For at least the past six years, the West Coast Shellfish industry has observed larval mortality in hatcheries and poor larval recruitment success for some species in the wild, especially during periods of high upwelling. One hypothesis is that these dramatic declines in productivity may be related to increasing ocean acidity and the corresponding decrease in the saturation state of carbonate minerals which shellfish use to create their shells. The West Coast shellfish industry sought help from scientists to explore the causes of the shellfish losses, what role ocean acidification and other factors might be playing, and how to adapt to sustain West Coast shellfish resources. Addressing questions about ocean acidification requires integration of ocean observing measurements, laboratory exposure studies, shellfish recruitment and production data, and field studies of organism performance in relation to ocean conditions. However, these data are collected by different sectors that, to date, have had limited interaction. To stimulate collaborations among these sectors, and at the request of the shellfish farming and wild harvest communities, the Integrated Ocean Observing Systems, California Sea Grant, USC Sea Grant, Oregon Sea Grant, Washington Sea Grant, and California Ocean Science Trust convened a workshop. Fifty‐one participants were invited, including state and federal managers, industry representatives, and leading academic researchers and oceanographers with expertise in larval recruitment, laboratory studies, and ocean chemistry.

Accurately measuring the marine CO2 system is imperative to assess the effect of oceanic uptake of anthropogenic CO2 and the consequences for marine biogeochemical processes. CO2 in the ocean is both a gas and an acid, so it is necessary to measure at least two parameters describing its chemistry, where two of the most commonly used parameters being pHT and total alkalinity (AT). While both are fairly straight forward to measure and have a long history in oceanography, they have unique challenges that can greatly reduce their quality for use in CO2 system calculations. For pHT measurements, especially electrometric methods involving a liquid junction, it is crucial to calibrate the measurement using a buffer prepared in a solution similar to seawater. Chapter 2 of this dissertation describes a method to prepare 0.04 mol kg-H2O−1 equimolar buffer 2-amino-2-hydroxymethyl-1,3-propanediol (TRIS)-TRIS·H+ in synthetic seawater. Its point of success is using a simple methodology that is also reproducible, and produces a buffer with a pHT within 0.006 of the assigned value 8.094 (at 25 °C). The measurement of AT and even its definition is simple, being the balance between bases and acids in seawater and measured by titration with acid. To use AT in CO2 system calculations, it is necessary to account for the non-carbonate alkalinity components. While most if not all inorganic bases and acids have been identified and can be accounted for, for decades there has been evidence for unidentified, likely organic, bases present at significant levels. Little advance has been made in understanding the alkalinity contribution from component “X” (AX) due to a lack of an unambiguous measurement. Chapter 3 describes an unambiguous, open-cell titration method to measure AX, which includes an uncertainty assessment informed both by ancillary measurements and by titration simulations using a custom chemical equilibrium model. Chapter 4 shows the success of this this titration method using a combination of well-characterized simple salt solutions and a simple seawater solution, by themselves and with the addition of one or two simple organic, proving that the system is capable of measuring AX at 3.4 micromol kg–1.

As pH measurement technologies evolve and are increasingly used to study the ocean’s CO2 system, there is a need to assess the uncertainty of seawater pH measurements, particularly those based on the spectrophotometric method using an indicator dye, which is used to calibrate alternative pH measurement methods, including autonomous pH sensors. In this dissertation, I investigated methodological and instrumental contributions to uncertainty in spectrophotometric pH measurements, developed tools for their quality control, and evaluated their likely quality based on their consistency with other seawater CO2 parameters. The accuracy of seawater pH measurements has been questioned due to observations from open ocean cruises of a significant pH-dependent discrepancy between measured pH and pH calculated from dissolved inorganic carbon (CT) and total alkalinity (AT), using a thermodynamic model of seawater acid-base systems. Based on an analysis of high quality CO2 measurements on four open ocean cruises, I showed that a combination of plausible biases in the constants and assumptions used to calculate pH can explain the observed inconsistencies and that there is likely an unaccounted, possibly organic, contribution to the AT measured in the open ocean. Next, I developed methods for analyzing spectra to identify and possibly correct instrumental contributions to spectrophotometric pH measurement error, such as those that may arise from degradation of the spectrophotometer lamp. In another chapter, laboratory and chemical modeling experiments were conducted to evaluate how adjustments for effect of the indicator addition on the sample pH contribute to uncertainty in the final pH result. Assumptions about the indicator’s behavior can result in error in the pH correction, but is minor, except when using high dye concentrations in short pathlength cells. Finally, I evaluated the performance of pH measurements using impure m-cresol purple, which contains absorbing impurities that can bias pH measurements. Calibrated impure dye measurements can still be inconsistent with purified dye measurements depending on the assumptions about the impurity absorption behavior or the purity of the reference dye. This dissertation contributes to understanding of the uncertainty of spectrophotometric pH measurements and our ability to use ocean pH data to characterize the CO2 system.

A large fraction of the carbon dioxide added to the atmosphere by human activity enters the sea, causing ocean acidification. We show that otoliths (aragonitic ear bones) of young fish grown under high CO2 (low pH) conditions are larger than normal, contrary to expectation. We hypothesize that CO2 moves freely through the epithelium around the otoliths in young fish, accelerating otolith growth while the local pH is controlled. This is the converse of the effect reported for structural biominerals.