Preface   Energy is the lifeline of modern world and this need is mainly fulfilled by the fossil fuels like petrol, diesel, natural gas etc. Due to increasing global population and industrialization, our dependence upon fossil fuels increased heavily during the last century. But today, India has 17% of the world’s population, and just 0.8% of the world’s known oil and natural gas resources. Transportation is the fastest growing energy consumer in India, now consuming nearly 112 million tons of oil annually. The complete substitution of oil imports for the transportation sectors and the depleting petroleum reserves in the world is the biggest and toughest challenge for the developing nations. The focus of researchers world over is to develop the cost effective technologies as well as searching alternative sources of energy which are eco-friendly, and easy to prepare to become energy independent in the years to come. One such class of fuels which have gained world-wide significance due to many advantages over the present fuels includes the biofuels which can be produced from renewable energy resource – the biomass, by the action of microorganisms. Microorganisms are ubiquitous and indispensable for the existence of mankind. They show diversity in size, shape, metabolism and the range of positive functions they perform for sustaining the life on this planet. Bacteria have been exploited by the mankind since times immemorial for the production of various foods and enzymes. They reveal several types of metabolic reactions which are absent in higher organisms. The scientific understanding of metabolic diversity in microorganisms has made it possible to exploit the selected strains of microbes for the commercial production of enormous useful commodities. Further, the biotechnological tools have made it possible to tailor useful strains of microorganisms for the new millennium which foresees upcoming applications for the sustainability of the society. The present book “Microbes: a source of energy for 21st century” highlights the potential of microorganisms in solving the global energy crisis and making this world as energy independent. The volume has been organized in 13 chapters which have been prepared to provide the readers with both an in-depth study and a broad perspective of microorganisms for sustainability of mankind. The book provides the fundamental knowledge about different types of microorganisms, overviews their distribution in nature and highlights their various applications and commercial uses. Further, it makes the readers familiar with the diversity in energy generating pathways among different groups of microbes and various possibilities which can be exploited for converting global biomass resources in to alternate biofuels. A great effort has been made to provide the readers a comprehensive knowledge about different alternative fuels from microbes for the 21st century. The use of various biotechnological tools for developing novel microorganisms and guidelines for the protection of intellectual property rights have also been discussed in this volume. I am indebted to all other co-authors including Dr. (Mrs) Raman Soni, Dr. D.K. Rahi, Ms. Nidhi Goyal and Ms. Bhavna Lumba who have contributed for this book. The assistance rendered by my research students, Ms. Sushma, Ms. Tammana Toor, Ms. Jasmine Sidhu, Ms. Garima Vasudev, my loving son, Dikshit and daughter, Lubna in the compilation of this manuscript is gratefully acknowledged. It is hoped that this volume will prove useful to the students and professionals who are pursuing their career in Microbiology, Biotechnology, Biochemistry, Environmental sciences and Energy studies related to the alternate biofuels to solve the global energy crisis. At the end, it is suggested that biofuel research should be extended in collaboration with R&D Laboratories, academic institutions and automobile industry to make it a “full fledged fuel” for the fleet running in the country in a time bound manner. The developing countries like India also need to evolve a comprehensive renewable energy policy for energy independence during the 21st century.

1.    Introduction    3 2.    History and Scope of Microbiology    4     2.1.    Controversy over the origin of microorganisms, 5     2.2.    Germ theory of fermentation, 6     2.3.    Germ theory of disease, 6     2.4.    Development of laboratory techniques and pure cultures, 7     2.5.    Discovery of immunization, 7     2.6.    Discovery of protection against infection, 8     2.7.    Discovery of chemotherapeutic agents, 8     2.8.    Microorganisms as geochemical agents, 9

1.    Introduction    71 2.    Microorganisms in Food Industry    72     2.1.    Microorganisms as the agents of fermentation in           traditional fermented foods, 73     2.2.    Microorganisms as the source of food, 83     2.3.    Microorganisms as a source of food supplements, 86 3.    Microorganisms in Pharmaceutical Industry    92     3.1.    Antimicrobial agents from microorganisms, 92     3.2.     Microorganisms as probiotics, 97     3.3.    Microbial enzymes in  pharmaceuticals, 98     3.4.    Mushroom nutriceuticals, 98

1.    Introduction    129 2.    Soil Microbiology    129     2.1.    Bacteria, 130     2.2.    Fungi, 132     2.3.    Algae and Cyanobacteria, 132     2.4.    Protozoa, 132     2.5.    Viruses, 135 3.    Water Microbiology    133 4.    Microbial Associations    133     4.1.    Neutral interactions, 133     4.2.    Positive interactions, 133     4.3.    Negative interactions, 133

1.    Introduction    174 2.    The Thermodynamic and Mechanistic basis of Cellular Metabolism    174     2.1.      Adenosine triphosphate, 175     2.2.    Coenzyme A, 176     2.3.    Modes of ATP synthesis, 177 3.      Components of Electron Transport Chain    181     3.1.    Electron carriers in ETC, 182     3.2.    Complex I - NADH dehydrogenase (NADH coenzyme Q reductase), 185     3.3.    Complex II - Succinate - coenzyme Q reductase, 187     3.4.    Complex III - Coenzyme Q - cytochrome c reductase, 187     3.5.    Complex IV - Cytochrome c oxidase, 188     3.6.    ATP synthese, 188

1.    Introduction    232 2.    Photosynthesis and Biomass Yields    232 3.    Biomass Properties    233     3.1.     Polymeric and chemical composition, 233     3.2.     Fuels analysis, 235     3.3.     Physical properties, 236

1.    Introduction    272 2.    Alcohols    273     2.1.    Methanol, 274     2.2.    Ethanol, 277     2.3.        Butanol, 283 3.    Biodiesel    284 4.    P-series fuels

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

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    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

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    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    496 2.    Strain Development Technologies    496     2.1.    Screening of natural variants of microorganisms, 496     2.2.    Genetic manipulation of microorganisms, 498         2.2.1.    Random mutagenesis and selection, 498         2.2.2.    Conjugation, 504         2.2.3.    Transduction, 504         2.2.4.    Transposition, 506         2.2.5.      Hybridization, 507         2.2.6.    Rare Mating, 509         2.2.7.    Cytoduction, 510         2.2.8.    Protoplast fusion, 511         2.2.9.    Transformation, 511         2.2.10.    Gene cloning and transformation (Recombinant DNA technology), 513

1    Introduction to Patent Laws    540 2.    An Overview of the Patenting Process    541     2.1.    Inventor’s disclosure, 542     2.2.    Patentability search, 542     2.3.    Patent application preparation, 542     2.4.    Patent application amendment, 542     2.5.    Patent application examination, 543     2.6    Main parts of a patent, 543     2.7.    Granting of patent, 544     2.8.    Date and term of patent, 544     2.9.    Provisional specification, 544     2.10.    Complete specification, 545     2.11.      Cost of patenting, 545

A Abiogenesis 5 Absolute Alcohol 303, 350 Acervulus 29 Acetic Acid 49, 65, 68, 73, 87, 89, 110, 144, 176, 177, 200, 251, 252, 276, 283, 283, 290, 318, 319, 331, 338, 353, 358, 399, 430, 476, 531 Acetic Acid Bacteria 200, 332 Acetobacter 87, 88, 89, 200, 332 Acetobacter Aceti 87 Acetogenesis 107, 226, 228, 402 Acetone-Butanol 110, 283 Acetyl Coa 208, 401, 526 Acetyl Phosphate 177, 219, 220, 223 Achromobacter 84, 141 Acid Esterification 261, 269, 371, 376, 378, 379 Acidianus 228 Acidification 78, 80, 81, 524, 530 Acidogenesis 291, 400, 401 Acidogenic Bacteria 290, 292, 293 Acidogenic Fermentation 402 Acidophiles 16, 23, 47, 129, 147, 228 Acinetobacter 84, 111 Actinobacteria 14 Actinomucor Elegans 81 Actinomyces 400 Actinomycetes 56, 57, 93, 94, 104, 105, 106, 107, 129, 130, 138, 140, 144, 211, 312, 369, 538 Activated Biofilters 153