http://lod.bco-dmo.org/id/dataset/995164
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
2026-03-18
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Coral biological data collected during acute and chronic stress exposures in outdoor mesocosms in Hawaii from January 2022 to March 2024
2026-09-01
publication
2026-09-01
revision
BCO-DMO Linked Data URI
2026-09-01
creation
http://lod.bco-dmo.org/id/dataset/995164
Keisha D. Bahr
Texas A&M, Corpus Christi
principalInvestigator
Conall McNicholl
Hawaii Institute of Marine Biology
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: Bahr, K. D., Armstrong, D. A., Bretzing-Tungate, R., McNicholl, C. (2026) Coral biological data collected during acute and chronic stress exposures in outdoor mesocosms in Hawaii from January 2022 to March 2024. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-09-01 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/995164 [access date]
Dataset Description: <p><strong>Note: This section includes a description of buoyant-weight data not included in this dataset. See "Related Datasets" section for buoyant-weight data.</strong></p> Methods and Sampling: <p><strong>Note: </strong><em>This section includes a description of buoyant-weight data not included in this dataset. See "Related Datasets" section for buoyant-weight data.</em><br />
<br />
<strong>Overview</strong></p>
<p>Seasonal mesocosm incubations of Montipora capitata and Pocillopora acuta were conducted over a two-year period (June 2022–March 2024) at the Hawai‘i Institute of Marine Biology (HIMB). Corals were collected from fringe reefs located around the institute.&nbsp;Experiments were carried out during winter (January 10–March 17) and summer (June 10–August 17) in outdoor flow-through mesocosms at the Hawaii Institute of Marine Biology in Kane`ohe, Hawai`i.&nbsp;Due to facility constraints, all treatments could not run simultaneously. Therefore, each seasonal experiment consisted of two consecutive 30-day exposures, each using newly collected coral colonies. All procedures were standardized across replicates, except for adjustments in total alkalinity (TA) and pH required to create the treatments.</p>
<p><strong>Coral Collection and Pre-Experiment Holding</strong></p>
<p>Coral colonies of Montipora capitata and Pocillopora acuta were collected by hand while snorkeling from shallow (1 m) fringing reef habitat surrounding HIMB in Kāne‘ohe Bay, Hawai‘i. Colonies were transported immediately to the mesocosm facility and held for one week in flow-through tanks that were identical in design to the experimental mesocosms.</p>
<p>One day prior to placement in experimental mesocosms, all colonies were stained for eight hours with alizarin red to mark the initial skeletal growth band (reference: Jokiel and Morrissey 1993).</p>
<p>At the start of each 30-day experiment, colonies were randomly assigned to mesocosms, buoyant weighed following Jokiel (1978), and placed into a standardized grid layout. Each mesocosm contained 20 colonies of each species arranged in alternating species order to avoid species-level clustering effects.</p>
<p><strong>Mesocosm Facility Design</strong></p>
<p>The flow-through mesocosm facility (Jokiel et al. 2014) consisted of twelve 450 L fiberglass tanks operating on continuous seawater flow. Tanks were arranged in four rows of three mesocosms, with each row supplied by a dedicated header tank. Water was pumped at ~3 m depth from the adjacent bay, supplying unfiltered seawater that preserved natural diel and seasonal variability.</p>
<p>Each header tank fed seawater into a 100 L mixing reservoir positioned above the system to facilitate chemical manipulation before seawater entered the mesocosms. Mesocosm residence time was greater than one hour. Each mesocosm contained two submersible circulation pumps and an airstone that ran continuously to maintain water movement and oxygenation.</p>
<p><strong>Treatment Conditions and Carbonate Chemistry Manipulation</strong></p>
<p>Four carbonate chemistry conditions were generated across consecutive 30-day exposures by altering total alkalinity (TA), dissolved inorganic carbon (DIC), and pH. Target conditions included:</p>
<p>1. Ambient control</p>
<p>2. Low pH (ΔpH ~ -0.3 from ambient)</p>
<p>3. High or low TA (±100 µmol kg-1 from ambient)</p>
<p>4. Combined low pH and TA alteration</p>
<p>TA adjustments were made using a peristaltic pump delivering either 1.0 M HCl (for low TA) at ~3 mL min-1 or 1.0 M Na2CO3 (for high TA) at ~2 mL min-1 directly into each row’s mixing tank.<br />
pH reductions were achieved by bubbling pure CO2 or a CO2-air mixture directly into designated mesocosms using a Maxi-Jet 1600 pump-driven venturi injector.</p>
<p>Because each row was supplied by a single header tank, only one direction of TA manipulation (increase or decrease) could be applied per row in a given 30-day experiment. The subsequent 30-day experiment performed the opposite TA manipulation, ensuring all conditions were tested each season.</p>
<p><strong>Seawater Sampling and Measurements</strong></p>
<p><strong>Daily Parameters</strong></p>
<p>Temperature, salinity, dissolved oxygen, and pHNBS were measured daily at mid-day in all mesocosms and header tanks using a YSI multimeter (YSI ProDSS or YSI 556 MPS).</p>
<p>pH electrodes were calibrated daily using NIST-traceable pH 4, 7, and 10 buffers and corrected to the total scale using Tris buffer from A. Dickson (Scripps Institution of Oceanography). Dissolved oxygen calibrations followed manufacturer water-saturated air calibration protocols.</p>
<p><strong>Total Alkalinity Sampling and Storage</strong></p>
<p>Discrete seawater samples (100 mL) for total alkalinity (TA) were collected twice weekly.</p>
<p>Sampling procedures followed best practices described in Dickson et al. (2007):</p>
<p>Rinsed sample bottles three times with sample water.</p>
<p>Collected seawater in acid-cleaned 100 mL borosilicate bottles.</p>
<p>No headspace was left to prevent gas exchange.</p>
<p>Samples were analyzed within 12 hours of collection and stored at ambient temperature in the dark until analysis.</p>
<p><strong>TA Determination</strong></p>
<p>TA was determined using open-cell potentiometric titration on a Metrohm 877 Titrino Plus equipped with a Metrohm 9101 Herisau glass pH electrode.</p>
<p>All titrations were standardized using certified reference materials (CRM, batch number provided by Dickson Laboratory). Electrode slope, offset, and drift were checked daily.</p>
<p>Carbonate system variables (DIC, pCO2, HCO3-, CO32-, and Omega aragonite) were calculated using the R package seacarb.</p>
<p><strong>Calcification Measurements</strong></p>
<p>Calcification rates were quantified using buoyant weighing following Jokiel (1978). Colonies were weighed on day 0 and day 30. Calcification rate (G) was calculated as:</p>
<p>G (g CaCO3 d-1) = 1.54 × (Wf – Wi) / d</p>
<p>where 1.54 g cm-3 is the density of aragonite, Wf and Wi are final and initial buoyant weights, and d is the exposure duration in days.</p>
<p>Three colonies per species per mesocosm were randomly selected for further biometric analysis. Three branch tips per colony were sampled immediately before and after the exposure period. Collected fragments were frozen at -20 C until post-processing.</p>
<p>Mortality was low and did not differ across treatments; dead colonies were excluded from analysis. All corals were returned to the reef at the conclusion of experiments.</p>
<p><strong>Post-Hoc Processing of Coral Samples</strong></p>
<p>At the end of each experimental season, all frozen branch tips were transported to Texas A&amp;M University–Corpus Christi for tissue, symbiont, pigment, and skeletal analysis.</p>
<p>Tissue Removal and Homogenization</p>
<p>Branch tips were thawed and sprayed with phosphate-buffered saline (PBS) using a Paasche airbrush.</p>
<p>Tissue slurry (25 mL) was sonicated for 20 seconds (Qsonica ultrasonic processor).</p>
<p>Samples were vortexed and centrifuged (VWR International centrifuge) to separate host tissue and symbionts.</p>
<p><strong>Host Tissue Analyses</strong></p>
<p>Aliquots of the host fraction were used to quantify protein concentration using spectrophotometry (SpectraMax M3). PBS was used as a blank.</p>
<p><strong>Symbiont Analyses</strong></p>
<p>Symbiont pellets were resuspended and counted using a Bright-Line hemocytometer (Hausser Scientific) under 10× magnification on a Leica ICC50W microscope.</p>
<p><strong>Pigment Analyses</strong></p>
<p>Chlorophyll a and c were extracted using 100 percent acetone. Absorbance was measured on a SpectraMax M3 spectrophotometer, with acetone blanks. Calculations followed Parsons et al. (1984).</p>
<p><strong>Skeletal Preparation and Biometric Measurements</strong></p>
<p>After tissue removal:</p>
<p>Skeletons were soaked in 10 percent bleach to remove remaining tissue.</p>
<p>Samples were dried for 4 hours at 60 C (DX302C drying oven).</p>
<p>Dry weights were recorded using a VWR-4002B2 analytical balance.</p>
<p>Skeletal volume was measured by water displacement in a 100 mL graduated cylinder.</p>
<p>Three-dimensional skeletal scans were generated using an Einscan-SE scanner and processed in MeshLab to estimate total surface area.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2049406 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2049406
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2049407 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2049407
onGoing
Keisha D. Bahr
Texas A&M, Corpus Christi
361-825-3707
6300 Ocean Drive, Unit 5800
Corpus Christi
TX
78412-5844
USA
Keisha.Bahr@tamucc.edu
pointOfContact
Conall McNicholl
Hawaii Institute of Marine Biology
cmcnic@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
experiment
season
mesocosm
treatment
species
coral
tp
chlorophyll_unit_630
chlorophyll_unit_663
protein_unit
symbiont_count_uL
density_g_mL
sa_cm
t_vol_ml
df_ch
df_p
df_s
Flow-through Mesocosm System
YSI Multiparameter Water Quality Meters
CO2 Gas Delivery System
Peristaltic Pumps for TA Manipulation
theme
None, User defined
experiment id
season
tank
treatment
species scientific name (binomial)
individual
sample description
chlorophyll a
chlorophyll c total
protein concentration
abundance
surface_area
sample_volume
featureType
BCO-DMO Standard Parameters
Aquarium
Diving Mask and Snorkel
Multi Parameter Portable Meter
no_bcodmo_term
Pump
Pump
Titrator
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Reevaluating calcification response to changes in seawater chemistry by testing the Proton Flux Hypothesis and the Coral Metabolism Model
https://osprey.bco-dmo.org/project/868178
Collaborative Research: Reevaluating calcification response to changes in seawater chemistry by testing the Proton Flux Hypothesis and the Coral Metabolism Model
<p><em>NSF Award Abstract:</em><br />
Corals build calcium carbonate skeletons to maintain the three-dimensional structure of a coral reef, which provides habitat for many organisms and protects shorelines from bioerosion and storm damage. However, changes in ocean chemistry threaten the ability of corals to build and sustain these ecological important structures. To further the understanding of how climate change impacts coral reefs, this project investigates how changes in ocean carbonate chemistry directly influence coral calcification. The researchers are conducting a series of experiments on corals grown in seawater tanks to study corals responses to seawater chemistry in a changing ocean. Broader impacts of the project include student research opportunities, science-inquiry labs, and virtual learning. This project supports the training of several early career researchers, Ph.D. students, undergraduates, and high school students in the disciplines of chemistry, engineering, and marine ecology. Researchers partner with the Texas State Aquarium to communicate with the general public through a virtual research expedition series that will focus on coral reef health. This series includes interviews, behind the scene tours, and virtual dives on coral reefs in Hawaii.</p>
<p>This project examines the fundamental connections between seawater chemistry and coral physiology by investigating the modulation of seawater chemistry in the microenvironment surrounding corals. Specifically, this project 1) examines the response of corals to differing carbonate chemistry and 2) characterizes the proton gradient across the corals' boundary layers under differing ocean acidification conditions. Results of this work isolate whether carbonate ions or hydrogen ions have a stronger influence on calcification rates. This work utilizes a state-of-the-art experimental mesocosm facility that combines an automated systems to simultaneously and independently control both total alkalinity and carbon dioxide in the tanks to examine coral response under different carbon chemistry scenarios. Small-scale gradients in carbon chemistry surrounding the corals are being characterized using an innovative solid-state, reagentless sensor capable of making simultaneous measurements of two critical carbon system parameters. Coral biological response variables are quantified during short-term incubations and long-term mesocosm manipulations to understand physiological implications across multiple scales (i.e., individual and community scales) and across boundary layers.</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>
Proton Flux Hypothesis
largerWorkCitation
project
eng; USA
oceans
-157.7877
-157.7877
21.4327
21.4327
2022-06-07
2024-03-18
Kaneohe, Hawaii
0
BCO-DMO catalogue of parameters from Coral biological data collected during acute and chronic stress exposures in outdoor mesocosms in Hawaii from January 2022 to March 2024
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/997880.rdf
Name: experiment
Units: unitless
Description: <p>the experiment ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/997881.rdf
Name: season
Units: unitless
Description: <p>the season in which measurements were conducted (smr = summer and wntr = winter)</p>
http://lod.bco-dmo.org/id/dataset-parameter/997882.rdf
Name: mesocosm
Units: unitless
Description: <p>tank identification number</p>
http://lod.bco-dmo.org/id/dataset-parameter/997883.rdf
Name: treatment
Units: unitless
Description: <p>treatment identification (amb = control, co2 = elevated pCO2, lta = lowered total alkalinity, hta = elevated total alkalinity)</p>
http://lod.bco-dmo.org/id/dataset-parameter/997884.rdf
Name: species
Units: unitless
Description: <p>coral species [mc = Montipora capitata (urn:lsid:marinespecies.org:taxname:287697), pa = Pocillopora acuta (urn:lsid:marinespecies.org:taxname:759099)]</p>
http://lod.bco-dmo.org/id/dataset-parameter/997885.rdf
Name: coral
Units: unitless
Description: <p>the coral identification number</p>
http://lod.bco-dmo.org/id/dataset-parameter/997886.rdf
Name: tp
Units: unitless
Description: <p>Timepoint indicator describing sampling day within the experiment since the start (1) before treatment, and (2) after treatment</p>
http://lod.bco-dmo.org/id/dataset-parameter/997887.rdf
Name: chlorophyll_unit_630
Units: micrograms per microliter (ug/uL)
Description: <p>chlorophyll a concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/997888.rdf
Name: chlorophyll_unit_663
Units: micrograms per microliter (ug/uL)
Description: <p>chlorophyll c concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/997889.rdf
Name: protein_unit
Units: micrograms per microliter (ug/uL)
Description: <p>protein concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/997890.rdf
Name: symbiont_count_uL
Units: number per microliter
Description: <p>symbiont abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/997891.rdf
Name: density_g_mL
Units: grams per milliliter
Description: <p>skeletal density</p>
http://lod.bco-dmo.org/id/dataset-parameter/997892.rdf
Name: sa_cm
Units: square centimeters
Description: <p>surface area</p>
http://lod.bco-dmo.org/id/dataset-parameter/997893.rdf
Name: t_vol_ml
Units: milliliters
Description: <p>total volume of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/997894.rdf
Name: df_ch
Units: unitless
Description: <p>dilution factor for chlorophyll</p>
http://lod.bco-dmo.org/id/dataset-parameter/997895.rdf
Name: df_p
Units: unitless
Description: <p>dilution factor for protein</p>
http://lod.bco-dmo.org/id/dataset-parameter/997896.rdf
Name: df_s
Units: unitless
Description: <p>dilution factor for symbiont abundances</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/995164/data/download
download
onLine
dataset
<p><strong>Note: </strong><em>This section includes a description of buoyant-weight data not included in this dataset. See "Related Datasets" section for buoyant-weight data.</em><br />
<br />
<strong>Overview</strong></p>
<p>Seasonal mesocosm incubations of Montipora capitata and Pocillopora acuta were conducted over a two-year period (June 2022–March 2024) at the Hawai‘i Institute of Marine Biology (HIMB). Corals were collected from fringe reefs located around the institute.&nbsp;Experiments were carried out during winter (January 10–March 17) and summer (June 10–August 17) in outdoor flow-through mesocosms at the Hawaii Institute of Marine Biology in Kane`ohe, Hawai`i.&nbsp;Due to facility constraints, all treatments could not run simultaneously. Therefore, each seasonal experiment consisted of two consecutive 30-day exposures, each using newly collected coral colonies. All procedures were standardized across replicates, except for adjustments in total alkalinity (TA) and pH required to create the treatments.</p>
<p><strong>Coral Collection and Pre-Experiment Holding</strong></p>
<p>Coral colonies of Montipora capitata and Pocillopora acuta were collected by hand while snorkeling from shallow (1 m) fringing reef habitat surrounding HIMB in Kāne‘ohe Bay, Hawai‘i. Colonies were transported immediately to the mesocosm facility and held for one week in flow-through tanks that were identical in design to the experimental mesocosms.</p>
<p>One day prior to placement in experimental mesocosms, all colonies were stained for eight hours with alizarin red to mark the initial skeletal growth band (reference: Jokiel and Morrissey 1993).</p>
<p>At the start of each 30-day experiment, colonies were randomly assigned to mesocosms, buoyant weighed following Jokiel (1978), and placed into a standardized grid layout. Each mesocosm contained 20 colonies of each species arranged in alternating species order to avoid species-level clustering effects.</p>
<p><strong>Mesocosm Facility Design</strong></p>
<p>The flow-through mesocosm facility (Jokiel et al. 2014) consisted of twelve 450 L fiberglass tanks operating on continuous seawater flow. Tanks were arranged in four rows of three mesocosms, with each row supplied by a dedicated header tank. Water was pumped at ~3 m depth from the adjacent bay, supplying unfiltered seawater that preserved natural diel and seasonal variability.</p>
<p>Each header tank fed seawater into a 100 L mixing reservoir positioned above the system to facilitate chemical manipulation before seawater entered the mesocosms. Mesocosm residence time was greater than one hour. Each mesocosm contained two submersible circulation pumps and an airstone that ran continuously to maintain water movement and oxygenation.</p>
<p><strong>Treatment Conditions and Carbonate Chemistry Manipulation</strong></p>
<p>Four carbonate chemistry conditions were generated across consecutive 30-day exposures by altering total alkalinity (TA), dissolved inorganic carbon (DIC), and pH. Target conditions included:</p>
<p>1. Ambient control</p>
<p>2. Low pH (ΔpH ~ -0.3 from ambient)</p>
<p>3. High or low TA (±100 µmol kg-1 from ambient)</p>
<p>4. Combined low pH and TA alteration</p>
<p>TA adjustments were made using a peristaltic pump delivering either 1.0 M HCl (for low TA) at ~3 mL min-1 or 1.0 M Na2CO3 (for high TA) at ~2 mL min-1 directly into each row’s mixing tank.<br />
pH reductions were achieved by bubbling pure CO2 or a CO2-air mixture directly into designated mesocosms using a Maxi-Jet 1600 pump-driven venturi injector.</p>
<p>Because each row was supplied by a single header tank, only one direction of TA manipulation (increase or decrease) could be applied per row in a given 30-day experiment. The subsequent 30-day experiment performed the opposite TA manipulation, ensuring all conditions were tested each season.</p>
<p><strong>Seawater Sampling and Measurements</strong></p>
<p><strong>Daily Parameters</strong></p>
<p>Temperature, salinity, dissolved oxygen, and pHNBS were measured daily at mid-day in all mesocosms and header tanks using a YSI multimeter (YSI ProDSS or YSI 556 MPS).</p>
<p>pH electrodes were calibrated daily using NIST-traceable pH 4, 7, and 10 buffers and corrected to the total scale using Tris buffer from A. Dickson (Scripps Institution of Oceanography). Dissolved oxygen calibrations followed manufacturer water-saturated air calibration protocols.</p>
<p><strong>Total Alkalinity Sampling and Storage</strong></p>
<p>Discrete seawater samples (100 mL) for total alkalinity (TA) were collected twice weekly.</p>
<p>Sampling procedures followed best practices described in Dickson et al. (2007):</p>
<p>Rinsed sample bottles three times with sample water.</p>
<p>Collected seawater in acid-cleaned 100 mL borosilicate bottles.</p>
<p>No headspace was left to prevent gas exchange.</p>
<p>Samples were analyzed within 12 hours of collection and stored at ambient temperature in the dark until analysis.</p>
<p><strong>TA Determination</strong></p>
<p>TA was determined using open-cell potentiometric titration on a Metrohm 877 Titrino Plus equipped with a Metrohm 9101 Herisau glass pH electrode.</p>
<p>All titrations were standardized using certified reference materials (CRM, batch number provided by Dickson Laboratory). Electrode slope, offset, and drift were checked daily.</p>
<p>Carbonate system variables (DIC, pCO2, HCO3-, CO32-, and Omega aragonite) were calculated using the R package seacarb.</p>
<p><strong>Calcification Measurements</strong></p>
<p>Calcification rates were quantified using buoyant weighing following Jokiel (1978). Colonies were weighed on day 0 and day 30. Calcification rate (G) was calculated as:</p>
<p>G (g CaCO3 d-1) = 1.54 × (Wf – Wi) / d</p>
<p>where 1.54 g cm-3 is the density of aragonite, Wf and Wi are final and initial buoyant weights, and d is the exposure duration in days.</p>
<p>Three colonies per species per mesocosm were randomly selected for further biometric analysis. Three branch tips per colony were sampled immediately before and after the exposure period. Collected fragments were frozen at -20 C until post-processing.</p>
<p>Mortality was low and did not differ across treatments; dead colonies were excluded from analysis. All corals were returned to the reef at the conclusion of experiments.</p>
<p><strong>Post-Hoc Processing of Coral Samples</strong></p>
<p>At the end of each experimental season, all frozen branch tips were transported to Texas A&amp;M University–Corpus Christi for tissue, symbiont, pigment, and skeletal analysis.</p>
<p>Tissue Removal and Homogenization</p>
<p>Branch tips were thawed and sprayed with phosphate-buffered saline (PBS) using a Paasche airbrush.</p>
<p>Tissue slurry (25 mL) was sonicated for 20 seconds (Qsonica ultrasonic processor).</p>
<p>Samples were vortexed and centrifuged (VWR International centrifuge) to separate host tissue and symbionts.</p>
<p><strong>Host Tissue Analyses</strong></p>
<p>Aliquots of the host fraction were used to quantify protein concentration using spectrophotometry (SpectraMax M3). PBS was used as a blank.</p>
<p><strong>Symbiont Analyses</strong></p>
<p>Symbiont pellets were resuspended and counted using a Bright-Line hemocytometer (Hausser Scientific) under 10× magnification on a Leica ICC50W microscope.</p>
<p><strong>Pigment Analyses</strong></p>
<p>Chlorophyll a and c were extracted using 100 percent acetone. Absorbance was measured on a SpectraMax M3 spectrophotometer, with acetone blanks. Calculations followed Parsons et al. (1984).</p>
<p><strong>Skeletal Preparation and Biometric Measurements</strong></p>
<p>After tissue removal:</p>
<p>Skeletons were soaked in 10 percent bleach to remove remaining tissue.</p>
<p>Samples were dried for 4 hours at 60 C (DX302C drying oven).</p>
<p>Dry weights were recorded using a VWR-4002B2 analytical balance.</p>
<p>Skeletal volume was measured by water displacement in a 100 mL graduated cylinder.</p>
<p>Three-dimensional skeletal scans were generated using an Einscan-SE scanner and processed in MeshLab to estimate total surface area.</p>
Specified by the Principal Investigator(s)
<p><strong>Note:&nbsp;</strong><em>This section includes a description of buoyant-weight data not included in this dataset. See "Related Datasets" section for buoyant-weight data.</em><br />
<br />
<strong>Overview</strong></p>
<p>Data processing included organization of raw seawater chemistry measurements, conversion of pH values to the total scale, calculation of carbonate system parameters, buoyant-weight based calcification calculations, and post-hoc biochemical and skeletal data extraction. All steps described below represent the procedures used to generate the submitted dataset. No statistical analysis, modeling, or graphing is included here.</p>
<p><strong>1. Seawater Chemistry Data Processing</strong></p>
<p><strong>pH Conversion</strong></p>
<p>Daily pHNBS measurements from the YSI multiparameter meter were converted to total scale (pHT) using Tris buffer reference standards prepared and certified by the Dickson Laboratory. Temperature-dependent conversion equations followed Dickson et al. (2007).<br />
All pH values were standardized across seasons using:</p>
<p>pHT = pHNBS + (Δbuffer offset)</p>
<p>where Δbuffer offset was determined daily from Tris-buffer calibration measurements.</p>
<p><strong>Total Alkalinity (TA)</strong></p>
<p>Raw potentiometric titration files from the Metrohm 877 Titrino Plus were exported using Metrohm tiamo software (version 2.5).<br />
Processing included:</p>
<p>Drift correction and electrode slope verification.</p>
<p>CRM standardization using certified values for TA (Dickson Laboratory, batch number provided in metadata).</p>
<p>Extraction of equivalence point and TA value using open-cell titration algorithms embedded in tiamo.</p>
<p>TA values were reported in µmol kg-1.<br />
If sample density was required, seawater density was calculated using temperature and salinity data following Fofonoff and Millard (1983).</p>
<p><strong>Carbonate System Calculations</strong></p>
<p>Carbonate chemistry parameters (DIC, pCO2, HCO3-, CO32-, and Omega aragonite) were calculated using the R package seacarb (version 3.3.1).<br />
Inputs included:</p>
<p>pHT (corrected)</p>
<p>Total alkalinity</p>
<p>Temperature</p>
<p>Salinity</p>
<p>Default seacarb constants (k1k2 = "l", kf = "pf", ks = "d") were applied unless otherwise noted.</p>
<p>Outputs were merged into the final seawater chemistry dataset with unique sample IDs matching mesocosm, date, and header source.</p>
<p>&nbsp;</p>
<p><strong>2. Coral Calcification Data Processing</strong></p>
<p><strong>Buoyant Weight</strong></p>
<p>Raw buoyant weight values (g) were recorded at day 0 and day 30 for each colony.<br />
Calcification rate (G) was calculated following Jokiel (1978):</p>
<p>G (g CaCO3 d-1) = 1.54 × (Wf – Wi) / d</p>
<p>where 1.54 g cm-3 is aragonite density, Wf is final buoyant weight, Wi is initial buoyant weight, and d is the exposure duration (30 days).<br />
Results were merged into a calcification table by colony ID, species, treatment, mesocosm, and season.</p>
<p>&nbsp;</p>
<p><strong>3. Tissue and Symbiont Processing</strong></p>
<p><strong>Coral Tissue Extraction</strong></p>
<p>Lab-generated tissue datasets included:</p>
<p>Host protein concentration</p>
<p>Symbiont cell density</p>
<p>Chlorophyll a and c concentrations</p>
<p>Processing steps:</p>
<p>Tissue slurry absorbance values were exported from the SpectraMax M3 software (SoftMax Pro, version 7.0).</p>
<p>Blanks (PBS for protein; acetone for chlorophyll) were subtracted from all readings.</p>
<p>Protein concentrations were calculated using standard curves prepared from bovine serum albumin (BSA).</p>
<p>Chlorophyll concentrations were calculated following Parsons et al. (1984) using:</p>
<p>Chl a = 11.85 A664 - 1.54 A647 - 0.08 A630<br />
Chl c = 24.52 A630 - 1.67 A664</p>
<p>Symbiont cell counts obtained via hemocytometer were converted to cells cm-2 by dividing by coral fragment surface area (see 3D scan section below).</p>
<p>All tissue-based metrics were matched to corresponding colony IDs using unique fragment barcodes.</p>
<p>&nbsp;</p>
<p><strong>4. Skeletal Processing</strong></p>
<p><strong>Dry Weight and Volume</strong></p>
<p>Dry weight (g) and volume (cm3) were combined to calculate skeletal density:</p>
<p>Density (g cm-3) = Dry mass / Volume</p>
<p>Volume was determined by water displacement using a 100 mL graduated cylinder.<br />
Each cylinder was checked against manufacturer volume tolerances.</p>
<p><strong>3D Scanning</strong></p>
<p>Skeletal fragments were scanned using the Einscan-SE scanner.<br />
Processing included:</p>
<p>Scan alignment and surface reconstruction in Einscan software (version 3.1).</p>
<p>Export of 3D mesh files (.stl format).</p>
<p>Mesh cleaning and area estimation in MeshLab (version 2022.02).</p>
<p>Surface area values (cm2) were merged into the biometric dataset using fragment ID numbers.</p>
<p>&nbsp;</p>
<p><strong>5. Data Organization and Quality Control</strong></p>
<p>Data Entry and Validation</p>
<p>All raw files (TA titrator outputs, YSI logs, spectrophotometer outputs, and 3D scanner files) were manually inspected before integration.<br />
Data validation steps included:</p>
<p>Removal of erroneous YSI readings (known sensor failure events, &gt;3 SD outliers).</p>
<p>Titration rejection if CRM recovery was outside ±1 percent.</p>
<p>Elimination of samples with visible air bubbles during buoyant weighing.</p>
<p>Duplicate measurements averaged when replicates differed by &lt;5 percent; otherwise re-measured.<br />
&nbsp;</p>
<p><strong>Data Integration</strong></p>
<p>All processed data were merged into the submission dataset using unique identifiers:</p>
<p>Season</p>
<p>Mesocosm number</p>
<p>Treatment</p>
<p>Species</p>
<p>Colony ID</p>
<p>Fragment ID (for biometrics)</p>
<p>Integrated datasets were exported as .csv files using R version 4.2.0.</p>
<p>&nbsp;</p>
<p><strong>6. Software Used</strong></p>
<p>R version 4.2.0</p>
<p>seacarb version 3.3.1</p>
<p>Metrohm tiamo version 2.5</p>
<p>Molecular Devices SoftMax Pro version 7.0</p>
<p>Einscan-SE Scanner Software version 3.1</p>
<p>MeshLab version 2022.02</p>
<p>Microsoft Excel 365 (data organization and file formatting only)</p>
Specified by the Principal Investigator(s)
- Loaded three CSV files (env_data.csv, sw_chem.csv, crm_tris_std.csv) using filenames as resource names, with missing values defined as "", "nd", and "NA"
- Loaded bio_data.csv as table "995164_v1_coral-biological-data" with missing values defined as "", "nd", and "NA"
- Renamed column "experiment (#)" to "experiment_num" in crm_tris_std
- Converted date col from %m/%d/%Y to ISO 8601 format (%Y-%m-%d) in crm_tris_std, env_data, and sw_chem; the tod column in sw_chem contains "day"/"night" text values, not actual times, so no ISO datetime conversion was applied to it
- Applied find/replace on tod_hr in env_data to add missing colons to time values in HHMM/HMM format (e.g., "2300" → "23:00")
- Applied second find/replace on tod_hr in env_data to standardize format to HH:MM by truncating seconds and zero-padding hours; values already containing colons (e.g., "23:00") were left unchanged
- Set col types for all four resources: numeric fields as number or integer, date fields as date with %Y-%m-%d format, tod_hr in env_data as time with %H:%M format, and various categorical fields as string
- Output written to env_data.csv, sw_chem.csv, crm_tris_std.csv, and 995164_v1_coral-biological-data.csv
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Flow-through Mesocosm System
Flow-through Mesocosm System
PI Supplied Instrument Name: Flow-through Mesocosm System PI Supplied Instrument Description:Reference: Jokiel et al. 2014
Description: Outdoor continuous-flow mesocosm facility at HIMB consisting of twelve 450 L fiberglass tanks (1 m x 1 m x 0.5 m) supplied by seawater pumped from ~3 m depth in Kāneʻohe Bay.
Flow: Adjustable head box delivering ~50 min-1 seawater residence time.
Notes: All mesocosms contained two submersible pumps and an airstone for continuous mixing. Instrument Name: Aquarium Instrument Short Name:Aquarium Instrument Description: Aquarium - a vivarium consisting of at least one transparent side in which water-dwelling plants or animals are kept
PI Supplied Instrument Name: PI Supplied Instrument Description:Snorkel-based Coral Collection Gear
Use: Hand-collection of coral colonies at 1 m depth surrounding HIMB.
Notes: Standard snorkeling gear (mask, snorkel, fins) and hand tools (bone cutters, chisels) were used; no specialized electronic instrumentation. Instrument Name: Diving Mask and Snorkel Instrument Short Name: Instrument Description: A diving mask (also half mask, dive mask or scuba mask) is an item of diving equipment that allows underwater divers, including, scuba divers, free-divers, and snorkelers to see clearly underwater.
Snorkel: A breathing apparatus for swimmers and surface divers that allows swimming or continuous use of a face mask without lifting the head to breathe, consisting of a tube that curves out of the mouth and extends above the surface of the water.
YSI Multiparameter Water Quality Meters
YSI Multiparameter Water Quality Meters
PI Supplied Instrument Name: YSI Multiparameter Water Quality Meters PI Supplied Instrument Description:YSI ProDSS
YSI 556 MPS
Manufacturer: YSI Inc.
Parameters Measured: Temperature, salinity, dissolved oxygen, and pHNBS.
Calibration:
DO probe calibrated daily using water-saturated air.
pH electrode calibrated daily using pH 4, 7, and 10 NIST buffers; corrected to total scale using Tris buffer from Dickson Laboratory.
Conductivity and temperature routinely checked using certified standards. Instrument Name: Multi Parameter Portable Meter Instrument Short Name: Instrument Description: An analytical instrument that can measure multiple parameters, such as pH, EC, TDS, DO and temperature with one device and is portable or hand-held.
CO2 Gas Delivery System
CO2 Gas Delivery System
PI Supplied Instrument Name: CO2 Gas Delivery System PI Supplied Instrument Description:Components: CO2 cylinder, regulator, and gas injection line.
Use: Manipulation of mesocosm pH by bubbling pure CO2 or CO2-air mixtures directly into individual mesocosms.
Calibration: Flow checked daily using bubble-rate timing; regulator pressures recorded each morning. Instrument Name: no_bcodmo_term Instrument Short Name: Instrument Description: No relevant match in BCO-DMO instrument vocabulary. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/999/
PI Supplied Instrument Name: PI Supplied Instrument Description:Submersible Pumps
Manufacturer: Maxi-Jet
Model: Maxi-Jet 1600
Use: Internal water circulation and CO2 injection mixing inside mesocosms.
Calibration: Flow rate verified twice per season using volumetric bucket timing. 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
Peristaltic Pumps for TA Manipulation
Peristaltic Pumps for TA Manipulation
PI Supplied Instrument Name: Peristaltic Pumps for TA Manipulation PI Supplied Instrument Description:Manufacturer: To be filled by user (brand not provided)
Flow Rate: 2–3 mL min-1
Use: Delivery of 1.0 M HCl or 1.0 M Na2CO3 to achieve target alkalinity offsets.
Calibration: Flow rate calibrated at the start of each 30-day experiment by measuring timed output volumes. 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
PI Supplied Instrument Name: PI Supplied Instrument Description:Open-cell Potentiometric Titrator for Total Alkalinity
Manufacturer: Metrohm
Model: 877 Titrino Plus with 9101 Herisau glass pH electrode
Use: Measurement of TA from discrete 100 mL seawater samples twice weekly.
Calibration:
Daily electrode slope and offset verification.
Weekly CRM calibration using certified reference materials from A. Dickson (batch number supplied by user).
Notes: All titrations performed at constant temperature. Instrument Name: Titrator Instrument Short Name:Titrator Instrument Description: Titrators are instruments that incrementally add quantified aliquots of a reagent to a sample until the end-point of a chemical reaction is reached. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB12/