Microbial ecology       Soil
Soil MicrohabitatsDifferent microhabitats favor different indigenousmicrobial populationsSurface horizons with rich litter...
Soil as a microbial habitat  Microorganisms are attached to the surface  of soil particles               Microcolonies
A soil particle has soil microenvironments        Decreasing O2 le vels                                anaerobes          ...
Soils: Microbial CommunitiesHigher microbial numbers – compared with freshwateror marine habitats      Algae      Bacteria...
Soils: Microbial CommunitiesAutochthonous microorganisms in soil  Can utilize humic substances     Gram-negative rod-shape...
Soils: Microbial CommunitiesZymogenous or opportunistic soil organisms  Not allochthonous  Intermittently active  True ind...
Soils: Microbial CommunitiesIndigenous soil microflora  Determined by the abiotic factors of the soil  Polar soils – psych...
Roles of soil microorganismsAgents of biodegradation     Degraders of cellulose and ligninAgents of mineral cyclingNitroge...
Biogeochemical CyclesRecycling (oxidation and reduction)       of chemical elements
The Carbon Cycle
The Nitrogen Cycle                     Figure 27.4
Nitrogen Cycle                                          Microbial decompositionProteins and waste products                ...
Formation of a Root Nodule                             Figure 27.5
Life Without Sunshine• Primary producers in most ecosystems are  photoautotrophs• Primary producers in deep ocean and  end...
The Sulfur Cycle
Sulfur Cycle                                         Microbial decompositionProteins and waste products                   ...
The Phosphorous Cycle
Degradation of Synthetic      ChemicalsNatural organic matter is easily degraded              by microbesXenobiotics are r...
Decomposition by Microbes• Bioremediation  – Use of microbes to detoxify or degrade pollutants;    enhanced by nitrogen an...
Decomposition by Microbes                            Figure 27.10
Biofilms           Figure 27.11
Freshwater Zonation
Microorganisms in water• Diverse• The numbers and types of bacteria present  will depend on:  – Amounts of organic matter ...
Water Quality• Microbes are filtered from water that percolates  into groundwater.• Some pathogens are transmitted to huma...
Water Quality• Most important source of infection is water   – Drinking   – Cooking   – Swimming• Common water borne disea...
Direct tests for pathogens• Involve selective cultivation to large numbers  – Time consuming  – Expensive  – Potentially d...
Indicator organisms for water• Indicators that water is contaminated with  pathogens• Criteria of good indicator  –   Suit...
Coliforms• Aerobic or facultatively anaerobic, gram-  negative, non–endospore forming rods that  ferment lactose to acid +...
Algal Blooms• Pollutants (nutrients) may cause algal blooms.• Algal blooms lead to eutrophication.
Multiple-Tube Method                       Figure 6.18a
Multiple-Tube Method                       Figure 6.18b
MUG Test• ONPG causes E. coli to make -galactosidase        - galactosidase MUG                      fluorescent compound
Municipal Water Treatment
Foods are preserved by:• Drying• Osmotic pressure (salt or sugar)• Fermentation
Industrial Food Canning                          Figure 28.1
Commercial Sterilization to Destroy    C. botulinum Endospores• 12D treatment kills 1012 endospores• Surviving endospores ...
Food Preservation• Pre-sterilized materials assembled into  packages and aseptically filled (Aseptic  packaging)• Gamma ra...
Cheese• Curd: solid casein from  lactic acid bacteria and  rennin• Whey: liquid separated  from curd• Hard cheeses produce...
Alcoholic Beverages and Vinegar• Beer and ale are fermented starch• Malting: Germinating barley converts starch to  maltos...
Yeast Fermentations
Making Red Wine
Microbial Metabolism         Saccharomyces cerevisiaeSugar                                   Ethyl alcohol + CO2          ...
Fermentation Technology                          Figure 28.10
Primary Fermentation                       Figure 28.11a
Secondary Fermentation                         Figure 28.11b
Industrial Microbiology•   Amino acids•   Citric Acid•   Enzymes•   Vitamins•   Antibiotics•   Steroids
Alternative Energy Sources Using          Microorganisms          BioconversionBiomass                   Methane or ethyl ...
Enviromental, industrial micro
Enviromental, industrial micro
Enviromental, industrial micro
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Enviromental, industrial micro

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Enviromental, industrial micro

  1. 1. Microbial ecology Soil
  2. 2. Soil MicrohabitatsDifferent microhabitats favor different indigenousmicrobial populationsSurface horizons with rich litter Indigenous microflora can tolerate high levels of organic nutrients Diverse groups Obligate aerobes Facultative anaerobes Microaerophiles Obligate anaerobes e.g. Waterlogged soils – anoxic conditons microflora – facultative and obligate anaerobes
  3. 3. Soil as a microbial habitat Microorganisms are attached to the surface of soil particles Microcolonies
  4. 4. A soil particle has soil microenvironments Decreasing O2 le vels anaerobes aerobes microaerophilic
  5. 5. Soils: Microbial CommunitiesHigher microbial numbers – compared with freshwateror marine habitats Algae Bacteria Cyanobacteria Bacteria Fungi Protozoa VirusesAbout 106 to 109 bacteria per gram soilDue to high organic matter content
  6. 6. Soils: Microbial CommunitiesAutochthonous microorganisms in soil Can utilize humic substances Gram-negative rod-shaped bacteria ActinomycetesZymogenous or opportunistic soil organisms Cannot utilize humic substances High metabolic activity Rapid growth due to presence of utilizable substrates (plant litter remains, fecal matter from other animals, carcasses) Bacillus Aspergillus Penicillium Mucor Penicillium
  7. 7. Soils: Microbial CommunitiesZymogenous or opportunistic soil organisms Not allochthonous Intermittently active True indigenous soil microflora
  8. 8. Soils: Microbial CommunitiesIndigenous soil microflora Determined by the abiotic factors of the soil Polar soils – psychrotrops or psychropiles Desert and arid soils – micrflora should be tolerant to extreme high temperatures and dessicationSome adaptive structures by indigenous soil microflora Bacillus spp. – endospores Arthrobacter spp. - pleomorphism
  9. 9. Roles of soil microorganismsAgents of biodegradation Degraders of cellulose and ligninAgents of mineral cyclingNitrogen-fixing activity – Makes nitrogen available for the plantsMinor role – primary production
  10. 10. Biogeochemical CyclesRecycling (oxidation and reduction) of chemical elements
  11. 11. The Carbon Cycle
  12. 12. The Nitrogen Cycle Figure 27.4
  13. 13. Nitrogen Cycle Microbial decompositionProteins and waste products Amino acids Microbial ammonificationAmino acids (–NH2) Ammonia (NH3) NitrosomonasAmmonium ion (NH4 +) Nitrite ion (NO2- ) Nitrobacter Nitrite ion (NO2 -) Nitrate ion (NO3- ) PseudmonasNitrate ion (NO3 -) N2 Nitrogen - fixationN2 Ammonia (NH3)
  14. 14. Formation of a Root Nodule Figure 27.5
  15. 15. Life Without Sunshine• Primary producers in most ecosystems are photoautotrophs• Primary producers in deep ocean and endolithic communities are chemoautotrophic bacteriaH2S SO42– Provides energy for bacteria which may be used to fix CO2 Calvin CycleCO2 Sugars Provides carbon for cell growth
  16. 16. The Sulfur Cycle
  17. 17. Sulfur Cycle Microbial decompositionProteins and waste products Amino acids Microbial dissimilationAmino acids (–SH) H2S ThiobacillusH2S SO42– (for energy) Microbial & plant assimilationSO4 2– Amino acids
  18. 18. The Phosphorous Cycle
  19. 19. Degradation of Synthetic ChemicalsNatural organic matter is easily degraded by microbesXenobiotics are resistant to degradation
  20. 20. Decomposition by Microbes• Bioremediation – Use of microbes to detoxify or degrade pollutants; enhanced by nitrogen and phosphorus fertilizer• Bioaugmentation – Addition of specific microbes to degrade of pollutant• Composting – Arranging organic waste to promote microbial degradation
  21. 21. Decomposition by Microbes Figure 27.10
  22. 22. Biofilms Figure 27.11
  23. 23. Freshwater Zonation
  24. 24. Microorganisms in water• Diverse• The numbers and types of bacteria present will depend on: – Amounts of organic matter present, – Presence of toxic substances, – water’s saline content, – environmental factors such as pH, temperature, and aeration
  25. 25. Water Quality• Microbes are filtered from water that percolates into groundwater.• Some pathogens are transmitted to human in drinking and recreational water.• Resistant chemicals may be concentrated in the aquatic food chain.• Mercury is metabolized by certain bacteria into a soluble compound, concentrated in animals
  26. 26. Water Quality• Most important source of infection is water – Drinking – Cooking – Swimming• Common water borne diseases: – Shigelosis (Shigella spp.) – Salmonellosis (Salmonella typhimurium) – Gastroenteritis (Campylobacter spp.) – Cholera (Vibrio cholerae) – Giardiasis (Giardia lambia) – Cryptosporidiosis (Cryptosporium parvum)
  27. 27. Direct tests for pathogens• Involve selective cultivation to large numbers – Time consuming – Expensive – Potentially dangerous to lab personnel• Molecular tests – Require testing for each pathogen – Expensive – Require expertise
  28. 28. Indicator organisms for water• Indicators that water is contaminated with pathogens• Criteria of good indicator – Suitable for all water types – Similar survival characteristics as pathogens in water – Present when pathogens are present – Present in greater number than pathogens – Correlate with the degree of pollution – Can be detected at low cost – Non-pathogenic
  29. 29. Coliforms• Aerobic or facultatively anaerobic, gram- negative, non–endospore forming rods that ferment lactose to acid + gas within 48 hr, at 35°C• Indicator organisms – Used to detect fecal contamination• MPN – Most probable number/100 ml of water
  30. 30. Algal Blooms• Pollutants (nutrients) may cause algal blooms.• Algal blooms lead to eutrophication.
  31. 31. Multiple-Tube Method Figure 6.18a
  32. 32. Multiple-Tube Method Figure 6.18b
  33. 33. MUG Test• ONPG causes E. coli to make -galactosidase - galactosidase MUG fluorescent compound
  34. 34. Municipal Water Treatment
  35. 35. Foods are preserved by:• Drying• Osmotic pressure (salt or sugar)• Fermentation
  36. 36. Industrial Food Canning Figure 28.1
  37. 37. Commercial Sterilization to Destroy C. botulinum Endospores• 12D treatment kills 1012 endospores• Surviving endospores of thermophilic anaerobes cause spoilage with gas• Or flat-sour spoilage
  38. 38. Food Preservation• Pre-sterilized materials assembled into packages and aseptically filled (Aseptic packaging)• Gamma radiation killsbacteria, insects, andparasitic worms• High-energy electrons
  39. 39. Cheese• Curd: solid casein from lactic acid bacteria and rennin• Whey: liquid separated from curd• Hard cheeses produced by lactic acid bacteria• Semisoft cheeses ripened by Penicillium on surface
  40. 40. Alcoholic Beverages and Vinegar• Beer and ale are fermented starch• Malting: Germinating barley converts starch to maltose and glucose• Yeast ferment sugars to ethyl alcohol + CO2
  41. 41. Yeast Fermentations
  42. 42. Making Red Wine
  43. 43. Microbial Metabolism Saccharomyces cerevisiaeSugar Ethyl alcohol + CO2 Lactic acid bacteriaMalic acid Lactic acid Acetobacter or GluconobacterEthyl alcohol Acetic acid
  44. 44. Fermentation Technology Figure 28.10
  45. 45. Primary Fermentation Figure 28.11a
  46. 46. Secondary Fermentation Figure 28.11b
  47. 47. Industrial Microbiology• Amino acids• Citric Acid• Enzymes• Vitamins• Antibiotics• Steroids
  48. 48. Alternative Energy Sources Using Microorganisms BioconversionBiomass Methane or ethyl alcohol
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