eChapters

It is well recognized that sustainable management and sustainable livelihoods are inseparable. If neglected and if the present trends are not corrected in time, everyone’s future is threated. On the other hand, there is increasing recognition of living examples and demonstrated evidences of how the eco agricultural practices can help provide a solution to some of the major problems of today and tomorrow. Also, the main stream international agencies are emphasizing that agro-ecological approaches are the way forward. What the policy makers, farmers and people would like to know is How !it has been our experience that in most countries of the developing world the answer to ‘How’ of eco-agricultural is being demanded!

Bhuva is a small village in north-west Gujarat – India.  My mother was born there. The loving people of Bhuva called me ‘Bhano’ (Sister’s Son / Nephew) and it was my favourite place to go as a child. I have my fondest memories of Bhuva, but could not visit for several decades, until when I was once at the Junagadh Campus of Gujarat Agricultural University, to inaugurate the International Conference on New Developments in Agriculture. Bhuva was not too far and I decided to go there. Soon as I reached, a familiar face, now aged with time, recognized me from a distance and with tears rolling from his old eyes (and mine) he hugged me, calling out “MaroBhano, MaroBhano” (My sister’s son, my sister’s son)! Now in his eighties, it was overwhelming to meet Nanji Ata, who I always remembered being wise, educated and cheerful. He was a relatively progressive farmer with about 6 to 7 acres of land, a few cows and a buffalo. Though water was scarce and saline, he managed to make a good living and was considered a well to do man.

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    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    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

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.

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

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

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

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

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

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

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.