http://lod.bco-dmo.org/id/dataset/960148
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
2025-05-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Coral physiologic response data from study of conspecific interactions between corals mediate the effect of submarine groundwater discharge on coral physiology in Mo'orea, French Polynesia in 2021
2025-05-05
publication
2025-05-05
revision
BCO-DMO Linked Data URI
2025-05-05
creation
http://lod.bco-dmo.org/id/dataset/960148
Nyssa Silbiger
California State University Northridge
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: Silbiger, N., Kerlin, J. R., Barnas, D. M. (2025) Coral physiologic response data from study of conspecific interactions between corals mediate the effect of submarine groundwater discharge on coral physiology in Mo'orea, French Polynesia in 2021. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-05-05 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/960148 [access date]
Methods and Sampling: <p><em>Porites rus </em>was chosen as the focal species for this experiment as it is common on tropical coral reefs worldwide, it is one of the dominant coral species at the study site, and it is often found in direct contact with both conspecific and heterospecific coral species. To test the hypothesis that coral neighbors mediate the effect of SGD on coral host and endosymbiont physiology, we placed living <em>P. rus </em>corals into four neighbor treatments placed at each of the 20 experimental locations, which included: 1) no neighbors (a solitary <em>P. rus</em>), 2) two dead skeletal fragments of <em>P. rus</em>, 3) two conspecific fragments (<em>P. rus</em> from a different colony than the focal colony), and 4) two heterospecific fragments (<em>Pocillopora acuta</em>) (Figure 1 in Kerlin et al. (2025)). The dead skeletal fragments acted as a non-coral control, but were not cleaned during the experiment; thus, algal growth mimicked the natural succession on dead coral.</p>
<p>Fragments (3 cm in height and 2 cm in width) of <em>P. rus </em>and <em>P. acuta </em>were collected haphazardly approximately 200-650 meters up current of the SGD seep in ambient seawater conditions. Six fragments were collected from each of 20 putative <em>P. rus </em>colonies (i.e., colonies at least 20-m apart from each other) for center (“focal”) coral fragments (n = 80), pre-deployment metabolism sampling fragments (n = 20), and pre-deployment endosymbiont measurement fragments (n = 20). All physiological measurements described below were conducted on these 120 <em>P. rus </em>fragments. Neighbor fragments of <em>P. rus </em>(n = 80)<em> </em>and <em>P. acuta </em>(n = 40)<em> </em>were collected from an additional 20 colonies of each species (two fragments from each colony). All coral fragments were collected using a chisel and hammer, placed in Ziploc bags underwater, and transported to Richard B. Gump South Pacific Research Station (“Gump Research Station”). At the Gump Research Station, fragments were placed in outside flow-through seawater tables and resized to 3 cm height by 2 cm width using bone cutters, as needed.&nbsp;All deployment<em> </em>fragments were randomly assigned to an experimental location, with the four focal fragments from the same putative colonies assigned to each neighbor treatment within an experimental location. The focal <em>P. rus </em>fragments were hot glued with Gorilla Glue Hot Glue&nbsp;to a nylon bolt connected to a 5-cm2 PVC plate. The neighbor fragments were hot glued to the PVC plate as close as possible to the focal fragment, with the neighbor corals in direct contact with the focal fragment. Four 5-cm<sup>2</sup> plates, one of each neighborhood treatment, were then attached to a larger 25-cm<sup>2</sup> PVC plate using bolts. Each plate was deployed at its experimental location for two weeks by attaching the plate to rebar epoxied to hard benthos and then collected to measure post-deployment response variables.&nbsp;</p>
<p>&nbsp; &nbsp; &nbsp; &nbsp; Endosymbiont density and chlorophyll <em>a</em> content were measured following methods within Becker and Silbiger (2020) at the start of the experiment from the pre-deployment fragments and at the end of the two-week SGD exposure period from each of the deployed center fragments. Coral fragments were frozen at -40°C immediately after collecting the pre-deployment corals or after respirometry measurements (described below) for the center corals. The fragments were thawed and airbrushed to remove tissue using an Iwata Eclipse HP-BCS airbrush (Oregon, USA) with 0.2 μm filtered seawater collected from the lagoon offshore of Gump Research Station. Coral tissue was transferred into falcon tubes, homogenized with a PRO Scientific Bio-Gen PRO200 Homogenizer (Oxford, Connecticut), and aliquoted into two 1 mL microcentrifuge tubes for endosymbiont density and chlorophyll <em>a</em> content. Samples were frozen again at -40°C until processing, and final tissue blastate volume was recorded for each coral fragment prior to aliquoting.</p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Samples aliquoted for chlorophyll <em>a</em> content were centrifuged (13,000 rpm for 3 minutes) (Labnet Spectrafuge 24D) and the supernatant was discarded to isolate the algal pellet. Acetone was added to extract the chlorophyll and the sample was vortexed and placed in 4°C in the dark for 24 hours. The samples were again vortexed and centrifuged at the same settings to separate out the debris and the extract was collected. The extract samples were processed on a Synergy HTX Multi-Mode Microplate Reader (BioTek, California, USA). Chlorophyll<em> a</em> content was calculated using equations from Jeffrey and Humphrey (1975) and normalized to surface area and endosymbiont density. E indicates the extinction at each wavelength (663 nm or 630 nm).</p>
<p>Chlorophyll <em>a</em> = 11.43(E<sub>663</sub>) – 0.64(E<sub>630</sub>)</p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Aliquot tissue slurries for endosymbiont density were sent to the University of Hawai’i at Mānoa and measured by flow cytometry following methodology from Fox et al. 2021. For each coral fragment, one sample of 150 μL was analyzed on a flow cytometer (Beckman Coulter CytoFLEX S) at a rate of 60 μL minute<sup>-1</sup> with excitation wavelengths of 375 nm, 405 nm, 488 nm, and 561 nm. Due to the uneven distribution of tissue blastate at the beginning of each run, the first 30 μL of each sample was removed from the analysis. Endosymbiont density was normalized to tissue blastate volume and coral surface area.</p>
<p>After removing the coral tissue using the airbrush methods described above, skeletal fragments were placed in a drying oven at 60°C to prepare for surface area measurements using the wax dipping method (Stimson and Kinzie 1991). First, a calibration curve (<em>r<sup>2</sup></em><sup> </sup>&gt; 0.9) of mass change of weight against surface area was created by using wooden dowels of known surface area. Coral fragments were then weighed, dipped in a 65°C Minerva paraffin wax bath (Georgia, USA) for two seconds, and then rotated in the air for two seconds at a constant rate. Fragments were set for 10 minutes to cool and then weighed again to obtain the mass change from wax dipping. The surface area of each coral fragment was calculated using the calibration curve obtained with wooden dowels.&nbsp;</p>
<p><em><strong>Coral metabolism</strong></em></p>
<p>All metabolism measurements were conducted following methods within Silbiger et al (2019). We first characterized the relationship between net photosynthesis and photon flux density, commonly known as a photosynthesis-irradiance (PI) curve, to ensure photosynthesis rates in the experimental fragments were measured at saturating light conditions. For the PI curve, additional fragments from six of the donor colonies were collected and placed in flow-through seawater tables for approximately 48 hours to recover from the collection process and handling. Fragments were then placed in 650 mL acrylic chambers full of seawater (collected from the flow-through system at the Gump Research Station and filtered to 5 µm) at ambient temperature (28.4℃) with no air bubbles, a stir bar, a fiber-optic oxygen probe (Presens Oxygen Dipping Probes DP-PSt7; calibrated by Presens; Regensburg, Germany), and a temperature probe (Presens Pt1000, Regensburg, Germany, precision:&nbsp; ± 0.1° C). The two probes were connected to a Presens Oxygen Meter [OXY-10 SMA (G2)], which measures oxygen percentage saturation and temperature (°C) at a frequency of 1 Hz. Oxygen concentrations (µmol L<sup>−1</sup>) were estimated from percent saturation accounting for a seawater salinity of 35 psu and standard oxygen solubility. Net photosynthesis was measured at eight light levels (µmol m<sup>−2</sup> s<sup>−1</sup>) using an LED light (Mars Aqua 300w LED Brand Epistar, LongGang District, ShenZhen, China) for 20 minutes at each light level: 0, 57, 144, 219, 300, 435, 573, and 809 µmol m<sup>−2</sup> s<sup>−1</sup>. Photosynthetically active radiation (PAR) was measured above each coral fragment with a cosine corrected MQ-510 Quantum Meter (error ± 2% and ± 5% at 45º and 75º from the light source, respectively; Apogee Instruments, Logan, UT, USA).</p>
<p>To calculate photosynthetic rates, the first two minutes of each run were removed to exclude the initial responses of the corals to changing light conditions and to ensure that the oxygen has reached equilibration within the chamber. The data were then thinned from every second to every 20 seconds to reduce noise in the data and to allow for processing of local linear regressions through the large dataset. Repeated local linear regressions were then used to calculate oxygen flux rates in the chambers using the R package <em>LoLinR.</em>&nbsp;Rates were normalized to the surface area (cm<sup>2</sup>) of each fragment after accounting for chamber seawater volume and blank control chamber rates. Saturating light (<em>I<sub>k</sub></em>) is the irradiance at which photosynthesis will no longer continue to increase.</p>
<p>Oxygen evolution was measured in all pre- and post-deployment coral fragments in 5 µm-filtered, ambient seawater (28℃) first in saturating light (approximately 590 µmol m<sup>−2</sup> s<sup>−1</sup>) for 20 minutes to measure the net photosynthesis and then in complete darkness for 20 minutes in the same seawater to measure light-adapted dark respiration. Ten chambers were measured at a time, with nine chambers having coral fragments and one chamber acting as a control seawater-only chamber to account for background fluctuation in oxygen. The volume of seawater in each chamber was measured with a graduated cylinder after each respirometry measurement. Metabolic rates were calculated using the same methods outlined above for the photosynthesis-irradiance curve. Gross photosynthesis was calculated by summing net photosynthesis and respiration rates (as absolute values).&nbsp;<br />
<br />
&nbsp;</p>
<p>Organism names and Life Sciences Identifiers (LSIDs):</p>
<p>Porites rus,urn:lsid:marinespecies.org:taxname:207231<br />
Pocillopora acuta, Pocillopora acuta,urn:lsid:marinespecies.org:taxname:759099</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924281 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924281
onGoing
Nyssa Silbiger
California State University Northridge
818-677-2901
HI
USA
silbiger@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
PlateID
FragmentID
Treatment
CCcm2_Final
CCcm2_Initial
CCED_Final
CCED_Initial
ED_Final
ED_Initial
GP_Final
GP_Initial
NP_Final
NP_Initial
R_Final
R_Initial
min_Temperature_C
max_Temperature_C
mean_Temperature_C
range_Temperature_C
min_NN_umolL
max_NN_umolL
mean_NN_umolL
range_NN_umolL
min_pH
max_pH
mean_pH
range_pH
min_Phosphate_umolL
max_Phosphate_umolL
mean_Phosphate_umolL
range_Phosphate_umolL
min_Salinity
max_Salinity
mean_Salinity
range_Salinity
Iwata Eclipse HP-BCS airbrush (Oregon, USA)
flow cytometer (Beckman Coulter CytoFLEX S)
PRO Scientific Bio-Gen PRO200 Homogenizer (Oxford, Connecticut)
MQ-510 Quantum Meter
fiber-optic oxygen probe (Presens Oxygen Dipping Probes DP-PSt7; calibrated by Presens; Regensburg, Germany)
Synergy HTX Multi-Mode Microplate Reader (BioTek, California, USA)
temperature probe (Presens Pt1000, Regensburg, Germany, precision: ± 0.1° C)
theme
None, User defined
sample identification
treatment
chlorophyll a
No BCO-DMO term
photosynthetic rate
respiration rate
water temperature at measurement depth
nitrate plus nitrite
pH
phosphate
salinity
featureType
BCO-DMO Standard Parameters
Airbrush
Flow Cytometer
Homogenizer
Light Meter
Oxygen Sensor
plate reader
Water Temperature Sensor
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.
RUI: Collaborative Research: Defining the biogeochemical context and ecological impacts of submarine groundwater discharge on coral reefs
https://osprey.bco-dmo.org/project/820158
RUI: Collaborative Research: Defining the biogeochemical context and ecological impacts of submarine groundwater discharge on coral reefs
<p><em>NSF Award Abstract:</em><br />
Submarine groundwater discharge (SGD) is the flow of water from land through the coastal seafloor into the nearby ocean. Approximately 13,000 cubic kilometers of groundwater is discharged into coastal environments every year, yet the effects of this fresh and often nutrient rich SGD are still poorly understood for coral reefs. This SGD input is driven by changes in precipitation, human land use, sea-level rise, tidal amplitude, and groundwater usage, many of which are rapidly changing with climate and human impacts. This project improves our understanding of SGD effects on coral reefs to better predict how both natural and human-induced changes will affect coastal ecosystem functioning in the future. Working in one of the most comprehensively studied coral reef ecosystems in the Pacific (Mo'orea, French Polynesia, home of the Mo'orea Coral Reef Ecosystem LTER); this project tests the influence of SGD on individual, community, and ecosystem-scale coral reef processes. Using mensurative studies, caging experiments, and a synthetic model, the investigators: 1) characterize SGD gradients and relate it to high resolution coral reef cover data, 2) determine how individual to ecosystem processes are influenced by SGD, and 3) develop a synthetic model to show how changes in SGD fluxes will alter reef ecosystem functioning. As SGD is a common feature on nearshore coral reefs worldwide, the results of this study have global implications for understanding the performance of coral reefs, which are essential economic, cultural, and scientific resources. This project is structured to provide training across multiple career levels, linking 13 undergraduate students, 2 graduate students, 2 senior personnel, 1 postdoctoral researcher, 1 female beginning lead investigator, and 2 senior co-investigators, with a focus on encouraging participation from underrepresented groups (e.g., through the Alaska Native and Native Hawaiian, Asian American and Native American Pacific Islander, and Hispanic-Serving Institutions of California State University Northridge, the University of Hawaiʻi at Mānoa, and California State University Long Beach). The investigators work with local K-12 students and teachers in Mo'orea and collaborate with an artist-in-residence to communicate science to the broader public through interactive and immersive art experiences in Mo'orea, Miami, and Los Angeles.</p>
<p>SGD is a natural and understudied feature of many nearshore coral reef ecosystems, which can contribute substantial changes to marine biogeochemistry, with impacts for coastal organisms such as reef-building corals, macroalgae, and bioeroders. SGD may play a key role in coral reef ecosystem functioning because it alters key physicochemical parameters (e.g., temperature, salinity, and nutrient and carbonate chemistry) that substantially affect both biotic and abiotic processes on coral reefs. This project (i) characterizes the spatial extent and biogeochemical signal of SGD in Mo'orea, French Polynesia, (ii) identifies how SGD influences microbial processes, benthic organism growth rates and physiology, species interactions between corals, macroalgae, and herbivores, and net ecosystem calcification and production rates, and (iii) quantitatively assesses how changes in SGD fluxes will alter reef biogeochemistry and ecosystem functioning through an integrative modelling effort. Specifically, the hydrogeological, biogeochemical, and ecological data collected in this study are synthesized in a Bayesian structural equation model. This project characterizes and quantifies how SGD directly and indirectly affects ecosystem functioning via changes in biogeochemistry and altered individual to ecosystem responses, thereby providing a better capacity to track and predict alterations in reef ecosystem function.</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>
Moorea SGD
largerWorkCitation
project
eng; USA
oceans
-149.903445
-149.896537
-17.5444
-17.538144
2021-08-03
2021-08-17
Mo'orea, French Polynesia
0
BCO-DMO catalogue of parameters from Coral physiologic response data from study of conspecific interactions between corals mediate the effect of submarine groundwater discharge on coral physiology in Mo'orea, French Polynesia in 2021
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/960540.rdf
Name: PlateID
Units: unitless
Description: <p>The plate that the corals were placed on in the field</p>
http://lod.bco-dmo.org/id/dataset-parameter/960541.rdf
Name: FragmentID
Units: unitless
Description: <p>The coral fragment ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/960542.rdf
Name: Treatment
Units: unitless
Description: <p>Coral species interaction treatment (Dead_Skelenton= Dead Coral Control; No_neighbor = Coral alone; Heterospecific = heterospecific Interaction; Conspecific = Conspecific interaction)</p>
http://lod.bco-dmo.org/id/dataset-parameter/960543.rdf
Name: CCcm2_Final
Units: micrograms per centimeter squared (ug/cm2)
Description: <p>Final chlorophyll Content (CCcm2). Measurement of coral biology at the end of two weeks.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960544.rdf
Name: CCcm2_Initial
Units: micrograms per centimeter squared (ug/cm2)
Description: <p>Chlorophyll Content (CCcm2). Measurement of coral biology before deplomyent.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960545.rdf
Name: CCED_Final
Units: micrograms per cell (ug/cell)
Description: <p>Final chlorophyll content per Endosymbiont (CCED). Measurement of coral biology at the end of two weeks.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960546.rdf
Name: CCED_Initial
Units: micrograms per cell (ug/cell)
Description: <p>Initial chlorophyll content per Endosymbiont (CCED). Measurement of coral biology before deplomyent.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960547.rdf
Name: ED_Final
Units: cells x 10^6/cm2
Description: <p>Final endosymbiont density (ED). Measurement of coral biology at the end of two weeks.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960548.rdf
Name: ED_Initial
Units: cells x 10^6/cm2
Description: <p>Initial endosymbiont density (ED). Measurement of coral biology before deplomyent.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960549.rdf
Name: GP_Final
Units: micromoles of O2 per square centimeter per hour (umol O2/ cm2 hr1)
Description: <p>Final gross photosynthesis (GP). Measurement of coral biology at the end of two weeks.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960550.rdf
Name: GP_Initial
Units: micromoles of O2 per square centimeter per hour (umol O2/ cm2 hr1)
Description: <p>Initial gross photosynthesis (GP). Measurement of coral biology at the end of two weeks.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960551.rdf
Name: NP_Final
Units: micromoles of O2 per square centimeter per hour (umol O2/ cm2 hr1)
Description: <p>Final net photosynthesis (NP). Measurement of coral biology at the end of two weeks.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960552.rdf
Name: NP_Initial
Units: micromoles of O2 per square centimeter per hour (umol O2/ cm2 hr1)
Description: <p>Initial net Photosynthesis (NP). Measurement of coral biology before deplomyent.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960553.rdf
Name: R_Final
Units: micromoles of O2 per square centimeter per hour (umol O2/ cm2 hr1)
Description: <p>Final respiration ("R"). Measurement of coral biology at the end of two weeks.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960554.rdf
Name: R_Initial
Units: micromoles of O2 per square centimeter per hour (umol O2/ cm2 hr1)
Description: <p>Initial respiration ("R"). Measurement of coral biology before deplomyent.</p>
http://lod.bco-dmo.org/id/dataset-parameter/960555.rdf
Name: min_Temperature_C
Units: Degrees Celcius
Description: <p>Minimum Temperature from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960556.rdf
Name: max_Temperature_C
Units: Degrees Celcius
Description: <p>Maximum Temperature from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960557.rdf
Name: mean_Temperature_C
Units: Degrees Celcius
Description: <p>Mean Temperature from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960558.rdf
Name: range_Temperature_C
Units: Degrees Celcius
Description: <p>Range Temperature from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960559.rdf
Name: min_NN_umolL
Units: micromolar (umol/L)
Description: <p>Minimum Nitrate+Nitrite (NO3_NO2) from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960560.rdf
Name: max_NN_umolL
Units: micromolar (umol/L)
Description: <p>Maximum Nitrate+Nitrite (NO3_NO2) from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960561.rdf
Name: mean_NN_umolL
Units: micromolar (umol/L)
Description: <p>Mean Nitrate+Nitrite (NO3_NO2) from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960562.rdf
Name: range_NN_umolL
Units: micromolar (umol/L)
Description: <p>Range Nitrate+Nitrite (NO3_NO2) from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960563.rdf
Name: min_pH
Units: pH units total scale
Description: <p>Minimum pH from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960564.rdf
Name: max_pH
Units: pH units total scale
Description: <p>Maximum pH from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960565.rdf
Name: mean_pH
Units: pH units total scale
Description: <p>Meani pH from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960566.rdf
Name: range_pH
Units: pH units total scale
Description: <p>Range pH from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960567.rdf
Name: min_Phosphate_umolL
Units: micromolar (umol/L)
Description: <p>Minimum Phosphate from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960568.rdf
Name: max_Phosphate_umolL
Units: micromolar (umol/L)
Description: <p>Maximum Phosphate from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960569.rdf
Name: mean_Phosphate_umolL
Units: micromolar (umol/L)
Description: <p>Mean Phosphate from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960570.rdf
Name: range_Phosphate_umolL
Units: micromolar (umol/L)
Description: <p>Range Phosphate from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960571.rdf
Name: min_Salinity
Units: Practical Salinity Units (PSU)
Description: <p>Minimum Salinity from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960572.rdf
Name: max_Salinity
Units: Practical Salinity Units (PSU)
Description: <p>Maximum Salinity from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960573.rdf
Name: mean_Salinity
Units: Practical Salinity Units (PSU)
Description: <p>Mean Salinity from Silbiger et al. 2023</p>
http://lod.bco-dmo.org/id/dataset-parameter/960574.rdf
Name: range_Salinity
Units: Practical Salinity Units (PSU)
Description: <p>Range Salinity from Silbiger et al. 2023</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
https://osprey.bco-dmo.org/dataset/960148/data/download
download
onLine
dataset
<p><em>Porites rus </em>was chosen as the focal species for this experiment as it is common on tropical coral reefs worldwide, it is one of the dominant coral species at the study site, and it is often found in direct contact with both conspecific and heterospecific coral species. To test the hypothesis that coral neighbors mediate the effect of SGD on coral host and endosymbiont physiology, we placed living <em>P. rus </em>corals into four neighbor treatments placed at each of the 20 experimental locations, which included: 1) no neighbors (a solitary <em>P. rus</em>), 2) two dead skeletal fragments of <em>P. rus</em>, 3) two conspecific fragments (<em>P. rus</em> from a different colony than the focal colony), and 4) two heterospecific fragments (<em>Pocillopora acuta</em>) (Figure 1 in Kerlin et al. (2025)). The dead skeletal fragments acted as a non-coral control, but were not cleaned during the experiment; thus, algal growth mimicked the natural succession on dead coral.</p>
<p>Fragments (3 cm in height and 2 cm in width) of <em>P. rus </em>and <em>P. acuta </em>were collected haphazardly approximately 200-650 meters up current of the SGD seep in ambient seawater conditions. Six fragments were collected from each of 20 putative <em>P. rus </em>colonies (i.e., colonies at least 20-m apart from each other) for center (“focal”) coral fragments (n = 80), pre-deployment metabolism sampling fragments (n = 20), and pre-deployment endosymbiont measurement fragments (n = 20). All physiological measurements described below were conducted on these 120 <em>P. rus </em>fragments. Neighbor fragments of <em>P. rus </em>(n = 80)<em> </em>and <em>P. acuta </em>(n = 40)<em> </em>were collected from an additional 20 colonies of each species (two fragments from each colony). All coral fragments were collected using a chisel and hammer, placed in Ziploc bags underwater, and transported to Richard B. Gump South Pacific Research Station (“Gump Research Station”). At the Gump Research Station, fragments were placed in outside flow-through seawater tables and resized to 3 cm height by 2 cm width using bone cutters, as needed.&nbsp;All deployment<em> </em>fragments were randomly assigned to an experimental location, with the four focal fragments from the same putative colonies assigned to each neighbor treatment within an experimental location. The focal <em>P. rus </em>fragments were hot glued with Gorilla Glue Hot Glue&nbsp;to a nylon bolt connected to a 5-cm2 PVC plate. The neighbor fragments were hot glued to the PVC plate as close as possible to the focal fragment, with the neighbor corals in direct contact with the focal fragment. Four 5-cm<sup>2</sup> plates, one of each neighborhood treatment, were then attached to a larger 25-cm<sup>2</sup> PVC plate using bolts. Each plate was deployed at its experimental location for two weeks by attaching the plate to rebar epoxied to hard benthos and then collected to measure post-deployment response variables.&nbsp;</p>
<p>&nbsp; &nbsp; &nbsp; &nbsp; Endosymbiont density and chlorophyll <em>a</em> content were measured following methods within Becker and Silbiger (2020) at the start of the experiment from the pre-deployment fragments and at the end of the two-week SGD exposure period from each of the deployed center fragments. Coral fragments were frozen at -40°C immediately after collecting the pre-deployment corals or after respirometry measurements (described below) for the center corals. The fragments were thawed and airbrushed to remove tissue using an Iwata Eclipse HP-BCS airbrush (Oregon, USA) with 0.2 μm filtered seawater collected from the lagoon offshore of Gump Research Station. Coral tissue was transferred into falcon tubes, homogenized with a PRO Scientific Bio-Gen PRO200 Homogenizer (Oxford, Connecticut), and aliquoted into two 1 mL microcentrifuge tubes for endosymbiont density and chlorophyll <em>a</em> content. Samples were frozen again at -40°C until processing, and final tissue blastate volume was recorded for each coral fragment prior to aliquoting.</p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Samples aliquoted for chlorophyll <em>a</em> content were centrifuged (13,000 rpm for 3 minutes) (Labnet Spectrafuge 24D) and the supernatant was discarded to isolate the algal pellet. Acetone was added to extract the chlorophyll and the sample was vortexed and placed in 4°C in the dark for 24 hours. The samples were again vortexed and centrifuged at the same settings to separate out the debris and the extract was collected. The extract samples were processed on a Synergy HTX Multi-Mode Microplate Reader (BioTek, California, USA). Chlorophyll<em> a</em> content was calculated using equations from Jeffrey and Humphrey (1975) and normalized to surface area and endosymbiont density. E indicates the extinction at each wavelength (663 nm or 630 nm).</p>
<p>Chlorophyll <em>a</em> = 11.43(E<sub>663</sub>) – 0.64(E<sub>630</sub>)</p>
<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Aliquot tissue slurries for endosymbiont density were sent to the University of Hawai’i at Mānoa and measured by flow cytometry following methodology from Fox et al. 2021. For each coral fragment, one sample of 150 μL was analyzed on a flow cytometer (Beckman Coulter CytoFLEX S) at a rate of 60 μL minute<sup>-1</sup> with excitation wavelengths of 375 nm, 405 nm, 488 nm, and 561 nm. Due to the uneven distribution of tissue blastate at the beginning of each run, the first 30 μL of each sample was removed from the analysis. Endosymbiont density was normalized to tissue blastate volume and coral surface area.</p>
<p>After removing the coral tissue using the airbrush methods described above, skeletal fragments were placed in a drying oven at 60°C to prepare for surface area measurements using the wax dipping method (Stimson and Kinzie 1991). First, a calibration curve (<em>r<sup>2</sup></em><sup> </sup>&gt; 0.9) of mass change of weight against surface area was created by using wooden dowels of known surface area. Coral fragments were then weighed, dipped in a 65°C Minerva paraffin wax bath (Georgia, USA) for two seconds, and then rotated in the air for two seconds at a constant rate. Fragments were set for 10 minutes to cool and then weighed again to obtain the mass change from wax dipping. The surface area of each coral fragment was calculated using the calibration curve obtained with wooden dowels.&nbsp;</p>
<p><em><strong>Coral metabolism</strong></em></p>
<p>All metabolism measurements were conducted following methods within Silbiger et al (2019). We first characterized the relationship between net photosynthesis and photon flux density, commonly known as a photosynthesis-irradiance (PI) curve, to ensure photosynthesis rates in the experimental fragments were measured at saturating light conditions. For the PI curve, additional fragments from six of the donor colonies were collected and placed in flow-through seawater tables for approximately 48 hours to recover from the collection process and handling. Fragments were then placed in 650 mL acrylic chambers full of seawater (collected from the flow-through system at the Gump Research Station and filtered to 5 µm) at ambient temperature (28.4℃) with no air bubbles, a stir bar, a fiber-optic oxygen probe (Presens Oxygen Dipping Probes DP-PSt7; calibrated by Presens; Regensburg, Germany), and a temperature probe (Presens Pt1000, Regensburg, Germany, precision:&nbsp; ± 0.1° C). The two probes were connected to a Presens Oxygen Meter [OXY-10 SMA (G2)], which measures oxygen percentage saturation and temperature (°C) at a frequency of 1 Hz. Oxygen concentrations (µmol L<sup>−1</sup>) were estimated from percent saturation accounting for a seawater salinity of 35 psu and standard oxygen solubility. Net photosynthesis was measured at eight light levels (µmol m<sup>−2</sup> s<sup>−1</sup>) using an LED light (Mars Aqua 300w LED Brand Epistar, LongGang District, ShenZhen, China) for 20 minutes at each light level: 0, 57, 144, 219, 300, 435, 573, and 809 µmol m<sup>−2</sup> s<sup>−1</sup>. Photosynthetically active radiation (PAR) was measured above each coral fragment with a cosine corrected MQ-510 Quantum Meter (error ± 2% and ± 5% at 45º and 75º from the light source, respectively; Apogee Instruments, Logan, UT, USA).</p>
<p>To calculate photosynthetic rates, the first two minutes of each run were removed to exclude the initial responses of the corals to changing light conditions and to ensure that the oxygen has reached equilibration within the chamber. The data were then thinned from every second to every 20 seconds to reduce noise in the data and to allow for processing of local linear regressions through the large dataset. Repeated local linear regressions were then used to calculate oxygen flux rates in the chambers using the R package <em>LoLinR.</em>&nbsp;Rates were normalized to the surface area (cm<sup>2</sup>) of each fragment after accounting for chamber seawater volume and blank control chamber rates. Saturating light (<em>I<sub>k</sub></em>) is the irradiance at which photosynthesis will no longer continue to increase.</p>
<p>Oxygen evolution was measured in all pre- and post-deployment coral fragments in 5 µm-filtered, ambient seawater (28℃) first in saturating light (approximately 590 µmol m<sup>−2</sup> s<sup>−1</sup>) for 20 minutes to measure the net photosynthesis and then in complete darkness for 20 minutes in the same seawater to measure light-adapted dark respiration. Ten chambers were measured at a time, with nine chambers having coral fragments and one chamber acting as a control seawater-only chamber to account for background fluctuation in oxygen. The volume of seawater in each chamber was measured with a graduated cylinder after each respirometry measurement. Metabolic rates were calculated using the same methods outlined above for the photosynthesis-irradiance curve. Gross photosynthesis was calculated by summing net photosynthesis and respiration rates (as absolute values).&nbsp;<br />
<br />
&nbsp;</p>
<p>Organism names and Life Sciences Identifiers (LSIDs):</p>
<p>Porites rus,urn:lsid:marinespecies.org:taxname:207231<br />
Pocillopora acuta, Pocillopora acuta,urn:lsid:marinespecies.org:taxname:759099</p>
Specified by the Principal Investigator(s)
<p>All code and data processing is available on Github at&nbsp;https://github.com/njsilbiger/Neighborhood_effects_and_SGD (DOI for archival copy of&nbsp;V1.0, doi:&nbsp;10.5281/ZENODO.14262764)</p>
Specified by the Principal Investigator(s)
* Table within submitted file "Kerlin et al coral data.csv" was imported into the BCO-DMO data system for this dataset. Values "NA" imported as missing data values. Table will appear as Data File: 960148_v1_sgd-response-conspecific-coral-physiology.csv (along with other download format options).
* BCO-DMO requires each column contain an individual Response_measurement (and units consistent per column). In order to meet this requirement, the BCO-DMO data manager transformed the data table and worked with the data contributor to review and make any additional changes needed. The original data format "Kerlin et al coral data.csv" provided to BCO-DMO was included as supplemental file 960148_v1_coral-phys-alternate-format.csv
Transformation notes (going from the originally provided file "Kerlin et al coral data.csv" to primary data table format 960148_v1_sgd-response-conspecific-coral-physiology.csv) :
* A table pivot was performed (transforming columns Response_measure, Initial, Final) to separate sets of columns per rate type (CCED_Initial,CCED_Final, etc)(See Parameters section for column descriptions).
* To do this tables were separated by filtering on rate_type (CCED,CCcm2,ED,GP,NP,R). Then joined to combine all columns using full joins on unique keys .
** "FragmentID" was unique per Rate_measure, Initial, Final so it was used as the join key.
Missing Data Identifiers:
* In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
* Date converted to ISO 8601 format
* Organism names in this dataset were matched to Life Science Identifiers (LSIDs) using the World Register of Marine Species (WoRMS) on 2025-05-06.
Specified by BCO-DMO Data Managers
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Iwata Eclipse HP-BCS airbrush (Oregon, USA)
Iwata Eclipse HP-BCS airbrush (Oregon, USA)
PI Supplied Instrument Name: Iwata Eclipse HP-BCS airbrush (Oregon, USA) PI Supplied Instrument Description:Airbrush corals with Iwata Eclipse HP-BCS airbrush (Oregon, USA) and homogenize coral slurries with PRO Scientific Bio-Gen PRO200 Homogenizer (Oxford, Connecticut). Instrument Name: Airbrush Instrument Short Name:Airbrush Instrument Description: Device for spraying liquid by means of compressed air.
flow cytometer (Beckman Coulter CytoFLEX S)
flow cytometer (Beckman Coulter CytoFLEX S)
PI Supplied Instrument Name: flow cytometer (Beckman Coulter CytoFLEX S) PI Supplied Instrument Description:Symbiont counts were collected on a flow cytometer (Beckman Coulter CytoFLEX S). Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
PRO Scientific Bio-Gen PRO200 Homogenizer (Oxford, Connecticut)
PRO Scientific Bio-Gen PRO200 Homogenizer (Oxford, Connecticut)
PI Supplied Instrument Name: PRO Scientific Bio-Gen PRO200 Homogenizer (Oxford, Connecticut) PI Supplied Instrument Description:Airbrush corals with Iwata Eclipse HP-BCS airbrush (Oregon, USA) and homogenize coral slurries with PRO Scientific Bio-Gen PRO200 Homogenizer (Oxford, Connecticut). Instrument Name: Homogenizer Instrument Short Name:Homogenizer Instrument Description: A homogenizer is a piece of laboratory equipment used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
MQ-510 Quantum Meter
MQ-510 Quantum Meter
PI Supplied Instrument Name: MQ-510 Quantum Meter PI Supplied Instrument Description:PAR was measured with MQ-510 Quantum Meter (error ± 2% and ± 5% at 45º and 75º from the light source, respectively; Apogee Instruments, Logan, UT, USA). Instrument Name: Light Meter Instrument Short Name:Light Meter Instrument Description: Light meters are instruments that measure light intensity. Common units of measure for light intensity are umol/m2/s or uE/m2/s (micromoles per meter squared per second or microEinsteins per meter squared per second). (example: LI-COR 250A)
fiber-optic oxygen probe (Presens Oxygen Dipping Probes DP-PSt7; calibrated by Presens; Regensburg, Germany)
fiber-optic oxygen probe (Presens Oxygen Dipping Probes DP-PSt7; calibrated by Presens; Regensburg, Germany)
PI Supplied Instrument Name: fiber-optic oxygen probe (Presens Oxygen Dipping Probes DP-PSt7; calibrated by Presens; Regensburg, Germany) PI Supplied Instrument Description:Oxygen and temperature in chambers was measured on fiber-optic oxygen probe (Presens Oxygen Dipping Probes DP-PSt7; calibrated by Presens; Regensburg, Germany), and a temperature probe (Presens Pt1000, Regensburg, Germany, precision: ± 0.1° C). Instrument Name: Oxygen Sensor Instrument Short Name:Dissolved Oxygen Sensor Instrument Description: An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed
Synergy HTX Multi-Mode Microplate Reader (BioTek, California, USA)
Synergy HTX Multi-Mode Microplate Reader (BioTek, California, USA)
PI Supplied Instrument Name: Synergy HTX Multi-Mode Microplate Reader (BioTek, California, USA) PI Supplied Instrument Description:Chlorophyll data was processed on a Synergy HTX Multi-Mode Microplate Reader (BioTek, California, USA) Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
temperature probe (Presens Pt1000, Regensburg, Germany, precision: ± 0.1° C)
temperature probe (Presens Pt1000, Regensburg, Germany, precision: ± 0.1° C)
PI Supplied Instrument Name: temperature probe (Presens Pt1000, Regensburg, Germany, precision: ± 0.1° C) PI Supplied Instrument Description:Oxygen and temperature in chambers was measured on fiber-optic oxygen probe (Presens Oxygen Dipping Probes DP-PSt7; calibrated by Presens; Regensburg, Germany), and a temperature probe (Presens Pt1000, Regensburg, Germany, precision: ± 0.1° C). Instrument Name: Water Temperature Sensor Instrument Short Name:Water Temp Sensor Instrument Description: General term for an instrument that measures the temperature of the water with which it is in contact (thermometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/134/