introduction to soil microbiology

The Life in Your SoilThe Life in Your SoilAn Introduction to Soil MicrobiologyThe Life in Your SoilThe Life in Your SoilAn Introduction to Soil Microbiology

Functions of agricultural soils

Functions of agricultural soils

• Anchor plant roots• Supply water to plant roots• Provide air for plant roots• Furnish nutrients for plant

growth• Release water with low levels

of nutrients

• Anchor plant roots• Supply water to plant roots• Provide air for plant roots• Furnish nutrients for plant

growth• Release water with low levels

of nutrients

Think of an ecosystem teeming with life…Think of an ecosystem teeming with life…

What comes to mind?What comes to mind?

Coral reef?Coral reef?

Savannah?Savannah?

Rainforest?Rainforest?

Who is at home in the soil?Who is at home in the soil?

Diversity of soil organismsDiversity of soil organisms

Soil organisms can be grouped on the basis of:– Size: how big they are– Species: who they are related to– Function: how they make their

living

Size of Soil OrganismsSize of Soil Organisms

Meso or mid-size(2–0.2 mm)

Micro or small(<0.2mm)

EarthwormEarthworm

Alfalfa rootAlfalfa root

MiteMite

BacteriaBacteria

YeastYeast

SpringtailSpringtail

Macro or large(>2 mm)

Species and functionSpecies and function• Animals

– Vertebrates: gophers, mice, voles, snakes– Arthropods: spiders, ants, beetles,

maggots– Annelids: earthworms– Mollusks: snails, slugs– Nematodes

Parasitic nematodes in insect larvae

Parasitic nematodes in insect larvae

Mouth parts of bacteria-feeding nematode

Mouth parts of bacteria-feeding nematode

Predatory nematodePredatory nematode

Species and functionSpecies and function

Plants, the primary producers

– Vascular plants: roots of all crop and vegetable plants

– Algae AlgaeAlgae

Legume roots with nitrogen fixing

nodules

Legume roots with nitrogen fixing

nodules

The rhizosphereThe rhizosphere

PlantRoot

• The zone of soil that is significantly influenced by living roots

• Usually extends about 2mm out from the root surface

• The rhizosphere is enriched in organic material due to root exudates and sloughed off root cells.

• Microbial activity in the rhizosphere may be 2 – 10 greater than in the bulk soil.

Species and functionSpecies and function

FungiFungi

AM fungusAM fungus

Slime moldSlime mold

MushroomMushroom

ProtistsProtists

Water bearWater bear

FlagellateFlagellateCiliateCiliate

AmoebaAmoeba

RedyeastRed

yeast

Water bearWater bear

Species and functionSpecies and functionMoneraMonera

BacteriaBacteria ActinomycetesActinomycetes

Numbers of SpeciesNumbers of Species

In a healthy soil one might find…Several species of vertebrate animalsSeveral species of earthworms20-30 species of mites50-100 species of insectsDozens of species of nematodesHundreds of species of fungiThousands of species of bacteria and

actinomycetes

Abundance of soil organismsAbundance of soil organisms

Number Biomass1

Organism per gram soil (lbs per(~1 tsp) acre 6”)

Earthworms – 100 – 1,500Mites 1-10 5 – 150Nematodes 10 – 100 10 – 150Protozoa up to 100 thousand 20 – 200Algae up to 100 thousand 10 – 500Fungi up to 1 million 1,000 – 15,000Actinomycetes up to 100 million 400 – 5,000Bacteria up to 1 billion 400 – 5,000

1 Biomass is the weight of living organisms

Number Biomass1

Organism per gram soil (lbs per(~1 tsp) acre 6”)

Earthworms – 100 – 1,500Mites 1-10 5 – 150Nematodes 10 – 100 10 – 150Protozoa up to 100 thousand 20 – 200Algae up to 100 thousand 10 – 500Fungi up to 1 million 1,000 – 15,000Actinomycetes up to 100 million 400 – 5,000Bacteria up to 1 billion 400 – 5,000

1 Biomass is the weight of living organisms

• Ecosystem Stability. Soil has several ways to accomplish the same function (system redundancy)

• Ecosystem Resilience. Soil has the ability to bounce back from a severe disturbance

• Ecosystem Stability. Soil has several ways to accomplish the same function (system redundancy)

• Ecosystem Resilience. Soil has the ability to bounce back from a severe disturbance

Benefits of diversityBenefits of diversity

CommensalistCommensalist

Dietrich Werner, Marburg, Germany

Interactions of soil organisms

Interactions of soil organisms

ParasiticParasitic

SymbioticSymbiotic

• Organic matter decomposition• Symbiotic Nitrogen Fixation• Mycorrhizal Fungi

• Organic matter decomposition• Symbiotic Nitrogen Fixation• Mycorrhizal Fungi

Beneficial microbe-plant-soil interactionsSome examples

Beneficial microbe-plant-soil interactionsSome examples

Organic matter decomposition

Everyone is involved


Everyone is involved• Earthworms

– Mix fresh organic materials into the soil

– Brings organic matter into contact with soil microorganisms

Corn leaf pulled into nightcrawler burrow

Corn leaf pulled into nightcrawler burrow

MillepedeMillepede

AntsAnts

•Soil insects and other arthropods

– Shred fresh organic material into much smaller particles

– Allows soil microbes to access all parts of the organic residue




Everyone is involved• Bacteria

– Population increases rapidly when organic matter is added to soil

– Quickly degrade simple compounds - sugars, proteins, amino acids

– Have a harder time degrading cellulose, lignin, starch

– Cannot get at easily degradable molecules that are protected

Bacteria on fungal strandsBacteria on fungal strands

Spiral bacteriaSpiral bacteria

Rod bacteriaRod bacteria




Everyone is involved•Fungi

– Grow more slowly and efficiently than bacteria when organic matter is added to soil

– Able to degrade complex organic molecules such as cellulose, lignin, starch

– Give other soil microorganisms access to simpler molecules that were protected by cellulose or lignin

Soil fungusSoil fungus

Fungus on poplar leafFungus on poplar leaf

Tree trunk rotted by fungi

Tree trunk rotted by fungi

Fairy ringFairy ring




Everyone is involved•Actinomycetes

– The cleanup crew– Become dominant in the

final stages of decomposition

– Attack the highly complex and decay resistant compounds

• Cellulose• Chitin (insect shells)• Lignin




Everyone is involved•Protists and

nematodes, the predators– Feed on the primary

decomposers (bacteria, fungi, actinomycetes)

– Release nutrients (nitrogen) contained in the bodies of the primary decomposers

AmoebaAmoeba

Bacteria-feeding nematodeBacteria-feeding nematode

Predatory nematodePredatory nematodeRotiferRotifer


Carbon and Nitrogen Cycling


Carbon and Nitrogen CyclingDuring each cycle of degradation about 2/3 of the organic carbon is used for energy and released as carbon dioxide (CO2)

Bacteria, FungiSoil organic matterBacteria, FungiSoil organic matter Nematodes, protists, humusNematodes, protists, humus

CO2CO2

CO2CO2

Plant litterPlant litter

During each cycle of degradation about 1/3 of the organic carbon is used to build microbial cells or becomes part of the soil organic matter


Carbon and Nitrogen Ratio


Carbon and Nitrogen Ratio

Average C/N ratio of bacteria and

fungi is 8:1

Litter C/N ratio around

24:1

CO2

C/N ratio 8:1

2/3 of carbon released as CO2

Microbial C/N ratio is maintained at 8:1 with no uptake or release of N


Carbon and Nitrogen Ratios





fungi is 8:1


90:1

CO2

C/N ratio 30:1

Immobilization

Soil N

Microbial C/N ratio is maintained at 8:1 by taking up N from soil






fungi is 8:1


9:1


9:1

CO2

C/N ratio 3:1


MineralizationSoil N

Microbial C/N ratio is maintained at 8:1 by releasing N to the soil

Symbiotic Nitrogen FixationSymbiotic Nitrogen Fixation• Many bacteria have the

ability to “fix” or convert atmospheric nitrogen into forms that plants can utilize.

• Some of these bacteria, notably the rhizobia species, form symbiotic relationships with legumenous plants– The plant provide Rhizobia

with a steady source of food (sugars)

– The rhizobia provides the plant with nitrate nitrogen

– Efficiency nitrogen fixation is greatly increased by this relationship

Rhizobia bacteriaRhizobia bacteria

Rhizobia nodules on bean roots

Rhizobia nodules on bean roots

Effect of rhizobia inoculation on soybeanEffect of rhizobia inoculation on soybean

InoculatedInoculated Not inoculatedNot inoculated

Mycorrhizal fungiPlant/fungi symbiosisMycorrhizal fungiPlant/fungi symbiosis

•Mycorrhizae means “fungus root”•Fungi live in close association with plant roots

• May live on the external surface of roots (ectomycorrhizal)

• Fungal hyphae may invade root cells (endomycorrhizal)

VAM fungi growing in symbiotic association with a plant root.

Root cells

Fungal hyphae

Vesicles – food storage

Arbuscule – exchanges nutrients with plant

Mycorrhizal fungiPlant/fungi symbiosisMycorrhizal fungiPlant/fungi symbiosis

With mycorrhizal fungi

Growth of Douglas Fir seedlings

No mycorrhizal fungi

•Plants supply fungi with sugars (energy)•Fungal hyphae grow 5 – 10 cm beyond plant

roots• Extend to soil pores too large for root hairs• Increase plant nutrient supply, especially

phosphorus • Increase plant water supply

Mycorrhizal fungiSoil structure benefitMycorrhizal fungiSoil structure benefit

Mycorrhizal fungi present•Soil structure stabilized and

strengthened•Structure is maintained

when immersed in water

Mycorrhizal fungi absent•Soil structure is weak•Structure is not maintained

when immersed in water

Soil factors that affect microorganism growthSoil factors that affect microorganism growth

• Organic matter• Aeration (oxygen)• Moisture and temperature• Soil fertility and pH

Effects of soil management practices on soil organismsEffects of soil management practices on soil organisms

ForestForest

Crop Monocultur

e

Crop Monocultur

e

GrasslandGrassland

Crop rotationCrop rotation

Diversity decreasesDiversi

ty incre

ases


Increased intensity of tillage tends to decrease microbial diversity and microbial biomass


Application of lime or fertilizer to infertile soils tends to increase microbial activity and biomass

Addition of organic materials such as manure tends to increase microbial biomass and activity


Maintaining high soil organic matter levels and residue cover on the soil surface (no till systems) tends to increase microbial diversity and activity

Pesticide applications have variable effects on

microbial populations

Herbicide Decomposition/FateHerbicide Decomposition/Fate

– Adsorption to soil components

– Leaching out of plant available zone

– Volatility - escapes into air and degrades

– Photodecomposition - degraded by sunlight

– Chemical decomposition - broken down by reactions

– Microbial degradation - primary means

Pesticides are degraded into inactive Pesticides are degraded into inactive substances (e.g., COsubstances (e.g., CO2 2 ) or rendered inactive ) or rendered inactive by several mechanisms:by several mechanisms:

Pesticide degradationPesticide degradation

Cl

Cl

OCH2COOH

Cl

Cl

OH

2,4-D

COOH

CH2

CH2

COOH

CO2

H2O

Cl-

CO2

H2O

Pesticide degradationPesticide degradation

Her

bic

ide

con

c. in

so

ilMinimum concentrationfor good weed control

Maximum concentration for safe recrop

Time

Critical concentrations for soil-applied or residual herbicides

Pesticide effects on non-target soil organisms

Pesticide effects on non-target soil organisms

• Herbicides– Minimal known effects soil microbes or soil

animals– Some may harm certain algae

• Insecticides– Some effects on non-target soil insects– Some effects on earthworms

• Fungicides and soil fumigants– Significant effects on a wide array of fungi and

soil animals.

Pesticide effects on earthwormsPesticide effects on earthworms• Most herbicides are harmless to earthworms

– Triazines (atrazine, simazine) appear to have moderate effects on earthworms

– Removing weeds may have indirect effects on earthworms by decreasing plant cover and food supply.

Pesticide effects on earthwormsPesticide effects on earthworms• Insecticides have varied effects on earthworms

– Most carbamates (Temik, Ficam, Sevin, Furadan) are highly toxic.

– Most organophosphates are low to moderate toxicity. Very toxic exceptions are:

• phorate (Thimet)

• chlopyrifos (Dursban, Equity, Tenure)

• ethoprophos (Mocap)

• ethyl-parathion

• isazophos

– Natural or synthetic pyrethroids are not known to be toxic

Pesticide effects on earthwormsPesticide effects on earthworms– Carbamate fungicides (carbendazim, benomyl) have toxic

effects on earthworms– Broad spectrum fumigants (fungicides, nematicides) tend

to be very toxic to earthworms.

– Reducing toxic effects• Occasional application of even toxic chemicals will have little

long-term impact on earthworm populations

• Repeated applications over a long period will decrease earthworm numbers and activity

• Avoid broadcasting toxic chemicals in spring and fall when earthworms are most active

• Band application of granular products greatly reduces earthworm mortality from highly toxic chemicals

The black box is openThe black box is open

•A healthy soil ecosystem is extremely diverse and complex

– Large numbers of organisms– Many different kinds organisms– Many different functions

•A diverse soil ecosystem is stabile and resilient

•A healthy soil ecosystem is extremely diverse and complex

– Large numbers of organisms– Many different kinds organisms– Many different functions

•A diverse soil ecosystem is stabile and resilient

•Soil organisms have developed many complex interdependencies that benefit agricultural soil functions.

•Soil management activities can significantly affect the life in your soil.

•Soil organisms have developed many complex interdependencies that benefit agricultural soil functions.

•Soil management activities can significantly affect the life in your soil.

Photo CreditsPhoto Credits

Pedatory nematode: Kathy Merifield, Oregon State Univ.

Bacterial and root feeding nematode: Elaine Ingham, Oregon State Univ.

Nematode: Mark Blaxter, Univ. EdinburghEarthworms: Clive Edwards, Ohio State Univ.Fungi on poplar: Bryce KendrickMycorrhizae and soil aggregation: Ted St.John,

USDA-ARSAmoeba: Ohio State Univ. – LimaWater bear: KamamusiCiliate: BioMedia ProductsBear in water: Katami Nat’l Park, Alaska

Rotifer: Nikon Microscopy, Inc.Fairy ring: Univ. Tenn.Millipede, mite, springtail: Penn State Univ.

Insect FairDisking: Colorado State Univ.Strip Crop: Ingolf VoglerNo till corn: Mich. State Univ.Rangeland: North Dakota St. Univ.Rhizobia: Frank Dazzo, Mich. State Univ.Actinomycetes: Paul R. August, Univ. Minn.Soybean growth: RIAL SiebersdorfRod bacteria: Univ. Georgia

Thanks to:Dr. Mary Ann Bruns, Soil Microbial Ecologist, Penn State Univ.

for reviewing this presentation and for providing some of the photographs

introduction to soil microbiology

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