Bioprospecting of microbial diversity : challenges and applications in bio-chemical industry, agriculture and environment protection

Bioprospecting of Microbial Diversity: Challenges and Applications in Biochemical Industry, Agriculture and Environment Protection gives a detailed insight into the utilization of microorganisms or microorganism-based bioactive compounds for the development of sustainable approaches, covering recent advances and challenges in the production and recovery of bioactive compounds such as enzymes, biopesticides, biofertilizers, biosensors, therapeutics, nutraceutical and pharmaceutical products. The challenges associated with the different approaches of microbial bioprospecting along with possible solutions to overcome these limitations are addressed. Further, the application of microbe-based products in the area of environmental pollution control and developing greener technologies are discussed. Providing valuable insight into the basics of microbial prospecting, the book covers established knowledge as well as genomic-based technological advancements to offer a better understanding of its application to various industries, promoting the commercialization of microbial-derived bioactive compounds and their application in biochemical industries, agriculture, and environmental protection studies. Describes the advanced techniques available for microbial bioprospecting for large-scale industrial production of bioactive compounds Presents recent advances and challenges for the application of microbe-based products in agriculture and environment pollution control Provides knowledge of microbial production of bioenergy and high-value compounds such as nutraceuticals and pharmaceuticals Front Cover Bioprospecting of Microbial Diversity: Challenges and Applications in Bio-chemical Industry, Agriculture and Environment Pr... Copyright Contents Contributors About the editors Preface Acknowledgment Chapter 1 Role of bioinformatics tools in microbial prospectives and its future 1.1 Introduction 1.2 Overview of the role of bioinformatics in microbiology 1.3 Prokaryotic genome sequencing 1.3.1 Finding genome variants with the help of bioinformatics 1.4 Prokaryotic genome annotation 1.5 Microbial profiling 1.6 Metagenomics and microbiome 1.7 Analysis of the human microbiome with the 16s rRNA gene 1.8 Phylogenetic microchips 1.9 Bacterial genetic barcode and their uses 1.10 NGS in microbial metabolism 1.11 The role of genomics in finding microbes 1.12 Genome scale metabolic reconstruction 1.13 Summary References Chapter 2 Recent trends in genomic approaches for microbial bioprospecting 2.1 Introduction 2.2 Overall scheme for genome-based bioprospecting 2.3 Culture-independent methods 2.3.1 16S rRNA 2.3.1.1 Limitations of 16S rRNA 2.3.2 MLSA technique 2.3.3 Other approaches 2.4 Bioprospecting through RT-PCR 2.4.1 Advantages of RT-PCR 2.4.2 Multiplex RT-PCR 2.5 Heterologous expression of secondary metabolite biosynthesis gene 2.6 DNA microarrays 2.6.1 Application of microarray technology 2.7 PCR-independent amplification techniques 2.8 Shift to metagenomic approach 2.8.1 Benefits of metagenomics 2.8.2 Types of metagenomic studies 2.8.3 Sequencing techniques for metagenomics 2.8.4 Process of metagenomics 2.8.5 Other insights in metagenomics 2.9 Synthetic biology approaches to hetero-expression of new gene clusters 2.10 Conclusion Acknowledgment Conflict of Interest References Chapter 3 Revolution in microbial bioprospecting via the development of omics-based technologies 3.1 Introduction 3.1.1 Microbial diversity 3.1.2 Bioprospecting 3.2 Loopholes in microbial cultivation and emergence of culture-independent methods 3.2.1 Modern approaches of microbial cultivation 3.3 Development of “omics-based” approaches for microbial cultivation 3.3.1 Metagenomics 3.3.2 Transcriptomics 3.3.3 Proteomics 3.3.4 Metabolomics 3.3.5 Lipidomics 3.3.6 Glycomics 3.4 Potential applications of “omics” technology in microbial bioprospecting 3.5 Conclusion Competing Interests References Chapter 4 Microbial assisted production of alcohols, acetone and glycerol 4.1 Introduction 4.2 Production of acetone, butanol and ethanol through ABE fermentation 4.2.1 Substrates used 4.2.2 Microorganisms 4.2.3 Fermentation process 4.2.4 Recovery of ABE 4.2.4.1 Pervaporation 4.2.4.2 Gas stripping 4.2.4.3 Hybrid gas stripping 4.2.4.4 Vacuum fermentation 4.2.4.5 Pervaporation 4.2.4.6 Liquid-liquid extraction 4.2.4.7 Perstraction (membrane extraction) 4.2.4.8 Adsorption 4.3 Fermentative production of bio-butanol 4.3.1 Recovery of bio-butanol 4.4 Fermentative production of acetone 4.5 Fermentative production of bio-ethanol 4.5.1 Ethanolic fermentation of sugar substrates 4.5.2 Ethanolic fermentation of corn starch 4.5.3 Ethanolic fermentation of lignocellulose biomass 4.5.4 Recovery of bioethanol 4.5.4.1 Pervaporation 4.5.4.2 Liquid-liquid extraction 4.5.4.3 Gas stripping 4.5.4.4 Adsorption 4.6 Fermentative production of bio-glycerol 4.6.1 Media used for glycerol production 4.6.2 Fermentation process 4.6.2.1 Heterotrophic glycerol production 4.6.2.2 Autotrophic glycerol production 4.6.3 Recovery of glycerol 4.7 Microbial production of bio-methanol 4.7.1 Recovery of methanol 4.8 Conclusion Competing Interests References Further reading Chapter 5 Assessing technical and commercial aspects of soil microbiome in growing leguminous plants and formation of bio- ... 5.1 Introduction 5.2 Microbial ecosystem in soil 5.2.1 Bacteria 5.2.2 Fungi 5.2.3 Nematodes 5.3 Significance of microbiome in soil fertility management 5.3.1 Soil organic matter improvement 5.3.2 Enhancement of nutrient mobilization 5.3.2.1 Phosphorus mobilization 5.3.2.2 Potassium mobilization 5.3.2.3 Iron mobilization 5.3.3 Soil quality improvement 5.4 Symbiotic interaction with plants 5.4.1 Nitrogen fixation 5.4.2 Disease or pest resistance 5.4.3 Growth promotion 5.5 Green manure as bio-fertilizer 5.6 Leguminous crops as bio-fertilizer 5.7 Commercial aspects of bio-fertilizer 5.8 Conclusion Competing Interests References Chapter 6 Mechanisms of multifarious soil microbial enzymes in plant growth promotion and environmental sustainability 6.1 Introduction 6.2 Microbial enzymatic indexes 6.3 Mechanisms of action of microbial enzymes 6.3.1 Catalase 6.3.2 Peroxidases 6.3.3 Phosphatases 6.3.4 Phytase 6.3.5 Dehydrogenase activity 6.3.6 Nitrogenase 6.3.7 Chitinases 6.3.8 Proteases 6.3.9 Arylsulfatases 6.3.10 Arylamidase enzyme 6.3.11 β -1,3-Glucanase 6.3.12 Myrosinase enzyme 6.3.13 Urease enzyme 6.3.14 Amylase enzymes 6.3.15 Invertase enzyme 6.3.16 Cellulase enzyme 6.3.17 Aminocyclopropane-1-carboxylate (ACC) deaminase 6.4 Factors affecting microbial enzyme activities 6.5 Microbial enzymes as potential indicators of soil contamination 6.6 Conclusions and future prospects References Chapter 7 Bioprospecting of endophytes: Recent advances in endophytic microbes for industrially important bioactive compounds 7.1 Introduction 7.2 Current scenario of endophytic bacteria 7.3 Current scenario of endophytic fungi 7.4 Conclusion and future prospects Conflicts of interest References Chapter 8 MnP enzyme: Structure, mechanisms, distributions and its ample opportunities in biotechnological application 8.1 Introduction and structure 8.2 Catalytic mechanisms of MnP enzyme 8.3 Distribution in fungi and bacteria 8.4 Physicochemical and molecular properties of MnP 8.5 Effects of various environmental and nutritional parameters on enzyme activity 8.6 Decomposition and action of mechanisms 8.6.1 Oxidation of polymers 8.6.1.1 Oxidation of phenolic and nonphenolic compounds by MnP 8.6.2 Other recalcitrant compounds degraded by MnP 8.7 Ample opportunities in biotechnological application 8.7.1 Pulp and paper industry 8.7.2 Distillery industries 8.7.3 Food industry 8.7.4 Textile industry 8.7.5 Organic, medical, pharmaceutical, cosmetic and nanotechnology applications 8.8 Conclusion Acknowledgment References Chapter 9 Microbes and their products as novel therapeutics in medical applications 9.1 Introduction 9.2 Prophylactic and therapeutic vaccines 9.2.1 Attenuated vaccines 9.2.2 Inactivated vaccines 9.2.3 Polysaccharide vaccines 9.2.4 Subunit vaccines 9.2.5 Toxoid vaccines 9.2.6 Recombinant vector vaccines 9.3 Virotherapy 9.3.1 Pro-apoptotic targeting 9.3.2 Transcriptional targeting 9.3.3 Translational targeting 9.3.4 Transduction targeting 9.3.5 Tumor microenvironment targeting 9.3.6 Cellular vehicle targeting 9.4 Microbes as source of antibiotics 9.4.1 Penicillin and its types 9.4.2 Microbes producing antibiotics 9.4.3 Classification of antibiotics 9.5 Clinical applications of microbial enzymes 9.6 Bacterial therapeutic products 9.6.1 Probiotics 9.6.2 Bacteriocin 9.7 Medical applications of fungi 9.7.1 Medicinal mushrooms 9.7.2 Therapeutic products from fungi 9.8 Conclusion 9.9 Summary Acknowledgment Competing interests References Chapter 10 Bioprospecting potential of microbes for the therapeutic application 10.1 Introduction 10.2 Microbial synthesized biologics 10.2.1 Antibiotics 10.2.2 Antifungal agents 10.2.3 Immunosuppressive agents 10.2.4 Anticancer agents 10.2.5 Anti-inflammatory agents 10.2.6 Biofilm inhibitory agents 10.2.7 Other microbial biologics 10.3 Microorganism: A potential source of bioactive compounds 10.3.1 Bacteria 10.3.1.1 Escherichia coli 10.3.1.2 Lactococcus lactis 10.3.1.3 Bacillus species 10.3.1.4 Streptomyces species 10.3.2 Yeast/fungi 10.3.2.1 Saccharomyces cerevisiae 10.3.2.2 Aspergillus species 10.3.2.3 Hansenula polymorpha 10.3.3 Microalgae as the potential source of biopharmaceutical 10.4 Upgradation of microorganisms and synthesis of new analogs 10.4.1 Microbial strain improvement 10.4.2 Product enhancement by precursor engineering 10.4.3 Metabolic pathway engineering 10.4.4 Novel analogs synthesis by mutasynthesis 10.5 Future prospects of microbial biologics and conclusion Acknowledgment Competing interests References Chapter 11 Microbial bioprospecting in development of integrated biomass based biorefineries 11.1 Introduction 11.2 Biorefinery concept in bioprocess industries 11.3 Screening and identification methods of potential microbes 11.3.1 Primary screening 11.3.2 Secondary screening 11.4 Biotechnology in bioprospecting of microbes 11.4.1 Bioprospecting of microbes for industrial production 11.4.1.1 Potential microbes for industrial enzymes 11.4.1.2 Potential microbes for industrial organic acids 11.4.1.3 Potential microbes for industrial pharmaceuticals 11.4.1.4 Potential microbes for industrial bioenergy 11.4.1.5 Potential microbes for other value-added industrial products 11.5 Case studies of successful biorefineries 11.6 Future prospects 11.7 Conclusion Competing interests References Chapter 12 Microbial bioprospecting for biorefinery application: Bottlenecks and sustainability 12.1 Introduction 12.2 Microbial bioprospecting 12.3 Biorefinery 12.3.1 Feedstock of biorefinery 12.3.1.1 Lignocellulosic biorefinery 12.3.1.2 Algal biorefinery 12.3.1.3 Waste materials biorefinery 12.3.2 Applications/products 12.4 Bioconversion routes 12.5 Sustainability aspects of microbial bioprospecting for biorefinery 12.5.1 Life cycle analysis 12.5.2 Techno-economic analysis 12.6 Challenges of microbial biorefinery applications 12.6.1 Genetics 12.6.2 Economical stability 12.6.3 Energy security 12.7 Conclusion Acknowledgment Declaration of competing interest statement References Chapter 13 Bioelectricity recovery from food waste using microbial fuel cell: Recent advances Practical application 13.1 Introduction 13.1.1 Food waste as a potential energy source 13.1.1.1 Animal based water 13.1.1.2 Brewery wastewater 13.1.1.3 Dairy waste industry 13.1.1.4 Molasses based wastewater 13.1.1.5 Palm oil mill effluent 13.1.1.6 Vegetable based waste 13.1.1.7 Other food industry wastewater 13.2 Traditional method for generation of bioelectricity from waster 13.2.1 Incineration 13.2.2 Landfill 13.2.3 Aerobic composting 13.2.4 Anaerobic digestion 13.2.5 Animal feed 13.2.6 Bio ethanol fermentation 13.3 Food waste generation in the globe and its energy analysis 13.4 Limitation of conventional food waste management technologies 13.4.1 Microbial cell versus anaerobic digestion 13.5 Microbial fuel cell—For simultaneous wastewater treatment and bioelectricity production 13.5.1 Brief history of MFC 13.5.2 Types of MFC 13.5.3 Classification of MFCs 13.5.3.1 Mediator-coupled microbial fuel cells 13.5.3.2 Microbial fuel cells without mediator 13.5.4 MFC design 13.5.5 Operating principle of MFC 13.6 Bioelectricity generation from food waste: Food sources as substrates for MFC 13.7 Factors affecting the performance of MFC utilizing food waste 13.7.1 pH 13.7.2 Substrate concentration 13.8 Strategy to enhance the efficiency of MFC performance 13.9 Techno-economic evaluation of microbial fuel cell 13.10 MFC commercialization 13.11 Challenges and limitation in MFC operation 13.12 Perspective and conclusion References Chapter 14 Bioprospecting of microalgae derived high value compounds with commercial significance 14.1 Introduction 14.2 Microalgae: Rich source of high-value compounds 14.3 Pigments from microalgae 14.3.1 Chlorophylls 14.3.2 Carotenoids 14.3.2.1 β -Carotene 14.3.2.2 Astaxanthin 14.3.2.3 Lutein 14.3.2.4 Other commercially important carotenoids 14.3.3 Phycobiliproteins 14.4 Source of proteins and amino acids 14.5 Functional carbohydrates 14.6 Essential fatty acids 14.7 Vitamins and minerals 14.8 Current and projected global market 14.9 Regulatory compliance 14.10 Challenges and limitations 14.11 Conclusion and future considerations Competing interests References Chapter 15 Microbial bioprospecting for nutraceuticals and value-added compounds 15.1 Introduction 15.2 Concept of nutraceuticals 15.3 Classification 15.4 Health benefits 15.5 Need for microbial production of nutraceuticals 15.5.1 Roadblocks in using conventional methods of nutraceuticals extraction: 15.5.2 Advantages of using microbes for nutraceuticals production: 15.5.3 Strategies/approaches used for microbial production of nutraceuticals 15.6 Microbes and nutraceuticals 15.6.1 Polysaccharides 15.6.2 Poly amino acids 15.6.3 Prebiotics 15.6.4 Probiotics 15.6.5 Polyphenolic compounds 15.6.6 Carotenoids 15.6.7 Marine microorganisms and their products 15.7 Developments in delivery systems 15.8 Microbiome for delivery of nutraceuticals 15.9 Relevance and challenges of commercial production 15.10 Conclusion/summary Competing interests References Chapter 16 Biofilm interceded microbial prospecting of bioremediation 16.1 Introduction 16.2 Bioremediation 16.2.1 Types of bioremediation 16.2.1.1 In situ bioremediation Biosparging Bio venting Bioaugmentation 16.2.1.2 Ex situ bioremediation 16.3 Role of biofilms in bioremediation 16.4 Strategies for use of biofilms in remediation 16.5 Bioremediation of various pollutants by biofilm 16.6 Assessment of various methods of biofilm interceded bioremediation 16.6.1 Microscopy 16.6.1.1 Light microscopy 16.6.1.2 Confocal laser scanning microscopy (CLSM) 16.6.1.3 Scanning electron microscopy (SEM) 16.6.1.4 Atomic force microscopy (AFM) 16.6.1.5 Transmission electron microscopy (TEM) 16.6.1.6 Scanning transmission X-ray microscopy (STXM) 16.6.2 Molecular methods 16.6.2.1 Clone libraries and sequencing 16.6.2.2 Genetic fingerprinting 16.7 Future perspectives for bioremediation 16.8 Summary Conflict of interest References Chapter 17 Microbial-based eco-friendly processes for the recovery of metals from E-waste 17.1 Introduction 17.2 Composition of E-waste 17.3 Biotechnological approach for the recovery of metals from E-waste 17.3.1 Bioleaching 17.3.1.1 Direct leaching 17.3.1.2 Indirect leaching 17.3.2 Biosorption process 17.3.2.1 Mechanism of biosorption 17.3.3 Bioaccumulation 17.3.4 Biotransformation 17.3.5 Biomineralization 17.4 Future R&D 17.5 Conclusion Competing interests References Chapter 18 Evaluation of environment by microbial sensors 18.1 Introduction of microbial sensor 18.2 Main components of a biosensor 18.3 Working principle of a biosensor 18.4 Types of biosensors 18.4.1 Electrochemical and optical biosensors 18.4.2 Microbial fuel cell 18.4.3 Enzyme-based biosensors 18.4.4 Bioluminescence-based biosensors 18.4.5 Fluorescence-based biosensors 18.4.6 Molecularly imprinted polymers 18.5 Other sensor systems 18.5.1 Bacterial systems as biosensors 18.5.2 Small vertebrates as biosensors 18.5.3 Plant species as biosensors 18.5.4 Lichens as biosensors 18.6 Implications of biosensor frameworks in the natural evaluation 18.7 Applications of biosensor frameworks in the natural evaluation 18.8 Pros and thorns of biosensor systems 18.8.1 Advantages 18.8.2 Disadvantages 18.9 Future viewpoints of microbial sensors in ecological assessment 18.10 Summary Conflict of interest References Chapter 19 Insight into microbial biosensors: Design, types and applications 19.1 Introduction 19.2 Advantages of microbial biosensors 19.3 Design of microbial biosensors 19.3.1 Selection of proper organism 19.3.2 Immobilization of microorganism 19.3.2.1 Chemical approaches 19.3.2.2 Physical approaches 19.4 Types of microbial biosensors based on types of sensing mechanism 19.4.1 Electrochemical biosensors 19.4.1.1 Amperometric biosensor 19.4.1.2 Conductimetric 19.4.1.3 Potentiometric 19.4.2 Optical based microbial biosensors 19.4.2.1 Fluorescent microbial biosensor 19.4.2.2 Bioluminescent microbial biosensor 19.4.3 Other types of microbial biosensors 19.5 Applications of microbial sensors in different areas 19.5.1 Heavy metals 19.5.2 Pesticides detection 19.5.3 BOD (biochemical oxygen demand) detection and water quality monitoring 19.5.4 Phenolic compounds, cyanide and alcohols 19.5.5 Genotoxicity 19.5.6 Surfactant 19.5.7 Food analysis 19.6 Conclusion References Chapter 20 New strategies in microbial screening for novel chemotherapeutics 20.1 Introduction 20.2 Conventional chemotherapeutics and their limitations 20.3 Microbial extracts as novel chemotherapeutics 20.4 New strategies for screening microbes to isolate chemotherapeutic metabolites 20.5 Future perspectives and conclusions Conflict of interest References Chapter 21 Seaweeds as potential source of bioactive compounds with special emphasis on bioprospecting in COVID-19 situation 21.1 Introduction 21.2 Current treatment scenario for COVID-19 21.2.1 Chloroquine and hydroxychloroquine 21.2.2 Ribavirin 21.2.3 Lopinavir and ritonavir 21.2.4 Oseltamivir 21.2.5 Umifenovir 21.2.6 Remdesivir 21.2.7 Favipiravir 21.3 Bioactive antiviral compounds from seaweeds 21.4 Bioactive compounds from seaweeds with a beneficial role in general human health and immunity 21.5 Bioactive compounds from seaweeds controlling secondary infections 21.6 Potential role of seaweed-derived bioactive compounds as a therapeutic agent in COVID-19 disease management 21.7 Conclusion Conflict of interest Acknowledgments References Chapter 22 Bioprospecting of extremophiles for industrial enzymes 22.1 Introduction 22.2 Extremozymes and their industrial significance 22.3 Extremozymes from thermophiles 22.3.1 Thermophilic microorganisms 22.3.2 Insight into the mechanism of action 22.3.3 Industrial applications of thermo-extremozymes 22.4 Extremozymes from psychrophiles 22.4.1 Psychrophililic microorganisms 22.4.2 Insight into the mechanism of action 22.4.3 Industrial applications of psychroextremozymes 22.5 Conclusion and future challenges Competing interests References Chapter 23 Bioenergy: An overview of bioenergy as a sustainable and renewable source of energy 23.1 Introduction 23.2 Bioethanol 23.2.1 Bioethanol feedstock 23.2.2 Feedstock type and its processing 23.2.2.1 1st Generation feedstock 23.2.2.2 2nd Generation feedstock 23.2.2.3 3rd Generation feedstock 23.3 Biodiesel 23.3.1 1st Generation biodiesel production 23.3.2 2nd Generation biodiesel production 23.3.3 3rd Generation from microorganisms 23.3.4 4th Generation from electrobiofuels and synthetic cells 23.4 Biogas and biohydrogen 23.4.1 Biogas 23.4.2 Bio‐hydrogen 23.4.3 Evolution of anaerobic digestion for production of biogas and biohydrogen 23.5 Advance bioenergy 23.5.1 Bio-butanol 23.5.2 Bioelectricity 23.6 Challenges 23.7 Conclusion Acknowledgments Competing interests References Chapter 24 Microbial diversity and bioprospecting potential of Phragmites rhizosphere microbiome through genomic approaches 24.1 Introduction 24.2 Structure and function of Phragmites microbiome 24.2.1 Culture-dependent insights into Phragmites microbiome 24.2.2 Culture-independent insights into Phragmites microbiome 24.2.2.1 Genomic techniques in the study of Phragmites rhizosphere microbiome 24.3 P. karka rhizosphere microbiome: An unexplored niche for bioprospecting 24.3.1 Draft genome sequencing of rhizospheric bacterial isolates from P. karka 24.3.2 Rhizosphere microbiome of P. karka 24.4 Conclusions and perspectives Acknowledgment References Index Back Cover Bioprospecting Of Microbial Diversity: Challenges And Applications In Bio-chemical Industry, Agriculture And Environment Protection Gives Detailed Insights Into The Utilization Of Microorganisms Or Microorganism-based Bioactive Compounds For The Development Of Sustainable Approaches. The Book Presents The Basics Of Microbial Prospecting, Past Knowledge, And Current Technological Advancements That Fill In The Gaps And Allow For A Better Understanding And Extension Of Application In Various Industries. The Challenges Associated With Different Approaches Of Microbial Bioprospecting, Along With Possible Solutions To Overcome Limitations Are Also Addressed. Further, The Book Presents The Application Of Microbes-based Products In The Area Of Environmental Pollution Control And Greener Technologies. The Collective Knowledge Of This Book Is A Source Of Inspiration For Promoting The Commercialization Of Microbial-derived Bioactive Compounds And Their Application In Biochemical Industries, Agriculture And Environmental Protection Studies. Covers Microbial Diversity And Its Role In The Importance Of Bioprospecting Outlines Recent Advances In Screening Methods For Identifying Microbes For The Production Of Different Bioactive Compounds Provides Knowledge Of Growth And Product Formation Kinetics Of Microbes, Along With Isolation, Media Formulation And Preservation Of Microbes Describes Various Available Techniques For Large-scale Industrial Production Of Bioactive Compounds Presents Current Advances And Challenges In The Production, Purification And Recovery Of Bioactive Compounds Such As Antibiotics, Organic Acids, Enzymes, Drugs, Vitamins, Therapeutic Peptides, Biopesticide, Biofertilizers, Biosensors And Pharmaceutical Products