3.2.

Soil Organisms

CO2
Solar radiation

CHO

CO2

Numbers of soil organisms

or organic matter content

Litter
Herbivores
Senescing roots
Root exudates
Mycorrhizal fungi

CHO

CO2

Soil
Depth

Figure 4.1. The photosynthetic transformation of solar energy to chemical energy

( reduced carbon ) by higher plants (producers). The transfer of reduced carbon to
the soil where it is oxidised back to CO2 to provide energy for soil organisms (consumers).

Page 1

Classification of soil microorganisms based on energy sources

Madigan et al. (2012)

Classification of soil microorganisms based electron acceptors

in chemotrophs
Electron acceptors

Anoxic conditions

Oxic conditions

Use of NO3-, Fe+3, Mn+4, SO42-, organic compounds

Use of O2
Aerobes

ATPs

Facultative
anaerobe

ATPs

Page 2

Anaerobes

ATPs

Photo by John A. Kelley, USDA Natural Resources Conservation Service

Classification of soil microorganisms based on carbon sources

Carbon sources

Inorganic C (CO2)

Organic C

Autotrophs

Heterotrophs

Synthesis of new substances

Synthesis of new substances

Page 3

CLASSIFICATION
Autotroph
Heterotroph

CARBON SOURCE
CO2
Organic compounds

ENERGY SOURCE
-

Chemotroph
Chemolithotroph
Chemoorganotroph
Phototroph

Chemical compounds
Inorganic compounds
Organic compounds
Light

Chemoautotroph
Photoautotroph
Chemoheterotroph
Photoheterotroph

CO2
CO2
Organic compounds
Organic compounds

Chemical compounds
Light
Chemical compounds
Light

Oxidation-reduction reactions
Regardless of how a microorganism makes a living, it
must be able to conserve some of the energy
released
The energy released in redox reactions is conserved
in compounds such as ATP
Oxidation: removal of electrons
H2 2 e- + 2 H+
Reduction: addition of electrons
O2 + 2 e- O2Formation of water
2 H+ + O2- H2O
Net reaction
H2 + O2 H2O

Madigan et al. (2012)

Page 4

The electron tower

Imagine electrons from an electron donor near the
top of the tower falling and being caught by
electrons acceptors at various levels.
The further the drop from a donor before they are
caught by an acceptor, the greater the amount of
energy released.
Oxygen, at the bottom of the redox tower, is the
strongest electron acceptor of any significance in
nature.
In the middle of the redox tower, redox couples can
be either electron donors or acceptors depending on
which redox couples they react with.

Madigan et al. (2012)

Madigan et al. (2012)

Page 5

Aerobic lithoautotroph

Aerobic organoheterotroph

CO2 Inorganic
compound
Organic compound

Organic compound

CO2

Carbon flow
Electron flow

Electron flow

Carbon flow

O2

O2

Fermentation (a type of anaerobic

Organoheterotroph)
Fermentation
Organic compound
products

Anaerobic organoheterotroph
CO2

Organic compound
Carbon flow
Electron flow

Biosynthesis

Carbon flow

Electron flow

NO3-, SO42-, other organic compounds

Internal oxidation-reduction

Algae
- Abundant in habitats in which moisture is adequate and light accessible
- Common forms in soil are green-algae, blue-green algae, diatoms and yellow-green algae
- Proliferation is usually a sign of water-logging conditions
- Most are single celled or small filaments
- Blue-green algae fix both N and C
- Some algae grow in close association with
fungi lichens

http://www.butterfly-conservation.org/text/362/lichen_feeders.html
http://www.google.co.nz/imgres?q=soil+bluegreen+algae&start=98&hl=en&gbv=2&biw=1680&bih=881&tbm=isch&tbnid=0m-X-bUZCUf4yM:&

http://squamules.blogspot.co.nz/

Page 6

Bacteria
- Bacteria are the most numerous organisms in the soil.
- In general, they do not grow well in soils of pH < 5
- Size is usually 0.5 to 1 m wide x 1-2 m long

http://silverfalls.k12.or.us/staff/read_shari/chapter_24_AB.htm

- Cells are spherical (cocci) or cylindrical (rods), but can also be short-curved rods, spirals
or chains. The most common soil bacteria are rod shaped.

http://www.google.co.nz/imgres?q=bacteria+cocci+rods&start=211&hl=en&biw=1680&bih=881&gbv=2&tbm=isch&tbnid=H7g7uqmgdw77rM:
&imgrefurl=http://textbook.s-anand.net/ncert/class-11/biology/2-biological-classification&docid=6r8gaS9K_RQZiM&imgurl=http://textbook.sanand.net/wp-content/uploads/2010/12/kebo102_page3_image99.png&w=640&h=176&ei=qVfT47sB4nLmAWq2v2FAg&zoom=1&iact=rc&dur=220&sig=116633157694015578981&page=7&tbnh=65&tbnw=237&ndsp=36&ved=1t:429,r:
10,s:211,i:106&tx=92&ty=51

Bacteria
- Classification based on morphology

http://silverfalls.k12.or.us/staff/read_shari/chapter_24_AB.htm

Page 7

Bacteria
- Some of the bacilli persist in unfavourable conditions by the formation of endospores
- Endospores often endure in adverse environments because of their great resistance to
both prolonged desiccation and to high temperatures.
- Spore-forming genera are present among the aerobic and anaerobic bacteria
- The endospore can persist in a dormant state long after the lack of food or water has led to
the death of vegetative cells.

http://micro.cornell.edu/cals/micro/research/labs/angert-lab/bacterialendo.cfm

Bacteria
- Classification based on metabolism. Bacteria are the group with the greatest metabolic
activity:
- Heterotrophic bacteria
-

The most common bacteria in soils

They obtain organic compounds for their energy and C needs by secreting
externally released extracellular enzymes, which attack live and dead animal and
plant material

The extracellular enzymes hydrolyse the more complex organic materials to simple
compounds that can be absorbed by the bacteria

http://simpert.com/technologies.html

Page 8

Bacteria
- Classification based on metabolism
- Heterotrophic bacteria
- Can attack a wide range of organic substrates, including organic
pesticides
- Bacteria have to compete for inorganic nutrients with plants and fungi
- Frequently detected bacteria in soil. Relative proportions of aerobic and
facultative anaerobic bacteria genera
Arthrobacter
Bacillus
Pseudomonas
Agrobacterium
Alcaligenes
Flavobacterium
Corynebacterium
Micrococcus
Staphylococcus
Xanthomonas
Mycobacterium

5-60%
7-67%
3-15%
1-20%
2-12%
2-10%
< 5%
< 5%
< 5%
< 5%
< 5%

Bacteria
- Classification based on metabolism
- Heterotrophic bacteria
- Rhizobium
- Heterotrophic bacteria that has a symbiotic relationship
with plant roots of legumes
- The soil bacteria infect the root hair which curls and
elongates, forming nodules
- The bacteria grow in the nodules, fixing N2 gas into NH4+
compounds which are available to plants
- The plant keeps the bacteria supplied with carbon
compounds

http://cropsoil.psu.edu/extension/facts/agronomy-facts-11

Page 9

Bacteria
- Classification based on metabolism
- Heterotrophic bacteria
- Rhizobium
- These bacteria have a very important role converting
unavailable atmospheric N2 gas into plant available N
- NZ pastoral farming is dependent upon biological N
fixation in the clover-ryegrass system

http://www.ctahr.hawaii.edu/mauisoil/c_nutrients01.aspx

Source: Legumes Inoculants and Their Use, 1984.

University of Hawaii NifTAL Project and FAO.

Bacteria
- Classification based on metabolism
- Heterotrophic bacteria
- Actinomycetes
- They are considered highly evolved bacteria
- They morphological similarities with fungi
- They are Gram+, usually filamentous
- Abundant not only in soils but also in compost and river muds
- Abundant in environments of high pH
- Streptomycete isolates may produce antibiotic agents
http://tunza.mobi/articles/2-actinomycetes/

Page 10

Bacteria
- Classification based on metabolism
- Chemolithoautotrophic bacteria
- Use of CO2 as the sole source of carbon
- Use of energy from the oxidation of inorganic substances
- The amount of CO2 fixed by these bacteria is negligible, but the
reactions producing the reducing power are important
pathways in the N and S cycles
- Nitrification
- Sulphur oxidation

Bacteria
- Classification based on metabolism
- Chemolithoautotrophic bacteria
- Nitrifiers
- NH4+

NO2-

Nitrosomonas

NO3Nitrobacter

- Both small flagellate rods

- Although they grow slowly, large quantities of
NH4+ can be converted to nitrate in soil
- Rates of nitrification are higher in moist neutral to
slightly alkaline soils
- Oxygen is required for growth

Page 11

Bacteria
- Classification based on metabolism
- Chemolithoautotrophic bacteria
- Nitrifiers
NO2-

- NH4+

Nitrosomonas

NO3Nitrobacter

- Nitrate can be:

- Taken up by plant
- Loss by leaching
- Loss through denitrification (NO3- used as
electron acceptor under anoxic conditions)

Bacteria

Jarosite
(KFe3(OH)6(SO4)2 +H2SO4

- Classification based on metabolism

- Chemolithoautotrophic bacteria
- Sulfur oxidation

Thiobacillus
FeS2

Page 12

Fungi
- Fungi are aerobic and heterotrophs
- As important as bacteria as decomposers in neutral to alkaline soils, but play the dominant
decomposing role in the soils of pH < 5, which are not suited for bacterial growth
- Fungi growth from spores by a threadlike structure
called hypha.
- A mass of hyphal threads is called mycellium and is
the growing, feeding part of the fungus.
- Mycelia grow into and invade organic material
- Typical hypha are 5 m wide and the extreme can be
meters in length
http://www.iaqinc.org/site-map.htm

Fungi
- Fungi are predominant in litter layers of soils and are either saprophytes, parasites, or
symbionts
- Like bacteria, fungi can use a wide range of organic compounds for food.
- Fungi are the major decomposers of lignin.

http://www.ozarkmountainimages.com/ForestFloor/ForestFloor.htm

http://www.davidlnelson.md/Cazadero/Fungi.htm

Page 13

Protozoa
- These are the smallest of soil animals
- They prey on soil bacteria and to some extent fungi
- They generally feed on dead bacterial cells and organic matter
- Some ingest solid food by engulfing (phagocytosis)
- Some eat live bacteria
- Few use only water-soluble compounds
- They are ecologically important in organic matter decomposition

Meso- and Macro-Fauna

- Micro-fauna is 200 m
- Meso-fauna = 200 m to 1 cm:
-

Nematodes
Rotifers
Springtails
Mites

- Meso- and macro-fauna are important in fragmenting

pieces of organic material and mixing soil
- Earthworms may release high levels of N and organic
matter in faeces and help in soil aggregation

- Macro-fauna 1 cm:
- Vertebrates
- Earthworms
- Big molluscs
- Arthropods

These microshredders, immature oribatid mites, skeletonise plant leaves. This starts the
nutrient cycling of carbon, nitrogen, and other elements. Collohmannia sp.

Credit: Roy A. Norton, College of Environmental Science & Forestry, State University of New York. Please contact the Soil and Water Conservation Society at
pubs@swcs.org for assistance with copyrighted (credited) images.

Page 14

Arthropods
-

Mites
Springtails
Insects
Millipedes
Centipedes

- Mites and springtails are often the most

numerous feeding on detritus in the lower
litter of the forests and undisturbed
grassland
- The most important role is that of
fragmenting litter, leading to easier decay by
fungi and bacteria
- Arthropods do not mix detritus with soil
minerals intimately, as they do not ingest
soil particles

Earthworms
- Earthworms feed exclusively on dead
organic matter, which they ingest with
large quantities of clay and silt size particles
- In soils with large earthworm populations,
organic and mineral matter are more
homogeneously mixed to a greater depth
than if the earthworms are absent
http://www.cheshirewildlifetrust.co.uk/watch_earthworms.htm

- Earthworms are rarely found in soils more

acid than pH 4.5 and most species prefer
neutral to calcareous soils and are active
only in moist soils

http://www.asknature.org/strategy/4c48cda5028087b65964b74e38fe2671

Page 15

Earthworms
- Earthworms increase the speed at which
organic matter is decomposed (the gut
contains cellulase and chitinase)
- The burrowing improves soil aeration
http://www.cheshirewildlifetrust.co.uk/watch_earthworms.htm

- They secrete a mucus which binds the walls

of their burrows and aid in soil structural
stability
- Burrows improve drainage and soil gas
exchange

http://www.asknature.org/strategy/4c48cda5028087b65964b74e38fe2671

Recommended videos

http://www.youtube.com/watch?v=0n04wCkIpuQ&feature=related
http://www.youtube.com/watch?v=puDkLFcCZyI&feature=related

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