Early Ocean Distribution of Juvenile Chinook Salmon in an Upwelling Ecosystem

Extreme variability in abundance of California salmon populations is often ascribed to ocean conditions, yet relatively little is known about their marine life-history. To investigate which ocean conditions influence their distribution and abundance, we surveyed juvenile Chinook salmon (Oncorhynchus tshawytscha) within the California Current (central California (37o 30’ N) to Newport, Oregon (44o 00’ N)) for a two-week period over three summers (2010-2012). At each station, we measured chlorophyll a as an indicator of primary productivity, acoustic-based metrics of zooplankton density as an indicator of potential prey availability, and physical characteristics such as bottom depth, temperature, and salinity. We also measured fork lengths and collected genetic samples from each salmon that was caught. Genetic stock identification revealed that the majority of juvenile salmon were from the Central Valley and the Klamath Basin (91-98%). We constructed generalized logistic-linear negative binomial hurdle models and chose the best model(s) using AIC to determine which covariates influenced salmon presence and, at locations where salmon were present, determined the variables that influenced their abundance. The probability of salmon presence was highest in shallower waters with high chlorophyll a concentration and close to an individual’s natal river. Catch abundance was primarily influenced by year, mean fork length, and proximity to natal rivers. At the scale of sampling stations, presence and abundance was not related to acoustic indices of zooplankton density. In the weeks to months following ocean entry, California’s juvenile Chinook salmon population appears to be primarily constrained to coastal waters near natal river outlets

Estuarine Recruitment of Longfin Smelt (Spirinchus thaleichthys) North of the San Francisco Estuary

Longfin Smelt (Spirinchus thaleichthys) was an important forage fish in the San Francisco Estuary (SFE) but was listed as threatened under the California Endangered Species Act in 2009. This has inspired research within the SFE at the southern edge of their distribution. However, populations also exist in other estuaries along the coast, which are far less described despite their potential importance in a metapopulation. We surveyed Longfin Smelt populations along the northern California coast for larval recruitment. We conducted surveys in 2019 and 2020 to (1) identify estuaries north of SFE where spawning occurs, and (2) evaluate how habitat features (e.g., salinity, temperature, dissolved oxygen, turbidity) influenced Longfin Smelt larvae abundance. We detected larvae in four of 16 estuaries we surveyed, and all were large estuaries north of Cape Mendocino. No larvae were detected in eight coastal estuaries in closer proximity to the SFE. Larvae catch probability increased with turbidity and decreased with salinity with no significant influence of temperature and dissolved oxygen. In the wet winter of 2019, we observed lower densities of larvae in Humboldt Bay and the Eel River and detected no Longfin Smelt in the Klamath and Mad Rivers, while in the dry winter of 2020, we detected larvae in two additional estuaries. Elevated freshwater outflow in 2019 possibly increased transport rates to sea, resulting in observed low larval recruitment. Our results sugget that, although populations of Longfin Smelt exist in large estuaries north of Cape Mendocino, coastal estuaries in proximity to the SFE were either under sampled or are not permanently inhabited by Longfin Smelt. Longfin Smelt in the SFE may therefore lack resilience normally afforded by metapopulations. Increased monitoring over their coastal range under varying hydrologic conditions is needed to assess gene flow between populations

Flow Augmentations Modify an Estuarine Prey Field

Zooplankton density and community composition in estuaries can be affected by variation in freshwater inputs, with important implications for higher trophic levels. In the San Francisco Estuary, management agencies have initiated autumn flow augmentations in the form of changes to reservoir releases or to exported water from the South Delta to increase and improve available habitat for endangered Delta Smelt, Hypomesus transpacificus, during the season when their body condition most influences fecundity. Autumn flow augmentation only occurs in years with higher precipitation, effectively moving the Low-Salinity Zone (LSZ) downstream to key foraging habitats for Delta Smelt in Suisun Bay and Suisun Marsh. To assess whether augmented flow enhanced prey resources for Delta Smelt, we compared autumn zooplankton abundance, biomass, spatial distribution, and community composition in years when flow was augmented (2017, 2019) with reference years when flow was not augmented (2018, 2020). In augmented years, we detected higher total zooplankton abundance and altered community composition in Suisun Bay and Suisun Marsh. Increased freshwater in these regions was associated with higher abundance of Pseudodiaptomus forbesi, a preferred prey of Delta Smelt, while species associated with higher salinities—Acartiella sinensis and Tortanus dextrilobatus—were less abundant. Thus, autumn flow augmentations can influence foraging habitat and prey availability for Delta Smelt, underscoring the complex responses of estuarine zooplankton communities to changes in response to flow and salinity regimes. This study is management- relevant because it shows that important Delta Smelt prey items increase in downstream regions when X2 is lower. Whether that results in a response in Delta Smelt abundance remains to be seen