http://lod.bco-dmo.org/id/dataset/925598
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
2024-04-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Incubation data for Mytilus californianus calcification from January to April 2022 (OA decoupling project)
2024-05-06
publication
2024-05-06
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-06-11
publication
https://doi.org/10.26008/1912/bco-dmo.925598.1
Brian Gaylord
University of California-Davis
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: Gaylord, B. (2024) Incubation data for Mytilus californianus calcification from January to April 2022 (OA decoupling project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-06 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.925598.1 [access date]
Incubation data for Mytilus californianus calcification Dataset Description: <p>Each row of the primary file of this&nbsp;dataset corresponds to incubation data collected while exposing an individual mussel to modified seawater.</p> Methods and Sampling: <p><strong>Sampling collection details</strong></p>
<p>We gathered naturally settled, adult California mussels (<em>M. californianus</em>&nbsp;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 (&lt; 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.&nbsp;</p>
<p><strong>Experiment details&nbsp;</strong></p>
<p>Incubations conducted according to published methods (Gazeau et al&nbsp; 2015).&nbsp;</p>
<p>Seawater chemistry was controlled to target unique combinations of alkalinity (between 337 and 9584&nbsp;µmol kg<sup>-1</sup>) and dissolved inorganic carbon (DIC,&nbsp;between 299 and 9322 µmol kg<sup>-1</sup>). 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.</p>
<p>Mussel response was quantified as the calcification rate measured with the alkalinity anomaly technique corrected for ammonia production (Gazeau et al&nbsp; 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.</p>
<p>&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2129942 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2129942
completed
Brian Gaylord
University of California-Davis
707-875-1940
Bodega Marine Laboratory & Department of Evolution and Ecology 2099 Westshore Road, P.O. Box 247
Bodega Bay
CA
94923
USA
bpgaylord@ucdavis.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
species
AphiaID
LSID
module
date_local
start_datetime_local
ISO_Start_DateTime_UTC
duration
salinity
temperature
calcification
tissue_mass
shell_mass
wet_mass
TA
ph_total
hco3
co3
omega
omegac
ca
ph_free
H
SIR
co2
pco2
dic
do
ci
incubation_water_mass
byssal_threads
delta_ta
delta_nh3
calc_diss
figure2
figure3
figure4
figureS45
Shimadzu spectrophotometer
theme
None, User defined
species scientific name (binomial)
taxon_code
Life Science Identifier (LSID)
sample type
date
time begin
incubation time or duration
salinity
incubation temperature
calcification
mass_dry
mass
total alkalinity (TA)
pH
bicarbonate concentration [HCO3]-
Carbonate concentration [CO3]2-
Aragonite Saturation State
Calcite Saturation State
Calcium
No BCO-DMO term
ratio
carbon dioxide
Partial pressure of CO2
dissolved inorganic Carbon
dissolved Oxygen
production
Ammonia (NH3) flux
featureType
BCO-DMO Standard Parameters
UV Spectrophotometer-Shimadzu
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.
Invertebrate calcification and behavior in seawater of decoupled carbonate chemistry
https://osprey.bco-dmo.org/project/886711
Invertebrate calcification and behavior in seawater of decoupled carbonate chemistry
<p><em>NSF Award Abstract:</em><br />
This research is exploring the capacity of coastal organisms to cope with alterations in seawater chemistry driven by both freshwater inputs and absorption of carbon dioxide into the world's oceans (ocean acidification). The project focuses on calcification responses and behavioral impairments of shoreline animals under altered seawater chemistry, and forefronts a common mussel species (the California mussel), and a common snail (the black turban snail), each abundant on rocky shores along the west coast of North America. The target species operate as exemplar organisms for characterizing the responses of marine invertebrates more generally. Methods involve experimental decoupling of multiple components of the carbonate system of seawater to isolate drivers that are difficult to separate otherwise. Broader impacts include transfer of scientific information to policy-makers, including legislators, as well as training and skill-set development of future generations of scientists and citizens. One Ph.D. student is supported, as are UC Davis undergraduates conducting mentored research. The project also provides research internships for undergraduates from a local community college (Santa Rosa Junior College), many of whom are from underrepresented groups. The latter project component substantially bolsters an ongoing program at Bodega Marine Laboratory that includes efforts in diversity, equity, and inclusion. Data and interpretations from the project are feeding into an existing educational program that links to local K-12 schools and reaches ~10,000 members of the public each year.</p>
<p>Overall, the research of the project is dissecting drivers of calcification and behavioral disruption in key shoreline invertebrates, across present-day and future carbonate system conditions appropriate to coastal marine environments. Efforts are exploring the extent to which calcification depends on one versus multiple parameters of the seawater carbonate system. In particular, existing conceptual models emphasize the importance of calcium carbonate saturation state (Ω) and/or the ratio of bicarbonate to hydrogen ion concentrations ([HCO3-]/[H+]), and the project is examining these mechanisms as well as the possibility that more than one driver acts simultaneously. It is doing so both in bivalves and in gastropods to test for generality across mollusks. The project is additionally examining whether pH is the only carbonate system factor contributing to known patterns of behavioral impairment in marine invertebrates. Leading explanations for debilitating behaviors induced by ocean acidification involve altered ion channel function, but discussion in the literature continues, and studies that explicitly decouple the carbonate system are necessary.</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>
OA decoupling
largerWorkCitation
project
eng; USA
oceans
-123.076306
-123.076306
38.371361
38.371361
2022-01-13
2022-04-23
California coast, USA
0
BCO-DMO catalogue of parameters from Incubation data for Mytilus californianus calcification from January to April 2022 (OA decoupling 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
http://lod.bco-dmo.org/id/dataset-parameter/926677.rdf
Name: species
Units: unitless
Description: <p>Mussel species used in incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926678.rdf
Name: AphiaID
Units: unitless
Description: <p>Unique identifier for the listed taxon in the Aphia database.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926679.rdf
Name: LSID
Units: unitless
Description: <p>Life Science Identifier (LSID) for the listed taxon.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926680.rdf
Name: module
Units: unitless
Description: <p>Experimental module corresponding to different mussel collection events.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926681.rdf
Name: date_local
Units: unitless
Description: <p>Incubation date in Pacific Standard Time.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926682.rdf
Name: start_datetime_local
Units: unitless
Description: <p>Start datetime of the incubation in Pacific Standard Time.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926683.rdf
Name: ISO_Start_DateTime_UTC
Units: unitless
Description: <p>Start datetime of the incubation in UTC.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926684.rdf
Name: duration
Units: hours
Description: <p>Duration of incubation in hours.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926685.rdf
Name: salinity
Units: PSU
Description: <p>Incubation salinity.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926686.rdf
Name: temperature
Units: degrees Celcius (c)
Description: <p>Incubation Temperature.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926687.rdf
Name: calcification
Units: umol hr^-1 g^-0.71592
Description: <p>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.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926688.rdf
Name: tissue_mass
Units: grams (g)
Description: <p>Dried mussel tissue mass.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926689.rdf
Name: shell_mass
Units: grams (g)
Description: <p>Dried mussel shell mass.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926690.rdf
Name: wet_mass
Units: grams (g)
Description: <p>Wet mass of mussel prior to incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926691.rdf
Name: TA
Units: umol kg-1
Description: <p>Mean alkalinity during incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926692.rdf
Name: ph_total
Units: unitless
Description: <p>Mean pH during incubation, total scale.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926693.rdf
Name: hco3
Units: umol kg-1
Description: <p>Mean bicarbonate ion concentration during incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926694.rdf
Name: co3
Units: umol kg-1
Description: <p>Mean carbonate ion concentration during incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926695.rdf
Name: omega
Units: unitless
Description: <p>Mean aragonite saturation state during incubation, corrected for calcium concentration where calcium was modified.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926696.rdf
Name: omegac
Units: unitless
Description: <p>Mean calcite saturation state during incubation, corrected for calcium concentration where calcium was modified.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926697.rdf
Name: ca
Units: mol kg-1
Description: <p>Calcium concentration during incubation, either calculated from salinity or measured with Ca ion selective electrode.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926698.rdf
Name: ph_free
Units: unitless
Description: <p>Mean pH during incubation, free scale.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926699.rdf
Name: H
Units: unitless
Description: <p>Mean proton concentration during incubation, calculated from ph_free.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926700.rdf
Name: SIR
Units: unitless
Description: <p>Mean substrate to inhibitor ratio, [HCO3-] [H+] during incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926701.rdf
Name: co2
Units: umol kg-1
Description: <p>Mean carbon dioxide concentration, including dissolved carbon dioxide and carbonic acid concentrations, during incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926702.rdf
Name: pco2
Units: uatm
Description: <p>Mean partial pressure of carbon dioxide during incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926703.rdf
Name: dic
Units: umol kg-1
Description: <p>Mean dissolved inorganic carbon concentration, [CO2] + [HCO3-] + [CO32-], during the incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926704.rdf
Name: do
Units: umol kg-1
Description: <p>Mean dissolved oxygen concentration during the incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926705.rdf
Name: ci
Units: umol kg-1
Description: <p>Mussel condition index, dry tissue mass divided by total dry mass.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926706.rdf
Name: incubation_water_mass
Units: kilograms (kg)
Description: <p>Mass of seawater in incubation vessel.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926707.rdf
Name: byssal_threads
Units: threads hr-1
Description: <p>Byssal thread production rate during incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926708.rdf
Name: delta_ta
Units: umol kg-1
Description: <p>Measured change in alkalinity during incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926709.rdf
Name: delta_nh3
Units: umol kg-1
Description: <p>Measured change in ammonia concentration during incubation.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926710.rdf
Name: calc_diss
Units: umol
Description: <p>Correction for alkalinity change due to abiotic dissolution calculated based on shell mass and seawater saturation state, see Figure S2 in related results publication, Romano de Orte et al. (2021).</p>
http://lod.bco-dmo.org/id/dataset-parameter/926711.rdf
Name: figure2
Units: unitless
Description: <p>Indicates if data were used to generate figures published in related results publication, Romano de Orte et al. (2021). 1= data used to generate Figure 3, 0 = data not used to generate Figure 3.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926712.rdf
Name: figure3
Units: unitless
Description: <p>Indicates if data were used to generate figures published in related results publication, Romano de Orte et al. (2021). 1 = data used to generate Figure 4, 0 = data not used to generate Figure 4.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926713.rdf
Name: figure4
Units: unitless
Description: <p>Indicates if data were used to generate figures published in related results publication, Romano de Orte et al. (2021). 1 = data used to generate Figure 5, 0 = data not used to generate Figure 5.</p>
http://lod.bco-dmo.org/id/dataset-parameter/926714.rdf
Name: figureS45
Units: unitless
Description: <p>Indicates if data were used to generate figures published in related results publication, Romano de Orte et al. (2021). 1=data used to generate Supplementary Figures 4 & 5, 0=data not used to generate Supplementary Figures 4 & 5.</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
96220
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/4ac6f161-5cbe-4e5c-ac28-19e45c48bb50/content
download
https://doi.org/10.26008/1912/bco-dmo.925598.1
download
onLine
dataset
<p><strong>Sampling collection details</strong></p>
<p>We gathered naturally settled, adult California mussels (<em>M. californianus</em>&nbsp;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 (&lt; 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.&nbsp;</p>
<p><strong>Experiment details&nbsp;</strong></p>
<p>Incubations conducted according to published methods (Gazeau et al&nbsp; 2015).&nbsp;</p>
<p>Seawater chemistry was controlled to target unique combinations of alkalinity (between 337 and 9584&nbsp;µmol kg<sup>-1</sup>) and dissolved inorganic carbon (DIC,&nbsp;between 299 and 9322 µmol kg<sup>-1</sup>). 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.</p>
<p>Mussel response was quantified as the calcification rate measured with the alkalinity anomaly technique corrected for ammonia production (Gazeau et al&nbsp; 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.</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
<p>We calculated net calcification rates with the ammonia-corrected alkalinity anomaly technique&nbsp;(Gazeau et al&nbsp; 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 CaCO<sub>3</sub>&nbsp;results in an equivalent reduction in seawater [CO<sub>3</sub><sup>2-</sup>] (or reduction of [HCO<sub>3</sub><sup>-</sup>] followed by an increase in [H<sup>+</sup>]) 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&nbsp;(Gazeau et al&nbsp; 2015).</p>
<p>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<sup>-1</sup>. The mean of the absolute values of alkalinity change during the incubations of these experimental blanks was 1.3 ± 1.2 µmol kg<sup>-1</sup>&nbsp;(n = 72).&nbsp;</p>
<p>We performed all computations with R statistical software, version 4.1.0. We performed carbonate system calculations using the package&nbsp;<em>seacarb</em>, using equilibrium constants from Lueker&nbsp;<em>et al</em>. We computed linear mixed models using the&nbsp;<em>lmer</em>&nbsp;function in in the&nbsp;<em>lmertest</em>&nbsp;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 R<sup>2</sup>&nbsp;was calculated with the package&nbsp;<em>MuMIn</em>. We determined parameters for non-linear fits employed to model dissolution rates by minimizing the sum of squares of model residuals using the&nbsp;<em>optim</em>&nbsp;function. Colors for plots were chosen from color palettes in the&nbsp;<em>cmocean</em>&nbsp;package in&nbsp;<em>R</em>.</p>
Specified by the Principal Investigator(s)
- 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
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
Shimadzu spectrophotometer
Shimadzu spectrophotometer
PI Supplied Instrument Name: Shimadzu spectrophotometer PI Supplied Instrument Description:A Shimadzu spectrophotometer was used to conduct spectrophotmetric pH and ammonia analyses. Instrument Name: UV Spectrophotometer-Shimadzu Instrument Short Name:UV Spectrophotometer-Shimadzu Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/