http://lod.bco-dmo.org/id/dataset/954197
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2025-02-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbiome Host Bleaching and Mortality Data for coral hosts collected in Moorea, French Polynesia from Jul 2018 to Aug 2020
2025-03-19
publication
2025-03-19
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-05-22
publication
https://doi.org/10.26008/1912/bco-dmo.954197.1
Tom C. Adam
University of California-Santa Barbara
principalInvestigator
Deron Burkepile
University of California-Santa Barbara
principalInvestigator
Thomas J. Sharpton
Oregon State University
principalInvestigator
Rebecca Vega Thurber
Oregon State University
principalInvestigator
Hannah E. Epstein
Oregon State University
principalInvestigator
Emily R. Schmeltzer
Oregon State University
principalInvestigator
Kelly E. Speare
University of California-Santa Barbara
principalInvestigator
Alex Dmitry Vompe
Oregon State University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Vompe, A. D., Epstein, H. E., Speare, K. E., Schmeltzer, E. R., Adam, T. C., Burkepile, D., Sharpton, T. J., Vega Thurber, R. (2025) Microbiome Host Bleaching and Mortality Data for coral hosts collected in Moorea, French Polynesia from Jul 2018 to Aug 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-03-19 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.954197.1 [access date]
RECHARGE 2018 - 2020 Microbiome Host Bleaching and Mortality Data Dataset Description: Methods and Sampling: <p>The relevant methods as described in Vompe et al. (2023):</p>
<h3><strong>Site and in&nbsp;situ experiment</strong></h3>
<p>Our experimental study site is located on the northern forereef in Mo'orea, French Polynesia (S17° 28.386′ W149° 49.059′). Mo'orea is a tropical, volcanic high island in the Central South Pacific Ocean. A shallow, ~1 km wide lagoon and barrier reef surround the island. The forereef gradually slopes downwards toward the open ocean and is composed of coral spur and sand groove formations. At the inception of our experiment in August 2018, this reef was dominated by scleractinian corals with low abundance of fleshy macroalgae. Coral cover was 56.0 ± 1.0% (mean ± SE) and macroalgae cover was 0.8 ± 0.2% (mean ± SE).</p>
<p>At this site, we have an ongoing in&nbsp;situ experiment investigating tipping points of coral benthic and microbial ecology in response to nutrient enrichment and herbivore reduction, as in Adam et&nbsp;al.&nbsp;(2022). Briefly, our experimental platform is a factorial design at 10 m depth on the forereef, consisting of four herbivore exclosures (~1 m2&nbsp;each) placed over eight natural 30-m2&nbsp;reef plots. The plots are exposed to two levels of nutrient enrichment (four plots ambient/four plots enriched) and four levels of herbivory (exclosures with different size holes of 2.5 cm × 2.5 cm, 5.0 cm × 5.0 cm, 7.5 cm × 7.5 cm, or open top, with one exclosure of each herbivory condition at each plot). Nutrient enrichment was achieved in the plots via PVC tubes with Osmocote® (19-6-12, N-P-K) slow-release garden fertilizer. These tubes were wrapped in plastic mesh to contain the fertilizer. The nutrient enrichment tubes were replaced every 12–16 weeks, except for two periods during the COVID-19 pandemic when travel to Mo'orea was not possible. See&nbsp;Supplementary Methods (Vompe et al. 2023) for a full description of the experimental setup.</p>
<h3><strong>Coral sampling for microbiome analysis</strong></h3>
<p>To investigate how the microbiomes of different coral species respond to environmental stress, samples of&nbsp;<em>Acropora retusa</em>,&nbsp;<em>Porites lobata</em>&nbsp;species complex, and&nbsp;<em>Pocillopora</em>&nbsp;spp. were collected over 2 years (July 2018–August 2020), 3× a year, in March, July or August, and November. Corals in the&nbsp;<em>P. lobata</em>&nbsp;species complex will be referred to as&nbsp;<em>P. lobata</em>&nbsp;below for brevity. However, we acknowledge there may be cryptic diversity in our samples (Brown et&nbsp;al.,&nbsp;2021). A nonmetric multidimensional scaling (NMDS) ordination of Bray–Curtis distances between&nbsp;<em>P. lobata</em>&nbsp;sample microbiomes from July 2018 suggests that the possible presence of cryptic members of the&nbsp;<em>P. lobata</em>&nbsp;species complex in our dataset was unlikely to affect&nbsp;<em>P. lobata</em>&nbsp;microbiome variation, as there are no obvious sample microbiome composition clusters. The taxonomic name&nbsp;<em>Pocillopora</em>&nbsp;spp. is used for this study because&nbsp;<em>Pocillopora</em>&nbsp;species have high cryptic diversity (Johnston et&nbsp;al.,&nbsp;2022), which makes it difficult to visually delineate among species. We selected&nbsp;<em>Pocillopora</em>&nbsp;spp. specimens that had consistent phenotypes similar to those now defined as&nbsp;<em>Pocillopora meandrina</em>&nbsp;or Haplotype 8a as described in Figure&nbsp;1 of Johnston et&nbsp;al.&nbsp;(2022). Different coral species, even genotypes, tend to have distinct microbiomes (Bourne et&nbsp;al.,&nbsp;2016; Dunphy et&nbsp;al.,&nbsp;2019; Rosales et&nbsp;al.,&nbsp;2019). A NMDS ordination of Bray–Curtis distances between&nbsp;<em>Pocillopora</em>&nbsp;spp. sample microbiomes from July 2018 suggests that the possible presence of cryptic&nbsp;<em>Pocillopora</em>&nbsp;species in our dataset was unlikely to affect&nbsp;<em>Pocillopora</em>&nbsp;spp. microbiome variation, as there are no obvious sample microbiome composition clusters.</p>
<p>All colonies of each coral species appeared healthy when initially selected for microbiome sampling. Live tissue on these focal colonies was repeatedly sampled throughout the study regardless of subsequent visual phenotype, as long as live tissue remained. Live tissue was sampled at haphazardly chosen locations on the colonies at each time point. For&nbsp;<em>A. retusa</em>&nbsp;and&nbsp;<em>Pocillopora</em>&nbsp;spp., haphazardly chosen live branch tips were sampled. For&nbsp;<em>P. lobata</em>, live tissue was sampled from haphazardly chosen locations around the center of the colony. Coral samples were collected in July 2018, November 2018, March 2019, August 2019, November 2019, March 2020, and August 2020, covering a 28-month period. Additional coral colonies were sampled in November 2018, March 2019, and August 2019 to increase sample sizes and to account for initial focal colony mortality. Colonies of each species were also added to the dataset in March 2020 and August 2020 to restore sample size due to colony mortality. Bleaching and mortality data for coral colonies added to the microbiome sampling effort after the start of the experiment were collected retroactively. This was possible because these corals were already present in the exclosures and data could be collected from our photomosaic time series from before they were added to the microbiome sampling effort.</p>
<p>During each sampling event, coral fragments &lt;1 cm3&nbsp;were snipped from each of the focal colonies using bone cutters that were flame-sterilized with 95% ethanol at the surface. Corals were sampled between 08:00 and 14:00 h to help minimize diel microbiome variation. Fragments were immediately placed in sterile 207 mL Whirl-Paks. This volume of sample is sufficient to produce accurate microbiome data without significantly damaging the focal colony (Zaneveld et&nbsp;al.,&nbsp;2016). Upon surfacing, Whirl-paks were placed on ice and transported to shore (~15 min) then transferred to Qiagen DNeasy PowerSoil lysis matrix tubes, containing a guanidinium thiocyanate preservative, using 95% ethanol flame-sterilized forceps. Tubes were stored at −40°C prior to transport on Techni Ice to Oregon State University where they were stored at −80°C until further processing.</p>
<h3><strong>Coral bleaching and mortality data collection and analyses</strong></h3>
<p>At each microbiome sample collection point, except during March 2020, ~64 high-resolution digital photographs were taken of each plot using an Olympus TG camera. The digital photographs were then used to generate orthorectified photomosaics using Agisoft Metashape Professional Version 1.7.0 (AgiSoft PhotoScan Professional, 2024) software. These high-resolution photomosaics allowed identification of benthic organisms to a low taxonomic resolution. Percent cover of benthic organisms was quantified using 225 random points per m2 plot using CoralNet software (Lozada-Misa at al., 2017) in manual annotation mode. Photomosaics were also used to create digital maps of the plots in which each focal coral was identified and circled. For each focal colony, we recorded whether coral bleaching or mortality was present (prevalence) and, if so, estimated the percentage of the colony surface area (to the nearest 5%) that was bleached or dead (severity). Because corals undergo natural, seasonal variation in Symbiodiniaceae density that can affect their coloration, we defined bleached tissue only as tissue that had lost all pigmentation.</p>
<p>Mortality and bleaching were tracked for focal corals at all time points, except March 2020. Comparisons between average per colony bleaching and mortality levels were assessed across coral species and time points using one-way analysis of variance (ANOVA) with TukeyHSD (honestly significant difference)&nbsp;post hoc tests. In March 2020, samples for microbiome analysis were collected, but the photomosaics were not conducted due to the interrupted field season resulting from the COVID-19 shutdown. However, qualitative notes on bleaching and health status during coral microbiome sample collection were recorded for focal colonies. Additionally, coral bleaching and mortality data were gathered for&nbsp;<em>A. retusa</em>&nbsp;and&nbsp;<em>Pocillopora</em>&nbsp;spp. during the peak of the 2019 heatwave in May, as described above; however, these data were collected from individual photos of coral plots taken from the top, not photomosaics. In this study, we only analyzed correlations between microbiome dynamics and host bleaching and mortality for months during microbiome sample collection so that phenotypic and microbiome data for each coral colony could be paired.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023701 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023701
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023424 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023424
completed
Tom C. Adam
University of California-Santa Barbara
805-893-7625
UCSB Marine Science Institute Bldg 520 Rm 4002 FI 4L
Santa Barbara
CA
93106
United States
thomascadam@gmail.com
pointOfContact
Deron Burkepile
University of California-Santa Barbara
805-893-3067
Department of Ecology, Evolution, and Marine Biology
Santa Barbara
CA
93106
USA
dburkepile@ucsb.edu
pointOfContact
Thomas J. Sharpton
Oregon State University
thomas.sharpton@oregonstate.edu
pointOfContact
Rebecca Vega Thurber
Oregon State University
rvegathurber@gmail.com
pointOfContact
Hannah E. Epstein
Oregon State University
hannah.epstein@essex.ac.uk
pointOfContact
Emily R. Schmeltzer
Oregon State University
eschmeltzer@usgs.gov
pointOfContact
Kelly E. Speare
University of California-Santa Barbara
kellyspeare@gmail.com
pointOfContact
Alex Dmitry Vompe
Oregon State University
vompealex@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample
Date
Coral
Herbivory
Nutrients
Plot
Tag
Run
Colony
percent_bleached
percent_dead
bone cutters
Olympus TG camera
theme
None, User defined
sample identification
date
taxon
treatment
site
sample description
seq_descrip
bleach percentage
mortality
featureType
BCO-DMO Standard Parameters
bone cutter
Camera
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Tipping points in coral reefs and their associated microbiomes: interactive effects of herbivory, nutrient enrichment, and temperature
https://osprey.bco-dmo.org/project/850105
Collaborative Research: Tipping points in coral reefs and their associated microbiomes: interactive effects of herbivory, nutrient enrichment, and temperature
<p><em>NSF Award Abstract:</em><br />
Coral reefs are some of the most diverse, yet most imperiled, ecosystems on the planet. Global change has driven the decline of corals worldwide with many reefs now lacking corals and being overrun by macroalgae. This research examines the impacts of several factors of thermal stress, overfishing of important herbivorous fishes, and nutrient pollution on the health of corals and their ability to recover after large coral-killing disturbances. Importantly, the investigators address the impacts of global change on the coral microbiome, the microbes that associate with corals and impact coral health. The overarching hypothesis is that factors such as overfishing and nutrient pollution impact coral health via impacts to their microbes. This 6-year experiment on the coral reefs of Mo’orea, French Polynesia examines what levels of herbivory, mostly by parrotfishes and surgeonfishes, are needed to provide resistance and resilience of corals and their microbiomes when reefs are exposed to elevated nutrients and ocean temperatures. Notably, the team tests how local stressors (overfishing, nutrient pollution) potentially interact with global stressors (climate change and rising ocean temperatures) to impact coral reef health. This research may yield insight into how to manage local factors (reducing fishing, mitigating nutrient pollution) to help corals survive the global stress of climate change. The field experiment provides a realistic platform to test questions about how local management of fisheries can alter reef health and provides data about the recoverability of reefs should new water quality management be put into place. This interdisciplinary work trains a new generation of both marine ecologists and microbiologists, including one postdoctoral researcher, two graduate students, as well as numerous undergraduates. The main international outreach effort is to map the microbiome of the island of Mo’orea. Mo’orea is approximately 130 square-kilometers in area and has five major watersheds that transport sediment and nutrients to the nearshore coral reef ecosystems. Thus poor stewardship of these watersheds likely contributes to the local phase shifts currently occurring in several areas of the lagoon. Therefore the team has engaged the local community to help collect microbiome samples from 50 terrestrial, 50 stream, 25 coastal sites, and 25 offshore sites around the island. The sampling effort is generating an island-wide map of the microbial communities associated with the soils, streams, and coastal waters that can be linked to adjacent coral reef health - The Moorea Microbiome! As part of this outreach effort, the team also collaborates with filmmakers to make a trilingual (English, French, and Tahitian) film about the project to serve as local engagement and teaching tool to help educate school groups and different stakeholders about both the seen and unseen connections between land and sea on their island.</p>
<p>On the island of Mo’orea, French Polynesia, coral communities have exhibited strikingly different trajectories, with some reefs recovering from disturbances and others undergoing protracted coral decline, accompanied by an increase in macroalgae. This diversity in coral community dynamics makes Mo’orea an excellent model system for testing why some reefs are resilient and return to abundant coral while others are not and undergo persistent phase shifts to macroalgal dominance. This 6-year experiment will measure the dynamics of benthic communities, coral demography, and the coral microbiome across seasonal change in ocean temperature, allowing the team to (1) link changes in coral microbiomes (e.g., a rise in pathogenic bacteria) to the trajectories of coral decline or recovery and (2) link nutrients, herbivory, and temperature to phase shifts in both benthic communities and coral microbiomes. Importantly, the team is testing the resistance of phase shifts of benthic communities and coral microbiomes by measuring their changes after removing the nutrient enrichment treatment at the end of year 3 and tracking recovery of the system for 3 more years. Thus, this project begins to answer whether reef and microbial community phase shifts can be easily reversed once they occur. Many studies have focused on the factors that disassemble coral reef communities, but this is the first to examine how reef communities can be reassembled from the microbiome upwards.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
RECHARGE
largerWorkCitation
project
eng; USA
biota
oceans
-149.81765
-149.81765
-17.4731
-17.4731
2018-07-01
2020-08-31
Mo’orea, French Polynesia
0
BCO-DMO catalogue of parameters from Microbiome Host Bleaching and Mortality Data for coral hosts collected in Moorea, French Polynesia from Jul 2018 to Aug 2020
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/958160.rdf
Name: Sample
Units: unitless
Description: <p>Associated sample taken for microbiome analyses</p>
http://lod.bco-dmo.org/id/dataset-parameter/958161.rdf
Name: Date
Units: unitless
Description: <p>Month of data collection as YYYY-MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/958162.rdf
Name: Coral
Units: unitless
Description: <p>Code for the coral species evaluated (Aret = Acropora retusa, Plob = Porites lobata, Poc = Pocillopora)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958163.rdf
Name: Herbivory
Units: unitless
Description: <p>Consumer pressure level created by the experimental exclosures (1x1, 2x2, 3x3, or open)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958164.rdf
Name: Nutrients
Units: unitless
Description: <p>Enrichment condition in the exclosures (Nutrient or Ambient)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958165.rdf
Name: Plot
Units: unitless
Description: <p>Unique plot containing a set of coral exclosures (A1, A2, B3, B4, C1, C3, D2, or D4)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958166.rdf
Name: Tag
Units: unitless
Description: <p>Unique colony identifier (numeric)</p>
http://lod.bco-dmo.org/id/dataset-parameter/958167.rdf
Name: Run
Units: unitless
Description: <p>Associated microbiome analysis sequencing run</p>
http://lod.bco-dmo.org/id/dataset-parameter/958168.rdf
Name: Colony
Units: unitless
Description: <p>Unique coral colony ID in the photomosaics</p>
http://lod.bco-dmo.org/id/dataset-parameter/958169.rdf
Name: percent_bleached
Units: percent
Description: <p>Partial colony bleaching percentage</p>
http://lod.bco-dmo.org/id/dataset-parameter/958170.rdf
Name: percent_dead
Units: percent
Description: <p>Partial colony mortality percentage</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
50019
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/55dac593-7b92-4476-b669-1610dc6bc63d/content
download
https://doi.org/10.26008/1912/bco-dmo.954197.1
download
onLine
dataset
<p>The relevant methods as described in Vompe et al. (2023):</p>
<h3><strong>Site and in&nbsp;situ experiment</strong></h3>
<p>Our experimental study site is located on the northern forereef in Mo'orea, French Polynesia (S17° 28.386′ W149° 49.059′). Mo'orea is a tropical, volcanic high island in the Central South Pacific Ocean. A shallow, ~1 km wide lagoon and barrier reef surround the island. The forereef gradually slopes downwards toward the open ocean and is composed of coral spur and sand groove formations. At the inception of our experiment in August 2018, this reef was dominated by scleractinian corals with low abundance of fleshy macroalgae. Coral cover was 56.0 ± 1.0% (mean ± SE) and macroalgae cover was 0.8 ± 0.2% (mean ± SE).</p>
<p>At this site, we have an ongoing in&nbsp;situ experiment investigating tipping points of coral benthic and microbial ecology in response to nutrient enrichment and herbivore reduction, as in Adam et&nbsp;al.&nbsp;(2022). Briefly, our experimental platform is a factorial design at 10 m depth on the forereef, consisting of four herbivore exclosures (~1 m2&nbsp;each) placed over eight natural 30-m2&nbsp;reef plots. The plots are exposed to two levels of nutrient enrichment (four plots ambient/four plots enriched) and four levels of herbivory (exclosures with different size holes of 2.5 cm × 2.5 cm, 5.0 cm × 5.0 cm, 7.5 cm × 7.5 cm, or open top, with one exclosure of each herbivory condition at each plot). Nutrient enrichment was achieved in the plots via PVC tubes with Osmocote® (19-6-12, N-P-K) slow-release garden fertilizer. These tubes were wrapped in plastic mesh to contain the fertilizer. The nutrient enrichment tubes were replaced every 12–16 weeks, except for two periods during the COVID-19 pandemic when travel to Mo'orea was not possible. See&nbsp;Supplementary Methods (Vompe et al. 2023) for a full description of the experimental setup.</p>
<h3><strong>Coral sampling for microbiome analysis</strong></h3>
<p>To investigate how the microbiomes of different coral species respond to environmental stress, samples of&nbsp;<em>Acropora retusa</em>,&nbsp;<em>Porites lobata</em>&nbsp;species complex, and&nbsp;<em>Pocillopora</em>&nbsp;spp. were collected over 2 years (July 2018–August 2020), 3× a year, in March, July or August, and November. Corals in the&nbsp;<em>P. lobata</em>&nbsp;species complex will be referred to as&nbsp;<em>P. lobata</em>&nbsp;below for brevity. However, we acknowledge there may be cryptic diversity in our samples (Brown et&nbsp;al.,&nbsp;2021). A nonmetric multidimensional scaling (NMDS) ordination of Bray–Curtis distances between&nbsp;<em>P. lobata</em>&nbsp;sample microbiomes from July 2018 suggests that the possible presence of cryptic members of the&nbsp;<em>P. lobata</em>&nbsp;species complex in our dataset was unlikely to affect&nbsp;<em>P. lobata</em>&nbsp;microbiome variation, as there are no obvious sample microbiome composition clusters. The taxonomic name&nbsp;<em>Pocillopora</em>&nbsp;spp. is used for this study because&nbsp;<em>Pocillopora</em>&nbsp;species have high cryptic diversity (Johnston et&nbsp;al.,&nbsp;2022), which makes it difficult to visually delineate among species. We selected&nbsp;<em>Pocillopora</em>&nbsp;spp. specimens that had consistent phenotypes similar to those now defined as&nbsp;<em>Pocillopora meandrina</em>&nbsp;or Haplotype 8a as described in Figure&nbsp;1 of Johnston et&nbsp;al.&nbsp;(2022). Different coral species, even genotypes, tend to have distinct microbiomes (Bourne et&nbsp;al.,&nbsp;2016; Dunphy et&nbsp;al.,&nbsp;2019; Rosales et&nbsp;al.,&nbsp;2019). A NMDS ordination of Bray–Curtis distances between&nbsp;<em>Pocillopora</em>&nbsp;spp. sample microbiomes from July 2018 suggests that the possible presence of cryptic&nbsp;<em>Pocillopora</em>&nbsp;species in our dataset was unlikely to affect&nbsp;<em>Pocillopora</em>&nbsp;spp. microbiome variation, as there are no obvious sample microbiome composition clusters.</p>
<p>All colonies of each coral species appeared healthy when initially selected for microbiome sampling. Live tissue on these focal colonies was repeatedly sampled throughout the study regardless of subsequent visual phenotype, as long as live tissue remained. Live tissue was sampled at haphazardly chosen locations on the colonies at each time point. For&nbsp;<em>A. retusa</em>&nbsp;and&nbsp;<em>Pocillopora</em>&nbsp;spp., haphazardly chosen live branch tips were sampled. For&nbsp;<em>P. lobata</em>, live tissue was sampled from haphazardly chosen locations around the center of the colony. Coral samples were collected in July 2018, November 2018, March 2019, August 2019, November 2019, March 2020, and August 2020, covering a 28-month period. Additional coral colonies were sampled in November 2018, March 2019, and August 2019 to increase sample sizes and to account for initial focal colony mortality. Colonies of each species were also added to the dataset in March 2020 and August 2020 to restore sample size due to colony mortality. Bleaching and mortality data for coral colonies added to the microbiome sampling effort after the start of the experiment were collected retroactively. This was possible because these corals were already present in the exclosures and data could be collected from our photomosaic time series from before they were added to the microbiome sampling effort.</p>
<p>During each sampling event, coral fragments &lt;1 cm3&nbsp;were snipped from each of the focal colonies using bone cutters that were flame-sterilized with 95% ethanol at the surface. Corals were sampled between 08:00 and 14:00 h to help minimize diel microbiome variation. Fragments were immediately placed in sterile 207 mL Whirl-Paks. This volume of sample is sufficient to produce accurate microbiome data without significantly damaging the focal colony (Zaneveld et&nbsp;al.,&nbsp;2016). Upon surfacing, Whirl-paks were placed on ice and transported to shore (~15 min) then transferred to Qiagen DNeasy PowerSoil lysis matrix tubes, containing a guanidinium thiocyanate preservative, using 95% ethanol flame-sterilized forceps. Tubes were stored at −40°C prior to transport on Techni Ice to Oregon State University where they were stored at −80°C until further processing.</p>
<h3><strong>Coral bleaching and mortality data collection and analyses</strong></h3>
<p>At each microbiome sample collection point, except during March 2020, ~64 high-resolution digital photographs were taken of each plot using an Olympus TG camera. The digital photographs were then used to generate orthorectified photomosaics using Agisoft Metashape Professional Version 1.7.0 (AgiSoft PhotoScan Professional, 2024) software. These high-resolution photomosaics allowed identification of benthic organisms to a low taxonomic resolution. Percent cover of benthic organisms was quantified using 225 random points per m2 plot using CoralNet software (Lozada-Misa at al., 2017) in manual annotation mode. Photomosaics were also used to create digital maps of the plots in which each focal coral was identified and circled. For each focal colony, we recorded whether coral bleaching or mortality was present (prevalence) and, if so, estimated the percentage of the colony surface area (to the nearest 5%) that was bleached or dead (severity). Because corals undergo natural, seasonal variation in Symbiodiniaceae density that can affect their coloration, we defined bleached tissue only as tissue that had lost all pigmentation.</p>
<p>Mortality and bleaching were tracked for focal corals at all time points, except March 2020. Comparisons between average per colony bleaching and mortality levels were assessed across coral species and time points using one-way analysis of variance (ANOVA) with TukeyHSD (honestly significant difference)&nbsp;post hoc tests. In March 2020, samples for microbiome analysis were collected, but the photomosaics were not conducted due to the interrupted field season resulting from the COVID-19 shutdown. However, qualitative notes on bleaching and health status during coral microbiome sample collection were recorded for focal colonies. Additionally, coral bleaching and mortality data were gathered for&nbsp;<em>A. retusa</em>&nbsp;and&nbsp;<em>Pocillopora</em>&nbsp;spp. during the peak of the 2019 heatwave in May, as described above; however, these data were collected from individual photos of coral plots taken from the top, not photomosaics. In this study, we only analyzed correlations between microbiome dynamics and host bleaching and mortality for months during microbiome sample collection so that phenotypic and microbiome data for each coral colony could be paired.</p>
Specified by the Principal Investigator(s)
- Imported "bleaching mortality data.xlsx" into BCO-DMO system
- Converted dates to YYYY-MM format
- Changed "ID" field to Colony to prevent confusion with the sample ID
- Exported file as "954197_v1_host_bleaching_mort.csv"
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
bone cutters
bone cutters
PI Supplied Instrument Name: bone cutters PI Supplied Instrument Description:During each sampling event, coral fragments less than 1 cm3 were snipped from each of the focal colonies using bone cutters that were flame-sterilized with 95% ethanol at the surface. Instrument Name: bone cutter Instrument Short Name: Instrument Description: A bone cutter is a surgical instrument used to cut bones or coral fragments.
Olympus TG camera
Olympus TG camera
PI Supplied Instrument Name: Olympus TG camera PI Supplied Instrument Description:At each microbiome sample collection point, except during March 2020, ~64 high-resolution digital photographs were taken of each plot using an Olympus TG camera. Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/