Interagency Ecological Program: Zooplankton abundance in the Upper San Francisco Estuary from 1972-2021, an integration of 7 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 CDWR Yolo Bypass Fish Monitoring
Program add zooplankton in 1999, the CDFW Summer Townet Survey added
zooplankton in 2005, and the Fall Midwater Trawl added zooplankton
in 2007. Two new sampling programs, the Fish Restoration Program and
Directed Outflow Project, began in 2015 and 2017, respectively. All
sampling programs continue today. Each survey samples once or twice
monthly at set of fixed or random 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 7 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.