Bioprospecting of Microbial Diversity: Challenges and Applications in Biochemical Industry, Agriculture and Environment Protection

566 Pages·2022·37.105 MB·English

by  Pradeep Verma, Maulin P. Shah

BIOPROSPECTING OF MICROBIAL
DIVERSITY
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BIOPROSPECTING
OF MICROBIAL
DIVERSITY
Challenges and Applications
in Biochemical Industry,
Agriculture, and Environment
Protection
Edited by
Pradeep Verma
Bioprocess and Bioenergy Laboratory, Department of Microbiology, Central University of Rajasthan, Bandarsindri,
Kishangarh, Ajmer, Rajasthan, India
Maulin P. Shah
Environmental Microbiology Lab, Bharuch, Ankleshwar, Gujarat, India
Elsevier
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Contents
Contributors xi 2.6 DNA microarrays 18
About the editors xv 2.7 PCR-independent amplification
techniques 19
Preface xvii
2.8 Shift to metagenomic approach 19
Acknowledgment xix 2.9 Synthetic biology approaches
to hetero-expression of new gene clusters 22
1. Role of bioinformatics tools 2.10 Conclusion 23
in microbial prospectives Acknowledgment 23
and its future Conflict of Interest 23
References 24
Ananya Nayak, Maheswata Sahoo, Swayamprabha Sahoo,
Ayushman Gadnayak, Jatindra Nath Mohanty,
Shivani Dave, Padmaja Mohanty, Sushma Dave, 3. Revolution in microbial
and Jayashankar Das bioprospecting via the development
1.1 Introduction 1 of omics-based technologies
1.2 Overview of the role of bioinformatics Megha Bansal, Neha Tiwari, and Jai Gopal Sharma
in microbiology 2
1.3 Prokaryotic genome sequencing 2 3.1 Introduction 27
1.4 Prokaryotic genome annotation 4 3.2 Loopholes in microbial cultivation and
1.5 Microbial profiling 4 emergence of culture-independent methods 30
1.6 Metagenomics and microbiome 5 3.3 Development of “omics-based” approaches for
1.7 Analysis of the human microbiome microbial cultivation 32
with the 16s rRNA gene 5 3.4 Potential applications of “omics” technology in
1.8 Phylogenetic microchips 6 microbial bioprospecting 41
1.9 Bacterial genetic barcode and their uses 6 3.5 Conclusion 41
1.10 NGS in microbial metabolism 6 Competing Interests 42
1.11 The role of genomics in finding microbes 8 References 43
1.12 Genome scale metabolic reconstruction 9
1.13 Summary 10 4. Microbial assisted production
References 11
of alcohols, acetone and glycerol
2. Recent trends in genomic approaches Anjali Yadav, Praveen Purohit, Abhishek Vashishtha,
P.D. Charan, and Gautam Kumar Meghwanshi
for microbial bioprospecting
4.1 Introduction 47
R. Nabil, M. Chamundeeswari, and K. Tamilarasan
4.2 Production of acetone, butanol and ethanol
2.1 Introduction 13 through ABE fermentation 48
2.2 Overall scheme for genome-based 4.3 Fermentative production of bio-butanol 60
bioprospecting 14 4.4 Fermentative production of acetone 61
2.3 Culture-independent methods 14 4.5 Fermentative production of bio-ethanol 62
2.4 Bioprospecting through RT-PCR 16 4.6 Fermentative production of bio-glycerol 73
2.5 Heterologous expression of secondary 4.7 Microbial production of bio-methanol 80
metabolite biosynthesis gene 17 4.8 Conclusion 83
v
vi Contents
Competing Interests 83 7.4 Conclusion and future prospects 179
References 84 Conflicts of interest 179
Further reading 92 References 179
5. Assessing technical and commercial 8. MnP enzyme: Structure, mechanisms,
aspects of soil microbiome in growing distributions and its ample opportunities
leguminous plants and formation in biotechnological application
of bio-fertilizer
Adarsh Kumar, Ajay Kumar Singh, Saroj Kumar, and Ram Chandra
Santosh Kodgire, Nishant Saxena, P.S. Chandrashekharaiah,
Debanjan Sanyal, and Santanu Dasgupta 8.1 Introduction and structure 185
8.2 Catalytic mechanisms of MnP enzyme 187
5.1 Introduction 93 8.3 Distribution in fungi and bacteria 188
5.2 Microbial ecosystem in soil 94 8.4 Physicochemical and molecular
5.3 Significance of microbiome in soil fertility properties of MnP 188
management 97 8.5 Effects of various environmental and nutritional
5.4 Symbiotic interaction with plants 101 parameters on enzyme activity 190
5.5 Green manure as bio-fertilizer 105 8.6 Decomposition and action of
5.6 Leguminous crops as bio-fertilizer 105 mechanisms 191
5.7 Commercial aspects of bio-fertilizer 106 8.7 Ample opportunities in biotechnological
5.8 Conclusion 107 application 193
Competing Interests 107 8.8 Conclusion 196
References 107 Acknowledgment 197
References 197
6. Mechanisms of multifarious soil
microbial enzymes in plant growth 9. Microbes and their products
promotion and environmental as novel therapeutics in medical
sustainability applications
Jay Kishor Prasad and Richa Raghuwanshi J. Chitra, S. Rajendren, J. Jeyakanthan, B. Gopal Samy,
J. Jeba Mercy, N. Manikandan, and N.K. Prasanna Kumari
6.1 Introduction 117
6.2 Microbial enzymatic indexes 118 9.1 Introduction 203
6.3 Mechanisms of action of microbial enzymes 121 9.2 Prophylactic and therapeutic vaccines 204
6.4 Factors affecting microbial enzyme 9.3 Virotherapy 207
activities 132 9.4 Microbes as source of antibiotics 210
6.5 Microbial enzymes as potential indicators of soil 9.5 Clinical applications of microbial enzymes 212
contamination 133 9.6 Bacterial therapeutic products 214
6.6 Conclusions and future prospects 135 9.7 Medical applications of fungi 216
References 135 9.8 Conclusion 218
9.9 Summary 219
7. Bioprospecting of endophytes: Acknowledgment 219
Recent advances in endophytic Competing interests 219
References 219
microbes for industrially important
bioactive compounds
10. Bioprospecting potential of microbes
Prashant Rajesh Wagh, Varsha Vasantrao Sonkamble,
for the therapeutic application
and Nilesh Shirish Wagh
Chetan Aware and Jyoti Jadhav
7.1 Introduction 145
7.2 Current scenario of endophytic bacteria 146 10.1 Introduction 223
7.3 Current scenario of endophytic fungi 159 10.2 Microbial synthesized biologics 227
Contents vii
10.3 Microorganism: A potential source of 13. Bioelectricity recovery from
bioactive compounds 234 food waste using microbial fuel
10.4 Upgradation of microorganisms and
cell: Recent advances
synthesis of new analogs 242
10.5 Future prospects of microbial biologics Shruti Rawat, Nishit Savlab, Marzuqa Quraishi,
Masirah Zahid Shah, Pooja Dange, Ayush Singha Roy,
and conclusion 247
Tushar Bharadwaj, Tanmai Agasam, Piyush K. Gupta,
Acknowledgment 249 and Soumya Pandit
Competing interests 249
References 249 13.1 Introduction 297
13.2 Traditional method for generation of
bioelectricity from waster 300
11. Microbial bioprospecting in
13.3 Food waste generation in the globe and its
development of integrated biomass energy analysis 302
based biorefineries 13.4 Limitation of conventional food waste
management technologies 302
Debapriya Sarkar, Rukmani Hansdah, Abhipsa Kar,
and Angana Sarkar 13.5 Microbial fuel cell—For simultaneous
wastewater treatment and bioelectricity
11.1 Introduction 257 production 305
11.2 Biorefinery concept in bioprocess 13.6 Bioelectricity generation from food
industries 259 waste: Food sources as substrates
11.3 Screening and identification methods for MFC 308
of potential microbes 260 13.7 Factors affecting the performance of MFC
11.4 Biotechnology in bioprospecting utilizing food waste 312
of microbes 261 13.8 Strategy to enhance the efficiency of MFC
11.5 Case studies of successful performance 314
biorefineries 269 13.9 Techno-economic evaluation of microbial
11.6 Future prospects 270 fuel cell 314
11.7 Conclusion 271 13.10 MFC commercialization 315
Competing interests 271 13.11 Challenges and limitation in MFC
References 271 operation 317
13.12 Perspective and conclusion 318
References 318
12. Microbial bioprospecting for
biorefinery application: Bottlenecks
14. Bioprospecting of microalgae
and sustainability
derived high value compounds with
Har Mohan Singh, Shubham Raina, V.V. Tyagi,
commercial significance
and Richa Kothari
Sunita Singh, Santosh Kodgire, Uma Shankar Sagaram,
12.1 Introduction 277 Debanjan Sanyal, and Santanu Dasgupta
12.2 Microbial bioprospecting 278
12.3 Biorefinery 279 14.1 Introduction 325
12.4 Bioconversion routes 288 14.2 Microalgae: Rich source of high-value
12.5 Sustainability aspects of microbial compounds 327
bioprospecting for biorefinery 288 14.3 Pigments from microalgae 327
12.6 Challenges of microbial biorefinery 14.4 Source of proteins and amino acids 334
applications 290 14.5 Functional carbohydrates 338
12.7 Conclusion 291 14.6 Essential fatty acids 339
Acknowledgment 291 14.7 Vitamins and minerals 342
Declaration of competing interest 14.8 Current and projected global market 343
statement 291 14.9 Regulatory compliance 344
References 292 14.10 Challenges and limitations 345
viii Contents
14.11 Conclusion and future considerations 346 17.3 Biotechnological approach for the recovery
Competing interests 347 of metals from E-waste 395
References 347 17.4 Future R&D 402
17.5 Conclusion 402
15. Microbial bioprospecting Competing interests 402
for nutraceuticals and value-added References 402
compounds
18. Evaluation of environment
Sharmili Jagtap
by microbial sensors
15.1 Introduction 357
G. Mahendran, T. Savitha, Ashraf Y.Z. Khalifa,
15.2 Concept of nutraceuticals 357 Abhishek Sharma, and A. Sankaranarayanan
15.3 Classification 358
15.4 Health benefits 358 18.1 Introduction of microbial sensor 407
15.5 Need for microbial production of 18.2 Main components of a biosensor 408
nutraceuticals 360 18.3 Working principle of a biosensor 408
15.6 Microbes and nutraceuticals 361 18.4 Types of biosensors 409
15.7 Developments in delivery systems 364 18.5 Other sensor systems 414
15.8 Microbiome for delivery of nutraceuticals 365 18.6 Implications of biosensor frameworks
15.9 Relevance and challenges of commercial in the natural evaluation 416
production 365 18.7 Applications of biosensor frameworks
15.10 Conclusion/summary 366 in the natural evaluation 417
Competing interests 367 18.8 Pros and thorns of biosensor systems 417
References 367 18.9 Future viewpoints of microbial sensors in
ecological assessment 420
16. Biofilm interceded microbial 18.10 Summary 421
Conflict of interest 421
prospecting of bioremediation
References 421
T. Savitha, Ashraf Y.Z. Khalifa, and A. Sankaranarayanan
19. Insight into microbial biosensors:
16.1 Introduction 371
16.2 Bioremediation 372 Design, types and applications
16.3 Role of biofilms in bioremediation 375
Pulkit Srivastava, Dinesh Prasad, and Vinod Kumar Nigam
16.4 Strategies for use of biofilms in
remediation 378 19.1 Introduction 425
16.5 Bioremediation of various pollutants 19.2 Advantages of microbial biosensors 426
by biofilm 379 19.3 Design of microbial biosensors 426
16.6 Assessment of various methods of biofilm 19.4 Types of microbial biosensors based
interceded bioremediation 379 on types of sensing mechanism 428
16.7 Future perspectives for bioremediation 384 19.5 Applications of microbial sensors
16.8 Summary 386 in different areas 431
Conflict of interest 386 19.6 Conclusion 437
References 386 References 437
17. Microbial-based eco-friendly 20. New strategies in microbial screening
processes for the recovery of metals for novel chemotherapeutics
from E-waste
Jaison Jeevanandam, Sharadwata Pan, and Michael K. Danquah
Muthu Kumar Sampath and Vinod Kumar Nigam
20.1 Introduction 441
17.1 Introduction 393 20.2 Conventional chemotherapeutics and their
17.2 Composition of E-waste 394 limitations 442
Contents ix
20.3 Microbial extracts as novel 22.3 Extremozymes from thermophiles 474
chemotherapeutics 444 22.4 Extremozymes from psychrophiles 476
20.4 New strategies for screening microbes to isolate 22.5 Conclusion and future challenges 478
chemotherapeutic metabolites 448 Competing interests 480
20.5 Future perspectives and conclusions 449 References 480
Conflict of interest 451
References 451 23. Bioenergy: An overview of
bioenergy as a sustainable and
21. Seaweeds as potential source of
renewable source of energy
bioactive compounds with special
Sangeeta Singh, Pradip Sarkar, and Kasturi Dutta
emphasis on bioprospecting in COVID-19
situation 23.1 Introduction 483
23.2 Bioethanol 485
Debanjan Sanyal, Dishant Desai, P.S. Chandrashekharaiah,
Vinay Dwivedi, and Santanu Dasgupta 23.3 Biodiesel 487
23.4 Biogas and biohydrogen 490
21.1 Introduction 455 23.5 Advance bioenergy 493
21.2 Current treatment scenario for 23.6 Challenges 496
COVID-19 456 23.7 Conclusion 497
21.3 Bioactive antiviral compounds from Acknowledgments 497
seaweeds 459 Competing interests 497
21.4 Bioactive compounds from seaweeds with a References 498
beneficial role in general human health and
immunity 462
24. Microbial diversity and bioprospecting
21.5 Bioactive compounds from seaweeds controlling
potential of Phragmites rhizosphere
secondary infections 462
microbiome through genomic
21.6 Potential role of seaweed-derived bioactive
compounds as a therapeutic agent in COVID-19 approaches
disease management 463
Stiti Prangya Dash, Madhusmita Mohapatra,
21.7 Conclusion 464 and Gurdeep Rastogi
Conflict of interest 464
Acknowledgments 465 24.1 Introduction 503
References 465 24.2 Structure and function of Phragmites
microbiome 506
22. Bioprospecting of extremophiles 24.3 P. karka rhizosphere microbiome: An
for industrial enzymes unexplored niche for bioprospecting 517
24.4 Conclusions and perspectives 523
Rehan Deshmukh and Sharmili Jagtap
Acknowledgment 524
References 524
22.1 Introduction 471
22.2 Extremozymes and their industrial
significance 472 Index 529