eChapters

Introduction to Antibiotic Discovery

Antibiotics are the drugs that are used to treat illnesses caused by bacteria in humans and animals. These act by killing or inhibiting the growth and multiplication of bacteria. Antibiotics were considered as “magic bullets” that selectively kills microbes responsible for disease causation, but at the same time would not affect the host (Zaman et al., 2017).

Louis Pasteur in 1877, first discovered the properties of antibacterial compounds with the inhibition of anthrax by saprophytic bacteria. In 1928, Alexander Fleming observed that the growth of Staphylococcus aureus in petri dishes was inhibited by substances produced by the fungus Penicillium chrysogenum, which led to the discovery of the first antibiotic, penicillin (Aminov, 2017). Selman Waksman, discovered multiple antibiotics from filamentous actinomycetes living in the soil and defined an antibiotic as “a compound made by a microbe to destroy other microbes”. Following the discovery of Penicillin, various antimicrobial compounds such as sulphonamides, aminoglycosides, tetracyclines, lipopeptides, oxazolidinones, glycopeptides, streptogramins, and quinolones were discovered in the “Golden era” of antibiotics during the period from the 1940s to the 1960s and most of the antibiotics still in current use were discovered during that period (Salam et al., 2023). Millions of metric tons of newer classes of antibiotics have been produced in last 60 years since its inception.

AMR has been prevalent in almost all European countries from past decades. A 2021-2022 report published by the European Food Safety Authority (EFSA) and the European Centre for Disease Prevention and Control (ECDC) on AMR in zoonotic and indicator bacteria from humans, animals and food origin reported vast differences in antimicrobials resistance levels among the European countries, with comparatively higher AMR percentages in the southern and eastern parts of Europe (ECDC, 2022, 2023). The resistance levels ranged from very high for tetracyclines, sulfonamides and ampicillin, moderate for ciprofloxacin to low levels for third-generation cephalosporins (cefotaxime and ceftazidime) in human cases infected with Salmonella spp. in 2022 (ECDC, 2023). The trends are dynamic and over a decade of 2013 2022, the human isolates from 12 and 15 countries reported a statistically significant reduction in tetracycline and ampicillin resistance, particularly for S. typhimurium (ECDC, 2023). The ciprofloxacin and cefotaxime combination, a highest priority critically important antimicrobials (CIA), had very low and rare resistance levels for Salmonella isolates of humans and animal and their derived meat.

Livestock species wise variation was also observed in the resistance pattern in imported meat, being higher in poultry meat isolates compared to pig or cattle meat for Escherichia coli (ECDC, 2023). High to extremely high levels of f luoroquinolone resistance from Campylobacter jejuni and C. coli of both human and animal origin isolates exist, due to which the fluoroquinolones can no more be used as a treatment option for human Campylobacter infections (ECDC 2023). The combined occurrence of erythromycin resistance and ciprofloxacin in Campylobacter spp is considered of high public health importance, and the report mentioned that the combined resistance for these antimicrobials was higher in C. coli compared to C. jejuni from food-producing animals and humans. However, while the ciprofloxacin resistance showed an increase in over 13 study countries, seven countries reported reduced erythromycin resistance for C. jejuni. Overall, resistance to conventional antimicrobials was frequent in Campylobacter and Salmonella from humans and animals. Increasing trend in resistance to one of two CIA for treatment in humans has been observed in poultry-originated Salmonella serovars and Campylobacter while combined resistance was is low in few Salmonella serovars and C. coli isolates from humans and animals in some countries (ECDC, 2023).

Antimicrobial Resistance abbreviated as AMR is defined as the process by which microorganisms like bacteria, fungi, viruses, and parasites change over a period and become resistant to a drug to which they were earlier susceptible to. This makes the medicines ineffective for treatment overtime, thus making infections difficult to treat thereby increasing the risk of spread of diseases caused by them and severe illness which may lead to death. This in turn necessitates the need for development of newer antibiotics. However, there has been a sharp decline in the development and manufacture of new antibiotics in the recent years resulting in development of only few antibiotics in the past two decades. The increase in emergence of antibiotic resistance concurrent with decline in development of newer antibiotics poses a serious threat to health of both humans and animals. Every year about 700,000 deaths have been reported to occur due to resistant infections and this rate is likely to increase further with estimated infections due to resistant pathogens expected to reach over 50 million globally by 2050 (O’Neill, 2016). The worrisome trends of increasing antimicrobial resistance across the globe poses a serious threat to both animal and human health as AMR not only increases the morbidity and mortality rates but also increases the economic burden on health care (Zhu et al., 2022). This presents an extremely grave situation as the supply of new antibiotics is inadequate to cope with the increase of AMR pathogens. The unnecessary use of antibiotics globally especially in the livestock sector as growth promoter further helps in selective enrichment of AMR pathogens which further increases health risks. It is well known that resistant pathogenic and commensal bacteria can persist and spread within and between premises despite zero antimicrobial drug use. This may be explained due to maintenance, replication, and further dissemination of resistance genes by horizontal transfer of genes via natural ecosystem and can occur either by conjugation, transformation and transduction; and these mechanisms can rapidly spread AMR genes among microbial community in natural environment and human microbiome, where these resistant bacterial species may be selected due to presence of antimicrobial drugs (Zhu et al., 2022). The physical transfer of bacteria via movement of animals, workers, and equipment and ineffective cleaning and disinfection may also be responsible for increasing the AMR pathogens in the natural environments.

Introduction

The antibiotics are low molecular weight natural, semi-synthetic, or synthetic substance that kills or slows the growth of germs while causing little or no harm to the host is considered an antimicrobial (Walsh, 2000). Antibiotics are the type of medicine produced by some microorganisms that kill or slow the growth of other microorganisms. It includes any of a large group of chemical substances, as penicillin or streptomycin, produced by various microorganisms and fungi, having the capacity in dilute solutions to inhibit the growth of or to destroy bacteria and other microorganisms, used chiefly in the treatment of infectious diseases (De Vetten et al., 2003). However today, a large number of bacteria are resistant to various antibiotics. Antibiotic resistance occurs when a bacterium becomes able to survive and multiply despite the presence of an antibiotic that would normally control or kill it. In other words, the bacteria become “resistant” and continue to grow even at therapeutic levels of the antibiotic. While antibiotic resistance is a natural phenomenon, it is accelerated by the selective pressure exerted when an antibiotic is used. Bacteria that are naturally resistant to the antibiotic have a better chance of survival compared to those that are susceptible. As the susceptible bacteria are killed or inhibited, resistant strains are favored and continue to thrive (Holme et al., 2006). Some resistance arises without human influence, as bacteria can naturally produce antibiotics against other microorganisms, resulting in a low-level, natural selection for antibiotic resistance. However, the current surge in antibiotic resistant bacteria is largely attributed to the overuse and misuse of antibiotics. One of the main issues facing public health is antimicrobial resistance, particularly in developing nations where access to and use of medications are easier than in developed nations, leading to a disproportionately higher rate of inappropriate antibiotic use and higher resistance levels (Ganguly et al., 2011). Antimicrobial resistance will make it more difficult to control infections in the community and make health care services less effective (Bhatia et al., 2010). It is well known that India has one of the highest rates of infectious disease burdens in the world, and that the country’s high rates of malnutrition and inadequate sanitation make these circumstances worse (http://www. resistancestrategies.org/wpcontent/uploads/2011/03/Indiareport).

Introduction

Today, antimicrobial resistance (AMR) has become a global issue, contributing to rise in mortality and cost of treatment. Antimicrobial resistance (AMR) is the resistance of a microorganism against an antimicrobial agent to which it was originally sensitive (WHO, 2013). Dispersion of antibiotics is done at large scale, in India even sometimes without any proper prescription. Animal Husbandry is not untouched and antibiotics are used to a great extent, which needs enforcement of strict government rules and regulations for their use in f ield conditions (PHFI, 2011).

Extended-spectrum β-lactamases (ESBLs) are enzymes that hydrolyse most of the β-lactam antibiotics and thus mediate resistance to penicillins, 3rd and 4th generation cephalosporins (Saravanan et al., 2018). Beta-lactamase inhibitors, inhibit these ESBLs such as clavulanic acid, sulbactam and tazobactam (Trott, 2013). The genes encoding for these enzymes are commonly found both on the chromosomes and plasmids among Enterobacteriaceae family (Kotsoana et al., 2019).

Among Enterobacteriacae, E. coli and Klebsiella species are main environmental pathogens associated with various illnesses such as acute bovine mastitis (Koovapra, 2015), pathogenic E. coli with diarrhoea and extra intestinal infections in humans and animals (Levine et al., 1987), K. pneumoniae with respiratory and urinary tract as well as bloodstream infections (Daehre et al., 2018). Resistance to extended-spectrum β-lactams occurs mainly in members of Enterobacteriaceae family through plasmids encoded ESBL genes. (Sharma et al., 2010).

Introduction

Antimicrobials, viz. antibiotics, antivirals, antifungals and anthelmintics are substances widely used to prevent and treat infections in humans, fish & prawn, livestock animals, and crops. In a situation where microorganisms such as bacteria, viruses, parasites or fungi become resistant to antimicrobial treatments to which they were previously susceptible, it is apprehended that antimicrobial resistance in the microbes has evolved. In fact, antibiotic resistant bacteria evade the effects of antibiotics and multiply in their own way leading to severe health consequences in human and animals. The menace is such that antimicrobial resistance (AMR) hinders treatment modalities targeted for infectious diseases. The hazards of antimicrobial resistance is frequently observed in various pathogenic and non-pathogenic organisms, viz. Salmonella spp., Campylobacter spp., Yersinia sp., E. coli serotype O157:H7, enterococci, Pasteurella sp., Actinobacillus sp. with varying severity (McEwen and Fedorka-Cray, 2002). Microorganisms that develop resistance to commonly used antimicrobials are referred to as superbugs. Globally it is a matter of great concern that it spreads rapidly and threatening the ability to treat common infectious diseases, resulting in prolonged illness, disability and death. Without any effective antimicrobial agent, treatment of infectious diseases, many medical procedures like cancer therapy, diabetes management, organ transplantation, and major surgery will not be possible. The microbes showing resistance to multiple antimicrobials are commonly known as multidrug resistance (MDR) organisms (Magiorakos et al., 2012).

Globally, antimicrobial resistance (AMR) is an important public health and development threat (WHO, 2020). Being one of the top 10 global public health threats, the ever-increasing rates in the occurrence of drug-resistant bacterial infections have become a grave public health concern for the governments (Laxminarayan et al., 2013). Moreover, such infections would be difficult to treat and therefore can lead to worse clinical outcomes (Laxminarayan et al., 2013). Worldwide, each year about 700,000 people die from antimicrobial resistant infections and the mortality figures are projected to reach 10 million/ year by 2050 (O’Neill, 2016). The crude infectious disease mortality rate in India is more than 400 per 100,000 persons and at least 23,000 deaths in adults and 58,000 neonatal deaths per year are caused by AMR bacteria (Laxminarayan and Chaudhury, 2016). A 2017 estimate puts the cost of developing an antibiotic at around US$1.5 billion (Towse, et al. 2017). Meanwhile, industry analysts estimate that the average revenue generated from an antibiotic’s sale is roughly $46 million per year. “That’s tiny and nowhere near the.

The response of any living cell to a xenobiotic (including antibacterial agent) is significantly affected by the prevailing local environmental conditions. In case of bacterial infection, it may include the presence of other microbes, no matter commensal or pathogenic, or biochemical alterations at that particular site of bacterial infection in host. All these host and bacterial factors play a critical role in the evolutionary responses of bacteria but usually go unconsidered while determining the microbial sensitivity to a particular antibiotic in a clinical setting. These also include the direct and indirect interspecies interactions that can affect the responses of individual bacterial species and surviving microbial communities to a particular antibiotic therapy. These interactions may significantly alter the qualitative and quantitative responses, potential phenotypic changes and the final trajectory of evolution of antimicrobial resistance. Due acknowledgement and plausible interpretation to these interactions may help to reduce the upsurge in AMR and its associated morbidity and fatality and pave path to more proficient clinical success.

The factors participating in drug- microbe interaction can be classified into two broad groups: host factors and microbial factors. The environmental milieu of the interaction is chiefly regulated by the gut microbiota with stressors causing deflections. The gastrointestinal bacteria amend host mental and physiological cadence via microbial metabolites such as butyrate, polyphenolic antioxidants, vitamins, and amines, affecting the overall ready perception and active rebuke to a stimulus. Lifestyle stressors such as fluctuating sleep and erratic eating patterns (western diet) disturb the host circadian system along with the gut microbiome. The overall impact is impaired detoxification (decreased conjugation of bile acids or increased production of hydrogen sulphide), substrate oxidation and energy regulation (reduced butyrate production) in the host affecting the overall health and productivity.

Antibiotics, often referred to as “magic bullets” in the battle against bacteria, stand out as one of the most remarkable medical breakthroughs of the 20th century. Their advent revolutionized the therapeutic landscape, consistently saving millions of lives from bacterial infections (WHO, 2020). Undoubtedly, antibiotics are a blessing to humanity, not merely for their medicinal applications but also for their diverse uses. They have long been employed in various contexts, including animal husbandry and production, serving as preventive measures in numerous underdeveloped and developing nations for decades (Majumder et al., 2020). A range of antimicrobial agents, including antibiotics, antifungals, antivirals, disinfectants, and food preservatives, function to either inhibit microbial growth or eradicate them altogether. Among these, antibiotics, specifically tailored to combat bacterial infections, are the most widely used class of antimicrobials. With their increasing and often improper use, microorganisms have developed antimicrobial resistance (AMR) (Murray et al., 2022).

Antimicrobial resistance is an inevitable evolutionary process observed in all microorganisms, and is driven by genetic mutations aimed at resisting the lethal pressures of selection. Bacteria, adapt to environmental selection pressures by developing resistance to antibacterial drugs, thereby diminishing the efficacy of these treatments (Murray et al., 2022). The widespread use of antibiotics, particularly in developing nations, further flares up the process, leading to significant repercussions such as increased rates of morbidity and mortality (WHO, 2020). The incidence and prevalence of antimicrobial resistant bacterial infections have reached alarming levels in the 21st century, posing a substantial threat to global public health akin to a silent pandemic. Antibiotic resistance knows no borders and can impact individuals of any age or gender, regardless of their location. In its present state, antimicrobial resistance (AMR) stands as one of the foremost threats, not only to global health but also to food security (Murray et al., 2022).

Microbial Resistance Mechanism

Huge use of antibiotics in nosocomical environment has lead to the occurrence of multidrug resistance mechanism by microorganism against particular antibiotics (Munita et al., 2016; Zhao et al., 2020). Main operation includes chemical modification, efflux pump through passivation, modification of drug targeting gene and systemic elimination of antibiotics as many of them can form biofilm (Rajput et al., 2018) which can show extreme resistance. Chemical and enzymatic mechanism can include inactivation, activity loss, degradation and derivatizaton of antibiotics chemical group (Liu et al., 2019). Best idea may include production of enzymes or they can also expel antibiotic to efflux pump. Antibiotics drug efflux resistance can be accomplished by drug efflux pump playing an important role in microbial resistance. A different type of efflux pump system has been identified that include lipophilic and hydrophilic efflux system targeting the drug at different chemical properties (Wasaznik et al., 2009; Kumar et al., 2012). Another strategy adopting in resistance mechanism is modification of drug targeting gene. This mechanism makes the changes in drug to lose its target through drug targeting gene modification. Another important resistance mechanism is effectiveness of antibiotics by interfering with the target site. Therefore, bacteria has evolved different mechanism that include target site protection. A bactericidal role played by beta lactum antibiotics in inhibition of mucopeptide synthase and bacterial penicillin binding protein (PBP) in cell wall transpeptidation reaction that prevents the formation of complete call wall and hence dies (Sauvage et al., 2016). Bacteria also developed its own strategies to cope up with the environmental stress that can also include human body. In course of gaining the advantage bacteria needs to compete for nutrients and to keep away from the molecules produced by other competing organism (Zhao et al., 2019). Recently researchers have found the importance of biofilm resistance in bacteria. Bacterial biofilm resistance produce by complex and systematic drug resistance mechanism.

Introduction

Antibiotic-resistant bacteria are a major cause of health care-associated infections around the world, and resistance has also emerged in infections in the wider community. Infections caused by multi resistant organisms significantly increase morbidity, mortality, and health care costs. Molecular analyses have revealed that widespread multi resistance has commonly been achieved by the acquisition of preexisting determinants followed by amplification in response to selection. The capture, accumulation, and dissemination of resistance genes are largely due to the actions of mobile genetic elements (MGE), a term used to refer to elements that promote intracellular DNA mobility (e.g., from the chromosome to a plasmid or between plasmids) as well as those that enable intercellular DNA mobility.

Insertion sequences (IS) and transposons (Tn) are discrete DNA segments that areable to move themselves (and associated resistance genes) almost randomly to newlocations in the same or different DNA molecules within a single cell. Other elements, such as integrons (In), use site-specific recombination to move resistance genes between defined sites. As these types of MGE are often present in multiple copies indifferent locations in a genome, they can also facilitate homologous recombination(exchange of sequences between identical or related segments). Intercellular mechanisms of genetic exchange include conjugation/mobilization (mediated by plasmidsand integrative conjugative elements [ICE]), transduction (mediated by bacteriophages), and transformation (uptake of extracellular DNA). Interactions between thevarious types of MGE underpin the rapid evolution of diverse multi resistant pathogens in the face of antimicrobial chemotherapy. Primarily the most important and/ or topical elements in Gram-negative and Gram-positive bacterial species of particular concern clinically, namely, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (the so-called ESKAPE group) (Rice LB., 2008) as well as Escherichia coli (giving the ESKAPEE group) (Llaca-Díaz J.M. et al.,2012); nonetheless, many of the MGE types described are of course broadly relevant to many other bacterial taxa.

Introduction

Resistance to antibiotics in the bacterial world is a genetically determined phenomenon that was first observed within a few years after the introduction of antibiotics for therapeutic purposes. In Nature, ARGs are believed to have originated about three billion years ago as an intrinsic defense mechanism in antibiotic-producing bacteria (Perry et al., 2016; Iskandar et al., 2022), and subsequently, evolved by complex and quantum jump trajectories to mobilize, diversify and interconnect all ecosystems in the micro-biosphere. Bacterial genomes exhibit plasticity and continue to evolve under the selection pressure of antibiotics and other stressors (Patel, 2016). The ARGs in circulation at present are thus a mixture of ancient and modern counterparts. Recently, the interplay between bacterial metabolism and antibiotic resistance has also been revealed (Zampieri, 2021).

The use of antimicrobials in health management, livestock, and food industry is driving the emergence of resistant microbes at a rapid pace (Wall et al., 2016; Adegoke et al., 2016; Hu et al., 2017). As a result, AR pathogens have spread globally to cause loss of lives, production, productivity, and negatively impact economic growth. Recently, AR pathogens in a large study have been found directly responsible for millions of deaths, and the figures are likely to increase in the coming decades (Murray et al., 2022). The pace of the emergence of AR can however be slowed down by improving human interventions. The global and local AR combat plans implemented during the past few years have enhanced the mass awareness of the pandemic problem (WHO, 2015; FAO, 2016; NAP, GOI, 2017; WHO, 2022; WOAH, 2022). These Action Plans on AR containment encourage avoiding of indiscriminate use of antibiotics for the treatment of sick humans and animals, recommend the ban on the use of antibiotics as growth promoters in food animals, promote AR surveillance and monitoring, and support the ‘One-Health’ strategy and application of the biosecurity principles for containment of the resistant microbes.

Introduction

Until the 20thcentury, bacterial infections were the number one cause of human death. In the 1940s, antibiotics became the lifelines for treating serious infections that saved millions of lives. Despite the advantages derived from the use of antibiotics, resistance to these drugs emerged. Unfortunately, resistance to most antibiotics emerged in time-course even for the most powerful antibiotics developed.Resistance to antibiotics is a challenge to the scientific community in keeping up the pace of antibiotic discovery.World Economic Forum’s Global Risks Reporthas listed antibiotic resistance as one of the greatest threats (WEF, 2020).United Nations (UN) has warned that drug-resistant diseases could account for 10 million deaths each year by 2050. By 2030, antimicrobial resistance (AMR) could likelylead up to 24 million people into extreme poverty(IACG,2019). Currently, at least 7,00,000 people die each year due to drug-resistant diseases (IACG,2019). The emergence and widespread of antibiotic-resistant organisms is a global challenge and needs a multi-dimensional approach to address the fundamental issues to minimize drug-resistance.The Antibiotic Resistance Genes Database (ARDB) contains a repository of around 23,000 antibiotic resistance gene or protein sequences conferring resistance against over 240 antibiotics (ARDB). Computational Biology (Bioinformatics) has become one of the important tools in studying antimicrobial resistance. It employs a range of computation techniques to make predictions about the biological phenomenon.

Introduction

The study of infectious diseases, alongside other clinical and natural strengths, is going through fast change introduced on by the approach of reasonable next generation sequencing (NGS) advancements (Koser et al., 2012).These technologies become adopted as routine methods easily, and laboratory techniques are transformed throughout the process. The amount of genomic bacterial data generated is huge. As of this writing, for example, over 200,000 Salmonella genomes alone are in the public domain with hundreds being added weekly. A whole genomic DNA sequence characterizes the maximum practicable level of structural detail on the individuating traits of an microbial organism or population. It can therefore be used to provide more accurate microbial genome recognition, evolutionary relations and a detailed catalogue of epidemiologically important characteristics. This has a significant role to play for outbreak research, diagnosis and treatment of infectious diseases, microbiology and epidemiology (Allard et al., 2019). Besides, DNA sequences are also a universal dataset which can theoretically be used to determine any biological function. This means that antimicrobial resistant (AMR) can be detected and to track the development and spread of AMR bacteria in a hospital or the community.

Introduction

The epidemiological risk and hazards to global health security posed by AMR has been reiterating in several World Health Assembly (WHA) declarations and has been prioritized under the Global Health Security Agenda (GHSA). The Indian Ministry of Health & Family Welfare (MoHFW) has also identified AMR as one of the top priorities for collaborative work with WHO and the first National Action Plan on AMR has been implemented (2017-2022). India ranked fifth in antibiotic consumption in food producing animals (ruminants, pigs, and poultry) in 2010. Even though there has been a gradual reduction of 3.6% in antibiotic consumption during 2011-2019 (Koya et al., 2022), with mounting incomes and shifting in dietary patterns in favour of the consumption of animal protein, especially for poultry, the veterinary antibiotic utilization is projected to further rise by 312%, elevating India to the fourth rank by 2030 (Van Boeckel et al., 2015). FAO has already reported some of the peak resistance rates among common commensal and environmental bacteria against antibiotics like penicillin, cephalosporins, erythromycin and co-trimazoles in India (INFAAR). Resistance to the broad spectrum fluoroquinolones and third generation cephalosporin antibiotics is already more than 70% in Escherichia coli, Klebsiella pneumoniae, and, Acinetobacter baumannii and more than 50% in Pseudomonas aeruginosa. Even the microbial resistance to carbapenems, the last-resort antibiotics, is extremely high among gram-negative microorganisms (Sumanth et al., 2016). To overcome these incidences, it is impulsive to understand the microbe and drug interaction in host system.

Introduction

Malnutrition remains a pervasive global challenge, affecting millions of individuals across the world, particularly in low- and middle-income countries. Despite significant advancements in agriculture and food production, a large segment of the population still lacks access to essential nutrients, leading to severe health consequences and perpetuating cycles of poverty and underdevelopment (Müller and Krawinkel, 2005). Malnutrition, defined as the inadequate intake of essential nutrients required for optimal health and development, encompasses both undernutrition and over-nutrition (WHO, 2023). While undernutrition, characterized by deficiencies in energy, protein, vitamins, and minerals, remains a significant concern, over nutrition, manifesting as obesity and diet-related non-communicable diseases, is also on the rise, particularly in urban settings (Wells et al., 2020). The consequences of malnutrition are far-reaching, impacting physical growth, cognitive development, immune function, and overall well-being, with long term implications for productivity, economic prosperity, and societal stability (Saunders and Smith, 2010).

Rice, a staple food for more than half of the world’s population, plays a central role in global food security and nutrition. However, conventional rice varieties often lack sufficient levels of key nutrients, such as iron, zinc, vitamin A, and certain amino acids, leaving populations reliant on rice-based diets vulnerable to micronutrient deficiencies and associated health risks (Peña-Rosas and Mithra, 2019). Iron deficiency anaemia, zinc deficiency, and vitamin A deficiency, are among the most prevalent forms of malnutrition worldwide, particularly affecting women and children in resource-constrained settings where rice consumption is high (Dipti et al., 2012)

Introduction: N metabolism

Nitrogen is one of the three essential macronutrients for plant growth and yield (Su et al., 2005) and most crucial elements for root growth also (Fageria, 2014). Most macromolecules and a variety of secondary and signalling substances, such as proteins, nucleic acids, cell wall components, hormones, and vitamins, contain nitrogen (N), an important element. In order to assimilate nitrogen, nitrate must be reduced to ammonium, and then ammonium must be converted into amino acids. Perez et al. (1973) pointed out that the rice genotype with high protein yield translocated N from leaf blade to the developing grains more efficiently than the low protein genotype. This was reported due to a high concentration of free amino acids in the sap translocated to the developing grains rather than to differences in translocation rates. Therefore, proper understanding of N metabolism and amino acid translocation are prerequisite to comprehend higher grain protein in high yielding rice genotypes. Use of N by plants involves several steps including uptake, assimilation, translocation and remobilization; and recycling and remobilization when the plant is ageing (Fig. 1). The enzyme nitrate reductase (NR) assimilates nitrate, the main form of nitrogen available to agricultural plants in the field. This enzyme and the nitrogen status of various higher plant systems have a strong positive link, and growth, yield, or protein content can occasionally be connected to this enzyme’s level in seeds or leaves. Nitrate intake occurs at the root level, and it has been demonstrated that plants have two nitrate transport systems that work together to cohabit, absorb, and distribute nitrate from the soil solution throughout the entire plant. (Srivastava 1980) Following NO3- uptake by NO3- transporters and reduction of NO3- to NO2- by nitrate reductase (NR) in the cytoplasm, the process of NO3- assimilation commences (Lea and Miflin, 1974).

Introduction

Understanding the variation in grain protein content is the pre-requisite of its improvement in modern rice varieties. The measure of quantitative and qualitative aspects of grain storage protein content includes estimation of soluble and total grain protein, quantifying various fractions, viz. glutelins, prolamins, globulins and albumins and their profiling through SDS-Page and  estimation of amino acid. As traditional chemical methods for protein content determination are destructive in nature. All these estimates comprehensively give insight into the diversity of storage protein in rice germplasm. The standard procedures followed for all these estimates are briefly stated in the  following sections.

Estimation of Total Grain Protein Content in Rice

The total protein is estimated via estimation of total N through the Kjeldahl method whereas soluble protein is estimated through Lowry method, Dumas method and Bradford method. But for estimation of large number of genotypes all these processes are tedious, time-consuming, and costly. Near-infrared spectroscopy (NIRS), as a non-destructive detection technique, can achieve rapid quantitative determination of protein contents and become an important development direction to replace traditional chemical detection methods.

Introduction

Rice is one of the most important staple foods among all cereals. The larger population in Asia and Africa depends on rice for their daily calorie and nutritional requirements. People are found to bank on rice as their main source of nutrition in emerging and underdeveloped nations (Yang et al. 2016). However, it is considered that the milled or polished rice is nutritionally poor as the majority of the essential micronutrients viz. iron (Fe) and zinc (Zn), and important vitamins are lost during the process of milling and polishing (Johnson et al. 2011). So, by the way, the poorer section of the worldwide population mainly depends on rice and is most vulnerable to ‘hidden hunger’ as they are unable to afford other micronutrients-rich non-staple foods for their balanced diet and are often at the maximum risk for micronutrients deficiencies (Bouis and Saltzman 2017). The only possible solution for such malnutrition is to have nutritionally enriched food in the daily foodstuff. However, approximately one third of the world’s population is facing the problem of hidden hunger (White and Broadley 2009). Prolonged utilization of carbohydrate-rich food mainly based on rice, wheat, or maize is contributing to such nutritional deficiency in the poorer section of our society as most of them are unable to supplement nutritionally rich food for their diet. The deficiency of micronutrients can be termed a silent epidemic because it slowly weakens our immune system and hampers physical and intellectual development which may lead to fatality in some severe conditions. In the case of micronutrient deficiencies, deficiencies  of iron or iron deficiency anaemia (IDA), zinc deficiency, and vitamin-A  deficiency (VAD) are common, and have serious consequences.

Introduction

Rice contains essential micronutrients such as iron (Fe), zinc (Zn), copper (Cu), calcium (Ca), manganese (Mn), magnesium (Mg), etc. which are generally lower when compared with other staple crops like wheat, maize, legumes, and tubers (Adeyeye et al. 2000). The most crucial micronutrients are iron and zinc, whose inadequacy is a leading cause of malnutrition. In this chapter we discuss estimation methodologies and diversity of Fe and Zn, its genetic basis, and improvement for micronutrient content through breeding techniques.

Procedure of Estimation of Fe and Zn Content in Rice Grain

Iron and zinc concentrations in rice samples were generally estimated by colorimetric method Atomic Absorption Spectrometry (AAS), X-ray Fluorescence (XRF), and Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES). X-Ray Fluorescence (XRF) Spectrometry is extremely helpful in the non-destructive estimation of relative Zn and Fe concentration in rice breeding lines and large germplasm collection (Paltridge et al. 2012). The majority of biofortification programs employ XRF as a metal analysis tool. For estimation of Fe and Zn, panicles of middle row plants of each replication were harvested, sun-dried for 4-5 days to reduce the moisture content to 11-12 %, and then seeds were dehusked. Each brown rice sample of about 5g was subjected to energy dispersive X-ray fluorescent spectrophotometer (ED-XRF) as per standard protocol (Stangoulis and Sison 2008, Rao et al. 2014) and expressed in ppm (µg g-1).

Introduction

Rice is the world’s most important staple crop and is a primary source of energy and nutrition for about half of the world’s population. So it is the most important cereal crop with respect to food security of common people. Due to increasing world population and shrinkage of farm land holdings there is an urgent need to increase the grain productivity. Therefore, increasing grain yield has become the primary objective in many rice-breeding programs. India is the second highest rice producer (about 120 million ton/year) in the world and able to meet the demand of rice for the entire Indian population. But along with yield improvement of rice, quality has now become a foremost consideration for rice consumers and millers. Quality is defined as “the totality of features and characteristics of a product or service that bears its ability to satisfy stated or implied needs” (International Standard Organization (ISO) 8402 1986). The concept of grain quality covers many physico-chemical properties such as grain shape and size, milling and cooking properties, amylose content, stickiness, chalkiness, texture, colour, gelatinization characters and various nutritional properties. Thus, rice grain quality generally includes five main classes i.e. (i) milling quality, (ii) physical quality, (iii) cooking and eating quality (iv) sensory quality and (v) nutritional quality. Grain quality and its assessment are very important to consumers, millers and rice breeders who are engaged in varietal improvement programme, related to new features such as high nutritional quality, high yield potential, highly resistant to abiotic or biotic stresses, higher water use efficiency etc.

Introduction

The transgenic approach can be an effective alternative for the development of biofortified crops when there is limited genetic variation for the targeted nutrient content among the germplasm (Zhu et al. 2007). Transgenic approaches have been used for the simultaneous integration of genes involved in the enhancement of micronutrient concentration as well as reduction in the concentration of antinutrients, resulting in enhancing the bioavailability of nutrients in plants. Development of biofortified crops employing the transgenic approaches, involves a significant amount of time, effort, and resources during the development stage, but it is a cost-effective and sustainable approach in a long run (Garg et al., 2018). For its wide consumption, rice has been targeted to address the global challenge of malnutrition. Vitamin deficiency can be considered as one of the significant challenges that affect poor section of populations due to low affordability. Development of ‘Golden Rice’ with provitamin A (beta-carotene) was recognized as an important breakthrough in this direction by expressing genes encoding PSY and carotene desaturase (Datta et al. 2003). Folic acid (vitamin B9) is important during pregnancy and reducing anemia. Rice was genetically modified to increase folate content (up to 150-fold) by overexpressing genes encoding Arabidopsis GTP-cyclohydrolase I (GTPCHI) and aminodeoxy-chorismate synthase (ADCS) (Blancquaert et al. 2015). Rice has also been targeted to address the global challenge of iron deficiency anemia. Multiple reports indicated an enhance in iron content by overexpressing a number of genes (Lee et al. 2009). Similarly, zinc content was also raised in rice by overexpressing OsIRT1 and mugineic acid biosynthesis genes from barley (HvNAS1, HvNAS1, HvNAAT-A, HvNAAT-B, IDS3) (Lee and An 2009, Masuda et al. 2008).

Significant Progress and Prospects

It is widely acknowledged that biofortification presents a promising and cost effective agricultural strategy to enhance the nutritional status of malnourished populations globally. Approaches to biofortification, including crop breeding, targeted genetic modification, and mineral fertilizer application, offer significant potential for combatting mineral deficiencies in human diets. The development of biofortified food crops with enhanced nutrient content such as iron, zinc, selenium, and provitamin A has shown promise in addressing micronutrient deficiencies prevalent in both developing and developed nations. Over the past decade, both national and international initiatives have made substantial contributions toward achieving these goals. These efforts have resulted in the release of biofortified varieties across various crops, including rice, maize, wheat, potatoes, vegetables, and millets. The majority of these varieties have been developed through conventional breeding methods without sacrificing crop yield, making them readily accepted by both growers and consumers.

One of the United Nations’ sustainable development goals is the cultivation of nutritionally rich crop varieties with heightened levels of micronutrients such as iron, zinc, calcium, total protein, lysine, tryptophan, anthocyanin, provitamin A, and oleic acid, coupled with reduced levels of anti-nutritional factors. In the past decade, 142 biofortified varieties, spanning rice, wheat, maize, pearl millet, small millet, lentil, chickpea, and other crops, have been developed under the auspices of the Indian Council of Agricultural Research (ICAR). Biofortified varieties typically do not impact ecological conditions, soil, or water requirements differently from traditional varieties. Additionally, they do not incur extra cultivation costs, and their economic output is comparable to traditional produce, leading to their widespread adoption. In India, the scale-up of biofortified varieties has gained momentum, with substantial quantities of breeder seeds being produced and distributed to public and private seed agencies for further multiplication and dissemination to farmers. Over the past six years, approximately 10 million hectares of land have been cultivated with biofortified rice, wheat, pearl millet, mustard, and lentil varieties.

Introduction

India’s policy in agriculture sector began in 1950 with a conscious effort to meet out the food needs of Indian population in view of famines but later on shifted to develop the agriculture education and research system for enhancing the productivity of staple crops and develop competent human resource to build skilled man power to strengthen agriculture and solve the problem of food & nutritional security at the nation level (1960,s to 1990,s) to the solution of global problems in agriculture through global solutions (2000,s onward) by forging the regional and global international corporation at different levels.

The closing years of the second decade of 21st century brought one of the most remarkable transitions in the international cooperation for strengthening the agriculture research and education in the history of agriculture in India. In most of the world the transition from a resource-based to a science-based system of agriculture is occurring within a single century.

Science, Technology and Skill Development in 21st Century

In the twenty first century, science and technology are viewed as the drivers of Indian economic growth; and agricultural R&D is expected to play a significant role in the process. Agriculture research and development is being affected by research and development at international level.

Introduction

Women in India constitute nearly half of the population. They contribute 75% to the development of our society as compared to men who only 25%. According to the census 2011, nearly 98 million women in India have agriculture jobs, but around 66.1 million of them are depended on others’ farms as agriculture labours. They are engaged largely in cotton, tea, oil seeds and vegetable production. It is also worth mentioning that from the basic level of work concerning farm related activities to unskilled farm jobs like sowing, transplanting, weeding, harvesting and post harvesting activities like winnowing, processing, storage etc. women are engaged right from the start.

Woman’s contribution to the fisheries sector is 22% according to the FAO. Food security, horticulture, sericulture, livestock production and collection of non- timber forest are some of the allied sectors in which they are involved. They are also involved in other allied sectors which include cattle management, milk and poultry farming, and fodder collection. At the same time, women’s domestic activities include cooking, child rearing water collection from the nearby and far-off places, fuel wood gathering and the overall upkeep of household. Ironically, women face disparities in terms of compensation, their share in properties and in representation in local bodies. Much of their contribution in the food production system as food producers and providers has not received effective recognition. This affects their lives and familial conditions in terms of poor health of children and low educational attainments.

Introduction

Millet is a very important cereal grain that many people around the world eat. In fact, over a third of the world’s population consumes millet. It’s the sixth most produced cereal crop globally. Some common types of millet include Jowar (Sorghum), Sama (Little millet), Ragi (Finger millet), Korra (Foxtail millet), and Variga (Proso millet). Among these, Bajra and Sama have more fat, while Ragi has the least. Millet has been cultivated for thousands of years and is used in many parts of the world. In the past, even the Romans and Gauls enjoyed millet-based porridges. Today, China, India, Greece, Egypt, and various African countries are the major producers of millet. In rural areas, some types of millet, like Finger millet and Sorghum, are eaten by people, while others are primarily used as animal feed. These millets have packed with several beneficial nutrients and play a crucial role in traditional diets in many regions. Compared to commonly used rice and wheat, millet is three to five times more nutritious. While wheat and rice mainly provide food security, millet offers not only food security but also health benefits and livelihood opportunities. It can help manage health issues like diabetes and high cholesterol.

In India, Karnataka is the top producer of millets, accounting for over 58% of global production. Despite its nutritional and health benefits, many people in India are not aware of the advantages of consuming millet. (Upadhyaya et al., 2007). Millets are fantastic crops when it comes to pest management. Traditionally grown millets don’t require pesticides and the land used for millet cultivation remains largely pest-free. Some millets, like foxtail millet, not only resist pests themselves but also serve as natural protectors against pests in storage conditions for other crops like green gram. This means there’s no need for fumigants to keep them safe. It has a treasure trove of micronutrients, including vitamins and beta-carotene, which are now seen as essential as pharmaceutical pills. In the present day, millets are exceptionally superior and serve as a solution to the widespread issues of malnutrition and obesity affecting a significant portion of the Indian population (Singh KP et al., 2012). Millets are rich in essential fatty acids, including linoleic, oleic, and palmitic acids, which are present in their free form. They also contain compounds like monogalactosyl, diacylglycerols, digalactosyl diacylglycerols, phosphatidylethanolamine, phosphatidylserine and phosphatidylcholine in bound forms. Although other fatty acids like arachidic acid, behenic acid and erucic acid are found in millets, they are in trace amounts. Millet oil can be a valuable source of linoleic acid and tocopherols. Additionally, millets are gluten-free and have an alkaline effect in the body. They contain essential B vitamins such as niacin, folacin, riboflavin, and thiamine, as well as phosphorus. These nutrients play a crucial role in energy synthesis within the body.

Introduction

In the middle of the 1900s, the world experienced a big increase in people, leading to a greater need for food. This demand for more food pushed for a farming revolution called the “green revolution.” This revolution used chemicals to help grow more crops and fight plant diseases. But using lots of these chemicals caused problems for the environment and people’s health. Even with all these chemicals, a large amount of food (up to 25% of what’s grown) is still lost to diseases each year. By 2050, we might need to double how much food we make. To do this without harming the environment or health, we’re looking for new ways. Some ideas include making plants that are genetically modified, creating plant varieties that resist pests naturally, and using helpful microorganisms like certain bacteria and fungi. These helpful organisms can be used in different ways, like making soil healthier or protecting plants.

The microorganisms colonizing plant roots generally include bacteria, algae, fungi, protozoa and actinomycetes. Enhancement of plant growth and development by application of these microbial populations is well evident. Among different microbial populations present in the rhizosphere, bacteria are the most abundant microorganisms. Various genera of bacteria, Pseudomonas, Enterobacter, Bacillus, Variovorax, Klebsiella, Burkholderia, Azospirillum, Serratia and Azotobacter, cause a pronounced effect on plant growth and are termed as plant growth promoting rhizobacteria (PGPR). PGPR play a significant role in enhancing plant growth and development both under non stress and stress conditions by a number of direct and indirect mechanisms. Microbes exert key functions in ecosystems being involved in nitrogen fixation, phosphorus solubilization, soil formation, and production of siderophores, plant growth regulators and organic acids as well as protection by enzymes like ACC-deaminase, chitinase and glucanase.

Introduction

Livestock sector has been an integral component of Indian agriculture since time immemorial due to its multifarious contributions to the society in the form of nutrient-rich food products, clothing, drought power, income and employment. India has huge population of livestock. Of the total livestock population of the world, India alone has about one-fifth cattle population. As per the 20th livestock census estimate, total livestock population in the year 2019 was over 535 million. Among the livestock products, milk is the most important. India has a glorious history of outstanding achievement in transforming itself from milk deficit country to world’s biggest milk producer over the span of three decades. With over 300 million bovines and producing over 198 million tonnes of milk in 2019-20, the Indian dairy sector exhibits strong growth potential. Despite COVID-19 induced restrictions, which has thrown the smallholder milk producers from the frying pan to fire, the organized dairy sector showed positive growth rate of around 1% in the last f iscal– the lowest in a decade. Despite these proud boasts, poor productivity potential of Indian milch herd is a major cause of concern that may threat its numero one position in future.

The major causes of low milk productivity in India are both intrinsic (low genetic potential) and extrinsic (poor nutrition/feed management). Empirical studies in India have shown that enhancing quality and quantity of feed and fodder has greater impact than breed improvement on increasing milk productivity (Lalwani, 1989; Gaddi and Kunal, 1996; IAEA, 2006; Roy et al., 2020). The timely unavailability of nutritionally rich feed and fodder is a major hitch that impinges on the productivity growth of farm animals in the country. Nonetheless, with increase in agricultural production over the time, the animal feed availability has also improved, but its supply always falls short of the aggregate demand. At national level, the recent reported shortage in green fodder, dry fodder and concentrates is 11.24%, 23.4% and 28.9%, respectively (Roy et al. 2019), and the scenario is more unnerving in few Indian states where the fodder deficit is above 25% (Fig 1).

1.1 Introduction

Water scarcity is seen as a major constraint to intensify agriculture in a sustainable manner as an attempt to meet the food requirements of a rapidly growing human population. The ever-increasing human population, climate change due to increased emissions of greenhouse gases (GHGs), and intensification of agriculture, are putting severe pressure on the world’s two major non-renewable resources of soil and water, and thus pose a big challenge to produce sufficient food to meet the current food demand. The present world population of 7.3 billion people is predicted to grow to over 9 billion by 2050, with the majority of this population increase occurring in developing countries, most of which already face food shortages. A 70% increase in current agricultural productivity will be required to produce sufficient food if these human population growth predictions prove to be correct. In this context, concerted efforts are being made globally to improve the effectiveness of water which will be used for enhancing the production of irrigated crops. Additionally, efforts are also being made to improve water harvesting and water conservation in rain-fed agriculture.

The injudicious use of saline/brackish water is all too often associated with the development of soil salinity, sodicity, ion toxicity, and groundwater pollution. Because of these negative effects, it is important to have a better understanding of exactly how the quality of water influences the management of irrigated agriculture, especially in arid and semi-arid regions.

2.1 Introduction

Water is the most precious gift of the nature and it is also the most crucial element for sustainability of the life in the earth. India is the largest user of freshwater in the world. India’s total water consumption alone is the higher than any other continents. The Agricultural sector is the largest consumer of water followed by the domestic sector and the industrial sector. The role of irrigation water as one of the most essential inputs for crop cultivation can’t be denied. As a traditional productive input, it ensures production by acting as an agent of insurance against inadequate and inconsistent monsoon. Ultimately the outcome provides agricultural production stability. Thus, irrigation is of prime importance in cultivation of vegetable crops as it ensures favourable water balance within the root zone in addition to natural precipitation. It fulfils the crop- water demand and improves the crop production and effectiveness of other agricultural inputs. It is also an important limiting factor of crop yield, because of its association with several factors of plant environment, which directly influence the crop growth and development (Yaghi et al., 2013). The various irrigation methods under different system of irrigation differ with regard to extent of control, timeliness and adequacy of supply of irrigation water for crop cultivation. Consequently, the economic benefits and the costs due to these irrigation methods vary among different irrigation systems. The dominant method of irrigation practiced in large parts of the country is surface irrigation (basin, border and furrow) where the entire soil surface is almost f looded without considering the actual consumptive requirements of the crops. Frequent over or under irrigation create the problems of water stress or water logging leading to reduced irrigation efficiency (less than 30%).

3.1 Introduction

Groundwater constitutes about 89% of the total fresh water resources in the planet. But in recent years, due to over exploitation of ground water and erratic nature of monsoon, there has been depletion of ground water across the world. Depletion of ground water has reached to the extent that it is virtually impossible to get the water table back. Even though there is a possibility of recharge of water from the other areas, the process is very slow and may take one year to replenish one meter. In view of this management of ground water has become one of the most significant issues in recent times. Added to it, there are also environmental problems such as aqua for mining, salt water intrusion, stream base flow reduction etc. For several reasons the efficient management of ground water resources through market mechanism has become difficult. Against this context the present article attempts to analyze the need for sustainable ground water management in India. The article also briefly discusses the concept of sustainable ground water management, factors affecting ground water availability, different approaches towards developing and using available ground water without adversely affecting the hydro geological balance. Further, the paper highlights strategies for sustainable groundwater management, including development of aquifers, rainwater harvesting and artificial recharge methods. The article offers some relevant policy recommendations for sustainable groundwater management in India.

4.1 Introduction

Water pollution is the contamination of water by an excess amount of a substance that can cause harm to human beings and/or the ecosystem. The level of water pollution depends on the abundance of the pollutant, the ecological impact of the pollutant, and the use of the water. Pollutants are derived from biological, chemical, or physical processes. Although natural processes such as volcanic eruptions or evaporation sometimes can cause water pollution, most pollution is derived from human, land-based activities (Figure 4.2). Water pollutants can move through different water reservoirs, as the water carrying them progresses through stages of the water cycle (Figure 4.1). Water residence time (the average time that a water molecule spends in a water reservoir) is very important to pollution problems because it affects pollution potential. Water in rivers has a relatively short residence time, so pollution usually is there only briefly. Of course, pollution in rivers may simply move to another reservoir, such as the ocean, where it can cause further problems. Groundwater is typically characterized by slow flow and longer residence time, which can make groundwater pollution particularly problematic. Finally, pollution residence time can be much greater than the water residence time because a pollutant may be taken up for a long time within the ecosystem or absorbed onto sediment.

5.1 Introduction

Out of the many climatic events that influence the earth’s environmental fabric, drought is perhaps the one that is most linked with desertification. Drought is a natural hazard originating from a deficiency of precipitation that results in a water shortage for some activities or some groups and is often associated with other climatic factors (such as high temperatures, high winds and low relative humidity) that can aggravate the severity of the event. Drought differs from aridity in that the latter is restricted to low rainfall regions and is a permanent feature of the climate. Drought occurrences are common in virtually all climatic regimes.

Widespread and severe drought conditions in Asia, Latin America and the Caribbean in 2000 have raised serious concerns about the continuing vulnerability of the world community to extended periods of droughts and water shortages. In 2000, major droughts affected much of south-eastern Europe, the Middle East, and the area through central Asia to northern China. Especially hard hit was Afghanistan, Bulgaria, Iraq and the Islamic Republic of Iran and parts of China. In North America, months of above-average temperature coincided with below-normal precipitation through northern Mexico and much of the southern and western regions of the USA, leading to one of the worst wildfires in the past 50 years.

By August 2001, much of Western Asia, Central Asia, and the Middle East was suffering the third year of a continuing drought that severely reduced many countries’ crop yields. The countries most affected were Afghanistan, India, Islamic Republic of Iran, Pakistan, and Tajikistan.

6.1 Introduction

Water deficit stress is a serious and frequently encountered abiotic stress in the terrestrial surface. Its deleterious effects on plant growth and productivity are well documented. Plant responses to water stress are believed to be complex as these operate at various levels of plant organization. Several in built physiological and biochemical mechanisms provide resistance to plants against stress. An understanding of the processes linked to these mechanisms is vital for optimizing crop growth and productivity under stress. Plants respond and adapt to water stress by altering cellular metabolism, thus invoking stress tolerance. Alteration in endogenous concentrations of growth regulators along with accumulation of osmolytes, modifications in antioxidant cascade, changes in protein profiles and induction of gene expression in plants under stress are important characteristic metabolic changes that invoke stress tolerance at the cellular level. Alteration in endogenous concentrations of plant bio-regulators under stress helps plants through better turgor maintenance and efficient water usage by influencing stomatal functioning, hydraulic conductivity and morphological adaptation. Progress made in plant adaptation to water stress is an outcome of advances made in analytical techniques on endogenous growth regulator analysis and powerful and reliable molecular and genetic techniques.

7.1 Introduction

Water is one of the most essential natural resources of the planet. Water is also the most critical resource for sustainable development in most of the developing countries. The quantities that are needed for drinking and sanitation purpose of humans are relatively small, and much larger quantities of water are required for many other purposes. It is essential not only for agriculture, industry and economic growth of a country, but also it is the most important component of the environment and ecosystem, with significant impact on overall wealth and nature conservation. Agricultural and industrial activities critically depend on a sufficient amount of fresh water that is withdrawn from rivers, lakes and groundwater aquifers. Currently, the rapid growth of world population along with the extension of irrigation dependent agriculture, development of industrial sector and climate change are stressing the quantity and quality of the natural water systems. Due to the increasing problems, human have begun to realize that they can no longer follow “use and discard” methodology either with water resources or any other natural resources. As a result, the need for water management has become evident. Climate change has already started to affect the hydrological cycle and the availability of freshwater for agriculture. So, proper water management practices play crucial roles in the food production and the management of ecosystems. Over the last century global irrigated area has increased more than sixfold from approximately 40 million hectares in 1900 to more than 260 million hectares in 2000. Today more than 40% of the world’s food comes from the irrigated cropland which is 18% of the total cultivated crop land. Irrigated area is increased by almost 1% every year and the demand for irrigation water will increase by 13.6% by 2025 (Jensen, 1993). On the other hand about 8-15% of fresh water supply will be diverted from agricultural sector to meet the increased demand of domestic and industrial use. On the other hand the efficiency of irrigation is very low, only 65% of the applied water is used by the crop (Fig. 1). So, to overcome shortage of irrigation water for agriculture, it is essential to increase the water use efficiency in the crop field and to use marginal water for irrigation.

Introduction

The foundation of agricultural productivity lies in the realm of weather and climate, a reality unaltered by technological progress. The consequences of climate change on agriculture represent a worldwide apprehension, particularly significant for India. Around 54.6% of the Indian population is engaged in agriculture and allied activities, contributing to 17.4% of the country’s total gross value added. The agriculture sector is battling a multitude of challenges, such as increasing food demand, depletion of agricultural lands and water resources, and the devastating effects of climate change. It is high time that we acknowledge and address these issues to safeguard the future of our food systems and ensure food security for all.

Climate change refers to the long-term variations in weather patterns and temperature over extended periods. Climate change occurs when earth’s climate system experiences variations in weather patterns that can last for decades or millions of years. These changes can arise naturally due to phenomena like volcanic eruptions or changes in solar activity. However, since the 1800s, human activities accelerate the natural pace of climate change, primarily due to the combustion of fossil fuels like coal, oil, and gas. These activities release greenhouse gases like carbon dioxide (CO2 ), methane (CH4 ), and nitrous oxide (N2 O) into the atmosphere, trapping heat and leading to a gradual increase in global temperatures. One of the most remarkable characteristics of climate change is the increase in temperature, which is widely referred to as global warming (Houghton, 2009). According to the report of Intergovernmental Panel for Climate Change, the release of greenhouse gases caused by human actions has contributed to around 1.1°C of warming since the period between1850-1900. The report also predicts that the global temperature will likely increase to 1.5°C or more in the next 20 years (IPCC, 2021).

Introduction

Soil is a silent foundation and a dynamic part of Earth’s complex ecosystem. It sustains life, influences plant growth and is involved in various environmental processes. However, the balance of this vital resource is increasingly threatened by the pervasive effects of climate change, manifested by rising temperatures, changing rainfall patterns and changes in atmospheric conditions. As global temperatures rise and weather patterns change, the relationship between soil and climate poses transformative challenges with far-reaching consequences. This research addresses the complexity of this interaction and examines how climate change affects agriculture, soil health, composition and functionality. Soil health, a holistic concept that includes physical, chemical and biological aspects of soils, is closely linked to climate change. A notable consequence of climate change is the increasing frequency and intensity of extreme weather events such as droughts and floods. These events disrupt the delicate balance of soil ecosystems and lead to erosion, loss of topsoil and reduced fertility. Additionally, increased temperatures contribute to soil moisture depletion, reducing water availability for plants and microorganisms and further compromising soil health. A central issue at the interface between soil science and climate change is the role of soil as a carbon sink. Soils store large amounts of carbon in the form of organic material, thereby influencing the environment.

Introduction

Climate plays a crucial role in shaping the agricultural landscape of a region, and the changing climatic conditions pose a significant threat to global food security. In developing countries in Asia and Africa, the primary challenges to realizing optimal crop yields are declining soil fertility, particularly soil organic carbon and drought. The unchecked emission of greenhouse gases is expected to lead to a considerable rise in the average global temperature by 6°C in the next century, primarily driven by activities such as fossil burning and urbanization. Over the past centuries, there has been a noticeable increase in the concentration of CO2 and CH4 , with up to a 35% expected rise in nitrous oxide due to the improper use of nitrogenous fertilizers. Climate models predict a substantial impact on agricultural productivity in the 21st century, with rising temperatures and more frequent extreme weather events (NASA, 2022). To maintain agricultural productivity, it is imperative to understand the effects of increasing temperatures, shifting precipitation patterns, and rising CO2 levels on soil health. It is noteworthy that climate is one of the key factors influencing soil formation, alongside four other factors. Temperature and precipitation directly affect soil formation by providing the necessary conditions for weathering and biomass production. The sum of active temperature and precipitation evaporation ratio are critical parameters that determine energy consumption for soil formation, water balances in soil, organic-mineral interactions, and the transformation processes within the soil. However, human activities such as population growth, deforestation, disruption of marine ecosystems, and the greenhouse effect contribute to climate change, leading to denudation, depletion of soil organic matter, destruction of soil structure, erosion, and desertification, ultimately causing a decline in soil health and environmental degradation (IMD, 2021). Despite being a gradual process, climate change, characterized by small, long-term changes in temperature and precipitation, significantly influences various soil processes, particularly those related to soil fertility. The anticipated effects of climate change on soils primarily involve alterations in soil moisture conditions, increased soil temperature, and elevated CO2 levels. Understanding the consequences of climate change on soil health is crucial, as it has far-reaching impacts on agriculture, biodiversity, carbon cycling, and ecosystem resilience in the face of an evolving climate (Nunez et al., 2019).

Introduction

Climate change has significant adverse implications on the physiological processes and metabolic machinery of plants, potentially affecting growth, development, and overall crop productivity. The rapid increase in global population exacerbates the threat to global food security, which is further impacted by changing climate conditions. The Intergovernmental Panel on Climate Change (IPCC) estimates that between 1850 and 1900 and 2011 and 2020, the global mean land surface air temperature increased by 1.6 °C. Predictions by the United Nations indicate that the global human population could reach 8.5 billion by 2023 and 9.7 billion by 2050, up from the current 8 billion. The National Centers for Environmental Information (NCEI) reported that 2022 was 0.86°C warmer than the average of the 20th century, making it the 6th warmest year on record. These data suggest an increased probability of unpredictable climate changes and harsh growing conditions, manifesting as various abiotic stresses on major cultivable lands. Climate change impacts CO2 concentration, temperature, precipitation, pollutants, and nutrient availability and uptake, leading to drought, salinity, irregular rainfall, f looding, high temperatures, and nutrient deficiencies in staple food crops, thereby threatening global food security. This review focuses on the effect of elevated CO2 and temperature on fundamental plant metabolic processes such as photosynthesis, respiration, transpiration, and nitrogen metabolism.

Introduction

The world’s food and nutritional security are under serious threat from climate change. Climate changes have significant effects on agriculture by affecting insect pests, their natural enemies, and pollinators as illustrated in Fig 1 (Eigenbrode and Adhikari, 2023). According to Benedict (2003), 13.6% of annual crop loss worldwide is attributed to insect pest attack. Crops, crop pests, natural enemies and pollinators are directly and indirectly impacted by erratic climate. The continuous and anticipated alterations in these insects vary across species, systems, and geographical areas, impeding the development of strong generalizations and forecasts. Moreover, the implementation of “climate-smart” agricultural methods, may have additional effects on ideal management of these insects.

Direct effects on insect pests

Temperature: The most reliable, well-researched, and easily modelled component of climate change is warming. Warming affects physiology, phenology, dispersal, reproduction, development, and survival of insect pests (Bale et al., 2002) as illustrated in Fig 2 (Skendži? et al., 2021). It can be inferred that increased herbivory would be associated with rising temperatures in many cases. High temperature and high humidity are key reasons for whitefly population increase (Pathania et al., 2020). Warming can alter the number of insect generations in Helicoverpa armigera (Lepidoptera: Noctuidae) in China (Huang and Hao, 2020).

Introduction

The “plant disease triangle” is a fundamental concept in plant pathology that illustrates the interaction between three essential components necessary for the development of a plant disease. Firstly, the host plant which refers to the plant species or cultivar that is susceptible to the pathogen. Host plants provide the necessary environment and resources for the pathogen to establish, grow, and reproduce. Secondly, the pathogen which is any organism (such as fungi, bacteria, viruses, nematodes, or other microorganisms) that can cause disease in plants. Pathogens can infect host plants through various means, including direct contact, airborne spores, soil-borne organisms, or vectors such as insects. And thirdly, the environment which encompasses all external factors that influence the interaction between the host plant and the pathogen. This includes abiotic factors such as temperature, humidity, soil moisture, light, and nutrient availability, as well as biotic factors such as the presence of other organisms (competitors, predators, symbionts) that may affect disease development.

The plant disease triangle illustrates that the occurrence of a disease requires the presence and interaction of all three components: a susceptible host, a virulent pathogen, and a conducive environment. If any of these components is missing or unfavourable, disease development may be inhibited or prevented. Any change in ecosystem can affect plant diseases, because plant disease is the result of interaction between a susceptible host, virulent pathogen and favourable environment. If any of the three factors are altered, the progress of any one disease can change. Although interactions among the three factors must be matched, weather is an important variable due to its dynamic behaviour.

Introduction

Rising temperature, decreasing precipitation, increased frequency in drought and flooding, etc. is making us realize climate change is not some cooked up story. Still there are people who believes climate change is not real. By definition, Climate change is a long-term shift in global or regional climate patterns. This will affect the life of people in many forms: health, food, water, etc. (Table 1). Agriculture is a highly vulnerable field to such weather and climate changes, they can have significant direct and indirect impacts on farm productivity and profitability. Climate change will have adverse effect on crop physiology, growth and chemistry and thus it will cause negative impact on agricultural production. Because of the variation in climate, moisture availability may change, which limits vegetation activity/plant growth, increase in drought/ heat/flooding will the crop growth and yield. Elevated CO2 does not have a profound effect on C4 plants. On the contrary, tissue nitrogen concentrations are higher for C3 species under increased CO2 . Intergovernmental Panel on Climate Change (IPCC) estimates that climate change and elevated CO2 is expected to increase competitiveness of invasive weed. IPCC also estimates that with 1°C rise in global temperature, 5 to 10 per cent yield reduction of major food and cash crops (Pachauri et al., 2014).

Introduction

Climate change is a deadliest hazard to life on Earth. Global temperature is rising due to greenhouse gas emissions from the usage of fossil fuels, this result in widespread agricultural and fisheries failure, the extinction of hundreds of thousands of species, and whole towns becoming uninhabitable (Lindwall, 2022). Rising global temperatures are severely killing humans and trees, forcing half of all species to move, worsening water-borne and respiratory ailments in people, and jeopardising millions’ food and water security (Isaacs-Thomas, 2022). Addressing these concerns necessitates a worldwide collaboration to minimise greenhouse gas emissions and promote sustainable behaviours. Climate change affects agriculture production, lowers crop nutritional value, and increases the frequency of extreme weather events. These interruptions jeopardise food production, availability, and access, especially in vulnerable countries. Microbes play an important role in soil health, nitrogen cycling, and ecosystem stability. They impact a variety of soil activities, such as organic matter breakdown, nutrient mobilisation, and plant growth stimulation. However, climate change poses a substantial danger to microbial communities, possibly changing their activities and altering ecosystem dynamics (Wang et al., 2022). Transitioning to a low-carbon economy requires a global effort. Mitigation strategies include enhancing energy efficiency, adopting renewable energy sources, electrifying industrial processes, implementing efficient transportation systems, and introducing carbon taxes or emissions markets.

Introduction

Climate change is widely acknowledged as the most significant contemporary challenge facing humanity. According to a recent report from the Intergovernmental Panel on Climate Change (IPCC, 2022), the situation has deteriorated further, with 3.3 billion people worldwide highly susceptible to climate change. Current unsustainable development practices are escalating the exposure of ecosystems and populations to climate-related risks. Human activities and their impact on the climate and environment are leading to unprecedented extinctions of animals and plants, resulting in a loss of biodiversity and posing a threat to life on Earth. The diversity of microorganisms is fundamental to maintaining a healthy global ecosystem, as the microbial world serves as the life support system of the biosphere. Although the influence of human activities on microorganisms is less conspicuous and less well understood, a significant concern is that changes in microbial biodiversity and functions will impact the resilience of other organisms, affecting their ability to adapt to climate change. Microorganisms play crucial roles in carbon and nutrient cycling, as well as in the health of animals (including humans), plants, agriculture, and the global food web. Microorganisms inhabit all environments on Earth occupied by larger organisms and are the exclusive life forms in certain environments such as the deep subsurface and extreme habitats. Dating back to the origin of life on Earth at least 3.8 billion years ago, microorganisms are likely to persist well beyond any future extinction events. Despite their vital role in regulating climate change, microorganisms are seldom the focal point of climate change studies and are typically overlooked in policy development. The challenge lies in understanding their intricate role in the ecosystem due to their vast diversity and varied responses to environmental changes.

Introduction

Climate change may advance more rapidly than anticipated, introducing novel environmental conditions for cultivating horticultural crops. The rise in atmospheric CO2 levels from non-renewable energy sources combustion drives global average temperatures, altering weather patterns worldwide with regional variations (Stocker et al., 2013). Currently, certain regions are already experiencing the effects of extreme weather events such as heat waves or frost, while prolonged droughts pose a growing threat to global food security elsewhere. Climate changes may yield both positive and negative outcomes, but they will undoubtedly alter production conditions and product quality (Kaufmann and Blanke, 2017).

Elevated temperatures can enhance the ability of air to hold water vapor, leading to increased water demand. This process can elevate evapotranspiration rates, potentially depleting soil water reserves and causing water stress in plants during dry periods. Fruit production is particularly vulnerable to water stress, especially in regions where trees lack irrigation. Numerous studies indicate that water stress diminishes crop yields and hastens fruit ripening (Henson, 2008).

Introduction

Agriculture is the backbone of every country. It largely depends on climate and its changes. Over the last few years climate change has affected crops, cropping systems, patterns and the ecosystem hugely. Climate change is caused by greenhouse gases in the atmosphere, which results in global warming (Aydinalp and Cresser, 2008). The rising temperature, melting of glaciers, loss in vegetation cover, frequent occurrences of drought and floods are some of the issues that have raised concern among the environmentalists. The change in temperature and precipitation patterns alters the traditional growing seasons. Climate change is expected to influence crop and livestock production, hydrologic balances, input supplies and other components of agricultural systems (Adams et. al., 1998). Vulnerability of climate change depends on physical, biological and socio-economic characteristics. Low income populations dependent on isolated agricultural systems are particularly vulnerable to hunger and severe hardship. These populations are already barely food-sufficient, even the slightest decline in yields could be very harmful in these areas. The most negative effects are foreseen in dry land areas at lower latitudes and in arid and semi-arid areas, especially for those reliant on rain fed, non-irrigated agriculture (Aydinalp and Cresser, 2008). The rise in temperature cause stress in crops and reduce yields and productivity. Crops that are sensitive to temperature during the growth stages are affected a lot. A shift in growing season is being seen due change in temperature. Irregular and altered patterns of rainfall are severely affecting the crops and water supplies for livestock, which in turn has increased the occurrence of floods and drought, causing soil erosion, disrupting harvesting schedules. Occurrence of new pests and diseases are seen in the places having warmer temperature. Altered temperature has altered the life cycle of pests and intensity of infestations. Rising of sea water level and increased evaporation leads to intrusion of salt water into fresh water making irrigation water more saline harmful to crops. Livestock are sensitive to heat stresses which in turn reduce livestock productivity and increase mortality rates.

Soil is a strange full of wisdom particularly in terms of biodiversity. Soil biota consists of the microbes (bacteria, fungi, archaea and algae), soil animals (protozoa, nematodes, mites, springtails, spiders, insects and earthworms) and plants, living all or part of their lives in or on the soil or pedosphere. Millions of species of soil organisms exist but only a fraction of them have been cultured and identified. Micro organisms (MOs) (fungi, archaea, bacteria, algae and cyanobacteria) are members of the soil biota but are not members of the soil fauna (Sachidanand et al., 2019). The soil fauna is the collection of all the microscopic and macroscopic animals in a given soil. The size of a soil organism can restrict its location in the soil habitat. Smaller members of the microfauna like nematodes are basically aquatic organisms that live in the thin water f ilms or capillary pores of aggregates preying or grazing on other aquatic microfauna such as amoebas. Soil has a direct effect on the environmental conditions, habitat and nutrient sources available to the soil biota. The term pedosphere is often used interchangeably with soil and captures the concept that the soil is a habitat where the integration of spheres occurs. These spheres include the lithosphere, atmosphere, hydrosphere and the biosphere. Numerous biogeochemical processes regulated by soil biota occur in the pedosphere.

The physical structure, aeration, water holding capacity and availability of nutrients are determined by the mineral constituents of soil, which are formed by the weathering of rock and the degradative metabolic activities of the soil MOs. Soil microbiology is the study of organisms in soil, their functions, and how they affect soil properties. It is believed that between two and four billion years ago, the first ancient bacteria and MOs came about in earth’s oceans. These bacteria could fix N2 , in time multiplied and as a result released oxygen into the atmosphere. This led to more advanced MOs. Soil biology plays a vital role in determining many soil characteristics. The decomposition of organic matter by soil organisms has an immense influence on soil fertility, plant growth, soil structure, and C storage. As a relatively new science, much remains unknown about soil biology and their effects on soil ecosystems. The soil is home to a large proportion of the world’s biodiversity.

2.1 Roots and the Rhizosphere

The rhizosphere, the region of soil surrounding plant roots in which soil and microbes closely interact–plays an important role in soil carbon cycling. The rhizosphere is only about 1-2% of Earth’s soil volume but can store up to 30-40% of Earth’s total soil organic matter. Plants secrete organic compounds such as amino acids or enzymes known as root exudates, which are key in recruiting and selecting relevant beneficial microbes to colonize in the rhizosphere (Julie Bobyock, 2023). Studying these microbial-plant interactions is critical to better understand the relationship between plant growth and the role soils play in keeping carbon from the atmosphere. It is the region that is a few distances (2-80 mm) extended from the root system. Rhizosphere zone is the region of intense microbial activity, and it is isolated from the bulk soil that often called as Edaphosphere or Non-rhizosphere.

Plant growth results from interaction of roots and shoots with the environment. The environment for roots is the soil or planting medium, and its importance is often not appreciated beyond the physical and nutritional aspects. Roots do provide structural support for the plant, and they absorb water and nutrients, but they also produce plant growth-regulating substances, such as cytokinins. The cortex of the root is largely starch storage tissue, and represents a transition zone from the soil to the stele. The cortex also provides a niche to be occupied by mycorrhizal fungi. It is not as generally appreciated, however, that roots also support the growth and functions of a complex of microorganisms that can have a profound effect on the growth and survival of plants. These microbes interact in the soil around the root that is influenced by root exudates; this zone is called the rhizosphere. The effects of rhizosphere microorganisms on plant growth or health often are ignored unless the microbes weaken or kill the plant through disease. There are, however, beneficial interactions that can occur and be enhanced if actively managed by the grower. Establishment and maintenance of rhizosphere microbial populations is a dynamic process affected by age and kind of plant, nature and treatment of soil, environmental factors, foliar applications of chemicals, and interactions of microorganisms. It is important to remember that selective or preferential development of rhizosphere populations occurs in the early stages of plant growth and root development when root exudation is maximal but, thereafter, is altered and maintained at some microbial equilibrium by both microbial and plant activity, with both being influenced by edaphic and other environmental factors.

3.1 Soil Inhabiting Fungi

There’s a wild and wonderful world that remains hidden for most of us, at least most of the time. It’s an amazing ecosystem filled with fascinating creatures interacting with one another to create an intricate, dynamic web of life. It’s right under our feet: the soil ecosystem! Many organisms make up this ecosystem, and some of the most important ones are the fungi. Healthy soil is alive and teeming with an array of fungus species, each playing a vital role in its environment. Healthy soils are alive with an especially diverse array of fungal species, and many are essential to the health of the plants growing in that soil. In fact, a soil devoid of fungi is a dead soil, and is unlikely to support thriving plants. Some soil fungi are single-celled and visible only through a microscope. Others form large, underground networks of filaments that can cover an area the size of a football field or larger. Most of us are familiar with the above-ground parts of some soil fungi, the mushroom.

Fungi are one of the key microbial groups in terrestrial ecosystems that enabled colonization of land by plants and facilitated development of soil that supports most of the biota on Earth. The kingdom Fungi is one of the most diverse groups of life with an estimated 1.5–6 million species that represent heterotrophic mutualists, pathogens, and saprotrophs (Tedersoo et al., 2017). The 70,000–100,000 currently recognized species are distributed among 156 orders, 46 classes, and 12 phyla. Fungi have traditionally been identified and classified based on morphological characters of fruiting bodies and living cultures. Similar to bacteria and archaea, merely <1% of fungal species have been cultivated with established protocols, which renders large taxonomic groups undescribed and virtually unknown to science. Roughly 80% of all soil-inhabiting fungal taxa cannot be identified at the species level, and 20% cannot be reliably assigned to known orders.

Biological control is defined broadly as the “use of natural or modified organisms, genes, or gene products” to reduce the effects of pests and diseases. The many approaches to biological control can be categorized conventionally into regulation of the pest population (the classical approach); exclusionary systems of protection (a living barrier of microorganisms on the plant or animal that deters infection or pest attack) and systems of self-defense (resistance and immunization) (Anchal Sharma et al., 2013). The agents of biological control include the pest- or disease-agent itself (sterile males or a virulent strain of pathogens), antagonists or natural enemies, or the plant or animal managed or manipulated (immunized) to defend itself. Principles of plant health care are offered, know the production limits of the agro-ecosystem, rotate the crops, maintain soil organic master, use clean planting material, plant well-adapted, pest resistant cultivars, minimize environmental and nutritional stresses, maximize the effects of beneficial organisms and protect with pesticides as necessary.

Biological control is the control of one organism by another. This control may be expressed as either a longer population of the pest or as a restriction or prevention of the severity or incidence of pest damage without regard to the pest population (Cook and Baker, 1983). Biological control depends on knowledge of biological interactions at the ecosystem, organism, cellular, and molecular levers and often is more complicated to manage compared with physical and chemical methods. Biological control is also likely to be less spectacular than most physical or chemical controls but is usually also more stable and longer lasting. In spite of biological controls having been used in agriculture for centuries, as an industry biological control is still in its infancy. Biological control is now being considered for an increasing number of crops and managed ecosystems as the primary method of pest control. One reason for its growing popularity is its record of safety during the past 100 years considered as the era of modem biological control (Anchal Sharma et al., 2013). No microorganism or beneficial insect deliberately introduced or manipulated for biological control purposes has, itself, become a pest so far as can be determined, and there is no evidence so far of measurable or even negligible negative effects of biocontrol agents on the environment. The new tools of recombinant DNA technology, mathematical modeling, and computer technology combined with a continuation of the more classical approaches such as importation and release of natural enemies and improved germplasm, breeding, and field testing should quickly move bio-control research and technology into a new era.