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Genomics-fueled approaches to current
challenges in marine ecology
Gretchen E. Hofmann1, Jennifer L. Burnaford2 and Kevin T. Fielman1
1
2
Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
Biology Department, University of Puget Sound, Tacoma, WA 98416, USA
As a result of recent advances in genomic technology, a
‘tool set’ is emerging that can be used by marine
ecologists to gain new perspectives on central questions
in the field. Techniques such as gene expression
profiling using DNA microarrays, when placed in an
ecological context, stand to advance greatly our understanding of how organisms respond to abiotic and biotic
stresses. Here, we target areas in which adding genomics to ecological and physiological investigations will
significantly advance our understanding of crucial issues
ranging from the general biological effects of environmental temperature changes on individuals and communities to the interactions between symbionts in coral
bleaching. At a time when both short- and long-term
perturbations of marine ecosystems are increasing in
severity, this kind of integrative approach could generate new and exciting hypotheses about the functioning of marine organisms and communities.
Introduction
Several recent reviews have underscored the advances
made using genomic technologies in ecologically relevant
studies (e.g. [1–4]), from the structural and functional
characterization of the Sargasso Sea microbial community
[5] to exploration of the molecular basis of behavioral
plasticity in honey bees Apis mellifera [6] (Box 1). As these
genomic technologies become increasingly available to
‘non-genomicists’, new opportunities to address challenging questions in ecology and evolution will continue to
emerge [7]. Given the synergy between ecologists and
genomicists in other fields (Box 1), we feel that the time is
right and the resources exist to gain new insights into
marine ecology via the application of genomic approaches.
Here, we highlight this potential by presenting four cases
where genomic-based data could make major contributions to our understanding of processes in marine
ecosystems. In addition, we present a survey of ongoing
projects that captures the state of genomics in studies of
marine systems, suggesting that genomic-based investigations will be increasingly possible in marine ecology
owing to an expanding genomic resource base for marine
organisms (Table 1, Online Supplementary Material).
A genomics-based approach, and the contribution that
these data can make to our understanding of the response
Corresponding author: Hofmann, G.E. ([email protected]).
Box 1. Recent advances in ecological functional genomics
The convergence of genomics with ecology and evolution has
yielded a wealth of new data with which to identify and to interpret
how species interact with their environment over multiple levels of
biological organization. Research areas with a long history of
organismal-level investigation have been greatly energized by this
synergy. Some exemplar studies are given below.
† Plant–herbivore interactions: key commonalities and differences
identified in stress-induced and herbivore-induced response pathways [63–65].
† Temperature acclimation in ectotherms: gene expression profiling
in response to high and low temperature regimes provides a
comprehensive view of the transitions between adaptive, thermotolerant phenotypes [10,11,65].
† Host–parasite interactions and infectious disease: expression
profiling of both host and symbiont in the mosquito–Plasmodium
system identified potential new genes of importance to life history
and infection [13,66,67].
† Reproductive biology of plants: vernalization found to be under
epigenetic control in Arabidopsis thaliana [68].
† Microbial community ecology: comprehensive analysis of the
Sargasso Sea microbial community metagenome characterized the
gene content, diversity and abundance of at least 1800 genomic
species, uncovered 148 new bacterial phylotypes and found O1.2
million previously unknown genes [6].
† Behavioral ecology: identification of genes associated with agespecific socially regulated division of labor in the honey bee, Apis
mellifera [7].
of organisms to environmental changes, is especially
timely. Marine ecosystems, particularly nearshore regions
such as coasts, estuaries and coral reefs, are experiencing
crises worldwide as environmental change places significant physiological stress on the resident organisms*.
Understanding ecosystem resilience and predicting the
impact of environmental stress on specific marine organisms depends on knowing the physiological status and
plasticity of key organisms in those ecosystems. Genomics
stands to provide a detailed and unprecedented view of
physiological diversity and function, and thus also
mechanistic insight into how organisms respond to
environmental stress. Such studies have already been
conducted on model organisms. For example, in yeast,
DNA microarray-based gene expression profiling has
revealed a complex pattern of gene up- and downregulation that suggested mechanistic underpinnings for how
cells tolerate and respond to an array of physiological
stresses [8]. Gene expression data sets can be grouped into
gene ontology groups that reflect categories of cellular
* Kenedy, V.S. et al. (2002) Coastal and Marine Ecosystems and Global Climate
Change, Report prepared for the Pew Center on Global Climate Change.
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function (e.g. general stress response, membrane
function, and protein degradation) and these clusters
of changing genes can be used to formulate hypotheses
about how different tissues, or the whole organism,
might be impacted by particular abiotic stresses at a
systems level. A better appreciation of physiological
diversity and how it plays out across large spatial
scales or in species interactions to determine largerscale ecological patterns (Figure 1) will be particularly
important if ecosystem disturbance becomes the norm
rather than the exception.
Progress is being made in genomic studies of nonmodel marine organisms, although most of these
studies are laboratory based. DNA microarrays have
been used to analyze the influence of physical factors,
such as temperature on aquatic organisms [9,10], and
to assess whether different populations have gene
expression profiles that correlate to organismal distributions [11]. Other examples include the identification
of genes that mediate host–parasite interactions in
diseases such as malaria [12] and in plant responses to
environmental stress [13]. Collectively, these studies
reveal significant changes in gene expression profiles
that provide insight into the phenotypic plasticity of
these study organisms and provide some perspective
on which genes might be ecologically relevant in these
environments. The next step is to venture into the
field, to attempt to use these techniques on marine
organisms in natural populations to reveal the physiological diversity that is operating at ecologically
significant scales in nature.
From a resource perspective, tools for marine
environmental genomics are developing rapidly. An
extensive suite of techniques traditionally reserved for
model systems, such as Drosophila, have recently been
pulled from the molecular toolbox and applied to the
study of genome and transcriptome (see Glossary)
organization in non-model marine species. The construction of a BAC library is often the starting point for a
eukaryotic genome-sequencing project and greatly
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Glossary
BAC: a bacterial artificial chromosome vector used to clone large fragments
(100–300 kb) of genomic DNA in Escherichia coli cells.
cDNA: a DNA copy of an RNA transcript produced by a reverse transcriptase
enzyme using RNA as a template.
Chromatin: a complex of DNA, proteins and the histones around which DNA is
wound; located in the cell nucleus.
DNA micro- and macroarray: DNA arrays are large collections of single DNA
sequences (i.e. a library) deposited as spots on a solid surface. The DNA can be
tens to thousands of base pairs in length and composed of sequences that are
synthetic, from cDNA or from genomic DNA. A macroarray is typically printed
onto a tough, reusable membrane (e.g. nylon) and holds hundreds to
thousands of large diameter spot features (R300 mm). By contrast, a typical
non-reusable microarray is printed onto a glass surface at much higher density
(tens to hundreds of thousands of features) with features that are necessarily
smaller in size (%200 mm). In both formats, labeled samples are hybridized to
the array to detect simultaneously differences in sequence representation at a
global scale within the genome or transcriptome.
Epigenetic: a mode of change in gene expression that is heritable but does not
involve a change in DNA sequence composition.
EST: an expressed sequence tag from a short stretch of sequenced cDNA that
uniquely identifies a gene locus. A quantitative transcriptome profile can be
produced from an EST library by determining the number of unique loci and
their EST abundance. Similar to SAGE, this method involves a substantial
sequencing effort, yet is a relatively inexpensive technique that does not require
previous sequence knowledge.
Library: a sequence collection obtained from genomic DNA or cDNA and
maintained as unique clones in a host cell (e.g. E. coli).
Metagenome: the collection of all genomes present within a community or
ecosystem, most commonly applied to characterization of microbial systems.
SAGE: serial analysis of gene expression is a quantitative transcriptome
profiling technique based on generating presumably unique cDNA ‘tags’ of
w15 base pairs that are sequenced to quantify transcript abundance and to
identify the transcribed gene. SAGE is relatively inexpensive and its subsequent
modifications increase the likelihood of unique tags, facilitate cloning of the
differentially expressed transcripts, and do not require previous sequence
knowledge.
Transcriptome: the collection of all RNA molecules that are present within a
defined cell or cell population (including whole tissues, organs and bodies).
Transcriptome profile: a quantitative or qualitative description of the
transcriptome. Methods and approaches for transcriptome profiling include
SAGE, the characterization of EST libraries and the use of macro- or
microarrays to generate a global gene expression profile. For a more detailed
review of the techniques, see [4]. For a broadly accessible alternative method
see [70].
facilitates genetic mapping [14]. At least 55 libraries,
as well as filters for screening clones, are now available
or under development for diverse marine taxa (Table 1,
Online Supplementary Material). Similarly, the
Environmental
stress
Genomics
Induced
Profile of
gene
gene
expression expression
Ecology
Distribution
and
abundance
Integration of
temperature
signal
Community
Species
structure
interactions and function
Differential
performance
TRENDS in Ecology & Evolution
Figure 1. Integration of genomics, physiology and ecology in the study of environmental stress. For example, in coral reefs, high temperature stress is often identified as the
cause of coral bleaching, a phenomenon that substantially alters community structure. within coral reef ecosystems. In this system, there is an urgent need to more
thoroughly understand the effects of environmental stressors on corals and their endosymbiotic algae because the consequences of physiological stress are manifested at
the community level through coral death.
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Table 1. Examples of marine and estuarine species with well developed structural or functional genomic resources
Taxon
Chordata
Fugu (Takifugu)
rubripes
Common name
Resources
Links
Japanese
pufferfish
BAC, cosmid, map,
EST, macroarray
Tetraodon
nigroviridis
Salmo salar
Green spotted
pufferfish
Atlantic salmon
BAC, map, EST
http://genome.jgi-psf.org/fugu6/fugu6.home.html
http://fugu.hgmp.mrc.ac.uk/
http://www.tigr.org/tdb/tgi/
http://www.genoscope.cns.fr/
http://www.broad.mit.edu/annotation/tetraodon/
http://web.uvic.ca/cbr/grasp/
http://www.thearkdb.org/browser?speciesZsalmon
http://www.tigr.org/tdb/tgi/
Sea squirt,
tunicate
BAC, EST,
macroarray lines
Sea squirt,
tunicate
Tunicate
BAC, macroarray
BAC, EST, map, lines
http://www.genoscope.cns.fr/externe/English/Projets/
Projet_HG/organisme_HG.html
ftp://ftp.jgi-psf.org/pub/JGI_data/CSP/
Purple urchin
BAC, PAC, EST,
macroarray, microarray
http://sugp.caltech.edu/
http://www.molgen.mpg.de/wag_seaurchin/
Pacific white
shrimp
Map, EST,
microarray, lines
Atlantic white
shrimp
Tiger prawn
Map, EST,
microarray, lines
Map, EST,
microarray, lines
Map, EST,
microarray, lines
http://www.tufts.edu/vet/aquatics/index.html
http://www.marinegenomics.org/
http://www.shrimp.ufscar.br/
http://www.marinegenomics.org/
Urochordata
Ciona intestinalis
C. savignyi
Oikoplura dioica
Echinodermata
Strongylocentrotus
purpuratus
Crustacea
Litopenaeus
vannamei
L. setiferus
Penaeus monodon
BAC, map, lines,
EST, macroarray,
microarray
http://genome.jgi-psf.org/ciona4/ciona4.home.html
http://ghost.zool.kyoto-u.ac.jp/indexr1.html
http://209.20.141.139/investigators/amemiya_chris/PACs.htm
http://www.tigr.org/tdb/tgi/
http://www.broad.mit.edu/annotation/ciona/
P. stylirostris
Pacific blue
shrimp
P. (Marsupenaeus)
japonicus
Kuruma prawn
Map, EST,
microarray, lines
http://www.aims.gov.au/pages/research/shrimpmap/pages/sm-05.html
http://www.intl-pag.org/pag/12/abstracts/P5o_PAG12_737.html
http://www.csusm.edu/dgarcia/
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmdZRetrieveanddbZPubMedandlist_uidsZ14648293anddoptZAbstract
http://www.intl-pag.org/pag/12/abstracts/P5o_PAG12_737.html
http://www.intl-pag.org/pag/10/abstracts/PAGX_W24.html
Atlantic oyster
BAC, EST, map, lines
http://www.intl-pag.org/pag/12/abstracts/P5o_PAG12_735.html
Pacific oyster
BAC, EST, map, lines
http://vertigo.hsrl.rutgers.edu/mapping.html
http://www.intl-pag.org/pag/12/abstracts/P5o_PAG12_735.html
https://www.genome.clemson.edu/orders/
http://www.ifremer.fr/GigasBase/
Pacific coral
EST, microarray
http://www.cmgd.adelaide.edu.au/research/dev_evo/index.html#Coral
http://cbis.anu.edu.au/coral/
Oyster ‘Dermo’
parasite
BAC, EST
http://www.tigr.org/tdb/e2k1/pmg/
Diatom
BAC, EST
http://genome.jgi-psf.org/thaps1/thaps1.home.html
http://avesthagen.sznbowler.com/chris/bowler/WEB/FRAMESET/frameset.php
Diatom
BAC, EST
http://www.jgi.doe.gov/sequencing/seqplans.html
http://www.ncbi.nlm.nih.gov/dbEST/dbEST_summary.html
http://avesthagen.sznbowler.com/chris/bowler/WEB/FRAMESET/frameset.php
Mollusca
Crassostrea
virginica
C. gigas
Cnidaria
Acropora millepora
Alveolata
Perkinsus marinus
Bacillariophyta
Thalassiosira
pseudonana
Phaeodactylum
tricornutum
application of techniques to quantify global gene
expression (reviewed from an ecological perspective in
[1,4]), including the construction and characterization of
expressed sequence tag (EST) libraries, serial analysis
of gene expression (SAGE), and macro- and microarrays,
will bring transcriptome-level analysis to at least 65
different marine organisms (Table 1, Online Supplementary Material). As suggested by others [7], we assert
that to advance truly marine environmental genomics,
additional species should be selected for resource
development on the basis of their ecological importance
(e.g. keystone species or ecosystem engineers) and fieldbased experimental tractability.
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Genomic-fueled insights into questions in marine
ecology
In this section, we present four case studies where the
application of genomics approaches would facilitate our
understanding of important processes in marine
ecosystems.
Insights into temperature and patterns of the distribution
of species
With regard to the ecological role of environmental
temperature, genomic-scale physiological studies have the
potential to reveal changes in gene expression that map
onto large-scale spatial patterns, such as biogeographical
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distribution (what factors determine the distribution
limits of species?) and global climate change (how will
the ranges of species change in response to changing
environmental conditions?)? In marine ecosystems, temperature has been recognized historically as a key abiotic
factor that influences the distribution of marine organisms
[15]. The modern synthesis of this perspective has yielded
varied studies of community structure (e.g. [16,17]), the
range boundaries of species (e.g. [18–20]), and predictions of
the response of species to global climate change [16,21–27].
However, there are few studies that have combined
genomics and the study of physiological traits over large
spatial scales (macrophysiology [28]); and, in spite of the
pervasive ecological effect of temperature on the marine
environment, the mechanisms linking temperature to
biogeography remain elusive. How does temperature
transduce its effects through the genotype of organisms
to alter the phenotype and, thus, organismal function? We
currently lack a clear understanding of the physiological
mechanisms by which environmental temperature is
translated into a physiological currency that affects
organismal performance, and thus alters how a species
reproduces and survives in its environment. These are
processes that, in combination, ultimately define the
limits of the biogeographical range of a species. On the
genomics side, studies of non-model aquatic organisms
have detected changes in the transcriptome as a function
of temperature change (e.g. [10]) and gene expression in
purple sea urchins exhibits changes in response to
thermal challenges that can be mapped onto latitudinal
distributions [29]. Although combining genomic-scale data
with large-scale spatial patterns is a nascent endeavor in
marine functional ecology, the future in this area is
exciting. A genomics approach provides the opportunity
to ‘mine’ for the genes that are varying in an ecological
context. These new data can then act as a platform upon
which to form hypotheses about the physiological and
cellular processes that might be varying in response to
environmental temperature, providing insight into organismal performance. Although some gene expression
patterns are not unexpected (e.g. the upregulation of
heat shock protein genes in response to heat stress), there
are sometimes unexpected patterns that are only detected
by examining expression at the genomic scale. For
example, studies have shown that genes that are normally
observed to be upregulated in response to heat stress are
also upregulated in response to cold temperatures [9,30],
suggesting that cold has a cost that is not detected by
standard analyses.
Insights into changing species interactions
In natural systems, stresses such as changes in temperature are applied at the community level. Therefore, the
responses of individual species will depend not only on
their physiology, but also on the physiology of the species
with which they interact. Recent ecological studies
examining the effect of elevated temperatures on laboratory species assemblages have shown that the outcome of
interactions such as competition and predation cannot be
predicted from the responses of single species in isolation
(e.g. [31–33]). Combining studies that use genomic tools to
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compare the ‘small-scale’ response of sets of interacting
species with studies that examine changes in species
interactions could lead to new research into the effects of
changing abiotic conditions on communities. Identifying
species with strong impacts (e.g. keystone or foundation
species) has been an important tool for determining the
mechanisms that structure communities [34–36]. We
propose that using genomics tools to investigate the
physiology of such species will similarly lead to rapid
advances in our understanding of how changes in abiotic
factors affect community functioning.
Ecological studies have already provided several
examples of important species interactions that are
contingent on abiotic conditions such as temperature. In
Oregon, USA, the foraging of the original keystone
species, the sea star Pisaster ochraceus, is strongly
affected by water temperatures [16]. Changes of as little
as 38C caused by periods of coastal upwelling significantly
reduced predation rates of the sea star, suggesting that
the annual effect of P. ochraceus on prey populations could
be governed by the frequency and intensity of upwelling
events. The prey of P. ochraceus also experience these
environmental fluctuations, and are also likely to experience alterations in metabolic rates (and possibly growth)
and reproduction (both total output and timing)*. Traditional approaches such as measuring LT50s† or respiration rates lend valuable insight into the ultimate effects
of stressors on individuals, but these measures have
limited ability to elucidate the mechanisms behind the
effects. The new perspective offered by genomics studies
could greatly improve our predictive capability. For
example, insight into physiological costs of temperature
change (e.g. elevated levels of gene transcription and
increased mRNA and protein synthesis) could enable
ecologists to better model long-term consequences of
thermal regime shifts by giving them estimates of the
potential energetic impacts of sub-lethal stressors.
The use of ecologically grounded genomics studies could
also provide new insights into the effects of how communities are affected by multiple stresses acting simultaneously. Environmental stress models (ESMs [37])
strongly influence the ways in which ecologists think
about the effects of abiotic factors on communities because
the models generate accurate predictions of community
structure in many marine systems (e.g. [38–40]). These
models assume a single stress axis, such that predator and
prey are responding either to the same stressor
(e.g. temperature) or to stressors that increase in parallel
(e.g. temperature stress and desiccation stress increase
from low to high in intertidal areas as the tide recedes). To
date, little attention has focused on situations in which
interacting species might be responding to different
stressors, or to stressors that do not increase in parallel;
yet, understanding these situations is likely to be a key
component in our understanding of how communities
respond to environmental change.
For example, in Washington, USA, the low intertidal
chiton Katharina tunicata experiences sub-lethal physiological stress at ambient summer temperatures and,
† LT50, temperature that is lethal for half of the organisms in an experimental trial.
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during these periods of high temperatures, seeks the
shade provided by the canopy of the kelp Hedophyllum
sessile [41]. The availability of shade strongly affects the
distribution and abundance of this major consumer and is
likely to reduce the metabolic costs associated with
thermal stress. Given that K. tunicata responds primarily
to low-tide air temperatures [41], it seems reasonable to
assume that canopy-provided shade would become more
important if the ambient temperature increases (sensu
[42]). However, because kelps are particularly sensitive to
increased water temperatures (such as the conditions that
accompany El Niño: e.g. [43,44]), changes in high-tide
conditions seem likely to determine the ability of the alga
to provide this crucial resource. Therefore, predicting the
outcome of this important species interaction requires
that we understand the relative importance of at least two
different stressors on the physiology of species that,
through their interactions, effectively alter abiotic conditions. This situation, in which species respond to
stressors that are not necessarily parallel, is likely to be
common but under-appreciated in marine systems. Using
genomics tools to compare the responses of species to a
suite of environmental stresses could offer fresh insights
and generate new hypotheses about how the small-scale
effects of abiotic factors are manifested in large-scale
changes in community structure and functioning.
New perspectives in environmental stress and
symbioses: coral bleaching and genomics
Perhaps no other marine ecosystem better exemplifies the
need to understand organismal physiological tolerances
than coral reefs. Currently suffering declines worldwide,
coral reefs are thought to be losing viability as a result of
coral bleaching, a phenomenon whereby stony corals lose
their algal endosymbionts and routinely die as a result
(reviewed in [45]). This loss of healthy coral has profound
consequences for reef ecosystems because decreased cover
shifts the community from a coral-dominated to an algaedominated assemblage [46], a situation that might not be
rapidly reversible. Because the health of corals is crucially
dependent on the maintenance of a functional symbiosis,
an understanding of this physiological relationship,
especially the thermotolerance of the association, is
crucial to our understanding of the mechanisms that
underlie bleaching [47], as well as to our ability to predict
the impacts of climate change [48,49].
As a process, bleaching is often considered to be a
general stress response of the coral and is thought to be
connected to a variety of factors, such as elevated seawater
temperatures and/or high light levels [50,51]. The factors
that drive the bleaching event might be acting on the host,
the symbiont, or both [52]. Alternatively, proponents of the
adaptive bleaching hypothesis have argued that bleaching
is not necessarily a stress-induced event, but rather, is an
acclimatization mechanism whereby the host has the
opportunity to repopulate with a symbiont that is more
physiologically tolerant of existing conditions [52–54].
Regardless of the causal mechanism of bleaching, there is
burgeoning evidence that both members of the symbiosis
respond to abiotic factors (e.g. [48,51,55–57]). From the
algal perspective, there might be stress-tolerant
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genotypes or ‘heat specialists’ within the dominant
zooxanthellae genus, Symbiodinium [49,55]. From the
animal perspective, studies have documented typical
metazoan physiological responses, such as the upregulation of stress-responsive genes [58]. How these individual
physiological reactions combine to alter the host–symbiont interaction during stressful events is unclear.
Future research using genomic tools stands to provide
new insight into the molecular cross-talk in this host–
symbiont relationship, identifying genes that are involved
in the bleaching process, from either the animal or algal
genomes, or both [47] (Box 2).
Diseases in the marine environment
Given the increased frequency of reports of marine
diseases [59] and their profound impact on community
structure in marine ecosystems, we need improved
molecular techniques with which to detect pathogens
and a better perspective of how environmental stressors
facilitate the outbreak of marine diseases. With regard to
these priorities, a genomics approach could contribute in
three major ways: (i) by improving our understanding of
infection mechanisms; (ii) by developing a physiological
perspective on the environmental facilitation of infection;
and (iii) as a mechanism with which to predict the spread
of disease, leading to better assessment and prediction of
environmental health [59].
Just as some methods have attempted to find indicators
of compromised health by looking at physiological indices
of stress (e.g. [60]), transcriptome profiling stands to
provide ‘physiological fingerprints’ of healthy versus
diseased organisms at the level of gene expression. By
providing early detection and potential for the high
throughput of samples, transcriptome profiling could be
a major tool for managers to use to detect the presence of
infected organisms in their systems. Gene expression
profiling will help target the processes that are generally
altered or compromised that might then link to reduced
resistance of organisms to disease. One example where
progress is rapidly being made is from the ongoing studies
of pathogenicity and the infection mechanism of white
spot shrimp virus (WSSV), the most important viral
infection affecting penaeid shrimp and other crustaceans
worldwide, which is thought to be transmitted via
aquacultural practices [61]. Even on a limited scale, the
application of DNA microarray technology to comparisons
of healthy and infected animals has provided marked
insight into the multiple strategies used to mitigate
infection, as well as to the global cellular response to
this virulent pathogen [62].
Concluding remarks
We believe that productive avenues of research in marine
systems will be those in which ecological knowledge and
the identification of the important species and species
interactions in a system are combined with genomics tools
and physiological perspectives on the responses of these
species to variable environmental conditions. Targeted
studies that characterize environmentally relevant physiological responses of species that are known to be
influential in communities could lead to a better general
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Box 2. The advancement of corals as marine models in
ecophysiological genomics
Tropical marine ecosystems based on scleractinian (stony) corals are
among the most productive and biodiverse systems on Earth,
providing food and shelter for many unique and irreplaceable
species. The great success of corals as ecosystem engineers might
lie in their own extraordinary ecology and physiology that is based
on a complex, mutualistic symbiosis between photosynthetic
dinoflagellate algae (zooxanthellae) and the anthozoan animal
host. A full understanding of this symbiosis remains elusive,
particularly at the molecular level. Unfortunately, there is a pressing
need to comprehend the coral system because of the global trend
towards failing coral health.
Our ability to deal directly with coral disease and to predict reef
change is dependent on how well we understand corals across
molecular, physiological and ecological scales. To address this
challenge and to further corals as a model system in marine
ecophysiological genomics, several research groups have undertaken the construction and characterization of the coral and
dinoflagellate genomes, and EST and cDNA libraries, with the
ultimate goal of collecting experimental field data on genome
function and evolution. In the USA, the Joint Genome Research
Institute (JGI; http://www.jgi.doe.gov/) has targeted two dominant
reef-building species from the Caribbean, the boulder star coral
Montastraea faveolata and the Elkhorn coral Acropora cervicornis.
The public resources of the JGI currently include a BAC library for
A. cervicornis containing 36 864 clones with an average size of
100 kb and 3.6X genome coverage [47]. The M. faveolata library has
an average insert size of 150 kb and clones from it are to be selected
and fully characterized. In the Pacific, Australian researchers have
taken the lead, with Acropora millepora as their model. Groups
collaborating at the national and international level from The
Australian National University (http://www.anu.edu.au/), James
Cook University (http://www.jcu.edu.au/), The University of Queensland (http://www.uq.edu.au/), as well as other institutions have
collectively assembled genomic libraries; cDNA libraries from
embryonic, larval and adult stages; a large collection of ESTs; and
a 3000 clone, sequenced EST microarray (Table 1, main text).
Exploitation of these resources has already brought new insight into
coral biology, as well as into general patterns of genome evolution
[69]. Thus, the coral reef community is eagerly awaiting the arrival of
similar resources for the common symbiotic dinoflagellate, Symbiodinium (http://oxytricha.princeton.edu/wacavalcanti/Symbiodinium_WP_distribute.pdf) and the synergistic progress that they
will promote.
understanding of marine systems and to a rapid increase
in the ability of ecologists to predict community responses
to environmental change.
Acknowledgements
We thank three anonymous reviewers for comments that improved the
article. We thank the National Science Foundation for financial support
during the course of this writing project (NSF grants INT-0243518 to
J.L.B. and OCE-0425107 to G.E.H.). This is contribution number 170 of
the Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO),
a long-term ecological consortium funded by the David and Lucile
Packard Foundation.
Supplementary data
Supplementary data associated with this article can be
found at doi:10.1016/j.tree.2005.03.006
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