ASSIGNMENT
SUBMITTED BY
ANAGHA BABU
M.SC ECOLOGY
REG NO. 23371004
Role of microbial communities in soil health
and agriculture
Soil microbial communities play an important role in agroecosystem functioning and are on
the field scale essential for plant nutrition and health. On a larger scale, they contribute to
global element cycling. Furthermore, they are involved in turnover processes of organic
matter, breakdown of xenobiotics and formation of soil aggregates. In contrast to plant
diversity, and the macro and meso fauna, the aspect of soil microbial diversity is a rather new
approach. A major problem in soil microbial analysis has been that most soil microorganisms
cannot be characterised by classical microbiological cultivation techniques. It is estimated
that approximately 80–90% of soil microorganisms are not yet cultured by means of classical
methods (Amann et al., 1995).
At the beginning of the last decades, cultivation-independent techniques became more
frequent, leading to a broader view of microbial life in soil. It is now widely accepted that a
given soil consists of members belonging to all three domains of the biosphere, the Bacteria,
the Eucarya and the Archaea (e.g. Liesack et al., 1997; Gattinger et al., 2002a). Cultivation-
independent molecular approaches are based on the direct extraction of DNA from soil and a
subsequent analysis molecular marker genes (e.g. genes coding for ribosomal RNA). These
genes are functionally conserved in all organisms and contain conserved, variable and highly
variable regions (Amann et al., 1995) and can therefore be used as marker genes to describe
structural microbial diversity. At present, more than 15 000 sequences of rRNA genes are
available in databases. Apart from structural genetic analyses, soil microbial communities can
also be studied in terms of their in situ functions by means of molecular techniques. There are
several PCR-based assays available for the detection of functional genes with respect to key
processes during C and N cycling (see Emmerling et al., 2002).
Another cultivation-independent technique for the analysis of the structural diversity of soil
microorganisms is the phospholipid approach. Phospholipids are essential components of
membranes of all living cells, and their fatty acid (PLFA: phospholipid fatty acids) or ether-
linked isoprenoid side chains (PLEL: phospholipid etherlipid) allow a taxonomic
differentiation within complex microbial communities (Zelles, 1999; Gattinger et al., 2002a,
b, 2003). This approach is now well established in soil ecology and serves as a phenotypic
and thus complementary tool to genotypic (molecular genetic) approaches.
Soil microbial communities and related functions were studied under the constraints of
agricultural land use in general and the specific aspects of Research Station Scheyern in
particular. Hence, the impact of copper from previous hop cultivation in Scheyern was also
investigated as well as the more general aspects of herbicide degradation and soil tillage
practices.
The aggregate of microorganisms in the soil environment is a microbiome that emerged as a
vital component of sustainable agriculture in the recent past. These beneficial
microorganisms perform multiple plant growth-promoting activities including fixation,
mineralization, solubilization, and mobilization of nutrients, production of siderophores,
antagonistic substances, antibiotics, and release of plant growth-promoting substances, such
as auxin and gibberellin hormones, mediated by interactions between host plant roots and
microbes in the rhizosphere. Numerous plant species forms symbiotic association with
microbes and draw the benefit of mineral nutrient supply with the expense of minimal
energy, and their distribution is governed by nature and the number of root exudates, crop
species, and cultivars. On the other hand, microorganisms with critical roles in the
microbiome can be isolated, formulated, and developed as a new biological product called
biofertilizers. Agriculturally, important microbes with Fe- and Zn-solubilizing attributes can
be used for the biofortification of micronutrients in different cereal crops. Regardless of the
approach to be used, innovations with the use of microbiomes represent the future of
sustainable agriculture. Probiotic microbes, such as Lactobacillus, etc., are increasingly being
used as dietary supplements in functional food products. Effective utilization of microbiome
aids in promoting sustainable agriculture that accomplishes a safe environment, which in turn
manifests positively on human health.
Soil Beneficial Microorganisms as a Link to Sustainable
Agriculture
Soil is a natural medium for plant growth and development. Soil is the most diverse and
complex habitat that consists of the smallest organisms in the soil and includes bacteria,
actinomycetes, fungi, algae, etc. The plant microbiome is a key determinant of plant health
and productivity and has received substantial attention in recent years. Microbes in the
rhizosphere can establish beneficial, neutral, or detrimental associations of varying intimacies
with their host plants. Specific interactions between microbes and model plants, such as in
Rhizobium–legume symbioses , are well understood. A significant amount, 5–20%, of the
products of photosynthesis (the photosynthate) is released, mainly into the rhizosphere (the
soil–root interface) through roots. These photosynthates include rhizodeposit exudates,
mucilage, and sloughed cells. Root exudates contain a variety of compounds, predominately
organic acids and sugars, and also amino acids, fatty acids, vitamins, growth factors,
hormones, and antimicrobial compounds. Root exudates are key determinants of rhizosphere
microbiome structure . The composition of root exudates can vary between plant species and
cultivars and with plant age and developmental stage.
Among the various advantages of the microbiome for plants, symbiotic associations between
nitrogen-fixing bacteria, mainly rhizobia, arbuscular mycorrhizal fungi, and phosphate-
solubilizing bacteria, are typical examples of the microbiome for how plants obtain nitrogen
and phosphorus, respectively. The interaction between nitrogen-fixing bacteria and legume
crops, and arbuscular mycorrhizal fungi and phosphate-solubilizing bacteria increases the
availability of nitrogen and phosphorus for plants since the bacteria fix the nitrogen and
solubilize phosphorus ions, while the fungi translocate them to the plant. Bacillus,
Azotobacter, Microbacterium, Erwinia, Beijerinckia, Enterobacter, Flavobacterium,
Pseudomonas, and Rhizobium bacteria are known as phosphate solubilizers. The microbiome
containing rhizobia, the legume nodule microbiome, consists of other endophytic bacteria,
both of which are responsible for direct and indirect growth promotion mechanisms in plants.
Some nitrogen-fixing endophytes are cyanobacteria (Anabaena, Nostoc, Calothrix),
Azotobacter, Azospirillum, and Gluconacetobacter. However, fixators can also be free living
and establish themselves in non-leguminous plants, as is the case, for example, with the
genera Beijerinckia, Klebsiella, and Bacillus.
Another method is phytostimulation or biostimulation intrinsically linked to plant growth and
made up of the production of phytohormones by the microbiome, such as indole-3-acetic acid
(IAA), auxin, gibberellins, cytokinins, and salicylic acid (SA). Besides, some bacteria can
secrete an enzyme, 1-carboxylic acid-1-aminocyclopropane (ACC) deaminase, which reduces
the level of ethylene in the plant. Aguiar-Pulido et al.reported that bacteria from the tomato
rhizospheric microbiome produced the hormone IAA, and promoted plant growth. Duran et
al. found, in the roots of cereals (wheat) and oilseed (soybeans) crops, rhizospheric bacteria
producing IAA and ACC deaminase, which were Pseudomonas spp. The microbiome also
plays an essential role in plant tolerance to extreme conditions, such as salinity, drought, and
exposure to heavy metals. Soil salinity has hindered the growth rates of plants and reduced
their yield. However, the negative impact of high levels of salt in the soil can be minimized
through the production of phytohormones by the microbiome, with a consequent increase in
plant resistance to these extreme environments. In a study in Ref., the rhizosphere
microbiome was able to promote germination and growth of Hibiscus hamabo under salinity
conditions. Recently, in Refs. a model was proposed to explain the establishment and
maintenance of the beneficial and degrading microbiome in the rhizosphere of contaminated
soil plants. Four strategies were identified, including plant selection based on the
microbiome, interference from root exudates, disturbance, and feeding of supply lines, to
ensure that the microbial community is kept under control in polluted environments. Plants
that live in oil-contaminated soils depend on their microbiome for survival, growth
optimization, and biomass production. At the same time, as the contamination of these areas
increases, there are changes in the composition of the microbiome, favoring hydrocarbon-
degrading microorganisms associated with plant growth. The plant–microbiome interaction
will not always be efficient for phytoremediation; therefore, human interventions are
necessary to optimize this interaction and promote the degradation of pollutants.
Understanding the potential of the microbiome for agriculture can lead to its use as an
inoculant or its manipulation, to select more efficient microbial groups for plant development.
Besides that, reducing the use of pesticides and chemical fertilizers based on an
understanding of the potential of the plant microbiome is of paramount importance in
advancing sustainable agricultural practices.
The microbiome can also be used as a biocontrol agent. There are a few examples of
biocontrol by the plant-associated microbiota through the production of siderophores, volatile
compounds, enzymes, and antibiotics, in addition to phytohormone levels being modulated.
The plant microbiome also inhibits the growth and activity of pathogens through competition
for nutrients and microenvironments through parasitism, antibiosis, and the resistance they
confer to the plants' immune system. Some soil bacteria are capable of protecting the plant
from pathogens belonging to the genera Pseudomonas, Streptomyces, Bacillus,
Paenibacillus, Enterobacter, Pantoea, Burkholderia, and Paraburkholderia. In the soil
microbiome, the phyla Acidobacteria, Actinobacteria, and Firmicutes were able to control the
wilt caused by Fusarium oxysporum, while the endophytes Serratia and Enterobacter were
able to control the pathogen Gaeumannomyces graminis, which caused take-all of wheat. Soil
microbiome promotes plant growth through the biocontrol mechanism. The microbiome
stimulates growth through bio-fertilization, that is, by controlling the availability and
acquisition of nutrients by plants. Manipulation of the plant microbiome has the potential to
reduce the incidence of plant disease, increase agricultural production , reduce chemical
inputs, and reduce emissions of greenhouse gases, resulting in more sustainable agricultural
practices. This goal is seen as vital in sustaining the world's growing population.
Although both soil and plant microbiomes have important roles in crop performance and
yield, the greater chance of success in using plant microbiomes is driven by eco-evolutionary
interactions between plant species and their microbiomes. However, to realize the full
potential of the crop microbiome to support productive and sustainable croplands would
require a better understanding of the structure and function of the crop microbiomes, and
their interactions with host species across the globe soil types at a level similar to the Human
Microbiome Project.
Role of Microbial Biotechnology in Agriculture
Agricultural technologies ensured a green revolution in the middle of the 20th century but
caused high ecological costs and contributed to global pollution, unfavorable climate change,
and loss of biodiversity. Biotechnology and microbiology together offer a broad field of
research for the improvement of crop quality, crop productivity, and sustainability of existing
systems to produce more and better quality agricultural products through genetically
modified organisms (GMO) and transgenic crops. Microbial biotechnology played a
sustainable role in sustainable agriculture in various ways, i.e., biofertilizers, biopesticides,
bioherbicides, bioinsecticides, etc. Microbial biotechnology reduces the dependence on
agrochemicals in sustainable agriculture by the management of biotic and abiotic stresses.
This management contains several steps from the selection of microorganisms, selection of
targets to the selection of genes from related or unrelated genetic resources. Microbial
biotechnology assisted with genetic engineering will lead to the advancement in
modifications of plant and animal pathogens for lesser virulence, disease-diagnostic tools,
and improvement in microbial agents for biological control of plant and animal pests, and
development of new and better microbial agents for bioremediation, etc. Soil microbiome is
considered as one of the major components for the microbial biotechnology tools to
sustainable agriculture. In that, rhizosphere acts as a microhabitat and are rich in diversity of
microorganisms. Microbial biotechnology assisted with genetic engineering will lead to the
advancement in modifications of plant and animal pathogens for lesser virulence, disease-
diagnostic tools, and improvement in microbial agents for biological control of plant and
animal pests, and development of new and better microbial agents for bioremediation, etc.
The tools of molecular biotechnology have augmented preciseness in plant breeding by
distinguishing, DNA isolation, gene cloning, and transferring of genes desired from one
species to another species.
Soil microbes are thought of jointly as the most important parts for the sustainable production
of sustainable and healthy food. Microhabitat for microorganisms in the rhizosphere is
enriched with a huge diversity of microorganisms. In biotechnology, rhizospheric microbes
play a vital role in creating agricultural sustainability by varied means, such as increasing N 2
fixation; increasing the availability of P, S, Zn, and Fe; managing abiotic and biotic stresses;
increasing productivity, quality of crops, and bioremediation. The major benefits of microbial
biotechnology are many. It helps to produce a crop without much application of chemical
fertilizers, pesticides, herbicides, etc. It also keeps our environment safe and clean for the use
of future generations. The benefit of microbial biotechnology helps us to avoid the use of
hazardous pollutants and wastes that affect natural resources and the environment.
The development of society should be done in such a way that it helps to protect our
environment and also helps us to develop it. Biotechnology and microbiology together offer a
broad field of research for the improvement of crop quality, crop productivity, and
sustainability of existing systems to produce more and better quality agricultural products
through genetically modified organisms (GMO) and transgenic crops. Some of the examples
of genetically manipulated crops for the global benefit are as follows: control ripening
improves shelf life and quality (e.g., tomatoes, peas, peppers, tropical fruits, broccoli,
raspberries, and melons), insect resistance to reduce insecticide use (e.g., tomatoes, potatoes,
corn, rice, lettuce, coffee, cabbage family, and apples), fungal resistance to reduce fungicide
use (e.g., peppers, tomatoes, and cucumbers), viral resistance to reduce diseases caused by
plant viruses and, since insects carry viruses, reduce the use of insecticides (e.g., potatoes,
tomatoes, cantaloupe, squash, cucumbers, corn, oilseed rape canola, soybeans, and grapes),
and herbicide tolerance improves weed control (e.g., soybeans, tomatoes, corn, cotton,
oilseed rape canola, and wheat).
Biotechnological intervention plays a pivotal role in this context regarding the identification
of the microbiome. In the recent past, genetic material sequencing and increment power of
computation is extensively used for the detection of microbes in the microbiomes of different
agro-ecologies, which makes it easy to identify microbiome in every feasible environment
bypassing the necessity to isolate and culture microbes. Extrapolating such diverse
knowledge is greatly worthwhile to develop approaches in the manipulation of the
microbiomes for the higher acquisition of nutrients and enhanced biotic and abiotic stress
tolerances causing better productivity of crops. As a matter of fact, the technology of
sequencing, synchronized with bioinformatic tools, has not only discovered speedy
microbiome identification but also made it feasible to rapid gene microbiome annotation
within a lesser period. Next-generation sequencing (NGS), a recently emerged technology, is
now being used because of its remarkable advantages over the conventional method of
Sanger sequencing. The advancement in this technology has caused high-throughput
sequencing, which has supplementarily enhanced the various outcomes, which previously
appeared to be hard and arduous by traditional techniques. The completed genome sequences
are of great quality by characterization, represent further precise genomic data, and can be
implemented for model organisms and agriculturally important microorganisms. Marching
ahead in this direction, the recently advanced sequencing tool metagenomics reveals the
study of genetic matter of microbes that exists in environmental samples, by employing high-
throughput sequencing tools. In studying the aboveground and belowground microbiomes,
metagenomic analysis has a huge potential to provide sufficient information about the
detection of microbial composition and diversity, novel genes, microbial pathways, and
interactions.
Due to the cheap cost of sequencing, an amazing number of microbiomes have been
discovered and identified in the earlier contemporary period using studies of metagenomics
through direct assessment of the sequence of the 16S/18S rDNA amplicons. Additionally, the
third-generation sequencing technique, SMRT (single-molecule real-time sequencing), does
not require a prior PCR process that relies upon a single molecule of DNA. The
pyrosequencing of 16S/18S rDNA amplicons is now in use to inspect the taxonomical
identification (from the phylum to the genus level) of the microbiome in various soils.
Agricultural practices are, as of now, implemented on a worldwide scale, and diverse
methodologies are being routed to meet sustainable environmental and economical
developments, with the final aims of maintaining yield while safeguarding the biosphere.
Agricultural microbiology is introduced as a synthetic research field responsible for the
exchange of knowledge from general microbiology and microbial ecology to agricultural
biotechnology. Analysis of the regular circulation of microorganisms between plants, animal,
and soil-borne niches is required to reconstruct the arrangement of the microbiota in natural
and agricultural ecosystems.
Soil Health and Crop Productivity
Earth crust is an important biological component for microbial activity. It is a natural habitat for
diversity of microbes, and it is estimated that one gram of soil contains up to ten billion bacterial cells.
Decline in soil fertility is major concern for food security. Soil microbes contribute to a wide range of
function in controlling soil health and crop productivity (Sahoo et al. 2015). It managed soil fertility
through the modification of soil properties either directly or indirectly. Plant–microbe interaction is
one of the important aspects for agriculture system. This association may help to achieve goal of
future sustainable agriculture. Soil held variety of microbial species such as bacteria, fungi, mosses,
and liverwort. Bacteria fungi and Actinomycetes are three groups of microbes that form major soil
biomass of microbes. Among these, rhizospheric bacteria are to establish relationship with plants and
promote nutrient uptake, water supply, and ameliorate various types ofabiotic and biotic stresses. The
presence of microbes is indicator of soil biological activities and regulates physical and chemical
properties of soil. Microorganism is fundamental component of soil for all nutrient cycles and plant
nutrient. Variation in temperature, low water content, anthropogenic, and grazing causes detrimental
impact on microbial diversity and soil process. Soil–root–microbes form a comparatively stable and
beneficial association. Some microbes have negative impactalso in rhizosphere zone and harmful for
plant growth and development (Ahmad et al. 2008). Due to intensive cropping and unhealthy effect of
fertilizers, this relation declines soil microbial diversity.
Conclusion
This review examined the role of the microbiome in sustainable agriculture and human
health. In sustainable agriculture, soil health is mainly determined by the presence and
diversity of microbes present in the soil rhizosphere. The diversity and abundance of soil and
rhizosphere microorganisms influence plant composition, productivity, and sustainability.
Deploying microbes to improve agriculture productivity is an extremely attractive approach
that is non-transgenic and can be viewed collectively as the extended plant genome. Because
these same microbes can contribute to restoring soil health and productivity, they have a
bright future in low-input, sustainable agriculture. Improved assessment of soil health
indicators is necessary to further enhance our understanding of how production strategies and
environmental factors affect the physical, biological, and chemical stability and dynamics of
the soil–rhizosphere–plant systems and their impact on short- or long-term sustainability.
Soil microbial communities extend various ecosystem services, and they are capable of
improving soil fertility, increase plant tolerance toward biotic and abiotic stresses, increase
crop productivity, and take part in nutrient cycling. Tailored selection of microbes from soil
environment for development of microbial inoculants may curtail chemical fertilizer
dependency of farmers. SH and quality aspects envisage integration of various soil physical,
chemical, and biological parameters for developing indices, which are specific to
agroecosystems. Future advances in SH practices include development of in situ sensors for
estimation of biotic and abiotic indicators, use of metaomics approaches under different land
use and environmental conditions, and for better understanding of microbial communities in
soils for sustainability. Also relating plant–microbe–soil interactions is utmost necessary for
climate change adaptations and building resilience in microbial communities.
References
https://link.springer.com
https://courseware.cutm.ac.in
https://www.sciencedirect.com
