Chapter 27

Environmental Microbiology

• Microbes live in the most widely varied habitats on Earth

– due to metabolic diversity – dynamic associations occur between microbes and

ecosystem

• Extremophiles– Most are Archaea – Produce specialized enzymes (extremozymes) that

allow them to tolerate extreme conditions

Metabolic Diversity

• Microbes live in an intensely competitive environment– High biodiversity

– Competitive exclusion

– Live in symbiotic relationships • Ruminants• Mycorhizae

Endomycorrhiza

Ectomycorrhiza

• Soil Microbiology• Billions of organisms in soil

– Over 80 % are bacteria• Millions in each gram of soil

– Most are in the top few centimeters of soil – Biomining – Many antibiotics come from Actinomycetes

• Streptomycin, tetracycline – Bacterial populations estimated by plate count

– Biogeochemical cycles for carbon, nitrogen, sulfur and phosphorus are vital for life

• Elements oxidized and reduced by microbes to meet their metabolic need

• Recycles elements into the environment– Production

– Consumption

– Decomposition

The Carbon Cycle

• All organisms contain large amounts of carbon

• Autotrophs fix CO2 into organics– 1st step of carbon cycle

• Heterotrophs consume autotrophs– 2nd step of carbon cycle

• Carbon reenters the environment as CO2

– due to respiration; decomposition by microbes; burning fossil fuels

• Global warming

The Nitrogen Cycle

• Nitrogen is needed for synthesis of proteins and nucleic acids

• Deamination– amino groups are removed and converted to

ammonia

• Ammonification– release of ammonia

• Nitrification – oxidation of ammonium into nitrate– nitrate can be fully oxidized and used as an electron

acceptor

• Denitrification – leads to loss of nitrogen back to the atmosphere as

nitrogen gas – Pseudomonas species are the most important soil

denitrifying bacteria– Occurs in waterlogged soils where little oxygen is

available

Nitrogen Cycle

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

• Nitrogen makes up ~ 80% of the Earth’s atmosphere– Exists as nitrogen gas (N2)

• Must be fixed into usable form – Specific microbes important in this conversion– Nitrogen fixation requires nitrogenase– Deactivated by oxygen

N2

Nitrogen - fixation

Ammonia (NH3)

• Two types of nitrogen fixers:– Free-living

• found in rhizosophere• Aerobic species - Azotobacter and Beijerinckia• Cyanobacteria –heterocysts• Anaerobic species - Clostridium

– Symbiotic

• Rhizobia form root nodules on legume plants • Frankia associated with alder trees• Lichens when containing a cyanobacteria • Cyanobacteria & Azolla in rice patty water

The Sulfur Cycle

• Involves numerous oxidation states

• Most reduced forms are sulfides like H2S gas– Generally forms under anaerobic conditions

• Source of energy for some autotrophic bacteria– Convert reduced sulfur in H2S into elemental sulfur

and oxidized sulfates – Thiobacillus– Endoliths

• Winogradsky studied filamentous aquatic bacteria Beggiatoa alba– Revealed much about bacterial sulfur

recycling and chemoautotrophy

• Primary producers in deep ocean and endolithic communities are chemoautotrophic bacteria

• Several photo-autotrophic bacteria use light for energy and use H2S to reduce CO2

• Sulfates are incorporated into plants, animals and bacteria as disulfide bonds in proteins

• Proteins decompose; sulfur released as H2S– Dissimilation

Sulfur Cycle

Proteins and waste products Amino acidsMicrobial decomposition

Amino acids (–SH)Microbial dissimilation

H2S

H2SThiobacillus

SO42– (for energy)

SO42–

Microbial & plant assimilationAmino acids

SO42– Desulfovibrio H2S (reduced)

The Phosphorus Cycle

• Limiting factor for plant and animal growth

• Exists primarily as phosphate ion (PO43-)

• Little change during oxidation – soluble to insoluble; organic to inorganic – Often related to pH – Can be solubilized in rock by acids produced by

bacteria like Thiobacillus

• There is no product to return it to atmosphere

• Accumulates in sea; certain islands are mined for phosphate deposits

• Used in detergents and fertilizers– Runoff may lead to eutrophication

The Phosphorous Cycle