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Soil
Mayrina Firdayati
Soil Biota (review)
helping soil to form from original parent rock
material,
contributing to the aggregation of soil particles,
enhancing cycling of nutrients,
transforming nutrients from one form to another,
assisting plants to obtain nutrients from soil,
degrading toxic substances in soil,
causing disease in plants,
minimizing disease in plants,
assisting or hindering water penetration into soil.
Role
Carbon Cycle
1. Primary producers fix CO2 convert to
organic material
- Plants – terrestrial ecosystem
- Algae and cyanobacteria (symbiotic as lichen
with fungi) in other ecosystem
- Autotroph microbes – soil ecosystem
2. Recyclers : converting OM to CO2 during
respiration. Heterotrophic bacteria and fungi.
Aided by higher animals that digest particulate
OM and microbes in intestinal tract
The process is known as decomposition and
involves the degradation OM to obtain energy
for growth
3. Mineralisation after degraded completely
into inorganic products such as carbon
dioxide, ammonia and water
In soil the major agents of OM decomposition are fungi
(saprotrofic fungi, mycorrhiza, the lichens)
Bacteria and fungi degrade complez OM that higher
organism cannot break down
Bacteria degradation
1. Actinobacteria and Proteobacteria that degrade soluble
organic molecules such as organic acids, amino acids,
and sugars
2. Bacteroidetes help degrade more recalcitrant carbon
compounds such as cellulose, lignin and chitin. The
bacteria need high levels of available N to support the
production of extracellular and transport enzymes
Anaerob/fermentative degradation of OM to organic acids
and generates gases such as hydrogen and carbon
dioxide
Strictly anaerobic conditions the hydrogen may be used
by methanogens to reduce carbon dioxide to produce
methane gas
Methanogens also can metabolise methanol, acetate or
methylamine to methane and carbon dioxide
Nitrogen fixation
Dssimilatory nitrate reduction to ammonia
Nitrification
Annamox
denitrification
Nitrogen fixation : reduction of atmospheric
nitrogen gas to ammonium
bacteria and archaea ( Azotobacter,
Burkholderia, Clostridium and some
methanogens associated with rhizosphere of
plants)
Cataliysed by the enzyme nitrogenase
Energetically expensive, consuming 16 moles
of ATP per mole of N fixed
The ammonium assimilated into amino acids
and subsequently polymerised into proteins
Nitrogen cycle
Formation of nitrite by Nitrosospira and
Nitrosomonas
Oxidation nitrite to nitrate mediated by bacteria
such as Nitrobacter and Nitrospira
Nitrification is important in soils, because the
oxidation of ammonium to nitrite and nitrate
ionschanges their charge from positive to
negative
This leads to nitrate leaching, because
ammonium tend to me nound by negatively
charges clay particles but the negatively charged
nitrate ions can be readily leached into
groundwaters
Nitrifications
Microbial respiratory process during which
soluble nitrogen oxides are used as an
alternative electron acceptor when oxygen
is limiting
Sequential reduction of nitrate, nitrite,
nitric oxide (NO) to the greenhouse gas
nitrous oxide (N2O) and nitrogen gas
Anaerobic area
Denitrification
P is not an abundant in the environment
Microbes transform P in 2 ways
1. Mineralise organic P to form inorganic
phosphate in a process catalysed by
phosphatase enzymes, produces by bacteria
and fungi
2. Transform insoluble, immobilised P to
soluble and mobile P in a process normally
mediated by the production of organic acids
3. Microbes release sufficient P for their own
use and plants and other soil organism
Phosphorus cycling
Bioremediation may be defined as the
controlled use of microorganisms for the
destruction of chemical pollutants. A large
number of processes have been developed to
handle various wastes and for the cleanup of
spilled organic materials. At the heart of all of
these processes lies the premise that the
metabolic activities of bacteria or fungi can
be used to degrade many of the organic
chemicals of commerce (solvents, pesticides,
hydrocarbon fuels, etc.).
Either of two forms of bioremediation is
commonly employed. In biostimulation the
environment into which the material has been
spilled or otherwise introduced is made favorable
for the rapid development of microbes. Typically,
this process involves adding sufficient nitrogen
and phosphorus fertilizer to overcome nutrient
limitations to microbial growth and providing
some mechanism for increased aeration of the
system. These practices encourage development
of the indigenous microbial population which
usually contains microbes able to degrade the
compounds of interest.
bioaugmentation, an external microbial population is added in
order to speed up the degradation process. Numerous microbes
have been developed for such purposes. However, the full
measure of the usefulness of such microbial products is not yet
known. Some inoculants have reportedly enhanced the
remediation process and others have had little or no effect on the
process. It is probable that in due time useful microbial products
or processes will be developed for use in the clean-up of oil or
other chemical spills. What is certain is that successful
bioremediation will require detailed knowledge of the factors
which make some microbes more competitive than others in a
given environment. Only when these details are established will
we know how to use sound ecological principles to add microbes
to these complex environments to insure their establishment and
function in the clean-up process.