Microorganisms for agricultural development

Overview

Microorganisms for agricultural development

By E. Sunil
Senior Research Fellow, AMAAS project,
Kerala Agricultural University, Thrissur

Published by Biology-Online on November 21, 2008


MICROBES are the oldest form of life on earth. These single cell organisms date back more than 3.5 billion years, to a time when the Earth was covered with oceans.

Without microbes, we can't eat or breathe. Thus, understanding microbes is vital to understanding our past and future. Microbes play many roles in the earth's environment, from recycling dead plant and animal matter through the soil, removing carbon dioxide from the atmosphere by photosynthesis in the oceans and fixing nitrogen from the atmosphere to form nitrogenous fertilizer for plants. They play an important role in nutrient recycling, nutrient management, organic matter decomposition and fermentation and in food industry.


Microbial biodiversity

Several countries have now come to realize the economic values of their microbial biodiversity. The direct commodity values of exploited microbial biological resources, such as different edible microorganisms/antibiotic producing strains, agriculturally important and industrial value of microbes are well established. These microbial genetic resources are available for commercial exploitation through biotechnology.

Developing countries are now demanding a greater share of the economic benefits arising from the use of resources within their boundaries, which until now have mainly accrued to the industrial countries with the technological capability to exploit them. India is home to millions of microbes, many of which are found nowhere else in the world. Therefore, it is imperative to conserve and characterize the variable agriculturally important microorganisms (AIMs) for its optimum utilization by the coming generations.

Some microbes can make humans very ill whilst others can help in maintaining our health. Likewise, plants suffer from diseases caused by microbes but other microbes can be very beneficial to them, for instance in assisting them to absorb nutrients such as phosphate nitrogen , potassium and other minerals Besides, they are a valuable source of industrial products like organic acids, alcohol, antibiotics, dyes and biopesticides.

During the last decades (1960s Green revolution) increased fertilizer and pesticide use contributed to a spectacular increase in crop production, especially in Asia and South America. However, the price of fossil-fuel-based inorganic fertilizers relative to the prices of most stable crops has increased and chemical pesticides are both costly and harmful when they persist in the soil and enter the food chain. This explains the emphasis on current attempts to control soil- and plant-associated microorganisms, to lower fertilizer production costs, reduce environmental pollution while ensuring fair or even high yields, and to expand the adaptability of plants to reputedly unfavorable situations.


Important micro-organisms

The agriculturally important microorganisms come from bacteria, actinomycetes, blue green algae (BGA), fungi - including vesicular arbuscular mycorrhizae (VAM) - and viruses. They thrive in a variety of habitats including soil, living body systems and dead/decayed matter, marine, snow bound mountains and desert systems, water bodies, etc. Their genetic factors underlying the differential adaptability to such diverse habitats indicate an invaluable treasure of genes for the benefit of agriculture. The sectoral importance of microorganisms in agriculture has also increased with the integration of agriculture, intellectual property and services with the world trade agreement.

'The developing world is keenly looking forward to harness the genic power from microorganisms through the rapid development of their institutional capacity, through building of state-of-the-art laboratories, biosafety and other regulatory mechanisms, and human resource.

Most of the chemical reactions that take place in the soil, leading to increased availability of several major and micronutrients, often have active contribution of microbes. The nitrogen-fixing bacteria, blue green algae, and phosphate solubilising bacteria are already well known to enhance availability of major nutritional elements like N and P to plants whereas the decomposer bacteria are instrumental for recycling, and thereby increasing, the availability of carbon and several micronutrients from plant residues to soil.

Some other microorganisms similarly contribute towards improved plant health and higher crop yield through the production of growth stimulators such as plant hormones and vitamins, such biofertilising and phyto-stimulating genes from microbes obviously require intensive study for their application and use in agriculture. Research efforts have to be essentially focused on prospecting and mining of the microbial genic potential for use in crop and animal improvement. The developments in genomics and gene transfer through biotechnology, their relevance and role has further increased. The agriculturally important microbes are increasingly seen to be much more dynamic and focused gene resource for developing transgenics to increase productivity of agri-based products and quality, and incorporating resistance to biotic/abiotic stress factors in the plants and livestock.

Microorganisms in the rhizosphere are known to act in synergy with crops. The rhizosphere is generally defined as the soil region under the influence of the root. It includes the rhizoplane (surface of the root) and the endorhizosphere (intercellular space between the root tissues inhabited by non-symbiotic bacteria). The rhizodeposition, one of the main factors influencing the rhizosphere is the organic or inorganic production of the root within the soil. It corresponds to 15-40% of the total photosynthetic production of the plant and secretes an important carbon and energetic source towards the micro-organisms of the rhizosphere. It comprises sloughed of cells, secreted mucilage (facilitates water exchanges), soluble exudates (e.g. sugars, amino acids, attractants or antibiotics). The root also influences the rhizosphere by creating a negative oxygen gradient (root respiration), by absorbing water (increasing the soil air conductivity) and by absorbing mineral salts.

Indian Council of Agricultural Research (ICAR), country's apex organization engaged in agricultural research, has taken a step in this direction by starting a project on Application of Microorganisms in Agriculture and Allied Sectors (AMAAS).Thus, to fully exploit potential of microorganisms in agriculture and allied sectors, AMAAS Project has been started involving various research centers spread all over country i.e. State Agricultural Universities (SAUs) as well as ICAR institutions having expertise in different fields of microbiology.

The major objectives of the project are (a) deciphering structural and functional diversity of AIMs and to develop microbial map of the country; (b) improving nutrient use efficiency through microbial interventions for sustainable crop production; (c) development of microbe based technologies for agro-waste management and biodegradation for sustainable crop production; (d) development of microbe-mediated processes for product development and value addition in agriculture etc. The project is expected to help increase the agricultural production on sustainable basis. It will help to reduce the usage of chemical fertilizers, pesticides, herbicides, and insecticides. The project will help to generate technologies like post harvest technologies, agro-waste management technologies, bio control agents, diagnostic kits for identification of pathogens and novel genes for both biotic and abiotic stress. These technologies are the need of hour, which will help in reducing huge losses due to biotic and abiotic losses that account to 30 per cent at present.


Plant growth promoting rhizobacteria

PGPR

Plant growth promoting rhizobacteria are bacteria that colonize plant roots, and in doing so, they promote plant growth and/or reduce disease or insect damage. There has been much research interest in PGPR and there is now an increasing number of PGPR being commercialized for crops. Organic growers may have been promoting these bacteria without knowing it. The addition of compost and compost teas promote existing PGPR and may introduce additional helpful bacteria to the field. The absence of pesticides and the more complex organic rotations likely promote existing populations of these beneficial bacteria. However, it is also possible to inoculate seeds with bacteria that increase the availability of nutrients, including solubilizing phosphate, potassium , oxidizing sulphur, fixing nitrogen, chelating iron and copper. Phosphorus (P) frequently limits crop growth in organic production. Nitrogen fixing bacteria are miniature of urea factories, turning N2 gas from the atmosphere into plant available amines and ammonium via a specific and unique enzyme they possess called nitrogenase. Although there are many bacteria in the soil that ‘cycle' nitrogen from organic material, it is only this small group of specialized nitrogen fixing bacteria that can ‘fix' atmospheric nitrogen in the soil. Arbuscular mycorrhizal fungi (AMF) are root symbiotic fungi improving plant stress resistance to abiotic factors such as phosphorus deficiency or deshydratation.

The fourth major plant nutrient after N, P and K is sulphur (S). Although elemental sulphur, gypsum and other sulphur bearing mined minerals are approved for organic production, the sulphur must be transformed (or oxidized) by bacteria into sulphate before it is available for plants. Special groups of microorganisms can make sulphur more available, and do occur naturally in most soils.
One of the most common ways that PGPR improve nutrient uptake for plants is by altering plant hormone levels. This changes root growth and shape by increasing root branching, root mass, root length, and/or the amount of root hairs. This leads to greater root surface area, which in turn, helps it to absorb more nutrients.

Disease control

PGPR have attracted much attention in their role in reducing plant diseases. Although the full potential has not been reached yet, the work to date is very promising and may offer organic growers some of their first effective control of serious plant diseases. Some PGPR, especially if they are inoculated on the seed before planting, are able to establish themselves on the crop roots. They use scarce resources, and thereby prevent or limit the growth of pathogenic microorganisms. Even if nutrients are not limiting, the establishment of benign or beneficial organisms on the roots limits the chance that a pathogenic organism that arrives later will find space to become established. Numerous rhizosphere organisms are capable of producing compounds that are toxic to pathogens like HCN

Challenges with PGPR

One of the challenges of using PGPR is natural variation. It is difficult to predict how an organism may respond when placed in the field (compared to the controlled environment of a laboratory. Another challenge is that PGPR are living organisms. They must be able to be propagated artificially and produced in a manner to optimize their viability and biological activity until field application. Like Rhizobia, PGPR bacteria will not live forever in a soil, and over time growers will need to re-inoculate seeds to bring back populations.

PGPR in Research

Over the years the PGPR (plant growth promoting rhizobacteria) have gained worldwide importance and acceptance for agricultural benefits. These microorganisms are the potential tools for sustainable agriculture and the trend for the future. Scientific researchers involve multidisciplinary approaches to understand adaptation of PGPR to the rhizosphere, mechanisms of root colonization, effects of plant physiology and growth, biofertilization, induced systemic resistance, biocontrol of plant pathogens, production of determinants etc. Biodiversity of PGPR and mechanisms of action for the different groups: diazotrophs, bacilli, pseudomonads, Trichoderma, AMF, rhizobia, Phosphate solubilising bacteria and fungi, Lignin degrading , chitin degrading , cellulose degrading bacteria and fungi are shown. Effects of physical, chemical and biological factors on root colonization and the proteomics perspective on biocontrol and plant defense have also shown positive results. Visualization of interactions of pathogens and biocontrol agents on plant roots using autofluorescent protein makers has provided more understanding of biocontrol processes with overall positive consequences.

Ways that PGPR promote plant growth

• Increasing nitrogen fixation in legumes
• Promoting free-living nitrogen-fixing bacteria
• Increasing supply of other nutrients, such as phosphorus, sulphur, iron and copper
• Producing plant hormones
• Enhancing other beneficial bacteria or fungi
• Controlling fungal diseases
• Controlling bacterial diseases
• Controlling insect pests


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