Industrial Applications of Soil Microbes

Microorganisms give life to the soil and provide a variety of ecosystem services to plants. Soil bacteria are the strongest candidates for determining soil health. Bacterial communities are important for the health and productivity of soil ecosystems. Therefore, we must have a thorough knowledge of the diversity, habitat, and ecosystem functioning of bacteria. In this chapter, we will discuss the functional, metabolic, and phylogenetic diversity of soil bacteria and highlight the role of bacteria in the cycling of major biological elements (C, N, P, and S), detoxification of common soil pollutants, disease suppression, and soil aggregation. This chapter also underlines the use of soil bacteria as indicators of soil health. We have concluded the chapter by taking note of the present agricultural practices that call for concern regarding the natural soil microflora and steps to return biological activity to the soil. 

The increasing need for environmentally friendly products or substances is driving the use of metabolites based on beneficial microorganisms. Soil is essential for the maintenance of biodiversity above and below ground. Millions of microorganisms live and reproduce in a few grams of topsoil, an ecosystem essential for life on earth. Moreover, microorganisms are capable of producing chemical compounds that have not been synthesized in the laboratory or can only be processed with considerable difficulty. Not only do these soil microflorae play a significant role in the conservation of soil quality, but they also play a vital role in biomedical, pharmaceutical, and industrial applications. In this chapter, we address recent advances in the industrial manufacture of chemical products by microorganisms. 

This chapter deals with the significance of soil microbes from an industrial perspective. Soil microbes are the most diverse populations to exist on earth, and they are known to have played a prominent role in the development of soil chemistry, soil texture, and soil suitability to sustain plant life. The chapter deals with the significance of cultural techniques for the isolation of desired microbial strains from the soil. The importance of screening techniques for isolates is emphasized, wherein the potential strains are tested for their physiological characteristics that are industrially beneficial. A few criteria are mentioned for judging the soil isolate’s capability to become an industrial strain. The difference between natural isolates and potential industrial strains is discussed. Useful strains are categorized based on their ability to produce primary and secondary metabolites with commercial applications in terms of economic, agricultural, and environmental significance. Industrially important microbes are listed with emphasis on the types of metabolites they produce and their applications. Knowledge of metabolic pathways involved in metabolite production and their regulation in terms of various feedback control systems are discussed. Strain improvement and its role in improving industrial aspects of microbes are highlighted. Bacillus sp. are given their due importance as the most diverse and dynamic forms of bacteria, contributing immensely to our knowledge and being the most beneficial forms of soil microbes. A few metabolites are discussed in detail, with emphasis given to enzymes, microbial polymers, amino acids, solvents, organic acids, and antibiotics. Microbial bioleaching mostly employs bacteria that could help in the recovery of metals from low-grade ores, and industries based on biomining have shown a renewed interest in this economically viable process.

 Soil is the basic and important medium that supports plant and microbial communities for their growth and development. Soil, plants, and microorganisms interact in various ways in nature. The interaction between plants and microbes may be harmful or beneficial in the soil environment. The phytopathogens have harmful effects, whereas antagonists may have beneficial effects on the plant community. The antagonists are capable of controlling phytopathogens through different modes of action. The antagonists may be fungi, bacteria, or actinomycetes under the category of biological control agents (BCAs). Amongst the antagonists, the genus Trichoderma is considered a superstar and the most widely exploited biological control agent. Besides plant disease management, it has the potential to enhance vegetative plant growth and resistance against biotic as well as abiotic stresses. In the last couple of years, public interest has been switching from synthetic fungicides to non-chemical fungicides in the agricultural sector. In such a situation, Trichoderma spp. could be an ideal option with zero harm to the ecosystem and human health. In India, there are hundreds of manufacturers and marketers of Trichoderma products. The majority of its products are available in the form of wettable powder (WP) formulations with variable active ingredients, whereas liquid formulations are very rare. Its formulations are mainly used to manage soil-borne fungal phytopathogens such as species of Fusarium, Pythium, Phytophthora, Rhizoctonia, Verticillium, etc., of cereals, pulses, vegetables, fruit, and plantation crops. It can also control certain air-borne fungal phytopathogens such as species of Alternaria, Curvularia, Colletotrichum, etc. It has great scope in the organic agriculture scenario, and its usage in the crop production system has been increasing day by day. The dose of its application for different crops, diseases, formulations, and manufacturers is variable. However, it should, like synthetic fungicides, be uniform to avoid unnecessary confusion and hesitation among the end-users. 

The effects of climate change on crop yields vary greatly from region to region across the globe. The projected climate change will also adversely affect soil quality by changing its physiochemical and biological properties. The soil's biological properties and processes are primarily mediated by microbial diversity and their distribution. The presence of soil microbes facilitates the production of greenhouse gases (GHGs). The microorganism also responded to global warming and climate change by either producing greenhouse gases or utilizing them in the environment. Soil microorganisms can recycle and transform the essential elements such as carbon and nitrogen that make up cells. Even small changes in the soil moisture content result in a change in the microbial habitat, particularly the fungal communities. However, the bacterial communities remain intact. The increase in the concentration of greenhouse gases like carbon dioxide not only increases methane production from the soil but also reduces the uptake of methane by up to 30% in the soil microbial population. The microbial communities of the tree leaves act on plant residue during this process. The increase in temperature is likely to accelerate the rate of decomposition that emits carbon dioxide from the soil. However, higher temperatures also elevate soil nitrogen levels, which suppresses the rates of fungal decomposition. This affects microbial communities. At the same time, trees and shrubs that advance towards the north in the tundra under the influence of temperature alteration can also influence microbes in unknown ways through the shadows they cast on the ground. 

Climate change is one of the minacious threats that is affecting agricultural production and food security the most. Agriculture is significantly involved in contributing to global warming with the use of chemical fertilizers. Soil microorganisms play an important role in several ecological processes in soil, such as the cycling of nutrients, nitrogen fixation, nitrification/denitrification, decomposition of organic matter, and mineralization/immobilization. These processes, carried out by microorganisms, are one of the most important components of organic farming. Climatic shifts are causing floods, droughts, and unseasonal rainfall and are showing potentially devastating effects on agricultural yields. Hence, there is an urgent need to develop strategies to make our farming systems more resilient to the consequences of climate change. This chapter presents the synergistic advantages of organic farming and the role of soil microbes, which could be effective climate change adaptation strategies for the agriculture sector, and will give information on the importance of soil microorganisms in organic farming. 

A microorganism is a term given to small living beings whose size is measured in microns. Bacteria, fungi, algae, and protozoans are a few of them that reside in the air, water, and soil. This review is about the microorganisms found in soil. These microorganisms have different functions in soil decomposition of dead organic matter, such as ecological food web balance, and making nutrients available to plants. Recently, their role in alleviating different abiotic stresses like salinity and drought has been marvelous. These microbes are also being used in biopesticide form, which is environmentally friendly and safe for other living organisms. Bacteria convert the inaccessible nutrients from dead matter into usable forms. Actinomycetes give off the typical smell of soil, and these microorganisms are also being used as a source of therapeutic medicines. Fungi are helpful in the way that they break down impossible nutrients, which are then available to other microbes. They also colonize plant roots and thus aid in plant growth. Algae promote submerged aeration as their photosynthesis is faster and adds more oxygen. Algae also help prevent the loss of nitrates that help in building soil structures by promoting the weathering of rocks. Nematodes help maintain the ecological equilibrium of their habitat. Viruses are the mode of gene transfer between organisms in the soil. Thus, these microorganisms have different functions in the soil to maintain the soil's structure and the balance between the environment and its living beings.

With the increasing population of the world and the daily life demands supplied through industries and modern industrialized agricultural systems, the need for the preservation of ecosystems is increasing day by day. Many industrial processes result in large amounts of organic waste as well as inorganic contaminants that deteriorate food and water quality. Immediate measures to avoid the negative impact on the environment are necessary. The generation of large quantities of hazardous materials in the form of heavy metals, radioactive substances, phenolic compounds, and volatile organic chemicals has resulted in the requirement for new and environmentally safe methods for their elimination. In situ degradation of hazardous organic materials by microbes is often the most cost-effective clean-up approach. Biological treatment of these hazardous wastes is potentially effective, practical, and economical. Bioremediation is measured as one of the safer, cleaner, cost-effective, and eco-friendly technologies for decontaminating sites. It uses numerous agents such as bacteria, yeast, fungi, algae, and higher plants as its main tools in treating oil spills, pesticides, radionuclides, polluted groundwater, and heavy metals existing in the environment. Currently, different methods and strategies are being applied in different parts of the world. Phytoextraction, biostimulation, fungal bioremediation, and rhizofiltration are some of the more common ones. Because of specific applications, all bioremediation techniques have their advantages and disadvantages.

Bioremediation is a prominent and novel technology among decontamination studies because of its economic practicability, enhanced proficiency, and environmental friendliness. The continuously deteriorating environment due to pollutants was taken care of by the use of various sustainable microbial processes. It is a process that uses microorganisms like bacteria and fungi, green plants, or their enzymes to restore the natural environment altered by contaminants to its native condition. Contaminant compounds are altered by microorganisms through reactions that come off as a part of their metabolic processes. Bioremediation technologies can be generally classified as in situ or ex situ. In situ bioremediation involves treating the pollutants at the site, while ex situ bioremediation involves the elimination of the pollutants to be treated elsewhere. This chapter deals with several aspects, such as the detailed description of bioremediation, factors of bioremediation, the role of microorganisms in bioremediation, different microbial processes and mechanisms involved in the remediation of contaminants by microorganisms, and types of bioremediation technologies such as bioventing, land farming, bioreactors, composting, bioaugmentation, biofiltration, and bio-stimulation.

Pedogenesis, or the formation of soil, takes decades along with a combination of parent geological material, natural biota, distinct climate, and topography. Soil, which hosts rich functional biodiversity ranging from microbes to higher plants, provides nutrients, anchorage for roots, holds water, and buffers against pollutants. After going through this chapter, readers will be able to appreciate how nature takes care of the nutritional requirements of its dwellers, how these nutrients, in turn, get transformed following the life-death cycle, and the infallible role that soil microbes play in this process. We aim to describe how the enormous but biounavailable nutrient sources, both in the atmosphere (nitrogen) and the earth’s crust (phosphorus, iron, etc.), are made accessible to plants in a multi-step mechanism. Curiosity and concern among mankind have provoked a wide range of scientific developments. Nevertheless, exploitative anthropogenic activities have degraded this vital life-supporting component. All kinds of pollutants and unsustainable agricultural practices over time have deposited harmful and toxic chemicals in the soil, the negative effects of which are being deliberated lately. Soil microbes hold promise in remediating these xenobiotic compounds and providing economically feasible and ecologically safe solutions. In the final section, we provide a brief overview of the ability of microbes to utilize a range of substrates that can prove detrimental to both modern infrastructure and archaeological artifacts. 

The use of nitrogen in an efficient way in agriculture has economic as well as environmental challenges. Bio-fertilizers and green manures are eco-friendly and economical sources for enhancing nitrogen use efficiency (NUE) for sustainable agriculture. In the era of climate change, conjunctive application of both bio-fertilizers and chemical fertilizers is required for soil health and sustainable yield as well. Azolla is one of the Biofertilizer that has the potential to fix nitrogen biologically, increase nitrogen recovery and enhance the rice yield. The regular application of Azolla significantly increases soil organic nitrogen content, which is much more beneficial than inorganic nitrogen. Azolla possesses the potential to mitigate major problems that are of global concern and can be used as a multi-faceted biofertilizer. Usage of Azolla in agriculture has various advantages as it has a positive impact on enhanced productivity and reduces input costs. They are also involved in the bioremediation of heavy metals and several toxic pollutants. Hence, it possesses great potential for its usage as a biofertilizer in the era of climate change.

Pomegranate and guavas are two important commercial fruit crops grown in India. These fruit crop plants can be attacked by insect pests, plant pathogens, and plant-parasitic nematodes, which can reduce the quality and quantity of fruit production. Diseases caused by plant-parasitic nematodes are of great economic importance. Many species of plant-parasitic nematodes are found associated with pomegranates and guavas. Root-knot nematodes, Meloidogyne incognita and M. javanica are among the economically important nematode pests of pomegranates in the world as well as India. In India, these nematodes are a serious problem in Maharashtra state. Guava orchards are facing symptoms of sudden decline and loss in productivity due to heavy infestation of a highly pathogenic species of root-knot nematode, M. enterolobii. The root-knot nematode is spreading to new areas through infected pomegranate and guava saplings. Management of this nematode is a challenge because of its polyphagous nature and ability to survive on weed hosts. Different scientific management strategies are discussed in this chapter. 

The coconut palms grown in homestead and plantation situations suffer considerable damage due to infestation by plant-parasitic nematodes right from the seedling stage. Many plant feeder nematodes have been reported from coconut. Economically, the most important key nematode pest in India is the burrowing nematode, Radopholus similis, a migratory endoparasite causing typical root lesions and rotting symptoms on tender roots. An extensive, widespread occurrence was recorded in Kerala, Tamil Nadu, and Karnataka, causing a 30% yield loss in the coconut cropping system. Root-knot nematode, Meloidogyne spp., the devastating nematode pest of vegetables, spices, medicinal and fruit intercrop/mixed crops under coconut cropping system, also caused significant yield loss. This chapter discussed symptoms caused by nematode pests and different management practices.

Biochemical interactions of nanoparticulate materials in the environment present a fairly complex situation due to a large number of available biochemical pathways. Insufficient knowledge about the interaction mechanisms involved means most of the experimental observations gathered are mixed up with ambiguous results. Taking the example of nanotechnology-enabled agriculture in the future, several beneficial impacts of green chemistry-based nanoparticulates (NPs) are expected to improve disease-tolerant crops with better yields. The critical issues involved in designing a plan of action in this context are briefly introduced in the present chapter after describing the agricultural bioorganisms and nanoparticulate species entering industrial plants on a large scale. This chapter aims to excite the imaginations of the readers by contributing to the future development of nanoagriculture. 

This document examines major economic issues for intellectual property rights protection (IPRs) in the context of the World Trade Organization (WTO). The idea is to look back on the establishment of TRIPS (trade-related aspects of intellectual property rights), which is an ongoing success of the Uruguay Round debate on free trade. This paper reviews the economic concept of harmonizing IPRs, drawing attention to economic theory and strong emerging evidence. The concept of linking IPR protection with trade in the context of the WTO is also being explored. Particular attention has been paid to the results of TRIPS on new agricultural and biotechnology innovations. The impact of IPR protection on promoting growth and development and the relationship between IPRs and other economic policies are discussed. This paper concludes with an analysis of the potential for more (or less) consensus related to IPRs in the current WTO negotiating cycle.