eChapters

Metabolic fingerprinting and profiling provide powerful approaches for investigating global biochemical changes within biological systems. This chapter explains the principles of metabolic fingerprinting and profiling and distinguishes between broad, untargeted characterization and targeted analysis of selected metabolites. It discusses experimental design, sample preparation, analytical platforms, data preprocessing, normalization, statistical analysis, and multivariate approaches used to identify meaningful metabolic patterns. Techniques such as principal component analysis and related statistical methods help reveal differences between biological conditions. The chapter highlights applications in disease investigation, agricultural research, environmental studies, food analysis, and biotechnology, while emphasizing the importance of reproducible analytical procedures and appropriate interpretation of complex metabolomic datasets.

Metabolism - sum total of all chemical reactions in living cells

Catabolic reactions - degrade macromolecules and other molecules to release energy

Anabolic reactions - used to synthesize macromolecules for cell growth, repair, and reproduction

Can divide metabolism into 4 groups: carbohydrates, lipids, amino acids, nucleotides.

Metabolomic databases provide essential information for identifying metabolites, interpreting experimental results, analyzing pathways, and understanding biochemical relationships. This chapter introduces major databases used in metabolomics and explains their roles in modern biological research. Resources such as KEGG, BRENDA, HMDB, MetaboLights, METLIN, and LIPID MAPS provide information on metabolites, enzymes, pathways, structures, spectra, diseases, and experimental datasets. The chapter discusses their applications in metabolite identification, pathway analysis, biomarker discovery, systems biology, and translational research. It also considers challenges including data volume, database completeness, continuous updating, standardization, and integration with other omics resources.

Metabolomic research depends on analytical technologies capable of detecting and characterizing large numbers of chemically diverse metabolites. This chapter introduces the principal analytical platforms used for metabolite analysis, with emphasis on mass spectrometry and nuclear magnetic resonance spectroscopy. Gas chromatography–mass spectrometry, liquid chromatography–mass spectrometry, capillary electrophoresis–mass spectrometry, and NMR are examined in relation to metabolite separation, identification, and quantification. The chapter also considers sample preparation, analytical workflows, advantages and limitations of different platforms, and complementary approaches for achieving broader metabolome coverage. These techniques provide the analytical foundation for metabolic profiling, biomarker discovery, pathway analysis, and systems-level biological investigations.

Surface-Enhanced Raman Spectroscopy (SERS) may detect and identify chemical and biological species ultrasensitively. Through localized surface plasmon resonance (LSPR) effects, metal nanostructures boost analyte Raman signals. This chapter covers current advances and essential principles in metal nanostructures for SERS chemical detection. It discusses SERS fundamentals and enhancing processes, such as metal nanostructure size, shape, and composition. Top-down and bottom-up processes including lithography, chemical synthesis, and self-assembly are used to create repeatable and controllable metal nanostructures. The complex interactions between light, metal nanostructures, and analyte molecules are best understood by combining theoretical modeling and experimental observations. 

Abstract

Microorganisms that produce methane as their metabolic end product are known as methanogens. Methanogens are prokaryotic, unicellular, obligate anaerobes having fastidious growth requirements making them difficult to isolate and preserve. They catalyse the terminal step in anaerobic breakdown of organic substances. Even though methanogenic archaea or methanogens show very limited metabolic diversity, they are one of the most phylogenetically and ecologically diverse group of Archaea. Methanogenic community varies greatly with respect to temperature. Methanogens have been reported from permanently frozen habitats like permafrost to hyperthermophilic environments such as hydrothermal vents. However, the metabolic and phylogenetic diversity of methanogens in these habitats vary greatly. Methanogens are the biocatalysts, having the ability to provide a solution to help solve energy crisis by producing methane as storable energy carrier. Methane being a flammable gas, can act as a clean and renewable source of energy. The biogenic methane gas thus produced may serve as an efficient alternative for fossil fuels in the future.

Bacterial biofertilizers are supplied as carrier based inoculants. Peat or lignite is used as carrier material. Carrier based bacterial inoculants are applied by the following methods.

1. Seed treatment or seed inoculation.
2. Seedling root dip and
3. Main field application

Seed Treatment

One packet of the inoculant (200 g) 7is mixed with 200 ml of rice kanji to make a slurry. The seeds required for an acre are mixed in the slurry so as to have a uniform coating of the inoculant over the seeds and then shade dried for 30 minutes. The shade dried seeds should be sown within 24 hours. One packet of the inoculant (200 g) is sufficient to treat 10 kg of seeds.

ABSTRACT

Methylotrophy is a phenomenon by which microorganisms derive energy, and in many cases, cell carbon from reduced molecules that have no C–C bond (also called C1compounds). This gains significance because of its unique mode of nutrition, the ability to utilize more than one metabolic pathway and its vast distribution among various groups of bacteria and yeasts. It is one of the earliest modes of energy metabolism present in microorganisms, through which microorganisms are able to utilize a wide range of compounds, which are considered unsuitable for most forms of life. In the present chapter we focus on various aspects of methylotrophy, and the application of methylotrophic bacteria in a spectrum of biological activities and commercial possibilities.

In genetics, microRNAs (miRNA) are single-stranded RNA molecules of 21-23 nucleotides in length, which regulate gene expression. miRNAs are encoded by genes from whose DNA they are transcribed but miRNAs are not translated into protein (i.e. they are non-coding RNAs); instead each primary transcript (a pri-miRNA) is processed into a short stem-loop structure called a pre-miRNA and finally into a functional miRNA. Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to down-regulate gene expression. They were first described in 1993 by Lee and colleagues in the Victor Ambros lab .

MicroRNAs can be encoded by independent genes, but also be processed (via the enzyme Dicer) from a variety of different RNA species, including introns, 3' UTRs of mRNAs, long noncoding RNAs, snoRNAs and transposons.

The genes encoding miRNAs are much longer than the processed mature miRNA molecule; miRNAs are first transcribed as primary transcripts or pri- miRNA with a cap and poly-A tail and processed to short, 70-nucleotide stem-loop structures known as pre-miRNA in the cell nucleus. These pre- miRNAs are then processed to mature miRNAs in the cytoplasm by interaction with the endonuclease Dicer, which also initiates the formation of the RNA-induced silencing complex (RISC). This complex is responsible for the gene silencing observed due to miRNA expression and RNA interference. The pathway in plants varies slightly due to their lack of Drosha homologs; instead, Dicer homologs alone effect several processing steps. The pathway is also different for miRNAs derived from intronic stem-loops; these are processed by Dicer but not by Drosha. Either the sense strand or antisense strand of DNA can function as templates to give rise to miRNA.

Microalgae have long been recognized as good potential sources for biofuel production due to their relatively high oil content and rapid biomass production (Schenk et al., 2008; Hu et al., 2008). These photosynthetic organisms thrive in a variety of aquatic habitats, including lakes, rivers, oceans, and even sewage, demonstrating their adaptability to diverse environmental conditions. They can tolerate a wide range of temperatures, salinities, and pH levels, as well as varying light intensities and aquatic or desert conditions. Additionally, microalgae can grow independently or in symbiosis with other organisms, making them highly versatile for various cultivation systems (Mutanda et al., 2011). Algae are generally grouped into three major categories: Rhodophyta (red algae), Phaeophyta (brown algae), and Chlorophyta (green algae), and are further classified by size into macroalgae and microalgae. Macroalgae are large, multicellular organisms visible to the naked eye, while microalgae consist of microscopic single cells that can be either prokaryotic, similar to cyanobacteria, or eukaryotic, similar to green algae (Fields et al., 2014; Maltsev & Maltseva, 2021). Microalgae are capable of producing a wide array of valuable bioproducts, including polysaccharides, lipids, pigments, proteins, vitamins, bioactive compounds, and antioxidants. They grow at a much faster rate compared to terrestrial crops and can be cultivated on non-agricultural land using non-potable saltwater or wastewater, reducing competition with food crops and ensuring sustainability (Lee et al., 2014). This has made microalgae an increasingly attractive alternative feedstock for biodiesel production, which relies heavily on the high lipid content of microalgae. The majority of these lipids are stored in the form of triacylglycerols, a type of oil that is ideal for biodiesel production. Beyond biodiesel, microalgae can also be utilized in various other energy production pathways. Some microalgal strains can produce hydrogen gas under specific growth conditions, while algal biomass can be combusted like wood or digested anaerobically to produce methane biogas, which can be used for heat and power generation. Additionally, algal biomass can be processed into crude bio-oil through pyrolysis, further expanding its applications as a renewable energy source (Mumtaz et al., 2019).

Introduction 
Fossil Fuels like Coal, Coal product, Natural Gas, Petroleum, Crude Oil provide 80% of the world’s energy. However, burning them releases harmful pollutants, including carbon dioxide, nitrogen oxides and the sulfur oxides, contributing to global warming. To combat this, the World is shifting towards cleaner, renewable energy sources called biofuels. Biofuels are made from organic materials like plants and waste, offering several benefits: Renewable and Sustainable, Less greenhouse gas emissions, non-toxic [6]. Common biofuels include are: Biodiesel, Biogas, Bioethanol. These alternative fuels help reduce our reliance on fossil fuels, mitigating climate change and promoting a healthier environment. Biodiesel replaces fossil-based diesel/petrol made through Trans-esterifi cation process. The benefi ts include clean energy, renewable resources and the domestic production. Generations of biodiesel are: First Generation include Edible crops (Soybean, Corn, Sugarcane). Second Generation includes Non-edible biomass(Straw, Hay). Third Generation include Microalgae (70% yield). Fourth Generation include the genetically modifi ed algae and electro-biofuel. [2] Biodiesel production has changed over time. Initially, edible vegetable oils like soybean, corn, sunfl ower and palm oil were used. However this raised concerns: using valuable farmland for fuel instead of food, competing with food production, weather and soil quality affecting the crop yield , fertilizer use releasing harmful nitrous oxide greenhouse gas. To address these issues, focus shifted to non-edible oils and now Microalgae, offering; sustainable, climate-resilient production, no competition with the food crops, reduced greenhouse gas emission, higher oil yield. Microalgae -based biodiesel is the future providing a cleaner, more effi cient alternative.[4]

Introduction 
Fuels are essential to human existence and account for 70% of the world’s energy use. The demand for fossil fuels is rising daily due to the ongoing global population boom and has now reached a crisis point. The world’s current reserves cannot keep up with the projected 40% rise in demand between 2010 and 2040 [1]. According to Energy Information Administration (EIA) statistics, the world’s fossil fuel sources will run out in fewer than 50 years [2]. In addition, burning fossil fuels and living in an industrialised environment have released large amounts of carbon dioxide (CO2), carbon monoxide (CO), sulphur dioxide (SO2), nitrogen oxides (NOx), as well as a significant number of potentially toxic compounds into the atmosphere. This has severely degraded the natural resources that are currently available, including fossil fuels. The human and natural ecology have suffered significant damages as a result of the effects of global warming in recent years [3]. As a result, cutting CO2 emissions is crucial to preventing the negative effects of global warming. Therefore, there has been a greater focus on the improvement of CO2 capture and sequestration systems to significantly lower CO2 emissions from a variety of sources, including vehicle exhaust emissions and industrial flue gas [4] . Fuel production needs to be sustainable in terms of the environment and the economy, meaning it needs to be able to reduce CO2. It is critical to find inexpensive, sustainable, and clean energy options in order to handle the current circumstances. Currently, several traditional renewable energy sources, such as solar, biofuels, hydroelectric, geothermal, or wind are being used with varying degrees of success and detriment. Biofuels are sustainable and renewable energy sources that have emerged as a superior alternative to traditional fossil fuels in energy production. Biofuels have a lot of potential because they are abundant environmentally favourable renewable resources and their production is expanding globally, even though they are still more expensive than fossil fuels [5]. Researchers are actively investigating biomasses as a means of obtaining energy from renewable sources. It is commonly known that through a process called photosynthesis, plants can transform sun energy into chemical forms. Microalgae are fast-growing microorganisms that develop 100 times quicker than terrestrial plants. Their photosynthetic efficiency is also higher (10–50 times greater than terrestrial plants) among biomasses [6]. In less than a day, they can double their biomass. Unicellular microalgae, in contrast to plants, do not divide substantial amounts of biomass into supporting structures like stems or roots, which are costly to create energetically and frequently challenging for harvesting and processing to produce biofuel. Furthermore, they have the ability to adapt to harsh aquatic environments and economically absorb helpful substances. Moreover, 1 kg of microalgae biomass is produced by microalgae cells that fix 1.8 kg of CO2 and have a 50% carbon content [7]. Microalgae can be grown on terrain that is inappropriate for food production because of their high total yield and hence small land use footprint [8]. Microalgal species including Scenedemus sp., Chlorella sp., and Botryococcus sp.; are common, easier to grow than other species and may have higher lipid contents [9].

Soil is the outer loose layer of earth consisting of layers of mineral material (regolith) whose properties differ from one another and these differences are largely due to the variation in biological activities. Soil micro-environment principally comprizes of inorganic particulates (sand, silt and clay) plus certain oxides and hydroxides, plant roots, organic matter, microbial biomass and aqueous and gaseous phases. The uneven distribution of these components provides a great variety of conditions from field to micropores. The interaction of physical and chemical factors contributes to the creation of varied soil habitat and hence determines the composition and activity of soil biota at a particular site and time. Over geological times, microorganisms have had great opportunity to become distributed worldwide. Such growth and development of microorganisms as well as species diversity is of considerable significance. The existing geographic distribution is reflective of long term adaptation of microorganisms to the various environmental conditions. The preferred environment of an organism is usually referred as ‘habitat’.

1.    Introduction    360
2.    Feedstocks for Biodiesel Production    361

    2.1.    Fats and oils, 362
    2.2.    Alcohols, 363
    2.3.    Catalysts and neutralizers, 367

1.    Introduction    468

2.    Biofuel Cell    470

    2.1.    Microbial-based Biofuel Cells, 471
        2.1.1.    Microbial bioreactors producing H2 for conventional fuel  cells, 475
        2.1.2.    Microbial fuel cells producing electrochemically active metabolites in  
                the anodic compartment, 476
        2.1.3.    Microbial fuel cells operating in the presence of artificial electron relays, 477
        2.1.4.    Microbial fuel cells producing electricity during wastewater treatment, 483
        2.1.5.    Microbial fuel cell producing  electricity from acetate or butyrate, 484

1.    Introduction    302
2.    Raw Materials for Alcohol Production    304

    2.1.    Sugary substrates, 306
    2.2.    Starchy residues (cereal grains), 309
    2.3.    Cellulosic materials (crop residues), 314

3.    Microorganisms for Alcohol Production    316

    3.1.    Comparision of ethanol production by bacteria and yeasts, 318

ABSTRACT

Microbes are integral part of the terrestrial ecosystem. Their function ranges from nutrients mineralization, stress alleviation to bioremediation in soils .There is a great possibility of using microbial inoculants as a biological tool for sustainable forestry and agriculture. This review gives an overview on the benefits of microbial technology and their contribution in development of green technology.

Keywords: Green technology, Microbes, AMF, PGPRs, Microbial consortium, Carbon sequestration.

1.     Introduction    424

2.    Conventional Methods of Hydrogen Production    426

3.    Biological Methods of Hydrogen Production    429

    3.1.    Hydrogen production by biophotolysis of water, 430
        3.1.1. Photolysis by cyanobacteria (Blue green algae), 430
            3.1.1.1. Nitrogenase dependent hydrogen production, 434
            3.1.1.2.  Hydrogenase-dependent hydrogen production, 437
            3.1.1.3.  Factors affecting  hydrogen production by cyanobacteria, 440
            3.1.1.4.   Bioreactors for cyanobacterial hydrogen production, 443
            3.1.1.5. Future prospects for cyanobacterial hydrogen production, 446

1.    Introduction    392

2.    Landfill Gas    393

3.    Biogas    394

    3.1.    Benefits of biogas, 394
    3.2.    Potential of biogas, 395
    3.3.    Biogas production system, 396
        3.3.1.    Raw materials, 396
        3.3.2.    Biogas technology, 398
        3.3.3.    Process of anaerobic fermentation for methane generation, 400
        3.3.4.    Conditions for anaerobic fermentation, 404
        3.3.5.    Sludge-algae-methane system, 407
        3.3.6.    Biogas plant, 408

Abstract

Microorganisms execute many key functions that regulate the processes related to the fertility status, nutrient transformation, nutrient conservation, and soil health management that are crucial for agronomic sustainability. Rice soils offer peculiar conditions for microorganisms that support diametrically opposite biochemical reactions under flooded conditions. It is pertinent to note that both reduction and oxidation reactions of several essential nutrients mediated by microbes occur simultaneously in the flooded soils at various depths, profiles and stages of rice crop growth in concurrence. This is peculiar and specific to rice soils as the cultivation process demands changes in water regimes, operative and management practices.