This dataset contains carbonate chemistry, physiological response, and incubation measurements from controlled static incubations of two Hawaiian coral species, Montipora capitata (branching and plating morphologies, urn:lsid:marinespecies.org:taxname:287697) and Pocillopora acuta (urn:lsid:marinespecies.org:taxname:759099). Corals were exposed to a series of experimental seawater chemistry treatments designed to independently manipulate proton concentration and carbonate ion availability through adjustments to total alkalinity and dissolved inorganic carbon. Treatments spanned ambient conditions as well as elevated and reduced total alkalinity, elevated and reduced pH, and combinations of altered pH and alkalinity. For each treatment, seawater parameters were measured, including temperature, salinity, dissolved oxygen, pH on the total scale, total alkalinity, bicarbonate, carbonate ion concentration, pCO2, dissolved inorganic carbon, and aragonite saturation state. Coral incubations were conducted under static conditions to quantify changes in carbonate chemistry associated with coral metabolic activity and to assess species- and morphology-specific calcification responses across distinct carbonate system states. This dataset supports the evaluation of the Proton Flux Hypothesis and Coral Metabolism Model by providing detailed carbonate chemistry conditions and coral responses across a spectrum of experimentally generated seawater states.

Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
  • Problem Description
• Data Files
• Related Publications
• Parameters
• Instruments
• Project Information
• Funding

Coral Collection and Pre-Experiment Holding

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.

Incubation Design

Incubations were conducted in a temperature-controlled water bath, under full-spectrum lighting (Wattshine 400w LEDs) set to ~800 PAR µmol m^-2 s^-1. Incubation chambers were closed-cell, with stirbars spinning via a belt-controlled magnet dial that was submerged entirely.  Corals were placed in a plug holder in the middle of each chamber, and chambers were numbered and haphazardly placed on the submerged racks. Corals were acclimated for 1 hr to treatment conditions before incubation, then closed in each chamber for either 1, 2, or 4 hr intervals based on preliminary assessments of calcification rates.  Seawater after this period was collected in borosilicate bottles for total alkalinity analysis, and separately in beakers for physical and chemical analysis with a YSI. 

Treatment Conditions and Carbonate Chemistry Manipulation

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:

1. Ambient control

2. Low pH (ΔpH ~ -0.3 from ambient)

3. High or low TA (±100 µmol kg-1 from ambient)

4. Combined low pH and TA alteration

5. High pH  (ΔpH ~ 0.3 from ambient)

6. Combined high pH and TA alteration

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.
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.

Seawater Sampling and Measurements

Daily Parameters

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).

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.

Total Alkalinity Sampling and Storage

Discrete seawater samples (100 mL) for total alkalinity (TA) were collected twice weekly.

Sampling procedures followed best practices described in Dickson et al. (2007):

Rinsed sample bottles three times with sample water.

Collected seawater in acid-cleaned 100 mL borosilicate bottles.

No headspace was left to prevent gas exchange.

Samples were analyzed within 12 hours of collection and stored at ambient temperature in the dark until analysis.

TA Determination

TA was determined using open-cell potentiometric titration on a Metrohm 877 Titrino Plus equipped with a Metrohm 9101 Herisau glass pH electrode.

All titrations were standardized using certified reference materials (CRM, batch number provided by Dickson Laboratory). Electrode slope, offset, and drift were checked daily.

Carbonate system variables (DIC, pCO2, HCO3-, CO32-, and Omega aragonite) were calculated using the R package seacarb.

Calcification Measurements

Calcification rates were quantified using buoyant weighing following Jokiel et al. (1978). Colonies were weighed on day 0 and day 30. Calcification rate (G) was calculated as:

G (g CaCO3 d-1) = 1.54 × (Wf – Wi) / d

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.

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.

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 the experiments.

Overview

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.

Seawater Chemistry Data Processing

pH Conversion

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).
All pH values were standardized across seasons using:

pHT = pHNBS + (Δbuffer offset)

where Δbuffer offset was determined daily from Tris-buffer calibration measurements.

Total Alkalinity (TA)

Raw potentiometric titration files from the Metrohm 877 Titrino Plus were exported using Metrohm tiamo software (version 2.5).
Processing included:

Drift correction and electrode slope verification.

CRM standardization using certified values for TA (Dickson Laboratory, batch number provided in metadata).

Extraction of equivalence point and TA value using open-cell titration algorithms embedded in tiamo.

TA values were reported in µmol kg-1.
If sample density was required, seawater density was calculated using temperature and salinity data following Fofonoff and Millard (1983).

Carbonate System Calculations

Carbonate chemistry parameters (DIC, pCO2, HCO3-, CO32-, and Omega aragonite) were calculated using the R package seacarb (version 3.3.1).
Inputs included:

pHT (corrected)

Total alkalinity

Temperature

Salinity

Default seacarb constants (k1k2 = "l", kf = "pf", ks = "d") were applied unless otherwise noted.

Outputs were merged into the final seawater chemistry dataset with unique sample IDs matching mesocosm, date, and header source.

Coral Calcification and Productivity Data Processing

Alkalinity Anomaly Technique
Calcification rate (G) was calculated utilizing the change in total alkalinity.

Gnet (umol CaCO3 g-1 h-1) = –0.5 × (ΔTA in µmol kg⁻¹) × (water mass in kg) ÷ (dry mass in g × time in hours)

Pnet (mol g⁻¹ h⁻¹) = (ΔDO in mg L⁻¹ × volume in L × 1×10⁻³ ÷ molecular weight of O₂ in g mol⁻¹) ÷ (dry mass in g × time in hours)

Data Organization and Quality Control

Data Entry and Validation

All raw files (TA titrator outputs, YSI logs, spectrophotometer outputs, and 3D scanner files) were manually inspected before integration.
Data validation steps included:

Removal of erroneous YSI readings (known sensor failure events, >3 SD outliers).

Titration rejection if CRM recovery was outside ±1 percent.

Elimination of samples with visible air bubbles during buoyant weighing.

Duplicate measurements averaged when replicates differed by <5 percent; otherwise re-measured.

Software Used

R version 4.2.0

seacarb version 3.3.1

Metrohm tiamo version 2.5

Microsoft Excel 365 (data organization and file formatting only)

Dataset Version 1 (2026-03-30)

Data File:
- Loaded "all_inc_final.csv" as resource "995172_v1_incubation-data" in CSV format with row 1 as headers; missing values coded as empty string, "nd", or "NA"
- Converted field "date" from format "%m/%d/%Y" to ISO date format "%Y-%m-%d", output as date type
- Set field types: "date" as date (%Y-%m-%d), "time" and "genotype" (as string and integer respectively — "time" as integer, "genotype" as string), numeric fields "TA_1", "TA_2", "beaker_mass", "bwt", "crm_205", "do_mg_l", "ph_mv", "ph_nbs", "sal", "sw_mass", "temp", "tris_41" as number, and string fields "condition", "genotype", "species", "titrator", "treatment"
- table sorted chronologically using column sort order '{date}{species}{treatment}{condition}{genotype}{time}'
- Output written to "995172_v1_incubation-data.csv"

None

Coverage: Kaneohe, Hawaii

NSF Award Abstract:
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.

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.

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.