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The goal of the Bio-ICE Task Team, convened from July 2020 - January 2022, was to advance the integration of biological observations from local, regional, and federal sources using best practices to inform national needs and ultimately feed into GOOS data visualizations and reporting. Using the GOOS marine mammals and corals EOVs as examples, the Task Team sought to: 1. Reconcile U.S. federal collection of these variables with GOOS EOVs and the Group on Earth Observations’ EBVs, identifying synergies in spatial and temporal observing requirements and with existing observation infrastructure and delivery, including use of documented best practices and standards. 2. Identify and improve pathways for data flow for observations of these variables from the IOOS Regional Associations and federal sources into common data portals. This included a focus on identifying and implementing best practices for standardized data collection and delivery adhering to the FAIR and CARE data principles, as appropriate. The Task Team effort focused on corals and marine mammals to ensure the work of the task team was achievable within the time frame. These two EOVs were selected because of their importance to multiple stakeholders, as well as offering opportunities to tie-in to several critical U.S. priorities in ocean science. While the team chose this focus, it acknowledged that there are activities and communities working to advance the other biology and ecosystem essential variables in ways that might be similar to or synergistic with the task team, such as SCOR Working Group 158: Coordinated Global Research Assessment of Seagrass System (C-GRASS), global efforts to coordinate ocean sound monitoring and data, GOOS BioEco panel community workshops and ongoing panel activities, and other efforts worth tracking or considering for future engagement with IOOC.

Reef-building corals rely on both heterotrophy and endosymbiotic dinoflagellate autotrophy to meet their metabolic needs. Those looking to culture these organisms for scientific or industrial purposes must therefore consider both feeding regimes and the light environment. Herein the effects of three photosynthetically active radiation (PAR) levels were assessed in fed and unfed specimens of the model coral Pocillopora acuta that were cultured in a recirculating aquaculture system (RAS). Half of the corals were fed Artemia sp. brine shrimp in a separate feeding tank to prevent biofouling, and fragments were exposed to PAR levels of 105, 157, or 250 μmol quanta m−2 s−1 over a 12-h period each day. All cultured corals survived the 140-day treatment, and the physiological response variables assessed-buoyant weight, specific growth rate, linear extension, color, and Fv/Fm-were significantly influenced by feeding, and, to a lesser extent, light. Specifically, fed corals grew faster and larger, and presented darker pigmentation; corals fed at the highest light levels grew at the fastest rate (6 cm year−1 or 175 mg g−1 week−1). Given the high physiological performance observed, we advocate the active feeding of brine shrimp in RAS by those looking to cultivate P. acuta, and likely other corals, over long-term timescales.

There is an urgent need to develop means of ex situ biobanking and biopreserving corals and other marine organisms whose habitats have been compromised by climate change and other anthropogenic stressors. To optimize laboratory growth of soft corals in a way that could also benefit industry (e.g., aquarium trade), three culture systems were tested herein with Sarcophyton glaucum: (1) a recirculating aquaculture system (RAS) without exogenous biological input (RAS−B), (2) a RAS with “live” rocks and an exogenous food supply (RAS+B), and (3) a simple flow-through system (FTS) featuring partially filtered natural seawater. In each system, the effects of two levels of photosynthetically active radiation (100 or 200 μmol quanta m−2 s−1) and flow velocity (5 or 15 cm s−1) were assessed, and a number of soft coral response variables were measured. All cultured corals survived the multi-month incubation, yet those of the RAS−B grew slowly and even paled; however, once they were fed (RAS−B modified to RAS+B), their pigmentation increased, and their oral discs readily expanded. Light had a more pronounced effect in the RAS−B system, while flow affected certain coral response variables in the FTS tanks; there were few effects of light or flow in the RAS+B system, potentially highlighting the importance of heterotrophy. Unlike the ceramic pedestals of the FTS, those of the RAS+B did not regularly become biofouled by algae. In concert with the aforementioned physiological findings, we therefore recommend RAS+B systems as a superior means of biopreservating and biobanking soft corals.

Naturally acidified environments, such as those caused by volcanic CO2 venting, reveal how complex coral reef ecosystems may respond to future ocean acidification conditions. Few of these sites have been described worldwide, and only a single such site is known from the Caribbean. Herein, we have characterized an area of volcanic acidification at Mayreau Island, St. Vincent and the Grenadines. Despite localized CO2 enrichment and gas venting, the surrounding area has high hard and soft coral cover, as well as extensive carbonate frameworks. Twice daily extremes in acidification, in some cases leading to undersaturation of aragonite, are correlated with tidal fluctuations and are likely related to water flow. Corals persisting despite this periodic acidification can provide insights into mechanisms of resilience and the importance of natural pH variability on coral reefs.

The recruitment of marine invertebrate larvae to coral reef ecosystems is critical for the continued productivity of these highly biodiverse habitats. Despite such importance, little is known about temporal variation patterns of invertebrate larval recruitment in coral reefs ecosystems, aside from studies focused only on reef corals themselves. Given this knowledge deficiency, recruitment onto dead coral branches was monitored over a one-year period in the Central Mexican Pacific, and recruit assemblage and density both changed over time. In particular, recruitment was higher in the warmer months, possibly due to reproductive processes and/or increases in metabolic rates associated with high temperatures and seasonal/local events such as upwellings that increase the food resources available for the recruits which just before the warm season, when the recruitment is more more prevalent during the warm season. The most common invertebrate recruits were malacostracans, ostracods, gastropods, maxillopods, and polychaetes, and foraminifers were commonly observed, as well. Future works in this region will seek to understand whether recruit density and diversity change in response to elevated temperatures associated with global climate change.

Increases in seawater temperature associated with global climate change are causing the mutualistic relationship between reef-building corals and the symbiotic dinoflagellates (genus Symbiodinium) that reside within their cells to break down. There is consequently an urgent need to develop tools for modeling coral biology in response to environmental shifts, an enterprise that is complicated by the fact that no pristine reefs remain on Earth. This work sought to 1) uncover the environmental factors that contribute most to observed spatio-temporal variation in coral physiology and 2) devise means of detecting anomalous behavior in field corals by analyzing a dataset from the Austral (French Polynesia) and Cook Islands of the South Pacific with a multivariate statistical approach. Upon employing this multi-tiered analytical platform, host genotype was found to be the most significant driver of variation in physiology of the pocilloporid coral colonies sampled across the two archipelagos. Furthermore, those colonies demonstrating the most extensive variation across the seven response variables assessed tended to deviate most significantly from the global mean response calculated across all samples, suggesting that high within-sample physiological variability may be one means of delineating aberrant coral behavior in the absence of data from pristine control reefs.

Although coral reef ecosystems across the globe are in decline due to climate change and other anthropogenic stressors, certain inshore reefs of the Upper Florida Keys reef tract have persisted, with some even thriving, under marginalized conditions. To better understand the molecular basis of the thermotolerance displayed by these corals, a laboratory-based temperature challenge experiment that also featured conspecifics from a more stress-susceptible offshore reef was conducted with the common Caribbean reef-builder Orbicella faveolata, and the proteomes of both the coral hosts and their endosymbiotic dinoflagellate communities were profiled in (1) controls, (2) corals that succumbed to high-temperature stress and bleached, and (3) those that instead acclimated to high temperatures ex situ. Proteomic signatures varied most significantly across temperatures, host genotypes, and Symbiodiniaceae assemblages, and the two eukaryotic compartments of this mutualism exhibited distinct proteomic responses to high temperatures. Both partners maintained high levels of molecular chaperones and other canonical (eukaryotic) stress response (CSR) proteins in all treatments (including controls). Instead, proteins involved in lipid trafficking, metabolism, and photosynthesis played greater roles in the holobionts’ high-temperature responses, and these energy mobilization processes may have sustained the elevated protein turnover rates associated with the constitutively active CSR.

Healthy coral communities can be found on artificial structures (concrete walls and riprap) within the Port of Miami (PoM), Florida. These communities feature an unusually high abundance of brain corals, which have almost entirely vanished from nearby offshore reefs. These corals appear to be thriving in very low-quality waters influenced by dense ship and boat traffic, dredging, and numerous residential and industrial developments. The PoM basin is part of Biscayne Bay, an estuarine environment that experiences frequent freshwater input, high nutrient loading, hypoxia, and acidification. To investigate if there is a molecular basis behind the ability of these corals to persist within these highly “urbanized” waters, we compared whole transcriptome expression profiles from 25 PoM Pseudodiploria strigosa colonies against six conspecifics from a nearby offshore reef. We found that the urban corals exhibited higher expression of (1) transcripts encoding pattern-recognition receptors which may allow these corals to better sense and detect food particles and pathogenic invaders; (2) digestive and degradation-associated enzymes, which may suggest an elevated capacity for heterotrophy and pathogen digestion; and (3) transcripts related to innate immunity, defense, and cellular detoxification, which may collectively protect against pathogenic organisms and water pollution impacts. Large ribosomal subunit rRNA gene mapping revealed that P. strigosa colonies from the PoM sites predominantly hosted heat-tolerant endosymbionts from the genus Durusdinium while offshore conspecifics’ communities were dominated by symbionts in the genus Breviolum. These findings reveal transcriptomic plasticity and molecular mechanisms contributing to the persistence of these corals within a highly urbanized habitat.

Coral bleaching is the single largest global threat to coral reefs worldwide. Integrating the diverse body of work on coral bleaching is critical to understanding and combating this global problem. Yet investigating the drivers, patterns, and processes of coral bleaching poses a major challenge. A recent review of published experiments revealed a wide range of experimental variables used across studies. Such a wide range of approaches enhances discovery, but without full transparency in the experimental and analytical methods used, can also make comparisons among studies challenging. To increase comparability but not stifle innovation, we propose a common framework for coral bleaching experiments that includes consideration of coral provenance, experimental conditions, and husbandry. For example, reporting the number of genets used, collection site conditions, the experimental temperature offset(s) from the maximum monthly mean (MMM) of the collection site, experimental light conditions, flow, and the feeding regime will greatly facilitate comparability across studies. Similarly, quantifying common response variables of endosymbiont (Symbiodiniaceae) and holobiont phenotypes (i.e., color, chlorophyll, endosymbiont cell density, mortality, and skeletal growth) could further facilitate cross-study comparisons. While no single bleaching experiment can provide the data necessary to determine global coral responses of all corals to current and future ocean warming, linking studies through a common framework as outlined here, would help increase comparability among experiments, facilitate synthetic insights into the causes and underlying mechanisms of coral bleaching, and reveal unique bleaching responses among genets, species, and regions. Such a collaborative framework that fosters transparency in methods used would strengthen comparisons among studies that can help inform coral reef management and facilitate conservation strategies to mitigate coral bleaching worldwide. published

The mutualistic symbiosis between anthozoans and intra-gastrodermal dinoflagellates of the family Symbiodiniaceae is the functional basis of all coral reef ecosystems, with the latter providing up to 95% of their fixed photosynthate to their hosts in exchange for nutrients. However, recent studies of sponges, jellyfish, and anemones have revealed the potential for this mutualistic relationship to shift to parasitism under stressful conditions. Over a period of eight weeks, we compared the physiological conditions of both inoculated and aposymbiotic anemones (Exaiptasia pallida) that were either fed or starved. By the sixth week, both fed groups of anemones were significantly larger than their starved counterparts. Moreover, inoculated and starved anemones tended to disintegrate into “tissue balls” within eight weeks, and 25% of the samples died; in contrast, starved aposymbiotic anemones required six months to form tissue balls, and no anemones from this group died. Our results show that the dinoflagellates within inoculated anemones may have posed a fatal metabolic burden on their hosts during starvation; this may be because of the need to prioritize their own metabolism and nourishment at the expense of their hosts. Collectively, our study reveals the potential of this dynamic symbiotic association to shift away from mutualism during food-deprived conditions.

Although reef-building corals are threatened by a number of anthropogenic impacts, certain scleractinian-dinoflagellate (genus Symbiodinium) endosymbioses have proven markedly resilient to environmental change. For instance, corals from upwelling habitats of Southern Taiwan withstand both short- and long-term increases in temperature, potentially due to their routine exposure to highly variable temperature regimes in situ. To gain a greater understanding of the proteomic basis for such acclimatization to unstable environmental conditions, specimens of the Indo-Pacific reef-building coral Seriatopora hystrix Dana 1846 were sampled during a period of stable temperature conditions from 1) a site characterized by frequent upwelling events in Southern Taiwan and 2) a nearby, non-upwelling control site in the Taiwan Strait. Two-dimensional gel electrophoresis followed by sequencing of differentially concentrated proteins with mass spectrometry unveiled significantly more proteins involved in the cellular stress response in coral hosts of the upwelling site. Although such stress protein signatures could be indicative of sub-lethal levels of cellular stress, especially given the relatively higher sediment loads characteristic of the upwelling site, these proteins may, in contrast, have been constitutively maintained at high levels in preparation for large fluctuations in temperature and other abiotic parameters (e.g., nutrient levels) brought upon by upwelling events.

Lipid bodies (LBs) in the coral gastrodermal tissues are key organelles in the regulation of endosymbiosis and exhibit a diel rhythmicity. Using the scleractinian Euphyllia glabrescens collected across the diel cycle, we observed temporally dynamic lipid profiles in three cellular compartments: host coral gastrodermal cells, LBs, and in hospite Symbiodinium. Particularly, the lipidome varied over time, demonstrating the temporally variable nature of the coral–Symbiodinium endosymbiosis. The lipidome-scale data highlight the dynamic, light-driven metabolism of such associations and reveal that LBs are not only lipid storage organelles but also act as a relay center in metabolic trafficking. Furthermore, lipogenesis in LBs is significantly regulated by coral hosts and the lipid metabolites within holobionts featured predominantly triacylglycerols, sterol esters, and free fatty acids. Given these findings through a time-varied lipidome status, the present study provided valuable insights likely to be crucial to understand the cellular biology of the coral–Symbiodinium endosymbiosis.

Fiddler crab burrow morphologies in tidal flat ecosystems depend largely on physical characteristics of the soil. Herein, we aimed to examine the relationship between soil texture profiles and the burrow depths and morphologies of four fiddler crab species: Tubuca arcuata , Gelasimus borealis , Xeruca formosensis , and Austruca lactea . We found that the burrow depths of T. arcuata , G. borealis , and A. lactea (range = 8–50 cm) were strongly affected by surface soil composition; only the burrow depth of X. formosensis (which reached 100 cm in some cases) was influenced by the presence of deeper, clay-rich soils. Specifically, X. formosensis relied more heavily on fine soils, such as clay or silt, when they burrowed deeper into sand-covered mudflats. We hypothesize that deep burrowers, such as X. formosensis, may coat clay-rich soils on their burrow walls to impede flooding and to prevent burrow collapse, suggesting that surface soil composition does not necessarily determine the burrow depth and composition for all fiddler crab species.

Ocean acidification (OA) and warming currently threaten coastal ecosystems across the globe. However, it is possible that the former process could actually benefit marine plants, such as seagrasses. The purpose of this study was to examine whether the effects of the seagrass Thalassia hemprichii can increase the resilience of OA-challenged coral reef mesocosms whose temperatures were gradually elevated. It was found that seagrass shoot density, photosynthetic efficiency, and leaf growth rate actually increased with rising temperatures under OA. Macroalgal growth rates were higher in the seagrass-free mesocosms, but the calcification rate of the model reef coral Pocillopora damicornis was higher in coral reef mesocosms featuring seagrasses under OA at 25 and 28 °C. Both the macroalgal growth rate and the coral calcification rate decreased in all mesocosms when the temperature was raised to 31 °C under OA. However, the variation in gross primary production, ecosystem respiration, and net ecosystem production in the seagrass mesocosms was lower than in seagrass-free controls, suggesting that the presence of seagrass in the mesocosms helped to stabilize the metabolism of the system in response to simulated climate change.

International audience; Seawater temperature rise in French Polynesia has repeatedly resulted in the bleaching of corals and giant clams. Because giant clams possess distinctive ectosymbiotic features, they represent a unique and powerful model for comparing molecular pathways involved in 1) maintenance of symbiosis and 2) acquisition of thermotolerance among coral reef organisms. Herein, we explored the physiological and transcriptomic responses of the clam hosts and their photosynthetically active symbionts over a 65-day experiment in which clams were exposed to either normal or environmentally relevant elevated seawater temperatures. Additionally, we used metabarcoding data coupled with in situ sampling/survey data to explore the relative importance of holobiont adaptation (i.e., a symbiont community shift) versus acclimation (i.e., physiological changes at the molecular level) in the clams' responses to environmental change. We finally compared transcriptomic data to publicly available genomic datasets for Symbiodiniaceae dinoflagellates (both cultured and in hospite with the coral Pocillopora damicornis) to better tease apart the responses of both hosts and specific symbiont genotypes in this mutualistic association. Gene module preservation analysis revealed that the function of the symbionts' photosystem II was impaired at high temperature, and this response was also found across all holobionts and Symbiodiniaceae lineages examined. Similarly, epigenetic modulation appeared to be a key response mechanism for symbionts in hospite with giant clams exposed to high temperatures, and such modulation was able to distinguish thermo-tolerant from thermo-sensitive Cladocopium goreaui ecotypes; epigenetic processes may, then, represent a promising research avenue for those interested in coral reef conservation in this era of changing global climate.

Herein we propose an ambitious confrontation of the current coral reef crisis through the establishment of a "Coral Hospital." In an analogous manner to a human hospital, "sick" corals will first be diagnosed either in situ or in the hospital's diagnostic "clinic" such that the root cause of illness can be discerned (e.g., disease, high temperatures, or pollutant stress). Then, corals will be "treated" (when necessary) and allowed to "convalesce" in precisely controlled coral husbandry facilities. Upon "rehabilitation," the recovered corals will be returned to their home reef (if this reef was not found to have degraded), or, alternatively, to a site featuring oceanographic conditions favoring a high level of health, as determined by husbandry experiments performed in other hospital "wards." When possible, diagnostic data from the sick corals (i.e., the underlying cause of sickness) will be used to guide environmental remediation schemes aimed at promoting coral resilience in the ocean. If the home reef improves to an appreciable extent during the time the corals are "hospitalized," these corals could be replanted there upon rehabilitation. Regardless of the site of outplanting, recuperated corals will be monitored over time to validate the "quality of care" in the hospital. In the event that the home reefs suffer to such an extent that environmental mitigation is no longer possible, coral gametes will be collected and cryopreserved such that they may be fertilized, reared in officinarum, and later reseeded once/if global marine conditions again permit coral survival.

As significant anthropogenic pressures are putting undue stress on the world's oceans, there has been a concerted effort to understand how marine organisms respond to environmental change. Transcriptomic approaches, in particular, have been readily employed to document the mRNA-level response of a plethora of marine invertebrates exposed to an array of simulated stress scenarios, with the tacit and untested assumption being that the respective proteins show a corresponding trend. To better understand the degree of congruency between mRNA and protein expression in an endosymbiotic marine invertebrate, mRNAs and proteins were sequenced from the same samples of the common, Indo-Pacific coral Seriatopora hystrix exposed to stable or upwelling-simulating conditions for 1 week. Of the 167 proteins downregulated at variable temperature, only two were associated with mRNAs that were also differentially expressed between treatments. Of the 378 differentially expressed genes, none were associated with a differentially expressed protein. Collectively, these results highlight the inherent risk of inferring cellular behaviour based on mRNA expression data alone and challenge the current, mRNA-focused approach taken by most marine and many molecular biologists.

El Nino-Southern Oscillation (ENSO) events can cause dramatic changes in marine communities. However, we know little as to how ENSO events affect tropical seagrass beds over decadal timescales. Therefore, a diverse array of seagrass (Thalassia hemprichii) habitat types were surveyed once every 3 months for 16 years (January 2001 to February 2017) in a tropical intertidal zone that is regularly affected by both ENSO events and anthropogenic nutrient enrichment. La Nina and El Nino events had distinct effects on the biomass and growth of T. hemprichii. During La Nina years, higher (a) precipitation levels and (b) seawater nitrogen concentrations led to increases in seagrass leaf productivity, canopy height, and biomass. However, the latter simultaneously stimulated the growth of periphyton on seagrass leaves; this led to decreases in seagrass cover and shoot density. More frequent La Nina events could, then, eventually lead to either a decline in intertidal seagrass beds or a shift to another, less drought-resistant seagrass species in those regions already characterized by eutrophication due to local anthropogenic activity.

Although most reef-building corals live near the upper threshold of their thermotolerance, some scleractinians are resilient to temperature increases. For instance, Pocillopora acuta specimens from an upwelling habitat in Southern Taiwan survived a 9-month experimental exposure to 30°C, a temperature hypothesized to induce stress. To gain a greater understanding of the molecular pathways underlying such high-temperature acclimation, the protein profiles of experimental controls incubated at 27°C were compared to those of conspecific P. acuta specimens exposed to 30°C for two, four, or eight weeks, and differentially expressed proteins (DEPs) were removed from the protein gels and sequenced with mass spectrometry. Sixty unique DEPs were uncovered across both eukaryotic compartments of the P. acuta-dinoflagellate (genus Symbiodinium) mutualism, and Symbiodinium were more likely to up-regulate protein expression in response to high temperature exposure than the coral hosts in which they resided at the 2-week sampling time. Furthermore, different cellular pathways were affected by elevated temperature exposure in each compartment; Symbiodinium tended to up-regulate the expression of proteins involved in the cellular stress response, whereas the differentially expressed host coral proteome featured numerous proteins involved in cytoskeletal structure, immunity, and metabolism. These proteome-scale data suggest that the coral host and its intracellular dinoflagellates have differing cellular strategies for acclimating to elevated temperatures.

Coral-reef ecosystems of the central Mexican Pacific have been routinely affected by both moderate and severe El Niño–Southern Oscillation (ENSO) events over the past 20 years. Such conditions are associated with abnormally high (1997–1998, 2002–2003, 2009–2010, and 2015–2016; ‘El Niño’) and low (1999–2000, 2008–2009, and 2010–2011; ‘La Niña’) seawater temperatures. Because few studies have documented how ENSO events affect both corals and key coral competitors such as macroalgae, we evaluated the short- and long-term changes in the cover of three reef coral genera, namely, Pocillopora, Pavona and Porites, as well as four coral competitors, namely, macroalgae, turf algae, coralline algae (CCA) and sponges, over a multi-year period that encapsulated two strong ENSO events: the 2010–2011 La Niña and the 2015–2016 El Niño. Such temperature anomalies caused a short-lived decrease in coral cover, alongside a concomitant increase in CCA. The communities eventually returned to their coral-dominated states within several months of the ENSO events, suggesting that these reef habitats can recover from such episodes of anomalous seawater temperatures.

Although rising ocean temperatures threaten scleractinian corals and the reefs they construct, certain reef corals can acclimate to elevated temperatures to which they are rarely exposed in situ. Specimens of the model Indo-Pacific reef coral Pocillopora damicornis collected from upwelling reefs of Southern Taiwan were previously found to have survived a 36-week exposure to 30°C, a temperature they encounter infrequently and one that can elicit the breakdown of the coral–dinoflagellate (genus Symbiodinium) endosymbiosis in many corals of the Pacific Ocean. To gain insight into the subcellular pathways utilized by both the coral hosts and their mutualistic Symbiodinium populations to acclimate to this temperature, mRNAs from both control (27°C) and high (30°C)-temperature samples were sequenced on an Illumina platform and assembled into a 236 435-contig transcriptome. These P. damicornis specimens were found to be ~60% anthozoan and 40% microbe (Symbiodinium, other eukaryotic microbes, and bacteria), from an mRNA-perspective. Furthermore, a significantly higher proportion of genes from the Symbiodinium compartment were differentially expressed after two weeks of exposure. Specifically, at elevated temperatures, Symbiodinium populations residing within the coral gastrodermal tissues were more likely to up-regulate the expression of genes encoding proteins involved in metabolism than their coral hosts. Collectively, these transcriptome-scale data suggest that the two members of this endosymbiosis have distinct strategies for acclimating to elevated temperatures that are expected to characterize many of Earth's coral reefs in the coming decades.

Fiddler crabs are deposit feeders that play critical roles as ecological engineers in tidal flats. Recently, anthropogenic disturbances have led to fiddler crab habitat loss and/or degradation; therefore, we developed a mathematically derived habitat suitability index (HSI) model to aid in habitat assessments of fiddler crabs. Based on what is known about the life histories of fiddler crabs, the variables of an HSI model included submersion time, interstitial salinity, and soil 1) grain size, 2) organic matter content, and 3) heat capacity. We acquired density data from four fiddler crab species—Xeruca formosensis, Tubuca arcuata, Austruca lactea, and Gelasimus borealis— at five sites on the western coast of Taiwan to develop the HSI models. Significant positive correlations existed between the HSI output and fiddler crab density for all target species except for those X. formosensis inhabiting the topsoil layer (0–20 cm). For the deep burrowers X. formosensis, however, a positive linear relationship was documented when only those data from the 40–60 cm layers were considered and if the habitat was a sand-covered mudflat. Mapping for each species was conducted using the HSI models with the highest reliability, and four classification levels were established for the habitat suitability of each species at one of the study sites. Based on this field test of a fiddler crab HSI model, we have developed a platform for the proactive conservation of fiddler crabs inhabiting subtropical tidal flats.

Coral reef ecosystems around the planet are threatened by an onslaught of anthropogenic stressors, most notably global climate change (GCC); indeed, no regions have been spared from our wide-ranging human impact. Consequently, there has been an urgent push to 1) model how marine organisms will respond to future changes in their environments and 2) make data-driven predictions as to which populations are most stress sensitive. Given our recently elevated level of understanding of the responses of reef-building corals to environmental change and GCC, we are now in a position in which it may be possible to make projections as to which corals are most susceptible to GCC, as well as which will likely demonstrate resilience. Herein I explore the potential for data-trained predictive modeling approaches based on artificial intelligence to generate models that can accurately predict coral stress susceptibility (CSS). Specifically, I advocate that coral reef-focused partial least squares and neural networking algorithms (trained with either molecular or environmental data) should be developed, with their prognostic capability then field-tested at sites that span a gradient of human impact and ecological resilience in the high-biodiversity “Coral Triangle.” If the developed predictive models are characterized by the analytical capacity to forecast CSS, we will possess one means of identifying reefs that should be prioritized for conservation in this era of rapidly changing global climate.

Although the importance of anthozoan-dinoflagellate (genus Symbiodinium) endosymbioses in the establishment of coral reef ecosystems is evident, little is known about the molecular regulation of photosynthesis in the intra-gastrodermal symbiont communities, particularly with respect to the rate-limiting Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco). In this study, we analyzed rubisco mRNA (rbcL) and protein (RBCL) concentrations over the diel cycle in both cultured and endosymbiotic Symbiodinium samples. In the former, rbcL expression increased upon illumination and decreased during the dark, a pattern that was upheld under continual dark incubation. A different trend in rbcL expression was observed in endosymbiotic Symbiodinium residing within sea anemone (Aiptasia pulchella) tissues, in which illumination gradually led to decreased rbcL mRNA expression. Unexpectedly, RBCL protein expression did not vary over time within anemone tissues, and in neither cultured nor endosymbiotic samples was a correlation between gene and protein expression documented. It appears, then, that photoperiod, lifestyle, and posttranscriptional regulation are all important drivers of RBCL expression in this ecologically important dinoflagellate.

Recent work has found that pocilloporid corals from regions characterized by unstable temperatures, such as those exposed to periodic upwelling, display a remarkable degree of phenotypic plasticity. In order to understand whether important reef builders from these upwelling reefs remain physiologically uncompromised at temperatures they will experience in the coming decades as a result of global climate change, a long-term elevated temperature experiment was conducted with Pocillopora damicornis specimens collected from Houbihu, a small embayment within Nanwan Bay, southern Taiwan that is characterized by 8–9 °C temperature changes during upwelling events. Upon nine months of exposure to nearly 30 °C, all colony (mortality and surface area), polyp (Symbiodinium density and chlorophyll a content), tissue (total thickness), and molecular (gene expression and molecular composition)-level parameters were documented at similar levels between experimental corals and controls incubated at 26.5 °C, suggesting that this species can readily acclimate to elevated temperatures that cause significant degrees of stress, or even bleaching and mortality, in conspecifics of other regions of the Indo-Pacific. However, the gastrodermal tissue layer was relatively thicker in corals of the high temperature treatment sampled after nine months, possibly as an adaptive response to shade Symbiodinium from the higher photosynthetically active radiation levels that they were experiencing at that sampling time. Such shading may have prevented high light and high temperature-induced photoinhibition, and consequent bleaching, in these samples.

Given the threat of climate change towards scleractinian corals, there is an urgent need to understand their physiological mechanisms of acclimation to increasing temperatures. To gain insight into this process, two mesocosm-based experiments were conducted in Southern Taiwan with the model reef-building coral Pocillopora damicornis. In the first study, temperature was gradually elevated to 32 °C, though reduced to ambient levels at night, in order to simulate a temperature profile that can characterize intertidal reefs of Southern Taiwan. All corals acclimated to such conditions over the course of the month-long experiment, as evidenced by a variety of physiological and sub-cellular responses. In the second experiment, corals were exposed continually to 31.5 °C for two weeks, and, in contrast to results from the first study, the majority of the corals died, revealing that prolonged exposure to this temperature is lethal for this dominant reef builder of many regions of the Pacific Ocean.

Given the significant threats towards Earth's coral reefs, there is an urgent need to document the current physiological condition of the resident organisms, particularly the reef-building scleractinians themselves. Unfortunately, most of the planet's reefs are understudied, and some have yet to be seen. For instance, the Kingdom of Tonga possesses an extensive reef system, with thousands of hectares of unobserved reefs; little is known about their ecology, nor is there any information on the health of the resident corals. Given such knowledge deficiencies, 59 reefs across three Tongan archipelagos were surveyed herein, and pocilloporid corals were sampled from approximately half of these surveyed sites; 10 molecular-scale response variable were assessed in 88 of the sampled colonies, and 12 colonies were found to be outliers based on employment of a multivariate statistics-based aberrancy detection system. These outliers differed from the statistically normally behaving colonies in having not only higher RNA/DNA ratios but also elevated expression levels of three genes: 1) Symbiodinium zinc-induced facilitator-like 1-like, 2) host coral copper-zinc superoxide dismutase, and 3) host green fluorescent protein-like chromoprotein. Outliers were also characterized by significantly higher variation amongst the molecular response variables assessed, and the response variables that contributed most significantly to colonies being delineated as outliers differed between the two predominant reef coral species sampled, Pocillopora damicornis and P. acuta. These closely related species also displayed dissimilar temporal fluctuation patterns in their molecular physiologies, an observation that may have been driven by differences in their feeding strategies. Future works should attempt to determine whether corals displaying statistically aberrant molecular physiology, such as the 12 Tongan outliers identified herein, are indeed characterized by a diminished capacity for acclimating to the rapid changes in their abiotic milieu occurring as a result of global climate change.

The Cnidaria have more symbiotic copepods than any other group of invertebrates, and the greatest numbers of these associates occur on hard corals. A review of the scattered literature on the diversity and taxonomic composition of scleractinian-associated copepods and their hosts revealed a total of 148 coral species, representing 66 genera and 15 families that serve as hosts to copepods. At present, 363 copepod species, representing 99 genera, 19 families and three orders, have been recorded as associates of scleractinian corals. The total included 288 cyclopoids, 68 siphonostomatoids and seven harpacticoids. Within the Cyclopoida the representation of species varied greatly among the 13 families, with a disproportionate number of species belonging to the Anchimolgidae (141 species) and Xarifiidae (92 species). Data on host utilization and geographical distribution of all copepods living symbiotically with hard corals is synthesized and host specificity patterns are highlighted. The prevalence, intensity, density, and biodiversity of copepod infection of 480 colonies of the reef-building coral Pocillopora damicorni s (Linnaeus, 1758) from Nanwan Bay, southern Taiwan were documented between July 2007 and November 2008. It was hypothesized that certain environmental factors and physiological coral traits, such as the density of Symbiodinium , could influence these infection parameters. Analysis revealed that ectoparasitic copepods were the most likely to infect P. damicornis , and that Asteropontius minutus Kim, 2003 accounted for more than 50% of total copepod density in July–September 2007 when temperatures were high and bleaching occurred in ~75% of the sampled colonies. The data further showed that copepod virulence may be related to their life history strategies, as well as to Symbiodinium density, surface area of the host coral colonies, and concentration of nitrate and chlorophyll- a in the surrounding seawater . By tracking the abundance, diversity, and performance of infectious copepods prior, throughout, and after a natural bleaching event, the potential to use these parasites as bioindicators for predicting the future physiological performance of P. damicornis in response to environmental change, particularly bleaching events, may ultimately be further explored, developed and maximized. Humesimyzon Kim, 2010, previously placed in the Asterocheridae, is tentatively transferred to the recently resurrected family Coralliomyzontidae. The authorship and spelling of Pseudanthessius thorellii (Brady, 1880) are corrected.

Background: Multivariate statistical approaches (MSA), such as principal components analysis and multidimensional scaling, seek to uncover meaningful patterns within datasets by considering multiple response variables in a concerted fashion. Although these techniques are readily used by ecologists to visualize and explain differences between study sites, they could theoretically be employed to differentiate organisms within an experimental framework while simultaneously identifying response variables that drive documented experimental differences. Methods: A meta-analysis employing various MSA was conducted to re-analyze data from two studies that sought to understand the response of the common, Indo-Pacific reef coral Seriatopora hystrix to temperature changes. Results: Gene expression and physiological data partitioned experimental specimens by time of sampling, treatment temperature, and site of origin upon employing MSA. Discussion: These findings 1) signify that S. hystrix and its dinoflagellate endosymbionts display physiological and molecular signatures that are characteristic of sampling time, site of colony origin, and/or temperature regime and 2) promote the utility of MSA for documenting biologically meaningful shifts in the physiological and/or sub-cellular response of marine invertebrates exposed to environmental change.

Given the threats of greenhouse gas emissions and a changing climate to marine ecosystems, there is an urgent need to better understand the response of not only adult corals, which are particularly sensitive to environmental changes, but also their larvae, whose mechanisms of acclimation to both temperature increases and ocean acidification are not well understood. Brooded larvae from the reef coral Pocillopora damicornis collected from Nanwan Bay, Southern Taiwan, were exposed to ambient or elevated temperature (25 or 29 °C) and pCO2 (415 or 635 μatm) in a factorial experiment for 9 days, and a variety of physiological and molecular parameters were measured. Respiration and rubisco protein expression decreased in larvae exposed to elevated temperature, while those incubated at high pCO2 were larger in size. Collectively, these findings highlight the complex metabolic and molecular responses of this life history stage and the need to integrate our understanding across multiple levels of biological organization. Our results also suggest that for this pocilloporid larval life stage, the impacts of elevated temperature are likely a greater threat under near-future predictions for climate change than ocean acidification.