Soil organisms & ecosystem function:

Bottom-up
MAMMALS/
PREDATORY MITES BIRDS

PREDATORY PREDATORY PREDATORY

COLLEMBOLA COLLEMBOLA INSECTS
tertiary
PREDATORY
NEMATODES

secondary
COLLEMBOLA MITES NEMATODES PROTOZOANS OLIGOCHAETES

PLANT-FEEDING
NEMATODES FUNGI BACTERIA primary

PLANT ROOTS PLANT DEBRIS ROOT DEPOSITIONS

 How might decomposers obtain
carbon from producers?
• Passivelly from dead biomass, excretions and
secretions
– Saprotrophs
• Actively from living biomass
– Necrotrophs, attack and decay biomass
– Biotrophs, obtain carbon from plant in exchange
for a microbe-supplied nutrient
 Saprotrophs
• Consume inanimate organic material
– Plant: litter, exudates
– Animal: bodies, excretions
– Microbial: cells, exudates
 Necrotrophs
• Plant pathogens
• Attack and decompose living plant parts
• Fungi (Pythium)
• Bacteria (Erwinia)
 Biotrophs
• Plant symbionts
• Bacteria = Nitrogen fixation
– Rhizobia (legumes)
– Actinorhiza (trees)
• Fungi = Phosphorus uptake
– Mycorrhizal fungi (woody and non-woody plants)
 Surface Soils
10 structure = soil particles + organic matter (humus) + roots +
microorganisms
20 structure = aggregate or ped = stability

Humic-like substances secretion

hydrophobic region
Polysaccharide secretion - hydrophobic region
Bacterial colonies binding of clay particles

Polysaccharide secretion
binding of clay particles

Fungi

Soil aggregate

Physical entanglement
Cross-section
 Where are the bacteria?
In soil 80 to 90% of the bacteria are attached to surfaces and only 10-20% are planktonic.
Cells have a patchy distribution over the solid surfaces, growing in microcolonies. Colony
growth allows sharing of nutrients and helps protect against dessication and predation or
grazing by protozoa.
 Similarly, bacteria are sorbed to soil. In this case the bacterium, which like the soil has
a net negative charge, is sorbed through a cation bridge.

+
+
-
- - ++
- - - ++
- +
2+
++ ---
Mg

C la y p a rtic le Bacterium negatively A tta c h m e n t o f b a c te riu m

n e g a tiv e ly c h a rg e d charged Divalent cation th ro u g h c a tio n b rid g in g
 Soil atmosphere

The composition of the earth’s atmosphere is approximately 79% nitrogen, 21%

oxygen, and 0.03% carbon dioxide. Microbial activity in the soil can change the local
concentration of these gases especially in saturated areas.

Composition (% volume basis)

Location Nitrogen (N2) Oxygen (O2) Carbon Dioxide (CO2)

Atmosphere 78.1 20.9 0.03

Well-aerated surface soil 78.1 18 - 20.5 0.3 – 3
Fine clay/saturated soil >79 0 - 10 Up to 10
Microorganisms in soil – an overview

• minor role as primary producers

• major role in cycling of nutrients

• role in soil formation

• role in pollution abatement

 Numbers and types of microbes in typical surface soils
Bacteria
Culturable counts 106 – 108 CFU/g soil
Highest
Direct counts 107 – 1010 cells/g soil numbers
Estimated to be up to 10,000 species of bacteria/g soil

Actinomycetes
Culturable counts 106 – 107 CFU/g soil
Gram Positive with high G+C content
Produce geosmin (earthy smell) and antibiotics

Fungi
Culturable counts 105 – 106/g soil Highest
Obligate aerobes biomass
Produce extensive mycelia (filaments) that can cover large areas.
Mycorrhizae are associated with plant roots.
White rot fungus, Phanerochaete chrysosporium is known for its ability to
degrade contaminants.
 Comparison of bacteria, actinomycetes, and fungi

Bacteria Actinomycetes Fungi

Numbers highest intermediate lowest
Biomass --- similar biomass --- largest
Cell wall --- PEP, teichoic acid, LPS --- chitin/cellulose

Competitiveness most least intermediate

for simple organics
Fix N2 Yes Yes No
Aerobic/Anaerobic both mostly aerobic aerobic
Moisture stress least tolerant intermediate most tolerant
Optimum pH 6-8 6-8 6-7
Competitive pH 6-8 >8 <5
Competitiveness all soils dominate dry, dominate
high pH soils low pH soils