1b:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1c:T778,

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.

1d:T863,

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.

1e:T460,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.1f:T502,

Definition from https://www.lsid.info/ (Accessed 2024-07-29):

The Life Sciences Identifier (LSID) is an Interoperable Informatics Infrastructure Consortium (I3C) and OMG Life Sciences Research (LSR) Uniform Resource Name (URN) specification in progress.

The LSID concept introduces a straightforward approach to naming and identifying data resources stored in multiple, distributed data stores in a manner that overcomes the limitations of naming schemes in use today. Almost every public, internal, or department-level data store today has its own way of naming individual data resources, making integration between different data sources a tedious, never-ending chore for informatics developers and researchers.

By defining a simple, common way to identify and access biologically significant data, whether that data is stored in files, relational databases, in applications, or in internal or public data sources, LSID provides a naming standard underpinning for wide-area science and interoperability.

A detailed LSID URN naming specification is available at the OMG LSR.

20:Tb9d,NSF Award Abstract: 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. 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. 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.6:["$","$L1b",null,{"dataset":{"_id":"925598","description":"

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

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Shimadzu manufacturers several models of spectrophotometer; refer to dataset for make/model information.","type_acronym":"UV Spectrophotometer-Shimadzu"}],"parameters":[{"_id":"926677","name":"species","format":"","frictionlessType":"string","description":"

Mussel species used in incubation.

","units":{"_id":"","name":"unitless"},"type":{"_id":"976","name":"species","description":"

a taxonomic binomial that consists of a genus name followed by the species name of an organism

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Unique identifier for the listed taxon in the Aphia database.

","units":{"_id":"","name":"unitless"},"type":{"_id":"995","name":"taxon_code","description":"

taxonomic group or entity code, such as the AphiaID (from the World Register of Marine Species), NCBI taxon_id, or the ten digit number from the NODC Taxonomic List, v. 8.

"}},{"_id":"926679","name":"LSID","format":"","frictionlessType":"string","description":"

Life Science Identifier (LSID) for the listed taxon.

","units":{"_id":"","name":"unitless"},"type":{"_id":"933996","name":"LSID","description":"$1f"}},{"_id":"926680","name":"module","format":"","frictionlessType":"string","description":"

Experimental module corresponding to different mussel collection events.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1742","name":"sample_type","description":"

text description of type of sample collected (rock, bio, fluid, etc)

"}},{"_id":"926681","name":"date_local","format":"%Y-%m-%d","frictionlessType":"date","description":"

Incubation date in Pacific Standard Time.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1070","name":"date","description":"

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

"}},{"_id":"926682","name":"start_datetime_local","format":"%Y-%m-%d %H:%M:%S","frictionlessType":"datetime","description":"

Start datetime of the incubation in Pacific Standard Time.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1117","name":"time_begin","description":"

time at start of measurement (GMT)

"}},{"_id":"926683","name":"ISO_Start_DateTime_UTC","format":"%Y-%m-%dT%H:%M:%SZ","frictionlessType":"datetime","description":"

Start datetime of the incubation in UTC.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1117","name":"time_begin","description":"

time at start of measurement (GMT)

"}},{"_id":"926684","name":"duration","format":"","frictionlessType":"number","description":"

Duration of incubation in hours.

","units":{"_id":"","name":"hours"},"type":{"_id":"489496","name":"incubation time","description":"

Duration of sample incubation; used in laboratory experiments. Refer to dataset for units of measure.

"}},{"_id":"926685","name":"salinity","format":"","frictionlessType":"number","description":"

Incubation salinity.

","units":{"_id":"","name":"PSU"},"type":{"_id":"955","name":"sal","description":"

Salinity: The amount (mass or quantity of matter) of salt per amount (volume or mass) of a body of water.

"}},{"_id":"926686","name":"temperature","format":"","frictionlessType":"number","description":"

Incubation Temperature.

","units":{"_id":"","name":"degrees Celcius (c)"},"type":{"_id":"489497","name":"temp_inc","description":"

Temperature at which samples were incubated.

"}},{"_id":"926687","name":"calcification","format":"","frictionlessType":"number","description":"

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.

","units":{"_id":"","name":"umol hr^-1 g^-0.71592"},"type":{"_id":"708750","name":"calcification","description":"

Accumulation of calcium salts including calcium carbonate (CaCO3) in various forms (e.g. aragonite, calcite). Can be a measured amount, percent of organism, or rate of accumulation.

"}},{"_id":"926688","name":"tissue_mass","format":"","frictionlessType":"number","description":"

Dried mussel tissue mass.

","units":{"_id":"","name":"grams (g)"},"type":{"_id":"1870","name":"mass_dry","description":"

mass of dried specimen (freeze-dried, ash free lean dry mass, and others).

"}},{"_id":"926689","name":"shell_mass","format":"","frictionlessType":"number","description":"

Dried mussel shell mass.

","units":{"_id":"","name":"grams (g)"},"type":{"_id":"1870","name":"mass_dry","description":"

mass of dried specimen (freeze-dried, ash free lean dry mass, and others).

"}},{"_id":"926690","name":"wet_mass","format":"","frictionlessType":"number","description":"

Wet mass of mussel prior to incubation.

","units":{"_id":"","name":"grams (g)"},"type":{"_id":"886","name":"mass","description":"

mass; the amount of matter in an object.

"}},{"_id":"926691","name":"TA","format":"","frictionlessType":"number","description":"

Mean alkalinity during incubation.

","units":{"_id":"","name":"umol kg-1"},"type":{"_id":"1224","name":"TALK","description":"

Total alkalinity

"}},{"_id":"926692","name":"ph_total","format":"","frictionlessType":"number","description":"

Mean pH during incubation, total scale.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1892","name":"pH","description":"

pH: The measure of the acidity or basicity of an aqueous solution

"}},{"_id":"926693","name":"hco3","format":"","frictionlessType":"number","description":"

Mean bicarbonate ion concentration during incubation.

","units":{"_id":"","name":"umol kg-1"},"type":{"_id":"489494","name":"bicarbonate","description":"

Concentration of bicarbonate ion ([HCO3]-) in seawater. Refer to dataset for units of measure.

"}},{"_id":"926694","name":"co3","format":"","frictionlessType":"number","description":"

Mean carbonate ion concentration during incubation.

","units":{"_id":"","name":"umol kg-1"},"type":{"_id":"489495","name":"carbonate","description":"

Concentration of carbonate ion ([CO3]2-) in seawater. Dissolved carbonate ion. Refer to dataset for units of measure.

"}},{"_id":"926695","name":"omega","format":"","frictionlessType":"number","description":"

Mean aragonite saturation state during incubation, corrected for calcium concentration where calcium was modified.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1963","name":"OM_ar","description":"

The saturation state of seawater with respect to aragonite (known as OMEGA_ar) is a measure of the thermodynamic potential for aragonite to form or to dissolve, and is defined as the product of the concentrations of dissolved calcium and carbonate ions in seawater, divided by their product at equilibrium.

"}},{"_id":"926696","name":"omegac","format":"","frictionlessType":"number","description":"

Mean calcite saturation state during incubation, corrected for calcium concentration where calcium was modified.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1964","name":"Calcite Saturation State","description":"

The saturation state of seawater with respect to calcite (known as OMEGA_ar) is a measure of the thermodynamic potential for calcite to form or to dissolve, and is defined as the product of the concentrations of dissolved calcium and carbonate ions in seawater, divided by their product at equilibrium.

"}},{"_id":"926697","name":"ca","format":"","frictionlessType":"number","description":"

Calcium concentration during incubation, either calculated from salinity or measured with Ca ion selective electrode.

","units":{"_id":"","name":"mol kg-1"},"type":{"_id":"527969","name":"Ca","description":"

Calcium (Ca). Concentrations may be reported in parts per million, nanomoles per liter, or other units. Refer to dataset metadata for units.

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Mean pH during incubation, free scale.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1892","name":"pH","description":"

pH: The measure of the acidity or basicity of an aqueous solution

"}},{"_id":"926699","name":"H","format":"","frictionlessType":"number","description":"

Mean proton concentration during incubation, calculated from ph_free.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"926700","name":"SIR","format":"","frictionlessType":"number","description":"

Mean substrate to inhibitor ratio, [HCO3-] [H+] during incubation.

","units":{"_id":"","name":"unitless"},"type":{"_id":"833208","name":"ratio","description":"

A ratio is the relative size of two quantities expressed as the quotient of one divided by the other. The numbers in a ratio may be quantities or measurements of any kind, such as counts, lengths, weights, or concentrations, for example. When two quantities are measured with the same unit, as is often the case, their ratio is a dimensionless number.

"}},{"_id":"926701","name":"co2","format":"","frictionlessType":"number","description":"

Mean carbon dioxide concentration, including dissolved carbon dioxide and carbonic acid concentrations, during incubation.

","units":{"_id":"","name":"umol kg-1"},"type":{"_id":"827442","name":"CO2","description":"

Carbon dioxide: A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi, and microorganisms that depend directly or indirectly on living or decaying plants for food.

"}},{"_id":"926702","name":"pco2","format":"","frictionlessType":"number","description":"

Mean partial pressure of carbon dioxide during incubation.

","units":{"_id":"","name":"uatm"},"type":{"_id":"1991","name":"pCO2","description":"

Partial pressure of carbon dioxide {pCO2} in the water body by computation from pH and alkalinity.

"}},{"_id":"926703","name":"dic","format":"","frictionlessType":"number","description":"

Mean dissolved inorganic carbon concentration, [CO2] + [HCO3-] + [CO32-], during the incubation.

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Dissolved Inorganic Carbon

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Mean dissolved oxygen concentration during the incubation.

","units":{"_id":"","name":"umol kg-1"},"type":{"_id":"910","name":"dissolved Oxygen","description":"

dissolved oxygen concentration

"}},{"_id":"926705","name":"ci","format":"","frictionlessType":"number","description":"

Mussel condition index, dry tissue mass divided by total dry mass.

","units":{"_id":"","name":"umol kg-1"},"type":{"_id":"886","name":"mass","description":"

mass; the amount of matter in an object.

"}},{"_id":"926706","name":"incubation_water_mass","format":"","frictionlessType":"number","description":"

Mass of seawater in incubation vessel.

","units":{"_id":"","name":"kilograms (kg)"},"type":{"_id":"886","name":"mass","description":"

mass; the amount of matter in an object.

"}},{"_id":"926707","name":"byssal_threads","format":"","frictionlessType":"number","description":"

Byssal thread production rate during incubation.

","units":{"_id":"","name":"threads hr-1"},"type":{"_id":"941","name":"production","description":"

carbon production, from simulated in situ experiments

"}},{"_id":"926708","name":"delta_ta","format":"","frictionlessType":"number","description":"

Measured change in alkalinity during incubation.

","units":{"_id":"","name":"umol kg-1"},"type":{"_id":"1224","name":"TALK","description":"

Total alkalinity

"}},{"_id":"926709","name":"delta_nh3","format":"","frictionlessType":"number","description":"

Measured change in ammonia concentration during incubation.

","units":{"_id":"","name":"umol kg-1"},"type":{"_id":"922923","name":"Ammonia flux","description":"

Fluctuation of Ammonia (NH3)

"}},{"_id":"926710","name":"calc_diss","format":"","frictionlessType":"number","description":"

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).

","units":{"_id":"","name":"umol"},"type":{"_id":"1224","name":"TALK","description":"

Total alkalinity

"}},{"_id":"926711","name":"figure2","format":"","frictionlessType":"number","description":"

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.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"926712","name":"figure3","format":"","frictionlessType":"number","description":"

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.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"926713","name":"figure4","format":"","frictionlessType":"number","description":"

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.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"926714","name":"figureS45","format":"","frictionlessType":"number","description":"

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.

","units":{"_id":"","name":"unitless"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}}],"related_publications":[{"id":"925651","citation":"Gazeau, F., Urbini, L., Cox, T., Alliouane, S., & Gattuso, J. (2015). Comparison of the alkalinity and calcium anomaly techniques to estimate rates of net calcification. Marine Ecology Progress Series, 527, 1–12. https://doi.org/10.3354/meps11287\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"747920","citation":"Lueker, T. J., Dickson, A. G., & Keeling, C. D. (2000). Ocean pCO2 calculated from dissolved inorganic carbon, alkalinity, and equations for K1 and K2: validation based on laboratory measurements of CO2 in gas and seawater at equilibrium. Marine Chemistry, 70(1-3), 105–119. doi:10.1016/s0304-4203(00)00022-0\r\n","relation_type":["Methods"],"relation_desc":""},{"id":"929672","citation":"Romanó de Orte, M., Koweek, D. A., Cyronak, T., Takeshita, Y., Griffin, A., Wolfe, K., Szmant, A., Whitehead, R., Albright, R., & Caldeira, K. (2021). Unexpected role of communities colonizing dead coral substrate in the calcification of coral reefs. Limnology and Oceanography, 66(5), 1793–1803. Portico. https://doi.org/10.1002/lno.11722\r\n","relation_type":["Results"],"relation_desc":""}],"related_datasets":[{"_id":"925664","name":"Shell dissolution data for Mytilus californianus","url":"","relation_type":"IsRelatedTo","type_desc":"

The dataset is related to another dataset.

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