http://lod.bco-dmo.org/id/dataset/960136
eng; USA
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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
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2025-05-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Coral reef metabolism data from in-situ experiments with submarine groundwater discharge (SGD) exposure treatments conducted in Mo'orea, French Polynesia in 2022 and 2023
2025-05-05
publication
2025-05-05
revision
BCO-DMO Linked Data URI
2025-05-05
creation
http://lod.bco-dmo.org/id/dataset/960136
Nyssa Silbiger
California State University Northridge
principalInvestigator
Danielle M Barnas
California State University Northridge
principalInvestigator
Maya Zeff
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., Barnas, D. M., Zeff, M. (2025) Coral reef metabolism data from in-situ experiments with submarine groundwater discharge (SGD) exposure treatments conducted in Mo'orea, French Polynesia in 2022 and 2023. 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/960136 [access date]
Dataset Description: <p>See the "Related Datasets" section or the project page for other data collected as part of this study.</p>
<p>See the Project Page for more data collected as part of the project.</p> Methods and Sampling: <p>Detailed methods are outlined in Barnas et al. (2025) and summarized here.&nbsp;</p>
<p>&nbsp;(a) Study site and experimental design .&nbsp; &nbsp; We created two SGD exposure treatments based on environmental data from Silbiger et al. (2023)&nbsp; and two SGD assemblage treatments based on benthic community surveys from naturally high or&nbsp; low SGD influence to test the effect of SGD on organismal growth and community metabolism (i.e., photosynthesis, respiration, and calcification). Specifically, we subjected multiple reef taxa&nbsp; in curated assemblages to high or low SGD exposure for six weeks during the rainy season,&nbsp; when SGD fluxes are highest. Ten replicate assemblages of the two community types were placed in each exposure treatment (two assemblage treatments ✕ two exposure treatments) for a&nbsp; total of 40 assemblages. This is an in situ experiment, with organisms soaking at the exposure sites for nearly 2 months, and then moved to the lab to measure community metabolism.</p>
<p>(b) SGD Exposure Treatments.&nbsp; &nbsp;Due to the predictable flow regime along the fringing reef, we selected two experimental locations: one 50 m upstream (low SGD&nbsp;exposure) and one 27 m downstream (high SGD&nbsp; &nbsp;exposure) of the known SGD seepage point. These sites were chosen to minimize&nbsp;differences in flow, sedimentation, and light regime, while also keeping distance offshore&nbsp; constant (18 m).&nbsp;</p>
<p>&nbsp;(c) SGD Assemblage Treatments.&nbsp; Benthic community composition surveys were used to determine the species identities of benthic communities to deploy at high and&nbsp;low SGD exposure locations. We selected eight total survey&nbsp; sites, four exhibiting highest and four exhibiting lowest environmental SGD exposure based on prior data.&nbsp;</p>
<p>Benthic communities were surveyed via snorkeling at each site from June-July&nbsp; &nbsp;2022 to estimate species composition of coral, macroalgae, sponges, corallimorphs,&nbsp;anemones,&nbsp;and cyanobacteria. Composition was assessed within 2 m ✕ 2 m plots using a uniform point-&nbsp; &nbsp;count method with 200 evenly distributed points at each site&nbsp;(4 m2 per site, 16 m2 total area per&nbsp; &nbsp;SGD exposure type). Organisms at each point were identified to species level when possible, or the lowest possible taxonomic unit.&nbsp;We determined the top eight most abundant benthic species from each environmental exposure area for our assemblage treatments). While species richness was&nbsp;consistent across assemblage types (n=8 species, abundance=1&nbsp; &nbsp;per species).</p>
<p>(d) Organism collection and deployment.&nbsp; &nbsp;A total of 320 organisms across all treatments (n = 80 individuals per treatment) were collected for this experiment. All species were hand collected by snorkel on the fringing reef at least 100m upcurrent of the known seepage point to avoid confounding effects of SGD on life history. To allow for direct comparison of individual response to SGD, replicate individuals of non-colonial&nbsp; organisms were collected in pairs to place one individual in each exposure treatment. Similarly,&nbsp; &nbsp;colonial species in each assemblage type were fragmented into two organisms, such that one organism was placed in high SGD exposure and one was placed in low SGD exposure. Both assemblage types therefore experienced each SGD exposure condition before being tested for&nbsp; changes in community metabolism (NEC and NEP). Replicates of species pairs or colonies were&nbsp; collected at least three meters away from each other to minimize genotypic duplication across&nbsp; assemblages in each exposure treatment.&nbsp;</p>
<p>(e) All organisms were transported submerged to the Richard B. Gump South Pacific Research&nbsp; Station on Mo'orea and held in flow-through water tables. A supply of&nbsp;fresh&nbsp; seawater was&nbsp; continuously pumped from nearshore to provide an ambient coastal environment similar to the collection site, and the water was supplementally&nbsp;oxygenated using air bubblers (Tetra Whisper&nbsp; Air Pump, Virginia, USA). Water tables were cleaned daily to remove algae and avoid&nbsp; &nbsp;settlement. Organisms were&nbsp;fragmented and cleaned to remove excessive epiphytes and epifauna. We used forceps to remove epiphytes and epifauna from organisms and additionally&nbsp;removed&nbsp;epifauna from interstitial spaces of L. kotschyanum by submerging fragments in&nbsp; freshwater for up to 15 seconds, following protocols from Glanz (2021). Species with&nbsp;hard&nbsp; substrate (Scleractinia: P. acuta, P. rus, M. grisea; crustose coralline algae [CCA]: L, kotschyanum; Corallimorpharia: D. nummiforme; sponge: Porifera unk) were&nbsp;attached to wide&nbsp; flat-headed bolts with hot super glue (Gorilla Hot Glue, The Gorilla Glue Company, Ohio).&nbsp; Species not attached to the bolts (macroalgae: D.&nbsp;bartayresiana, T. ornata, H. opuntia, V.&nbsp; fastigiata; sponge: L. chondrodes) were wrapped loosely in clear nylon netting to allow sufficient space and light for growth (8 mm ✕&nbsp; 8 mm mesh size).</p>
<p>(f) Organisms were deployed in either the high or low exposure location in situ for 5-6 weeks from February 8 - March 24, 2023. Species were held in situ in a metal cage (13&nbsp;mm x 13 mm mesh&nbsp; size) at each exposure site to reduce grazing and predation. Cages were fastened atop cinder&nbsp; block platforms raised above the benthos to 0.6 m&nbsp;depth at each site. Bolt-mounted species were fastened to the cage along the mesh base with washers and nuts, while netted organisms were attached to the base&nbsp;with zip ties. Cages were consistently cleaned and checked for overall health condition of species throughout deployment.</p>
<p>(g) Community metabolism.&nbsp; &nbsp;After deployment at high and low SGD locations, we formed complete assemblages based on the species in Table 1 from Barnas et al. (2025) through random selection of healthy individuals from each species group. We measured four biomass-normalized community metabolism rates for each of the 40 assemblages: dark respiration (Rd), net photosynthesis (NP), gross photosynthesis (GP), and net calcification (NC). Community respiration and net photosynthesis were calculated from oxygen evolution, and community&nbsp; calcification was estimated using the total alkalinity anomaly technique in closed-system chambers (6 L) with ambient filtered seawater (20 µm-rated sand filter). For each community metabolism trial, we placed four high SGD assemblages and four low SGD assemblages (two&nbsp; from high SGD exposure and two from low SGD exposure per assemblage type) each in&nbsp; &nbsp;individual 6 L water-tight transparent chambers (Rubbermaid, Georgia; n=8 chambers) with a&nbsp; circulation pump (Aquaneat Submersible Pump, 80 GPH), fiber optic oxygen sensor (PSt7,&nbsp; &nbsp; accuracy ± 0.05 % O2) and temperature sensor (Pt100, accuracy ± 1.0 °C)&nbsp; (PreSensPrecision&nbsp; &nbsp;Sensing GmbH, Germany), and overhead light source (Prime 16 HD LED Reef Light,&nbsp; Aqua Illumination) equipped for each chamber. A ninth chamber without organisms was also&nbsp; included as a control to account for any background changes in oxygen or total alkalinity from&nbsp; the seawater.</p>
<p>NP and NC were measured simultaneously for 60 minutes under saturating light conditions (Ik =&nbsp; 440 μmol photons m-2 s-1). Saturating light was determined from photosynthesis-irradiance curves from prior coral and algal studies conducted at fringing reef sites at the same depth in Mo’orea (Edmunds et al. 2012; Becker and&nbsp; Silbiger 2020; Perng 2019). Notably, the organisms in the current study experienced in situ light conditions ranging from 0 to 1800 µmol photons m-2 s-1 (miniPAR, accuracy ± 5% in air traceable to NIST, Precision Measurement Engineering, California). Given the high light intensity experienced in situ, we do not anticipate photo- inhibition of communities at 440 µmol photons m-2 s-1. After refilling the chambers with oxygenated filtered seawater, chambers were&nbsp; &nbsp; then run in darkness for 20 minutes to measure Rd. Oxygen concentration (µmol/L) and&nbsp; &nbsp;temperature (℃) were recorded at a frequency of 1 Hz (Oxy10 St, PreSens Measurement Studio2, PreSens Precision Sensing GmbH, Germany).&nbsp; &nbsp;Rates of oxygen evolution (net photosynthesis [NP]) and uptake (Rd) were calculated by repeated&nbsp; local linear regressions used to obtain the best-fit linear regression through a bootstrapping&nbsp; &nbsp;technique with the package LoLinR in R, corrected for chamber volume, blank rates,&nbsp; and normalized to the&nbsp; total organic biomass of each assemblage. We calculated gross&nbsp; photosynthesis (GP) of assemblages by:&nbsp; GP&nbsp; =&nbsp; NP + |Rd|, where the absolute value of Rd is added to&nbsp; NP to account for O2 consumption.&nbsp; To measure NC, water samples were collected before and after each 60 min light trial in triple-&nbsp; &nbsp;rinsed 120 mL acid- washed Nalgene bottles. We measured AT using the same methods detailed above. Net calcification (NC, µmol CaCO3 g-1 h-1) was calculated by the total alkalinity anomaly technique using the following equation: NC = [(ΔAT sample - ΔAT blank) X V X ρSW]\(2 X t X AFWD).</p>
<p>&nbsp;ΔAT (µmol kg-1) is the change in AT from initial to post-trial water samples, with ΔAT blank as the control chamber, V is total water volume in each chamber (mL), ρSW is the average density of seawater (1.023 g cm-3), t relates to total incubation time of assemblages in their respective&nbsp;chambers (h-1), and AFDW is the total ash-free dry weight of each assemblage relating to total&nbsp;organic biomass (g-1). An individual’s AFDW was calculated by drying and ashing the organisms, and AFDW of each assemblage was obtained through the sum of its respective set of organisms.<br />
<br />
Organism names:</p>
<p>Name used in metadata, Full SciName, LSID<br />
L. kotschyanum, Lithophyllum kotschyanum,urn:lsid:marinespecies.org:taxname:213889<br />
P. acuta,Pocillopora acuta,urn:lsid:marinespecies.org:taxname:759099<br />
P. rus,Porites rus,urn:lsid:marinespecies.org:taxname:207231<br />
M. grisea,Montipora grisea,urn:lsid:marinespecies.org:taxname:287709<br />
Corallimorpharia,Corallimorpharia,urn:lsid:marinespecies.org:taxname:1362<br />
D. nummiforme,Discosoma nummiforme, urn:lsid:marinespecies.org:taxname:411031<br />
Porifera unk, Porifera spp.,&nbsp; urn:lsid:marinespecies.org:taxname:558</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
Danielle M Barnas
California State University Northridge
dmbarnas@hawaii.edu
pointOfContact
Maya Zeff
California State University Northridge
mayazeff@ucsc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
SampleID
Assemblage_Treat
Environmental_Treat
Date
Location
NC_Rate
NP_Rate
R_Rate
GP_Rate
Presens Oxy-19
theme
None, User defined
sample identification
treatment
date
site
calcification
photosynthetic rate
respiration rate
featureType
BCO-DMO Standard Parameters
Oxygen 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
2022-06-01
2023-04-01
Mo'orea, French Polynesia
0
BCO-DMO catalogue of parameters from Coral reef metabolism data from in-situ experiments with submarine groundwater discharge (SGD) exposure treatments conducted in Mo'orea, French Polynesia in 2022 and 2023
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/960519.rdf
Name: SampleID
Units: unitless
Description: <p>Unique Sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/960520.rdf
Name: Assemblage_Treat
Units: unitless
Description: <p>Assemblage Treatment (High = assemblage from High SGD; LOW = Assemblage from low SGD site)</p>
http://lod.bco-dmo.org/id/dataset-parameter/960521.rdf
Name: Environmental_Treat
Units: unitless
Description: <p>Environment Treatment</p>
http://lod.bco-dmo.org/id/dataset-parameter/960522.rdf
Name: Date
Units: unitless
Description: <p>Date of metabolism measurement</p>
http://lod.bco-dmo.org/id/dataset-parameter/960523.rdf
Name: Location
Units: unitless
Description: <p>Location of experimental Site</p>
http://lod.bco-dmo.org/id/dataset-parameter/960524.rdf
Name: NC_Rate
Units: mmol CaCO3 per g per hour
Description: <p>net calcification</p>
http://lod.bco-dmo.org/id/dataset-parameter/960525.rdf
Name: NP_Rate
Units: O2 per g per hour
Description: <p>net photosynthesis</p>
http://lod.bco-dmo.org/id/dataset-parameter/960526.rdf
Name: R_Rate
Units: O2 per g per hour
Description: <p>Respiration</p>
http://lod.bco-dmo.org/id/dataset-parameter/960527.rdf
Name: GP_Rate
Units: O2 per g per hour
Description: <p>gross photosynthesis</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/960136/data/download
download
onLine
dataset
<p>Detailed methods are outlined in Barnas et al. (2025) and summarized here.&nbsp;</p>
<p>&nbsp;(a) Study site and experimental design .&nbsp; &nbsp; We created two SGD exposure treatments based on environmental data from Silbiger et al. (2023)&nbsp; and two SGD assemblage treatments based on benthic community surveys from naturally high or&nbsp; low SGD influence to test the effect of SGD on organismal growth and community metabolism (i.e., photosynthesis, respiration, and calcification). Specifically, we subjected multiple reef taxa&nbsp; in curated assemblages to high or low SGD exposure for six weeks during the rainy season,&nbsp; when SGD fluxes are highest. Ten replicate assemblages of the two community types were placed in each exposure treatment (two assemblage treatments ✕ two exposure treatments) for a&nbsp; total of 40 assemblages. This is an in situ experiment, with organisms soaking at the exposure sites for nearly 2 months, and then moved to the lab to measure community metabolism.</p>
<p>(b) SGD Exposure Treatments.&nbsp; &nbsp;Due to the predictable flow regime along the fringing reef, we selected two experimental locations: one 50 m upstream (low SGD&nbsp;exposure) and one 27 m downstream (high SGD&nbsp; &nbsp;exposure) of the known SGD seepage point. These sites were chosen to minimize&nbsp;differences in flow, sedimentation, and light regime, while also keeping distance offshore&nbsp; constant (18 m).&nbsp;</p>
<p>&nbsp;(c) SGD Assemblage Treatments.&nbsp; Benthic community composition surveys were used to determine the species identities of benthic communities to deploy at high and&nbsp;low SGD exposure locations. We selected eight total survey&nbsp; sites, four exhibiting highest and four exhibiting lowest environmental SGD exposure based on prior data.&nbsp;</p>
<p>Benthic communities were surveyed via snorkeling at each site from June-July&nbsp; &nbsp;2022 to estimate species composition of coral, macroalgae, sponges, corallimorphs,&nbsp;anemones,&nbsp;and cyanobacteria. Composition was assessed within 2 m ✕ 2 m plots using a uniform point-&nbsp; &nbsp;count method with 200 evenly distributed points at each site&nbsp;(4 m2 per site, 16 m2 total area per&nbsp; &nbsp;SGD exposure type). Organisms at each point were identified to species level when possible, or the lowest possible taxonomic unit.&nbsp;We determined the top eight most abundant benthic species from each environmental exposure area for our assemblage treatments). While species richness was&nbsp;consistent across assemblage types (n=8 species, abundance=1&nbsp; &nbsp;per species).</p>
<p>(d) Organism collection and deployment.&nbsp; &nbsp;A total of 320 organisms across all treatments (n = 80 individuals per treatment) were collected for this experiment. All species were hand collected by snorkel on the fringing reef at least 100m upcurrent of the known seepage point to avoid confounding effects of SGD on life history. To allow for direct comparison of individual response to SGD, replicate individuals of non-colonial&nbsp; organisms were collected in pairs to place one individual in each exposure treatment. Similarly,&nbsp; &nbsp;colonial species in each assemblage type were fragmented into two organisms, such that one organism was placed in high SGD exposure and one was placed in low SGD exposure. Both assemblage types therefore experienced each SGD exposure condition before being tested for&nbsp; changes in community metabolism (NEC and NEP). Replicates of species pairs or colonies were&nbsp; collected at least three meters away from each other to minimize genotypic duplication across&nbsp; assemblages in each exposure treatment.&nbsp;</p>
<p>(e) All organisms were transported submerged to the Richard B. Gump South Pacific Research&nbsp; Station on Mo'orea and held in flow-through water tables. A supply of&nbsp;fresh&nbsp; seawater was&nbsp; continuously pumped from nearshore to provide an ambient coastal environment similar to the collection site, and the water was supplementally&nbsp;oxygenated using air bubblers (Tetra Whisper&nbsp; Air Pump, Virginia, USA). Water tables were cleaned daily to remove algae and avoid&nbsp; &nbsp;settlement. Organisms were&nbsp;fragmented and cleaned to remove excessive epiphytes and epifauna. We used forceps to remove epiphytes and epifauna from organisms and additionally&nbsp;removed&nbsp;epifauna from interstitial spaces of L. kotschyanum by submerging fragments in&nbsp; freshwater for up to 15 seconds, following protocols from Glanz (2021). Species with&nbsp;hard&nbsp; substrate (Scleractinia: P. acuta, P. rus, M. grisea; crustose coralline algae [CCA]: L, kotschyanum; Corallimorpharia: D. nummiforme; sponge: Porifera unk) were&nbsp;attached to wide&nbsp; flat-headed bolts with hot super glue (Gorilla Hot Glue, The Gorilla Glue Company, Ohio).&nbsp; Species not attached to the bolts (macroalgae: D.&nbsp;bartayresiana, T. ornata, H. opuntia, V.&nbsp; fastigiata; sponge: L. chondrodes) were wrapped loosely in clear nylon netting to allow sufficient space and light for growth (8 mm ✕&nbsp; 8 mm mesh size).</p>
<p>(f) Organisms were deployed in either the high or low exposure location in situ for 5-6 weeks from February 8 - March 24, 2023. Species were held in situ in a metal cage (13&nbsp;mm x 13 mm mesh&nbsp; size) at each exposure site to reduce grazing and predation. Cages were fastened atop cinder&nbsp; block platforms raised above the benthos to 0.6 m&nbsp;depth at each site. Bolt-mounted species were fastened to the cage along the mesh base with washers and nuts, while netted organisms were attached to the base&nbsp;with zip ties. Cages were consistently cleaned and checked for overall health condition of species throughout deployment.</p>
<p>(g) Community metabolism.&nbsp; &nbsp;After deployment at high and low SGD locations, we formed complete assemblages based on the species in Table 1 from Barnas et al. (2025) through random selection of healthy individuals from each species group. We measured four biomass-normalized community metabolism rates for each of the 40 assemblages: dark respiration (Rd), net photosynthesis (NP), gross photosynthesis (GP), and net calcification (NC). Community respiration and net photosynthesis were calculated from oxygen evolution, and community&nbsp; calcification was estimated using the total alkalinity anomaly technique in closed-system chambers (6 L) with ambient filtered seawater (20 µm-rated sand filter). For each community metabolism trial, we placed four high SGD assemblages and four low SGD assemblages (two&nbsp; from high SGD exposure and two from low SGD exposure per assemblage type) each in&nbsp; &nbsp;individual 6 L water-tight transparent chambers (Rubbermaid, Georgia; n=8 chambers) with a&nbsp; circulation pump (Aquaneat Submersible Pump, 80 GPH), fiber optic oxygen sensor (PSt7,&nbsp; &nbsp; accuracy ± 0.05 % O2) and temperature sensor (Pt100, accuracy ± 1.0 °C)&nbsp; (PreSensPrecision&nbsp; &nbsp;Sensing GmbH, Germany), and overhead light source (Prime 16 HD LED Reef Light,&nbsp; Aqua Illumination) equipped for each chamber. A ninth chamber without organisms was also&nbsp; included as a control to account for any background changes in oxygen or total alkalinity from&nbsp; the seawater.</p>
<p>NP and NC were measured simultaneously for 60 minutes under saturating light conditions (Ik =&nbsp; 440 μmol photons m-2 s-1). Saturating light was determined from photosynthesis-irradiance curves from prior coral and algal studies conducted at fringing reef sites at the same depth in Mo’orea (Edmunds et al. 2012; Becker and&nbsp; Silbiger 2020; Perng 2019). Notably, the organisms in the current study experienced in situ light conditions ranging from 0 to 1800 µmol photons m-2 s-1 (miniPAR, accuracy ± 5% in air traceable to NIST, Precision Measurement Engineering, California). Given the high light intensity experienced in situ, we do not anticipate photo- inhibition of communities at 440 µmol photons m-2 s-1. After refilling the chambers with oxygenated filtered seawater, chambers were&nbsp; &nbsp; then run in darkness for 20 minutes to measure Rd. Oxygen concentration (µmol/L) and&nbsp; &nbsp;temperature (℃) were recorded at a frequency of 1 Hz (Oxy10 St, PreSens Measurement Studio2, PreSens Precision Sensing GmbH, Germany).&nbsp; &nbsp;Rates of oxygen evolution (net photosynthesis [NP]) and uptake (Rd) were calculated by repeated&nbsp; local linear regressions used to obtain the best-fit linear regression through a bootstrapping&nbsp; &nbsp;technique with the package LoLinR in R, corrected for chamber volume, blank rates,&nbsp; and normalized to the&nbsp; total organic biomass of each assemblage. We calculated gross&nbsp; photosynthesis (GP) of assemblages by:&nbsp; GP&nbsp; =&nbsp; NP + |Rd|, where the absolute value of Rd is added to&nbsp; NP to account for O2 consumption.&nbsp; To measure NC, water samples were collected before and after each 60 min light trial in triple-&nbsp; &nbsp;rinsed 120 mL acid- washed Nalgene bottles. We measured AT using the same methods detailed above. Net calcification (NC, µmol CaCO3 g-1 h-1) was calculated by the total alkalinity anomaly technique using the following equation: NC = [(ΔAT sample - ΔAT blank) X V X ρSW]\(2 X t X AFWD).</p>
<p>&nbsp;ΔAT (µmol kg-1) is the change in AT from initial to post-trial water samples, with ΔAT blank as the control chamber, V is total water volume in each chamber (mL), ρSW is the average density of seawater (1.023 g cm-3), t relates to total incubation time of assemblages in their respective&nbsp;chambers (h-1), and AFDW is the total ash-free dry weight of each assemblage relating to total&nbsp;organic biomass (g-1). An individual’s AFDW was calculated by drying and ashing the organisms, and AFDW of each assemblage was obtained through the sum of its respective set of organisms.<br />
<br />
Organism names:</p>
<p>Name used in metadata, Full SciName, LSID<br />
L. kotschyanum, Lithophyllum kotschyanum,urn:lsid:marinespecies.org:taxname:213889<br />
P. acuta,Pocillopora acuta,urn:lsid:marinespecies.org:taxname:759099<br />
P. rus,Porites rus,urn:lsid:marinespecies.org:taxname:207231<br />
M. grisea,Montipora grisea,urn:lsid:marinespecies.org:taxname:287709<br />
Corallimorpharia,Corallimorpharia,urn:lsid:marinespecies.org:taxname:1362<br />
D. nummiforme,Discosoma nummiforme, urn:lsid:marinespecies.org:taxname:411031<br />
Porifera unk, Porifera spp.,&nbsp; urn:lsid:marinespecies.org:taxname:558</p>
Specified by the Principal Investigator(s)
<p>All data and code are available on GitHub (https://github.com/dbarnas/SGD_drives_both_direct_and_indirect_effects_on_organismal_and_community_metabolism_on_coral_reefs) and&nbsp;archival copy is available at Zenodo (Version 1.2, doi: 10.5281/zenodo.14285978)</p>
Specified by the Principal Investigator(s)
* Table within submitted file "Community_Metabolism .csv" was imported into the BCO-DMO data system for this dataset. Table will appear as Data File: 960136_v1_sgd-response-reef-metabolism.csv (along with other download format options).
* BCO-DMO requires each column contain an individual measurement type (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 "Respirometrydata.csv" provided to BCO-DMO was included as supplemental file 960136_v1_sgd-response-reef-metabolism-alternate-format.csv
Transformation notes (going from the originally provided file "Community_Metabolism .csv" to primary data table format 960136_v1_sgd-response-reef-metabolism.csv) :
* A table pivot was performed (transforming columns Rate_type, Rate) to separate sets of columns per rate type.
* To do this tables were separated by filtering on rate_type (NP,NC, R, GP). Then joined to combine all columns using full joins on unique keys ("SampleID", "Assemblage_Treat","Environmental_Treat","Date","Location").
** Data were evaluated to determine a unique set of columns corresponding to the rate_type before the pivot operation was performed.
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 2025-05-09. Partial names used in metadata (e.g. L. kotschyanum) were matched to full names as used in the related dataset for organism growth in this study which specified full names. (e.g. Lithophyllum kotschyanum) (matched to LSID urn:lsid:marinespecies.org:taxname:213889)
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
Presens Oxy-19
Presens Oxy-19
PI Supplied Instrument Name: Presens Oxy-19 PI Supplied Instrument Description:Presens Oxy-19 with fiber optic oxygen sensor (PSt7, accuracy ± 0.05 % O2) and temperature sensor (Pt100, accuracy ± 1.0 °C) (PreSensPrecision Sensing GmbH, Germany) was used for respirometry. 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