eChapters

INTRODUCTION

Biodiversity can be useful as an ecosystem indicator for conservation and monitoring, through continuous assessment of its main properties including stability, primary productivity, exploitation tolerance and even global environmental changes (Douglas et al., 2012). Crustaceans are found one of the most morphologically diverse taxonomic groups on the planet (Martin and Davis, 2001). Among them, decapods are the most studied taxon, mainly on account of the commercial interest of some species and their great diversity (Isarch and Munoz, 2015). Decapods are chiefly composed of marine species that live in waters depths ranging from shallow to deeper than 5000 m. Isarch and Munoz (2015) described the importance of this group lies in several factors such as the great biomass they represent, their significant role in marine food webs and the commercial interest of many decapod species. Order Decapoda comprises the commercially important shrimps, crabs and lobsters. Out of 649 species of marine crabs so far recorded from Indian waters, only 12 species of edible crabs namely Portunus sanguinolentus, P. plagicus, Charybdis feriatus, C. lucifera, C. annulata, C. natator, Scylla serrata, S. tranquebarica, Matuta lunaris, Sesarma tetragonum and Varuna litterata, which inhabit the coastal waters and adjoining brackishwater environments, support commercial fisheries (Menon and Pillai, 1996). However substantial quantities of crabs are landed every year as by-catches of shrimp trawlers and indigenous fishing units throughout the county.

India represents one of the major contributors to the world production of marine crustaceans. Shrimps constitute as the main seafood export industry for the major foreign exchange earner as well as a source of livelihood for millions of fish workers. As shrimps are targeted for fishing, information on the present status of the fishery is critical for implementation of proper management. Some of the important penaeid shrimps that support commercial fisheries along the Indian seas are Fenneropenaeus indicus, P.semisulcatus P.monodon, P.merguiensis, P.japonicus, P.penicillatus, Metapenaeus dobsoni, M.monoceros, M. affinis, M. kutchensis , M. brevicornis, Parapenaeopsis stylifera, P.hardwickii, P.sculptilis, P.maxillipedo, P.uncta, Trachypenaeus curvirostris, Metapenaeopsis stridulans, Parapenaeus longipes, Solenocera crassicornis and S.choprai (Mohan Joseph and Jayaprakash, 2003). Rajkumar et al. (2015) carried out molecular identification of shrimp species, Penaeus semisulcatus, Metapenaeus dobsoni, Metapenaeus brevicornis, Fenneropenaeus indicus, Parapenaeopsis stylifera and Solenocera crassicornis from Tamil Nadu, India.

Mastitis is a global problem as it adversely affects animal health, quality of milk and economics of milk production. Bovine Mastitis is reported to be the most costly disease of dairy cattle, causing huge economic losses in terms of reduced milk yield, milk discard after treatment, cost of veterinary services and premature culling. While reviewing status of mastitis in India, subclinical mastitis is more important (10–50%) than the clinical mastitis (1-10%). Estimated annual economic losses incurred due to mastitis estimates to Rs.7165.57 crores to dairy farmers (Bansal and Gupta, 2009).

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).

Abstract

Nematodes are non-segmented worms typically 50 µm in diameter and 1 mm in length. Those few species responsible for plant diseases have received a lot of attention, but far less is known about the majority of the nematode community that plays beneficial roles in soil. Nematode diversity tends to be greatest in ecosystems with the least disturbance. Species of Aphelenchoides, Ditylenchus spp, Helicotylenchus, Meloidogyne spp., Pratylenchus, Scutellonema  and Rotylenchulus are obnoxious plant parasitic nematode beside Heterodera and Globodera. Soil temperature, soil structure, soil pH, soil moisture and soil texture play major role in movement of nematode, infestation and completion of life cycle under abiotic and biotic stresses.

Introduction

Lactic acid bacteria (LAB) are characterized as Gram-positive cocci or rods, non-aerobic but aerotolerant, able to ferment carbohydrates for production of energy and lactic acid. Lactic acid bacteria includes different major genera: Lactococcus, Enterococcus, Lactosphaera, euconostoc, Melissococcus, Oenococcus, Pediococcus, Streptococcus, Tetragenococcus, Vagococcus and Weissella. Other genera are Aerococcus, Microbacterium, Propionibacterium and Bifidobacterium. Through carbohydrate fermentation along with lactic acid, various organic acids are produced due to which there is a fall in pH level and creates unfavorable environment or inhibits growth of some undesired microorganisms. The low pH makes organic acids lipo -soluble, allowing them to invade into cytoplasm of pathogens by rupturing cell membrane. LAB are generally regarded as safe (GRAS), and have a significant role in the preservation of foods and fermented products. Under controlled conditions they can be used as natural competitive microbiota or as specific starter cultures. Antagonistic substance like bacteriocins are produced from lactic acid bacteria that inhibits the activity and growth of other bacteria and these bacteriocins are active against various pathogens in minimum concentration. These are antimicrobial peptides modified by post -translational mechanisms and exported to the extracellular medium. Till date about 239 bacteriocin producing LAB genome and 789 putative bacteriocin producing genes cluster are stored in the public databases. Many gram positive and gram negative bacteria in the environment produce bacteriocins.

Abstract

Desert or arid regions present a unique environment for microbial growth. Thar Desert of India harbours a plethora of nitrogen fixing bacteria ranging from symbiotic nitrogen fixers, free living nitrogen fixers, associative nitrogen fixers and blue green algae or cyanobacteria. But the knowledge and extent of diversity is still limited to explore their full potential. On top of that, the documentation of the available knowledge is also scattered. Nitrogen-fixing bacteria are crucial for the protection of the nitrogen supply for vegetation in the arid region. Since deserts are poor in soil nitrogen, biological nitrogen fixation plays a crucial role in maintaining soil fertility. In this article, an attempt has been made to cover the nature and extent of diversity in nitrogen fixing bacteria in Indian arid zone.

ABSTRACT

Pesticide degradation is the breaking down of toxic pesticides into a non-toxic compounds and, in some cases, down to the original elements from which they were derived. The most common type of degradation is carried out in the soil by microorganisms, especially the fungi and bacteria. Microbial degradation depends not only on the presence of microbes with the appropriate degradative enzymes, but also on a wide range of environmental parameters. Pesticides which are rapidly degraded are called non-persistent while those which resist degradation are termed as recalcitrant (persistent). Microorganisms are able to degrade a large variety of compounds, including pesticides under laboratory conditions. However, methods have yet to be developed to decontaminate the environment from pesticide residues. Continuous efforts are required in this direction, and at present several PGPR capable of degrading pesticides have been isolated from the natural environment. Catabolic genes responsible for the degradation of several xenobiotics, including pesticides, have been identified, isolated, and cloned into various other organisms such as Streptomyces, algae, fungi, etc. In addition, recombinant DNA studies have made it possible to develop DNA probes that are being used to identify microbes from diverse environmental communities with a unique ability to degrade pesticides. Bioremediation treatment still requires more intense research through specific microbial degradation of broad range of organic pollutants. This review describes recent advances in biodegradation of pesticides by addressing the microbes involved in pesticide degradation.

Microbial diversity is the key to human survival and economic well being. It provides a huge reservoir of resources which can be utilized for our benefit. Yeasts have been isolated from many sources for industrial purposes. The impact of yeasts on food and beverage production extends many fold beyond the popular notions of bread, beer and wine fermentations by Saccharomyces cerevisiae.

Diverse dynamic mixed populations of prokaryotic and lower eukaryotic microorganisms govern the fermentation and maturation processes and, finally, impact the quality of wine. Both of these parameters apparently contribute to regional differences in the quality of produced wines and characterization of regional wines should involve the study of microbial populations and their members active in the given region.

ABSTRACT

The current paper discusses the diversity, distribution and commercial importance of Indian Magnolias. Globally, these species are found in tropical, subtropical and temperate forests of southeastern Asia and tropical America. In India, there are 25 species of Magnolias and most of them are distributed in Northeast India, with highest number in Assam. Of all the species, two (Magnolia gustavii and M. pleiocarpa) are critically endangered, one (M. pealiana) endangered, two (M. manii and M. nilagirica) vulnerable, nine least concern and ten data deficient at global level. The highly threatened nature of most of the magnolias species calls for their immediate conservation and protection measures. Members of this genus are known to be rich in a wide variety of biologically active compounds including alkaloids, flavonoids, lignans, neolignans and terpenoids. Many of the species have been found to possess potent procognitive activity, anti-oxidative, anti-microbial, anti-inflammatory, anti-angiogenic, diuretic, anti-ulcer, analgesic, anti-helmintholytic, and anti-cancer activities. The species have huge economic potential and are used for a number of purposes including ornamental, medicinal, culinary, timber and joinery works.

INTRODUCTION

The entire Himalayan region is vast and its diverse geographical grouping is unique and has complex ecosystem and occupies about 18% of the total geographical area of India. Indian Himalaya (27O 50' – 37O 06' N and 72O 30' – 97O 25' E) includes the parts of trans, north-west, west, central and east Himalaya and covers approximately an area of 4,19,873 Km2 with 2500 Km length and 240 Km width. The north-western Himalayas generally represent the Himalayan tract from Kumaon in Uttar Pradesh to Chitral in Gilgit. The Himalayan ranges situated in this region exhibit a diverse climate, topography, vegetation, ecology and land use pattern. The annual average rainfall varies from 8 cm in Ladakh to over 200 cm in some parts of Himachal Pradesh and Uttar Pradesh. The vegetation may vary from the scrub in the lower hills to arctic in the Greater Himalayas. The unique physiography, climatic conditions and soil characteristics of the area has resulted in a variety of habitats and a significant biological and cultural diversity. Along the altitudinal gradient (300-800 m.a.s.l) the vegetation varies from sub-tropical, temperate, sub-alpine to alpine types. It supports about 8000 species (47.06% of the total flowering plants of India) of which 30% are endemics, 10.2% trees, 8.44% wild edibles and over 15% medicinal (Samant and Dhar 1997).

Abstract

Lianas are slightly lesser known angiosperms, grows typically in the form of climbing vines mostly in tropical and subtropical forests. Such plants are characterized by scandent thick stems, woody stem in nature and vary in shape and size. They depend on supports in the form of trees, fence and usually climb upward towards the sunlight as they needed for their survival. Keeping the importance of lianas in forests and household, this study was conducted to document the liana angiosperms growing in Western Himalaya along with their medicinal potential for human and animals. This study reveals a total 64 lianas species belonging to 24 families recorded from Jammu and Kashmir, Ladakh, Uttarakhand, Himachal Pradesh and Punjab. This investigation also provided with medicinal potential of these species, which is used as ethnomedicine by local people living in the interior regions of hills and mountains of Himalaya. In this communication, we highlight lianas as an example of an underestimated forest element that, on the one hand, is a key component in and around forests. This study also helps in conservation of endangered liana species in Himalaya.

1. Introduction

Fungi are ubiquitously present in air, water, soil and organisms, or on organism surfaces. They are a group of eukaryotic system that are of great applied and scientific interest to common man, microbiologists, agriculturists and industrialists. They are a diverse group of organisms with respect to taxonomy, size, morphological appearance, mode of nutrition and reproduction. Fungi are eukaryotic spore bearing protists that lack chlorophyll. Fungi comprise the molds and yeasts. Yeasts are usually unicellular measuring only several microns in diameter, whereas molds are filamentous and multicellular which may grow up to several meters in diameter like the extremely large polypores. Fungi generally reproduce both sexually and asexually (Gow and Gadd 1995).

Although it is not easy to define fungi, biologists currently use the term “Fungus” to include nucleated, spore bearing, achlorophyllous organisms with absorptive nutrition which generally reproduce sexually and asexually, and whose filamentous branched somatic structures are typically surrounded by cell walls containing cellulose of chitin or both. A feature which all fungi have in common is their mode of nutrition. Like animals, fungi are heterotrophic organisms, which must consume preformed organic matter. They may live as saprophyte or parasites. They are of great economic importance to man and play an important role in the disintegration of organic matter and affect us directly by destroying food, fabric, leather and other commercial goods. They are responsible for a large number of diseases of plants, animals and man.

Horticulture is a wide field and includes a great variety and diversity of crops. In general, these crops are classified as follows:

1. Crops grown for the food and/or vitamin and mineral content, for e.g., apple and sweet potato.

2. Crops grown for their beverage properties, for e.g., tea and coffee.

3. Crops grown to beautify the environment, for e.g., the grasses of the well planned lawn.

4. Crops grown to express sentiments, for e.g., cut roses, jasmine.

5. Crops grown for perfume for e.g., rose, jasmine.

6. Crops grown for spices for e.g., pepper, nutmeg.

UNTIL THE 1940S BIOLOGISTS ARGUED ABOUT WHETHER DNA OR PROTEIN WAS THE MOLECULE OF HEREDITY

Nuclei observed to divide when cells reproduced themselves

Large amounts of both DNA & protein in the nucleus

Many though protein was most likely molecule of heredity

Proteins made of 20 different amino acids- could have more variety than DNA (made of only 4 different bases)

Abstract

Despite several controversies surrounding the genetically modified (GM) crops or their produce, the production of such crops is constantly increasing, especially in developing countries. To regulate the GM produce in the market, several countries have set very strict regulatory procedures for the approval to grow, import or utilize these GM crops as food or food ingredients. Hence, for regulatory compliance on GM labeling and identification of genetic traits, the development of reliable, sensitive and precise detection assays have become essential. The detection of GM produce is carried out by detecting either the inserted foreign DNA or the novel transgenic protein specifically expressed in GM crops. This article broadly focuses on some DNA and protein-based detection methods employed for GM produce and significant current advances in such detection technologies.

Delineating species boundaries correctly and also identifying species are crucial to the discovery of life’s diversity because it determines whether different individual organisms are members of the same entity or not (Dayrat, 2005). The identification of species depends on the knowledge held by taxonomists whose work cannot cover all taxon identification requested by non-specialists. To deal with these difficulties, the ‘DNA Barcode of Life’ project aims to develop a standardized, rapid and inexpensive species identification method accessible to non-taxonomists.

DNA barcoding is a technique in which species identification is performed by determining and comparing the sequences of several hundred base pairs of nucleotides from a small fragment of an identified gene, with the aim of contributing to a wide range of ecological and conservation studies in which traditional taxonomic identification is not practical (Krishnamurthy and Francis, 2012). The two main ambitions of DNA barcoding are to assign unknown specimens to species and to enhance the discovery of new species and facilitate identification, particularly in cryptic, microscopic and other organisms with complex or inaccessible morphology (Hebert et al., 2003a). Apart from these, identification of species previously defined by other criteria to also is an objective of barcoding. Another major objective could be the definition of operational units for ecological studies. This may also be used for forensic purposes by linking the specimens with already identified databases.

Introduction
DNA barcoding is a molecular taxonomic method used to identify species by analyzing variations in conserved DNA sequences that differ among species. The concept of “barcoding” refers to pooling multiple samples and sequencing and analysing them collectively. This technique has been widely applied to identify organisms ranging from simple to complex forms. Unlike other genetic markers, such as short tandem repeats (STR), which are typically used to identify individual organisms, DNA barcoding enables broader species identification. However, identifying species-specific DNA sequences across different taxa can be complex and time-consuming. For accurate species differentiation, the variation in DNA sequences must be sufficiently high to clearly distinguish between closely related species (Antil et al., 2023).
DNA barcode sequences are stored in databases like the Barcode of Life Data Systems (BOLD), which is an online repository containing reference DNA sequences for comparison with unknown samples. These databases store speciesspecific genetic sequences, specimen images, and related data, and also track updates to barcode libraries (Jin et al., 2020). DNA barcoding has progressed alongside genomics research, with large online libraries serving as reference databases for identifying samples from various environments like gardens, forests, and even commercial products (Seethapathy et al., 2019).
As research advances, the number of conserved genomic regions used for DNA barcoding continues to grow. For phylogenetic analysis, the rbcL gene locus is commonly used, along with other regions such as the trnL-F intergenic spacer, matK, ndhF, and atpB (Shaw et al., 2005). The CoxI gene has been wellestablished for barcoding animals and plant species. The trnH, psbA region of the plastid has been proposed as a universal barcode for terrestrial plants (Ward et al., 2005). Several other conserved genomic regions have been established by a “plant working group” for molecular taxonomy (Singh et al., 2012). Despite these advancements, further critical evaluations of the authenticity of these DNA barcoding markers in assessing biological diversity are still needed. Over the last few decades, DNA barcoding has become a widely used tool for confirming species identification, as evidenced by the growing body of research publications on the topic (Rob et al., 2019).Publications on DNA barcoding have seen a notable increase, as shown by a search using specific keywords in the CabDirect database (http://www.cabdirect.org/). This trend highlights the growing importance of DNA barcoding in taxonomic research

Introduction
Pathogenic organisms that cause diseases in plants are generally referred to as plant pathogens. Fungi, bacteria, viruses, viroids, algae and protozoa are the important phytopathogenic organisms responsible for plant diseases and they cause immense economic losses to growers. Recent estimates indicate that crop losses due to diseases range from 17-30%, primarily caused by fungal, oomycete, and nematode pathogens (Agrios, 2005). Beyond biotic factors, crop losses can also be attributed to abiotic causes, such as poor agricultural practices, nutrient deficiencies, changes in temperature and rainfall patterns, inadequate/overirrigation and weather extremes, all of which exert selection pressure on plant pathogens, potentially leading to new host infections. Hence, for effective disease management strategy, accurate identification and diagnosis of plant pathogens are of paramount importance before the pathogen induces any epidemic leading to immense loss of crop plants which is certain. Often, identification can be accomplished either visually through microscopic observation of disease-causing micro-organisms or molecular diagnosis based on nucleic acid detection methods. Microscopic observations alone are inadequate for species-level identification of plant pathogens and can often lead to taxonomic errors due to the potential for misidentification of organisms. Nucleic acid-based diagnostic tools allow for the sensitive detection, precise quantification, and specific differentiation of pathogens.Although numerous nucleic acid-based methods are available for plant pathogen detection, PCR-based diagnostics, especially those employing DNA barcodes, are still considered highly reliable and accurate. Scientists, especially plant pathologists, can now easily identify and diagnose most plant diseases as many standardized phytopathogen barcodes facilitate rapid, early, and accurate identification of plant diseases.