Drivers of plankton community structure in intermittent and continuous coastal upwelling systems-from microscale in-situ imaging to large scale patterns

Eastern Boundary Systems support major fisheries whose early life stages depend on upwelling production. Upwelling can be highly variable at the regional scale, with substantial repercussions for new productivity and microbial loop activity. A holistic assessment of plankton community structure is challenging due to the range in body forms and sizes of the taxa. Thus, studies that integrate the classic trophic web based on new production with the microbial loop are rare. Underwater imaging can overcome this limitation, and together with machine learning, enables fine resolution studies spanning large spatial scales. We used the In-situ Ichthyoplankton Imaging System (ISIIS) to investigate the drivers of plankton community structure in the northern California Current, sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA, respectively. The non-invasive imaging of particles and plankton (250m -15cm) over 1644km (30 transects) in the winters and summers of 2018 and 2019 yielded 1.194 billion classified plankton images. The imaged plankton community ranged from protists, crustaceans, and gelatinous taxa to larval fishes. To assess community structure, >2000 single-taxon distribution profiles were analyzed using high resolution spatial correlations. Co-occurrences on the NH line were consistently significantly higher off-shelf while those at TR tended to be highest on-shelf. Taxa co-occurrences at TR increased significantly with upwelling strength and in 2019 TR summer co-occurrences were similar to those on the NH line. Random Forests models identified the concentrations of microbial loop taxa such as protists, Oithona copepods, and appendicularians as important drivers of co-occurrences at NH line, while at TR, cumulative upwelling and chlorophyll a were of the highest importance. Our results indicate that the microbial loop is actively driving plankton community structure in intermittent upwelling systems such as the NH line and may induce temporal stability. Where upwelling is more continuous such as at TR, primary production may dominate patterns of community structure, obscuring the underlying role of the microbial loop. Future changes in upwelling strength are likely to disproportionately affect plankton community structure in continuous upwelling regions, while high microbial loop activity enhances community structure resilience.