SOIL MICROBIOLOGY

KEY POINTS
 Biological fertility is under-studied and our scientific knowledge of it is incomplete.
 In addition to fertility, soil microorganisms also play essential roles in the nutrient cycles that are
fundamentally important to life on the planet.
 In the past, agricultural practices have failed to promote healthy populations of microorganisms,
limiting production yields and threatening sustainability.
 Scientific research is exploring new and exciting possibilities for the restoration and promotion of
healthy microbial populations in the soil.

‘Soil is essential for the maintenance of biodiversity above and below ground. The wealth of
biodiversity below ground is vast and unappreciated: millions of microorganisms live and
reproduce in a few grams of topsoil, an ecosystem essential for life on earth…’

Soil has traditionally been seen as a "dead" agricultural medium – something to keep crops upright.
Soil physicochemical analyses were conducted to determine the application rate of chemical
fertilizers to sustain/increase the season's yields. Soils were injudiciously ploughed, drenched in
herbicides and pesticides, crop residues were burned, and fields were left bare and vulnerable to
nature's elements, with precious fertile topsoil being blown away or carried off during wind and
rainstorms. The vital role of soil microorganisms in agriculture have only recently gained
popularity with South African farmers after they experimented with various agricultural practices
in an effort to increase their yields and soil's health/fertility in a sustainable way. Before this
paradigm shift, we never realized that only 6-8 cm of fertile soil was naturally formed over a period
of 2000 years; that soil-life consisted of thousands of different insects, earthworms, mites,
nematodes, fungi, yeasts, and single-cell organisms; that a teaspoon of fertile soil could contain a
billion bacteria and almost 5,000 different species of bacteria per gram of soil.
After decades of collaboration between researchers and farmers, conservation agriculture
(CA) was promoted as the most probable solution to sustainable agriculture. Conservation
agriculture aims to improve/sustain productivity, increase profits and food security while
preserving and enhancing the resource base and the environment. Long-term implementation of
CA's three main principles, i.e. minimum soil disturbance, permanent organic soil cover, and crop
diversification, will inevitably lead to healthier soil and sustainable agriculture.
Nematodes, fungi and bacteria are usually associated with large-scale yield-losses, but
what we fail to realize in a healthy soil with its high microbial diversity and activity, is that
beneficial and harmful organisms are present in a very fine balance. With this sensitive balance
maintained, plant-pathogens are suppressed and/or out-competed by the indigenous soil life, and
vital soil processes are optimally executed. This attribute is highly beneficial, especially when
external forces, such as drought and diseases, disrupt soil processes performed by specific species.
In the event of such an external force, these vital processes can immediately be re-initiated and
maintained by other individual or groups of species, thus strengthening the soil's resilience and
resistance to disruptive forces.
Due to the sensitive nature of soil microbial populations, they could be used as "early
warning systems" or sentinel organisms to detect deterioration or improvement in soil quality –
almost like the canaries that were historically carried into the coal mine tunnels by the miners to
detect the collection of dangerous gases. If the canary was killed by the gases, it served as a
warning to coal miners to exit the tunnels immediately. With the case of soil microbial populations,
for example, when a soil's microbial diversity (the number of different microorganisms) decreases
but the activity (how hard/fast they work) increases, or vice versa, it indicates a disturbance in the
soil's balance and that the soil's health might be compromised. Such an imbalance typically occurs
during injudicious ploughing and fertiliser application, extended fallow periods, or continuous
monocropping.
Soil microbiology is the study of organisms in soil, their functions and how they affect soil
properties. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae, protozoa
and viruses. Each of these groups has different characteristics that define the organisms and
different functions in the soil it lives in. Importantly, these organisms do not exist in isolation; they
interact and these interactions influence soil fertility as much or more than the organism’s
individual activities.

Bacteria: Bacteria are organisms that have only one cell and are, therefore, microscopic. There
are anywhere from 100 million to one billion bacteria in just a teaspoon of moist, fertile soil. They
are decomposers, eating dead plant material and organic waste. By doing this, the bacteria release
nutrients that other organisms could not access. The bacteria do this by changing the nutrients from
inaccessible to usable forms. The process is essential in the nitrogen cycle.
Actinomycetes: Actinomycetes are soil microorganisms like both bacteria and fungi, and have
characteristics linking them to both groups. They are often believed to be the missing evolutionary
 link between bacteria and fungi, but they have many more characteristics in common with bacteria
than they do fungi. Actinomycetes give soil its characteristic smell. They have also been the source
of several significant therapeutic medicines.

Fungi: Fungi are unusual organisms, in that they are not plants or animals. They group themselves
into fibrous strings called hyphae. The hyphae then form groups called mycelium which are less
than 0.8mm wide but can get as long as several metres. They are helpful, but could also be harmful,
to soil organisms. Fungi are helpful because they have the ability to break down nutrients that other
organisms cannot. They then release them into the soil, and other organisms get to use them. Fungi
can attach themselves to plant roots. Most plants grow much better when this happens. This is a
beneficial relationship called mycorrhizal. The fungi help the plant by giving it needed nutrients
and the fungi get carbohydrates from the plant, the same food that plants give to humans. On the
other hand, fungi can get food by being parasites and attaching themselves to plants or other
organisms for selfish reasons.
Some of the functions performed in soil by fungi are:
 Decomposers – saprophytic fungi – convert dead organic material into fungal biomass, carbon
dioxide (CO2), and small molecules, such as organic acids.
 Mutualists – the mycorrhizal fungi – colonise plant roots. In exchange for carbon from the plant,
mycorrhizal fungi help to make phosphorus soluble and bring soil nutrients (phosphorus,
nitrogen, micronutrients and, perhaps, water) to the plant. One major group of mycorrhizae,
the ectomycorrhizae, grow on the surface layers of the roots and are commonly associated with
trees. The second major group of mycorrhizae are the endomycorrhizae that grow within the root
cells and which are commonly associated with grasses, row crops, vegetables and shrubs.
 Parasites: The third group of fungi, pathogens or parasites, causes reduced production or death
when they colonise roots and other organisms.
 Algae: Algae are present in most of the soils where moisture and sunlight are available. Their
number in the soil usually ranges from 100 to 10,000 per gram of soil. They are capable of
photosynthesis, whereby they and obtain carbon dioxide from atmosphere and energy from
sunlight and synthesise their own food.
The major roles and functions of algae in soil are:
 Playing an important role in the maintenance of soil fertility, especially in tropical soils.
 Adding organic matter to soil when they die and thus increasing the amount of organic carbon in
soil.
 Acting as a cementing agent by binding soil particles and thereby reducing and preventing soil
erosion.
 Helping to increase the water retention capacity of soil for longer time periods.
 Liberating large quantities of oxygen in the soil environment through the process of photosynthesis
and, thus, facilitating submerged aeration.
 Helping to check the loss of nitrates through leaching and drainage, especially in
un-cropped soils.
 Helping in the weathering of rocks and the building up of soil structure.
Protozoa: These are colourless, single-celled animal-like organisms. They are larger than bacteria,
varying from a few microns to a few millimetres. Their population in arable soil ranges from
10,000 to 100,000 per gram of soil and they are abundant in surface soil. They can withstand
adverse soil conditions, as they are characterised by a protected, dormant stage in their life cycle.
The major functions, roles and features of protozoa are:
 Most protozoans derive their nutrition from feeding or ingesting soil bacteria and, thus, they play
an important role in maintaining microbial/bacterial equilibrium in the soil.
 Some protozoa have been recently used as biological control agents against organisms that cause
harmful diseases in plants.
 Several soil protozoa cause diseases in human beings that are carried through water and other
vectors. Amoebic dysentery is an example.
Viruses: Soil viruses are of great importance, as they may influence the ecology of soil biological
communities through both an ability to transfer genes from host to host and as a potential cause of
microbial mortality. Consequently, viruses are major players in global cycles, influencing the
turnover and concentration of nutrients and gases.
Despite this importance, the subject of soil virology is understudied. To explore the role of the
viruses in plant health and soil quality, studies are being conducted into virus diversity and
abundance in different geographic areas (ecosystems). It has been found that viruses are highly
abundant in all the areas studied so far, even in circumstances where bacterial populations differ
significantly in the same environments. Soils probably harbour many novel viral species that,
together, may represent a large reservoir of genetic diversity. Some researchers believe that
investigating this largely unexplored diversity of soil viruses has the potential to transform our
understanding of the role of viruses in global ecosystem processes and the evolution of microbial
life itself.
Nematodes: Not microorganisms (strictly speaking), nematode worms are typically 50 microns in
diameter and one millimetre in length. Species responsible for plant diseases have received much
attention, but far less is known about much of the nematode community, which play beneficial
roles in soil. An incredible variety of nematodes have been found to function at several levels of
the soil food web. Some feed on the plants and algae (the first level), others are grazers that feed
on bacteria and fungi (second level), and some feed on other nematodes (higher levels).
Free-living nematodes can be divided into four broad groups based on their diet. Bacterial-
feeders consume bacteria. Fungal-feeders feed by puncturing the cell walls of fungi and sucking
out the internal contents. Predatory nematodes eat all types of nematodes and protozoa. They eat
smaller organisms whole or attach themselves to the cuticle of larger nematodes, scraping away
until the prey’s internal body parts can be extracted.Like protozoa, nematodes are important in
mineralising, or releasing, nutrients in plant-available forms. When nematodes eat bacteria or
fungi, ammonium is released because bacteria and fungi contain much more nitrogen than the
nematodes require.
Nematodes may also be useful indicators of soil quality because of their tremendous
diversity and their participation in many functions at different levels of the soil food web.
Role and Functions
Collectively, soil microorganisms play an essential role in decomposing organic matter, cycling
nutrients and fertilising the soil. Without the cycling of elements, the continuation of life on Earth
would be impossible, since essential nutrients would rapidly be taken up by organisms and locked
in a form that cannot be used by others. The reactions involved in elemental cycling are often
chemical in nature, but biochemical reactions, those facilitated by organisms, also play an
important part in the cycling of elements. Soil microbes are of prime importance in this process.
Soil microbes are also important for the development of healthy soil structure. Soil microbes
produce lots of gummy substances (polysaccharides and mucilage, for example) that help to
cement soil aggregates. This cement makes aggregates less likely to crumble when exposed to
water. Fungal filaments also stabilise soil structure because these threadlike structures branch out
throughout the soil, literally surrounding particles and aggregates like a hairnet. The fungi can be
thought of as the “threads” of the soil fabric. It must be stressed that microbes generally exert little
influence on changing the actual physical structure of the soil; that is performed by larger
organisms.
Soil microorganisms are both components and producers of soil organic carbon, a
substance that locks carbon into the soil for long periods. Abundant soil organic carbon improves
soil fertility and water-retaining capacity. There is a growing body of research that supports the
hypothesis that soil microorganisms, and fungi in particular, can be harnessed to draw carbon out
of the atmosphere and sequester it in the soil. Soil microorganisms may provide a significant means
of reducing atmospheric greenhouse gasses and help to limit the impact of greenhouse gas-induced
climate change.