Systems Biology of Marine Ecosystems PDF
Preview Systems Biology of Marine Ecosystems
Manoj Kumar · Peter Ralph Editors Systems Biology of Marine Ecosystems Systems Biology of Marine Ecosystems Manoj Kumar • Peter Ralph Editors Systems Biology of Marine Ecosystems Editors Manoj Kumar, PhD Peter Ralph, PhD Climate Change Cluster Climate Change Cluster Faculty of Science Faculty of Science University of Technology Sydney (UTS) University of Technology Sydney (UTS) Sydney, NSW, Australia Sydney, NSW, Australia ISBN 978-3-319-62092-3 ISBN 978-3-319-62094-7 (eBook) DOI 10.1007/978-3-319-62094-7 Library of Congress Control Number: 2017953394 © Springer International Publishing AG 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland v Preface Marine organisms are exposed to diverse environmental fluctuations, anthropogenic stresses, and threats from invasive species and pathogens. Increasing ocean tempera- ture and acidification in a changing climate continually alter the structure and func- tion of marine ecological systems, thereby forcing the marine organisms to either tolerate or adapt to new ocean conditions. Ecophysiology-based approaches in studies of ecological adaptation to altered environmental conditions, such as measur- ing photosynthesis, growth, and morphological changes, have generally been unable to precisely predict future changes in the performance and persistence of marine organisms under a scenario of global climate change and increased anthropogenic activities. In terrestrial ecosystems, however, approaches in systems biology have played a major role in elucidating the functional adaptation of land plants to biotic and abiotic stress conditions. Systems biology integrates data from various disciplines, such as physiology, genomics, transcriptomics, proteomics, and metabolomics, into numerical models in order to simulate the physiology of a whole organism. It not only analyzes the topology of biochemical and signaling networks in response to stress but also captures the dynamics of these responses. Systems biology has been used extensively to study terrestrial vegetation and their ecological adaptation to future climate change scenarios, but to a lesser extent in the study of marine organisms. This book, Systems Biology in Marine Ecosystem, describes current advances in the biological and functional interplay within four marine ecosystems: seaweed (Chaps. 1–5), seagrasses (Chaps. 6–9), microorganisms and microalgae (Chaps. 10–13), and their bacterial interactions (Chaps. 14–16). It describes how systems biology has been applied to advance knowledge of the stress response in these important marine ecosystems to climatic and anthropogenic perturbations. This knowledge is linked to mechanisms of resilience and persistence under varying environmental scenarios, which have important implications for the conservation and management of these ecosystems. In addition, the book describes how systems biology has been used in research and discovery to benefit the marine biotechnology sector. Seaweeds are the focus of Chaps. 1–5. Seaweeds, also known as macroalgae, are the dominant flora of coastal ecosystems globally. Among the most important primary vii viii Preface producers, seaweeds are of great importance both ecologically and economically. Seaweeds are exposed to a variety of stressors which affect their physiological and ecological performance. Integrated “omics” is a powerful technique to identify the genes, proteins, and metabolic pathways that respond to biotic and abiotic stresses in plants. Chapter 1 focuses on the application of functional genomics to study stress physiology in seaweeds and the challenges associated with this approach. It also describes how functional genomics has been used to identify the mechanism of bio- synthesis of secondary metabolites that comprise the cell wall of seaweeds. This knowledge is highly beneficial when genetically altering the cell wall composition of seaweeds; such alterations can facilitate oil extraction for biofuel production and the production high-value bio-products from diverse seaweeds. In recent years, with the availability of genomic and transcriptomic (expressed sequence tags or ESTs) resources, several studies have integrated physiological, transcriptomic, and/or pro- teomic approaches to determine stress tolerance mechanisms in seaweeds. Chapters 2 and 3 summarize how integrated omics approaches, when coupled with physiological observations, have led to new mechanistic understandings of stress tolerance in seaweeds. For example, it was discovered that biochemical pathways/networks coordinate within the cell to scavenge reactive oxygen species in order to increase tolerance in seaweeds to desiccation and to detoxify heavy metals. These path- ways/networks included the upregulation of antioxidant machinery, phycobili- somes (light-harvesting complexes), vesicular trafficking, heat shock proteins, polyamines, phytochelatins, lipoxygenases, and ATP-binding cassette transporter proteins. These findings may explain the permanence of stress-tolerant algal species in the upper intertidal zone, compared with sensitive algal species located in the lower intertidal zone. In recent years, another allied omics platform, “lipidomics,” has gained momentum in marine science to reveal the role of diverse lipids and fatty acids and their oxidized counterparts (commonly known as oxylipins) in biological systems. These studies have shown how lipid metabolites influence membrane architecture and the modulation of transcription and translation and thus provide tolerance and acclima- tion to marine organisms in altered environmental conditions. In Chap. 4, current knowledge of lipidomics, advanced analytical tools, and techniques to examine lipids and their derivatives are given. The integration of lipidomics with allied sister omics branches to identify unknown gene/protein functions and the development of systems biology networks to advance knowledge of lipid biochemistry in seaweed development and acclimation to stress conditions are also discussed. Chapter 5 describes recent advances in understanding how volatile compounds emitted from seaweeds, such as ethylene and DMSP, affect seaweeds’ physiology, reproduction, and developmental biology. Seagrasses are the focus of Chaps. 6–9. Seagrasses are monocotyledonous flow- ering plants that have adapted to the marine environment for over 130 million years. Despite their immense ecological (carbon sink) and commercial value, they are declining at an alarming rate due to climate change and anthropogenic activities attributed directly (e.g., dredging) or indirectly (e.g., eutrophication) to light stress. Chapter 6 provides an overview of the development of high-throughput molecular Preface ix technologies (e.g., omics) to bridge the gap between the genome and phenotype in order to elucidate the molecular mechanisms that underpin tolerance to abiotic stress in seagrass. Seagrasses live in dynamic coastal aquatic environments and experience complex photosynthetic and respiratory responses. Chapter 7 describes systems biology approaches to the understanding of photosynthetic processes in seagrasses and the accurate estimation of the carbon budgets of seagrass meadows. Furthermore, Chapter 8 summarizes how system-based approaches are crucial in predicting the fitness and response of seagrasses to the combined impacts of envi- ronmental constraints and how their interactions with other organisms in their eco- logical niche at different trophic levels affect the marine system dynamics at numerous points in the network. The adaptive fitness of seagrasses to any environ- ment requires a mechanistic understanding of environmental influence on metabolic networks that eventually control energy assimilation, growth, and reproduction. Chapter 9 explores nontargeted metabolite profiling and how metabolomic informa- tion in seagrasses is integral to linking genotype to phenotype in the context of global climate change. Marine microalgae and microorganisms are the focus of Chaps. 10–13. Chapter 10 describes the availability of complete marine microalgal genome sequences, meta-transcriptomic data, and other omics-based datasets. These molecular resources have enabled precise molecular descriptions of complete biological systems and have enabled rigorous hypothesis testing to study the connections between genotype and phenotype, phenotype and the environment, species and ecosystems, and the interspecies evolution and adaptation of microalgae. A discussion of the potential of meta-barcoding and meta-genomics to characterize ocean microbial communities rapidly and effectively is given in Chap. 11. In addition, this chapter describes the potential of cultivation-independent omics approaches to understand how microbial taxa adjust their molecular and physiological machinery to take advantage of chang- ing environmental conditions and, in turn, shape microbial community structure. Chapter 12 summarizes the individual and combined effects of ocean acidification and ultraviolet radiations on marine photosynthetic carbon fixation. Chapter 13 provides a comprehensive overview of bioprospecting of microalgae while culturing under stress conditions to enhance secondary metabolite production and biofuel potential. This chapter further highlights how the integration of multiple omics is effective for discovering new metabolic pathways that are integral for the use of microalgae as biofactories. Chemical communications between host and microbial community are the focus of Chaps. 14–16. The host (marine macro- and microalgae/corals)-microbial interaction and its significance within a hostile marine environment are described. Furthermore, the interactions that are essential to regulate the host defense system, their morphology and development, quorum sensing, and exchange of info-chemicals informed by sys- tems biology approaches, together with meta-genomics and meta-transcriptomics, are discussed. This book describes the latest advances in systems biology in four pillars of the marine ecosystems: seaweed, seagrasses, microalgae, and corals. This knowledge will not only benefit marine biology students and researchers but also resource man- x Preface agers and marine biotechnologists. We thank all the authors for their generous contribution to this book and collaboration in revising the manuscript. We are also indebted to the consistent support from the reviewers for providing their critical inputs to improve the articles and eventually this book. We are extremely thankful to the entire team of Springer for their support and effort in producing this book. Sydney, New South Wales, Australia Manoj Kumar Peter Ralph Contents Part I 1 Macroalgal Functional Genomics: A Missing Area ............................ 3 Vishal Gupta, Mukesh Jain, and C.R.K. Reddy 2 Tolerance Pathways to Desiccation Stress in Seaweeds ...................... 13 Loretto Contreras-Porcia, Camilo López-Cristoffanini, Andrés Meynard, and Manoj Kumar 3 Marine Metal Pollution and Effects on Seaweed Species ................... 35 Loretto Contreras-Porcia, Andrés Meynard, Camilo López-Cristoffanini, Nicolas Latorre, and Manoj Kumar 4 Seaweed Lipidomics in the Era of ‘Omics’ Biology: A Contemporary Perspective ................................................................ 49 Puja Kumari 5 Volatiles in the Aquatic Marine Ecosystem: Ethylene and Related Plant Hormones and Sporulation in Red Seaweeds ...... 99 P. Garcia-Jimenez and R.R. Robaina Part II 6 Abiotic Stress of Seagrasses: Recent Advances in Transcriptomics, Genomics, and Systems Biology ......................... 119 E.E. Malandrakis, T. Danis, A. Iona, and A. Exadactylos 7 Photobiology of Seagrasses: A Systems Biology Perspective ............. 133 Pimchanok Buapet 8 Systems Biology and the Seagrass Paradox: Adaptation, Acclimation, and Survival of Marine Angiosperms in a Changing Ocean Climate ............................................................... 167 Richard C. Zimmerman xi
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