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Menara Perkebunan 2009, 77 (1), 58-67. Review

Introduction of microbial inoculants to improve fungsional
relationship between above- and below-ground bio-diversity

Didiek Hadjar GOENADI & Laksmita Prima SANTI
IndonesianBiotechnology Research Institute for Estate Crops, Bogor 16151


Sebagaimana telah diketahui bahwa
keragaman di muka bumi memainkan peran
yang sangat penting dalam menciptakan
lingkungan yang berkelanjutan. Bagaimana-
pun juga, aktivitas manusia sampai tingkat
tertentu mengurangi kompleksitas agro-
ekosistem. Beberapa di antaranya adalah
perubahan proses bio-fisik-kimia yang
mengakibatkan tidak dapat menopang
produktivitas. Untuk mengatasi masalah ini,
banyak upaya telah dipusatkan pada
peningkatan aktivitas mikrob di dalam tanah
dengan menggunakan teknologi yang disebut
bio-fertilizer (pupuk hayati), pengomposan
residu tanaman secara modern, dan membatasi
penggunaan pestisida sintetik. Teknologi
tersebut diyakini dapat meningkat-kan
keragaman hubungan antara bagian per-
mukaan dan bawah tanah yang akhirnya
berkontribusi terhadap perubahan dan
membawa fungsi penting secara biologi.
Makalah ini memaparkan hubungan
keragaman yang menguntungkan secara
fungsional antara keaneka-ragaman
permukaan dan bawah tanah untuk
pengelolaan dan pengembangan pertanian
atau perkebunan secara berkelanjutan.


It has been very well understood that bio-
diversity on the earth plays a very important
role on governing the sustainability of the
environment. However, anthropogenic
activities have to some extent reduced
drastically the complexity of the agro-
ecosystem. Many of these bio-physic-chemical
processes will be changed and as a result they
can not sustain productivity. To overcome this
problem, a great effort was focused at
improving microbial activities in the soil by
using the so-called bio-fertilizer technology,
new-modern composting plant residues, and
limited use of synthetic pesticides. It is
believed that enhanced relationship between
above-and below-ground biodiversity
contributes to the re-establishment and able to
carry out essential biological functions. This
paper discusses functional relationship between
above- and below-ground bio-diversity
beneficial for sustainable management and
plant development.

[Keywords: Biodiversity, plant development,
microbial inoculants, biofertilizer,
sustainable management, legume
cover-crop ].


Global food supply depends on
intensive agriculture. In Indonesia, large
numbers of farmers have limited access to
inputs but are nonetheless forced by
circumstances to drastically reduce the
complexity of their agro ecosystems in an
attempt to intensify production. As
intensification proceeds, above-ground
biodiversity is reduced, one consequence
of which is that the biological regulation
of soil processes is altered and often
substituted by the use of mechanical

Goenadi & Santi

tillage, chemical fertilizers and pesticides.
This is assumed to reduce below-ground
diversity. On the other hand, crop
productivity is closely related to the ability
of plant roots to extract water and
nutrients efficiently out of the soils. The
function of the roots is governed by an
integrated set of biological processes. In
addition to plants, soil is the habitat of a
diverse array of organisms, which their
activities are contribute to the maintenance
and productivity of agro ecosystem by
their influence on soil fertility. In this
case, there are functional relationships
between above and below-ground in agro
ecosystem. Swift & Bignell (2001)
suggested that maintenance of diversity of
crops, other plants, and below-ground in
cropping systems is widely accepted as a
management practice which buffer
farmers against short-term risks.
Enhanced relationship between above
and below-ground biodiversity contributes
to the re-establishment and able to carry
out essential biological functions. To be
more precise, the enhancement of soil
biodiversity by the retention of crop
residues and other organic matter, induced
microbe inoculants, and limitations in the
use of pesticides will also have associated
labor costs which are part of the
assessment on efficiency economic value
of management farming. Soil micro-
organism especially bacteria and fungi
contribute a wide range of essential
service to the sustainable function of all
ecosystem, such as regulating nutrient
cycles and the dynamics of soil organic
matter, soil carbon sequestration, green-
house gas emission, bioremediation of
toxics and pollutants, and enhancing the
amount and efficiency of soil nutrient for
crops. In the tropical region, the diversity
of the soil microorganism (bacteria and
fungi) commonly even greater than that of
other soil organism. Directly target the
joint conservation of both above (crops)
and bellow-ground (soil microbial)
components of biological diversity will
have environmental benefits at ecosystem
and agricultural production.
This paper is, therefore, aimed to
present basic information regarding to
microbial inoculants to improve functional
relationship between above and below-
ground bio-diversity for sustainable
management and plantation development.

Potential use of bio-fertilizer to improve
functional relationship above- and
below-ground bio-diversity

The influence of plants on microbial
population structure and function in the
rhizosphere has important ecological
implications for soil function, including
biogeochemical cycles. Similarly, soil
microbes have a tremendous influence on
plant health and productivity (Bloemberg
& Lugtenberg, 2001). For example, large
areas of marginal soils in Indonesia have
been developed for plantation. These soils
have been characterized by low organic
matter content, predominant low activity
clays, and strongly acid in reaction. These
in effect will depress the microbial
activities which in turn disturb the nutrient
cycle in the soils. On the other hand,
under humid-tropic conditions, fertilizer
loss through leaching, volatilization,
and/or fixation represents an economic
loss as well as a potential environmental
contamination. A biotechnological
approach is then assumed to be able to
enhance the emergence of biotechnology
in soil management provides a new
approach in tackling efficiently many
problems which remain unsolved by

Introduction of microbial inoculants to improve fungsional..

current conventional technology. Mani-
pulation of soil microbes offers an
efficient technique to stabilize soil
aggregates, increase nutrient uptake,
control soil-borne pathogen, and
accelerate the decomposition of solid
organic wastes, without adding new
pollutants to the environment. Bio-
fertilizers are basically microorganisms
which can improve the availability of
nutrient to plants. They have been
believed to be an important component of
sustainable agriculture, as they can reduce
significantly the use of chemical
fertilizers. It is hypothesized that by
improving rhizospheric microbial acti-
vities via bio-fertilizer application,
nutrient solubilization can be enhanced
and consequently less conventional
fertilizers will be needed (Goenadi et al.,
2005). An efficient bio-fertilizer product
i.e. EMAS (Enhancing Microbial Activity
in the Soils) has been successfully
development by using active ingredients
consisting of Azospirillum lipoferum,
Azotobacter beijerinckii, Aeromonas
punctata, and Aspergillus niger native of
tropical soils (Goenadi et al., 2000). The
application of 6.25 g EMAS per plant
(equivalent with 83.125 kg/ha) + 50%
inorganic fertilizer recommended dosage
for tea, could reduce application of
inorganic fertilizer dosage until 50% and
resulted in the growth of the plant which
was better than that of inorganic fertilizer
(Wachjar et al., 2006). In addition,
evaluate the effectiveness of EMAS bio-
fertilizer in reducing dosage of conven-
tional fertilizers used in corn at Pelaihari,
South Kalimantan indicated that based on
the current production value and total of
cost production, reducing 25, 50 and 75%
conventional fertilizer provides the
planters with 1.44, 1.13, and 1.12 revenue
cost ratio. Yield of dry grain of corn was
higher (+41.8%) by application of 75%
standard dosage and 1 gram EMAS
biofertilizer/tree (53.3 kg/ha) than by
standard dosage of conventional fertilizer
(Santi et al., 2007).
One straightforward and visible
benefit for the plant is a better supply of
and access to nutrients. The role of
mutualistic nitrogen-fixating rhizobia has
been well documented for decades, but
recent data detail the intimate exchange of
nutrients during the symbiosis of plant
roots and bacteria (Lodwig et al., 2003).
The plant attracts nitrogen-fixating
bacteria to invade the cells in the root and
provides them with carbohydrates as a
food source while the bacteria reduce
nitrous compounds in the soil that are then
used by the plant. These microbes use
root exudates as a source of energy and
cellular carbon. Endophytic associations
in rice have a N-fixing potential of 150 kg
N/ha/year, but are at times unreliable
(Shenoy et al., 2001). Similarly, inter-
actions between plants and fungi can also
provide nutrients for the plant. Arbuscular
mycorrhizal fungi, which form an intricate
internal symbiosis with the roots of most
flowering plants, are associated with the
provision of phosphorous to the plant in
exchange for organic carbohydrates
(Smith & Read, 1997).
Microbes also indirectly aid nutrient
uptake bacteria of the Azospirillum genus
promote increased root mass and more
efficient nitrogen uptake from the soil in
response to the plant hormone indole-3-
acetic acid. Using these bacteria and fungi
could provide significant environmental
benefits as they would allow a reduction in
the application of nitrogen and phos-
phorous fertilizers. The overuse of such
fertilizers has become a major concern

Goenadi & Santi

because they cause nitrate contamination
of soil and groundwater by leachates and
because microbial denitrification converts
residual nitrogen into the greenhouse gas
nitrous oxide (Nosengo, 2003; Reay,
2004). Equally, excess phosphorous
compounds leach into groundwater, rivers
and streams, where they promote algal
growth and other environmental problems.
Microbial seed inoculants are able to
enhance biological nitrogen fixation. The
inoculants are claimed to be cost effective,
eco-friendly, renewable and generally
capable of supplementing chemical ferti-
lizers in sustainable agricultural system.
Amongst nitrogen fixing bacteria such as
Rhizobium (symbiotic), Azotobacter and
Azospirillum (non-symbiotic), the most
widely used inoculant is Rhizobium. It has
long been known that the inoculation of
effective strains of the symbiotic
Rhizobium can be beneficial for legu-
minous pulses and oilseed (Isherwood,
2002). Inoculation with effective
Rhizobium is a well known agronomic
practice to insure adequatenitrogen
nutrition of legume instead of fertilizer N.
Although commercial fertilizer
products based on below-ground diversity
are already available, their effectiveness
depends on the natural conditions and
plant clay organic soil and microbe
interaction. Regarding the product itself,
the inoculants is a living material and
there are problem due to the needs to
select the most effective strains, the
difficulty of quality control, the short
shelf-life, and the need to avoid high
temperatures in storage. The Food and
Fertilizer Technology Center for the Asia
and Pacific Region (FFTC, 1997)
reported that, while there is an increasing
interest in Asia in the use of N-fixing
bacteria, the technology of producing and
using them still at an early stage. There are
a very large number of different
microorganisms in microbial products and
they are often not identified yet, whereas
some are crop-specific. There is a great
need for standards, simple and accurate
ways of measuring their effectiveness.
Therefore, an appropriate management of
bio-fertilizer in agriculture and plantation
soil quality could be maintained.

Benefits of legume cover crops as
above-ground bio-diversity and its
relationship with below-ground bio-

In the land farming, legume cover
crops can reduce fertilizer costs and
herbicide or other pesticides, improve
yields by enhancing soil health, prevent
soil erosion, conserve soil moisture,
protect water quality, and help safeguard
personal health. Many legume cover crop
offer harvest possibilities as forage,
grazing or seed that work well in system
with multiple crop enterprises and
livestock. For instance, fertilizer
recommendation made for oil palm
plantation is of higher dosages on non-
legume cultivation than on legume
cultivation. In addition, Sarrantonio
(1998) stated that cover crops provide
many benefits, but they are not do-it-all
wonder crops. To find a suitable cover
crop or mix of covers need to identify the
best time and place for a cover crop in
farming system. Cover crops improve soil
by (i) speeding infiltration of excess
surface water, (ii) relieving compaction
and improving structure of over tilled soil,
(iii) adding organic matter that encourages
beneficial soil microbial life, and (iv)
enhancing nutrient cycling. Further,
nitrogen is a central component of cell

Introduction of microbial inoculants to improve fungsional..

proteins and is used for seed production. It
exists in several chemical forms and
various microorganisms are involved in its
transformation. Legume cover crops, in
association with specialized bacteria
called rhizobia are able to convert nitrogen
gas in the atmosphere into soil nitrogen
that plants can use. Crops grown in fields
after legumes can take up at least 30 60
percent of the N by legumes.
Consequently, the farmer can reduce
N fertilizer applications. The beneficial of
N value of legume cover crop could
evaluated, both agronomically and
economically. The nitrogen provided by
N-fixation is used efficiently in natural
ecosystems. Sarrantonio (1998) suggest
that in an agricultural system, however,
soil and crop management factor often
interfere with natures ultra-efficient use
of organic or inorganic N. Learning a bit
about the factors affecting N-use
efficiency from legume plants will help
build the most sustainable cropping
Management of above-ground covers
is an important aspect of rubber and oil
palm cultivation. In these area, Pueraria
phaseoloides, Calopogonium caeruleum,
and Centrosema pubescens are widely
cultivated for rubber and oil palm.
Legume cover crops, normally compete
successfully against volunteer weed
growths, particularly Mikania and
Asystasia. Therefore, a good legume
cover crops should be maintained for as
long as possible after planting. In some
environments it will be possible to
maintain legume cover crops throughout
the life of the rubber and oil palm. Also,
Ahmad Tajuddin & Wan Zahari (1991)
stated that forage species that grow in oil
palm and rubber plantations include all the
palatable plant species that thrive under
this microenvironment. The leguminous
cover crops are grown at early stages of
the tree crop development in first five
years, and they are gradually replaced by
the shade-tolerant species when the
canopies close. Some common goals for
cover crops are to provide nitrogen, add
organic matter, improve soil structure,
reduce soil erosion, provide weed control,
manage nutrients, and furnish moisture-
conserving mulch. Like other plants,
legumes cover crops need nitrogen to
grow. They can take it from soil if present
enough in forms they can use. Legume
roots also seek out specific strains of soil-
dwelling bacteria that can fix nitrogen gas
from the air for use by the plant. While
many kinds of bacteria compete for space
on legume roots, the root tissues will only
begin this symbiotic N-fixing process
when they encounter a specific species of
Rhizobium bacteria.

The nitrogen fixation bacteria as a
simple model for expressing rela-
tionship between above- and below-
ground bio-diversity

Plants of the family Leguminoseae
play many roles in agriculture, but perhaps
most important is their ability to use free
nitrogen gas (N
) in the atmosphere as a
source of nitrogen. Only certain
prokaryotes possess the nitrogenase
enzyme required to convert N
ammonia (NH
), a process called nitrogen
fixation. Legumes fix atmosphere N by
establishing a functional relationship
(symbiotic) with a group of soil bacteria
collectively called rhizobia. The life cycle
of the rhizobia has been intensively
studied. It is now understood that a
particular strain of Rhizobium in the soil is

Goenadi & Santi

attracted to its particular host. Since the
rhizobia are motile, they actually swim to
their host. Once they reach the hosts root
system they attach to single root hair and
release substances that stimulate the hair
to allow the Rhizobium to penetrate it.
The Rhizobium proceeds to invade
certain cells in the root where they
produce chemicals that stimulate the
growth of these cells to produce the
tumor-like nodule (Hurlbert, 1999).
Nitrogen gas (N
) from air in the spaces
between soil particles enters the nodule.
The bacteria contribute an enzyme that
helps convert the gas to ammonia (NH
The plant uses this form of N to construct
amino acids, the building blocks for
protein. In return, the host legume supplies
the bacteria with carbohydrates to fuel the
N-fixation process. The nitrogen fixed by
rhizobia gives benefits to legume cover
crops production in two ways: (i) by
meeting most of the legume cover crops
nitrogen needs and (ii) by enriching the
soil for the benefit of subsequent crops.
The rate of N fixation is determined
largely by genetic potential of the legume
species and by the amount of plant-
available N in the soil. Rhizobium
inoculation should be considered in all
legume green manure crops to gain
maximum benefit from nitrogen fixation
in the shortest possible time. The fixed
nitrogen is subsequently made available to
the host plant. When the host plants die,
their nitrogen is returned to the soil for use
by other organisms.

Inoculants technology for functional
relationship induction between above-
and below-ground bio-diversity

Although rhizobia seem to be as
widely distributed as the legumes
themselves, many soils used for legume
cultivation do not contain adequate
numbers of highly effective rhizobia.
They may be devoid of rhizobia, they may
contain low numbers of effective strains or
they may contain high numbers of
ineffective or partially effective strain
(Herridge et al. 2002). Allen & Allen
(1961) listed four indicator that, if
positive, would necessitate inoculation
rhizobia for optimum growth of legume
i.e. (i) the absence of the same or
symbiotically-related legume in the
immediate past history of the land, (ii)
poor nodulation when the same crop was
grown on the land previously, (iii) when
the legume followed a non-legume in the
rotation, (iv) when the land was
undergoing reclamation. Microbial ino-
culants have received only limited
acceptance by farmers in developing
countries. They show considerable
promise but more development is
required. Inoculants technology is used
widely on commercial scale in the
development countries, specifically in
South East Asia i.e. Thailand, Philippines,
Vietnam, and Indonesia. Research is
necessary to adapt legume nodulating
bacteria technology and develop
appropriate Rhizobium strains and ino-
culation procedures for use in the tropical
area. Current inoculation technology from
Indonesian Biotech-nology Research
Institute for Estate Crops (IBRIEC),
Indonesia, i.e. RhiPhosant have been used
in North Sumatera, East J ava and Papua.
In these area, legumes are grown under
marginal conditions with minimal input
and confronted with one or more soil and
climatic stresses. Field experiment in
Ngawi (East J ava), indicated that by
inoculating Rhiphosant to soybean
(Glycine max var. Wilis), the yield could
increase up to 16.8-48%/ha (Rijono,
personal communication).

Introduction of microbial inoculants to improve fungsional..

In other case, Hatfindo (2000)
suggested that the biodiversity of below-
ground communities, as well as their
functions are strongly influenced by the
diversity of above-ground communities.
Rapid rates of land-form disturbances
followed by land degradation due to
mining operations and infrastructure
development activities at PT. Freeport
Indonesia, in Papua, may result in
reduction in soil-biota biodiversity. In
addition, alterations of biological regu-
lation activities within soil may lead to
loss of ecosystem function. Consequently,
the ability of the ecosystem to recover and
the sustainability of land system may be
reduced. Hatfindo have applied inoculant
technology of RhiPhosant to identify
potential entry points for improving
tailings reclamation through the
introduction or management of potential
soil microorganism and plantation
development in tailing areas. The number
of nodule of Pterocarpus indicus,
Paraserianthes falcataria, and
Enterolobium cyclocarpum could increase
38.7, 63.7, and 30.9% respectively by
inoculating RhiPhosant to seeds before
putting them in the seeder.
RhiPhosant (Rhizobial & Phosphate
Solubilizing Inoculants) consisting of
Bradyrhizobium japonicum a symbiotic N
fixation and Aeromonas punctata a
phosphate solubilizing bacteria. The
commercial inoculants are formulated by
growing the bacteria in broth and mixing
the broth with ground peat and highly
active mineral as a carrier which is stored
dry. Application technology is carrier
based inoculants. The inoculant that has
been formulated with a carrier was mixed
with seed just before putting it in the
seeder. Development of this inoculants
technology was bases on interaction of
soil minerals with natural organic and
Peat is the most commonly-used
carrier for rhizobial inoculants because of
its high moisture-holding capacity and
dual abilities to foster multiplication or
rhizobia in the peat itself and protect the
rhizobia once they are applied to the seed
coat, however, it by no means the only
carrier tested or used. Brockwell et al.
(1995) presented an imposing list of
alternative inoculants carriers that
included the following: coal, charcoal
alone or with composted straw, mixtures
of soil and compost, mixtures of soil, peat,
composted bark and wheat husks, bagasse,
coir dust, composted corn cobs, filter mud,
lignite, bentonite and talc. Goenadi
(1995) have been determined most
suitable carrier material, particularly in the
form of clay and organic minerals. The
quality of the mixture as carrier was
evaluated on the basis of microbial
population dynamic. As the results of
these, addition of humic substance to
minerals up to 2.5% (v/w) yielded a
significant increase to the bacterial
population at two weeks after inoculation.
Keyser et al. (1992) regarded the
properties of a good inoculants carrier as:
(i) high water holding capacity, (ii) non-
toxic to the rhizobia, (iii) easy to sterilise
by autoclaving or gamma irradiating, (iv)
readily available and inexpensive, (v)
sufficiently adhesive for effective
application to seed, (vi) pH buffering
capacity, and (vii) cation and anion-
exchange capacities.
Furthermore, the rhizobial strain used
in inoculants should have the ability to
form nodules and fix N
with the target
legume, compete in nodule formation with
populations of rhizobia already present in
the soil, fix N
with a wide range of host

Goenadi & Santi

genotypes and across different
environments, form nodules and fix N
the presence of soil nitrate, grow in
artificial media, in inoculants carrier and
in the soil, persist in the soil, particularly
for annually regenerating legumes,
migrate from the initial site of inoculation,
colonize the soil in the absence of the
legume host, maintain genetic stability,
and be compatible with agrochemicals.
They should also have as wider host range
as possible, have low mortality on
inoculated seed and have the ability to
colonize the rhizosphere or the host plant.
Strains of rhizobia used in inoculants are
selected in strain trials that ideally cover
the physical environments and soil types
that the inoculants are to cover. This may
mean a number of multi-site evaluations
over a number of seasons. Legume cover
crops inoculants are prone to loss of
quality because of variation in the
organism and from unforeseen factors
affecting some aspect of growth or
survival. It is therefore essential that a
quality control system be established. The
control laboratory maintains and supplies
recommended strains annually for ability
to fix nitrogen, assess quality of culture
during and after manufacture, and
conductany research that is necessary to
overcome problems associated with
production and survival.


Soil organisms as a below-ground
bio-diversity are contribute a wide range
of essential services to the sustainable
function of all ecosystems, such as
regulating nutrient cycles and the
dynamics of soil organic matter, soil
carbon sequestration and greenhouse
emission, enhancing the amount and
efficiency of nutrient acquisition by the
vegetation. Few data are available from
Indonesia regions, where it is suspected
that the highest level of bio-diversity may
be found. Although the bio-diversity of
the community of organism below-ground
is probably higher in most cases than that
above-ground, it has generally been
ignored in surveys of ecosystem bio-
The process of land conversion and
agricultural intensification are significant
cause of below-ground biodiversity loss
with risks of impact on ecosystem service.
Enhancement of below-ground bio-
diversity may be accomplished by direct
manipulation, such as re-inoculation with
indigenous of N
-fixing bacteria and other
microbes. Agro technology based on
relationship between above and below-
ground bio-diversity have beneficial effect
on development of agriculture.
A lack of domestic inoculants
production plants also constrains research,
development, and production enterprises.
Relationship between above and below-
ground technology would benefit for
increasing economic and political pressure
for greater energy efficiency in
agriculture, increased recognition by
decision makers in funding agencies and
in governments of the potential for
exploiting below-ground diversity in
developing country. With the advent of
modern biotechnology, there is potential
to develop crops suited to diverse agro-
ecological conditions. By using the case
study of functional relationship between
above and below-ground biodiversity, this
paper examines to extent to which
smallholder access to modern
biotechnology innovations.


Introduction of microbial inoculants to improve fungsional..


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