Microbial Ecology

1. 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 geologicalcomponent of the world

2. 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)

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

4. 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

5. 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

6. Siklus Karbon • Fiksasi Karbondioksida • Degradasi selulosa/karbohidrat

7. 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.

8. 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

10. Contoh dekomposisi komponen substrat daun pohon Oak

11. 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

12. 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)

13. 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

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

15. Phosphorus Cycle phytoplankton Higher plant bacteria zooplankton Dissolved org.ortho-P Precipitated inorg.-P Dissolved org.-P Sediment

16. 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

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

18. 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

19. 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

20. 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.

21. 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 Microbes and Soil

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

23. they are responsible for many of the biochemical changes in soil the most common soil bacteria : Arthrobacter, Bacillus, Pseudomonas, Agrobacterium, Alcaligenes, Flavobacterium, Streptomyces, andNocardia (Actinomyces) Bacteria are the dominant m.o. in soil

24. 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

25. 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

26. 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 roote.g. mycorrhiza • cause disease in human, plants, and animals

27. 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

28. 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

29. 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

30. 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

31. 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

33. 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

34. Mycorrhiza certain types of soil fungi are closely associated with the roots of vascular plants

35. 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

36. 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

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

38. 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

39. 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

40. Benefit: Microbial leaching in Copper mining • low grade Cu ores contain <0.5% 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

42. 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

43. 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

44. 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)

45. 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

46. 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 lake’s nutrient content, thermal stratification, and light compensation level

47. 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

48. 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)

49. 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

50. 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 ColiformsG-ve, aerobic or facultative anaerobic, nonspore- forming rods,