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Microbial ecology
Soil
Different microhabitats favor different indigenous microbial populations
Soil Microhabitats
Surface horizons with rich litter Indigenous microflora can tolerate high levels of organic nutrients Diverse groups
Obligate aerobesFacultative anaerobesMicroaerophilesObligate anaerobes
e.g. Waterlogged soils – anoxic conditons microflora – facultative and obligate anaerobes
Soil as a microbial habitat Microorganisms are attached to the surface of soil particles
Microcolonies
A soil particle has soil microenvironments
aerobes
anaerobes
microaerophilic
Decreasing O2 le vels
Higher microbial numbers – compared with freshwateror marine habitats
AlgaeBacteriaCyanobacteriaBacteriaFungiProtozoaViruses
About 106 to 109 bacteria per gram soilDue to high organic matter content
Soils: Microbial Communities
Autochthonous microorganisms in soil Can utilize humic substances
Gram-negative rod-shaped bacteriaActinomycetes
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 AspergillusPenicillium Mucor
Penicillium
Soils: Microbial Communities
Zymogenous or opportunistic soil organisms Not allochthonous Intermittently active True indigenous soil microflora
Soils: Microbial Communities
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
Roles of soil microorganisms
Agents of biodegradationDegraders of cellulose and lignin
Agents of mineral cycling
Nitrogen-fixing activity – Makes nitrogen available for the plants
Minor role – primary production
Biogeochemical CyclesRecycling (oxidation and reduction)
of chemical elements
The Carbon Cycle
The Nitrogen Cycle
Figure 27.4
Nitrogen Cycle
N2
Nitrogen - fixationAmmonia (NH3)
Nitrate ion (NO3-)
PseudmonasN2
Nitrite ion (NO2-)
NitrobacterNitrate ion (NO3
- )
Ammonium ion (NH4+)
NitrosomonasNitrite ion (NO2
- )
Amino acids (–NH2)Microbial ammonification
Ammonia (NH3)
Proteins and waste productsMicrobial decomposition
Amino acids
Formation of a Root Nodule
Figure 27.5
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
CO2 Sugars Provides carbon for cell growthCalvin Cycle
The Sulfur Cycle
Sulfur Cycle
Proteins and waste products Amino acidsMicrobial decomposition
Amino acids (–SH)Microbial dissimilation
H2S
H2SThiobacillus
SO42– (for energy)
SO42–
Microbial & plant assimilationAmino acids
The Phosphorous Cycle
Degradation of Synthetic Chemicals
Natural organic matter is easily degraded by microbes
Xenobiotics are resistant to degradation
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
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 present, – Presence of toxic substances, – water’s saline content, – environmental factors such as pH, temperature,
and aeration
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
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)
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
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
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
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
MUG fluorescent compound- galactosidase
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 of thermophilic anaerobes cause spoilage with gas
• Or flat-sour spoilage
Food Preservation
• Pre-sterilized materials assembled into packages and aseptically filled (Aseptic packaging)
• Gamma radiation kills bacteria, insects, and parasitic worms
• High-energy electrons
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
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
Yeast Fermentations
Making Red Wine
Microbial Metabolism
Sugar Ethyl alcohol + CO2
Saccharomyces cerevisiae
Malic acid Lactic acidLactic acid bacteria
Ethyl alcohol Acetic acidAcetobacter or Gluconobacter
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
Biomass Methane or ethyl alcoholBioconversion