic

Nitrogen fixation

NO2-

N2

NO3-

Assimilation Ammonification

(Nitrosococcus)

(Rhizobium)

(Nitrococcus)

Assimilation

Page 3: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

3

Siklus Nitrogen• Fiksasi NitrogenKonversi nitrogen atmosfer

menjadi amoniak

• AmonifikasiAsam amino menjadi

13

amonia

• NitrifikasiKonversi amonia menjadi

nitrat

• DenitrifikasiReduksi nitrat menjadi gas

nitrogen

Fiksasi Nitrogen• Nitrogenase• Fiksasi nitrogen

1.Simbiotik :Rhizobium2. Non simbiotik : mikroorganisme bebas dan

independen

Genus/Species Karakteristik FisiologiAzotobacter chroococcum

Beijerinckia indica

14

Heterotrof AerobDerxia gummosa

Cyanobacteria Fotosintetik

Clostridium sp Heterotrof

AnaerobDesulvovibrio spp.

Chromatium vinosum

Fotosintetik

Chlorobium

Rhodospirillum rubrum

Rhodomicrobium vanielli

Higher plant

zooplanktonphytoplanktonbacteria

Dissolved

15

Precipitated inorg.-PDissolved

org.-P

Dissolved org.ortho-P

Sediment

•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

17

•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

SoR-SH

sulfateassimilation

sulfateassimilation

desulfurylation Aerobic

BeggiatoaThiothrix

Thiobacillus(some procaryotes)

18

R-SH H2S SO42- R-SH

Dissimilatory sulfate reduction

SoS2O3

2-

assimilationy

Anaerobic

Aerobic

ChromatiumChlorobium Chromatium

ChlorobiumDesulfovibrio

Page 4: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

4

Siklus Sulfur

19

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

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

20

some plants), reduced to sulfide in the atmosphere, or oxidized to sulfate in the atmosphere as sulfuric acid, a principal component of acid rain.

Microbes and Soil

• soil consists of organic and mineral matter and capable of supporting life

• soil characteristics depend on

21

soil characteristics depend on1. Climate and availability

of water2. Geologic age (young-old)3. Biological inhabitants

• many kinds of bacteria, fungi, algae, and protozoa are found in soil

22

• they are responsible for many of the

biochemical changes in soil

• the most common soil bacteria : Arthrobacter,

Bacteria are the dominant m.o. in soil

23

Bacillus, Pseudomonas, Agrobacterium, Alcaligenes, Flavobacterium, Streptomyces, and Nocardia (Actinomyces)

• 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

24

Pseudomonas Different typesof CHO

Bacillus Starch, cellulose, gelatin

Arthrobacter Pesticides, caffeine, phenol

Page 5: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

5

Fungi

• account for a large part of microbial

population in well-aerated, cultivated soil

• make up a significant part of total biomass

25

because of their large size and extensive

network of filaments

• most common fungi isolated from soil :

Penicillium and Aspergillus

Role and activity of fungiRole and activity of fungi• degrade organic matters

• control growth of other organisms e.g.

Predator protozoa, nematode

• humus formation

26

• humus formation

• improve soil aggregation

• help in the nutrient adsorption

of plant root e.g. mycorrhiza

• cause disease in human, plants, and animals

Algae

• eucaryotic algae and cyanobacteria are found

in the upper layers of soil

algae do not require a source of organic

27

• algae do not require a source of organic

carbon because …????…

• light accessibility, N, and P are the limiting

factor in the distribution of algae

Role and activity of algaeRole and activity of algae

increase organic carbon in soil

CO2 org.-C

soil corrosion (from respiration product)

28

CO2 + H2O H2CO3

prevent soil erosion and improve soil

aggregation

nitrogen fixation blue-green algae

• are found in greatest abundance near the soil surface (104 -105 cells)

• why ?

Protozoa

adequate food supply

water availability and

29

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

• different types of viruses persist in soil

- Bacteriophages of soil bacteria- viruses that cause human, animal, and plant dieases e g hepatitis virus tobacco

Virus

30

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

Page 6: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

6

rhizosphere = the region of soil closely surrounding the roots

rhizosphere effect = a consequence of the

31

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

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

33

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

MycorrhizaMycorrhizacertain types of soil fungi are closely associated with the roots of vascular plants

34

they significantly increase the absorption

area of the roots for minerals and water

Mycorrhizae are especially important in

nutrient-poor and water-limited environments

35

the fungus benefits from the carbohydrates

made available to it by plant

the plants benefit from the increased

absorption area provided by the fungus

Endomycorrhiza

36

• 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

Page 7: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

7

Ectomycorrhiza

37

• are typically found in trees and shrubs,

particularly in temperate forests

• the plant roots are surrounded but not penetrated by fungal hyphae

Microbial LeachingMicrobial LeachingLeaching : is commercially used for the extraction of Cu, Pb, Zn, and Ur from sulfide-containing ores

Thiobacillus thiooxidans and Thiobacillus

38

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

Fe2+ Fe3+

So S2- S2O32- SO4

2-

Acid mine drainage serious problem

39

FeS2 + H2SO4 + 1/2 O2 FeSO4 + 2 So + H2O

2 So + 2 H2O + 3 O2 2 H2SO4

Acidification of water and surrounding soil

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 H2OT.

ferrooxid

40

2 2

CuS + 8 Fe3+ + 4 H2O Cu2++ 8 Fe2++ SO42-+ 8

H+

ferrooxidans

• microbial leaching of low-grade copper ores

is important in the mining industry

• typical aquatic environments are the oceans,

estuaries, salt marshes, lakes, ponds, rivers,

and springs

42

and springs

• because aquatic environments differ considerably

in chemical and physical properties, so their

microbial species compositions also differ

Page 8: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

8

• saltwater organisms differ from freshwater

organisms based upon osmotic properties

• Algae (phytoplankton) are common in

marine habitats and provide significant i b

43

organic carbon

• the bacterial population in estuaries

consists of Pseudomonas, Flavobacterium,

and Vibrio, as well as enteric organisms

• 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

44

microorganisms

• Rivers may contain large numbers of soil bacteria (Bacillus, Actinomyces), fungi

(Penicillium, Aspergillus), and algae (Microcystis, Nostoc)

• 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

45

esp. E. coli, Enterococcus faecalis, Proteus vulgaris, Clostridium sp., and other intestinal bacteria

Littoral zone

Limnetic zone

LakesLakes are relatively stagnant bodies of water

that can be divided into

- zone of light penetration

- temperature

46

profundal zonep

epilimnion hypolimnion

The microflora of a lake is determined by lake’s nutrient content, thermal stratification, and light compensation level

Cyanobacteria and algae are abundant in the littoral and limnetic zonesPhotoautotrophic bacteria (Clorobium, Rhodopeudomonas, and Chromatium ---- use reduced org. and inorg. substanses as e donors) are found at lower depths

47

e-donors) are found at lower depthsChemolithotrophic 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

QualityQuality of Waterof 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

48

C e ca a d b o og ca co a a s a ecthe quality of water

Chemical contaminant

Inorg. : metals (Fe, Cd, Hg, Cu)

Org. : pesticides, petroleum wastes, detergents, etc.

Page 9: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

9

biological biological contaminantcontaminant

Microbes (bacteria and

viruses)

• physical properties such as pH, temperature,

di l d d li it l ff t th

49

dissolved oxygen, and salinity also affect the

quality of biological life in water

• Biochemical Oxygen Demand (BOD) is one

method to monitor water quality

indicator organisms are frequently used to monitor bacterial contamination of water

those generally used are associated with the gastrointestinal tract, since many waterborne

50

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,

ferment lactose with gas production within 48 hours at 35oC

they are in the family Enterobacteriaceae ; E. coli, Enterobacter aerogenes, and Klebsiella pneumoniae

51

Detection for presence and quantity Detection for presence and quantity of coliformsof coliforms

- The most probable number (MPN)- The membrane filtration (MF)

52

53 54

Page 10: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

10

Biological Wastewater TreatmentBiological 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

56

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

Tertiary additional purification, either through filtration or chlorination

in 2nd treatment, organic matter in the wastewater is oxidized by m.o.

O id ti d

57

Aerobic process

Anaerobic process

Oxidation pond, activated sludge, trickling filter

septic tank, anaerobic

digestion, UASB

CHONPS + O2 CO2 + H2Om.o.

58Oxidation pond

59

Activated sludge60Trickling filter

Page 11: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

11

61Wastewater treatment plant

CHONPS org. acids CO2 + H2S

+ NH3 + CH4

m.o. m.o.

62Septic tankSeptic tank

63Anaerobic digestionAnaerobic digestion

64

65

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 t h i

66

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

Page 12: Microbial Ecology Biogeochemical Cyclingkuliah.ftsl.itb.ac.id/wp-content/uploads/2016/10/bahan-kuliah-mi... · Microbial Ecology Microbial Ecology ... - major waste product of respiration

5/15/2009

12

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

67

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