Bioprospecting of Microorganism-Based Industrial Molecules

Sudhir P. Singh, Scientist-D, Biotechnology & Synthetic Biology, Center of Innovative and Applied Bioprocessing, Mohali, India. He has been working in the field of molecular biology and biotechnology for more than a decade. His current research is focused on gene mining and biocatalyst engineering for the development of approaches for transformation of agro-industrial residues and under- or un-utilized side-stream biomass into value-added bio-products.Santosh Kumar Upadhyay, Assistant Professor, Department of Botany, Panjab University, Chandigarh, India. He has been working in the field of plant biotechnology for more than 14 years. His current research focuses on functional genomics.

• About the Editors xviList of Contributors xviiiPreface xxiiiAcknowledgments xxiv1 An Introduction to Microbial Biodiversity and Bioprospection 1Tomoya Shintani, Santosh Kumar Upadhyay, and Sudhir P. Singh1.1 Introduction 11.1.1 Microorganisms 11.1.2 Bioprospecting 11.1.3 Bioprospection of Microorganisms 21.2 Conclusions and Perspectives 3Acknowledgment 4References 42 Application of Microorganisms in Biosurfactant Production 6Lorena Pedraza- Segura, Luis V. Rodríguez- Durán, Gerardo Saucedo- Castañeda, and José de Jesús Cázares- Marinero2.1 Biosurfactants Nature and Classification 62.2 Biosynthesis of BS by Archaea and Bacteria 122.3 Biosynthesis of BS by Yeasts and Molds 142.4 Screening for BS Producers 152.5 A Case Study: SL by Solid- State Fermentation (SSF), Kinetics, and Reactor Size Estimation 162.6 Conclusions and Perspectives 23References 243 Microbial Gums: Current Trends and Applications 31Rwivoo Baruah and Prakash M. Halami3.1 Introduction 313.2 Biosynthesis of Microbial Gums 323.3 Production of Microbial Gums 333.4 Structure and Properties of Microbial Gums 343.5 Types of Microbial Gums 343.5.1 Xanthan Gum 363.5.2 Sphingans 363.5.2.1 Gellan Gum 363.5.2.2 Welan Gum 373.5.2.3 Rhamsan Gum 373.5.2.4 Diutan Gum 383.5.3 Pullulan 383.5.4 Other Microbial Gums 383.6 Applications of Microbial Gums 393.6.1 Food Applications 403.6.2 Biomedical Applications 413.6.3 Applications in Nanotechnology 423.7 Conclusions and Perspectives 42Acknowledgments 43References 434 Antiaging and Skin Lightening Microbial Products 47Prabuddha Gupta, Ujwalkumar Trivedi, Mahendrapalsingh Rajput, Tejas Oza, Jasmita Chauhan, and Gaurav Sanghvi4.1 Introduction 474.2 Aging 484.2.1 Structure of Skin 484.2.2 Skin Aging Factors 504.2.3 Intrinsic Skin Aging Factors 504.2.3.1 Anatomical and Histological Changes 504.2.3.2 Telomere Shortening 504.2.3.3 Metabolic ROS Production 514.2.3.4 Upregulation of Matrix Metalloproteinases 514.2.3.5 Mitochondrial Dysfunction 514.2.3.6 Mutations and Oncogenesis 514.3 Extrinsic Skin Aging Factors 524.3.1 Photoaging 524.3.2 Tobacco Smoking 524.3.3 Air Pollution 534.4 Why Microbes 534.4.1 Bacterial Compounds 544.4.2 Polysaccharides and Oligosaccharides 544.4.2.1 Hyaluronic Acid 544.4.2.2 Bacterial Cellulose 554.4.2.3 Astaxanthin and Equol 554.4.3 Fungi Compounds 564.4.3.1 Tyrosinase Inhibition 564.4.3.2 Hyaluronidase Inhibition 564.4.3.3 Collagenase and Elastase Inhibition 574.4.4 Algae Compounds 574.4.4.1 Carbohydrates from Algae 584.4.4.2 Fucoidan 604.4.4.3 Laminaran 604.4.4.4 Ulvans 604.4.4.5 Porphyran 614.4.4.6 Carrageenan 614.4.4.7 Agar 614.4.4.8 Alginic Acids 624.4.5 Pigments from Algae 624.4.5.1 Phycobiliproteins 624.4.5.2 Chlorophylls 644.4.5.3 Carotenoids 644.4.5.4 β- carotene 644.4.5.5 Canthaxanthins 664.4.5.6 Astaxanthin 664.4.5.7 Fucoxanthin 664.4.5.8 Zeaxanthin 664.4.5.9 Violaxanthin 664.4.6 Secondary Metabolites 674.5 Conclusions and Perspectives 67References 685 Application of Microorganisms in Bioremediation 77Himani Thakkar and Vinnyfred Vincent5.1 Introduction 775.2 Microbial Bioremediation 785.3 Microbial Bioremediation of Organic Pollutants 795.3.1 Bioremediation of Alkanes 795.3.2 Bioremediation of Benzene, Toluene, Ethylbenzene, and Xylenes (BTEX) 805.3.3 Bioremediation of Polyaromatic Hydrocarbons 805.3.3.1 Degradation of High- Molecular- Weight Polyaromatic Hydrocarbons 835.3.4 Fungal Degradation of Polyaromatic Hydrocarbons 835.3.4.1 Bioremediation of PAHs by Ligninolytic Fungi 845.3.4.2 Catabolism of PAHs by Non- Ligninolytic Fungi 845.3.5 Bioremediation of Pesticides by Microbes 845.4 Microbial Degradation of Heavy Metals 875.5 Factors Affecting Bioremediation 895.5.1 Abiotic Factors 905.5.2 Biotic Factors 915.6 Advances in Bioremediation 915.7 Conclusions and Perspectives 94References 956 Microbial Applications in Organic Acid Production 104Jyoti Singh Jadaun, Amit K. Rai, and Sudhir P. Singh6.1 Introduction 1046.2 Glycolic acid (2C) 1056.3 Acetic Acid (2C) 1086.4 Pyruvic Acid (3C) 1086.5 Lactic Acid (3C) 1096.6 Succinic Acid (4C) 1096.7 Fumaric Acid (4C) 1106.8 Malic Acid (4C) 1116.9 Itaconic Acid (5C) 1126.10 Gluconic Acid (6C) 1136.11 Citric Acid (6C) 1146.12 Kojic Acid (6C) 1146.13 Muconic and Adipic Acid (C6) 1156.14 Conclusions and Perspectives 117Acknowledgments 117References 1177 Production of Bioactive Compounds vs. Recombinant Proteins 125Maria F. Salazar Affonso, Débora Bublitz Anton, Daniel Kuhn, Bruno Dahmer, Camile Wünsch, Verônica Contini, Luís F. Saraiva Macedo Timmers, Claucia F. Volken de Souza, Márcia I. Goettert, and Rodrigo G. Ducati7.1 Introduction 1257.2 In vitro Cell-Based Assays 1267.3 Cell Viability Assays 1277.4 Cell Metabolic Assays 1277.5 Cell Survival Assays 1287.6 Cell Transformation Assays 1297.7 Cell Irritation Assays 1297.8 Heterologous Expression of Recombinant Proteins of Biomedical Relevance 1307.9 Lactic Acid Bacteria and the Production of Metabolites with Therapeutic Roles 1327.10 Preclinical Studies 1347.10.1 Acute Toxicity 1357.10.2 Repeated Dose Toxicity 1367.10.3 Genotoxicity 1367.10.4 Carcinogenicity 1367.10.5 Reproductive Toxicity 1377.11 Computer-aided Drug Design 1377.12 Conclusions and Perspectives 140References 1408 Microbial Production of Antimicrobial and Anticancerous Biomolecules 147M. Indira, T. C. Venkateswarulu, S. Krupanidhi, and K. Abraham Peele8.1 Introduction 1478.2 Microbial Sources 1488.2.1 Bacteria 1488.2.2 Fungi 1498.2.3 Actinomycetes 1508.2.4 Extremophiles 1508.3 Microbial Bioprospecting Methods 1518.3.1 Cultural Bioprospecting 1518.3.2 Nonculturable Microorganism’s Bioprospecting 1528.3.3 In Silico Bioprospecting of Microorganisms 1528.4 Bioactive Compounds 1538.4.1 Antibiotics 1558.4.2 Bacteriocins 1558.4.3 Biosurfactants 1568.4.4 Exopolysaccharides 1568.4.5 Enzymes 1578.4.6 Biopolymers 1588.4.7 Bioenergy Compounds 1588.4.8 Anticancer Compounds 1588.5 Future Prospects 1608.6 Conclusions and Perspectives 160Acknowledgments 161References 1619 Microbial Fuel Cells and Plant Microbial Fuel Cells to Degradation of Polluted Contaminants in Soil and Water 170Chung-Yu Guan and Chang-Ping Yu9.1 Introduction 1709.2 History 1729.3 Electricigens 1739.3.1 Electricigens of Bacteria 1739.3.2 Electrocigens of Fungi 1759.4 Electron Generation and Transfer Mechanisms of Electricigens 1759.4.1 Electron Generation Mechanism 1759.4.2 Electron Transfer Mechanism 1759.4.3 Biofilm Mechanism 1769.4.4 Electron Shuttle Mechanism 1769.4.5 Electron Transfer by Exogenous Mediators 1769.4.6 Microbial Secondary Metabolites for Electron Transfer 1779.4.7 Oxidation of Reduced Primary Metabolites 1779.5 Materials 1779.5.1 Anode Materials 1779.5.2 Base Materials of the Anode 1779.5.3 The Modification of Anode Materials 1789.5.4 Cathode Materials 1799.5.5 Carbon-Based Materials of Cathodes 1799.5.6 Non-Carbon-Based Materials 1799.5.7 Cathode Catalyst 1809.5.8 Biocathode 1819.5.9 Separator Materials 1819.5.9.1 Conventional Separator Materials 1819.5.9.2 New Separator Materials 1819.6 Design and Operation of Bioelectrochemical Systems 1829.6.1 MFC Configuration 1829.6.1.1 Two-Compartment MFCs 1829.6.1.2 Air Cathode MFC 1849.6.1.3 Other Configurations 1859.6.2 Soil MFC and PMFC Configurations 1859.6.2.1 Dual-Chamber of Soil MFCs and PMFCs 1859.6.2.2 Single-Chamber MFCs 1869.6.2.3 Air-Diffusion Cathode System 1869.6.2.4 Other Configuration of PMFCs 1879.7 Performances of the MFCs in Actual Wastewater Treatment 1879.7.1 Industrial Wastewater 1879.7.2 Domestic and Livestock Wastewater 1889.8 Soil MFCs for Soil Remediation 1899.8.1 Remediation of Organic Contaminated Soils 1899.8.2 Remediation of Heavy Metal Contaminated Soils 1899.9 PMFCs for Environmental Remediation 1909.9.1 PMFCs for Wastewater Treatment 1909.9.2 PMFCs for Soil Remediation 1909.10 Prospectives 1919.11 Conclusions 191References 19210 Microalgae- Based UV Protection Compounds 201Jorge Alberto Vieira Costa, Juliana Botelho Moreira, Gabrielle Guimarães Izaguirres, Liliane Martins Teixeira, and Michele Greque de Morais10.1 Introduction 20110.2 UV Radiation 20210.3 Protection Compounds Induced by UV Radiation 20210.3.1 Mycosporine- Like Amino Acids 20310.3.2 Phenolic Compounds 20310.3.3 Carotenoids 20310.3.4 Phycocyanin 20410.3.5 Polyamines 20410.3.6 Scytonemin 20510.4 Microalgal Biotechnology for the Production of Photoprotective Compounds 20610.5 Effects of UV Radiation on the Growth, Morphology, and Production of Lipids, Proteins, and Carbohydrates 20910.6 Extraction Methods of Photoprotective Compounds 21110.7 Prospects for Commercial Applications 21310.8 Conclusion and Perspectives 215References 21511 Microorganisms as a Potential Source of Antioxidants 225Ayerim Hernández-Almanza, Nathiely Ramírez-Guzman, Gloria A. Martínez-Medina, Araceli Loredo-Treviño, Deepak Kumar Verma, and Cristobal N. Aguilar11.1 Introduction 22511.2 Antioxidant-Producing Microorganisms 22511.3 Production of Some Microbial Antioxidants and Their Action Mechanisms 22611.3.1 Peptides 22611.3.2 Pigments 22711.3.3 Polyphenols 22911.4 Extraction and Purification of Microbial Antioxidants 23011.4.1 Extraction of Microbial Antioxidants 23011.4.2 Purification of Microbial Antioxidants 23111.5 Evaluation of Antioxidant Activity 23111.5.1 Classical Methods 23211.5.2 Cellular Methods 23411.6 Conclusions and Perspectives 235References 23612 Microbial Production of Biomethane from Digested Waste and Its Significance 242Arun Kumar Pal, Vijay Tripathi, Prashant Kumar, and Pradeep Kumar12.1 Introduction 24212.2 Methane 24312.2.1 Source of Methane 24312.2.1.1 Industry 24412.2.1.2 Agriculture 24412.2.1.3 Waste 24412.2.2 Biomethane 24512.3 Types of Waste 24512.3.1 Biological Waste 24712.3.2 Household Waste 24712.3.3 Agricultural Waste 24812.4 Digestion Processes of Organic Wastes 24812.4.1 Hydrolysis of Organic Waste 24812.4.2 Acidogenesis of Hydrolyzed Matter 24912.4.3 Acetogenesis 24912.4.3.1 Methanogenesis 25012.5 Conclusions and Perspectives 250Acknowledgments 250Conflicts of Interest 250References 25013 Enzymatic Biosynthesis of Carbohydrate Biopolymers and Uses Thereof 254Manisha Sharma, Jyoti Singh Jadaun, Santosh Kumar Upadhyay, and Sudhir P. Singh13.1 Introduction 25413.2 Dextran 25513.2.1 Mechanism of Dextran Production 25513.2.2 Production of Dextran at Industrial Level 25513.2.3 Applications of Dextran 25613.3 Chitin and Chitosan 25613.3.1 Biological Extraction of Chitin 25713.3.1.1 Biosynthesis of Chitin and Chitosan 25713.3.1.2 Chitin and Chitosan- Producing Fungi 25713.3.1.3 Enzymatic Deproteinization 25713.3.1.4 Fermentation 25913.3.1.5 Enzymatic Deacetylation 25913.3.2 Applications of Chitin and Chitosan 25913.4 Xanthan Gum 26013.4.1 Xanthan Gum Production 26013.4.2 Microbial Production 26113.4.3 Applications of Xanthan Gum 26113.5 Bacterial Cellulose 26113.5.1 Biosynthetic Pathway for Cellulose Production 26113.5.2 Cellulose Precursor 26213.5.3 Microbial Source for Cellulose Production 26213.5.4 Applications of Cellulose 26313.6 Levan 26313.6.1 Levan Producing Organism 26413.6.2 Mechanism for Levan Biosynthesis 26413.6.3 Strategies for Levan Production 26513.6.4 Applications of Levan 26513.7 Conclusions and Perspectives 266Acknowledgments 266References 26614 Polysaccharides from Marine Microalgal Sources 278Ratih Pangestuti, Evi Amelia Siahaan, Yanuariska Putra, and Puji Rahmadi14.1 Introduction 27814.2 Polysaccharides from Marine Microalgae 27914.2.1 Subcritical Water Hydrolysis 28014.2.2 Ultrasonic- Aided Extraction 28114.2.3 Microwave- Assisted Extraction 28214.2.4 Enzyme- Assisted Extraction 28214.3 Optimization of Microalgae Culture Conditions 28214.4 Bioactivities and Potential Health Benefits 28514.4.1 Antiviral Activity 28514.4.2 Antioxidant 28614.4.3 Anticancer 28714.4.4 Immunomodulatory 28814.5 Conclusions and Perspectives 288Acknowledgment 288References 28915 Microbial Production of Bioplastic: Current Status and Future Prospects 295Karishma Seem15.1 Introduction 29515.2 General Structure of PHA 29715.3 Physical Properties 29815.4 Biodegradability of PHA 29815.5 Biosynthesis of PHA 29915.6 Challenges of Scaling Up of PHA Production on an Industrial Scale 30015.6.1 Renewable Sources as Feedstock for PHA Production 30015.6.1.1 Food Processing and Agricultural Industries Discharge 30015.6.1.2 Glycerol 30115.6.1.3 Agro- Industrial Oily Wastes 30115.6.2 Cyanobacteria 30215.6.3 Bacteria from Extreme Niches 30315.6.3.1 Halophilic Bacteria 30315.6.3.2 Thermophiles for PHA 30415.6.3.3 Psycrophiles for PHA 30415.7 Co- synthesis of PHA with Value- Added Products 30415.8 Blends of PHA 30515.9 Applications of PHA 30615.9.1 Biomedical Applications 30615.9.2 Soft Tissue Implants 30715.9.3 Esophagus, Pericardial Patches 30715.9.4 Heart Valve Tissue Engineering 30715.9.5 Nerve Regeneration 30815.9.6 Drug Delivery System 30815.10 Conclusions and Perspectives 309References 30916 Microbial Enzymes for the Mineralization of Xenobiotic Compounds 319Ankita Chatterjee, Pritha Chakraborty, and Jayanthi Abraham16.1 Introduction 31916.2 Major Pollutants and Their Removal with White- Rot Fungi 32016.2.1 Pesticides 32016.2.2 Polychlorinated Biphenyls 32116.2.3 Polycyclic Aromatic Hydrocarbons 32116.2.4 Synthetic Dyes 32216.2.5 Synthetic Polymers 32216.2.6 Phenolic Compounds 32216.2.7 Petroleum Hydrocarbons 32316.3 Enzyme System of White- Rot Fungi 32316.3.1 Laccase 32316.3.1.1 Mechanisms 32716.3.2 Lignin Peroxidase 32816.3.3 Manganese Peroxidase 32916.3.3.1 Mechanism 32916.3.4 Other Enzymes 33016.4 Molecular Aspect 33016.5 Conclusions and Perspectives 331Acknowledgement 331Compliance with Ethical Guidelines 332References 33217 Functional Oligosaccharides and Microbial Sources 337SA Belorkar17.1 Introduction 33717.1.1 What Are Functional Foods? All You Need to Know 33817.2 Inulin and Oligofructose: The Preliminary Functional Oligosaccharides 33917.3 GRAS and FOSHU Status 33917.4 Conventional and Upcoming Oligosaccharides 33917.5 Microbes and Functional Oligosaccharides 34017.6 Arabinoxylo- Oligosaccharides 34017.7 Sources and Properties 34117.8 Approaches for AXOS Production 34117.9 Isomaltooligosaccharides 34217.10 Sources and Properties 34317.11 Production of IMO 34417.12 Approaches to Improve IMO Production 34417.13 Lactosucrose 34517.14 Novel Approaches in Lactosucrose Preparation 34717.15 Xylooligosaccharides 34717.16 Occurrence and Properties 34817.17 Approaches to Improve the Efficiency of XOS 34917.18 Conclusions and Perspectives 349References 35018 Algal Biomass and Biofuel Production 357Suman Sanju, Aditi Thakur, Pragati Misra, and Pradeep Kumar Shukla18.1 Introduction 35718.2 Biofuels 35718.2.1 First-Generation Biofuels 35818.2.2 Second-Generation Biofuels 35818.2.3 Third-Generation Biofuels 35918.3 Algae: The Biomass 35918.4 Microalgae as Biofuel Biomass 36018.5 Microalgae Culture Systems 36218.5.1 Open Algal Systems 36218.5.2 Closed Algal Systems 36318.5.3 Hybrid Algal Systems 36318.6 Microalgae Harvesting 36418.7 Processing and Extraction of Components 36418.8 Biofuel Conversion Processes 36418.8.1 Transesterification 36518.8.2 Biochemical Methods 36618.8.2.1 Fermentation 36618.8.2.2 Anaerobic Digestion 36618.8.3 Thermochemical Conversions 36718.8.3.1 Gasification 36718.8.3.2 Pyrolysis 36718.8.3.3 Liquefaction 36818.8.4 Direct Combustion 36818.9 Microalgal Biofuels 36818.9.1 Biodiesel 36818.9.2 Bioethanol 36918.9.3 Biogas 37018.9.4 Bio-Oil and Bio-Syngas 37018.9.5 Biohydrogen 37118.10 Conclusions and Perspectives 371References 37119 Microbial Source of Insect- Toxic Proteins 377Tripti Yadav and Geetanjali Mishra19.1 Introduction 37719.2 Fungi 37819.3 Bacteria 38419.4 Virus 38619.5 Conclusions and Perspectives 387References 38820 Recent Trends in Conventional and Nonconventional Bioprocessing 404Saswata Goswami, Keyur Raval, Anjana, and Priyanka Bhat20.1 Advances in Conventional Bioprocessing 40420.1.1 The Stirred- Tank Bioreactor Systems 40720.2 Nonconventional Bioprocessing 40920.2.1 Wave Bioreactors 40920.2.2 Orbital Shaken Bioreactors 41020.2.3 Stirred Tank Bioreactors 41120.3 Brief Note on the Recent Trends in Downstream Bioprocessing 41320.4 Perfusion Culture for Bioprocess Intensification 41320.5 Conclusions and Perspectives 416References 416Index 418