Microbial wealth regulates crop quality and soil health

D.P. Singh and H. B. Singh

 Interaction, whether mutualistic, symbiotic or suppressive, that coexists in soil ecosystem within the plants, microbes or micro-fauna is among the most important phenomenon regulating the soil and plant health. The most intense interactions between microbes and plants take place at the rhizosphere, the root zone in the close vicinity of the soil. This is the zone where complex biological and biochemical activities between microbes-microbes, microbes-plants and plants-plants are continuously going on to influence the biodiversity of the beneficial organisms, suppression of pathogenic microflora and the physicochemical behaviour of the soil. The concept of the rhizosphere was first developed by the German biologist Lorenz Hiltner some 100 years ago, who pointed out that the area around the roots is the region of high microbial activity. However, even after a longer time, despite significant work and research on the biology and biochemistry of the rhizosphere, very little has been extracted and documented about the detailed mechanisms that take place in the soil and how such activities influence microbial community, soil health and plant productivity. Although most research focus on what is happening aboveground level, researchers have demonstrated direct link between “above-ground” and “below-ground” biodiversity. The biological cost-benefits and ecological impacts of this phenomenon remain elusive, but the overall findings suggest that the maintenance of high plant diversity as well as good crop quality requires a correspondingly high level of soil microbial biodiversity.

Soils are the natural home of enormous numbers of diverse living organisms assembled in varied communities. A complex soil biodiversity reflects a great variability among the living entities in the soil – ranging from the myriad of invisible microbes, bacteria, fungi, protozoans, nematodes to the familiar macro-fauna such as earthworms and termites. Plant roots are also living components to act as soil organisms in view of their active physiological activities, symbiotic relationships and interactions with soil microbes residing in their vicinity. These diverse organisms interact with one another in a fascinating manner, either to suppress the growth and development of their counterparts or to promote the beneficial organisms. While a number of soil-borne disease causing conditions have been observed due to the presence of harmful fungi and bacteria, suppression of these organisms by other beneficial microbes is also a common observation. One such fungus, Trichoderma is now widely acceptable as biological control agents for suppressing soil borne diseases of many crops.

Interaction among various plant roots, microbes and animals in the belowground soil ecosystem forms a complex web of biological activity. Soil organisms contribute to a wide range of natural services to render smooth and sustainable functioning of rhizosphere ecosystems. They are the primary driving forces regulating the nutrient cycling, maintaining the dynamics of soil organic matter, balancing soil carbon sequestration and checking greenhouse gas emissions, modifying soil physico-chemical structure and water regime and enhancing the efficient capability of nutrient acquisition by plant roots. These entire phenomena ultimately lead to enrich soil with extraordinary capacity to enhance plant health. The role of mutualistic nitrogen-fixing bacteria, Rhizobia has been well documented for a long time and recent research has emphasized the intimate exchange of nutrients during the symbiosis of plant roots and bacteria. Such services are not only critical to the functioning of natural ecosystems but constitute an important resource for sustainable agricultural systems.

Beneficial microbes improve soil health

Microbes being an integral component of any soil ecosystem provide life to the soil. Native soils minus microbes are merely dead material. In the present era of agriculture, unfortunately many unscientific activities have caused a huge threat to the soil microbial community. Actually this observation remained un-noticed in the farms unless the soils in many parts of the world have shown loss of response towards nutrient supply and decline in crop productivity even after maintaining high farm inputs. It is now widely being recognized that the presence and abundance of microbial wealth provide soils richness in terms of making available slow-release nutrients, continuous breaking down of complex macro-molecules and natural products into simpler ones to enrich beneficial substances, maintaining physico-chemical properties of the soils and most essentially, providing supports to the plants in terms of growth enhancement and protection against diseases and pests through their metabolic activities that goes on in the soil along day and night. The metabolic activities of the microbes such as rhizosphere bacteria, beneficial mycorrhizal fungi, biological control agents e.g. species and strains of Aspergillus niger, Bacillus spp., Burkholderia cepacia, Candida oleophila I-182, Coniothyrium minitans, Coniothyrium sclerotiorum, Fusarium oxysporum (Nonpathogenic), Gliocladium spp., Phlebia gigantean, Pseundomonas cepacia, Pythium oligandrum, Streptomyces griseoviridis and Trichoderma spp., the biological nitrogen fixers e.g. cyanobacteria (blue green algae), Azolla-Anabaena symbiont  and soil fauna like nematodes, worms, protozoans etc., continuously add to the soil health and promote crop productivity through diverse mechanisms. The organisms such as Rhizobium, Azotobacter, Azospirillum, phosphate solubilizing micro-organisms etc. that are currently being used as the formulations of biofertilizers have been put under the schedule of Fertilized Control Order (FCO), 1985 amended vide S.O. 391 (E) dated 24.03.2006 wherein, the state governments are asked to enforce quality control of these biofertilizers and organic fertilizers as per the specifications of the FPO act.

“Promotion of low-input biofarming practices based on integrated use of biopesticides, rhizobacteria, vermicompost and neem products among rural population is perhaps the best way in the present time to obtain sustainable food security”

There is growing interest in the presence of certain naturally occurring, beneficial microorganisms in agricultural wastes (e.g. processing wastes, composts and anaerobic slurries) that have considerable potential to enhance the growth, health and protection of crops. Further their numbers can be increased through incubation procedures and they can be applied as mixed or pure culture inoculants to soils and plants in waste materials or as sprays and suspensions. The various mechanisms of disease suppression and plant protection imparted by these beneficial microorganisms may be related to (a) microbe-microbe interactions, (b) plant-microbe interactions, (c) metabolites produced and/or, (d) induced systemic-acquired resistance. To share our more than a decade experience with the farming communities, we have started promoting the usage of beneficial microbes in as an component of integrated farming practices and farmers in the villages of Varanasi, Ghazipur, Chandauli and Azamgarh districts are adopting seed treatment techniques with Trichoderma formulation, rural production technology of Trichoderma on cow dung, use of microbial consortia of Pseudomonas and Bacillus, use of vermicompost in the field and its in-house production with simple and repetitive technology. All these microbes are being promoted in vegetable crops like tomato, potato, brinjal, cabbage, cauliflower, ladyfinger etc., fruit crops, pulses like chickpea, pigeonpea, masoor etc. and cereals wheat, bajra, rice etc. Case studies indicated that these microbes possess the potential to suppress soil borne plant diseases, promote plant growth due to the release of plant hormones and by nutrient acquisition and keep soils in good physicochemical conditions. Further research is being carried out in many premier institutions to elucidate exact mechanisms or modes-of-action to determine the optimum time, rate and frequency of application for improving plant health and protection.

Microbial interactions, biological control and plant health

The rhizosphere or the zone of influence around roots harbors a multitude of microorganisms that are affected by both abiotic and biotic stresses. Among these are the dominant rhizobacteria that prefer living in close vicinity to the roots or on their surface and play a crucial role in soil health and plant growth. Both free-living and symbiotic bacteria are involved in such specific ecological niches and help in plant matter degradation, nutrient mobilization and biocontrol of plant disease. These are the real players in a defined ecosystem whose beneficial effects boosts and detrimental effects diminish soil health and crop production. Overall, the population of all these inhabitants is directly dependent on the organic matter content of the agro-ecosystem. Within the plant roots, the loss of carbon sources provides the desired energy for the development of active microbial populations in the rhizosphere around the root. Generally, saprotrophs or biotrophs such as mycorrhizal fungi grow in the rhizosphere in response to this carbon loss, but plant pathogens may also develop and infect a susceptible host, resulting in a diseased condition. This complete cycle of fetching carbon from the roots, flourishing in the vicinity of roots on their exudates, and in turn, providing essential minerals for plant growth and development, is one of the most important natural way of living together while helping each other. This way of living is very similar to what humans are maintaining in their own society to flourish and make sustained growth.

Microbial interactions that take place in the rhizosphere and are involved in biological disease suppression are very important from the view of sustainable crop productivity. These organisms have evolved many mechanisms such as antibiosis, competition, parasitism and resistance induction in plants to provide effective disease suppression and plant growth promotion. It has been well documented that such interactions not only provide plants the needed resistance against pathogenic attacks or environmental stress but, at the same time metabolites constituted due to such interactions either in plants or in microbes are beneficial to each other. Production of a vast range of secondary metabolites such as polyphenols, flavonoids, alkaloids, peptides, lipids and steroidal compounds with diverse biological properties in plants and production and excretion of plant growth harmones e.g. indole acetic acid, siderophores, amino acids, proteins, enzymes and other nutrients into the medium, etc. by the microbes interacting the plant roots are some beautiful examples of such a highly complex interactive system needed for the survival of each other. The significance of plant growth promotion, rhizosphere competence and the suppression of diseases and pests on the plants is much considered research theme in present days. Multiple microbial interactions involving bacteria and fungi in the rhizosphere are shown to provide enhanced biocontrol in many cases in comparison with biocontrol agents used singly.

Organic practices nurture microbial biodiversity and soil health 

Scientific research has shown that organic farming practices essentially based on natural resource management significantly increase the population density and species diversity to improve soil’s life. It is being realized that suitable organic practices that favour soil micro-fauna and flora also favors soil conditioning and nutrient re-cycling. Manipulation of crop rotations, strip-cropping, green manuring and organic fertilization (animal manure, compost, crop residues), zero or minimum tillage and avoidance of chemical pesticides and herbicides, all nurtures good soil conditions and support plant health.

Organic practices favour arthropod and earthworm abundance

Organic farming practices increases the species abundance and richness of beneficial arthropods inhabiting aboveground and earthworms, thus improves the soil conditions. Increased predator population helps to suppress harmful organisms in the soil. In organic systems the density and abundance of arthropods such as carabids increases up to 100%, staphylinids up to 60-70% and spiders up to 70-120% as compared to conventional farming systems. Such a vast difference is explained by prey deficiency due to pesticide influence as well as by a richer weed flora in the standing crop that is less dense than in conventional plots. With the presence of field margins and hedges, beneficial arthropods are further enhanced, as these habitats are essential for over-wintering and hibernation. The biomass of earthworms in organic systems is 30-40% higher than in conventional systems with 50-80% more population density. When compared to the chemical fertilizer based farming system, this difference may be even more pronounced.

High occurrence of symbionts essential for good soil

Organic crops benefit from symbiotic mechanisms undergoing with the root systems that better enable plants to utilize the soil minerals. On an average, mycorrhizal colonization of roots is highest in crops of unfertilized systems, followed by organic systems. Conventional crops with chemical farm inputs have lower mycorrhizal colonization to a level of up to 30%. The most intense mycorrhizal root colonization is found in grass-clover, followed by the vetch rye intercrop. Roots of winter wheat are scarcely colonized. Even when all soils are inoculated with active micorrhizae, colonization is far better enhanced and supported in organic soil. This indicates that, even at surplus inoculum, soil nutrients at elevated levels and plant protection suppress symbiosis. This underpins the importance of appropriate living conditions for specific organisms.

 Abundance of micro-organisms relates with soil health

Earthworms are the natural plow in the soil and work hand in hand with fungi, bacteria, and numerous other microorganisms in the soil. In organically managed soils, the activity of these organisms is much higher as compared to conventional farming systems. Micro-organisms in organic soils not only mineralize more actively, but also contribute to the build up of stable soil organic matter like humus and other natural carbon complexes. By this way nutrients are recycled faster and soil structure is improved. The amount of microbial biomass and decomposition is correlated, at high microbial biomass levels, only small fractions of complex carbon materials remains undecomposed adding to crop health. The total mass of micro-organisms in organic systems is 20-40% higher than that in the conventional system with manure and 60-85% than that in the conventional system without manuring. The ratio of microbial carbon to total soil organic carbon is higher in organic system as compared to conventional systems. Therefore, organic management practices promote microbial carbon and ultimately enhance soil carbon sequestration potential.

 Microbial wealth supports biochemical activity in soils

Microbes have activities with important functions in the soil ecosystem. Soil enzymes are indicative of these functions. The total activity of micro-organisms can be estimated by measuring the activity of a living cell-associated enzyme, dehydrogenase. This enzyme plays a major role in the respiratory pathway. Proteases in soil, where most organic N is protein, cleave protein compounds into simpler constituents. Phosphatases cleave organic phosphorus compounds and thus establish link between the plant uptake and the reservoir of organic phosphorus in the soil. Enzyme activity in organic soils is markedly higher than in conventional soils. Microbial biomass and enzyme activities are closely related to soil acidity and soil organic matter content. A diverse microbial population, as observed in the organic fields, may divert a greater part of the available carbon to microbial growth rather than maintenance. In agricultural practice this may be interpreted as an increased turnover of organic matter with a faster mineralization and delivery of plant nutrients. Finally, more organic matter is diverted to build-up stable soil humus.

 Microbial biodiversity is vital for ecosystem functioning

While the rhizosphere as a domain of fierce microbial activity has been studied for over a century, the availability of modern tools in microbial ecology has now permitted the study of microbial communities associated with plant growth and development, in situ localization of important forms, as well as the monitoring of introduced bacteria as they spread in the soil and root environment. 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. These bacteria and fungi could provide significant environmental benefit as they may cause reduction in the application of nitrogen and phosphorous fertilizers. The overuse of such fertilizers has become a major concern because they cause nitrate contamination in the soil and groundwater by leachates. Thus, this interest is also linked with environmental concerns for reduced use of chemicals for growth promotion and disease control. Diversity of rhizobacteria microbes in a variety of plants, cereals, legumes and others is closely linked with their functionality based on the release of enzymes (soil dehydrogenase, phosphatase, nitrogenase, etc.), metabolites (siderophores, antifungals, HCN, etc.), growth promoters (IAA, ethylene) and as inducers of systemic disease resistance (ISR). Based on such primary screening protocols, effective rhizobacteria have been field tested with success stories from various agroecological zones of the country, as reflected in the control of root and soil-borne diseases, improved soil health and increased crop yields. Several commercial formulations, mostly based on dry powder (charcoal, lignite, farmyard manure, etc.) have been prepared and field tested, however, problems of appropriate shelf-life and cell viability are still to be solved. Also, inherent in such low cost technologies are the problems of variability in field performance and successful establishment of introduced inoculants in the root zone. In addition, most products available in the market are not properly monitored for quality before they reach the farmer. As a consequence, the acceptance of rhizobacterial formulations in the country is limited. However, several laboratories have now developed protocols for the rapid characterization of effective isolates based on molecular fingerprinting and other similar tools. The government initiative in integrated nutrient management and pest management systems has provided additional incentives to relate rhizobacterial science to other ongoing activities so that the benefit of this research may lead to technologies that are environmentally and socially acceptable.

Acknowledgement: DPS is thankful to Council of Scientific and Industrial Research (CSIR), New Delhi for financial Support.

D.P. Singh and H. B. Singh

Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221 005, E mail- dpsfarm@sancharnet.in; hbs1@rediffmail.com

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