Introduction
In circa 1500 Leonardo da Vinci said: ”We know more about
the movement of celestial bodies than about the soil
underfoot”. Although our knowledge of both these fields of
science has developed immensely over the last five
centuries, this statement undoubtedly remains true. Soil
life, and especially the soil microbial system, is very
dynamic and sensitive, and the potential impacts on its
composition are so vast in number that it is very
difficult to predict its characteristics under all
possible circumstances.
Since the living part of soil consists of a huge number of
different species that live in a dynamic ecosystem, where
they prey on one another and other times live
symbiotically together, the science of soil microbiology
is complicated. As a result, very few scientists will
claim to be specialists in more than one or two components
of soil microbiology. Because of the interest in this
topic that has developed among grape producers in recent
years, this article attempts to apply relevant elements of
this biological science to grape production systems and to
address some of the factors that impact vineyard soil-
ecosystems.
Soil Organic Matter
Organic matter is a critical component in the microbial
ecosystem of soil since it is the energy source of soil
micro-organisms. With a reduction in soil organic matter
content, microbial activity decreases. The presence of
soil organic matter therefore ensures microbial activity
and affects the characteristics of the soil in various
ways. Whilst attempting to manage his vineyard soil
responsibly, a viticulturalist will benefit from having
some knowledge regarding the properties of soil organic
matter.
Organic matter is defined as all carbon compounds formed
by living organisms. In soil it consists of three
components, namely dead organic matter, living parts of
plants (eg. roots) and living microbes and animals (Figure
1). Of these three, the first is the largest component,
comprising between 70% and 90% of the soil organic matter
(Gregorich et al., 1997). Recently died plant material,
soil microbes and insects/animals are in a very dynamic
state in that it quickly develops into humus. As a result,
humus is the largest component of the dead organic matter
fraction.
The dead organic matter (humus and fresh soil organic
matter) consists of various chemical compounds that
individually plays a role in the ecosystem, breaks down at
different rates, and gives each soil its own unique
character. The most important compounds, that make up the
bulk of the material, are: (1) cellulose, (2) lignin, (3)
chitin, (4) lipids, (5) protein, and (6) simple soluble
molecules.
Cellulose is a carbohydrate that composes of glucose that
is bound together in long chains (Figure 2). Carbon (C),
oxygen (O) and hydrogen (H) are the main elements of this
compound. It is prominent in woody substances, straw,
stubble and leaves. Through hydrolysis fungi and bacteria
convert it to carbon dioxide (CO2) or cell carbon.
Cellulose is relatively resistant to microbial attack and
the chemical process of hydrolysis. The initial pace of
cellulose hydrolysis is therefore slow, often making it
the rate limiting reaction in microbial breakdown of soil
organic material.
Lignin is a complex long-chain compound (polymer) that is
made up of thousands of rings of C atoms joined together
in a long chain. The way in which they are linked up
varies along the chain. It also contains only C, H and O,
but is aromatic compared to cellulose in that it contains
phenolic groups. Lignin binds to cellulose fibers to
harden and strengthen cell walls of plants. It is
plentiful in older higher woody plants, especially in the
branches and trunks (Table 1). The most important
characteristic of lignin is its high resistance to
enzymatic breakdown. The result is that, with the
exception of a few specialized fungi and actinomycetes
(unicellular filamentous microorganisms that possess
properties intermediate between the fungi and the
bacteria), soil organisms cannot digest wood. Decomposed
soil organic matter will therefore often end up having
high lignin contents but little cellulose.
Chitin is also a polymer, analogous in chemical structure
to cellulose, but consists of units of a nitrogenous
derivative of glucose. It is, therefore a polysaccharide,
with amino sugars as its basic structural unit. Like
cellulose, chitin contributes strength and protection to
organisms. Soil chitin originates from the remains of
insect cells and fungi, as well as some actinomycetes and
yeasts. It is mainly broken down by actinomycetes, which
proliferate in its presence, especially those that excrete
anti-fungal substances.
Lipids are substances produced by organisms that are
insoluble in water. It includes a lot of compounds like
pigments, fats, waxes, phospholipids, sterols, di- &
triglycerides, etc. They generally are hydrophobic. Lipids
are broken down by specific groups of bacteria that
secrete an enzyme (lipase) which hydrolyze it to break
down to fatty acids. Last mentioned are then broken down
further through oxidation.
Protein is a group of complex organic compounds, mainly
one or more chains of amino acids that are linked together
by peptide bonds. It therefore contains C, H, O, sulphur
(S) and very characteristically, nitrogen (N). They are
broken down very easily through hydrolyses of the peptide
bonds by enzymes that are excreted by an innumerable
amount of heterotrophic soil organisms (organisms which
require carbon in organic form). Thereby the amino acids
are released which then serve as sources of C and N to the
soil organisms. Because of its high N content, protein
contributes to the N in soil organic matter and therefore
increases the C:N ratio of the soil.
Simple soluble molecules are usually the product of
microbial breakdown of organic matter. Examples are, as
mentioned above, amino acids, also acids, sugars, alcohols
and aromatic groups. These are readily available for
uptake or utilization by the soil micro-organisms.
As dead organic matter breaks down, it forms into the most
important part of dead soil organic matter, i.e. humus.
Last mentioned can be defined as a mixture of colloidal
degradation products that accumulates in the soil because
it breaks down slower than the products it was formed
from. Humus is therefore relatively resistant to microbial
breakdown. One of the major substances of humus is
residual lignin. Despite its resistance to microbial
breakdown, it oxidizes to give humus its black colour.
Furthermore, the phenolic groups also contribute to the
characteristic smell of humus. The slow process of humus
decay happens in two ways, namely oxidation in hot dry
climates and microbial breakdown in warm wet climates. A
flux in humus decay usually occurs after a dry spell. This
is due to the oxidation that takes place in the dry period
whereby C is lost from the humus as CO2 and the chemical
composition of the resistant compounds in the humus is
altered. Afterwards, when the soil is moistened, an
explosion in the population of soil organisms occurs due
to the sudden increase in digestible compounds and the
favourable climatic conditions.
Breakdown of Soil Organic Matter
By now it must be clear that the process of soil organic
matter breakdown is complex. It involves different stages
of breakdown taking place simultaneously, with different
compounds breaking down at different rates and due to the
activity of different organisms (Figure 3). The stages of
breakdown can be separated into (1) the colonization and
physical fragmentation of fresh organic matter, (2) the
chemical alteration of the organic matter and, finally,
(3) the release of mineral nutrients.
Leaf- and root surfaces are colonised by micro-organisms
even before they die. Once the dead organic matter lands
on the soil, they immediately excrete enzymes that oxidize
the organic matter to obtain energy and C. In the process
C is lost through the release of CO2. The result is a
decrease in the C:N ratio of the organic matter.
Simultaneously, earthworms and other larger soil animals
such as mites and ants, start fragmenting the fresh
organic matter. The surface area is thereby increased
allowing more micro-organisms to colonise and decompose
it. Soil animals, especially earthworms, assist with the
colonisation process by incorporating organic matter into
the soil (where conditions for microbial colonization are
more favourable) and mixing it with intestinal microbes as
they digest the material. The fungi, bacteria and
actinomycetes secrete enzymes to break up the organic
compounds which all are, as mentioned above, long and
complex chains. Simpler molecules are then formed from
which, with further decomposition, are mineral nutrients
finally released. This process is called mineralization,
i.e. the biological process by which organic compounds are
chemically converted to simpler organic compounds and
finally to mineral nutrients (Figure 4).
Because of the large amount of N that can be released from
incorporated soil organic matter for plant nutrition,
N-mineralization is of economic importance.
It consists of two steps:
-
Ammonification - the release of N as
ammonium (NH +) from organic molecules through enzyme
activity of bacteria & fungi (Figure 5).
-
Nitrification - the release of N as
ammonium (NH +) from organic molecules through enzyme
activity of bacteria & fungi (Figure 5).
From Figure 5 it can be deduced that urea, being an
organic molecule, also requires mineralization before the
N therein is released for uptake. This process of urea
breakdown, however, is done by a very specific group of
bacteria that are able to release an enzyme called
“urease”. Low microbial activity is the reason why the use
of urea is not recommended as fertilizer on coarse sandy
soils. Furthermore, it is worthwhile noticing that two
hydrogen ions (H+) are released to the soil for every NH +
-ion that is nitrified. The implication is that the
mineralization of all organic matter (especially urea)
acidifies the soil. Where the use of urea or organic
matter applications is frequent, maintenance lime
applications should be considered for soils with a pH(KCl)
lower than 6,0.
The amount of N, as well as the rate by which it is
released, is determined by the C:N ratio of the soil
organic matter. The C:N ratio is an expression of the
amount of C compared to N that are in the soil, but does
not give an indication of the forms that the C and N are
in. The value of knowing this ratio is that one can deduce
the potential N- availability to both soil micro-organisms
and plants. The lower the C:N ratio, the more of the N in
the organic matter will be available for mineralization
and, therefore, for plant nutrition. On the other hand, a
high C:N ratio causes periodic plant N deficiency because
the soil micro-organism population is under-supplied by N
and as a result consume all the available N, both in the
organic and mineral form. This is called immobilisation of
mineral N. The addition of organic matter with a high C:N
ratio to the vineyard soil can therefore lead to a
periodic N deficiency in the vines. In Table 2 an
indication of the C:N ratio of some fresh organic
materials are given with an indication of its
corresponding rate of N-release.
The Rhizosphere
Related to a grape production system, the rhizosphere is
the most important facet of soil microbiology. It is the
region of soil immediately adjacent to, and directly
affected by, the vine roots.
Active growing roots exude organic compounds (exudates)
into the soil. These compounds are a food source for
micro-organisms, causing their number to be up to 500
times higher than in the rest of the soil (McLaughlin et
al., 2000). The characteristics of the exudates changes
according to the age of the plant, season, chemical
inputs, water availability and nutritional status. The
rhizosphere is therefore a constantly changing
environment, in which the relative number of each member
group adjusts according to the nature of the exudates and
the environmental conditions. For example, when a vine
wilts due to water stress, more amino acids are released
by the roots to the rhizosphere. Likewise, some plants
release organic acids into the rihizosphere in response to
iron (Fe) or P deficiency, which then solubilise Fe, P, Zn
and other metals, thereby enhancing their bioavailability
(McLaughlin et al., 2000).
Chemicals also affect the microbial situation of the
rihizosphere. It happens in three ways, namely (1) through
its direct influence thereon by being incorporated into
the soil; (2) by being absorbed by the plant leaves and
translocated to other plant parts where it alters the
plant’s metabolism and, as a result, affects the
composition of the exudates; and (3) by being absorbed by
the plant, translocated to the roots and exuded by the
roots into the rhizosphere. For example, application of a
Bordeaux mixture to the leaves of bean plants was found to
increase the Cu in the rhizosphere, reducing the bacterial
numbers therein (Wilhelm, 1966).
Relating to soil pathogenic infections, the rhizosphere is
often called “the first line of defence”. Pathogens can
only cause a disease by entering the root from the
rhizosphere. For it to successfully establish itself as a
member of the rhizosphere, it must be able to compete with
the other saprophytes for nutrients. But because of the
high numbers of microbial organisms and their enhanced
activity, which is associated with antagonistic and
competing reactions, the rhizopshere generally protects
the roots against infection. However, if the balance of
this micro-habitat is disturbed by a chemical or
detrimental environmental conditions (drought,
water-logging, nutritional deficiencies) the effectiveness
of the saprophytes to compete with the parasites/pathogens
reduces and results in root-infections. In terms of the
root environment, biological control of fungal diseases
would therefore entail the maintenance of a high activity
of beneficial organisms in the root-zone.
Managing Soil Biological Fertility
Although management practices are known to impact the
biology of vineyard soils, there is limited knowledge to
support the development of detailed management strategies.
A particular practice may have the desired result in one
situation but have little effect in another because
biological communities respond to the interaction of
multiple factors including food sources, moisture,
historical land use and physical habitat.
A common denominator is that soil potential improves when
the number and complexity, or diversity, of the soil
biological community increases. There, however, is also an
economic limit to the amount of diversity that one might
want to obtain. Some practical ideas on increasing and
maintaining biological activity and diversity are
therefore suggested below.
Firstly, supply organic matter to the
soil. It is known that over time, the organic matter
content of cultivated soils decreases, especially during
the first years after development (Figure 6). Organic
matter can be added to the soil by utilising crop residue
maximally, i.e. do not remove shoots after pruning, by
applying compost or manure (if available and affordable)
and by planting cover crops. Surface residue, like shoots
and stubble, encourages the decomposers, especially fungi
because they have an advantage over bacteria in digesting
surface residue. Earthworms and arthropods are also
benefited. In addition to above ground residue produced,
cover crops increase the sub-soil organic matter content
through its dense root system. The rhizosphere of cover
crop roots also increases the biological activity of the
soil significantly. Compost inoculates the soil with a
wide variety of organisms while animal manure provides
food and mineral nutrients to both larger organisms and
micro-organisms. A combination of manure and plant matter
will obviously support a larger mixture of soil organisms
(Anonymous, 2005).
Secondly, rotate crops. This practice
regularly puts a different food source into the soil that
results in a wider variety of organisms and prevents the
build-up of a single pest species. Within a vineyard
context, this can be achieved through rotation of cover
crops. For example, on a sandy soil saia oats can be
followed up after two years by grazing vetch, which is
followed up by pink seradella (personal communication: J.
Fourie).
Thirdly, protect the habitat of soil
organisms. Soil organisms need air, moisture, a constant
food supply and protection against adverse elements. Soil
compaction changes the movement of air and water through
soil, and may cause a switch from aerobic to anaerobic
organisms. It also reduces the space available for larger
organisms to move through the soil. The ecosystem is
therefore affected, with the result that the population of
fungi, larger predators and arthropods declines. Among the
nematodes, the predatory species are the most affected,
followed by the fungal feeders and then the bacterial
feeders. Root-feeding nematodes, however, are the least
sensitive to compaction – perhaps because they do not need
to move through the soil in search for food (Anonymous,
2005).
Clean cultivation leads to the migration of most
arthropods or to their starvation. The soil climatic
conditions are also adverse to any biological activity,
while cover crops will stabilize the soil moisture and
temperature conditions and maintain the biological
habitat. Although tillage enhances bacterial growth in the
short term by aerating the soil and mixing the organic
matter with the soil, it leads to an accelerated loss of C
as CO2 and it triggers explosions of bacterial predators
like protozoa. Over the long term the soil organic matter
that fuels the organism population reduces and as a result
the populations of fungi, earthworms, nematodes and
arthropods will decline due to a lack of food, rather than
the (also detrimental) mechanical action of tillage.
Pesticides also impacts non-target organisms. It feed some
organisms and harms others. Few pesticides have been
studied for their effect on a wide range of soil
organisms, so that the net effect of moderate chemicals is
not well understood. We do know, however, that many of the
well-known pesticides reduce soil biological complexity
(van Zwieten, 2004). Herbicides often do not affect soil
organisms directly, but the weed loss (in clean
cultivation) changes the food sources and habitats
available to organisms. Fertilisers provide some nutrients
to organisms and favour those species that can utilize
mineral nutrients. The pH and salt effect of fertilizers
like ammonium nitrate and potassium chloride reduces
populations of bacteria, fungi and nematodes temporarily
(Anonymous, 2005). On the other hand, responsible
fertilizer use increases plant growth, and therefore
organic inputs into the soil which benefits biological
activity. This is especially applicable to cover crops.
In conclusion, it is important to consider the fact that
soil biological processes can develop slowly and it can
take time before changes are noticed. Some processes can
take place at enormous rates, eg. bacterial population
growth after soil cultivation, affecting the soil within
days, while other processes takes many months or even
years to impact the soil.
Practical considerations to keep in mind
The presence of organic matter is a prerequisite for
microbial activity. One therefore must ensure its
presence. Clean cultivation leads to a loss of soil
organic matter, increases soil density and soil erosion,
while temperature extremes also develop in the topsoil.
All are detrimental conditions to soil biological
activity. Rotated cover crop cultivation and the
maintenance of pruning material in the vineyard should be
an integral part of a viticulturalist’s soil management
strategy.
The use of organic matter and urea acidifies the soil,
regular monitoring of the soil pH.
The C:N ratio of applied organic matter will determine
whether N is released rapidly, slowly or whether mineral N
in the soil is immobilized periodically. As a general
rule, an estimated 50% of all organic N applied to soil
will be released during the course of the first year.
Thereafter 25% is released in the second year and 10% in
the third. Through annual additions of organic material
the N released from the soil organic matter will therefore
increase continuously. Mineral N-fertilisation will
therefore have to be decreased.
The health of the rhizosphere determines to a large extent
the health of the vine, particularly its roots system.
Many chemicals affect it and as a result, soil conditions
that contributes to the rapid restoration of the
rihzosphere ecosystem benefits the health and performance
of the vine. A high microbial activity in the soil,
maintained by the presence of organic matter, is the
crucial aspect.
Literature Cited
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