Abstract Long-term biological time series that monitor ecosystems across the ocean’s full water column are extremely rare. As a result, classic paradigms have yet to be tested. One such paradigm is that variations in coastal upwelling drive changes in marine ecosystems throughout the water column. We examine this hypothesis by using data from three multi-decadal time series spanning surface (0 m), midwater (200-1000 m), and benthic (~ 4000 m) habitats in the central California Current Upwelling System. Data include microscopic counts of surface plankton, video quantification of midwater animals, and imaging of benthic seafloor invertebrates. Taxon-specific plankton biomass and midwater and benthic animal densities were separately analyzed with principal component analysis. Within each community, the first mode of variability corresponds to most taxa increasing and decreasing over time, capturing seasonal surface blooms and lower-frequency midwater and benthic variability. When compared to local wind-driven upwelling variability, each community correlates to changes in upwelling damped over distinct timescales. This suggests that periods of high upwelling favor increases in organism biomass or density from the surface ocean through the midwater down to the abyssal seafloor. These connections most likely occur directly via changes in primary production and vertical carbon flux, and to a lesser extent indirectly via other oceanic changes. The timescales over which species respond to upwelling are taxon-specific and are likely linked to the longevity of phytoplankton blooms (surface) and of animal life (midwater and benthos), that dictate how long upwelling-driven changes persist within each community. Data set description This data set includes 3 files, one for each community. The files contain plankton biomass (for the surface community) or animal density (for midwater and benthos communities) as a function of sampling time and taxonomic group. surface.csv: autotrophic and heterotrophic surface plankton sampled in Monterey Bay by CTD-rosette and analyzed by epifluorescence microscopy and flow cytometry midwater.csv: midwater animals observed by ROV in the Monterey Bay mesopelagic zone from 200-1000m benthos.csv: benthic animals observed by ROV in a ~ 4000 m abyssal seafloor habitat at the base of the Monterey deep-sea fan Detailed description (see additional details and references in Messié et al., 2023): Surface time series: Plankton biomass was estimated from surface plankton counts collected using ship-based CTD-rosette at station M1 in Monterey Bay (122.022°W, 36.747°N). This station is part of a 3-station time series program operating in Monterey Bay since 1989 at 3-4 week intervals. Epifluorescence microscopy was used to enumerate and size auto- and heterotrophic plankton. Starting in 1998, flow cytometry samples provided more precise numbers for Synechococcus and eukaryotic picoplankton (Prochlorococcus was not included as no information is available prior to 1998). Standard geometric equations (e.g., ellipsoid, sphere, cylinder, pennate diatom shape) were used to calculate biovolumes of individual cells, and biomass of each plankton group was assessed using biovolume-based carbon conversions. For picoplankton an average value per cell was used: 82 fgC cell-1 for Synechococcus and 530 fgC cell-1 for eukaryotic picophytoplankton (red fluorescing picoplankton). Diatom biovolumes were converted to biomass using log10(Biomass) = 0.76 log10(Volume) - 0.29 where Biomass is in gC and Volume is in 𝜇m3. The ciliate conversion was Biomass = 0.08 * Volume. For all other plankton we used log10(Biomass) = 0.94 log10(Volume) - 0.6. Midwater time series: Quantitative mesopelagic video transects were conducted at a single station in Monterey Bay (Midwater 1, 36°42′N, 122°02′W). The station is located over the axis of the Monterey Submarine Canyon, where the water column is approximately 1600 m deep. Data were collected using remotely operated vehicles (ROVs). Estimates of animal densities using ROV imaging underestimate some groups (notably fishes), but provide a more complete view of life in the ocean than traditional methods such as nets and acoustics, particularly for gelatinous animals. The ROVs conducted horizontal video transects while moving at about 0.5 m s-1 for 10 min. Data for this paper come from approximately monthly transects made at 100 m intervals between 200 - 1000 m from 1997-2017. These years were chosen because the entire mesopelagic water column was more evenly surveyed than in the years prior. In each transect, the community of animals was annotated by professional annotators using the open-source Video Annotation and Referencing System (VARS) software. Annotators identified organisms in transect video to the lowest taxon possible; in many cases to species. We selected 63 taxonomic groups defined at the highest possible taxonomic resolution; annotations not included represent 31% of the total (84% of which are euphausiids, chaetognaths, and unidentified appendicularians). Calibrated cameras on MBARI ROVs and accurate measurement of ROV speed through water, allow for the calculation of volume for each transect. Animal density was calculated for each taxonomic group and each depth-specific transect as the number of individuals divided by the corresponding transect volume, further averaged over the water column from 200 - 1000 m. Midwater transecting methods and their efficacy are well-documented. Benthic time series: Two comparable methods were used to assess benthic communities at Station M (34°50′N, 123°00′W). From 1989-2005, the identification to the lowest possible taxon, and quantity of benthic animals were recorded from images taken by a camera-sled towed along a horizontal transect above the sea floor at a speed of approximately 1 m s-1, taking a film image every 4-5 seconds (water depth ~ 4,100 m). The developed film was projected by a Beseler model 23C-II enlarger for annotation of identifiable animals in images. From 2006-2018, benthic communities were assessed using ROV video transects recorded from approximately 1.3 m above the sea floor, with a view of approximately 1 m wide, and length typically approximately 1 km. Water depth for these transects was approximately 4,000 m, the lower depth limit of the ROV. Animals visible in the video were identified and annotated using VARS. The 2006 change in sampling method and in time series location and depth was found to have little impact on the megafauna time series.

{"references": ["Monique Messi\u00e9, Rob E. Sherlock, Christine L. Huffard, J. Timothy Pennington, C. Anela Choy, Reiko P. Michisaki, Kevin Gomes, Francisco P. Chavez, Bruce H. Robison, and Kenneth L. Smith Jr. (2023). Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor. Proceedings of the National Academy of Sciences, 120 (13) e2214567120, https://doi.org/10.1073/pnas.2214567120"]}

The Monterey Bay Aquarium Research Institute time series programs and this work were funded by the David and Lucile Packard Foundation.