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 7, Issue 1, 2009
Abstracts are not presented with Editorials. -SFEWS Editors
A review of the geologic literature regarding sedimentation in the San Francisco Bay estuarine system shows that the main part of the bay occupies a structural tectonic depression that developed in Pleistocene time. Eastern parts, including San Pablo Bay and Suisun Bay, have had sedimentation throughout late Mesozoic and Tertiary. Carquinez Strait and the Golden Gate may represent antecedent stream erosion. Sedimentation has included estuarine, alluvial, and eolian deposition. The ages of estuarine deposition includes the modern high sea level stand and earlier Pleistocene interglacial periods. Sediment sources can be generally divided into the Coast Ranges, particularly the Franciscan Complex, and “Sierran.” Much of the estuarine system is floored by very fine sediment, with local areas of sand floor. Near the Golden Gate, sediment size decreases in both directions away from the deep channel. Bedforms include sand waves (submarine dunes), flat beds, and rock and boulders. These are interpreted in terms of dominant transport directions. Near the Golden Gate is an ebb-tidal delta on the outside (including San Francisco bar) and a flood-tidal delta on the inside (parts of Central Bay). The large tidal prism causes strong tidal currents, which in the upper part of the estuary are normally much stronger than river currents, except during large floods. Cultural influences have altered conditions, including hydraulic mining debris, blasting of rocks, dredging of navigation channels, filling of the bay, and commercial sand mining. Many of these have served to decrease the tidal prism, correspondingly decreasing the strength of tidal currents.
Old School vs. New School: Status of Threadfin Shad (Dorosoma petenense) Five Decades After Its Introduction to the Sacramento–San Joaquin Delta
Threadfin shad (Dorosoma petenense) is a schooling pelagic forage fish native to watersheds of the Gulf Coast of North America. Around 1962 it invaded the Sacramento-San Joaquin Delta from upstream reservoirs, where it was stocked to support sport fisheries. It quickly became, and continues to be, one of the most abundant fishes collected by ongoing monitoring programs in the delta. A substantial portion of the delta provides suitable abiotic habitat and so the species is widely distributed. However, in routine sampling it is most commonly collected and most abundant in the southeastern delta, where suitable abiotic habitat (relatively deep, clear water with low flow) coincides with high prey abundance. Apparent growth rate appears to be relatively fast with summer-spawned age-0 fish attaining fork lengths of 70 to 90 mm by the onset of winter. During fall months (September through December) apparent growth rate of age-0 fish has exhibited no long-term trend but has been negatively related to abundance, suggesting that density-dependent factors may be important to the population. Although abundance has fluctuated since its introduction almost five decades ago, it has recently dropped to persistent near-record lows since 2002, which has been coincident with similar declines for other pelagic species in the delta. The recent decline is apparent in two long-term monitoring programs, fish salvaged from the diversions of the state and federal water projects, and commercial fishing harvest. It appears that the decline is, at least in part, a function of fewer and smaller schools of threadfin shad encountered relative to the past. There was little evidence from the data examined for consistent stock-recruit or stage-recruit effects on the population. It is likely that a combination of abiotic and biotic factors regionally-focused where threadfin shad are most abundant, which may sometimes be episodic in nature, have a large effect on abundance. Focused studies and sampling of threadfin shad are lacking but are necessary in order to better understand population dynamics in the delta.
Quantifying Activated Floodplains on a Lowland Regulated River: Its Application to Floodplain Restoration in the Sacramento Valley
We describe a process and methodology for quantifying the extent of a type of historically prevalent, but now relatively rare, ecologically-valuable floodplains in the Sacramento lowland river system: frequently-activated floodplains. We define a specific metric the “Floodplain Activation Flow” (FAF), which is the smallest flood pulse event that initiates substantial beneficial ecological processes when associated with floodplain inundation. The “Activated Floodplain” connected to the river is then determined by comparison of FAF stage with floodplain topography. This provides a simple definition of floodplain that can be used as a planning, goal setting, monitoring, and design tool by resource managers since the FAF event is the smallest flood and corresponding floodplain area with ecological functionality—and is necessarily also inundated in larger flood events, providing additional ecological functions. For the Sacramento River we selected a FAF definition to be the river stage that occurs in two out of three years for at least seven days in the mid-March to mid-May period and "Activated Floodplains" to be those lands inundated at that stage. We analyzed Activated Floodplain area for four representative reaches along the lower Sacramento River and the Yolo Bypass using stream gauge data. Three of the most significant conclusions are described: (1) The area of active functional floodplain is likely to be less than commonly assumed based on extent of riparian vegetation; (2) Levee setbacks may not increase the extent of this type of ecologically-productive floodplain without either hydrologic or topographic changes; (3) Within the Yolo Bypass, controlled releases through the Fremont Weir could maximize the benefits associated with Activated Floodplain without major reservoir re-operation or grading. This approach identifies a significant opportunity to integrate floodplain restoration with flood management by establishing a FAF stage metric as an engineering design criterion alongside the commonly-used 100-year flood stage for flood hazard reduction.