Vivek˜Kumar˜· Manoj˜Kumar Shivesh˜Sharma · Ram˜Prasad … · 2017. 9. 29. · Editors Vivek...
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Vivek Kumar · Manoj Kumar Shivesh Sharma · Ram Prasad Editors Probiotics in Agroecosystem
Transcript of Vivek˜Kumar˜· Manoj˜Kumar Shivesh˜Sharma · Ram˜Prasad … · 2017. 9. 29. · Editors Vivek...
Vivek Kumar · Manoj Kumar Shivesh Sharma · Ram Prasad Editors
Probiotics in Agroecosystem
Probiotics in Agroecosystem
Vivek Kumar • Manoj Kumar Shivesh Sharma • Ram PrasadEditors
Probiotics in Agroecosystem
EditorsVivek KumarHimalayan School of BiosciencesSwami Rama Himalayan UniversityJolly GrantDehradunUttarakhandIndia
Manoj KumarAmity Institute of Microbial TechnologyAmity UniversityNoidaUttar PradeshIndia
ISBN 978-981-10-4058-0 ISBN 978-981-10-4059-7 (eBook)DOI 10.1007/978-981-10-4059-7
Library of Congress Control Number: 2017953188
© Springer Nature Singapore Pte Ltd. 2017This 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, express 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.
Printed on acid-free paper
This Springer imprint is published by Springer NatureThe registered company is Springer Nature Singapore Pte Ltd.The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore
Shivesh SharmaDepartment of BiotechnologyMotilal Nehru National Institute
of TechnologyAllahabadUttar PradeshIndia
Ram PrasadAmity Institute of Microbial TechnologyAmity UniversityNoidaUttar PradeshIndia
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Preface
Probiotics in Agro-Ecosystems
As a general notion, probiotics are beneficial microbes for human health, and are, by definition, living microbes, which when administered appropriately confer a benefit to the host. Advertisements and recent research claim that probiotic products are good for our health, resulting in improved digestion, immunity, and manage-ment of allergies and colds. However, the probiotic prospective applications in nondairy- food products and agriculture have not received proper recognition. Presently there is increased interest in food and agricultural applications of probiot-ics, selection of new probiotic strains, and the development of new applications. The agricultural applications of probiotics with regard to animal, fish, and crop plants have increased steadily, yet a number of uncertainties concerning technological, microbiological, regulatory, and ignored aspects do exist.
Human systems obtain benefits from the beneficial bacteria of probiotics. Likewise, plants also reflect a dependency on certain eco-friendly microbes that act in symbiosis, i.e. plant strengtheners, bioinoculants, phytostimulators, and biopesti-cides, which eventually benefit human health and agro-ecosystems. The way these microbes are associated with or inhabit plant systems and the fate of their interac-tion are still poorly understood at a metabolic level. It most likely differs according to microbial plethora, age, and species of the plant, although numerous environmen-tal factors do influence this association.
Scientists have known for decades that legume plants harbor beneficial bacteria in nodules, which fix unavailable nitrogen into a form the plant can easily use. On the other hand, the plant root surface, especially the rhizosphere region, harbors diverse beneficial bacteria and fungi along with various types of endophytes, which are present in the host tissue. This endophytic plant relationship is a matter of adap-tation during the process of evolution. Plants have a restricted capacity to geneti-cally adapt to rapidly changing environmental conditions such as temperature, water stress, pathogens, or limited nutrient resources. Therefore, plants may use microbes that have the potential to evolve rapidly owing to their short life cycles and simple genetic material, and help the plant to overcome unfavorable conditions. During the
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process of selection, the host plant chooses or favors the right microbes for particu-lar conditions, which helps the plants to be healthier and competitive. In this way, it is comparable to humans taking probiotics to improve their health.
The increasing interest in the preservation of the environment and the health of consumers is demanding change in production methods and food consumption hab-its. Consumers demand functional foods because they contain bioactive compounds in bioavailable forms that are involved in health protection. To fulfill consumers’ demands, plants are inoculated with biofertilizers, which are linked to the roots or move inside them, thus acting as plant probiotics and to some extent they become reliable substitutes for chemical fertilizers.
These beneficial microbes are plant probiotics, which promote plant growth through diverse mechanisms such as phosphate solubilization, nitrogen fixation, phytohormone and siderophore production, and by mitigating abiotic and biotic stress. They act as vector carriers that take up unavailable nutrients, move them through the soil, and mobilize them to the root. This concept posits that less is wasted, whatever is available is utilized, and that less needs to be applied. The plant thrives in an environment of lower pollution, and nutrients taken up by the organisms are not available to be leached into the ground and surface waters. In addition, this concept creates a healthy soil that produces superior and healthy plants and involves much more than using only chemical inputs. Regular applica-tion of only synthetic inputs leads to reduced soil quality and fortifies plants with chemicals, which results in unhealthy produce, imparting negative effects on human health.
Health-conscious society has encouraged farmers and organic growers to adopt these microbial-based probiotic technologies to inoculate seeds/soils/roots to pro-vide nutrients like phosphate, nitrogen, and other phytostimulatory compounds. In addition, microorganisms have also attracted worldwide consideration owing to their role in disease management, drought tolerance, and remediation of polluted soils. Accordingly, selected and potentially selected microbial communities are pos-sible tools for sustainable crop production and can set a trend for a healthy future. Scientific researchers draw on multidisciplinary approaches to understanding the complexity and practical utility of a wide spectrum of microbes for the benefit of crops. The success of crop improvement, however, largely depends on the perfor-mance of microbes and the willingness and acceptance by growers to cooperate. A substantial amount of research has been carried out to highlight the role of microbes in the improvement of crops, but very little attempt is made to organize such find-ings in a way that can significantly help students, academics, researchers, and farmers.
“Plant Probiotics in Agro-Ecosystems” is conceptualized by experts providing a broad source of information on strategies and theories of probiotic microbes with sustainable crop improvement in diverse agro-ecosystems. The book presents strat-egies for nutrient fortification, adaptation of plants in contaminated soils, and miti-gating pathogenesis, and explores ways of integrating diverse approaches to accomplish anticipated levels of crop production under outdated and conventional
Preface
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agro-ecosystems. It is believed that the enthusiasm and noteworthy opportunities presented in this work regarding our recent understanding of the challenges and relationships that bring about learning plant probiotic and synergistic approaches towards plant and human health will inspire readers to push the field forward to new frontiers.
Dehradun, Uttarakhand, India Vivek KumarNoida, Uttar Pradesh, India Manoj Kumar Allahabad, Uttar Pradesh, India Shivesh SharmaNoida, Uttar Pradesh, India Ram Prasad
Preface
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Contents
1 Role of Endophytic Bacteria in Stress Tolerance of Agricultural Plants: Diversity of Microorganisms and Molecular Mechanisms . . . . 1Inga Tamosiune, Danas Baniulis, and Vidmantas Stanys
2 The Interactions of Soil Microbes Affecting Stress Alleviation in Agroecosystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31M. Miransari
3 Phosphate-Solubilizing Microorganisms in Sustainable Production of Wheat: Current Perspective . . . . . . . . . . . . . . . . . . . . . . 51Mohammed Saghir Khan, Asfa Rizvi, Saima Saif, and Almas Zaidi
4 Arbuscular Mycorrhization and Growth Promotion of Peanut (Arachis hypogaea L.) After Inoculation with PGPR . . . . . . . . . . . . . . . 83Driss Bouhraoua, Saida Aarab, Amin Laglaoui, Mohammed Bakkali, and Abdelhay Arakrak
5 Biosynthesis of Nanoparticles by Microorganisms and Their Significance in Sustainable Agriculture . . . . . . . . . . . . . . . . . . . . . . . . . 93Deepika Chaudhary, Rakesh Kumar, Anju Kumari, Rashmi, and Raman Jangra
6 Soil Microbiome and Their Effects on Nutrient Management for Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117Rosangela Naomi Inui Kishi, Renato Fernandes Galdiano Júnior, Silvana Pompéia Val-Moraes, and Luciano Takeshi Kishi
7 Rhizobacterial Biofilms: Diversity and Role in Plant Health . . . . . . . 145Mohd. Musheer Altaf, Iqbal Ahmad, and Abdullah Safar Al-Thubiani
8 How Can Bacteria, as an Eco-Friendly Tool, Contribute to Sustainable Tomato Cultivation?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163Vivian Jaskiw Szilagyi Zecchin and Átila Francisco Mógor
9 Development of Future Bio-formulations for Sustainable Agriculture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175Veluswamy Karthikeyan, Kulliyan Sathiyadash, and Kuppu Rajendran
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10 Plant Growth-Promoting Rhizobacteria and Its Role in Sustainable Agriculture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195Sunita J. Varjani and Khushboo V. Singh
11 Simultaneous P-Solubilizing and Biocontrol Activity of Rhizobacteria Isolated from Rice Rhizosphere Soil . . . . . . . . . . . . 207Saida Aarab, Francisco Javier Ollero, Manuel Megias, Amin Laglaoui, Mohammed Bakkali, and Abdelhay Arakrak
12 Efficient Nutrient Use and Plant Probiotic Microbes Interaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217Moses Awodun, Segun Oladele, and Adebayo Adeyemo
13 Exploring the Plant Microbiome Through Multi-omics Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233Rubén López-Mondéjar, Martin Kostovčík, Salvador Lladó, Lorena Carro, and Paula García-Fraile
14 Microbial Inoculants: A Novel Approach for Better Plant Microbiome Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269Satwant Kaur Gosal and Jupinder Kaur
15 Siderophores: Augmentation of Soil Health and Crop Productivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291Rizwan Ali Ansari, Irshad Mahmood, Rose Rizvi, Aisha Sumbul, and Safiuddin
16 Growth Stimulation, Nutrient Quality and Management of Vegetable Diseases Using Plant Growth-Promoting Rhizobacteria . . . . . . . . . . . 313Almas Zaidi, Mohammad Saghir Khan, Ees Ahmad, Saima Saif, and Asfa Rizvi
17 Azospirillum and Wheat Production . . . . . . . . . . . . . . . . . . . . . . . . . . . 329Mohammad Javad Zarea
18 Current Scenario of Root Exudate–Mediated Plant-Microbe Interaction and Promotion of Plant Growth . . . . . . . . . . . . . . . . . . . . 349Kanchan Vishwakarma, Shivesh Sharma, Vivek Kumar, Neha Upadhyay, Nitin Kumar, Rohit Mishra, Gaurav Yadav, Rishi Kumar Verma, and Durgesh Kumar Tripathi
19 Mycorrhiza: An Alliance for the Nutrient Management in Plants . . . 371Aisha Sumbul, Irshad Mahmood, Rose Rizvi, Rizwan Ali Ansari, and Safiuddin
20 Sustainable Management of Waterlogged Areas Through a Biodrainage and Microbial Agro-ecosystem . . . . . . . . . . . . . . . . . . . 387Kumud Dubey, Alok Pandey, Praveen Tripathi, and K.P. Dubey
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21 Traditional Ecological Knowledge-Based Practices and Bio-formulations: Key to Agricultural Sustainability . . . . . . . . . . . . . 407Seema B. Sharma
22 Influence of Arbuscular Mycorrhizal Fungal Effect and Salinity on Curcuma longa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 417B. Sadhana and S. Muthulakshmi
23 Microbes and Crop Production . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 437Priyanka Arora and Archana Tiwari
24 Probiotic Microbiome: Potassium Solubilization and Plant Productivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451Priyanku Teotia, Vivek Kumar, Manoj Kumar, Ram Prasad, and Shivesh Sharma
25 Earthworms and Associated Microbiome: Natural Boosters for Agro-Ecosystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469Khursheed Ahmad Wani, Mamta, Razia Shuab, and Rafiq A. Lone
26 Organic Farming, Food Quality, and Human Health: A Trisection of Sustainability and a Move from Pesticides to Eco-friendly Biofertilizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491Nitika Thakur
27 Role of Bioremediation Agents (Bacteria, Fungi, and Algae) in Alleviating Heavy Metal Toxicity . . . . . . . . . . . . . . . . . . . . . . . . . . . 517Zaid ul Hassan, Shafaqat Ali, Muhammad Rizwan, Muhammad Ibrahim, Muhammad Nafees, and Muhammad Waseem
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About the Editors
Vivek Kumar, PhD is Associate Professor, involved in teaching, research and guidance, with a pledge to enduring knowledge. Dr. Kumar works at Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, India. He obtained his Masters and Ph.D degrees from CCS Haryana Agricultural University, Hisar, Haryana, India. He serves as an editor and reviewer of several reputed inter-national journals. He has published 61 research papers, 30 book chapters, six review articles, and four books. Dr. Kumar has also served as a microbiologist for 8 years in the Department of Soil and Water Research, Public Authority of Agricultural Affairs and Fish Resources, Kuwait. He has been credited with first-time reporting and identification of pink rot inflorescence disease of the date palm in Kuwait caused by Serratia marcescens. He has also organized a number of conferences/workshops as convener/organizing secretary.
Dr. Kumar’s research areas are plant-microbe-interactions, environmental micro-biology, and bioremediation. He was awarded the ‘Young Scientist Award’ for the year 2002 in ‘Agricultural Microbiology’ by the Association of Microbiologists of India (AMI).
Manoj Kumar, PhD is a positive-minded scientist who has a passion for research and development, with a commitment to lifelong learning. He is devoted to high quality science that contributes broadly to both increasing the intellectual knowl-edge of plant development and to increasing the ecological niche. He has a high level of professional desire and intellectual curiosity, and the potential to fulfil the dream of his high impact publications and the future recognition of these by aca-demic peers.
Dr. Kumar completed his PhD in plant biotechnology at the prestigious Jawaharlal Nehru University and was then awarded two post-doctoral fellowships consecu-tively: i) DBT-PDF from IISc Bangalore in 2005 and then NRF-PDF from University of Pretoria.
Dr. Manoj Kumar is a researcher of plant biotechnology in the Amity University Uttar Pradesh, India. His present research goal is to understand the metabolic fate of microbial-mediated precursors in whole plant physiology and genetics through pro-cesses occurring at the level of metabolism, particularly through processes of
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rhizosphere communication under in situ and in vitro plant conditions. Many gradu-ate and undergraduate students who have worked with him have been placed in prestigious organizations worldwide.
Dr. Kumar has published his research work in many prestigious journals and played the role of reviewer for many of his peers.
Shivesh Sharma, PhD is Associate Professor and Head of the Department of Biotechnology at Motilal Nehru National Institute of Technology (MNNIT), Allahabad, Uttar Pradesh, India. Dr. Shivesh Sharma has completed his Masters and Ph.D. in the field of Microbiology. His research interests include environ-mental microbiology/biotechnology, plant-microbe interaction and bioformula-tions. Before joining MNNIT Allahabad, Dr. Shivesh Sharma worked at S.B.S (PG) Institute of Biomedical Sciences and Research, Balawala, Dehradun Uttarakhand from 2002–2009. He has been involved in a number of research projects funded both externally (DBT, UGC, DST, MHRD) and internally in the fields of his research interests. His teaching interests include microbiology, environmental microbiology/biotechnology, food biotechnology, bacteriology, and IPR.
He has successfully supervised seven Ph.D., eight M. Tech. and 28 M.Sc. stu-dents. He has more than 80 publications in different research journals and various book chapters to his credit. He has also organized various outreach activities.
Ram Prasad, PhD is Assistant Professor at the Amity University, Uttar Pradesh, India. Dr. Prasad completed his Ph.D. from the Department of Microbiology, Chaudhary Charan Singh University, Meerut, UP, India, in collaboration with the School of Life Sciences, Jawaharlal Nehru University (JNU), New Delhi, India. Dr. Prasad received his M.Sc. in Life Sciences at JNU and also qualified CSIR-NET, ASRB-NET, and GATE. His research interest includes plant-microbe inter-actions, sustainable agriculture, and microbial nanobiotechnology. Dr. Prasad has 93 publications to his credit including research papers and book chapters, five patents issued or pending, and has edited or authored several books. Dr. Prasad has 11 years of teaching experience and he has been awarded the Young Scientist Award (2007) and Prof. J.S. Datta Munshi Gold Medal (2009) by the International Society for Ecological Communications; FSAB fellowship (2010) by the Society for Applied Biotechnology; Outstanding Scientist Award (2015) in the field of Microbiology by Venus International Foundation, and the American Cancer Society UICC International Fellowship for Beginning Investigators (USA, 2014). In 2014–2015, Dr. Prasad served as Visiting Assistant Professor in the Department of Mechanical Engineering at Johns Hopkins University, USA.
About the Editors
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Contributors
Saida Aarab Département de Biologie, Faculté des Sciences et Techniques d’Al Hoceima, Al Hoceima, Morocco
Equipe de Recherche de Biotechnologies et Génie des Biomolécules (ERBGB), Faculté des Sciences et Techniques de Tangier, Tangier, Morocco
Adebayo Adeyemo Department of Crop, Soil and Pest Management, Federal University of Technology, Akungba-Akoko, Ondo State, Nigeria
Department of Agronomy, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
Ees Ahmad Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Iqbal Ahmad Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
Shafaqat Ali Department of Environmental Sciences and Engineering, Government College University, Faisalabad, Pakistan
Mohd Musheer Altaf Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
Abdullah Safar Al-Thubiani Department of Biology, Umm Al-Qura University, Makkah, Saudi Arabia
Rizwan Ali Ansari Section of Plant Pathology and Nematology, Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Abdelhay Arakrak Equipe de Recherche de Biotechnologies et Génie des Biomolécules (ERBGB), Faculté des Sciences et Techniques de Tangier, Tangier, Morocco
Priyanka Arora School of Sciences, Noida International University, Greater Noida, India
Moses Awodun Department of Crop, Soil and Pest Management, Federal University of TechnologyAkure, OndoState, Nigeria
Department of Agronomy, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
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Mohammed Bakkali Equipe de Recherche de Biotechnologies et Génie des Biomolécules (ERBGB), Faculté des Sciences et Techniques de Tangier, Tangier, Morocco
Danas Baniulis Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Babtai, Lithuania
Driss Bouhraoua Equipe de Recherche de Biotechnologies et Génie des Biomolécules (ERBGB), Faculté des Sciences et Techniques de Tangier, Tangier, Morocco
Lorena Carro School of Biology, Newcastle University, Tyne, UK
Deepika Chaudhary Department of Microbiology, CCS Haryana Agricultural University Hisar, Haryana, India
Kumud Dubey Centre for Social Forestry and Eco-Rehabilitation, Allahabad, Uttar Pradesh, India
K.P. Dubey CCF/General Manager, (East), Uttar Pradesh Forest Corporation Allahabad, Allahabad, Uttar Pradesh, India
Renato Fernandes Galdiano Júnior Department of Technology, State Paulista University – UNESP, São Paulo, Brazil
Paula García-Fraile Institute of Microbiology of the CAS, v. v. i, Vestec, Czech Republic
Satwant Kaur Gosal Department of Microbiology, Punjab Agricultural University, Ludhiana, India
Zaid ul Hassan Department of Environmental Sciences and Engineering, Government College University, Faisalabad, Pakistan
Muhammad Ibrahim Department of Environmental Sciences and Engineering, Government College University, Faisalabad, Pakistan
Rosangela Naomi Inui Kishi Department of Technology, State Paulista University – UNESP, São Paulo, Brazil
Veluswamy Karthikeyan Centre for Research, Department of Botany and Biotechnology, Thiagarajar College, Madurai, Tamil Nadu, India
Jupinder Kaur Department of Microbiology, Punjab Agricultural University, Ludhiana, India
Mohd Saghir Khan Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Mohammad Saghir Khan Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Contributors
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Luciano Takeshi Kishi Department of Technology, State Paulista University – UNESP, São Paulo, Brazil
Martin Kostovčík Institute of Microbiology of the CAS, v. v. i, Vestec, Czech Republic
Manoj Kumar Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, India
Nitin Kumar Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, Uttar Pradesh, India
Rakesh Kumar Department of Microbiology, CCS Haryana Agricultural University Hisar, Hisar, Haryana, India
Vivek Kumar Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India
Anju Kumari Centre of Food Science and Technology CCS Haryana Agricultural University Hisar, Hisar, Haryana, India
Amin Laglaoui Equipe de Recherche de Biotechnologies et Génie des Biomolécules (ERBGB), Faculté des Sciences et Techniques de Tangier, Tangier, Morocco
Salvador Lladó Institute of Microbiology of the CAS, v. v. i, Prague, Czech Republic
Rafiq A. Lone School of Studies in Botany, Jiwaji University, Gwalior, Madhya Pradesh, India
Department of Natural Sciences, SBBS University, Khiala (Padhiana), Jalandhar, Punjab, India
Rubén López-Mondéjar Institute of Microbiology of the CAS, v. v. i, Vestec, Czech Republic
Mamta Department of Environmental Science, Jiwaji University, Gwalior, Madhya Pradesh, India
Irshad Mahmood Section of Plant Pathology and Nematology, Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Manuel Megias Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
Inga Tamosiune Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Babtai, Lithuania
M. Miransari Department of Book & Article, AbtinBerkeh Scientific Ltd. Company, Isfahan, Iran
Rohit Mishra Centre for Medical Diagnostic and Research MNNIT, Allahabad, Uttar Pradesh, India
Contributors
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Átila Francisco Mógor Federal University of Paraná, Department of Plant Science and Crop Protection, Curitiba, Paraná, Brazil
S. Muthulakshmi P.G and Research Centre, Department of Botany, Thiagarajar College, Madurai, Tamil Nadu, India
Muhammad Nafees Institute of Soil & Environmental Sciences. University of Agriculture Faisalabad, Faisalabad, Pakistan
Segun Oladele Department of Crop, Soil and Pest Management, Federal University of Technology, Akungba-Akoko, Ondo State, Nigeria
Department of Agronomy, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
Francisco Javier Ollero Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
Alok Pandey Centre for Social Forestry and Eco-Rehabilitation, Allahabad, Uttar Pradesh, India
Ram Prasad Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, India
Kuppu Rajendran Center for Research, Department of Botany and Biotechnology, Thiagarajar College, Madurai, Tamil Nadu, India
Raman Jangra Department of Microbiology, CCS Haryana Agricultural University Hisar, Haryana, India
Rashmi Department of Microbiology, CCS Haryana Agricultural University Hisar, Haryana, India
Asfa Rizvi Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Rose Rizvi Section of Plant Pathology and Nematology, Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Muhammad Rizwan Department of Environmental Sciences and Engineering, Government College University, Faisalabad, Pakistan
B. Sadhana P.G and Research Centre, Department of Botany, Thiagarajar College, Madurai, Tamil Nadu, India
Safiuddin Section of Plant Pathology and Nematology, Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Saima Saif Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Kulliyan Sathiyadash Center for Research, Department of Botany and Biotechnology, Thiagarajar College, Madurai, Tamil Nadu, India
Contributors
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Seema B. Sharma Department of Earth and Environmental Science, KSKV Kachchh University, Gujarat, India
Shivesh Sharma Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Uttar Pradesh, India
Centre for Medical Diagnostic and Research MNNIT, Allahabad, Uttar Pradesh, India
Razia Shuab School of Studies in Botany, Jiwaji University, Gwalior, Madhya Pradesh, India
Khushboo V. Singh Department of Microbiology, Gujarat University, Ahmedabad, Gujarat, India
Vidmantas Stanys Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Babtai, Lithuania
Aisha Sumbul Section of Plant Pathology and Nematology, Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Vivian Jaskiw Szilagyi Zecchin Federal University of Paraná, Department of Plant Science and Crop Protection, Curitiba, Paraná, Brazil
Priyanku Teotia Department of Botany, CCS University, Meerut, India
Nitika Thakur Shoolini University of Biotechnology and Management Sciences, Solan, HP, India
Archana Tiwari School of Sciences, Noida International University, Greater Noida, India
Praveen Tripathi Centre for Social Forestry and Eco-Rehabilitation, Allahabad, Uttar Pradesh, India
Neha Upadhyay Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, Uttar Pradesh, India
Silvana Pompéia Val-Moraes Department of Technology, State Paulista University – UNESP, São Paulo, Brazil
Sunita J. Varjani School of Biological Sciences and Biotechnology, University and Institute of Advanced Research, Gandhinagar, Gujarat, India
Rishi Kumar Verma Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, Uttar Pradesh, India
Kanchan Vishwakarma Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, Uttar Pradesh, India
Khursheed Ahmad Wani Department of Environmental Science, ITM University, Gwalior, Madhya Pradesh, India
Contributors
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Muhammad Waseem Department of Microbiology, Government College University, Faisalabad, Pakistan
Gaurav Yadav Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, Uttar Pradesh, India
Centre for Medical Diagnostic and Research MNNIT, Allahabad, Uttar Pradesh, India
Almas Zaidi Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
Mohammad Javad Zarea Faculty of Agriculture, University of Ilam, Ilam, Iran
Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
Contributors
1© Springer Nature Singapore Pte Ltd. 2017V. Kumar et al. (eds.), Probiotics in Agroecosystem, DOI 10.1007/978-981-10-4059-7_1
1Role of Endophytic Bacteria in Stress Tolerance of Agricultural Plants: Diversity of Microorganisms and Molecular Mechanisms
Inga Tamosiune, Danas Baniulis, and Vidmantas Stanys
AbstractBacterial endophytes are a group of endosymbiotic microorganisms widespread among plants. An association of plants with endophytic bacteria includes a vast diversity of bacterial taxa and host plants. In this review we present an overview of taxonomic composition of the bacterial endophytes identified in common agricultural crops with special emphasis on the most recent results obtained using metagenomic analysis. Endophytic microbiome constitutes a part of larger soil microbial community and is susceptible to direct or indirect effect of agricul-tural practices: soil tillage, irrigation, use of pesticides and fertilizers has a major effect on function and structure of soil and endophytic microbial populations. Therefore, the use of agricultural practices that maintain natural diversity of plant endophytic bacteria becomes important element of sustainable agriculture that ensures plant productivity and quality of agricultural production. On the other hand, the endophytic microbiome itself have been shown to have multiple effects on their host plant, including modulation of phytohormone signaling, metabolic activity, and plant defense response pathways. It has been demon-strated that these effects could be helpful for plant adaptation to abiotic or biotic stresses. Therefore, application of endophytic bacteria to improve crop perfor-mance under cold, drought, salinity, and heavy metal contamination stress condi-tions or to enhance disease resistance presents an important potential for sustainable agricultural production.
I. Tamosiune • D. Baniulis • V. Stanys (*) Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas str. 30, Babtai, Kaunas reg, Lithuaniae-mail: [email protected]; [email protected]; [email protected]
2
1.1 Introduction
An intensification of agricultural production has been crucial in sustaining popula-tion growth throughout civilization history (Ellis et al. 2013). During the last cen-tury, the agricultural intensification has been largely achieved through improvement in crop productivity and the use of farm equipment, irrigation, intensive tillage, fertilizers, pesticides, and other manufactured inputs (Foley et al. 2005; 2011). However, these agricultural practices often lead to detrimental effects on environ-ment as well as human health. Therefore, new environmentally benign pathways have to be employed to maintain increase in agricultural production while greatly reducing unsustainable uses of water, nutrients, and agricultural chemicals. This requires new means to overcome threats that cause loss of crop yield, including plant stresses associated with unfavorable environmental conditions, such as drought, temperature extremes, or soil salinity, as well as biotic stress induced by plant pathogens and pests. Therefore, the attention is drawn to exploitation of mutu-alistic and antagonistic biotic interactions within agroecosystems that would increase crop productivity and improve sustainability of pest control technologies (Gaba et al. 2014).
Plants live in intimate association with microorganisms that fulfill important functions in agricultural ecosystems and represent an important resource for improvement of plant performance through enhancing crop nutrition or reducing damages caused by pathogens or environmental stress (Jha et al. 2013; Singh et al. 2011). Bacteria constitute the most numerous group of microorganisms in soil (Whitman et al. 1998). They exist as free-living organisms, attached to the surface of roots or phyllosphere, and establish interactions with plants. The extreme forms of plant–microbe interactions could be categorized into commensal (acquire nutri-ents from the plant without damaging), mutualistic (positively influence plant health), and pathogenic (damage plant) type, yet many microorganisms exploit dif-ferent forms of relationship with plants during their life cycles (Newton et al. 2010). Endophytic bacteria are a group of endosymbiotic microorganisms that live in inter-nal plant tissues of apparently healthy host plants and do not normally cause any substantial disease symptoms (Schulz and Boyle 2006).
Endophytic bacteria colonize intercellular spaces of the cell walls and xylem vessels of plant roots, stems, and leaves, and they are also found in tissues of flowers (Compant et al. 2011), fruits (de Melo Pereira et al. 2012), and seeds (Cankar et al. 2005; Johnston-Monje and Raizada 2011; Trognitz et al. 2014). Meanwhile it is generally believed that endophytic bacteria reside in apoplast of plant cells, several studies of intracellular colonization of cytosol have been published (Cocking et al. 2006; Koskimaki et al. 2015; Thomas and Sekhar 2014; White et al. 2014). Plant roots have been established as the main entry point of the potential endophytes from soil and provide a base camp for colonization of other plant organs. Higher density of endophyte populations is characteristic to plant roots and other belowground tis-sues as compared to phyllosphere, and an ascending migration of endophytic bacte-ria from roots to leaves of rice plants has been demonstrated (Chi et al. 2005). It has been also shown that plant roots are capable to take up bacteria from surrounding
I. Tamosiune et al.
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environment (Paungfoo-Lonhienne et al. 2010). Isolation of endophytic bacteria from seeds suggests an alternative transmission route (Cankar et al. 2005; Johnston- Monje and Raizada 2011; Trognitz et al. 2014). Structure of the endophytic com-munity is defined by abiotic and biotic factors such as environmental conditions, microbe–microbe interactions, and plant–microbe interactions (Ryan et al. 2008).
Diverse effects of endophytic bacteria on plant health and growth have been well documented. The endophytes aid nutrient availability and uptake, enhance stress tolerance, and provide disease resistance (Hamilton et al. 2012; Ryan et al. 2008). The plant growth-promoting capability of endophytes is established through activ-ity that increases accessibility of nutrients, such as nitrogen and phosphorus, or is mediated by compounds produced by the microorganisms and the host cells, such as plant growth hormones (Brader et al. 2014; Glick 2012; Reinhold-Hurek and Hurek 2011). Disease protection properties are associated with ability of endophytic bacteria to produce compounds, such as antibiotics and fungal cell-wall lytic enzymes, which can inhibit growth of plant pathogens (Brader et al. 2014; Christina et al. 2013; Raaijmakers and Mazzola 2012; Wang et al. 2014) or priming plant response to pathogens by induced systemic resistance (ISR) mechanism (Pieterse et al. 2014). Owing to their plant growth-promoting and disease control properties, endophytes can be used in the form of bioinoculants in agriculture to benefit devel-opment of sustainable agricultural production practices (Mei and Flinn 2010).
The aim of this review is to outline the understanding about diversity of endo-phytic bacterial communities of agricultural crops and their implication in plant adaptation to stress and disease resistance. We provide a summary of the extensive information on taxonomic composition of bacterial endophytes identified in major agricultural crop plants that has been remarkably expanded due to application of advanced metagenomic analysis methods. Effect of different agricultural practices on the diversity of endophytic bacterial communities is assessed. Further, an impli-cation of endophytes in plant adaptation to stress and disease resistance through modulation of phytohormone balance or induction of stress-related metabolites or systemic resistance signaling pathway is presented.
1.2 Assessment of Diversity of Bacterial Endophytes Using Cultivation Techniques and Metagenomic Analysis
Plants are naturally associated with continuum of other organisms, the majority of which are bacterial endophytes. Population densities of endophytic bacteria are extremely variable in different plants and tissues and have been shown to vary from hundreds to reaching as high as 9 × 109 of bacteria per gram of plant tissue (Chi et al. 2005; Jacobs et al. 1985; Misaghi and Donndelinger 1990). Initial studies of diversity of endophyte community were mostly based on the classic microbial cul-ture techniques; therefore, bacterial endophytes isolated using surface sterilization methods have been reported for most species of agricultural plants (Rakotoniriana et al. 2013). One of the early reviews by Hallman et al. (1997) presented the list of isolated bacterial endophytes from various plant parts of different agricultural crops.
1 Role of Endophytic Bacteria in Stress Tolerance of Agricultural Plants
4
The list was supplemented by latter studies on endophyte diversity (Bacon and Hinton 2007; Lodewyckx et al. 2002; Rosenblueth and Martinez-Romero 2006; Ryan et al. 2008; Sturz et al. 2003).
Innovative culture-independent sequencing technologies allow much deeper assessment of microbial communities and improve our understanding about diverse microbiomes occupying plants. In recent years, extensive information about diversity of endophytic microbiota has been gathered using metagenomic sequencing platforms. Application of hypervariable regions from small subunit ribosomal RNA gene (16S rRNA) for the metagenomic sequencing allows precise taxonomic identification (Turner et al. 2013). Direct amplification of microbial DNA from plant tissue samples and application of modern bioinformatics tools allow analysis of growing numbers of plant material samples, and such studies have revealed rarely reported endophyte species of δ- and ε-Proteobacteria (Sun et al. 2008). In addition, culture-independent high-throughput sequencing tech-nologies reflect variations of total microbial diversity and their physiological potential and ecological functions (Akinsanya et al. 2015; Turner et al. 2013; van Overbeek and van Elsas 2008). For example, Tian and associates (Tian et al. 2015) used second-generation sequencing technology to assess diversity of bacterial endophytes before and after nematode attack, and the study revealed that nema-tode infection was associated with variation and differentiation of the endophyte bacterial populations.
Studies of microbial diversity using culture-independent molecular techniques could be limited by relatively low abundance of endophytic bacteria that results in underrepresentation in metagenomic library. This problem is associated with diffi-culties in separation and high sequence homology of endophytic bacteria, plant nuclei, plastids, mitochondria, and plant-associated microbial DNA (Govindasamy et al. 2014). In recent years, gene enrichment strategies have been broadly used. Bacterial DNA extraction from host plant tissues and enrichment is the key step in preparation of the metagenomic library harboring representative sample of micro-bial diversity. In order to recover target genes of metagenome, a suitable enrichment method should be used before DNA amplification (Mutondo et al. 2010). Jiao et al. (2006) enriched target genes from a metagenome by optimized hydrolysis of the plant cell walls, followed by differential centrifugation. Wang et al. (2008) effi-ciently enriched bacterial DNA from medicinal plant by specific enzymatic treat-ment. The same method increased representation of less abundant grapevine-associated bacteria (Bulgari et al. 2009). Series of differential centrifuga-tion steps followed by a density gradient centrifugation efficiently enriched propor-tion of microbial DNA in stems of soybean (Ikeda et al. 2009). Maropola and colleagues (2015) analyzed the impact of metagenomic DNA extraction procedures on the endophytic bacterial diversity in sorghum and found that different DNA extraction methods introduce significant biases in community diversities. The authors stated that despite the differences in results of extraction of DNA, the agri-culturally important genera such as Microbacterium, Agrobacterium, Sphingobacterium, Herbaspirillum, Erwinia, Pseudomonas, and Stenotrophomonas were predominant. An enrichment method useful for extraction of plant-associated
I. Tamosiune et al.
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bacteria of potato tubers was developed by Nikolic et al. (2011) and involved over-night shaking of small pieces of potato tubers in sodium chloride solution.
Although 16S rRNA gene clone library technique provides efficient means to study different agricultural plant microbiota in detail (genetics and physiology), however, not all endophytes are easily amenable using this method as well (Sessitsch et al. 2012). The methods for microbe enrichment in plant tissues may lead to over-representation of high-abundance bacterial species and reduced representation of low-abundance species. Therefore, a combination of microbial cultivation and culture- independent metagenomic analysis methods provides broader perspective of the diversity of endophytes.
A summary of the most widespread bacterial isolates identified in common agri-cultural crop plants is presented in Table 1.1. Due to a vast diversity of bacterial species and host plants described to this day, the list is not complete and presents a sample of important agricultural crops and overview of associated endophytic bacte-rial species identified using both, cultivation and metagenomic, analysis methods.
A study of direct comparison of culture-dependent and culture-independent approaches for assessing bacterial communities in the phyllosphere of apple has been published by Yashiro et al. (2011). Among the cultivated isolates only order of Actinomycetales has been found, while metagenomic approach has revealed the presence of Bacteroidales, Enterobacteriales, Myxococcales, and Sphingobacteriales. Differences between plant-associated microbial phyla are revealed when comparing the niches of rhizosphere, endosphere, and phyllosphere. The largest diversity is found in the roots, as it is the primary site of interaction between plants and soil microorganisms (Hardoim et al. 2011). Maropolla and colleagues (2015) found that diversity of sorghum-associated endophytic bacteria is lower in stems than that of rhizospheric communities. Rhizospheric endophytic species mostly belong to α-, β-, and γ-Proteobacteria subgroups and are closely related to epiphytic species (Kuklinsky-Sobral et al. 2004). The group of γ-Proteobacteria is found to be the most diverse. Culture-dependent methods revealed bacteria species that belong to the Proteobacteria, meanwhile Firmicutes, Actinobacteria, and also Bacteroides are less common (Reinhold-Hurek and Hurek 2011).
Culture-independent approach suggests a 100–1000-fold higher diversity of the bacterial communities in economically important crops (Suman et al. 2016; Turner et al. 2013). Sessitsch with associates (Chi et al. 2005) investigated genomic char-acteristics of the most abundant bacterial endophytes colonizing rice roots under field conditions without cultivation bias. In this study, the members of γ-Proteobacteria, comprising mostly Enterobacter-related endophytes, were pre-dominant. Metagenomic analyses demonstrated that rhizobia (and other α-Proteobacteria) were the most abundant plant-associated endophytes, including β-Proteobacteria, γ-Proteobacteria, and Firmicutes (Turner et al. 2013). However, it was found that only culture-independent techniques were able to identify endo-phytic archaea (Euryarchaeota) (Suman et al. 2016). In general, the species of Pseudomonas, Bacillus, Enterobacter, Klebsiella, Rhizobium, Sphingomonas, Pantoea, Microbacterium, Acinetobacter, Erwinia, and Arthrobacter were defined as the most dominant using both methods.
1 Role of Endophytic Bacteria in Stress Tolerance of Agricultural Plants
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Tab
le 1
.1
End
ophy
tic b
acte
ria
isol
ated
fro
m c
omm
on a
gric
ultu
ral c
rop
spec
ies
plan
ts
Phyl
umSu
bgro
upG
enus
Oni
onSo
rghu
mW
heat
Ric
eSu
garc
ane
Mai
zePo
tato
Tom
ato
Soyb
ean
Stra
wbe
rry
Suga
r be
etB
ean
Pepp
erC
arro
tG
rape
vine
Pro
teob
acte
ria
αA
grob
acte
rium
sp.
■■
■■
■B
rady
rhiz
obiu
m s
p.■
■■
■B
revu
ndim
onas
sp.
■■
■■
■■
Cau
loba
cter
sp.
■■
■D
evos
ia s
p.■
■■
Mes
orhi
zobi
um s
p.■
■■
Met
hylo
bact
eriu
m
sp.
■■
■■
■■
Nov
osph
ingo
bium
sp
.■
■
Nov
osph
ingo
bium
sp
.■
■
Rhi
zobi
um s
p.■
■■
■■
■■
Rho
dops
eudo
mon
as
sp.
■■
Sino
rhiz
obiu
m s
p.■
■■
■Sp
hing
omon
as s
p.■
■■
■■
■■
■Sp
hing
opyx
is s
p.■
■β
Ach
rom
obac
ter
sp.
■■
■■
Aci
dovo
rax
sp.
■■
Bur
khol
deri
a sp
.■
■■
■■
■■
Com
amon
as s
p.■
■■
■D
elft
ia s
p.■
■■
■D
ugan
ella
sp.
■■
■G
alli
onel
la s
p.■
■
I. Tamosiune et al.
7
Her
basp
iril
lum
sp.
■■
■■
■R
alst
onia
sp.
■■
■■
Vari
ovor
ax s
p.■
■■
■■
γA
cine
toba
cter
sp.
■■
■■
■■
Azo
toba
cter
sp.
■■
Ent
erob
acte
r sp
.■
■■
■■
■■
■■
Erw
inia
sp.
■■
■■
■■
Kle
bsie
lla
sp.
■■
■■
■■
■■
Klu
yver
a sp
.■
■P
anto
ea s
p.■
■■
■■
■■
Pse
udom
onas
sp.
■■
■■
■■
■■
■■
■■
■■
■P
sych
roba
cter
sp.
■■
Serr
atia
sp.
■■
■■
■St
enot
roph
omon
as
sp.
■■
■■
■■
■■
Xan
thom
onas
sp.
■■
■■
■G
eoba
cter
sp.
■■
■Sy
ntro
phus
sp.
■■
Fir
mic
utes
Bac
illu
s sp
.■
■■
■■
■■
■■
■■
■■
Bre
viba
cill
us s
p.■
■■
Clo
stri
dium
sp.
■■
■E
xigu
obac
teri
um s
p.■
■L
acto
baci
llus
sp.
■■
Lysi
niba
cill
us s
p.■
■■
■■
Pae
niba
cill
us s
p.■
■■
■■
■■
■St
aphy
loco
ccus
sp.
■■
■■
■■
(con
tinue
d)
1 Role of Endophytic Bacteria in Stress Tolerance of Agricultural Plants
8
Act
inob
acte
ria
Act
inom
yces
sp.
■■
Am
ycol
atop
sis
sp.
■■
Art
hrob
acte
r sp
.■
■■
■■
■A
ureo
bact
eriu
m s
p.■
■B
rach
ybac
teri
um s
p.■
■C
lavi
bact
er s
p.■
■■
Cor
yneb
acte
rium
sp
.■
■■
■■
Cur
toba
cter
ium
sp.
■■
■■
■D
acty
losp
oran
gium
sp
.■
■
Fra
nkia
sp.
■■
Koc
uria
sp.
■■
■M
icro
bact
eriu
m s
p.■
■■
■■
■■
■■
Mic
roco
ccus
sp.
■■
■■
■■
Mic
rom
onos
pora
sp.
■■
■M
ycob
acte
rium
sp.
■■
Noc
ardi
oide
s sp
.■
■R
hodo
cocc
us s
p.■
■■
■■
Rot
hia
sp.
■St
rept
omyc
es s
p.■
■■
■■
Chr
yseo
bact
eriu
m
sp.
■■
■
Tab
le 1
.1
(con
tinue
d)
Phyl
umSu
bgro
upG
enus
Oni
onSo
rghu
mW
heat
Ric
eSu
garc
ane
Mai
zePo
tato
Tom
ato
Soyb
ean
Stra
wbe
rry
Suga
r be
etB
ean
Pepp
erC
arro
tG
rape
vine
I. Tamosiune et al.
9
Cyt
opha
gale
s sp
.■
■F
lavo
bact
eriu
m s
p.■
■■
■■
■■
Ped
obac
ter
sp.
■■
■■
Sphi
ngob
acte
rium
sp
.■
■■
■
Oni
on (
All
ium
cep
a L
.) (
From
mel
et a
l. 19
91; W
eilh
arte
r et
al.
2011
), s
orgh
um (
Sorg
hum
bic
olor
) (J
ames
et a
l. 19
97; M
arop
ola
et a
l. 20
15),
whe
at (
Trit
icum
aes
tivu
m)
(Bal
andr
eau
et a
l. 20
01;
Coo
mbs
and
Fra
nco
2003
; Ini
guez
et a
l. 20
04; J
ha a
nd K
umar
200
9; L
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2002
; Mav
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92; V
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; Ver
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13, 2
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201
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iva)
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Fis
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Die
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otat
o (S
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um tu
bero
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e B
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and
Cop
eman
197
4; H
allm
an
et a
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97;
Han
et
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Hol
lis 1
951;
Man
ter
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Page
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. 201
3; P
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011;
Rad
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; Se
ssits
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t al
. 200
4; S
turz
et
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988,
200
3), t
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olan
um ly
cope
rsic
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Hal
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et a
l. 19
97; L
i et a
l. 20
14; P
atel
et a
l. 20
12; P
illay
and
Now
ak 1
997;
Sam
ish
et a
l. 19
61; Y
ang
et a
l. 20
11),
soy
bean
(Gly
cine
max
) (H
ung
and
Ann
apur
na 2
004;
K
uklin
sky-
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; Min
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; Zin
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Mel
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reir
a et
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; Dia
s et
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, 201
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85; T
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ean
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ris)
(de
Oliv
eira
Cos
ta e
t al.
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; Suy
al e
t al.
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rics
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s ca
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(Su
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1 Role of Endophytic Bacteria in Stress Tolerance of Agricultural Plants
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1.3 Effect of Agricultural Practices on Diversity of Endophytic Bacterial Communities
Bacteria constitute the most numerous group of microorganisms in soil (Whitman et al. 1998), and many endophytic bacteria originate from the population of plant- associated microorganisms in rhizosphere (Hardoim et al. 2008). Microbial diver-sity of the plant rhizosphere itself is defined by overall composition of microbial pool of soil and further refined by specific plant–microbe interactions that are largely mediated by root exudates (Sorensen and Sessitsch 2006). It has been dem-onstrated that endophytic community represents a plant genotype-specific subset of the wider microbial population of soil (Bulgarelli et al. 2012; Lundberg et al. 2012). Agricultural land management, such as tillage or irrigation, greatly alters soil char-acteristics that may lead to reduction in soil microbial diversity due to mechanical destruction, soil compaction, reduced pore volume, desiccation, and disruption of access to food resources (Garcia-Orenes et al. 2013; Jangid et al. 2008). Several studies have established the effect of tillage systems on soil microbial communities in different soils and cropping systems (Balota et al. 2003; Dorr de Quadros et al. 2012; Mathew et al. 2012). The effect of excessive use of pesticides can induce significant changes in the function and structure of soil microbial populations due to direct inhibition of microbial growth or overall changes in the structure of agricul-tural ecosystems (Pampulha and Oliveira 2006). Balanced mineral or organic fertil-izers have been shown to have positive effect on diversity and metabolic activity of the soil microbial community (Zhong et al. 2010).
The effect of the agronomic practices on the overall soil microbial community could be expected to reflect differences in endophyte populations of agricultural crop plants. However, the research aimed to elicit effect of agricultural practices on composition of the endophytic bacteria populations is limited to several studies. An early study by Fuentes-Ramirez et al. (1999) demonstrated that colonization ability of nitrogen-fixing endophytic bacterium Acetobacter diazotrophicus was largely decreased in the sugarcane plants fertilized with high levels of nitrogen. A recent study using automated ribosomal intergenic spacer analysis showed that structure of rice root endophytic community was affected by the nitrogen fertilization level (Sasaki et al. 2013). Another study assessed root bacterial endophyte diversity in maize grown using different fertilizer application conditions. Application of PCR- based group-specific markers revealed that type I methanotroph patterns were dif-ferent for plants cultivated using mineral and organic fertilizer (Seghers et al. 2004).
Recently, culture-based and metagenomic analyses were employed to assess bacterial endophyte diversity of plants grown using conventional and organic prac-tices. An extensive study by Xia et al. (2015) evaluated diversity of culturable bacte-rial endophytes in different tissues of corn, tomato, melon, and pepper grown using organic or conventional practices. The endophyte diversity was significantly higher among all the crops grown organically versus those grown using conventional prac-tices. There were 32 species isolated from organically grown plants and 28 species from plants grown using conventional practices.
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No significant effect of herbicide treatment on composition of the maize root endophyte population was detected using the PCR-based group-specific markers (Seghers et al. 2004). However, recent study using automated ribosomal intergenic spacer fingerprinting and metagenomic analysis using 16S rDNA pyrosequencing identified differences in the composition of endophytic communities in grapevines cultivated using organic and integrated pest management conditions (Campisano et al. 2014a). While a different outcome of the two studies might be a consequence of improvement in the capability of the analysis methods, it could as well be related to differences specific to the plant species or pesticide treatment conditions.
The studies described in this section showed that agricultural conditions could alter diversity of endophytic bacteria populations; however, further insight would be required to elucidate the mechanisms that mediate such changes. The variation in bacterial diversity could be a consequence of changes in overall soil microbial pop-ulation upon the fertilizer treatment or application of other agronomic practices. On the other hand, the agronomical conditions potentially had a direct effect on the root endophytic bacterial community as was suggested by Xia et al. (2015). In addition, an important role might be attributed to differences in plant physiological state and changes in composition of the plant root exudates that influence growth of endo-phytic bacteria (Paungfoo-Lonhienne et al. 2010). This notion that factors related to plant biochemistry regulate endophyte diversity was supported by the study demon-strating that application of chitin resulted in changes in bacterial communities in soil, rhizosphere, and cotton roots, and the organic amendment supported the endo-phytic species in cotton roots that otherwise did not occur (Hallman et al. 1999). Intriguingly, it was shown that composition of the endophytic community was largely different from that of the rhizosphere; therefore, the amendment of chitin, which enhanced chitinase and peroxidase concentrations, might have changed pref-erence of the plants for certain bacterial endophytes.
Another aspect related to the effect of agricultural practices on soil and plant microbiome is reflected by disease-suppressive soil phenomenon that is associated with the capability of soils to suppress or reduce plant disease of susceptible host plants in the presence of virulent pathogen (Weller et al. 2002). It was shown several decades ago that disease-suppressive properties of soil were largely induced by long-term cultivation of wheat and potato monoculture leading to buildup of host- specific microbial community (Lorang et al. 1989; Scher and Baker 1980; Whipps 1997). Further studies elucidated possible mechanisms of disease suppression that include competition for space and nutrients, antagonism due to production of sec-ondary metabolites, and elicitation of ISR by soil microbiota (Philippot et al. 2013; Pieterse et al. 2014). Specific role of the endophytic bacteria in the development of the disease-suppressive traits was rarely addressed in the studies on disease- suppressive soil communities; however, bacteria of genus Streptomyces, Bacillus, Actinomyces, and Pseudomonas that are known to lead endophytic lifestyle were shown to contribute to the disease-suppressive traits of soils (Haas and Defago 2005; Kinkel et al. 2012; Mendes et al. 2011; Siddiqui and Ehteshamul-Haque 2001; Weller et al. 2002).
1 Role of Endophytic Bacteria in Stress Tolerance of Agricultural Plants
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The importance of agricultural practices that maintain natural diversity of plant endophytic bacteria is emphasized by the observations that agricultural plants may become a niche for human pathogens and a source for outbreaks of food-borne ill-ness (Brandl 2006). Use of manures contaminated with virulent bacteria was identi-fied as a main source of human pathogens (Brandl 2006; Holden et al. 2009; van Overbeek et al. 2014). Other routes included irrigation water (Erickson et al. 2010) or flies (Talley et al. 2009). Meanwhile a decline of species antagonistic to the pathogenic bacteria in soil and endosphere was associated with plant colonization by human pathogen species (Latz et al. 2012); it was also demonstrated that the presence of certain plant pathogens and other species living in soil plays an impor-tant role in colonization of plants by human pathogens (Barak and Liang 2008; Brandl 2008; Brandl et al. 2013). On the other hand, typical plant-associated bacte-ria species belonging to the genera of Enterobacter, Serratia, and Klebsiella could become virulent to humans by acquisition of mobile genetic elements from human pathogens through horizontal gene transfer (van Overbeek et al. 2014). Pathogenic bacteria of the family Enterobacteriaceae, including pathogenic Salmonella genus strains, E. coli, Klebsiella pneumoniae, and Vibrio cholerae strains, and the human opportunistic pathogens Pseudomonas aeruginosa and Propionibacterium acnes were described as endophytic colonizers of plants (Campisano et al. 2014b; Deering et al. 2012; El-Awady et al. 2015; Kumar et al. 2013; Kutter et al. 2006; Schikora et al. 2008).
1.4 Role of Endophytic Bacteria in Adaptation of Agriculture Crops to Biotic and Abiotic Environmental Stress
1.4.1 Induction of Accumulation of Stress-Related Metabolites and Enzymes
Plants are capable to acclimate to environmental stresses by altering physiology to attain state adopted to overcome stress factors such as dehydration, mechanical injury, nutrient deficiency, high solar radiation, or stress-induced increase in con-centration of reactive oxygen species. This acclimation is associated with enhanced production of compounds that mediate osmotic adjustment, stabilize cell compo-nents, and act as free radical scavengers. It has been observed that plant inoculation with endophytic bacteria leads to accumulation of such compounds, including pro-line, phenolic compounds, carbohydrates, and antioxidants.
It was shown that bacterial endophyte Burkholderia phytofirmans PsJN enhances cold tolerance of grapevine plants by altering photosynthetic activity and metabo-lism of carbohydrates involved in cold stress tolerance (Ait Barka et al. 2006; Fernandez et al. 2012). The presence of the bacterium in the plant promoted accli-mation to chilling temperatures resulting in lower cell damage, higher photosyn-thetic activity, and accumulation of cold-stress-related metabolites such as starch, proline, and phenolic compounds (Ait Barka et al. 2006). Fernandez et al. (2012)
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