http://lod.bco-dmo.org/id/dataset/924650
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
2024-04-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Coral area from a study of year-long effects of high pCO2 on the community structure of a tropical fore reef assembled in outdoor flumes in Moorea, French Polynesia from 2017 to 2018
2024-04-09
publication
2024-04-09
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-04-18
publication
https://doi.org/10.26008/1912/bco-dmo.924650.1
Robert Carpenter
California State University Northridge
principalInvestigator
Peter J. Edmunds
California State University Northridge
principalInvestigator
Steve Doo
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: Edmunds, P. J., Carpenter, R., Doo, S. (2024) Coral area from a study of year-long effects of high pCO2 on the community structure of a tropical fore reef assembled in outdoor flumes in Moorea, French Polynesia from 2017 to 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-04-09 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.924650.1 [access date]
Dataset Description: <p>See "Related Datasets" and "Supplemental Files" sections for access to related data published as part of these pCO2 flume experiments published in Edmunds et al., (2020, doi:10.1093/icesjms/fsaa015).&nbsp;&nbsp;<br />
<br />
Related metabolism data was published in Edmunds et al. (2024, doi:10.1002/lno.12504).</p> Methods and Sampling: <p>Fore reef communities were assembled in three outdoor flumes in Mo'orea, which were assigned randomly to a pCO<sub>2</sub>&nbsp;treatment targeting ambient (400 μatm), 700 μatm, and 1300 μatm pCO<sub>2</sub>. The elevated pCO<sub>2</sub>&nbsp;treatments approximated atmospheric conditions projected for about the year 2140 under representative concentration pathways (RCP) 2.6, 4.5, and 8.5. Treatments were maintained for one year beginning in late Austral spring (November 2017), and actual pCO<sub>2</sub>&nbsp;treatments over the year differed from target values (described below). In brief, each flume consisted of a working section that was 5.0-m long, 30-cm wide and filled to ~ 30-cm depth with ~ 500 L of seawater. The fixed and unfixed communities within each fume occupied a 4.7 × 0.3 m portion of the floor of the working section of each flume. Seawater was circulated continually through a return section, and was supplied with fresh seawater at ~ 5 L min<sup>-1</sup>. Seawater was pumped from Cook’s Bay (14-m depth) and filtered through sand (pore size ~ 450–550 µm) before entering the flumes. With this pore size, small particulates passed through the filter and were added to the flumes where they were available as food for heterotrophic organisms.</p>
<p><strong>Fore reef communities:</strong></p>
<p>The reef communities were assembled to correspond to the mean percent cover of the major benthic space holders recorded in 2006 at 17-m depth on the fore reef of the north shore of Mo'orea. A historic community structure (rather than present day) was used because 2006 represented the long-term community structure on this reef, and it created the capacity to compare aspects of the present experiment with a previous experiment. Based on six sites sampled around Mo'orea in 2006, the community structure in the flumes was targeted to ~ 11% cover of&nbsp;<em>Pocillopora</em>&nbsp;spp., ~ 8% massive&nbsp;<em>Porites</em>&nbsp;spp., 8%&nbsp;<em>Acropora</em>&nbsp;spp., and ~ 53% reef rock. This construct created a community with ~ 27% coral cover, which was slightly lower than the actual mean coral cover in 2006 (32%), because the remaining 14 genera of scleractinians and&nbsp;<em>Millepora</em>&nbsp;contributed 5% coral cover. The&nbsp;<em>Pocillopora</em>&nbsp;conformed to the classic morphology of&nbsp;<em>P. verrucosa</em>, but it is likely that other&nbsp;<em>Pocillopora</em>&nbsp;spp. were present in the flumes. Likewise,&nbsp;<em>Acropora</em>&nbsp;spp. were selected to represent&nbsp;<em>A. hyacinthus</em>&nbsp;and&nbsp;<em>A. retusa</em>, which were common on the fore reef when the experiment was completed, and colonies of these species were scattered haphazardly among the flumes. Given the morphological complexity of&nbsp;<em>Acropora</em>&nbsp;spp., it is possible that other species were placed into the flumes. Pieces of coral rubble (~ 11.5-cm diameter) were added to achieve ~ 29% cover. Coral and rubble were haphazardly scattered along the working section of each flume to approach the targets for percentage cover, and this resulted in portions of the flumes having slightly different covers of coral. This was important for the central 2.4-m portion of the flume, where community members were fixed to allow the community structure to be quantified monthly using planar photographs. In the adjacent portions of the flumes, community members were unfixed (and rested on the floor of the flumes) so that they could be removed monthly for buoyant weighing (described below).&nbsp;</p>
<p>Corals and rubble were collected from ~ 17-m depth on the north shore fore reef, epoxied (Z-Spar A788, Pettit Marine Paint, Rockaway, NJ, USA) to plastic bases, and placed in a seawater table for at least 2 d before being added to the flumes. This time allowed the epoxy to cure and for the corals to recover from collection. Fore reef communities were assembled in the flumes on 27 October 2017, where they were maintained under ambient seawater conditions until 3 November. At this time, treatment pCO<sub>2</sub>&nbsp;levels were initiated in two flumes (one remained at ambient pCO<sub>2</sub>), with pCO<sub>2&nbsp;</sub>gradually increased to target values over 24 h.</p>
<p><strong>Physical and chemical parameters&nbsp;</strong>(see "Supplemental Files" for data access)<strong>:</strong></p>
<p>Seawater was circulated in the flumes at ~ 0.1 m s<sup>-1</sup>&nbsp;using a pump (Wave II 373 J s<sup>-1</sup>, W. Lim Co., El Monte, CA, USA), and flow speeds were measured across the working sections using a Nortek Vectrino Acoustic Doppler Velocimeter. This flow speed was ecologically relevant for 15-m depth on the fore reef of Mo’orea (14-y mean = 0.065 m s<sup>-1</sup>). The flumes were exposed to natural sunlight that was reduced with a blue filter (LEE #183, Lee Filters, Andover, England) to photon flux densities (PFD) in the range of photosynthetically active radiation (400–700 nm) that approximated those at 17-m depth. Light in the flumes was measured continuously (at 0.0006 Hz) using cosine-corrected sensors (Odyssey, Dataflow Systems Ltd, Christchurch, New Zealand) that recoded PAR. Odyssey sensors were calibrated with a&nbsp;Li-COR meter [LI-1400, Li-COR Biosciences, Lincoln, NE, USA] attached to a 2p&nbsp;sensor [LI 192A]). Temperatures in the flumes were regulated with chillers (heaters were not required) and were maintained close to the mean monthly seawater temperature at 17-m depth on the fore reef.</p>
<p>Seawater carbonate chemistry was uncontrolled in one flume (ambient, ~ 400 μatm pCO<sub>2</sub>), and controlled in two others to simulate conditions arising from seawater pCO<sub>2</sub>&nbsp;targeted at 700 μatm and 1300 μatm. Seawater pH was not altered in the ambient flume, but was controlled in the treatment flumes by bubbling CO<sub>2</sub>&nbsp;into the seawater to alter pH relative to a set-point (regulated using an Aquacontroller, Neptune Systems, Morgan Hill, CA, USA) that operated a solenoid supplying pure CO<sub>2</sub>&nbsp;gas to a diffuser stone submerged in each flume. A diurnal upward pH adjustment of ~ 0.1 unit was applied to the two treatment flumes to simulate natural diurnal variation in seawater pCO<sub>2</sub>&nbsp;on the reef of Mo’orea. The ambient flume also maintained a diurnal variation in pCO<sub>2</sub>&nbsp;with a night time pH ~ 0.1 unit lower than in the daytime. Ambient air was bubbled continuously into all flumes. Periodic measurements of pCO<sub>2</sub>&nbsp;in the flumes confirmed that nocturnal pCO<sub>2</sub>&nbsp;met, or exceeded day-time target values (described in results).</p>
<p>Throughout the experiment, logging sensors (described above) recorded PAR, and temperature (Hobo Pro v2 [± 0.2 °C], Onset Computer Corp., Bourne, MA, USA). pH was measured daily on the total hydrogen ion scale (pH<sub>T</sub>) using a handheld meter (see below). The values from the temperature and pH measurements were used to adjust the thermostat and pH-set points to achieve target pCO<sub>2</sub>&nbsp;values. Seawater carbonate chemistry (pH and A<sub>T</sub>) and salinity were measured during the day (14:00 hrs) and night (20:00 hrs) and were obtained weekly. A bench-top conductivity meter (Thermo Scientific, Orionstar A212, Waltham, MA, USA) was used to measure salinity. The remaining parameters of the seawater carbonate system were calculated from temperature, salinity, pH<sub>T</sub>, and&nbsp;<em>A</em><sub>T</sub>, using the R package Seacarb.</p>
<p>pH<sub>T</sub>&nbsp;was measured using a DG 115-SC electrode (Mettler Toledo, Columbus, OH, USA) that was calibrated with a TRIS buffer.&nbsp;<em>A</em><sub>T</sub>&nbsp;was measured using open-cell, acidimetric titration using a certified titrant with an automatic titrator (T50, Mettler Toledo) fitted with a DG 115-SC electrode (Mettler Toledo). The accuracy and precision of measurements were determined by processing certified reference materials (CRMs batch numbers 158 and 172; from A. Dickson Laboratory, Scripps Institution of Oceanography, CA, USA), against which measured values of&nbsp;<em>A</em><sub>T</sub>&nbsp;maintained an accuracy of 1.7 ± 0.3 μmol kg<sup>-1</sup>&nbsp;(<em>n</em>&nbsp;= 15) and precision of 1.8 ± 0.1 μmol kg<sup>-1</sup>&nbsp;(<em>n</em>&nbsp;= 475).</p>
<p><strong>Response variables:</strong></p>
<p>See more details about coral weight and Gnet calculation&nbsp;in&nbsp;the related dataset "Edmunds et al. 2020 ICES: pCO2 flume - Coral weight"&nbsp;https://www.bco-dmo.org/dataset/924603.&nbsp;&nbsp;</p>
<p><strong>Community structure:</strong><br />
* This section describes the methodology of the "percent_area" column in this dataset.<br />
* The images of each flume (1-3) are in the "Supplemental Files" section of this dataset.</p>
<p>The effects of the treatments on the community structure were described using photographs recorded monthly in planar view. The image-based technique strengthened the ability to address the effects of OA on the community ecology of coral reefs, which frequently is recorded using planar photographs (including in Mo'orea). Photographs were recorded in ambient light using a GoPro Hero 4 camera (12 MP, 3-mm focal length) that was fitted to a stand and positioned on the upper edge of the flumes to record the benthic community through the air-water interface. At each sampling, the camera was sequentially moved along the flume to record the community in the middle 2.4 m of the working section using ~ 15 contiguous photographs.</p>
<p>Photographs were analyzed using ImageJ software after they were stitched together to make a single image for each sampling. This image covered the ~ 2.4-m length of the central portion of the flume where the corals were secured to a plastic-coated metal grid with a mesh size of 5 × 5 cm. The stitching of photographs sometimes was imperfect due to parallax errors, and in such cases, separate pictures were evaluated to assess organism size. The planar area of living tissue on corals was quantified by outlining organisms in ImageJ, after scaling the image using the metal grid as a size reference. Organism size (cm<sup>2</sup>) was expressed as a percentage of the area (7200 cm<sup>2</sup>) occupied by the fixed portion of the community. The summed area of community members was used to determine cover of the benthic community, and the areas of each organism were used to quantify growth (and shrinkage). Where organisms died, their area was set to zero.</p>
<p><strong>Organism identifiers</strong>&nbsp;(Taxon, LifeSciences Identifier (LSID), name as appears in Species column):</p>
<p>Acropora hyacinthus, urn:lsid:marinespecies.org:taxname:207044,&nbsp;A. hyacinthus<br />
Acropora retusa, urn:lsid:marinespecies.org:taxname:430653, A. retusa<br />
Porites, urn:lsid:marinespecies.org:taxname:206485, Massive Porites<br />
Pocillopora damicornis, urn:lsid:marinespecies.org:taxname:206953,<br />
Pocillopora verrucosa, urn:lsid:marinespecies.org:taxname:206954,</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1041270 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1041270
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1415268 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1415268
completed
Robert Carpenter
California State University Northridge
818-677-3256
Department of Biology 18111 Nordhoff Street
Northridge
CA
91330-8303
USA
robert.carpenter@csun.edu
pointOfContact
Peter J. Edmunds
California State University Northridge
818-677-2502
Department of Biology 18111 Nordhoff Street
Northridge
CA
91330-8303
USA
peter.edmunds@csun.edu
pointOfContact
Steve Doo
California State University Northridge
doos@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Flume
Year_Month
Sample
Type
Species
percent_area
Nortek Vectrino Acoustic Doppler Velocimeter
A bench-top conductivity meter (Thermo Scientific, Orionstar A212, Waltham, MA, USA)
Hobo Pro v2
Wave II 373 J s-1, W. Lim Co., El Monte, CA, USA
GoPro Hero 4
theme
None, User defined
treatment
Date_Month
sample identification
sample description
taxon
area
featureType
BCO-DMO Standard Parameters
Acoustic Doppler Velocimeter
Conductivity Meter
Onset HOBO Pro v2 temperature logger
pH Sensor
Photosynthetically Available Radiation Sensor
Pump
Underwater 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.
Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA)
https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503477
Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA)
NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707).
In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.
Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.
PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)
NSF media releases for the Ocean Acidification Program:
Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification
Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?
Discovery nsf.gov - National Science Foundation (NSF) Discoveries - Trouble in Paradise: Ocean Acidification This Way Comes - US National Science Foundation (NSF)
Press Release 12-179 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: Finding New Answers Through National Science Foundation Research Grants - US National Science Foundation (NSF)
Press Release 13-102 World Oceans Month Brings Mixed News for Oysters
Press Release 13-108 nsf.gov - National Science Foundation (NSF) News - Natural Underwater Springs Show How Coral Reefs Respond to Ocean Acidification - US National Science Foundation (NSF)
Press Release 13-148 Ocean acidification: Making new discoveries through National Science Foundation research grants
Press Release 13-148 - Video nsf.gov - News - Video - NSF Ocean Sciences Division Director David Conover answers questions about ocean acidification. - US National Science Foundation (NSF)
Press Release 14-010 nsf.gov - National Science Foundation (NSF) News - Palau's coral reefs surprisingly resistant to ocean acidification - US National Science Foundation (NSF)
Press Release 14-116 nsf.gov - National Science Foundation (NSF) News - Ocean Acidification: NSF awards $11.4 million in new grants to study effects on marine ecosystems - US National Science Foundation (NSF)
SEES-OA
largerWorkCitation
program
RUI: Ocean Acidification- Category 1- The effects of ocean acidification on the organismic biology and community ecology of corals, calcified algae, and coral reefs
https://osprey.bco-dmo.org/project/2242
RUI: Ocean Acidification- Category 1- The effects of ocean acidification on the organismic biology and community ecology of corals, calcified algae, and coral reefs
<p>While coral reefs have undergone unprecedented changes in community structure in the past 50 y, they now may be exposed to their gravest threat since the Triassic. This threat is increasing atmospheric CO2, which equilibrates with seawater and causes ocean acidification (OA). In the marine environment, the resulting decline in carbonate saturation state (Omega) makes it energetically less feasible for calcifying taxa to mineralize; this is a major concern for coral reefs. It is possible that the scleractinian architects of reefs will cease to exist as a mineralized taxon within a century, and that calcifying algae will be severely impaired. While there is a rush to understand these effects and make recommendations leading to their mitigation, these efforts are influenced strongly by the notion that the impacts of pCO2 (which causes Omega to change) on calcifying taxa, and the mechanisms that drive them, are well-known. The investigators believe that many of the key processes of mineralization on reefs that are potentially affected by OA are only poorly known and that current knowledge is inadequate to support the scaling of OA effects to the community level. It is vital to measure organismal-scale calcification of key taxa, elucidate the mechanistic bases of these responses, evaluate community scale calcification, and finally, to conduct focused experiments to describe the functional relationships between these scales of mineralization.</p>
<p>This project is a 4-y effort focused on the effects of Ocean Acidification (OA) on coral reefs at multiple spatial and functional scales. The project focuses on the corals, calcified algae, and coral reefs of Moorea, French Polynesia, establishes baseline community-wide calcification data for the detection of OA effects on a decadal-scale, and builds on the research context and climate change focus of the Moorea Coral Reef LTER.</p>
<p>This project is a hypothesis-driven approach to compare the effects of OA on reef taxa and coral reefs in Moorea. The PIs will utilize microcosms to address the impacts and mechanisms of OA on biological processes, as well as the ecological processes shaping community structure. Additionally, studies of reef-wide metabolism will be used to evaluate the impacts of OA on intact reef ecosystems, to provide a context within which the experimental investigations can be scaled to the real world, and critically, to provide a much needed reference against which future changes can be gauged.</p>
<p><strong>Datasets listed in the "Dataset Collection" section include references to results journal publications published as part of this project.</strong></p>
OA_Corals
largerWorkCitation
project
eng; USA
oceans
-149.84705
-149.80817
-17.48437
-17.47495
2017-01-01
2018-01-01
Moorea, French Polynesia
0
BCO-DMO catalogue of parameters from Coral area from a study of year-long effects of high pCO2 on the community structure of a tropical fore reef assembled in outdoor flumes in Moorea, French Polynesia from 2017 to 2018
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/924717.rdf
Name: Flume
Units: unitless
Description: <p>Flume number (1-3) and target treatment pCO2 (400, 700, 1300 uatm)</p>
http://lod.bco-dmo.org/id/dataset-parameter/924718.rdf
Name: Year_Month
Units: unitless
Description: <p>Year and month of experiment</p>
http://lod.bco-dmo.org/id/dataset-parameter/924719.rdf
Name: Sample
Units: unitless
Description: <p>Reference tag for each corals</p>
http://lod.bco-dmo.org/id/dataset-parameter/924720.rdf
Name: Type
Units: unitless
Description: <p>Specimen type that either were mobile and taken out every month for weighing, or permanent and not disturbed for weighing</p>
http://lod.bco-dmo.org/id/dataset-parameter/924721.rdf
Name: Species
Units: unitless
Description: <p>Species used</p>
http://lod.bco-dmo.org/id/dataset-parameter/924722.rdf
Name: percent_area
Units: percent (%)
Description: <p>size of the coral as a % of the area of the flume floor</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
91676
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/5d8f89a1-9ef2-43a4-be80-52dd383ec491/content
download
https://doi.org/10.26008/1912/bco-dmo.924650.1
download
onLine
dataset
<p>Fore reef communities were assembled in three outdoor flumes in Mo'orea, which were assigned randomly to a pCO<sub>2</sub>&nbsp;treatment targeting ambient (400 μatm), 700 μatm, and 1300 μatm pCO<sub>2</sub>. The elevated pCO<sub>2</sub>&nbsp;treatments approximated atmospheric conditions projected for about the year 2140 under representative concentration pathways (RCP) 2.6, 4.5, and 8.5. Treatments were maintained for one year beginning in late Austral spring (November 2017), and actual pCO<sub>2</sub>&nbsp;treatments over the year differed from target values (described below). In brief, each flume consisted of a working section that was 5.0-m long, 30-cm wide and filled to ~ 30-cm depth with ~ 500 L of seawater. The fixed and unfixed communities within each fume occupied a 4.7 × 0.3 m portion of the floor of the working section of each flume. Seawater was circulated continually through a return section, and was supplied with fresh seawater at ~ 5 L min<sup>-1</sup>. Seawater was pumped from Cook’s Bay (14-m depth) and filtered through sand (pore size ~ 450–550 µm) before entering the flumes. With this pore size, small particulates passed through the filter and were added to the flumes where they were available as food for heterotrophic organisms.</p>
<p><strong>Fore reef communities:</strong></p>
<p>The reef communities were assembled to correspond to the mean percent cover of the major benthic space holders recorded in 2006 at 17-m depth on the fore reef of the north shore of Mo'orea. A historic community structure (rather than present day) was used because 2006 represented the long-term community structure on this reef, and it created the capacity to compare aspects of the present experiment with a previous experiment. Based on six sites sampled around Mo'orea in 2006, the community structure in the flumes was targeted to ~ 11% cover of&nbsp;<em>Pocillopora</em>&nbsp;spp., ~ 8% massive&nbsp;<em>Porites</em>&nbsp;spp., 8%&nbsp;<em>Acropora</em>&nbsp;spp., and ~ 53% reef rock. This construct created a community with ~ 27% coral cover, which was slightly lower than the actual mean coral cover in 2006 (32%), because the remaining 14 genera of scleractinians and&nbsp;<em>Millepora</em>&nbsp;contributed 5% coral cover. The&nbsp;<em>Pocillopora</em>&nbsp;conformed to the classic morphology of&nbsp;<em>P. verrucosa</em>, but it is likely that other&nbsp;<em>Pocillopora</em>&nbsp;spp. were present in the flumes. Likewise,&nbsp;<em>Acropora</em>&nbsp;spp. were selected to represent&nbsp;<em>A. hyacinthus</em>&nbsp;and&nbsp;<em>A. retusa</em>, which were common on the fore reef when the experiment was completed, and colonies of these species were scattered haphazardly among the flumes. Given the morphological complexity of&nbsp;<em>Acropora</em>&nbsp;spp., it is possible that other species were placed into the flumes. Pieces of coral rubble (~ 11.5-cm diameter) were added to achieve ~ 29% cover. Coral and rubble were haphazardly scattered along the working section of each flume to approach the targets for percentage cover, and this resulted in portions of the flumes having slightly different covers of coral. This was important for the central 2.4-m portion of the flume, where community members were fixed to allow the community structure to be quantified monthly using planar photographs. In the adjacent portions of the flumes, community members were unfixed (and rested on the floor of the flumes) so that they could be removed monthly for buoyant weighing (described below).&nbsp;</p>
<p>Corals and rubble were collected from ~ 17-m depth on the north shore fore reef, epoxied (Z-Spar A788, Pettit Marine Paint, Rockaway, NJ, USA) to plastic bases, and placed in a seawater table for at least 2 d before being added to the flumes. This time allowed the epoxy to cure and for the corals to recover from collection. Fore reef communities were assembled in the flumes on 27 October 2017, where they were maintained under ambient seawater conditions until 3 November. At this time, treatment pCO<sub>2</sub>&nbsp;levels were initiated in two flumes (one remained at ambient pCO<sub>2</sub>), with pCO<sub>2&nbsp;</sub>gradually increased to target values over 24 h.</p>
<p><strong>Physical and chemical parameters&nbsp;</strong>(see "Supplemental Files" for data access)<strong>:</strong></p>
<p>Seawater was circulated in the flumes at ~ 0.1 m s<sup>-1</sup>&nbsp;using a pump (Wave II 373 J s<sup>-1</sup>, W. Lim Co., El Monte, CA, USA), and flow speeds were measured across the working sections using a Nortek Vectrino Acoustic Doppler Velocimeter. This flow speed was ecologically relevant for 15-m depth on the fore reef of Mo’orea (14-y mean = 0.065 m s<sup>-1</sup>). The flumes were exposed to natural sunlight that was reduced with a blue filter (LEE #183, Lee Filters, Andover, England) to photon flux densities (PFD) in the range of photosynthetically active radiation (400–700 nm) that approximated those at 17-m depth. Light in the flumes was measured continuously (at 0.0006 Hz) using cosine-corrected sensors (Odyssey, Dataflow Systems Ltd, Christchurch, New Zealand) that recoded PAR. Odyssey sensors were calibrated with a&nbsp;Li-COR meter [LI-1400, Li-COR Biosciences, Lincoln, NE, USA] attached to a 2p&nbsp;sensor [LI 192A]). Temperatures in the flumes were regulated with chillers (heaters were not required) and were maintained close to the mean monthly seawater temperature at 17-m depth on the fore reef.</p>
<p>Seawater carbonate chemistry was uncontrolled in one flume (ambient, ~ 400 μatm pCO<sub>2</sub>), and controlled in two others to simulate conditions arising from seawater pCO<sub>2</sub>&nbsp;targeted at 700 μatm and 1300 μatm. Seawater pH was not altered in the ambient flume, but was controlled in the treatment flumes by bubbling CO<sub>2</sub>&nbsp;into the seawater to alter pH relative to a set-point (regulated using an Aquacontroller, Neptune Systems, Morgan Hill, CA, USA) that operated a solenoid supplying pure CO<sub>2</sub>&nbsp;gas to a diffuser stone submerged in each flume. A diurnal upward pH adjustment of ~ 0.1 unit was applied to the two treatment flumes to simulate natural diurnal variation in seawater pCO<sub>2</sub>&nbsp;on the reef of Mo’orea. The ambient flume also maintained a diurnal variation in pCO<sub>2</sub>&nbsp;with a night time pH ~ 0.1 unit lower than in the daytime. Ambient air was bubbled continuously into all flumes. Periodic measurements of pCO<sub>2</sub>&nbsp;in the flumes confirmed that nocturnal pCO<sub>2</sub>&nbsp;met, or exceeded day-time target values (described in results).</p>
<p>Throughout the experiment, logging sensors (described above) recorded PAR, and temperature (Hobo Pro v2 [± 0.2 °C], Onset Computer Corp., Bourne, MA, USA). pH was measured daily on the total hydrogen ion scale (pH<sub>T</sub>) using a handheld meter (see below). The values from the temperature and pH measurements were used to adjust the thermostat and pH-set points to achieve target pCO<sub>2</sub>&nbsp;values. Seawater carbonate chemistry (pH and A<sub>T</sub>) and salinity were measured during the day (14:00 hrs) and night (20:00 hrs) and were obtained weekly. A bench-top conductivity meter (Thermo Scientific, Orionstar A212, Waltham, MA, USA) was used to measure salinity. The remaining parameters of the seawater carbonate system were calculated from temperature, salinity, pH<sub>T</sub>, and&nbsp;<em>A</em><sub>T</sub>, using the R package Seacarb.</p>
<p>pH<sub>T</sub>&nbsp;was measured using a DG 115-SC electrode (Mettler Toledo, Columbus, OH, USA) that was calibrated with a TRIS buffer.&nbsp;<em>A</em><sub>T</sub>&nbsp;was measured using open-cell, acidimetric titration using a certified titrant with an automatic titrator (T50, Mettler Toledo) fitted with a DG 115-SC electrode (Mettler Toledo). The accuracy and precision of measurements were determined by processing certified reference materials (CRMs batch numbers 158 and 172; from A. Dickson Laboratory, Scripps Institution of Oceanography, CA, USA), against which measured values of&nbsp;<em>A</em><sub>T</sub>&nbsp;maintained an accuracy of 1.7 ± 0.3 μmol kg<sup>-1</sup>&nbsp;(<em>n</em>&nbsp;= 15) and precision of 1.8 ± 0.1 μmol kg<sup>-1</sup>&nbsp;(<em>n</em>&nbsp;= 475).</p>
<p><strong>Response variables:</strong></p>
<p>See more details about coral weight and Gnet calculation&nbsp;in&nbsp;the related dataset "Edmunds et al. 2020 ICES: pCO2 flume - Coral weight"&nbsp;https://www.bco-dmo.org/dataset/924603.&nbsp;&nbsp;</p>
<p><strong>Community structure:</strong><br />
* This section describes the methodology of the "percent_area" column in this dataset.<br />
* The images of each flume (1-3) are in the "Supplemental Files" section of this dataset.</p>
<p>The effects of the treatments on the community structure were described using photographs recorded monthly in planar view. The image-based technique strengthened the ability to address the effects of OA on the community ecology of coral reefs, which frequently is recorded using planar photographs (including in Mo'orea). Photographs were recorded in ambient light using a GoPro Hero 4 camera (12 MP, 3-mm focal length) that was fitted to a stand and positioned on the upper edge of the flumes to record the benthic community through the air-water interface. At each sampling, the camera was sequentially moved along the flume to record the community in the middle 2.4 m of the working section using ~ 15 contiguous photographs.</p>
<p>Photographs were analyzed using ImageJ software after they were stitched together to make a single image for each sampling. This image covered the ~ 2.4-m length of the central portion of the flume where the corals were secured to a plastic-coated metal grid with a mesh size of 5 × 5 cm. The stitching of photographs sometimes was imperfect due to parallax errors, and in such cases, separate pictures were evaluated to assess organism size. The planar area of living tissue on corals was quantified by outlining organisms in ImageJ, after scaling the image using the metal grid as a size reference. Organism size (cm<sup>2</sup>) was expressed as a percentage of the area (7200 cm<sup>2</sup>) occupied by the fixed portion of the community. The summed area of community members was used to determine cover of the benthic community, and the areas of each organism were used to quantify growth (and shrinkage). Where organisms died, their area was set to zero.</p>
<p><strong>Organism identifiers</strong>&nbsp;(Taxon, LifeSciences Identifier (LSID), name as appears in Species column):</p>
<p>Acropora hyacinthus, urn:lsid:marinespecies.org:taxname:207044,&nbsp;A. hyacinthus<br />
Acropora retusa, urn:lsid:marinespecies.org:taxname:430653, A. retusa<br />
Porites, urn:lsid:marinespecies.org:taxname:206485, Massive Porites<br />
Pocillopora damicornis, urn:lsid:marinespecies.org:taxname:206953,<br />
Pocillopora verrucosa, urn:lsid:marinespecies.org:taxname:206954,</p>
Specified by the Principal Investigator(s)
<p>SEACARB for the analysis of seawater chemistry: Lavigne, H. and Gattuso, J. P. 2013. Seacarb, seawater carbonate<br />
chemistry with, R. R package version 2.4.10. Available at: http://CRAN.R-project.org/package=seacarb (last accessed 11 July 2014).</p>
Specified by the Principal Investigator(s)
* Sheet 2 of submitted file "Areas.xlsx" was imported into the BCO-DMO data system for this dataset. Values "nd" imported as missing data values. Sheet 1 contained metadata added to Parameters section.
** Missing data values are displayed differently based on the file format you download. They are blank in csv files, "NaN" in MatLab files, etc.
* 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]
* dataset Lon bounds corrected from deg 149... to -149...
* quote characters removed from some species values so entire column is consistent.
* Year and month reformatted for consistency within the dataset and between related coral weight datast. Variable full month and abbreviated month in month column, and separate column for year converted to one Year_Month column formatted to match related datasets.
* Sheet 2 of "Physical _and_Chemical_conditions.xlsx" exported as a supplemental file. Column names adjusted to BCO-DMO conventions. Column values with micron (greek mu character) changed to -> u replaced in the flume identifier column and – replaced with standard hyphen character -.
* Site list added for LTER sites from the existing table included for datasets "Edmunds et al. 2024 Oecologia..."
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
Nortek Vectrino Acoustic Doppler Velocimeter
Nortek Vectrino Acoustic Doppler Velocimeter
PI Supplied Instrument Name: Nortek Vectrino Acoustic Doppler Velocimeter Instrument Name: Acoustic Doppler Velocimeter Instrument Short Name:ADV Instrument Description: ADV is the acronym for acoustic doppler velocimeter. The ADV is a remote-sensing, three-dimensional velocity sensor. Its operation is based on the Doppler shift effect. The sensor can be deployed either as a moored instrument or attached to a still structure near the seabed.
Reference:
G. Voulgaris and J. H. Trowbridge, 1998. Evaluation of the Acoustic Doppler Velocimeter (ADV) for Turbulence Measurements. J. Atmos. Oceanic Technol., 15, 272–289. doi: http://dx.doi.org/10.1175/1520-0426(1998)0152.0.CO;2 Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/384/
A bench-top conductivity meter (Thermo Scientific, Orionstar A212, Waltham, MA, USA)
A bench-top conductivity meter (Thermo Scientific, Orionstar A212, Waltham, MA, USA)
PI Supplied Instrument Name: A bench-top conductivity meter (Thermo Scientific, Orionstar A212, Waltham, MA, USA) Instrument Name: Conductivity Meter Instrument Short Name:Conductivity Meter Instrument Description: Conductivity Meter - An electrical conductivity meter (EC meter) measures the electrical conductivity in a solution. Commonly used in hydroponics, aquaculture and freshwater systems to monitor the amount of nutrients, salts or impurities in the water.
Hobo Pro v2
Hobo Pro v2
PI Supplied Instrument Name: Hobo Pro v2 PI Supplied Instrument Description:Throughout the experiment, logging sensors (described above) recorded PAR, and temperature (Hobo Pro v2 [± 0.2 °C], Onset Computer Corp., Bourne, MA, USA). Instrument Name: Onset HOBO Pro v2 temperature logger Instrument Short Name:HOBO U22-001 Instrument Description: The HOBO Water Temp Pro v2 temperature logger, manufactured by Onset Computer Corporation, has 12-bit resolution and a precision sensor for ±0.2°C accuracy over a wide temperature range. It is designed for extended deployment in fresh or salt water.
Operation range: -40° to 70°C (-40° to 158°F) in air; maximum sustained temperature of 50°C (122°F) in water
Accuracy: 0.2°C over 0° to 50°C (0.36°F over 32° to 122°F)
Resolution: 0.02°C at 25°C (0.04°F at 77°F)
Response time: (90%) 5 minutes in water; 12 minutes in air moving 2 m/sec (typical)
Stability (drift): 0.1°C (0.18°F) per year
Real-time clock: ± 1 minute per month 0° to 50°C (32° to 122°F)
Additional information (http://www.onsetcomp.com/)
Onset Computer Corporation
470 MacArthur Blvd
Bourne, MA 02532 Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/134/
PI Supplied Instrument Name: PI Supplied Instrument Description:pHT was measured using a DG 115-SC electrode (Mettler Toledo, Columbus, OH, USA) that was calibrated with a TRIS buffer Instrument Name: pH Sensor Instrument Short Name:pH Sensor Instrument Description: An instrument that measures the hydrogen ion activity in solutions.
The overall concentration of hydrogen ions is inversely related to its pH. The pH scale ranges from 0 to 14 and indicates whether acidic (more H+) or basic (less H+).
PI Supplied Instrument Name: PI Supplied Instrument Description:Light in the flumes was measured continuously (at 0.0006 Hz) using cosine-corrected sensors (Odyssey, Dataflow Systems Ltd, Christchurch, New Zealand) that recoded PAR. Odyssey sensors were calibrated with a Li-COR meter [LI-1400, Li-COR Biosciences, Lincoln, NE, USA] attached to a 2p sensor [LI 192A]) Instrument Name: Photosynthetically Available Radiation Sensor Instrument Short Name:PAR sensor Instrument Description: A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/122/
Wave II 373 J s-1, W. Lim Co., El Monte, CA, USA
Wave II 373 J s-1, W. Lim Co., El Monte, CA, USA
PI Supplied Instrument Name: Wave II 373 J s-1, W. Lim Co., El Monte, CA, USA Instrument Name: Pump Instrument Short Name: Instrument Description: A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps
GoPro Hero 4
GoPro Hero 4
PI Supplied Instrument Name: GoPro Hero 4 PI Supplied Instrument Description:Photographs were recorded in ambient light using a GoPro Hero 4 camera (12 MP, 3-mm focal length) that was fitted to a stand and positioned on the upper edge of the flumes to record the benthic community through the air-water interface. Instrument Name: Underwater Camera Instrument Short Name: Instrument Description: All types of photographic equipment that may be deployed underwater including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/180/