SFEWS Vol. 20, Issue 2 | June 2022
#ChinookSalmon #SacramentoSplittail #tidalmarsh #floodplain #openwater #drought #flood #juvenileproductionestimate #JPE #lifehistory #raceidentification #springrun #SacramentoRiver #CADelta #quantile #regressionforest #Steelhead #machinelearning #entrainmentloss #SanFrancisco #estuary #SFE #BayDelta #gillnet #gearselectivity #Drainage #waterquality #agriculturaldrainage #returnflow #diversions #Delta #island #groundwater #nitrogen #phosphorous #metals
Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon
Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley.
Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California
Incidental entrainment of fishes at large-scale state and federal water diversion facilities in the Sacramento-San Joaquin Delta, California, can trigger protective management actions when limits imposed by environmental regulations are approached or exceeded. These actions can result in substantial economic costs, and likewise they can affect the status of vulnerable species. Here, we examine data relevant to water management actions during January–June; the period when juvenile salmonids are present in the Delta.
Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary
Gill-net size selectivity for 15 fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies which together contained 7,096 individual fish observations from 882 gill net sets. The gill nets considered in this study closely resembled the American Fisheries Society’s recommended standardized experimental gill nets for sampling inland waters. Relationships between gill-net mesh sizes and the sizes for each fish species retained in them were estimated indirectly using generalized linear modeling and maximum likelihood.
Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California
Inventorying nutrient and trace element sources in the Sacramento-San Joaquin Delta (the Delta) is critical to understanding how changes—including alterations to point source inputs such as upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) and landscape-scale changes related to wetland restoration—may alter the Delta’s water quality. While island drains are a ubiquitous feature of the Delta, limited data exist to evaluate island drainage mass fluxes in this system. To better constrain inputs from island drains, we measured monthly discharge along with nutrient and trace element concentrations in island drainage on three Delta islands and surrounding rivers from June 2017 to September 2018.
Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review ample header
In the San Francisco Estuary, signals of climate change are apparent in the long-term monitoring record. Here we synthesize current and potential future climate change effects on three main ecosystems (floodplain, tidal marsh, and open water) in the upper estuary and two representative native fishes that commonly occur in these ecosystems (anadromous Chinook Salmon, Oncorhynchus tshawytscha and estuarine resident Sacramento Splittail, Pogonichthys macrolepidotus).
Volume 3, Issue 2, 2005
The delta smelt (Hypomesus transpacificus) is a small and relatively obscure fish that has recently risen to become a major focus of environmental concern in California. It was formally abundant in the low-salinity and freshwater habitats of the northeastern San Francisco Estuary, but is now listed as threatened under the Federal and California State Endangered Species Acts. In the decade following the listings scientific understanding has increased substantially, yet several key aspects of its biology and ecological relationships within the highly urbanized estuary remain uncertain. A key area of controversy centers on impacts to delta smelt associated with exporting large volumes of freshwater from the estuary to supply California’s significant agricultural and urban water demands. The lack of appropriate data, however, impedes efforts to resolve these issues and develop sound management and restoration alternatives.
Delta smelt has an unusual life history strategy relative to many fishes. Some aspects of its biology are similar to other coastal fishes, particularly salmonids. Smelts in the genus, Hypomesus, occur throughout the Pacific Rim, have variable life history strategies, and are able to adapt rapidly to local environments. By comparison, delta smelt has a tiny geographic range being confined to a thin margin of low salinity habitat in the estuary. It primarily lives only a year, has relatively low fecundity, and pelagic larvae; life history attributes that are unusual when compared with many fishes worldwide. A small proportion of delta smelt lives two years. These individuals are relatively highly fecund but are so few in number that their reproductive contribution only may be of benefit to the population after years of extremely poor spawning success and survival. Provisioning of reproductive effort by these older fish may reflect a bet-hedging tactic to insure population persistence.
Overall, the population persists by maximizing growth, survival, and reproductive success on an annual basis despite an array of limiting factors that can occur at specific times and locations. Variability in spawning success and larval survival is induced by climate and other environmental and anthropogenic factors that operate between winter and mid-summer. However, spawning microhabitats with egg deposition have not been discovered. Spawning success appears to be timed to lunar periods within a water temperature range of about 15 to 20°C. Longer spawning seasons in cooler years can produce more cohorts and on average higher numbers of adult delta smelt. Cohorts spaced in time have different probabilities of encountering various sources of mortality, including entrainment in freshwater export operations, pulses of toxic pesticides, food shortages and predation by exotic species. Density dependence may provide an upper limit on the numbers of juvenile delta smelt surviving to the adult stage. This may occur during late summer in years when juvenile abundance is high relative to habitat carrying capacity. Factors defining the carrying capacity for juvenile delta smelt are unknown, but may include a shrinking volume of physically suitable habitat combined with a high density of competing planktivorous fishes during late summer and fall.
Understanding the relative importance of anthropogenic effects on the population can be improved through better estimates of abundance and measurements of potentially limiting processes. There is little information on losses of larval delta smelt (less than 20 mm fork length, FL) to the export facilities. Use of a population model suggests that water export operations can impact the abundance of post-larval (about 20 mm FL) delta smelt, but these effects may not reflect on adult abundance due to other processes operating in the intervening period. Effects from changes to the estuarine food web by exotic species and toxic chemicals occur but measuring their influence on population abundance is difficult.
Although delta smelt recently performed well enough to meet the current restoration criteria, analyses presented here suggest that there is still a high probability that the population will decline in the near future; the most recent abundance index (2004) is the lowest on record. Overall, the limited distribution, short life span and low reproductive capacity, as well as relatively strict physical and feeding requirements, are indications that delta smelt is at risk to catastrophe in a fluctuating environment. Unfortunately, options for avoiding potential declines through management and restoration are currently limited by large gaps in knowledge. Monitoring of spring water temperatures, however, may provide a useful tool for determining when to reduce entrainment in water export facilities. Actions that target carrying capacity may ultimately provide the most benefit, but it is not clear how that can be achieved given the current state of knowledge, and the limited tools available for restoration. Overall, a better understanding of the life history, habitat requirements, and limiting factors will be essential for developing tools for management and restoration. Therefore, given the implications for managing California water supply and the current state of population abundance, a good investment would be to fill the critical data gaps outlined here through a comprehensive program of research.
Low Dissolved Oxygen in an Estuarine Channel (San Joaquin River, California): Mechanisms and Models Based on Long-term Time Series
The Stockton Deep Water Ship Channel, a stretch of the tidal San Joaquin River, is frequently subject to low dissolved oxygen conditions and annually violates regional water quality objectives. Underlying mechanisms are examined here using the long-term water quality data, and the efficacy of possible solutions using time-series regression models. Hypoxia is most common during June-September, immediately downstream of where the river enters the Ship Channel. At the annual scale, ammonium loading from the Regional Wastewater Control Facility has the largest identifiable effect on year-to-year variability. The longer-term upward trend in ammonium loads, which have been increasing over 10% per year, also corresponds to a longer-term downward trend in dissolved oxygen during summer. At the monthly scale, river flow, loading of wastewater ammonium and river phytoplankton, Ship Channel temperature, and Ship Channel phytoplankton are all significant in determining hypoxia. Over the recent historical range (1983–2003), wastewater ammonium and river phytoplankton have played a similar role in the monthly variability of the dissolved oxygen deficit, but river discharge has the strongest effect. Model scenarios imply that control of either river phytoplankton or wastewater ammonium load alone would be insufficient to eliminate hypoxia. Both must be strongly reduced, or reduction of one must be combined with increases in net discharge to the Ship Channel. Model scenarios imply that preventing discharge down Old River with a barrier markedly reduces hypoxia in the Ship Channel. With the Old River barrier in place, unimpaired or full natural flow at Vernalis would have led to about the same frequency of hypoxia that has occurred with actual flows since the early 1980s.
Genetic variation at 11 microsatellite loci described population genetic structure for Oncorhynchus mykiss in the Central Valley, California. Spatial and temporal variation was examined as well as relationships between hatchery and putative natural spawning anadromous stocks. Genetic diversity was analyzed at two distinct spatial scales: fine-scale within drainage for five populations on Clear Creek; between and among drainage diversity for 23 populations. Significant regional spatial structure was apparent, both within Clear Creek and among rainbow trout populations throughout the Central Valley. Significant differences in allelic frequencies were found among most river or drainage systems. Less than 1% of the molecular variance could be attributed to differences found between drainages. Hatchery populations were shown to carry similar genetic diversity to geographically proximate wild populations. Central Valley M = 0.626 (below the M < 0.68 threshold) supported recent population reductions within the Central Valley. However, average estimated effective population size was relatively high (Ne = 5066). Significant allelic differences were found in rainbow trout collected above and below impassable dams on the American, Yuba, Stanislaus and Tuolumne rivers. Rainbow trout sampled in Spring Creek were extremely bottlenecked with allelic variation at only two loci and an estimated effective population size of 62, suggesting some local freshwater O. mykiss stocks may be declining rapidly. These data support significant genetic population structure for steelhead and rainbow trout populations within the Central Valley across multiple scales. Careful consideration of this genetic diversity and its distribution across the landscape should be part of future conservation and restoration efforts.
A review of the science and practice of ecosystem restoration led me to identify key ecological theories and concepts that are relevant to planning, implementing, and sustaining restoration efforts. From experience with actual restoration projects, I provide guidance for improving the restoration process. Despite an abundance of theory and guidance, restoration goals are not always achieved, and pathways toward targets are not highly predictable. This is understandable, since each restoration project has many constraints and unique challenges. To improve restoration progress, I advise that sites be designed as experiments to allow learning while doing. At least the larger projects can be restored in phases, each designed as experimental treatments to test alternative restoration approaches. Subsequent phases can then adopt one or more of the treatments that best achieved goals in earlier phases while applying new tests of other restoration measures. Both science and restoration can progress simultaneously. This phased, experimental approach (called “adaptive restoration”) is an effective tool for improving restoration when monitoring, assessment, interpretation and research are integrated into the process.