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Methylotrophic bacterial community is very important group of bacteria utilizing reduced carbon compounds and plays significant role in plant growth promotion (PGP), crop yield and soil fertility for sustainable agriculture. Abiotic and biotic stresses are very important factors affecting PGP in agriculture. A vast number of microbial communities play an important role in abiotic stress tolerance. The PGP methylotrophic microbes have been reported well enough to mitigate different types of biotic and abiotic stresses. The abiotic stress tolerance was well documented by several methylotrophic bacterial communities such as Hyphomicrobium, Methylarcula, Methylobacillus, Methylobacterium, Methylocapsa, Methylocella, Methyloferula, Methylohalomonas, Methylomonas, Methylophilus, Methylopila, Methylosinus, Methylotenera, Methylovirgula and Methylovorus. The abiotic stress tolerance ability of different methylotrophs and their colonization in different parts of plants under severe low temperature, high temperature, drought and salt stress conditions have been investigated in various studies. The methylotrophic communities help in proliferation of plant directly through solubilization of phosphorus, potassium and zinc, production of phytohormones viz., auxins and cytokinins; production of Fe-chelating compound, biological nitrogen fixation and ACC-deaminase activities or indirectly through productions of ammonia, siderophores and secondary metabolites. The auxin and cytokinin secreted by methylotrophs influence seed germination and plant root growth and help plants to endure water stress. On the plant surface, the abundant methylotrophs exude osmo-protectants such as sugars and alcohols which ultimately help to protect the plants from desiccation and excessive radiations. The utilisation of these potent methylotrophic strains may facilitate proper crop production, PGP by ameliorating abiotic stresses.

Industrialization and modernization of agricultural systems contaminated lithosphere, hydrosphere, and biosphere of the Earth. Sustainable remediation of contamination is essential for environmental sustainability. Myco-remediation is proposed to be a green, economical, and efficient technology over conventional remediation technologies to combat escalating pollution problems at a global scale. Fungi can perform remediation of pollutants through several mechanisms like biosorption, precipitation, biotransformation, and sequestration. Myco-remediation significantly removes or degrades metal metals, persistent organic pollutants, and other emerging pollutants. The current review highlights the species-specific remediation potential, influencing factors, genetic and molecular control mechanism, applicability merits to enhance the bioremediation efficiency. Structure and composition of fungal cell wall is crucial for immobilization of toxic pollutants and a subtle change on fungal cell wall structure may significantly affect the immobilization efficiency. The utilization protocol and applicability of enzyme engineering and myco-nanotechnology to enhance the bioremediation efficiency of any potential fungus was proposed. It is advocated that the association of hyper-accumulator plants with plant growth-promoting fungi could help in an effective cleanup strategy for the alleviation of persistent soil pollutants. The functions, activity, and regulation of fungal enzymes in myco-remediation practices required further research to enhance the myco-remediation potential. Study of the biotransformation mechanisms and risk assessment of the products formed are required to minimize environmental pollution. Recent advancements in molecular "Omic techniques"and biotechnological tools can further upgrade myco-remediation efficiency in polluted soils and water.

This chapter discusses the knowledge extreme microbiomes and their biotechnological applications. Extremophilic microbiome has a wide range of applications from bioremediation of toxic elements to production of biomolecules for industrial and medical purposes to an agricultural application. The potential applications of extremophiles have formed a great impact in the field of biotechnology which has been described. Extremophiles microbiome has been providing an extensive and versatile metabolic diversity with astonishing physiological capabilities to colonize extreme environments. Recently according to frontier work extremophiles are channeled to consider their peculiar electrology, and survival mechanism as well as physiology. Since the last two decades, the research data on extremophiles has increased exponentially as the enzymes extracted from the extremophilic microbiome have been shown in various industries such as biotechnological industries, diary textiles, detergent, food and beverages, leather pulp and paper and the pharma medicines.

The tiny organism of soil, known as soil microbes have several functional annotations like nutrients cycling and their fixation, mineralization and solubilization, alleviation of biotic caused by pest-insects, microbial pathogens as well as abiotic stresses by harsh environmental conditions, degradation of polluting elements in the environment. Their functional abilities can be utilized in the different fields of biotechnology i.e. environment and agriculture because these are one the best sustainable technique over others like conventional methods as already environment is heavily polluted by the activities of mankind. In agriculture, soil microbes can be used as a biofertilizer and biopesticides. Soil microbes as biofertilizers help in providing nutrients like nitrogen, phosphorus, potassium, zinc and iron. Along with nutrients, these microbes also help in releasing plant growth regulators that help in increasing plant development. These use various mechanisms like fixation, solubilization and scavenging (of iron) for providing nutrients. Soil microbes also help in alleviating biotic stress by releasing antibiotics, siderophores and hydrogen cyanide to kill unwanted or pathogenic pest and microbes. Such microbes can also be applied in the environment for various applications like alleviation stress, pollution which cannot be degraded naturally. The present chapter deals with the functional annotation and biotechnological applications of beneficial soil microbiomes for agricultural sustainability.

Fungi are an incredible group of organisms that are grouped under eukaryotes. The organism falls under the fungi was earlier viewed as damaging and pathogenic organisms that infect and kill plants and animals, but as the time flew and researches were being conducted, dark ages of fungi have fallen away and their benefits got the spotlight. Now days, this group of organism has been using in the fields agriculture, environment and industries. The fungal species ease the life of mankind have been distributed in the wide range of habitats including soil, water having moderate and extreme conditions like hypersalinity, extreme temperatures, pressure and heavy metals accumulated areas which were being used in the field of environment and industries. In environment, this group of organism can be applied for clean pollutants (heavy metals, oil, xenobiotics including DDT, pesticides, halogenated hydrocarbon and synthetic azo dyes) as they are good decomposer of pollutants of the ecosystem created by the human’s activity. On the other hand, fungi can also be applied in the industries as they have a capability of producing several types of extra-cellular digestion enzymes and secondary metabolites which can be used in the several foods, pharmaceuticals, textiles, detergents and paper and pulp industries. This chapter detailed the perspectives of fungi in the field of environment and industrial sectors.

One of the diverse groups of organisms after insects, fungi and its diversification are one of the debated topics among the mycologists because they are one important organism that plays various roles in the ecosystem. In the ecosystem, fungi exist in various environments like soil and water and in association with plants as well as animals in which they work as decomposers mainly. Earlier, fungi were under the black box and known as only pathogens but as the research was being conducted these organisms got the spotlight and began to be considered as beneficial. Nowadays, fungi are being used for industrial, agriculture, and environmental purposes like to make various products like dyes, medicines, and food; for protection and as nutrient provider; and for cleaning and removing harmful pollutants. In this chapter, the capabilities and their role in various fields have been explained.

Over the past few decades, the rapid development of agriculture and industries has resulted in contamination of the environment by diverse pollutants, including heavy metals, polychlorinated biphenyls, plastics, and various agrochemicals. Their presence in the environment is of great concern due to their toxicity and non-biodegradable nature. Their interaction with each other and coexistence in the environment greatly influence and threaten the ecological environment and human health. Furthermore, the presence of these pollutants affects the soil quality and fertility. Physicochemical techniques are used to remediate such environments, but they are less effective and demand high costs of operation. Bioremediation is an efficient, widespread, cost-effective, and eco-friendly cleanup tool. The use of microorganisms has received significant attention as an efficient biotechnological strategy to decontaminate the environment. Bioremediation through microorganisms appears to be an economically viable and efficient approach because it poses the lowest risk to the environment. This technique utilizes the metabolic potential of microorganisms to clean up contaminated environments. Many microbial genera have been known to be involved in bioremediation, including Alcaligenes, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Mucor, Penicillium, Pseudomonas, Stenotrophomonas, Talaromyces, and Trichoderma. Archaea, including Natrialba and Haloferax, from extreme environments have also been reported as potent bioresources for biological remediation. Thus, utilizing microbes for managing environmental pollution is promising technology, and, in fact, the microbes provide a useful podium that can be used for an enhanced bioremediation model of diverse environmental pollutants.

Microbial biotechnology is an emerging field with greater applications in diverse sectors involving food security, human nutrition, plant protection, and overall basic research in the agricultural sciences. The environment has been sustaining the burden of mankind since decades and indiscriminate use of the resources has led to the degradation of the environment, loss of soil fertility, and has created a need for sustainable strategies. The major focus in the coming decades would be on a green and clean environment by utilizing the plant-associated beneficial microbial communities. These beneficial microbial communities represent a novel and promising solution for a sustainable environment. Microbial communities possess a huge sink of mechanisms by which they act as biofertilizers, bioprotectants, and biostimulants as well as the alleviators of abiotic stress conditions. Thus, utilizing plant-associated microbiomes will surely support sustainable agriculture thereby reducing the production costs and environmental pollution. The present chapter exclusively concluded the horizon covered book content of microbial biotechnology for sustainable agriculture.

Endophytic microbes are known to live asymptomatically inside their host throughout different stages of their life cycle and play crucial roles in the growth, development, fitness, and diversification of plants. The plant–endophyte association ranges from mutualism to pathogenicity. These microbes help the host to combat a diverse array of biotic and abiotic stressful conditions. Endophytic microbes play a major role in the growth promotion of their host by solubilizing of macronutrients such as phosphorous, potassium, and zinc; fixing of atmospheric nitrogen, synthesizing of phytohormones, siderophores, hydrogen cyanide, ammonia, and act as a biocontrol agent against wide array of phytopathogens. Endophytic microbes are beneficial to plants by directly promoting their growth or indirectly by inhibiting the growth of phytopathogens. Over a long period of co-evolution, endophytic microbes have attained the mechanism of synthesis of various hydrolytic enzymes such as pectinase, xylanases, cellulase, and proteinase which help in the penetration of endophytic microbes into tissues of plants. The effective usage of endophytic microbes in the form of bioinoculants reduce the usage of chemical fertilizers. Endophytic microbes belong to different phyla such as Actinobacteria, Acidobacteria, Bacteroidetes, Deinococcus–thermus, Firmicutes, Proteobacteria, and Verrucomicrobia. The most predominant and studied endophytic bacteria belonged to Proteobacteria followed by Firmicutes and then by Actinobacteria. The most dominant among reported genera in most of the leguminous and non-leguminous plants are Bacillus, Pseudomonas, Fusarium, Burkholderia, Rhizobium, and Klebsiella. In future, endophytic microbes have a wide range of potential for maintaining health of plant as well as environmental conditions for agricultural sustainability. The present review is focused on endophytic microbes, their diversity in leguminous as well as non-leguminous crops, biotechnological applications, and ability to promote the growth of plant for agro-environmental sustainability.

A biofilm comprises any group of microbes (archaea, bacteria, cyanobacteria, diatoms, fungi, microalgae, protozoa) in which cells stick to each other. The cells within the biofilms produce extracellular polymeric substances (EPS) components, which are typically a polymeric conglomeration of extracellular polysaccharides, proteins, lipids, and DNA. The microbes in biofilm formations have been reported worldwide and belong to all three domain systems of life: archaea, bacteria, and eukarya. Microbial biofilms is an attractive field as these play very important role in different sectors including environmental, industrial, and medicine. Microbial biofilms have been focused on health and industrial sectors only, but now the role of the biofilms is greatly gaining attention in the field of agriculture for sustainable agriculture. Biofilms colonize soil, roots, and shoots where they facilitate proliferation in the desired niche as well as increase the fertility of the soil. Further, they play a significant role in improving the production of crops. There are even reports evaluating the plant growth-promoting attributes of microbial biofilms including antifungal activity as well as the production of ammonia, indole acetic acid, and siderophores, which have shown far better results when compared with individual microbes. With the advancement of biochemical and molecular techniques, knowledge of the structure and development of the biofilms has also increased, however, more research is still required. The association of microbes within biofilms with plant growth-promoting traits will surely prove to be superior bioinoculants to improve the productivity of the crops for sustainable agriculture.

Genetically varying, wild, traditional, or ancient food crops were nutritional-rich compounds such as micronutrients. But, nowadays, level of micronutrients has been declined and even some has been vanished from the food crops because farmers chose to grow more productivity of the crops and make more profits. The reduced amount of micronutrients in food crops causes micronutrient deficiencies or hidden hunger in human, which is one of the serious global threats that affect more than two million people worldwide. Hidden hunger can cause dangerous health conditions and diseases such as birth defect, cancer, cardiovascular disease, osteoporosis, neurodegenerative disorders, and many more. To overcome these issues, microbes-mediated biofortification is a new and promising option for the bioavailibity of nutrient to plants. Biofortification is getting more attention to increase phytoavailability of micronutrients, especially Fe, Zn, Mg, and Se, in the major food crops. Utilization of diverse types of microbes that promote plant growth is becoming an effective approach to substitute synthetic fertilizers, pesticides, and supplements. Microbes mobilize the nutrients by various mechanisms such as acidification, chelation, exchange reactions, and release of organic acids.

This chapter contains current knowledge of role of microbial biotechnology for sustainable biomedicine systems, which included the perspective of human microbiomes and other beneficial microbiomes and their biotechnological applications. The book deals about recent techniques and method used to study the beneficial microbiomes and their potential applications. The human microbiome plays a role in the maintenance of a healthy state in adulthood. With the increase in knowledge about gut microbiome functions, it is becoming increasingly more possible to develop novel diagnostic, prognostic and, most important, therapeutic strategies based on microbiome manipulation. The use of novel pharmaceuticals and nutraceuticals to modulate microbial colonization and development of a healthy gut microbial community in early childhood will support healthy adult human body functions and prevent the occurrence of several diseases. There is an increasing interest and demand for probiotics today, after a long history of safe use in fermented dairy products, due to greater recognition of its beneficial effects to the human gut health. The probiotic strains such as Bacillus, Bifidobacterium, Methanosphaera, Paralactobacillus, Pediococcus, Saccharomyces, and Streptococcus exhibit powerful antiinflammatory, antiallergic, and other important properties. Probiotics have demonstrated significant potential as therapeutic options for a variety of diseases, but the mechanisms responsible for these effects have not been fully elucidated yet. This chapter covered conclusion of book content of Trends of Microbial Biotechnology for Sustainable Agriculture and Biomedicine Systems: Perspectives for Human Health. The concluding remark envisioned the future beneficial microbes with the use of new biotechnological techniques with potential application in medical, industry, pharmaceutical, and other allied sectors.

Plants reveal diverse associations with microbes and the importance of these associations for growth and health of the plants is the area of focus of this study because the research on the role of microbes associated with the seeds mainly the seed endophytes is very limited. A great diversity of endophytic microbes has been reported including the species of Acidovorax, Aspergillus, Aureimonas, Bacillus, Chaetomium, Curtobacterium, Enterobacter, Fusarium, Kocuria, Leucobacter, Microbacterium, Micrococcus, Novosphingobium, Penicillium, Pseudacidovorax, Pseudomonas, Rahnella, Sphingomonas, Staphylococcus, and Trichoderma. Seed microbiome is surely a rich pool of diverse species with high genetic complexity, possessing capability of rapid evolution, further allowing responsive selection of additional functionality depending on the environmental conditions in which there is emergence of the seedling and hence the selected microbe may be used to deliver traits of interest to the host plants. This chapter deals with the diversity and distribution of seed microbes, endophytic lifestyle, i.e., mechanisms of colonization, the relationship that seed microbiomes possess with the flower microbiomes, the interactions that occur between bacteria and fungi in the root zone, endosphere, genes involved in the endophytic behavior.

Endophytes exist within the plant tissues without causing any harm to their host plants. Endophytic microbes have been conferred to provide various benefits to the host such as enhancing their growth rate, higher biomass, making the availability of the phosphorus, zinc, potassium, fixing atmospheric nitrogen, producing various phytohormones, provides tolerance to abiotic stresses. Thus, the interest in role of these microbiomes especially the seed-associated microbiomes is growing day by day as they play a very vital role in the life cycle of the plants. Seed microbiomes greatly influence the seed health, prepare them for germination, further also act as the founder of microbial communities of newly developed plants and very important, for multigenerational maintenance of these beneficial associations plants can use seeds as carriers of microbes. This chapter deals with the potential biotechnological applications of seed microbiomes in agriculture and allied sectors.

Plant microbiomes have profound effects on seed germination, seedling vigor, growth of the plants and development, nutrition, diseases, crop productivity, and soil fertility. The microbial communities associated with plant as epiphytic, endophytic, and rhizospheric influence their composition and activities in plant surrounding systems. The rhizospheric region is defined as the narrow zone in top soil which encompasses the root system and it has been known to be the hot spot for several microorganisms and is among one of the most complex ecosystems on the earth. Rhizospheric microbes that have been well-studied for their beneficial effects on the plant growth as well as health include nitrogen-fixers, phosphorus solubilizers and mobilizers, phytohormones producers, and biocontrol microorganisms. These mostly include the species of genera Arthrobacter, Azospirillum, Azotobacter, Bacillus, Burkholderia, Cellulomonas, Enterobacter, Erwinia, Flavobacterium, Gluconacetobacter, Klebsiella, Pseudomonas, Rhizobia, Serratia, Streptomyces, and Xanthomonas. Sustainable agricultural systems utilize the natural processes so as to attain adequate degree of output as well as the quality of food concurrently reducing the adverse ecological effects. There are numerous soil fertility factors which impart sustainability to agriculture by acting as the biocontrol agent of the soil-borne disease, along with enlarged activity of microbes in the soil that leads to the enhanced competition and parasitism within the rhizosphere. The use of the plant growth-promoting microbes in agronomy can support a decline in utilization of chemical fertilizers and can boost the crops’ productivity in an eco-friendly manner.

Fungi are known to produce a wide range of secondary metabolites such as pigments, antibiotics, vitamins, amino acids, and organic compounds that have several useful biological activities such as antifungal, antiinflammatory, antioxidant, antimicrobial, and anticancer and also have wide range of biotechnological applications in food, pharmaceutical, and cosmetic industries as well as in agriculture. Antibiotics such as β-lactam, cholesterol-lowering drug, lovastatin, and penicillin are some of the important fungal metabolites that have diverse biotechnological applications in pharmaceutical industries and in the field of medicine. On the other hand, several of these fungal secondary metabolites also have potentially harmful biological activities such as mycotoxins and phytotoxins. There are various biosynthetic pathways followed by the fungi to produce secondary metabolites such as β-lactam, cyclic peptide, diterpenes, diketopiperazines, polyketides, sesquiterpenes, and a combination of these pathways. There are wide ranges of fungal communities producing potentially important secondary metabolites including Penicillium notatum, Cephalosporium acremonium, Penicillium griseofulvum, Streptomyces griseus, Monascus purpureus, Micromonospora purpurea, Tolypocladium inflatum, Aspergillus niger, Aspergillus parasiticus, and Beauveria bassiana. The potential biological applications of secondary metabolites of fungi will be useful for sustainable development.

The endophytes from medicinal plants are important resources for discovery of natural products and bioactive compounds having the potential biotechnological applications in agriculture, industry, medicine, and allied sectors. Endophytes have been sorted out from all the parts of medicinal plant such as roots, stem, leaves, fruits, flowers, bark, scales, resin canals, and even from meristem. The medicinal plants which are known to be used since centuries as a substitute of medicine are a precious source for bioprospecting endophytes. The endophytic fungi such as Acremonium, Alternaria, Apiospora, Aspergillus, Aureobasidium, Bartalinia, Cephalosporium, Chaetomium, Chloridium, Choanephora, Colletotrichum, Cryptosporiopsis, Emericella, Eupenicillium, Eutypella, Eutypella, Fusarium, Gliocladium, Hypoxylon, Paecilomyces, Penicillium, Pestalotiopsis, Pseudomassari, Quercina, Talaromyces, and Trichoderma have been reported from different medicinal plants. These endophytic fungi have ability to produce the natural and potential bioactive compounds for different processes. The present chapter reveals the importance of endophytic fungi from medicinal plants as a source of bioactive and chemically novel compounds as well as its use in the pharmaceutical and agrochemical industries.

Plant pathogens and pest are one of the major destroyers of plants that affect the crop productivity. To control phytopathogens, various types of chemical is being used, which severely affects the environment. Agricultural beneficial fungi can be used as the biopesticides that can minimize the pesticides exercise and also help in reducing the attack of phytopathogens on plants. There are different kinds of mechanism used by fungi to restrict the pest and phytopathogens growth like siderophore production that limits the iron in soil that is not available for pathogens. Another mechanism is production of HCN, hydrolytic enzymes, antibiotics by fungi to control the several phytopathogens. This chapter discussed about the current research and future prospect of fungi that are agriculturally important and act as a biocontrol agent.

A biofilm is an assemblage, aggregation, or community of microbial cells bounded by a polymeric matrix comprising polysaccharides that are associated with an inert or biotic surface. Biofilm formation is a universal trait, exhibited by microbes, when growing attached to natural and artificial surfaces. Microbial biofilms are an attractive subject, due to their important roles in the different sectors including agriculture, environment, industry, and health. Biofilms in agriculture have acquired interest due to their immense possibilities in crop production, protection, and improvement through their role in colonization of surface soils, roots/shoots of plants, and enabling proliferation in the desired niche, as well as enhancing soil fertility. Biofilm-forming microbes have been reported worldwide and they belong to Gram-positive, Gram-negative species, cyanobacteria, archaea, fungi, and microalgae. The microbial biofilm formation has been reported by all three domain systems of archaea, bacteria, and eukarya of different phylum including Actinobacteria, Ascomycota, Bacteroidetes, Basidiomycota, Chloroflexi, Crenarchaeota, Cyanobacteria, Euryarchaeota, Firmicutes, Oomycetes, and Proteobacteria. The most dominant genera involve in biofilms formation belong to Agrobacterium, Anabaena, Azospirillum, Azotobacter, Bacillus, Bradyrhizobium, Burkholderia, Gluconacetobacter, Paenibacillus, Pseudomonas, Rhizobium, Trichoderma, Xanthomonas, and Xylella. The agriculturally-important microbial communities and their interactions can have several implications on climate change, plant nutrition, plant protection, biofertilization, and bioremediation for sustainable agriculture and environments. This chapter deals with the fundamental aspects of biofilms, mechanisms of formation, the genes that are involved, biodiversity, and biotechnological applications in agriculture, industry, environmental studies, and allied sectors.

Nanotechnology is a promising field as wide range of research is ongoing in this field throughout the world. Nanotechnology has revolutionized the agronomy system with the development of new tools. Nanotechnology provides a stage for the development of the essential characteristics of metal in the form of nanoparticles (NPs) having promising use in diagnostics, biomarkers, cell labeling, antimicrobial agents, nano-drugs, etc. for treatment of various disease. The synthesis of NPs by chemical and physical methods is extremely costly and utilizing toxic or hazardous chemicals for their formulation which causes threat to ecosystem. In the present time, there is need to develop NPs which are eco-friendly and cost effective. It is well known that biological entities like microorganisms and living cells are the example of machines that possess operating parts at the nanoscale and performing their action with very high efficiency. Endophytes are microorganisms (bacteria and fungi) that are present in living tissue of various plants like root, fruit, stem, seed, leaf, etc. establishing mutual relationship without apparently any symptoms of diseases. The plants are known to harbor endophytic microbes that are believed to be associated with the production of pharmaceutical products. The microbes have a number of advantages for green synthesis of NPs. The use of microbes for the synthesis of NPs could be more advantageous, because of the tolerance, bioaccumulation, and extracellular production of enzymes at large scale. Therefore, synthesis of NPs from microbes is a boon for advance research in nanotechnology.

Agriculture is the most expanded sector that uses wide range chemical based fertilizers to increase the productivity in order to feed the growing population. Chemical based fertilizers are causing serious threat to human health as well as to environment. To overcome this problem, ecofriendly techniques are being implemented for increasing crop productivity. Use of beneficial microbes as biofertilizers and biopesticides in agriculture sector are one of the methods that can pave way for the next agricultural green revolution. Beneficial fungi, associated with plants are playing essential role in the development and growth of plants through various mechanisms including solubilization of different insoluble and unavailable nutrients and production of plant growth regulators. Fungi also helps in alleviation biotic stresses like plant pest and pathogen and abiotic stresses like drought, salinity, temperature, heavy metals. Fungi as biofertilizers in agriculture sector is one the emerging area for growth and enhance crop prodcution for sustainable agriculture. This chapter exclusively concluded the horizon covered book content of agriculturally important fungi for sustainable agriculture. The concluding remark envisioned the future beneficial role of plant growth promoting fungal communities in plant growth promotion and soil fertility.

Microbial biofilm is known to be structured consortium surrounded by self-produced polysaccharide matrix. The capability of microbes to develop biofilms is a significant element of their pathogenicity and is a serious challenge for today’s medicine. The biofilms are responsible for many chronic infections because they are highly resistant to most of the antimicrobials. A number of antibiotics have been tested against the biofilms, but microbes in biofilm mode have been found to be less sensitive to the treatments. In past few decades, there is a dramatic increase in the antibiotic resistance either to one or many antibiotics. It has been estimated that biofilm-associated infections reoccur in approximately 65–80% of cases. Thus, developing strategies against increasing antibiotic resistance is a major global challenge for scientific community and, in fact, important for public health. The present chapter describes the major steps involved in the formation of the biofilms, highlighting the biofilm-forming pathogenic microbes, their role in device-related, and other infections. Further, the chapter also takes into account the mechanisms behind antibiotic resistance in biofilms and what could be the successful strategies to control and treat these biofilms.

Injudicious application of chemical fertilizers in world has a considerable negative impact on economy and environmental sustainability. There is a growing need to turn back to nature or sustainable agents that promote evergreen agriculture. Potassium is important and well-known constraint to crop production. Plant growth promoting microbes (PGPMs) promote the growth of the plants by diverse mechanisms including they make the availability of various nutrients to the plants such as potassium, phosphorus, and zinc, and they produce various plant growth regulators, protect plants from pathogens, and help the plants to survive under stress conditions. A wide range of potassium-solubilizing microbes have been reported, viz., Acidithiobacillus, Agrobacterium, Arthrobacter, Aspergillus, Bacillus, Burkholderia, Enterobacter, Pantoea, Flectobacillus, Klebsiella, Microbacterium, Myroides, Paenibacillus, Pseudomonas, and Stenotrophomonas. This chapter deals with diversity of potassium solubilizing from diverse habitats, mechanism of potassium solubilization and mobilization, and their potential biotechnological applications for sustainable agriculture and environments. K-solubilizing PGP bacteria may have exploited as agricultural agent for wheat crop under different stresses condition, critical diseases and may have also used in the amelioration of K-deficient soils.

Long ago, fossil fuel likes coal, oil, and natural gases have been exploited massively to run various engines, automobiles, and other purposes. Presently, also demand for fossils is increasing with the increasing population, and its global reserves are depleting speedily and will disappear in the future. Apart from the depletion, fossil fuel use also has some destructive effects on environment as it releases huge amounts of carbon dioxide (CO2) and some other pollutants in the atmosphere when burned. Considering all the fossil fuels deleterious factors, a substitute has been searched and named biofuel. Biofuels are the liquid or gaseous fuels (bioethanol, biomethanol, biodiesel, biohydrogen) which are a renewable source and also environmentally friendly. Various bioresources are being utilized for biofuels’ production such as agriculture byproducts, food processing wastes or lignocellulosic waste, animal and poultry wastes, and microbial biomass. Microbial bioresources are the most significant resource for the production of biofuel as they can be achieved in less time and can be cultivated using CO2 which provides greenhouse gas alleviation benefits. Diverse microbes have the ability to produce biofuels like algae, bacteria, cyanobacteria, and fungi by using different methods that have been discussed in this chapter.

Worldwide, plant growth and productivity are majorly affected by the extreme environment of soil salinity, which is one of the major limiting factors. Numerous studies are increasing day by day to explore microbial diversity form saline environments and its application for crop improvements. Halophilic microbes are reported from diverse saline habitat including food crops growing under saline conditions, halophytic plants, saline lakes, sea, hypersaline soil, and mangrove. The microbiomes of saline habitats have the ability to survive in hypersaline conditions and colonized in rhizospheric/phyllospheric and internal tissue of plants. It promotes the plant growth by production of phytohormones and other important metabolites as well as produces some chemicals such as siderophore, hydrogen cyanide, ammonia, and hydrolytic enzymes for defenses of host plant from pathogenic microbes. The biodiversity of halophilic microbes will be illustrated in terms of different phylum, class, genera, and species and their mechanisms of action for the enhancement of plant growth, salt stress, and soil health for sustainable agriculture. All three domain archaea, bacteria and eukaryote with different phylum, e.g., Actinobacteria, Ascomycota, Bacteroidetes, Balneolaeota, Basidiomycota, Cyanobacteria, Euryarchaeota, Firmicutes, Proteobacteria (α/β/γ/δ), and Spirochaetes obtained from diverse saline habitat have been reported. Among all halophilic microbes, the phylum Firmicutes was found to be most dominant followed by Proteobacteria whereas phylum Balneolaeota was found less in numbers. The microbes with ecological significance were reported, e.g., many microbes such as Alternaria, Arthrobacter, Bacillus, Halobacillus, Halomonas, Oceanobacillus, Penicillium, Pseudomonas, and Sediminibacillus have been sorted out to be common at all site studies/survey, whereas microbes Alcaligenes, Amycolatopsis, Cladosporium, Haloarchaeobius, Myrothecium, Salinibacter, Soortia, and Spirochaeta have been reported as niche specific. This chapter is a critical and comprehensive review on biodiversity of microbiomes in saline environments, its ecological significance, and potential biotechnological applications for the betterment of salt stress, soil health, and plant growth for agriculture sustainability. These halophilic microbes help in promoting plant growth by increasing uptake of nutrients, plant growth and yield under the saline habitat, which could be utilized as biofertilizers/bioinoculants for crops growing in saline habitat.

Phytases are known to be pro-nutritional enzymes hydrolyzing phytate and making associated nutrients, for instance, phosphorus, iron, and zinc, are bioavailable. Phytase is reported in diverse groups of microbes, plants, and animals, but microbial sources are the most promising ones. Many bacterial and fungal strains have been reported as phytase producers from different environments. Phytases are of commercial importance and play a fundamental role in the animal feed industry and in agriculture. The foremost step to evaluate its efficacy as a feed additive, the study of its characteristic properties such as pH and temperature optimum, proteolytic stability and thermostability is important. It is achieved by producing these enzymes using microbes on large scale and purifying it. Many phytase genes from different microbes have been expressed in different hosts for achieving maximum yields and stability. In fact, many transgenic plants with phytase genes from microbes have been also developed that have ability to grow on phytate as only source of phosphorus. This chapter deals with biodiversity of phytase-producing microbes, production methods, and techniques used to purify microbial phytases for maximum product recovery, further also taking into account the molecular biology for maximum yields and maximum utilization of organic phosphorus. Finally, the chapter also highlights the biotechnological applications of phytases.

The plant ecosystem is very prone to unfavorable environmental conditions. Plants are directly or indirectly affected by several biotic and abiotic factors facing everyday triggers causing the underdevelopment of plants leading disease. The agricultural soil and water system inhabit numerous natural microbial flora. Researchers are deeply working in the field of development of strategies to enhance plant growth promotion. One peculiar group of microbes called PGPR (Plant growth-promoting rhizobacteria) alleviates the effect of biotic and abiotic stress factors directly or indirectly. The plant growth-promoting bacteria have several properties such as iron chelating ability, phosphate solubilization, ACC deaminase enzyme production under saline stress, phytohormone production, and many more. This significant potential makes them a very unique microbial candidate as bioinoculants enhancing plant growth both in favorable and unfavorable conditions. They play a very important role in sustaining all different geochemical cycles in the environment such as the carbon cycle, phosphorus cycle, sulfur cycle, and nitrogen cycle. PGPR may present as normal and as an extremophilic microorganism. The current compilation and description inculcate various types of compatibility of PGPR with plants in different climatic conditions. Few PGPRs such as Bacillus, Klebsiella, Pseudomonas, Azobacter, Enterobacter, Serratia, Variovorax, and Azospirillum are commercialized in the agriculture system to make it more sustainable.

Psychrotrophic microbes from the cold habitats have been reported worldwide. The psychrotrophic microbes from diverse cold habitats have biotechnological potential applications in agriculture as they can possess different direct and indirect plant growth-promoting (PGP) attributes such as solubilization of micronutrients (P, K, and Zn), 1-aminocyclopropane-1-carboxylate deaminase production, Fe-chelating compounds, indole-3-acetic acid, and bioactive compounds. Psychrophilic and psychrotrophic microbes are ubiquitous in nature and have been reported worldwide from various cold environments. The microbial communities from cold deserts have been reported using both culture-dependent techniques and metagenomic techniques, which belong to diverse major groups, viz., Verrucomicrobia, Thaumarchaeota, Spirochaetes, Proteobacteria, Planctomycetes, Nitrospirae, Mucoromycota, Gemmatimonadetes, Firmicutes, Euryarchaeota, Cyanobacteria, Chloroflexi, Chlamydiae, Basidiomycota, Bacteroidetes, Ascomycota, and Actinobacteria. Cold-adapted microbes, isolated from the low-temperature condition, are belonging to different genera such as Arthrobacter, Bacillus, Exiguobacterium, Paenibacillus, Providencia, Pseudomonas, and Serratia. On review of different research, it was found that inoculation with psychrotrophic strains significantly enhanced plant growth, crop yield, and soil fertility. The present book chapter deals with the biodiversity of psychrotrophic or cold-adapted microbes from diverse cold habitats, and their potential biotechnological applications in agriculture have been discussed.

Soil consists of diverse microscopic life forms such as actinomycetes, algae, bacteria, fungi, nematodes, and protozoans. But, the rhizospheric region is the most widely colonized regions of the soil due to the secretion of various nutrients by plant roots which attract microbes toward it with bacteria being the dominant one in this region. The bacteria in the rhizospheric region are highly beneficial for the plants as they directly or indirectly stimulate growth of the plants by nitrogen fixation; production of various phytohormones including auxins, cytokinins, and gibberellins; solubilization of phosphorus; production of 1-aminocyclopropane-1-carboxylate deaminase (ACC), siderophores, HCN, ammonia, and various lytic enzymes; and induction of systemic resistance. These plant growth-promoting bacteria of rhizospheric region are referred to as plant growth-promoting rhizobacteria (PGPR). The phyla involving major groups of PGPR include Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria belonging to different genera Acetobacter, Achromobacter, Arthrobacter, Azospirillum, Azotobacter, Bacillus, Burkholderia, Exiguobacterium, Flavobacterium, Gluconacetobacter, Herbaspirillum, Methylobacterium, Paenibacillus, Pseudomonas, Rhizobium, Serratia, and Staphylococcus. Furthermore, the use of PGPR offers an eco-friendly and an attractive way of replacing the chemical fertilizers, pesticides. In fact, there are many reports on use of rhizobacteria for improving the productivity and also protection of plants against pathogens and pests. In this way, benefits of using PGPR for sustainable agriculture is gaining a greater attention as well as acceptance worldwide, and the progress that has been made to date in using the rhizospheric bacteria with various applications, for agricultural improvement with reference to plant growth-promoting mechanisms, has been summarized and discussed in the present chapter.

Prokaryotic methylotrophic bacteria are able to consume a number of C1-carbon compounds such as methane, methylamine and methanol, whereas only methanol can be consumed by eukaryotic methylotrophic bacteria as source of carbon and methylamine as a source of nitrogen. The intensive researches explain the beneficial relationship between plants and methylotrophic bacterial communities earlier. Different genera of methylotrophic yeasts such as Candida, Pichia, Torulopsis and Hansenula are able to metabolise C1 corbon compound like formaldehyde and methanol.and a number of genes are involved in the methanol and other substrate utilisation pathways such as AOX (alcohol oxidase), DAS (dihydroxyacetone synthase), FDH (format dehydrogenase) and DAK (dihydroxyacetone kinase). The phylogeny and identification of these methylotrophic yeast strains are done based on either conserved gene sequences or functional gene sequences. The current description involves the genetic diversity of different strains of methylotrophic yeast from various ecosystems, identified at gene level.

The microbial secondary metabolites have great importance for humans and agriculture. They are widely used as active drug ingredients in medicine (e.g., many antibiotics, antitumor agents, and antivirals are derived from secondary metabolites, as are antipyretics like aspirin, hallucinogenics like LSD, and cholesterol-lowering drugs like lovastatin), as herbicides or phytotoxins in agriculture, and as food additives (color, flavors, and sweeteners), fragrances, and even as precursors for the synthesis of plastics. Biotechnology has opened up new possibilities for potential applications of beneficial microbiomes producing secondary metabolites in agriculture, industrial, pharmaceuticals, and allied sectors. The microbes from diverse habitats including plant microbiomes (epiphytic, endophytic rhizospheric) and extreme microbiomes (psychrophilic, thermophilic, acidophilic, alkaliphilic, xerophilic, and halophilic) produce the necessary secondary metabolites for diverse applications. The present book chapter provides complete, comprehensive, and broad subject-based reviews on existing microbial biodiversity with the production of potential secondary metabolites for different biotechnological applications. Here we have also discussed metabolic engineering for the production of secondary metabolites from different groups of microbes including archaea, bacteria, and eukarya and their applications in agriculture, medicine, and industry.

Drought is one of the major abiotic stresses accepted as the main constraint for loss of the crop yield worldwide. Further, problems are created by nutrient limitations particularly low phosphorus (P). Soils though have higher concentration of total phosphorus but are actually deficient in available orthophosphate due to which modern agricultural systems are highly dependent on chemical fertilizers. These chemical fertilizers are neither eco-friendly nor economically feasible and sustainable. Biotechnology offers a number of sustainable solutions to mitigate these problems by using plant growth-promoting (PGP) microbes. The PGP microbes colonize the rhizospheric region, or they may be endophytic or epiphytic and are beneficial for plant growth and adaptation to abiotic stresses. These microbes help the crops to tolerate drought conditions by different mechanisms including the production of exopolysaccharide (EPS), various phytohormones, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and a number of volatile compounds, enhancement of nutrient uptake, induction of the accumulation of osmolytes and antioxidants, upregulation or downregulation of the stress-responsive genes, or bringing about of alterations in root morphology. Inoculating plants with PGP microbes can increase tolerance against abiotic stresses such as drought, salinity, and metal toxicity. Systematic identification of bacterial strains providing cross-protection against multiple stressors would be highly valuable for agricultural production in changing environmental conditions. Among the PGP microbes, P-solubilizing microbes play an important role in plant growth and soil health, which belong to diverse genera such as Arthrobacter, Azospirillum, Azotobacter, Bacillus, Burkholderia, Enterobacter, Klebsiella, Lysinibacillus, Paenibacillus, Pseudomonas, Serratia, and Streptomyces. The present chapter deals with biodiversity of P-solubilizing drought-tolerant microbes, mechanisms of plant growth promotion, and mitigation of drought stress in the plants.

Bacteria are ubiquitous organisms, inhabiting almost every part of earth including the extreme habitats, and in aquatic ecosystems they represent dense assemblages with varied morphological, physiological and ecological preferences. In these freshwater ecosystems bacterial community composition is determined by using various culture-dependent as well as culture-independent techniques (DNA isolation, PCR amplifications, amplified ribosomal DNA restriction analysis, sequencing, and phylogenetic profiling). The chapter deals with the bacterial community composition of lakes, their diversity, distribution, functional annotations, and their relationship with other organisms in aquatic ecosystem. Later in the chapter the bacterial community's responses to disturbance (natural as well as anthropogenic) are discussed. The chapter further reviews the bacterial community composition of various lakes, novel species obtained from these lakes, and the dominant phyla (Actinobacteria, Cyanobacteria, Acidobacteria, Caldeserica, Calditrichaeota, Verrucomicrobia, Chlorobi, Planctomycetes, Nitrospirae, Chloroflexi, Bacteriodetes, Firmicutes, and Proteobacteria) found in these freshwater ecosystems.

Endophytic fungi are abundant and have been reported from all tissues such as roots, stems, leaves, flowers, and fruits. In recent years, research into the beneficial use of endophytic fungi has increased worldwide. In this chapter, we critically review the production of a wide range of secondary metabolites, bioactive compounds from fungal endophytes that are a potential alternative source of secondary plant metabolites and natural producers of high-demand drugs. One of the major areas in endophytic research that holds both economic and environmental potential is bioremediation. During their life span, microbes adapt fast to environmental pollutants and remediate their surrounding microenvironment. In the last two decades, bioremediation has arisen as a suitable alternative for remediating large polluted sites. Endophytic fungi producing ligninolytic enzymes have possible biotechnological applications in lignocellulosic biorefineries. This chapter highlights the recent progress that has been made in screening endophytic fungi for the production and commercialization of certain biologically active compounds of fungal endophytic origin.

The global energy demand is increasing day by day, with which substantial risk to the environment is also increasing. The consumption of the fuel, as well as the demand, is expected to grow rapidly side by side, and use of fossil energy is causing harmful impacts on the environment. All these factors have greatly attracted the attention of the researchers to find some alternative renewable resources of energy. Biofuels are an outstanding instance of renewable energy which can be produced using biological organisms which will ultimately cause a reduction in dependence on fossil fuels. Thus, biofuels are an attractive and feasible source of renewable energy on contrary to the geopolitical instability, finite nature, and deleterious global effects of fossil fuel energy. Biofuels are basically the energy-enriched chemicals that are generated either directly through the biological processes or from the chemical conversion of the biomass of prior living organisms. Biofuels are chiefly produced by photosynthetic organisms, including photosynthetic bacteria, micro- and macroalgae, and vascular land plants. Among all these organisms utilized, microalgae are being considered to be the most attractive source for production of biofuels. The biofuels production is still challenging at commercial scale, and new strains with commercial potential are still needed to be explored more. The combination of multiple genetic engineering strategies for optimizing the biofuels production will surely be useful. Thus, to overcome the energy crisis, the global cooperative efforts are very important for transforming biofuels into our current energy system that will further aid in cultivation methodology development as well as technology advancement of biofuels production.

With the expanding population, the environment is changing greatly, and agriculture is one of the most exposed sectors to these changes and faces a number of challenges like pollution, pathogenic attack, salinity, drought, high and low temperature, and so on. All these challenges ultimately affect productivity. To overcome such issues, eco-friendly approaches are very vital. The use of fungi as biofertilizers is one emerging area which is getting greater attention as it is proving its importance by enhancing plant growth and productivity by diverse plant growth-promoting traits including production of phytohormones, siderophores, and hydrolytic enzymes; making available different nutrients; and protecting plants against pathogens. Further, fungi are also becoming a center of focus for the industrial sector as fungal enzymes play a chief role in industries and their requirement is at the top position and in fact their influence will be felt more in coming years. Thus, keeping in view the importance of fungi especially for the agriculture as well as industrial sector, the following chapter has been designed which will take into consideration the plant growth-promoting traits of fungi, role of fungi in abiotic stress tolerance, value-added products from fungi, use of fungal enzymes in diverse industries, and fungi as a source of various secondary metabolites.

Heavy metal (Pb, Cd, Cr, Ni, As, Se, etc.) contaminations in fertile soils and fresh water are one of the worldwide growing issues along with the modernization of the life style. Contamination in natural resources due to heavy metals is a serious threat to sustainability of ecosystems and human life. A special urge is needed to restore the natural resources in its natural state. Based on the contamination type, various site-specific physical, chemical, and biological bioremediation strategies could be applied. However, the major limitation of physicochemical approaches is its higher cost and relatively low competence. Conversely, the biotic action of contaminated environment is slightly economical and ecologically attractive alternative to the present physicochemical methods of treatment. Among different bioremediation techniques, phytoremediation and mycoremediation are having its merit of eco-friendliness. Microorganisms play an important role in heavy metal bioremediation from contaminated resources attributed to its easy operation, without any secondary pollution and showing higher efficiency at low metal concentrations. Mycoremediation is the utilization of fungi for remediation of the contaminated natural resources. Unlike bacteria, the fungal phytoremediation does not require absolute water phase as fungus can grow of air-water interface. The pH, moisture, substrate, and species specificity are the important factors which highly influence the fungal phytoremediation. This chapter mainly emphasizes the detailed mechanism of fungal phytoremediation. Some potential species are provided for abatement of heavy metals from contaminated water and soil. The heavy metals toxicity, stress response and their impact on humans as well as on plants are described in brief. Further, it also highlights the utilization efficiency of fungal phytoremediation for sustainable removal of toxic heavy metals from contaminated natural soil and water resources.

The genus Trichoderma is ubiquitous in the environment, particularly in soils. Trichoderma species could be readily isolated from soil by all available conventional methods, largely because they grow rapidly and also because of their abundant conidiation. Based on the phylogenetic study, several researchers reported that Trichoderma and Hypocrea form a single holomorph genus, within which two major clades can be distinguished. The species of Trichoderma possess diverse biotechnological applications such as they act as biofungicide for controlling various plant diseases, as biofertilizers for plant growth promotion. Trichoderma secrete diverse volatile compounds including alcohols, aldehydes and ketones, ethylene, hydrogen cyanide, and monoterpenes, as well as nonvolatile compounds including peptaibols and diketopiperazine-like gliotoxin and gliovirin which are known to exhibit antibiotic activity. The interaction of Trichoderma with the host plant results in parasitism/predation; production of antibiotic is combined with mycoparasitism (penetration and infection), production of cell wall-degrading enzymes or lytic enzymes, competition for nutrients or for space, and establishment of induced resistance in the plant.