Table Of ContentManoj 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
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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
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