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