Going with the flow: How corals in high-flow environments can beat the heat

Cryptic coral diversity is associated with symbioses, physiology, and response to thermal challenge

Coral persistence in the Anthropocene depends on interactions among holobiont partners (coral animals and microbial symbionts) and their environment. Cryptic coral lineages-genetically distinct yet morphologically similar groups-are critically important as they often exhibit functional diversity relevant to thermal tolerance. In addition, environmental parameters such as thermal variability may promote tolerance, but how variability interacts with holobiont partners to shape responses to thermal challenge remains unclear. Here, we identified three cryptic lineages of Siderastrea siderea in Bocas del Toro, Panamá that differ in distributions across inshore and offshore reefs, microbial associations, phenotypic traits of holobiont partners (i.e., phenomes), and skeleton morphologies. A thermal variability experiment failed to increase thermal tolerance, but subsequent thermal challenge and recovery revealed that one lineage maintained elevated energetic reserves, photochemical efficiency, and growth. Last, coral cores highlighted that this lineage also exhibited greater growth historically. Functional variation among cryptic lineages highlights their importance in predicting coral reef responses to climate change.

Interspecies differences in the transcriptome response of corals to acute heat stress

Rising sea surface temperatures threaten the survival of corals worldwide, with coral bleaching events becoming more commonplace. However, different coral species are known to exhibit variable levels of susceptibility to thermal stress. To elucidate genetic mechanisms that may underlie these differences, we compared the gene repertoire of four coral species, Favites colemani, Montipora digitata, Acropora digitifera, and Seriatopora caliendrum, that were previously demonstrated to have differing responses to acute thermal stress. We found that more tolerant species, like F. colemani and M. digitata, possess a greater abundance of antioxidant protein families and chaperones. Under acute thermal stress conditions, only S. caliendrum showed a significant bleaching response, which was accompanied by activation of the DNA damage response network and drastic upregulation of stress response genes (SRGs). This suggests that differences in SRG orthologs, as well as the mechanisms that control SRG expression response, contribute to the ability of corals to maintain stability of physiological functions required to survive shifts in seawater temperature.

Symbiodiniaceae phenotypic traits as bioindicators of acclimatization after coral transplantation

Coral-dinoflagellate symbiosis underpins coral reef resilience and influences conservation success, given the relationship's role in coral bleaching. Here, we transplanted Guam's dominant staghorn coral, Acropora pulchra, across four coral gardens and monitored their endosymbiotic dinoflagellates (family Symbiodiniaceae) for ∼15 months (May 2021-August 2022). Transplantation and predation resulted in temporary symbiotic destabilization, as signaled by increased cell roughness and decreased cell density. Eventually, the Symbiodiniaceae phenotypic profile mostly converged with the wild population, although cell density and red fluorescing photopigments remained modified. In March, corals paled, which allowed us to evaluate the Symbiodiniaceae assemblage's relationship with host color. Interestingly, cell density was not the most informative when predicting host color. Instead, fluorescence from antioxidant-associated pigments were most informative. We conclude that Symbiodiniaceae phenotypic traits respond differently depending on the condition, supporting their development as acclimatization bioindicators.

Impacts of marine heatwaves in coastal ecosystems depend on local environmental conditions

Marine heatwaves (MHWs), increasing in duration and intensity because of climate change, are now a major threat to marine life and can have lasting effects on the structure and function of ecosystems. However, the responses of marine taxa and ecosystems to MHWs can be highly variable, making predicting and interpreting biological outcomes a challenge. Here, we review how biological responses to MHWs, from individuals to ecosystems, are mediated by fine-scale spatial variability in the coastal marine environment (hereafter, local gradients). Viewing observed responses through a lens of ecological theory, we present a simple framework of three 'resilience processes' (RPs) by which local gradients can influence the responses of marine taxa to MHWs. Local gradients (1) influence the amount of stress directly experienced by individuals, (2) facilitate local adaptation and acclimatization of individuals and populations, and (3) shape community composition which then influences responses to MHWs. We then synthesize known examples of fine-scale gradients that have affected responses of benthic foundation species to MHWs, including kelp forests, coral reefs, and seagrass meadows and link these varying responses to the RPs. We present a series of case studies from various marine ecosystems to illustrate the differential impacts of MHWs mediated by gradients in both temperature and other co-occurring drivers. In many cases, these gradients had large effect sizes with several examples of local gradients causing a 10-fold difference in impacts or more (e.g., survival, coverage). This review highlights the need for high-resolution environmental data to accurately predict and manage the consequences of MHWs in the context of ongoing climate change. While current tools may capture some of these gradients already, we advocate for enhanced monitoring and finer scale integration of local environmental heterogeneity into climate models. This will be essential for developing effective conservation strategies and mitigating future marine biodiversity loss.

Gene expression response under thermal stress in two Hawaiian corals is dominated by ploidy and genotype

Transcriptome data are frequently used to investigate coral bleaching; however, the factors controlling gene expression in natural populations of these species are poorly understood. We studied two corals, Montipora capitata and Pocillopora acuta, that inhabit the sheltered Kāne'ohe Bay, Hawai'i. M. capitata colonies in the bay are outbreeding diploids, whereas P. acuta is a mixture of clonal diploids and triploids. Populations were sampled from six reefs and subjected to either control (no stress), thermal stress, pH stress, or combined pH and thermal stress treatments. RNA-seq data were generated to test two competing hypotheses: (1) gene expression is largely independent of genotype, reflecting a shared treatment-driven response (TDE) or, (2) genotype dominates gene expression, regardless of treatment (GDE). Our results strongly support the GDE model, even under severe stress. We suggest that post-transcriptional processes (e.g., control of translation, protein turnover) modify the signal from the transcriptome, and may underlie the observed differences in coral bleaching sensitivity via the downstream proteome and metabolome.

Seasonal dynamics and environmental drivers of tissue and mucus microbiomes in the staghorn coral Acropora pulchra

Background

Rainfall-induced coastal runoff represents an important environmental impact in near-shore coral reefs that may affect coral-associated bacterial microbiomes. Shifts in microbiome community composition and function can stress corals and ultimately cause mortality and reef declines. Impacts of environmental stress may be site specific and differ between coral microbiome compartments (e.g., tissue versus mucus). Coastal runoff and associated water pollution represent a major stressor for near-shore reef-ecosystems in Guam, Micronesia.

Methods

Acropora pulchra colonies growing on the West Hagåtña reef flat in Guam were sampled over a period of 8 months spanning the 2021 wet and dry seasons. To examine bacterial microbiome diversity and composition, samples of A. pulchra tissue and mucus were collected during late April, early July, late September, and at the end of December. Samples were collected from populations in two different habitat zones, near the reef crest (farshore) and close to shore (nearshore). Seawater samples were collected during the same time period to evaluate microbiome dynamics of the waters surrounding coral colonies. Tissue, mucus, and seawater microbiomes were characterized using 16S DNA metabarcoding in conjunction with Illumina sequencing. In addition, water samples were collected to determine fecal indicator bacteria (FIB) concentrations as an indicator of water pollution. Water temperatures were recorded using data loggers and precipitation data obtained from a nearby rain gauge. The correlation structure of environmental parameters (temperature and rainfall), FIB concentrations, and A. pulchra microbiome diversity was evaluated using a structural equation model. Beta diversity analyses were used to investigate spatio-temporal trends of microbiome composition.

Results

Acropora pulchra microbiome diversity differed between tissues and mucus, with mucus microbiome diversity being similar to the surrounding seawater. Rainfall and associated fluctuations of FIB concentrations were correlated with changes in tissue and mucus microbiomes, indicating their role as drivers of A. pulchra microbiome diversity. A. pulchra tissue microbiome composition remained relatively stable throughout dry and wet seasons; tissues were dominated by Endozoicomonadaceae, coral endosymbionts and putative indicators of coral health. In nearshore A. pulchra tissue microbiomes, Simkaniaceae, putative obligate coral endosymbionts, were more abundant than in A. pulchra colonies growing near the reef crest (farshore). A. pulchra mucus microbiomes were more diverse during the wet season than the dry season, a distinction that was also associated with drastic shifts in microbiome composition. This study highlights the seasonal dynamics of coral microbiomes and demonstrates that microbiome diversity and composition may differ between coral tissues and the surface mucus layer.

Characterizing transcriptomic responses to sediment stress across location and morphology in reef-building corals

Anthropogenic activities increase sediment suspended in the water column and deposition on reefs can be largely dependent on colony morphology. Massive and plating corals have a high capacity to trap sediments, and active removal mechanisms can be energetically costly. Branching corals trap less sediment but are more susceptible to light limitation caused by suspended sediment. Despite deleterious effects of sediments on corals, few studies have examined the molecular response of corals with different morphological characteristics to sediment stress. To address this knowledge gap, this study assessed the transcriptomic responses of branching and massive corals in Florida and Hawai'i to varying levels of sediment exposure. Gene expression analysis revealed a molecular responsiveness to sediments across species and sites. Differential Gene Expression followed by Gene Ontology (GO) enrichment analysis identified that branching corals had the largest transcriptomic response to sediments, in developmental processes and metabolism, while significantly enriched GO terms were highly variable between massive corals, despite similar morphologies. Comparison of DEGs within orthogroups revealed that while all corals had DEGs in response to sediment, there was not a concerted gene set response by morphology or location. These findings illuminate the species specificity and genetic basis underlying coral susceptibility to sediments.

A Decade of Death and Other Dynamics: Deepening Perspectives on the Diversity and Distribution of Sea Stars and Wasting

AbstractMass mortality events provide valuable insight into biological extremes and also ecological interactions more generally. The sea star wasting epidemic that began in 2013 catalyzed study of the microbiome, genetics, population dynamics, and community ecology of several high-profile species inhabiting the northeastern Pacific but exposed a dearth of information on the diversity, distributions, and impacts of sea star wasting for many lesser-known sea stars and a need for integration across scales. Here, we combine datasets from single-site to coast-wide studies, across time lines from weeks to decades, for 65 species. We evaluated the impacts of abiotic characteristics hypothetically associated with sea star wasting (sea surface temperature, pelagic primary productivity, upwelling wind forcing, wave exposure, freshwater runoff) and species characteristics (depth distribution, developmental mode, diet, habitat, reproductive period). We find that the 2010s sea star wasting outbreak clearly affected a little over a dozen species, primarily intertidal and shallow subtidal taxa, causing instantaneous wasting prevalence rates of 5%-80%. Despite the collapse of some populations within weeks, environmental and species variation protracted the outbreak, which lasted 2-3 years from onset until declining to chronic background rates of ∼2% sea star wasting prevalence. Recruitment began immediately in many species, and in general, sea star assemblages trended toward recovery; however, recovery was heterogeneous, and a marine heatwave in 2019 raised concerns of a second decline. The abiotic stressors most associated with the 2010s sea star wasting outbreak were elevated sea surface temperature and low wave exposure, as well as freshwater discharge in the north. However, detailed data speaking directly to the biological, ecological, and environmental cause(s) and consequences of the sea star wasting outbreak remain limited in scope, unavoidably retrospective, and perhaps always indeterminate. Redressing this shortfall for the future will require a broad spectrum of monitoring studies not less than the taxonomically broad cross-scale framework we have modeled in this synthesis.

Ciliary flows in corals ventilate target areas of high photosynthetic oxygen production

Most tropical corals live in symbiosis with Symbiodiniaceae algae whose photosynthetic production of oxygen (O₂) may lead to excess O₂ in the diffusive boundary layer (DBL) above the coral surface. When flow is low, cilia-induced mixing of the coral DBL is vital to remove excess O₂ and prevent oxidative stress that may lead to coral bleaching and mortality. Here, we combined particle image velocimetry using O₂-sensitive nanoparticles (sensPIV) with chlorophyll (Chla)-sensitive hyperspectral imaging to visualize the microscale distribution and dynamics of ciliary flows and O₂ in the coral DBL in relation to the distribution of Symbiodiniaceae Chla in the tissue of the reef building coral, Porites lutea. Curiously, we found an inverse relation between O₂ in the DBL and Chla in the underlying tissue, with patches of high O₂ in the DBL above low Chla in the underlying tissue surrounding the polyp mouth areas and pockets of low O₂ concentrations in the DBL above high Chla in the coenosarc tissue connecting neighboring polyps. The spatial segregation of Chla and O₂ is related to ciliary-induced flows, causing a lateral redistribution of O₂ in the DBL. In a 2D transport-reaction model of the coral DBL, we show that the enhanced O₂ transport allocates parts of the O₂ surplus to areas containing less chla, which minimizes oxidative stress. Cilary flows thus confer a spatially complex mass transfer in the coral DBL, which may play an important role in mitigating oxidative stress and bleaching in corals.

Coral physiology: Going with the ciliary flow

Corals have long been known to generate local fluid flows using ciliary beating, but the importance of these ciliary flows is just being discovered. Two new papers shed light on how ciliary-flow physics plays a key role in shaping coral physiology.

Contrasting hydrodynamic regimes of submerged pinnacle and emergent coral reefs

Hydrodynamics on coral reefs vary with depth, reef morphology and seascape position. Differences in hydrodynamic regimes strongly influence the structure and function of coral reef ecosystems. Submerged coral reefs on steep-sided, conical bathymetric features like seamounts experience enhanced water circulation as a result of interactions between currents and the abrupt physical structure. There may also be similar interactions between smaller pinnacles and regional water currents in offshore locations (crests > 10 m), while shallow reefs (crests <10 m) may be more subject to surface currents driven by wind, waves and tide. Here we tested whether coral pinnacles experienced stronger and more variable currents compared to emergent reefs at the same depth in both nearshore and offshore positions. Current speeds and temperature were monitored for 12 months at 11 reefs, representing the three different reef categories: submerged offshore pinnacles, emergent offshore reefs and emergent nearshore reefs. We found different patterns in current speeds and temperature among reef types throughout the year and between seasons. Submerged pinnacles exhibited stronger, more variable current speeds compared to both near and offshore emergent reefs. We found seasonal changes in current speeds for pinnacle and nearshore reefs but no variation in current strength on offshore reefs. Whilst instantaneous current directions did reflect the seascape position of individual sites, there was no difference in the directional variability of current speeds between reef types. Annual daily average temperatures at all reef types were not strongly seasonal, changing by less than 2 °C throughout the year. Daily temperature ranges at specific sites however, exhibited considerable variability (annual range of up to 6.5 °C), particularly amongst offshore emergent reefs which experienced the highest temperatures despite greater exposure to regional-scale circulation patterns. Additionally, we found a consistent mismatch between satellite sea surface temperatures and in-situ temperature data, which was on average 2 °C cooler throughout the annual study period. Our results suggest that distinct hydrodynamic processes occur on smaller submerged structures that are physically analogous to seamounts. Our findings highlight important nuances in environmental processes that occur on morphologically distinct coral reef habitats and these are likely to be important drivers for the community dynamics of organisms that inhabit these reefs.

Frontloading of stress response genes enhances robustness to environmental change in chimeric corals

Background

Chimeras are genetically mixed entities resulting from the fusion of two or more conspecifics. This phenomenon is widely distributed in nature and documented in a variety of animal and plant phyla. In corals, chimerism initiates at early ontogenic states (larvae to young spat) and results from the fusion between two or more closely settled conspecifics. When compared to genetically homogenous colonies (non-chimeras), the literature has listed ecological and evolutionary benefits for traits at the chimeric state, further positioning coral chimerism as an evolutionary rescue instrument. However, the molecular mechanisms underlying this suggestion remain unknown.

Results

To address this question, we developed field monitoring and multi-omics approaches to compare the responses of chimeric and non-chimeric colonies acclimated for 1 year at 10-m depth or exposed to a stressful environmental change (translocation from 10- to 2-m depth for 48h). We showed that chimerism in the stony coral Stylophora pistillata is associated with higher survival over a 1-year period. Transcriptomic analyses showed that chimeras lose transcriptomic plasticity and constitutively express at higher level (frontload) genes responsive to stress. This frontloading may prepare the colony to face at any time environmental stresses which explain its higher robustness.

Conclusions

These results show that chimeras are environmentally robust entities with an enhanced ability to cope with environmental stress. Results further document the potential usefulness of chimeras as a novel reef restoration tool to enhance coral adaptability to environmental change, and confirm that coral chimerism can be an evolutionary rescue instrument.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01371-7.

Coral-bleaching responses to climate change across biological scales

The global impacts of climate change are evident in every marine ecosystem. On coral reefs, mass coral bleaching and mortality have emerged as ubiquitous responses to ocean warming, yet one of the greatest challenges of this epiphenomenon is linking information across scientific disciplines and spatial and temporal scales. Here we review some of the seminal and recent coral-bleaching discoveries from an ecological, physiological, and molecular perspective. We also evaluate which data and processes can improve predictive models and provide a conceptual framework that integrates measurements across biological scales. Taking an integrative approach across biological and spatial scales, using for example hierarchical models to estimate major coral-reef processes, will not only rapidly advance coral-reef science but will also provide necessary information to guide decision-making and conservation efforts. To conserve reefs, we encourage implementing mesoscale sanctuaries (thousands of km² ) that transcend national boundaries. Such networks of protected reefs will provide reef connectivity, through larval dispersal that transverse thermal environments, and genotypic repositories that may become essential units of selection for environmentally diverse locations. Together, multinational networks may be the best chance corals have to persist through climate change, while humanity struggles to reduce emissions of greenhouse gases to net zero.

Nitric oxide production rather than oxidative stress and cell death is associated with the onset of coral bleaching in Pocillopora acuta

Elevated seawater temperatures associated with climate change lead to coral bleaching. While the ultimate causes of bleaching are well understood, the proximate physiological mechanisms underlying the bleaching response are not as well defined. Here we measured nitric oxide synthase activity, oxidative stress, and cell death in algal symbionts (Symbiodinaceae) freshly isolated from the reef-building coral Pocillopora acuta collected in the field under natural non-bleaching conditions and from corals experimentally exposed to elevated temperatures. Nitric oxide synthase activity in the algal symbionts was >3 orders of magnitude higher than that of the host and increased dramatically with increasing temperature and time of exposure (up to 72 h), consistent with the onset of bleaching for these corals. Oxidative stress and cell death among the algal symbionts were highest in coral holobionts exposed to intermediate as opposed to maximal temperatures, suggesting that these mechanisms are not proximal triggers for bleaching in this species. Our results point to nitric oxide production by the algal symbionts, rather than symbiont dysfunction, as a more important driver of coral bleaching under acute thermal stress in this coral.

Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance

Corals from the northern Red Sea, in particular the Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching >5℃ above their maximum monthly mean (MMM) temperatures. These elevated thresholds are thought to be due to historical selection, as corals passed through the warmer Southern Red Sea during recolonization from the Arabian Sea. To test this hypothesis, we determined thermal tolerance thresholds of GoA versus central Red Sea (CRS) Stylophora pistillata corals using multi-temperature acute thermal stress assays to determine thermal thresholds. Relative thermal thresholds of GoA and CRS corals were indeed similar and exceptionally high (~7℃ above MMM). However, absolute thermal thresholds of CRS corals were on average 3℃ above those of GoA corals. To explore the molecular underpinnings, we determined gene expression and microbiome response of the coral holobiont. Transcriptomic responses differed markedly, with a strong response to the thermal stress in GoA corals and their symbiotic algae versus a remarkably muted response in CRS colonies. Concomitant to this, coral and algal genes showed temperature-induced expression in GoA corals, while exhibiting fixed high expression (front-loading) in CRS corals. Bacterial community composition of GoA corals changed dramatically under heat stress, whereas CRS corals displayed stable assemblages. We interpret the response of GoA corals as that of a resilient population approaching a tipping point in contrast to a pattern of consistently elevated thermal resistance in CRS corals that cannot further attune. Such response differences suggest distinct thermal tolerance mechanisms that may affect the response of coral populations to ocean warming.