Metagenomics and Microbial Ecology: Techniques and Applications

214 Pages·2021·20.786 MB·English

by  Amrita Kumari Panda, Satpal Singh Bisht, Fengliang Jin, Surajit De Mandal, N. Senthil Kumar

Metagenomics and
Microbial Ecology

Metagenomics and
Microbial Ecology
Techniques and Applications
Edited by
Surajit De Mandal, Amrita Kumari Panda,
Nachimuthu Senthil Kumar, Satpal Singh Bisht,
and Fengliang Jin
First edition published 2022
by CRC Press
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Library of Congress Cataloging‑in‑Publication Data
Names: De Mandal, Surajit, editor. | Panda, Amrita Kumari, editor. | Senthil Kumar, N., editor. | Bisht, Satpal Singh,
editor. | Jin, Fengliang, editor.
Title: Metagenomics and microbial ecology : techniques and applications / edited by Surajit De Mandal, Amrita
Kumari Panda, N. Senthil Kumar, Satpal Singh Bisht, Fengliang Jin.
Description: First edition. | Boca Raton : CRC Press, 2022. | Includes bibliographical references and index.
Identifiers: LCCN 2021031758 | ISBN 9780367487348 (hardback) | ISBN 9781032140209 (paperback) |
ISBN 9781003042570 (ebook)
Subjects: MESH: Metagenomics | Environmental Microbiology | Microbiological Phenomena
Classification: LCC QH434 | NLM QU 460 | DDC 572.8/629—dc23
LC record available at https://lccn.loc.gov/2021031758
ISBN: 9780367487348 (hbk)
ISBN: 9781032140209 (pbk)
ISBN: 9781003042570 (ebk)
DOI: 10.1201/9781003042570
Typeset in Times LT Std
by Apex CoVantage, LLC
Contents
Preface .....................................................................................................................................................vii
Editors .......................................................................................................................................................ix
Contributors ..............................................................................................................................................xi
Section I An Overview of Metagenomics ����������������������������������������������1
1 Principles and Analysis of Metagenomics Data ����������������������������������������������������������������������������3
A. Rawat, P. Singh, S. Al Khodor
Section II Metagenomics Tools to Access Microbial Diversity �������������19
2 Metagenomic Tools for Taxonomic and Functional Annotation �����������������������������������������������21
Yordanis Pérez‑ Llano, Sara Cuadros‑O rellana, Alma Delia Nicolás‑ Morales,
Ramon Alberto Batista‑ García, María del Rayo Sánchez‑ Carbente,
Natividad Castro‑ Alarcón, Jorge Luis Folch‑ Mallol
Section III Metagenomics of Extreme Environments ����������������������������45
3 Metagenomic Insights into the Microbial Communities of Desert Ecosystems ����������������������47
Satish Kumar, Bharat Bhushan, G.C. Wakchaure, Kamlesh K. Meena, Mahesh Kumar,
Ajay Kumar Singh, Ajinath Shridhar Dukare, Jagadish Rane
4 Metagenomic Approaches for Exploration of Halophile Prokaryotes in Coastal Areas ��������63
Jamseel Moopantakath, Madangchanok Imchen, Athira CH, Ranjith Kumavath
5 Metagenome Assembly for Gut Microbial Functional Diversity Associated with
Xenobiotic Degradation �����������������������������������������������������������������������������������������������������������������79
Ashok Kumar Sharma, Vinay Shankar Dubey
Section IV Metagenomics of Various Ecotypes �������������������������������������89
6 Earthworm Gut Microbiome: The Uncharted Microbiome ������������������������������������������������������91
Rashi Miglani, Amrita Kumari Panda, Monu Bala, Jyoti Upadhyay, Nagma Parveen,
Ankit Kumar, Surajit De Mandal, Satpal Singh Bisht
7 Metagenomics of Pollen-Borne Microbes and Gut Microbiota of the Honey Bee �����������������105
Sampat Ghosh, Saeed Mohamadzade Namin, Chuleui Jung
8 Viral Metagenomics ����������������������������������������������������������������������������������������������������������������������117
Hugo G. Castelán‑ Sánchez, Xiaolong Liang, María del Rayo Sánchez‑ Carbente,
Sonia Dávila Ramos
v
vi Contents
9 Freshwater Metagenomics: Overall Scenario ���������������������������������������������������������������������������139
D. Patel, P. Chunarkar Patil
Section V Applications �������������������������������������������������������������������������153
10 Microbiomes in the Rice Ecosystem �������������������������������������������������������������������������������������������155
Arabinda Mahanty, Srikanta Lenka, Prabhukarthikeyan SR, Totan Adak, Raghu S.,
Prakash Chandra Rath, Koustav Kumar Panda, Amrita Kumari Panda
11 Ecosystem Services of Microbes �������������������������������������������������������������������������������������������������165
Joystu Dutta, Tirthankar Sen
12 Commercial Exploitation of Microbial Communal Services to Enrich
Plant Microbiome �������������������������������������������������������������������������������������������������������������������������181
Adhikesavan Harikrishnan, Ramasamy Shanmugavalli, Oshin K, Vijaykumar Veena,
Basavegowda Lakshmi
Index ������������������������������������������������������������������������������������������������������������������������������������������������������193
Preface
Natural environments have unique ecosystems with a large diversity of microbial dark matter.
Understanding and characterizing these microorganisms will be an important step toward discovering
novel products or understanding complex biological systems. Researchers working in the field of micro-
bial taxonomy are well aware of the remarkable changes that have occurred over the last decade through
next- generation sequencing (NGS) technology. The introduction of high- throughput cost- effective NGS
technology has expanded the possibilities of genomic research in various biological systems, allowing
parallel sequencing analyses of multiple genes effectively at any desired depth of coverage. These methods
are currently considered an important tool for studying the taxonomic and functional characteristics of
microorganisms in various ecosystems. This also led to the discovery of rare microorganisms present
in low abundance. However, it is often difficult for young researchers to fully understand and apply
NGS in their research due to the sophisticated instrumentation, large amounts of generated data, and
complex bioinformatics tools for annotation. Metagenomics completely revolutionized microbial dark
matter research by exploring environmental samples. Metagenomics diverges from genomics study, as
it focuses on intricate biological interactions such as horizontal gene transfer, population dynamics, and
nutritional complementation among microbial consortia. Metagenomics projects mainly use two types
of methods: amplicon sequencing and shotgun sequencing, but the experimental strategy, sequencing
technology, and analytical bioinformatics tools vary per the requirements to facilitate microbial ecol-
ogy research.
The purpose of this book is to present these advances to better understand the status and application
of NGS technology in microbial ecology projects. This book will also help young researchers to under-
stand and learn new scientific tools and their subsequent applications to address future challenges. In
this book, Metagenomics and Microbial Ecology: Techniques and Applications, renowned scientists and
professors explore the most recent advances in the landscape of next- generation sequencing technolo-
gies for studying microorganisms and their communities in different environments. The whole book
is divided into five sections. Section I deals with an overview of metagenomics. Section II describes
various metagenomic tools used to assess microbial diversity. Section III describes metagenomic studies
conducted under extreme conditions, including halophiles in the coastal area, desert ecosystems, and
xenobiotics. Section IV of this book describes the metagenomic studies in various ecotypes. Finally, the
recent application of metagenomics is discussed in Section V.
vii

Editors
Surajit De Mandal, Ph.D., is a post- doctoral researcher at the College of Agriculture, South China
Agricultural University, Guangzhou, P. R. China. He has eight years of research experience and has
published several research articles in international journals. He also acts as an editorial board mem-
ber/reviewer for various international journals. His fields of interest include microbial diversity and
metagenomics, molecular phylogeny, bioinformatics, and microbial control of insect pests. He is pres-
ently working on microbial community analysis using next- generation sequencing methods.
Amrita Kumari Panda, P h.D., is currently working as an assistant professor of biotechnology at the
Department of Biotechnology, Sant Gahira Guru Vishwavidyalaya Sarguja, Chhattisgarh, India. She
obtained her doctoral degree in biotechnology from Berhampur University, Odisha, India. Dr. Panda
received a Fast Track Post Doctoral fellowship from the Science and Engineering Research Board,
Government of India, New Delhi. She has more than eight years of research experience in the field
of molecular microbiology and microbial diversity and has published several articles in national and
international peer- reviewed journals. She received the Federation of European Microbiological Society
(FEMS) Meeting grant award in the year 2014. Her research interests include metagenomics and micro-
bial diversity.
Nachimuthu Senthil Kumar, P h.D., is Professor in the Department of Biotechnology, Mizoram
University, with 20 years of teaching and research experience. His fields of interest include genom-
ics, molecular phylogeny, and bioinformatics. He is presently working on metagenomics, cancer DNA
markers, and mutation analysis. During his post- doctoral stint at Sun Yat- sen University, China, he was
involved in RNAi studies with the chitin synthase gene. He has authored more than 120 research papers,
and he is the investigator of various national research projects.
Satpal Singh Bisht, D.Sc., has been an inspiring professor and researcher in the field of life sciences
for 20 years. Dr. Bisht is an internationally acclaimed biologist/academician and an administrator. He
completed his doctoral degree in 1992 from Kumaun University, Nainital Uttarakhand, India. Dr. Bisht
presently works as Professor of Zoology and Dean of Biomedical Sciences at Kumaun University. He has
published many research papers and articles in journals of international repute and visited many coun-
tries on academic assignments. Prof. Bisht is a member of various academic bodies at many universities
and colleges. His major research interests include exploring the gut microbiome of earthworms using
next- generation sequencing and DNA barcoding of mountain earthworms. He has served as an editor
and reviewer for many journals and has been nominated for and received many professional awards from
many academic organizations.
Fengliang Jin, Ph.D.,  is presently working as a professor in the Department of Entomology, College of
Agriculture, South China Agricultural University, Guangzhou, P.R. China. His major research interest
is in the role of non- coding RNAs in the regulation of insect immune signal transduction, exploring the
interaction mechanism of insects to entomopathogens using next- generation sequencing, bioinformatic
analysis, and RNAi-b ased functional analysis of immune- related genes and their role in the regulation
of antimicrobial peptides of insects. Prof. Jin served as a principal investigator for several research proj-
ects related to the development of biopesticides at various agencies. He has several patents and scientific
articles and is currently serving as a reviewer and editor for many international journals.
ix