Soil Microbiology

Soil

Soils correspond to the surface layer of the Soils correspond to the surface layer of the

Earth's crust (lithosphere: litho = rock). Earth's crust (lithosphere: litho = rock).

They develop as a result of the weathering of They develop as a result of the weathering of

geological rock formations. geological rock formations.

Soil

Soil consist of Soil consist of

mineral particlesmineral particles (from the eroded rocks) and (from the eroded rocks) and

organic mattersorganic matters (from the remains of plants, (from the remains of plants, animals, and microorganisms). animals, and microorganisms).

Mineral and organic particles are intimately Mineral and organic particles are intimately mixed in soil, forming various types of soil mixed in soil, forming various types of soil aggregates.aggregates.

Soil microbiology

They are found in association with air (i.e. the soil They are found in association with air (i.e. the soil

atmosphere) and an aqueous phase (i.e. the soil atmosphere) and an aqueous phase (i.e. the soil

solution) in the pores existing between particles solution) in the pores existing between particles

and/or aggregates. and/or aggregates.

Air and water = limiting factorAir and water = limiting factor

Limit number and type of microorganismsLimit number and type of microorganisms

Oxygen level in sandy soil particle.O2

Microorganisms:The soil represents a favorable habitat for microorganisms and is inhabited by a wide range of microorganisms, including bacteria, fungi, algae, viruses and protozoa.

Microorganisms are found in large numbers in soil - usually between one and ten million microorganisms are present per gram of soil.

Microorganisms:

Bacteria and fungi being the most prevalent.

However, the availability of nutrients is often

limiting for microbial growth in soil and most soil

microorganisms may not be physiologically active

in the soil at a given time.

Microorganisms and their significance:

Almost every chemical transformation taking Almost every chemical transformation taking place in soil involves active contributions from soil place in soil involves active contributions from soil microorganisms. microorganisms.

Active role in soil fertility as a result of their Active role in soil fertility as a result of their involvement in the cycle of nutrients like carbon involvement in the cycle of nutrients like carbon and nitrogen, which are required for plant growth. and nitrogen, which are required for plant growth.

Microorganisms and their significance:

Soil microorganisms are responsible for the Soil microorganisms are responsible for the

decomposition of the organic matter entering the soil decomposition of the organic matter entering the soil

and therefore in the recycling of nutrients in soil. and therefore in the recycling of nutrients in soil.

Certain soil microorganisms such as mycorrhizal fungi Certain soil microorganisms such as mycorrhizal fungi

can also increase the availability of mineral nutrients can also increase the availability of mineral nutrients

(e.g. phosphorus) to plants. (e.g. phosphorus) to plants.

1. CO2 fixation by photoautotrophs and chemoautotrophs.

2. Methanogenesis from inorganic (CO2+H2) or organic matter, involves

various archaea methanogens (Methanobacterium, others). Global CH4

production ~1011 kg / yr (~85% biogenic)

Microorganisms in C cycle:

Carbon fixerCarbon fixer

PhotoautotrophsPhotoautotrophs

Anaerobic Anaerobic –– ChromatiumChromatium (purple, sulfur bacteria)(purple, sulfur bacteria)

Aerobic Aerobic –– cyanobacteriacyanobacteria

Chemoautotrophs Chemoautotrophs -- anaerobicanaerobic

Methanotrophs: Methanotrophs: MethylomonasMethylomonas

Sulfur oxidizer:Sulfur oxidizer: ThiobacillusThiobacillus

Microorganisms in C cycle:

Methanogenesis Methanogenesis –– anaerobic degradation of anaerobic degradation of carbon: strictly by microbes.carbon: strictly by microbes.

Anaerobic respiration involves the complete oxidation of Anaerobic respiration involves the complete oxidation of organic substancesorganic substances

(CH(CH22O)O)nn + X+ Xoxox ----------> CO> CO22 + X+ Xredred

XX = electron acceptor= electron acceptor

(NO(NO33--, SO, SO44

22--, S, S00, Fe, Fe3+3+))

Methanobacterium

Microorganisms in C cycle:Anaerobic decomposition of organic substances to COAnaerobic decomposition of organic substances to CO22

and CHand CH44 involving many different reactions and species of involving many different reactions and species of microorganisms. This is also called interspecies hydrogen microorganisms. This is also called interspecies hydrogen transfer [the gut,sediments, soils, and the rumen].transfer [the gut,sediments, soils, and the rumen].

a. Complex polymers a. Complex polymers →→monomersmonomers

b. The monomeric subunits b. The monomeric subunits →→ organic acidsorganic acids

c. Fermentations c. Fermentations →→ acetate, COacetate, CO22, and H, and H22

d. Methanogens produce methane (i.e. CHd. Methanogens produce methane (i.e. CH44))

1. Nitrogen fixation

2. NH3 assimilation

3. Ammonification

4. Nitrosification

5. Nitrification

6. Nitrate assimilation

7. Dissimilatory nitrate reduction

8. Denitrification

• Nitrogen fixation N2 → NH3 (aerobic)

• free-living: Azotobacter, cyanobacteria;

• symbiotic: Rhizobium, Frankia

• (anaerobic): Clostridium perfringens, purple & green sulfur phototrophs.

2. NH3 assimilation (aerobic & anaerobic)

3. Ammonification (organic N→ NH3)

4. Nitrosification (aerobic), Nitrosomonas

5. Nitrification (aerobic), Nitrobacter

6. Nitrate assimilation (NO3-→ NH3 → amino acids)

7. Dissimilatory nitrate reduction (NO3 -→ NO2

-)

8. Denitrification (NO3- → N2) Bacillus, Pseudomonas,

Biogeochemical Sulfur Cycle:

1. Sulfur oxidation (S°→ SO3-2→ SO4

-2): (aerobic) many

chemolithotrophs; (anaerobic) purple & green

photoautotrophs

2. Assimilatory sulfate reduction (SO4-2→ organic S)

3. Desulfurylation (organic S decomposition → H2S)

4. H2S oxidation (H2S → S°)

Aerobic: Thiobacillus, Beggiotoa (chemolithotrophs).

Anaerobic: Chlorobium, Chromatium

Biogeochemical Sulfur Cycle:5. Dissimilatory sulfate and sulfite reduction (solid purple

arrows) SO4

-2 or SO3-2 → H2S:

Desulfovibrio and related organisms6. Elemental sulfur reduction (S°→ H2S) Desulfuromonas,

thermophilic archaea, cyanobacteria in hypersaline sediments.

Microorganisms and their significance:

Other soil microorganisms can increase the Other soil microorganisms can increase the

amount of nutrients present in the soil. amount of nutrients present in the soil.

The microorganisms, which improve the fertility The microorganisms, which improve the fertility

status of the soil and contribute to plant growth, status of the soil and contribute to plant growth,

have been termed 'have been termed 'biofertilizersbiofertilizers‘‘..

Microorganisms and their significance:

Similarly, other soil microorganisms have been Similarly, other soil microorganisms have been

found to produce compounds (such as vitamins found to produce compounds (such as vitamins

and plant hormones) that can improve plant and plant hormones) that can improve plant

health and contribute to higher crop yield. health and contribute to higher crop yield.

These microorganisms (called 'phytostimulators') These microorganisms (called 'phytostimulators')

are currently studied for possible use as microbial are currently studied for possible use as microbial

inoculants to improve crop yield. inoculants to improve crop yield.

Microorganisms and their significance:

Some soil microorganisms are pathogenic to Some soil microorganisms are pathogenic to

plants. Large numbers are routinely found in the plants. Large numbers are routinely found in the

soil and many of them can infect the plant through soil and many of them can infect the plant through

the roots.the roots.

Microorganisms and their significance:

Some native microorganisms present in the soil are Some native microorganisms present in the soil are

antagonistic to the pathogens and can prevent the antagonistic to the pathogens and can prevent the

infection of crop plants. infection of crop plants.

Competition for nutrients and/or production of inhibitory Competition for nutrients and/or production of inhibitory

compounds such as secondary metabolites (antimicrobial compounds such as secondary metabolites (antimicrobial

metabolites and antibiotics) and extracellular enzymes. metabolites and antibiotics) and extracellular enzymes.

Microorganisms and their significance:

Other soil microorganisms produce compounds Other soil microorganisms produce compounds that stimulate the natural defense mechanisms of that stimulate the natural defense mechanisms of the plant and improve its resistance to pathogens. the plant and improve its resistance to pathogens.

The last two groups have been termed The last two groups have been termed 'biopesticides' (= biological control).'biopesticides' (= biological control).

Major groups of soil microorganisms :Bacteria:

Numerically abundant (109 cells/g soil) but most

non-culturable

Along with fungi, most important decomposers of

organic matter

Major groups of soil microorganisms :Bacteria:

Specialized groups participate in all biogeochemical cycles

Their extracellular polymers help bind soil particles into aggregates

Some form beneficial or pathogenic interactions with plants

Important group of bacteria

Actinomycetes sp. Rhizobium sp.

Pseudomonas aeroginosa Bacillus sp.

Major groups of soil microorganisms :Nitrogen fixing organisms: bacteria

Symbiotic with plants Free living

FrankiaAzospirillum

RhizobiumClostridium (some)Desulfovibrio

Purple sulphur bacteria*Purple non-sulphur bacteria*

Green sulphur bacteria*

AzotobacterBeijerinckia

Klebsiella (some)Cyanobacteria

(some)*

Other plantsLegumesAnaerobicAerobic

Examples of nitrogen-fixing bacteria (* denotes a photosynthetic bacterium)

Major groups of soil microorganisms :

Actinomycetes:specialized filamentous prokaryotesparticipate in decomposition of complex organic compoundsproduce many 2nd metabolites, e.g., antibiotics, geosmins (earth odor) that give soil its characteristic distinctive aroma

Major groups of soil microorganisms :

Fungi:the major component of microbial biomass in soilsmajor participants in decomposition of organic matterhyphal growth helps bind soil particles into stable aggregates

Ectomycorrhizae - sheath

Major groups of soil microorganisms :

Fungi:Some associate with plant roots: major plant pathogens,

Beneficial symbionts

increase nutrient uptake

and decrease disease incidence

Major groups of soil microorganisms :Protozoa:

major predators of soil bacteria,

grazing activities accelerate decomposition of organic matter in soil

Very abundant in well drained surface soils.

There are some 250 different species in soils

Major groups of soil microorganisms :

Cyanobacteria and algae (green algae, diatoms):

Photoautotrophs, form surface algal crusts important in

H2O retention

Some cyanobacteria carry out free-living and symbiotic

N2-fixation

Major groups of soil microorganisms :Viruses:

Numerically abundant, ecology not well defined

Both lytic and lysogenic bacteriophage (latter very common)

Persistance and migration of human enteroviruses pose serious health issues with land disposal of sewage and fecal wastes

Winogradsky column

Metagenomics method

Using 5S and 16S rRNA gene sequence analysis.Using 5S and 16S rRNA gene sequence analysis.

Can use to study uncultivated microbial majorityCan use to study uncultivated microbial majority

Main reason Main reason ––

cannot culture cannot culture –– nutrition and physiological nutrition and physiological

Nature of culture does not reflect natural behaviorNature of culture does not reflect natural behavior