Plant Growth Promoting Rhizobacteria for Agricultural Sustainability: From Theory to Practices [1st ed.] 978-981-13-7552-1;978-981-13-7553-8

Table of contents :
Front Matter ....Pages i-xi
Plant Growth-Promoting Bacteria: Strategies to Improve Wheat Growth and Development Under Sustainable Agriculture (Éva Abod, Éva Laslo, Sarolta Szentes, Szabolcs Lányi, Gyöngyvér Mara)....Pages 1-17
Rhizospheric Microbiomes: Biodiversity, Mechanisms of Plant Growth Promotion, and Biotechnological Applications for Sustainable Agriculture (Divjot Kour, Kusam Lata Rana, Neelam Yadav, Ajar Nath Yadav, Ashok Kumar, Vijay Singh Meena et al.)....Pages 19-65
Advances in the Application of Plant Growth-Promoting Rhizobacteria in Horticulture (Ragini Maurya, Shivani Verma, Indra Bahadur)....Pages 67-76
Agriculture Application of Pseudomonas: A View on the Relative Antagonistic Potential Against Pests and Diseases (K. Sankari Meena, M. Annamalai, S. R. Prabhukarthikeyan, U. Keerthana, M. K. Yadav, P. C. Rath et al.)....Pages 77-93
Plant Growth-Promoting Rhizobacteria as Biological Tools for Nutrient Management and Soil Sustainability (Temoor Ahmed, Muhammad Shahid, Muhammad Noman, Sabir Hussain, Muhammad Asaf Khan, Muhammad Zubair et al.)....Pages 95-110
Rhizobacteria-Mediated Root Architectural Improvement: A Hidden Potential for Agricultural Sustainability (Sakthivel Ambreetha, Dananjeyan Balachandar)....Pages 111-128
Role of Rhizobia for Sustainable Agriculture: Lab to Land (Ashok Kumar, Vijay Singh Meena, Pratiti Roy, Vandana, Renu Kumari)....Pages 129-149
Plant Growth-Promoting Rhizobacteria: Harnessing Its Potential for Sustainable Plant Disease Management (S. Harish, S. Parthasarathy, D. Durgadevi, K. Anandhi, T. Raguchander)....Pages 151-187
Soil Microbial Hotspots and Hot Moments: Management vis-a-vis Soil Biodiversity (R. K. Yadav, M. R. Yadav, D. M. Mahala, Rakesh Kumar, Dinesh Kumar, Neelam Yadav et al.)....Pages 189-202
Surfactin: An Emerging Biocontrol Tool for Agriculture Sustainability (Fauzia Yusuf Hafeez, Zakira Naureen, Ambrin Sarwar)....Pages 203-213
Molecular Approaches to Study Plant Growth-Promoting Rhizobacteria (PGPRs) (Munazza Ijaz, Roshina Shahzadi, Mahmood-ur Rahman, Muhammad Iqbal)....Pages 215-232
Impact of Land Uses on Microbial Biomass C, N, and P and Microbial Populations in Indian Himalaya (R. P. Yadav, B. Gupta, J. K. Bisht, R. Kaushal, T. Mondal, Vijay Singh Meena)....Pages 233-255
Potassium-Solubilizing Bacteria (KSB): A Microbial Tool for K-Solubility, Cycling, and Availability to Plants (Indra Bahadur, Ragini Maurya, Pratiti Roy, Ashok Kumar)....Pages 257-265
ACC Deaminase-Producing Bacteria: A Key Player in Alleviating Abiotic Stresses in Plants (Swapnil Sapre, Iti Gontia-Mishra, Sharad Tiwari)....Pages 267-291
Sustainability of Crop Production by PGPR Under Abiotic Stress Conditions (Muzaffer İpek, Şeyma Arıkan, Lütfi Pırlak, Ahmet Eşitken)....Pages 293-314

Citation preview

Ashok Kumar · Vijay Singh Meena Editors

Plant Growth Promoting Rhizobacteria for Agricultural Sustainability From Theory to Practices

Plant Growth Promoting Rhizobacteria for Agricultural Sustainability

Ashok Kumar  •  Vijay Singh Meena Editors

Plant Growth Promoting Rhizobacteria for Agricultural Sustainability From Theory to Practices

Editors Ashok Kumar Department of Genetics and Plant Breeding Banaras Hindu University Mirzapur, Uttar Pradesh, India

Vijay Singh Meena Crop Production Division ICAR-Vivekananda Institute of Hill Agriculture Almora, Uttarakhand, India

ISBN 978-981-13-7552-1    ISBN 978-981-13-7553-8 (eBook) https://doi.org/10.1007/978-981-13-7553-8 © Springer Nature Singapore Pte Ltd. 2019 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, 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. This Springer imprint is published by the registered company Springer Nature Singapore Pte Ltd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore

Contents

1 Plant Growth-Promoting Bacteria: Strategies to Improve Wheat Growth and Development Under Sustainable Agriculture������    1 Éva Abod, Éva Laslo, Sarolta Szentes, Szabolcs Lányi, and Gyöngyvér Mara 2 Rhizospheric Microbiomes: Biodiversity, Mechanisms of Plant Growth Promotion, and Biotechnological Applications for Sustainable Agriculture����������������������������������������������   19 Divjot Kour, Kusam Lata Rana, Neelam Yadav, Ajar Nath Yadav, Ashok Kumar, Vijay Singh Meena, Bhanumati Singh, Vinay Singh Chauhan, Harcharan Singh Dhaliwal, and Anil Kumar Saxena 3 Advances in the Application of Plant Growth-Promoting Rhizobacteria in Horticulture����������������������������������������������������������������   67 Ragini Maurya, Shivani Verma, and Indra Bahadur 4 Agriculture Application of Pseudomonas: A View on the Relative Antagonistic Potential Against Pests and Diseases��������������������������������   77 K. Sankari Meena, M. Annamalai, S. R. Prabhukarthikeyan, U. Keerthana, M. K. Yadav, P. C. Rath, M. Jena, and P. Prajna 5 Plant Growth-Promoting Rhizobacteria as Biological Tools for Nutrient Management and Soil Sustainability����������������������   95 Temoor Ahmed, Muhammad Shahid, Muhammad Noman, Sabir Hussain, Muhammad Asaf Khan, Muhammad Zubair, Muhammad Ismail, Natasha Manzoor, Tanvir Shahzad, and Faisal Mahmood 6 Rhizobacteria-Mediated Root Architectural Improvement: A Hidden Potential for Agricultural Sustainability������������������������������  111 Sakthivel Ambreetha and Dananjeyan Balachandar 7 Role of Rhizobia for Sustainable Agriculture: Lab to Land����������������  129 Ashok Kumar, Vijay Singh Meena, Pratiti Roy, Vandana, and Renu Kumari

v

vi

Contents

8 Plant Growth-Promoting Rhizobacteria: Harnessing Its Potential for Sustainable Plant Disease Management ��������������������������������������������������������������������  151 S. Harish, S. Parthasarathy, D. Durgadevi, K. Anandhi, and T. Raguchander 9 Soil Microbial Hotspots and Hot Moments: Management vis-a-vis Soil Biodiversity ������������������������������������������������  189 R. K. Yadav, M. R. Yadav, D. M. Mahala, Rakesh Kumar, Dinesh Kumar, Neelam Yadav, S. L. Yadav, V. K. Sharma, and Sunita Yadav 10 Surfactin: An Emerging Biocontrol Tool for Agriculture Sustainability ����������������������������������������������������������������  203 Fauzia Yusuf Hafeez, Zakira Naureen, and Ambrin Sarwar 11 Molecular Approaches to Study Plant Growth-Promoting Rhizobacteria (PGPRs) ��������������������������������������������������������������������������  215 Munazza Ijaz, Roshina Shahzadi, Mahmood-ur Rahman, and Muhammad Iqbal 12 Impact of Land Uses on Microbial Biomass C, N, and P and Microbial Populations in Indian Himalaya������������������������������������  233 R. P. Yadav, B. Gupta, J. K. Bisht, R. Kaushal, T. Mondal, and Vijay Singh Meena 13 Potassium-Solubilizing Bacteria (KSB): A Microbial Tool for K-Solubility, Cycling, and Availability to Plants ����������������������������  257 Indra Bahadur, Ragini Maurya, Pratiti Roy, and Ashok Kumar 14 ACC Deaminase-Producing Bacteria: A Key Player in Alleviating Abiotic Stresses in Plants ������������������������������������������������  267 Swapnil Sapre, Iti Gontia-Mishra, and Sharad Tiwari 15 Sustainability of Crop Production by PGPR Under Abiotic Stress Conditions������������������������������������������������������������  293 Muzaffer İpek, Şeyma Arıkan, Lütfi Pırlak, and Ahmet Eşitken

Editors and Contributors

About the Editors Ashok  Kumar is Assistant Professor at the Department of Genetics and Plant Breeding (Plant Biotechnology), Banaras Hindu University (BHU), Uttar Pradesh, India. He received his PhD in Biotechnology from the BHU, where he also completed his doctoral studies. His research chiefly focuses on the effective use of plant growth promoting rhizobacteria (PGPR) for sustainable agricultural development, and on soil-microbe-plant-interactions. He has submitted 44 bacterial sequences to the NCBI Genebank. Dr. Kumar has served as an editorial board member for the International Journal of Applied Agricultural Sciences and is a lifetime member of the Asian PGPR Society of Sustainable Agriculture and Society and Nature.  

Vijay Singh Meena is currently working as a soil scientist at the ICAR–Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand. He received his BSc from SKRAU, Bikaner, Rajasthan, and his MSc and PhD with a specialization in Soil Science and Agricultural Chemistry from Banaras Hindu University (BHU), Uttar Pradesh, India. He has completed vital work on potassium-solubilizing microbes, soil biological fertility, rhizospheric chemistry, and conservation agriculture, and has published more than 45 original research articles in national and international peer-reviewed journals. In addition, he has published 6 books and 15 book chapters.  

List of Contributors Éva  Abod  Faculty of Technical and Human Sciences, Sapientia Hungarian University of Transylvania, Târgu-Mureş, Romania Temoor  Ahmed  Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan Sakthivel  Ambreetha  Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, India

vii

Editors and Contributors

viii

K.  Anandhi  Krishi Vigyan Kendra, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu, India M. Annamalai  ICAR National Rice Research Institute, Cuttack, Odisha, India Şeyma Arıkan  Faculty of Agriculture, Department of Horticulture, The Alaeddin Keykubat Campus, Selçuk University, Konya, Turkey Indra Bahadur  Soil and Land Use Survey of India, Ministry of Agriculture and Farmers Welfare, GOI, Kolkata Centre, Kolkata, India Dananjeyan Balachandar  Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, India J. K. Bisht  ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, India Vinay  Singh  Chauhan  Department of Biotechnology, Bundelkhand University, Jhansi, India Harcharan  Singh  Dhaliwal  Department of Biotechnology, Akal College of Agriculture, Eternal University, Sirmour, Himachal Pradesh, India D. Durgadevi  Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India Ahmet Eşitken  Faculty of Agriculture, Department of Horticulture, The Alaeddin Keykubat Campus, Selçuk University, Konya, Turkey Iti  Gontia-Mishra  Biotechnology University, Jabalpur, India

Centre,

Jawaharlal

Nehru Agriculture

B. Gupta  Dr. Y.S. Parmar University of Horticulture and Forestry, Nauni, Solan, India Fauzia  Yusuf  Hafeez  Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan S.  Harish  Department of Plant Pathology, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu, India Sabir Hussain  Department of Environmental Sciences & Engineering, Government College University, Faisalabad, Pakistan Munazza Ijaz  Department of Bioinformatics and Biotechnology, GC University– Faisalabad, Faisalabad, Pakistan Muzaffer İpek  Faculty of Agriculture, Department of Horticulture, The Alaeddin Keykubat Campus, Selçuk University, Konya, Turkey Muhammad  Iqbal  Department of Environmental Science and Engineering, GC University–Faisalabad, Faisalabad, Pakistan

Editors and Contributors

Muhammad  Ismail  Department of Bioinformatics Government College University, Faisalabad, Pakistan

ix

and

Biotechnology,

M. Jena  ICAR National Rice Research Institute, Cuttack, Odisha, India R.  Kaushal  ICAR-Indian Institute of Soil and Water Conservation, Dehradun, India U. Keerthana  ICAR National Rice Research Institute, Cuttack, Odisha, India Muhammad  Asaf  Khan  Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan Divjot Kour  Department of Biotechnology, Akal College of Agriculture, Eternal University, Sirmour, Himachal Pradesh, India Dinesh Kumar  ICAR-National Dairy Research Institute, Karnal, Hariyana, India Rakesh Kumar  ICAR-National Dairy Research Institute, Karnal, Hariyana, India Renu Kumari  Department of Genetics and Plant Breeding (Plant Biotechnology), Rajiv Gandhi South Campus, Banaras Hindu University, Mirzapur, Uttar Pradesh, India Szabolcs Lányi  Faculty of Economics, Socio-Human Sciences and Engineering, Sapientia Hungarian University of Transylvania, Miercurea-Ciuc, Romania Éva  Laslo  Faculty of Economics, Socio-Human Sciences and Engineering, Sapientia Hungarian University of Transylvania, Miercurea-Ciuc, Romania D. M. Mahala  ICAR-Indian Institute of Maize Research, Ludhiana, Punjab, India Faisal  Mahmood  Department of Environmental Sciences & Engineering, Government College University, Faisalabad, Pakistan Mahmood-ur  Rahman  Department of Bioinformatics and Biotechnology, GC University–Faisalabad, Faisalabad, Pakistan Central Hi-Tech Laboratory, GC University–Faisalabad, Faisalabad, Pakistan Natasha  Manzoor  Department of Soil and Water Sciences, China Agricultural University, Beijing, China Gyöngyvér Mara  Faculty of Economics, Socio-Human Sciences and Engineering, Sapientia Hungarian University of Transylvania, Miercurea-Ciuc, Romania Ragini  Maurya  Department of Horticulture, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India Tilak  Mondal  ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, India Zakira Naureen  Department of Biological Sciences and Chemistry, University of Nizwa, Birkat Al Mawz, Sultanate of Oman

x

Editors and Contributors

Muhammad  Noman  Department of Bioinformatics Government College University, Faisalabad, Pakistan

and

Biotechnology,

S.  Parthasarathy  Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India Lütfi  Pırlak  Faculty of Agriculture, Department of Horticulture, The Alaeddin Keykubat Campus, Selçuk University, Konya, Turkey S.  R.  Prabhukarthikeyan  ICAR National Rice Research Institute, Cuttack, Odisha, India P. Prajna  ICAR National Rice Research Institute, Cuttack, Odisha, India Pratiti  Roy  Department of Genetics and Plant Breeding (Plant Biotechnology), Rajiv Gandhi South Campus, Banaras Hindu University, Mirzapur, Uttar Pradesh, India T.  J.  Purakayastha  ICAR-Indian Agricultural Research Institute, New Delhi, India T.  Raguchander  Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India Kusam  Lata  Rana  Department of Biotechnology, Akal College of Agriculture, Eternal University, Sirmour, Himachal Pradesh, India P. C. Rath  ICAR National Rice Research Institute, Cuttack, Odisha, India K. Sankari Meena  ICAR National Rice Research Institute, Cuttack, Odisha, India Swapnil  Sapre  Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur, India Ambrin  Sarwar  Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan Anil  Kumar  Saxena  ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, Uttar Pradesh, India Muhammad  Shahid  Department of Bioinformatics Government College University, Faisalabad, Pakistan

and

Biotechnology,

Roshina  Shahzadi  Department of Bioinformatics and Biotechnology, GC University–Faisalabad, Faisalabad, Pakistan Tanvir  Shahzad  Department of Environmental Sciences & Engineering, Government College University, Faisalabad, Pakistan V. K. Sharma  ICAR-Indian Agricultural Research Institute, New Delhi, India Bhanumati Singh  Department of Biotechnology, Bundelkhand University, Jhansi, India

Editors and Contributors

xi

Sarolta Szentes  Faculty of Economics, Socio-Human Sciences and Engineering, Sapientia Hungarian University of Transylvania, Miercurea-Ciuc, Romania Sharad  Tiwari  Department of Plant Breeding and Genetics, Jawaharlal Nehru Agriculture University, Jabalpur, India Vandana  Department of Genetics and Plant Breeding (Plant Biotechnology), Rajiv Gandhi South Campus, Banaras Hindu University, Mirzapur, Uttar Pradesh, India Shivani Verma  Department of Genetics and Plant Breeding (Plant Biotechnology), Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India Ajar  Nath  Yadav  Department of Biotechnology, Akal College of Agriculture, Eternal University, Sirmour, Himachal Pradesh, India M. R. Yadav  Rajasthan Agricultural Research Institute, Jaipur, Rajasthan, India M. K. Yadav  ICAR National Rice Research Institute, Cuttack, Odisha, India Neelam Yadav  Gopi Nath P.G. College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh, India R.  K.  Yadav  Agricultural Research Station, Agriculture University, Kota, Rajasthan, India R. P. Yadav  ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, India S. L. Yadav  Agricultural Research Station, Agriculture University, Kota, Rajasthan, India Sunita Yadav  ICAR-Indian Agricultural Research Institute, New Delhi, India Muhammad  Zubair  Department of Bioinformatics Government College University, Faisalabad, Pakistan

and

Biotechnology,

1

Plant Growth-Promoting Bacteria: Strategies to Improve Wheat Growth and Development Under Sustainable Agriculture Éva Abod, Éva Laslo, Sarolta Szentes, Szabolcs Lányi, and Gyöngyvér Mara

Contents 1.1  Introduction 1.2  Strain Identification and Characterization 1.3  Siderophore Production 1.4  Organic Compound (Cellulose, Phytic Acid, and Lecithin) Degradation 1.5  Alkaline Protease and Phosphatase Enzyme Assays 1.6  Growth-Promoting Effect of Bacterial Treatment on Wheat 1.7  Conclusion and Future Perspectives References

   2    3    7    8    8  10  13  14

Abstract

A part of rhizospheric bacteria are considered plant growth-promoting bacteria (PGPB) due to their positive effect on the plant growth and development. Plant growth-promoting bacteria based on their metabolic activity can be grouped as biofertilizers, fitostimulants, or biopesticides. These efficient bacteria due to various direct or indirect effects exerted on plants have crucial role in agricultural sustainability. Recently were reported diverse genera as PGPB like Acetobacter, Achromobacter, Arthrobacter, Azoarcus, Azospirillum, Azotobacter, Bacillus, Burkholderia, Frankia, Phyllobacterium, Pseudomonas, Serratia, and Rhizobium. Bacterial strains for this study were isolated from a natural habitat (raised bog) and agricultural environment. Selected bacterial strains based on 16S rRNA gene sequence analysis were identified as Achromobacter spanius, É. Abod Faculty of Technical and Human Sciences, Sapientia Hungarian University of Transylvania, Târgu-Mureş, Romania É. Laslo (*) · S. Szentes · S. Lányi · G. Mara (*) Faculty of Economics, Socio-Human Sciences and Engineering, Sapientia Hungarian University of Transylvania, Miercurea-Ciuc, Romania e-mail: [email protected]; [email protected] © Springer Nature Singapore Pte Ltd. 2019 A. Kumar, V. S. Meena (eds.), Plant Growth Promoting Rhizobacteria for Agricultural Sustainability, https://doi.org/10.1007/978-981-13-7553-8_1

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É. Abod et al.

Delftia lacustris, Pseudomonas protegens, P. jessenii, and Acinetobacter lwoffii. These bacterial strains  have different plant growth-promoting (PGP) activities like multi-stress resistances (temperature, pH, salinity) and others such as cellulose, phytin, and lecithin degradation, alkaline phosphatase and alkaline protease activity, and siderophore production. The selected strains were tested on plants either alone or in consortia. Based on the reports, it was confirmed that Delftia lacustris BI5, P. jessenii BI7, bacterial strains, and the bacterial consortia P. jessenii BI7 and A. lwoffii BI13 showed positive effect due to their PGP characteristics on wheat shoot growth under laboratory conditions. These promising strains have potential as inoculation agents in eco-friendly crop production contributing to environmental sustainability. Keywords

Rhizosphere · Microorganisms · Plant growth · Synergy · Crop production

1.1

Introduction

Plant growth-promoting bacteria (PGPB) are soil and rhizosphere bacteria that can promote plants growth through various direct and indirect mechanisms. These bacteria based on their effect on plant growth and development, due to different metabolic activities, can be grouped as biofertilizers, phytostimulants, and biopesticides. Bacteria with role in biofertilization can provide inaccessible nutrients for plants, due to atmospheric nitrogen fixing and phosphorus, iron or potassium solubilizing. They are able to increase the availability of nutrients through the decomposition of organic compounds, expected to enzymes such as phytase, acid or alkaline phosphatase, and esterase (Lü et al. 2005; Sarikhani et al. 2010). In iron insufficiency conditions, iron could be solubilized by the production of iron-binding molecules like siderophores which can form Fe-siderophore complex, readily available to plants (Kumar et  al. 2017b). Phytostimulants produce different phytohormones (auxins, gibberellins, cytokinins, and ethylene) and fulfil a role in plant growth promotion (Shukla 2019). Due to the synthetized hormones, these microbes can also improve plant tolerance in various abiotic stress circumstances (Gupta et  al. 2015). Biopesticides are able to control the growth of deleterious microorganisms due to the deliberation of different secondary metabolites or extracellular cell wall decomposing enzymes (cellulose, alkaline or neutral protease, siderophores, antibiotics, HCN, and induced systemic resistance) (El-Sayed et al. 2014; Akram et al. 2017; Barnawal et al. 2017). From the recent observations were reported diverse genera as PGPB with important role in different crop or vegetable nutrition like Agrobacterium, Acetobacter, Achromobacter, Arthrobacter, Azoarcus, Azospirillum, Azotobacter, Bacillus, Burkholderia, Erwinia, Flavobacterium, Frankia, Herbaspirillum, Klebsiella, Kluyvera, Paenibacillus, Phyllobacterium, Pseudomonas, Proteus, Serratia, Rahnella, and Rhizobium (Babalola 2010; Ahemad and Kibret 2014; Chatterjee et al. 2017; Shukla 2019).

1  Plant Growth-Promoting Bacteria: Strategies to Improve Wheat Growth…

3

The current agricultural practice due to intensive use of agrochemicals faces difficulties due to the pollution and nonrenewable resource use, having a significant effect on the state of the environment. The solution relies on a more resource-­ preserving and environmentally friendly practice so-called sustainable agriculture. In sustainable agricultural practice, the maintenance of soil health and its microbial community is crucial. Microbial products contribute to the plant nutrient status without pollution and depletion of natural resources and also protect plant under stress conditions (Bhattacharyya et al. 2016; Prasad et al. 2019). These microbes with plant nutrition enhancement, phytostimulation, or biocontrol effect can replace or complete the chemicals used in agriculture. Microbial inoculants are getting focus and are widely accepted in sustainable development of agriculture (Bhattacharyya et al. 2016; Prasad et al. 2019). PGP bacteria from different ecological habitats, regions, and plant rhizosphere were described for their beneficial activities and impact on plant growth in order to be used in sustainable agriculture. Crop and wild plants and their rhizosphere represent a potential origin of new PGP bacterial strains. The wild plant rhizosphere, due to the harsh environment, is considered as a good source for competitive PGP bacteria (Gopalakrishnan et al. 2015). Nevertheless, a high percentage of studied PGP bacteria were isolated from crop plants as soybean (Sugiyama et  al. 2014), pea (Meena et al. 2015), wheat (Majeed et al. 2015), and maize (Shahzad et al. 2013; Qaisrani et al. 2014). Data on PGP bacteria isolated from wild plants are deficient; several findings were published regarding the native plant-associated rhizobacteria from Saudi Arabia (El-Sayed et  al. 2014) and India (Singh et  al. 2015). It was observed also that the performance of the PGPB varies due to environmental factors and local conditions (Shukla 2019). The aim of the research was to isolate PGP bacteria from wild and crop plants adapted to local conditions in order to be used in microbial inoculants in this region. This chapter presents a comparative study of plant growth-stimulating aspects (production of siderophores, protease, and phosphatase and degradation of cellulose, phytin, and lecithin) of bacterial strains originated from natural and agricultural ecosystems. Furthermore, the plant growth-promoting potential of the strains used either single or in consortia was assessed in vivo on wheat growth. The present study identified novel PGP characters for Achromobacter spanius, Acinetobacter lwoffii, Delftia lacustris, Pseudomonas jessenii, and P. protegens strains. D. lacustris BI5, P. jessenii BI7, and A. lwoffii BI13 bacterial strains were found to be efficient on wheat plant growth based on a single and multistrain microbial formulation, making them good candidates to be used as microbial inoculants.

1.2

Strain Identification and Characterization

These efficient bacterial isolates were isolated from soil and rhizosphere of Carex sp. from Borsáros raised bog natural reserve (Harghita County, Romania, GPS coordinates: 46°18′37.6″ N, 25°50′24.8″ E) and from soil and rhizosphere of Zea mays from Cristuru Secuiesc (Romania, GPS coordinates: 46°28′62.4″ N, 25°03′85.3″ E).

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É. Abod et al.

Among 13 isolates studied, 7 (53.8%) were sequestered from natural raised bog environment, whereas the remaining 6 (46.2%) from agricultural environment. The 13 bacterial isolates were identified by their 16S rRNA gene sequence. Genomic DNA was isolated from strains after cultivation of cells on King’s B agar for 24 h. The 16S rRNA gene sequence was amplified by PCR using primers 27f (5′-AGAGTTTGATCMTGGCTCAG-3′) and 1401r (5′-CGGTGTGTACA AGGCCCGGGAACG-3′) and purified by PCR-MTM Clean-Up System (Viogene, Sunnyvale, USA). The partial 16S rRNA gene sequence was obtained by sequencing the gene in both directions (AmpliTaq® FS Big Dye TM Terminator sequencing kit, Applied Biosystems). The bacterial isolates were identified using partial 16S rDNA gene sequence alignment to database (Table 1.1) as follows: Achromobacter spanius BI1 and BI4; Delftia lacustris BI2, BI5, and BI6; Pseudomonas protegens BI3; P. jessenii BI7; and Acinetobacter lwoffii BI8, BI9, BI10, BI11, BI12, and BI13 strains. The strains isolated from the natural raised bog environment showed higher taxonomic diversity, being identified to belong to three different genera (Achromobacter, Delftia, and Pseudomonas), whereas from the agricultural area, Acinetobacter sp. strains were isolated. The capacity to grow at different temperatures (4, 24, 25, 26, 28, 32, and 37 °C), various salinities (0, 1, 2, 3, 4, 5, 6, 8, 10, and 12 g L−1 NaCl), and pH (pH 6, 6.5, 7, 7.5, and 8) was tested in flasks containing 20 mL tryptic soy broth (TSB) incubated at 28 °C (4–37 °C for temperature preference analysis) on 150 RPM. Cellular morphology and cell diameter of the strains were determined from overnight culture using optical microscopy (Olympus, BX53). The morphological, physiological, and biochemical profile of the isolated strains was realized. The Achromobacter spanius BI1 and BI4; the Delftia lacustris BI2, BI5, and BI6; and the Pseudomonas protegens BI3 (Table  1.1) bacterial strains were Gram-­ negative, nonspore-forming, short rods with 2.2 ± 0.5 μm length. Growth occurred between 4 and 37 °C with an optimum growth at 25 °C, salinity from 0 to 12 g L−1 NaCl with an optimum between 4 and 6 g L−1, and pH values from 6 to 8 with an optimum between pH 7.0 and 7.5. The abovementioned bacterial strains proved to be aerobe and oxidase positive and were able to degrade glucose. Achromobacter spanius sp. nov., originated from medical samples, was first reported by Coenye et al. (2003) as Gram-negative, oxidase-positive bacteria, with optimal growth temperature range between 28 and 37 °C and salinity between 0 and 4.5 g L−1 NaCl. Delftia lacustris sp. nov. was first isolated from freshwater environment by Jorgensen et al. (2009). It was described as rod-shaped bacteria, with the same optimal growth as in the current study (25 °C); the growth to 12 g L−1 NaCl salinity was supported by the strains isolated from raised bog environment (BI2, BI5, and BI6), whereas in case of the first described strain, growth to 6  g  L−1 NaCl salinity was observed (Jorgensen et al. 2009). Similar morphological and biochemical characteristics were observed in case of Pseudomonas protegens sp. nov. isolated from tobacco roots (Ramette et al. 2011) and Pseudomonas protegens BI3 strain isolated from raised bog environment. The isolate Pseudomonas jessenii BI7 was proved to be Gram-­ negative, nonspore-forming, oxidase-positive aerobic bacteria, and it was first isolated and described showing similar growth parameters and biochemical

BI9

BI8

BI7

BI6

BI5

BI4

BI3

BI2

Strain code BI1

Identified strain, similarity (%), the 16S rDNA sequence length (base pair) Achromobacter spanius LMG 5911(T) AY170848, 99.7%, 484 bp Delftia lacustris DSM 21246(T) EU888308, 98.9%, 482 bp Pseudomonas protegens CHA0(T) AJ278812, 99.1%, 483 bp Achromobacter spanius LMG 5911(T) AY170848, 100%, 483 bp D. lacustris DSM 21246(T) EU888308, 98.9%, 479 bp D. lacustris DSM 21246(T) EU888308, 98.9%, 478 bp Pseudomonas jessenii CIP 105274(T) AF068259, 99%, 467 bp Acinetobacter lwoffii strain MBW4 JX966447.1, 99%, 482 bp A. lwoffii strain MBW4 JX966447.1, 99%, 474 bp + +

− −

+ +

+

+

+

+

−

−

−

−

+

+

−

+

+

−

−

−

−

+

−

−

−

+

+

+

−

−

+

+

+

+

+

−

+

+

Phytin degradation −

Cellulose degradation +

Lecithin degradation +

Siderophore production +

Oxidase test +

Table 1.1  The resulted morphological, biochemical, and PGP characteristics of the isolates

0.04 ± 0.02

ND

0.33 ± 0.01

0.21 ± 0.03

0.24 ± 0.02

ND

ND

0.08 ± 0.05

Alkaline protease activity (mol tyrosine/h) 0.13 ± 0.04

ND

ND

ND

ND

(continued)

0.25 ± 0.04

0.12 ± 0.03

0.24 ± 0.05

ND

Alkaline phosphatase activity (μ mol p-NP/h) ND

1  Plant Growth-Promoting Bacteria: Strategies to Improve Wheat Growth… 5

Siderophore production + + + −

Oxidase test −

−

−

−

−

−

−

Lecithin degradation −

−

−

−

Cellulose degradation −

−

−

−

Phytin degradation −

ND

ND

ND

Alkaline protease activity (mol tyrosine/h) ND

1.83 ± 0.05

1.75 ± 0.01

1.43 ± 0.04

Alkaline phosphatase activity (μ mol p-NP/h) 1.12 ± 0.03

“−” negative result, “+” positive result, all bacterial isolates having aerobic and glucose-degrading capacity as well as negative in Gram staining along with no spore forming ability

BI13

BI12

BI11

Strain code BI10

Identified strain, similarity (%), the 16S rDNA sequence length (base pair) A. lwoffii strain MBW4 JX966447.1, 99%, 474 bp A. lwoffii strain MBW4 JX966447.1, 99%, 480 bp A. lwoffii strain MBW4 JX966447.1, 99%, 481 bp A. lwoffii strain MBW4 JX966447.1, 99%, 480 bp

Table 1.1 (continued)

6 É. Abod et al.

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characteristics from mineral water by Verhille et  al. (1999). The six studied Acinetobacter lwoffii strains isolated from agricultural area (BI8, BI9, BI10, BI11, BI12, and BI13) were Gram-negative, nonspore-forming, short rods with 1.73 ± 0.45 μm length. Growth occurred between 3 and 37 °C with an optimum growth at 32 °C, salinity from 0 to 12 g L−1 NaCl with an optimum between 10 and 12 g L−1, and pH values from 6 to 8 with an optimum at pH 7.5–8.0. The Acinetobacter strains were aerobe and oxidase negative and were able to degrade glucose. Acinetobacter lwoffii sp. nov. was first described by Bouvet and Grimont (1986) as rods with similar characteristics, differences in growth on various temperature were observed among strains, and those isolated in the present study were able to grow on lower temperature ranges (3–15 °C).

1.3

Siderophore Production

Siderophores are low molecular weight organic compounds produced by bacteria and fungi to enhance the iron uptake and are believed an efficient iron source also for the plants, therefore promoting plant growth (Saha et al. 2016). For siderophore production screening chrome azurol S (CAS) plates were used (Oldal et al. 2002). The plates were point inoculated and incubated for 24 h at 28 °C. Eleven strains from the studied 13 (~85%) were able to produce siderophore, a high-affinity iron-chelating compound. Two strains, A. spanius BI4 isolated from raised bog environment and A. lwoffii BI13 isolated from agricultural environment, showed no siderophore production ability (Table 1.1). Although Achromobacter sp. strains are widely described as potential human pathogens, they were isolated also from rhizosphere environment, and PGP characteristics such as phosphate solubilization, plant hormone production ability, acetylene reduction, and direct plant growth promotion have been recently described (Gopal 2013; Abdel-Rahman et al. 2017). The study is the first record of siderophore production ability of an A. spanius BI1 strain. Morel et al. (2011) report Delftia sp. strains as having siderophore and indole acetic acid (IAA) production capacity, but Delftia lacustris strains were not mentioned previously as siderophore producers. D. lacustris strains were previously reported as having biocontrol potential against fungal pathogens (Janahiraman et al. 2016). P. protegens strains were previously described as siderophore producers (Ruiz et al. 2015; Sexton et al. 2017). No data about the siderophore production potential of P. jessenii was found in the literature; it was reported as capable of phosphate solubilization (Valverde et  al. 2007). Acinetobacter sp. strains were described by Trotel-Aziz et  al. (2008) as biocontrol agents and by Farokh et  al. (2011) showing PGP characteristics as siderophore and P-solubilization. As the result of the screening for PGP potential according to our best knowledge, this is first recorded for siderophore-producing ability of A. spanius, D. lacustris, and P. jessenii.

8

1.4

É. Abod et al.

 rganic Compound (Cellulose, Phytic Acid, O and Lecithin) Degradation

The cellulose degradation potential of the isolated bacterial strains was exploited on carboxymethylcellulose (2% CMC, minimal salt media) containing agar plates using clearing assay. Bacterial strains were point inoculated on agar plates in triplicate and incubated for 5 days at 28 °C. To visualize the producing halos around the bacterial culture, plates were stained with 0.1% Congo red dye. The cellulose degradation ability was recorded if a clear zone around the colonies was observed. Five strains (71.4%, A. spanius BI1; D. lacustris BI2, BI5, and BI6; and P. jessenii BI7) isolated from natural raised bog environment and one strain (16.66%, A. lwoffii BI8) isolated from agricultural environment (Table 1.1) were able to degrade CMC. Screening methods were used in order to elucidate the organic phosphorus-­ degrading capacity of the strains. The analysis of the phytic acid utilization was conducted on Sperber agar (Sarikhani et al. 2010), while the lecithin degradation was performed on egg yolk agar (Lü et al. 2005). Each bacterial strain was point inoculated in triplicate on agar plates. After incubating at 28  °C for 5  days, the phytic acid or lecithin degradation was recorded for each strain that produced a clearing zone. Lecithin degradation was observed only for two bacterial strains (15.3%): A. spanius BI1 and P. protegens BI3 isolated from the natural raised bog environment. The lecithinase activity of a P. protegens strain isolated from tobacco roots was previously described by Ramette et al. (2011). Phytic acid degradation was detected in four bacterial strains (30.76%): D. lacustris BI2, BI5, and BI6 and A. spanius BI4. The six studied A. lwoffii strains were unable to degrade any of the phosphorus-­ containing organic compounds. In case of Achromobacter sp., Pseudomonas jessenii, and Acinetobacter sp., only inorganic phosphate solubilization was previously reported (Valverde et al. 2007; Farokh et al. 2011; Abdel-Rahman et al. 2017); no data on phosphorus-containing organic compound degradation were found in literature. We provide new evidence of organic matter decomposing activity of the two Achromobacter and one Acinetobacter strain. A. spanius BI1 strain was able to decompose lecithin and cellulose, and A. spanius BI4 utilized phytic acid, whereas in case of A. lwoffii BI8 strain, cellulose-degrading capacity was detected.

1.5

Alkaline Protease and Phosphatase Enzyme Assays

The bacterial strains were grown in culture broth containing casein as substrate (Adinarayana et al. 2005). After incubation on a rotary shaker (28 °C, 140 RPM) for 24 h, the culture media was centrifuged at 10000 RPM for 10 min, and the supernatants were gathered for enzyme assay. The absorbance of the resulted tyrosine was determined using a microplate reader (Fluostar Optima, BMG Labtech), and from the absorbance values, the protease enzyme activities (mol tyrosine/mL/h) of the strains were determined. The alkaline protease enzyme activity was proved for six (D. lacustris BI2, BI5, BI6, A. spanius BI4, P. jessenii BI7, A. lwoffii BI9) bacterial

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strains (Table  1.1). The protease enzyme activities ranged from 0.04  ±  0.02  mol tyrosine/mL/h to 0.33 ± 0.01 mol tyrosine/mL/h. In most studies published in the last years, the protease activity of the PGP bacterial strains was detected on skim milk agar (Hantsis-Zacharov and Halpern 2007; Suresh et  al. 2010; Yuttavanichakul et  al. 2012; Sadeghi et  al. 2014; Masciarelli et al. 2014). Quantitative determinations of the protease enzyme activities were performed for several PGP bacterial strains as follows: Bacillus subtilis 333 (0.162 mmol tyrosine/h), Tatumella ptyseos (0.162  mmol tyrosine/h), B. megaterium 817 (0.157 mmol tyrosine/h), Acinetobacter sp. 378 (0.065–0.126 mmol tyrosine/h on different pH values) (Rodarte et al. 2011), P. putida MSC1 (0.0057 mol tyrosine/h), P. pseudoalcaligenes MSC4 (0.012 mol tyrosine/h) (Saraf et al. 2013), and B. cereus PM2 strain (0.0029 mmol tyrosine/h) (Anwar et al. 2014). No previous evidence for the alkaline protease activity of the studied taxa, Delftia lacustris, Achromobacter spanius, Pseudomonas jessenii, and Acinetobacter lwoffii, was found in the scientific literature. Alkaline protease activity of strains affiliated to Acinetobacter sp. genera was determined by Rodarte et al. (2011). Phosphatase activity was tested by using a chromogenic substrate p-nitrophenyl phosphate (pNPP) (Wu et  al. 2007). The bacterial strains were grown in pNPP-­ containing broth in an incubator shaker (24 h, 28 °C, and 140 RPM). Cells were lysed by sonication, and the debris was separated by centrifugation at 10000 RPM for 10 min at 25 °C. The absorbance of the resulted p-nitrophenol was quantified using microplate reader (Fluostar Optima, BMG Labtech), and from the absorbance values, the phosphatase enzyme activities (μmol p-NP/mL/h) of the strains were determined. In case of eight bacterial strains (D. lacustris BI2 and BI5, P. protegens BI3, A. spanius BI4, A. lwoffii BI10, BI11, BI12, and BI13), the alkaline phosphatase enzyme activity was determined, varying between 0.12  ±  0.03 and 1.83 ± 0.05 μmol p-NP/mL/h. The values obtained for the PGP bacteria and presented here are higher than those reported previously. Alkaline phosphatase enzyme activity varied between 1.41 and 2.15  μmol p-NP/mL/h in case of four bacterial strains (Bacillus brevis 2W4W1, B. polymyxa 1W5W5, B. thuringiensis 2P1M3, Xanthomonas maltophilia R85) isolated from wheat and pea plants (De Freitas et al. 1997). Viruel et al. (2011) determined values between 0.24 and 4.92 μmol p-NP/mg protein/h enzyme activities in soil with small Pi values for four bacterial strains (Serratia marcescens EV1, Pantoea eucalypti EV4, Pseudomonas tolaasii IEXb, Enterobacter aerogenes IEY). Rana et  al. (2012) investigated the effects of PGP bacterial strains on wheat plants and observed in case of inoculation with two bacterial consortia (Bacillus sp. AW1 and Brevundimonas sp. AW7 consortia, Providencia sp. AW5 and Brevundimonas sp. AW7 consortia, respectively) 1.4–1.94  μmol p-NP/g soil/h alkaline phosphatase enzyme activities in soil. Kang et  al. (2013) determined 0.022 and 0.13 μmol p-NP/g soil/h alkaline phosphatase enzyme activities from soil inoculated with Bacillus pumilus WP8 and Pseudomonas chlororaphis RA6 bacterial strains. This study confirms the alkaline phosphatase activity of Delftia lacustris, Achromobacter spanius, Pseudomonas protegens, and Acinetobacter lwoffii. Acid and alkaline phosphatase activity of Delftia lacustris strain when first described was

10

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also mentioned by Jorgensen et al. (2009), but no activity was measured. According to our best knowledge, we provide new evidence of alkaline protease activity for A. spanius, P. jessenii, D. lacustris, and A. lwoffii and alkaline phosphatase activity for A. spanius, P. protegens, D. lacustris, and A. lwoffii strains. In case of two D. lacustris strains (BI1, BI5) and one A. spanius BI4 strain, both alkaline phosphatase and protease activity was observed.

1.6

 rowth-Promoting Effect of Bacterial Treatment G on Wheat

Seeds of the same weight (0.3–0.4 g) of Triticum aestivum (wheat) were surface sterilized and germinated on filter paper for 48 h. The seedlings (1.5–2 cm shoot length) were transferred into autoclavable polypropylene boxes (size 34 × 23 × 16 cm) with lid. In these boxes steel sieves were made (25 × 15 cm, height 2 cm), with 4-mm-diameter holes, and the distance between the holes were 20 mm. The boxes with the sieves were sterilized by autoclaving at 121 °C, 15 min. Seedlings were wrapped in sterile buds and were placed 4 cm from each other (20–30 seedlings/box). For plant growth a nutrient solution was used containing the minimum necessary elements as follows: macroelements, 1.85 g L−1 MgSO4‧7H2O, 1.66 g L−1 CaCl2‧2H2O, 5 g L−1 peptone, and 2.5 g L−1 phytic acid sodium salt as organic nitrogen and phosphorus source, and microelements, 0.44  mg  mL−1 MnSO4‧4H2O, 0.16  mg  mL−1 H3BO3, 0.15  mg  mL−1 ZnSO4‧7H2O, 0.08  mg  mL−1 KI Fe-EDTA, 3.73 mg mL−1 Na2EDTA, and 2.78 mg mL−1 FeSO4‧7H2O. Bacterial cultures were grown for 24 h in a rotary shaker (150 RPM) in 100 mL flasks filled with 25  mL TSB broth. Following the seedling transplant, each was inoculated with 1 ml bacterial inoculum (108 CFU mL−1) of the selected bacterial strains or bacterial consortium. Plants were placed in an environmental growth chamber (Sanyo MLR-351) at 25 °C, 70% relative humidity using a lighting program of 12 h/day with 2500 lx. After 11 days of growth, plants were harvested, and the shoot and root length and wet and dry biomass were determined. The tests were carried out in 8–15 replicates for each plant. Data obtained were compared to uninoculated control, using PAST statistical program. The treatment of wheat plants with three selected isolates resulted different effects on dry and wet biomass production. Table  1.2 presents the results of the bacterial inoculation experiment on plant growth and biomass under gnotobiotic conditions. Bacterial isolates D. lacustris BI5 and P. jessenii BI7 significantly increased the shoot length of plants compared to the uninoculated plants; the relative increase was of 33.05% (11.43  ±  1.32  cm) and 25.27% (10.76  ±  1.4  cm), respectively. The inoculation with A. lwoffii BI13 strain showed no significant effect on the shoot length of wheat plants. However, A. lwoffii BI13 strain used in consortia with P. jessenii BI7 strain showed a higher increase on wheat shoot length (43.48%) than the P. jessenii BI7 strain alone (Fig. 1.1a). Regarding the total weight of the plants, the inoculation with D. lacustris BI5 slightly stimulated (9.37%), whereas P. jessenii BI7 strain had no influence on the plant growth (Fig.  1.1b).

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11

Table 1.2  Influence of the bacterial treatments on wheat growth Bacterial strains Total weight (g) Shoot length (cm) Wet weight of the shoot (g) Dry weight of the shoot (g) Wet weight of the root (g) Dry weight of the root (g)

D. lacustris BI5 0.084 ± 0.012* 11.43 ± 1.32*

P. jessenii BI7 0.080 ± 0.01 10.76 ± 1.40*

A. lwoffii BI13 0.068 ± 0.01 8.44 ± 1.81

P. jessenii BI7 + A. lwoffii BI13 0.083 ± 0.009* 12.32 ± 1.02*

0.058 ± 0.01

0.058 ± 0.01

0.046 ± 0.011

0.0616 ± 0.0068*

0.010 ± 0.001*

0.010 ± 0.001*

0.007 ± 0.001

0.009 ± 0.001*

0.021 ± 0.007

0.017 ± 0.006

0.018 ± 0.005

0.018 ± 0.006

0.004 ± 0.001

0.002 ± 0.000

0.003 ± 0.001

0.004 ± 0.001

*Significantly different from the control for p 20 Above mineral soil surface, topsoil Regular + occasional Weeks–months

Variable Below Ah/Ap, subsoil

10–20 Below Ah/Ap, subsoil

Occasional

Occasional

Days–weeks

Days

Occasional + regular A day (weeks)

are not constant; it varies temporally. The extent and regularity of hot moments generally depend upon (1) regular availability of labile C or the input source and (2) the rates of microbial use of input (Herron et al. 2013). Accordingly, hotspot formation requires variability. Many properties and process rates in soil surrounding hotspots vary by orders of scale within very short distances and periods. The duration of the hotspot is determined by the dynamic nature of C input. Constant availability of inputs or labile carbon source led to the longer existence of hotspots.

9.3

Microbial Activities as a Driver of Hotspot Performance

The microbial hotspots have two to three times greater diversity and microbial biomass over bulk soil (Marschner et al. 2012). However, the dominant part of this total biomass is shared by dormant microbes, while active microbes represent a small share is known to perform a range of biochemical processes. Populations of active microorganism in the root rhizosphere are two to three times more compared to bulk soil (Blagodatskaya et al. 2014). In the detritusphere, a zone where C liberation is taking place for longer and the microbial root competition is fairly weaker compared to rhizosphere, the population and biomass of active microbes reported to 4–20 times greater than that of in bulk soil (Blagodatskaya et al. 2009). Microbial hotspots because of their high density of C substrate and longer hot moments are generally outstanding in terms of active microorganisms’ biomass, particularly in a physiologically alert stage (Table  9.2). For example, due to some reason, many researchers reported that the activity of hydrolytic enzymes in rhizosphere zone was 3–5 times greater (Lee et al. 2013), whereas the N2O emissions from the detritusphere region were 2–9 times more intensive (Blagodatskaya et al. 2010) compared to bulk soil. Therefore, it is very clear that hotspots are not only rich in total microbial biomass, but also the portion of active microbes is also higher in hotspots which are very important for biochemical processes within the soil (Table 9.2).

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Table 9.2  Relative changes of PLFA content by activation/deactivation of soil microbial community during hot moments (Kuzyakov and Blagodatskaya 2015) Relative changes in PLFA content Bacterial Effect of Total Fungal Gram + Hotspots in comparison with bulk soil Plant roots ↑ 1.5–1.7 ↓ 1.1–1.3 ↑↓ 1.1 (rhizosphere) Plant growth ↑ 1.7 ↑ 1.8 Plant species ↑ 1–1.7 ↑ 1.4–2 ↑ 1–1.2 Detritusphere Detritusphere

↑ 1.8–5.1 ↑ 1.1–1.4

↑ 11–68 ↑ 2–2.3

↑ 2.1–↓ 1.6 ↑ 1.5–↓ 1.3

Detritusphere

↑ 1.2

↑ 2.5–4

↑ 1.1–1.3

Activation during hot moments Rewetting ↑ 1.4–1.6 Available ↑ 2.4 ↑ 50 nutrients 1.1 Wheat straw ↑ 1.7 and fertilizer Barley straw ↑4 Leaf litter ↑ 1.5–4.7 Sorghum ↑ 1.7–2 ↑ 2.3–3 residues Hotspot expiration–end of hot moments One-year ↓ 3.5–3.6 ↓ 6–10 incubation Soil depth ↓3 ↓ 3.5 Decreasing pH ↓ 2.1 ↑ 1.3 Grazing ↓2

Gram −

Source

↑ 1.1–1.3

Denef et al. (2009)

↑2 ↑ 1–1.3

Lu et al. (2004) Hamer and Makeschin (2009) Baldrian et al. (2010) Marschner et al. (2012) Rousk and Bååth (2007) McIntyre et al. (2009) Ehlers et al. (2010)

↑ 1.2 ↑ 1.7

↑ 5.5

↑ 1.3 ↑ 1.5

↑2

↓ 2.7–5

↓ 2.9–6

↓ 1.5 ↓ 1.7 ↑2

↓ 2.7

Pietri and Brookes (2009) Rousk and Bååth (2007) McIntyre et al. (2009) White and Rice (2009)

Feng and Simpson (2009) White and Rice (2009) Djukic et al. (2010) Klumpp et al. (2009)

9.3.1 Microbial Diversity and Community Structure in Hotspots The microbial hotspots are rich in microbial diversity especially of active microbes over bulk soil (Marschner et al. 2012). The principal reason for higher biomass of microbes in these microbial hotspots is higher substrate or C input availability which stimulates their growth and shapes community structure. Size and shape of the microbial community affected by locality of hotspot and type of substrate availability (Table 9.2).

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9.3.2 Microbial Strategies and Competition in Hotspots Microbial functions within microbial hotspot region are defined by the supremacy of the ecological groups, i.e., r- and K-strategists (Nottingham et al. 2009). However, the phylogenic structure of the microbial community is not directly governed by supremacy as most of the bacterial and fungal phyla are reported to have both r- and K-strategists. The dominant type of strategy within the microbial hotspots can be analyzed by the kinetics and effectiveness of microbial growth. Kinetic parameters of microbial communities suggest that the addition of very minute amounts of labile carbon substrates can be able to activate fast-increasing strategists in the microbial hotspots (Blagodatskaya et al. 2010). Many studies proved that rhizosphere, detritusphere, and biopores are the microbial hotspots with great microbial biomass and activity compared to bulk mineral soil, but a few reports have been found on the aspect of competition between microbes in these hotspot sites. The amount and availability of labile C substrates in detritusphere and rhizosphere are known to define their competition structure. For example, the detritusphere is the preferred site for the competition between microbial species, whereas in rhizosphere this occurs mainly between microbes and plants (Kuzyakov and Xu 2013).

9.3.3 Signal Pathways at Hot Moments Microorganisms change physiological states (i.e., from active stage to dormant stage and vice versa) on the basis of availability of labile C substrates. So, labile C availability plays an important role in the adaptation of microbes to dynamic environmental conditions in the hotspots. However, some of the physicochemical factors of soil (i.e., moisture and temperature) are also known to play a vital role in the switching of physiological states of soil microbes in the hotspots. Apart from these factors, signaling molecules are also of a prime significant factor in activation/deactivation mechanisms of the microbes. Many studies suggested that transition of active cells to dormancy is mainly governed by quorum sensing, i.e., a phenomenon in which secretion of sensing molecules stirs up the reduction of population density of microbes in subjected hotspots (Gray and Smith 2005).

9.3.4 Instruments for Characterization of Hotspots The pH changes within microbial hotspot can be reported with gels (Hinsinger et al. 2009) or by placing pH and redox microelectrodes near to the root zone of the plant. Autoradiography and its follow-up imaging are also good means for localization of rhizodeposits and of uptake of nutrients by microbes in the hotspot sites (Rasmussen et al. 2013). However, many times this type of localizations through autoradiography does not necessarily reveal the exact location and pattern of microbial hotspots. These parameters can use to define the microbial activity (CO2/O2 changes) of the microbial hotspot. Recently developed soil zymography technology is able to locate

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the hotspots by analyzing the activities of various soil enzymes, i.e., protease, amylase, acid and alkaline phosphatases, cellulase, and chitinase (Eickhorst and Tippkotter 2008).

9.4

Ecological Significance of Microbial Hotspot

The higher rates of biochemical processes within the hotspot zone over bulk soil are of special ecological significance as this directly or indirectly associated with substrate availability. Microbial hotspots directly affects decomposition and mineralization of crop residue, amount of rhizodeposits and soil organic matter, microbial populations, and release of nutrients. The hotspots of soil also govern the rates of processes related to C transformation, i.e., microbial immobilization of soil N and other plant nutrients as well as consumption of O2 and electron acceptors available in the soil and root sites (Rudolph et al. 2013).

9.5

Strategies for Hotspot Management

Rhizospheric and detrituspheric soils are characterized by high concentrations of labile C and hence are hotspots of microbial activity. Furthermore, the microbial community structure modifies with distance from roots or residues. Marschner et al. (2012) reported the higher activities of ß-glucosidase, xylosidase, and phosphatase in the vicinity (1–2 mm) of roots and residue-amended soil at 2 weeks after planting, with usually greater activities in the vicinity of the residue-amended soil over roots (Fig. 9.1).

Manipulated crop type and cropping systems Effecient species

Manipulated root system

Cropping system

Rhizosphere

Root proliferation; Root activity Root exudation; Effecient genotypes

Manipulated microbes

Microorganisms; PGPR Mycorrhiza

Fig. 9.1  Strategies for hotspot management

Manipulated rhizoenvironment

Localized nutrient supply; Rhizosphere fertilization; Rhizosphere nutrient intensity; transplant with rhizo-soil

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R. K. Yadav et al.

9.5.1 M  icroscale Distribution and Function of Soil Microbes in the Interface Between Rhizosphere and Detritusphere In general, results of a case study involving samples amended with maize residue show that the degree of microbial structure did not overlap resulting in a U-shaped pattern of activities in the rhizosphere-detritusphere interface. The amount of PLFAs which is directly associated with activity and biomass of soil microbes was nearly 30% more in detritusphere zone over rhizosphere. The major part of reported PLFAs primarily belongs to fungal communities and their activities, and biomass was 5–7 times higher in the roots of plants of residue-amended soil as compared to unamended soil. Plant roots and soils amended with crop residue have the potential to strongly affect the amount of PLFAs especially in the root vicinity zone due to their richness in terms of easily degradable carbon substances. The microscale gradients of various soil enzymes and bacterial and fungal PLFAs within interface and between rhizosphere and detritusphere zones are directly controlled by carbon inputs of the soil. Due to their higher density of carbon, the overall effect of crop residue was larger than that of root compartment.

9.5.2 Role of Organic Layer-Mediated Microbial Hotspots Soils with high density of organic carbon are treated as organic layer which strongly acts as hotspots for microbes in respect to their activity, abundance, and diversity. A microbial enzymatic activity was found much higher in soils rich in organic carbon compared to mineral soils. In comparison to mineral soil, the organic-rich soils may be a good representative for a hotspot resulted in higher productivity and faster cycling of various essential nutrients in the associated agroecosystem (Lee et  al. 2012). Archaeal diversity was found to be greatly affected with changes in soil types, while diversity index of bacteria and fungi did not exhibit any significant change with respect to type of soil. The dissimilarity in microbial abundance and diversity indicated that there was geographical aberration in the microbial community even in Arctic tundra regions with similar temperature conditions. This may be due to historical difference in the development of the soil layer between each tundra region resulting to different evolutionary processes in the microbial populations. The identification of active microbes in context of the spatial heterogeneity of tundra soils, temperature, and moisture conditions is necessary to know the understanding of nutrient cycling in Arctic systems (Lee et al. 2012).

9.5.3 M  icrobial Community and Their Structures in Residue-­ Amended Soil Microbiological processes are playing a great role for the various ecological functions of soils due to their extended role in input and output dynamics of soil organic matter (SOM) content. Organic carbon content of soil which may lose through

9  Soil Microbial Hotspots and Hot Moments: Management vis-a-vis Soil Biodiversity

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erosion or mineralization can be balanced by the incorporation of crop straw (Singh et  al. 2015, 2016; Meena et  al. 2013, 2015). A comprehensive study of samples (residues, detritusphere, and bulk soil) regarding diversity and structure of different bacterial and fungal communities in terms of PLFAs of soil amended with wheat residue highlighted the existence of a succession of populations following wheat straw incorporation, as proved in recent studies focused on plant residue decay in soil (Ranjard et al. 2003). A Monte Carlo test of samples amended with wheat straw has been executed to assess the significant level of the imbalance between incubation times and has allowed the deduction of magnitude for community that was found in following sequence: bulk soil