The Life in Your Soil

An Introduction to Soil Microbiology

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
 Think of an ecosystem teeming with life…
What comes to mind?
Rainforest?

Savannah?

Coral reef?
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
Macro or large Meso or mid-size Micro or small
(>2 mm) (2–0.2 mm) (<0.2mm)

Mite

Earthworm Yeast

Alfalfa root Bacteria

Springtail
 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 Predatory
nematode nematode
 Species and function
Plants, the primary producers
– Vascular plants: roots of all Legume roots with
crop and vegetable plants nitrogen fixing nodules

– Algae

Algae
 The rhizosphere

• The zone of soil that is

significantly influenced by living
Plant roots
Root • 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 Protists
AM fungus Amoeba

Flagellate
Ciliate

Slime mold

Water bear

Red
Mushroom
yeast
Water bear
 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
11
Biomass is the weight of living organisms
 Benefits of diversity

• 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
 Interactions of soil organisms

Commensalist

Parasitic

Dietrich Werner, Marburg, Germany

Symbiotic
 Beneficial microbe-plant-soil
interactions
Some examples

• Organic matter decomposition

• Symbiotic Nitrogen Fixation
• Mycorrhizal Fungi
 Organic matter decomposition
Everyone is involved
• Earthworms Corn leaf pulled into
– Mix fresh organic materials nightcrawler burrow
into the soil
– Brings organic matter into
contact with soil
microorganisms

Millepede
• Soil insects and other
arthropods
– Shred fresh organic material
into much smaller particles
– Allows soil microbes to access
Ants all parts of the organic residue
 Organic matter decomposition
Everyone is involved
• Bacteria
Bacteria on fungal strands
– Population increases
rapidly when organic
matter is added to soil
– Quickly degrade simple
compounds - sugars,
proteins, amino acids Spiral bacteria
– Have a harder time
degrading cellulose, lignin,
starch
– Cannot get at easily
degradable molecules that
are protected
Rod bacteria
 Organic matter decomposition
Everyone is involved
• Fungi
– Grow more slowly and Fungus on poplar leaf
efficiently than bacteria when
organic matter is added to soil Tree trunk
– Able to degrade complex rotted by fungi
organic molecules such as
cellulose, lignin, starch
– Give other soil microorganisms
access to simpler molecules
that were protected by
cellulose or lignin
Fairy ring

Soil fungus
 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, Amoeba
the predators
– Feed on the primary
decomposers (bacteria,
fungi, actinomycetes)
– Release nutrients (nitrogen) Bacteria-feeding nematode
contained in the bodies of
the primary decomposers

Rotifer
Predatory nematode
 Organic matter decomposition
Carbon and Nitrogen Cycling
During each cycle of
degradation about 2/3 of
the organic carbon is
used for energy and During each cycle of
released as carbon CO2 degradation about 1/3 of
the organic carbon is
dioxide (CO2)
used to build microbial
cells or becomes part of
Plant litter the soil organic matter

CO2

Bacteria, Fungi
Soil organic matter Nematodes, protists, humus
 Organic matter decomposition
Carbon and Nitrogen Ratio
CO2
Litter
2/3 of carbon
C/N ratio
released as CO2
around C/N
24:1 ratio
8:1

Average C/N ratio Microbial C/N ratio is

of bacteria and maintained at 8:1 with no
fungi is 8:1 uptake or release of N
 Organic matter decomposition
Carbon and Nitrogen Ratios
CO2
Litter 2/3 of carbon
C/N ratio released as CO2
around C/N
90:1 ratio
30:1

Average C/N ratio Microbial C/N ratio is

of bacteria and maintained at 8:1 by
taking up N from soil
fungi is 8:1
Soil N

Immobilization
 Organic matter decomposition
Carbon and Nitrogen Ratios
CO2
Litter 2/3 of carbon
C/N ratio released as CO2
around C/N
9:1 ratio
3:1

Average C/N ratio Microbial C/N ratio is

maintained at 8:1 by
of bacteria and releasing N to the soil
fungi is 8:1

Soil N
Mineralization
 Symbiotic Nitrogen Fixation
• Many bacteria have the Rhizobia bacteria
ability to “fix” or convert
atmospheric nitrogen into Rhizobia nodules on
bean roots
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 Effect of rhizobia inoculation on
(sugars) soybean
– The rhizobia provides the
plant with nitrate nitrogen
– Efficiency nitrogen fixation
is greatly increased by this
relationship 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)

Root cells VAM fungi growing in symbiotic

association with a plant root.
Fungal hyphae

Vesicles – food storage

Arbuscule – exchanges nutrients with

plant
 Mycorrhizal fungi
Plant/fungi symbiosis
• 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

Growth of Douglas Fir seedlings

No mycorrhizal fungi

With mycorrhizal fungi

 Mycorrhizal fungi
Soil structure benefit

Mycorrhizal fungi present Mycorrhizal fungi absent

• Soil structure stabilized and • Soil structure is weak
strengthened • Structure is not maintained
• Structure is maintained when when immersed in water
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 Grassland

Crop Crop rotation

Monoculture

Div ses
ers
it y r ea
dec inc
r ea s it y
es rs
ve
Di
Effects 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 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 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/Fate
Pesticides are degraded into inactive
substances (e.g., CO2 ) or rendered inactive
by several mechanisms:
– 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
 Pesticide degradation
CO2
OCH2COOH CO2
H2O
H2O
Cl OH Cl-

Cl

Cl COOH
CH2
2,4-D Cl CH2
COOH
 Pesticide degradation
Critical concentrations for soil-applied or
residual herbicides

Minimum concentration
for good weed control
Herbicide conc. in soil

Maximum concentration
for safe recrop

Time
 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 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 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 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 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.
 Thanks to:
Dr. Mary Ann Bruns, Soil Microbial Ecologist, Penn State Univ.
for reviewing this presentation and for providing some of the photographs

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