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- 5. Sustainable Development andBiodiversity 27 Ajar NathYadav Editor Soil Microbiomes for Sustainable Agriculture Functional Annotation
- 6. Sustainable Development andBiodiversity Volume 27 Series Editor Kishan Gopal Ramawat Botany Department, Mohanlal Sukhadia University, Udaipur, India
- 7. Sustainable Development Goalsare best achieved by mechanisms such as research, innovation, and knowledge sharing. This book series aims to help researchers by reporting recent progress and providing complete, comprehensive, and broad subject-based reviews about all aspects of sustainable development and ecological biodiversity. The series explores linkages of biodiversity with delivery of various ecosystem services and it offers a discourse in understanding the biotic and abiotic interactions, ecosystem dynamics, biological invasion, ecological restoration and remediation, diversity of habitats and conservation strategies. It is a broad scoped collection of volumes, addressing relationship between ecosystem processes and biodiversity. It aimstosupporttheglobaleffortstowardsachievingsustainabledevelopmentgoalsby enriching the scientific literature. The books in the series brings out the latest reading material for botanists, environmentalists, marine biologists, conservationists, policy makers and NGOs working for environment protection. We welcome volumes on the themes – Agroecosystems, Agroforestry, Biodiversity, Biodiversity conservation, Conser- vation of ecosystem, Ecosystem, Endangered species, Forest conservation, Genetic diversity, Global climate change, Hotspots, Impact assessment, Invasive species, Livelihood of people, Plant biotechnology, Plant resource utilization, Sustainability of the environment, Sustainable management of forests, Sustainable use of terrestrial ecosystems and plants, Traditional methods, Urban horticulture. More information about this series at http://www.springer.com/series/11920
- 8. Ajar Nath Yadav Editor SoilMicrobiomes for Sustainable Agriculture Functional Annotation
- 9. Editor Ajar Nath Yadav Departmentof Biotechnology Eternal University Baru Sahib, Himachal Pradesh, India ISSN 2352-474X ISSN 2352-4758 (electronic) Sustainable Development and Biodiversity ISBN 978-3-030-73506-7 ISBN 978-3-030-73507-4 (eBook) https://doi.org/10.1007/978-3-030-73507-4 © Springer Nature Switzerland AG 2021 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland
- 10. Foreword by DavinderSingh Microbes are ubiquitous in the environment and can survive in most habitats. They play a major role in the ecosystem and are even excellent for plant growth promotion foragro-environmentalsustainability.Itisexpectedthatthefast-growingworldpopu- lation will make food security a big issue in the future. Agricultural sustainability is facing to be a formidable task by using chemical-based fertilizers and pesticides in order to increase the yield of the crop plants. To fulfill the increasing demand of food supply with the problems like shrinking farmlands, and global warming is one of the major challenges. The soil microbiome has found diverse and complex habitats, which consist of billions of bacteria, fungi, and other living organisms. Beneficial microbes play an essential role in nutrient cycling and plant shielding from destructive effects of biotic and abiotic stresses. Intensive farming practices lead to an increase in crop production, but they also have detrimental effects on the biolog- ical and physiological properties of soils. The macronutrients for plant growth are generally provided via chemical fertilizers. In comparison to chemical and synthetic fertilizers, biofertilizers and biopesticides improve plant growth and crop produc- tivity in an eco-friendly way. Along with plant growth promotion, beneficial microbes v
- 11. vi Foreword byDavinder Singh could be used for mitigation of diverse abiotic stresses using diverse plant growth- promoting mechanisms such as fixation of atmospheric nitrogen, solubilization of macronutrients (phosphorus, potassium, and zinc) and micronutrients (magnesium, selenium), production of ACC deaminase, antagonistic substances, plant growth hormones (auxin, cytokinin, and gibberellins), and siderophores (iron chelators). Thus, using beneficial soil microbiomes for sustainable agriculture is gaining vast attention worldwide. I recommend this book to researchers and students working on the emerging and fascinating field of microbiology, biotechnology, and related subjects. The book will advance the knowledge to a greater extent in these areas with significant broader research on soil microbial communities and their biotechnological role for agricul- tural sustainability. The editor of this book deserves credit for such a splendid and innovative contribution to microbiology research. Dr. Davinder Singh Vice Chancellor Eternal University, Baru Sahib, Himachal Pradesh, India
- 12. Foreword by AmrikSingh Ahluwalia Microbes are the hidden wonders of the planet Earth that stuns humans with their diversity, habitats, and functional capabilities. Archaea, bacteria, and fungi are the three major microbial domains that comprise millions of microbes that are present in various habitats like soil, water, air, plant, and animal externals and irrefutably play various roles. Among all habitats, the soil is the one habitat that is known to comprise a large portion of microbial diversity and these microbes are believed to play a large number of ecosystem processes. Nitrogen fixation, carbon cycling, phos- phorus cycling, weathering of rocks, decomposition of dead, and decay matter are some of the roles that soil microbes play in the ecosystem. The functional annotation of microbes could be advantageous to many sectors including the agriculture envi- ronment and industry. Nowadays, plant growth-promoting microbes as biofertilizers and biopesticides are known as the sustainable input that enhances crop produc- tivity and soil fertility. Soil microbes undergo different mechanisms to improve crop productivity like solubilization of micro- and macronutrients, fixation of nitrogen, chelation, and mitigation of biotic and abiotic stress. vii
- 13. viii Foreword byAmrik Singh Ahluwalia ThepresentbookSoilMicrobiomesforSustainableAgriculture:FunctionalAnno- tation is to provide the recent advances in mechanisms of plant growth promotion and applications of soil microbiomes for mitigation of different abiotic stresses in plants. The proposed book encompasses current knowledge of soil microbiomes and their potential biotechnological applications for plant growth, crop yield, and soil health under the natural as well as harsh environmental conditions for sustain- able agriculture. The book volume comprises 19 chapters. The Chap. 1 by Bose et al. describes the soil microbiomes, their beneficial attributes of the plant growth promotion, and potential applications in agriculture, whereas Mokrani and Nabti highlight diverse soil microbial communities from different crops and their roles for crop productivity in Chap. 2. Chapter 3 by Boroujeni et al. describes soil microbes with multifarious plant growth-promoting attributes for enhanced production of food crops. Chapter 4 by Emami-Karvani and Chitsaz-Esfahani highlights the mecha- nisms, recent advancement, and future challenge of phosphorus solubilizing micro- biomes. Berde et al. describe potassium solubilization, its mechanism, and functional impact on plant growth in Chap. 5. In Chap. 6, Kumar et al. have given the details about soil microbiomes with siderophores production and zinc solubilizing attributes for cereals biofortification. Jatav et al. highlights the diverse soil microbes for plant growth promotion and mitigation of abiotic stress of drought in Chap. 7. In Chap. 8, Maitra et al. describe the current status and future outlook of mitigation of heat stress by thermotolerant soil microbes. Mukhtar et al. highlight the potential applications of halophilic soil microbes for the mitigation of salt stress in Chap. 9. Jha et al. explain the role of psychrotrophic soil microbes in the alleviation of cold stress in plants in Chap. 10. Mitigation strategies for abiotic stress tolerance in plants through stress-tolerant PGP microbes have been described by Dhevagi et al. in Chap. 11. Chapter 12 by Maitra et al. describes the omics strategies for abiotic stress responses and microbe-mediated mitigation in plants. Zia et al. highlight the technical chal- lenges and emerging solutions for enhancing food crops using plant probiotics in Chap. 13. Salimi and Hamedi highlight the soil microbes as biofertilizers for agri- cultural productivity in Chap. 14 and soil microbes as biopesticides for agricultural sustainability in Chap. 15. Mycorrhiza as a plant growth-promoting and biocon- trol agent for crops growing under the stress condition is discussed in Chap. 16 by Hussain et al. Thakur et al. highlights entomopathogenic soil microbes for sustain- able crop protection in Chap. 17. Subrahmanyam et al. explain global scenario of soil microbiome research in Chap. 18. Finally, the conclusion and future prospects of functional annotation and biotechnological applications of soil microbiomes have been described by the editor and co-authors in the last chapter.
- 14. Foreword by AmrikSingh Ahluwalia ix Overall, great efforts have been carried out by Dr. Ajar Nath Yadav, his reviewer team, and scientists from different countries to compile this book as a highly unique and up-to-date source on soil microbiome for sustainable agriculture for the students, researchers, scientists, and academicians. I hope that the readers will find this book highlyusefulandinterestingduringtheirpursuitofmicrobiologyandrelatedsubjects. Prof. Amrik Singh Ahluwalia Pro-Vice Chancellor Eternal University, Baru Sahib, Himachal Pradesh, India
- 15. Preface The microbes areubiquitous in nature. The soil is a natural hotspot of the soil micro- biome. The soil microbiome plays a critical role in the maintenance of global nutrient balance and ecosystem functioning. The soil microbiomes are associated with plant ecosystems through the intense network of plant–microbe interactions. The microbes present in bulk soil move toward the rhizospheric region due to the release of different nutrients by plant systems. The rhizospheric microbes may survive or proliferate in the rhizospheric zone depending on the extent of influences of the chemicals secreted into the soil by roots. The root exudates contain the principal nutrients factors (amino acids, glucose, fructose, and sucrose). The microbes present in the rhizospheric region have the capabilities to fix atmospheric nitrogen, produce different phyto- hormones, and solubilize phosphorus, potassium, and zinc. The plant systems take these nutrients for their growth and development. These soil- and plant-associated microbes also play an important role in the protection of plants from different plant pathogenic organisms by producing a wide range of secondary metabolites such as ammonia, hydrogen cyanide, siderophores, and hydrolytic enzymes. The soil micro- biomes with plant growth-promoting (PGP) attributes have emerged as an important and promising tool for sustainable agriculture. The soil microbiomes promote plant growth, enhance crop yield and soil fertility via different direct or indirect plant growth-promoting mechanisms. The soil microbes help the plant for adaptation in extreme habitats by mitigating the abiotic stress of high/low temperatures, hyper- salinity, drought, and acidic/alkaline soil. These PGP microbes could be used as biofertilizers/bioinoculants to replace the harmful chemical fertilizers for sustainable agriculture and environments. The aim of volume Soil Microbiomes for Sustainable Agriculture: Functional Annotation is to provide the recent advances in mechanisms of plant growth promo- tion and applications of soil microbiomes for mitigation of different abiotic stresses in plants. The proposed book encompasses current knowledge of soil microbiomes and their potential biotechnological applications for plant growth, crop yield, and soil health under the natural as well as harsh environmental conditions for sustainable xi
- 16. xii Preface agriculture. Thebook will be useful to scientists, researchers, and students related to microbiology, biotechnology, agriculture, molecular biology, environmental biology, and related subjects. Baru Sahib, Himachal Pradesh, India Ajar Nath Yadav
- 17. Contents 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes and Potential Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Pragya Tiwari, Subir Kumar Bose, and Hanhong Bae 2 Microbes Associated with Crops: Functional Attributes for Crop Productivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Slimane Mokrani and El-hafid Nabti 3 Soil Microbes with Multifarious Plant Growth Promoting Attributes for Enhanced Production of Food Crops . . . . . . . . . . . . . . . 55 Yasaman Kiani Boroujeni, Vahid Nikoubin Boroujeni, Ali Asghar Rastegari, Neelam Yadav, and Ajar Nath Yadav 4 Phosphorus Solubilization: Mechanisms, Recent Advancement and Future Challenge . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 Zarrindokht Emami-Karvani and Zahra Chitsaz-Esfahani 5 Potassium Solubilization: Mechanism and Functional Impact on Plant Growth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 Chanda Vikrant Berde, Sonal Suresh Gawde, and Vikrant Balkrishna Berde 6 Fe Chelation and Zinc Solubilization: A Promising Approach for Cereals Biofortification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 Upendra Kumar, Priyanka, Rashmi Malik, Prexha, Yogita, and Kamla Malik 7 Soil Microbes in Plant Growth Promotion and for Mitigation of Abiotic Stress of Drought . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175 Surendra Singh Jatav, Manoj Parihar, Abhik Patra, Satish Kumar Singh, Manoj Kumar Chitara, Kiran Kumar Mohapatra, and Kiran Rana xiii
- 18. xiv Contents 8 ThermotolerantSoil Microbes and Their Role in Mitigation of Heat Stress in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203 Sagar Maitra, Biswajit Pramanick, Prithwiraj Dey, Preetha Bhadra, Tanmoy Shankar, and Kumar Anand 9 Microbiomes of Hypersaline Soils and Their Role in Mitigation of Salt Stress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243 Salma Mukhtar, Dalaq Aiysha, Samina Mehnaz, and Kauser Abdulla Malik 10 Psychrotrophic Soil Microbes and Their Role in Alleviation of Cold Stress in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267 Yachana Jha, Anjali Kulkarni, and R. B. Subramanian 11 Strategies for Abiotic Stress Management in Plants Through Soil Rhizobacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287 Vinay Kumar, Balram Sahu, Deep Chandra Suyal, P. Karthika, Manali Singh, Dipti Singh, Saurabh Kumar, Ajar Nath Yadav, and Ravindra Soni 12 The Omics Strategies for Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants . . . . . . . . . . . . . . . . . . . . . 315 Sagar Maitra, Preetha Bhadra, Ajar Nath Yadav, Jnana Bharati Palai, Jagadish Jena, and Tanmoy Shankar 13 Plant Probiotics: Technical Challenges and Emerging Solutions for Enhancing Food Crops . . . . . . . . . . . . . . . . . . . . . . . . . . . . 379 Ramna Zia, Malik Nawaz Shuja, Muhammad Ali, and Muhammad Sohail Afzal 14 Biofertilizers: Microbes for Agricultural Productivity . . . . . . . . . . . . 407 Fatemeh Salimi and Javad Hamedi 15 Biopesticides: Microbes for Agricultural Sustainability . . . . . . . . . . . 471 Fatemeh Salimi and Javad Hamedi 16 Mycorrhiza: Plant Growth-Promoting and Biocontrol Agent Ability Under the Abiotic Stress Conditions . . . . . . . . . . . . . . . . . . . . . . 503 Tayyaba Hussain, Muhammad Usmaan, Muhammad Numan, Aamir Abdullah Khan, Faiza Abbas, and Alvina Gul 17 Entomopathogenic Soil Microbes for Sustainable Crop Protection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 529 Neelam Thakur, Preety Tomar, Simranjeet Kaur, Samiksha Jhamta, Rajesh Thakur, and Ajar Nath Yadav
- 19. Contents xv 18 GlobalScenario of Soil Microbiome Research: Current Trends and Future Prospects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 573 Gangavarapu Subrahmanyam, Amit Kumar, Reeta Luikham, Jalaja S. Kumar, and Ajar Nath Yadav 19 Functional Annotation and Biotechnological Applications of Soil Microbiomes: Current Research and Future Challenges . . . . 605 Ajar Nath Yadav, Tanvir Kaur, Divjot Kour, Rubee Devi, Geetika Guleria, Rajeshwari Negi, Ashok Yadav, and Amrik Singh Ahluwalia
- 20. Editor and Contributors Aboutthe Editor Ajar Nath Yadav is an Assistant Professor (Senior Scale) and Assistant Controller of Examinations at Eternal University, Baru Sahib, Himachal Pradesh, India.Hehas8yearsofteachingand12yearsofresearch experience in the field of Microbial Biotechnology, Microbial Diversity, and Plant-Microbe-Interactions. He obtained a doctorate in Microbial Biotechnology, jointly from IARI, New Delhi, and BIT, Mesra, Ranchi, India; M.Sc. (Biotechnology) from Bundelk- hand University and B.Sc. (CBZ) from the University of Allahabad, India. He has 250 publications, with an h-index of 58, i10-index of 160, and 9050 citations (Google Scholar- on 06/06/2021), and 112 research communications in different national and international conferences. He is the editor of 18 Springer-Nature, 7 Taylor & Francis, 2 Elsevier, and 1 Wiley book. In his credit, one granted patent “Insecticidal formu- lation of novel strain of Bacillus thuringiensis AK 47”. He has got 12 Best Paper Presentation Awards and 1 Young Scientist Award (NASI-Swarna Jayanti Puraskar). He received the “Outstanding Teacher Award” in the 6th Annual Convocation 2018 by Eternal University, Baru Sahib, Himachal Pradesh. He has a long-standing interest in teaching at the UG, PG, and Ph.D. levels and is involved in taking courses in micro- biology and microbial biotechnology. He is currently handling two projects, one funded by the Department of Environments, Science & Technology (DEST), Shimla, and one by the HP Council for Science, Technology & xvii
- 21. xviii Editor andContributors Environment (HIMCOSTE). He has guided two Ph.D. candidates and one M.Sc. scholar, and presently, he is guiding four scholars for Ph.D. degree and one M.Sc. In his credit, ~6700 microbes (Archaea, bacteria, and fungi)areisolatedfromdiversesources,and~550poten- tial and efficient microbes are deposited at the culture collection ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, India. He has deposited 2423 nucleotide sequences and 3 whole- genome sequences (Bacillus thuringiensis AKS47, Arthrobacter agilis L77, and Halolamina pelagica CDK2) and 2 transcriptomes to NCBI GenBank databases: in the public domain. The niche-specific microbes from extreme environments were reported as specific bioinoculants (Biofertilizers) for crops growing in normal and diverse abiotic stress conditions. He and his group have developed technology for screening archaea for phosphorus solubilization for the first time. He is the editor-in-chief for “Journal of Applied Biology and Biotechnology”. He has been serving as an editor/editorial board member and a reviewer for 49 different national and international peer-reviewed journals. He has lifetime membership in the Associa- tion of Microbiologist in India and the Indian Science Congress Council, India. Please visit https://sites.goo gle.com/view/ajarnathyadav/ for more details. Contributors Faiza Abbas Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan Muhammad Sohail Afzal Department of Life Sciences, School of Science, University of Management and Technology (UMT), Johar Town, Lahore, Pakistan Amrik Singh Ahluwalia Department of Botany, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India Dalaq Aiysha Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan Muhammad Ali Department of Life Sciences, School of Science, University of Management and Technology (UMT), Johar Town, Lahore, Pakistan Kumar Anand Department of Biotechnology, Vinoba Bhave University, Hazaribag, India
- 22. Editor and Contributorsxix Hanhong Bae Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea Chanda Vikrant Berde Marine Microbiology, School of Earth, Ocean and Atmo- sphere Sciences (SEOAS), Goa University, Taleigao Plateau, Goa, India Vikrant Balkrishna Berde Department of Zoology, Arts, Commerce and Science College, Lanja, Maharashtra, India Preetha Bhadra Department of Biotechnology, M.S. Swaminathan School of Agri- culture, Centurion University of Technology and Management, Paralakhemundi, Odisha, India Vahid Nikoubin Boroujeni Department of Microbiology, Science and Research Branch, Islamic Azad University, Tehran, Iran Yasaman Kiani Boroujeni Department of Molecular and Cell Biochemistry, Falavarjan Branch, Islamic Azad University, Isfahan, Iran Subir Kumar Bose Department of Agriculture Science, Himalayan Garhwal University, Pokhara, Pauri Garhwal, Uttarakhand, India Manoj Kumar Chitara Department of Plant Pathology, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India Zahra Chitsaz-Esfahani Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Rubee Devi Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India Prithwiraj Dey Department of Agronomy, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India El-hafid Nabti Laboratoire de Maitrise Des Energies Renouvelables, Faculté Des Sciences de La Nature Et de La Vie, Université de Bejaia, Bejaia, Algeria Zarrindokht Emami-Karvani Department of Microbiology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran Sonal Suresh Gawde Department of Microbiology, Gogate Jogalekar College, Ratnagiri, Maharashtra, India Alvina Gul Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan Geetika Guleria Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India Javad Hamedi Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny Living Organisms, College of Science, Microbial Technology and Products (MTP) Research Center, University of Tehran, Tehran, Iran
- 23. xx Editor andContributors Tayyaba Hussain Department of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan Surendra Singh Jatav Department of Soil Science and Agricultural Chemistry, InstituteofAgriculturalSciences,BanarasHinduUniversity,Varanasi,UttarPradesh, India Jagadish Jena Department of Agronomy, Indira Gandhi Krishi Viswavidyalaya, Raipur, India Yachana Jha N. V. Patel College of Pure and Applied Sciences, S. P. University, Anand, Gujarat, India Samiksha Jhamta DepartmentofZoology,AkalCollegeofBasicSciences,Eternal University, Sirmour, Rajgadh, India P. Karthika Department of Agricultural Microbiology, Indira Gandhi Krishi Vish- wavidhyalaya, Raipur, Chhattisgarh, India Simranjeet Kaur Department of Zoology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, India Tanvir Kaur Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India Aamir Abdullah Khan Department of Plant Biology and Ecology, Nankai Univer- sity Tianjin, Tianjin, China Divjot Kour Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University Baru Sahib, Sirmour, Himachal Pradesh, India Anjali Kulkarni N. V. Patel College of Pure and Applied Sciences, S. P. University, Anand, Gujarat, India Amit Kumar Central Muga Eri Research & Training Institute, Central Silk Board, Lahdoigarh, Jorhat, Assam, India Jalaja S. Kumar Central Muga Eri Research & Training Institute, Central Silk Board, Lahdoigarh, Jorhat, Assam, India Saurabh Kumar Division of Crop Research, ICAR Research Complex for Eastern Region, Patna, Bihar, India Upendra Kumar Department of Molecular Biology, Biotechnology & Bioin- formatics, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar, India Vinay Kumar ICAR-National Institute of Biotic Stress Management, Baronda Farm, Raipur, Chhattisgarh, India Reeta Luikham Central Muga Eri Research & Training Institute, Central Silk Board, Lahdoigarh, Jorhat, Assam, India
- 24. Editor and Contributorsxxi Sagar Maitra Department of Agronomy, Centurion University of Technology and Management, Paralakhemundi, Odisha, India Kamla Malik Department of Microbiology, College of Basic Sciences & Human- ities, CCS Haryana Agricultural University, Hisar, India Kauser Abdulla Malik KAM School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan Rashmi Malik Department of Genetics & Plant Breeding, College of Agriculture, G.B. Pant University of Agriculture & Technology, Pantnagar (Udham Singh Nagar), Uttarakhand, India Samina Mehnaz KAM School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan Kiran Kumar Mohapatra Department of Soil Science and Agricultural Chem- istry, Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India Slimane Mokrani Department Agronomy, Laboratory of Research On Biological Systems and Geomantic (L.R.S.B.G), University of Mustapha Stumbouli, Mascara, Algeria; Laboratoire de Maitrise Des Energies Renouvelables, Faculté Des Sciences de La Nature Et de La Vie, Université de Bejaia, Bejaia, Algeria Salma Mukhtar KAMSchool of Life Sciences, Forman Christian College (AChar- tered University), Lahore, Pakistan; School of Biological Sciences, University of the Punjab, Lahore, Pakistan Rajeshwari Negi Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University Baru Sahib, Sirmour, Himachal Pradesh, India Muhammad Numan Laboratory of Molecular Biology and Biotechnology, University of North Carolina, Chapel Hill, USA Jnana Bharati Palai Department of Agronomy, Centurion University of Tech- nology and Management, Paralakhemundi, Odisha, India Manoj Parihar ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, India Abhik Patra Department of Soil Science and Agricultural Chemistry, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India Biswajit Pramanick Department of Agronomy, Dr. Rajendra Prasad Central Agri- cultural University, Pusa, Samastipur, Bihar, India Prexha Department of Molecular Biology, Biotechnology & Bioinformatics, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar, India
- 25. xxii Editor andContributors Priyanka Department of Botany, Deva Nagri P.G. College, Meerut, Uttar Pradesh, India Kiran Rana Department of Agronomy, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India Ali Asghar Rastegari Department of Molecular and Cell Biochemistry, Falavarjan Branch, Islamic Azad University, Isfahan, Iran Balram Sahu Department of Agricultural Microbiology, Indira Gandhi Krishi Vishwavidhyalaya, Raipur, Chhattisgarh, India Fatemeh Salimi Cellular and Molecular Group, Department of Biology, Damghan University, Damghan, Iran Tanmoy Shankar Department of Agronomy, Centurion University of Technology and Management, Paralakhemundi, Odisha, India Malik Nawaz Shuja Department of Microbiology, Kohat University of Science and Technology (KUST), Kohat, Pakistan Dipti Singh Division of Genetics, Indian Agricultural Research Institute, New Delhi, India Manali Singh Invertis Institute of Engineering and Technology (IIET), Invertis University, Bareilly, UP, India Satish Kumar Singh Department of Soil Science and Agricultural Chemistry, InstituteofAgriculturalSciences,BanarasHinduUniversity,Varanasi,UttarPradesh, India Ravindra Soni Department of Agricultural Microbiology, Indira Gandhi Krishi Vishwavidhyalaya, Raipur, Chhattisgarh, India Gangavarapu Subrahmanyam Central Muga Eri Research & Training Institute, Central Silk Board, Lahdoigarh, Jorhat, Assam, India R. B. Subramanian B R D School of Biosciences, Sardar Patel University, Anand, Gujarat, India Deep Chandra Suyal Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India Neelam Thakur Department of Zoology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, India Rajesh Thakur Krishi Vigyan Kendra Kandaghat, Solan, Dedgharat, Himachal Pradesh, India Pragya Tiwari Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
- 26. Editor and Contributorsxxiii Preety Tomar Department of Zoology, Akal College of Basic Sciences, Eternal University, Sirmour, Rajgadh, India Muhammad Usmaan Central Cotton Research Institute CCRI Multan, Multan, Pakistan Ajar Nath Yadav DepartmentofBiotechnology,Dr.KhemSinghGillAkalCollege of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India Ashok Yadav Department of Botany, Institute of Sciences, Banaras Hindu Univer- sity, Varanasi, Uttar Pradesh, India Neelam Yadav Department of Food Technology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India Yogita Department of Molecular Biology, Biotechnology & Bioinformatics, College of Basic Sciences & Humanities, CCS Haryana Agricultural University, Hisar, India Ramna Zia Department of Life Sciences, School of Science, University of Manage- ment and Technology (UMT), Johar Town, Lahore, Pakistan
- 27. Chapter 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes and Potential Applications Pragya Tiwari, Subir Kumar Bose, and Hanhong Bae Abstract Soil microbiome constitutes an integral component of plant–soil–microbe associations and has a key impact on the ecosystem. The soil microbiome influ- ences key biological processes namely bio-geochemical cycling, plant nutritional uptake and carbon sequestration. The present era has witnessed the emerging signif- icance of soil microbiome as a dynamic system influencing plant productivity and conferring stress tolerance to the plants, having a major impact on the ecosystem. Comprehensive knowledge about plant–soil microbiome is essential for increasing agricultural output, maintenance of soil health towards more sustainable agriculture. Discussing the emerging significance of soil microbiomes in the recent perspective, this chapter extensively focuses on the soil microbiome diversity and distribution in nature, providing an overview of its integral association and dynamics in association with the plants. Moreover, the beneficial attributes of the soil microbiome and its socio-economic applications in a biotechnological perspective are herein discussed. Recent approaches in bioengineering soil microbiomes provide a key platform to enhance food security and sustainable agriculture for millions across the globe. Keywords Metabolic engineering · Metagenomics · Plant colonization · Plant growth promotion · Secondary metabolites · Soil microbiomes · Sustainable agriculture P. Tiwari · H. Bae (B) Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea e-mail: [email protected] S. K. Bose Department of Agriculture Science, Himalayan Garhwal University, Pokhara, Pauri Garhwal, Uttarakhand, India © Springer Nature Switzerland AG 2021 A. N. Yadav (ed.), Soil Microbiomes for Sustainable Agriculture, Sustainable Development and Biodiversity 27, https://doi.org/10.1007/978-3-030-73507-4_1 1
- 28. 2 P. Tiwariet al. 1.1 Introduction Soil microbiome constitutes a plethora of diverse microbes in close proximity with plants and influences plant growth. Plant-associated microbial communities enhance plant tolerance to environmental stress, nutrition uptake and contributing to plant growth (Bakker et al. 2018; Kour et al. 2020). Recent statistics by the Food and Agri- culture Organization (FAO, United Nations) suggests that to sustain an estimated 10 billion world population, the global food production has to be increased up to 70% by 2050. This can be achieved by the increase in crop production through agricul- ture to compensate for the depleting natural resources, indiscriminate use of natural products, threatened plant species, among others (Sergaki et al. 2018; Sharma et al. 2021). The vital functions in the ecosystem are governed by soil microbes, ranging from carbon sequestration, nutrient re-cycling to agricultural output. The soil micro- biome comprises of microbial communities exhibiting enormous diversity and abun- dance (Thakur and Geisen 2019). Moreover, the microbial communities inhabiting the rhizosphere include mainly soil bacteria and fungi, performing multiple func- tions in the ecosystem (Bardgett and Van Der Putten 2014; Kour et al. 2019). Any fluctuations in climatic condition directly or indirectly affect the plant–soil micro- biome and its dynamics (Tripathi et al. 2015). The existence of microbial diversity in the ecosystem and its association with plants highlight the beneficial prospects in biotechnological applications, restoration of ecological balance, agriculture and pharmaceutical sectors (Dubey et al. 2019; Hesham et al. 2021). Therefore, understanding the dynamics of plant–soil microbiome and their main- tenance is the key to sustainable agriculture and crop productivity. In the present context, researchers across the globe are working on increasing the beneficial prospects of soil microbiome, aiming for increased agricultural production. Plant– soil microbiome is indispensable to plant productivity with significant role in cycling of nutrients, carbon sequestration and increase in plant growth (Verma et al. 2017a, b; Yadav et al. 2021). Modern scientific techniques for plant–soil microbiome profiling hold potential for the identification of plant-associated microbes and their func- tional dynamics, providing insights into the influence of climate changes on their distribution and diversity in the soil. With an overview of microbial communities in soil microbiomes and their distribution, the chapter discusses the importance of understanding plant–soil microbiome dynamics in the context of sustainable agri- culture. Moreover, recent trends in genetic engineering approach towards synthetic symbiosis and bioengineering plant–soil microbiomes hold enormous potential towards maximum utilization of these beneficial microbes towards increased crop productivity in agriculture.
- 29. 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes … 3 1.2 Plant and Soil Microbiomes The naturally occurring microbes in the rhizosphere include a group of microor- ganisms classified as bacteria, fungi, protozoans, nematodes and micro-arthropods. The plant rhizosphere consists of the upper surface of the soil, with widespread root networks (Kumar et al. 2015b; Singh et al. 2019). The plant root secretes several primary and secondary metabolites comprising of amino acids, lipids and carbohy- drates, which promotes microbial population towards the plant (Yadav 2021). The above soluble metabolites bind to receptors on bacterial membrane and attract micro- bial communities, which colonize and adhere to the roots of the plant (rhizosphere). This is correlated and promotes plant tolerance to environmental stress, plant growth promotion and plant productivity (Singh et al. 2019; Santoro et al. 2015; Kumar et al. 2015a; Subrahmanyam et al. 2020). Moreover, plant growth-promoting bacteria (PGPB) are defined as the microorganisms, which promote plant growth, yield and production (Glick et al. 1999; Babalola 2010) (Table 1.1). Studies have discussed the association of complex microbial communities with a diverse group of plants including herb, shrub and trees (Yasmin et al. 2016; Sandhya et al. 2017). The microbial components of the plant holobiont comprise of microbiota and microbiome (Lucaciu et al. 2019). The presence of plant microbiota and micro- biome (microorganisms and microbial genomes) in endosphere, phyllosphere and rhizosphere demonstrates significant functions in plant growth and disease manage- ment (Sczyrba et al. 2017; Sanchez-Canizares et al. 2017; Lucaciu et al. 2019; Yadav 2020). Nowadays, crop production is challenged by exposure to toxic chemicals and heavy metals, climate changes, and an ever-increasing need to enhance global agri- cultural output. Plant growth-promoting rhizobacteria (PGPR) improves plant health and aids in higher crop yield and production, these microorganisms are desig- nated as biofertilizers (Prasad et al. 2021). In the present context, there has been a growing scientific interest in employing biofertilizers in agricultural practices (Di- Benedetto et al. 2017). Presently, biofertilizers are commercially marketed in many brand names, such as Galltrol, Diegall, Gmax PGPR, Nitromax, Azo-Green, Custom N2, Custom GP, BaciGold, Subtilex, YieldShield, RootShield, Plus WP and others (Table 1.2). Microorganisms that are closely associated with a particular plant species are specific for exudate secretion of plants roots (Fig. 1.1) and not dependent on soil conditions, respectively. 1.2.1 Diversity and Composition Microbial communities are present in close proximity with plant species and consti- tute the “soil microbiome”. Plants display interaction with the microbial commu- nities, namely the phyllosphere and soil/rhizosphere, among others (Hardoim et al. 2015). The microbiota associated with roots is horizontally transferred, although
- 30. 4 P. Tiwariet al. Table 1.1 Plant growth-promoting bacteria as bio-fertilizer and their functional role in plant growth promotion Host/Microorganism Region PGP attributes Host plant References Alcaligenes faecalis str. S8 Endophyte P-solubilization IAA production Withania somnifera Abdallah et al. (2016) Pseudomonas putida Rhizosphere P- solubilization Siderophore production IAA production M. piperita Santoro et al. (2015) Enterobacter sp. TAP02 Rhizosphere IAA production N2 fixation P-solubilization T. amplexicaulis El-Sayed et al. (2014) Pseudomonas fluorescens WCS417r Bacillus amyloliquefaciens GB03 Root inoculation Increase the drought tolerance M. piperita Chiappero et al. (2019) Bacillus subtilis P-20 B. subtilis Daz-26 Rhizosphere PGPRs Essential oil yield M. arvensis Maji et al. (2013) Achromobacter xylosoxidans Fd2 Herbaspirillum seropedicae Oci9 Ochrobactrum rhizosphaerae Oci13 Rhizosphere IAA production Siderophore production Ocimum sanctum Barnawal et al. (2012) Serratia ureilytica Bac5 Rhizosphere Siderophore production ACCdeaminase P-solubilization O. sanctum Barnawal et al. (2012) Pseudomonas stutzeri CSP03, Bacillus subtilis TTP02 Pseudomonas putida PHP03 Rhizosphere IAA production N2 fixation P-solubilization Siderophore production Capparis spinosa El-Sayed et al. (2014) Arthrobacter sp. SMR3, B.subtilis SMR15 Endophyte IAA production ACC deaminase Papaver somniferum Pandey et al. (2016) Bacillus sp. Pseudomonas putida (ECL5) Endophyte, IAA P-solubilization Siderophore production Curcuma longa Kumar et al. (2016a, b) Clavibacter michiganensis Endophyte IAA production C. longa Kumar et al. (2016a, b) Azotobacter chroococcum CL13 Rhizosphere IAA, HCN, ammonia P-solubilization C. longa Kumar et al. (2014) (continued)
- 31. 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes … 5 Table 1.1 (continued) Host/Microorganism Region PGP attributes Host plant References Bacillus subtilis LK14 Endophyte P-solubilization IAA production Moringa peregrine Khan et al. (2016) B. subtilis CT-1 A. tumefaciens CT-2 P. putida CT-4 Pseudomonas sp. CT-5 Endophyte IAA production, Ammonia production P-solubilization Cassia tora L. Kumar et al. (2015a) Achromobacter xylosoxidansAUM54 Endophyte IAA production, Phosphate solubilization Siderophore production Catharanthus roseus Karthikeyan et al. (2012) Rhizobium sp. Rhizosphere Cytokinin production Mimosa pudica Sabat et al. (2014) Pseudomonas stutzeri P3 Endophyte IAA production Echinacea Lata et al. (2006) Paenibacillus borealis BR 32 Rhizosphere IAA production N2 fixation Phosphate solubilization Juniperus sp. Navarro-Noyaa et al. (2012) Acinetobacter sp. ALEB16 Endophyte Abscisic acid production Salicylic acid production Atractylodes lancea Wang et al. (2015) Paenibacillus durus BR 30 Rhizosphere IAA production N2 fixation Phosphate solubilization Asphodelus sp. Navarro-Noyaa et al. (2012) Brevundimonas diminuta EGEB-1 Agrobacterium tumefaciens EGE-B-5 Stenotrophomonas rhizophilia EGE-B-6 Endophyte IAA production Phosphate solubilization Prunus persica Liaqat and Eltem (2016) Bacillus strains OSU-142 and M3 Rhizosphere Auxin and cytokinin production (N2 fixing) and phosphate solubilizing) M3 produce Zeatin Raspberry Orhan et al. (2006) (continued)
- 32. 6 P. Tiwariet al. Table 1.1 (continued) Host/Microorganism Region PGP attributes Host plant References Pseudomonas BA-8 Bacillus OSU-142 Bacillus M-3 Rhizosphere Auxin and Cytokinins Fragaria × ananassa Pırlak and Kose (2009) Stenotrophomonas maltophilia R551-3 Endophyte IAA synthesis ACC deaminase Populus sp. Taghavi et al. (2009) Paenibacillus graminis BR 35 Rhizosphere N2 fixation Phosphate solubilization Aster gymnocephalus Navarro-Noyaa et al. (2012) Azospirillum lipoferum KYR F6 Rhizosphere IAA synthesis N2 fixation Phosphate solubilization Haplopappus sp. Navarro-Noyaa et al. (2012) Rhizobium sp. Azospirillum sp. Endophyte IAA synthesis N2 fixation Oryza sativa Sev et al. (2016) Pseudomonas aeruginosa FTR, Enterobacteras buriae MRC12 Acitenobacter brumalii MZ30V92 Endophyte Ammonia production Phosphate solubilization Siderophore production Zea mays Sandhya et al. (2017) Pseudomonas monteilii FMZR2 Sinorhizobium meliloti MRC31 Endophyte Ammonia production Phosphate solubilization, Z. mays Sandhya et al. (2017) Serratia sp. Rh269 Rhizosphere IAA synthesis Siderophore production Phosphate solubilization Oryza sativa Yasmin et al. (2016) Bacillus sp. Rh219 Rhizosphere Siderophore production O. sativa Yasmin et al. (2016) Pseudomonas sp. E227 Rhizosphere IAA synthesis Siderophore production HCN Phosphate solubilization O. sativa Yasmin et al. (2016) Azospirillum brasilense Pseudomonas fluorescens Rhizosphere – Triticum aestivum Naiman et al. (2009) Azospirillum sp. Azotobacter sp. – – T. aestivum Namvar and Khandan (2013) Azospirillum brasilense Inoculation of seeds with bacteria culture – T. aestivum cultivar CD 150 Piccinin et al. (2011) (continued)
- 33. 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes … 7 Table 1.1 (continued) Host/Microorganism Region PGP attributes Host plant References Glomus intraradices BEG72, Glomus mossae Trichoderma atroviride MUCL 45632 Coated seeds of wheat with a microbial consortium Enhance growth, nutrient uptake, yield and grain quality Triticum durum Colla et al. (2015) vertical transmission for bacteria through seeds has also been observed in nature (Rana et al. 2020; Rana et al. 2019b). The microbial communities present in rhizo- sphere colonize the plant through roots, which offers a unique ecological niche (Hart- mann et al. 2009). However, some studies also suggested that the microbial commu- nities present in rhizosphere show variation with time. Plant roots are colonized by diverse bacterial endophytes, in a symbiotic network with the plant species. Diverse bacterial species present as endophytes in grapevine roots comprise of Acidobac- teria, Actinobacteria, Chloroflexi, Planctomycetes, Proteobacteria, Verrucomicrobia, beside others (Fierer 2017). The aboveground zone, the phyllosphere provides a unique environment for the epiphytes microbial communities. The endophytes may enter the plant tissues through aerial parts or from xylem to the stem, and leaves, respectively (Compant et al. 2011). The plant microbiota, which is above ground, mainly thrives from soil, air and seed and several environmental factors affect their presence and distribution. The epiphytes and endophytes enhance plant growth and improve stress (biotic and abiotic) tolerance, respectively (Hardoim et al. 2015; Rana et al. 2019a). 1.2.2 Factors Affecting the Soil Microbiomes Soil and rhizosphere microbial communities (soil microbiomes) are affected by the environmental stresses: biotic factors–host genotypes, cultivars, developmental stages, proximity to root and root architecture. In the case of abiotic factors, these influence soil composition of microbial communities including soil type and soil quality (Buyer et al. 1999; Li et al. 2018), the physical factor includes light, pH, seasonal variation, moisture content, temperature and soil mineral composition. The soil porosity is a critical determinant of plant growth and development because it provides oxygen (O2) to the roots of the plants (Berendsen et al. 2012; Chaparro et al. 2012; Turner et al. 2013; Kumar et al. 2019). 1.2.2.1 Soil Type and Composition Soil environment plays a key role in rhizosphere microbial communities’ growth, in direct and indirect manner. The root secretions (exudates) have a key effect on the
- 34. 8 P. Tiwariet al. Table 1.2 The commercial products (based on plant growth-promoting rhizobacteria) marketed for plant growth promotion and disease management Bioagents/microbial source Trade name/formulation Use/Recommended crops Weblink Agrobacterium radiobacter strain K1026 Nogall Block infections by crown gall-causing pathogenic agrobacteria http://bio-caretechn ology.com A. radiobacter strain K84 Galltrol Diegall Prevention and eradication of crown gall https://agbiochem. com/wpcontent/upl oads/2014/08/Revised- Galltrol-Gallex-Pam phle Azospirillum brasilense Azotobacter chroococcum Gmax PGPR Nitromax Nitrogen nutrition, phosphate nutrition, plant protection from diseases https://www.greenm axagrotech.com A. brasilense Azo-Green (Azospirillum) N-supplementation contains an efficient strain of Azospirillum https://pdf.indiamart. com/impdf/417723 7333/MY-863282/azo green-azospirillum Nitrogen-fixing bacteria Custom N 2 Nitrogen-fixing bacteria http://living-soils.com/ custom-n2-nitrogen-fix ing-bacteria Trichoderma sp. Custom GP Increase soil performance http://living-soils.com/ trichoderma-benefits- plants B. subtilis MB1600 BaciGold (Fungicide) Fungicide https://www.indiamart. com/proddetail/bac igold-4576463473. html (continued)
- 35. 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes … 9 Table 1.2 (continued) Bioagents/microbial source Trade name/formulation Use/Recommended crops Weblink Bacillus subtilis strain MBI 600 Subtilex (Bio-Fungicide) Bio-fungicide and protection against diseases caused by Rhizoctonia solani, Fusarium sp. and Pythium sp. https://www.seedra nch.com/Subtilex-NG- Fungicide-6-X-2-Oz- p/subtilex-ng-case.htm Bacillus pumilus GB 34 YieldShield (biological seed treatment) Yield Shield 200 FS applied as a water-based slurry either alone or with other registered seed treatment insecticides and fungicides https://www3.epa.gov/ pesticides/chem_s earch/ppls/000264- 01117-20101020 Trichoderma harzianum—1.15% Trichoderma virens—0.61% RootShield Plus WP (Biological Fungicide) It mainly grows on roots and shielding them against root-damaging fungi https://www.seedra nch.com/RootShield- Plus-WP-Biological- Fungicide-1-Lb-p/roo tshield-plus-wp-1 B. pumilus QST2808 Sonata ASO Control or suppression of many plant diseases https://agrobaseapp. com/unitedstates/pes ticide/sonata-aso Beneficial bacteria, fungi/mycorrhiza Microbeact (growth accelerator) For garden plants, vegetables, fruits, shrubs, trees, lawn, sod and turf (contains photosynthetic cultures) https://www.microb eact.com/growth-acel Bacillus licheniformis SB3086 EcoGuard, Green Releaf (Biofungicide) It is used on ornamental plants and ornamental turf to prevent and treat many fungal diseases https://patents.google. com/patent/CA2451 555C/en Burkholderia cepacia Blue Circle, Deny, Intercept Increase plant P nutrition in high P-fixing soils Pseudomonas fluorescens A506 (71%) BlightBan A506 Suppression or control of fire blight on pome fruits and the suppression of frost damage on cherry, apple, pear, almond, peach, tomato, potato and strawberry https://nufarm.com/usc rop/product/blightban a506 (continued)
- 36. 10 P. Tiwariet al. Table 1.2 (continued) Bioagents/microbial source Trade name/formulation Use/Recommended crops Weblink Pseudomonas syringae ESC-100 Bio-Save 10, 11, 100, 110,1000, and 10 LP Biological decay control agent. Bio-Save is labelled for post-harvest applications for the control and prevention of disease on a variety of fruits and vegetables that include, among others: seed and storage white potatoes and sweet potatoes https://iviair.com Pseudomonas chlororaphis Cedomon (Biological seed dressing solution) Biological seed dressing solution Cedomon ® is commonly used, especially in Sweden http://orgprints.org/ 11271/1/fnytt105 Streptomyces griseovirdis K61 Mycostop (Biological fungicide) Mycostop is used by farmers for diseases caused by Pythium, fusarium, botrytis, alternaria, phomopsis, rhizoctonia and phytophthora. It also increases plant vigour and yields even in the absence of root pathogen activity https://www.planetnat ural.com/product/myc ostop 4 species of beneficial soil fungi and 5 species of beneficial soil bacteria Biota Green™ It is a probiotics for golf courses http://living-soils.com/ biota-green-probiotic- for-golf-greens Beneficial bacteria and fungi spore BiotaMax Soil probiotics, seed germination, root developments and plant growth http://living-soils.com/ product/biotamax
- 37. 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes … 11 Induced IAAProduction Induced Cytokinin Production Induced Gibberellin Production Induced Abscisicacid Production Induced EthyleneProduction Plant development & abiotic stress Fig. 1.1 Diagrammatic representation of the influence of the soil factors and PGPR on plant roots and soil microbes, which modify the soil environment and induce chemical signalling and growth hormone production, promoting plant health and yield soil microbes as signalling molecules for microbes, creating a complex and intricate interaction between plants and the microbiome (Chaparro et al. 2012). A key study by Broeckling et al. (2008) suggested a close dynamics between the composition of soil microbial population and their interaction with the plant species. Some fungal communities (soil-borne fungus) altered the composition and nature of soil and decreased the total biomass of a non-native model plant (Broeckling et al. 2008). The experiments were conducted in two plant species, Arabidopsis thaliana and Medicago truncatula. Both plants were cultivated in their natural environments (presence of their natural microbiomes) and in the non-native soil. Arabidopsis plants (root secretions) supported the native fungal community in natural soil conditions (as compared to non-native soil), when cultivated alone. The beneficial microbial popu- lation was disproportionate (in non-native soil) and while other microbial species were increased due to this uneven population of microbes (fungal biomass), micro- bial population and plant growth were also affected, when compared with or without treatment with root exudates in Arabidopsis plants. The similar observation was recorded in case of M. truncatula plants. These results strongly suggested that the
- 38. 12 P. Tiwariet al. secretion of chemicals from plant roots (roots exudates) and, therefore, individual plants influenced the total population and composition of soil microbiomes. 1.2.2.2 Soil pH Effect Soil pH is a measure of soil acidity/alkalinity and governs the composition of micro- bial communities (Fierer and Jackson 2006; Yang et al. 2017). The soil pH showed a negative correlation with soil biomass and a positive correlation with average well colour development (AWCD) (Zhong et al. 2010; Chen et al. 2015), distinct fungal and bacterial interactions with soils of diversified texture, nitrogen and phosphorous content (Frey et al. 2004; Chaparro et al. 2012; Girvan et al. 2003; Yadav et al. 2020b), and pH of the soil (Fierer and Jackson 2006; Rousk et al. 2010). The optimum soil pH range for plant growth is 5.5–7.5. Soil pH influences the plant nutrients avail- ability, micro or macronutrient and directly affects the growth of plants and their productivity. Therefore, soil pH governs the growth of the plant and adaptation to the environment. Moreover, a plant may be sensitive to a pH range in some soil condi- tions but not for others, for example, a low concentration of molybdenum (Mo) in soil may not be optimum for Glycine max (pH 5.5), but soils with optimum Mo leads to better growth at that pH (Sumner and Yamada 2002). Bacterial decomposition of organic contents and some fertilizers release nitrogen (chemically synthesized fertil- izers), which influence soil properties and pH, the optimum pH for bacterial growth being 5.5–7.0 range. In soil with pH < 5.0, most of the plant nutrients demonstrate soil leaching (mainly acidic condition) (Loncaric et al. 2008). Recent research evidence proves that the pH of the soil may critically affect the soil bacterial communities (Fierer and Jackson 2006). Soil sample analysis by Rousk et al. (2010) was performed in pH range that varies from 4.0 to 8.3, while all other factors and variables in soil were regulated. In the above study, the diversity and composition of the bacterial population showed correlation with soil pH (Rousk et al. 2010). It was assumed that the correlation between soil bacterial communities and soil pH structure was attributed to the pH sensitivity of bacterial cells, the bacterial taxa being tolerant to a relatively narrow pH range (Rousk et al. 2010). Other evidence suggested that soil pH was a key factor for soil microbial diversity, highlighting that altitude, phosphorous concentration and the ratios of Ca2+ , Mg2+ , and Al3+ ions in the soil, are key determinants (Faoro et al. 2010). 1.2.2.3 Nutrient Composition The nutrient composition of soil is a key determinant of soil health and has a crit- ical effect on plant growth (Ryan and Sommer 2012). Soil basically comprises of three nutrients: nitrogen (N), phosphorus (P) and carbon (C) (Ryan and Sommer 2012), while other factors, namely iron, also influence the presence of rhizosphere microbiome (Yang and Crowley 2000). Optimum nutrient content in soil is crucial to plant growth and deficiency of any factor is overcome by the application of chemical
- 39. 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes … 13 fertilizers (Geiger et al. 2010). Moreover, the fertility of the soil is determined by a complex interaction between the biotic and the abiotic components, the soil microbes aiding the organic content decomposition and nutrient generation for plant growth. The growth of the plant facilitates the acquisition of nutrients and root colonization by the microbes (Berendsen et al. 2012). In addition, disproportionate soil nutrient content also has a critical impact on biodiversity in ecosystem and cultural practices for land use, thereby having a profound effect on the soil microbiome (Joergensen and Emmerling 2006). Another key nutrient, phosphorous modulates the microbiome in rhizosphere (Kour et al. 2021). A study by Coolon et al. (2013) showed that grassland burning would increase phosphorous and nitrogen availability and studied the effect of phos- phorous and nitrogen increase on grasslands in North America. The study showed the effect of soil phosphorous and nitrogen on natural ecosystems. Moreover, the presence of nitrogen in the soil has a profound effect on plant productivity and bacte- rial communities (Clark et al. 2007). Studies have shown that an increase in nitrogen enhanced plant productivity but adversely affected lower plants and bacterial commu- nities (Suding et al. 2005). This study demonstrates the significance of soil nutrients in diversity and distribution of soil microbes and plant growth, respectively. 1.2.2.4 Climate Changes The global rising temperature results in fluctuating climatic conditions, thereby adversely affecting the soil microbiome. Studies have shown that the microbial communities, which were selective for Arabidopsis root exudates, responded to changes in the environment (Badri et al. 2013). In another study, the structure and function of rhizosphere microbes were modified by increased CO2 concentration in root exudates. The changes in climatic conditions altered the gene expression in microbial communities (Bardgett et al. 2013). Moreover, the depletion in ozone layer had increased the penetration of UV-B radiations (Müller et al. 1997), and ecosys- tems in the polar region been prone to climatic changes (Caldwell et al. 1982). UV-B radiation directly affects soil microbes leading to altered growth, carbon assimila- tion, changes in pigments, synthesis of amino acids, among others (Formanek et al. 2014). Compared to the rhizosphere, the phyllosphere microbes are more sensitive to ultraviolet (UV) radiations, thereby only a few taxa are present in the phyllosphere as compared to rhizosphere regions (Dohrmann and Tebbe 2005). The soil microbiomes are directly affected by increased UV-B radiation levels (Johnson et al. 2002); but the microbial communities in rhizosphere display different levels of sensitivity to damage by UV-B radiation (Arrage et al. 1993). The bacterial population adopts multiple mechanisms to tolerate UV radiations. The bacterium, Pseudomonas syringae, includes a plasmid having rulAB operon functions in DNA repair process (Cazorla et al. 2008), as a protective mechanism. In Xanthomonas campestris, the bacteria show UV tolerance by producing an extracellular polysac- charide, which absorbs UV radiations (Hugenholtz et al. 1998). Moreover, the bacte- rial communities in phyllosphere produce pigments as a UV protection mechanism
- 40. 14 P. Tiwariet al. (Whipps et al. 2008). The UV-B radiation affects the nutrient cycle in soil, thereby having a key effect on soil microbes (Caldwell et al. 2007). The root biomass is reduced on exposure to UV radiation, leading to less colonization and little nutrients in the soil, disturbing the soil microbiome. Moreover, the increase in atmospheric CO2 (Hu et al. 2001) and elevated temperature (global warming) directly affects the soil microbial communities (Carson et al. 2010). 1.2.2.5 Geographical Factors Few studies have shown the effect of latitude, longitude and altitude on the diversity and distribution of the soil microbiome. Van Horn et al. (2013), suggested that abiotic factors, namely organic content, pH, etc., govern the biodiversity of Antarctic soil. The study further discussed the importance of geographical sampling for the deter- mination of geographical factors affecting soil microbial communities. Moreover, studies have shown that the combinations of different abiotic factors are responsible for biogeographical changes, rather than altitude, latitude and longitude, respectively (Chu et al. 2010). 1.3 Scientific Techniques for Plant–Soil Microbiome Profiling For gaining insights into the beneficial plant and microbe interaction and dynamics (Fierer 2017; Singh et al. 2019), the plant–soil microbiome needs to be explored using scientific approaches (Lucaciu et al. 2019). Nowadays, sophisticated scientific techniques are employed to decipher information and correlate them (Fierer 2017; Singh et al. 2019; Lucaciu et al. 2019). The newer scientific techniques comprise of microbiome 16S r-RNA gene-sequencing technique, sequence analysis, microarrays analysis, shotgun metagenomics approaches, among others (Table 1.3). Table 1.3 discusses modern techniques and scientific tools used for plant–soil microbiome profiling. The techniques specifically employed for the insilico studies of shotgun metagenomes include target-gene assembly, taxonomic profiling, and genome binning and taxonomic binning. From whole-genome sequence data, scientists collect and use genomic data, which improves phylogenetic resolution and functional annotation. The strategy employed to estimate the extent of sequencing essential to delineate information for a particular genome requires preliminary metagenomics data and existing 16S rDNA amplicon data, respectively (Tamames et al. 2012; Ni et al. 2013; Rodriguez et al. 2018). Other techniques are meta-transcriptomics, and meta-proteomics employed in plant–microbe association studies. Additionally, sequencing of amplicon of functional genes acting in key biogeochemical reac- tion in soil and the rhizosphere zone is done. The important ones include pmoA
- 41. 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes … 15 Table 1.3 Modern techniques and scientific tools used for plant–soil microbiome profiling Name of techniques/approaches Main function References 16S r-RNA gene-sequencing technique (Using sequencing technique and databases platform e.g. Greengenes, Silva and RDP) Sequencing analysis strategies to estimate how much sequencing is necessary to recover information for a target genome require existing 16S r-DNA amplicon data and/or a preliminary metagenomics data set Tamames et al. (2012) Shotgun metagenomic approaches (computational analysis of genomic DNA sequence) There are four techniques typical for the computational analysis of shotgun metagenomes: including, taxonomic binning, taxonomic profiling, target-gene reassembly and genome binning Ni et al. (2013) Metagenomics (Microarray-based Metagenomics analysis) It is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics Riesenfeld et al. (2004) Meta-transcriptomics (RNA-sequencing analysis) Transcript sequences from the organisms in a microbiome Chaparro et al. (2014) Meta-proteomics (meta-proteomics mostly utilizes methods originating from mass spectrometry (MS)-based proteomics) Meta-proteomics is the study of the proteins in a microbial community from an environmental sample Hettich et al. (2013) Metabolomics (Nuclear magnetic resonance (NMR), and liquid chromatography–mass spectrometry (LC-MS) and gas chromatography–mass spectrometry (GC-MS)) It is the large-scale study of metabolites molecules, within cells, biofluids, tissues or organisms. Collectively, these small molecules and their interactions within a biological system are known as the metabolome Cajka and Fiehn (2016) and amoA (methanotrophs) and ammonia oxidizers (Suddaby and Sourbeer 1990; Pester et al. 2012), mcrA gene (methanogens) (Zeleke et al. 2013) and dsrB for sulphite and sulphate reducers (Jochum et al. 2017; Vigneron et al. 2018; Zeleke et al. 2013), nifH for diazotrophs (Collavino et al. 2014; Angel et al. 2018) nxrB for nitrite oxidizers (Pester et al. 2014), a comprehensive overview and omics database platform of functional genes may be retrieved from Fungene (Fish et al. 2013). The analytical methods and technologies employed for the study of metabolomics include nuclear magnetic resonance (NMR), liquid chromatography–mass spectrom- etry (LC-MS) and gas chromatography–mass spectrometry (GC-MS). The estima- tion of metabolites employing MS-based techniques provides better resolution than
- 42. 16 P. Tiwariet al. NMR (Emwas 2015). However, an extensive MS sample preparation method and the detection of metabolites (that ionize into the detectable mass range) project few limitations. The NMR-based metabolic profiling works well with compounds that are difficult to ionize or derivatization is required (Markley et al. 2017). 1.4 Beneficial Attributes of Soil Microbiomes The constant applications of synthetic chemical fertilizers and pesticides have a harmful consequence on the natural microbiomes, which include bacteria, archaea, protozoan, cyanobacteria, fungi, nematodes and micro-arthropods inhabiting the rhizosphere (microbiomes) and the frequent use leads to disturbance in soil natural ecosystem and chemical properties of the soil (pH, bacterial population) and correla- tion between them (Mazid and Khan 2014; Devi et al. 2020). Moreover, the extended use of synthetic chemical fertilizers and pesticides leads to damage of soil property, texture quality and soil microbial communities influencing the yield and productivity of plants. To address this concern, scientists are focusing on sustainable agriculture for restoration of soil health and promote crop yield and production, by employing natural methods without affecting natural soil microflora. For sustainable agricul- ture, the concerns associated with chemical fertilizers and pesticides for mitigation of climate influence need to be addressed (Kumar et al. 2017a, b). Sustainable agri- culture is the possible way to compensate for the rising demand for organic fertilizers of biological origin, then employing agro-chemicals. Organic farming maintains the diversity of natural microbes in the soil and natural microflora contribute to plant growth. The microflora comprise of bacteria, actinomycetes, fungi including arbus- cular mycorrhiza fungi (AMF), cyanobacteria, to manage disease (disease manage- ment), salt tolerance, drought toleranceandheavymetal toxicity(Gupta 2012; Mishra et al. 2014; Kumar et al. 2021). The rhizosphere zone constitutes the upper soil layer; in close proximity to the root surface (Kumar et al. 2015b). In the rhizosphere zone, root secretion comprises of lipids, amino acids and carbohydrates, respectively. These chemicals attract micro- bial population, which colonize the plant roots, and participate in promoting plant growth and tolerance to diseases (Oku et al. 2012; Kumar et al. 2015a, b). Plant- associated beneficial microbes influence the biomass, yields and productivity of the host plant and are known as plant growth-promoting bacteria (PGPB) (Babalola 2010; Kumar et al. 2016a, b). The PGPB also induce phytohormone production, ammonia production, phosphate solubilization, siderophores and hydrogen cyanide (HCN) production, among other functions (Yadav et al. 2020c). Nitragin is a potent biofertilizer (legume inoculants and growth promotants) marketed by Merck KGaA, Darmstadt, Germany. The statistics suggested that the global market of Nitragin is $85 million dollar in agriculture because the farmers prefer organic and sustainable agriculture. Presently, the global market for bio- inoculants is projected at an annual cost of $85 million (with $50 million in the USA alone).
- 43. 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes … 17 Azotobacter is a free-living Gram-negative bacteria (diazotrophic), primarily found in neutral to alkaline soils (pH range 7.0), on some plants and in aquatic environments. One of the distinct abilities of Azotobacter is that it can survive in dry soils, in the form of cysts for up to 24 years. Moreover, it fixes atmospheric nitrogen by conversion to ammonia (biological nitrogen fixation). Blue-green algae (BGA) (cyanobacteria) are prokaryotes, consisting of free-living bacteria and the endo-symbiotic plastids, found in some eukaryotes. They perform photosynthesis for energy generation and shows freshwater or terrestrial origin. Few cyanobacteria perform biological nitrogen fixation in anaerobic conditions by specialized cells called heterocysts. The heterocysts of BGA are able to fix atmospheric nitrogen (N2) into ammonia (NH3), nitrites (NO2 − ) or nitrates (NO3 − ), readily assimilated by the plants (Golden and Yoon 1998; Fay 1992). Free-living cyanobacteria inhabit the water content of rice paddies and play important role in increasing the yield and production of rice crop through a biological process. Considering the current demand for organic farming, PGPB is a potential biofer- tilizer, safe and effective for increasing crop yields and productivity in agri- culture. Recently in organic farming, several bacterial species were used, such as Arthrobacter, Azospirillum, Azotobacter, Bacillus, Burkholderia, Enterobacter, Klebsiella, Pseudomonas and Serratia (Saharan and Nehra 2011; Kumar et al. 2015a, b). In plants, phytohormones play a major role in the growth and secondary metabo- lites production (Bose et al. 2013). Azospirillum fixes atmospheric nitrogen, produces phytohormones and confers abiotic and biotic stresses tolerance to the plants (Fukami et al. 2018; Bashan and de-Bashan 2010; Naiman et al. 2009). The study of beneficial plant–microbe interactions and the increase in plant growth by Hordelymus europaeus (also known as wood-barley) were undertaken. In this study,theeffectofmicroorganisms(Protozoa,NematodaandLumbricidae)increased shoot/root ratio up to 3.4–5.6 in H. europaeus (Alphei et al. 1996). The N2-fixing bacteria, Azospirillum lipoferum and Azotobacter chroococcum, were used as biofer- tilizers and its effect on the growth and productivity of three Mentha species was studied (El-Hadi et al. 2009). The study showed that microbiological parameters (total fungi, total microbial counts, Azotobacter and Azospirilla) were enhanced with the treatments of above biofertilizers, and Mentha essential oil yield was also increased. 1.5 Biotechnological Applications in Agriculture To improve crop productivity and sustainable agriculture, researchers are exploring innovative methods in agriculture. Approaches for enhancing sustainable agricul- ture are required to boost crop productivity and maintain ecological balance. The plants showing higher adaptation to changing environmental conditions and biotic and abiotic stress tolerance would lead to a higher agricultural output (Pretty et al. 2011; Singh et al. 2020) (Tiwari et al. 2021). The soil microbiomes comprise of the rhizosphere and phyllosphere microbes in close association with the plant. The
- 44. 18 P. Tiwariet al. beneficial microbe in soil serves as an important bioresource for nutrition uptake (mineral solubilization) and siderophores production. The plant growth-promoting microbes or biofertilizers define an eco-friendly method for sustainable agriculture. Besides agriculture, microbes producing phytases show good prospects in nutritional applications as human food (Kumar et al. 2016a, b, 2017a, b). Moreover, the mineral bioavailability was increased by exogenous phytase addition (Penella et al. 2008), while improved iron bioavailability was seen in oat, rice and maize porridges by phytase supplementation (Hurrell et al. 2003). The bio-fortification method has been used to increase micronutrients in the major food crops. PGP bacteria were used in place of synthetic pesticides and fertilizers, which mobilize nutrients by chelation, organic acids release and acidification (Verma et al. 2017a, b; Kaur et al. 2020). Probiotics are defined as food supplements made to improve human health and consist of live microbes, which positively influence the host by the maintenance of microbial balance. Probiotics were prepared for pharmaceutical application and showed improvement in the immune system in a host (Rekha et al. 2020). A better immune response to Salmonella typhi oral vaccine in a person taking Lactobacillus johnsonii and Bifidobacterium lactis as probiotic was observed (Olivares et al. 2007) and Lactobacillus fermentum showed promising effects in influenza (Arunachalam et al. 2000). Moreover, probiotics also affects the behaviour of a person and initial human trials suggested that probiotic consumption may induce gastro-intestinal symptoms and behaviour (Yadav et al. 2017; Benton et al. 2010). 1.6 Presence of Soil Microbiomes and Management Practices The agricultural management practices affect the diversity of soil microbiomes. These management practices are classified as conventional and organic: the organic farming was defined as “an ecological production management system that promotes and enhances biodiversity, biological cycles and soil biological activity”. The organic farming targets replenishing and maintains ecological balance (Gold 1995) and does not use synthetic fertilizers. However, the conventional farming practice employs pesticides and synthetic chemicals for crop protection and crop production. These management practices greatly affect the soil microbiome, the use of synthetic pesti- cides in conventional agriculture may change the diversity of soil microbial commu- nities (Liu et al. 2007; Sugiyama et al. 2010; Yadav et al. 2020a). However, the organic farming may combat plant pathogens by methods that promote the diversity of microbial communities (Sugiyama et al. 2010). Moreover, studies have suggested that soil microbiome is affected by stress and environmental changes (Degens et al. 2001), agri-management practices, etc. (Lumini et al. 2011).
- 45. 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes … 19 1.7 Towards Synthetic Symbiosis: Bioengineering Plant–Soil Microbiomes Soil microbiomes influence the distribution and productivity of plants (Lau and Lennon 2011; van der Heijden et al. 2008), therefore, studies in the present time are investigating the functional dynamics of microbial communities and plants. More- over, studies in the past have highlighted that plant health and yield may be predicted by an increase in soil microbial communities (Lau and Lennon 2011; Schnitzer et al. 2011). Advances in scientific technologies have provided significant information on the diversity and functions of soil microbiome (Nannipieri et al. 2003), for instance, plant growth and productivity increased with a diversity of fungal species (Maherali and Klironomos 2007). Moreover, the plant–microbe association displays a feedback mechanism, the soil microbiome and the plant community changes in response to each other. The presence of soil microbiome is critical for plant productivity and intensive agriculture practices hamper the diversity and functions of associated microbes, which in turn leads to less crop yield and production. To address this concern, collaborative UK research projects (funded by the Soil Security Programme) are co- integrating genomics and field studies to gain insight into the functional dynamics of the soil microbiomes and to manipulate them for benefit of farmers. In a related “Roots of Decline” project, the researchers studied the outcome of continuous crop- ping on causing diseased microbiomes in oilseed rape and how to use different OSR varieties for disease improvement (www.soilsecurity.org/roots-of-decline). Addi- tionally, the “MycoRhiza soil” project aims to study the different combination of wheat varieties and their cultivation may promote beneficial crop–microbe associa- tions, leading to better soil health and disease resistance (www.soilsecurity.org/myc arhizasoil). Advances in synthetic biology approaches have put forth possibilities of bioengi- neering “soil microbiome” for more sustainable agriculture. For example, the legu- minous crops have an inherent property to fix atmospheric nitrogen but not present in cereal crops (maize, wheat, etc.). Researchers are exploring the possibilities to transfer genes from nitrogen-fixing bacteria to bacteria associating with cereal crops (www.synthsym.org). The advantages include the increased crop yield in low-income areas and would improve the damages caused by intensive agricultural practices. However, the science of “synthetic symbiosis” by bioengineering soil microbiomes needs to find scientific approval since genetic manipulations remain a controversial area in scientific research.
- 46. 20 P. Tiwariet al. 1.8 Perspectives in Sustainable Agriculture and Food Security With the rising global population and a requirement to provide food to the billions, agriculture calls for a more sustainable approach by increasing food production and security (Gupta 2012). The agricultural methods should focus on enhancing the plant–microbe associations to promote diversity of soil microbiome. This will increase the crop yield and production while utilizing the minimum use of resources (Chaparro et al. 2012). Research studies have demonstrated the beneficial effects of plant microbial communities in improving plant growth and productivity (Lambers et al. 2009; van der Putten et al. 2009). According to guidelines of U.S. National Research Council, the objectives of sustainable agriculture should focus on the devel- opment of productive farming systems that conserve energy and are environmentally sound (Lakshmanan et al. 2014). In this direction, the ideal approach would be to use beneficial microbes for nutritional enhancement and tolerance to biotic and abiotic and stress conditions. Different formulations of beneficial microbes were used in soil applications, bio-priming, seed treatment, etc. in the respective plant. Several key areas in sustainable agriculture include microbial isolate optimization, identifi- cation of healthy microbiomes and their agricultural applications (Lakshmanan et al. 2014). Moreover, comprehensive knowledge about plant–soil microbiome interac- tion will serve as a platform to increase crop productivity, stress tolerance and plant growth. 1.9 Recent Trends and Outcome in Plant–Soil Microbiome Research The “soil microbiome” represents a diverse ecosystem with interacting microbial communities. With the changing environmental conditions, the microbial commu- nities have evolved mechanism for adaptation and survival (Jansson and Hofmockel 2020), however, the impact of changing climatic conditions has a major impact on the presence and stability of the soil microbial communities. With the progress in high-throughput methods, it is possible to determine the effect of climatic change on the diversity of soil microbial communities and their composition. Moreover, the determination of functional mechanisms of soil microbial communities, for example, soil respiration process, is a very critical aspect in understanding soil microbiome science and may be studied by multi-omics strategies. The presence and functions of the soil microbiome in maintaining healthy soil and providing nutrition to the plants are vital for optimum functioning of ecosystem. The recent trends in the maintenance of soil microbiome and sustainable agriculture call for a more integrated approach to use soil management practices, biodiversity maintenance, carbon sequestration and increased tolerance to climate changes (Jansson and Hofmockel 2020). Moreover, different omics-technologies, namely proteomics, metabolomics, transcriptomics,
- 47. 1 Plant Growth-PromotingSoil Microbiomes: Beneficial Attributes … 21 etc., provided clear insights into the plant–microbe dynamics, contributing to better genetic and functional prospects of soil microbiome (Dubey et al. 2018; Malla et al. 2018a, b). Additionally, advanced methods, namely stable isotope probing, helped in the estimation of diversity and function of soil microbial communities (Mau et al. 2015; Zhang et al. 2018). In the present era, emerging, sophisticated technologies, namely amplicon sequencing, had been employed for taxonomic classification of bacterial communities within ecosystems (Sanschagrin and Yergeau 2014). More- over, the large dataset obtained by 16SrRNA gene sequencing provided details about the presence of microbial species but no insight into the function (Fierer et al. 2012). To address this concern, metagenomics approaches were employed to decipher the diversity and functional mechanisms of microbial communities (Zhou et al. 2015). The bioinformatics resources namely Functionalize R (Kristiansson et al. 2009), MG-RAST (Glass and Meyer 2011), Galaxy portal (Goecks et al. 2010) and others are available to analyze and interpret the biological data. A key area in this direc- tion defines exploring the molecular basis of plant–microbe interactions, in order to promote the functioning of plant and thereby respective ecosystem. 1.10 Conclusion and Future Prospects Soil microbes constituting the “soil microbiome” are the key soil components of soil, which provide nutrients to the plants and protection against pests. Soil microbiome constitutes a determining factor of ecosystem health, and there has been increasing momentum in deciphering the functional dynamics of soil microbiome as a compo- nent of ecosystem and climate change. Studies have shown the emerging importance of soil microbial communities in plant associations and as plant pathogens, having a major impact on the ecosystems. However, high-throughput technologies and omics approaches are required for gaining insights into the microbial pathways and their functional mechanism. Moreover, next-generation sequencing and metagenomics are promising areas employed to monitor climate changes. In the present era, with the global population increase and climate changes, it is necessary to adopt scien- tific methods to boost sustainable agriculture. These scientific methods to study soil microbial communities would aim at delineating information about microbial communities sensitive to climate changes and its influence on microbial community and its function. Such studies exhibit significant prospects in the maintenance of soil health and a productive ecosystem. Attempts towards understanding the dynamics of soil microbiomes and adopting scientific approaches towards maintaining and improving soil microbiomes and their beneficial functions would be the prospective approaches towards sustainable agriculture. Acknowledgements The authors are thankful to their respective institutions for encouragement and support. No conflict of interests was declared.
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- 55. Discovering Diverse ContentThrough Random Scribd Documents
- 56. Mr. Wade. Withthe press, midnight, radio, television, and everything else. I think if you will get a copy of that you will find they asked me lots of questions about fingerprints and evidence. I refused to answer them because I said it was evidence in the case. The only thing that I told them that you might get the impression was evidence but is really not evidence, I told them that the man's wife said the man had a gun or something to that effect. The reason, maybe good or bad, but that isn't admissible in Texas. You see a wife can't testify. It is not evidence, but it is evidence but it is inadmissible evidence actually is what it was. So I think if you find anything in that interview that deals with the evidence you are going to feel that it dealt only with that piece of testimony of Marina Oswald, which someone had told me she said about the gun was missing from the house, which I think later was corroborated. Mr. Rankin. At that time, had you filed on the assassination? Mr. Wade. Yes, sir; we had filed upstairs prior to this. He had been filed on for murder with malice. Mr. Rankin. But he hadn't been brought before the justice of the peace or magistrate yet on that complaint, had he? Mr. Wade. The justice of the peace was there in the office and took it in the homicide. Oswald was in homicide, also, but he is in a separate office. Like I told you, I never did see Oswald except in that lineup downstairs. That was the first time I had seen him. Mr. Rankin. Was that when you told the justice of the peace that he ought to have him before him to tell him his rights and so forth? Mr. Wade. Yes; it was some time during that hour, this went on for about an hour down there, everything. Well, during that interview somebody said, and the thing— Oswald belonged to, was he a Communist, something generally to that effect. Mr. Rankin. They asked you that?
- 57. Mr. Wade. Iwas asked that. And I said, well, now, I don't know about that but they found some literature, I understand, some literature dealing with Free Cuba Movement. Following this—and so I looked up and Jack Ruby is in the audience and he said, no, it is the Fair Play for Cuba Committee. Well, he corrected me, you see, to show you why I got attracted to his attention, why someone in the audience would speak up and answer a question. Mr. Dulles. You hadn't known him before? Mr. Wade. I had never known him, to my knowledge. He is a man about town, and I had seen him before, because when I saw him in there, and I actually thought he was a part of the press corps at the time. Mr. Rankin. Were any of your assistants or people working for you there at that showup? Mr. Wade. I don't believe there were any of them there now. If there is any of them, it is Alexander, because he is the only one down there, but I think he is still up in homicide. I will go further on that, some of my assistants know him, but he was in my office 2 days before this with a hot check or something where he was trying to collect a hot check or pay someone. I think he was trying to pay someone else's hot check off, I don't know what it was, I didn't see him. He talked to my check section. I found this out later. Mr. Rankin. By "he" you mean—— Mr. Wade. Ruby, Jack Ruby. Mr. Rankin. Yes. Mr. Wade. He was in another office of mine, since this all came out, he was in there with a bunch of the police, we were trying a case on pornography, some of my assistants were, and my assistant came in his office during the noon hour after coming from the court, this was 2 or 3 days before the assassination and Ruby was sitting there in his office with five or six Dallas police officers. In fact, he
- 58. was sitting inmy assistant's desk and he started to sit down and asked who he was and the officer said, "Well, that is Jacky Ruby who runs the Carousel Club," so he had been down there. I don't know him personally—I mean I didn't know who he was. It was one of these things I had seen the man, I imagine, but I had no idea who he was, and I will even go further, after it was over, this didn't come out in the trial, as they left down there, Ruby ran up to me and he said, "Hi Henry" he yelled real loud, he yelled. "Hi, Henry," and put his hand to shake hands with me and I shook hands with him. And he said, "Don't you know me?" And I am trying to figure out whether I did or not. And he said, "I am Jack Ruby, I run the Vegas Club." And I said, "What are you doing in here?" It was in the basement of the city hall. He said, "I know all these fellows." Just shook his hand and said, "I know all these fellows." I still didn't know whether he was talking about the press or police all the time, but he shook his hands kind of like that and left me and I was trying to get out of the place which was rather crowded, and if you are familiar with that basement, and I was trying to get out of that hall. And here I heard someone call "Henry Wade wanted on the phone," this was about 1 o'clock in the morning or about 1 o'clock in the morning, and I gradually get around to the phone there, one of the police phones, and as I get there it is Jack Ruby, and station KLIF in Dallas on the phone. You see, he had gone there, this came out in the trial, that he had gone over there and called KLIF and said Henry Wade is down there, I will get you an interview with him. Mr. Rankin. Who is this? Mr. Wade. KLIF is the name of the radio station. You see, I didn't know a thing, and I just picked up the phone and they said this is so and so at KLIF and started asking questions. But that came out in the trial. But to show that he was trying to be kind of the type of person who was wanting to think he was important, you know.
- 59. Mr. Rankin. Didyou give him an interview over the telephone to KLIF? Mr. Wade. Ruby? Mr. Rankin. No. Mr. Wade. I answered about two questions and hung up, but they had a man down there who later interviewed me before I got out of the building. But they just asked me had he been filed and one or two things. Mr. Dulles. It was a KLIF reporter that you gave this to, not Ruby? Mr. Wade. Not Ruby. Ruby was not on the phone, he had just gone out and called him and handed the phone to me. I thought I got a call from somebody, and picked it up and it was KLIF on the phone. Mr. Rankin. On the pornography charge, was Ruby involved in that? Mr. Wade. No, sir; I don't know why he was down there, actually. But there were six or seven police officers, special services of the Dallas police were officers in the thing and I don't know whether he was just interested in it or what he was down there for but he was down there, and I didn't know him. He has tried to leave the impression that he had known me a long time but it is one of those things, I have been in politics and sometimes there are a lot of faces I know that I don't know actually who they are, but I didn't know who he was and he actually introduced himself to me that night. Well, that is about all I can recall of that night. I went home then. Mr. Rankin. You have told us all you remember about the showup? Mr. Wade. I told you all, and, of course, all I know about it as far as my interview with the press. You can get more accurate, actually,
- 60. by getting atranscript of it because I don't remember what all was asked, but I do remember the incident with Ruby and I know I told them that there would be no evidence given out in the case. At that time, most of it had already been given out, however, by someone. I think by the police. Now, the next morning, I don't know of anything else until the next morning. I went to the office about 9 o'clock. Mr. Dulles. Could I ask a question? Mr. Wade. Yes, sir. (Discussion off the record.) Mr. Rankin. Do you have any particular transcript that you are speaking about? Mr. Wade. No; I don't have anything. The thing about it is this was taken, this was on television and radio and all the networks. They had everything there set up and that is the only—that is the first of, I think, three times I was interviewed, but it was Friday night around between 12 and 1 o'clock. It was actually Saturday morning between 12 and 1. Mr. Rankin. So there were a number of networks, possibly, and a number of the radio stations and television stations from the whole area? Mr. Wade. The whole area and it actually wasn't set up for an interview with me. It was an interview, what I thought, with Fritz and Curry, and I thought I would stay for it, but when they got into the interviewing, I don't know what happened to them but they weren't there. They had left, or I was the one who was answering the questions about things I didn't know much about, to tell you the truth. Has that got it cleared? Can I go to the next morning? I will try to go a little and not forget anything.
- 61. The next morningI went to my office, probably, say, 9 o'clock Saturday morning. Waiting there for me was Robert Oswald, who was the brother of Lee Harvey Oswald. You probably have met him, but I believe his name is Robert is his brother. I talked to him about an hour. Mr. Rankin. What did you say to him and what did he say to you? Mr. Wade. Well, we discussed the history of Lee Harvey Oswald and the—one of the purposes he came to me, he wanted his mother, Oswald's mother, and wife and him to see Oswald. Mr. Rankin. Did he say this to you? Mr. Wade. Yes; but we had already set it up, somebody, I don't know whether my office or the police, but he was set up to see him that morning at 11 o'clock, I believe, or 12 o'clock, some time. Mr. Rankin. Did you do anything about it? Mr. Wade. Yes, sir; I checked to see if it was arranged. I called Captain Fritz and told him that he wanted to see him, and he said they were going to let him see him. I don't know. I don't know the name, but it was either 11 o'clock or 12 o'clock Saturday morning. I don't know whether he had requested or not, but that was the first time I had seen him. I don't know why he came to my office, but I used it to try to go into Lee Harvey Oswald's background some, and I also told him that there is a lot involved in this thing from a national point of view, and I said, "You appear to be a good citizen," which he did appear to me, "and I think you will render your country a great service if you will go up and tell Oswald to tell us all about the thing." That was part of the deal of my working for a statement from Oswald which didn't pan out, of course. Because I was going to interview Oswald Sunday afternoon when we got him into the county jail and I was going to attempt to get a statement from him. Mr. Rankin. Did Robert tell you anything about Lee Harvey Oswald's background at that time?
- 62. Mr. Wade. Hetold me about in Europe, how in Russia, how they had had very little correspondence with them and he wrote to them renouncing or telling them he wanted to renounce his American citizenship and didn't want to have anything else to do with him. He said later that one of the letters changed some, I mean back, and then he said he was coming home, coming back and he had married and kind of his general history of the thing and he came back and I believe stayed with this Robert in Fort Worth for 2, 3, or 4 months. Now I say this is from memory, like I don't have—and they had helped him some, and said that Marina, the thing that impressed her was most your supermarkets, I think, more than anything else in this country, your A. & P. and the big, I guess you call them, supermarkets or whatever they are. And he told me something about him going to New Orleans, but I gathered that they were not too close. I believe he told me this, that he hadn't seen him in close to a year prior to this, or a good while. Now, it seemed to me like it was a year, and he said their families, they didn't have anything in common much, and he said, of course—I said "Do you think"—I said, "the evidence is pretty strong against your brother, what do you think about it?" He said, "Well, he is my brother, and I hate to think he would do this." He said, "I want to talk to him and ask him about it." Now, I never did see him. Roughly, that is about all I remember from that conversation. We rambled around for quite a bit. I know I was impressed because he got out and walked out the front of my office and in front of my office there were 15 or 20 press men wanting to ask him something, and he wouldn't say a word to them, he just walked off. I told him they would be out there, and he said, "I won't have anything to say." Mr. Dulles. Was this the morning after the assassination? Mr. Wade. Yes, sir; Saturday morning.
- 63. Mr. Dulles. Aboutwhat time? Mr. Wade. I would say between 9 and 10 is when I talked with him. And so the main purpose in the office, we believed, the main purpose of me and the lawyers in the office were briefing the law on whether to try Oswald for the murder of the President, whether you could prove the flight and the killing of Officer Tippit, which we became satisfied that we could, I mean from an evidentiary point of view. Mr. Rankin. By "we" who do you mean, in your office? Mr. Wade. Well, I think I had seven or eight in there, Bowie, and Alexander, and Dan Ellis, Jim Williamson, but there was a legal point. My office was open, but that, with reference to this case, there were other things going on, but in reference to this case, this is what we spent our time trying to establish whether that would be admissible or not. Mr. Rankin. Did you consult with any Federal officers in regard to how you should handle the case or what you should say about it at any time? Mr. Wade. No; I didn't discuss, consult with any of them. I did talk to some of the FBI boys and I believe there was an inspector. Mr. Rankin. Secret Service? Mr. Wade. No. Mr. Rankin. FBI? Mr. Wade. There was an inspector of the FBI who called me two or three times. I don't remember. Mr. Rankin. Did they tell you how to handle the case in any way? Mr. Wade. I don't think so. I mean it wasn't really up to them. Mr. Rankin. The only time you ever talked to Barefoot Sanders about it was in regard to this conspiracy, possibility of, that you have
- 64. already described? Mr. Wade.Frankly, that is hard to say. I think we talked off and on every day or two about developments in it, because, you see, well, I don't know whether we talked any more but before the killing by Ruby, but we had nearly a daily conversation about the files in the Oswald case, what we were going to do with them. You see, they were going to give them all to me, and at that stage we didn't know whether it was going to be a President's Commission or a congressional investigation or what. After the President's Commission was set up, I arranged through him and Miller here in the Justice Department that rather than give the files to me, to get the police to turn them over to the FBI and send them to you all, or photostat them and send them to you all. Barefoot and I talked frequently, but I don't know of anything significant of the Oswald angle that we discussed, and we spent the last 2 months trying to get some of the FBI files to read on the Ruby trial. I mean we talked a lot but I don't know anything further about Oswald into it or anything on Ruby of any particular significance. Mr. Rankin. Was Barefoot Sanders suggesting how you should handle the Oswald case except the time you already related? Mr. Wade. I don't recall him doing, suggesting that. Mr. Rankin. Any other Federal officers suggesting anything like that to you? Mr. Wade. The only thing I remember is the inspector of the FBI whom I don't think I ever met. I was there in the police one time during this shuffle, and I think it was some time Saturday morning, and he said they should have nothing, no publicity on the thing, no statements. Now, I don't know whether that was after Ruby shot Oswald or before, I don't know when it was, but I did talk with him and I know his concern which was that there was too much publicity. Mr. Rankin. And he told you that, did he?
- 65. Mr. Wade. Atsome stage in it. I am thinking it was Sunday night which I know I talked with him Sunday night, but we are not that far along with it yet. But I don't know whether I talked to him previously or not. Mr. Rankin. That is the only conversation of that type that you recall with any Federal officer? Mr. Wade. That is all I recall. I am sure Barefoot and I discussed the publicity angle on it some, but I don't remember Barefoot suggesting how we handle it, but neither one of us knew whether it was his offense or mine, to begin with, for 2 or 3 hours because we had to select it. Mr. Rankin. Do you know what Barefoot said about publicity when you did discuss it with him? Mr. Wade. I don't recall anything. Mr. Rankin. All right. What happened next, as you recall? Mr. Wade. I was going home. I went by the police station to talk to Chief Curry. Mr. Rankin. Did you discuss the evidence then? Mr. Wade. Well, at that time—you see, Chief Curry knew very little of the evidence at that stage. He should have known, but he didn't. But I discussed the thing with him and I told him there was too much evidence being put out in the case from his department, that I wish he would talk to Fritz and have no further statements on it. Mr. Rankin. What did he say about that? Mr. Wade. He said, "That is fine. I think that is so." Mr. Rankin. Now, going back just a moment, you spoke out about a map earlier that you had been told they had as evidence, do you recall, of the parade route. Did you look at the map at the time?
- 66. Mr. Wade. Idon't think I ever saw the map. Mr. Rankin. You don't know what it contained in regard to the parade route? Mr. Wade. I was told by Fritz that it had the parade route and it had an X where the assassination took place and it had an X out on Stemmons Freeway and an X at Inwood Road and Lemon, is all I know, a circle or some mark there. Mr. Rankin. But you have never seen the map? Mr. Wade. So far as I know, I have never seen the map. I don't know even where it was found, but I think it was found in his home, probably. But that is my recollection. But I don't even know that. I told Chief Curry this. Then I walked out, and Tom Pettit of NBC said, "We are all confused on the law, where we are really on this thing." Mr. Rankin. What did you say? Mr. Wade. At that time I said, "Well, I will explain the procedure, Texas procedure in a criminal case," and I had about a 10-minute interview there as I was leaving the chief's office, dealing entirely with the procedure, I mean your examining trial and grand jury and jury trial. I mean as to what takes place. You see, they had all kinds of statements and other countries represented and they were all curious to ask legal questions, when bond would be set and when it would be done. Mr. Rankin. Did you discuss the evidence at that time? Mr. Wade. No, sir; I refused. You will find that I refused to answer questions. They all asked questions on it, but I would tell them that is evidence and that deals with evidence in the matter. Mr. Rankin. Did you tell them why you wouldn't answer those questions? Mr. Wade. I told them we had to try the case, here, and we would have to try the case and we wouldn't be able to get a jury if
- 67. they knew allthe evidence in the case. You will find that in those interviews most, I think. I haven't seen them. As a matter of fact, didn't see them myself even. But I went home that day, and—— Mr. Dulles. That day is Saturday? Mr. Wade. Saturday; yes, sir. Mr. Rankin. About what time? Do you recall? Mr. Wade. I guess I got home 2:30 probably. I must have eaten on the way home or somewhere. Mr. Rankin. In the afternoon? Mr. Wade. Yes, sir; and I know I was amazed as I walked through the television room there and saw Chief Curry with that gun. You see, at that time they had not identified the gun as his gun, but he was telling about the FBI report on it. Mr. Rankin. Will you just describe what you saw there at that time? Mr. Wade. Well, I know he was in a crowd, and it seems to me like he had the gun, but on second thought I am not even sure whether he had the gun, but he was tracing the history of how that the gun was bought under the name, under an assumed name from a mail-order house in Chicago and mailed there to Dallas, and that the serial number and everything that had been identified, that the FBI had done that, something else. I believe they said they had a post office box here, a blind post office box that the recipients of that had identified as Oswald as the guy or something that received it. In other words, he went directly over the evidence connecting him with the gun. Mr. Rankin. You say there was a crowd there. Who was the crowd around him?
- 68. Mr. Wade. Newsmen.You see, I was at home. I was watching it on television. Mr. Rankin. I see. Did you do anything about that, then? Did you call him and ask him to quit that? Mr. Wade. No; I felt like nearly it was a hopeless case. I know now why it happened. That was the first piece of evidence he got his hands on before Fritz did. Mr. Rankin. Will you explain what you mean by that? Mr. Wade. Well, this went to the FBI and came to him rather than to Captain Fritz, and I feel in my own mind that this was something new, that he really had been receiving none of the original evidence, that it was coming through Fritz to him and so this went from him to Fritz, you know, and I think that is the reason he did it. So I stayed home that afternoon. I was trying to think, it seems like I went back by the police station some time that night, late at night. Mr. Rankin. This way of giving evidence to the press and all of the news media, is that standard practice in your area? Mr. Wade. Yes; it is, unfortunately. I don't think it is good. We have just, even since this happened we have had a similar incident with the police giving all the evidence out or giving out an oral confession of a defendant that is not admissible in court. You know, oral admissions are not generally admissible in Texas. And they gave all the evidence out in it. Mr. Rankin. Have you done anything about it, tried to stop it in any way? Mr. Wade. Well, in this actually, in the same story they quoted me as saying, I mean the news quoted me as saying they shouldn't give the information out, that is the evidence, we have got to try the case, we will get a jury, it is improper to do this, or something to that effect. So far as taking it up with—I have mentioned many times that they shouldn't give out evidence, in talking to the police
- 69. officers, I meanin there in training things, but it is something I have no control over whatever. It is a separate entity, the city of Dallas is, and I do a little fussing with the police, but by the same token it is not a situation where—I think it is one of your major problems that are going to have to be looked into not only here but it is a sidelight, I think, to your investigation to some extent, but I think you prejudice us, the state, more than you do the defense by giving out our testimony. You may think that giving out will help you to convict him. I think it works the other way, your jurors that read, the good type of jurors, get an opinion one way or another from what they read, and you end up with poor jurors. If they haven't read or heard anything of the case—well, not generally the same type of juror. The only thing I make a practice of saying is that I reviewed the evidence in this case in which the State will ask the death penalty, which may be going too far, but I tell them we plan to ask the death penalty or plan to ask life or plan to ask maximum jail sentence or something of that kind. Mr. Rankin. Did you say that at any time about the Oswald case? Mr. Wade. Oh, yes, sir; I have said that about both Oswald and Ruby. Mr. Rankin. When did you say it about the Oswald case? Mr. Wade. I guess it was Friday night probably. I was asked what penalty we would ask for. Mr. Rankin. When the police made these releases about the evidence, did they ever ask you whether they should make them? Mr. Wade. No, sir; like I told you. I talked Saturday morning around between 11 and 12, some time. I told him there was entirely too much publicity on this thing, that with the pressure going to be on us to try it and there may not be a place in the United States you can try it with all the publicity you are getting. Chief Curry said he
- 70. agreed with me,but, like I said about 2 hours later, I saw him releasing this testimony. Mr. Rankin. Did you consult any State officials about how you should handle either the Oswald or the Ruby case? Mr. Wade. I don't know. It seems like I talked to Waggoner Carr that night, but I don't remember. Didn't we talk some time about it? I don't know whether it was consulting about how to try it or anything. But I know I talked to Waggoner's office some time within 2 or 3 days, but I don't know whether it was before the Ruby assault or not. But he doesn't actually—— Mr. Rankin. Does the Texas attorney general have any jurisdiction to tell you how to try such cases? Mr. Wade. No sir; I think Waggoner will agree with that. They don't have any jurisdiction to try criminal cases other than antitrust, but I assume we would ask for their assistance if we wanted it. We don't generally, and I don't, the law doesn't contemplate that. Mr. Rankin. Mr. Carr didn't try to tell you in any way how to handle either case? Mr. Wade. Not that I know of. Mr. Carr. Off the record. (Discussion off the record.) Mr. Dulles. May we proceed. Mr. Rankin. Mr. Wade, will you give us the substance of what Mr. Carr said to you and what you said to him at that time? Mr. Wade. All I remember—I don't actually remember or know what night it was I talked to him but I assume it was that night because he did mention that the rumor was out that we were getting ready to file a charge of Oswald being part of an
- 71. international conspiracy, andI told him that that was not going to be done. It was late at night and I believe that is—— Mr. Dulles. It must have been Saturday night, wasn't it? Mr. Wade. No; that was Friday night. Mr. Dulles. Friday night. Mr. Wade. And I told him, and then I got a call, since this happened, I talked to Jim Bowie, my first assistant who had talked to, somebody had called him, my phone had been busy and Barefoot Sanders, I talked to him, and he—they all told that they were concerned about their having received calls from Washington and somewhere else, and I told them that there wasn't any such crime in Texas, I didn't know where it came from, and that is what prompted me to go down and take the complaint, otherwise I never would have gone down to the police station. Mr. Rankin. Did you say anything about whether you had evidence to support such a complaint of a conspiracy? Mr. Wade. Mr. Rankin, I don't know what evidence we have, we had at that time and actually don't know yet what all the evidence was. I never did see, I was told they had a lot of Fair Play for Cuba propaganda or correspondence on Oswald, and letters from the Communist Party, and it was probably exaggerated to me. I was told this. I have never seen any of that personally. Never saw any of it that night. But whether he was a Communist or whether he wasn't, had nothing to do with solving the problem at hand, the filing of the charge. I also was very, I wasn't sure I was going to take a complaint, and a justice of the peace will take a complaint lots of times because he doesn't have to try it. I knew I would have to try this case and
- 72. that prompted meto go down and see what kind of evidence they had. Mr. Rankin. Will you tell us what you mean by taking a complaint under your law. Mr. Wade. Well, a complaint is a blank form that you fill out in the name, by the authority of the State of Texas, and so forth, which I don't have here, but it charged, it charges a certain person with committing a crime, and it is filed in the justice court. The law permits the district attorney or any of his assistants to swear the witness to the charge. The only place we sign it is over on the left, I believe sworn to and subscribed to before me, this is the blank day of blank, Henry Wade, district attorney. Over on the right the complainant signs the complaint. We mean when we say take or accept a complaint is when we swear the witness and we draw it up ourselves and word it and take it. Mr. Rankin. Is that what you did in the Oswald-Ruby case? Mr. Wade. Yes, sir; we did that. Now, as a practical matter that is not really filing the complaints. The complaint is not really legally filed until a justice of the peace takes it and records it on his docket. Now, it goes to the justice of the peace court to clear the whole thing up and his purpose, he has—the law says you shall take him immediately before a magistrate, which is the justice of the peace. The courts have held that it is not necessary in Texas, but there is a statute that says that, and then he—his purpose is to hold an examining trial to see whether it is a bailable case or not. Then he sends it to the grand jury and the grand jury hears it and returns an indictment or a no bill and then it is in a certain court set with a docket number and then it is ours to try. Does that answer some of the questions? (At this point, Senator Cooper returned to the hearing room.)
- 73. Mr. Rankin. Whichroute did you follow in regard to the Oswald case? Mr. Wade. The same route. I accepted the complaint on him in the homicide department, and gave it to David Johnston, the justice of the peace who was there incidentally, or there in the homicide department. But I didn't actually type it up. I don't know who actually typed it up, somebody typed it up, but we file about a 100 a year, murders "did with malice aforethought." It was a straight murder indictment, murder with malice charge, and that was the procedure we followed in the Oswald case. Mr. Rankin. Why did you not include in that complaint a charge of an international conspiracy? Mr. Wade. Well, it is just like I said, it is surplusage to begin with. You don't need it. If you allege it you have to prove it. The U.S. attorney and the attorney general had called me and said that if it wasn't absolutely necessary they thought it shouldn't be done, and— Mr. Rankin. By the "attorney general" who do you mean? Mr. Wade. Mr. Carr. And actually it is never done. I mean, you see that got clear, apparently you had the press writing that up, radio or whoever was saying that was—had no idea about what murder was. Now, to write in there, assume he was, assume we could prove he was, a Communist, which I wasn't able to prove because all I heard was he had some literature there on him and had been in Russia, but assume I knew he was a Communist, can I prove it, I still wouldn't have alleged it because it is subject actually to be removed from the indictment because it is surplusage, you know, and all a murder indictment, the only thing that a murder indictment varies on is the method of what they used, did kill John Doe by shooting him with a gun or by stabbing him or by drowning him in water or how, the manner and means is the only thing that varies in
- 74. a murder indictment,all other wordage is the same. Does that clear that up? (Discussion off the record.) Senator Cooper. As I understand it, under Texas law there is no crime which is denominated under the term "international conspiracy." Mr. Wade. No, sir. Senator Cooper. I assume that conspiracy is a crime in Texas, isn't it, conspiracy to commit a crime? Mr. Wade. Conspiracy is a crime. It is a joining together of a group, your conspiracy where they enter into an agreement to commit a crime, and that is usually the one is indicted as a conspirator, the one who doesn't participate in the crime. Senator Cooper. My point is, though, that conspiracy is a crime under Texas law? Mr. Wade. Yes, sir; conspiracy to commit murder is a crime. Senator Cooper. Yes. Let me ask this question. Mr. Wade. Yes, sir. Senator Cooper. As I understand it then, one of the reasons that no warrant of indictment was rendered upon, touching upon an international conspiracy is that there is just no such crime in Texas as an international conspiracy? Mr. Wade. There was no such crime. If it was any such crime it would be a Federal rather than a State offense. If there is such crime as being a part of an international conspiracy it would deal with treason rather than murder, I would think. But there is no such thing as being a part of any organization that makes that it is a crime to commit murder. This was a straight murder charge.
- 75. If we wouldhave had four or five co-conspirators who conspired with him, planned the thing and could prove it we would have. That would have been a conspiracy to, conspiracy to commit murder. Senator Cooper. But conspiracy is not essential to the crime, to describe the person accused as belonging to any organization? Mr. Wade. No, sir; it is not necessary and it is entirely what they call surplusage. Senator Cooper. Now the last question, was there any evidence brought to you or any evidence of which you had knowledge upon which you could base an indictment or a warrant for conspiracy to commit murder in this case? Mr. Wade. No, sir; you mean parties other than Oswald? Senator Cooper. Yes. Mr. Wade. No. I might say on that score, to clear that up, I haven't seen any evidence along that line. I haven't even seen any of the correspondence that they had, allegedly had with the Communist Party here in New York or the Fair Play for Cuba, I haven't seen his little black book where he is supposed to have had the Russian Embassy's telephone numbers in it which I am sure you all have gone into it. I never did see the book, none of that. Of course, I have been told by a lot of people and undoubtedly a lot of it was exaggerated that he was a Communist, and you have had people say he was a Communist who might say I was a Communist, you know, if they didn't agree with me on something, so I have absolutely no evidence that he was a Communist of my own knowledge, I have heard a lot, of course. Mr. Dulles. What you are saying in this last answer relates to the present time, not only the way your knowledge has—— Mr. Wade. At that time and up to the present. Mr. Dulles. Rather than the day of assassination.
- 76. Mr. Wade. Ihave no evidence myself now that he was a Communist, or ever was a Communist, and I never did see what evidence that they had on him there gathered on him. I never saw any of the physical evidence in the Oswald case other than one or two statements, and I think I saw the gun while they were taking it out of there bringing it to Washington, because I told them at that stage, they didn't want to take it out, didn't want to let the FBI have it and I told them I thought they ought to let them bring it on up here that night and get it back the next night. There was arguing over that. I am getting off, rambling around, but their argument over that was they were still trying to identify the gun through a pawn broker or something like that and the police wanted to keep it but I said, "Let it go up there and they said they would have it back the next afternoon." Mr. Rankin. Have you ever had any evidence that Oswald was involved with anyone else in actually shooting the President? Mr. Wade. Well, I will answer that the same way. I have absolutely no evidence myself. Now, of course, I might have some type of opinion or some connection with reference to the Fair Play for Cuba and these letters that they told me about. If that was so there may have been some connection or may not, but I have no evidence myself on it. Mr. Rankin. Do you have any evidence as to whether Jack Ruby was involved with anyone else in the killing of Oswald? Mr. Wade. No, sir; I have no evidence on that. We have some and I think you have them all, some 8 or 10 witnesses who have said they had seen Ruby and Oswald together at various times. Some of them were, I know one of them during the trial was a lawyer there in Dallas, which I presume you all got his four-page statement, said he heard them discussing killing Connally a week before then, came out to my house and that had been sent to the FBI, and that was during the trial, and I gave him a lie detector which showed that he didn't have, this was a fanciful thing.
- 77. That, I can'tthink of his name, some of you all may know it, but he is a lawyer there in Dallas. Mr. Rankin. You found that was not anything you could rely on. Mr. Wade. I didn't use him as a witness and after giving him the polygraph I was satisfied that he was imagining it. I think he was sincere, I don't think he was trying—I don't think he was trying to be a hero or anything. I think he really thought about it so much I think he thought that it happened, but the polygraph indicated otherwise. Mr. Dulles. Did you have any other evidence than the polygraph on this point that he was not telling the truth or that this was a fiction? Mr. Wade. No, but I didn't—but I did see a report where the FBI interviewed the girl that was allegedly with him in Ruby's place in October, and she didn't corroborate all of it. I think she did say he was in there but I am not even sure of that. I didn't interview her but I just read a report on it. I read where they checked with the Department of Public Safety and they did not, were not able to—he said he reported all this to the Department of Public Safety, and I don't think they found any record of him reporting it. It is very difficult to get him to come in to see me. He didn't just walk in, this went on for a month, I kept hearing that there was a certain person knew about it and I kept telling him to come on and talk to me and he finally came out to my house late one night. The reason I think he actually must have thought it was so, but —I wasn't too interested in that theory of the case on this thing because I had a theory on this Ruby case from the start because I, even before you are going to get into some of these officers' testimony in a minute, but when this happened I was going home from church, and my own mind I said I believe that was Jack Ruby who shot him because from that Friday night, and from my theory has been from that Friday night, when he saw him there he made up his mind to kill him if he got a chance and I have had that—I didn't
- 78. even know aboutDean's testimony which you are going to hear today, I didn't know about his testimony until the day before I put him on the stand because I had not been preparing the evidence, I had been picking a jury for 2 weeks but that was my theory from the start. We had a waitress that I think you are all familiar with that was out at B&B Cafe at 3 a.m. on the 22d who said she served Ruby and Oswald there. B&B Cafe on Oak Lane, I know you have got that, I have seen it somewhere. I don't think she was ever given a polygraph test. You have about four homosexuals, I think that is probably the word, that have said they have seen them together places. There was some indication that Ruby was either bisexual or homosexual, but at least, I think they testified to that in the trial, I think by mistake. Belli asked the man, meant to ask him another word and says, he meant to say homicidal tendencies and he said homosexual tendencies and his one witness said yes, sir. That is in the record which you will get of the trial, I guess. Mr. Rankin. I understood you to say when you came home from church, after the killing of Oswald that you thought it was Ruby before you had heard that it was Ruby. Mr. Wade. You see, they announced Dallas businessman kills him. Mr. Rankin. Yes. Mr. Wade. I took my family, I was in church with the family. I took them on home and on the way down there they kept—they didn't say who it was but this ran through my mind, a businessman. I said that must be Jack Ruby the way he looked. He looked kind of wild to me down there Friday night the way he was running everywhere, you know, and I said to myself that must be him. I didn't tell my wife. You can't prove that. It is one of those things,
- 79. that was mytheory that he was likely the one. I couldn't, you know, out of a million people I couldn't say he was the one but when they announced his name I will say it didn't surprise me. Mr. Rankin. Mr. Chairman, what do you want to do about Mr. Carr? Senator Cooper. Mr. Wade, can you name to the Commission the names of the persons who told you or who stated in your presence that they had seen Lee Oswald and Jack Ruby together? Mr. Wade. Well—— Senator Cooper. Start out with the first one, his name. Mr. Wade. If anybody would mention the lawyer's name, I know him—he has run for the legislature a number of times. Senator Cooper. A lawyer who lives in Dallas? Mr. Wade. A lawyer in Dallas, and he has—we have, he made a four-page affidavit about this thing, and mailed it to J. Edgar Hoover. Senator Cooper. You can supply his name. Mr. Wade. We can supply his name and I would supply you with copies of his affidavit which I think you have. Don't you have it, isn't that up here? Senator Cooper. Without going into that in a moment, you can refresh your recollection and supply to the Commission the name of this lawyer. Mr. Wade. Yes, sir. Senator Cooper. Had he talked to you? Mr. Wade. Yes, sir. Senator Cooper. What did he say? Did he make a written statement to you or just talk to you? Mr. Wade. He handed me a written statement. He said, "The day after this happened I made this," it was a copy of a written
- 80. statement, he said,"I sent this to J. Edgar Hoover in Washington." I am talking to him, we will say, the 10th to the 20th of February, the first time I talked with him. He said, "I sent this to the FBI, to J. Edgar Hoover, special delivery air mail within a day or two after the assassination," and he left that and as far as I know I have got a copy of that, he left it with me. He talked to me at length there at my house, just us, and I would say at 11 o'clock at night, it was on a Sunday night I know, but what Sunday night I don't know. It was on a Sunday night in February. I read that statement over. It is a rather startling thing. It didn't ring true to me. It all deals with a conversation between Oswald and Ruby about killing John Connally, the Governor of Texas, over, he says, they can't get syndicated crime in Texas without they kill the Governor. I know enough about the situation, the Governor has practically nothing to do with syndicated crime. It has to be on a local, your district attorney and your police are the ones on the firing line on that, and they discussed at length killing him, how much they are going to pay him, "He wants five thousand, I believe or half of it now, and half of it when it is done." Don't you have this memorandum? Mr. Rankin. Yes. Mr. Wade. There is no use of me trying to give it to you. Senator Cooper. I was just personally trying to get your recollection about it. Mr. Wade. He told me this is what happened, and I said, "I can't put you on the stand without I am satisfied you are telling the truth because," I said, "We have got a good case here, and if they prove we are putting a lying witness on the stand, we might hurt us," and I said, "The only thing I know to do I won't put you on the stand but to take a polygraph to see if you are telling the truth or not."
- 81. He said, "Iwould be glad to." And I set it up and I later ran into him in the lawyers' club there and he handed me another memorandum which amplified on the other one, which all have been furnished to the attorney general or if we didn't lose it in the shuffle. This was during the trial actually, and then when the man called me he took a lie detector. There was no truth in it. That he was in the place. He was in the place, in Ruby's Carousel, but that none of this conversation took place. He said he was in one booth and Ruby was in another booth. Senator Cooper. Did anyone else tell you that they had seen Ruby and Oswald talking together? Mr. Wade. No one else personally has told me this. Senator Cooper. You mentioned a girl. Mr. Wade. No, I never talked to her but we had the Dallas Police take an affidavit from her and so did the FBI of that which is in all your files. What her name is, I just know it is a waitress out at the B&B Cafe. She lived in Mesquite, Tex., and some of my people interviewed her and she told them the same thing she told the FBI. The other information was in your FBI reports of where people or somebody who claimed he had seen them together in a YMCA, if I recall correctly, and another one in a store. The report indicated these, all these people were homosexuals as I believe, or there was an indication of that. I have an interview, in answering your question, in Lynn's first, but this is the only one I have talked personally about it. But the rest of them I got from reading the FBI and police files. Senator Cooper. Lynn? Mr. Wade. I believe that is his first name, and he is a lawyer there. Senator Cooper. He is the lawyer?
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