Day 2 Soil Organisms

3.2. Soil Organisms

Litter

HerbivoresSenescing rootsRoot exudatesMycorrhizal fungi

CO2

CHO

CHO CO2

CO2

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).

Solar radiation

Numbers of soil organisms

SoilDepth

or organic matter content

Classification of soil microorganisms based on energy sources

Madigan et al. (2012)

Classification of soil microorganisms based electron acceptorsin chemotrophs

AnaerobesAerobes

Electron acceptors

Anoxic conditionsOxic conditions

ATPs ATPs

Use of O2 Use of NO3-, Fe+3, Mn+4, SO42-, organic compounds

Facultative anaerobe

ATPs

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

Classification of soil microorganisms based on carbon sources

AutotrophsHeterotrophs

Carbon sources

Inorganic C (CO2)Organic C

Synthesis of new substances Synthesis of new substances

CLASSIFICATION CARBON SOURCE ENERGY SOURCEAutotroph CO2 -Heterotroph Organic compounds -

Chemotroph - Chemical compoundsChemolithotroph - Inorganic compounds

Chemoorganotroph - Organic compoundsPhototroph - Light

Chemoautotroph CO2 Chemical compoundsPhotoautotroph CO2 LightChemoheterotroph Organic compounds Chemical compoundsPhotoheterotroph Organic compounds Light

Oxidation-reduction reactionsRegardless 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- O2-Formation of water

2 H+ + O2- H2ONet reaction

H2 + O2 H2O


The electron towerImagine 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.



Organic compound CO2

O2

Electron flow

Carbon flow


NO3-, SO42-, other organic compounds

Electron flow

Carbon flow


O2

Electron flow

Carbon flow

Biosynthesis

Aerobic organoheterotroph

Anaerobic organoheterotrophFermentation (a type of anaerobic Organoheterotroph)

Organic compound

Internal oxidation-reduction

Fermentationproducts

Carbon flowElectron flow

Inorganic compound

Aerobic lithoautotroph

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

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

- 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+blue-green+algae&start=98&hl=en&gbv=2&biw=1680&bih=881&tbm=isch&tbnid=0m-X-bUZCUf4yM:&

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

- 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.s-anand.net/wp-content/uploads/2010/12/kebo102_page3_image99.png&w=640&h=176&ei=qV-fT47sB4nLmAWq2v2FAg&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

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

Bacteria- Classification based on morphology

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

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

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 5-60%Bacillus 7-67%Pseudomonas 3-15%Agrobacterium 1-20%Alcaligenes 2-12%Flavobacterium 2-10%Corynebacterium < 5%Micrococcus < 5%Staphylococcus < 5%Xanthomonas < 5%Mycobacterium < 5%



- 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



- 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.



- 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 agentshttp://tunza.mobi/articles/2-actinomycetes/


- 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



- Nitrifiers

Nitrosomonas- NH4+ NO2- NO3-

Nitrobacter

- 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



- Nitrifiers

Nitrosomonas- NH4+ NO2- NO3-

Nitrobacter

- Nitrate can be:- Taken up by plant- Loss by leaching- Loss through denitrification (NO3- used as

electron acceptor under anoxic conditions)



- Sulfur oxidation

FeS2

Thiobacillus

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

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

http://www.iaqinc.org/site-map.htm

- 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

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

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

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

- 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

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 [email protected] for assistance with copyrighted (credited) images.

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

- 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

http://www.cheshirewildlifetrust.co.uk/watch_earthworms.htm

Earthworms

- Earthworms increase the speed at which organic matter is decomposed (the gut contains cellulase and chitinase)

- The burrowing improves soil aeration

- 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

http://www.cheshirewildlifetrust.co.uk/watch_earthworms.htm

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

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

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Day 2 Soil Organisms