Metabarcoding supports regional ocean acidification monitoring and identifies novel bioindicators in the Southern California Bight

Ashton Margaret Bandy , Christina Frieder, Susanna Theroux, Zachary Gold , Sean M. McAllister , Katherine R. M. Mackey, Karen McLaughlin, Nataly Pineda, Melissa Brock, Martha Sutula, Adam C Martiny

The impacts of ocean acidification (OA) on marine communities are a growing concern for coastal upwelling ecosystems, such as the Southern California Bight (Bight). Successful management of coastal resources in the face of OA requires accurate assessment tools to understand the status and trends of OA impacts on biological communities. Current methods often rely on the condition of individual organisms (e.g., shell dissolution) and are resource- and labor-intensive. As a result, they are difficult to scale to population-level effects or to impacts on the community as a whole, which limits impact assessments and hinders implementation by coastal resource managers. DNA-based monitoring methods can address these gaps, and represent a scalable and cost-effective complement to traditional OA biomonitoring efforts. We applied a DNA metabarcoding approach to analyze mesozooplankton (>200 µm) samples in the Bight to investigate novel OA biomonitoring approaches and target organisms. We sequenced the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene and analyzed mesozooplankton community composition across 20 locations and four seasons. We found communities largely structured by seasonal gradients and dominated by copepods and krill. A subset of taxa corresponded strongly to carbonate chemistry variability; taxa in the Order Cheilostomatida (encrusting bryozoans), along with the copepod species Clausocalanus furcatus and Oncaea scottodicarloi corresponded to high aragonite saturation state values. In contrast, other species like Calanus pacificus (calanoid copepod) and Euphausia pacifica (krill) corresponded with low aragonite saturation state. We also investigated the ubiquity and relative abundance of routine target organisms (pteropods and larval crabs) versus alternative targets. Pteropods were rare and only found in the wintertime, while other larval stages of benthic calcifiers were more relatively abundant and ubiquitous. Our findings highlight the utility of DNA-based methods to guide OA biomonitoring and lay the groundwork for future research on OA indicators in this region.