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Microorganisms in terrestrial environments
Soil is dominated by inorganic material that is modified by
microorganisms and plants
Soil microorganisms include bacteria, archaea, fungi, algae,
protozoa and viruses
Only about 10% of the microorganisms found in soil have been
cultured
Oxygen concentrations in soil
Soil microorganisms tend to be
located in thin films of water on the
particle surfaces
Oxygen diffuses rapidly in this
environment
Oxygen diffuses very slowly in
water-logged soils
Oxygen concentrations in soil
Less oxygen is available at lower depths, especially in wetter
soils
Microorganisms in soil
Microscopic and macroscopic organisms contribute to the
formation and characteristics of soil
 nematodes, earthworms, protozoa, fungi and bacteria
All contribute to the decomposition of plant material and the
turnover of nutrients
Microorganisms in soil
Many important soil bacteria have only recently been cultured
Microorganisms and the formation of soils
Rate at which nutrients in
plant material is released is
dependent on activity of soil
microorganisms
Influences the soil and
manner in which plants adapt
Microorganisms and the formation of soils
Nutrients released rapidly in
tropical forests so plant roots
do not penetrate far
Slow release in temperate
grasslands causes deep root
penetration  fertile soil
Microorganisms and the formation of soils
Release of acid compounds
in temperate coniferous
forests results in a bleached
zone
 Accumulation of litter and
increased risk of fire (need
for controlled burns)
Microorganisms and the formation of soils
Low oxygen content in bogs
results in slow
decomposition and the
formation of peat
Microorganisms and the formation of soils
Microorganisms also
involved in the formation of
soil in cold moist regions,
desert regions and
geologically heated regions
Microorganisms and plants
Microorganisms are associated with various parts of plants
Some are commensals, some are symbionts and some are
pathogens
Phyllosphere microorganisms are found on the aerial surfaces
of plants (leaves, stems, etc.)
Microorganisms and plants
Rhizosphere microorganisms are found in the area surrounding
and influenced by the plant roots
Rhizoplane microorganisms are found on the surface of plant
roots
Microorganisms and the formation of soils
Many bacteria grow within
plants and can induce
formation of nodules
(nitrogen-fixation)
These include species of
Rhizobium and related
bacteria
Microorganisms and plants
Microorganisms and plants
Microorganisms and plants
Microorganisms and plants
Some nitrogen-fixing bacteria can
induce the formation of nodules on
the stems of some tropical legumes
Plant pathogens
A number of fungi and bacteria are capable of causing diseases in
plants
Plant pathogens
Infection of plants with
Agrobacterium tumefaciens
causes the formation of tumorlike growths on plants
Plant pathogens
Tumor formation due to the Ti
plasmid which integrates into
the host chromosome
Ti plasmid is being used to
genetically modify plants
(e.g. insertion of resistance
genes)
Soils, plants and nutrients
Microorganisms have a
profound influence on the
cycling of nutrients in soils
Excessive ammonium in
fertilizer is oxidized to nitrite
and nitrate
These anions enter the surface
and ground waters (harmful to
animals and humans)
Soils, plants and the atmosphere
Some soil microorganisms nucleate ice and can increase
precipitation and frost damage to crops
Plants sprayed with genetically modified “ice-minus” bacteria
can protect crops from frost
Soil microorganisms can degrade airborne pollutants such as CO,
benzene and methane (1 plant/ 100 ft2 of living space)
The subsurface biosphere
Microbial processes take place in different subsurface regions
The shallow subsurface where water flows below the
plant root zone
Regions where organic matter has been transformed into
hydrocarbons
Regions where methane is being synthesized
The subsurface biosphere
Microorganisms appear to be growing in high temperature
(60-90 C) oil reserves
Soil microorganisms and human health
Most soil microorganisms are harmless but a few can cause diseases
in humans
Species of Clostridium can cause gangrene and tetanus
Many fungi (molds) and some bacteria can cause respiratory diseases
when they grow in buildings (“sick-building syndrome”)
Microbial diversity in the soil
Only 1-10% of soil microorganisms can be grown in the laboratory
Diversity can be assessed by extracting and analyzing DNA in a soil
sample
Growth of identified organisms will ultimately be required for a
complete understanding of their role in the environment