README: Dataset for Oyster reefs’ control of carbonate chemistry – implications for oyster reef restoration in estuaries subject to coastal ocean acidification

This set of files contains the primary data supporting the results/figures for this study. The data are grouped into relevant subfolders:

Discrete sampling 2021 data
High frequency environmental monitoring data
Juvenile oyster experimental data
Oyster reef growth and calcification data

Description of the Data files

All data are stored in csv file formats.
Missing data are coded as nan.

Discrete sampling 2021

carbchem.csv - all discrete measures of DIC and TA along with relevant environmental variables

The following columns are included in the dataset:
'datetime_utc' (date and time in Coordinated Universal Time),
'site' (site, sc: 'Sedge Control', sr1: 'Sedge Reef 1', sr2: 'Sedge Reef 2')
'ta_µmolkg-1' (total alkalinity in micromoles per kilogram)
'dic_µmolkg-1' (dissolved inorganic carbon in micromoles per kilogram)
'sal' (salinity)
'temp_degc' (temperature in degrees celsius)
'do_sat' (dissolved oxygen in percent saturation)
'do_mgl' (dissolved oxygen in milligrams per liter)
'aou'(apparent oxygen utilization in micromoles per kilogram)

chlorophyll.csv - raw chlorophyll measurements by date and site

The following columns are included in the dataset:
'date' (date),
'chl' (chlorophyll in micrograms per liter),
'site' (site; sc: 'Sedge Control', sr1: 'Sedge Reef 1', sr2: 'Sedge Reef 2')

macroalgae.csv - replicate quadrat measurements of macroalgae percent cover by date and site

The following columns are included in the dataset:
'date' (date),
'quadrat' (quadrat number, n=8 per date),
'site' (site; sc: 'Sedge Control', sr1: 'Sedge Reef 1', sr2: 'Sedge Reef 2')
'coverage_pct' (estimated percent cover of macroalgae within quadrat)

High frequency environmental monitoring

environmental_hf.csv - high frequency biogeochemical monitoring data at reef and control sites

The following columns are included in the dataset:
'datetime_utc' (date and time in Coordinated Universal Time)
'temp' (temperature in degrees celsius)
'sal' (salinity)
'vert' (depth in meters)
'tide' (tidal depth in meters)
'dosat' (dissolved oxygen in percent saturation)
'domgl' (dissolved oxygen in milligrams per liter)
'phn' (pH on NBS scale)
'site' (site; qc: 'Quogue Control', qr: 'Quogue Reef', sc: 'Sedge Control', sr1: 'Sedge Reef 1', sr2: 'Sedge Reef 2')
'note' (codes for missing data; 'cle_cal': cleaning or recalibration occurred, 'qc' flagged during qc process, 'bat': battery issue prevented collection, 'uer' : user error inhibited logging at sites)

sc_daily.csv - daily means, minima, maxima, and ranges of pH and dissolved oxygen at the 'Sedge Control' site

sr1_daily.csv - daily means, minima, maxima, and ranges of pH and dissolved oxygen at the 'Sedge Reef 1' site

sr2_daily.csv - daily means, minima, maxima, and ranges of pH and dissolved oxygen at the 'Sedge Reef 2' site

qc_daily.csv - daily means, minima, maxima, and ranges of pH and dissolved oxygen at the 'Quogue Control' site

qr_daily.csv - daily means, minima, maxima, and ranges of pH and dissolved oxygen at the 'Quogue Reef' site

The following columns are included in the above datafiles:
'date' (date in Coordinated Universal Time),
'phn_mean' (mean daily pH on the NBS scale),
'phn_min' (minimum daily pH on the NBS scale),
'phn_max' (maximum daily pH on the NBS scale),
'phn_range' (daily pH range on the NBS scale),
'dosat_mean' (mean daily dissolved oxygen in percent saturation),
'dosat_min' (minimum daily dissolved oxygen in percent saturation),
'dosat_max' (maximum daily dissolved oxygen in percent saturation),
'dosat_range' (daily dissolved oxygen range in percent saturation)

Data coded as nan indicates that at least one dissolved oxygen and/or pH measurement (collected at a 15-min frequency) was missing on a particular date.

Juvenile oyster experimental data

juvexpt_2020.csv - Juvenile oyster heights measured during the 2020 field experiment in the Sedge region

juvexpt_2021.csv - Juvenile oyster heights measured during the 2021 field experiment in the Sedge region

The following columns are included in the above datafiles:
'date' (date),
'height' (oyster height in millimeters),
'site' (site; sc: 'Sedge Control', sr1: 'Sedge Reef 1', sr2: 'Sedge Reef 2')
'tray' (replicate experimental tray; naming indicates site and tray number, e.g., sc-1: sedge control tray 1)

Oyster reef growth and calcification data

reefheight.csv - Average oyster heights measured in replicate 'monitoring spat on shell bags' seasonally on 'Quogue Reef', 'Sedge Reef 1', and 'Sedge Reef 2'

The following columns are included in the dataset:
'date' (date)
'mbag' (replicate 'monitoring spat on shell bag' number)
'avg_sh' (average shell height)
'site' (site; qc: 'Quogue Control', qr: 'Quogue Reef', sc: 'Sedge Control', sr1: 'Sedge Reef 1', sr2: 'Sedge Reef 2')

reefdensity.csv - Average density of oysters on 'Quogue Reef', 'Sedge Reef 1', and 'Sedge Reef 2' by year

The following columns are included in the dataset:
'year' (year)
'mbag' (replicate 'monitoring spat on shell bag' number)
'r_density' (oyster density per meter squared, based on counts of live oysters in monitoring spat on shell bags)
'o_growth' (average oyster growth in millimeters, based on the annual difference in average oyster height of oysters on replicate 'monitoring spat on shell bags')

sr_massheight.csv - shell masses and heights of oysters located on reefs within the Sedge region

The following columns are included in the dataset:
'age' (age class of individual oyster in years)
'height_mm' (height in millimeters)
'mass_g' (mass in grams)

calcification.csv - Approximations of reef-wide calcification of Sedge reefs in 2021 utilizing allometric relationship established in Fig. S2

The following columns are included in the dataset:
'site' (reef site; sr1: 'Sedge Reef 1' and sr2: 'Sedge Reef 2')
'mbag' (replicate 'monitoring spat on shell bag' number)
'2020_hgt' (average shell height of individual oysters in 2020)
'2021_hgt' (average shell height of individual oysters in 2021)
'2020_mass' (average shell mass of individual oysters in 2020; derived from allometric relationship established in Fig. S2)
'2021_mass' (average shell mass of individual oysters in 2021; derived from allometric relationship established in Fig. S2)
'2021_gain' (average shell mass gained per individual oyster from 2020 to 2021; derived by subtracting '2020_mass' from '2021_mass')
'2021_caco3' (average mass of calcium carbonate added from 2020 to 2021 per individual oyster; derived by multiplying 2021 gain by 0.95)
'density' (2021 oyster density per meter squared, based on counts of live oysters in monitoring spat on shell bags)
'reef_calc' (estimates of reef-wide calcification in g of calcium carbonate per meter squared; derived by multiplying '2021_caco3' by 'density')