This document discusses soil microbial ecology and the role of microorganisms in soil. It notes that different microhabitats in soil favor different indigenous microbial populations. Soil particles provide microenvironments with decreasing oxygen levels from the surface. Indigenous soil microflora are determined by abiotic soil factors and some have adaptive structures like endospores. Soil microorganisms play important roles in biodegradation, mineral cycling like nitrogen fixation, and biogeochemical cycles.

1. Microbial ecology
Soil

2. Soil Microhabitats
Different microhabitats favor different indigenous
microbial populations
Surface 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. Soil as a microbial habitat
Microorganisms are attached to the surface
of soil particles
Microcolonies

4. A soil particle has soil microenvironments
Decreasing O2 le vels
anaerobes
aerobes
microaerophilic

5. Soils: Microbial Communities
Higher microbial numbers – compared with freshwater
or marine habitats
Algae
Bacteria
Cyanobacteria
Bacteria
Fungi
Protozoa
Viruses
About 106 to 109 bacteria per gram soil
Due to high organic matter content

6. Soils: Microbial Communities
Autochthonous microorganisms in soil
Can utilize humic substances
Gram-negative rod-shaped bacteria
Actinomycetes
Zymogenous 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. Soils: Microbial Communities
Zymogenous or opportunistic soil organisms
Not allochthonous
Intermittently active
True indigenous soil microflora

8. Soils: Microbial Communities
Indigenous 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 dessication
Some adaptive structures by indigenous soil microflora
Bacillus spp. – endospores
Arthrobacter spp. - pleomorphism

9. Roles of soil microorganisms
Agents of biodegradation
Degraders of cellulose and lignin
Agents of mineral cycling
Nitrogen-fixing activity – Makes nitrogen available for
the plants
Minor role – primary production

10. Biogeochemical Cycles
Recycling (oxidation and reduction)
of chemical elements

11. The Carbon Cycle

12. The Nitrogen Cycle
Figure 27.4

13. Nitrogen Cycle
Microbial decomposition
Proteins and waste products Amino acids
Microbial ammonification
Amino acids (–NH2) Ammonia (NH3)
Nitrosomonas
Ammonium ion (NH4 +) Nitrite ion (NO2- )
Nitrobacter
Nitrite ion (NO2 -) Nitrate ion (NO3- )
Pseudmonas
Nitrate ion (NO3 -) N2
Nitrogen - fixation
N2 Ammonia (NH3)

14. Formation of a Root Nodule
Figure 27.5

15. Life Without Sunshine
• Primary producers in most ecosystems are
photoautotrophs
• Primary producers in deep ocean and
endolithic communities are chemoautotrophic
bacteria
H2S SO42– Provides energy for bacteria
which may be used to fix CO2
Calvin Cycle
CO2 Sugars Provides carbon for cell growth

16. The Sulfur Cycle

17. Sulfur Cycle
Microbial decomposition
Proteins and waste products Amino acids
Microbial dissimilation
Amino acids (–SH) H2S
Thiobacillus
H2S SO42– (for energy)
Microbial & plant assimilation
SO4 2– Amino acids

18. The Phosphorous Cycle

19. Degradation of Synthetic
Chemicals
Natural organic matter is easily degraded
by microbes
Xenobiotics are resistant to degradation

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. Decomposition by Microbes
Figure 27.10

22. Biofilms
Figure 27.11

23. Freshwater Zonation

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. 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. 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)

28. 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

30. 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

31. 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

32. Algal Blooms
• Pollutants (nutrients) may cause algal blooms.
• Algal blooms lead to eutrophication.

33. Multiple-Tube Method
Figure 6.18a

34. Multiple-Tube Method
Figure 6.18b

35. MUG Test
• ONPG causes E. coli to make -galactosidase
- galactosidase
MUG fluorescent compound

37. Municipal Water Treatment

38. Foods are preserved by:
• Drying
• Osmotic pressure (salt or sugar)
• Fermentation

39. Industrial Food Canning
Figure 28.1

40. 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

41. Food Preservation
• Pre-sterilized materials assembled into
packages and aseptically filled (Aseptic
packaging)
• Gamma radiation kills
bacteria, insects, and
parasitic worms
• High-energy electrons

42. 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

43. 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

44. Yeast Fermentations

45. Making Red Wine

46. Microbial Metabolism
Saccharomyces cerevisiae
Sugar Ethyl alcohol + CO2
Lactic acid bacteria
Malic acid Lactic acid
Acetobacter or Gluconobacter
Ethyl alcohol Acetic acid

47. Fermentation Technology
Figure 28.10

48. Primary Fermentation
Figure 28.11a

49. Secondary Fermentation
Figure 28.11b

50. Industrial Microbiology
• Amino acids
• Citric Acid
• Enzymes
• Vitamins
• Antibiotics
• Steroids

51. Alternative Energy Sources Using
Microorganisms
Bioconversion
Biomass Methane or ethyl alcohol