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хөрсний микробиологи by R. Chinzorig Ph.D.
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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
Prepared by: Richard Stehouwer Department of Crop & Soil
Sciences
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
Water bearWater bear
Predatory nematode
Bear in waterBear in water
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
FlagellateFlagellateCiliateCiliate
AmoebaAmoeba
RedyeastRed
yeast
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
Organic matter decomposition
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
Organic matter decomposition
Everyone is involved
Organic matter decomposition
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
Organic matter decomposition
Everyone is involved
Organic matter decomposition
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
Organic matter decomposition
Everyone is involved
Organic matter decomposition
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
Organic matter decomposition
Everyone is involved
Organic matter decomposition
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
Organic matter decomposition
Carbon and Nitrogen Cycling
Organic matter decomposition
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
Organic matter decomposition
Carbon and Nitrogen Ratio
Organic matter decomposition
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
Organic matter decomposition
Carbon and Nitrogen Ratios
Organic matter decomposition
Carbon and Nitrogen Ratios
2/3 of carbon released as CO2
Average C/N ratio of bacteria and
fungi is 8:1
Litter C/N ratio around
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
Organic matter decomposition
Carbon and Nitrogen Ratios
Organic matter decomposition
Carbon and Nitrogen Ratios
Average C/N ratio of bacteria and
fungi is 8:1
Litter C/N ratio around
9:1
Litter C/N ratio around
9:1
CO2
C/N ratio 3:1
2/3 of carbon released as CO2
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
Effects of soil management practices on soil organismsEffects of soil management practices on soil organisms
Increased intensity of tillage tends to decrease microbial diversity and microbial biomass
Effects of soil management practices on soil organismsEffects of soil management practices on soil organisms
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
Effects of soil management practices on soil organismsEffects of soil management practices on soil organisms
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