This dataset contains a number of files related to a project that characterizes the sensitivity of the Puget Sound ecosystem to ocean acidification by estimating, at a number of taxonomic levels, the direct sensitivity of its species. It includes a database of marine species in Puget Sound (.csv) with estimates of species mineralogy in the adult and early life stages, and a list (.docx) of references called to in the database. It also includes a list (.csv) of species in the Puget Sound that are also included in a second database that collects the results of studies on the sensitivity of temperate marine species to ocean acidification (Busch and McElhany 2016, https://doi.org/10.1371/journal.pone.0160669). This latter database (.csv) is presented in an abbreviated format here including only species taxonomy, reference for the manuscript presenting data on the species, scores estimating the relevance of these studies to understanding the sensitivity of Puget Sound species to ocean acidification, and the direction of the species’ response to low pH conditions. Information on pH sensitivity from this database is rolled into scalars summarized at the family, order, and class levels (.csv) and these scalars are assigned to the species included in the Puget Sound species database.

This is data from a laboratory experiment in which mature female Tanner crabs were held at three different pHs (ambient, pH 7.8, and pH 7.5) for approximately two years. The laboratory exposure started on 2011-06-21 and ended on 2013-07-14. At the end of the exposure period samples of both the exoskeleton and claw were taken. Exoskeleton mechanical and elemental properties were analyzed in both the carapace and the claw. This dataset includes only the data from the cuticle analysis. The results of this work are published as: Dickenson, G.H., Bejerano, S., Salvador, T., Makdisi, C., Patel, S., Long, W.C., Swiney, K.M., Foy, R.J., Steffel, B.V., Smith, K.E., and Aaronson, R.B. 2021. Ocean acidification alters exoskeleton properties in adult Tanner crabs, Chionoecetes baridi. J. Exp. Biol. 224: jeb232819. https://doi.org/10.1242/jeb.232819.

This dataset contains laboratory experiment data that were collected to examine the effects of elevated levels of CO2 on the growth, survival, otolith (ear bone) condition and the skeleton of juvenile scup, Stenotomus chrysops, a species that supports both commercial and recreational fisheries. Increasing amounts of atmospheric carbon dioxide from human industrial activities are causing changes in global ocean carbon chemistry resulting in a reduction in pH, a process termed ocean acidification. Studies have demonstrated adverse effects on calcifying organisms, particularly some invertebrates, corals, sea urchins, pteropods, and coccolithophores. It is important to determine which species are sensitive to elevated levels of CO2 because of the potential impacts to ecosystems, marine resources, biodiversity, food webs, populations and effects on human communities and economies. There have been few studies examining the effects of ocean acidification on marine fish, particularly the juvenile stages of species that support important fisheries. These data demonstrated that elevated levels of pCO2 (>1300 micro-atm) had no statistically significant effect on growth, survival, or otolith condition after 8 weeks of rearing. There was a trend towards a greater gain in weight and length in scup exposed to the mid-level (1726 micro-atm) and the high level (2614 micro-atm) treatments of pCO2 when compared to the fish in the control (1205 micro-atm) treatments, but these differences were not statistically significant. X-ray analysis of the fish revealed a slightly higher incidence of hyper-ossification in the vertebrae of a few scup from the highest treatments compared to fish from the control treatments. The study's results show that juvenile scup are tolerant to increases in levels of environmental pCO2, possibly due to conditions this species encounters in their naturally variable environment.

This dataset contains laboratory experiment data that were collected to examine the effects of ocean acidification on the Atlantic surfclam, Spisula solidissima, a species worth $31 million in 2009. Ocean acidification has negatively impacted growth and survival of multiple bivalve species, but because each species and developmental stage can show different responses, these studies were designed to determine potential impacts of increased CO2 on the larvae of the commercially important surfclam. Additionally, the role of nutrition (i.e., phytoplankton concentration) was included in a portion of these experiments because food availability may be able to mitigate the stress of ocean acidification and because ocean acidification has the potential to impact marine phytoplankton communities. During the summer of 2011, three different experiments were conducted at Woods Hole Oceanographic Institution examining the effects of three different pCO2 concentrations on larval surf clams. Two short term experiments (~70h) examined the effect of food availability on early shell development (fed vs unfed). One long term experiment (~21d) was conducted to examine the effects of pCO2 on shell development and metamorphic success (all animals well fed). Carbonate data is reported from these preliminary short-term experiments, and survival and shell length data is reported, in addition to carbonate data, from the long-term experiment. During 2012, one 6 day experiment was conducted examining the role and potential interactive effects of high and low food availability (400 and 40,000 cells ml-1 Tiso) and differential CO2 concentrations (ambient, ~1200 ppm and ~2200ppm). From these experiments, carbonate data, shell length, mass and biochemical compositions are reported. In 2013, two additional experiments were conducted to confirm results obtained in 2012. Unfortunately we observed stunted larval growth, no feeding effect on growth, high mortalities and a general failure to thrive. Given this, we infer poor gamete quality may have been the cause, and have chosen not to interpret these data as results are suspect. Therefore, 2013 data are therefore not included in this data submission.

This dataset contains a laboratory experiment study with the goal of understanding the effects of ocean acidification on the embryos and larvae of red king crab, Paralithodes camtschaticus. The effects of the decline in ocean pH, known as ocean acidification, on marine species are not well understood. To test the effects on embryos and larvae of red king crab, Paralithodes camtschaticus, ovigerous crab and their larvae were held in CO2-acidified (pH 7.7) and control (ambient; pH 8.0) seawater during development. Morphometrics, hatch duration, fecundity, survival, mineral content, and condition were measured. Acidified embryos had 4% larger eyes and 5% smaller yolks, while mean hatch duration was 33% longer and female fecundity was unaffected. Acidified embryos also resulted in 4% longer larvae while acidified larvae had lower survival. Calcium content of both larvae and female carapaces after molting increased by 5% and 19%, respectively. Although ocean acidification may increase larval size and calcium content, the implications of this are unclear and decreased survival is likely to harm red king crab populations.

This dataset contains data for a study of the effect of ocean acidification (OA) on the behavioral responses of a coastal flatfish. In laboratory experiments, we first characterized speckled sanddab (Citharichthys stigmaeus) behavioral responses to potential predation cues (predator odor, damaged skin cues from injured conspecifics, and sight of a predator) under ambient CO2 levels (~400 uatm). Sanddab reduced conspicuousness and foraging at the sight of a predator, but increased activity and conspicuousness when exposed to damaged skin cues. We then examined the effects of elevated CO2 levels (~900 uatm and ~1500 uatm) on posture, activity, and foraging of sanddab, and the behavioral responses to damaged skin cues. Sanddab behavior appeared generally resilient to the effects of elevated CO2 levels, but there were non-significant trends of fish from the medium CO2 treatment exhibiting lower posture and activity scores, and reduced feeding activity. The resiliency of speckled sanddab to OA conditions may be related to their distribution in a coastal upwelling region with seasonally elevated CO2 levels. Alternatively, prolonged acclimation to elevated CO2 may have mitigated the effects observed in other fishes following shorter-term exposures. Additional studies of ecologically relevant behaviors across diverse species assemblages are necessary to evaluate the impact of ocean acidification on marine food webs.

This dataset contains laboratory experimental data that were collected to examine the effects of elevated levels of carbon dioxide on the growth of Atlantic surfclam (Spisula solidissima), a species that supports both commercial and recreational fisheries in the Northeast United States. Three levels of carbon dioxide enrichment (low, medium, and high) were delivered to surfclams in a 12-week exposure experiment. All treatments were done in 3 replicates (A, B, C). Approximately every 2 to 3 weeks, 12 individuals were removed from each treatment and measurements of length, width, height, dry tissue, and dry shell were recorded. Length was measured across the longest part of the shell, parallel to the hinge. Width was the thickness of the shell, and height was measured form the hinge to the outer edge of the shell. Dry tissue and dry shell samples were dried at 60°C until constant weight was achieved (~5 days). DIC measurements of carbon dioxide enrichment were taken and analyzed on an Apollo SciTech, while pH was measured weekly with a spectrophotometer. Values reported for DIC, pH, temperature, and salinity are the mean of each treatment during the 12-week experiment. The data indicated that increased carbon dioxide affected growth, tissue mass, and shell weight for Atlantic surfclam.

Multiple stressor studies are needed to better understand the effects of oceanic changes on marine organisms. To determine the effects of near-future ocean acidification and warming temperature on young of the year red king crab (Paralithodes camtschaticus) survival, growth, and morphology, we conducted a long-term (184 d) fully crossed experiment with two pHs and three temperatures: ambient pH (~7.99), pH 7.8, ambient temperature, ambient +2 degrees Celsius, and ambient +4 degrees Celsius, for a total of 6 treatments. Mortality rate increased with both reduced pH and by higher temperatures, but interpretation of the multistressor effects is not straightforward as a clear trend was not observed. A synergetic effect was observed; the pH 7.8 and ambient +4 degrees Celsius temperature treatment had the lowest survival, with only 3% surviving to the end of the experiment. However, antagonistic effects were observed in the pH 7.8 ambient +2 degrees Celsius temperature treatment; the mortality rate in this treatment was less than the mortality rate of each of the stressors individually. Despite the effects on mortality, neither decreased pH nor increased temperature had an effect on growth or morphology. The results of this study combined with other studies suggest that ocean acidification and warming may have profound negative effects on red king crab populations in the upcoming decades unless the species is able to quickly adapt or acclimate to changing conditions.

Impacts of elevated carbon dioxide on marine ecosystems depend on physiological responses to consequential decreased pH and increased temperature. Responses to these environmental factors vary among species and life stages, and interactive effects can be significant. To study effects of decreased pH and increased temperature on juvenile red king crab (RKC, Paralithodes camtschaticus) we exposed individuals to three levels of temperature: 11 degrees Celsius (ambient), 13 degrees Celsius, and 14 degrees Celsius, crossed with three levels of pH: 8.0, 7.8 and 7.5, for a total of nine treatments. To better understand the effect of these environmental changes at the level of genome regulation, we analyzed total RNA of whole crabs using Illumina-based RNA-seq whole-transcriptome sequencing. We assembled a RKC transcriptome using Trinity, annotated the transcriptome using Trinotate, and estimated expression levels using bowtie2, samtools and eXpress. Differentially expressed genes were identified using EdgeR. Genes were clustered by expression patterns. Interactive effects were determined by comparing sets of differentially expressed genes using three statistical models to examine the effect of temperature, the effect of pH, and the interaction between temperature and pH in EdgeR. The largest set of differentially expressed genes encoded proteins involved in regulation of extracellular and cuticular structures, including chitin-binding and calcification related proteins.