Biological Process in

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 of soil organism in soil fertility

(review)
6 function that perform by soil
microorganism
Releasing
 nutrients from organic matter
Soil microorganisms are responsible for most of the
nutrient release from organic matter. When microorganisms
decompose organic matter, they use the carbon and nutrients
in the organic matter for their own growth. They release
excess nutrients into the soil where they can be taken up by
plants. If the organic matter has a low nutrient content, micro-
organisms will take nutrients from the soil to meet the
requirements.
For example, applying organic matter with carbon to nitrogen
ratios lower than 22:1 to soil generally increases mineral
nitrogen in soil. In contrast, applying organic matter with
carbon to nitrogen ratios higher than 22:1, generally results in
microorganisms taking up mineral nitrogen from soil
 Cont.
Fixing atmospheric nitrogen
Symbiotic nitrogen fixation is a significant source of and may
account for up to 80% of total nitrogen inputs.In the symbiosis,
rhizobia or fix nitrogen gas from the atmosphere and make it
available to the legume. In exchange, they receive carbon from
the legume. The symbiosis is highly specific and particular species
of rhizobia are required for each legume.

Increasing phosphorus availability

Most agricultural plants (except lupins and canola) form a
symbiosis with arbuscular mycorrhizal (AM) fungi ) that can
increase phosphorus uptake by the plant. The hyphal strands of
AM fungi extend from plant roots into soil and have access to
phosphorus that plant roots cannot reach. The AM fungi can
provide phosphorus to plants and in return they receive the
carbon they need to grow. 
Importantly, this symbiosis is only beneficial for plants when
available phosphorus in soil is insufficient for the plant’s
requirements.
 Cont.

Degrading pesticides
The degradation of agricultural pesticides in soil is primarily performed by
microorganisms. Some microorganisms in soil produce enzymes that can break
down agricultural pesticides or other toxic substances added to soil. The length
of time these substances remain in soil is related to how easily they are
degraded by microbial enzymes.
Controlling pathogens
Some microorganisms and soil animals infect plants and decrease plant
yield. However many organisms in the soil control the spread of pathogens.
For example, the occurrence of some pathogenic fungi in soil is decreased by
certain protozoa that consume the pathogenic fungi. The soil food web
contains many relationships like this that decrease the abundance of plant
pathogens.
Improving soil structure
Biological processes in soil can improve soil structure. Some bacteria and
fungi produce substances during organic matter decomposition that chemically
and physically bind soil particles into micro-aggregates. The hyphal strands of
fungi can cross-link soil particles helping to form and maintain aggregates
(figure 3). A single gram of soil can contain several kilometres of fungal
hyphae (Young and Crawford 2007). In addition, soil animals increase pores by
tunnelling through soil and increase aggregation by ingesting soil.
Soil microbes play major rules in cycling
Carbon, Nitrogen, Phosphorus (essential
for producing biomolecules such as amino
acids, proteins, DNA, RNA)
Soil bacteria and fungi plays significant
role in ion cycling and plant nutrition by
mineral weathering

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.