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Manoj Nath · Deepesh Bhatt Prachi Bhargava D. K. Choudhary Editors Microbial Metatranscriptomics Belowground Microbial Metatranscriptomics Belowground Manoj Nath • Deepesh Bhatt • Prachi Bhargava • D. K. Choudhary Editors Microbial Metatranscriptomics Belowground Editors Manoj Nath Deepesh Bhatt Indian Council of Agricultural Research Shree Ram Krishna Institute of Computer (ICAR)-Directorate of Mushroom Education and Applied Science, Sarvajanik Research (DMR) Education Society Solan, Himachal Pradesh, India Surat, Gujarat, India Prachi Bhargava D. K. Choudhary Institute of Biosciences and Technology Amity Institute of Microbial Technology Shri Ramswaroop Memorial University Amity University Barabanki, Uttar Pradesh, India Noida, Uttar Pradesh, India ISBN 978-981-15-9757-2 ISBN 978-981-15-9758-9 (eBook) https://doi.org/10.1007/978-981-15-9758-9 # The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2021 This work is subject to copyright. All rights are solely and exclusively licensed 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. 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The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Preface For the compilation of this book, emphasis has been given on the role of functional microbes belowground, i.e., in the rhizosphere to know the response to their metatranscriptomics level and impact on aboveground response. The functional or metatranscriptomics learning provides the detailed acclimation about the functional or transcriptional profiles of discrete microbial populations within a phytomicrobiome that reveals the molecular action of a microbiome and their regulatory mechanisms around the phytosphere. In the present compendium, main emphasis has been given on the following points: • Occurrence and distribution of microbial communities • In situ active microbial quorum in the rhizosphere • Metatranscriptomics for microflora- and fauna • Functional diversity in the rhizosphere • Importance of PGPRs in the rhizosphere • Root endotrophic microbes • Functional AM fungi in the rhizosphere • Functional protozoans belowground • Functional infochemicals • Location of microbe in plant • Root epiphytic microbes • Nitrogen-fixing bacteria • Functional microbial determinants • Functional niche under biotic stress • Functional niche under abiotic stress • Functional root-derived signals • Functional microbe-derived signals • Approaches deployed in metatranscriptomics • Functional defence signals • Molecular Tools used in the rhizosphere • Perspectives of metatranscriptomic in belowground functioning • Metatranscriptomics for siderophore producing microbes • Metatranscriptomics for microbe–plant signals v vi Preface • Metatranscriptomics for Pi-solubilizing producing microbes • Metatranscriptomics for improving soil fertility • Metatranscriptomics for pathogenic microbes in the rhizosphere This book is organized in 31 chapters that deliberate on microbial transcriptomics belowground and their response aboveground wherein structural and functional divergences of microbes rely on the deployment of various phenotypic and molecular approaches incurred. Chapter 1 seeks to get comprehensive knowledge on soil metatranscriptomics analysis including obtaining biologically important information from transcriptome datasets, comparative information to other transcriptome analysis techniques, bioinformatics tools and technical challenges applied to soil metatranscriptomics. Chapter 2 concludes with a brief reference to some of the advanced molecular tools available to explore microbial diversity in belowground. Chapter 3 discusses on the role of the functional rhizosphere in phytomicrobiome wherein extraction and purification of mRNA immediately from plant, decomposi- tion of natural material and soil, accompanied with pooling of expressed genes by using high-throughput sequencing, have spawned metatranscriptomics a new rising area of research. Chapter 4 defines the utilization of functional infochemicals that provide the pathways for insect management by mating disruption, mass trapping, monitoring of pest infestation, mass annihilation. Thereby, these infochemicals can be an important component of sustainable management of insect pests and also Integrated Pest Management (IPM). Chapter 5 encompasses the deployment of synthetic biology in the genetics of the nitrogenase enzyme and its engineering in phytomicrobiome responses. Chapter 6 encompasses the role of functional AM fungi on various fruit crops that considered for useful organic cultivation and also for expanding the fruit crop in low fertility degraded soil with less expenditure and minimum reduction to yield. Chapter 7 encompasses the role of PGPRs in the rhizosphere and activities performing in that zone with varied potential of PGPRs in crop production for commercial uses. Chapter 8 seeks to disclose the role of flavonoid infochemicals in the modifier of the rhizospheric ecosystem favouring plant growth and development. These biochemicals play the role of signals to call the beneficial microbes towards plant root and deterring the pathogenic species away from the rhizosphere due to which they are also described as “Infochemicals”. Chapter 9 discusses various mechanisms adopted by the soil microbes to abrogate the negative effects of abiotic stresses in plants for their better growth and productivity. Chapter 10 defines the signalling molecules including transcription factors and volatile compounds and their role in plant defence response. Chapter 11 seeks to get comprehensive knowledge of techniques that are used to study metatranscriptomics and bioinformatics tools to interpret the most valuable knowledge from sequencing data. Preface vii Chapter 12 discusses the functional role of rhizobacteria such as biocontrol activity, phytohormone secretion, siderophore production, mineral solubilization, nitrogen fixation and enzyme production and their occurrence, distribution and functions belowground. Chapter 13 encompasses insights into the biodiversity of psychrotrophic microbes, their adaptation strategies and their potential applications in agriculture, medicine, industry, food and allied sectors. Chapter 14 defines the functional role of microbial diversity in the rhizosphere zone and its significance to the crop and soil. A diverse population of microbes associated with different activities in the rhizosphere zone is discussed in detail in this chapter. Chapter 15 seeks to get knowledge of various abiotic stress conditions including temperature, salt, drought, water-logging and metal toxicity stress, and how they influence the structure and diversity of the inhabiting microbial community structure and diversity. Chapter 16 summarizes the functional behaviour of the microbial communities which may include a group of species trait represented as an individual or species leads to the functional diversity in the rhizosphere. Chapter 17 provides an insight into the diverse and compact world of root surface associated microbes with their structural and functional divergence. Chapter 18 reviews the plant root associated endophytes, factor affecting, functionalities and understanding interaction between microbiome associated within plant root. Chapter 19 focuses on the strategies and methods that are adopted to manipulate the plant–soil microbiome interactions, various mechanisms that are involved in the interactions and the impact of this technology on the plant and soil. Chapter 20 seeks to get comprehensive knowledge wherein Sundarbans replan- tation schemes require the microbiome niche to be maintained if successful restora- tion is to be achieved either in the form of suitable site-specific plantations or microbial consortium based supplementations. Chapter 21 discusses the major headway in this exponentially proliferating field, comparing the various options used in the computational bioinformatical analysis of data and the challenges associated with them. Chapter 22 discusses the concepts, tools and techniques used to investigate metatranscriptome and will further highlight its application in understanding the microbial structure and function. Chapter 23 defines a microbiome wide association study with known disease causing microbial datasets and predict the potential pathogenic microorganisms that are

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