eChapters

Before the invention of N fertilizer, mineralization of organic N ( present in dead plants and animals or manure) was the main method used to obtain ammonium and nitrate nitrogen. Mineralization is conducted by soil microbes resulting in ammonium ion. Most Nitrogen is absorbed by plants in the form of Nitrate (NO-₃). Ammonium is converted to Nitrate with the help of  soil bacteria. Nitrogen is a very mobile element and is easily lost from the soil. Ammonium (NH₄+) can be converted to Ammonia (NH₃). The gaseous ammonia can be lost to the atmosphere.  Nitrate can be lost through denitrification. Nitrate nitrogen is reduced to nitrous oxide (N₂O), elemental nitrogen (N₂) and nitric oxide (NO). All are volatile. Denitrification occurs under conditions of high water availability and temperatures higher than 10^ºC.

Plant hormones (phytohormones) are chemicals that regulate plant growth and are termed as ‘plant growth substances’. Plant hormones are signal molecules produced within the plant, and are present in extremely low concentrations. Hormones regulate cellular processes in targeted cells. Hormones also determine the formation of flowers, stems, leaves, the shedding of leaves, and the development and ripening of fruit. Every cell is capable of producing hormones in plants. They shape the plant, affecting seed growth, time of flowering, the sex of flowers, senescence of leaves, and fruits. Plant hormones affect gene expression and transcription levels, cellular division, and growth.They direct which tissues grow upward and which grow downwards. Hormones are vital to plant growth. Hence, they are also known as growth factors or growth regulators.

Vitamins are essential organic nutrients required by an organism in small quantities. They are essential since they cannot be synthesized in sufficient quantities by an organism, and must be obtained from the diet. The term vitamin does not include other essential nutrients like dietary minerals, essential fatty acids, or essential amino acids which are needed in larger quantities than vitamins. The term vitamin is derived from “vitamine,” coined in 1912 by the Polish biochemist Funk. The name is from vital and amine, meaning amine of life. Thirteen vitamins are generally recognized presently. Vitamins are used in small quantities by an organism to keep it in a healthy condition.

Vitamins are given letters of alphabet (A,B, C, D, etc.) in the order in which they have been discovered. The letters do not bear any relation to their structures or their importance. Vitamins are classified by their biological and chemical activity and not by their structure. Thus, each “vitamin” refers to a number of vitamer compounds that all show the biological activity associated with a particular vitamin. Vitamin A includes the compounds retinal, retinol, and four known carotenoids. Vitamers by definition are convertible to the active form of the vitamin in the body, and are sometimes inter-convertible to one another, as well.

Alkaloids are naturally occurring substances of plant origin that are alkaline in reaction. They are optically active, contain nitrogen as part of a heterocyclic ring and have varying degrees of psychological responses in man and animals. They exhibit significant pharmacological activity. Alkaloids are mostly basic in character but also includes some related compounds with neutral and even weakly acidic properties. Presently more than 2000 alkaloids are known.

Nomenclature of alkaloids
Alkaloids are named by adding the suffix ‘ine’ to various distinguishable features such as sources, physiological action in animals, their properties etc. Thus, 1. The name of the genera of the plants containing them Ex. Atropine (Atropa), nicotine (Nicotiana) etc. 2. The names of the species of the plants producing them Ex. Cocaine (Erythroxolon coca). 3. The common name of the organism producing them Ex. Ergotamine (ergot fungus). 4. The specific physiological activity observed in animals Ex. Emetine (emetic – causing vomiting), narcotine (narcotic-alters mind).

Sterols are derivatives of a complex ring system called cyclopentano perhydro phenanthrene. The term sterol means solid alcohol. Sterols, though alcohols, are solids with a M.P. of 100-120^ºC. The 27 carbon atoms impart hydrocarbon character, namely, solubility in non-polar solvents. Free sterols in plants are mono hydroxy  secondary alcohols varying in the constitution of methyl or ethyl group and in double bonds. Cholesterol, ergosterol, bile acids, sex harmones, cortical harmones and D-vitamins are some of the sterol derivatives.
   
The most widely distributed sterols in higher plants are the C₂₉ sterols, stigmasterol, β sitosterol and g sitosterol. Together, they are called steroids. In plants, steroids are present as glycosides. Cholesterol was first isolated from gall stones. The word cholesterol means “solid alcohol from bile”. Bile is a fluid which is formed and stored in the gall bladder. It aids in the digestion of fats in the digestive tract. Sterols form an important group among the steroids. Unsaturated steroids with most of the skeleton of cholestane containing a 3β-hydroxyl group and an aliphatic side chain of 8 or more carbon atoms attached to position 17 form the group of sterols.

Plant pigments impart colour to the different components like leaves, flowers, fruits etc. They in turn are responsible for the colour of raw food, we eat. Pigments like chlorophyll, anthocyanins, flavonoids, tannins, xanthones etc. are the different pigments that are present in plants. The primary function of pigments in plants is photosynthesis, which uses the green pigment chlorophyll along with several red and yellow pigments that help to capture as much light energy as possible. Other functions of pigments in plants include attracting insects to flowers to encourage pollination.

Phenol is normally a benzene ring containing an –OH group, and hence an aromatic alcohol. The term phenolic refers to similar aromatic compounds with one or more -OH groups. Phenolics constitute one of the most widespread classes of secondary metabolites. Commonly talked about class of compounds like anthocyanins, flavonoids, lignins, tannins, coumarins and chalcones are all phenolic substances. Phenolics are water insoluble substances. However, the water solubility increases with the increase in the number of -OH groups. Phenolics absorb electromagnetic radiation strongly. Many of the phenolics absorb in the visible part of the spectrum (Ex. anthocyanins) and are coloured. Phenolics are produced in plants by 1. Shikimate pathway through phenylalanine (C6.C3)  and 2. Acetate/ malonate pathway.

Primary metabolism in a plant comprises all metabolic pathways that are essential to the plant’s survival. Primary metabolites, namely, carbohydrates, lipids and proteins are compounds that are directly involved in the growth and development of a plant whereas the secondary metabolites are compounds produced in other metabolic pathways that, although important, are not essential to the functioning of the plant. However, secondary plant metabolites are useful in the long term, often for defense purposes, and give plants characteristics such as color.
 
Secondary plant metabolites are used in signalling and regulation of primary metabolic pathways. Plant hormones, which are secondary metabolites, are often used to regulate the metabolic activity within cells. Secondary plant metabolites help the plant maintain an intricate balance with the environment, often adapting to match the environmental needs. Plant metabolites that color the plant are a good example of this, as the coloring of a plant can attract pollinators and also defend against attack by animals. Terpenes, alkaloids, sterols, pigments, growth regulators, and phenolics are the important secondary plant metabolites.

Amino acids serve as the building blocks of proteins and as precursors of many other important biomolecules such as hormones, purines, pyrimidines, porphyrins and some vitamins. They also serve as sources of energy when present in excess amounts and when they are used as fuel, amino acids undergo deamination reactions. The remaining carbon skeleton will either convert itself into glucose or undergoes oxidation to CO₂ via TCA cycle.

Central dogma: The Central dogma of molecular biology, which has been formulated as a simple linear progression of information from DNA to RNA to Protein, is summarized in the illustration. The replication process on the left consists of   passing  information from a parent DNA molecule to daughter molecules. The middle  transcription process copies this information to a mRNA molecule.  Finally, this information is used by the chemical machinery of the ribosome to make polypeptides.

Plants can synthesize all the 20 amino acids, which include essential and non-essential amino acids. They can be degraded by removal of the amino group and conversion of the remaining skeleton to useful metabolic intermediates which participate in the synthesis of glucose and other ketone bodies.
 
Biosynthesis of amino acids
 
The biosyntheses of amino acids have an important feature. Their carbon skeletons come from intermediates from glycolysis, pentose phosphate pathway and citric acid cycle etc. The biosynthetic pathways depend on the intermediates from which they are derived. The primary amino group normally comes from the transamination of glutamate. Glutamine synthetase is a central control point in nitrogen metabolism, since glutamine is the amino group donor in the formation of many biosynthetic products as well as being a storage form of ammonia. Glutamate is the precursor of proline, ornithine, and arginine. Serine, cysteine, and glycine are derived from 3-phosphoglycerate. Glycine is synthesized from serine by removing CH2OH group. Tyrosine is synthesized from phenylalanine. Asparagine and glutamine are amides that are synthesized from aspartate and glutamate.

The importance of lipids have already been elaborated. They play a major role as source of energy and as components of membranes which have implications in plant growth regulation. The complete metabolism of fat leads to oxidation, the final products being CO₂ and water. The burning of one mole of palmitic acid gives 2340 kcal.  The molecular weight of palmitic acid is 256. This works out to approximately 9 kcal/g of palmitic acid. This energy is twice that derived from either sugars or proteins. Fats and oils are thus better and more efficient forms of storage of energy in living beings.

Carbohydrate metabolism in the cell is essentially the metabolism of glucose and other substances related to glucose in their metabolic processes. The chemical reactions involved in carbohydrate metabolism represents complex groups, sequences, and cycles of reactions which integrate at various points with the reactions concerned in the metabolism of lipids and proteins. The major types of chemical processes involved in carbohydrate metabolism may be grouped as follows: a) Anabolism of starch – Photosynthesis, b) Catabolism of starch, c) Catabolism of glucose – 1. Glycolysis and TCA cycle and 2. Oxidative pentose   phosphate pathway.
 
Plant cells “burn “ glucose for energy. Plants also produce sugars through photosynthesis. This is roughly the reverse of the burning process.

Plants are responsible for highly useful molecular reactions. All the enzymatic  reactions  that  occur in the cell are  termed  as metabolic reactions.  They  take place within organisms in an orderly and regulated way.  They  are  the  metabolic pathways and the compounds  resulting from the process, namely,  metabolism are called  the metabolites. Metabolism in Greek means change. It is the set of life sustaining chemical transformations within the cells of living organisms. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to the environments around them.
 
Metabolism is a highly organized,   coordinated and purposeful enzymatic activity inside a cell. Metabolism has four functions: 1. To obtain energy from the environment, 2. To convert molecules into building blocks, 3. To convert the building blocks into proteins, lipids, sugars, nucleic acids and other cell components and 4. To synthesize and degrade organic molecules for specific needs of the cell.

Nucleic acids were first discovered in 1868 by Friedrich Meischer. Nucleic acids are high molecular weight polymers that are present in our cells. They  store and transfer genetic material from generation to generation. Knowledge of how genes are expressed and how they can be manipulated is becoming increasingly important for understanding   of nearly every aspect of biochemistry. These macromolecules pass on information for cellular growth and reproduction.  All the genetic information in the cells is called the genome. Every time a cell divides, the information is copied and passed on to the new cells.
 
Nucleic acids fall into two main classes according to the type of sugar they contain: the Deoxyribonucleic acids (DNA) and Ribonucleic acids (RNA). Some sections  of  the  DNA  called  genes contain the information to make a protein. RNA translates the genetic information in the DNA to the ribosomes, where the synthesis of proteins takes place.

Enzymes are organic catalysts produced by living organisms. They make possible biochemical reactions. Hence they are called biocatalysts. They are mostly a specialized class of proteins. However, there are some non-protein enzymes like ribozymes, which are RNAses. Enzymes speed up reactions at ambient temperatures. This is in contrast to chemical reactions like saponification of lipids which take place when lipids are boiled for a few hours with concentrated alkali.  Enzymes, namely, lipases, hydrolyze lipids at body temperatures in minutes. They are superior to chemical catalysts by a factor of 107 to 1014 .  An enzyme may be a simple protein or a complex protein. They are produced by cells and are mostly globular proteins. Each cell contains an estimated 3000 different enzymes.

The word protein was first coined in 1838 to emphasize the importance of this class of molecules. The word is derived from the Greek word proteios which means “of the first- rank”. Proteins are polymers/macro molecules made up of several amino acids. When there are more than 50 amino acids in a chain, the polypeptide is normally called a protein. Each protein in the cells of living beings has a unique sequence of amino acids that determines its biological function. The proteins are folded into specific defined structures, which are maintained by a large number of relatively weak bonds. The  three  dimensional structure is well defined and suited to it’s specific function.

Very small changes in the structure can modify the function. Hence, it is important to know the structure of proteins to understand their behavior and function. The biological activity of proteins depends on maintenance of folded conformation. Proteins fold into well defined three dimensional shapes and they are able to recognize their corresponding substrates or antigen molecules and bind them tightly. The protein structure has been classified into four different levels based on the folded conformation of the protein.

An amine reacts with a carboxylic acid to form an amide. Similarly, the amino group  on one amino acid molecule reacts with the carboxyl group of another amino acid  to form a compound called peptide. A peptide bond is an amide bond that forms when the –COO- group of one amino acid reacts with the -NH₃+ group of another amino acid. The resulting compounds are called peptides. Even after this there is a reactive amino group and a carboxyl group in the peptide. If these groups react further a poly peptide can form and later a polymer called protein can form.

Amino acids are the building blocks of proteins. They occur in all living plant cells as constituents of proteins and as free acids or amides. More than 200 naturally occurring amino acids have been identified in higher plants. Around 20 different amino acids have been observed to be incorporated into proteins. They have two functional groups, an amino group (-NH2) and a carboxylic group(-COOH). Both these groups are attached to the a carbon atom only. Amino acids with this structure are called a amino acids or 2-aminoacids. The unique characteristics of the 20 amino acids are due to the side chain (R), which can be an alkyl, hydroxyl, thiol, amino, sulphide, aromatic, or heterocyclic group.

Amino acids have the general formula, R-CH(NH₂)-COOH. The R represents a side chain. If R=H, the simplest amino acid glycine (NH₂ -CH₂ –COOH) results. Amino acids are alpha (a ) amino carboxylic acids. The carbon atom is tetrahedral in shape. The various groups attached to it are placed in different positions. Since the valence of the carbon atom is four, four groups can be attached to the carbon atom. Based on the groups attached to the carbon atom it may be of two types.

Lipids are non polar substances of biological origin that are sparingly soluble in water, but soluble in organic solvents like chloroform, hexane, benzene etc. The word lipid comes from the Greek word lipos meaning lard or fat. The lipids present in biological systems are either hydrophobic (non polar) or amphipathic (both polar and non polar). Lipids like fats, oils or glycerophospholipids can be hydrolyzed to get fatty acids and other products. Hydrophobic nature is useful in making lipids as membranes which act as effective barriers to more polar molecules. Steroids are also considered lipids, but cannot be hydrolysed and are components of non-saponifiables in fats. Waxes, which are esters of fatty acids with long chain alcohols are also considered as lipids.

Carbohydrates are the most abundant biomolecules on earth. They occur in nature as glucose, starch and cellulose etc. Each year, photosynthesis converts more than 100 billion metric tonnes of carbon dioxide and water into starch, cellulose and other plant products. Carbohydrates are polyhydroxy aldehydes or ketones and their derivatives. They provide 4k calories energy per gram. They promote utilization of lipids and reduce wastage of proteins. They are readily available in roots, tubers, cereal grains, sugarcane and sugar beet.

Carbohydrates have the general formula C_n( H₂O)n, indicting that they are the hydrates of carbon. Some carbohydrates also contain nitrogen, phosphorous or sulfur. They are characterized by the number of carbon atoms they contain. If n=3, they are trioses, n=4 tetroses, n=5 pentoses, n=6 hexoses and n=7 heptoses. The most common sugars in plants are the hexoses. Two or more simple carbohydrates condense together to form polymer sugars like sucrose, starch and cellulose etc. The basic condensing bond is glycosidic bond.

All living organisms are basically made up of chemical components. The chemistry, composition and energy management of living organisms is what we call biochemistry. It tries to explain life processes at the molecular level. Although different organisms differ outwardly in their life processes, there are striking similarities in executing the different tasks. Genetic code, metabolic pathways, enzymes, coenzymes and even regulatory mechanisms are similar to a large extent in all the living organisms. Living organisms have certain extraordinary properties. They can grow, respond to stimuli and replicate themselves with high fidelity. All these activities are ultimately interpretable in chemical terms. The components that constitute organisms are all inanimate. The lifeless organic molecules with appropriate complexity and properties make a living being.

Biochemistry helps us understand how the inanimate molecules that constitute living organisms interact with each other to maintain life. The basic life processes or the biochemistry remains broadly the same in either the unicellular microorganism or the higher organisms such as the plants or the human beings. Life is nothing but thousands of ordered chemical reactions. In other words, chemistry is the logic of all biological phenomena.

14.1. INTRODUCTION

The climate of a place is the average weather that is experiences over a period of time. It is the natural phenomenon that has occurred throughout the history of the earth. Climate change is strongly associated with higher temperature, altered precipitation, and higher levels of atmospheric CO₂ and other greenhouse gases. It is a very slow process; it takes a long time to settle in. Climate change in IPCC (2007) usage refers to any change in climate over time, whether due to natural variability or as a result of human activities. Over the last 150-200 years the changes to our climate are happening more quickly now than they have ever done before in the geological past. Human activities have altered natural climatic processes at a geographically rapid pace by booting atmospheric concentrations of several greenhouse gasses. Following are the changes taken place over years of industrial age (IPCC, 2007):

13.1. INTRODUCTION

Photosynthetically active radiation is a primary energy resource for terrestrial plants, necessary for the plant growth. Plants receives this photosynthetically active radiation from sunlight as a consequence, plants are also exposed to the ultraviolet (UV)-radiation. Seven percent of the electromagnetic radiation emitted by the sun is the UV range (200-400 nm). Though representing only a small portion of the total solar electromagnetic spectrum, UV-B has a disproportionately large photobiological effect. As it passes through the atmosphere, the flux transmitted is greatly reduced, and the composition of the UV-radiation is modified. This UV-radiation is mainly divided into three classes, namely UV-A, UV-B and UV-C. The UV-A region of the spectrum (wavelengths from 320 to 400 nm) are not attenuated by ozone, so their influence will be unaffected by ozone layer reduction. This portion of the UV radiation is less damaging and important for photomorphogenic signal in plant development (Bjorn, 1994). The wavelength of UV-B portion ranges from 280 to 320 nm. This region of UV is very energetic and effectively absorbed by ozone in the stratosphere. Thus, only a very small portion, approximately 4% is transmitted to the earths. Shortwave UV-C radiation (200-280 nm) is highly energetic and strongly absorbed by atmospheric oxygen and ozone. Thus, none of this sterilizing radiation is present in terrestrial sunlight.

12.1. INTRODUCTION

Air is polluted when it contains enough unhealthy particles and gases to harm human beings, animals, plants and even objects such as building and statues. Air pollutant may present as solid, liquid or gas form. Industrial revaluation in the 19th and 20th centuries leads faster increase in concentration of air pollutants in the atmosphere. The most important air pollutants that damage the plants’ growth and development, subsequently the economic yields of crop plants are ozone (O₃), nitrous oxides (NO₂ and NO), carbon monoxide (CO), ammonia (NH₄), peroxiacetyl nitrate (PAN), sulphur dioxide (SO₂), hydrogen fluorides (HF), particulate matters (cement dust, magnesium-lime dust, carbon shoot etc.), smoke etc. Burning of hydrocarbons in motor vehicle engines gives rise to CO₂, CO, SO₂, and NO in varying proportions and ethylene (C₂H₄) as well as other hydrocarbons. Industrial plants release SO₂, H₂S, NO₂ and HF into atmosphere. Hydrogen peroxide (H₂O₂) is another potentially injurious molecule, can form by the reaction between O₃ and naturally release volatiles (terpenes) from forest trees.

11.1. BORON TOXICITY
11.1.1. Introduction

Boron (B) is essential micro-nutrient. It is necessary for cell wall formation, membrane integrity, calcium uptake and carbohydrate synthesis and transportation. B affects many functions in plants, which includes flowering, pollen germination, fruiting, cellular activities (division, differentiation, maturation, respiration etc.), water relationships and the movement of hormones. It is not translocated and leached easily from soils.

10.1. CADMIUM
10.1.1. Introduction

Cadmium (Cd) is a strongly phytotoxic heavy metal in an increasing environmental problem worldwide. It is one of the most dangerous metal due to its high mobility and the small concentration at which its effects on the plants being to appear. It is released into the environment by the power stations, heating systems, metal-working industries or urban traffic. It is recognized as an extremely significant pollutant due to its high toxicity and large solubility in water (Pinto et al., 2004). Soil solutions which have a Cd concentration ranging from 0.32 to 1.00 mM can be regarded as polluted to a moderate level (Sanita di Toppi and Garbrielli, 1999).

9.1. INTRODUCTION

Iron (Fe) is important component of a plant’s energy-power house chlorophyll. It also interacts with all the major enzymes and proteins at higher concentration in the soil, and it is toxic to plants. Fe-toxicity creates a range of nutrient disorders and deficiencies of P, K, Ca, Mg, Mn and Zn in plants. These elements were reported to play decisive roles in manifesting toxicity symptoms in rice (Sahu, 1968; Ottow et al., 1983; Yamauchi, 1989; Sahrawat et al., 1996). Excess absorption and translocation of Fe in the rice plants led to toxicity, which has been a major limiting factor in wetland rice. Average yield loss due to Fe-toxicity accounts to 50% and in fact ranges from 10-100% (Brigit et al., 1993).

8.1. INTRODUCTION

Aluminium (Al) is not considered as essential nutrient, but at low concentrations it may increase plant growth or induce other desirable effects (Bollard and Butler, 1966; Foy, 1988; Huang et al., 1992a, b; Roy and Mandal, 2005). Al affects about 40-70% of the world arable land, which has the potential for food crops biomass production (Haug and Caldwell, 1985). Acid soils constitute about 3.95 billion hectares globally. About 38% of those are present in Tropical Asia (Datta, 2002). It is believed to cover more than 800 million hectares of forest and tropical Savana ecosystems of tropical America (Jaffe and Rojar, 1994; Prakash 2000). Nearly 75% of Amazon Basin contains acid and infertile soil classified as oxisols and utisols. About 383 million hectares (79%) of the Amazon area, suffers from Al toxicity. Acid soil occurs extensively in the some of the Mediterranean countries and Southern Australia. Low laying acid sulfate of Bay Islands in India chronically suffer from Al-toxicity (Chowdhury et al., 2001).

7.1. INTRODUCTION

Abiotic stress is a major limiting factor in crop productivity. Several stresses, such as high temperature, high light intensity, osmotic stress, heavy metals, and several herbicides and toxin lead to over production of reactive oxygen species (ROS), causing extensive cellular damage and inhibition of photosynthesis (Allen, 1997). ROS is produced in both unstressed and stressed cells. Plants have well developed mechanisms against ROS, involving both limiting the formation of ROS as well as instituting its removal. Under unstressed conditions, the formation and removal of O₂ are balance. Introduction of molecular oxygen (O₂) into atmosphere by O₂- evolving photosynthetic organisms, ROS has been the unwelcome companion of anaerobic metabolism. In contrast to O₂, these partially reduced or activated derivatives of oxygen (O₂¹, O2-, H₂O₂, and HO) are highly reactive and toxic and can lead to the oxidative destruction in tissues during stress.

6.1. INTRODUCTION

Low temperature is one of the major environmental factors that limit the plant growth. Many plants of tropical origin suffer cold damage when exposed to temperature below 20ºC (Graham and Patterson, 1982, Andrews, 1987). Cold temperature in crop plants are compounded by cold snap– a lower than usual drop in temperature that causes the crop to fail. Low temperature in growing season may reduce germination, retard vegetative growth by inducing metabolic imbalances and can delay or prevent productive development. Each plant species has an optimum range of temperature for its normal growth and development. It varies among the genotypes within a species, the specific temperature also depends on the growth stage and development of the particular genotype.

5.1. INTRODUCTION

Temperature is the one of the most important environmental element influencing the plant growth and development limiting the productivity and adaptation of crops, especially when it coincides with critical ranges (Chen et al., 1982; Paulsen, 1994). Nearly all commercial crops in the arid and semi-arid tropics often suffer from heat stress. Every plant has an optimal temperature for its normal growth, deviation from this may cause stress to plants. The adverse effects on plant of temperatures higher than the optimal considered as heat stress. Crops are exposed to periods of heat stress during their life-cycle. The optimum temperature for the most species ranges from 25 to 35 0C. Above this value, a decline in the photosynthesis rate is observed (Berry and Bjorkman, 1980; Pimentel, 1998). Even brief periods of heat-shock between temperature ranges of 45-50 0C induce marked change in plant growth processes.

4.1. INTRODUCTION

Water stress is the single most severe limitation to the productivity of rice in the rainfed ecosystem (Widawsky and O’Toole, 1990). Drought has been defined as the inadequacy of water availability, including precipitation and soil moisture storage capacity, in quantity and distribution during the life cycle of the crop to restrict expression of its full genetic yield potential. Drought is actually a meteorological event which implies the absence of rainfall for a period of time, long enough to cause moisture-depletion in soil and water deficit with a decrease of water potential in plant tissues. Under drought conditions, water stress develops in the plants as the demand exceeds supply of water; this may occur either/or both due to atmospheric or soil conditions, and is reflected in a gradient of water potentials developed between the soil or soil-root interface and leaf, the transpiring organ. Moisture stress is likely to develop to a different rate in different plant organs along with the gradient. Drought like many other environmental stresses has adverse effects on plant growth and yield.

3.1. INTRODUCTION 

Transitory waterlogging occurs extensively in both irrigated and dry land agriculture on clay flats and duplex soils. Most of the humid tropical lowlands, with adequate, rain-fed but poor drainage, have the problems of waterlogging, which is further intensified by low water table and poor root aeration. In submerged condition, only root is exposed to excess water and the injury to the shoot is not a primary effect.

The term ‘waterlogging’ is defined as a condition of the soil where excess water inhibits gas exchange of roots with the atmosphere. Waterlogging is different from ‘flooding’ because the latter results in addition factors of partial or complete submergence of the shoot. The waterlogging replaces a gaseous air by liquid water, leading to the gas stresses. Schematic representation of adverse effects of waterlogging on plant growth and survival has been given in Fig. 3.1.

2.1. INTRODUCTION

Salt stress has become an ever increasing threat to food production. It is a major factor limiting the crop productivity in the arid and semi-arid areas of the world (Ashraf, 1994; Foolad and Jones, 1992) and it affects about 10% of the total global land area (Richards, 1995). Increased salinization of arable lands is expected to have devastating global effects, resulting in 30% land losses within the next 25 years and up to 50% by the year 2050 (Wang et al., 2003).

Soluble salts can cause harm to plant, if they are in high concentration in water or soils and it limit crop cultivation world wide. Generally an array of stresses interplay in saline soils and reduces productivity of salt sensitive crops. In India, about 12 mha of land has been affected with salinity and alkalinity (Yadav and Gupta, 1984); an area of nearly 4 mha of land suitable for rice affected with salinity (Paul and Ghosh, 1986). The optimum salt concentration for the growth of halophytes is found to be about 0.5 M NaCl (Flower and Yeo, 1981). Most of the crop plants are salt sensitive glycophytes.

Abiotic stresses are major constraints for many crop plants in specific areas over the globe which limits the crop production. Dudal (1976) estimated that only 10% of world’s arable land may be categorized as free from stress. The rapid change in environmental conditions likely to override the adaptive potential of plants, this environmental changes mainly originated from anthropogenic activities, which has caused soil and air pollution, plant are exposed to natural climatic or edaphic stresses, such as, high irradiation, heat, chilling, freezing, drought, excess water and waterlogging and nutrient imbalance. Among abiotic stresses drought is the main abiotic factor as it affects 26% of arable area (Table 1.1). Water stress is a single most severe, limitation to the productivity of rice in the rainfed ecosystem (Widawgky and O’Toole, 1990). Mineral toxicity/deficiencies are second in importance. Among mineral toxicity, salinity is wide spread and is estimated to affect 10% of the world land surface (Richards, 1995).

Abstract

Microbiological synthesis of nanoparticles has emerged as rapidly developing research area in nanotechnology across the globe with various biological entities being employed in production of nanoparticles constantly forming an impute alternative for conventional methods. Simple prokaryotes to complex eukaryotic organisms including higher plants are used for the fabrication of nanoparticles. In the present article, the synthesis of important plant nutrients like Mg, Zn, Ag, Au, Ti, P and Fe nanoparticles from different fungal species, their characterization and application potential of nanonutrients in agriculture is elaborately discussed.

Abstract

Microorganisms inhabiting in the rhizosphere play a vital role in ecosystem functioning. Rhizosphere is an area around the root surface where pathogenic and beneficial microorganisms repose and influence the plant growth and health. These microbial groups of bioagents found in the rhizosphere include bacteria, fungi, nematodes, protozoa, algae and micro-arthropods. Because of their rich diversity, complexity of interactions and numerous metabolic pathways, microbes are an amazing resource for biological activity. These microorganisms require organic matter for their growth and activity in soil and provide valuable nutrients to the plants and hence maintaining the plant health. The most promising fields for the use of bioinoculants are agriculture, horticulture and forestry. There are many reports on the inoculation of bioagents in agriculture and horticulture crops but only a few reports are available in forestry. This article is an overview on various bioinoculants which are used during inoculation and a compilation of scattered reports of bioinoculants in forestry only.

Abstract

Amongst various oilseed crops grown across the world, soybean (Glycine max L. Merrill) is globally important as a high source of protein and oil for human consumption and is also being used as potential feed for animals. Soybean is grown under rain-fed conditions in the tropics and subtropics in the marginal lands with less amount of external application of chemical fertilizers. The frequent climate variations have created a number of biotic and abiotic stresses, drought being a major abiotic stress which adversely affects the soybean productivity. Thus, to enhance the productivity of soybean, besides managing the nutrients, stress management is of utmost importance. There is a great opportunity of application of microbes especially arbuscular mycorrhizal fungi (AMF) where its application alone or in combination with plant growth promoting rhizobacteria (PGPR) can help in nutrient mobilization and remediation of plant stresses.

Abstract

Soil salinization is an important factor limiting crop production, mainly in the arid and semiarid regions of the world. Nevertheless, plants naturally have evolved several physiological, biochemical and molecular mechanisms to establish and thrive in salt stressed soils. In addition to breeding crops for salt tolerance, recent emphasis is on exploring the possible role of plant-microbe interactions in amelioration of salt stress in plants. It is now well established that arbuscular mycorrhizal (AM) symbiosis alleviates the effect of salt stress in plants. Further, available evidence does suggest that AM symbiosis regulates many of the plant’s salt stress alleviation mechanisms. However, the molecular basis for many of these mechanisms is yet to be ascertained. In this chapter, we summarize the current knowledge on the role of AM symbiosis in alleviation of salt stress in crop plants, which now appears to be a promising strategy to improve crop yield in salt stressed soils.

Abstract

Abiotic stresses lead to the overproduction of reactive oxygen species (ROS) in plants which are highly reactive and toxic and cause damage to proteins, lipids, carbohydrates and DNA which ultimately results in oxidative stress. The arbuscular mycorrhizal fungi (AMF)-symbiosis can confer a greater degree of tolerance against drought stress in many cash crops. The significance of heat shock proteins (Hsps) and chaperones in abiotic stress responses in plants, and co-operation among their different classes and their interactions with other stress-induced components is well known. Soil salinity is a major abiotic stress adversely affecting plant growth and crop production worldwide. Phyto-mycoremediation utilizing AMF as plant inoculants is regarded as a promising strategy to heavy metal pollution remediation. Plants have stress specific adaptive responses as well as responses which protect the plants from more than one environmental stress. The potential of phytoremediation of contaminated soil can be enhanced by inoculating hyper-accumulator plants with mycorrhizal fungi most appropriate for the contaminated site.

Abstract

Drought and salinity are two major abiotic stresses that affect various aspects of human lives of one third world population including human health and agricultural productivity. Abiotic stresses such as salinity, drought, nutrient deficiency or toxicity, and flooding limit crop productivity world-wide. A living organism is considered resistant if it tolerates a given physicochemical stress. The presence of microorganisms within the soil, specially a main group known as arbuscular mycorrhizal fungi (AMF), is a key factor in the adaptation of plants to the different ecosystems. The AMF colonizing within the plant roots can determine the success of plants in salt- and/or drought-affected areas. The symbiosis with AMF has been proposed as one of the mechanisms of salinity and water stress avoidance. Studies have shown greater drought and salinity tolerance in AMF-colonized plants by a number of mechanisms. These mechanisms include enhanced water and nutrient uptake directly by extraradical hyphae, higher leaf stomatal conductance and/or better root system architecture, higher capacity of osmotic adjustment and antioxidant defense systems, better soil structure due to higher glomalin and over expression of genes encoding antioxidant enzymes.

Abstract

A majority of the plants studied in natural ecosystems are symbiotic with microorganisms that either reside entirely (endophytes) or partially within plants. These microorganisms express different associations ranging from mutualism to parasitism. These symbiotic relationships appear to impart tolerance to various types of abiotic stresses such as heat, drought, salinity, heavy metals, etc. and sometimes may be responsible for the survival of both plant hosts and microbial symbionts in high stress habitats. The amelioration of the abiotic stresses by the endophytes assumes increasing significance in the light of rapidly changing global climate, which is likely to face frequent incidences of extreme weather conditions like high temperature, droughts, etc.

Abstract

Variously defined endophytes are highly diverse in plants in natural ecosystems, and most of them are symbiotic with of them are Asymptomatic presence of endophytic fungi in internal tissues on healthy host plants are able to play vital roles in physiology and biochemical processes. As a result of this interaction endophyte produces chemical substances having various applications. This chapter provides a brief review of certain grass and non-grass endophytes capable to extend beneficial impacts on host plants to sustain the unfavourable conditions of abiotic stresses. However, biotic stresses are also a matter of great concern, where endophytes can play important roles in combating the unfavourable situation. Endophytic fungi used in bio-control and other agriculture related sectors are also  highlighted in this review. Endophytic fungi producing volatile organic compounds reported from all over the world and their various applications find place in this article which has opened new frontiers of bioprospecting of endophytic fungi.

Abstract

Microbes are endowed with a high and exploitable potential of being useful associates with their surrounding environment and host in case of symbiotic relationship. Most of the microbes live alone but many of them require association of other living system for its survival. Hence, the beneficial role of microbes is always correlated with growth promotion and survivability of other associated living system. Now it is established that microbes play an important and key role in plant growth and development, even its survivability in case of symbiotic mycorrhizal association with orchids. They are nothing but potential tool protecting plants from different adverse conditions like diseased state, environmental stress like cold temperature, drought, metal contamination, salt and acidic or alkaline stress.

Abstract

In its natural environment, a plant faces various types of stressors. In fact, stress in moderation is a welcome event in plants. Only when it is in excess, would it compromise the productivity of plants. Beyond a threshold, stress (biotic and abiotic) has a detrimental effect on plant growth causing extensive yield losses in crop plants worldwide. Plants being sessile, have evolved a complex set of mechanisms to perceive the changes in the environment. Plants respond to minimize the potential damage due to stress while simultaneously preserving resources vital for their growth and development. The chapter presents an overview of various types of biotic and abiotic factors that act as plant stressors and the mechanisms by which plants respond to these stresses. The chapter concludes with a perspective on how the plant’s innate stress response machinery can be exploited for achieving higher tolerance to stress in crop plants.

Abstract

Impact of climate change and related stresses on plant productivity are being witnessed worldwide with developing countries being more vulnerable due to more dependency on agriculture. Microorganisms can play important role as economic and farmer’s friendly strategy to combat abiotic stress in agriculture. A wide range of microorganisms associate with plants, and many of them confer beneficial effects to their hosts through different mechanisms like production of growth promoting substances, nutrient acquisition, protection against plant pathogens etc. In the last few decades, role of microorganisms in imparting tolerance to plants against different abiotic stress has been reported in many crop plants. Under stresses conditions, plant-microbe interactions become more common towards coping with the stress. Selection and application of efficient abiotic stress tolerant microorganisms can be a fruitful strategy to alleviate negative effects of abiotic stresses in plants.

Abstract

With increasing population and subsequent human requirements; the generation of municipal solid waste (MSW) has increased all over the world. In India, the safe disposal of the municipal solid waste still remaines a problem for the authorities concerned. Depending upon the nature and type of the MSW, there are physical and chemical methods for the disposal of the waste, but these methods have their own limitations. Those limitations may be overcome by biological methods. Higher number of microorganisms are present in MSW which may either be pathogenic or nonpathogenic. These microorganisms may play a vital role in bioconversion of MSW into compost. The compost thus produced is useful in increasing soil fertility and reducing the concentration of the waste.

Abstract

The rhizomicrobiome plays a vital role in maintaining plant health and is highly influenced by the root exudates of the host plant. Plants select a subset of microbes at different stages of their development, and determine the microbiome community composition in its immediate vicinity presumably for specific functions. The rhizomicrobiome is composed of diversified microbial community with specific functions and is highly influenced by the plant type, soil type and environmental conditions. The rhizomicrobiome communities apart from promoting plant growth also elicit induced systemic tolerance to salinity and drought in stressed plants. Bacterial communities producing 1-aminocyclopropane-1-carboxylate (ACC) deaminase modulate stress ethylene in plants and alleviate the effects of abiotic stress and increases plant adaptability to stressed environment.

Abstract

Ever growing population and associated food scarcity are the major issues of concern globally. Microorganisms are the ultimate solution for addressing this severe problem in association with recent advances made in genomics and molecular biology. Many bacterial and fungal species which are in association with plant rhizosphere soil can immensely contribute in better growth and developments, ultimately leading to better yield. Exploring these novel organisms happens to be the need of an hour. Metagenomics and next generation sequencing technologies can contribute in identifying those microbes which are otherwise impossible to cultivate traditionally.

Pollution is continuously increasing in India. To control ambient air pollution CPCB has prescribed National Ambient Air Quality Standards