Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications Tulasi Satyanarayana • Subrata Kumar Das Bhavdish Narain Johri Editors Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications Volume 2. Soil & Agroecosystems Editors Tulasi Satyanarayana Subrata Kumar Das Division of Biological Sciences Division of Molecular Microbiology and Engineering Institute of Life Sciences Netaji Subhas University Bhubaneshwar, Odisha, India of Technology (NSUT) New Delhi, Delhi, India Bhavdish Narain Johri Department of Biotechnology Barkatullah University Bhopal, Madhya Pradesh, India ISBN 978-981-13-8486-8 ISBN 978-981-13-8487-5 (eBook) https://doi.org/10.1007/978-981-13-8487-5 © 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 Preface The outer loose material of the Earth’s surface, which is distinctly different from underlying bedrock, is soil. This originates from physico-chemical and biological weathering of rocks. Soil is an admixture of five major components, viz. mineral matter, organic matter, soil-air, soil water and soil organisms. Soil is not a mass of debris, but teeming with life. Every small particle of soil contains numerous types of living organisms belonging to the Bacteria, Archaea and Eucaryota domains, and viruses; living organisms which are too small to be seen with the naked eye are microbes, microorganisms or microscopic organisms. Soil microorganisms are vital for the continuing cycling of nutrients and for driv- ing aboveground ecosystems. It is important to study microbial diversity not only for basic scientific research, but also to understand the link between diversity and com- munity structure and function. Soil microorganisms influence aboveground ecosys- tems by contributing to plant nutrition, plant health, soil structure and soil fertility. The activity and species composition of microbes are, however, generally influenced by many factors including physico-chemical properties of the soil, temperature and vegetation. The dynamics of soil microbes have important implications for the response of subsurface soil ecosystems to perturbations. Despite all attempts to mea- sure fluxes and gross microbial pools, the soil and its microbiota still remain a black box. Most soil microorganisms are still unknown. The comparison between direct microscopic counts and plate counts indicates that less than 0.1% of agricultural soil microorganisms are culturable. Understanding the diversity and dynamics of indig- enous microbial populations represents a challenge to modern soil ecology. The rhizosphere, the narrow zone of soil that is influenced by root secretions, can contain up to 1011 microbial cells per gram root and more than 30,000 prokaryotic species. The collective genome of this microbial community is much larger than that of the plant, which is also known as the plant’s second genome. The microflora of most soils is carbon starved. Since plants secrete up to 40% of their photosyn- thates into the rhizosphere, the microbial population densities in the rhizosphere are much higher than those in the surrounding bulk soil; this phenomenon is known as the ‘rhizosphere effect’. In general, rhizosphere microbial communities are less diverse than those in bulk soil. The mesmerizing diversity of microbes settling down in the rhizosphere are termed “root microbiome,” while their interaction with roots can result in a positive or negative outcome for plant fitness. Increasing evidence suggests that the v vi Preface microbial communities dominating the rhizosphere are influenced by the host geno- type. It appears that plants actively select and determine the composition of the root microbiome by releasing compounds in the rhizosphere which selectively stimulate microorganisms promoting plant growth and health or repress organisms that are deleterious to plants. Root microbiome is, therefore, a subset of a more diverse microbial community recruited from the surrounding bulk soil. The involvement of root microbiome on plant health becomes more evident in disease-suppressive soils. In these soils, a plant is unlikely to become infected by a soil-borne pathogen even when the pathogen is present and favoured by the plant. The phenomenon of disease suppression is well-known and is associated with the indigenous microbiota and activity. The mechanisms underlying this phenomenon have not, however, been fully understood. In this volume, Dubey and Sharma (Chap. 11) discuss the concept of rhizosphere engineering by employing synthetic microbial communities and the prospects of the rhizosphere microbiome engineering. Microbial diversity represents the variability among all types of microbes (pro- karyotes [archaea and bacteria], eukaryotes [algae, fungi, protozoa] and acellular viruses and others) in the natural world. Interest in the exploration of microbial diversity has stemmed from the fact that microbes are essential for life because they perform numerous functions essential for the biosphere that include nutrient cycling and environmental detoxification. The vast array of microbial activities and their importance to the biosphere and to human economies provide strong rationale for understanding their diversity, conservation and exploitation for society. For long, microbial diversity has been explored by conventional culture-­ dependent methods, which allow access to only 0.1–1.0% of the extant microbes in any ecosystem. Over the past two decades, several methods, such as rRNA gene sequencing, fluorescence in situ hybridization (FISH), denaturing gradient gel elec- trophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), restriction fragment length polymorphism and terminal restriction fragment length polymor- phism (T-RFLP), have been developed to assess microbial diversity and catalogue microbes without the need for isolation. The use of molecular techniques over the past 20 years has shown that only a very small fraction of microbial diversity so far has been catalogued from all the habitats investigated. Earth is considered to be inhabited by close to a trillion bacterial and archaeal species, and 10–15 million eukaryotic species; this prediction is based on ecological theory reformulated for large-scale predictions, an expansive dominance scaling law, a richness scaling relationship with empirical and theoretical support and the largest molecular surveys compiled to date [PNAS (2016) 113: 5970–5975]. The profound magnitude of our prediction of Earth’s microbial diversity emphasizes the need for continued investigation. Extensive and intensive efforts are being made to understand microbial diversity by both culture-dependent and culture-independent metagenomics approaches. Despite significant advances made in understanding microbial diversity, most microbes are characterized only by ‘molecular fingerprints’ and have resisted culti- vation. The microbiomics approach is now being adopted for surveying total Preface vii microbes present in different ecosystems (e.g. earth microbiome, ocean microbi- ome, human microbiome and rhizosphere microbiome, to mention a few). In order to analyse microbial populations in ecosystems such as skin and mucosal surfaces of humans and animals, plants, soil and oceans, Next Generation Sequencing (NGS) and advanced bioinformatics have become valuable tools. The Earth Microbiome Project (EMP), launched in 2010, is a landmark study for investigating large-scale microbial diversity. Bacterial and archaeal 16S rRNA diversity in 27,751 samples was analysed from 97 independent studies, which produced 2.2 billion sequence reads [PNAS (2018) 115: 4325–4333]. Only two-thirds of EMP reads could be mapped to the existing 16S references, which prevented meaningful Operational Taxonomic Unit (OTU) analysis. By leveraging metagenomics and metabarcoding of global top soil samples (189 sites, 7,560 subsamples), it has recently been observed that bacterial genetic diver- sity is very high in temperate habitats in comparison with fungi, and microbial gene composition varies more strongly with environmental variables than with geo- graphic distance [Nature (2018) 560: