SFEWS Vol. 20, Issue 1 | March 2021
#CentralValley #ChinookSalmon #otolithchemistry #Steelhead #monitoring #surveys #catchability #detectionefficiency #DeltaSmelt #supplementation #Ich #pathogens #organiccarbon #stablecarbon #nitrogen #inputs #YubaRiver #watersheds
Variation in Juvenile Salmon Growth Opportunities Across a Shifting Habitat Mosaic
Coleman et al. found that juvenile Chinook Salmon grew faster in the Delta in some years (2016), but slower in the Delta during drought conditions (2014 to 2015). Habitat that featured faster growth rates varied within and among years, suggesting the importance of maintaining a habitat mosaic for juvenile salmonids, particularly in a dynamic environment such as the California Central Valley.
Counting the Parts to Understand the Whole: Rethinking Monitoring of Steelhead in California’s Central Valley
Eschenroeder et al. argue that a reallocation of monitoring resources to better understand the interaction between resident and anadromous Steelhead would provide better data to estimate the vital rates needed to evaluate the effects of recovery actions.
Relative Bias in Catch Among Long-Term Fish Monitoring Surveys Within the San Francisco Estuary
Huntsman et al. assessed relative catchability differences among four long-term fish monitoring surveys from the San Francisco Estuary. Their results demonstrate that catchability is a source of bias among monitoring efforts within the San Francisco Estuary, and assuming equal catchability among surveys, species, and size classes could result in significant bias when describing spatio-temporal patterns in catch if ignored.
Investigation of Molecular Pathogen Screening Assays for Use in Delta Smelt
Gille et al. conducted a pilot study that applied molecular assays originally developed in salmonids to assess the presence of a wide variety of pathogens in the gill tissue of cultured and wild Delta Smelt—as well as cultured fish—deployed in enclosures in the estuary. Although disease is not an overt cause of population decline of Delta Smelt in the San Francisco Estuary, comprehensive pathogen presence and prevalence data are lacking, and unintended transmission of pathogens can have devastating effects on populations already at-risk or on the natural ecosystem at large. Their results corroborate previous work that cultured Delta Smelt do not appear to present a high risk for pathogen transmission during population supplementation or reintroduction.
Multi-Biomarker Analysis for Identifying Organic Matter Sources in Small Mountainous River Watersheds: A Case Study of the Yuba River Watershed
Pondell and Canuel's study focused on identifying the composition of watershed-derived organic matter (OM). To better understand inputs to inland waters and improve distinguish between terrigenous and aquatic sources in downstream systems, such as estuaries and coasts, they surveyed OM sources from the Yuba River watershed in northern California to identify specific biomarkers that represent aquatic and terrigenous OM sources. Results demonstrate the utility of multi-biomarker studies for distinguishing between OM from different sources and land uses, offering new insights for biogeochemical studies in aquatic systems.
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.