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.