SFEWS: Volume 19, Issue 3
In our September issue new research and commentary provide insights on several topics: how to integrate zooplankton science to inform estuary management; how simulated fishing can avoid missed fish and detect gear bias in the water; why juvenile Chinook Salmon length-at-date criteria don't match genetic run assignments; whether declines in breeding waterfowl population relate to wetland habitat and salinity; and what kinds of food web support can be achieved by use of a managed flow pulse.
Photo: Forster’s Terns at Crown Beach, public domain. Attribution: © Ingrid Taylar, Creative Commons 2.0 Generic license.
Catch as Catch Can
"Catchability" refers to the relationship between catch rate and the true population. Ecological monitoring programs use catch per unit of effort (CPUE) to standardize catch and monitor changes in fish populations; however, CPUE is proportional to the portion of the population that is vulnerable to the type of gear used in sampling, which is not necessarily the entire population. Tobais' simulation combines a module for sampling conditions with a module for individual fish behavior to estimate the proportion of available fish that would escape from the sample. The method is applied to the case study of the well monitored fish species Delta Smelt (Hypomesus transpacificus) in the San Francisco Estuary, where it has been hypothesized that changing water clarity may affect catchability for long-term monitoring studies.
Waterfowl Reproductive Success Depends on High Water, Low Salt
Availability of wetlands with low salinities during the breeding season can influence waterfowl reproductive success and population recruitment. Salinities as low as 2 ppt (3.6 mS/cm) can impair duckling growth and influence behavior, with mortality occurring above 9 ppt (14.8 mS/cm). Schacter et al. used satellite imagery to quantify the amount of available water, and sampled surface water salinity at Grizzly Island, in the brackish Suisun Marsh, at three time-periods during waterfowl breeding (April, May, July) over 4 years (2016–2019). Among their findings was during peak duckling production in May, 81%–95% of available water had salinity above 2 ppt, and 5%–21% was above 9 ppt. Local waterfowl populations would benefit from management practices that provide fresher water during peak duckling production in May and retain more water through July.
Deep Dives Among Waterbird Populations in South SF Bay
In south San Francisco Bay, former salt ponds now managed as wildlife habitat support large populations of breeding waterbirds. In 2006, the South Bay Salt Pond Restoration Project began the process of converting 50% to 90% of these managed pond habitats into tidal marsh. Hartman et al. compared waterbird populations in south San Francisco Bay before (2001) and after (2019) approximately 1,300 ha of managed ponds were breached to tidal action to begin tidal marsh restoration. Study results showed average annual nest abundance declined during 2017–2019 by 53%, 71%, and 36%, for American Avocets, Back-necked Stilts, and Forster’s Terns, respectively. All three species established nesting colonies on newly constructed islands within remaining managed ponds; however, these new colonies did not make up for the steep declines observed at other historical nesting sites. For future wetland restoration, retaining more managed ponds that contain islands suitable for nesting may help to limit further declines in breeding waterbird populations.
Managed Pulse Flows as Food Web Support
While freshwater inflow has been a major focus of resource management in estuaries, including the upper San Francisco Estuary, there is a growing interest in using focused flow actions to maximize benefits for specific regions, habitats, and species. To test this concept, in summer 2016, Frantzich et al. used a managed flow pulse to target an ecologically important region: a freshwater tidal slough called the Cache Slough Complex. Their goal was to improve estuarine habitat by increasing net flows through CSC to enhance downstream transport of lower trophic-level resources, an important driver for fishes such as the endangered Delta Smelt. Simulations using a 3-D hydrodynamic model (UnTRIM) indicated that the managed flow pulse had a large effect on the net flow of water through Yolo Bypass, and between the CSC and further downstream. The managed flow pulse resulted in increased densities of zooplankton (copepods, cladocerans) demonstrating potential advection from upper floodplain channels into the target CSC and Sacramento River regions. Though conducted during a single year, this study may provide an instructive example of how a relatively modest change in net flows can generate measurable changes in ecologically relevant metrics, and how an adaptive management action can help inform resource management.
Length-at-Date Criteria and Genetic Run Assignments
Four distinct runs of Central Valley Chinook Salmon are named after their primary adult return times: fall, late-fall, winter, and spring run. Estimating the run-specific composition of juveniles entering and leaving the Sacramento–San Joaquin Delta is crucial for assessing population status and processes that affect juvenile survival through the Delta. Historically, the run of juvenile Chinook Salmon captured in the field has been determined using a length-at-date criteria (LDC); however, LDC run assignments may be inaccurate if there is high overlap in the run-specific timing and size of juveniles entering and leaving the Delta. In this study, Brandes et al. use genetic run assignments to assess the accuracy of LDC at two trawl locations in the Sacramento River (Delta entry) and at Chipps Island (Delta exit).Across years, there was extensive overlap among the distributions of run-specific fork lengths of genetically identified juveniles, indicating that run compositions based on LDC assignments would tend to underestimate fall-run and especially late-fall-run compositions at both trawl locations, and greatly overestimate spring-run compositions (both locations) and winter-run compositions (Chipps Island). We therefore strongly support ongoing efforts to include tissue sampling and genetic run identification of juvenile Chinook Salmon at key monitoring locations in the Sacramento–San Joaquin River system.
Pelagic fish in the San Francisco Estuary are harder to catch in recent decades. Over the past thirty years, Delta Smelt catch in the Fall Midwater Trawl Survey has declined by 99%, Longfin Smelt catch has declined by over 95%, and even the notoriously hardy Striped Bass have declined by over 75%. To manage the system and reverse these declines, we need a better understanding of the “bottom-up” processes that exert control on these populations—we need to study fish food. In other words, in addition to studying fish directly, we need to increase our understanding of what pelagic fish eat: zooplankton. In this essay, Hartman et al. break down not only what fish eat (zooplankton) and why they are important drivers of species abundance in higher trophic areas of the food web, but also how scientists and natural resources managers can communicate better to understand which zooplankton data can inform and develop management-relevant questions.
Volume 4, Issue 1, 2006
CalJep is a spatially enabled database that reconciles or cross-walks the two prominent electronic plant distribution lists for California: CalFlora and Jepson. We intersected the distribution information from the two data sources to create a refined spatial distribution repository that can be used to examine patterns of plant diversity, distribution ranges of individual plant species or infrataxa, or vegetation associations. These data will allow scientists and resource managers to examine potential range maps for non-native plants, create range maps for plant species of restoration interest, and corroborate lines of evidence for determining appropriate management and conservation activities. We present here a detailed description of the methods used to create the CalJep geodatabase, data rendered from its creation, and a discussion of its applicability to a wide range of biogeographical and ecological questions, including restoration planning and adaptive management for the Bay-Delta ecosystem. CalJep records 7,887 plant species, subspecies, and varieties mapped onto 228 ecological subunits with corresponding distributional information for vascular plant species at varying levels of confidence. Information derived from this geodatabase is inherently as accurate as the digital floras used to create it; hence, its utility is best realized when implemented at the regional or statewide scale. CalJep provides a previously unavailable service to vegetation science in California and to resource managers operating within the Bay-Delta ecosystem.
Infectious Hematopoietic Necrosis Virus Transmission and Disease among Juvenile Chinook Salmon Exposed in Culture Compared to Environmentally Relevant Conditions
The dynamics of IHNV infection and disease were followed in a juvenile Chinook salmon population both during hatchery rearing and for two weeks post-release. Cumulative weekly mortality increased from 0.03%–3.5% as the prevalence of viral infection increased from 2%–22% over the same four-week period. The majority of the infected salmon was asymptomatic. Salmon demonstrating clinical signs of infection shed 1000 pfu mL-1 of virus into the water during a 1 min observation period and had a mean concentration of 106 pfu mL-1 in their mucus. The high virus concentration detected in mucus suggests that it could act as an avenue of transmission in high density situations where dominance behavior results in nipping. Infected smolts that had migrated 295 km down river were collected at least two weeks after their release. The majority of the virus positive smolts was asymptomatic. A series of transmission experiments was conducted using oral application of the virus to simulate nipping, brief low dose waterborne challenges, and cohabitation with different ratios of infected to naïve fish. These studies showed that asymptomatic infections will occur when a salmon is exposed for as little as 1 min to >102 pfu mL-1, yet progression to clinical disease is infrequent unless the challenge dose is >104 pfu mL-1. Asymptomatic infections were detected up to 39 d post-challenge. No virus was detected by tissue culture in natural Chinook juveniles cohabitated with experimentally IHNV-infected hatchery Chinook at ratios of 1:1, 1:10, and 1:20 for either 5 min or 24 h. Horizontal transmission of the Sacramento River strain of IHNV from infected juvenile hatchery fish to wild cohorts would appear to be a low ecological risk. The study results demonstrate key differences between IHNV infections as present in a hatchery and the natural environment. These differences should be considered during risk assessments of the impact of IHNV infections on wild salmon and trout populations.
Effective conservation and recovery planning for Central Valley steelhead requires an understanding of historical population structure. We describe the historical structure of the Central Valley steelhead evolutionarily significant unit using a multi-phase modeling approach. In the first phase, we identify stream reaches possibly suitable for steelhead spawning and rearing using a habitat model based on environmental envelopes (stream discharge, gradient, and temperature) that takes a digital elevation model and climate data as inputs. We identified 151 patches of potentially suitable habitat with more than 10 km of stream habitat, with a total of 25,500 km of suitable habitat. We then measured the distances among habitat patches, and clustered together patches within 35 km of each other into 81 distinct habitat patches. Groups of fish using these 81 patches are hypothesized to be (or to have been) independent populations for recovery planning purposes. Consideration of climate and elevation differences among the 81 habitat areas suggests that there are at least four major subdivisions within the Central Valley steelhead ESU that correspond to geographic regions defined by the Sacramento River basin, Suisun Bay area tributaries, San Joaquin tributaries draining the Sierra Nevada, and lower-elevation streams draining to the Buena Vista and Tulare basins, upstream of the San Joaquin River. Of these, it appears that the Sacramento River basin was the main source of steelhead production. Presently, impassable dams block access to 80% of historically available habitat, and block access to all historical spawning habitat for about 38% of the historical populations of steelhead.
A two-dimensional, depth-averaged kinetic model of copper cycling was developed for the San Francisco Bay estuary. Adsorption and desorption reaction rate constants were determined from experimental sorption experiments. To calibrate the model, processes related to aqueous speciation were included. The model was used to predict spatial and seasonal trends in the adsorption and desorption of copper. Model predictions show that copper is continually being re-partitioned between sediment and water. Re-partitioning is prevalent near tributary and anthropogenic sources. It also occurs between segments of the bay, in response to differences in salinity and the availability of organic ligands dissolved in the water. In areas of restricted circulation such as the South Bay, copper adsorbed onto settling particles during wet season storm events acts as a source to the water column during the dry season. The relative contribution of resuspended benthic sediment to dissolved copper concentrations is highly variable in the bay. In the North Bay, dissolved copper is principally introduced from the San Joaquin-Sacramento Delta. In the South and lower South bays, desorption from sediment during the dry season may contribute as much as 20% of the total mass input of dissolved copper. Improvement of water quality can be achieved by reducing loads; however, changes are predicted to take years.