Bacteria and
archaea (initially classified as bacteria), the smallest organisms in soil apart from
viruses, are
prokaryotic. They are the most abundant microorganisms in the soil, and serve many important purposes, including
nitrogen fixation and organic matter
decomposition for bacteria. Soil archaea are still poorly known but they could play a significant role in
nitrification and
methanogenesis. Some bacteria can colonize
minerals in the soil and help influence
weathering and the breaking down of these minerals. The overall composition of the soil can determine the amount and distribution of bacteria growing in it. The more clay minerals that are found in an area can result in a higher abundance of bacteria living as
biofilms at their surface. Soil bacteria also contribute to the formation of
soil aggregates, which increases the overall
health of the soil. Apart from the
rhizosphere, where bacterial activity is stimulated by
rhizodeposition and
root exudation, most bacteria of the
bulk soil are in a quiescent state, in the form of bacterial
colonies embedded in a
polysaccharidic matrix covered with clay platelets, and resistant to drought. These bacterial microaggregates may remain in this state of quiescence for a long time, until being reached by
exudates from growing
root tips or the
mucus of burrowing earthworms. Accordingly, sugar-rich
lixiviates (e.g. after a
pollen rain) may also stimulate respiration, reproduction and dissemination of resting soil bacteria, exerting a
priming effect on soil
microbial activity. In the
mycorhizosphere mycorrhiza helper bacteria form symbiotic associations with
mycorrhizal fungi, assisting
mycorrhiza formation or enhancing their functions.
Biochemical processes One of the most distinguished features of bacteria is their
biochemical versatility. A bacterial genus called
Pseudomonas can
metabolize a wide range of
chemicals and
fertilizers. In contrast, another genus known as
Nitrobacter can only derive its energy by oxidizing
nitrite to
nitrate. The genus
Clostridium is an example of bacterial versatility because it, unlike most species, can grow in the absence of oxygen, respiring
anaerobically. Several species of
Pseudomonas, such as
Pseudomonas aeruginosa are able to respire both aerobically and anaerobically, using nitrate as the terminal
electron acceptor.
Archaea are particularly adapted to chemically and physically harsh environments, with their unique
membrane lipids, and their
methanogenic pathways which incorporate a number of
coenzymes unique to this microbial group.
Nitrogen fixation Nitrogen is often the most limiting
nutrient in soil and water. Bacteria are responsible for the process of
nitrogen fixation, which is the conversion of atmospheric
dinitrogen into nitrogen-containing compounds (such as
ammonia) that can be used by plants. Some nitrogen-fixing bacteria (e.g.
cyanobacteria) are
autotroph and derive their carbon from the atmosphere through
photosynthesis while others are
heterotroph and derive their carbon either from
soil organic matter (e.g.
Clostridium) of from a
symbiotic host (e.g.
Rhizobium). Some soil
chemotroph bacteria derive their energy through the
oxidation of
nitrite ions, which they transform in
nitrate ions, like
Nitrobacter. These bacteria are not
nitrogen-fixing microorganisms but contribute to
nitrification, an important step in the
nitrogen cycle. == Actinomycetes ==