In the past few decades course, the global human population has grown tremendously and reached 7.712 billion counts by 2019. It is expected to cross the whopping mark of 10 billion by 2053. This every second escalating growth has also directly increased the application of human-made fertilizers, the intensity of agricultural practices, and much wider use of chemicals like weedicides, insecticides, and multiple diseases controlling agents. However, along with other anthropogenic activities, the situation has somewhere worsened. As a result, the primary focus of the current age researchers is to increase the overall output yield of every crop as well as maintaining or enhancing soil fertility in an eco-friendly manner. Currently, various groups of researchers are working throughout the globe via different approaches. One of the prominent options that emerged during the last decade is microbiome engineering. It includes the engineering of every component of epiphytic, endophytic, and rhizospheric microbiome. It creates a unique set of conditions to enhance the interaction between plants and their associated microbes. However, the prerequisite for microbial engineering is the ample amount of knowledge of the plant’s microbiome. One of the prominent global crops in which the microbiome studies have been conducted in maize (Zea mays L., family Poaceae). Therefore, in the current book chapter, we have critically reviewed the relevant literature regarding the maize microbiome chiefly from the last decade. Additionally, the isolation method of maize microbiome and microbiome targeted maize breeding has been discussed.

Endophytes are symptomless microbes found in different plant tissues. Endophytes are beneficial for the growth of the host plant and essential part of biogeochemical cycling in the environment. The host range of endophytes is comprehensive, that is, cereals, pulses, oilseeds, medicinal plants, and trees. The habitat of endophytes is host-dependent and varies from tissue to tissue. They produce growth hormones, antibiotics, secondary metabolites, siderophores, and volatile compounds, which help in plant health management (PHM). The role of plant–endophyte interactions thoroughly investigated for PHM, especially in some cereal and vegetable (CV) crops. Recently, microbial formulations, including endophytes, are one of the most innovative and attractive approaches for organic farming and alternative biocontrol agents. Before commercial exploitation of beneficial properties of CV endophytes in agriculture, further research is needed about their mode of action, host interaction, and suitable delivery methods before application into the open fields. In this chapter, the biology of CV endophytes, mechanisms of plant–endophyte interactions, mode of action for plant growth promotion activity, biotic and abiotic stress management are discussed.

Viruses are capable of causing epidemics on all significant crops of agronomic importance across the world. They can infect all the species of cultivated and wild plants, thus threating global food security. However, this “invisible foe” has variable host range. For instance, Indian citrus ringspot virus infects few species in the genus Citrus, whereas Cucumber mosaic virus infects over >1200 species in 100 plant families. For best or for worst, plant viruses have a remarkable capacity to reprogram plant growth and development. With the advent of next-generation sequencing technologies and bioinformatics analysis, the discovery, abundance, and species richness of plant viruses, more aptly “the plant virome” has become easier to decipher. In this chapter, the plant virome, its composition, and methods to study, interaction with other biotic components of phytobiome have been discussed.

The structure and function of every living organism in the biosphere are shaped and directed by its genome, respectively. The genome of an organism is an abode of all the genes and other DNA segments, known and yet to be known, responsible for its metabolism, survival, growth, development, interaction with the environment, defense, reproduction, senescence, etc. To exploit any species as a biological resource at molecular level to serve human kind in form of good(s) and/or service(s), primarily requires a thorough understanding of its genes and their locations in the genome. Genome mapping is a technique that aids in determining the location of genes, and/or its(or their) markers(s), of interest in relation to other gene(s), and/or its (or their) marker(s), within the genome. Since all the genes of commercial interest are nor present in the same individual/taxa, it is essential to move gene(s) of interest from available source(s) to the required target(s), which is made easy with the knowledge of genome map. Genome mapping has wider applications in modern molecular biology: from the applied areas, such as genetic improvement of organisms, to the fundamental research such as genome sequencing. It needs proper tools and techniques such as various kinds of markers and mapping populations. To choose an appropriate tool and method requires thorough knowledge of myriad basket of available genome mapping tools. This chapter brings a complete, comprehensive and updated information that is necessary to understand genome of interest and use appropriate mapping tools, such as markers and mapping populations, for mapping of genes of interest in the genome of an organism of interest, ultimately to help deriving useful product(s) and/or service(s) to meet various needs of humankind in the wake of everchanging environment and never-receding human populations. This chapter also offers future prospects of available genome mapping tools and opportunities to develop new tools in the light of advanced techniques available for DNA sequencing and rapid generation advancement of mapping populations.

Enhanced chemical input in the agricultural field for the increased crop yield and plant disease management has resulted in the development of the resistant form of phytopathogens, loss of soil structure and fertility, and harmful effect on the ecosystem and human health. At this point, there is a necessity of sustainable alternative methods to compensate issues with injudicious use of agrochemicals. Application of plant beneficial microorganisms executed in the form of biofertilizer and biocontrol agents hence has significant application. Most remarkably, plant microbiome is unique in their biosynthetic potential, antimicrobial, and plant beneficial properties and hence has immense promises to boost agricultural production. This chapter mainly focused on multifaceted applications of plant-associated microorganisms including plant growth promotion, biocontrol properties, stress tolerance, and bioremediation.

In the classical era, the application of microbial technology was restricted to foods and beverages. With the progress in physical sciences, microbial biotechnology accelerated and led to innovations in biological science, food science, sustainable agriculture, and medical science. Development in biotechnological techniques allows the quick identification of novel molecules, accurate nomenclature of microorganisms, or strains improvement of known species through the involvement of genetic manipulations techniques. Currently, several beneficial microbes have been exploited for various purposes; however, the role of microbes in agriculture as plant growth promoters and biocontrol against phytopathogens have been widely explored. Besides the crucial role of microbes in agriculture, various microbes are also discovered and manipulated for industries application and value addition in food products, search and production of secondary metabolites of wide uses, drug productions through microbial interventions, and microbial biosensors are the prime attractions of microbial biotechnology in the modern era. Further, microbes have been recognized as biofactories and have been utilized for the synthesis of diverse chemicals, fuel molecules, industrial polymers, and genetically modified strains which are environmentally important due to their decomposing or adsorption capacity. Hence, in the current chapter, an attempt has been made to cover the wide application of microbial biotechnology that benefited not only humanity but also extended benefits for attaining environmental sustainability in the modern era.

Plants are associated with the combination of microbiomes, which can improve plant growth, stress tolerance, and control plant pathogens. The incorporation of a beneficial microbiome represents a promising sustainable key to enhance agricultural production. Sugarcane is an essential crop with many agricultural and industrial uses including animal feed, biofuels and bagasse. There is a need to strengthen sugarcane crop production sustainably and to locate solutions to control pathogens, abiotic stress, and pests. The utilization of beneficial microbes as a biofertilizer has become essential in sugarcane agriculture for sustainable crop production. In this perspective, the sugarcane microbiome becomes a promising approach for sustainable production. The chapter describes the application of sugarcane-associated microbiome.

The environmental interaction of the entire plant’s community along with micro- and macroorganisms at a specific niche with diverse bacteria, archaea, fungi, viruses, nematodes, insects, animals, birds, and climatic conditions contributes the term “Phytobiomes.” Such interaction has profound effects on the agroecosystem of the plant-like soil fertility, crop yield, productivity, food quality, and safety. When these plants and plant products are consumed, it influences the entire health and other ecosystems tremendously. Therefore necessary actions should be taken to ameliorate the efficiency of crops to shuck off these interactions that affect the plant ecosystem. Recent research has been involved in introducing analytical tools to manage and protect crop production for the future. Increased agricultural practices play a key role in enhancing crop yield and food productivity worldwide to sustain phytobiomes. Steps involving bioremediation also develop phytobiome-based management approaches. For interdisciplinary cooperation in phytobiome management, ultimate studies of phytobiome mechanisms, their interaction, dynamics, functions, generation of integrated system-based models for phytobiome investigation and prediction, expansion of effective phytobiome-based crop administration policies and establishment of the combined worldwide platform open communication among agronomists, scientists, industries, farming counselors, advisors, and traders. Hence, to improve global crop productivity, a strategic plan with available resources and tools can optimize phytobiome-based solutions in the next generation.

Actinobacteria are a group of microorganisms reflecting standard behavior of both bacteria and fungi and are known to play a multifunctional role in agricultural production systems. The primary functions include the production of a wide array of growth-promoting compounds and metabolites, including antibiotics that provide the host plants resistance to withstand both biotic and abiotic stress conditions. Consequently, actinobacteria are often employed as a biocontrol agent against dreadful plant pathogens. Further, actinobacteria colonize host plants and elute growth-promoting substances that assist in favoring accelerated growth of plants even under harsh environmental conditions such as nutrient deficiencies, drought, salinity, and heavy metal contaminated soils. Several actinobacteria are involved in nutrient solubilization and mobilization, particularly phosphates and iron, besides facilitating as helper bacteria in mycorrhizal symbiosis and biological nitrogen fixation.

Phyllosphere is an abode for different kinds of microorganisms. Recent developments in the advancements of molecular and computational tools, high-throughput screening procedures, and amalgamation of omics techniques have significantly enhanced the understanding of phyllosphere-associated microbial communities in relation to their structural, functional, and ecological properties. Several research findings indicated that phyllosphere microbiome has played an important role in sustaining crop growth and health management by regulating plant physiological processes under ever-changing environmental conditions. Briefly, the current chapter provides an overview of current understanding on the diversity of phyllosphere microbiome, microbial engagements linked with phyllosphere colonization, and further addresses the significance of phyllosphere microbiome in enhancing plants’ tolerance to withstand various biotic and abiotic stress conditions in the current facet of climate change. Besides this, efforts have been made to highlight approaches and emerging areas for future research on phyllosphere microbiome in the context of sustainable agriculture.