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Coral reefs provide habitat for approximately 25% of all extant marine species, including 845 species of scleractinian corals. These rich ecosystems are becoming increasingly degraded in many regions by a range of anthropogenic factors, including recurrent bleaching episodes associated with rising sea surface temperatures. Within the northern Red Sea, coral reef communities appear to be faring relatively better than global trends and continue to exhibit remarkable diversity and thermal tolerance. However, recent reports of coral bleaching in the region highlight the urgent need for comprehensive ecological surveys to provide a baseline for long-term monitoring of biodiversity and potential species loss. This field report aims to support the tracking of diversity and growth form distributions of scleractinian corals at two reef sites at Mangrove Bay, El Qoseir, Egypt. Over time, it is our hope that such reports will contribute to broader databases and analyses focused on the biodiversity of reef-building coral species in the northern Red Sea.This study presents the first comprehensive checklist of scleractinian coral species (Scleractinia Bourne, 1900) in Mangrove Bay, El Qoseir, Egypt. As a result of our 2023 field survey, we identified a total of 68 species across 29 genera and 14 families, spanning six reef habitats — three per study site — at two study locations (sheltered and current-exposed), with depths ranging from 0 to 9.5 m. We found that both scleractinian coral diversity and coral growth forms varied amongst the six habitats. Branching corals were found in each habitat, but were particularly abundant at the current-exposed reef edge, where they covered 67% of the habitat. Encrusting and massive corals became more prevalent with increasing depth at both study sites, with massive corals covering 72% at the sheltered deeper reef slope and encrusting corals covering 24% at the current-exposed deeper reef slope. Species of the genus Porites dominated the sheltered site at all depths and the deeper reef slope at the current-exposed site, while Pocillopora verrucosa was most abundant at the exposed site’s reef edge and shallow slope.We provide photographs confirming these new records and access to the raw data on the abundance, distribution and conservation status of these taxa. Forty-three percent of the scleractinian species are classified as "Least Concern," but six are identified as "Vulnerable" (9%). Reef cover analyses revealed algae as the dominant group in most habitats, while scleractinian coral cover ranged between approximately 17% at the current-exposed reef edge and almost 35% at the current-exposed shallow reef slope. Millepora contributed the most at the exposed reef edge with nearly 28% cover, but was scarce elsewhere; soft corals exhibited their highest abundance on the deeper slope.Our observations serve as a critical baseline for future research and conservation efforts at Mangrove Bay by presenting an initial inventory of the local scleractinian communities and emphasise the importance of detailed species data in understanding and preserving coral reef ecosystems.

Abstract Background Subtropical coral reefs are comparatively understudied compared to tropical coral reef ecosystems, yet also host a diverse and abundant array of marine life and provide substantial socio-economic benefits to communities. Research into the impacts of ocean warming on subtropical coral reefs has increased over the past two decades due to increase frequency and intensity of bleaching and degradation of these ecosystems. Understanding the extent of research effort and type of evidence assessing the response of subtropical corals and reefs to ocean warming provides valuable insight into global patterns in research efforts allowing critical knowledge gaps to be identified. A comprehensive understanding the impact of ocean warming on these systems will underpin our ability to predict and respond to future changes on subtropical coral reefs. Here, a systematic-map approach is used to identify recent research effort, from 2010 to 2023, and highlight patterns in the type, scale, and location of research conducted and as well as identify the availability of data and evidence reported. Methods Primary literature was identified by searching Scopus and Science Citation Index Expanded through Web of Science Core Collection databases. The methodologies provided in a previously published systematic map protocol were applied, and 90 primary research publications were subsequently identified. Data extraction from the identified literature included bibliometric data, discipline and type of research, type of data reported and how it was recorded, and data availability. Findings The identified literature consisted primarily of experimental (49%) and observational (39%) studies. The majority of the primary literature investigated corals in the ecoregions of Southern China (13%), Western Mediterranean (10%) and across a total of seven ecoregions grouped within Oceania (29%). Stressors reported in the literature as drivers of ocean warming reflect the standardisation of methods applied in reporting of events within the literature. Standardised metrics related to degree heating weeks (DHW) and marine heatwaves (MHW) have been reported when assessing the occurrence and severity of drivers, and are increasing in recent years, particularly in Australia. Finally, the need for increased research effort across much of the subtropics is evident, particularly for understudied regions such as the Western Indian Ocean where there are far fewer studies than other similar subtropical coral reef ecosystems. Conclusions Climatic change, increasing ocean temperatures, and the impacts to subtropical and temperate coral reefs are of increasing concern to policy makers and researchers alike. This systematic map provides a broad overview of research topics and effort around the globe since 2010 and identifies areas where more research effort is urgently needed. Our study has identified major research clusters in Asia, Australia, the Mediterranean, and North America and gaps of research in regions such as the East Indian Oceans. Of the research conducted to date approximately one third reports on evidence related to marine protected areas and the vast majority of evidence is from close/territorial sea locations, providing important knowledge base for management of these areas. Of the 17 studies reporting on specific extreme events (rather than experimental studies which is the majority of evidence identified here) 13 have been published since 2019, with the majority reporting on events occurring in 2019/20 indicating a trend of increasing evidence in recent years (a total of 7 studies from 2010 to 2013, compared to over 10 studies published annually since 2019 up to mid-2023).

Background: Subtropical coral reefs are comparatively understudied compared to tropical coral reef ecosystems, yet also host a diverse and abundant array of marine life and provide substantial socio-economic benefits to communities. Research into the impacts of ocean warming on subtropical coral reefs has increased over the past two decades due to increase frequency and intensity of bleaching and degradation of these ecosystems. Understanding the extent of research effort and type of evidence assessing the response of subtropical corals and reefs to ocean warming provides valuable insight into global patterns in research efforts allowing critical knowledge gaps to be identified. A comprehensive understanding the impact of ocean warming on these systems will underpin our ability to predict and respond to future changes on subtropical coral reefs. Here, a systematic-map approach is used to identify recent research effort, from 2010 to 2023, and highlight patterns in the type, scale, and location of research conducted and as well as identify the availability of data and evidence reported. Methods: Primary literature was identified by searching Scopus and Science Citation Index Expanded through Web of Science Core Collection databases. The methodologies provided in a previously published systematic map protocol were applied, and 90 primary research publications were subsequently identified. Data extraction from the identified literature included bibliometric data, discipline and type of research, type of data reported and how it was recorded, and data availability. Findings: The identified literature consisted primarily of experimental (49%) and observational (39%) studies. The majority of the primary literature investigated corals in the ecoregions of Southern China (13%), Western Mediterranean (10%) and across a total of seven ecoregions grouped within Oceania (29%). Stressors reported in the literature as drivers of ocean warming reflect the standardisation of methods applied in reporting of events within the literature. Standardised metrics related to degree heating weeks (DHW) and marine heatwaves (MHW) have been reported when assessing the occurrence and severity of drivers, and are increasing in recent years, particularly in Australia. Finally, the need for increased research effort across much of the subtropics is evident, particularly for understudied regions such as the Western Indian Ocean where there are far fewer studies than other similar subtropical coral reef ecosystems. Conclusions: Climatic change, increasing ocean temperatures, and the impacts to subtropical and temperate coral reefs are of increasing concern to policy makers and researchers alike. This systematic map provides a broad overview of research topics and effort around the globe since 2010 and identifies areas where more research effort is urgently needed. Our study has identified major research clusters in Asia, Australia, the Mediterranean, and North America and gaps of research in regions such as the East Indian Oceans. Of the research conducted to date approximately one third reports on evidence related to marine protected areas and the vast majority of evidence is from close/territorial sea locations, providing important knowledge base for management of these areas. Of the 17 studies reporting on specific extreme events (rather than experimental studies which is the majority of evidence identified here) 13 have been published since 2019, with the majority reporting on events occurring in 2019/20 indicating a trend of increasing evidence in recent years (a total of 7 studies from 2010 to 2013, compared to over 10 studies published annually since 2019 up to mid-2023). [ABSTRACT FROM AUTHOR]

Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from nine species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019). While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together, these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals. [ABSTRACT FROM AUTHOR]

Aim: Efficiently protecting species requires knowing their ecological, life‐history and reproductive traits. This is particularly decisive for scleractinian corals, key components of coral reefs, which are experiencing critical declines. Yet their connectivity remains insufficiently documented. Here, we focused on four distinct species of the coral genus Pocillopora found in diverse habitats of the southwestern Indian Ocean and presenting various reproductive strategies. We aimed to understand whether these traits affect species connectivity. Location: Archipelagos and islands of the southwestern Indian Ocean. Taxon: Pocillopora spp. Methods: We used target capture to collect single‐nucleotide polymorphisms (SNPs) from over a thousand colonies sampled across nine localities. From the ca. 1400 SNPs retained per species, Bayesian clustering methods, networks and demographic inferences were applied to first infer the population genetic structure and connectivity of each species, then the demographic history of each population. Results: All four Pocillopora species exhibited almost the same genetic structuring pattern, reflecting the sampled ecoregions (Madagascar and surrounding islands vs. Mascarene Islands). However, the genetic differentiation was stronger (FST about 10 times higher) for P. acuta, the species inhabiting more enclosed habitats, such as lagoons and shallow waters, and reproducing mainly asexually. Similarly, all populations, except those from P. acuta, showed a signature of population expansion ca. 100,000 years ago, following the penultimate glacial period. Main Conclusions: These results indicate reduced gene flow between Madagascar and the Mascarene Islands, probably linked to currents, suggesting distinct connectivity networks that should be considered independently when setting up conservation plans. In addition, shared demographic histories reflect that populations from these species have probably met the same environmental constraints and reacted similarly, something that should be considered in light of the ongoing rapid climate change. [ABSTRACT FROM AUTHOR]

For many organisms, early life stages experience significantly higher rates of mortality relative to adults. However, tracking early life stage individuals through time in natural settings is difficult, limiting our understanding of the duration of these 'mortality bottlenecks', and the time required for survivorship to match that of adults. Here, we track a cohort of juvenile corals (1-5 cm maximum diameter) from 12 taxa at a remote atoll in the Central Pacific from 2013 to 2017 and describe patterns of annual survivorship. Of the 537 juveniles initially detected, 219 (41%) were alive 4 years later, 163 (30%) died via complete loss of live tissue from the skeleton, and the remaining 155 (29%) died via dislodgement. The differing mortality patterns suggest that habitat characteristics, as well as species-specific features, may influence early life stage survival. Across most taxa, survival fit a logistic model, reaching > 90% annual survival within 4 years. These data suggest that mortality bottlenecks characteristic of 'recruitment' extend up to 5 years after individuals can be visually detected. Ultimately, replenishment of adult coral populations via sexual reproduction is needed to maintain both coral cover and genetic diversity. This study provides key insights into the dynamics and time scales that characterize these critical early life stages.

Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from nine species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019). While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together, these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.

Corals' endosymbiotic algae (Symbiodiniaceae) supply much of the energetic demands of the host, and some symbionts, such as Durusdinium spp., may confer higher thermal tolerance than others. However, there may be physiological tradeoffs during non-bleaching periods or across environmental gradients. The common Hawaiian reef-building coral, Montipora capitata, hosts the symbionts Cladocopium C31 and/or Durusdinium glynnii. Here, we measured growth of these holobionts over two months to test whether the higher heat tolerance of D. glynnii involved a tradeoff of lower growth, which could impact survivorship and competition for space on the reef. Additionally, we tested whether any such tradeoffs were modulated by light, which is a major driver of the ecological distribution of these symbionts in Kāneʻohe Bay. During the first month, when water temperatures were warmer (median 25.5 °C), there was no effect of symbiont on growth. However, over the cooler second month (median 23.4 °C), C31-dominated corals grew up to 77% faster than D. glynnii-dominated corals, and this growth advantage increased in higher light treatments (up to a daily light integral of 3.8 mol m−2 d−1, corresponding to 3.8–6.4 m depth). This advantage may explain why C31-dominated colonies are more prevalent at most depths; however, their increasing advantage at higher light levels is not reflected in the shallowest parts of Kāneʻohe Bay, where D. glynnii-dominated colonies become more prevalent. This may indicate that in these warmer surface waters, D. glynnii's higher heat tolerance outweighs the growth advantage that would otherwise favor C31 during the cooler parts of the year, providing a net ecological benefit. As oceans continue to warm, understanding how symbionts and the environment mediate coral performance outcomes will help predict reef futures and inform conservation interventions where coral stocks are selected for specific traits or symbionts. [ABSTRACT FROM AUTHOR]

The three‐dimensional structure of habitats is a critical component of species' niches driving coexistence in species‐rich ecosystems. However, its influence on structuring and partitioning recruitment niches has not been widely addressed. We developed a new method to combine species distribution modelling and structure from motion, and characterized three‐dimensional recruitment niches of two ecosystem engineers on Caribbean coral reefs, scleractinian corals and gorgonians. Fine‐scale roughness was the most important predictor of suitable habitat for both taxa, and their niches largely overlapped, primarily due to scleractinians' broader niche breadth. Crevices and holes at mm scales on calcareous rock with low coral cover were more suitable for octocorals than for scleractinian recruits, suggesting that the decline in scleractinian corals is facilitating the recruitment of octocorals on contemporary Caribbean reefs. However, the relative abundances of the taxa were independent of the amount of suitable habitat on the reef, emphasizing that niche processes alone do not predict recruitment rates. [ABSTRACT FROM AUTHOR]

Abstract Background Tropical coral reefs cover only ca. 0.1% of the Earth’s surface but harbour exceptional marine biodiversity and provide vital ecosystem services to millions of people living nearby. They are currently threatened by global (e.g. climate change) and local (e.g. chemical pollution) stressors that interact in multiple ways. While global stressors cannot be mitigated by local actions alone, local stressors can be reduced through ecosystem management. Here, we aimed to systematically review experimental studies assessing the toxicity of chemical pollutants to tropical reef-building corals to generate accessible and usable knowledge and data that can be used to calculate measurement endpoints in ecological risk assessment. From the quantitative estimates of effects, we determined toxicity thresholds as the highest exposures tested at which no statistically significant adverse effects were observed, and we compared them to regulatory predicted no effect concentrations for the protection of marine organisms, to assess whether these reference values are indeed protective of corals. Methods The evidence was taken from a systematic map of the impacts of chemicals arising from human activity on tropical reef-building corals published in 2021. All studies in the map database corresponding to the knowledge cluster “Evidence on the ecotoxicological effects of chemicals on corals” were selected. To identify subsequently published literature, the search was updated using a subset of the search string used for the systematic map. Titles, abstracts and full-texts were screened according to the criteria defining the selected cluster of the map. Because the eligibility criteria for the systematic review are narrower than the criteria used to define the cluster in the systematic map, additional screening was performed. Studies included were critically appraised and each study was rated as low, unclear, medium, or high risk of bias. Data were extracted from the studies and synthesised according to a strategy dependent on the type of exposure and outcome. Review findings The systematic review reports the known effects of chemical exposures on corals from 847 studies corresponding to 181 articles. A total of 697 studies (161 articles) were included in the quantitative synthesis and 150 studies (50 articles) in the narrative synthesis of the findings. The quantitative synthesis records the effects of 2706 exposure concentrations-durations of 164 chemicals or mixtures of chemicals, and identifies 105 toxicity thresholds corresponding to 56 chemicals or mixtures of chemicals. When toxicity thresholds were compared to reference values set for the protection of marine organisms by environmental agencies, the reference values appear to be protective of corals for all but three chemicals assessed: the metal copper and the pesticides diuron and irgarol 1051. Conclusions This open-access database of known ecotoxicological effects of chemical exposures on corals can assist managers in the ecological risk assessment of chemicals, by allowing easy determination of various ecotoxicological thresholds. Several limitations of the toxicity tests synthesised here were noted (in particular the lack of measurement of effective concentrations for more than half of the studies). Overall, most of the currently available data on coral toxicity should be replicated independently and extended to corals from less studied geographical regions and functional groups.

Background: Tropical coral reefs cover only ca. 0.1% of the Earth's surface but harbour exceptional marine biodiversity and provide vital ecosystem services to millions of people living nearby. They are currently threatened by global (e.g. climate change) and local (e.g. chemical pollution) stressors that interact in multiple ways. While global stressors cannot be mitigated by local actions alone, local stressors can be reduced through ecosystem management. Here, we aimed to systematically review experimental studies assessing the toxicity of chemical pollutants to tropical reef-building corals to generate accessible and usable knowledge and data that can be used to calculate measurement endpoints in ecological risk assessment. From the quantitative estimates of effects, we determined toxicity thresholds as the highest exposures tested at which no statistically significant adverse effects were observed, and we compared them to regulatory predicted no effect concentrations for the protection of marine organisms, to assess whether these reference values are indeed protective of corals. Methods: The evidence was taken from a systematic map of the impacts of chemicals arising from human activity on tropical reef-building corals published in 2021. All studies in the map database corresponding to the knowledge cluster "Evidence on the ecotoxicological effects of chemicals on corals" were selected. To identify subsequently published literature, the search was updated using a subset of the search string used for the systematic map. Titles, abstracts and full-texts were screened according to the criteria defining the selected cluster of the map. Because the eligibility criteria for the systematic review are narrower than the criteria used to define the cluster in the systematic map, additional screening was performed. Studies included were critically appraised and each study was rated as low, unclear, medium, or high risk of bias. Data were extracted from the studies and synthesised according to a strategy dependent on the type of exposure and outcome. Review findings: The systematic review reports the known effects of chemical exposures on corals from 847 studies corresponding to 181 articles. A total of 697 studies (161 articles) were included in the quantitative synthesis and 150 studies (50 articles) in the narrative synthesis of the findings. The quantitative synthesis records the effects of 2706 exposure concentrations-durations of 164 chemicals or mixtures of chemicals, and identifies 105 toxicity thresholds corresponding to 56 chemicals or mixtures of chemicals. When toxicity thresholds were compared to reference values set for the protection of marine organisms by environmental agencies, the reference values appear to be protective of corals for all but three chemicals assessed: the metal copper and the pesticides diuron and irgarol 1051. Conclusions: This open-access database of known ecotoxicological effects of chemical exposures on corals can assist managers in the ecological risk assessment of chemicals, by allowing easy determination of various ecotoxicological thresholds. Several limitations of the toxicity tests synthesised here were noted (in particular the lack of measurement of effective concentrations for more than half of the studies). Overall, most of the currently available data on coral toxicity should be replicated independently and extended to corals from less studied geographical regions and functional groups. [ABSTRACT FROM AUTHOR]

Coral reefs are the most diverse habitat per unit area in the world's oceans, supporting an estimated 1–3 million species in only 0.2% of its area. These ecosystems have suffered severe declines since the 1970s, largely as a result of climate change, ocean acidification, pollution, disease, and overfishing. Porites astreoides is a shallow species that is able to thrive in a variety of environmental conditions and has been a clear 'winner' on Atlantic reefs in the last decades. This, coupled with its ease of identification and wide distribution, has caused P. astreoides to become a focal species in many scientific studies. Given the current and increasing significance of P. astreoides, this review sought to (i) identify the key life history traits that allowed this species to thrive under stressful conditions; (ii) compile aspects of its biology and ecology to understand its future contribution to Atlantic reefs, and (iii) identify knowledge gaps. To date, no comprehensive overview of the literature exists for P. astreoides. All articles available on Google Scholar up to the time of submission containing the terms 'Mustard Hill Coral', 'Porites astreoides', or 'P. astreoides' were examined for potential inclusion in this review. Papers were assessed based on whether they captured the most influential or widespread theories, represented an important trend in the research, or contained novel findings relevant to the understanding of this species. This review provides a scholarly resource and wide-ranging synthesis of P. astreoides on Atlantic reefs of today and the future. [ABSTRACT FROM AUTHOR]

Dissolved inorganic phosphorus (DIP) is a limiting nutrient in the physiology of scleractinian corals. Anthropogenic addition of dissolved inorganic nitrogen (DIN) to coastal reefs increases the seawater DIN:DIP ratio and further increases P limitation, which is detrimental to coral health. The effects of imbalanced DIN:DIP ratios on coral physiology require further investigation in coral species other than the most studied branching corals. Here we investigated the nutrient uptake rates, elemental tissue composition and physiology of a foliose stony coral, Turbinaria reniformis, and a soft coral, Sarcophyton glaucum, exposed to four different DIN: DIP ratios (0.5:0.2, 0.5:1, 3:0.2, 3:1). The results show that T. reniformis had high uptake rates of DIN and DIP, proportional to the seawater nutrient concentrations. DIN enrichment alone led to an increase in tissue N content, shifting the tissue N:P ratio towards P limitation. However, S. glaucum had 5 times lower uptake rates and only took up DIN when the seawater was simultaneously enriched with DIP. This double uptake of N and P did not alter tissue stoichiometry. This study allows us to better understand the susceptibility of corals to changes in the DIN:DIP ratio and predict how coral species will respond under eutrophic conditions in the reef. [ABSTRACT FROM AUTHOR]

As climate change drives health declines of tropical reef species, diseases are further eroding ecosystem function and habitat resilience. Coral disease impacts many areas around the world, removing some foundation species to recorded low levels and thwarting worldwide efforts to restore reefs. What we know about coral disease processes remains insufficient to overcome many current challenges in reef conservation, yet cumulative research and management practices are revealing new disease agents (including bacteria, viruses, and eukaryotes), genetic host disease resistance factors, and innovative methods to prevent and mitigate epizootic events (probiotics, antibiotics, and disease resistance breeding programs). The recent outbreak of stony coral tissue loss disease across the Caribbean has reenergized and mobilized the research community to think bigger and do more. This review therefore focuses largely on novel emerging insights into the causes and mechanisms of coral disease and their applications to coral restoration and conservation.

Abstract Background Tropical coral reefs cover only ca. 0.1% of the Earth’s surface but host an outstanding biodiversity and provide important ecosystem services to millions of people living nearby. They are currently threatened by global (e.g., climate change) and local (e.g., chemical pollution) stressors that interact in different ways. While global stressors cannot be mitigated by local actions alone, local stressors can be reduced through ecosystem management. A systematic map on the impacts of chemicals arising from anthropogenic activities on tropical reef-building corals, which are the main engineer species of reef ecosystems, was published in 2021. This systematic map gathered an abundant literature (908 articles corresponding to 7937 studies), and identified four well-represented subtopics, amenable to relevant full syntheses. Here, we focused on one of the four subtopics: we aimed to systematically review the evidence on the ecotoxicological effects of chemicals on tropical reef-building corals. Methods The evidence will be identified from the recent systematic map on the impacts of chemicals arising from anthropogenic activities on tropical reef-building corals. Especially, all studies in the map database corresponding to the knowledge cluster “evidence on the ecotoxicological effects of chemicals on corals” will be selected. To identify the evidence produced since then, a search update will be performed using a subset of the search string used for the systematic map, and titles, abstracts and full-texts will be screened according to the criteria defining the selected cluster of the map. In addition, as the eligibility criteria for the systematic review are narrower than those used to define the cluster in the systematic map, additional screening will be carried out. The included studies will then be critically appraised and a low, medium, or high risk of bias will be assigned to each study. Data will be extracted from studies and synthesised according to a strategy depending on the type of exposure and outcome. Synthesis will be mainly quantitative but also narrative, aiming to identify toxicity thresholds of chemicals for corals.

Abstract Background Tropical coral reefs cover ca. 0.1% of the Earth’s surface but host an outstanding biodiversity and provide important ecosystem services to millions of people living nearby. They are currently threatened by local stressors (e.g. nutrient enrichment and chemical pollution arising from poor land management, sewage effluents, agriculture, industry) and global stressors (mainly seawater warming and acidification, i.e. climate change). Global and local stressors interact in different ways, but the presence of one stressor often reduces the tolerance to additional stress. While global stressors cannot be mitigated solely by local actions, local stressors can be reduced through ecosystem management, therefore minimizing the impact of climate change on coral reefs. We systematically mapped the evidence of impacts of chemicals arising from anthropogenic activities on tropical reef-building corals, which are the main engineer species of reef ecosystems, to inform decision-makers on the available evidence on this topic. Methods We searched the relevant literature using English terms combined in a tested search string in two publication databases (Scopus and Web Of Science Core Collection). The search string combined terms describing the population (tropical reef-building corals) and the exposure (chemicals). We searched for additional literature through three search engines, three dissertations repositories, 11 specialist websites, and through a call to local stakeholders. Titles, abstracts, and full-texts were successively screened using pre-defined eligibility criteria. A database of all studies included in the map with coded metadata was produced. The evidence was described and knowledge clusters and gaps were identified through the distribution and frequency of studies into types of exposure and/or types of outcomes and/or types of study. Review findings The initial searches identified 23,403 articles which resulted in 15,177 articles after duplicate removal. Among them, 908 articles were retained after screening process, corresponding to 7937 studies (a study being the combination of a taxon, an exposure, and an outcome). Among these studies, 30.5% dealt with the impact of nutrient enrichment on corals while 25% concerned the impact of human activities without reference to a chemical. The most measured outcomes were those related to the chemical concentration in corals (bioaccumulation, 25.8%), to coral physiology (16.9%), cover (14%), and mortality (9%). Half of the studies (48.4%) were experimental—the exposure was controlled by the researchers—and were conducted in laboratory conditions (39.4%) and in situ (9%). The most studied taxa, exposure, and outcomes were different between experimental and observational studies. Conclusions We identified four well-represented subtopics that may be amenable to relevant full syntheses via systematic reviews: (1) evidence on bioaccumulation of chemicals by corals; (2) evidence on the effects of nutrient enrichment on corals; (3) evidence on the effects of human activities on corals; and (4) evidence on the ecotoxicological effects of chemicals on corals (except nutrient enrichment). The systematic map shows that corals in their natural environment can be exposed to many categories of chemicals, and that there is a complete gap in experimental research on the combined effects of more than two categories of chemicals. We therefore encourage research on this topic.

In corals, pH regulation of the extracellular calcifying medium (ECM) by the calcifying cell layer is a crucial step in the calcification process and is potentially important to influencing how corals respond to ocean acidification. Here, we analyzed the growing edge of the reef coral Stylophora pistillata to make the first characterization of the proton gradient across the coral calcifying epithelium. At seawater pH 8 we found that while the calcifying epithelium elevates pH in the ECM on its apical side above that of seawater, pH on its basal side in the mesoglea is markedly lower, highlighting that the calcifying cells are exposed to a microenvironment distinct from the external environment. Coral symbiont photosynthesis elevates pH in the mesoglea, but experimental ocean acidification and decreased seawater inorganic carbon concentration lead to large declines in mesoglea pH relative to the ECM, which is maintained relatively stable. Together, our results indicate that the coral calcifying epithelium is functionally polarized and that environmental variation impacts pHECM regulation through its effects on the basal side of the calcifying cells.

Abstract Background Tropical coral reefs cover ca. 0.1% of the Earth’s surface but host an outstanding biodiversity and provide important ecosystem services to millions of people living nearby. However, they are currently threatened by both local (e.g. nutrient enrichment and chemical pollution of coastal reefs, arising from poor land management, agriculture and industry) and global stressors (mainly seawater warming and acidification, i.e. climate change). Global and local stressors interact together in different ways, but the presence of one stressor often reduces the tolerance to additional stress. While global stressors cannot be halted by local actions, local stressors can be reduced through ecosystem management, therefore minimizing the impact of climate change on reefs. To inform decision-makers, we propose here to systematically map the evidence of impacts of chemicals arising from anthropogenic activities on tropical reef-building corals, which are the main engineer species of reef ecosystems. We aim to identify the combinations of chemical and coral responses that have attracted the most attention and for which evidence can be further summarized in a systematic review that will give practical information to decision-makers. Methods The systematic map will follow the Collaboration for Environmental Evidence Guidelines and Standards for Evidence Synthesis in Environmental Management. We will search the relevant literature using English terms combined in a tested search string in two publication databases (Web Of Science Core Collection and Scopus). The search string will combine terms describing the population (tropical reef-building corals) and the exposure (chemicals). We will supplement this literature with some more obtained through search engines, specialist websites, and through a call to local stakeholders. Titles, abstracts, and full-texts will then be successively screened using pre-defined eligibility criteria. A list of pre-defined variables will then be extracted from full-texts. Finally, a database of all studies included in the map with coded metadata will be produced. The evidence will be described in a map report with text, figures and tables, and a matrix showing the distribution and frequency of included study into types of exposure and types of outcomes will be computed to identify potential knowledge gaps and knowledge clusters.

Abstract We investigated the occurrence of intracolonial genetic variability (IGV) in Pocillopora corals in the southwestern Indian Ocean. Ninety‐six colonies were threefold‐sampled from three sites in Reunion Island. Nubbins were genotyped using 13 microsatellite loci, and their multilocus genotypes compared. Over 50% of the colonies presented at least two different genotypes among their three nubbins, and IGV was found abundant in all sites (from 36.7% to 58.1%). To define the threshold distinguishing mosaicism from chimerism, we developed a new method based on different evolution models by computing the number of different alleles for the infinite allele model (IAM) and the Bruvo's distance for the stepwise mutation model (SMM). Colonies were considered as chimeras if their nubbins differed from more than four alleles and if the pairwise Bruvo's distance was higher than 0.12. Thus 80% of the IGV colonies were mosaics and 20% chimeras (representing almost 10% of the total sampling). IGV seems widespread in scleractinians and beyond the disabilities of this phenomenon reported in several studies, it should also bring benefits. Next steps are to identify these benefits and to understand processes leading to IGV, as well as factors influencing them.

Cryptic species and lineages have been widely reported during the last decades, particularly in the marine realm. Misidentifications and ignoring species complexes imply many consequences, notably biasing biodiversity and connectivity assessments, which in turn mislead our understanding of ecosystems and impact the effective design and management of conservation plans. Focusing on the Indo-Pacific coral genus Pocillopora, playing key roles in reef ecosystems as one of the main bio-constructors, we report the first Pocillopora PSH16 (ORF53; sensu Gélin et al. 2017) colonies (N = 19) in the Western Indian Ocean (Nosy Tanikely, Madagascar), 6000 km further from its current distribution. Colonies were identified according to their mitochondrial open reading frame (ORF) haplotype and Bayesian assignment tests based on 13-microsatellite genotypes. Additionally, we performed genetic structure and diversity analyses with sympatric colonies from other Pocillopora species and Pocillopora PSH16 colonies from the tropical southwestern Pacific, revealing (1) a weak clonal richness, (2) a weak genetic diversity and (3) a relative isolation for the newly reported PSH16 colonies. These colonies thus represent either a new, distinct and uncommon, genetic lineage or isolated remnants of a wider one. In any case, unless specific management measures are implemented, their long-term maintenance seems compromised due to restricted gene flow within a restricted pool of genes. [ABSTRACT FROM AUTHOR]

Background: Tropical coral reefs cover only ca. 0.1% of the Earth's surface but host an outstanding biodiversity and provide important ecosystem services to millions of people living nearby. They are currently threatened by global (e.g., climate change) and local (e.g., chemical pollution) stressors that interact in different ways. While global stressors cannot be mitigated by local actions alone, local stressors can be reduced through ecosystem management. A systematic map on the impacts of chemicals arising from anthropogenic activities on tropical reef-building corals, which are the main engineer species of reef ecosystems, was published in 2021. This systematic map gathered an abundant literature (908 articles corresponding to 7937 studies), and identified four well-represented subtopics, amenable to relevant full syntheses. Here, we focused on one of the four subtopics: we aimed to systematically review the evidence on the ecotoxicological effects of chemicals on tropical reef-building corals. Methods: The evidence will be identified from the recent systematic map on the impacts of chemicals arising from anthropogenic activities on tropical reef-building corals. Especially, all studies in the map database corresponding to the knowledge cluster "evidence on the ecotoxicological effects of chemicals on corals" will be selected. To identify the evidence produced since then, a search update will be performed using a subset of the search string used for the systematic map, and titles, abstracts and full-texts will be screened according to the criteria defining the selected cluster of the map. In addition, as the eligibility criteria for the systematic review are narrower than those used to define the cluster in the systematic map, additional screening will be carried out. The included studies will then be critically appraised and a low, medium, or high risk of bias will be assigned to each study. Data will be extracted from studies and synthesised according to a strategy depending on the type of exposure and outcome. Synthesis will be mainly quantitative but also narrative, aiming to identify toxicity thresholds of chemicals for corals. [ABSTRACT FROM AUTHOR]

Caribbean coral cover has decreased substantially in recent decades, with much of the live coral being replaced by macroalgae. Encrusting red algae in the genus Ramicrusta have become abundant throughout the region and have demonstrated widespread harm to corals by overgrowing living tissue, causing colony mortality, and impairing coral recruitment. In this research, Ramicrusta textilis was identified by morpho-anatomy and DNA sequencing from nine sites around St. Thomas, US Virgin Islands, and 3D photogrammetry was used to measure the rate of algal growth on stony corals. 3D models of individual coral colonies (five species plus controls, N = 72) competing with R. textilis revealed differential competitive abilities among taxa, with Siderastrea siderea being the only species capable of inhibiting overgrowth by the alga (mean linear algal growth − 1.1 mm yr−1). Important reef building coral species such as Orbicella annularis and Orbicella faveolata were poor competitors (mean linear algal growth + 15 mm yr−1 and + 7.7 mm yr−1, respectively), indicating that the emergence of the alga could have significant impacts on Caribbean coral reef species diversity, community composition, and structural complexity. [ABSTRACT FROM AUTHOR]

Cold-water corals (CWC) can be found throughout a wide range of latitudes (79°N–78°S). Since they lack the photosymbiosis known for most of their tropical counterparts, they may thrive below the euphotic zone. Consequently, their growth predominantly depends on the prevalent environmental conditions, such as general food availability, seawater chemistry, currents, and temperature. Most CWC communities live in regions that will face CaCO3 undersaturation by the end of the century and are thus predicted to be threatened by ocean acidification (OA). This scenario is especially true for species inhabiting the Chilean fjord system, where present-day carbonate water chemistry already reaches values predicted for the end of the century. To understand the effect of the prevailing environmental conditions on the biomineralization of the CWC Tethocyathus endesa, a solitary scleractinian widely distributed in the Chilean Comau Fjord, a 12-month in situ experiment was conducted. The in situ skeletal growth of the test corals was assessed at two sites using the buoyant weight method. Sites were chosen to cover the naturally present carbonate chemistry gradient, with pH levels ranging between 7.90 ± 0.01 (mean ± SD) and 7.70 ± 0.02, and an aragonite saturation (Ωarag) between 1.47 ± 0.03 and 0.98 ± 0.05. The findings of this study provide one of the first in situ growth assessments of a solitary CWC species, with a skeletal mass increase of 46 ± 28 mg per year and individual, at a rate of 0.03 ± 0.02% day. They also indicate that, although the local seawater chemistry can be assumed to be unfavorable for calcification, growth rates of T. endesa are comparable to other cold-water scleractinians in less corrosive waters (e.g., Lophelia pertusa in the Mediterranean Sea).

Growth anomalies (GAs) are a morphologically diverse and poorly understood group of lesions affecting corals. The aim of this study was to describe the prevalence and morphology of GAs affecting the faviid corals Diploria labyrinthiformis, Pseudodiploria strigosa, Psudodiploria clivosa, and Colpophyillia natans on St. Kitts. Three gross morphological variants of GAs (exophytic, nodular, and ruminate) were equally prevalent, together affecting 7.8% of corals surveyed across 5 reefs. Prevalence varied by reef and coral species, being highest in C. natans (35.7%). Median colony diameter was larger in corals with GAs relative to those without (Mann-Whitney U test, P <.001). Histopathological examination of exophytic GAs consistently showed corallite and polyp gigantism (n = 7), characterized by polyp enlargement and retained microanatomical structures. In contrast, nodular GAs (n = 9) were consistently hyperplasia of the basal body wall with skeletal dystrophy, composed of micronodular skeletal deposits with abundant hyaline lamellae, bordered by calicoblastic epithelial hyperplasia, interspersed with distorted gastrovascular canals and islands of mesoglea. Endolithic organisms, particularly fungi and algae, were common among GA and apparently healthy biopsies. While pathogenesis of these lesions remains uncertain, a neoplastic basis for GAs on Caribbean faviids could not be established using diagnostic criteria conventionally applied to tumors of vertebrate taxa, in line with other recent observations of coral GAs. [ABSTRACT FROM AUTHOR]

Background: Tropical coral reefs cover ca. 0.1% of the Earth's surface but host an outstanding biodiversity and provide important ecosystem services to millions of people living nearby. They are currently threatened by local stressors (e.g. nutrient enrichment and chemical pollution arising from poor land management, sewage effluents, agriculture, industry) and global stressors (mainly seawater warming and acidification, i.e. climate change). Global and local stressors interact in different ways, but the presence of one stressor often reduces the tolerance to additional stress. While global stressors cannot be mitigated solely by local actions, local stressors can be reduced through ecosystem management, therefore minimizing the impact of climate change on coral reefs. We systematically mapped the evidence of impacts of chemicals arising from anthropogenic activities on tropical reef-building corals, which are the main engineer species of reef ecosystems, to inform decision-makers on the available evidence on this topic. Methods: We searched the relevant literature using English terms combined in a tested search string in two publication databases (Scopus and Web Of Science Core Collection). The search string combined terms describing the population (tropical reef-building corals) and the exposure (chemicals). We searched for additional literature through three search engines, three dissertations repositories, 11 specialist websites, and through a call to local stakeholders. Titles, abstracts, and full-texts were successively screened using pre-defined eligibility criteria. A database of all studies included in the map with coded metadata was produced. The evidence was described and knowledge clusters and gaps were identified through the distribution and frequency of studies into types of exposure and/or types of outcomes and/or types of study. Review findings: The initial searches identified 23,403 articles which resulted in 15,177 articles after duplicate removal. Among them, 908 articles were retained after screening process, corresponding to 7937 studies (a study being the combination of a taxon, an exposure, and an outcome). Among these studies, 30.5% dealt with the impact of nutrient enrichment on corals while 25% concerned the impact of human activities without reference to a chemical. The most measured outcomes were those related to the chemical concentration in corals (bioaccumulation, 25.8%), to coral physiology (16.9%), cover (14%), and mortality (9%). Half of the studies (48.4%) were experimental—the exposure was controlled by the researchers—and were conducted in laboratory conditions (39.4%) and in situ (9%). The most studied taxa, exposure, and outcomes were different between experimental and observational studies. Conclusions: We identified four well-represented subtopics that may be amenable to relevant full syntheses via systematic reviews: (1) evidence on bioaccumulation of chemicals by corals; (2) evidence on the effects of nutrient enrichment on corals; (3) evidence on the effects of human activities on corals; and (4) evidence on the ecotoxicological effects of chemicals on corals (except nutrient enrichment). The systematic map shows that corals in their natural environment can be exposed to many categories of chemicals, and that there is a complete gap in experimental research on the combined effects of more than two categories of chemicals. We therefore encourage research on this topic. [ABSTRACT FROM AUTHOR]

Abstract Maintaining the coexistence of algae and corals depends on the interactions between them. We investigated these interactions to assess: (1) recruitment patterns of algal turfs over time in dead areas on live corals; (2) the influence of fine-scale differences in coral-dominated environments on algal colonisation; (3) the influence of coral as a substrate for algal recruitment; (4) the invasion potential of algal turf on live coral tissue. This study compared algal colonisation directly on dead or damaged coral areas with algal colonisation on recruitment plates in coral-dominated or -free areas at 23, 154, and 230 days. We also monitored coral colonies over 1.5 years. Filamentous and articulated coralline algae were primarily evident in the early colonisation, reaching stability after 154 days. On a fine scale, the coral-dominated environment showed an increase in number of algal species and coverage. However, coral substrate was selective, with fewer species recruited to this substrate compared to the artificial plates. Furthermore, the competitive dynamics between corals and algal turfs did not result in a winner over time. Thus, algal turf colonisation was influenced not only by coral substrate but also by the reef environment on a fine scale.

Framework‐building corals create the three‐dimensional structure of coral reefs and are subject to predation from fishes, echinoderms, and gastropods. Anthropogenic stressors can magnify the effects of such top‐down pressure on foundation species. The gastropod Coralliophilaviolacea (Kiener, 1836) depletes coral energy reserves via predation, potentially increasing coral susceptibility to land‐based pollution (i.e., sediment accumulation and nutrient pollution). We hypothesized that sedimentation would worsen coral mortality, while nutrient enrichment would mitigate the harmful effects of sediment and predation on coral mortality by increasing the densities of algal symbionts. To test these hypotheses, we conducted in situ surveys of the fringing reefs in Mo'orea, French Polynesia to explore the relationships among massive Poritesspp. cover, C. violacea densities, and sediment accumulation on coral colonies across low and high nutrient sites. We also conducted a factorial field experiment to test the interactions among these stressors on coral tissue mortality, symbiont densities, and chlorophyll. Massive Porites colonies at higher nutrient sites had C. violacea densities 13 times higher than at low nutrient sites but there was no difference in the amount of live tissue on coral colonies with or without snails among these sites. In our experiment, there were interactions between predation and nutrients as well as nutrients and sediment that impacted coral mortality. Sedimentation and predation by C. violacea increased coral tissue mortality independently by ~20%. Nutrient enrichment reduced this effect in corals under sedimentation or predation pressure by lowering coral tissue mortality by 18% and increasing algal symbiont densities by ~28%. Our results indicate that sediment does not magnify top‐down pressure on this coral, and that moderate nutrient enrichment may interact with predation in complex, unexpected ways to alter the responses of corals to top‐down pressure. [ABSTRACT FROM AUTHOR]

Deep-sea scleractinian cup corals are prominent members of Southern Ocean megabenthic communities, though little is known about their life history. This study used paraffin histology and scanning electron microscopy to characterize the reproduction of the scleractinian coral Balanophyllia malouinensis (Squires, 1961) from Burdwood Bank in the Drake Passage. Samples were taken in April and May via otter trawls, Blake trawls, and dredges on three separate cruises: one on the RV Lawrence M. Gould in 2006, and two on the RV Nathaniel B. Palmer in 2008 and 2011. B. malouinensis is gonochoric with rare hermaphroditism. All four spermatocyst stages were seen simultaneously in males; similarly, most females contained oocytes at varying stages of development, though seasonality or periodicity could not be determined without a wider range of sample dates. Average fecundity was 241 ± 184 oocytes/individual (n = 38) and not correlated to cup size. Maturing larvae were found in the mesenteries and coelenteron of females, indicating B. malouinensis broods its larvae. This study was the first to characterize the reproduction of a deep-sea Balanophyllia species and adds to a small but growing body of work seeking to understand the unique benthic communities of Burdwood Bank. [ABSTRACT FROM AUTHOR]

Within the past decade, a functional group of encrusting red macroalgae defined as peyssonnelid algal crusts (PAC) has been rapidly spreading on shallow Caribbean reefs, frequently encrusting corals and sponges. This study focused on PAC growing on the reefs of St. John, US Virgin Islands, to (1) expand the monitoring of PAC abundance in this location, and (2) test two mechanisms, rapid linear growth and competitive dominance, by which PAC is hypothesized to enhance its capacity to spread. In August 2019, we found that the percentage coverage of PAC reached 46.6% at Tektite (3 m depth), and 63.8% at Cabritte Horn (3 m depth). Overall, the cover of PAC at these sites in 2019 was identical to, or up to 2.4-fold higher than in August 2017, and 2.1–3.7-fold higher than in November 2017, just after two category 5 storms impacted St. John. PAC was 1.8–29.1-fold more abundant at 3 m versus 9 m depth, and 1.4–22.0-fold more abundant at sites close to the tips of headlands than sites sheltered within bays. From August 2019 to January 2020, the rate of linear extension of PAC at each site and depth ranged from 26 to 43 µm d − 1, and of 80 PAC-coral interactions that were tagged in August 2019, none involved corals that had become completely overgrown by PAC by January 2020. The slow linear growth and absence of cases in which PAC completely overgrew coral colonies in 6 months are inconsistent with the high rate at which PAC has occupied space on Caribbean reefs over the past decade. One means to reconcile these observations is the possibility that recruitment of peyssonnelid spores to benthic surfaces facilitates the rapid spread of PAC. [ABSTRACT FROM AUTHOR]

The extent to which populations persist under environmental stress depends on the reproductive output of individuals that survive the stress. In coral systems, corals bleach in response to stress from elevated water temperature. However, little is known of the extent to which thermal stress impairs the reproductive capacity of the survivors over the following years, limiting the capacity to predict how populations will persist in the Anthropocene.Using histology to quantify the abundance and size of oocytes and spermaries per polyp, we tested how bleaching impairs the reproductive response of the coral Pocillopora meandrina over two reproductive seasons following the 2015 mass bleaching event in the Hawaiian Islands.We found that smaller colonies not only had a greater probability of bleaching but also suffered greater reproductive impacts over a longer time. In contrast, larger colonies generated comparable reproductive output regardless of bleaching severity, although bleached colonies generated smaller oocytes the year after bleaching.These results show that reproductive impacts of bleaching are more complex and size‐specific than commonly assumed. Therefore, estimates of bleaching mortality may underestimate the true impact of thermal stress on populations, especially as populations lose larger individuals from repeated and co‐occurring stressors. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

We investigated the occurrence of intracolonial genetic variability (IGV) in Pocillopora corals in the southwestern Indian Ocean. Ninety‐six colonies were threefold‐sampled from three sites in Reunion Island. Nubbins were genotyped using 13 microsatellite loci, and their multilocus genotypes compared. Over 50% of the colonies presented at least two different genotypes among their three nubbins, and IGV was found abundant in all sites (from 36.7% to 58.1%). To define the threshold distinguishing mosaicism from chimerism, we developed a new method based on different evolution models by computing the number of different alleles for the infinite allele model (IAM) and the Bruvo's distance for the stepwise mutation model (SMM). Colonies were considered as chimeras if their nubbins differed from more than four alleles and if the pairwise Bruvo's distance was higher than 0.12. Thus 80% of the IGV colonies were mosaics and 20% chimeras (representing almost 10% of the total sampling). IGV seems widespread in scleractinians and beyond the disabilities of this phenomenon reported in several studies, it should also bring benefits. Next steps are to identify these benefits and to understand processes leading to IGV, as well as factors influencing them. [ABSTRACT FROM AUTHOR]

Despite increased attention over the last decade on Mesophotic Coral Ecosystems (MCEs) [...]

Coral reefs are one of the most diverse marine ecosystems on Earth and one of the richest in terms of species interactions. Scleractinian corals are usually the most likely to provide numerous different habitats and to support many symbiotic relationships. However, many other invertebrate groups, such as sponges, bryozoans, and other cnidarians, establish strict symbiotic relationships with other marine organisms. Despite the nature of these relationships—as well as the factors that drive their establishment—being unclear in most cases, a few studies have already shown that some associations may increase the resistance of their hosts to external disturbances. Thus, the potential ability of each member of these diverse symbiotic assemblages to influence the fitness and long-term survival of their hosts bring the coral-associated fauna to the top of the list of coral reef studies. Unfortunately, the widespread degradation of coral reef ecosystems may threaten the existence of the intimate relationships that may go unrecognized complicating our understanding of the intricate networks connecting the fates of reef species. Therefore, this unprecedented loss of biodiversity calls for synergic conservation and monitoring actions aimed at significantly increasing our efforts to search for and describe as much of the diversity of coral-associated organisms as possible, shedding new light on the complex, elusive mechanisms controlling coral reef functioning.

This study is aimed at establishing a baseline on the genetic diversity of the Acropora corals of Sabah, North Borneo based on variations in the partial COI and CYB nucleotide sequences. Comparison across 50 shallow-water Acropora morphospecies indicated that the low substitution rates in the two genes were due to negative selection and that rate heterogeneity between them was asymmetric. CYB appeared to have evolved faster than COI in the Acropora as indicated by differences in the rate of pairwise genetic distance, degrees of transition bias (Ts/Tv), synonymous-to-nonsynonymous rate ratio (dN/dS), and substitution patterns at the three codon positions. Despite the relatively high haplotype diversity (Hd), nucleotide diversity (π) of the haplotype datasets was low due to stringent purifying selection operating on the genes. Subsequently, we identified individual COI and CYB haplotypes that were each extensively shared across sympatrically and allopatrically distributed Indo-Pacific Acropora. These reciprocally common mtDNA types were suspected to be ancestral forms of the genes whereas other haplotypes have mostly evolved from autoapomorphic mutations which have not been fixed within the species even though they are selectively neutral. To our knowledge, this is the first report on DNA barcodes of Acropora species in North Borneo and this understanding will play an important role in the management and conservation of these important reef-building corals. [ABSTRACT FROM AUTHOR]

Abstract: Eighteen microsatellite sequences were isolated from Platygyra acuta through magnetic bead hybridization enrichment method, and the site primers were used to analyze the genetic diversity of P. acuta, Platygyra daedalea, Favites flexuosa, and Porites lutea. Results showed that among the 18 microsatellites of P. acuta, 12 (66.67%) were perfect, 3 (16.67%) were imperfect, and the remaining 3 (16.67%) were compound type. P. acuta, P. daedalea, F. flexuosa, and P. lutea were detected to have 39, 28, 40, and 21 alleles using 12 pairs of common primers. The genetic diversity analysis of the four scleractinian populations indicated that the average polymorphism information contents were 0.5168, 0.4250, 0.5286, and 0.3409; the average expected heterozygosity values were 0.6667, 0.6042, 0.5972, and 0.4702; and the average effective numbers of allele were 2.7112, 2.5376, 2.6860, and 2.0081, respectively. All results indicated that the P. acuta and the F. flexuosa populations had high levels of genetic diversities, whereas P. daedalea and P. lutea had moderate levels of genetic diversities. In addition, environment stresses and the modes of reproduction of corals may be the main reasons for the deviation from Hardy-Weinberg equilibrium. [ABSTRACT FROM AUTHOR]

Abstract The plating coral, Agaricia lamarcki is a widely distributed species inhabiting reefs across the Caribbean basin and Florida. This species is of interest since it is considered a depth-generalist, found from 10 to 70 m. Given the scope of contemporary studies on this coral's population dynamics and physiology, as well as, the potential of mesophotic reefs to be refuge habitats for deteriorated shallow water reefs, we present the first de novo transcriptome assembly of an important mesophotic coral. Using next-generation paired-end sequencing (Illumina Hiseq4000; 2 × 150 bp), we obtained a total of 82,506,058 raw reads. The novel transcriptome assembly strategy included the recently developed National Center for Genome Analysis Support de novo transcriptome assembly pipeline. Assembly produced a total of 101,322 biologically true, non-redundant transcripts with an average contig length of 959 and N50 of 1830. EvidentialGene and TransDecoder were used to identify open reading frames (ORFs) with homology insight provided by the UniProtKb and PFAM databases. ORF prediction resulted in 38,517 putative ORFs of which 12,107 ORFs were annotated as genes dealing with molecular function, 1266 with biological processes and 416 with cellular components. [ABSTRACT FROM AUTHOR]

Ocean acidification changes the carbonate chemistry of seawater in a manner that reduces the biomineralisation rate of reef-building corals. Other effects of acidification on coral physiology are less well explored, and recent debate has focused on whether ocean acidification causes a change in Symbiodinium densities within tropical and subtropical reef-building corals. Within the framework of null-hypothesis significance testing, some aquaria experiments have provided evidence for a decrease in symbiont densities within coral tissue under ocean acidification (whilst others have suggested an increase). However, null effects have prevailed in the majority of such experiments, and so the question has remained unresolved. This study attempted to resolve this question using a meta-analytic framework, by establishing the effect sizes for symbiont density change under ocean acidification from a structured search of the literature. A regression of effect size (Hedge’s d) versus level of ocean acidification revealed a statistically significant negative relationship, with symbiont density per cm2 decreasing as the level of ocean acidification increased. The decline amounted to an additional 0.07 standard deviations of difference in symbiont density between corals in control (near present day) and acidified seawater with every 100 μatm of increase in partial pressure of CO2 in seawater (a relationship with an r2 of 0.24). A further unresolved question is whether ocean acidification will synergistically exacerbate (or diminish) symbiont density reductions caused by elevated temperature. An analysis of covariance did not reveal a greater decline in symbiont densities with increasing acidification at elevated temperature compared to non-stressful temperature, though this latter analysis should be viewed as exploratory due to a lower sample size. The well-supported evidence for a decline in symbiont densities in tropical and subtropical corals under ocean acidification now provides an impetus for sustained investigation of the consequences of such a change for holobiont functioning and the broader function of the coral reef ecosystem. [ABSTRACT FROM AUTHOR]

Over the last decade, publications on deep-sea corals have tripled. Most attention has been paid to Lophelia pertusa, a globally distributed scleractinian coral that creates critical three-dimensional habitat in the deep ocean. The bacterial community associated with L. pertusa has been previously described by a number of studies at sites in the Mediterranean Sea, Norwegian fjords, off Great Britain, and in the Gulf of Mexico (GOM). However, use of different methodologies prevents direct comparisons in most cases. Our objectives were to address intra-regional variation and to identify any conserved bacterial core community. We collected samples from three distinct colonies of L. pertusa at each of four locations within the western Atlantic: three sites within the GOM and one off the east coast of the United States. Amplicon libraries of 16S rRNA genes were generated using primers targeting the V4–V5 hypervariable region and 454 pyrosequencing. The dominant phylum was Proteobacteria (75–96%). At the family level, 80–95% of each sample was comprised of five groups: Pirellulaceae, Pseudonocardiaceae, Rhodobacteraceae, Sphingomonadaceae, and unclassified Oceanospirillales. Principal coordinate analysis based on weighted UniFrac distances showed a clear distinction between the GOM and Atlantic samples. Interestingly, the replicate samples from each location did not always cluster together, indicating there is not a strong site-specific influence. The core bacterial community, conserved in 100% of the samples, was dominated by the operational taxonomic units of genera Novosphingobium and Pseudonocardia, both known degraders of aromatic hydrocarbons. The sequence of another core member, Propionibacterium, was also found in prior studies of L. pertusa from Norway and Great Britain, suggesting a role as a conserved symbiont. By examining more than 40,000 sequences per sample, we found that GOM samples were dominated by the identified conserved core sequences, whereas open Atlantic samples had a much higher proportion of locally consistent bacteria. Further, predictive functional profiling highlights the potential for the L. pertusa microbiome to contribute to chemoautotrophy, nutrient cycling, and antibiotic production.

Coral reefs are under increasing pressure from a variety of stressors, highlighting the need for information about the status of coral reef communities including the distribution, abundance and composition of juvenile and adult coral assemblages. This information is currently limited for the Great Barrier Reef (GBR) and is necessary for understanding the impacts of disturbances and the system’s potential for recovery. This study reports juvenile and adult hard coral abundance and composition from 122 reefs on the GBR during a period of limited acute disturbance. The data represent baseline observations for juvenile hard coral assemblages spanning the longitudinal cross-shelf gradient of the GBR and 12 degrees of latitude and augment reported distribution of adult coral assemblages over the same scale with inclusion of additional reefs. Juvenile and adult coral assemblages reflected broad differences imposed by the gradient of environmental conditions across the GBR. The mean density of juvenile hard corals was lower in the inshore reefs (5.51 m2) than at either the mid-shelf (11.8 m2) or outer shelf reefs (11.2 m2). The composition of juvenile and adult coral assemblages covaried overall, although there were different relationships between these two life stages across the continental shelf and among community types. Dissimilarity between juvenile and adult coral assemblages was greater on inshore and outer shelf reefs than on reefs in the mid-shelf, although, there were differences in community types both within these shelf positions and those that spanned mid- and outer shelf reefs. Dissimilarity was greatest for Inshore branching Acropora and high for Southern Acropora communities, although very high coral cover and very low juvenile densities at these reefs precluded interpretation beyond the clear competitive dominance of Acropora on those reefs. Dissimilarity was also high between juvenile and adult coral assemblages of Turbid inshore communities suggesting water quality pressures, along with synergistic effects of other stressors, pose ongoing selective pressures beyond the juvenile stage. Conversely, relatively low dissimilarity between juvenile and adult coral assemblages on mid-shelf and lower latitude outer shelf reefs suggests pressures beyond those influencing settlement and early post-settlement survival were having less influence on the composition of adult coral assemblages.

Over the last decade, publications on deep-sea corals have tripled. Most attention has been paid to Lophelia pertusa, a globally distributed scleractinian coral that creates critical three-dimensional habitat in the deep ocean. The bacterial community associated with L. pertusa has been previously described by a number of studies at sites in the Mediterranean Sea, Norwegian fjords, off Great Britain, and in the Gulf of Mexico (GOM). However, use of different methodologies prevents direct comparisons in most cases. Our objectives were to address intra-regional variation and to identify any conserved bacterial core community. We collected samples from three distinct colonies of L. pertusa at each of four locations within the western Atlantic: three sites within the GOM and one off the east coast of the United States. Amplicon libraries of 16S rRNA genes were generated using primers targeting the V4-V5 hypervariable region and 454 pyrosequencing. The dominant phylum was Proteobacteria (75-96%). At the family level, 80-95% of each sample was comprised of five groups: Pirellulaceae, Pseudonocardiaceae, Rhodobacteraceae, Sphingomonadaceae, and unclassified Oceanospirillales. Principal coordinate analysis based on weighted UniFrac distances showed a clear distinction between the GOM and Atlantic samples. Interestingly, the replicate samples from each location did not always cluster together, indicating there is not a strong site-specific influence. The core bacterial community, conserved in 100% of the samples, was dominated by the operational taxonomic units of genera Novosphingobium and Pseudonocardia, both known degraders of aromatic hydrocarbons. The sequence of another core member, Propionibacterium, was also found in prior studies of L. pertusa from Norway and Great Britain, suggesting a role as a conserved symbiont. By examining more than 40,000 sequences per sample, we found that GOM samples were dominated by the identified conserved core sequences, whereas open Atlantic samples had a much higher proportion of locally consistent bacteria. Further, predictive functional profiling highlights the potential for the L. pertusa microbiome to contribute to chemoautotrophy, nutrient cycling, and antibiotic production. [ABSTRACT FROM AUTHOR]

Species delimitation methods based on genetic information, notably using single locus data, have been proposed as means of increasing the rate of biodiversity description, but can also be used to clarify complex taxonomies. In this study, we explore the species diversity within the cnidarian genus Pocillopora , widely distributed in the tropical belt of the Indo-Pacific Ocean. From 943 Pocillopora colonies sampled in the Western Indian Ocean, the Tropical Southwestern Pacific and Southeast Polynesia, representing a huge variety of morphotypes, we delineated Primary Species Hypotheses (PSH) applying the Automatic Barcode Gap Discovery method, the Poisson Tree Processes algorithm and the Generalized mixed Yule-coalescent model on two mitochondrial markers (Open Reading Frame and Dloop) and reconstructing a haploweb using one nuclear marker (Internal Transcribed Spacer 2). Then, we confronted identified PSHs to the results of clustering analyses using 13 microsatellites to determine Secondary Species Hypotheses (SSH). Based on the congruence of all methods used and adding sequences from the literature, we defined at least 18 Secondary Species Hypotheses among 14 morphotypes, confirming the high phenotypic plasticity in Pocillopora species and the presence of cryptic lineages. We also identified three new genetic lineages never found to date, which could represent three new putative species. Moreover, the biogeographical ranges of several SSHs were re-assessed in the light of genetic data, which may have direct implications in conservation policies. Indeed, the cryptic diversity within this genus should be taken into account seriously, as neglecting its importance is source of confusion in our understanding of ecosystem functioning. Next generation sequencing, combined with other parameters (i.e. microstructure, zooxanthellae identification, ecology even at a micro-scale, resistance and resilience ability to bleaching) will be the next step towards an integrative framework of Pocillopora taxonomy, which will have profound implications for ecological studies, such as studying biodiversity, response to global warming and symbiosis. [ABSTRACT FROM AUTHOR]

Preventing the loss of biodiversity is a major challenge in mega-diverse ecosystems such as coral reefs where there is a critical shortage of baseline demographic data. Threatened species assessments play a valuable role in guiding conservation action to manage and mitigate biodiversity loss, but they must be undertaken with precise information at an appropriate spatial scale to provide accurate classifications. Here we explore the regional conservation status of scleractinian corals on isolated Pacific Ocean atolls in the Republic of the Marshall Islands. We compile an integrated regional species list based upon new and historical records, and compare how well the regional threat classifications reflect species level priorities at a global scale. A similar proportion of the 240 species of hard coral recorded in the current survey are classified as Vulnerable at the regional scale as the global scale using the International Union for the Conservation of Nature (IUCN) Red List criteria (23% and 20% respectively), however there are distinct differences in the composition of species. When local abundance data is taken into account, a far greater proportion of the regional diversity (up to 80%) may face an elevated risk of local extinction. These results suggest coral communities on isolated Pacific coral reefs, which are often predicted to be at low risk, are still vulnerable due to the small and fragmented nature of their populations. This reinforces that to adequately protect biodiversity, ongoing threatened species monitoring and the documentation of species-level changes in abundance and distribution is imperative.

Ocean acidification (OA) is predicted to reduce reef coral calcification rates and threaten the long-term growth of coral reefs under climate change. Reduced coral growth at elevated pCO2 may be buffered by sufficiently high irradiances; however, the interactive effects of OA and irradiance on other fundamental aspects of coral physiology, such as the composition and energetics of coral biomass, remain largely unexplored. This study tested the effects of two light treatments (7.5 versus 15.7 mol photons m−2 d−1) at ambient or elevated pCO2 (435 versus 957 µatm) on calcification, photopigment and symbiont densities, biomass reserves (lipids, carbohydrates, proteins), and biomass energy content (kJ) of the reef coral Pocillopora acuta from Kāne‘ohe Bay, Hawai‘i. While pCO2 and light had no effect on either area- or biomass-normalized calcification, tissue lipids gdw−1 and kJ gdw−1 were reduced 15% and 14% at high pCO2, and carbohydrate content increased 15% under high light. The combination of high light and high pCO2 reduced protein biomass (per unit area) by approximately 20%. Thus, under ecologically relevant irradiances, P. acuta in Kāne‘ohe Bay does not exhibit OA-driven reductions in calcification reported for other corals; however, reductions in tissue lipids, energy content and protein biomass suggest OA induced an energetic deficit and compensatory catabolism of tissue biomass. The null effects of OA on calcification at two irradiances support a growing body of work concluding some reef corals may be able to employ compensatory physiological mechanisms that maintain present-day levels of calcification under OA. However, negative effects of OA on P. acuta biomass composition and energy content may impact the long-term performance and scope for growth of this species in a high pCO2 world.