Environmental and Agricultural Microbiology

Bibhuti Bhusan Mishra is working as the ICAR-Emeritus Professor at the P.G. Department of Microbiology, College of Basic Science & Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India. He obtained his PhD Degree in 1987 from Berhampur University, Odisha. He has more than 60 research publications to his name.Suraja Kumar Nayak obtained his PhD from Odisha University of Agriculture and Technology in 2013 and is currently an assistant professor in the Department of Biotechnology, College of Engineering and Technology, Biju Patnaik University of Technology, Bhubaneswar, Odisha, India. His areas of teaching and research include general and environmental microbiology, soil microbiology, industrial & food biotechnology, microbial biotechnology. Dr. Nayak has published 18 scientific papers including book chapters in various journals and national & international books. Swati Mohapatra is a research Professor in Wankwong University South Korea. She obtained her PhD in Microbiology from Orissa University of Agriculture and Technology in 2015. Her areas of teaching and research include environmental microbiology, polymer chemistry, industrial and material science, microbial molecular biology, infection biology, agriculture microbiology. Dr. Mohapatra has published 32 scientific articles in various national and international journals and 07 book chapters. D. P. Samantaray obtained his PhD in Microbiology (2013) from Utkal University, Bhubaneswar, Odisha, India. He is an assistant professor in the Post Graduate Department of Microbiology, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha. He is working in the field of bioenergy, bioremediation, biopolymer & composite materials including its biomedical and agricultural applications. He has published more than 70 scientific publications.

• Preface xviiPart 1: Microbial Bioremediation and Biopolymer Technology 11 A Recent Perspective on Bioremediation of Agrochemicals by Microalgae: Aspects and Strategies 3Prithu Baruah and Neha Chaurasia1.1 Introduction 41.2 Pollution Due to Pesticides 61.2.1 Acute Effects 81.2.2 Chronic Effects 91.3 Microalgal Species Involved in Bioremediation of Pesticides 91.4 Strategies for Phycoremediation of Pesticides 131.4.1 Involvement of Enzymes in Phycoremediation of Pesticides 131.4.2 Use of Genetically Engineered Microalgae 131.5 Molecular Aspects of Pesticide Biodegradation by Microalgae 141.6 Factor Affecting Phycoremediation of Pesticides 161.6.1 Biological Factor 161.6.2 Chemical Factor 161.6.3 Environment Factor 171.7 Benefit and Shortcomings of Phycoremediation 171.7.1 Benefits 171.7.2 Shortcomings 171.8 Conclusion and Future Prospects 18References 182 Microalgal Bioremediation of Toxic Hexavalent Chromium: A Review 25Pritikrishna Majhi, Satyabrata Nayak and Saubhagya Manjari Samantaray2.1 Introduction 252.1.1 Chromium Cycle 272.2 Effects of Hexavalent Chromium Toxicity 272.2.1 Toxicity to Microorganisms 272.2.2 Toxicity to Plant Body 282.2.3 Toxicity to Animals 292.3 Chromium Bioremediation by Microalgae 302.3.1 Cyanobacteria 302.3.2 Green Algae 312.3.3 Diatoms 312.4 Mechanism Involved in Hexavalent Chromium Reduction in Microalgae 322.5 Conclusion 33References 343 Biodetoxification of Heavy Metals Using Biofilm Bacteria 39Adyasa Barik, Debasish Biswal, A. Arun and Vellaisamy Balasubramanian3.1 Introduction 403.2 Source and Toxicity of Heavy Metal Pollution 413.2.1 Non-Essential Heavy Metals 423.2.1.1 Arsenic 423.2.1.2 Cadmium 433.2.1.3 Chromium 433.2.1.4 Lead 443.2.1.5 Mercury 453.2.2 Essential Heavy Metals 453.2.2.1 Copper 453.2.2.2 Zinc 463.2.2.3 Nickel 463.3 Biofilm Bacteria 473.4 Interaction of Metal and Biofilm Bacteria 473.5 Biodetoxification Mechanisms 483.5.1 Biosorption 483.5.2 Bioleaching 503.5.3 Biovolatilization 523.5.4 Bioimmobilization 543.6 Conclusion 55References 554 Microbial-Derived Polymers and Their Degradability Behavior for Future Prospects 63Mohammad Asif Ali, Aniruddha Nag and Maninder Singh4.1 Introduction 634.2 Polyamides 654.2.1 Bioavailability and Production 664.2.2 Biodegradability of Polyamides 664.2.3 Degradation of Nylon 4 Under the Soil 674.2.4 Fungal Degradation of Nylon 6 and Nylon 66 (Synthetic Polyamide) 674.2.5 Itaconic Acid-Based Heterocyclic Polyamide 684.2.6 Summary and Future Development 694.3 Polylactic Acid 694.3.1 Availability and Production 704.3.2 Polymerization Method 714.3.3 Biodegradability of Polylactic Acid 734.3.4 Copolymerization Method 734.3.5 Blending Method 734.3.6 Nanocomposite Formation 744.3.7 Summary 744.4 Polyhydroxyalkanoates 744.4.1 Biosynthesis of Polyhydroxyalkanoates 754.4.2 Application of PHAs 754.4.3 Biodegradability of PHAs 764.4.4 Degradability Methods 764.4.5 Summary 774.5 Conclusion and Future Development 77References 785 A Review on PHAs: The Future Biopolymer 83S. Mohapatra, K. Vishwakarma, N. C. Joshi, S. Maity, R. Kumar, M. Ramchander, S. Pattnaik and D. P. Samantaray5.1 Introduction 845.2 Green Plastic: Biodegradable Polymer Used as Plastic 855.3 Difference Between Biopolymer and Bioplastic 885.4 Polyhydroxyalkanoates 885.5 Polyhydroxyalkanoates and Its Applications 895.6 Microorganisms Producing PHAs 905.7 Advantages 965.8 Conclusion and Future Prospective 96References 966 Polyhydroxybutyrate as an Eco-Friendly Alternative of Synthetic Plastics 101Shikha Sharma, Priyanka Sharma, Vishal Sharma and Bijender Kumar Bajaj6.1 Introduction 1026.2 Bioplastics 1046.3 Bioplastics vs. Petroleum-Based Plastics 1066.4 Classification of Biodegradable Polymers 1076.5 PHB-Producing Bacteria 1096.6 Methods for Detecting PHB Granules 1136.7 Biochemical Pathway for Synthesis of PHB 1146.8 Production of PHB 1166.8.1 Process Optimization for PHB Production 1176.8.2 Optimization of PHB Production by One Variable at a Time Approach 1186.8.3 Statistical Approaches for PHB Optimization 1206.9 Production of PHB Using Genetically Modified Organisms 1236.10 Characterization of PHB 1256.11 Various Biochemical Techniques Used for PHB Characterization 1266.11.1 Fourier Transform Infrared Spectroscopy 1276.11.2 Differential Scanning Calorimetry 1276.11.3 Thermogravimetric Analysis 1286.11.4 X-Ray Powder Diffraction (XRD) 1286.11.5 Nuclear Magnetic Resonance Spectroscopy 1286.11.6 Microscopic Techniques 1296.11.7 Elemental Analysis 1306.11.8 Polarimetry 1306.11.9 Molecular Size Analysis 1306.12 Biodegradation of PHB 1316.13 Application Spectrum of PHB 1326.14 Conclusion 1356.15 Future Perspectives 135Acknowledgements 136References 1367 Microbial Synthesis of Polyhydroxyalkanoates (PHAs) and Their Applications 151N.N.N. Anitha and Rajesh K. Srivastava7.1 Introduction 1537.2 Conventional Plastics and Its Issues in Utility 1567.2.1 Synthetic Plastic and Its Accumulation or Degradation Impacts 1587.3 Bioplastics 1597.3.1 Polyhydroxyalkanoates 1607.3.1.1 Microorganisms in the Production of PHAs 1647.4 Fermentation for PHAs Production 1717.5 Downstream Process for PHAs 1737.6 Conclusions 175References 1768 Polyhydroxyalkanoates for Sustainable Smart Packaging of Fruits 183S. Pati, S. Mohapatra, S. Maity, A. Dash and D. P. Samantaray8.1 Introduction 1838.2 Physiological Changes of Fresh Fruits During Ripening and Minimal Processing 1858.3 Smart Packaging 1868.4 Biodegradable Polymers for Fruit Packaging 1888.5 Legal Aspects of Smart Packaging 1898.6 Pros and Cons of Smart Packaging Using PHAs 1898.7 Conclusion 190References 1919 Biosurfactants Production and Their Commercial Importance 197Saishree Rath and Rajesh K. Srivastava9.1 Introduction 1989.2 Chemical Surfactant Compounds 2009.2.1 Biosurfactant Compounds 2029.3 Properties of Biosurfactant Compound 2059.3.1 Activities of Surface and Interface Location 2059.3.2 Temperature and pH Tolerance 2059.3.3 Biodegradability 2069.3.4 Low Toxicity 2069.3.5 Emulsion Forming and Breaking 2069.4 Production of Biosurfactant by Microbial Fermentation 2069.4.1 Factors Influencing the Production of Biosurfactants 2099.4.1.1 Environmental Conditions 2099.4.1.2 Carbon Substrates 2109.4.1.3 Estimation of Biosurfactants Activity 2119.5 Advantages, Microorganisms Involved, and Applications of Biosurfactants 2119.5.1 Advantages of Using Biosurfactants 2119.5.1.1 Easy Raw Materials for Biosurfactant Biosynthesis 2119.5.1.2 Low Toxic Levels for Environment 2119.5.1.3 Best Operation With Surface and Interface Activity 2129.5.1.4 Good Biodegradability 2129.5.1.5 Physical Variables 2129.5.2 Microbial Sources 2129.5.3 Production of Biosurfactants 2139.5.3.1 Production of Rhamnolipids 2139.5.3.2 Regulation of Rhamnolipids Synthesis 2149.5.3.3 Commercial Use of Biosurfactants 2149.6 Conclusions 215References 216Part 2: Microbes in Sustainable Agriculture and Biotechnological Applications 21910 Functional Soil Microbes: An Approach Toward Sustainable Horticulture 221C. Sarathambal, R. Dinesh and V. Srinivasan10.1 Introduction 22110.2 Rhizosphere Microbial Diversity 22210.3 Plant Growth–Promoting Rhizobacteria 22310.3.1 Nitrogen Fixation 22410.3.2 Production of Phytohormones 22510.3.3 Production of Enzymes That can Transform Crop Growth 22510.3.4 Microbial Antagonism 22610.3.5 Solubilization of Minerals 22610.3.6 Siderophore and Hydrogen Cyanide (HCN) Production 22810.3.7 Cyanide (HCN) Production 22910.3.8 Plant Growth–Promoting Rhizobacteria on Growth of Horticultural Crops 22910.4 Conclusion and Future Perspectives 235References 23511 Rhizosphere Microbiome: The Next-Generation Crop Improvement Strategy 243M. Anandaraj, S. Manivannan and P. Umadevi11.1 Introduction 24411.2 Rhizosphere Engineering 24511.3 Omics Tools to Study Rhizosphere Metagenome 24611.3.1 Metagenomics 24611.3.2 Metaproteomics 24811.3.3 Metatranscriptomics 24911.3.4 Ionomics 25011.4 As Next-Generation Crop Improvement Strategy 25111.5 Conclusion 252References 25212 Methane Emission and Strategies for Mitigation in Livestock 257Nibedita Sahoo, Swati Pattnaik, Matrujyoti Pattnaik and Swati Mohapatra12.1 Introduction 25812.2 Contribution of Methane from Livestock 25912.3 Methanogens 25912.3.1 Rumen Microbial Community 26012.3.2 Methanogens Found in Rumen 26012.3.3 Enrichment of Methanogens from Rumen Liquor 26112.3.4 Screening for Methane Production 26112.3.5 Isolation of Methanogens 26112.3.6 Molecular Characterization 26112.4 Methanogenesis: Methane Production 26212.4.1 Pathways of Methanogenesis 26212.4.2 Pathway of CO2 Reduction 26212.4.3 CO2 Reduction to Formyl-Methanofuran 26312.4.4 Conversion of the Formyl Group from Formyl-Methanofuran to Formyl-Tetrahydromethanopterin 26312.4.5 Formation of Methenyl-Tetrahydromethanopterin 26312.4.6 Reduction of Methenyl-Tetrahydromethanopterin to Methyl-Tetrahydromethanopterin 26312.4.7 Reduction of Methyl-Tetrahydromethanopterin to Methyl-S-Coenzyme M 26412.4.8 Reduction of Methyl-S-Coenzyme M to CH4 26412.5 Strategies for Mitigation of Methane Emission 26412.5.1 Dietary Manipulation 26412.5.1.1 Increasing Dry Matter Intake 26412.5.1.2 Increasing Ration Concentrate Fraction 26512.5.1.3 Supplementation of Lipid 26512.5.1.4 Protozoa Removal 26612.5.2 Feed Additives 26612.5.2.1 Ionophore Compounds 26612.5.2.2 Halogenated Methane Compound 26712.5.2.3 Organic Acid 26712.5.3 Microbial Feed Additives 26812.5.3.1 Vaccination 26812.5.3.2 Bacteriophages and Bacteriocins 26912.5.4 Animal Breeding and Selection 27012.6 Conclusion 270References 27113 Liquid Biofertilizers and Their Applications: An Overview 275Avro Dey13.1 Introduction 27513.1.1 Chemical Fertilizer and its Harmful Effect 27713.2 Biofertilizers “Boon for Mankind” 27813.3 Carrier-Based Biofertilizers 27913.3.1 Solid Carrier-Based Biofertilizers 27913.3.2 Liquid Biofertilizer 27913.4 Sterilization of the Carrier 28213.5 Merits of Using Liquid Biofertilizer Over Solid Carrier-Based Biofertilizer 28213.6 Types of Liquid Biofertilizer 28313.7 Production of Liquid Biofertilizers 28513.7.1 Isolation of the Microorganism 28513.7.2 Preparation of Medium and Growth Condition 28513.7.3 Culture and Preservation 28613.7.4 Preparation of Liquid Culture 28613.7.5 Fermentation and Mass Production 28713.7.6 Formulation of the Liquid Biofertilizers 28713.8 Applications of Biofertilizers 28813.9 Conclusion 290References 29114 Extremozymes: Biocatalysts From Extremophilic Microorganisms and Their Relevance in Current Biotechnology 293Khushbu Kumari Singh and Lopamudra Ray14.1 Introduction 29414.2 Extremophiles: The Source of Novel Enzymes 29514.2.1 Thermophilic Extremozymes 29614.2.2 Psychrophilic Extremozymes 29914.2.3 Halophilic Extremozymes 30014.2.4 Alkaliphilic/Acidiophilic Extremozymes 30014.2.5 Piezophilic Extremozymes 30114.3 The Potential Application of Extremozymes in Biotechnology 30114.4 Conclusion and Future Perspectives 303References 30415 Microbial Chitinases and Their Applications: An Overview 313Suraja Kumar Nayak, Swapnarani Nayak, Swaraj Mohanty, Jitendra Kumar Sundaray and Bibhuti Bhusan Mishra15.1 Introduction 31415.2 Chitinases and Its Types 31515.3 Sources of Microbial Chitinase 31715.3.1 Bacterial Chitinases 31715.3.2 Fungal Chitinases 31915.3.3 Actinobacteria 32115.3.4 Viruses/Others 32215.4 Genetics of Microbial Chitinase 32215.5 Biotechnological Advances in Microbial Chitinase Production 32315.5.1 Media Components 32415.5.2 Physical Parameters 32515.5.3 Modes and Methods of Fermentation 32515.5.4 Advances Biotechnological Methods 32615.6 Applications of Microbial Chitinases 32715.6.1 Agricultural 32815.6.1.1 Biopesticides 32815.6.1.2 Biocontrol 32815.6.2 Biomedical 32915.6.3 Pharmaceutical 32915.6.4 Industrial 33015.6.5 Environmental 33015.6.5.1 Waste Management 33115.6.6 Others 33115.7 Conclusion 332References 33216 Lithobiontic Ecology: Stone Encrusting Microbes and their Environment 341Abhik Mojumdar, Himadri Tanaya Behera and Lopamudra Ray16.1 Introduction 34116.2 Diversity of Lithobionts and Its Ecological Niche 34216.2.1 Epiliths 34216.2.2 Endoliths 34316.2.3 Hypoliths 34416.3 Colonization Strategies of Lithobionts 34516.3.1 Temperature 34616.3.2 Water Availability 34616.3.3 Light Availability 34716.4 Geography of Lithobbiontic Coatings 34816.4.1 Bacteria 34816.4.2 Cyanobacteria 34916.4.3 Fungi 34916.4.4 Algae 34916.4.5 Lichens 35016.5 Impacts of Lithobiontic Coatings 35116.5.1 On Organic Remains 35116.5.2 On Rock Weathering 35116.5.3 On Rock Coatings 35216.6 Role of Lithobionts in Harsh Environments 35216.7 Conclusion 353Acknowledgement 353References 35317 Microbial Intervention in Sustainable Production of Biofuels and Other Bioenergy Products 361Himadri Tanaya Behera, Abhik Mojumdar, Smruti Ranjan Das, Chiranjib Mohapatra and Lopamudra Ray17.1 Introduction 36217.2 Biomass 36317.3 Biofuel 36417.3.1 Biodiesel 36517.3.1.1 Microalgae in Biodiesel Production 36517.3.1.2 Oleaginous Yeasts in Biodiesel Production 36617.3.1.3 Oleaginous Fungi in Biodiesel Production 36617.3.1.4 Bacteria in Biodiesel Production 36717.3.2 Bioalcohol 36717.3.2.1 Bioethanol 36717.3.2.2 Biobutanol 36817.3.3 Biogas 36917.3.4 Biohydrogen 36917.4 Other Bioenergy Products 37017.4.1 Microbial Fuel Cells 37017.4.1.1 Microbes Used in MFCs 37217.4.1.2 Future Aspects of Microbial Fuel Cells 37217.4.2 Microbial Nanowires in Bioenergy Application 37417.4.2.1 Pili 37517.4.2.2 Outer Membranes and Extended Periplasmic Space 37517.4.2.3 Unknown Type—MNWs Whose Identity to be Confirmed 37517.4.3 Microbial Nanowires in Bioenergy Production 37617.5 Conclusion 376References 37618 Role of Microbes and Microbial Consortium in Solid Waste Management 383Rachana Jain, Lopa Pattanaik, Susant Kumar Padhi and Satya Narayan Naik18.1 Introduction 38418.2 Types of Solid Waste 38418.2.1 Domestic Wastes 38518.2.2 Institutional and Commercial Wastes 38518.2.3 Wastes From Street Cleansing 38518.2.4 Industrial Wastes 38518.2.5 Nuclear Wastes 38518.2.6 Agricultural Wastes 38518.3 Waste Management in India 38618.4 Solid Waste Management 39018.4.1 Municipal Solid Waste Management 39018.5 Solid Waste Management Techniques 39018.5.1 Incineration 39218.5.2 Pyrolysis and Gasification 39218.5.3 Landfilling 39318.5.4 Aerobic Composting 39418.5.5 Vermicomposting 39718.5.6 Anaerobic Digestion 40118.5.6.1 Enzymatic Hydrolysis 40218.5.6.2 Fermentation 40218.5.6.3 Acetogenesis 40318.5.6.4 Methanogenesis 40318.5.7 Bioethanol From Various Solid Wastes 40418.6 Conclusion 413References 413Index 423