The Life in Our Soil An Introduction to Soil

Microbiology

Slides Prepared by: Richard Stehouwer Department of Crop & Soil Sciences

Adapted and presented by John Paul, PhD with permission

Function of soil

• 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

Soil Components The 4 parts of soil

MineralMatter45%

SoilWater25%

SoilAir

25%

OrganicMatter

5%

About ½ of the soil volume is

solid particles

About ½ of the soil volume is pore space

Why should you care

about soil organic matter

(SOM)?

SOM Improves Soil Physical Properties

– Increased granulation and aggregate stability

– Makes heavy soils easier to work

– Increases water infiltration rates

– Increases water holding capacity

– Decreases erosion

If your soil looks like this…

You can avoid this!

Soil aggregates held together by: – Fungal hyphae

– Bacterial “glues”

– Organic matter

sand

silt

hyphae clay

bacteria

SOM Improves Soil Chemical Properties

– Increases Cation Exchange Capacity so the soil is better able to store and supply plant nutrients

– Increases pH buffering so the soil resists changes in pH

– Reduces Aluminum, Iron, and Manganese toxicity in acidic soil

Why should you care

about soil organic

matter (SOM)?

• SOM Improves Soil Biological Properties – Greater abundance, diversity and activity of soil microbes

– Increased nutrient cycling

– Increased root elongation and abundance

– Increased access to water and nutrients

Why should you care about soil organic

matter (SOM)?

What is Soil Organic

Matter?

• All material in soil that contains (reduced) carbon.

• SOM is derived from – Plant residue (both litter

and roots)

– Animal remains and excreta

– Living soil microbes (microbial biomass)

• Over time microbes transform fresh organic material into stable soil organic matter

Crop residue

Bacteria

Fungi Actinomycetes

SOM

Who is at home in the soil?

Diversity 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 Organisms

Meso or mid-size

(2–0.2 mm)

Micro or small

(<0.2mm)

Earthworm

Alfalfa root

Mite

Bacteria

Yeast

Springtail

Macro or large

(>2 mm)

Species and function • Animals

– Vertebrates: gophers, mice, voles, snakes

– Arthropods: spiders, ants, beetles, maggots

– Annelids: earthworms

– Mollusks: snails, slugs

– Nematodes Parasitic nematodes in insect larvae

Mouth parts of bacteria-feeding nematode

Water bear

Predatory nematode

Species and function

Plants, the primary producers

– Vascular plants: roots of all crop and vegetable plants

– Algae

Algae

Legume roots with nitrogen fixing nodules

The rhizosphere

Plant Root

• 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 function

Fungi

AM fungus

Slime mold

Mushroom

Protists

Flagellate Ciliate

Amoeba

Red yeast

Species and function

Monera

Bacteria Actinomycetes

Numbers of Species

In a healthy soil one might find… Several species of vertebrate animals Several species of earthworms 20-30 species of mites 50-100 species of insects Dozens of species of nematodes Hundreds of species of fungi Thousands of species of bacteria and

actinomycetes

Abundance of soil organisms

Number Biomass1

Organism per gram soil (lbs per (~1 tsp) acre 6”) Earthworms – 100 – 1,500 Mites 1-10 5 – 150 Nematodes 10 – 100 10 – 150 Protozoa up to 100 thousand 20 – 200 Algae up to 100 thousand 10 – 500 Fungi up to 1 million 1,000 – 15,000 Actinomycetes up to 100 million 400 – 5,000 Bacteria 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

Benefits of diversity

Commensalist

Dietrich Werner, Marburg, Germany

Interactions of soil organisms

Parasitic

Symbiotic

• Organic matter decomposition

• Symbiotic Nitrogen Fixation

• Mycorrhizal Fungi

Beneficial microbe-plant-soil

interactions Some examples

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

Millepede

Ants

• 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

• 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 strands

Spiral bacteria

Rod bacteria

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 fungus

Fungus on poplar leaf

Tree trunk rotted by fungi

Fairy ring

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

• Protists and nematodes, the predators – Feed on the primary

decomposers (bacteria, fungi, actinomycetes)

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

Amoeba

Bacteria-feeding nematode

Predatory nematode Rotifer

Organic matter decomposition Carbon and Nitrogen Cycling

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

Bacteria, Fungi Soil organic matter Nematodes, protists, humus

CO2

CO2

Plant 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

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

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

Average C/N ratio of bacteria and

fungi is 8:1

Litter C/N ratio

around 9:1

CO2

C/N ratio 3:1

2/3 of carbon released as CO2

Mineralization Soil N

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

Symbiotic 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 bacteria

Rhizobia nodules on bean roots

Effect of rhizobia inoculation on soybean

Inoculated Not inoculated

Mycorrhizal fungi Plant/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 fungi Plant/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 fungi Soil 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 growth

• Organic matter

• Aeration (oxygen)

• Moisture and temperature

• Soil fertility and pH

Effects of soil management

practices on soil organisms Forest

Crop Monoculture

Grassland

Crop rotation

Effects 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

The 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

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

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

Photo Credits

Pedatory nematode: Kathy Merifield, Oregon State Univ.

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

Nematode: Mark Blaxter, Univ. Edinburgh

Earthworms: Clive Edwards, Ohio State Univ.

Fungi on poplar: Bryce Kendrick

Mycorrhizae and soil aggregation: Ted St.John, USDA-ARS

Amoeba: Ohio State Univ. – Lima

Water bear: Kamamusi

Ciliate: BioMedia Products

Bear in water: Katami Nat’l Park, Alaska

Rotifer: Nikon Microscopy, Inc.

Fairy ring: Univ. Tenn.

Millipede, mite, springtail: Penn State Univ. Insect Fair

Disking: Colorado State Univ.

Strip Crop: Ingolf Vogler

No 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 Siebersdorf

Rod 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