Agro-Environmental Sustainability

Sustainability in agroecosystems is governed primarily by the functional balance between soil processes and plant productivity. Microorganisms are key drivers of important soil processes such as nutrient recycling, and their activity directly influences the functional stability and sustainability of the soil ecosystem. In nature, microbes tend to function as functional guilds or communities, thereby creating a complex network of microbial interactions. Therefore, microbial signalling processes play an important role in communication within a particular functional guild or among different guilds. Numerous chemical compounds acting as signalling molecules in the soil-plant system have been identified. However, the understanding of how these molecules contribute to soil ecosystem stability and sustainability through inter- and intra-species chemical signalling is incomplete. In particular, it is known that chemical inputs in agroecosystems can suppress some microbes (e.g. nitrogen fixers), which can also reduce the interactions between microbes due to destruction of the signalling networks, consequently breaking the delicate balance of the soil ecosystem. Understanding the impact of microbial signalling processes on soil ecosystem sustainability is imperative if we are to address this issue. This chapter reviews the current knowledge on the mechanisms of microbial signalling in plant–microbe interactions and technical advances in identifying signalling pathways between plants and soil and also proposes avenue for future research in this field.

Plants have recently been recognized as meta-organisms harboring distinct microbiome and reveling close symbiotic relationship with the associated microflora. Each plant has a unique niche and possesses species-specific microbes to a certain proportion and majority of the ubiquitous microbes that fulfill important host as well as ecosystem function. Currently, agricultural crops are facing challenges due to imbalance of micronutrients, deterioration of soil health, fluctuating environmental conditions, and increasing pest and pathogen attack. The rhizosphere region of the plants is the most extensively studied area due to its remarkable microbial diversity. Fluorescent pseudomonads are Gram-negative, motile, rod-shaped bacteria predominantly inhabiting the vicinity of rhizosphere and sometimes even the root interior. They effectively colonize the plant roots and rhizosphere soil because of their excellent ability to utilize a variety of organic substrates exuded by the plant roots. The study on the role of fluorescent pseudomonads in agriculture has been a matter of great interest attributable to their ability to control plant diseases, maintain soil health, and influence the plant growth directly or indirectly. They directly promote the plant growth by producing secondary metabolites such as siderophores and phosphatases that can chelate iron and solubilize phosphorus, respectively, from the soil and make them available to the plants. They also produce indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase that sequesters ACC, the precursor of ethylene. They also indirectly promote the plant growth mainly by suppressing the plant pathogens by producing an array of antibiotics and fungal cell wall degrading enzymes. Specific metabolites produced by fluorescent pseudomonads may elicit defense reactions and induce systemic resistance of the host plants. Introduction of such multifunctional rhizobacteria to the plant roots can lead to increased plant growth and protection against phytopathogens. This chapter reviews the beneficial traits of the fluorescent pseudomonads and their relationship to the functioning in the rhizosphere.

Soil and water surfaces, as well as plant surfaces and tissues are the known locations that harbor free-living phototrophic N₂-fixing cyanobacteria. These organisms are known to contribute substantial amounts of fixed nitrogen (20–30 kg N ha⁻¹annually). In continents where rice is the prime crop for majority of the population (amounting to over 40 % of world’s population), these organisms assume great importance. Two third of the total of 180 million tons of fixed nitrogen that gets added to the earth’s surface globally, comes from biological activities mainly contributed by these and other microbes. Rice field ecosystems are ideal for cyanobacterial growth as they provide optimum growth conditions. Azolla-Anabaena symbiotic association, another cyanobacterial system has been exploited as a biofertilizer in many Asian countries. This symbiosis is very important agronomically because its contribution has been estimated to be ~600 kg N ha⁻¹. With the adverse consequences of chemical agriculture, focus on nitrogen enrichment has shifted again to biological nitrogen fixation, especially towards both free-living and symbiotic cyanobacteria. During past few decades, research studies have yielded a large quantity of information on cyanobacterial nitrogen fixation from isolation, molecular understanding and manipulations to large-scale production for agriculture. Substantial research studies have also been devoted towards creating and understanding the artificial associations of cyanobacteria with crop plants. In this chapter, various N₂-fixing cyanobacterial systems in light of their use as biofertilizers are reviewed.

Exploitation of agriculturally important microorganisms in plant growth promotion and antagonistic potential is a well-investigated area. Trichoderma spp. are widely acknowledged for their potential to parasitize plant pathogenic fungi and have been efficiently utilized for biocontrol of wide range of seed and soil-borne phytopathogens. The antagonistic activity of Trichoderma spp. is largely credited to production of various antimicrobial secondary metabolites and has also been reported for plant growth promotion, management of the phytopathogens, and induction of systemic resistance in plants. Secondary metabolites-based formulation may have an additional benefit of longer shelf-life and immediate effect in comparison to spore-based formulations. Hence, this chapter will focus on the role of biosynthesized antimicrobial secondary metabolites of Trichoderma in tripartite interactions.

Soil fertility is the inherent capacity of a soil to provide the essential plant nutrients in adequate amounts and proper proportions for plant growth. There is an immense possibility to enhance soil fertility through microbes, as microbes are “built-in” soil regulators and catalysts contributing to recycling of nutrients into available inorganic forms and provide early warning of land degradation. The focus of this chapter is on the prospect of using microbes as decomposers (cellulose, protein and lignin), formers (humus, nitrate and nitrite), nitrogen fixers, ammonifiers, oxidizers (iron, hydrogen and sulfur), phosphorus solubilizers and denitrifiers. In this context, the factors viz. environmental contaminants and climate change that limit the enhancement of soil fertility through microbes are also discussed. In the latter part of the chapter, the strategies like practising organic farming, zero-tillage, mixed cropping, nano-biofertilizer, biopesticides and soil carbon sequestration for management of soil fertility through microbes are highlighted.

Trichoderma species are free-living fungi that occur in nearly all the soils and other natural habitats. They can be easily isolated from soil and decomposing organic matter. The genus Trichoderma comprises a great number of fungal strains that act as biological control agents, the antagonistic properties of which are based on the activation of multiple mechanisms. A successful biocontrol system is one which is easy and economical to produce, safe, stable in the environment, and easily applied during the conventional agricultural practices. Biofungicides include in a broader sense fungicides of biological origin, i.e., botanical and microbial. The use of microbial fungicides as one of the major components of IPM is gaining acceptance, as these are generally specific, apparently harmless to the beneficial insects, animals, and human beings with no residue problems and environmental hazards. Microbial fungicides are made of microbes such as eco-friendly fungi. Trichoderma strains exert biocontrol against fungal phytopathogens either indirectly, by competing for nutrients and space, modifying the environmental conditions, or promoting plant growth and plant defensive mechanisms and antibiosis, or directly, by mechanisms such as mycoparasitism. These indirect and direct mechanisms may act coordinately and their importance in the biocontrol process depends on the Trichoderma strain, the antagonized fungus, the crop plant, and the environmental conditions, including nutrient availability, pH, temperature, and iron concentration. Activation of each mechanism implies the production of specific compounds and metabolites, such as plant growth factors, antibiotics, and carbon and nitrogen permeases. These metabolites can be either overproduced or combined with appropriate biocontrol strains in order to obtain new formulations for use in more efficient control of plant diseases and postharvest applications.

At present, agricultural systems are under immense pressure to fulfill the increasing demand of food and feed in the context of global climate change with expanding populations. It is an established fact that the global temperature is likely to increase in upcoming decades resulting in the alteration of the edaphic attributes. The change in the edaphic factors due to climatic variations such as annual rainfall, events of drought and flood results in the decrease in soil fertility with water salinization which ultimately results in the reduction of crop yield. Hence in the contemporary era of scientific advancement, it is of central significance to develop mitigation strategies using analytical and forward looking concepts to fulfill the rapidly increasing food demands with ecological sustainability. In recent years, transgenic technology has proven to be very effective in terms of developing stress tolerant crops and use of microbes. This is a relatively simple alternative in terms of cost, unique properties, and ease of handling for broad-spectrum resistance/tolerance against combination of different stresses. Thus, the emphasis is now shifted to the bioprospecting of microbiota to explore the molecular and biochemical potential of microbes towards stress alleviation in crop plants. This book chapter includes an updated progress in microbial gene prospecting and their contemporary use in different plants to enhance their stress tolerance potential. Moreover, the chapter also emphasizes the different metabolic pathways which were previously targeted towards the development of stress tolerant plants and simultaneously proposed theoretical perspective and a baseline knowledge which could be further harnessed in future research towards sustainable agriculture and ecosystem.

Cover cropping with graminoids or legumes represents an important strategy in agricultural production systems for the improvement of soil fertility and soil functioning. The organic carbon derived from both aboveground littering and root deposition of cover crops can greatly regulate the functional microbial groups involved in the substance cycling of nitrogen, carbon, and phosphorus. This regulation normally improves soil quality from a long-term perspective, and the effects can vary much depending on cover crop species or soil types. On the other hand, symbiotic microbes, such as arbuscular mycorrhizal fungi and rhizobia, can bring great benefits to cover crops and the associated soils. They regulate the soil fertility and soil functioning via the direct effects on native soil microbial communities or the indirect effects through altered plant growth of cover crops. Recently, the synergic effects of cover crops and symbiotic microbes are explored, and the combination of cover cropping and symbiotic microbial inoculation is emerging as a potential technology for sustainable agriculture, mainly in the horticulture area. This chapter reviews the recent progresses in the improvement of soil fertility and soil functioning with cover crops via the soil functional microbial groups, with special focus on the addictive effects of symbiotic microbes.

The advent of green revolution or high input agrotechnologies have led to self-reliance in food production. Modern agriculture methods are getting increasingly dependent on the steady supply of synthetic inorganic fertilizers and pesticides, which are products of fossil fuels. There is an increasing concern about the excessive dependence on the supply of chemical fertilizers and pesticides, and the adverse effects of the indiscriminate use of synthetic inputs in soil productivity and environmental quality. The cumulative effect of environmental degradation due to application of agrochemicals has led to a decline in food production during the last two decades. In order to overcome these adverse effects, there is an urgent need to develop new strategies for ensuring further growth in agricultural output. By adapting a strategy involving integrated supply of nutrients from a combination of chemical fertilizers and pesticides, organic manures, and biofertilizers and biopesticides, the soil can be saved from further impoverishment and environmental degradation. The use of microbes as bioinoculants for promoting plant growth and/or bioremediation purposes gives a new dimension to agricultural and environmental biotechnology. Actinobacteria are considered as the most prominent source of bioactive compounds (antibiotics, enzymes, and plant growth modulators) facilitating plant growth promotion and plant disease suppression. Attempts are being made to utilize actinobacteria that produce antibiotics and agro-active compounds as biofertilizers and biopesticides; these aids in mitigating the use of harmful chemical fertilizers and pesticides. Besides making agriculture systems sustainable, soil inhabiting actinobacteria play important roles in various ecological processes such as organic matter decomposition and toxic pollutant and heavy metal bioremediation, thus contributing to the restoration of soil fertility and environmental sustainability.

Microalgae are considered to be suitable candidates for atmospheric carbon sequestration by virtue of attributes such as faster growth, ability to grow in low-quality water, and tolerance towards a wider range of temperature, salinity and nutrient-deficient environment. Further, the downstream processing of microalgal biomass yields a variety of value-added products including biodiesel which is considered to be a lucrative alternative to fossil-based fuels. In this review, the potentialities of microalgae for atmospheric carbon sequestration are discussed with reference to present status of microalgae biomass production systems, strategies for enhancing the growth of natural populations of microalgae in marine environment, status of knowledge about downstream processing of biomass for biodiesel production and its implications on global warming mitigation. In concluding part, the prospects and challenges pertaining to microalgal biomass production and its utilization are highlighted. Based on an overview of the state of knowledge, few recommendations are submitted for the consideration of the scientific community.

Since their original isolation from rice paddies near Hanoi, the set of microbial strains comprising the biofertilizer BioGro have been subjected to extensive and intensive experimentation in both laboratory and the field. Based on a hypothesis that such strains inoculated onto rice and other plants could significantly reduce the need for chemical fertilizers, this has been successfully tested using numerous procedures, documented in a series of peer-reviewed papers. The BioGro strains have been examined by a range of molecular and biochemical techniques, also providing means of quality control of inoculants. A positive response by rice plants to BioGro strains has been confirmed by proteomics. More than 20 randomized block design field experiments conducted in Vietnam or Australia have confirmed their effectiveness under a range of field conditions, reviewed here. Interactions with different rice cultivars have also been examined. While the response to inoculation is complex, the hypothesis of increased nutrient efficiency has been amply confirmed as consistent with observations. Finally, an extensive participatory research project over 3 years in the Mekong Delta showed reductions in fertilizer needs as high as 52 % as rice farmers learned to apply the technology. This result shows the importance of such adaptive practices for successful application of this biofertilizer technology in field condition.

Mycorrhizal symbiosis has an important impact on plant interactions with pathogens and insects. Direct competition has been suggested as mechanism by which arbuscular mycorrhizae (AM) fungi can reduce the abundance of pathogenic fungi in roots. Priming set the plant to an “alert” state in which defenses are not actively expressed but in which the response to an attack occurs faster and/or stronger compared to plants not previously exposed to the priming stimulus, efficiently increasing plant resistance. Thus, priming confers important plant fitness benefit thereby defense priming by AM has a great ecological relevance. With regard to its bioprotective properties, the mycorrhizal symbiosis has become a focal point of research as an alternative to chemical fertilizers and pesticides in sustainable agriculture. In this chapter, we summarize the information available regarding mycorrhiza-induced resistance (MIR) with special emphasis in those involving plant defense responses.

Phosphorous (P) is an essential macronutrient required for plant growth and development and comes next to Nitrogen (N). The quantity of phosphorous present in soil is huge but is unavailable to the plants due to its fixation with the other elements in soil necessitating the application of chemical phosphatic fertilisers to the soil for plant growth and development. Injudicious use of phosphatic fertiliser though has resulted in enhancement of crop yield but had left an adverse effect on the ecosystem. In the present scenario, to manage the nutritional security and the environment, sustainable agriculture holds the key which uses phosphate solubilising microorganisms (PSM’s) as an important alternative, which can solubilise soil phosphate and supply it to the plants in a more eco-friendly and sustainable manner. PSM’s are diversified in nature and are abundant in normal to stressed environments. They include bacteria, fungi, algae, actinomycetes and mycorrhizae which solubilises soil phosphate by different mechanisms including production of organic acids and enzymes, thus making phosphorous available to the plants for their growth and development. Molecular biotechnology brings out a better technique that could help researchers to understand the mechanisms responsible for solubilisation and also improve the performance of PSM’s by manipulating the genes responsible for phosphorous solubilisation for the betterment of crops and also in managing a sustainable environment system.