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![TABLE 1.1 Calculating microbial diversity indices using alpha diversity.
Diversity indices Equation Variables Description Reference
Alpha diversity
Fisher’s Index (S) S 5 αln 1 1 N
α
S 5 Total number of species; α 5 Index of diversity of
population; N 5 Total number of individuals
Estimates logarithmic
distribution of number of
individuals of different species
Fisher
et al.
(1943)
Simpson’s Index
(D)
D 5 1
P
s
i51
Pi2
D 5 Simpson’s dominance index; S 5 Total number of
species in the community; pi 5 Proportion of
community represented by Operational taxonomic
unit (OTU)
Quantify number of species
present as well as their
abundance
Simpson
(1949)
Odum’s Index
(Rodum)
Rodum 5 S
ln N
ð Þ
Rodum 5 Odum’s Index; S 5 Total number of species;
N 5 Total number of individuals in the sample
Estimates species diversity Odum
et al.
(1960)
McIntosh Index Mc 5 [NO(Σni 2)]/[NON] Mc 5 McIntosh Diversity Index; ni 5 Number of
individuals belonging to i species; N 5 Total number
of individuals
Estimates species richness McIntosh
(1967)
McIntosh
Evenness Index
E 5 N 2 U
N 2 N=
ffiffi
S
p E 5 McIntosh Evenness Index; N 5 Total number of
individuals; S 5 Total number of species; U 5 Sample
size
Estimates species evenness McIntosh
(1967)
BergerParker
Index
D IBP 5 Nmax
Ntot
DIBP 5 BergerParker Index; Nmax 5 Number of
individuals of most abundant species; Ntot 5 Total
number of individuals of all the species in the sample
Estimates species abundance Berger
and
Parker
(1970)
Species Richness
Index
EðSÞ 5 fðk; NÞ E(S) 5 Expected value for number of species;
N 5 Number of individuals; k 5 Richness index
Estimates species diversity Peet
(2003)
Pielou Evenness J
0
5 H
0
H0
max
J0
5 Pielou evenness; H0
5 Number derived from
Shannon Diversity Index; H0
max 5 maximum possible
value of H0
Estimates species evenness Pielou
(1975)
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- 6. MICROBIAL DIVERSITY AND ECOLOGYIN HOTSPOTS
- 7. This page intentionallyleft blank
- 8. MICROBIAL DIVERSITY AND ECOLOGYIN HOTSPOTS Edited by APARNA GUNJAL Department of Microbiology, Dr. D.Y. Patil, Arts, Commerce & Science College, Pimpri, Pune, India SONALI SHINDE Annasaheb Kulkarni Department of Biodiversity, MES Abasaheb Garware College, Pune, India
- 9. Academic Press isan imprint of Elsevier 125 London Wall, London EC2Y 5AS, United Kingdom 525 B Street, Suite 1650, San Diego, CA 92101, United States 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom Copyright © 2022 Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress ISBN: 978-0-323-90148-2 For Information on all Academic Press publications visit our website at https://www.elsevier.com/books-and-journals Publisher: Stacy Masucci Acquisitions Editor: Linda Versteeg-Buschman Editorial Project Manager: Megan Ashdown Production Project Manager: Maria Bernard Cover Designer: Christian J. Bilbow Typeset by MPS Limited, Chennai, India
- 10. Contents List of Contributorsxi Preface xv Acknowledgments xvii 1. Exploration of microbial ecology and diversity in hotspots 1 SONALI SHINDE, PRATIK MUNOT, YOGESHWARI HIVARKAR, SHRUSHTI PATIL AND ANKUR PATWARDHAN 1.1 Introduction 1 1.2 Meaning of biodiversity, threats associated and need for its protection 2 1.3 Biodiversity hotspots: a brief overview 4 1.4 Tools for systematically studying the biodiversity hotspots through various aspects 4 1.5 Biodiversity hotspots and microbial ecology 6 1.6 Microbial hotspots: an overview 7 1.7 Microbial ecology: microbial habitats and the distribution of microbes 8 1.8 Microbial diversity indices: application in studying community ecology 10 1.9 Microbial composition and succession 10 1.10 Microbial interactions 15 1.11 Hotspots bioindicators/indicating unique environment of hotspots 17 1.12 Conclusion and way forward 18 References 18 2. Habitat-specific microbial community associated with the biodiversity hotspot 25 SARITA TIWARI, SANDHYA MOGHE, W.B. GURNULE, DEVIDAS S. BHAGAT AND APARNA GUNJAL 2.1 Introduction 25 2.2 Biodiversity hotspot in the Indian continent 26 2.3 Factors affecting biodiversity hotspots in India 26 2.4 The Himalayas 27 2.5 The Indo-Burma region 27 2.6 The Sundaland 28 2.7 The Western Ghats 28 2.8 Approach to safeguard biodiversity hotspots in India 29 2.9 Habitat-specific microbes of hotspot region 30 v
- 11. 2.10 Factors responsiblefor the diversity of habitat-specific microbial community in the Western Ghats 32 2.11 Habitat-specific microbes 33 2.12 The utility of microbial diversity 35 2.13 Importance of habitat-specific microorganisms in agriculture 35 2.14 Techniques used for assessing microbial diversity 36 2.15 Conclusion 38 2.16 Future prospects 39 References 39 3. Microbial diversity and ecology of saline environments from India 45 REBECCA S. THOMBRE AND AMITSINH V. MANGROLA 3.1 Introduction 45 3.2 Microbial diversity of saline lakes of India 47 3.3 Microbial diversity of Indian deserts 50 3.4 Microbial diversity of Indian solar salterns and halite deposits 53 3.5 Conclusion and future outlook 55 Acknowledgment 55 References 55 4. Marine microbial hotspots—especially related to corals 61 SHRUTI GUPTA, JULIUS EYIUCHE NWEZE AND SHARAD DNYANDEV SUBUGADE 4.1 Introduction 61 4.2 Symbiosis within the coral holobionts 63 4.3 Microhabitats of the coral microbiome 63 4.4 Profiling of coral-associated microbial diversity 65 4.5 Importance of coral microbiome for marine ecosystem 73 4.6 Conclusion and future perspectives 75 References 75 5. Phyllosphere microbiomes: implications and ecofunctional diversity 81 MOHAMMAD YASEEN MIR, SAIMA HAMID AND JAVID A. PARRAY 5.1 Introduction 81 5.2 Leaf surface and microbial growth 82 5.3 Phyllosphere microbiome: nature and composition 84 5.4 Bacterial diversity in the phyllosphere 86 5.5 Fungal microbiota of phyllosphere 86 5.6 Actinomycetes diversity in phyllosphere 87 5.7 Microbial interaction and phyllosphere 87 vi Contents
- 12. 5.8 Omics approachesand future prospective 92 References 92 6. Fungal association in hotspot of rhizosphere 97 MANJU SHREE SHAKYA HADA, RESHMA TULADHAR, ANIMA SHRESTHA, SARITA MANANDHAR AND ANJANA SINGH 6.1 Introduction 97 6.2 Fungal association in rhizosphere 98 6.3 Outcomes of fungal rhizosphere association 106 6.4 Application of fungal rhizosphere association 110 6.5 Conclusion 111 References 111 7. Diversity of actinomycetes in Western Ghats 117 APARNA GUNJAL AND DEVIDAS S. BHAGAT 7.1 Introduction 117 7.2 Actinomycetes 118 7.3 Habitat of actinomycetes 119 7.4 Growth of actinomycetes on different media 122 7.5 Diversity in enzyme production by actinomycetes isolated from the Western Ghats 122 7.6 Antimicrobial diversity of actinomycetes isolated from the Western Ghats 123 7.7 Biotechnological applications of actinomycetes from the Western Ghats 125 7.8 Conclusion 128 7.9 Future prospects 129 References 129 8. Microbial diversity at the polluted sites 135 SUNEETA GIREESH PANICKER 8.1 Introduction 135 8.2 Uranium 141 8.3 Thorium IV 141 8.4 Neptunium-237 141 8.5 Plutonium 141 8.6 Mechanisms involved in bioremediation 143 8.7 Biosorption 144 8.8 Bioaccumulation 144 8.9 Biotransformation 146 8.10 Biosolubilization 146 8.11 Bioprecipitation 147 8.12 Chelation 147 8.13 Complexation 148 vii Contents
- 13. 8.14 Conclusion 148 References148 9. Microbial diversity in termite gut ecosystem and their role in lignocellulosic degradation 155 GINCY MARINA MATHEW, RAVEENDRAN SINDHU, CHIEH CHEN HUANG, ASHOK PANDEY AND PARAMESWARAN BINOD 9.1 Introduction 155 9.2 Termite gut 156 9.3 Lignocellulose and their degradation in termites 161 9.4 Metagenomic approaches in termites for detecting glycosyl hydrolase genes for lignocellulosic degradation 163 9.5 Future perspectives of termites/their gut microbes in lignocellulosic degradation 169 9.6 Conclusion 170 Acknowledgments 170 References 170 10. Bacterial diversity from Garampani warm spring, Assam 177 JOYASREE DAS, PRADIPTA SAHA AND SRINIVASAN KRISHNAMURTHI 10.1 Introduction 177 10.2 Methods 178 10.3 Results 183 10.4 Discussion 199 10.5 Conclusion 201 Acknowledgments 201 References 202 11. Diversity and biotechnological importance of cellulolytic microorganisms from biodiversity hotspots 207 HIMANSHU AND JITENDRA KUMAR SAINI 11.1 Lignocellulose: composition and availability 207 11.2 Lignocellulolytic enzyme system 209 11.3 Applications of ligninolytic enzymes 212 11.4 Applications of cellulolytic and xylanase enzymes 212 11.5 Diversity of culturable cellulolytic microbes 213 11.6 Metagenomic diversity of cellulolytic microbes 219 11.7 Metaproteomic analysis of cellulolytic microbes 221 viii Contents
- 14. 11.8 Metatranscriptomic analysisof cellulolytic microbes 222 11.9 Conclusion 223 References 223 12. Biodiversity of cold-adapted extremophiles from Antarctica and their biotechnological potential 231 LAXMI JADHAV, VRUSHALI PHALKE, STUTEE PANSE, SMITA PATIL AND ASHOK BANKAR 12.1 Introduction 231 12.2 Biodiversity of extremophiles from Antarctica 233 12.3 Potential hotspots in Antarctica 235 12.4 Cold adaption mechanisms in psychrophiles 239 12.5 Biotechnological applications of psychrophiles from Antarctica 239 12.6 Bioremediation 250 12.7 Pharmaceutical and medical applications 251 12.8 Conclusions 253 Acknowledgments 253 Conflict of interest 253 References 253 13. Isolation methods for evaluation of extremophilic microbial diversity from Antarctica region 267 JANKI RUPARELIA, ANIRUDDH RABARI, NISHRA JOSHI AND CHAITANYA KUMAR JHA 13.1 Introduction 267 13.2 Diversity of extremophilic organisms in Antarctic hotspot 268 13.3 Isolation and identification methodology 271 13.4 Future prospects 282 13.5 Concluding remarks 283 Acknowledgment 283 Conflict of interest 283 References 283 14. Recent advances in microbial databases with special reference to kinetoplastids 291 DIVYA NARAYANAN PRAKASH, CHINMAYEE BAR ROUTARAY, RENUKA BHOR AND KALPANA PAI 14.1 Introduction 291 14.2 Classification of biological databases 294 14.3 Global resources/comprehensive databases 294 14.4 Community/specialized databases 305 ix Contents
- 15. 14.5 Future perspectives314 14.6 Conclusions 314 References 314 15. Advances in sequencing technology, databases, and analyses tools for the assessment of microbial diversity 317 SHAIMA RIFAIE, VIKAS PATIL AND KAMLESH JANGID 15.1 Introduction 317 15.2 Advances in sequencing technology 319 15.3 Development of databases 325 15.4 Advancements in analyses tools 328 15.5 How to study microbial diversity? 332 15.6 Conclusion 339 Acknowledgments 339 References 339 16. Legal protection of microbial biodiversity 349 RASHMI ARYA AND SONALI SHINDE 16.1 Introduction 349 16.2 Biodiversity Hotspots: Introduction 350 16.3 Protection of microbial diversity in hotspot regions 351 16.4 Existing framework for the research and exploration of microbiome 351 16.5 Patents and microorganisms 353 16.6 Microbial access and research: pipeline 357 References 362 Index 365 x Contents
- 16. List of Contributors RashmiArya CSIR-Unit for Research & Development of Information Products, Pune, India Ashok Bankar Department of Microbiology, MES Abasaheb Garware College, Savitribai Phule Pune University, Pune, India Devidas S. Bhagat Department of Forensic Chemistry and Toxicology, Government Institute of Forensic Science, Aurangabad, India Renuka Bhor Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune, India Parameswaran Binod Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum, India Joyasree Das Microbial Type Culture Collection & Gene Bank (MTCC), CSIR- Institute of Microbial Technology, Chandigarh, India Julius Eyiuche Nweze Soil and Water Research Infrastructure, Biology Centre CAS, Ceske Budejovice, Czech Republic; Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic Aparna Gunjal Department of Microbiology, Dr. D. Y. Patil Arts, Commerce & Science College, Pune, India Shruti Gupta Soil and Water Research Infrastructure, Biology Centre CAS, Ceske Budejovice, Czech Republic W.B. Gurnule Department of Chemistry, Kamla Nehru Mahavidyalaya, India Saima Hamid Centre of Research for Development, University of Kashmir, Hazratbal, India; Department of Environmental Sciences, University of Kashmir, Hazratbal, India Yogeshwari Hivarkar Annasaheb Kulkarni Department of Biodiversity, MES Abasaheb Garware College, Pune, India Chieh Chen Huang Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan Laxmi Jadhav Department of Microbiology, MES Abasaheb Garware College, Savitribai Phule Pune University, Pune, India Kamlesh Jangid National Centre for Microbial Resource, National Centre for Cell Science, SP Pune University Campus, Pune, India Chaitanya Kumar Jha Microbiology Department, Gujarat Arts and Science College, Ahmedabad, India xi
- 17. Nishra Joshi MicrobiologyDepartment, Gujarat Arts and Science College, Ahmedabad, India Srinivasan Krishnamurthi Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, India Sarita Manandhar Department of Microbiology, Tri-Chandra Multiple College, Tribhuvan University, Kathmandu, Nepal Amitsinh V. Mangrola Department of Biochemistry, Shri Alpesh. N. Patel P. G. Institute of Science & Research, Charotar Education Society, India Gincy Marina Mathew Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum, India Mohammad Yaseen Mir Centre of Research for Development, University of Kashmir, Hazratbal, India Sandhya Moghe Department of Biotechnology, Kamla Nehru Mahavidyalaya, India Pratik Munot MIT-School of Bioengineering Sciences and Research, MIT-ADT University, India Divya Narayanan Prakash Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune, India Kalpana Pai Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune, India Ashok Pandey Center for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, India Suneeta Gireesh Panicker Department of Microbiology, D.Y. Patil Arts Commerce and Science College, Pune, India Stutee Panse Department of Microbiology, PES Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, India Javid A. Parray Department of Environmental Sciences, Government Degree College Eidgah, India Shrushti Patil Annasaheb Kulkarni Department of Biodiversity, MES Abasaheb Garware College, Pune, India Smita Patil Department of Microbiology, Camp Education Society’s Arvind B. Telang Senior College of Arts, Commerce and Science, Savitribai Phule Pune University, Pune, India Vikas Patil National Centre for Microbial Resource, National Centre for Cell Science, SP Pune University Campus, Pune, India Ankur Patwardhan Annasaheb Kulkarni Department of Biodiversity, MES Abasaheb Garware College, Pune, India Vrushali Phalke Department of Microbiology, MES Abasaheb Garware College, Savitribai Phule Pune University, Pune, India xii LIST OF CONTRIBUTORS
- 18. Aniruddh Rabari MicrobiologyDepartment, Gujarat Arts and Science College, Ahmedabad, India Shaima Rifaie National Centre for Microbial Resource, National Centre for Cell Science, SP Pune University Campus, Pune, India Chinmayee Bar Routaray Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune, India Janki Ruparelia Microbiology Department, Gujarat Arts and Science College, Ahmedabad, India Pradipta Saha Department of Microbiology, The University of Burdwan, Golapbag Campus, Burdwan, India Jitendra Kumar Saini Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana, India Himanshu Departmentof Microbiology, Central University of Haryana, Mahendergarh, Haryana, India Sonali Shinde Annasaheb Kulkarni Department of Biodiversity, MES Abasaheb Garware College, Pune, India Manju Shree Shakya Hada Department of Microbiology, Tri-Chandra Multiple College, Tribhuvan University, Kathmandu, Nepal Anima Shrestha Department of Microbiology, Tri-Chandra Multiple College, Tribhuvan University, Kathmandu, Nepal Raveendran Sindhu Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum, India Anjana Singh Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal Sharad Dnyandev Subugade Department of Biotechnology, Vidya Pratishthan’s Art, Science & Commerce College, Pune, India Rebecca S. Thombre Blue Marble Space Institute of Science, Seattle, WA, United States; Department of Biotechnology, Modern College of Arts, Science and Commerce, India Sarita Tiwari Department of Biotechnology, Kamla Nehru Mahavidyalaya, India Reshma Tuladhar Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal xiii LIST OF CONTRIBUTORS
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- 20. Preface Being researchers andenthusiasts of Ecology, contemplating for pro- tracted hours on subject matters of biodiversity, its associated flora and fauna and such is allegorically labor of loves! Having assumed the role of a past master with regards to Intellectual Property and its associated rights at an Institute, this thought struck us—“How would Ecological factors be blended in contemporary times?” To our consternation, the postulations dealing with the Intellectual Properties associated with microbes with respect to their Ecological Niche was an underenvisaged subject matter for research. Eyeballing further, we decided to get down into venturing the prospects of patent- ing and legitimately procuring the microbial subjects from their inherent habitats—that too particularly from the Biodiversity Hotspot regions distributed across the world. Brevity is the soul of wit, they say! For it was a collective effort from all the authors involved in carrying out an intensely vigorous sense of study and research. In a chucklesome sense, our research methodology can be manifested into a computer code with “if, while and for”—loops repeating ad nauseam. Collating and juxtaposing the resulting endea- vors of ours was a quenching task—for we received wise counsels from many eminent personalities of this field. We present this book that covers wide range of topics, namely, microbial diversity and ecology in hotspots; actinobacteria diversity in Western Ghats; habitat-specific microbial community associated with biodiversity hotspots; ecology of saline environments in India; marine microbial hotspots related to corals; phyllosphere microbiome diversity; microbial diversity at the polluted sites; bacterial diversity in termite gut ecosystem. The book has also given importance and covered topics such as bacterial diversity from warm springs; diversity of cellulase degrading organisms from hotspots; diversity and isolation methods for evaluation of extremophiles from Antarctica region. The aspects such as advances in microbial databases, sequencing technology, and various tools for studying microbial diversity are also taken into consideration in this book. Last but not least, the legal protection of microbial diver- sity is also beautifully highlighted in this book. This book will serve the purpose of rightfully shepherding aspiring researchers and erudite cerebrals to understand and formulate a xv
- 21. legitimate approach towardprocuring and wielding subject matters involving the use of microbial life forms, especially from the Biodiversity Hotspot regions. It contains deliberate use of flowcharts and diagrams, quintessentially to simplify the whole understanding of the subject matter. Special efforts have been made to acknowledge the sources from where the information has been collated vis-à-vis through the bibliographical content. Suggestions for the improvement of the book will be thankfully acknowledged and incorporated in further editions. Aparna Gunjal and Sonali Shinde xvi Preface
- 22. Acknowledgments • The editors—AparnaGunjal and Sonali Shinde—are thankful to all the authors for the contribution of their chapters for the book Microbial Diversity and Ecology in Hotspots. • The editors are also thankful to the publisher and their whole team for their management of book publication process. • The editors are thankful to Vighnesh Shinde, Content Developer and Outreach Person at Arannya Environment Research Organisation, pursuing MSc Biodiversity, Annasaheb Kulkarni Department of Biodiversity, MES Abasaheb Garware College, Pune, Maharashtra, India, for preparing the excellent Cover Page Design for our book Microbial Diversity and Ecology in Hotspots. The Cover Page is of bracket fungi, which was taken at Bhagwan Mahaveer Wildlife Sanctuary, Goa, India. The spectrum of colors can be seen by illuminating artificial light. These spores are dispersed during monsoon nights. **Cover Page Copyright—Photograph was taken by Omkar Dharwadkar, Naturalist, Partner at Mrugaya Xpeditions and President of Goa, Bird Conservation Network. • Last but not least, the editors are thankful to their family members for their support and cooperation during this book publication process. Aparna Gunjal and Sonali Shinde xvii
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- 24. C H AP T E R 1 Exploration of microbial ecology and diversity in hotspots Sonali Shinde1 , Pratik Munot2 , Yogeshwari Hivarkar1 , Shrushti Patil1 and Ankur Patwardhan1 1 Annasaheb Kulkarni Department of Biodiversity, MES Abasaheb Garware College, Pune, India, 2 MIT-School of Bioengineering Sciences and Research, MIT-ADT University, India 1.1 Introduction “Man is a microcosm”—so rightly said by Democritus, an ancient Greek philosopher, as the Alchemy of Nature is boundless, seamless— as if nature talks and whispers to us! As mankind strives toward scien- tific and technological progresses, it is a mere wonderful sight to watch earth, revealing its hidden gems and secrets in front of us. Delighted, as every being is, we can experience the spread of different forms of life and its supporting elements throughout the span of this planet. Astrophysicists are now even exploring the possibilities of life being present in other regions of the Universe as well (Steven et al., 2015). While these are significant steps toward ensuring an unimaginable world of possibilities, it is ironic to learn that even on our planet, plants and animals on land have yet to be named and cataloged (Mora et al., 2011). The case for microbes is even more surprising as a recent study estimates that a significant portion of the microbial species present on the earth are yet to be discovered (Locey & Lennon, 2016). A series of such serious facts strengthens and encapsulates the importance of studying the biodiversity and natural heritage spanning the earth in a systematic and sustainable way, in order to discover life to its fullest! 1 Microbial Diversity and Ecology in Hotspots DOI: https://doi.org/10.1016/B978-0-323-90148-2.00015-8 © 2022 Elsevier Inc. All rights reserved.
- 25. 1.2 Meaning ofbiodiversity, threats associated and need for its protection First used by Thomas Lovejoy in the year 1980, the term Biological Diversity or simply put, biodiversity, was meant to quantitatively include the variety of species of living organisms on earth. However, the brief definition of biodiversity can be obtained from the charter of the Convention on Biodiversity (CBD). Article 2 of the CBD describes biologi- cal diversity as “the variability among living organisms from all sources including inter alia, terrestrial, marine and other aquatic ecosystems and the ecological complexes of which they are part; this includes diversity within species, between species and of ecosystems” (refer to Chapter 16: Legal Protection of Microbial Biodiversity, for further reading on the legal status of biodiversity conservation). With the advancements made in molecular biology and genome sequencing technologies (refer to Chapter 14: Recent Advances in Microbial Databases with Special Reference to Kinetoplastids, and Chapter 15: Advances in Sequencing Technology, Databases and Analyses Tools for the Assessment of Microbial Diversity), the science of exploring, understanding, protecting, and utilizing components of biodiversity in a sustainable manner, has emerged to be an important aspect of Conservational Biology. Various scientists from different domains such as ecology, botany, zoology, micro- biology, biogeography, genetics, and other life sciences’ subjects, actively engage themselves in conserving the biodiversity by chalking out strate- gies and implementing sustainable policies, taking into account the inter- ests of different stakeholders involved in the conservation work. Every subject expert from the aforementioned domain explores the subject from different perspectives and with different hypotheses (Klinkenberg, 2020). They study various aspects involving population dynamics, the function- ing of ecosystems, species distributions, and other factors of biodiversity, in order to understand and ascertain the scope of protection. In recent times, a plethora of threats has been incurred upon the bio- logical diversity of almost all the regimes over the globe resulting from unreasonable utilization and overexploitation of natural resources, with increased urbanization and unaccountable industrial development (refer to Chapter 8: Microbial Diversity at the Polluted Sites). These factors have especially undermined the viability of wild populations of flora and fauna, collectively (Wake & Vredenburg, 2008). For instance, this trend of overexploitation of resources has predominately been wit- nessed in the nations consisting of a rich heritage of biological diversity. In order to understand the basis of this trend, it is essential to first understand the factors forcing such countries to attain a “compulsive- state-of-mind” in which they are at vulnerable economic position and naturally, the exploitation of their natural resources is the only option 2 1. Exploration of microbial ecology and diversity in hotspots Microbial Diversity and Ecology in Hotspots
- 26. left with them.However, while the abundance of natural resources in different regions of the globe quite necessarily implies a seemingly vast potential for the economic development of the region as a whole by sus- tainable usage of the natural components (OECD, 2011), the recent times have accounted for a rather paradoxical situation. Termed as the “Resource Curse” or the “paradox of plenty,” it is a surprisingly contra- dictory situation, in which the countries with an abundance of nonre- newable resources experience shunted economic growth (Chandra et al., 2013). This theory is intricately applicable to the components of biodi- versity as well. The theory of Resource Curse is dependent on a couple of essential con- cepts, namely the Resource-Ratio Theory and the Carrying Capacity (in ecological terms). The “Resource-Ratio theory” or the “R* rule,” (Wilson et al., 2007), is an essential framework in community ecology to under- stand and hypothesize the influence of competition for growth-limiting resources on the biological diversity of a region (Smith et al., 1998). The theory predicts in a mathematical way the coexistence of two or more spe- cies in a particular ecosystem in the presence of growth-limiting nutrients with the condition that each species is limited by such a resource, which it (the species) is least prone or able to deplete (Mazancourt & Schwartz, 2010). The second concept, called the “Carrying Capacity” (in ecological terms), is described as the limiting factor of the population size which is supported by a particular regional environment, is the availability of the natural resources in that environment (Rachlow, 2008). However, the pop- ulation size can also be altered by other limiting factors such as food, pre- dation, and diseases, which do not account for inclusion as the limiting factor in ecological carrying capacity. In simpler words, the ecological car- rying capacity is the level of production (i.e., the population size of a spe- cies) that does not affect the equilibrium of the surrounding ecosystem or its environmental carrying capacity (TettPaul et al., 2015). Coming back to the implication of Resource Curse theory with respect to Microbial Ecology and Biological characteristics of a particular region, when the natural resources are abundant at a particular place, microbes tend to increase in their colony size and populations, thereby making way for strong competi- tive behavior and instincts for survival, a phenomenon that can be explained by the Resource-Ratio hypothesis. Regions bearing high Carrying Capacity, tend to provide survival edge on species adopting R* behavior in which there is aggression and competition among species to survive, while the low Carrying Capacity regions tend to show mutualistic behavior adopted by different species by not adopting the R* behavior, to sustain in that particular environment (Marcel, 2002). The essence of this mentality (unaccounted exploitation of natural resources), adopted by such countries with abundant biodiversity, can lead to an increase in the environmental misfortunes and maybe threatening in 3 1.2 Meaning of biodiversity, threats associated and need for its protection Microbial Diversity and Ecology in Hotspots
- 27. the form ofspecies elimination, that would result into unbalancing of the earth’s natural diversity. Hence, a dire need can be felt for adopting a con- servation strategy in order to minimize and counter the biodiversity loss. Also, we must realize that the biodiversity is not consistently spread across the globe and there are hardly any zones where we observe the exception- ally rich diversity of endemic species, which are unfortunately threatened by irresponsible human activities (Habel et al., 2019; Myers et al., 2000). So, in order to protect such regions possessing high numbers of endemic spe- cies, the concept of Biodiversity Hotspots has been upheld by the Conservationists, with the aid of participation of all the major stakeholders (governmental, nongovernmental) at various conservation levels and dif- ferent strategies, culminating into a potentially fruitful and sustainable out- come in the near future (Christian, 2015). 1.3 Biodiversity hotspots: a brief overview Put forward as a sustainable conservation strategy for biodiversity by Norman Myers and supported thereafter by Conservation International, bio- diversity hotspots, simply, are miscellanies providing a unique niche with a significant reservoir of diverse flora, fauna, and landscape. Every hotspot region features unique characteristics and adaptability with significant eco- logical balance for organisms to thrive in. The considerably high diversity, especially with respect to endemic species present in these regions, is termed as mega diversity. Such a region necessarily constitutes an area that contains at least 0.5% of total plant species as endemic species and with the implication that the area has lost a minimum of 75% of its original vegetation (Myers, 1988, 1990; the conditions for declaring a region as a Biodiversity Hotspot are detailed in Chapter 16: Legal Protection of Microbial Biodiversity). The idea of Biodiversity Hotspots is much more than a conservation tool as it quantifies the effect of environmental pressure due to human activities. Till now (with the last one being recently announced in February, 2016), a total of 36 hotspots have been reported and defined as places of biodiversity with vulnerability and irreplaceability (Mittermeier, 2004; Mittermeier et al., 2011). The term Hotspots’ Ecosystem is a geographic niche where plants, animals, and different microorganisms interact together constituting natural energy cycles and processes, along with its weather and landscape. 1.4 Tools for systematically studying the biodiversity hotspots through various aspects Advancements in scientific and technological progress have ushered the way biological elements and components of biodiversity were 4 1. Exploration of microbial ecology and diversity in hotspots Microbial Diversity and Ecology in Hotspots
- 28. previously understood. Researchersuse these tools for understanding the micronature and relations among biodiversity, species, populations, and ecosystems. Fig. 1.1 explains excerpts of tools used in studying Biological diversity. 1.4.1 Mathematical and statistical tools for data analysis Downstream analysis of ecological data can be performed by the simplest and most efficient approach by estimating the biodiversity. Large varieties of bioinformatics tools have been developed to analyze and compare the microbial diversity from the array of a microbial sample. Though ecological data have been substantially less explored in contrast to molecular research and bioinformatics, still many computational tools can be used to explore the patterns involved in studying biodiversity, as well. A classic example, that of Bayesian Networks, can be cited in this context which can be used for interpreting and studying interdependence and relationships among dif- ferent organisms, especially in studying the biodiversity distribution in a particular region (Tucker & Duplisea, 2012; for more information refer to Chapter 14: Recent Advances in Microbial Databases with Special Reference to Kinetoplastids, and Chapter 15: Advances in Sequencing Technology, Databases and Analyses Tools for the Assessment of Microbial Diversity). 1.4.2 Molecular tools In particular, molecular biology tools, especially the use of ribosomal RNA (rRNA), in particular, the 16S or small subunit (SSU) RNA and Internal Transcribed Spacer (ITS) sequences have proved to be important in the history of biodiversity exploration and its conservation (Rappé & Giovannoni, 2003; for more information refer to Chapter 13: Isolation Methods for Evaluation of Extremophilic Microbial Diversity From Antarctica Region). Apart from them, DNA markers such as mini- and FIGURE 1.1 Tools for studying biodiversity. 5 1.4 Tools for systematically studying the biodiversity hotspots through various aspects Microbial Diversity and Ecology in Hotspots
- 29. microsatellite DNA sequences,Restriction Fragment Length Polymorphism (RFLPs) and genomic sequence data can also be effectively used as a reli- able tool for ecological data analysis, especially in the cases of microbes, where culturing techniques are also well suited for the same purpose (Allan & Max, 2010). 1.4.3 Technological tool and specialized equipment Other equipment such as remote sensing modules, biometric devices, etc. are proactively used in monitoring and tracking the movement of biodiver- sity elements, especially those like tigers, snakes, etc. Among them, the use of actively monitoring animal locations is through global positioning system (GPS) and digital images for visualization (Alexander et al., 2020). 1.5 Biodiversity hotspots and microbial ecology Biodiversity hotspots are not only diverse in flora and fauna but may also show immense variation in microbial diversity with respect to their unique ecosystems. Microbial diversity hotspots could be deemed to necessarily include temperature, pressure, nutrients, and energy- exchange acting on the system, that is, niche, containing the microbes. For instance, Biodiversity hotspot of the Hawaiian Archipelago has sub- stantial endemism (Donachie et al., 2004; for more information refer to Chapter 2: Habitat-Specific Microbial Community Associated With the Biodiversity Hotspot). It is well known that the relationship between species and the existing environmental conditions is embodied by the concept of ecological niche (Begon et al., 2006). The term Ecological Niche encapsulates the position of a species within an ecosystem, describing both the range of conditions its ecological role in the ecosys- tem (Polechová & Storch, 2008). Extending this concept for aiding the inclusion of microbes, it is imperative to note that microbial community of a particular niche has an important feature, characterized by the number of species and their composition diversity. Hence, the develop- ments and advancements made in genome sequencing technologies with respect to their efficacy, accuracy, cost-effectiveness, and reliability (Roderic & Michiel, 2018; for more information refer to Chapter 15: Advances in Sequencing Technology, Databases and Analyses Tools for the Assessment of Microbial Diversity) and the use of environmental amplicon sequencing survey has built to a large number of biodiversity estimates for analysis of microbial studies. With the knowledge of microbial taxa and the resources available, we can march toward under- standing the complexity and diversity of an organism in that particular 6 1. Exploration of microbial ecology and diversity in hotspots Microbial Diversity and Ecology in Hotspots
- 30. habitat. It isimportant to consider the interactions between these ele- ments (biotic and abiotic) when studying the biogeographical or spatio- temporal patterns and not just the isolated being. On a practical note instead of knowing who all are there, it will be easy to find what are they doing and later find out who they were. 1.6 Microbial hotspots: an overview When defining microbial hotspots, the obvious difficulty will be to understand what should be the exact definition of microbial hotspots. Irrespectively the importance of measuring biodiversity lies more in adjust- ing the downward scale and unmapped terrain (Wilson, 1994). The study of microbes in biodiversity hotspots for their uniqueness is somewhat discouraging as microbes survive and grow almost every- where on earth, dramatically extending our perception of the limits of the biosphere and unclear definition of species. In line with the Baas- Becking hypothesis which states, “Everything is everywhere, but the environment selects” (Baas-Becking, 1934). Our understanding to find a specific microbe in a specific geographic location is limited. In compli- ance with this, whatever one has to study on Mars can be studied in the regions on earth where the spatial conditions are similar (Martiny et al., 2006; for more information refer to Chapter 2: Habitat-Specific Microbial Community Associated With the Biodiversity Hotspot). Microscale dis- tribution is definitely a tedious job and may often get a heterogeneous result. Some studies have demonstrated a no-point connection with spe- cies richness, a threat to the habitat and endemism do not show the same geographical distribution (Orme et al., 2005). Within the currently recognized 36 biodiversity hotspot regions, few of them highlighted for the microorganisms are studied. For example, Atlantic forest is a dense ombrophilous forest that has high variations creating vegetation gradi- ent ranging from shrubs to well-developed Montane forest (CEPF, 2001). Thermophilic Proteobacteria are unique to obsidian hot spring pool with 75 C95 C in Southern Brazilian Atlantic forest (Faoro et al., 2010). California floristic province is a Mediterranean-type climate divided into hot-dry summers and cold-dry winters (Burge et al., 2016). Rhodobacter capsulatus, a purple nonsulfur bacterium is studied in the region that grows in anaerobic conditions also responsible for denitrifi- cation (Costa et al., 2017). Cape Floristic region is evergreen fire- dependent scrubland, divided in the tropical, subtropical dry broadleaf forest. Amphora diatoms are highly studied in this region. The presence of this species indicates high pH (Rea De Stefano, 2019). The Caribbean Island consists of diverse ecosystem ranging from Montane cloud forest to cactus scrubland. Rhodococcus rhodochrous actinobacteria 7 1.6 Microbial hotspots: an overview Microbial Diversity and Ecology in Hotspots
- 31. were studied inthis region (CEPF, 2011). Presence of Salinispora and nonacid fast bacteria indicates organic contamination (Bauermeister et al., 2018). Himalaya which is rich in psychrophiles, that is, Pseudomonas palleroniana N26 was studied at low temperature and nitrogen-deficient ecosystem (Joshi et al., 2017). Indo-Burma hotspot is wet and dry ever- green, deciduous forest, swamps, and mangrove ecosystem. Tepidimonas taiwanensis and Tepidimonas fonticoldi thermophilic bacteria are found in the hot spring of Southern Thailand (CEPF, 2020). Coastal forest of Eastern Africa are characterized with small and fragmented forest has different diatoms species indicators like Nitzschia asterionelloides, Nitzschia forticola, and Fragillaria (Descy) (Jean-Pierre Hugo, 2008). 1.7 Microbial ecology: microbial habitats and the distribution of microbes As extreme and far-reaching and diverse environmental conditions can only be manifested supporting life, in reality, the microbial habitats consist of some of the wildest places on the globe including hot springs (Panosyan et al., 2018), steam-heated soils, different soil horizons (sur- face, subsurface, vertical, and depth), cryoconite holes (Sanyal et al., 2018), mud holes, surface waters (Bhattacharyya Jha, 2015; Lan et al., 2019; Yoshitake et al., 2018), geothermal power plants (Hou et al., 2020), drylands (Wang et al., 2018), and coral reefs (Tout et al., 2014). An interesting case, that of cryoconite holes in the chilling biodiversity hotspots of the Himalayan region and Antarctica provides a suitable habitat for the growth of microbial communities dominated by Proteobacteria, Bacteroidetes, Actinobacteria. Apart from these, there are many other microbial communities present in assemblages, which are specific to these regions characterized by the presence of cryoconites, which assist in shaping the microbial interactions, in part, the unique eco- system of this region (Sanyal et al., 2018; for more information refer to Chapter 10: Bacterial Diversity From Garampani Warm Spring, Assam; Chapter 12: Biodiversity of Cold Adapted Extremophiles From Antarctica and Their Biotechnological Potential; and Chapter 13: Isolation Methods for Evaluation of Extremophilic Microbial Diversity From Antarctica Region). Apart from these, the other commonly found ecosystems include the diverse soil types characterized with respective nutrient contents, gut and rumen of animals, aquatic environments, rhizosphere, phyllosphere, and others. A change in the habitat by natural fragmentation of the area leads to a change in the microbial interactions and networks and increases their geographical isolation (Speer et al., 2020; for more information refer to Chapter 2: Habitat-Specific Microbial Community Associated With the 8 1. Exploration of microbial ecology and diversity in hotspots Microbial Diversity and Ecology in Hotspots
- 32. Biodiversity Hotspot). Asdiscussed in the introductory paragraph of this part, some of the microbiota, termed as extremophiles, are located in harsh and extreme environmental conditions Fig. 1.2. These extremophilic microbial life forms, tend to sustain in these harsh and extreme conditions, where no other life forms would ostensi- bly sustain and thrive for longer periods, are conditioned by virtue of their great and unique ability to survive in array of habitats like hyper extremophile environment. At the center-stage, the microbial distribution is governed by nutrients, water, and other resources present in the habitat, habitat complexity, flora and fauna of that habitat as well as the anthropogenic activities (Young et al., 2008). One study shows microbial density is higher in the soil in the summer and spring due to increased soil moisture and nutrients which plays an important role in their distribution (Bhattacharyya Jha, 2015). Distributions of microbes such as algae found in the red snow of Svalbard and Arctic Sweden are uncul- tured Chlamydomonaceae species, of Green snow are Microglena sp. and Raphidonema sempervirens in Svalbard and Chloromonaspolyptera in Sweden is diverse (Lutz et al., 2017). The distribution pattern in the environment can be beneficial for understanding the ecological theories, recognizing and predict- ing the changes in community structures with environmental alterations (Bhattacharyya Jha, 2015; Valdespino-Castillo et al., 2018). Microbial distri- bution in psychrophilic biota and limnetic microbial mats favors a huge por- tion of the biomass in extreme environmental conditions with respect to inland Antarctica. While the conditions affecting microbial composition over successional and prolonged time periods with the environmental changes and imbalances may be disclosed by the distribution patterns or microbial assem- blages, the microbial distribution is also altered as a result of unaccounted and overly done anthropogenic activities like agricultural processes, especially the unwarranted use of artificial pesticides which accounts for drastic pH changes in the soil of that region, thus causing a significant reduction of biodiversity and the instability of that region’s ecosystem (2018). FIGURE 1.2 Types of extremophiles. 9 1.7 Microbial ecology: microbial habitats and the distribution of microbes Microbial Diversity and Ecology in Hotspots
- 33. 1.8 Microbial diversityindices: application in studying community ecology In spite of being the most commonly manifested form of explaining the Ecological Diversity in a particular region, the concept of Species Diversity subtly differs in its meaning and application, as compared to Biodiversity. For describing this sophisticated concept, ecologists tend to explain species diversity as a function of two factors—species rich- ness and relative species abundance (Hamilton, 2005). Species richness means the number of species present in a particular region and species abundance means the number of individuals per species. Relative spe- cies abundance means the evenness of distribution among individuals among species in a community (Baillie Upham, 2012). An important approach in measuring the species diversity is to construct the mathe- matical diversity indices. These indices are used for quantification of heterogeneous microbial distribution. Different microbial diversity indi- ces are shown in Tables 1.1 and 1.2. 1.9 Microbial composition and succession Depending upon the biogeography, the microbial composition is often determined at the community level, as microbial structures and functions/ processes are determined by their characteristic community, that is, popula- tion dependent (Martiny et al., 2006; Martiny et al., 2006; Nemergut et al., 2014). The assemblage of microbes helps in signaling between the microbial networks and also helps in the degradation of complex organic compounds to simpler ones. For instance, the degradation of xenobiotics or recalcitrant compounds by certain species of Pseudomonas and Rhodococcus is an efficient bioremediation technique being highly potentialized in contemporary times (Phale et al., 2019). Some bacterial and fungal species are however unable to convert and utilize complex molecules such as cellulose and lignin and do initiate the enzymatic process of converting these complex molecules to sim- pler forms by producing extracellular enzymes (Selim Zayed, 2017; Tribedi, 2016). Apart from that, the microbial assemblages are responsible to alter microbial structures and compositions, which obstruct the stabilization of microbial communities (Martiny et al., 2006; Martiny et al., 2006; Nemergut et al., 2014). As microbial communities play an important role in maintaining a healthy soil ecosystem, microbial succession is responsible for bringing in changes in the microbial composition. Microbial succession changes with change in the habitats, such as changes taking place when the ice melts with that the nutritional concentration changes leading to change 10 1. Exploration of microbial ecology and diversity in hotspots Microbial Diversity and Ecology in Hotspots
- 34. TABLE 1.1 Calculatingmicrobial diversity indices using alpha diversity. Diversity indices Equation Variables Description Reference Alpha diversity Fisher’s Index (S) S 5 αln 1 1 N α S 5 Total number of species; α 5 Index of diversity of population; N 5 Total number of individuals Estimates logarithmic distribution of number of individuals of different species Fisher et al. (1943) Simpson’s Index (D) D 5 1 P s i51 Pi2 D 5 Simpson’s dominance index; S 5 Total number of species in the community; pi 5 Proportion of community represented by Operational taxonomic unit (OTU) Quantify number of species present as well as their abundance Simpson (1949) Odum’s Index (Rodum) Rodum 5 S ln N ð Þ Rodum 5 Odum’s Index; S 5 Total number of species; N 5 Total number of individuals in the sample Estimates species diversity Odum et al. (1960) McIntosh Index Mc 5 [NO(Σni 2)]/[NON] Mc 5 McIntosh Diversity Index; ni 5 Number of individuals belonging to i species; N 5 Total number of individuals Estimates species richness McIntosh (1967) McIntosh Evenness Index E 5 N 2 U N 2 N= ffiffi S p E 5 McIntosh Evenness Index; N 5 Total number of individuals; S 5 Total number of species; U 5 Sample size Estimates species evenness McIntosh (1967) BergerParker Index D IBP 5 Nmax Ntot DIBP 5 BergerParker Index; Nmax 5 Number of individuals of most abundant species; Ntot 5 Total number of individuals of all the species in the sample Estimates species abundance Berger and Parker (1970) Species Richness Index EðSÞ 5 fðk; NÞ E(S) 5 Expected value for number of species; N 5 Number of individuals; k 5 Richness index Estimates species diversity Peet (2003) Pielou Evenness J 0 5 H 0 H0 max J0 5 Pielou evenness; H0 5 Number derived from Shannon Diversity Index; H0 max 5 maximum possible value of H0 Estimates species evenness Pielou (1975) (Continued)
- 35. TABLE 1.1 (Continued) Diversityindices Equation Variables Description Reference Chao’s Index SðmaxÞchao 5 Sobs 1 a2 1 b2 S(max) 5 Maximum number of species; Sobs 5 Number of species observed in different samples; a 5 Singletons (number of species represented by one individual each); b 5 Doubletons (number of species represented by two individuals each) Abundance-based estimates species richness Chao (1984, 1988) ShannonWiener Diversity Index (H) H0 5 2 P s i 5 1 piln pi H0 5 ShannonWiener Diversity Index; S 5 Number of OTUs; pi 5 Proportion of the community represented by OTU ShannonWiener Diversity Index measures the rarity and commonness of species in a habitat. Lemos et al. (2011) Menhinick’s Index Dmn 5 S ffiffiffi N p Dmn 5 Menhinick’s Index; S 5 Number of species; N 5 Total number of individuals Estimates species richness Kim et al. (2017) Margalef’s Index Dmg 5 S 2 1 ln N ð Þ Dmg 5 Margalef’s Index; S 5 Total number of species; N 5 Total number of individuals in the sample Estimates dependence between species diversity and number of organisms sampled Kim et al. (2017) Abundance-based coverage estimator (ACE) Index SACE 5 Sabund 1 Srare CACE 1 F1 CACE γ2 ACE Sabund and Srare 5 Number of abundant and rare OTUs; CACE 5 Sample abundance coverage estimator; F1 5 Frequency of singletons; γ2 ACE 5 Estimated coefficient of variation for rare OTUs Abundance-based coverage estimator of species richness Kim et al. (2017) Brillouin Index HB 5 ln N 2 P ln ni N HB 5 Brillouin Index; N 5 Total number of individuals; ni 5 The number of individuals in the ith species Estimates species richness similar to Shannon diversity index Kim et al. (2017)
- 36. TABLE 1.2 Betadiversity—microbial index. Diversity indices Equation Variables Description Reference Beta diversity Jaccard Index J 5 Sc Sa 1 Sb 1 Sc J 5 Jaccard Index, Sa and Sb are the numbers of species unique to samples a and b, respectively, Sc 5 Number of species common to the two samples It is the fraction of species shared between the samples. Jaccard (1912) Sorensen Index Ss 5 2a 2a 1 2b 1 2c Ss 5 Sorensen’s similarity coefficient; a is the species common to both samples; b is the species in sample 1; and c is the species in sample 2 Used for comparing the similarity of two samples. Sorenson (1948) BrayCurtis BCij 5 1 2 Cij Si 1 Sj BCij 5 BrayCurtis Index; Cj 5 Sum of the lesser values for only those species in common between both sites; Si and Sj 5 The total number of specimens counted at both sites Quantify the compositional dissimilarity between two different sites, based on counts at each site. Bray and Curtis (1957) Morista- Horn CD 5 2 P s i51 xiyi Dx 1 Dy ð Þxy CD 5 0 if the two samples do not overlap in terms of species; CD 5 1 if the species occur in the same proportions in both samples; xi 5 Number of times species i is represented in the total X from one sample; yi is the number of times species i is represented in the total Y from another sample; Dx and Dy are the Simpson index values for the x and y samples, respectively. S is the number of unique species Estimate the measure of dispersion of individuals in a population. Morisita (1959) (Continued)
- 37. TABLE 1.2 (Continued) Diversity indices EquationVariables Description Reference Wilson and Shmida Index βT 5 gðHÞ 1 lðHÞ ½ 2α βT 5 Beta turnover; H is habitat gradient; g 5 Species gained; l 5 Species lost; α 5 Average number of species found within the community samples Estimates changes, additivity in the alpha diversity. Wilson and Shmida (1984) Colwell and Coddington Index S 5 Sobs 1 F2 1 2F2 Sobs 5 Number of species in the sample; F1 5 Number of singletons (i.e., the number of species with only a single occurrence in the sample); F2 5 Number of doubletons (the number of species with exactly two occurrences in the sample) Estimate species diversity. Colwell and Coddington (1994) Shannon Beta Index Hβi 5 P j Cij Ci11 1 P k Cjk Cij1 ln Cijk Cij1 = Ci1k C111 H(βi) 5 Shannon Beta Index; Cijk 5 The sequence count for subject i, from time j and taxon k; 1 (plus) in the subscript denotes the summation of the counts over the specified indicator Measures multiple alpha and beta components when community weights are unequal. Marcon et al. (2012) These listed microbial indices are used for analyzing the numerical composition of microbial diversity in a complex community of microbes.
- 38. in the microbialcommunity (Valdespino-Castillo et al., 2018). Some of the bacterial species, discovered in the early stages of ecological succes- sion with respect to the glacial soil in the mountain ranges of the Alps in Switzerland, including Proteobacteria (alpha . betaproteobacteria) has shown a gradual decline in the soil percentage with age over a pro- longed time period. The process of a generalized microbial succession is slowed down due to decreasing mineralization in the soil nutrients such as carbon and nitrogen (Bhattacharyya Jha, 2015). The succession results in diverse microbial composition in a single habitat, for instance as observed in the deep seas. A hydrothermal vent sulfide chimney is another suitable example as the habitat showing the microbial succes- sion of chemoautotrophic microorganisms, on and around the walls of the chimneys. Some microbes are dominant when the chimney is active as it may supply the growth conditions. The succession depends on the source of nutrients, temperature condition, and other conditions for the growth of microbes from thermophilic to mesophilic to psychrophilic microorganisms (Hou et al., 2020). The ground surface after the glacial retreat is covered by a primary succession of microbes and these stimu- late physical and biological processes which lead to favorable conditions for further microbial and ecosystem succession (Yoshitake et al., 2018). 1.10 Microbial interactions Microorganisms interact with one another and the other elements of the ecosystem in a host by ways called microbial interactions Fig. 1.3, during which the genetic material and biologic molecules are exchanged FIGURE 1.3 Types of microbial interactions. 15 1.10 Microbial interactions Microbial Diversity and Ecology in Hotspots
- 39. and processed (Bragaet al., 2016). These interactions can be classified as being intraspecific or interspecific (Selim Zayed, 2017) depending upon the nature of the involvement of various interacting elements. These interactions can also be classified as being positive or negative, depend- ing upon the benefits derived by interacting elements, or the harmful product resulting out of such involvements (Shimane et al., 2018). The microbial communities are actively involved in creating favorable environmental conditions, that too, for other microbial communities to survive and carry out their interactions with each other and in an ecosys- tem as well. For instance, the snow and ice algae present in the cryoconite holes act as a source of nutrients and carbon for heterotrophic communi- ties (Lutz et al., 2017). The ecosystem and hotspot regions characterized with cryoconite holes are governed by the microbial interactions which play an important role in influencing and vitalizing the carbon cycle in these ecosystems. The microbial interactions within the cryoconite debris form a microenvironment and matrix, promoting biochemical interac- tions, many of them, yet to be explored (Sanyal et al., 2018). The microbial communities interact for certain functional and meta- bolic activities, the establishment and maintenance of which, determines a successful establishment of the microbial community. An outcome of these interactions is the coevolution process, which guides the microbial adaptations in different habitats (Braga et al., 2016). Microbes associated with different chemical processes may be driven by localized growth enhancement or chemotaxis into chemical microniches (Mitchell, 2002). These interactions help in improving their activities like signaling, exchange of compounds and involve the physicochemical changes, meta- bolites exchange and conversion, chemotaxis, and many more processes. Some microbes are known to interact with the roots and seeds through chemotaxis or chemotropism activated by plant exudates. Some processes like the root nodule factors released by Rhizobia are perceived by root cells leading to alteration of calcium flux and activates signaling pathway for the production of cytokinins, which also acts as symbiotic interaction of microbes (Braga et al., 2016; Moënne-Loccoz et al., 2015; Tribedi, 2016). It is a well-established fact that the microbes, by virtue of exchang- ing the vital materials produced through their interactions with each other and the environment, can regulate the plant development pro- cess, indirect way, by releasing phytohormones, contributing to the ecosystem processes, producing biocontrol compounds and different signaling compounds. Diverse communities of bacteria and fungi live in close association with each other and on the surfaces of plant roots (rhizosphere) and leaves (phyllosphere) and inside the plant tissues (endosphere) (Kent Triplett, 2002). These are highly diverse and have a fundamental role in water economy, nutrient acquisition, growth, and disease tolerance. Some examples are arbuscular 16 1. Exploration of microbial ecology and diversity in hotspots Microbial Diversity and Ecology in Hotspots
- 40. mycorrhizal fungi (AMF),Basidiomycetes, Penicillium, Archeospora, Glomus, Actinomycetes, Proteobacteria. While such microbial interactions help in stabilizing and understand- ing the dynamics of the biological communities, these interactions, can show both positive as well as a negative effect in their relationship with the host (Fig. 1.3). 1.11 Hotspots bioindicators/indicating unique environment of hotspots A characteristic exhibited by every microorganism in an ecosystem to potentially indicate the environmental health of the surrounding region can be accounted on the basis that they can tolerate a limited range of chemical, physical, and biological conditions (Holt Miller, 2010). Through the utilization of bioindicators, researchers can anticipate the common conditions for a specific region or the level and/or the degree of environmental contamination (Parmar et al., 2016). Some bioluminescent bacteria belonging to the genus Photobacterium from the North- Western Mediterranean Sea Hotspot region can effectively be used to test water for environmental toxins with the help of stress proteins. Toxins released by microbes affect the cellular metabolism of bacteria (Martini et al., 2016). Microorganisms also encompass the oceanic biomass and are respon- sible for the majority of productivity and nutrient cycle in a marine eco- system, as they have a rapid rate of growth, and react to even low levels of contaminants and other physicochemical and biological changes. One such example is of the bacterium Vogesella indigofera from the Mediterranean basin region which reacts to heavy metals quantitatively. Under conditions influenced by no metal pollution, blue pigment is a significant marker of the underlying morphological change that has occurred (Krieg, 2015). On the other hand, under the presence of hexa- valent chromium ions, the production of pigment is blocked. This can be attributed to the fact that there is an essentially important relation- ship between the concentration of chromium ions and the generation of blue pigment by the bacterium (Aslam et al., 2012). An interesting fact is that some microbes are adaptable to extreme environmental conditions and habitats by showing different strategies for their existence, such as the generation of pigments like violacein, carotenoids, melanin, β-carotene, etc. These pigments help the microbes to get adopted to harsh conditions like ultraviolet radiance, the genetic ability for carbon and nitrogen cycling and the capacity to degrade com- plex organic compounds (Sajjad et al., 2020; Valdespino-Castillo et al., 2018). 17 1.11 Hotspots bioindicators/indicating unique environment of hotspots Microbial Diversity and Ecology in Hotspots
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- 48. C H AP T E R 2 Habitat-specific microbial community associated with the biodiversity hotspot Sarita Tiwari1 , Sandhya Moghe1 , W.B. Gurnule2 , Devidas S. Bhagat3 and Aparna Gunjal4 1 Department of Biotechnology, Kamla Nehru Mahavidyalaya, India, 2 Department of Chemistry, Kamla Nehru Mahavidyalaya, India, 3 Department of Forensic Chemistry and Toxicology, Government Institute of Forensic Science, Aurangabad, India, 4 Department of Microbiology, Dr. D. Y. Patil Arts, Commerce Science College, Pune, India 2.1 Introduction India is ranked as a mega-diverse country enduring four biodiversity hotspots among the 36 proclaimed sites situated worldwide (De Mandal et al., 2015; Rajkhowa et al., 2015). The four regions are the Himalayas, the Indo-Burma region, Western Ghats, and the Sundaland. The arena tagged as hotspots are known for their rich and discrete biological combo witnessing biological activity par the normal limit but having fear of extinction is marked as biodiversity hotspots. The overall survey in India reports the existence of over 91,000 species of animals, and 45,500 plant species have been documented in India. The major factors responsible for creating a diverse aura are climate, temperature, soil quality, rainfall percentage, and the presence of many rivers culpable for vegetation cover and microbes dwelling in soil (Rathour et al., 2017). The soil in the biodiversity zone is laced with a unique natural envi- ronment in which, inhabitant special microbes with distinctive charac- teristics also involved in plant growth, etc. have the possibility of 25 Microbial Diversity and Ecology in Hotspots DOI: https://doi.org/10.1016/B978-0-323-90148-2.00018-3 © 2022 Elsevier Inc. All rights reserved.
- 49. encouraging diversified species.Within the microbial community, pro- karyotes are the dominant group in comparison to others and are actively involved in ecosystem functioning (Powell, 1993). In the biodi- versity hotspot region, the microbial world is still to uncover which is a large pool of biodiversity on land (Vibha Neelam, 2012). The study of microbial ecology is gaining immense interest. Members of the micro- bial family, that is, bacteria, fungi, and actinomycetes are at the fore- front in shaping the morphology, physiology, functioning, and overall working of living systems (Braga et al., 2016; Briones Raskin, 2003). As most of the findings are based on discovering microbes of surface soil (about 1040 cm depth), the data on identification of the microor- ganisms are not sufficient (Martı́nez-Alonso et al., 2010). 2.2 Biodiversity hotspot in the Indian continent India is blessed with a diverse climatic condition which is the basis for biological diversity, ultimately maintains equity relations amidst humans and organisms. The well-known biodiversity hotspots of the Indian subcontinent are the Himalayas, Indo Burma Region, Sundaland, and the Western Ghats situated in different parts of India. They are listed in the top 36 biodiversity hotspot around the world. However, these hotspots are under threat and on the verge of extinction of many rare species. Thus it is the need of time to conserve these species as it is a heritage of the country. Conserving this biodiversity amid many development projects going on in a country like India is challenging but essential for sustainable development. 2.3 Factors affecting biodiversity hotspots in India The presence of green hills, clear water, fantastic caves, and variety had made this biodiverse area alluring. But recent activities like fraternization of trade, human, and geogenic action to a certain extent has dragged the cleaner zone of biodiversity toward containment of pollutants (Vareda et al., 2019; Yang et al., 2018). Different actions responsible for deteriorating the habitats in the hotspots are listed in Fig. 2.1. One of the activities which are done for human welfare is dam construction. The dam is a modern- day technology having double facet, that is, affirmative as well as the pes- simistic outcome. Even this biodiversity zone is not left alone by today’s world mechanistic engineering action. Even the emergence of toxicants like metal imparts toxicity to reachable biota belonging to nearby ranges depending on its type and chemical form. Escorted with cytotoxicity, mutagenicity, and carcinogenic character, they are a big threat to animals 26 2. Habitat-specific microbial community associated with the biodiversity hotspot Microbial Diversity and Ecology in Hotspots
- 50. and plants especiallyto human health, calling an emergency for imple- mentation of an appropriate technique for abatement and inhibition of its entry into the natural environment (Hadjiliadis, 2012). 2.4 The Himalayas The Himalayan region has spread in the arena of country like Bhutan, Northern India, and major parts of Nepal. They are well known for their high peaks mountain comprising about more than 100 mountains higher than 7200 m height and also marked as highest mountains in the world including Mount Everest and K2 (Rüber et al., 2020). There are about 163 species declared on the verge of extinction belonging to the group of mam- mals, birds, reptiles, invertebrate, and plant species. In case of plants, the Himalayan valley is densely populated with varied species of plants and about 300 varied species of animals including wild water buffalo, sloth bear, big squirrel, and requires urgent attention. The issues faced by these regions are imparting harm to local medicinal plants, black bears, etc. (Pandit et al., 2007; Tali et al., 2019). For example, some of the species are on the verge of extinction such as Namdapha’s flyinal plants like Himalayan Yew, Blue- poppy, Snow Lotus plants for profiteering purposes. 2.5 The Indo-Burma region The Indo-Burma region is the second biodiversity hotspot that belongs to the Indian subcontinent. The regions stretch over different countries FIGURE 2.1 Factors responsible for creating disturbances in biodiversity hotspot of India. 27 2.5 The Indo-Burma region Microbial Diversity and Ecology in Hotspots
- 51. including India’s Northeasternstates, Myanmar, Cambodia, Laos, Thailand, Vietnam, and the southern part of China, covering about 23 lakh km2 area. This hotspot consists of 13,500 plant species, 1260 marine fishes, reptiles, mammals, etc. (Jose et al., 2016). Among these, the botanical cover is threat- ened to be extinct which is clear from the fact that only 1.18 lakh km2 vege- tation cover is remaining. Factors dragging the priceless rare species to extinction are farming activity, commercial plantation, fisheries, etc. which has to drop down the original habitat to 5% (Dudgeon, 2012). These areas are known for its unique biota and environ created due to its unique habitat. Also known for its superiority in biological values, provide and promote diverse niche for existence of microbes with beneficial characteristic (Jose et al., 2016). However, regrettably, because of its tough and high mountains, its extreme environment construct, researchers find it difficult to attend and explore the microbial communities dwelling in this ecological condition. 2.6 The Sundaland The Sundaland biodiversity hotspot region exists in the Nicobar group of Islands—Borneo, Java and Sumatra, Singapore, the Philippines which covers 15 lakh km2 area. The Nicobar Islands constitute India. These islands have been declared as the sector biosphere reserve in 2013 through the United Nations. These islands have wealthy terrestrial as nicely as marine ecosystems together with mangroves, seagrass beds, and coral reefs. Also, it is accompanied by various marine fishes, rep- tiles, etc. dwelling in the water bodies (Giam et al., 2012). The Sundaland comprises 25,000 species of plants, 380, 770, 450, 245, 950 mammals, birds, reptiles, amphibians, freshwater fishes, respectively. Presently only 1 lakh km2 vegetation cover is remaining while the area under protection is 1.79 lakh km2 . Fifteen thousand plants, almost half of mammals and reptiles are endemic to the region. These islands are an abode to unique orchids and tropical plant species of high economic value, like oil palm, rubber, etc. The endangered species in this hotspot are turtles, pangolins, orangutans, tigers, rhinoceros, the Bali starling, straw-headed bulbul, and many more. The Sundaland biodiversity hot- spot faces red danger and has lost most of its habitat due to deforesta- tion, intensive commercial agriculture, man-made forest fires, extensive illegal hunting, and poaching of animals (Verma et al., 2020). 2.7 The Western Ghats Another hotspot of India is the Western Ghats (the Sahayadri range) which is also listed as a biodiversity zone with a unique climate and 28 2. Habitat-specific microbial community associated with the biodiversity hotspot Microbial Diversity and Ecology in Hotspots
- 52. environmental ecosystem. Thereare over 7000 plant species in the Western Ghats, of which about 5600 are endemic (Bossuyt et al., 2004). The rare and susceptible species include Nilgiri Tahr, Lion-tailed macaque, parakeets, laughing thrush birds, and more. The biotic group of Western Ghats is also under extinction and needs attention for the preservation of endangered species. Due to the proximity of this region to the ocean, they receive a higher volume of rainfall. Most of the spe- cies belonging to the group of amphibians and reptiles present in this region are rare and not found in other parts of the world. Also, another country like Srilanka, situated extreme south of India is known for rus- tic and wealthy species too and connected with India through an extended stretch of bridge having 140 Km. There is more than 6000 vas- cular flora present here belonging to 2500 genus. Within these, 3000 plants are prevalent in this area. Even the world famous spices like black pepper, cardamom have been known to be evolved from the Western Ghats. Majorly, of the total plant species, most of the plants are situated on Agasthyamalai Hills located in the acute South. The area is likewise domestic to round 450 species of birds, 140 mammals, 260 rep- tiles, and 175 amphibians. Such variety is pretty lovely in addition to uncommon, however, now lies at the verge of extinction. The plants on this area became firstly unfold over 190,000 rectangular kilometers, however, has decreased to 43,000 rectangular kilometers today. Presently, most effective 1.5% of the authentic woodland, nevertheless, exists in Sri Lanka. The mountains of the Western Ghats in Peninsular India are an international biodiversity hotspot (Garg et al., 2017). An exponential twofold increment withinside the counted number of spe- cies during the last decade and a half (200115) has evidenced that a vast majority of amphibians of this place had still to be discovered (Biju Bossuyt, 2005), and there is probability that the original diversity is far greater in number than the estimated value (Biju Bossuyt, 2005). In terms of species diversity, the Western Ghats positioned at the fourth position which ranked next to Indo-Burma, also grabbed the foremost spot among another hotspot region in terms of amphibian’s range. The speedy disclosure of these species becomes possible due to the vast range of available advanced molecular tools and a synchronized step- wise approach. 2.8 Approach to safeguard biodiversity hotspots in India Industralization, urbanization and other human activities are respon- sible for aggravating pollution, deforestration etc. which cause uncon- trolled impact on their habitats, inturn causing nuisance. The conservation of biodiversity is the need of time. The negligence of the 29 2.8 Approach to safeguard biodiversity hotspots in India Microbial Diversity and Ecology in Hotspots
- 53. government toward precautionaryinvestment, monitoring, and mainte- nance also lead to dwindling this diversity zone. Depicting the menac- ing state of art can overture for fastening policy and administrative action toward this crisis. In such circumstances, paramount involvement of government and policymakers for sustainable preservation model and definitive protocol for species restoration is required, also demands effective policy and financial commitments at large scale. The protection of biodiversity in India also requires the involvement of residents who indirectly get benefited from this diverse heritage. Many policies are already introduced by the Indian government such as Marine Turtle Policy and Marine Standing Policy for marine biodiversity protection from pollution. Ministry of Environment, Forest, and Climate Change is the heading agency that has been administered by the Indian Government; they also highlighted the Biological Diversity Act in 2002. International Union for Conservation of Nature has categorized the bio- logical entity into different groups depending upon their present status as threatened, vulnerable, endangered, critically endangered, and extinct. Also, many international agencies are actively involved in fund- ing the plan/policy for the preservation of threatened species in the hot- spot region. 2.9 Habitat-specific microbes of hotspot region The microorganisms play a vital and frequently specific position withinside the functioning of the ecosystems in preserving equality amidst biosphere and productivity. The harm in biodiversity and the approach to revive for human welfare is the thrust area seeking atten- tion. Each habitat comprises a specific group of microbes which differ from site to site. Microbes present in this region are mostly in symbiotic association with other members of microbes pertaining in the soil (Taylor et al., 2007). For instance, the coexistence of algae and bacterial diversity determines the number of the carbon source utilized by bacte- ria, which directly symbolizes direct relation of nutrient cycling with microbial exploitation suggesting linkage between bacterial diversity and algal production. The major reason for inhabitant of special com- munity is competition between microbial species, resultant into decre- ment in the microbial diversity of specific habitats. Specific habitat is a battle field where microbes are engaged in a fight for dominance defeat- ing existence of other species. In case of some microbes, they are backed with genetic setup which makes them behave in ecologically aggressive manner. The characteristics laced with these microbes are high resis- tance against abiotic stress, tolerance against viral infection, varied sub- strate intake, out-grow competitors. However, there are some concepts 30 2. Habitat-specific microbial community associated with the biodiversity hotspot Microbial Diversity and Ecology in Hotspots
- 54. which are unexplainedconcerned to adherence of particular microbial species within communities (Yadav et al., 2015). A genetically diverse group of microbes depending upon their meta- bolic need, environmental conditions, etc. persist in a particular niche (Kühl et al., 2012). Invertebrate-microbe symbioses additionally play essential roles in host ecological achievement via the supply of supple- mental vitamins and the manufacturing of protective secondary metabo- lites. The total pull of DNA in soil signifies cumulative genomes of microbes, small eukaryotes, and many plants and animals, which is used for tracking by the individual. In the Indo-Burman region, the presence of strains Trichoderma has been reported to synthesize three important enzymes, namely, chitinase, protease, and β-1,3-glucanase. Tayang and Jha (2010) detected the presence of an endophytic fungus Fusarium sp. having antimicrobial effect against most of the pathogens. In another study by Jose et al. (2016), they identified three cellulolytic fungal isolates displaying excessive FPase pastime and their information had been submitted in NCBI, GenBank as Talaromyces verruculosus SGMNPf3 (KC937053), Trichoderma gamsii SGSPf7 (KC937055), and Trichoderma atroviride SGBMf4 (KC937054). Bhattacharyya et al. (2014) used a metagenomics approach to assess the different soil bacterial com- munities of five varied zones in terms of geology and hydrology, target- ing mainly floor and subsurface soil habitats of Brahmaputra valley, tagged as mega-biodiversity hotspot. Identifying the total microbial spe- cies persistence in this unique zone can definitely add on to the diverse beneficial role of microbes performed with the aid of using extraordi- nary microbial companies inside an ecosystem. Microbial diversity also had a pivotal involvement the diversification of a particular ecosystem. The Northeastern part of the Indian continent is covered by natural forest and many parts of the zone are untouched and uncovered by the discoverer/researcher and from industrial inter- ference. This region provides varied niches that trigger the propagation of novel microorganisms in the soil which are still unexplored. Many microbes are unidentified, undiscovered, and many are unculturable which are putting a big constrain in exploring. According to the study of De Mandal et al. (2015), Indo-Burman hotspot consists of a total of 29 phyla, within which the dominant phyla have been Acidobacteria (39.45%) accompanied with the aid of using Proteobacteria (26.95%), Planctomycetes (7.81%), Actinobacteria (7.18%), Bacteroidetes (6.65%), Chloroflexi (4.11%), and Nitrospirae (3.33%) (Bhattacharyya et al., 2014) while the study on a microbial pool of Indo-Burman hotspot used a culture-independent metagenomic approach for the identification of microbial population. By following 16s rRNA housekeeping gene for identification of microbes, the authors found dominancy of microbes belonging to the genera Proteobacteria, Acidobacterium, and 31 2.9 Habitat-specific microbes of hotspot region Microbial Diversity and Ecology in Hotspots
- 55. Another Random ScribdDocument with Unrelated Content
- 59. The Project GutenbergeBook of Half a Hundred Hero Tales of Ulysses and The Men of Old
- 60. This ebook isfor the use of anyone anywhere in the United States and most other parts of the world at no cost and with almost no restrictions whatsoever. You may copy it, give it away or re-use it under the terms of the Project Gutenberg License included with this ebook or online at www.gutenberg.org. If you are not located in the United States, you will have to check the laws of the country where you are located before using this eBook. Title: Half a Hundred Hero Tales of Ulysses and The Men of Old Editor: Francis Storr Illustrator: Frank Cheyne Papé Release date: January 3, 2013 [eBook #41765] Most recently updated: October 23, 2024 Language: English Credits: Produced by Greg Bergquist, JoAnn Greenwood, and the Online Distributed Proofreading Team at http://www.pgdp.net (This file was produced from images generously made available by The Internet Archive/American Libraries.) *** START OF THE PROJECT GUTENBERG EBOOK HALF A HUNDRED HERO TALES OF ULYSSES AND THE MEN OF OLD ***
- 61. HERCULES AND THEGOLDEN APPLES HALF A HUNDRED HERO TALES OF ULYSSES AND THE MEN OF OLD
- 62. EDITED BY FRANCIS STORR EDITOROF THE JOURNAL OF EDUCATION, LONDON WITH ILLUSTRATIONS BY FRANK C. PAPÉ NEW YORK HENRY HOLT AND COMPANY 1913 Copyright, 1911, by HENRY HOLT AND COMPANY Published January, 1911
- 63. THE QUINN BODEN CO. PRESS RAHWAY, N. J.
- 64. PREFACE The apology offeredfor adding yet another book of Classical Stories to the endless existing versions, ancient and modern, in verse and in prose, is the plea that Vivien offers to Merlin for her tender rhyme: It lives dispersedly in many hands, And every minstrel sings it differently. You Greeks, said the Egyptian priest to Herodotus, are always children, and Greece will never lose the secret of eternal youth. The tale of Troy divine, of Thebes and Pelops' line, the song of sweet Colonus, the most cruel death of Pyramus and Thisby, Dido with a willow in her hand—these old stories of Homer and Sophocles, of Virgil and Ovid, have not lost their gloss and freshness. The innocent brightness of a new-born day is lovely yet. They have been sung or said by Wace and Caxton, by Chaucer and Wordsworth, by Keats and William Morris; they have been adapted for young readers by Fénelon, by Niebuhr, by Kingsley, by Hawthorne, and yet the last word has not been said. Each new editor makes his own selection, chooses some new facet, or displays the jewel in a new light. As Sainte-Beuve remarks of Don Quixote and other world classics, One can discover there something more than the author first of all tried to see there, and certainly more than he dreamed of putting there. The present collection of Fifty Stories (there might well have been five hundred) makes no pretense either of completeness or of uniformity. Some of the contributors have followed closely the texts, others have given free play to their fancy, but in every case the myths have been treated simply as stories and no attempt has been made either to trace their origin or to indicate their religious or
- 65. ethical significance. Mostof the stories point their own moral, and need no more commentary than Jack the Giant-killer or the Sleeping Beauty. Young readers of to-day resent the sermons even of a Kingsley. From Tanglewood Tales, a book that was the joy of our childhood, we have borrowed ten stories, and have taken the liberty of dividing into chapters and slightly abridging the longest of Hawthorne's Tales. All but one of the remaining forty are original versions. CONTENTS PAGE Pluto and Proserpine 1 By H. P. Maskell Pan and Syrinx 5 By Mrs. Guy E. Lloyd The Story of Phaeton 13 By M. M. Bird Arethusa 19 By V. C. Turnbull The Story of Daphne 24 By M. M. Bird Deucalion and Pyrrha 28 By M. M. Bird Epimetheus and Pandora 33
- 66. By Nathaniel Hawthorne Europaand the God-Bull 50 By Nathaniel Hawthorne Cadmus and the Dragon's Teeth 65 By Nathaniel Hawthorne Orpheus and Eurydice 83 By V. C. Turnbull Hercules and the Golden Apples 89 I. Hercules and the Old Man of the Sea By Nathaniel Hawthorne Hercules and the Golden Apples 98 II. Hercules and Atlas By Nathaniel Hawthorne Hercules and Nessus 107 By H. P. Maskell The Quest of the Golden Fleece 111 By M. M. Bird How Theseus Found His Father 124 By Nathaniel Hawthorne Theseus and the Witch Medea 131 By Nathaniel Hawthorne Theseus Goes to Slay the Minotaur 138 By Nathaniel Hawthorne
- 67. Theseus and Ariadne144 By Nathaniel Hawthorne Paris and Œnone 154 By V. C. Turnbull Iphigenia 161 By Mrs. Guy E. Lloyd Protesilaus 166 By Mrs. Guy E. Lloyd The Death of Hector 173 By V. C. Turnbull The Wooden Horse 180 By F. Storr The Sack of Troy 185 By F. Storr The Death of Ajax 191 By F. Storr The Flight of Æneas from Troy 196 By F. Storr Æneas and Dido 201 By V. C. Turnbull Æneas in Hades 209 By V. C. Turnbull
- 68. Nisus and Euryalus217 By F. Storr Ulysses in Hades 224 By M. M. Bird Circe's Palace 232 By Nathaniel Hawthorne Ulysses and the Cyclops 262 By Hope Moncrieff The Sirens 271 By V. C. Turnbull The Story of Nausicaa 275 By M. M. Bird The Homecoming of Ulysses 283 By M. M. Bird Baucis and Philemon 292 By H. P. Maskell Hypermnestra 296 By V. C. Turnbull Œdipus at Colonos 302 By Mrs. Guy E. Lloyd Midas 308 By H. P. Maskell
- 69. Perseus and Andromeda313 By V. C. Turnbull Meleager and Atalanta 320 By H. P. Maskell The Story of Dædalus and Icarus 326 By M. M. Bird Scylla, the Daughter of Nisus 330 By Mrs. Guy E. Lloyd The Story of Pyramus and Thisbe 340 By M. M. Bird Hero and Leander 344 By Mrs. Guy E. Lloyd Pygmalion and the Image 352 By F. Storr Cephalus and Procris 359 By H. P. Maskell Echo and Narcissus 364 By Thomas Bulfinch The Ring of Polycrates 369 By M. M. Bird Romulus and Remus 375 By Mrs. Guy E. Lloyd
- 70. ILLUSTRATIONS Hercules and theGolden Apples Frontispiece FACING PAGE The Story of Daphne 26 Hercules and Nessus 108 Theseus Goes to Slay the Minotaur 138 Æneas in Hades 212 Ulysses and the Cyclops 266 Perseus and Andromeda 316 Romulus and Remus 380 HALF A HUNDRED HERO TALES
- 71. PLUTO AND PROSERPINE BYH. P. MASKELL In the very heart of Sicily are the groves of Enna—a land of flowers and rippling streams, where the spring-tide lasts all through the year. Thither Proserpine, daughter of Ceres, betook herself with her maidens to gather nosegays of violets and lilies. Eager to secure the choicest posy, she had wandered far from her companions, when Pluto, issuing, as was his wont, from his realm of shadows to visit the earth, beheld her, and was smitten by her childlike beauty. Dropping her flowers in alarm, the maiden screamed for her mother and attendants. 'Twas in vain; the lover seized her and bore her away in his chariot of coal-black steeds. Faster and faster sped the team as their swart master called to each by name and shook the reins on their necks. Through deep lakes they sped, by dark pools steaming with volcanic heat, and on past the twin harbors of Syracuse. When they came to the abode of Cyane, the nymph rose up from her crystal pool and perceived Pluto. No farther shalt thou go! she cried. A maiden must be asked of her parents, not stolen away against her mother's will! For answer the wrathful son of Saturn lashed his foam-flecked steeds. He hurled his royal scepter into the very bed of the stream. Forthwith the earth opened, making a way down into Tartarus; and the chariot vanished through the yawning cave, leaving Cyane dissolved in tears of grief for the ravished maiden and her own slighted domain. Meanwhile Ceres, anxious mother, had heard her daughter's cry for help. Through every clime and every sea she sought and sought in vain. From dawn to dewy eve she sought, and by night she pursued the quest with torches kindled by the flames of Ætna. Then, by
- 72. Enna's lake, shefound the scattered flowers and shreds of the torn robe, but further traces there were none. Weary and overcome with thirst, she chanced on a humble cottage and begged at the door for a cup of water. The goodwife brought out a pitcher of home-made barley wine, which she drained at a draught. An impudent boy jeered at the goddess, and called her toss-pot. Dire and swift was the punishment that overtook him. Ceres sprinkled over him the few drops that remained; and, changed into a speckled newt, he crept away into a cranny. Too long would be the tale of all the lands and seas where the goddess sought for her child. When she had visited every quarter of the world she returned once more to Sicily. Cyane, had she not melted away in her grief, might have told all. Still, however, on Cyane's pool the girdle of Proserpine was found floating, and thus the mother knew that her daughter had been carried off by force. When this was brought home to her, she tore her hair and beat her breast. Not as yet did she know the whole truth, but she vowed vengeance against all the earth, and on Sicily most of all, the land of her bereavement. No longer, she complained, was ungrateful man worthy of her gifts of golden grain. A famine spread through all the land. Plowshares broke while they were turning the clods, the oxen died of pestilence, and blight befell the green corn. An army of birds picked up the seed as fast as it was sown; thistles, charlock, and tares sprang up in myriads and choked the fields before the ear could show itself. Then Arethusa, the river nymph, who had traveled far beneath the ocean to meet in Sicily her lover Alpheus, raised her head in pity for the starving land, and cried to Ceres: O mourning mother, cease thy useless quest, and be not angered with a land which is faithful to thee. While I was wandering by the river Styx I beheld thy Proserpine. Her looks were grave, yet not as of one forlorn. Take comfort! She is a queen, and chiefest of those who dwell in the world of darkness. She is the bride of the infernal king.
- 73. Ceres was buthalf consoled, and her wrath was turned from Sicily to the bold ravisher of her daughter. She hastened to Olympus, and laid her plaint before Jupiter. She urged that her daughter must be restored to her. If only Pluto would resign possession of Proserpine, she would forgive the ravisher. Jupiter answered mildly: This rape of the god lover can scarce be called an injury. Pluto is my brother, and like me a king, except that he reigns below, whereas I reign above. Give your consent, and he will be no disgrace as a son-in-law. Still Ceres was resolved to fetch her daughter back, and Jupiter at length agreed that it should be so on condition that Proserpine, during her sojourn in the shades, had allowed no food to pass her lips. In joy the mother hurried down to Tartarus and demanded her daughter. But the fates were against her. The damsel had broken her fast. As she wandered in the fair gardens of Elysium she had picked a pomegranate from the bending tree, and had eaten seven of the sweet purple seeds. Only one witness had seen her in the fatal act. This was Ascalaphus, a courtier of Pluto, who some say had first put it into the mind of the king to carry off Proserpine. In revenge for this betrayal, Ceres changed him into an owl, and doomed him ever after to be a bird of ill-omen who cannot bear the light of day, and whose nightly hooting portends ill tidings to mortals. But Ceres was not doomed to lose Proserpine utterly. Jupiter decreed that for six months of each year her daughter was to reign in dark Tartarus by Pluto's side; for the other six months she was to return to earth and dwell with her mother. Joy returned to the mother's saddened heart; the barren earth at her bidding once more brought forth its increase. Soon the fields were smiling with golden corn, and the mellow grapes hung heavy on the vines, and once again that favored land became the garden of the world.
- 75. PAN AND SYRINX BYMRS. GUY E. LLOYD Long ages ago in the pleasant land of Arcadia, where the kindly shepherds fed their flocks on the green hills, there lived a fair maiden named Syrinx. Even as a tiny child she loved to toddle forth from her father's house and lose herself in the quiet woods. Often were they forced to seek long and far before they found her, when the dew was falling and the stars coming out in the dark blue sky; but however late it was, they never found her afraid nor eager to be safe at home. Sometimes she was curled up on the soft moss under the shelter of a spreading tree, fast asleep; sometimes she was lying by the side of a stream listening to the merry laughter of the water; sometimes, sitting over the stones upon the hillside, she would be watching with wonder and delight the lady moon, with her bright train of clouds, racing across the sky as if in hot chase. Years passed on, and Syrinx grew into a tall and slender maiden, with long fair hair and great gray eyes, with a look in them that made her seem to be always listening. Out in the woods there are so many sounds for any one who has ears to hear—the different notes of the birds, the hum of the insects, the swift, light rustle as some furry four-legged hunter creeps through the underwood. Then there is the pleasant, happy murmur of the breeze among the leaves, with a different sound in it for every different tree, or the wild shriek of the gale that rends the straining branches, or the bubbling of the spring, or the prattle of the running stream, or the plash of the waterfall. Many are the sounds of the woods, and Syrinx knew and loved them all until Beauty born of murmuring sound, Had passed into her face.
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