Data from: Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor [updated]

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. When using these time series, please cite the original reference listed below each time series description in addition to this dataset. 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 In addition, following the time series update to v2.0.0, the paper figures reproduced using these time series are provided here. 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 pgC 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. Reference: Chavez, F. P., Pennington, J. T., Michisaki, R. P., Blum, M., Chavez, G. M., Friederich, J., ... & Messié, M. (2017). Climate variability and change: response of a coastal ocean ecosystem. Oceanography, 30(4), 128-145. https://doi.org/10.5670/oceanog.2017.429 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. Reference: Robison, B. H., Reisenbichler, K. R., & Sherlock, R. E. (2017). The coevolution of midwater research and ROV technology at MBARI. Oceanography, 30(4), 26-37. https://doi.org/10.5670/oceanog.2017.421 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. Reference: Smith Jr, K. L., Sherman, A. D., McGill, P. R., Henthorn, R. G., Ferreira, J., & Huffard, C. L. (2017). Evolution of monitoring an abyssal time-series station in the northeast Pacific over 28 years. Oceanography, 30(4), 72-81. https://doi.org/10.5670/oceanog.2017.425摘要 能够监测全水柱海洋生态系统的长期生物时间序列极为稀缺，致使诸多经典生态学范式尚未得到验证。其中一个典型范式为：沿岸上升流（coastal upwelling）的变化驱动全水柱海洋生态系统的改变。本研究借助加利福尼亚中部沿岸上升流系统中覆盖表层（0米）、中层（200~1000米）及底栖（约4000米）生境的3套多年代时间序列数据，对该假说展开验证。数据集包含表层浮游生物显微计数数据、中层水生动物视频量化数据，以及底栖海底无脊椎动物成像数据。研究分别采用主成分分析（Principal Component Analysis）对分类群特异性浮游生物生物量、中层与底栖动物密度进行分析。在每个群落中，第一变异模态对应多数类群随时间的增减变化，捕捉到了表层季节性水华以及低频的中层与底栖群落变异。将其与局地风驱上升流变异对比后发现，各群落均与不同时间尺度下衰减的上升流变化存在相关性。这表明，高上升流时段有利于从表层海洋到中层再到深渊海底的生物体生物量或密度提升。这种关联最可能直接通过初级生产与垂直碳通量的变化实现，次要程度上则通过其他海洋过程间接产生。物种对上升流响应的时间尺度具有类群特异性，且可能与浮游植物水华（表层群落）以及动物寿命（中层与底栖群落）的持续时长相关，而这些因素决定了上升流驱动的变化在各群落中能够维持的时长。 数据集说明 本数据集包含3个文件，分别对应3类海洋群落。文件内容为采样时间与分类群维度下的浮游生物生物量（表层群落）或动物密度（中层与底栖群落）数据。使用本时间序列数据时，除引用本数据集外，还需引用各时间序列描述下方标注的原始参考文献。 surface.csv：取自蒙特利湾的自营与异养表层浮游生物样本，通过CTD罗塞塔系统（CTD-rosette）采集，经落射荧光显微镜与流式细胞术分析 midwater.csv：蒙特利湾200~1000米中层带内通过遥控水下机器人（Remotely Operated Vehicle，ROV）观测得到的中层水生动物数据 benthos.csv：蒙特利深海扇基部约4000米深渊海底生境内通过ROV观测得到的底栖动物数据 此外，本数据集已更新至v2.0.0版本，随附利用本时间序列复刻的论文图表。 详细说明（更多细节与参考文献详见Messié等人，2023年）： 表层群落时间序列：样本取自蒙特利湾M1站（122.022°W，36.747°N）的表层浮游生物，通过船载CTD罗塞塔系统采集，浮游生物生物量由计数结果估算得到。该站位是蒙特利湾自1989年起运行的3站位时间序列项目的一部分，采样间隔为3~4周。研究采用落射荧光显微镜对自营与异养浮游生物进行计数与尺寸测定。1998年起，流式细胞术为聚球藻属（Synechococcus）与真核超微型浮游生物提供了更精准的计数数据（原绿球藻属（Prochlorococcus）未纳入统计，因1998年前无相关观测数据）。通过标准几何方程（如椭球、球体、柱体、羽纹硅藻形态）计算单个细胞的生物体积，并基于生物体积的碳转换系数估算各浮游类群的生物量。超微型浮游生物采用单细胞平均碳含量：聚球藻属为82 fgC cell⁻¹，真核超微型浮游植物（红色荧光超微型浮游生物）为530 fgC cell⁻¹。硅藻生物体积至生物量的转换公式为：log₁₀(生物量) = 0.76log₁₀(体积) - 0.29，其中生物量单位为pgC，体积单位为μm³。纤毛虫的转换公式为：生物量 = 0.08 × 体积。其余浮游类群采用转换公式：log₁₀(生物量) = 0.94log₁₀(体积) - 0.6。 参考文献：Chavez, F. P., Pennington, J. T., Michisaki, R. P., Blum, M., Chavez, G. M., Friederich, J., 等 & Messié, M. (2017). 气候变异与变化：沿岸海洋生态系统的响应. 海洋学(Oceanography), 30(4), 128-145. https://doi.org/10.5670/oceanog.2017.429 中层群落时间序列：在蒙特利湾单一站位（中层1站，36°42′N，122°02′W）开展定量中层带视频样带调查，该站位位于蒙特利海底峡谷轴线上方，水柱深度约1600米。数据通过遥控水下机器人（ROV）采集。尽管利用ROV成像估算动物密度会低估部分类群（尤其是鱼类），但相较于拖网、声学探测等传统方法，该方案能够更全面地展现海洋生物群落，尤其适用于凝胶状动物。ROV以约0.5 m s⁻¹的速度行进10分钟，完成水平视频样带采集。本研究使用1997~2017年间的数据集，该时段内以100米为间隔在200~1000米水深范围内开展近似月度的样带调查，相较于此前年份，该时段对整个中层带水柱的调查更为均匀。每条样带的动物群落均由专业标注人员利用开源视频标注与引用系统（Video Annotation and Referencing System, VARS）进行注释，标注人员尽可能将观测生物鉴定至最低分类阶元，多数类群可鉴定至物种水平。本研究选取了63个以最高分类分辨率定义的类群，未纳入标注的类群占总观测量的31%，其中84%为磷虾类、毛颚类以及未鉴定的尾海鞘类。MBARI的ROV搭载校准后的摄像头，并可精准测量水下行进速度，据此可计算每条样带的水体体积。针对每个分类群与每个水深样带，动物密度以个体数除以对应样带水体体积计算得出，并进一步在200~1000米水柱范围内取平均。中层带样带调查方法及其有效性已有充分文献记录。 参考文献：Robison, B. H., Reisenbichler, K. R., & Sherlock, R. E. (2017). MBARI中层带研究与ROV技术的协同发展. 海洋学(Oceanography), 30(4), 26-37. https://doi.org/10.5670/oceanog.2017.421 底栖群落时间序列：在M站（34°50′N，123°00′W）采用两种可比方法评估底栖生物群落。1989~2005年，通过在海底上方以约1 m s⁻¹速度拖行的摄像雪橇开展水平样带调查，每4~5秒拍摄一张胶片图像（水深约4100米），记录可鉴定至最低分类阶元的底栖动物种类与数量。冲洗后的胶片通过Beseler 23C-II型放大仪投影，对图像中可识别的动物进行标注。2006~2018年，改用ROV视频样带调查：在海底上方约1.3米处录制视频，视野宽度约1米，样带长度通常约1公里，调查水深约4000米，为该ROV的最大作业水深。视频中可见的动物通过VARS软件进行鉴定与标注。研究表明，2006年采样方法、时间序列站位与水深的变更，对大型底栖生物时间序列几乎无影响。 参考文献：Smith Jr, K. L., Sherman, A. D., McGill, P. R., Henthorn, R. G., Ferreira, J., & Huffard, C. L. (2017). 东北太平洋深渊时间序列站位28年监测工作的演进. 海洋学(Oceanography), 30(4), 72-81. https://doi.org/10.5670/oceanog.2017.425