Microbial Inoculants in Sustainable Agricultural Productivity

Dhananjaya Pratap Singh Harikesh Bahadur Singh • Ratna Prabha Editors

Microbial Inoculants in Sustainable Agricultural Productivity Vol. 1: Research Perspectives

ISBN 978-81-322-2645-1 ISBN 978-81-322-2647-5 (eBook) DOI 10.1007/978-81-322-2647-5

Library of Congress Control Number: 2015960842

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Editors Dhananjaya Pratap Singh ICAR-National Bureau of Agriculturally

Important Microorganisms Maunath Bhanjan , UP , India

Ratna Prabha ICAR-National Bureau of Agriculturally

Important Microorganisms Maunath Bhanjan , UP , India

Harikesh Bahadur Singh Department of Mycology and Plant

Pathology, Institute of Agricultural Sciences

Banaras Hindu University Varanasi , UP , India

v

Sustainable agriculture without bargaining environmental quality is among a global concern. In the era of hugely applied chemical inputs (fertilizers, nutri-ents and pesticides etc.) in farming systems, serious threats are being observed on the reduced crop productivity and nutritional quality, decline in soil fertil-ity, resistance among pests and phytopathogens, contamination of agroeco-system with over and above health problems for humans and animals. Since last few decades, viable biological options based on the basic principles of environmental protection and ecological sustenance have been widely worked out to minimize the threats of huge chemicalization in agricultural systems. Agriculturally important microorganisms have been found to have vast poten-tial to minimize the ecological threats arising due to chemical inputs in soils and crops. Inoculation of a number of microbial strains in agriculture as soil or seed treatment have been shown proven benefi ts to the crop plants as well as the soils making both of them healthier, safer and sustainable. This is why the research in exploring microbial population with higher impacts of plant growth promotion, biological control of pests and diseases and soil fertility increased exponentially in the last few decades and many microbes have been identifi ed, characterized and their multifarious mode of action benefi tting plants and soils have been established. The prospects of manipulating soil biology and plant root rhizosphere with microbial population by inoculating benefi cial microbes (bacteria, actinobacteria, cyanobacteria, fungi, mycorrhi-zal fungi etc.) have been well documented on the growth and development of plants, enhancement of intrinsic resistance against biotic and abiotic factors, tolerance against diseases and pests and improvement in the soil fertility sta-tus. This eco-friendly approach will lead to the reduction in dependence on chemicals. Moreover, recent progress in understanding of the biological interactions of microbes within their communities, with hosts, biotic and abi-

Foreword

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otic stresses in the rhizosphere, delivery system, viability issues and techno-logical reliability has led to the development of practical requirements for microbial inoculant formulation development and commercialization.

This edited volume, ‘ Microbial Inoculants in Sustainable Agricultural Productivity Vol. I – Research Perspectives ’ is a comprehensive effort con-cerning research perspectives on the identifi cation, characterization, func-tional community analysis, mode of interactions, delivery models and formulations and benefi ts of inoculating benefi cial microbes in the agricul-tural system as inoculants. The efforts of the editors is commendable, and the book would be useful for the entine-scientifi c community.

New Delhi (S. Ayyappan) 27 July 2015

Foreword

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M icrobial communities have potential to play a vital role in solving many if not all problems of present-day agriculture and environment and can be equally benefi cial for crop production and protection management, food security, public health, and societal well-being. Microbes are the key living components crucial for the ecological harmony, ecosystem function, agricul-tural sustainability, environmental wellness, and human and livestock health. They are the most important components of soil biodiversity contributing to the valued agroecological services with their vast functional gene pool and metabolic capabilities. In the era of huge chemicalization and industrializa-tion of agricultural ecosystems, microbes are fundamentally important for natural ecological functioning and balance, biotic and abiotic stress manage-ment, mineralization and nutrient recycling, bioconversion of complex ani-mal and plant residues and bioremediation of soil contaminants, and, therefore, support of plant growth and development. Very close interactive mechanisms have been observed within the root rhizosphere of plants with microbial communities that survive on root exudates and strengthen plants in terms of growth, immunity, and resistance against abiotic and biotic stresses. This is why the task of identifi cation, characterization, judicious exploitation of microbes and their communities, and fi nally utilization of an array of their functional characteristics has been taken at priority in the past several decades. The whole exercise is to come up with such effi cient microbial sys-tems that can offer their services at the farming level. Such microbial systems can be termed as “microbial inoculants” that provide benefi cial agricultural services like plant growth promotion, nutrient use effi ciency, bioremediation, and control of pests/phytopathogens.

Our understanding of the microbial communities, their specifi c functions, responses of plants and soils to such communities, and ecological impacts of such communities on other biotic and abiotic mechanisms has increased in the past to a greater extent. With the advent of technological advancements in the area of molecular biology and biotechnology, new avenues have been established to identify and characterize microbes and their communities and in assigning functions to them. Cumulatively, all these studies have led to the identifi cation of several microbial species that were proved potential candi-dates for offering plant growth promotion, soil fertility management, biologi-cal control of pests and diseases, and bioremediation of environmental pollutants. The book Microbial Inoculants in Sustainable Agricultural

Pref ace

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Productivity Vol. I Research Perspectives presents a holistic view of analyzing microbes and their communities and describing their functional role during the endeavor of developing microbial inoculants for the benefi t of agricul-tural productivity. While going through the book, readers can fi nd a detailed account of all such aspects that are required for making a microbe “microbial inoculant.” The views of the authors are thorough and authoritative and based on their long research experience in the subject area. We are thankful to all the contributing authors for making their efforts to provide their valuable inputs in this volume. We hope that this Volume of the book will be very use-ful for all those who are actively involved in the endeavor of developing microbial inoculants for reaping their benefi ts in sustainable agricultural productivity.

Maunath Bhanjan , Uttar Pradesh , India Dhananjaya Pratap Singh Varanasi , Uttar Pradesh , India Harikesh Bahadur Singh Maunath Bhanjan , Uttar Pradesh , India Ratna Prabha

Preface

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1 Strategies for Characterization of Agriculturally Important Bacteria ....................................................................... 1 V. J. Szilagyi-Zecchin , Á. F. Mógor , and G. G. O. Figueiredo

2 Microbial Inoculants as Agents of Growth Promotion and Abiotic Stress Tolerance in Plants ........................................ 23 Ahmed Idris Hassen , F. L. Bopape , and L. K. Sanger

3 A Renaissance in Plant Growth- Promoting and Biocontrol Agents by Endophytes ........................................ 37 Rajendran Vijayabharathi , Arumugam Sathya , and Subramaniam Gopalakrishnan

4 Omics-Driven Approaches in Plant–Microbe Interaction ..................................................................................... 61 V. Swarupa , K. Pavitra , K. S. Shivashankara , and K. V. Ravishankar

5 Strategies for Taxonomical Characterisation of Agriculturally Important Microorganisms ............................ 85 Om Prakash , Rohit Sharma , Prashant Singh , and Amit Yadav

6 Microbial Inoculants: Identification, Characterization, and Applications in the Field........................................................ 103 Ashutosh Kumar Rai , D. P. Singh , Ratna Prabha , Manish Kumar , and Lalan Sharma

7 Endophytic Microbes in Crops: Diversity and Beneficial Impact for Sustainable Agriculture ............................................. 117 Archna Suman , Ajar Nath Yadav , and Priyanka Verma

8 Exploiting PGPR and AMF Biodiversity for Plant Health Management ..................................................... 145 Suseelendra Desai , G. Praveen Kumar , Leo Daniel Amalraj , D. J. Bagyaraj , and R. Ashwin

9 Biopesticides: An Eco-Friendly Approach for the Control of Soilborne Pathogens in Peanut ................................................ 161 Javier A. Andrés , Nicolás A. Pastor , Mauricio Ganuza , Marisa Rovera , María Marta Reynoso , and Adriana Torres

Contents

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10 Strategies for High-Density Cultivation of Bio-inoculants in Submerged Culture with Special Reference to Pseudomonads ........................................................................... 181 S. Mutturi , V. Sahai , S. Sharma , and V. S. Bisaria

11 Microbial Inoculants as Biofertilizers and Biopesticides .......... 197 D. V. Pathak and Mukesh Kumar

12 Seed Bio-priming for Biotic and Abiotic Stress Management .................................................................................. 211 S. Rajendra Prasad , Umesh R. Kamble , K. V. Sripathy , K. Udaya Bhaskar , and D. P. Singh

13 Azotobacter: PGPR Activities with Special Reference to Effect of Pesticides and Biodegradation ................................. 229 Chennappa Gurikar , M. K. Naik , and M. Y. Sreenivasa

14 Beneficial Effects and Molecular Diversity of Endophytic Bacteria in Legume and Nonlegumes ................. 245 Surjit Singh Dudeja

15 Pseudomonas fluorescens: A Promising Biocontrol Agent and PGPR for Sustainable Agriculture ........................... 257 Deepak G. Panpatte , Yogeshvari K. Jhala , Harsha N. Shelat , and Rajababu V. Vyas

16 Isolation, Characterization of Nematode-Controlling Bacteria and Fungi from Nature ................................................................. 271 S. B. Wann , B. Borah , R. Ahmed , B. Gogoi , P. Phukon , J. Baruah , D. K. Sharma , and B. S. Bhau

17 Eco-friendly Plant Growth Promoting Rhizobacteria for Crop Improvement .................................................................. 297 K. V. B. R. Tilak and C. Manoharachary

18 Microbial Inoculants as Biofertilizer........................................... 311 Deep Chandra Suyal , Ravindra Soni , Santosh Sai , and Reeta Goel

19 Microbial Inoculant: Modern Era of Fertilizers and Pesticides .......................................................... 319 Hemant J. Patil and Manoj K. Solanki

Contents

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R. Ahmed Biotechnology Division , CSIR-Northeast Institute of Science & Technology (CSIR-NEIST) , Jorhat , Assam , India

Leo Daniel Amalraj Division of Crop Sciences , Central Research Institute for Dryland Agriculture , Hyderabad , India

Javier A. Andrés Laboratorio de Microbiología Agrícola, Facultad de Agronomía y Veterinaria , Universidad Nacional de Río Cuarto , Río Cuarto , Córdoba , Argentina

R. Ashwin Centre for Natural Biological Resources and Community Development (CNBRCD) , Bangalore , India

D. J. Bagyaraj Centre for Natural Biological Resources and Community Development (CNBRCD) , Bangalore , India

J. Baruah Plant Genomics Laboratory, Medicinal Aromatic and Economic Plant Division , CSIR-Northeast Institute of Science & Technology (CSIR- NEIST) , Jorhat , Assam , India

K. Udaya Bhaskar ICAR-Directorate of Seed Research , Maunath Bhanjan , India

B. S. Bhau Plant Genomics Laboratory, Medicinal Aromatic and Economic Plant Division , CSIR-Northeast Institute of Science & Technology (CSIR- NEIST) , Jorhat , Assam , India

V. S. Bisaria Department of Biochemical Engineering and Biotechnology , Indian Institute of Technology , New Delhi , India

F. L. Bopape Agricultural Research Council , Plant Protection Research (ARC-PPR) , Pretoria , South Africa

B. Borah Plant Genomics Laboratory, Medicinal Aromatic and Economic Plant Division , CSIR-Northeast Institute of Science & Technology (CSIR- NEIST) , Jorhat , Assam , India

Suseelendra Desai Division of Crop Sciences , Central Research Institute for Dryland Agriculture , Hyderabad , India

Contributors

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Surjit Singh Dudeja Department of Microbiology , Chaudhary Charan Singh Haryana Agricultural University , Hisar , India

Department of Bio- & Nanotechnology , Guru Jambeshwar University of Science & Technology , Hisar , India

G. G. O. Figueiredo Departamento de Fitotecnia e Fitossanitarismo , Universidade Federal do Paraná-UFPR , Curitiba , PR, Brazil

Mauricio Ganuza Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales , Universidad Nacional de Río Cuarto , Río Cuarto , Córdoba , Argentina

Reeta Goel Department of Microbiology , CBSH, G. B. Pant University of Agriculture and Technology , Pantnagar , Uttaranchal , India

B. Gogoi Plant Genomics Laboratory, Medicinal Aromatic and Economic Plant Division , CSIR-Northeast Institute of Science & Technology (CSIR- NEIST) , Jorhat , Assam , India

Subramaniam Gopalakrishnan International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) , Patancheru , Telangana , India

Chennappa Gurikar Department of Studies in Microbiology, Manasagangothri , University of Mysore , Mysore , Karnataka , India

Ahmed Idris Hassen Agricultural Research Council , Plant Protection Research (ARC-PPR) , Pretoria , South Africa

Yogeshvari K. Jhala Department of Agricultural Microbiology, B.A. College of Agriculture , Anand Agricultural University , Anand , Gujarat , India

Umesh R. Kamble ICAR-Directorate of Seed Research , Maunath Bhanjan , India

K. Pavitra Division of Biotechnology , ICAR-Indian Institute of Horticultural Research , Bengaluru , India

Manish Kumar ICAR-National Bureau of Agriculturally Important Microorganisms , Maunath Bhanjan , Uttar Pradesh, India

Mukesh Kumar Krishi Vigyan Kendra , CCS Haryana Agricultural University , Bawal (Rewari) , Haryana , India

G. Praveen Kumar Division of Crop Sciences , Central Research Institute for Dryland Agriculture , Hyderabad , India

C. Manoharachary Department of Botany , Osmania University , Hyderabad , Telangana , India

Á. F. Mógor Departamento de Fitotecnia e Fitossanitarismo , Universidade Federal do Paraná-UFPR , Curitiba , PR, Brazil

S. Mutturi Microbiology and Fermentation Technology Department , Central Food Technology Research Institute , Mysuru , India

Contributors

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M. K. Naik Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences , Raichur , Karnataka , India

Deepak G. Panpatte Department of Agricultural Microbiology, B.A. College of Agriculture , Anand Agricultural University , Anand , Gujarat , India

Nicolás A. Pastor Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales , Universidad Nacional de Río Cuarto , Río Cuarto , Córdoba , Argentina

D. V. Pathak CCS Haryana Agricultural University, Regional Research Station , Bawal (Rewari) , Haryana , India

Hemant J. Patil Institute of Soil, Water and Environmental Sciences, Volcani Center , Agricultural Research Organization , Bet Dagan , Israel

P. Phukon Plant Genomics Laboratory, Medicinal Aromatic and Economic Plant Division , CSIR-Northeast Institute of Science & Technology (CSIR- NEIST) , Jorhat , Assam , India

Ratna Prabha ICAR-National Bureau of Agriculturally Important Microorganisms , Maunath Bhanjan , Uttar Pradesh, India

Om Prakash Microbial Culture Collection , National Centre for Cell Science , Pune , Maharashtra, India

S. Rajendra Prasad ICAR-Directorate of Seed Research , Maunath Bhanjan , India

Ashutosh Kumar Rai ICAR-National Bureau of Agriculturally Important Microorganisms , Maunath Bhanjan , Uttar Pradesh, India

K. V. Ravishankar Division of Biotechnology , ICAR-Indian Institute of Horticultural Research , Bengaluru , India

María Marta Reynoso Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales , Universidad Nacional de Río Cuarto , Río Cuarto , Córdoba , Argentina

Marisa Rovera Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales , Universidad Nacional de Río Cuarto , Río Cuarto , Córdoba , Argentina

V. Sahai Department of Biochemical Engineering and Biotechnology , Indian Institute of Technology , New Delhi , India

Santosh Sai Department of Agricultural Microbiology, College of Agriculture , Indira Gandhi Krishi VishvaVidyalaya , Raipur , Chhatisgarh , India

L. K. Sanger Agricultural Research Council , Plant Protection Research (ARC-PPR) , Pretoria , South Africa

Arumugam Sathya International Crops Research Institute for the Semi- Arid Tropics (ICRISAT) , Patancheru , Telangana , India

Contributors

xiv

D. K. Sharma Plant Genomics Laboratory, Medicinal Aromatic and Economic Plant Division , CSIR-Northeast Institute of Science & Technology (CSIR-NEIST) , Jorhat , Assam , India

Rohit Sharma Microbial Culture Collection , National Centre for Cell Science , Pune , Maharashtra, India

S. Sharma Department of Biochemical Engineering and Biotechnology , Indian Institute of Technology , New Delhi , India

Lalan Sharma ICAR-National Bureau of Agriculturally Important Microorganisms , Maunath Bhanjan , Uttar Pradesh, India

Harsha N. Shelat Department of Agricultural Microbiology, B.A. College of Agriculture , Anand Agricultural University , Anand , Gujarat , India

K. S. Shivashankara Division of Plant Physiology and Biochemistry , ICAR-Institute of Horticultural Research , Bengaluru , India

Prashant Singh Microbial Culture Collection , National Centre for Cell Science , Pune , Maharashtra, India

D. P. Singh ICAR-National Bureau of Agriculturally Important Microorganisms , Maunath Bhanjan , India

Manoj K. Solanki Guangxi Crop Genetic Improvement and Biotechnology Lab , Guangxi Academy of Agricultural Sciences , Nanning , China

Ravindra Soni Department of Agricultural Microbiology, College of Agriculture , Indira Gandhi Krishi VishvaVidyalaya , Raipur , Chhatisgarh , India

M. Y. Sreenivasa Department of Studies in Microbiology , Manasagangothri, University of Mysore , Mysore , Karnataka , India

K. V. Sripathy ICAR-Directorate of Seed Research , Maunath Bhanjan , India

Archna Suman Division of Microbiology , Indian Agricultural Research Institute , New Delhi , India

Deep Chandra Suyal Department of Microbiology, CBSH , G. B. Pant University of Agriculture and Technology , Pantnagar , Uttaranchal , India

V. Swarupa Division of Biotechnology , ICAR-Indian Institute of Horticultural Research , Bengaluru , India

V. J. Szilagyi-Zecchin Departamento de Fitotecnia e Fitossanitarismo , Universidade Federal do Paraná-UFPR , Curitiba , PR, Brazil

K. V. B. R. Tilak Department of Botany , Osmania University , Hyderabad , Telangana , India

Adriana Torres Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales , Universidad Nacional de Río Cuarto , Río Cuarto , Córdoba , Argentina

Contributors

xv

Priyanka Verma Division of Microbiology , Indian Agricultural Research Institute , New Delhi , India

Rajendran Vijayabharathi International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) , Patancheru , Telangana , India

Rajababu V. Vyas Department of Agricultural Microbiology, B.A. College of Agriculture , Anand Agricultural University , Anand , Gujarat , India

S. B. Wann Biotechnology Division , CSIR-Northeast Institute of Science & Technology (CSIR-NEIST) , Jorhat , Assam , India

Amit Yadav Microbial Culture Collection , National Centre for Cell Science , Pune , Maharashtra, India

Ajar Nath Yadav Division of Microbiology , Indian Agricultural Research Institute , New Delhi , India

Contributors

xvii

Dhananjaya Pratap Singh is presently Senior Scientist (Biotechnology) with the Indian Council of Agricultural Research-National Bureau of Agriculturally Important Microorganisms (ICAR-NBAIM) at Maunath Bhanjan, India. He obtained his master’s degree from G.B. Pant University of Agriculture and Technology, Pantnagar, India, and Ph.D. in Biotechnology from Banaras Hindu University, India. His research interests lie in microbial diversity, bioprospecting of metabolites, microbe-mediated stress manage-ment in plants, metabolomics-driven search for small molecules, and bioin-formatics. He has been engaged with the development of supercomputational infrastructure for agricultural bioinformatics at ICAR-NBAIM under the National Agricultural Bioinformatics Grid project of ICAR. He has overall 112 publications including 60 research papers, two edited books, 22 book chapters, 20 popular articles, 15 reviews, and one Indian patent to his credit.

Harikesh Bahadur Singh is presently Professor and Head at the Department of Mycology and Plant Pathology in the Institute of Agricultural Sciences, Banaras Hindu University. He served the State Agriculture University, Central University, and CSIR Institute in teaching, research, and extension roles. His major research focus is on bioinoculants, biological control of plant patho-gens, and nano-biotechnology. In recognition of Prof. Singh’s scientifi c con-tributions and leadership in the fi eld of plant pathology, he is honored with several prestigious awards, notable being CSIR Technology Prize for Biological Sciences; Vigyan Bharti Award; Prof. V.P. Bhide Memorial Award; Society for Plant Research, Scientist of Excellence Awards; BRSI Industrial Medal Award; Jyoti Sangam Award; Akshyavat Samman; Distinguish Scientist Award by the Society for Research Development in Agriculture; Prof. Panchanan Maheshwari Medal by the Indian Botanical Society; Rashtriya Gaurav Award by IIFS; Plant Pathology Leader Award by IPS; CSIR Award for S&T Innovation for Rural Development (CAIRD); Environment Conservation Award; and Vigyan Ratna by the UP Council of Science and Technology. Dr. Singh has been a fellow of the National Academy of Agricultural Sciences. Professor Singh has written two books, several training modules/manuals, and more than 275 publications and has more than 18 US patents and 3 PCTs to his credit.

About the Editors

xviii

Ratna Prabha obtained her Master’s degree in Bioinformatics from Banasthali Vidyapeeth, Rajasthan, and Ph.D. in Biotechnology from Mewar University, India. She is presently associated with ICAR-National Bureau of Agriculturally Important Microorganisms, India in the Network Project on Agricultural Bioinformatics and Computational Biology of Indian Council of Agricultural Research. Dr. Prabha has been engaged in developing various bioinformatics tools, digital databases on plants and microbes and genomic and metagenomics data analysis and published many research papers in jour-nals of international repute along with book chapters. Her current research interest lies in microbe-mediated stress management in plants, database development, comparative microbial genome analysis, phylogenomics, and pangenome analysis. She is also engaged in developing various online inter-active demonstration tools/kits for researchers and students on bioinformatics and computational biology.

About the Editors