Microbial Diversity and the Impact of Agricultural Practices
|B. Venkateswarlu and Ch. Srinivasarao Central Research
Institute for Dryland Agriculture Santoshnagar, Saidabad
(PO) Hyderabad -500 059
of microbial population in soil in relation to various
agricultural practices was evaluated. In the soil profile,
the microbial population mostly occurs within 40 cm
of top soil. Bacteria are predominant followed by actinomycetes
and fungi. Management practices such as irrigation,
tillage, cropping, fertilizer application, residue incorporation,
manuring and microbial inoculation have major impact
on diversity of biological population in soil. Diversity
index was much higher in Alfisols than Vertisols under
different crop management practices. In both the soils,
addition of organic manure (FYM) showed greater species
diversity over control and inorganic fertilizer application.
Continuous monoculture had a negative impact on species
diversity as compared to crop rotations. Future research
needs on understanding microbial diversity and its relationship
with sustaining soil quality are highlighted.
microbial diversity, agricultural practices, soil degradation
a vibrant living community in the soil contributing
to a number of nutrient transformations. They are involved
in organic matter decomposition, N2-fixation, solubilization
and immobilization of several major and minor nutrients
(Alexander, 1971). Microbes also play an important role
in soil structure maintenance, soil borne disease control
and plant growth promotion through secretion of hormones.
The diversity and richness of soil microorganisms has
been a fascinating subject for scientists over the years,
but till today relatively little is known on the complex
living biota in the soil and their biophysical and biochemical
functions in the soil ecosystem. But during the last
50 years, many beneficial effects of microbes in soil
have been discovered (Alexander, 1971; Subba Rao and
Gaur, 2000) and we have been making use of microorganisms
for improving productivity in agriculture, industry
and pharmaceuticals. With growing awareness on agro
biodiversity conservation and management during the
last decade, a parallel interest has been generated
on understanding soil microbial biodiversity (SMD) as
well. SMD is a vast frontier of potential gold mine
for the biotechnology industry as it offers countless
new genes and biochemical pathways (Tilak, 2000). This
paper summarizes the recent advances in understanding
soil microbial diversity, its functional significance
and the impact of agricultural practices with particular
reference to semi arid tropics.
of microbial diversity in soil
One cubic meter of soil may house many hundreds of
species of bacteria, actinomycetes, fungi and algae.
The distribution of microorganisms in a typical soil
profile has been described by Alexander (1971). The
numerical dominance of bacteria and its significance,
each group has its unique contribution to the nutrient
cycles and as source of useful chemicals like antibiotics,
vitamins and enzymes.
Although extensive information has been generated
on plant and animal biodiversity, little is known
on microbial diversity and our knowledge on soil biodiversity
is still a miniscule. About 45,000 species of plants,
67,000 species of insects and 61,000 of invertebrates
have been described in India. No specific information
on bacteria is available for the country but an estimated
50 percent of all living population on earth is microbial.
There may be 1.5 million species of fungi but only
5 percent are described and as many as one million
species of bacteria but only about 5,000 have been
described (Tilak, 2000). The estimated and the actually
described number of species of bacteria, fungi, algae
and viruses are compared with the culture collections
of Hawksworth (1991). Compared to number of species
estimated, the described ones are few and those actually
cultured in the laboratory are still fewer. The data
indicate the dominance of fungi in the estimated species
but very small percentage of them had been cultured.
Two parameters become important while evaluating
the significance of microorganisms in soil i.e., abundance
and diversity. While abundance may increase or decrease
over short periods of time in response to management
practices and inputs, diversity is a more complex
and stable attribute and reflects a state of near
equilibrium. The latter is more important to understand
the functional significance of microorganisms at a
given site. High variation can be found for abundance
between different soil types, seasons and land uses.
In view of the large fluctuations and the undependability
of numbers, microbial biomass is often used as a more
reliable parameter to assess the abundance. The populations
and biomass levels of major groups of organisms in
a typical soil profile (0-25cm) has already been described
by Miller (1990). In terms of biomass, fungi dominate
in the soil followed by bacteria and actinomycetes.
The total populations and live biomass are only reflections
of the status of the soil at a given point of time,
but do not give a clear picture of the living diversity
as influenced by different land use practices over
time. The greatest uncertainty in population counts
is our inability in recovering all the organisms in
the culture. Generally only about 5-10 percent of
the organisms in the soil can be recovered through normal viable counts. Even direct counting methods
do not reflect the true composition of the population
in the soil. Therefore in most studies, what is being
determined is only the cultureable biodiversity.
Despite these limitations, conventional studies on
soil microbiology have always relied on total population
counts, enrichment and isolation of pure cultures
to study their practical significance, estimation
of microbial biomass and carbon dioxide evolution
(Alexander, 1971). Only recently, studies on soil
microbial diversity have been initiated using the
standard methods developed for eukaryotes. Kennedy
and Smith (1995) reviewed the various components of
microbial diversity and the different indices normally
used for its measurement. Although diversity can be
studied at the level of genera, species, community
and ecosystem, species diversity is the most commonly
studied parameter in the soil. Many indices have been
described for assessing the species richness and evenness
(Kennedy and Smith, 1995). More recently molecular
genetics tools have also been used to study microbial
diversity in soil (Ogram, 2000).
practices and soil biodiversity:
Microorganisms are involved in a number of biochemical
processes that contribute to improved plant nutrient
availability. These include 1) mineralization 2) nitrogen
fixation 3) nitrification/denitrification 4) phosphate
solubilization 5) antibiosis 6) siderophores production
7) plant growth regulation and 8) induced resistance.
Several groups of organisms act both competitively
and synergistically to mediate the above processes.
Soil and crop management research over the years has
helped in understanding the impact of various natural
factors and agricultural practices on the population
and diversity of microorganisms in soil. Soil management
practices in general and those that influence the
fertility in particular have an immediate impact on
microbial population. Swift et al. (1996) has summarized
the general typical soil management practices and
their impact on biotic activity. In view of the practical
importance, most of the studies have been focused
on agriculturally useful organisms like nitrogen fixers
and phosphate solubilizers. Tillage, soil erosion,
crop rotations, manuring, burning and pesticide application
were the major agricultural practices whose impact
has been studied in detail. However, most studies
focused on the population and activity of individual
organisms of specific physiological significance are
not on the diversity per se.
Species diversity at a particular site is not always
related with the microbial biomass or carbon dioxide
evolution, which indicates the total microbial activity.
In general, cultivated soils have greater diversity
than fallow lands (Kennedy and Smith, 1995). The impact
of land use is highly variable. Each kind of vegetation
(natural or crop) provides a particular substrate,
which encourages some microbial species over others
in the rhizosphere. Although several studies indicate
that cultivation increases the population and diversity
in soils, there have been few reports of increased
population under minimum tillage with residue incorporation
as compared to conventional tillage (Linn and Doran,
1984). However, this superiority was restricted to
surface soil (0-75mm) and in deeper layers conventional
tillage caused more population build up. Soil biota
influence soil properties through the formation of
stable aggregates, bonding through fungal hyphae and
polysaccharides, but accelerated erosion and loss
of clay and organic carbon fractions can cause significant
decline in microbial population and diversity (Venkateswarlu,
1998). In a comprehensive study in Alfisols and Vertisols
in peninsular India, Venkateswarlu (2000) observed
a considerable decline in population and diversity
as a result of top soil erosion. (Table 1).
Table 1. Population and diversity indices (DI) of
bacteria, fungi, actinomycetes and nitrifying bacteria
in control and eroded sites of Hayatnagar Research
Farm near Hyderabad (Population of bacteria, fungi
and actinomycetes by plate counts, while Nitrosomonas
and Nitrobactor by MPN method. Ten randomly collected
samples (0-30 cm) were analysed twice during July
and October for each treatment)
DI was determined based on operational taxonomic
unit (OTU); ** Not applicable
Manuring and fertilizer application also have a significant
impact on the species diversity of bacteria and fungi.
They cause significant changes in the microbial populations
which are largely mediated through changes in soil
pH. Sharma et al. (1983) reported that application
of nitrogen fertilizers like ammonium sulfate increase
the fungal population whereas FYM and NPK application
increased the population of fungi, bacteria and actinomycetes.
Certain species of microorganisms like Azotobacter
are very sensitive to soil acidity while others like
Nitrosomonas and Nitrobacter are more sensitive to
erosion of top soil (Venkateswarlu, 2000). Such organisms
can be used as indicators of degradative processes
in soil or the extent of degradation of given soil.
Samples analyzed from long term fertilizer trial
plots in Alfisols at Bangalore revealed greater species
diversity in FYM plots as compared to chemical fertilizer
and control plots. While organic manured plots showed
greater population and species richness, continuous
application of NPK did not cause any significant change
in the diversity of fungi or bacteria as compared
to control plots
Table 2. Microbial populations and diversity
indices (Mean ± SD) in long term experimental
plots receiving only chemical fertilisers
or FYM at Bangalore (Alfisols) and Indore (Vertisols).
Fertilisation includes recommended level i.e. 40-26-0
of NPK at Indore and 50-50-25 at Bangalore .
A critical analysis of the qualitative composition
of the microflora indicated that certain species like
Chaetomium, Monilia, Trichoderma and Spicaria
were more frequently isolated in FYM plots than
control or chemical fertilizer plots (Table
3) . In Vertisols, few species not found
in chemical fertilizer or control plots could be isolated
from FYM plots. Similar trend was noted with Nocardia
and Streptomyces . Actinoplanes
could be detected only in FYM plots of Alfisols.
Aspergillus and Penicillium together
constituted 80% of the total colonies in control and
chemical fertilizer plots while in FYM plots it did
not exceed 65%. Similarly, Streptomyces
comprised 60% of the total actinomycete colonies in
control and chemical fertilizer plots, but in FYM
plots this did not exceed 50%.
Table 3: Frequency of occurrence of genera
of fungi and actinomycetes in control (C) and chemical
fertilised (CF) and organic manure (FYM) plots in
Alfisol and Vertisol
+++ Abundant; ++ Frequent occurrence; + Rare occurrence;
0 Not detected
The crops and cropping systems grown on cultivated
fields over a period of time also significantly influence
their population and diversity. Certain crops encourage
a particular group of genera of fungi and actinomycetes
in rhizosphere while others do not exhibit any specific
effect. For example, in a study of two sites near
Hyderabad under sorghum - castor - sorghum rotation
for twelve years and continuous castor for ten years,
a differential distribution of fungal genera was noted.
More diversity was recorded in rotation plots as compared
to monoculture ( Table 4 ). In monoculture
plots, there was a predominance of one or two genera
(mostly Streptomyces ) representing 80% of
the actinomycetes. These preliminary studies indicate
the negative effects of monoculture, over crop rotations
on the soil biota, but more detailed studies are required
to understand the cropping system effect by not only
studying the effect of root exudates, leaf leachates
from standing biomass but also of the residues after
the crop harvest. Allelopathic effect of crops on
soil microbes is yet another area very little understood.
Table 4. List of genera of fungi and actinomycetes
isolated in plots under Sorghum-Castor-Sorghum (SCS)
rotation (12 yrs.) and continuous castor (CC) cultivation
(10 yrs.) in an Alfisol near Hyderabad
and Future Research Needs:
The available information on changes in soil microbial
diversity in response to agricultural practices is
quite scanty. However even this limited data indicate
that significant changes occur in the diversity of
important microorganisms involved in nutrient transformations,
antibiosis, plant disease control and growth promotion
in response to various soil managing practices which
are part of intensive agriculture. Therefore, there
is need to understand the following aspects of microbial
diversity in order to sustain the soil productivity
on a long term basis, particularly in tropical soils.
- What are the changes in rhizosphere biology under
continuous monocropping? Are there any microbial
factors involved in yield declines under continuous
- What are the impacts of long term use of agrochemicals
like fertilizers and pesticides on the diversity
of important functional groups?
- Do the soil management practices cause selective
stimulation of particular species of microbes. If
so, can it be used to suppress pathogenic organisms
- What are the microbial indicators of sustainable
soil fertility? Can particular species of microbe
be used as early indicators of land degradation?
- What are the best biological indicators of soil
The future research on soil microbiology particularly
using the frontier techniques like molecular biology
including PCR, 16S rRNA study and gene tagging might
provide answers to some of the above questions. Species
diversity studies on unique habitats might inadvertently
show up useful gene products, which can be used outside
the agriculture. Thus soil microbial diversity studies
in future might transcend beyond the academic level
and prove to be a source of large economic gains in
agriculture, bio-pharmaceuticals and environmental
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