Data from: Spatiotemporal variability from physics to plankton ecology in an upwelling bay

Abstract Bays play a critical role in Eastern Boundary Upwelling Systems (EBUS) as hotspots of biological productivity and incubators for commercially important species. Within the California EBUS, Monterey Bay is a well-studied upwelling bay located downstream of the Año Nuevo upwelling center. Spatial structuring includes enhanced phytoplankton blooms in the northern and southern bay due to the influx of nutrient-rich upwelled water and locally enhanced residence time and stratification. Temporal structuring includes a clear seasonal succession in phytoplankton taxa, as first diatoms and then dinoflagellates bloom. These characteristics have been described from satellite data, fixed-point time series, and process studies. However, characterizing spatiotemporal patterns of variability within Monterey Bay, their relation to environmental forcing, and physical-biological coupling requires a long-term, multidisciplinary, spatially and vertically resolved time series. Here, we summarize monthly high-resolution autonomous underwater vehicle (AUV) transects from 2016 to 2024 that survey Monterey Bay from inner to outer shelf habitats. The AUV measures physical (temperature, salinity), chemical (oxygen, nitrate), and biological (fluorescence, bioluminescence) parameters, and provides qualitative ecological information on photosynthetic and heterotrophic plankton communities. Our results highlight the importance of upwelling in shaping the Monterey Bay ecosystem. Dominant variability for most parameters is found to be strongly seasonal and coherent across the bay, and to be correlated with upwelling and each other for physics, chemistry, and part of the plankton community (i.e. diatoms). Dinoflagellates and zooplankton display contrasting dynamics apparently unrelated to upwelling, likely associated with stratification (dinoflagellates) and the end of blooms (zooplankton). Dataset description This dataset includes 2 files: gridded AUV surveys, collected approximately monthly in a diamond pattern in Monterey Bay from 2016 to 2024, saved as a NetCDF file. Metadata is given in the NetCDF file. the corresponding gulper data used to evaluate plankton proxies, saved as a csv file where columns G-L are the 18S eDNA read counts summed by broad taxonomic groups, columns M-N are matching variables measured by autonomous sensors onboard the vehicle, and columns O-R are matching proxies computed from full-resolution bioluminescence and/or fluorescence data. Details regarding data sources and calculations can be found in Messié et al. (2026).摘要 海湾作为生物生产力热点与经济物种繁育场，在东边界上升流系统（Eastern Boundary Upwelling Systems, EBUS）中发挥着至关重要的作用。在加利福尼亚东边界上升流系统范围内，蒙特雷湾是一处研究较为充分的上升流海湾，坐落于阿尼奥新诺（Año Nuevo）上升流中心的下游区域。其空间结构表现为：受富营养上升流输入以及局地滞留时间延长与层化作用增强的影响，海湾南北两侧的浮游植物水华规模显著提升。时间结构则体现为浮游植物类群呈现清晰的季节演替规律：硅藻（diatoms）率先形成水华，随后由甲藻（dinoflagellates）接替。上述特征已通过卫星遥感数据、定点时间序列观测与过程研究得到了阐释。然而，若要刻画蒙特雷湾内的时空变异模式、阐明其与环境强迫的关联以及物理-生物耦合机制，则需要长期、多学科且具备空间与垂直分辨率的时间序列观测数据。本研究汇总了2016至2024年间的逐月高分辨率自主水下航行器（autonomous underwater vehicle, AUV）走航观测数据，观测覆盖了蒙特雷湾从近岸陆架到外陆架的所有生境。该自主水下航行器可采集物理（温度、盐度）、化学（溶解氧、硝酸盐）与生物（荧光、生物发光）参数，并可为光合型与异养型浮游生物群落提供定性生态学信息。本研究结果凸显了上升流作用对蒙特雷湾生态系统的塑造意义。多数参数的主导变异模式呈现显著的季节性特征，且在全湾范围内具有一致性；物理、化学参数以及部分浮游生物类群（即硅藻）的变异与上升流作用及彼此间均存在显著相关性。甲藻与浮游动物则呈现出与上升流无关的迥异动态，其变异可能分别与层化作用（甲藻）以及水华消退过程（浮游动物）相关。 数据集说明 本数据集包含2个文件： 1. 网格化自主水下航行器观测数据：2016至2024年间以菱形航线逐月在蒙特雷湾采集，存储为NetCDF格式文件，元数据已包含在该NetCDF文件中。 2. 配套gulper数据：用于评估浮游生物替代指标，存储为csv格式文件，其中G-L列为按大类群汇总的18S环境DNA（18S environmental DNA, eDNA）测序读长计数，M-N列为搭载于航行器的自主传感器所测得的匹配变量，O-R列为由全分辨率生物发光和/或荧光数据计算得到的匹配替代指标。 有关数据来源与计算方法的详细信息，请参见Messié等人（2026）的研究成果。