Molecular and Physiological Insights into Plant Stress Tolerance and Applications in Agriculture- Part 2

Genetic information is fundamental in biology. It is stored in all genomes, crucial to generating and maintaining a new organism. The biological importance of DNA lies in its role as a carrier of genetic information and how it is expressed under specific conditions. Among the different ways of controlling the manifestation of genomic information (or gene expression), epigenetic mechanisms have been highlighted. These mechanisms are diverse, multifunctional, and profoundly affect the plant's molecular physiology. Cytosine methylation and demethylation - one of the best-studied epigenetic mechanisms - is a dynamic process that influences, respectively, the down- and up-regulation of target genes. The referred chemical modifications occur in response to developmental processes and environmental variations, and have their biological value accentuated as they can be passed on to subsequent generations. This inheritance mechanism conducts ‘states of gene expression’ to new cells and even to the offspring, allowing them to be ‘more adequate’ to the changing environment. The possibility of inheriting such chemical modifications defies our understanding of the hereditary process, opening new perceptions and practical implications. This chapter aims to address the cytosine methylation and demethylation effects in plants. In the present review, we deal with how cytosine (de)methylation occurs in plant genomes, their participation in the biotic and abiotic stress responses, the recent studies for its use in crop breeding, and the epigenetic inheritance issue, which is a matter of intense debate.

Numerous anthropogenic activities, such as novel agricultural practices, coal mining, industrial pollution, etc., pose a negative impact on the environment. Such factors cause the accumulation of different pollutants within the ecosystem, ultimately hampering the plants as well as animals. However, plants possess a series of physiological as well as molecular mechanisms for defense and resistance. The global population has posed a significant food challenge, therefore, to ensure food security, soil nutrition, agricultural productivity as well as fertility, different sustainable aspects should be kept in mind. Chemical fertilizers dilapidate the ecological balance along with human health, henceforth the microflora present in the rhizosphere acts as quintessential elements. Microbes such as plant growth-promoting rhizobacteria and mycorrhizae have been formulated as biofertilizers in agriculture that enhance their nutrient uptake as well as yield, along with providing resistance against different stressors. Biofertilizers have been shown to provide a positive outcome for plants, therefore, an array of microbial strains have been selected and formulated to be used in the agricultural sector. These are based on rhizobacterial species, endophytes, and mycorrhizae. Regardless of the challenges observed in the production, usage, and application, these have been proven to be the exclusive alternatives for chemical-based fertilizers. Therefore, their elaborate understanding will offer new approaches to sustainable agriculture. Biofertilizers not only boost crop yield and soil fertility but also interact with plants to trigger their immune systems, physiological processes, growth, and development. They also enable solubilization of essential nutrients such as nitrogen, phosphorous, zinc, potassium, and silica that promote plant growth. Most importantly, they are cost-effective, toxin-free, eco-friendly, and serve as the best alternative for chemical fertilizers. In this chapter, we have highlighted the microbial dynamics within the rhizospheric zone and its significance in agriculture by its usage as biofertilizers for sustainable crop production. 

Plant terpenoids and their precursors, terpenes, are among the most important classes of plant secondary metabolites that have provoked increased interest regarding their application in the medical field to treat different health issues. Additionally, terpenoids are known to play a crucial role in many different plant processes, such as photosynthesis, root growth, flower production, fruit set, and plant interaction with the environment. A plant can produce different kinds of terpenoids with diverse structures and functions. These compounds are usually liberated in the atmosphere in the form of flavors or fragrance compounds or stored in plant organs, such as glandular trichomes. Due to increased water scarcity, salt stress, mineral deficit, temperature level, and pathogens resistance, it has become difficult to provide natural conditions for the development of some plant species, which has led to a shortage in levels of some naturally occurring compounds, such as terpenoids. So, to reduce the alteration of terpenoid production, some strategies have been recently applied, like metabolic engineering and applying biofertilizers. Thus, this chapter will define the different classes of terpenoids produced by plants, their metabolic pathways, and their roles in plant development and physiology, nodule formation, mycorrhizal symbiosis, wounding healing, and plant defense as well as recent advances regarding the increase in the accumulation of terpenoids through metabolic engineering and exogenous application of natural substances.

With the rise in rampant anthropogenic activities, the contamination of the environment due to heavy metals is increasing at an alarming rate. This poses a serious threat to both the plant and animal world, including poor human health and disturbed crop physiology and yield. Heavy metal pollution commonly leads to oxidative stress in sensitive plants, thereby altering the entire homeostasis within the plant system. Therefore, plants have evolved certain regulatory circuits for combating the resulting stress ensuing from the excess concentration of heavy metals in the soil. Certain plants have the immense potential to accumulate such heavy metals, followed by their detoxification via a range of mechanisms, inherent to the plant system. This process is commonly referred to as phytoremediation, which is an efficient, cost-effective and sustainable approach for the rejuvenation of contaminated soil. In present times, medicinal plants are not only exploited as a source of different traditionally available medicines, but have also displayed the immense capacity of cleaning up heavy metalcontaminated soil and serve as sinks for the toxic effects of heavy metals to clean up the environment. The present chapter, therefore, focuses on medicinal plants as potential phytoremediation agents.

Plants, throughout their life cycle, are exposed to vagaries of biotic and abiotic stresses. To alleviate the stresses, plants have developed different molecular response systems. One such response is the high-level accumulation of Late Embryogenesis Abundant (LEA) proteins, a group of hydrophilic proteins encoded by a set of genes during seed dehydration, at the late stage of embryogenesis. These proteins are reported not just in plants, but also in algae, bacteria, and nematodes. LEA proteins are reported to play a versatile role in stress tolerance. This chapter discusses the classification, distribution, characterization, and functions of LEA proteins and their implications for plant stress tolerance.

In a natural system, plants are experienced adverse effects of continuously changing climatic conditions and various types of stress throughout their life in which abiotic stresses are the major constraints that affect the growth and development of plants. Metal-based nanoparticles are emerging as a new pollutant of concern because of their widespread application in consumer products, which pose new challenges to the environment due to their complex interaction and possible toxic effects on plants. Plants absorb these metal nanoparticles (MNPs) from the soil along with other minerals and nutrients. Nanoparticles cause phytotoxicity by adversely affecting plants at the morphological, biochemical, physiological, and molecular levels. Various MNPs alter growth, yield, photosynthesis, and mineral nutrient uptake and induce oxidative stress, cytotoxicity, and genotoxicity in plants. Although plants have evolved various mechanisms to cope with nanoparticles-induced stress. Coordinated activities of antioxidants, some key regulatory genes and proteins regulate cellular function under stress conditions. Understanding the interaction of MNPs with plants and elucidating the behavior of genes and proteins in response to NPs stressors could lead to the development of novel approaches to mitigate stress which will support agricultural production. In this chapter, nanoparticle-induced physiological and molecular responses and tolerance mechanisms in plants against the mechanistic action of nanoparticles were described.

Rice is one of the most important cereals, as it feeds over half of the world's population. Rice production is limited by different abiotic stresses, which would probably worsen with climate change. Also, we must expect a rapid increase in food demand. Therefore, there is an urgent need for innovative agricultural technologies able to increase cereal amounts without increasing arable lands. The inoculation of plant growth-promoting bacteria (PGPB) from paddy soil can improve plant response to abiotic stresses; however, the mechanisms involved in such protective response are largely unknown. The current chapter comprehensively analyses and presents the state-of-the-art inoculation of selected PGPB aiming to improve rice tolerance to abiotic stress conditions. Different plant responses at the molecular, biochemical, physiological, and agronomical levels will also be appraised. This summary can stimulate the producers to inoculate rice plants, contributing to rice production in abiotic stress-impacted regions.

Modern agricultural practices rely on the excessive use of chemical fertilizers to increase crop yields to meet the growing population's demand. It has exploited the inherent biological potential of soil and plant systems. Sustainable agricultural practices focus on equal attention to soil and plant health. Plant growthpromoting rhizobacteria (PGPR) serve the plants by combating abiotic and biotic stressors in the environment. These microorganisms aid plants in multiple ways by colonizing the plant roots. They work effectively as biofertilizers and as biocontrol agents and help in fostering plant growth through either direct (potassium and phosphorous solubilization, siderophore production, nitrogen fixation) or indirect (production of VOCs, antibiotics, lytic enzymes) mechanisms. To upgrade their application to agro-ecosystems, modern technologies are being worked out. These aim at improving the efficacy of PGPR and uplifting agricultural sustainability. Therefore, in this book chapter, the role and mechanism of PGPR as soil health boosters and plant growth enhancers were discussed. Further, it sheds light on recent developments made to strongly present PGPR as a potent candidate for green agriculture.

ABC transporters (ATP-binding cassette transporters) are dynamic proteins found in both types of organisms, prokaryotes and eukaryotes. They play pivotal roles in the transportation of various substances along cellular membranes by utilizing ATPs. ABC transporters consist of four domains: two NBDs with highly conserved motifs and two TMDs. They have a large diverse family, which is grouped into 8 subfamilies (A, B, C, D, E, F, G, H, I), though the H subfamily is not found in plants. ABC transporters are well-defined for transporting xenobiotic compounds, secondary metabolites, phytohormones, toxic heavy metal ions, chlorophyll catabolites, lipids, and drugs across cellular membranes. Importantly, several kinds of ABC transporters investigation discovered their functions in plant growth, development, and defense. Commonly localized on plasma membranes, they are also found on the membranes of vacuoles and various cellular organelles. Under stress, these are known to contribute to various physiological, developmental, and metabolic processes by helping plants adapt. Initially, they were recognized as tonoplast intrinsic transporters, but now they are well-known in cellular detoxification mechanisms which protect plants and maintain homeostasis. This chapter presents a comprehensive account of the roles of ABC transporters with insights into molecular and physiological leading to stress tolerance. 

 The use of endophytic bacteria is an emerging trend in agriculture since they can promote plant growth under normal conditions and abiotic and biotic stresses. In this regard, endophytic bacteria have been used to deal with the consequences of the climate crisis in global crops, as alternatives to ecologically unsustainable chemical pesticides and fertilizers. These bacteria can benefit plant growth by direct mechanisms, such as hormone production and nutrient solubilization, and indirect mechanisms, which involve protecting the plant against pathogens and suppressing disease. Thus, this chapter aims to present the main mechanisms of plant growth promotion by endophytic bacteria, focusing on the genetic and physiological processes of biocontrol of pathogen growth and induction of systemic plant resistance. Genome sequencing data from endophytic bacteria provide information about genes involved in the synthesis of enzymes and antimicrobial compounds, such as siderophores and hydrocyanic acid, among others. Furthermore, genetic pathways involved in plant response induction were characterized using sequencing experiments and differential RNA expression analysis. Jasmonic acid and salicylic acid biosynthesis genes are differentially expressed in response to plant interaction with endophytic bacteria. Therefore, data from the most current methodologies of genetic and molecular analysis will be condensed here to provide an overview to respond to the question that heads the chapter.

Food security has become the biggest challenge today due to the burgeoning population and environmental impacts on crops. The agriculture system needs to meet the food demand by using appropriate sustainable approaches while exerting minimum impact on the ecosystem. Multiomics is one of the successful sustainable technologies that contribute toward crop improvement and acceleration in food production. Progressive development in next-generation sequencing for various omics like genomics, transcriptomics, proteomics, metabolomics, ionomics and phenomics have provided desired genetic resources for crop improvement. With the development of molecular technology, new breeding tools are used for the transfer of genes from one species to another. Biotic and abiotic stress-resistant traits are incorporated in cultivating varieties to make them superior and produce a good yield. This chapter solely summarizes the development of new traits with the help of new breeding tools such as TALENs and CRISPR in plant breeding. The high throughput multi-omics techniques are not only applicable for enhancing agricultural growth and yield but also helpful in refining food security.