Interagency Ecological Program: Zooplankton abundance in the Upper San Francisco Estuary from 1972-2018, an integration of 5 long-term monitoring programs

The upper San Francisco Estuary is an inland inverse delta formed by the confluence of 5 major rivers that drain 40% of the land in California (USA). It is a central hub of water delivery in California and home to a number of commercially important and endangered fish, such as Chinook Salmon, Green Sturgeon, and Delta Smelt. To monitor the environmental impacts of water exports from this system, extensive ecological monitoring has been conducted since the 1960s. To track lower trophic levels, zooplankton abundance has been monitored from 1972 to present. Starting with just one survey (the CA Department of Water Resources’ [CDWR] and California Department of Fish and Wildlife’s [CDFW] Environmental Monitoring Program) in 1972, the suite of zooplankton surveys gradually expanded with time. Several surveys traditionally focused on monitoring fish abundance added zooplankton nets to their sampling programs. The CDFW 20-mm larval fish survey added zooplankton sampling in 1995, the CDFW Summer Townet Survey added zooplankton in 2005, and the Fall Midwater Trawl added zooplankton in 2007. A new sampling program, the Fish Restoration Program, began in 2015 and included both fish and zooplankton. All sampling programs continue today. Each survey samples once or twice monthly at set of fixed stations that varies across surveys depending on their objectives. While the Environmental Monitoring Program samples year-round, the other surveys are mostly seasonal, although additional months were sampled in some years. Most surveys target open channels although the Fish Restoration Program samples in or near shallow tidal wetlands. Three size classes of zooplankton are targeted by these sampling programs with different net mesh sizes: micro zooplankton (copepods and rotifers) are targeted with a 43 µm mesh net, meso zooplankton (copepods and cladocerans) are targeted with 150 - 160 µm mesh nets, and macro zooplankton (mysids and amphipods) are targeted with 500-505 µm mesh nets. We have integrated data from all 5 surveys and 3 size classes into a powerful long-term record of zooplankton in the San Francisco Estuary, representing over 80,000 zooplankton samples and over 2 billion estimated zooplankton captured by the nets in these surveys. Over the duration of this zooplankton dataset, the zooplankton community species composition has almost completely turned over after a series of species invasions from East Asia, numerous drought cycles have come and gone, and important fish species have dramatically declined during the Pelagic Organism Decline in 2002, likely due in part to reduced food supply from zooplankton. Data from the individual surveys have been used in prior studies to investigate issues related to species invasions, flows, fish diets and population dynamics, zooplankton population dynamics, and community ecology. Our integrated dataset offers new and unparalleled spatiotemporal resolution to address these and other questions with greater statistical power.圣弗朗西斯科河口上游（upper San Francisco Estuary）是由5条主要河流汇流形成的内陆逆三角洲，其流域覆盖美国加利福尼亚州40%的陆地面积。它是加州核心输水枢纽，同时栖息着多种兼具商业价值与保护价值的濒危鱼类，例如奇努克鲑鱼（Chinook Salmon）、绿色鲟鱼（Green Sturgeon）以及三角洲胡瓜鱼（Delta Smelt）。为监测该系统水体外调对环境的影响，研究团队自20世纪60年代起便开展了大规模生态监测工作。为追踪低营养级（lower trophic levels）生物，研究人员自1972年起至今持续监测浮游动物（zooplankton）丰度。 1972年，该监测体系最初仅包含一项由加州水资源部（California Department of Water Resources, CDWR）与加州鱼类与野生动物部（California Department of Fish and Wildlife, CDFW）联合实施的环境监测计划（Environmental Monitoring Program），随时间推移，浮游动物调查的覆盖范围逐步拓展。多项原本以鱼类丰度监测为核心的传统调查项目，也将浮游动物网采样纳入了自身的采样方案：CDFW的20毫米仔鱼调查（20-mm larval fish survey）于1995年新增浮游动物采样环节，CDFW夏季托内特拖网调查（Summer Townet Survey）于2005年加入该采样内容，秋季中层拖网调查（Fall Midwater Trawl）则于2007年将浮游动物采样纳入工作范畴。2015年，全新的鱼类恢复计划（Fish Restoration Program）正式启动，该项目同时涵盖鱼类与浮游动物监测。目前所有采样项目均持续开展至今。 各项调查均在固定站位每月开展1至2次采样，不同调查的固定站位设置因研究目标各有差异。其中，环境监测计划全年不间断采样，其余调查多为季节性开展，部分年份会增设额外采样月份。多数调查以开阔水道为采样区域，唯有鱼类恢复计划的采样点设置于浅潮湿地带或其邻近区域。 本次采样体系针对3个粒径等级的浮游动物设置了不同网孔尺寸的采样网：微型浮游动物（micro zooplankton，涵盖桡足类与轮虫）采用43 μm网孔的采样网；中型浮游动物（meso zooplankton，涵盖桡足类与枝角类）采用150~160 μm网孔的采样网；大型浮游动物（macro zooplankton，涵盖糠虾与端足类）则采用500~505 μm网孔的采样网。 研究团队将上述5项调查与3个粒径等级的浮游动物数据整合，构建了圣弗朗西斯科河口高质量的长期浮游动物监测数据集，涵盖超过8万个浮游动物采样样本，以及各次调查中采样网捕获的逾20亿只估算浮游动物个体。 在该数据集的监测周期内，受一系列东亚物种入侵的影响，浮游动物群落的物种组成几乎完成完全更替；多轮干旱周期循环往复；2002年爆发的浮游生物衰退事件（Pelagic Organism Decline）期间，重要鱼类种群数量大幅下降，该现象部分归因于浮游动物提供的食物资源减少。 此前已有多项研究利用各单项调查的数据，探讨了物种入侵、水文径流、鱼类食性与种群动态、浮游动物种群动态以及群落生态学等相关科学议题。本整合数据集提供了前所未有的时空分辨率，能够以更强的统计效力解决上述及其他相关科学问题。