The mechanisms by which tropical hermatypic corals biomineralize to build aragonite skeletal material has received increased attention in recent years, but uncertainties remain regarding the relative importance of different biomineralization processes. In particular, the biological modification of a semi-isolated calcification fluid pH (pHCF) and other carbonate chemistry parameters ([CO32-]CF, DICCF, and ΩAR-CF) within an extra-cellular calcifying space may be critical to facilitate biomineralization, and thus, a determining factor for coral growth responses to anthropogenic carbon dioxide induced reductions in seawater pH and aragonite saturation state (ΩAR). The extent to which a coral’s inability to compensate for external seawater carbonate chemistry changes govern coral calcification responses to ocean acidification and temperature stress remains debated. This work builds on a prior study by Bove et al. (2019) that tested the calcification responses of four common Caribbean coral species - Porites astreoides, Psuedodiploria strigosa, Undaria tenuifolia, and Siderastrea siderea - under a range of experimental pCO2 and temperature culture conditions. We utilize skeletal boron geochemistry (B/Ca and δ11B) to probe the pHCF, [DIC]CF, and ΩAR-CF regulation in these corals, finding evidence for modest declines in pHCF but stable or increasing [DIC]CF across increasing seawater pCO2 treatments, with subtle variations in responses between species as well as subtle differences between temperature treatments. Combining our results with boron-isotope, pH-microprobe and pH-sensitive dye data from the literature on scleractinian corals reveals that almost all studied species show evidence of pHCF buffering against changes in external seawater pH (pHSW) but that, in many cases, this compensation is imperfect (i.e. pHCF is not maintained at a constant level across all pHSW conditions). In total, these data suggest that corals do invest additional energy into actively regulating pHCF in high CO2 conditions but that perfect pH compensation by the coral may not be necessary to maintain [CO32-]CF and DICCF at levels required for calcification. In addition, we report δ13C, δ18O, and carbonate “clumped” isotope (Δ47) measurements on the same specimens. δ18O and Δ47 exhibit characteristic scleractinian coral disequilibrium “vital effects” compared to expected values for inorganic aragonite and occasionally show an influence of culture temperature. In some species, variable pCO2 culture experiments at constant temperature produce significant changes in skeletal δ18O and Δ47. Observed pH driven effects on carbonate δ18O and Δ47 in controlled abiogenic precipitation experiments have been attributed to changes relative abundance of CO32- and HCO3- in the calcification fluid DIC pool as different DIC species have different δ18O and multiply substituted isotopologue (Δ47) compositions. However, with our unique combination of δ11B, δ18O, and Δ47 measurements, we are able to determine that the magnitude of the pHCF change indicated by the δ11B-pHCF proxy indicates that observed trends in the δ18O and clumped isotope composition are not solely driven by this mechanism in tropical shallow water scleractinian corals. Instead, trends in δ18O and Δ47 with external pCO2 manipulation may be better explained by changes in the residence time of the DIC in the parent fluid for calcification, which will influence the time available for DIC to equilibrate with water and therefore change the potential for kinetic isotope effects generated by physiological processes to be recorded in the coral skeleton.

Environmental DNA metabarcoding (eDNA) is an evolving methodology of biodiversity monitoring. By leveraging shed and excreted DNA from organisms in a marine environment, researchers can perform DNA amplification and sequencing to identify what species were present at a site without the need for visual identification. This thesis uses eDNA to evaluate conservation efforts in Southern California as well as further establish and refine eDNA as a survey tool. In Chapter 1, I evaluate seagrass beds in three distinct geographic settings in Southern California. We demonstrate that nearly half of community composition is associated with whether seagrass was found off the mainland, off an island, or in an embayment. In addition, when compared to traditional monitoring, eDNA was able to identify roughly ~50% to 400% greater number of fish species at each site. In Chapter 2, I create a novel eDNA droplet digital PCR assay for the detection of the invasive species Caulerpa prolifera that was found in Newport Bay in 2021 and found it to have the lowest eDNA steady state of any previously tested species. We demonstrate the critical importance of benchmarking eDNA assays before their use by managers and highlight some limitations for using eDNA in species detection. In Chapter 3, we perform two years of monthly sampling of MPAs using community scientists and UCLA researchers. We find that MPAs are distinct from nonMPAs in multivariate space for both fish and metazoan communities and that metazoan communities in MPAs are more diverse and stable compared to nonMPAs. We also show the scalability that eDNA has in biodiversity monitoring through the incorporation of volunteers into field sampling. Together, these chapters better our understanding of marine conservation in Southern California and further demonstrate the utility and limitations of eDNA metabarcoding for monitoring marine biodiversity.

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