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Microbial Communities in Coastal Sediments: Structure and Functions Microbial Communities in Coastal Sediments This page intentionally left blank Microbial Communities in Coastal Sediments Structure and Functions SALOM GNANA THANGA VINCENT Professor, Department of Environmental Sciences, University of Kerala, India TIM JENNERJAHN Senior Scientist & Group Leader, Working Group Ecological Biogeochemistry, Leibniz Centre for Tropical Marine Research, Bremen, Germany KUMARASAMY RAMASAMY Director, Faculty and Academics, SRM Institute of Science and Technology, India Elsevier Radarweg 29, PO Box 211, 1000 AE Amsterdam, Netherlands The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States Copyright © 2021 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: 978-0-12-815165-5 For Information on all Elsevier publications visit our website at https://www.elsevier.com/books-and-journals Publisher: Candice Janco Acquisition Editor: Louisa Munro Editorial Project Manager: Mona Zahir Production Project Manager: Joy Christel Neumarin Honest Thangiah Cover Designer: Miles Hitchen Typeset by MPS Limited, Chennai, India Contents Introduction vii 1. Source and composition of organic matter and its role in designing sediment microbial communities 1 1.1 Introduction 1 1.2 Organic matter in coastal sediments 2 1.3 Source of organic matter: autochthonous and allochthonous 5 1.4 Quality of organic matter in sediments 10 1.5 Microbial degradation of organic matter 12 1.6 Role of organic matter in designing sediment microbial communities 17 1.7 Microbial diversity and ecology in coastal sediments 19 1.8 Diversity of archaeal communities 30 References 34 2. Sources, types, and effects of nutrients (N and P) in coastal sediments 47 2.1 Introduction 47 2.2 Nutrient sources of coastal ecosystems 50 2.3 Nutrient enrichment: forms and types 59 2.4 Effect of hypernutrification 61 References 73 3. Environmental variables and factors regulating microbial structure and functions 79 3.1 Introduction 79 3.2 Spatial and temporal heterogeneity 80 3.3 Geological factors 82 3.4 Hydrological factors 85 3.5 Physicochemical factors 85 3.6 Biological factors 95 3.7 Nutritional factors 105 3.8 Natural and anthropogenic disturbances 106 3.9 Presence of contaminants/toxic substances 107 References 108 v vi Contents 4. Biogeocycling of nutrients (C, N, P, S, and Fe) and implications on greenhouse gas emissions 119 4.1 Introduction 119 4.2 Biogeocycling of nutrients 120 4.3 Greenhouse gas dynamics in coastal ecosystems 133 References 139 5. Biodegradation and biotransformation of persistent organic pollutants by microbes in coastal sediments 147 5.1 Introduction 147 5.2 Why persistent organic pollutants? 148 5.3 Anaerobic degradation and pathways 149 5.4 Anaerobic microorganisms involved 159 5.5 Limitations for anaerobic degradation: electron acceptors 161 5.6 Future prospects 161 References 162 6. Assessment of microbial structure and functions in coastal sediments 167 6.1 Introduction 167 6.2 Culture-dependent methods: the “great plate count anomaly” 168 6.3 Molecular tools used to examine microbial diversity of coastal sediments 169 6.4 High-throughput sequencing technologies 175 6.5 Functional diversity of coastal sediment microbes 177 6.6 Microbial activity in coastal sediment: study of biogeochemical reaction rates in laboratory microcosms 180 6.7 Conclusion and future prospects 181 References 182 Appendix 1: Conclusions and future perspectives 187 Index 189 Introduction The complex mixture of nutrient and organic matter inputs from marine and terrestrial ecosystems into the coastal zone fuels rich and diverse microbial communities in the sediments, which have an important role in ecosystem processes. These include mineralization of organic matter and assimilation of nutrients that serve as sources of food. The structure (abun- dance, diversity, and taxonomic composition) and functions (metabolic activities, biodegradation, and nutrient cycling) of microbial communities are controlled by multiple factors that vary in space and time. As marine sediments cover more than two-thirds of the earth’s surface and are also regarded as the largest reservoir of organic carbon on earth, the spatial and temporal variations in microbial activity are primarily attributed to the quality and quantity of organic matter. Moreover, the availability of inor- ganic nutrients and terminal electron acceptors also influences the abun- dance and activity of sediment microbes. Hence, Baas Becking’s hypothesis, “everything is everywhere; but the environment selects” is also relevant with regard to sediment microbial community structure. Studies on the microbial ecology of sediments have been increasing largely in the recent past owing to the advent of molecular tools for charac- terization and quantification of microbial community structure. The recent progress in knowledge on coastal microbiology provided motivation for this book. A citation network analysis using the keywords “microbial commu- nities—coastal sediments—organic matter” displays the progress and inter- linking of various research topics regarding the structure and functions of coastal microbial communities. A total of 5854 papers grouped in five clus- ters numbered from 0 to 4 different clusters are based on the relevant sub- themes of the subject area. The themes for clusters were ecology and diversity of sediment microbes, organic matter sedimentation and microbial dynamics, microbial abundance and diversity in sediments, microbial inter- actions in sediments, and influence of sediment disturbance like bioturba- tion on sediment microbial communities. Fig. 1 represents the most cited research papers in the clusters. Chapter 1, Source and Composition of Organic Matter and Its Role in Designing Sediment Microbial Communities, delineates how the qual- ity and availability of sedimentary organic carbon drive the composition and activities of microbial communities. In coastal sediments, vii viii Introduction Biddle Jf, 2006, P N... Parkes Rj, 2000, Hyd... Parkes Rj, 2005, Nat... Parkes Rj, 1994, Nat... Whitman Wb, 1998, P ... Hedges Ji, 1995, Mar... Martin Jh, 1987, Dee... Ploug H, 1999, Mar E... White Dc, 1979, Oeco... Alldredge Al, 1988, ... Hoppe Hg, 1983, Mar ... Alldredge Al, 1986, ... Smith Dc, 1992, Natu... Simon M, 2002, Aquat... Aller Rc, 1994, Chem... Delong Ef, 1993, Lim... Grossart Hp, 1998, A... Kristensen E, 2000, ... Bligh Eg, 1959, Can ... Azam F, 1998, Scienc... Porter Kg, 1980, Lim... Rich J, 1997, Deep-s... Simon M, 1989, MarPomeroy E... Lr, 2001, Aq... Fuhrman Ja, 1980, Ap... Hobbie Je, 1977, App... Fuhrman J, 1992, Env... Fuhrman Ja, 1995, Li... Wommack Ke, 2000, Mi... Middelboe M, 1996, A... Noble Rt, 1998, Aqua... Figure 1 Citation network of highly cited research publications relating to microbial communities in coastal sediments. microorganisms create their own microhabitats within which several types of interactions occur within and between communities. Geochemical zonation is a well-documented factor responsible for microbial distribu- tion. However, exceptional reports on the cooccurrence of microbes that occupy different metabolic niches, for example, methanogenic archaea and sulfate-reducing bacteria, contradict the concept of geochemical zonation. Under anoxic conditions, organic matter degradation and remineralization are carried out by the concerted action of diverse microbial communities through a “microbial food chain” and a “microbial loop,” which are key processes in coastal sediment biogeochemistry. In the microbial food chain, initially, large substances are hydrolyzed by extracellular enzymes of hydrolytic bacteria, and the organic products released during this reaction are trans- formed
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