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International Journal of
Agriculture and Biosciences
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Review Article
The Role of Microorganisms in Nutrient Status of Forest Soil
Amonum Joseph Igba1 and Unanaonwi Okpo Esio2
Department of Forest and Forest Production, Federal University of Agriculture Makurdi, Benue State, Nigeria
2
Department of Biology, Federal University Otuoke, Otuoke, Nigeria
*Corresponding author: [email protected]
Article History:
Received: March 23, 2016
Revised: June 26, 2016
Accepted: July 17, 2016
AB S T RA CT
Microorganisms maintain a healthy soil by enhancing soil fertility in which other biota benefit from. The diversity of
microorganisms in soil is enormous and they drive many soil services. These roles are highlighted in the cycling of
major biological elements such as carbon (C), nitrogen (N), phosphorus (P), potassium (K), in the recycling of wastes,
and the detoxification of environmental pollutants. Microorganisms play a pivotal role in the cycling of nitrogen; they
exclusively mediate nitrogen fixation, denitrification, and nitrification. They also play a role in the decomposition of
organic matter, transformation of phosphorous, potassium and other secondary and micro nutrients which presence
confers fertility of the soil. A fertile soil is judge by the amount of organic matter present and the volume of bacteria
population in the soil. Apart from artificial fertilizer application to upgrade soil nutrients, a practice widely
condemned by environmentalists, soil microorganisms are the major organizers of soil nutrients. This paper discusses
soil nutrients and the role of microorganisms in the provisioning of fertile soil.
Key words: Microorganism, Soil nutrients, Forest soil, Fertility, Environmental pollutants
because they affect soil structure and fertility through
their activities (Weil et al., 2012).
INTRODUCTION
Soil is one the most dynamic site of biological
interactions in nature. It is the region where most of the
physical, biological and biochemical reactions related to
decomposition of organic weathering of parent rocks
take place. Soil represent the interface of three material
status; solid (geological and dead biological materials),
liquid (water), and gases (air in soil pores) (Dominati et
al., 2010). Soils are the foundation of all terrestrial
ecosystems and are home to vast diversity of bacteria,
archaea, fungi, insects, annelids, and other invertebrates
as well as plants and algae (Dominati et al., 2010).
These soil dwellers provide nutrients that support
organisms that live above and below the ground. Soil
productivity depends upon several factors including
heavy presence of bacteria and organic matter (Harrison
and Strahm, 2008). Microorganisms are microscopic
organisms that are so small that that they can only be
visualized by the aid of a compound-brightfield
microscope. We generally cannot see individual
microorganisms with the naked eye and they are present
in virtually every habitat known to man (Prey et al.,
2010). Soil microorganisms are those (microorganisms)
that dwells in/on the soil. These organisms are important
Types of soil microorganisms
Soil microorganisms can be classified as bacteria,
actinomycetes, fungi, algae and protozoa (Bassuk et al.,
2010, Heartmann et al., 2008). These microorganisms
play a pivotal role in soil nutrient transformation. The
activities of these organisms drive soil nutrient from
complex forms to forms that are usable by plants meaning
that they serves as plant nutrients.
Bacteria
Bacteria are important in agricultural soils because
they contribute to the carbon cycle by fixation and
decomposition. Some bacteria are important decomposers
and others such as actinomycetes are particularly effective
at breaking down tough substances such as cellulose
(which makes up the cell walls of plants) and chitin
(which makes up the cell walls of fungi) (Brady et al.,
2012, Hodge et al., 2000). One group of bacteria
(Nitrobacter species) is particularly important in nitrogen
cycling. Free-living bacteria fix atmospheric N, adding it
to the soil nitrogen pool; this is called biological nitrogen
fixation (Weil et al., 2012).
Cite This Article as: Igba AJ and UO Esio, 2016. The role of microorganisms in nutrient status of forest soil. Inter J
Agri Biosci, 5(5): 296-300. www.ijagbio.com (©2016 IJAB. All rights reserved)
296
Inter J Agri Biosci, 2016, 5(5): 296-300.
Actinomycetes
Actinomycetes are a broad group of bacteria that
form thread-like filaments in the soil. The distinctive scent
of freshly exposed, moist soil is attributed to these
organisms, especially to the nutrients they release as a
result of their metabolic processes (Brady et al., 2012).
Actinomycetes form associations with some nonleguminous plants and fix N, which is then available to
both the host and other plants in the near vicinity (Miniaci
et al., 2007).
Fungi grow in the form of a finely-branched network
of strands called hyphae. These hyphae can release
digestive enzymes and take up nutrients over their entire
length. Fungi secrete enzymes that can break down
cellulose into glucose. Fungi are the only known
organisms that degrade lignin completely (Hoorman et al.,
2010).
The role of fungi in the soil includes:
• Nutrient cycling.
• Disease suppression.
• Water dynamics - since they release hyphae and
sporulate in the soil, they trap water and even in
period of dryness, they produce moisture to the soil
due to water accumulation in the hyphae, and this
help the plants to get nutrient as nutrients are
normally found in soluble form.
• Decomposition of pectin, cellulose, lignin and
hemicelluloses.
• Saprophytic fungi convert dead organic matters into
their own biomass, CO2, and organic acids.
• Help in removing rubbish which otherwise must have
covered the entire earth surface.
(Eilers et al., 2012).
Contribution of microorganisms to soil nutrient status
In soils, microorganisms play a pivotal role in cycling
nutrients essential for life. For example, soil microbes
play major roles in cycling elements which are essential
for producing biomolecules such as amino acids, proteins,
DNA and RNA – the fundamental compounds of life
(Eilers et al., 2010). Many plant nutrients are ultimately
derived from weathering of minerals.
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. It is only through the
actions of soil microorganisms that the nutrients in
organic fertilizers are liberated for plants use. (Rifat et al.,
2010). Soil microbiologists call this process
mineralization [the conversion of organic complexes of
the elements to their inorganic forms, e.g., conversion of
proteins to carbon dioxide (CO2) ammonium (NH4+) and
sulfate (SO4)]. It is perhaps the single-most important
function of soil microbes as it recycles nutrients tied up in
organic materials back into forms useable by plants and
other microbes (Rifat et al., 2010).. It is through the
process of mineralization that crop residues, grass
clippings, leaves, organic wastes, etc., are decomposed
and converted to forms useable for plant growth as well as
converted to stable soil organic matter called humus
(Bhardwaj et al., 2014). The soil microbial population
also further decomposes the waste products of the larger
animals. Thus, the activities of different groups of soil
organisms are linked in complex "food webs" (Rogers and
Burns, 2001).
In terrestrial environments, fungi promote rock
weathering and contribute to the dissolution of mineral
aggregates in soil through excretion of H+, organic acids
and other ligands, or through redox transformations of
mineral constituents. Fungi also play an active or passive
role in mineral formation through precipitation of
secondary minerals, e.g. oxalates, oxides, carbonates and
phosphates and through the nucleation of crystalline
material onto cell walls (Swer et al., 2011). Such
interactions between fungi and minerals are of importance
to biogeochemical cycles including those of carbon (C),
nitrogen (N), sulphur (S) and phosphorus (P), as well as
being of relevance to bioremediation approaches for
contaminated soil (Towe et al., 2010).
Another benefit of soil microbes is their ability to
degrade pest control chemicals and other hazardous
materials reaching the soil. Thus through the actions of
the soil microflora, pesticides may be degraded or
rendered nontoxic lowering their potential to cause
environmental problems such as ground and surface water
contamination.
One beneficial process carried out exclusively by soil
microbes is called nitrogen fixation, the capture of inert
N2 gas (dinitrogen) from the air for incorporation into the
bodies of microbial cells. In one well-known form of this
process, symbiotic nitrogen fixation, soil bacteria such as
Rhizobium and Bradyrhizobium actually inhabit
specialized structures on the roots of leguminous plants
(soybeans, cowpeas, beans clovers, etc.) where they fix
substantial quantities of nitrogen that becomes available to
the host plant (Fierer et al., 2012, Nordin et al., 2004).
Algae
Algae play an important role in every ecosystem.
They contribute to the fertility and the stability of the soil
through fixation of carbon and nitrogen, release of organic
compounds, and binding together of soil particles to
reduce soil erosion hence, reduces nutrient loss
(Janusauskaite et al., 2013).
Soil nutrients
Soil nutrient can be defined as any substance found in
the soil and being used by plants, in large or small
quantity as food in order to grow. Soil is a major source
of nutrients needed by plants for growth. The three main
plant nutrients are nitrogen (N), phosphorus (P) and
potassium (K) (Nasholm et al., 2009; Slovd et al., 2011).
Together they make up the trio known as NPK. Other
important nutrients are calcium, magnesium and sulfur.
Plants also need small quantities of iron, manganese, zinc,
copper, boron and molybdenum, known as trace elements
because only traces are needed by the plants. Soil
nutrients play a key role in plant growth through mineral
nutrition and toxicity. Nutrients must be available not only
in sufficient amounts but also in appropriate ratio. These
nutrients if present at low levels may cause deficiency
symptoms, and toxicity is possible at levels too high.
Furthermore, deficiency of one element may present as
symptoms of toxicity from another element, and vice
versa (Wayne et al., 2011).
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Inter J Agri Biosci, 2016, 5(5): 296-300.
Fig. 1: The nitrogen cycle. Adapted from EPA, 2014.
Nitrogen is essential to life because it is a key
component of proteins and nucleic acids. Nitrogen occurs
in many forms and is continuously cycled among these
forms by a variety of bacteria. Although nitrogen is
abundant in the atmosphere as diatomic nitrogen gas (N2),
it is extremely stable, and conversion to other forms
requires a great deal of energy. The cycling of nitrogen
among its many forms is a complex process that involves
numerous types of bacteria and environmental conditions.
In general, the nitrogen cycle has five steps namely:
Nitrogen
fixation,
Nitrification,
Assimilation,
Ammonification and Denitrification.
Assimilation
Assimilation is the process by which plants and
animals incorporate the NO3- and ammonia formed
through nitrogen fixation and nitrification. Plants take up
these forms of nitrogen through their roots, and
incorporate them into plant proteins and nucleic acids.
Animals are then able to utilize nitrogen from the plant
tissues (Coleman, D.C. 2004, Hayat et al., 2010).
Ammonification
Assimilation produces large quantities of organic
nitrogen, including proteins, amino acids, and nucleic
acids (Kumar, 2005). Ammonification is the conversion of
organic nitrogen into ammonia. The ammonia produced
by this process is excreted into the environment and is
then available for either nitrification or assimilation
(Alam, 2001; Fan et al., 2013).
Nitrogen fixation
Bacteria are responsible for the process of nitrogen
fixation, which is the conversion of atmospheric nitrogen
into nitrogen-containing compounds (such as ammonia)
that can be used by plants (Kenneth, 2012). Autotrophic
bacteria derive their energy by making their own food
through oxidation, like the Nitrobacter species, rather than
feeding on plants or other organisms. These bacteria are
responsible for nitrogen fixation. The amount of
autotrophic bacteria is small but they are very important
because almost every plant and organism requires
nitrogen in some way, and would have no way of
obtaining it if not for nitrogen-fixing bacteria (Torsvik
and Ovreas, 2002; Hoorman et al., 2010).
Denitrification
While nitrogen fixation converts nitrogen from the
atmosphere into organic compounds, a series of processes
called denitrification returns an approximately equal
amount of nitrogen to the atmosphere (Bardgett, 2011).
Denitrifying bacteria tend to be anaerobes, or facultative
anaerobes (can alter between the oxygen dependent and
oxygen independent types of metabolisms), including
Achromobacter and Pseudomonas. The purification
process caused by oxygen-free conditions converts
nitrates and nitrites in soil into nitrogen gas or into
gaseous compounds such as nitrous oxide or nitric oxide
(Alexander, 2012). In excess, denitrification can lead to
overall losses of available soil nitrogen and subsequent
loss of soil fertility. However, fixed nitrogen may
circulate many times between organisms and the soil
before denitrification returns it to the atmosphere. The
diagram above (Fig. 1) illustrates the nitrogen cycle.
Nitrification
Nitrification is a two-step process in which NH3/
NH4+ is converted to NO3 -. First, the soil bacteria
Nitrosomonas and Nitrococcus convert NH3 to NO2-, and
then another soil bacterium, Nitrobacter, oxidizes NO2- to
NO3-. These bacteria gain energy through these
conversions, both of which require oxygen to occur
(Kowalchuk and Stephen, 2001).
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Inter J Agri Biosci, 2016, 5(5): 296-300.
photosynthesize) are “subsidized” by well-illuminated
trees. It is possible that young trees in shady environments
are enabled to survive by this mechanism, at least until
they can extend their branches into the canopy. It has been
speculated that forests are less competitive than they
appear, particularly if the mycorrhizae act to reduce
competition for nutrients by equitable distribution. In one
experiment, tree seedlings were found to transfer carbon
between species bidirectionally (Simard, et al., 1997).
However, Proctor, (1995) warns that little is known about
the role of mycorrhizae in tropical forests, and therefore
one must be cautious about assessing the roles of these
fungi in these ecosystems.
In tropical forests all organisms are dependent to
some extent on bacteria and fungi. Some animals such as
wood and leaf-eating insects depend on symbiotic gut
microbes to digest cellulose in their food supply, while
other insects utilize fungi directly as a food source (Higa
and Parr, 1994; Gupta and Roget, 2004). Without
microbes, organic matter on the forest floor and in the soil
would never decompose. The rate at which these
microorganisms decompose dead material is directly
responsible for the availability of nutrients for plants. As
the humidity and temperatures in rainforests are high,
conditions are ideal for rapid microbial decomposition.
However, the rates of decomposition will differ according
to which microorganisms are present, the character of the
organic matter, and the physical and chemical
environment of the soil and so forth (Raina et al., 2009;
Leahy and Colwell, 1990). Apparently microbial and
fungal populations are quite sensitive to fluctuations in
soil moisture and other disturbances.
Nitrogen fixation is an essential function of microbes
in forests. Without bacteria which are capable of
converting gaseous nitrogen into nitrates and nitrites
which plants can utilize, rainforest soils would rapidly
become depleted of this essential mineral in usable form.
Many million tons of nitrogen are converted annually and
added to the soil by these organisms. In the many tropical
soils which are nutrient-poor, only nitrogen-fixing
bacteria allow plants to survive (Kenneth, 2012).
Many fungi are present in rainforest soils, and some
form close associations with tree roots. These presumably
symbiotic associations are known as mycorrhizae.
Certainly the associations, in which the fungal hyphae
penetrate or ensheathe the root, are very close, although
they may not all be beneficial to the plant (Joauset et al.,
2011). Up to 90% of all tree roots are involved in these
associations. The fungi colonize roots through the spread
of the hyphae or the dispersion of spores. The exact role
of mycorrhizae in forest ecology is not clear. Some
believe that they are involved in nutrient capture and that
much carbon and other minerals (nitrogen and
phosphorus, especially) are transferred from the soil to the
roots by mycorrhizal associations. In turn, the plant passes
manufactured carbon compounds to the fungi, and since
the mycorrhizae are themselves eaten by soil organisms,
carbon is transferred rapidly from the host tree to the soil
ecosystem. Mycorrhizae apparently facilitate the uptake of
water by roots and increase the resistance of roots to
pathogens. All in all, mycorrhizal associations appear to
play key roles in growth, nutrient cycling and primary
productivity in tropical rainforests. They also appear to
have some control over the structure of the plant
community and the course of succession. Where forest is
disturbed, plants which do not form mycorrhizal
associations will predominate; later, as the fungi invade
the area, there will be a succession of plants which
tolerate and, later, require these associations. This
scenario is complicated by the fact that fungi also undergo
succession, and that these changes may play a role in the
successional dynamics of plant species. Mycorrhizal fungi
also act as social agents, as they interconnect trees
through their hyphae. This may mean that trees can
transfer carbon among themselves via the fungal mat, so
that trees in the shade (and thus less able to
Conclusion
The soil is home to a large proportion of the world's
biodiversity. The links between soil organisms and soil
functions are observed to be incredibly complex. The
interconnectedness and complexity of soil ‘food web’
means any appraisal of soil function must necessarily take
into account interactions with the living communities that
exist within the soil. We know that soil organisms break
down organic matter, making nutrients available for
uptake by plants and other organisms. The nutrients stored
in the bodies of soil organisms prevent nutrient loss by
leaching.
Plants grow in an active and steady environment. The
mineral content of the soil and its heartiful structure are
important for their well-being, but it is the lives in the soil
that powers its cycles and provides its fertility. Without
the activities of soil organisms, organic materials would
accumulate and litter the soil surface, and there would be
no food for plants.
At present context in the globe, forest soil is being
compacted with heavy agricultural equipment which have
created soil horizon devoid of air space. The soil density
has increased resulting in the decrease in the porosity of
the soil and limiting the microorganism population and
growth. Similar is the case with the organic matter.
Present agricultural practice uses chemical fertilizers,
thereby limiting use of organic matter. As a consequence
the microorganisms are deprived of food and their growth
has been checked. This has created imbalance in the soil
ecosystem which have resulted in poor structure and less
fertile soil.
To create healthy and fertile soil we must provide the
environment that favours the growth of microorganism.
The addition of organic matter, loosening the soil mass,
providing optimum moisture in soil, reducing heavy
agricultural equipment, replacing chemicals with
alternative source of manure, could be few steps towards
eco-friendly soil with high microbial population.
REFERENCES
Alam SN, 2001. Microorganisms and soil Fertility. NIA,
Tando Jam, Pakistan, pp: 218.
Bardgett RD, 2005. The biology of soil: A community and
Ecosystem Approach, Oxford University press. pp: 361.
Bhardwaj D, MW Ansari, RK Sahoo and N Tuteja, 2014.
Biofertilizers function as key player in sustainable
agriculture by improving soil fertility, plant tolerance
and crop productivity. Microbe Cell Fact, 13: 66.
299
Inter J Agri Biosci, 2016, 5(5): 296-300.
Silva AP, LC Babujia, LS Matsumoto, MF Guimaraes and
M Hungaria, 2013. Bacterial diversity under different
tillage and crop rotation systems in an oxisol of
southern brazil. The Open Agric J, 7(Supp 11-M6):
40-47.
Swer H, MS Dkhar and H Kayang, 2011. Fungal
population and diversity inorganically amended
agricultural soils of meghalaya, India. J Organic Syst,
6: 3-12.
Prey B, SR Rirder, I Brunner, M Plotze, S Koetzsch and A
Lapanje, 2010. Weathering associated bacteria from
Damma glacier forefield. Appl Environ Microbiol,
76: 4788-4796.
Harrison RB and B Strahm, 2008. Soil Formation,
Encyclopedia of Ecology, 3291-3295.
Hartmann A, M Rothballer and H Lorenz, 2008. A
pioneerrhizoosphere microbial ecology and soil
bacteriology research. Plant Soil, 312: 7-14.
Hodge A, D Robinson and A Fitter, 2000. Are
microorganisms more effective than plants at
competing for nitrogen?. Trends Plant Sci, 5: 304308.
Kowalchuk GA and JR Stephen, 2001. Ammonia
oxidizing bacteria, a model for molecular microbial
ecology. Ann Rev Microbiol, 55: 485-529.
Leahy JG and RR Colwell, 1990. Microbial degradation
of hydrocarbons in the environment Microbial
Review, 53: 305-315.
Lipson DA and RK Monson, 1998. Plant-microbe
competition for soil amino acids in the alpine tundra:
effects of breeze-thaw and dry-rewet events.
Oecologia, 113: 406-414.
Miniaci C, M Bunge, L Duuc, H Burmann and J Zeyer,
1999. Effects of pioneering plants on microbial
structures and functions in a glacier forefield, Bio
Fert Soils. 44: 289-297.
Nasholm T, K Kielland and U Ganeteg, 2009. Uptake of
organic nitrogen by plants, New Phytol, 182: 31-48.
Nordin A, IK Schmidt and GR Shaver, 2004. Nitrogen
uptake by artic soil microbes and plants in relation to
soil nitrogen supply. Ecology, 85: 955-962.
Proctor RH, 1995. Reduced incidence of Gibberela zeae
caused by disruption of a Trichothecene toxin
biosynthetic gene. Mol. Plant Microbe Interact, 4:
593-601.
Raina MM, LP Ian and PG Charles, 2009. Environmental
microbiology” Second edition, Elsevier Inc, pp: 209.
Rogers SL and RG Burns, 1994. Changes in aggregate
stability, nutrient status, indigenous microbial
populations, and seedling emergence, following
inoculation of soil. Biol. Fert Soils, 18: 209-215.
Simard WS, AP David, DJ Melanie and D David, 1997.
Net transfer of carbon between ectomycorrhizal free
species in the field. Nature, 388: 577-582.
Torsvik V and L Ovreeas, 2002. Microbial diversity and
function in soil: from genes to ecosystems. Curr Opin
Microbiol, 5: 240-245.
Towe N, A Albert and R Kleineidam, 2010. Abundance of
microbes involved in nitrogen transformation in the
rhizosphere of Leucanthemosis (L) Heywood grown
in soils from different sites of the Damma glacier
forelands. Mircobiol Ecol, 60: 762-770.
Coleman DC, 2004. Fundamentals of Soil Ecology.
Second edition, Academic press, UK, pp: 245.
Brady NC and RC Weil, 2012. The Nature and Properties
of Soils. (14th edn), Dorling Kindersley India Pvt.
Ltd, Noida, India.
Eilers KG, S Debenport, S Anderson and N Fierer, 2012.
Digging deeper to find unique microbial
communities, The strong effect of depth on the
structure of bacterial and archaeal communities in
soil. Soil Biol Biochem, 50: 58-65.
Eilers KG, CL Lauber, R Knight and N Fierer, 2010.
Shifts in bacterial community structure associated
with inputs of low molecular weight carbon
compounds to soil. Soil Biol Biochem, 42: 896-903.
Fan MY, RJ Xie and G Qin, 2013. Bioremediation of
petroleum contaminated soil by a combined system of
biostimulation-bioaugmentation
with
yeast.
Environmental, Tech, 35: 4.
Fierer N, CL Lauber, SK Ramirez, J Zaneveld and MA
Bradford,
2012.
Comparative
metagenomic,
phylogenetic and physiological analyses of soil
microbial communities across nitrogen gradients. The
ISME J, 6: 1007–1017.
Goldfarb KC, U Karaoz, CA Hanson, CA Santee, MA
Bradford and KK Treseder, 2011. Differential growth
responses of soil bacterial taxa to carbon substrates of
varying chemical recalcitrance. Frontiers in
Microbiology, 2: Article 94.
Griffiths RI, BC Thomson, P James, T Bell, M Bailey and
AS Whiteley, 2011. The bacterial biogeography of
British soils. Environm Microbiol, 13: 1642-1654.
Gupta V and DK Roget, 2004. Unde4rstanding soil biota
and biological functions. Soil Sci and Nutr, 34: 256265.
Hayat R, S Ali and U Amara, 2010. Soil beneficial
bacteria and their role in plant growth promotion: A
review in; Soil Sci. and Nutrition. Retrieved from
http:/www.seedbuzz.com
Higa T and FJ Parr, 1994 Beneficial and Effective
microorganism. International nature Farming
Research centre, Atami, Japan, 65-80.
Humbert S, S Tarnawski, N Fromin, MP Mallet, M
Aragno and J Zopfi, 2010. Molecular detection of
anammox bacteria in terrestrial ecosystems:
distribution and diversity. The ISME J, 4: 450–454.
Janusauskaite D, G Kadziene and O Auskalniene, 2013.
The effect of tillage system on soil microbiota in
relation to soil structure. Pol J Environ Stud, 22:
1387-1391.
Jouset A, 2011. Intraspecific genotypic richness and
relatedness prrdict the invisibility of microbial
communities. Pub Med. Publishers, London, pp: 127.
Kenneth T, 2012 The impact of Microbes on the
Environment and Human activities. Today’s online
textbook of bacteriology Page 1.
Kumar AS, 2005. Rhizobacteria Bacillus subtilis restricts
foliar pathogen entry through stomata, Black well
publishing Ltd, pp: 556.
Rifat H, A Safdar, A Ummay, K Rabia and A Iftikhar,
2010. Soil beneficial bacteria and their role in plant
growth promotion: a review. Ann Microbiol 60: 579598.
300