Papers by Stéphane De Palmas
Authorea (Authorea), Jun 16, 2021
The decline of coral reefs has fueled interest in determining whether mesophotic reefs can shield... more The decline of coral reefs has fueled interest in determining whether mesophotic reefs can shield against disturbances and help replenish deteriorated shallower reefs. In this study, we characterized spatial (horizontal and vertical) and seasonal patterns of diversity in coral recruits from Dabaisha and Guiwan reefs at Ludao, Taiwan. Concrete blocks supporting terra cotta tiles were placed at shallow (15m) and mesophotic (40m) depths, during 2016-2018. Half of the tiles were retrieved and replaced biannually over three 6-month surveys (short-term); the remainder retrieved at the end of the 18-month (long-term) survey. 451 recruits were located using fluorescent censusing and identified by DNA barcoding. Barcoding the mitochondrial cytochrome oxidase I (COI) gene resulted in 17 molecular operational taxonomic units (MOTUs). To obtain taxonomic resolution beyond the generic level, Pocillopora were phylotyped using the mitochondrial open reading frame (ORF), resolving eight MOTUs. Acropora, Isopora or Montipora recruits were identified by the nuclear PaxC intron, yielding ten MOTUs. Overall, 35 MOTUs were generated and were comprised primarily of Pocillopora, and in fewer numbers, Acropora, Isopora, Pavona, Montipora, Stylophora, among others. 40% of MOTUs recruited solely within mesophotic reefs while 20% were shared by both depth zones. MOTUs recruiting across a broad depth distribution appear consistent with the hypothesis of mesophotic reefs acting as a refuge for shallow water coral reefs. In contrast, Acropora and Isopora MOTUs were structured across depth zones representing an exception to this hypothesis. This research provides an imperative assessment of coral recruitment in understudied mesophotic reefs and imparts insight into the refuge hypothesis.
Marine Biodiversity, Dec 24, 2014
Frontiers in Marine Science, Aug 13, 2021
Taninaka et al. Phylogeography of Genus Heliopora Heliopora coerulea has a wider distribution, be... more Taninaka et al. Phylogeography of Genus Heliopora Heliopora coerulea has a wider distribution, being across the Indian Ocean and western Pacific. This study highlights the effectiveness of phylogenetic analysis using genomewide markers and the importance of examining populations across their distribution range to understand localized genetic structure and speciation patterns of corals.
PLOS ONE, Jan 14, 2013
Background: Seawater temperature is the main factor restricting shallow-water zooxanthellate cora... more Background: Seawater temperature is the main factor restricting shallow-water zooxanthellate coral reefs to low latitudes. As temperatures increase, coral species and perhaps reefs may move into higher-latitude waters, increasing the chances of coral reef ecosystems surviving despite global warming. However, there is a growing need to understand the structure of these high-latitude coral communities in order to analyze their future dynamics and to detect any potential changes. Methodology/Principal Findings: The high-latitude (32.75uN) community surveyed was located at Tatsukushi, Shikoku Island, Japan. Coral cover was 6062% and was composed of 73 scleractinian species partitioned into 7 functional groups. Although only 6% of species belonged to the 'plate-like' functional group, it was the major contributor to species coverage. This was explained by the dominance of plate-like species such as Acropora hyacinthus and A. solitaryensis. Comparison with historical data suggests a relatively recent colonization/development of A. hyacinthus in this region and a potential increase in coral diversity over the last century. Low coverage of macroalgae (2% of the benthic cover) contrasted with the low abundance of herbivorous fishes, but may be reasonably explained by the high density of sea urchins (12.963.3 individuals m 22). Conclusions/Significance: The structure and composition of this benthic community are relatively remarkable for a site where winter temperature can durably fall below the accepted limit for coral reef development. Despite limited functionalities and functional redundancy, the current benthic structure might provide a base upon which a reef could eventually develop, as characterized by opportunistic and pioneer frame-building species. In addition to increasing seawater temperatures, ongoing management actions and sea urchin density might also explain the observed state of this community. A focus on such 'marginal' communities should be a priority, as they can provide important insights into how tropical corals might cope with environmental changes.
PLOS ONE, Sep 11, 2014
The identification of coral recruits has been problematic due to a lack of definitive morphologic... more The identification of coral recruits has been problematic due to a lack of definitive morphological characters being available for higher taxonomic resolution. In this study, we tested whether fluorescent detection of coral recruits used in combinations of different DNA-barcoding markers (cytochrome oxidase I gene [COI], open reading frame [ORF], and nuclear Pax-C intron [PaxC]) could be useful for increasing the resolution of coral spat identification in ecological studies. One hundred and fifty settlement plates were emplaced at nine sites on the fringing reefs of Kenting National Park in southern Taiwan between April 2011 and September 2012. A total of 248 living coral spats and juveniles (with basal areas ranging from 0.21 to 134.57 mm 2) were detected on the plates with the aid of fluorescent light and collected for molecular analyses. Using the COI DNA barcoding technique, 90.3% (224/248) of coral spats were successfully identified into six genera, including Acropora, Isopora, Montipora, Pocillopora, Porites, and Pavona. PaxC further separated I. cuneata and I. palifera of Isopora from Acropora, and ORF successfully identified the species of Pocillopora (except P. meandrina and P. eydouxi). Moreover, other cnidarian species such as actinarians, zoanthids, and Millepora species were visually found using fluorescence and identified by COI DNA barcoding. This combination of existing approaches greatly improved the taxonomic resolution of early coral life stages, which to date has been mainly limited to the family level based on skeletal identification. Overall, this study suggests important improvements for the identification of coral recruits in ecological studies.
<p>Boxplots display median, first, and third quartiles (hinges); 95% confidence interval of... more <p>Boxplots display median, first, and third quartiles (hinges); 95% confidence interval of median (notches) and outliers.</p
<p>Percentage cover of major benthic categories. <b>b.</b> Appearance of coral ... more <p>Percentage cover of major benthic categories. <b>b.</b> Appearance of coral community at Tatsukushi dominated by <i>Acropora</i> spp (at 5 m in depth).</p
Taiwan straddles tropical and subtropical latitudes in the North Pacific Ocean. While shallow-wat... more Taiwan straddles tropical and subtropical latitudes in the North Pacific Ocean. While shallow-water coral reefs in Taiwan have been studied for many years, mesophotic coral ecosystems (MCEs) have recently enjoyed a surge of interest because they are hypothesized to provide a refuge for some reef species in distress. The distribution of MCEs in Taiwan is influenced by numerous biophysical and environmental variables including substrate availability, temperature, light irradiance, and sedimentation. In 1991, an early survey of the diversity of MCEs off Taiwan’s southern coast highlighted sedimentation and the lack of suitable substrates as important factors restricting reef communities at depths below 30 m. The steeply sloping east coast of Taiwan supports well-developed and more accessible MCEs and has therefore been the focus of recent research. Preliminary surveys have documented 18 macroalgal, 95 scleractinian, 33 octocoral, 2 antipatharian, 14 sponge, and 76 fish species. With th...
Frontiers in Marine Science, 2022
Coral endolithic microbes can be an important nutrients support for hosts while under stresses. P... more Coral endolithic microbes can be an important nutrients support for hosts while under stresses. Previous studies have found that the endolithic microbial composition of a single coral species can be biogeographical diverse. However, the potential environmental factors, such as salinity, temperature, pH, and nutrient, that might influence the composition of the endolithic microbes remain unclear. In this study, we used both amplicon sequence variants (ASV) and a kmer-based taxonomic unit (KTU) to characterize the endolithic bacterial constitution of Isopora spp. located in the western Pacific Ocean—where it is subjected to the Kuroshio Current (in Okinawa, Japan and Green Island, Taiwan)—and the South China Sea (Dongsha Atoll). The endolithic bacterial community compositions showed a significant geographical difference, and we suggest that the ocean current and primary productivity are the most essential environmental factors influencing the bacterial communities in the skeleton of I...
It can be challenging to identify scleractinian corals from the genus Pocillopora (Lamarck 1816) ... more It can be challenging to identify scleractinian corals from the genus Pocillopora (Lamarck 1816) in the field because of their large range of inter- and intra-specific morphological variation that co-occur with changes in the physical environment. This task is made more arduous in the context of a depth gradient, where light and water current could greatly affect the morphology of the corallum. Pocillopora verrucosa (Ellis and Solander, 1786) in Taiwan was previously reported exclusively from shallow waters (40m in depth) questions this bathymetric distribution. We used the mitochondrial open reading frame and the histone 3 molecular markers to investigate the vertical and horizontal spatial distribution of P. verrucosa around Ludao (Green Island), Taiwan. We genotyped 101 Pocillopora verrucosa-like colonies collected from 4 depth zones, ranging from 7 to 45m, at 3 sites around the island. Of the 101 colonies sampled, 85 were genotyped as P. verrucosa, 15 as P. meandrina, and one specimen as an undescribed Pocillopora species. P. verrucosa was found at all depths, while P. meandrina and the undescribed Pocillopora specimen were limited to 15m depth. P. verrucosa has a large bathymetric distribution around Ludao and could benefit from the refuge that the mesophotic zone offers. This study illustrates the difficulty of identifying Pocillopora corals in the field and emphasizes the relevance of molecular taxonomy as an important and complementary tool to traditional taxonomy for clarifying vertical and horizontal species distribution. Our results also illustrate the need in conservation biology to target species genetic diversity rather than just species diversity
PloS one, 2018
Pocillopora verrucosa is a widely distributed depth-generalist coral that presents plasticity in ... more Pocillopora verrucosa is a widely distributed depth-generalist coral that presents plasticity in its skeletal macro- and microstructure in response to environmental gradients. Light and water movement, which covary with depth, are the main environmental drivers of morphological plasticity in this genus; however, assessing environmentally-induced plasticity may be confounded by the extent of interspecific variation in Pocillopora. We examine the morphology of 8 typed P. verrucosa specimens collected along a depth gradient ranging from 7 to 45 meters and comprising 3 sites throughout Ludao, Taiwan. We measured 36 morphological characters, 14 which are novel, in 3 regions on the corallum-the apex, branch and base-in order to quantify their relationship to site and depth. We found significant correlation between depth and 19 morphological characters, notably branch verruca area, branch verruca height, base verruca spacing, base spinule length, and branch corallite area. 60% of microstru...
Scientific Reports, 2013
Stylophora pistillata is a widely used coral ''lab-rat'' species with highly variable morphology ... more Stylophora pistillata is a widely used coral ''lab-rat'' species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the
Marine Ecology Progress Series, 2011
The capacity of corals for repairing partial mortality is a fundamental determinant of reef resil... more The capacity of corals for repairing partial mortality is a fundamental determinant of reef resilience. This capacity was assessed in the major reef-building coral Porites lutea by monitoring the regeneration of artificially induced lesions of standard size (330 ± 50 mm 2 , 3 mm deep) in 4 shallow reef flat populations at Réunion Island, under different environmental conditions related to sites and seasons, during a period without positive temperature anomalies. An exponential decay model with an asymptote described the lesion regeneration through 14 experiments. In spite of fast initial lesion regeneration, limited capacity for repair in this massive coral was indicated, as only 18% of the inflicted lesions healed completely within 6 to 9 mo. Lesion regeneration was fastest and most complete in the cooling and cool seasons, and may be impaired during the warming and hot seasons. Both solar radiation and seawater temperature contributed to seasonal changes in regeneration capacity, although they had opposite effects. While high radiation during the warming season decreased lesion regeneration rate, potentially through reduction of the photosynthetic efficiency of zooxanthellae, high temperature boosted it but also increased the amount of lesion area that could not be regenerated. Study sites were characterised by different temperature and radiation regimes, but these parameters alone could not explain all site effects on lesion regeneration capacity. Additional factors, most probably chronic stress caused by inputs of organic matter and runoff from land, may further compromise the regeneration capacity of corals and the resilience of coral populations.
Coral Reefs, 2014
The resilience of coral reefs relies significantly on the ability of corals to recover successful... more The resilience of coral reefs relies significantly on the ability of corals to recover successfully in algaldominated environments. Larval settlement is a critical but highly vulnerable stage in the early life history of corals. In this study, we analyzed how the presence of two upright fleshy algae, Sargassum mcclurei (SM) and Padina australis (PA), and one crustose coralline algae, Mesophyllum simulans (MS), affects the settlement of Acropora muricata larvae. Coral larvae were exposed to seawater flowing over these algae at two concentrations. Larval settlement and mortality were assessed daily through four variables related to their behavior: swimming, substratum testing, metamorphosis, and stresses. Temperature, dissolved oxygen, pH, algal growth, and photosynthetic efficiency were monitored throughout the experiment. Results showed that A. muricata larvae can settle successfully in the absence of external stimuli (63 ± 6 % of the larvae settled in control treatments). While algae such as MS may stimulate substrate testing and settlement of larvae in the first day after competency, they ultimately had a lower settlement rate than controls. Fleshy algae such as PA, and in a lesser measure SM, induced more metamorphosis than controls and seemed to eventually stimulate settlement. A diverse combination of signals and/or modifications of microenvironments by algae and their associated microbial communities may explain the pattern observed in coral settlement. Overall, this study contributes significantly to the knowledge of the interaction between coral and algae, which is critical for the resilience of the reefs. Keywords Mesophyllum Á Padina Á Sargassum Á Coral larvae Á Coral-algal interactions Á Reef recovery Communicated by Biology Editor Dr. Mark Vermeij V. Denis and M. Loubeyres have contributed equally to this work.
PLOS ONE, 2017
Environmental impacts can alter relationships between a coral and its symbiotic microbial communi... more Environmental impacts can alter relationships between a coral and its symbiotic microbial community. Furthermore, changes in the microbial community associated with increased seawater temperatures can cause opportunistic infections, coral disease and death. Interactions between soft corals and their associated microbes are not well understood. The species Scleronephthya gracillimum is distributed in tropical to temperate zones in coral assemblages along the Kuroshio Current region. In this study we collected S. gracillimum from various sites at different latitudes, and compared composition of their bacterial communities using Next Generation Sequencing. Coral samples from six geographically distinct areas (two sites each in Taiwan, Japan, and Korea) had considerable variation in their associated bacterial communities and diversity. Endozoicimonaceae was the dominant group in corals from Korea and Japan, whereas Mycoplasma was dominant in corals from Taiwan corals. Interestingly, the latter corals had lower relative abundance of Endozoicimonaceae, but greater diversity. These biogeographic differences in bacterial composition may have been due to varying environmental conditions among study locations, or because of host responses to prevailing environmental conditions. This study provided a baseline for future studies of soft coral microbiomes, and assessment of functions of host metabolites and soft coral holobionts.
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Papers by Stéphane De Palmas