Industrial Applications of Soil Microbes

The symbiotic association between green plants and fungi is called mycorrhiza. The plant makes organic products by photosynthesis and supplies them to the fungus, and the fungus from the soil supplies water and mineral nutrients, such as phosphorus, etc., to the plant. These fungi establish a mild form of parasitism, a form of mutualism, where both the plant and the fungus benefit from the association. Mycorrhizal fungi are soil fungi that play an important role in plant growth, protection of plants from pathogens, and improving the quality of the soil. Abiotic components and living communities of soil and soil organisms, particularly microbes, can have direct and indirect impacts on land productivity. Direct impacts are those where specific organisms affect the crop yield immediately. Indirect impacts that affect the functions include those provided by soil organisms participating in carbon and nutrient cycles, soil structure modification, and food web interactions that generate ecosystem services that ultimately affect plant productivity. Selected organisms from different functional groups, like microsymbionts (symbiotic fungi, bacteria, etc.), decomposers, elemental transformers, soil ecosystem engineers, soil-borne pests and pathogens, and micro regulators, are used to illustrate the linkages between soil biota and ecosystem processes. There are various groups of fungi that form different types of symbiotic associations with almost all groups of plants, from bryophytes to seed plants, i.e., gymnosperms and angiosperms, on the earth. Out of the seven types of mycorrhizae (ectomycorrhizae, ectendomycorrhizae, ericoid mycorrhizae, arbuscular mycorrhizae, orchidoid mycorrhizae, arbutoid mycorrhizae, and monotropoid mycorrhizae), the endomycorrhizae (arbuscular) and ectomycorrhizae are the most abundant and widespread. The molecular basis of nutrient exchange between ectomycorrhizal and arbuscular mycorrhizal fungi and host plants proved the role of mycorrhizal fungi in disease control, the alleviation of heavy metal stress, and increasing production in sustainable agriculture, horticulture, and forest plants or trees, etc. Arbuscular mycorrhizal fungi play a major role in the restoration of native ecosystems, and mycorrhizae transform a disturbed ecosystem into productive land. Ectomycorrhizae play an important role in forestation, forest ecosystems, and horticultural systems, and they maintain monodominance in tropical rainforests. Apart from the nutrient benefits to the plants,the mycorrhizae are presently employed in the colonization of barren soil and improving the transplantability of forest plants. Mycorrhizae create resistance against insect pests, various root diseases, toxicity, and reduced susceptibility in plants. The presence of mycorrhizae also favours the growth of beneficial microbiota, converting the rhizosphere into a mycorrhizosphere and increasing tolerance to adverse conditions like drought, salinity, and stress in the plants.

The role of fungi, particularly those selectively colonizing the root surfaces of growing plants, in increasing the availability of phosphorus has received scanty attention. The fungi arbuscular mycorrhiza (AM) has many beneficial effects on plant growth, including enhanced nutrition, improved plant growth, and better biotic and abiotic stress tolerance. Moreover, by improving the soil properties, the hyphal networks of these AM fungi will minimize the risk of water and wind erosion. This potential of AM fungi encourages a flourishing industry of AM-related substrates, mainly in the plant production and landscaping sectors. Although the potential benefits of AM fungi for some crops have been well documented, more research is needed to determine their suitability for other crops. The various aspects, which are fully reflected in this chapter, are mycorrhiza-history, classification, mode of action, crop specificity, AM production technology, quality standards, and methods of analysis, along with future opportunities for AM application.

Over the past few decades, the growing body of research on mycorrhizal fungi has been exploring their roles in maintaining and enhancing a wide range of ecosystem functions. These functions include, and are not limited to, maintenance of soil health, plant nutrition, removing hazardous contaminants from soil, prevention of soil erosion, and suppressing pathogens in the soil. As a result, mycorrhizae offer great potential as ecosystem engineers, capable of meeting various objectives of sustainable agriculture, forestry, ecological restoration, and biodiversity conservation. In this chapter, we attempt to offer an insight into the fascinating world of such mutualistic interaction, some of the benefits it offers to our planet, some of its industrial applications, and why it is imperative to integrate mycorrhizae into discussions for a more sustainable future. We consider various types of mycorrhizae present in our ecosystems and their defining features and differences. After all, we discuss some of the major roles they play in ecosystem functioning. We then explore a few facets of their industrial importance in biofertilization and phytoremediation, which are increasingly recognized globally. We also discuss the issues that hinder the full-fledged utilization of such a mutualistic interaction. In conclusion, we will look at new avenues of research that mycorrhizal research is poised to explore. This chapter will give the readers a holistic view of the exciting world of plant-fungal mutualism and trigger them to explore the growing body of work probing into such fascinating members of our ecosystems.

Weeds are a serious problem in agriculture, causing major losses in crop production. Chemical methods for weed control, including herbicide use, may have a harmful impact not only on untargeted plants but also on other beneficial organisms, such as arbuscular mycorrhizal fungi (AMF), which form with plant roots, one of the most widespread symbioses on Earth. AMF forms a profuse mycorrhizal mycelial network that explores and scavenges the soil for nutrients and water and links neighbouring plants, thus supporting the transfer of nutrients from one plant to another.

This chapter focuses on the interrelationships between weeds and cultivated plants through mycorrhizal networks, as well as on possible herbicide-mediated changes in fungal and plant communities. An overview of the influence of herbicides showing the different modes of action on the formation and functioning of arbuscular mycorrhizal (AM) symbiosis is given. Different issues, such as direct and indirect effects of herbicides on the abundance and diversity of AMF, impact and species-specific responses of AMF to herbicides, and other factors (i.e., mode of action, rate, application method) influencing the effect of herbicides on the abundance and diversity of AMF and AM formation are considered. The possible protective effect of AM symbiosis on crops due to alleviation of herbicide-mediated stress is considered, which could be an important clue for increasing herbicide efficiency. Indeed, in this sense, the use of modern molecular biological tools seems promising. 

Mycorrhizae are important mutualistic associations seen among the majority of terrestrial plants. The plant’s roots get infected by a specific group of fungi that enrich the plant in various ways. Though the degree of association varies from one plant to another, researchers and agricultural experts are well aware of the numerous benefits it imparts to the plant. In turn, the fungi gain a nutritional and niche advantage over the other microorganisms in the soil. The fungi involved in mycorrhizal association usually belong to the Ascomycetes or Basidiomycetes groups. Some of these fungi can form simultaneous mycorrhizal associations with multiple plant partners. The specificity and great beneficial aspects of mycorrhizal associations have been adopted to design strategies for increased yield of commercial crops.

Arbuscular mycorrhiza (AM), a symbiosis between plants and members of the Glomeromycota, an ancient phylum of fungi, boosts the availability of water and nutrients to the host plant, such as phosphate and nitrogen. In exchange, the fungus receives up to 20% of the carbon fixed by the plants. Arbuscules, symbiotic entities found inside plant root cells, are responsible for nutrient delivery. The formation of AM is accompanied by a signalling molecule exchange between the symbionts. Plant roots secrete strigolactones, a new class of plant hormones, which help in host recognition. In India, chilli (Capsicum annuum L.) is one of the most important commercial spice crops. After looking over the literature on chilli wilt complex disease, it appears that it causes a major constraint in production. The major diseases affecting chilli production are anthracnose, Phytophthora leaf blight, Fusarium wilt, bacterial wilt, damping-off, root rot, etc. Arbuscular mycorrhiza (AM) is well known for its plant growth-promoting efficiency and providing bioprotection against soilborne pathogens (bacteria, fungal and parasitic nematodes). Soil-borne plant pathogens are difficult to control by conventional fungicidal methods; therefore, an attempt was made to control the wilt of chilli by eco-friendly management. Increased and efficient use of mycorrhizal fungi may reduce the use of fertilizer.

 Mycorrhizae and plants have a well-established symbiotic relationship, and play an important role in better plant growth, disease protection, and improving soil quality. Arbuscular and ectomycorrhizae are the most common of the seven species of mycorrhizae described in the scientific literature (arbuscular, ecto-, ectendo-, arbutoid-, monotropoid-, ericoid-, and orchidaceous mycorrhizae). This chapter presents a summary of current knowledge of mycorrhizal interactions, processes, and potential benefits to society. The molecular basis for genetic exchange between arbuscular mycorrhizal (AM) fungi and host crops, the role of AM fungi in disease protection, in promoting plant growth, in reducing heavy metal load, and in increasing grain production, and their impact on sustainable agriculture are presented in this chapter. The impact of AM-fungal incorporation and beneficial saprophytic mycoflora on the promotion of plant growth and root colonization, the role of AM fungus in restoring indigenous ecosystems, and the impact of the mycorrhizosphere on multitrophic interactions have been summarized. The ways in which the mycorrhizae transform the disturbed ecosystem into productive land are discussed. The importance of restoring mycorrhizal systems in the rhizosphere is emphasized, and their impact on land reclamation and environmental remediation of polluted soils is also discussed. The importance of ectomycorrhiza in forest ecosystems, ectomycorrhizal association in tropical rain forests and their role in maintaining thermal monodominance, are briefly explained.

Mycorrhiza, meaning fungus root, is a typical example of an endophytic biotrophic and symbiotic relationship rampant in most cultivated and natural ecosystems. Mycorrhizal fungi are fungal species that are closely associated with plant roots, forming a symbiotic relationship resembling legume-rhizobium symbiosis with the plant providing carbohydrates for the fungi and the fungi providing mineral nutrients such as phosphorus and zinc to the plants. Mycorrhizae can enhance the growth of plant roots and even the whole plant system. In addition to nutrient transport, mycorrhizal associations can also impart considerable plant disease resistance against certain plant pathogens. Because of their greater surface area, mycorrhizae can improve plant vigour and soil quality. This chapter deals with the origin and evolution of mycorrhiza using paleontological evidence and phylogenetic analysis of its evolution and its agricultural and commercial applications. Mycorrhizae are important biofertilizers that improve plant nutrition and, thus, productivity by imparting tolerance and resistance to abiotic and biotic stresses and improving soil structure fertility and health and quality. 

The rhizosphere is the most active zone of soil and plays a significant role in soil health management. The rhizosphere concept is more than a century old and has played a pivotal role in understanding the mutual association of microbes and plants over that period. This has opened many interesting facts about wonderful plant-microbe associations. During these years, the concept has evolved from the rhizosphere to the phyllosphere and more recently, to the holosphere/holobiont level. The earlier understanding of how bacteria inhabit plants and, in particular, how bacteria feed plants, has greatly expanded. Recently, it has been observed that plants take bacteria inside their cells and use them as a source of nutrients (rhizophagy). This understanding has completely changed the dimensions of the rhizosphere concept, and we need to think more rationally to understand the bacteria-plant association during the coming years. This chapter covers the wonderful overview of soil-inhabitant bacteria with special emphasis on rhizobacteria in general and plant growth promotion for an enhanced yield of crop plants in particular.

Cyanobacteria continue to produce various biologically active compounds of antibacterial, antifungal, antifungal, and antiviral potential. These bioactive compounds also belong to the groups of polyketides, amides, alkaloids, fatty acids, indoles, and lipopeptides. In addition, these cyanobacteria often produce a broad spectrum of antialgal compounds that attempt to inhibit the growth of pathogens by inhibiting their metabolic and physiological activities. We all know that cyanobacteria were among the first microorganisms to live on Earth. Long ago, about billions of years ago, they played a major role in shaping the Earth into the planet we live on today, and they play an important role in a variety of functions in addition to our daily lives. Despite the small genome of cyanobacteria, marine cyanobacteria are also prolific secondary metabolite producers, along with being an essential source of atmospheric oxygen. With the ever-increasing human population and higher post-production waste emissions and increased use of fossil fuels based on food requirements, its concentration in the atmosphere is expected to increase steadily. Since most of the attention related to metabolite production has historically been focused on their freshwater counterparts, marine cyanobacteria present a relatively untapped resource in terms of evolutionary diversity and industrial potential. They are also producers of several complex secondary metabolites with potential applications in human health, biofuels, and bioengineering. 

The multifaceted potential of soil microorganisms is being exploited in various fields like agriculture, food and cosmetic industries, for the sustainability of the environment and in the industrial production of useful compounds. On the one hand, these microorganisms play an essential role in the nutrient cycling of minerals like phosphorus and nitrogen that are crucial for their survival and sustenance, along with making the soil fertile by releasing important growth-promoting hormones like ethylene, auxin, and cytokinin. On the other hand, the potential of soil actinomycetes like Dactylosporangium, Ampullariella, Actinoplanes, Actinomadura, and Actinosynnema is being explored extensively for the industrial production of new lifesaving antibiotics. Many of the enzyme producing species like Streptomyces ruber, S. lividan, and S. rutgersensis are used in supplements for detergents, textiles, animal additives, paper, and pulp. Xanthomonas produces xanthan gum, which is used to thicken and stabilize foods and cosmetics. Screening desired microorganisms and manipulating them to obtain maximum production is a crucial step in industrial production. Hence, it can be concluded that soil microorganisms are important for diverse metabolite production useful in agriculture and industry as well as having the capability to transform recalcitrant compounds to reduce environmental pollution.

Biocatalysis is also widely applicable for the enhancement of bioprocess productivity, selectivity of target reactions, and production of valuable chemicals, pharmaceutical ingredients, precursors, and key intermediates. The vast majority of such enzymes are of microbial origin and include dehydrogenases, oxygenases, hydrolases, transferases, and lyases. These enzymes may introduce minor molecule changes, such as the insertion of a hydroxyl or keto function or the saturation or desaturation of a complex cyclic structure. Microorganisms and cell suspension cultures of the plant are applied in biotransformations of steroidal drugs to generate high regio-and stereo-selective products. Studies of steroid modifications catalyzed by microbial or plant cell cultures represent a well-established research approach and methodology in biotechnology. Bioconversion can occur at a position of the steroid molecule that is rarely accessible to chemical agents; the molecule can function stereospecifically, and several reactions can be completed in a single biotechnological step.

The world faces new challenges every decade in the form of calamities, pandemics, and deadly diseases. The increase in the population and limited resources has led the human race towards many ailments that are incurable, but the potency of the human brain and in collusion with natural resources can reveal the remedy to many diseases. Cancer is one of the major reasons for mortality at present, which is a global challenge. The search for new anticancer drugs is a necessity of the present day. Researchers are urged to explore alternative and new potent sources of anticancer drugs. Natural sources include plant products or some plant-derived bioactive compounds. Endophytes manifest as an acceptable source of bioactive compounds of medicinal value. Endophytes are microorganisms present asymptomatically inside the plant parts. These are known to produce several metabolites with antifungal, antiviral, antioxidant, and anticancerous activity. Some major metabolites include taxol, alkaloids, camptothecin, chromones, etc. These produced metabolites can also be manipulated for the production of novel chemotherapeutic agents. The incessant need for these anticancer drugs has escalated the search for novel natural compounds. The present chapter attempts to summarize different endophytic metabolites that serve as an alternative source for an ailment of the deadly cancer disease.

Naturally occurring carotenoids’ demand is increasing because of their need in the pharmaceuticals, food, cosmetics, flavor, and animal feed industries. Extraction and synthesis of carotenoids are expensive and technically challenging. To fulfil the ever-increasing demand for the production of carotenoids, microbial production of carotenoids seems to be an attractive alternative to current extraction from natural sources. For carotenoid overproduction in microorganisms, metabolic engineering as well as synthetic biology strategies, have been extensively used to reconstruct and optimize pathways of carotenoid production. Modified and advanced strategies such as the novel and specific enzymes, protein engineering, target gene screening, and regulation tools should be used to improve carotenoid production. The applications of carotenoids, biosynthetic pathways of metabolic engineering of microbial carotenoid production, molecular breeding of carotenoids, and prospects of carotenoids are discussed in the present review.

Phytoparasitic nematodes are highly dangerous to the global agricultural production of a variety of crops. Chemical nematode overuse necessitates the creation of new nematode control strategies. Filamentous fungi could be a feasible biocontrol alternative in this case. Trichoderma, mycorrhizae, and endophytic fungi are the most common filamentous fungi studied and used as biological control agents (BCAs) against nematodes as resistance inducers. Several pathways have been linked to the biocontrol effect of fungi on plant-parasitic nematodes. Increased plant tolerance, direct competition for nutrients and space, induced systemic resistance (ISR), and altered rhizosphere interactions are all possible pathways. Several mechanisms, as well as a detailed discussion of their plausibility in the biocontrol of plant-parasitic nematodes, in particular, have been postulated. Mycorrhizal fungi are not yet widely utilized in conventional agriculture, but recent data is assisting in the development of a better understanding of the mechanisms of action. This will eventually lead to mycorrhizal fungi being used in the field to combat plant-parasitic nematodes.

Agricultural production is affected by both biotic and abiotic stresses. To increase production to meet the demands of the population (agrochemical products), pesticides are heavily used, which are toxic to the environment as well as to humans and animals, and also very cost-effective. For the development of sustainability in agriculture, minimum use of pesticides is recommended. In this context, microorganisms like endophytic fungi and bacteria are used to promote plant growth and productivity. Endophytic organisms live inside plant tissues and can improve plant growth under normal and challenging conditions. They provide benefits to host plants directly or indirectly by improving plant nutrient uptake, production of phytohormones, targeting pests and pathogens with antibiotics, hydrolytic enzyme production, and inducing plant defence mechanisms. This chapter elaborates on the beneficial uses of endophytic organisms in the agriculture system.