Industrial Applications of Soil Microbes

Mycorrhizae are mutualistic associations between plant roots and fungi, conferring several advantages to plants, improving their survival and growth even under harsh soil conditions such as drought, acidic pH, the presence of toxic compounds, low nutrient availability, the presence of soil pathogens, etc., and hence act as nature’s own biofertilizers. The importance of mycorrhizal associations is signified by the fact that almost all the plant species on our planet carry these associations at least for some part and typically for most of their life cycle. In this chapter, our focus is to provide undergraduate and graduate students with an overview of three different types of mycorrhizae, namely endo-mycorrhizae, ectomycorrhizae, and ectendomycorrizae, based primarily on their macro- and microscopic structures. Further classification of endomycorrhizae into vesicular arbuscular mycorrhizae (VAM), arbuscular mycorrhizae, orchid, and ericoid mycorrhizae and classification of ectendomycorrhizae into monotropoid and arbutoid mycorrhizae are based on further details of microscopic features and the fungal and plant species involved. This chapter also aims at providing the reader with an insight into the advantages conferred by the fungal partner to the plants and the accelerated use of these fungi as inoculants for various applications such as agriculture, afforestation, and reclamation of waste lands.

Mycorrhizae are mutualistic symbiotic associations between fungi and plants. Mycorrhizal associations are believed to be established between the Ordovician and Devonian periods. The mycorrhizal association is prevalent in almost all ecosystems with a high degree of host specificity. About 40,000–50,000 fungal species colonize the roots of nearly about 250,000 plant species. These symbiotic relations benefit associated plants by providing up to 80% of N and P and also help in plant growth and fitness by different mechanisms. A look into the recent literature suggests that mycorrhizal fungi are not only involved in improving crop yield but also increase the quality of products through the increase in antioxidants, vitamins, and essential trace elements in plants. Due to eco-friendly and sustainable aspects, widespread research and industrial applications of AM fungi are trending in today’s world. During recent years of urbanization and industrialization, the concentration of trace elements has increased in soil and water. Recovery of contaminated areas is very crucial as it may get into the food chain and the process is generally complex. For this, mycorrhizae have evolved as an efficient and sustainable aspect. Ecological restoration of mining sites using AM fungi is considered necessary and useful.

AMF displays significant positive effects, such as increased plant survival under unfavourable growth conditions, enhanced growth and nutrition, improved soil structure and quality, and greater plant re-establishment. Implementation of various molecular techniques and advanced scientific knowledge on AM fungal symbioses, mycorrhizal biotechnology has reached various application domains such as horticulture, agriculture, soil reclamation, bioremediation, gardening, landscaping, and other areas of the plant market.

Abiotic pressures interfere with plant growth and production. Climate change and agricultural stress, including the overuse of chemical fertilizers and pesticides, have worsened the effects of abiotic stress on crop yields and damaged ecosystems and their environment. There is an urgent need for environmentally friendly management techniques such as the use of arbuscular mycorrhizal fungi (AMF) to increase crop productivity. AMF is best accepted as a biofertilizer. Additionally, it is broadly believed that the inclusion of AMF provides plant tolerance to a variety of stressful conditions such as temperature, salt, drought, and metals. AMF can provide essential plant nutrients that can hold plants, resulting in enhanced growth and harvest under less stressful and oppressive conditions. The role of AMF as a biofertilizer may improve plant flexibility in a changing environment. Therefore, further research focusing on promoting and producing plant quality produced by AMF is needed. The current review provides an in-depth knowledge of AMF and its impact on plants beyond the various stages of growth and, consequently, the importance of the relationship between different plant nutrients and AMF.

Mycorrhiza is the mutually beneficial relationship between a plant and a fungus colonizing its roots wherein the plant provides carbohydrates to fungi, in return Mycorrhizal fungal partner imparts several advantages to plants viz., making otherwise unavailable nutrients available to the plant, imparting resistance to diseases. It also has the potential to be used extensively not only for growth and yield but also for disease and insect control along with nutrient cycling, heavy metal assimilation, land reclamation, restoration and so on. The application of mycorrhizal biotechnology has great potential and can play an essential role in the restoration of degraded lands in many surface-mined areas. This chapter is an overview of the prospects, potential and possibilities of Mycorrhiza in agriculture, industry and other environmental applications.

The present investigation deals with the effect of six different species of mycorrhizal inoculation on the germination and growth of Lycopersicon esculentum Mill (Tomato). This experiment was conducted to observe the efficient VAM inoculation that would be beneficial for plant growth. Tomato occupies a prominent position in vegetables and is a commercially exploited crop. The local variety of tomatoes (1057) was inoculated with six different AM fungal inoculums in the germinating media. The germination percentage and plant vigour were increased by different VA mycorrhizal fungi. The minimum number of days taken for germination was observed by Glomus fasciculatum (6 days) followed by G. mosseae, G. monosporum, G. heterosporum, G. geosporum and G. multicaule (7 days). The highest germination percent was recorded with G. fasciculatum (96%) followed by G. geosporum (94.12 per cent) when compared to the control. The highest shoot height, root length, fresh shoot weight and the highest fresh root weight were recorded with Glomus fasciculatum compared to the control and other VA fungal species. Hence, it is concluded that AM fungi help in better seed germination by mutualistic symbiosis.

The existence of microorganisms in nature has been under speculation since ancient times, and they were exploited for beer and vinegar production long before anything was known about their existence. The scientific study of microorganisms began with their observation under the microscope in the 1670s by Antony van Leeuwenhoek. Louis Pasteur, in 1860, reported the first synthetic medium for microorganisms and introduced the biological concept of alcohol fermentation. The next phase started with the use of modern industrial fermentation, aiming for largescale aerobic fermentation facilities. Selected strains of yeast, Saccharomyces cerevisiae, are commonly used for the fermentation of commercial alcohols, namely wine, beer, and distilled liquor. Vinegar is prepared by allowing a wine to go sour with the aid of a specific microbe under controlled conditions. Cider vinegar is made from alcohol in fermented apple cider, whereas wine vinegar comes from grapes. Genetic alteration of microorganisms has been an important practice in many industries, including agriculture, the beverage industry, the pharmaceutical industry, etc. The prerequisites to a practical industrial microbiological process are the organisms, medium, and product upon which the whole gamut of production depends. The discovery of penicillin by Alexander Fleming in 1929 triggered an intensive search for antibiotics during the Second World War, and several other antibiotics were discovered. The wonderful activities of the microbial community are now exploited by industrial microbiologists to find suitable microorganisms for desired products such as antibiotics, amino acids, food products, enzymes, amino acids, vaccines, organic solvents, and other value-added products. The benefits of microbial activities are also widened commercially in other fields, like the agriculture sector, through biofertilizer and biopesticide preparations. Carrier based bio-inoculants are agriculturally useful in terms of nitrogen fixation, phosphorus solubilization, or nutrient mobilization, to increase the productivity of soil and crop. Most commercial biopesticides are of microbial origin and are primarily based on the Bacillus thuringiensis (Bt) microorganism. Potential microorganisms are exploited in many other sectors, from petroleum, mining, textiles, polymers, cosmetics, waste treatment, health care, and so on. Industrial production of citric acid is also accomplished by microbial fermentation using the fungus. Many microorganisms are capable of synthesizing bioactive L-optical isomers of amino acids from inorganic nitrogen compounds. Commercially useful enzymes are manufactured from microorganisms using 'immobilized enzyme technology'. Among the commercially available enzymes, proteases and amylases are produced in maximum quantities. Insulin is another very important pharmaceutical product, produced commercially by a genetically engineered bacteria. Recombinant (r-) DNA technology has been exploited in order to provide selective improvements in various specialties that include crop agriculture, pharmaceutics, gene therapy, vaccine design, and bioremediation. The technology has now become the mainstay of the pharmaceutical industry. Natural genetic engineering uses ‘forced evolution’ and ‘adaptive mutation’. Such ‘environmentally directed mutation’ can produce microbes with new biosynthetic capabilities. Extremozymes from extremophiles are becoming increasingly attractive as biocatalysts for industrial applications, particularly at high temperatures. However, a vast microbial world is yet to be examined for its efficacy towards new industrial products. So, research on industrially useful microorganisms has tremendous potential and a long way to go.

Soils are a rich source of biologically active industrial and medical compounds arising from microbial populations and their ecosystem services that comprise soil microbiome. The research of soil microbial ecosystems has supported the development of a complete knowledge of the earth's microbial community's (bacteria, archaea, lower and higher eukaryotes, and viruses) important role in repairing soil structure and function and making it active. Soil microbiome discovery has transformed environmental problems, agricultural productivity, bio-manufacturing and medical science. Soil microbes are an obligatory fundamental form of life affecting us in a variety of ways, helping as tools in industry and research. Soil microorganisms in the biosphere play a crucial role in supporting life in the face of increasing 21st century challenges such as soil fertility, food insecurity, epidemics, and a global energy dilemma.

Algae, fungi, mushrooms, protozoa, seaweeds, and, in particular, soil microorganisms now represent an unlimited source and ingredients used in pharmaceuticals for the manufacture of antibiotic compounds, in food industries for the advancement of human nutrition, in medication and beauty care products, in climate control, in the industry for the creation of fuel, chemicals, and other bioactive mixtures, and in research. A detailed knowledge of soil microorganism resilience might lead to new advances in agriculture, energy, healthcare, and the environment.

The major global challenge in the present scenario is to provide nutritional security to the growing population without affecting the ecosystem or the environment. Crop productivity mainly suffers because of various pests, diseases, and other problems caused by the use of pesticides during the management. Pesticide residue is now being considered as more detrimental to human health. Hence to overcome these biotic problems, the use of biological organisms such as arbuscular mycorrhizal fungi (AMF), Trichoderma spp., plant growth-promoting rhizobacteria (PGPR) and endophytes are gaining popularity to achieve sustainable agriculture. Still, many microorganisms should be identified in order to know their ecological significance. The proper selection and the application of the microbes have huge potential to safeguard our food and environment. Furthermore, novel and modern techniques like clustered regularly interspaced short palindromic repeats (CRISPR/Cas), transcriptomics, proteomics, genomics, etc., can be exploited for the sustainability of the crop ecosystem. The microorganisms can be improved by gene engineering techniques, which will improve the overall health of the plants. Thus, this chapter presents a brief overview of recent trends in the application of various microbial interactions with the twenty-first century technology for crop productivity and the overall sustainability of our agricultural ecosystem for our future generation.

Endophytes are considered all microorganisms present within plants that can be cultured in suitable media (MEA, PDA). In addition to mutualistic and commensalistic symbionts, endophytes could include latent pathogens, latent saprotrophs, and early stages of colonization by mycorrhizal fungi and rhizobia. Endophytes inhabit the interior of plant tissues, causing no harm to the host and do not develop external structures, excluding in this way modulating bacteria and mycorrhizal fungi.

The intimate relationship between endophytic microorganisms and their hosts involves co-evolutionary processes and may influence the physiology of the plant and also interfere with the presence of other endophytes. This endophyte-plant interaction may have been naturally selected during long climatic changes thus allowing a great genetic variability in endophyte populations that open perspectives for the discovery of improved or new enzymes, drugs, and other products with new and useful properties. In this chapter, endophytes, their ubiquitous occurrence, transmission, techniques of isolation, molecular characterization, biodiversity evaluation and future directions for endophytic exploitation have been focused. In the literature, examples have been summarized that show the functional significance and importance of endophytic fungi and bacteria.

Recent studies have demonstrated that these endophytes can be used as vectors to provide new characteristics with biotechnological interest to the host plant. In this aspect, endophytic fungi can be genetically modified and express heterologous genes. They can be used to control pathogens, promote plant growth and produce vitamins, amino acids and vaccines inside the host plant. Therefore, it is extremely important to look at endophytes as microorganisms with biotechnological potential besides their biological role.

Medicinal plants have been known for their therapeutic properties for centuries, as they are rich in uncountable and valuable phytochemical compounds. Synthesis as well as different biological aspects of such compounds in plants increases many folds in association with endophytes. These microbial endophytes reside in host plants without causing any symptoms of infection so they are gaining the attention of researchers for research in many fields such as in agriculture, medicines, environmental studies, etc. In the recent development of research, the medicinally important family Zygophyllaceae has a limited extent of microbial endophytes’ specificity. Very limited studies have been conducted on bioactive compounds isolated from endophytes and their role in health-related benefits. Therefore, this article presents a review of the evaluation of endophytes studied in plants of Zygophyllaceae for the study of bioactive compounds along with various biological activities. This review article will prominently contribute to the exploration of endophytes from medicinal plants of Zygophyllaceae as a source of bioactive and chemically novel compounds.

Antibiotics are low molecular microbial metabolites that have been used since the 1950s to control bacterial diseases of high-value horticulture and ornamental plants. Bactericidal and bacteriostatic antibiotics were used in agriculture. Although antibiotics were produced primarily for the medical profession and their use was limited by cost, some experiments were conducted soon after they were first produced commercially to determine their effectiveness in the control of plant diseases. In present days, streptomycin and oxytetracycline antibiotics are the most commonly used bacterial disease management in plants. The effectiveness of antibiotics is influenced by a number of factors including antibiotic concentration, method of application, temperature and humidity in addition to host and pathogen factors. The prolonged application of antibiotics in an inappropriate manner is triggering the problem of antibiotic resistance depending on the modes of action, structures, and functional and biochemical properties of antibiotics. A variety of antibiotic resistance mechanisms were expressed in various genes present in pathogens which encode some specific types of enzymes to alter antibiotics into being non-toxic. The main mechanisms of antibiotic resistance were expressed in targeted pathogens by various means of mutation, modification, and replacement of various genes and target sites of antibiotics. The rational use of antibiotics is one of the key approaches to increasing the efficacy of antibiotics and prevention of resistance in future for the bacterial disease management. 

Proteases are degradative enzymes, which catalyze the total hydrolysis of proteins. Advances in analytical techniques have demonstrated that proteases conduct highly specific and selective modifications of proteins such as the activation of zymogenic forms of enzymes by limited proteolysis blood clotting and processing and transport of secretory proteins across the membranes. The main sources of proteases are animals, plants, and microbes. Proteases from microbial sources are preferred to enzymes from plant and animal sources since they possess almost all the characteristics desired for their biotechnological applications. Proteases are further categorized as serine proteases, Aspartic proteases, cysteine proteases or metalloproteases – depending on their catalytic mechanisms. Moreover, proteases are also classified based on their pH –being acidic, neutral or alkaline proteases. Microbial proteases have numerous applications in different sectors like leather, detergent, food, photographic industry, etc.

Plant and animal diseases continue to pose a significant and long-term shortage of food, food hygiene, foreign business, bio-diversity, and the ecological system. Numerous questions, such as global warming, regulatory developments, changes in the geographical size and concentration of farm animals’ assets, and increased trade, create this an excellent time to assess the level of research on disease effect and biocontrol product management and control. This paper examines the rationale for conducting an integrative study to investigate the management practices of contagious plant and animal diseases. Finally, the organisation of the content under this chapter provides a picture of current plant and animal diseases.

Lack of sustainability in agricultural production owing to the gradual deterioration in soil health is emerging as a major concern in Indian agriculture. This behavior has largely been attributed to over-dependence on mineral fertilizers and limited use of organic matter during the last several decades. To come out from this situation, the necessity of larger incorporation of organic materials in the agricultural soils is being emphasized at different levels. Since the availability of traditional organic manures is gradually reducing in the country, while a plentiful amount of wide ranges of biodegradable organic waste materials are being generated every day, growing attention is now being paid to the recycling of these wastes as organic manures for improving the health conditions of our arable soils. However, most of these organic wastes cannot be directly added to the soils due to some limitations in their chemical as well as biological properties and, therefore, adoption of various composting processes is being suggested for this purpose. With the present thrust and encouragement from the Government on waste recycling under the “Swachh Bharat Yojna”, a good number of small and medium-scale industries have come up in this composting sector and many more are in the pipe line. Now, composting is basically a process of microbiological degradation of various organic materials to form humified end products along with the release of various nutrient elements. Hence, for successful implementation of any waste management program through composting, a thorough knowledge of the roles of various microorganisms in the decomposition of varying natures of organic wastes, their behaviors, successions, relative efficiency levels, etc., need to be understood thoroughly. In this article, various aspects of composting microbiology have been discussed with special reference to the occurrence and behavior of different microbes during the process of composting. Several aspects like the relative efficiency of the microorganisms in degrading varying components of organic wastes, microbial acceleration of composting, biological fortification of compost quality, etc., have been discussed to provide a gross idea for efficient microbiological management of the composting process. 

Plant-parasitic nematodes (PPNs) are a serious threat to the quantity and quality of many economic crops around the world. As a result of rising dissatisfaction with the hazards of chemical nematicides, interest in microbial control of PPNs is developing, and biological nematicides are becoming an important component of ecologically acceptable management strategies. Bionematicides can be employed in integrated nematode management (INM) programs to maximize their benefits, with techniques that make them complementary or superior to chemical nematode control approaches. This is especially relevant in integrated pest control systems because bionematicides can operate synergistically or additively with other crop inputs. bionematicides and other pesticides should be used in a more coordinated manner. This is especially relevant because numerous bionematicides are already or will soon be commercially available. It is still necessary to identify research objectives for using fungal and bacterial nematicides in sustainable agriculture, as well as to get a better knowledge of their ecology, biology, mode of action, and interactions with other agricultural inputs. As a consequence, utilizing a microbial nematicide from the stated category as a plant-parasitic nematode biocontrol agent is a viable long-term biocontrol technique in agriculture.

Several plant viruses infecting temperate fruit crops are extremely infectious and have devastating effects on the host trees. They all have a significant effect on yield and yield-related efficiency. Others cause a slew of problems, necessitating a large sum of money to save these infectious diseases from wreaking havoc. Yield and other economic losses are the most visible manifestations of this effect. These viruses cause economic loss to the farmers/producers and consumers by affecting plant growth and reproduction, causing sterility, yield and/or quality reduction, increased susceptibility to other stresses, crop failure, loss of aesthetic value, quarantine, and the need for eradication of the infected plants, thus increasing the cost of control measures as well as detection programs. Since future yield and risks are so unpredictable, losses incurred by any viral disease cannot be calculated explicitly. Experimental evaluation of the losses due to viral diseases is difficult because the infection of safe, controlled plants is rarely possible, and inoculations under vector-proof conditions do not adequately represent what occurs in natural conditions. Viruses are also unusual, and their structures are deceptively simple. However, this simplicity leads to a stronger reliance on the host, and the two have a complicated relationship. This complicates plant-virus management strategies as well as the damage caused by them. Plant virus control systems rely on our knowledge of the virus-vector/host relationship and will remain one of the most difficult tasks faced by plant virologists, growers, and nurserymen in the future.

Mushrooms are fleshy or macro fungi, belong to a special group in biological science, the Mycota and their descriptive science is called Mycology. Mushrooms have considerable interest in the most important civilizations in history because of their sensory characteristics. They have been recognized for their attractive culinary attributes. Presently mushrooms are common valuable foods because they have low calories, carbohydrates, fat, and sodium and are cholesterol-less vegetables. Besides, mushrooms have important nutrients, and are rich in selenium, potassium, riboflavin, niacin, vitamin D, proteins, and fiber. Mushrooms have healing capacities and many properties of traditional medicines. They act as anti-fungal, antibacterial, immune system enhancers and cholesterol-lowering agents, and also are an important source of bioactive compounds. Due to the presence of these properties, a variety of mushroom extracts are used to promote human health and are found as dietary supplements. It has been reported that mushrooms have beneficial effects on health and are a good source of treatment for some diseases and disorders. Some of the nutraceutical properties in mushrooms are seen in the treatment of hypertension, high risk of stroke, Alzheimer’s, in reducing the likelihood of cancer invasion and metastasis due to anti-tumoral attributes. Although there are a number of mushroom varieties having nutritional and nutraceutical properties, mostly are collected from nature (wild), whereas a few are cultivated on marginal and commercial label. Agaricus bisporus, species of Lentinula (Lentinus), Volvariella, Pleurotus, Calocybe, Auricularia, Flammulina, Ganoderma, Schizophyllum, Trametes and few others are among cultivated varieties in India and abroad. Considering the tremendous nutritional and medicinal qualities of different groups of these fleshy fungi, the cultivation of different varieties of mushrooms is increasing globally day by day. 

Size and surface modifications of a nanoparticle (NP) make it easy to cross several physiological barriers and mix with the transport of numerous bio-actives not only to selectively interact with different molecular species but also adopt characteristic pathways depending upon their physicochemical properties. Successful realizations of these possibilities associated with the development of biomedicines have already been realized in several cases published recently. Drawing a parallel from these observations the next question is whether similar possibilities can be availed in the case of agricultural crop management, especially with an eye on improving crop health to meet the global need for food security without any adverse effect on the natural ecological balance. The interaction space of nanoparticulate species, prepared separately, is more heterogeneously complex due to additional contributions from the ecosystem.

For appreciating the numerous advantageous applications of the NPs in crop health management, first, it is necessary to know about the constituents of the soil including bio-organisms that facilitate supplying adequate micronutrients to the plants through their roots along with the coexistence of various families of fungi and pathogenic species. In this chapter, an attempt has been made to examine the interactions of numerous types of metal-NPs on the populations of fungi and bacteria at molecular levels for using the relevant interactions to improve plant health, growth, and yield with adequate protections from harmful species also present there. The experimental assays made ex-situ and in-situ in simulated models as well as actual cases of different crops are included in the descriptions to provide a more integrated understanding of the interactions involved. The contributions from very recent reviews already published are acknowledged duly for providing input for the discussions regarding the prospects.

Sustainable farming is an emerging trend in recent decades to improve ecosystem health. However, little is known about to what extent and how this process affects the taxonomic diversity and functional capacities of above-ground microbes. Consequently, a metagenomics approach was applied to investigate how agricultural management practices, including organic, and conventional management, govern the structure and function of soil microbial communities. In a metagenome analysis, farming practices are strongly influenced by taxonomic and functional microbial diversity, and interactions of microbes. In agricultural soil, the most complex microbial network was observed that can be used for bioinoculant production and their applications for bioremediation of contaminated agricultural soil, indicating a strong resilience of the microbial community to withstand environmental stresses.

The metagenomics of soils can provide an assessment of the largely untapped genetic resources of soil microbial communities independent of cultivation for bioinoculant production. Novel biomolecules and genes have been identified by this approach. It also helps to study the metabolism of microorganisms that change in response to different environmental conditions. This chapter describes the use of these novel tools in the exploration of soil microbiota and its use to innovate new farming practices for a sustainable environment.

Soil microbial communities are the most complex of any other microbial communities. Methods based on sequencing remain the most effective way to analyze soil metagenomes. Future strategies to overcome this difficulty include comparative sequence analysis using soil metagenome sequences to identify microbial enzymes and novel bioactivities. The Metagenomics approach provides benefits over the restrictions of culture-dependent procedures along with the study of the community structure and function of microbes in the soil.