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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. This metric would allow for a more robust scientific assessment of the population, which is needed to effectively manage water to reduce effects on spring run, a key condition of state permit requirements. To help guide this effort, we organized a workshop for stake-holders, managers, and scientists to review some of the key aspects of spring-run biology, examine the management and conservation importance of a JPE, identify knowledge gaps, introduce new tools, and discuss alternative approaches to forecasting the number of spring run emigrating from the Sacramento River drainage and into the Delta. This paper summarizes the spring-run biology, monitoring, and emergent methods for assessment considered at the workshop, as well as the guiding concepts identified by workshop participants necessary to develop a JPE for spring-run Chinook Salmon.

Extirpation of the Central Valley spring-run Chinook salmon (Oncorhynchus tshawytscha) evolutionary significant unit (ESU) from the San Joaquin River is emblematic of salmonid declines across the western seaboard of the United States. Habitat restoration and fish reintroduction efforts are ongoing, but recent telemetry studies have revealed low outmigration survival of juveniles to the ocean. Previous investigations have focused on modeling survival relative to river discharge and geographic regions, but have largely overlooked the effects of habitat variability. To evaluate the link between environmental conditions and survival of juvenile spring-run Chinook salmon, we combined high spatial resolution habitat mapping approaches with acoustic telemetry along a 150 km section of the San Joaquin River during the spring of 2019. While overall outmigration survival was low (5%), our habitat-based classification scheme described variation in survival of acoustic-tagged smolts better than other candidate models based on geography or distance. Two regional mortality sinks were evident along the longitudinal profile of the river, revealing poor survival in areas that shared warmer temperatures but that diverged in chlorophyll a, fluorescent dissolved organic matter (fDOM), turbidity, and dissolved oxygen levels. These findings demonstrate the value of integrating river habitat classification frameworks to improve our understanding of survival dynamics of imperiled fish populations. Key words: juvenile salmon, migration, habitat, survival, FLAMe La disparition locale de l'unite evolutionnaire significative (UES) du saumon chinook (Oncorhynchus tshawytscha) a migration printaniere de la vallee centrale dans la riviere San Joaquin est representative des declins de salmonides a la grandeur de la cote ouest des Etats-Unis. Si des efforts de restauration d'habitats et de reintroduction de poissons sont en cours, des etudes telemetriques recentes revelent une faible survie des juveniles lors de la devalaison vers l'ocean. Les etudes anterieures se sont axees sur la modelisation de la survie en fonction du debit et de la region geographique, mais n'ont generalement pas considere les effets de la variabilite des habitats. Afin d'evaluer le lien entre les conditions environnementales et la survie des saumons chinooks a migration printaniere juveniles, nous avons jumele des approches de cartographie d'habitats a haute resolution spatiale a la telemetrie acoustique le long d'un troncon de 150 km de la riviere San Joaquin durant le printemps 2019. Si la survie globale durant la devalaison etait faible (5 %), notre schema de classification base sur l'habitat decrit mieux les variations de la survie de saumoneaux dotes d'etiquettes acoustiques que d'autres modeles possibles bases sur la geographie ou la distance. Deux puits de mortalite regionaux sont ressortis le long du profil longitudinal de la riviere, revelant une faible survie dans des secteurs ayant en commun des temperatures elevees, mais dont les valeurs de chlorophylle a, matiere organique dissoute fluorescente (MODf), turbidite et oxygene dissous different. Ces constatations demontrent la pertinence d'integrer des cadres de classification des habitats fluviaux pour ameliorer la comprehension de la dynamique de la survie de populations de poissons menacees. [Traduit par la Redaction] Mots-cles : saumon juvenile, migration, habitat, survie, FLAMe, Introduction Pacific salmon populations native to California, USA have declined throughout the last century, shifting once economically viable runs to critically low numbers (Yoshiyama et al. 1998; Katz et al. [...]

Conceptual models underpin river ecosystem research. However, current models focus on continuously flowing rivers and few explicitly address characteristics such as flow cessation and drying. The applicability of existing conceptual models to nonperennial rivers that cease to flow (intermittent rivers and ephemeral streams, IRES) has not been evaluated. We reviewed 18 models, finding that they collectively describe main drivers of biogeochemical and ecological patterns and processes longitudinally (upstream-downstream), laterally (channel-riparian-floodplain), vertically (surface water-groundwater), and temporally across local and landscape scales. However, perennial rivers are longitudinally continuous while IRES are longitudinally discontinuous. Whereas perennial rivers have bidirectional lateral connections between aquatic and terrestrial ecosystems, in IRES, this connection is unidirectional for much of the time, from terrestrial-to-aquatic only. Vertical connectivity between surface and subsurface water occurs bidirectionally and is temporally consistent in perennial rivers. However, in IRES, this exchange is temporally variable, and can become unidirectional during drying or rewetting phases. Finally, drying adds another dimension of flow variation to be considered across temporal and spatial scales in IRES, much as flooding is considered as a temporally and spatially dynamic process in perennial rivers. Here, we focus on ways in which existing models could be modified to accommodate drying as a fundamental process that can alter these patterns and processes across spatial and temporal dimensions in streams. This perspective is needed to support river science and management in our era of rapid global change, including increasing duration, frequency, and occurrence of drying.

Acoustic telemetry, a commonly used tool for examining movements and survival of aquatic species, is often applied without a comprehensive understanding of transmitter implantation effects. This can be problematic when the goal of the study is to use telemetry results to make inferences regarding broader populations. Here, we examined juvenile Chinook Salmon Oncorhynchus tshawytscha at varying time intervals after transmitter implantation to assess the behavioral implications of tagging. The following behavioral metrics in response to a novel environment were compared across treatment and control groups: time to emergence from shelter into the open portion of the test arena, rheotactic response, total activity, and rates of exploration. Tagged fish (114–132 mm FL) were tested at 0, 1, or 4 d postsurgery (day-0, day-1, and day-4 groups, respectively), and their behavior was compared to that of similarly handled control fish. Emergence from refuge was the only metric that differed significantly between treatment and control groups. Fish tested on the same day as the surgery were less likely to emerge from the refuge, with only 46% of the day-0 tagged fish emerging compared to 88, 93, and 80% of the day-1, day-4, and control groups, respectively. However, day-0 fish that did emerge from the refuge had rheotactic responses, total activity, and exploration rates similar to those of fish from the other treatment and control groups. This study may have fisheries research and management implications, especially for telemetry studies and monitoring efforts. We encourage researchers using this technology to consider (1) observing a post-transmitter-implantation recovery period of at least 24 h prior to release, adjusting study plans and logistics accordingly; (2) applying sufficient scientific rigor to emerging tagging technology prior to wide-scale adoption; and (3) when possible, conducting concurrent battery life and tag effects studies with any field release of tagged fishes, as differing relationships between fish size, tag size, and tagging techniques may yield variable results.

Variations in species distribution, population structure, and behavior can provide a portfolio effect that buffers populations against rapid environmental change. Although diversity has been identified as a goal for effective resource management and genetic and demographic tools have been developed, life history remains challenging to quantify. In this study, we demonstrate a novel metric of life history diversity using telemetry data from migratory fish. Here, we examined diversity in the outmigration behavior of juvenile Chinook salmon (Oncorhynchus tshawytscha) released in the Sacramento River, California, between 2007 and 2017. In this synthesis, we examined a wide variety of landscape and demographic drivers at high resolution by incorporating many individual telemetry studies, with variability in release location by year, environmental conditions, and all runs of salmon that are present in the watershed. When years were grouped by shared hydrologic conditions, variation in travel time was significantly higher in wet years. Further, our model showed a negative effect of warm temperatures at low flows on the variation in migration movements. This suggests that enhanced hydrologic connectivity increases the variation in migration time, a representation of habitat complexity and biocomplexity, despite the degraded state of this watershed and the weakened state of these populations. Variation in migration behavior could buffer species from current and future environmental changes, such as climate effects on precipitation and temperature. Hence, behavioral metrics generated from telemetry studies can be used to understand life history diversity and the potential effects of environmental fluctuations. [ABSTRACT FROM AUTHOR]

Non-flow periods in fluvial ecosystems are a global phenomenon. Streambed drying and rewetting by sporadic rainfalls could drive considerable changes in the microbial communities that govern stream nitrogen (N) availability at different temporal and spatial scales. We performed a microcosm-based experiment to investigate how dry period duration (DPD) (0, 3, 6, and 9 weeks) and magnitude of sporadic rewetting by rainfall (0, 4, and 21 mm applied at end of dry period) affected stocks of N in riverbed sediments, ammonia-oxidizing bacteria (AOB) and archaea (AOA) and rates of ammonia oxidation (AO), and emissions of nitrous oxide (N2O) to the atmosphere. While ammonium (NH4 +) pool size decreased, nitrate (NO3 -) pool size increased in sediments with progressive drying. Concomitantly, the relative and absolute abundance of AOB and, especially, AOA (assessed by 16S rRNA gene sequencing and quantitative PCR of ammonia monooxygenase genes) increased, despite an apparent decrease of AO rates with drying. An increase of N2O emissions occurred at early drying before substantially dropping until the end of the experiment. Strong rainfall of 21 mm increased AO rates and NH4 + in sediments, whereas modest rainfall of 4 mm triggered a notable increase of N2O fluxes. Interestingly, such responses were detected only after 6 and 9 weeks of drying. Our results demonstrate that progressive drying drives considerable changes in in-stream N cycling and the associated nitrifying microbial communities, and that sporadic rainfall can modulate these effects. Our findings are particularly relevant for N processing and transport in rivers with alternating dry and wet phases - a hydrological scenario expected to become more important in the future.

Outmigration survival of acoustic-tagged, hatchery-origin, late-fall-run Chinook salmon (Oncorhynchus tshawytscha) smolts from the Sacramento River was estimated for 5 years (2007-2011) using a receiver array spanning the entire outmigration corridor, from the upper river, through the estuary, and into the coastal ocean. The first 4 years of releases occurred during below-average river flows, while the fifth year (2011) occurred during above-average flows. In 2011, overall outmigration survival was two to five times higher than survival in the other 4 years. Regional survival estimates indicate that most of the improved survival seen in 2011 occurred in the riverine reaches of the outmigration corridor, while survival in the brackish portions of the estuary did not significantly differ among the 5 years. For the 4 low-flow years combined, survival rate in the river was lower in the less anthropogenically modified upper reaches; however, across all regions, survival rate was lowest in the brackish portion of the estuary. Even in the high-flow year, outmigration survival was substantially lower than yearling Chinook salmon populations in other large rivers. Potential drivers of these patterns are discussed, including channelization, water flow, and predation. Finally, management strategies are suggested to best exploit survival advantages described in this study.

Rivers significantly contribute to global biogeochemical cycles; however, we have a limited understanding of how drying may influence these cycles. Drying fragments river networks, thereby influencing important ecosystem functions such as the processing of carbon and nitrogen, and associated fluxes of greenhouse gases (GHGs) both locally, and at the river network scale. Our objective was to assess, using a network‐scale approach, the lateral, longitudinal, and temporal dynamics of GHG fluxes in a river network naturally fragmented by drying. We used a closed‐loop chamber with automated analyzers to measure carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) fluxes from dry sediments, flowing waters, isolated pools, and riparian soils, along with a suite of environmental variables, over 9 months at 20 sites across a non‐perennial river network in France. Network‐scale drying had a spatial and temporal legacy effect on GHG fluxes. On average, CO2 fluxes were up to 29 times higher from perennial than non‐perennial sites under flowing conditions. At non‐perennial sites, CO2 and N2O fluxes positively covaried with time since rewetting. In addition, CO2 and N2O fluxes at perennial sites positively covaried with the percent of non‐perennial reaches upstream, indicating a spatial effect of drying. GHG fluxes from riparian soil and dry riverbed sediments had markedly different magnitudes and covariates. This research demonstrates that drying not only has a local‐scale impact but also influences GHG fluxes at the network scale, contributing valuable insights for upscaling global riverine GHG estimates. [ABSTRACT FROM AUTHOR]

The contribution of two basal energy sources - detrital organic matter and primary producers - as part of aquatic food webs varies typically along river continua. A host of barriers to river flow increase the water residence time and sediment and nutrient retention in reservoirs worldwide, and potentially alter the balance between detritus-based and algae-based energy pathways in the downstream food webs. We explored this issue on the Sélune River (Normandy, France), a small coastal stream that drains an agricultural catchment with high sediment runoff. Seasonal measurements of the following parameters were compared upstream and downstream of the reservoirs of two large dams (16 m and 36 m high): sediment fluxes, nutrient and chlorophyll a concentrations, algal communities in the epilithic biofilm (taxonomic composition, biomass and growth), and benthic invertebrate communities (abundance and trophic guild structure). As anticipated, annual sediment fluxes were much lower downstream of the reservoirs, where significant decreases in water turbidity, phosphate and silicate concentrations were recorded. A higher chlorophyll a concentration in water and a higher contribution of pelagic algae taxa to the photosynthetic biofilm suggested drifting and deposition of reservoir-borne phytoplankton downriver. Photosynthetic biofilm growth was higher downstream of the reservoirs in spring and fall, and so was the abundance of herbivores in the invertebrate community, notably scrapers and algae eaters. Energy pathways within riverine food webs were traced using stable isotope analyses of carbon (C) and nitrogen in the tissues of aquatic consumers (invertebrates and fish). Mixing models revealed a discontinuity in the origin of the C entering the food webs along the river continuum, confirming a greater contribution of algal C to aquatic consumers downstream of the reservoirs. These results illustrate mechanisms whereby large reservoirs can modulate C flow in food webs along a small coastal river with high sediment loads, and make it possible to anticipate the effects of dam removal on the future river ecosystem. [ABSTRACT FROM AUTHOR]

Green sturgeon (Acipenser medirostris) and white sturgeon (A. transmontanus) are closely related, sympatric species that inhabit the San Francisco estuary. Green sturgeon have a more marine life history but both species spawn in the Sacramento River and reside for some duration in San Francisco Bay. These sturgeons are of conservation concern, yet little is known about their dietary competition when they overlap in space and time. To examine evidence of dietary differentiation, we collected whole blood and blood plasma from 26 green sturgeon and 35 white sturgeon in San Francisco Bay. Using carbon and nitrogen stable isotope analyses, we compared their relative trophic levels and foraging locations along the freshwater to marine gradient. Sampling blood plasma and whole blood allowed comparison of dietary integration over shorter and longer time scales, respectively. Plasma and whole blood δ13C values confirmed green sturgeon had more marine dietary sources than white sturgeon. Plasma δ15N values revealed white sturgeon fed at lower trophic levels than green sturgeon recently, however, whole blood δ15N values demonstrated the two species fed at the same trophic level over longer time scales. Larger individuals of both species had higher δ13C values than smaller individuals, reflecting more marine food sources in adulthood. Length did not affect δ15N values of either species. Isotope analyses supported the more marine life history of green than white sturgeon and potentially highlight a temporary trophic differentiation of diet between species during and preceding the overlapping life stage in San Francisco Bay. [ABSTRACT FROM AUTHOR]