Dataset: Incubation data for Mytilus californianus calcification

Name: Incubation data for Mytilus californianus calcification from January to April 2022 (OA decoupling project)
Published: 2024-05-06
Keywords: calcification, ocean acidification, carbonate chemistry, mussel, oceans

Cite This Dataset

Spatial Extent: N:38.371361 E:-123.076306 S:38.371361 W:-123.076306

Laboratory experiments were conducted at the Bodega Marine Laboratory in Bodega Bay, CA, USA and specimens were collected from Carmet Beach

Temporal Extent: 2022-01-13 - 2022-04-23

Project:

Invertebrate calcification and behavior in seawater of decoupled carbonate chemistry (OA decoupling)

Principal Investigator:

Brian Gaylord (University of California-Davis, UC Davis)

Student:

Aaron T. Ninokawa (University of California-Davis, UC Davis-BML)

Alisha Saley (University of California-Davis, UC Davis-BML)

Roya Shalchi (University of California-Davis, UC Davis-BML)

Contact:

Aaron T. Ninokawa (State University of New York College of Environmental Science and Forestry, SUNY ESF)

BCO-DMO Data Manager:

Sawyer Newman (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-05-06

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Incubation data for Mytilus californianus calcification from January to April 2022 (OA decoupling project)

Abstract:

Calcification is vital to marine organisms that produce calcium carbonate shells and skeletons. However, how calcification is impacted by ongoing environmental changes, including ocean acidification, remains incompletely understood due to complex relationships among the carbonate system variables hypothesized to drive calcification. Here, we experimentally decouple these drivers in an exploration of shell formation in adult marine mussels, Mytilus californianus. In contrast to models that focus on single parameters like calcium carbonate saturation state, our results implicate two independent factors, bicarbonate concentration and seawater pH, in governing calcification. While qualitatively similar to ideas embodied in the related substrate-inhibitor ratio (bicarbonate divided by hydrogen ion concentration), our data highlight that merging bicarbonate ion and hydrogen ion concentrations into a simple quotient obscures important features of calcification. Considering a dual-parameter framework improves mechanistic understanding of how calcifiers interact with complex and changing chemical conditions.

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Description

Each row of the primary file of this dataset corresponds to incubation data collected while exposing an individual mussel to modified seawater.

Methods & Sampling

Sampling collection details

We gathered naturally settled, adult California mussels (M. californianus between 30 and 80 mm in maximum shell length) by hand from the mid-intertidal zone of Carmet Beach, along the northern California coast. We cleaned mussels of all epibionts and external byssal threads, then transported them in buckets (< 0.5 hr transit time) to Bodega Marine Laboratory, where we acclimated individuals for seven days in flow-through seawater tables prior to subsequent experiments.

Experiment details

Incubations conducted according to published methods (Gazeau et al 2015).

Seawater chemistry was controlled to target unique combinations of alkalinity (between 337 and 9584 µmol kg-1) and dissolved inorganic carbon (DIC, between 299 and 9322 µmol kg-1). Carbonate chemistry manipulations were accomplished by first acidifying seawater to an alkalinity of 0 and allowing DIC to offgas. Then alkalinity and DIC were replaced by adding a known amount of a DIC stock (sodium carbonate and sodium bicarbonate) to each incubation vessel and alkalinity adjusted with either HCl or NaOH. Additional incubations further modified salinity and calcium concentrations by the addition of known amounts of distilled water and calcium chloride.

Mussel response was quantified as the calcification rate measured with the alkalinity anomaly technique corrected for ammonia production (Gazeau et al 2015). Calcification rates are expressed as gross calcification where net calcification = gross calcification - dissolution. Dissolution rates were quantified separately and can be found in the dataset: Shell dissolution data for Mytilus californianus from March to July 2020 (OA decoupling project). A link to this dataset can be found within the Related Datasets section of this metadata page.

Data Processing Description

We calculated net calcification rates with the ammonia-corrected alkalinity anomaly technique (Gazeau et al 2015), divided by incubation duration and mussel dry tissue mass raised by a factor of 0.72 (see related dataset). The alkalinity anomaly technique builds on the observation that precipitation of CaCO3 results in an equivalent reduction in seawater [CO32-] (or reduction of [HCO3-] followed by an increase in [H+]) which contributes two equivalents of total alkalinity—simultaneous production of ammonia is the major metabolic process in mussels that can obscure this and its signal must be removed (Gazeau et al 2015).

Following the incubation, we dissected each mussel and dried it at 60 °C for at least 24 hours to obtain the dry tissue mass (excluding byssal threads) and dry shell mass of each individual mussel. We conducted additional incubations (n=87, between 3 and 9 per experiment day) without mussels throughout the trials as experimental blanks to determine background changes in alkalinity (Figure S7). We excluded from our analysis any experimental days where background alkalinity changes exceeded 5 µmol kg-1. The mean of the absolute values of alkalinity change during the incubations of these experimental blanks was 1.3 ± 1.2 µmol kg-1 (n = 72).

We performed all computations with R statistical software, version 4.1.0. We performed carbonate system calculations using the package seacarb, using equilibrium constants from Lueker et al. We computed linear mixed models using the lmer function in in the lmertest package in R and focused on assessing likely candidate parameters as fixed factors, and mussel collection date as a random intercept to account for natural seasonal differences between cohorts. Conditional R2 was calculated with the package MuMIn. We determined parameters for non-linear fits employed to model dissolution rates by minimizing the sum of squares of model residuals using the optim function. Colors for plots were chosen from color palettes in the cmocean package in R.

BCO-DMO Processing

- Removed special characters (e.g., periods) from column names and replaced with underscores
- Converted dates and datetimes from Excel format to %Y-%m-%d and %Y-%m-%dT%H:%M:%S, respectively
- Changed the presentation of species values from "mytilus_californianus" to "Mytilus californianus" and added AphiaID and LSID to the data file
- ph_total and ph_free columns rounded to 3 degrees of precision, and all other float numeric fields rounded to 2 degrees of precision

Data Files

File
925598_v1_incubation_data_for_Mytilus_californianus_calcification.csv (Comma Separated Values (.csv), 93.96 KB) MD5:7871de9e437a4da1dcd21393967e144e Primary data file for dataset ID 925598, version 1

Supplemental Files

File
Figure 1.png (Portable Network Graphics (.png), 129.29 KB) MD5:32303e0bfe3af910de45537d43db2d02 Figure 1 referenced in data file from pending results publication.
Figure 2.png (Portable Network Graphics (.png), 154.10 KB) MD5:7cb2a82b72aa6f9b41c646d94589a002 Figure 2 referenced in data file from pending results publication.
Figure 3.png (Portable Network Graphics (.png), 76.03 KB) MD5:ed9d51894f77775f6afc338b17f8a486 Figure 3 referenced in data file from pending results publication.
Figure 4.png (Portable Network Graphics (.png), 63.74 KB) MD5:5c6d4e49edc46f55a0d036082b739b8e Figure 4 referenced in data file from pending results publication.
Figure 5.png (Portable Network Graphics (.png), 158.75 KB) MD5:608433f0f4966ef4ca1f534fed3d1bbe Figure 5 referenced in data file from pending results publication.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2129942

Deployments

None available yet

Instruments

UV Spectrophotometer-Shimadzu

Supplied Name: Shimadzu spectrophotometer

Supplied Description:

A Shimadzu spectrophotometer was used to conduct spectrophotmetric pH and ammonia analyses.

Instrument Type

Generic Name: UV Spectrophotometer-Shimadzu

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/

Generic Description:

The Shimadzu UV Spectrophotometer is manufactured by Shimadzu Scientific Instruments (ssi.shimadzu.com). Shimadzu manufacturers several models of spectrophotometer; refer to dataset for make/model information.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
species	Mussel species used in incubation	unitless	species
AphiaID	Unique identifier for the listed taxon in the Aphia database	unitless	taxon_code
LSID	Life Science Identifier (LSID) for the listed taxon	unitless	taxon_code
module	Experimental module corresponding to different mussel collection events	unitless	sample_type
date_local	Incubation date in Pacific Standard Time Format: %Y-%m-%d	unitless	date
start_datetime_local	Start datetime of the incubation in Pacific Standard Time Format: %Y-%m-%d %H:%M:%S	unitless	time_begin
ISO_Start_DateTime_UTC	Start datetime of the incubation in UTC Format: %Y-%m-%dT%H:%M:%SZ	unitless	time_begin
duration	Duration of incubation in hours	hours	time_inc
salinity	Incubation salinity	PSU	sal
temperature	Incubation Temperature	degrees Celcius (c)	temp_inc
calcification	Calcification rate of mussel, can be calculated within this dataset as ( (-0.5 * (delta.ta - delta.nh3) * incubation.water.mass) - calc.diss) /duration/ tissue.mass^0.71592	umol hr^-1 g^-0.71592	calcification
tissue_mass	Dried mussel tissue mass	grams (g)	mass_dry
shell_mass	Dried mussel shell mass	grams (g)	mass_dry
wet_mass	Wet mass of mussel prior to incubation	grams (g)	mass
TA	Mean alkalinity during incubation	umol kg-1	TALK
ph_total	Mean pH during incubation, total scale	unitless	pH
hco3	Mean bicarbonate ion concentration during incubation	umol kg-1	bicarbonate
co3	Mean carbonate ion concentration during incubation	umol kg-1	carbonate
omega	Mean aragonite saturation state during incubation, corrected for calcium concentration where calcium was modified	unitless	OM_ar
omegac	Mean calcite saturation state during incubation, corrected for calcium concentration where calcium was modified	unitless	OM_ca
ca	Calcium concentration during incubation, either calculated from salinity or measured with Ca ion selective electrode	mol kg-1	Ca
ph_free	Mean pH during incubation, free scale	unitless	pH
H	Mean proton concentration during incubation, calculated from ph_free	unitless	no_bcodmo_term
SIR	Mean substrate to inhibitor ratio, [HCO3-] [H+] during incubation	unitless	ratio
co2	Mean carbon dioxide concentration, including dissolved carbon dioxide and carbonic acid concentrations, during incubation	umol kg-1	CO2
pco2	Mean partial pressure of carbon dioxide during incubation	uatm	pCO2
dic	Mean dissolved inorganic carbon concentration, [CO2] + [HCO3-] + [CO32-], during the incubation	umol kg-1	DIC
do	Mean dissolved oxygen concentration during the incubation	umol kg-1	O2
ci	Mussel condition index, dry tissue mass divided by total dry mass	umol kg-1	mass
incubation_water_mass	Mass of seawater in incubation vessel	kilograms (kg)	mass
byssal_threads	Byssal thread production rate during incubation	threads hr-1	production
delta_ta	Measured change in alkalinity during incubation	umol kg-1	TALK
delta_nh3	Measured change in ammonia concentration during incubation	umol kg-1	NH3_f
calc_diss	Correction for alkalinity change due to abiotic dissolution calculated based on shell mass and seawater saturation state, see Figure S2	umol	TALK
figure2	1=data used to generate Figure 3, 0=data not used to generate Figure 3	unitless	no_bcodmo_term
figure3	1=data used to generate Figure 4, 0=data not used to generate Figure 4	unitless	no_bcodmo_term
figure4	1=data used to generate Figure 5, 0=data not used to generate Figure 5	unitless	no_bcodmo_term
figureS45	1=data used to generate Supplementary Figures 4 & 5, 0=data not used to generate Supplementary Figures 4 & 5	unitless	no_bcodmo_term
normcalc	description needed	unitless	no_bcodmo_term

Database

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Dataset: Incubation data for Mytilus californianus calcification