Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications Tulasi Satyanarayana • Subrata Kumar Das Bhavdish Narain Johri Editors

Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications Volume 2. Soil & Agroecosystems Editors Tulasi Satyanarayana Subrata Kumar Das Division of Biological Sciences Division of Molecular Microbiology and Engineering Institute of Life Sciences Netaji Subhas University Bhubaneshwar, Odisha, of Technology (NSUT) New , Delhi, India

Bhavdish Narain Johri Department of Biotechnology Barkatullah University Bhopal, Madhya Pradesh, India

ISBN 978-981-13-8486-8 ISBN 978-981-13-8487-5 (eBook) https://doi.org/10.1007/978-981-13-8487-5

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This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Preface

The outer loose material of the Earth’s surface, which is distinctly different from underlying bedrock, is soil. This originates from physico-chemical and biological weathering of rocks. Soil is an admixture of five major components, viz. mineral matter, organic matter, soil-air, soil water and soil organisms. Soil is not a mass of debris, but teeming with life. Every small particle of soil contains numerous types of living organisms belonging to the Bacteria, Archaea and Eucaryota domains, and viruses; living organisms which are too small to be seen with the naked eye are microbes, microorganisms or microscopic organisms. Soil microorganisms are vital for the continuing cycling of nutrients and for driv- ing aboveground ecosystems. It is important to study microbial diversity not only for basic scientific research, but also to understand the link between diversity and com- munity structure and function. Soil microorganisms influence aboveground ecosys- tems by contributing to plant nutrition, plant health, soil structure and soil fertility. The activity and species composition of microbes are, however, generally influenced by many factors including physico-chemical properties of the soil, temperature and vegetation. The dynamics of soil microbes have important implications for the response of subsurface soil ecosystems to perturbations. Despite all attempts to mea- sure fluxes and gross microbial pools, the soil and its microbiota still remain a black box. Most soil microorganisms are still unknown. The comparison between direct microscopic counts and plate counts indicates that less than 0.1% of agricultural soil microorganisms are culturable. Understanding the diversity and dynamics of indig- enous microbial populations represents a challenge to modern soil ecology. The rhizosphere, the narrow zone of soil that is influenced by root secretions, can contain up to 1011 microbial cells per gram root and more than 30,000 prokaryotic species. The collective genome of this microbial community is much larger than that of the plant, which is also known as the plant’s second genome. The microflora of most soils is carbon starved. Since plants secrete up to 40% of their photosyn- thates into the rhizosphere, the microbial population densities in the rhizosphere are much higher than those in the surrounding bulk soil; this phenomenon is known as the ‘rhizosphere effect’. In general, rhizosphere microbial communities are less diverse than those in bulk soil. The mesmerizing diversity of microbes settling down in the rhizosphere are termed “root microbiome,” while their interaction with roots can result in a positive or negative outcome for plant fitness. Increasing evidence suggests that the

v vi Preface microbial communities dominating the rhizosphere are influenced by the host geno- type. It appears that plants actively select and determine the composition of the root microbiome by releasing compounds in the rhizosphere which selectively stimulate microorganisms promoting plant growth and health or repress organisms that are deleterious to plants. Root microbiome is, therefore, a subset of a more diverse microbial community recruited from the surrounding bulk soil. The involvement of root microbiome on plant health becomes more evident in disease-suppressive soils. In these soils, a plant is unlikely to become infected by a soil-borne pathogen even when the pathogen is present and favoured by the plant. The phenomenon of disease suppression is well-known and is associated with the indigenous microbiota and activity. The mechanisms underlying this phenomenon have not, however, been fully understood. In this volume, Dubey and Sharma (Chap. 11) discuss the concept of rhizosphere engineering by employing synthetic microbial communities and the prospects of the rhizosphere microbiome engineering. Microbial diversity represents the variability among all types of microbes (pro- karyotes [archaea and bacteria], eukaryotes [algae, fungi, protozoa] and acellular viruses and others) in the natural world. Interest in the exploration of microbial diversity has stemmed from the fact that microbes are essential for life because they perform numerous functions essential for the biosphere that include nutrient cycling and environmental detoxification. The vast array of microbial activities and their importance to the biosphere and to human economies provide strong rationale for understanding their diversity, conservation and exploitation for society. For long, microbial diversity has been explored by conventional culture-­ dependent methods, which allow access to only 0.1–1.0% of the extant microbes in any ecosystem. Over the past two decades, several methods, such as rRNA gene sequencing, fluorescencein situ hybridization (FISH), denaturing gradient gel elec- trophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), restriction fragment length polymorphism and terminal restriction fragment length polymor- phism (T-RFLP), have been developed to assess microbial diversity and catalogue microbes without the need for isolation. The use of molecular techniques over the past 20 years has shown that only a very small fraction of microbial diversity so far has been catalogued from all the habitats investigated. Earth is considered to be inhabited by close to a trillion bacterial and archaeal species, and 10–15 million eukaryotic species; this prediction is based on ecological theory reformulated for large-scale predictions, an expansive dominance scaling law, a richness scaling relationship with empirical and theoretical support and the largest molecular surveys compiled to date [PNAS (2016) 113: 5970–5975]. The profound magnitude of our prediction of Earth’s microbial diversity emphasizes the need for continued investigation. Extensive and intensive efforts are being made to understand microbial diversity by both culture-dependent and culture-independent metagenomics approaches. Despite significant advances made in understanding microbial diversity, most microbes are characterized only by ‘molecular fingerprints’ and have resisted culti- vation. The microbiomics approach is now being adopted for surveying total Preface vii microbes present in different ecosystems (e.g. earth microbiome, ocean microbi- ome, human microbiome and rhizosphere microbiome, to mention a few). In order to analyse microbial populations in ecosystems such as skin and mucosal surfaces of humans and animals, plants, soil and oceans, Next Generation Sequencing (NGS) and advanced bioinformatics have become valuable tools. The Earth Microbiome Project (EMP), launched in 2010, is a landmark study for investigating large-scale microbial diversity. Bacterial and archaeal 16S rRNA diversity in 27,751 samples was analysed from 97 independent studies, which produced 2.2 billion sequence reads [PNAS (2018) 115: 4325–4333]. Only two-thirds of EMP reads could be mapped to the existing 16S references, which prevented meaningful Operational Taxonomic Unit (OTU) analysis. By leveraging metagenomics and metabarcoding of global top soil samples (189 sites, 7,560 subsamples), it has recently been observed that bacterial genetic diver- sity is very high in temperate habitats in comparison with fungi, and microbial gene composition varies more strongly with environmental variables than with geo- graphic distance [Nature (2018) 560: 233–237]. Fungi and bacteria show global niche differentiation which is associated with contrasting diversity responses to pre- cipitation and soil pH. Both competition and environmental filtering have been seen to affect the abundance, composition and encoded gene functions of bacterial and fungal communities, suggesting that the relative contributions of these microorgan- isms to global nutrient cycling varies spatially. Good understanding of microbial diversity will allow us to cure diseases, engineer and conserve our environment, manufacture better products, grow more food, colo- nize other worlds, and much more. In practical and scientific terms, microorganisms give us the power to ask new questions and solve previously intractable problems. Voluminous data have accumulated on the microbial diversity of various ecosys- tems. The present attempt is to briefly review the developments in understanding microbial diversity and its role in ecosystem sustainability and biotechnological applications. The second volume of the book focuses on Soil and Agroecosystems. Very comprehensive reviews are included in this volume on aspects such as micro- bial diversity in caves, jhum agroecosystem, metal rich mine leachates, ectomycor- rhizal and VAM fungi, mangroves, Himalayan edible mushrooms, microbes producing industrially useful enzymes and several others. We wish to thank all the contributors for readily accepting our invitation and submitting well-written chapters in their areas of specialization within the pre- scribed timelines. The opinions expressed by the contributors are their own. We sincerely hope and wish that the book will serve as a ready reference for students, scholars, teachers and scientists in broad areas of life sciences, microbiology and biotechnology. We wish to thank Springer Nature for publishing the book to dis- seminate knowledge from innumerable sources in two volumes.

New Delhi, Delhi, India Tulasi Satyanarayana Bhubaneshwar, Odisha, India Subrata Kumar Das Bhopal, Madhya Pradesh, India Bhavdish Narain Johri Contents

Part I Soil and Agroecosystem 1 Cave Microbiome for Human Welfare...... 3 Subhro Banerjee, D. K. Jha, and S. R. Joshi 2 Diversity of Nitrogen-Fixing Symbiotic Rhizobia with Special Reference to Indian Thar Desert...... 31 Nisha Tak and Hukam Singh Gehlot 3 Soil Microbiota and Sustainable Jhum Agroecosystem...... 57 S. R. Joshi, Donald Bareh, and Aishiki Banerjee 4 Diversity in Type III Secreting Systems (T3SSs) in Legume-Rhizobium Symbiosis...... 83 M. Senthilkumar, K. Swarnalakshmi, and K. Annapurna 5 Microbe-Based Novel Biostimulants for Sustainable Crop Production...... 109 Rahul Singh Rajput, Ratul Moni Ram, Anukool Vaishnav, and Harikesh Bahadur Singh 6 Ectomycorrhizal Diversity and Tree Sustainability...... 145 Shikha Khullar and M. Sudhakara Reddy 7 Diversity of Arbuscular Mycorrhizal Fungi in Relation to Sustainable Plant Production Systems...... 167 Manju M. Gupta, Dipanti Chourasiya, and Mahaveer P. Sharma 8 Microbial Diversity on Grapes and Other Fruits: Role and Significance in Fermentation...... 187 M. V. Deshpande 9 Harnessing Entomopathogenic Fungi for Enhanced Farm Productivity and Profitability...... 205 Suseelendra Desai, T. V. Prasad, G. Praveen Kumar, John Peter, and Leo Danile Amalraj

ix x Contents

10 Microbial Diversity of the Sundarbans, the World’s Largest Tidal Mangrove Forest, and Its Bioprospects...... 231 Kaushik Biswas and Joydeep Mukherjee 11 Rhizospheric Microbiome Engineering as a Sustainable Tool in Agriculture: Approaches and Challenges...... 257 Shubham Dubey and Shilpi Sharma 12 Dynamics of Plant Microbiome and Its Effect on the Plant Traits...... 273 Shivali Sharma, Shanu Magotra, Sneha Ganjoo, Tabia Andrabi, Rikita Gupta, Shilpi Sharma, and Jyoti Vakhlu

Part II Diversity of Specific Microbial Groups 13 Diversity of Photobionts: Their Coevolution and Bioprospecting Potential...... 307 Khem Chand Saini, Sanjeeva Nayaka, and Felix Bast 14 Diversity in Xylan-degrading Prokaryotes and Xylanolytic Enzymes and Their Bioprospects...... 325 Digvijay Verma, Ravi Kumar, and Tulasi Satyanarayana 15 Diversity in Cellulose-Degrading Microbes and Their Cellulases: Role in Ecosystem Sustainability and Potential Applications...... 375 Anica Dadwal, Shilpa Sharma, and Tulasi Satyanarayana 16 New Paradigm in Degradation of Lignocellulosic Biomass and Discovery of Novel Microbial Strains...... 403 Rohit Rai, Dhruv Agrawal, and B. S. Chadha 17 Secondary Metabolism in Trichoderma: Chemo- and Geno-Diversity...... 441 Shikha Pachauri, Pramod D. Sherkhane, and Prasun K. Mukherjee 18 Diversity of Chitinase-Producing Bacteria and Their Possible Role in Plant Pest Control...... 457 Sandipan Banerjee and Narayan Chandra Mandal 19 Endophytic Fungi As the Alternate Source of High-Value Plant Secondary Metabolites...... 493 Sunil K. Deshmukh, Manish K. Gupta, and Sangram K. Lenka 20 Wild Edible Mushrooms of North West Himalaya: Their Nutritional, Nutraceutical, and Sociobiological Aspects...... 533 N. S. Atri, Y. P. Sharma, Sanjeev Kumar, and Mridu Contents xi

21 Methanogens for Human Welfare: More Boon Than Bane...... 565 Prashant K. Dhakephalkar, Om Prakash, Vikram B. Lanjekar, Manasi P. Tukdeo, and Dilip R. Ranade 22 Genetic Diversity of Pathogenic Yeasts...... 593 Kunal Ranjan and Marcio José Poças-Fonseca

Index...... 617 About the Editors and Contributors

Editors

Prof. T. Satyanarayana is a Faculty Fellow at the Division of Biological Sciences & Engineering, Netaji Subhas University of Technology, . He received his M.Sc. and Ph.D. from Saugar University, India, and pursued postdoctoral stud- ies in France. He has over four decades of research and teaching experience, and has received the Association of Microbiologists of India’s Dr. G.B. Manjrekar Memorial Award, the Mycological Society of India’s Dr. V. Agnihotrudu Memorial Award, and the Biotech Research Society’s Malaviya Memorial Award for his valu- able contributions. He is a Fellow of NAAS, AMI, BRSI, MSI and Telengana Academy of Sciences and a member of the Editorial Board of several journals. He has also served as reviewer for various respected journals. He has edited several books, published scientific papers, and has three patents to his credit.

Dr. Subrata K. Das is currently a Scientist F. at the Institute of Life Sciences, Bhubaneswar, Department of Biotechnology, Govt of India. He received his Ph.D. degree from Bose Institute, Kolkata and conducted postdoctoral research at the University of Texas Medical Branch, Galveston, USA. His research interests include geomicrobiology, metagenomics, and archaeal and bacterial origin and adaptation in geothermal springs. He has received the E.K. Janaki Ammal National Award from the Ministry of Environment, Forest and Climate Change, Government of India; Prof. KS Bilgrami Memorial Award from the Society for Plant Research, India; Outstanding contribution award from the Association for the Advancement of Science and is a Fellow of West Bengal Academy of Science and Technology (FAScT) and the Association for the Advancement of Biodiversity Science (FABSc).

Prof. B. N. Johri received his PhD from the University of Alberta, and gained postdoctoral experience at Alberta and the University of British Columbia, Canada. He has taught microbiology at Sagar, Bhopal, and Pantnagar. He is a recipient of several awards including INSA Young Scientist, KN Katju and the ICAR Rafi Ahmed Kidwai Award. He is a Fellow of the National Academy of Sciences India,

xiii xiv About the Editors and Contributors

National Academy of Agricultural Sciences, and National Institute of Ecology. He also received a Life Time Achievement Award from the AMI and Life Time Devotion Award from the Microbiologist Society of India. He has authored over 100 research papers and co-edited five books. He has recently retired after a long stint as Senior Scientist at the National Academy of Sciences at the Department of Biotechnology, Barkatullah University, Bhopal.

Contributors

Dhruv Agrawal Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India Leo Danile Amalraj Varsha Bioscience and Technology India Pvt. Ltd., Vinaynagar, , India Tabia Andrabi Microbiomics Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India K. Annapurna Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, India N. S. Atri Department of Botany, Punjabi University, Patiala, Punjab, India Aishiki Banerjee Microbiology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India Sandipan Banerjee Mycology and Plant Pathology Research Laboratory, Department of Botany, Visva-Bharati, Santiniketan, West Bengal, India Subhro Banerjee Department of Botany, Gauhati University, Guwahati, Assam, India Microbiology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India Donald Bareh Microbiology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India Felix Bast Department of Plant Sciences, Central University of Punjab, Bathinda, Punjab, India Kaushik Biswas School of Environmental Studies, Jadavpur University, Kolkata, West Bengal, India B. S. Chadha Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India Dipanti Chourasiya ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh, India About the Editors and Contributors xv

Anica Dadwal Division of Biological Sciences and Engineering, Netaji Subhas University of Technology (NSUT), New Delhi, Delhi, India Suseelendra Desai Plant Pathology, ICAR-Central Research Institute for Dryland Agriculture, Santoshnagar, Hyderabad, Telangana, India Sunil K. Deshmukh TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute (TERI), New Delhi, Delhi, India M. V. Deshpande Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India Prashant K. Dhakephalkar Bioenergy Group, MACS-Agharkar Research Institute, Pune, Maharashtra, India Shubham Dubey Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, Delhi, India Sneha Ganjoo Microbiomics Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India Hukam Singh Gehlot BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur, Rajasthan, India Manish K. Gupta TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute (TERI), New Delhi, Delhi, India Manju M. Gupta Sri Aurobindo College, , New Delhi, Delhi, India Rikita Gupta Microbiomics Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India D. K. Jha Department of Botany, Gauhati University, Guwahati, Assam, India S. R. Joshi Microbiology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India Shikha Khullar Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India G. Praveen Kumar Drugs Control Laboratory, Govt. of , SMC Campus, Vijayawada, Andhra Pradesh, India Ravi Kumar Division of Biological Sciences and Engineering, Netaji Subhas University of Technology (NSUT), New Delhi, Delhi, India Sanjeev Kumar Department of Botany, University of Jammu, Jammu, Jammu and Kashmir, India Vikram B. Lanjekar Bioenergy Group, MACS-Agharkar Research Institute, Pune, Maharashtra, India xvi About the Editors and Contributors

Sangram K. Lenka TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute (TERI), New Delhi, Delhi, India Shanu Magotra Microbiomics Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India Narayan Chandra Mandal Mycology and Plant Pathology Research Laboratory, Department of Botany, Visva-Bharati, Santiniketan, West Bengal, India Mridu Department of Botany, Punjabi University, Patiala, Punjab, India Joydeep Mukherjee School of Environmental Studies, Jadavpur University, Kolkata, West Bengal, India Prasun K. Mukherjee Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, , Maharashtra, India Sanjeeva Nayaka Laboratory, CSIR – National Botanical Research Institute, , , India Shikha Pachauri Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India HomiBhabha National Institute, Mumbai, Maharashtra, India John Peter Varsha Bioscience and Technology India Pvt. Ltd., Vinaynagar, Hyderabad, India Marcio José Poças-Fonseca Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasilia, Brazil Om Prakash NCCS-National Centre for Microbial Resource, Pune, Maharashtra, India T. V. Prasad Agricultural Entomology, ICAR-Central Research Institute for Dryland Agriculture, Santoshnagar, Hyderabad, Telangana, India Rohit Rai Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India Rahul Singh Rajput Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India Ratul Moni Ram Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India Dilip R. Ranade NCCS-National Centre for Microbial Resource, Pune, Maharashtra, India Kunal Ranjan Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, Brasilia, Brazil M. Sudhakara Reddy Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India About the Editors and Contributors xvii

Khem Chand Saini Centre for Biosciences, Central University of Punjab, Bathinda, Punjab, India Tulasi Satyanarayana Division of Biological Sciences and Engineering, Netaji Subhas University of Technology (NSUT), New Delhi, Delhi, India M. Senthilkumar Division of Basic Sciences, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India Mahaveer P. Sharma ICAR-Indian Institute of Soybean Research, Indore, Madhya Pradesh, India Shilpa Sharma Division of Biological Sciences and Engineering, Netaji Subhas University of Technology (NSUT), New Delhi, Delhi, India Shilpi Sharma Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, Delhi, India Shilpi Sharma Microbiomics Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India Shivali Sharma Microbiomics Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India Y. P. Sharma Department of Botany, University of Jammu, Jammu, Jammu and Kashmir, India Pramod D. Sherkhane Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India Harikesh Bahadur Singh Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India K. Swarnalakshmi Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, India Nisha Tak BNF and Microbial Genomics Lab., Department of Botany, Center of Advanced Study, Jai Narain Vyas University, Jodhpur, Rajasthan, India Manasi P. Tukdeo Department of Microbiology, Modern College of Arts, Science and Commerce, Ganeshkhind, Pune, Maharashtra, India Anukool Vaishnav Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India Jyoti Vakhlu Microbiomics Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India Digvijay Verma Department of Microbiology, Babasaheb Bhimrao Ambedkar (Central) University, Lucknow, Uttar Pradesh, India