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4,207 results for “Corals”
Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs (Raw data)
<p>Datasets for the analysis developed in the Article "<em><strong>Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs</strong></em>". For more information, please refer to the original publication.</p> <p>Network_Structural_Index_&_SpogeTraits.csv <- Structural Index for the sponge-dwelling fauna network, sponge accumulated area and sponges’ morphology.</p> <p>NWTA_CoralReefs_Sponges_ interactions.csv <- Relationship between host sponges and guest fauna in the Northwester Atlantic coral reefs</p> <p>NWTA_CoralReefs_Sponge_reacords.csv <- Sponge species incidence records in the Northwester Atlantic coral reefs</p> <p>sponges_morphological_description.csv <- Sponge morphological standardization</p> <p>Network.html <- Interactive sponge-dwelling fauna network</p> <p>Enjoy!<br> </p>
Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts
<p>Sequencing reads were assembled using the genome assembler pipeline Shovill v1.1.0. Briefly, the Shovill pipeline included read trimming using Trimmomatic v0.39, de novo assembly with SPAdes v3.15.5 and genome polishing with Pilon v1.24. After the pipeline, additional polishing was performed by mapping the reads back to the contigs with BWA v0.7.17 and sorting the resulting SAM/BAM files using SAMtools v1.15.1. Pilon v1.24 was then used to correct bases, fix mis-assemblies and fill gaps. The reformat.sh script from the Bbmap package v38.76 (-minlength=1000) was used to filter out contigs less than 1000bp. The draft genome assemblies were then annotated with Bakta v1.7.0. </p> <p>Single nucleotide polymorphism (SNP) detection between WT (WTref) and SS (SSref) samples were then performed using snippy v4.6.0, where both WT and SS samples were inputted as the reference genome in turn.</p> <p>A subset of the snippy output files are uploaded here and contain all variants found.</p>
Mapping literature reviews on coral health: A review map, critical appraisal, and bibliometric analysis - Data and Code
<p>Data, code, and supplementary materials for "Mapping literature reviews on coral health: A review map, critical appraisal, and bibliometric analysis" by Burke et al., published in Ecological Solutions and Evidence.</p>
Virgin Islands National Park: Coral Reef: Population Dynamics: Landscape-scale Variation in Scleractinian Corals
This study provides a landscape-scale context to a decadal-scale analysis of community structure on shallow reefs along 4 km of the south shore of St. John, US Virgin Islands. By focusing on 12-14 sites along ~100 km of the shores of St. John and St. Thomas, surveys conducted in 2011 were used to contrast: (1) a local-scale with a landscape-scale analysis on two islands, (2) reefs around St. John and St. Thomas, and (3) reefs on north and south shores. Reefs were censused using photoquadrats that were analyzed for percentage cover first by functional groups (coral, macraolagae and CTB), and then by coral genus. In general, among-site variation for the coarse-resolution analysis eclipsed shore and island effects, but the fine-resolution analysis revealed strong site-specific differences for multiple coral genera that could be the product of priority effects in community succession. Over the next decade these differences probably will create unique community trajectories at each site.
Bioerosion on Fungia pieces and coral recruits, calcification and settlement data on Palmyra Atoll reef.
Coral recruitment and calcium carbonate (CaCO₃) accretion are fundamental processes that help maintain coral reefs. Many reefs worldwide have experienced degradation, including a decrease in coral cover and biodiversity. Successful coral recruitment helps degraded reefs to recover, while CaCO₃ accretion by early successional benthic organisms maintains the topographic complexity of a coral reef system. It is therefore important to understand the processes that affect coral recruitment and CaCO₃ accretion rates in order to understand how coral reefs recover from disturbances. The aim of this thesis was to determine how biophysical forcing factors affect coral recruitment, calcification and bioerosion on a pristine coral reef.
Nitrogen cycling and metabolic rates of aquacultured and wild Acropora coral from Guam in response to ammonium loading rates during 2020-2022
Rates from aquacultured corals and coral fragments collected in Guam in response to ammonium loading. These data are from two separate experiments, one using aquacultured corals and artificial seawater and light. The second was done with wild collected Acropora pistillata from two reef sites in Guam. The first site was West Hagåtña Bay (N13.479650, E144.741750; N13.479833, E144.741733) which had more nearby urban influences and was near the sewage outfall for the city (Redding et al. 2013). The second site was Luminao Reef (N13.4652417, E144.6477483; N13.465467, E144.648050) which was a more isolated reef on the seaward side of the breakwater for Guam’s major port. We measured respiration, gross primary production, 15N ammonium uptake to corals, related nitrogen cycling fluxes in the tanks (reminerization, net uptake, nitrification).
Virgin Islands National Park: Coral Reef: Decadal-scale changes in community structure from 1987 to 2011
These time series data sample percent cover of Scleractinian corals by genus measured from photo quadrats. Percent cover is given for each quadrat, each site, each year from 1987 to 2011. Counts of juvenile corals conducted in situ and small colonies less than 4 cm diameter are pooled from all sites. Supplementary data include in situ seawater temperature daily mean from 1989 to 2011. These data were used to create the figures in Edmunds, P.J., 2013, Decadal-scale changes in the community structure of coral reefs in St. John, US Virgin Islands, Marine ecology Progress Series. doi:10.3354/meps10424
Virgin Islands National Park: Coral Reef: Populations Dynamics: Population Projections
In this study, size-based matrix models for the reef-building coral Orbicella annularis at 14-m depth on the Tektite reef in St. John, U.S. Virgin Islands, were used to: (1) explore the demography of changing coral cover over 25 yr, (2) test for spatial homogeneity in demographic properties through a contrast with a previous study (at Yawzi Point, Edmunds and Elahi 2007), and (3) evaluate the potential for future population stability. During three, five year intervals from 1988 to 2002, St. John was affected by hurricanes and bleaching, yet coral cover at Tektite increased from 33% to 49%; from 2002 to 2007, it declined to 27%; and from 2010 to 2013, it stabilized at ∼ 28%. Over a quarter-century, colonies > 50 cm2 became rare, the abundance of colonies ≤ 50 cm2 increased from 58% (1988) to 92% (2013), and population density doubled to 67 colonies m-2 by 2013. Population growth (λ) was greater at Tektite (1.152 ≥ λ ≥ 1.018) than Yawzi Point (0.679 ≥ λ ≥ 0.586), and while population size at Tektite declined due to bleaching and disease in 2005 (λ = 0.753 over 2003–2008), it recovered between 2008 and 2013 (λ = 0.966); the population at Yawzi Point declined from 1988 to 2003 without signs of recovery. Projections suggest a continuation of recent conditions could allow O. annularis at Tektite to retain ∼ 9% cover after 100 yr, but with a return to the rates of growth and survival of 1993–1998, it could attain coverage similar to that of 1988 (33%) in ∼ 15 yr.
Virgin Islands National Park: Coral Reef: Population Dynamics: Octocorals
These data are evidence of the the long-term dynamics of shallow coral reefs along the south coast of St. John from as early as 1987. These data describe coral reef community structure by density based on the analysis of color photographs. All of these data originate from color images of photoquadrats recorded annually (usually in the summer) from as early as 1987. The data falls into three groups. The two groups that are contained in this data package are (1) Tektite & Yawzi and (2) Random sites. Tektite – this is at 14 m depth on the eastern side of Great Lameshur Bay and is the original site of the Tektite man-in-the sea project in 1969; this project marked the birth of the Virgin Islands Ecological Research Station (later the Virgin Islands Environmental Resource Station) that hosts the field component of the project. The reef in this location consists of a single buttress that has remained dominated by Montastraea anularis since the start of the research (1987). These surveys consist of 30 photoquadrats (1 x 1 m) distributed along three, 10 m transects. Yawzi – this is at 9 m depth and is on the western side of Great Lameshur Bay and has been recorded photographically since 1987. This reef also started the study period dominated by Montastraea annularis, but has degraded much more rapidly that the Tektite site. These surveys consist of 30 photoquadrats (1 x 1 m) distributed along three, 10 m transects. Random sites – were added in 1992 to address the concern that the original sites (Yawzi and Tektite) were selected on “good” areas of reef and, therefore, could only decline in condition. The Random sites were selected using random coordinates in 1992, and consist of 6 sites (at 7-9 m depth) scattered between Cabritte Point and White Point. All lie a little shoreward of Yawzi and Tektite, and have always been characterized by low coral cover (< 10% cover). The surveys consist of 18-40 photoquadrats (0.5 x 0.5 m; with sample size determined by the exposures on a 3
Virgin Islands National Park: Coral Reef: Reference: Taxonomy
In early years photos were analyzed with less refined taxonomic classsification. This reference table may be used to aggregate taxa to align with coarse analysis. Use this table to define sub-categories and super-categories such as the M. annularis complex. This is a reference dataset containing the taxonomic classifications, groupings of taxonomic classifications, and functional groups. It has been updated in accordance with Budd, et al., 2012.
Virgin Islands National Park: Coral Reef: Population Dynamics: Scleractinian corals (Reformatted to a Darwin Core Archive)
This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/357/2, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/291/2. The abstract below was extracted from the Level 0 data package and is included for context: These data are evidence of the the long-term dynamics of shallow coral reefs along the south coast of St. John from as early as 1987. These data describe coral reef community structure as percent cover based on the analysis of color photographs. All of these data originate from color images of photoquadrats recorded annually (usually in the summer) from as early as 1987. The data falls into three groups. The two groups that are contained in this data package are (1) Tektite & Yawzi and (2) Random sites. The juvenile coral density is packaged separately. Tektite – this is at 14 m depth on the eastern side of Great Lameshur Bay and is the original site of the Tektite man-in-the sea project in 1969; this project marked the birth of the Virgin Islands Ecological Research Station (later the Virgin Islands Environmental Resource Station) that hosts the field component of the project. The reef in this location consists of a single buttress that has remained dominated by Montastraea anularis since the start of the research (1987). These surveys consist of 30 photoquadrats (1 x 1 m) distributed along three, 10 m transects. Yawzi – this is at 9 m depth and is on the western side of Great Lameshur Bay and has been recorded photographically since 1987. This reef also started the study period dominated by Montastraea annularis, but has degraded much more rapidly that the Tektite site. These surveys consist of 30 photoquadrats (1 x 1 m) distributed along three, 10 m transects. Random sit
Scott Reef and Rowley Shoals Coral Bleaching Data
Coral reefs have evolved over millennia to survive disturbances. Yet, in just a few decades chronic local pressures and the climate catastrophe have accelerated so quickly that most coral reefs are now threatened. Rising ocean temperatures and recurrent bleaching pose the biggest threat, affecting even remote and well-managed reefs on global scales. We illustrate how coral bleaching is altering reefs by contrasting the dynamics of adjacent reef systems over more than two decades. Both reef systems sit near the edge of the northwest Australia’s continental shelf, have escaped chronic local pressures and are regularly affected by tropical storms and cyclones. The Scott reef system has experienced multiple bleaching events, including mass bleaching in 1998 and 2016, from which it is unlikely to fully recover. The Rowley Shoals has maintained a high cover and diversity of corals and has not yet been impacted by mass bleaching. We show how the dynamics of both reef systems were driven by a combination of local environment, exposure to disturbances and coral life history traits, and consider future shifts in community structure with ongoing climate change. We then demonstrate how applying knowledge of community dynamics at local scales can aid management strategies to slow the degradation of coral reefs until carbon emissions and other human impacts are properly managed.
MCR LTER: Coral Reef: Community Dynamics: Abundance and Species Richness of Fishes Associated with the Coral Porites rus 2000 thru 2011
These data describe the species richness and abundance as part of MCR LTER's reef fish monitoring program to track long-term patterns in species abundance and diversity. This study began in 2000 in the lagoons off of the north shore of the island of Moorea, French Polynesia and the dataset is updated annually. The abundance and life history stage (adults, juveniles or recruits) of all taxa of fishes associated with selected colonies (5-16 colonies per site) of the mound forming coral Porites rus are recorded at seven reef sites located along the north shore of Moorea. These sites are characterized by differences in water depth, distance to the fore reef and the number and types of neighboring corals. Counts are performed by a pair of divers using SCUBA and include semi-cryptic species. The collection of these data was suspended following the last survey conducted in July 2011 due to the extremely low abundance of live P. rus at these locations.
MCR LTER: Coral Reef: Bathymetry Grid for North Shore
These bathymetric data are a combined product of digitized SHOM nautical charts, SRTM30plus bathymetry, small boat surveys, and bathymetry derived from Worldview-2 satellite imagery. Satellite data were collected in collaboration with Le centre de L'Environment de Moorea (CRIOBE). Data products are (x,y,z) point data and images in Coordinate system: UTM zone 6S and Datum: WGS-84.
MCR LTER: Coral Reef: Water Column nutrient data in lagoons of Moorea, French Polynesia
Nutrients are important for ecosystem structure and community dynamics. To quantify fine-scale patterns of variation in water column nutrients in tropical lagoon ecosystems, nitrite + nitrate, phosphate, and silicate were quantified from water column samples collected in lagoons around Moorea, French Polynesia during April-May starting in 2021 using flow injection with an automated ion analyzer. Over the first three years, water column nitrite + nitrate and silicate were higher in bays and fringing reef habitats, and phosphate was higher in bays.
MCR LTER: Coral Reef: Growth and scaling of photosynthetic energy intake in Fungia concinna: Elahi & Edmunds 2007 JEMBE
For many marine invertebrates, the maximum size of an individual is influenced heavily by environmental factors and may be limited by energetic constraints. In this study, an energetic model developed originally for anemones was applied to the free-living scleractinian Fungia concinna (Verrill) from Moorea, French Polynesia to test the hypothesis that energetic constraints limit the size of this solitary coral. The modified model assumed that photosynthesis was the primary source of metabolic energy, and that metabolic costs were represented by aerobic respiration; these sources and sinks of energy were compared using daily energy budgets that were analyzed using double logarithmic regressions of energy against coral size. These data were published in Elahi, R. and P.J. Edmunds. 2007. Determinate growth and the scaling of photosynthetic energy intake in the solitary coral Fungia concinna (Verrill). Journal of Experimental Marine Biology and Ecology 349:183-193. and were part of the masters thesis of R. Elahi (2005). This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2018). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
MCR LTER: Coral Reef: Diadema predation and recruitment in Moorea, French Polynesia
These are field data from Moorea, French Polynesia regarding the population dynamics of Diadema savignyi. Data were collected during the austral winters in 2009 and 2010. Four datasets are provided: (1) recruitment data of Diadema savignyi over the course of ~9 weeks during the austral winter of 2010, (2) predation data of adult Diadema using a tethering experiment, (3) urchin abundance surveys for 2009 and 2010, and (4) a 9 week weekly survey of newly recruited Diadema (test diameter). These data are part of a PhD dissertation, "Herbivore Community Dynamics and Functional Compositions in Moorea, French Polynesia", 2014, published by ProQuest.
MCR LTER: Coral Reef: pH Time Series from Bottom-mounted SeaFET on the Fringing Reef, January-February 2011
Bottom-mounted instrumentation (SeaFET, Seabird thermistors) sampled for 6 weeks on the fringing reef of Moorea Island, French Polynesia at site LTER Fringe 1. Sampling began in January 2011. The instruments were secured to a cement piling at 3.3 meters depth and 0.7 meters above the sandy bottom. The SeaFET recorded voltages from a thermistor and pH electrodes at a 10-minute sampling interval. Discrete seawater samples were collected using a Niskin bottle during the deployment; pH, salinity, and total alkalinity of this sample were measured to calculate seawater pH (total scale) from raw SeaFET data as well as other carbonate chemistry parameters. The Seabird thermistors provided measures of seawater temperature at 10-minute sampling intervals. These data are published in Rivest, E.B. and G.E. Hofmann. 2014. Responses of the metabolism of the larvae of Pocillopora damicornis to ocean acidification and warming. PLoS ONE DOI:10.1371/journal.pone.0096172
MCR LTER: Coral Reef: Effects of Flow and Temperature on Growth and Photophysiology of Scleractinian Corals in Moorea, French Polynesia
To test for threshold effects in the response of coral physiology to increasing seawater flow, field and laboratory experiments were conducted in Moorea. First, the growth of juvenile massive Porites spp. and branching P. irregularis was compared among habitats differing in water motion. Growth of massive Porites spp. responded to flow in a pattern consistent with a threshold effect, whereas growth of P. irregularis increased linearly with flow. Second, a recirculating flume was used to test the effect of flow on photophysiology (ΔF⁄Fm'), effective photochemical efficiency) for massive Porites spp.; ΔF⁄Fm' displayed a threshold response at 23 cm/sec and 28 °C, but not at 31 °C. Finally, intra-colony variation in the response of ΔF⁄Fm' to flow and temperature was explored to evaluate the functional significance of colony shape in small corals. ΔF⁄Fm' on the top and upstream surfaces of massive Porites spp. responded with a threshold effect of flow at 28 °C (but not 31 °C), but ΔF⁄Fm' on downstream surfaces was unresponsive to flow. ΔF⁄Fm' for P. irregularis was less responsive to flow than for massive Porites spp., suggesting that the photophysiological response of corals to varying flow speeds may differ between species and morphologies. Together, these results emphasize that flow can have diverse effects on the physiology of corals, with the outcome depending on flow speed, temperature, location on the colony, and perhaps morphology. These data were published in The Biological Bulletin and were part of the masters thesis of W. Goldenheim (2011).
MCR LTER: Coral Reef: Coral Larval Metabolism in pH and Temperature Treatments
In this study, we explored plasticity of physiological responses of coral larvae from a reef in French Polynesia. The study was motivated by these questions: (1) what is the present-day exposure of Pocillopora damicornis to natural variability of pH and temperature on the natal reef?, (2) what is the response of P. damicornis larvae to conditions of decreased pH and warming, measured via two indices of metabolism - rates of oxygen consumption and citrate synthase activity?, and (3) are there differences in larval sensitivity to environmental change between cohorts that are released from adult colonies at different times? P. damicornis larvae were incubated for 6 hours in seawater containing combinations of CO2 concentration (450 and 950 μatm) and temperature (28 and 30C). Rates of larval oxygen consumption were higher at elevated temperatures. In contrast, high CO2 levels elicited depressed metabolic rates, most dramatically for larvae released later in the spawning period. Rates of citrate synthase, a rate-limiting enzyme in aerobic metabolism, suggested a biochemical limit for increasing oxidative capacity in a warming, acidifying ocean. Biological responses were also compared between cohorts, larvae released from adult colonies on the same day. The metabolic physiology of P. damicornis larvae varied significantly by day of release. Without adaptation or acclimatization, only a portion of naive P. damicornis larvae may have suitable metabolic phenotypes for maintaining function and fitness in an end-of-the century ocean. These data are published in Rivest, E.B. and G.E. Hofmann. 2014. Responses of the metabolism of the larvae of Pocillopora damicornis to ocean acidification and warming. PLoS ONE DOI:10.1371/journal.pone.0096172
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