Climate change is reshaping thermal regimes worldwide, threatening species whose early development depends on narrow temperature ranges. Yet directly linking warming to reproductive failure in wild populations remains intractable, particularly in aquatic ecosystems. We developed an empirical framework integrating stable isotope thermometry of archival tissues, landscape-scale temperature modeling, and field surveys to identify when and where successful reproduction occurs. Applying this approach to endangered winter-run Chinook salmon confined below a large dam, we revealed a narrow “critical thermal window” during early development. Surviving juveniles experienced temperatures below 12.5°C within ∼15 days of fertilization, and modest warming during this period sharply reduced survival. In warm years, dam-released cold-water overlapped only briefly with this window, restricting successful reproduction to a small fraction of the total spawning season. These results show how climate warming and river regulation interact to constrain population persistence and provide a framework to guide research on assessing climate vulnerability in temperature-sensitive species.

Many once coupled habitats are now disconnected due to human infrastructure that prevents not only the transfer of organisms but also fundamental ecosystem processes. Here we investigate the importance of hydrologic connectivity between remnant floodplain and freshwater intertidal marsh habitats for zooplankton metacommunity dynamics and juvenile Chinook salmon growth in the Sacramento-San Joaquin Delta, California, U.S.A. during a connected flood and disconnected drought year. Hydrological connection led to highly similar zooplankton communities between habitats. Further, we found that connected intertidal marsh habitats had approximately twice the total abundance of zooplankton of upstream floodplains and, in some cases, 15 times greater abundance than during disconnection. Gut content analysis demonstrated that salmon in our study utilized these abundant zooplankton food resources which likely contributed to elevated juvenile salmon growth rates in connected intertidal marsh habitats, where salmon had 25% greater growth rates (mm day-1) than those reared in disconnected marsh habitats. These results provide strong evidence for the importance of connectivity for metacommunity dynamics as well as productivity in historically coupled ecosystems and provide important information for future management and restoration.

Nutrient deficiency can cause increased susceptibility to infectious diseases in fish, thus leading to high rates of morbidity and mortality. Thiamine deficiency complex (TDC) in fish can lead to low reproductive success and high mortality rates. Columnaris disease in salmonids, caused by Flavobacterium columnare, has resulted in devastating losses in aquaculture production and wild populations of Pacific salmon particularly associated with climate change and high water temperatures. There is growing awareness that both TDC and columnaris are emerging diseases of salmonids on the west coast of North America; however, it is unknown whether fish that survive from low/intermediate thiamine level eggs will experience latent mortality due to susceptibility to infectious diseases like columnaris. To investigate the interaction of TDC survivors and columnaris, Chinook salmon Oncorhynchus tshawytscha fry reared from either thiamine-deficient (n = 120) or thiamine-replete (n = 120) eggs were challenged with F. columnare using an immersion challenge model of infection, and morbidity/mortality, immune responses, and bacterial load were evaluated. The cumulative mortalities between the treatment groups were significantly different, with the thiamine-deficient, F. columnare-exposed fry ending the challenge with an 80.3% survival rate and the thiamine-replete, F. columnare-exposed fry ending with a 29.03% survival rate (p < 0.0001). Different transcript abundance was detected in gills and spleen of thiamine-deficient and thiamine-replete fry exposed to F. columnare. This study demonstrated that fry reared from eggs low in thiamine have an altered immune response and warrants further studies to better understand interaction with potential pathogens at different life stages.

Measuring the growth of migratory fish across habitats is difficult because field observations only provide a snapshot into their life; yet, understanding which habitats provide better growth opportunities is crucial for their conservation. We experimentally enclosed individually tagged juvenile Chinook salmon (Oncorhynchus tshawytscha) in habitats with known differences in growth potentials to evaluate four different models (Dahl–Lea, Fraser–Lee, Biological Intercept, and Modified Fry) used to back-calculate size-at-age from otoliths. We found that otolith-derived fish size reconstructions were most accurate using the Biological Intercept or Modified Fry model, though bias remains for slow growing fish. This tool was then used in a case study to reconstruct the mosaic of inter- and intra-habitat growth opportunities available to fishes, providing a useful framework for assessing and monitoring fish responses to habitat restoration and a changing environment.

Stable oxygen isotopes (delta O-18) in biogenic carbonates serve as a valuable proxy for reconstructing thermal history. Fish otoliths (ear stones) are particularly useful, as they precipitate continuously throughout life, creating a temporally resolved archive of water temperature. Here, we calibrate the temperature-dependent oxygen isotope fractionation equation for Chinook salmon (Oncorhynchus tshawytscha) using two analytical methods, secondary ion mass spectrometry (SIMS) and isotope ratio mass spectrometry (IRMS), to assess method-specific effects on fractionation equations and their implications for otolith-based thermometry. Juvenile fish were reared for 15 weeks under controlled freshwater conditions (salinity < 0.1 ppt) with a stable ambient water delta O-18 of -5.54 parts per thousand (VSMOW) (+/- 0.10, 1 SD) at three temperatures (11, 16, 20 degrees C). Otolith delta O-18 values measured by SIMS showed a significant linear inverse relationship with ambient water temperature: 1000ln alpha = 11.51( +/- 1.39, 1SE) x 10(3)T(K)(-1)-10.94( +/- 4.80, 1SE) delta O-18(otolith(VPDB))-delta(18)(Owater(VSMOW) )=-0.14( +/- 0.02, 1SE) x T(C- degrees) + 0.64( +/- 0.27, 1SE) Applying this equation yielded water temperature reconstructions with an accuracy of +/- 1.97 degrees C and a precision of +/- 0.70 degrees C (1 SD). A paired comparison revealed SIMS delta O-18 values were on average 1.97 parts per thousand lower than IRMS values, likely due to matrix effects and organic content. This offset produced large differences in equation intercepts, leading to reconstructed temperatures from IRMS-based equations that deviated similar to 10 degrees C from observed temperatures when applied to SIMS data. In contrast, the slopes (thermal sensitivity) of SIMS and IRMS equations were highly consistent, indicating that relative temperature changes can still be reliably inferred from SIMS delta O-18 values using IRMS-based equations. Greater variability in SIMS delta O-18 values compared to IRMS may partly reflect fine-scale isotopic heterogeneity within otoliths, suggesting that SIMS-based temperature reconstructions may require larger sample sizes or additional calibration tailored to specific contexts. Across-species comparison of fractionation equations revealed that inter-method differences exceeded inter-species differences, highlighting the need for method-matched equations for accurate absolute temperature reconstructions. Despite these challenges, once calibrated, SIMS-based otolith thermometry provides a powerful tool for reconstructing fine-scale fish thermal histories and assessing habitat refugia and resilience to climate change.

Understanding dissolved concentrations of the essential coenzyme thiamin (vitamin B-1) can provide insights into the biological controls on highly productive upwelling systems such as the California Current Ecosystem. To connect thiamin availability with microbial communities in the California Current Ecosystem, we measured concentrations of dissolved thiamin and its biochemically related moieties (thiamin congeners) and 16S rRNA gene-based microbial communities during the spring. We found that strong upwelling caused a depletion of dissolved thiamin precursor compounds and abiotic degradation products relative to periods of weak upwelling. Specific microbial taxa, including species of SAR11 ecotypes, Candidatus Nitrosopumilus, and SUP05 cluster, were also significantly enriched with strong upwelling. Our data provide evidence that alterations to microbial communities in the mixed layer that occur as a result of upwelling could constrain the availability of dissolved thiamin and its chemical congeners in the California Current Ecosystem.

As fish populations face compounding pressures under climate change, highly modified rivers are receiving increasing research and conservation attention as important sites for restoration. Across the North Pacific Ocean, Chinook salmon (Oncorhynchus tshawytscha) have experienced unprecedented declines and extirpations because of habitat loss and fragmentation and climate variability. Here, we studied a rare example of a novel salmon population developing in Putah Creek, California, a dam-controlled stream flowing through an area of intensive agriculture where salmon were unlikely to occur prior to the rehabilitation of a more natural flow regime. We used otoliths from adult Chinook salmon carcasses recovered from Putah Creek to determine river or hatchery of origin for five spawning year classes. Our results provide evidence of successful salmon reproduction, outmigration survival, and natal homing of individuals back to Putah Creek in recent years. Although hatchery-origin fish that strayed to Putah Creek to spawn dominated returns each year, this study documents life-cycle completion required for the potential development of a self-sustaining salmon population. This study demonstrates that targeted restoration and flow rehabilitation efforts can generate viable new salmon spawning habitat in dam-controlled river systems, which could help mitigate habitat lost to dams and developments. Further, successful anadromous life-cycle completion can occur in new spawning habitat within the first several generations, which will help inform efforts to restore or reintroduce salmon in other altered river systems.

Mobile consumers track fluctuating resources across heterogeneous landscapes to grow and survive. In river networks, the abundance and accessibility of food and the energetic consequences of foraging vary among habitats and through time, providing a shifting mosaic of growth opportunities for mobile consumers. However, a framework integrating the spatiotemporal dynamics of growth potential within riverscapes has been lacking. We present the concept of foodscapes to depict the dynamic changes in food abundance, food accessibility, and consumer physiology that contribute to spatial and temporal variation of fish growth in rivers. Drawing on case studies of salmonid fishes from Alaska to California, we illustrate how foodscapes can provide a plethora of foraging, growth, and life history opportunities that potentially contribute to population resilience. We identify knowledge gaps in understanding foodscapes and approaches for stewardship that focus on restoring diverse foraging and growth opportunities for fish and other mobile consumers in river networks.

ObjectiveThe illegal introduction of fish species can disrupt ecosystems, collapse food webs, and undermine recreational fishing opportunities. Determining whether introduced fish are locally reproducing is important for resource managers. Here, we used the geochemical analysis of otoliths to investigate the potential illegal introduction of a Walleye Sander vitreus caught in 2022, in Lake Cascade, Idaho. Lake Cascade is known for its recreational Yellow Perch Perca flavescens fishery and has no documented resident population of Walleye.MethodsTo determine if the Walleye was spawned in Lake Cascade or introduced from elsewhere, we analyzed otoliths for strontium isotopes (87Sr/86Sr) and compared them to local water samples and three locally caught Yellow Perch.ResultThe Walleye otolith revealed a shift from higher 87Sr/86Sr values (0.70878) in its early life to a period of intermediate value (0.70842) equal to Payette Lake water, then finally to a lower value (0.70807) comparable to the Lake Cascade water and resident Yellow Perch otoliths.ConclusionThese results suggest that the Walleye was initially transplanted to the Payette Lake area from a currently unknown source in 2020, 2 years before its capture. It resided there briefly before migrating south into Lake Cascade. This study further highlights the benefit of geochemical analyses to identify the illegal introduction of fish and to provide resource managers with a powerful tool for early detection and prevention of the establishment of illegally introduced fish species. Otolith geochemical analyses reveal that an invasive Walleye caught in Lake Cascade, Idaho, did not originate there but was instead illegally introduced. This showcases the potential of this tool to provide independent evidence of illegal introductions.Impact statement

AbstractPhenotypic diversity and abundance drive salmon resilience in the face of increasing environmental variability. But what happens when human activities fundamentally alter the habitat complexity that drives this diversity? And how can we restore habitats to recover both diversity and abundance to support salmon persistence in a warming climate? Here, we looked at the impact of a large watershed restoration effort on the abundance and climate resilience of the three remaining core natural spring‐run Chinook Salmon populations in the California Central Valley (Butte, Mill, and Deer Creek). Butte Creek fish, which have floodplain access, had higher overall productivity and faster juvenile growth compared with Mill and Deer Creek populations, and the proportion of floodplain inundation was positively correlated with Butte Creek adult abundance two years later. While Butte Creek exhibited significant increases in abundance post‐restoration (~2000%), it generally exhibited lower phenotypic diversity and only a marginal increase in population stability after restoration based on the coefficient of variation (CV). In particular, Butte Creek salmon tended to exhibit larger drops in escapement following dry years (e.g., return years 2010, 2017) compared with Mill and Deer Creek populations, presumably due to limited inundation of its downstream floodplain. The late‐migrating juvenile strategy (i.e., yearling), which disproportionately supported Mill and Deer Creek populations during droughts, was uncommon among Butte Creek adults (averaging 60% of returns for Mill and Deer Creek vs. 0.3% for Butte Creek). Increased spring‐run stock complex stability was found, post‐restoration, when combining the three spring‐run populations (i.e., lower aggregate CV). However, among‐river pairwise correlations also suggested increased synchronization in population abundances post‐restoration, potentially due to increasing frequency and severity of extreme climatic events (e.g., droughts and ocean warming). This study underscores the importance of restoring a connected mosaic of aquatic habitats across modified landscapes, such as cold water refugia and floodplains, to preserve multiple (across‐population) life history pathways for increasing salmon stock complex stability and abundance. These landscape‐scale process‐based habitat restoration efforts are likely to be crucial for the successful long‐term recovery of vulnerable species in a rapidly changing climate.

There is growing interest to integrate conservation initiatives into agricultural practices using a reconciliation ecology framework. In California's Central Valley, one approach to improving crucial nursery habitat for threatened and endangered fish species is by re-creating floodplain habitats through the inundation of agricultural fields during the non-growing season. We conducted a series of field experiments in agricultural floodplains (winter-flooded rice fields that historically were natural floodplains) to examine whether different field preparation methods enhanced growth and survival of floodplain-dependent fish species. Approximately 8000 juvenile fall-run Chinook Salmon (Oncorhynchus tshawytscha) were reared for at least 28 days on eight, 0.2 hectares (ha) experimental fields. Each experimental field represented one of four treatments (two replicates per treatment): addition of large wood, addition of in-field canals, addition of both large wood and in-field canals, and control. Controls fields received no additional field preparations beyond standard post-growing practices: that is chopping rice into stubble, baling, and removing excess rice straw, and discing the field with a single pass by plowing rice straw into the ground to promote decomposition. We found no significant difference in water temperature, fish growth or fish survival among habitat treatments. Across treatments, survival ranged from 50.1% to 78.3% and averaged 65.75% (+/- 7.89% SE). These findings suggest agricultural floodplains require no additional modifications to promote fish growth and survival. Results illustrate the benefits of integrating working landscapes with conservation initiatives, as this approach creates more accessible and beneficial habitat for native fish species.

The abundance and dispersion of plastic particles in aquatic ecosystems has become pervasive resulting in the incorporation of these materials into food webs. Here we describe the first record of plastic ingestion by the freshwater white-blotched river stingray Potamotrygon leopoldi (Potamotrygonidae), an endemic and threatened species in the Xingu River, Amazon basin. Potamotrygonidae stingrays inhabit exclusively Neotropical rivers, occupying rocky substrate habitats and feeding mainly on benthic macroinvertebrates. The gastrointestinal tract of 24 stingrays were analyzed, 16 (66.6 %) of which contained plastic particles. In total, 81 plastic particles were recorded and consisted of microplastics (< 5 mm, n = 57) and mesoplastics (5-25 mm, n = 24). The plastic particles found were classified into fibers (64.2 %, n = 52) and fragments (35.8 %, n = 29). The predominant color was blue (33.3 %, n = 27), followed by yellow (18.5 %, n = 15), white (14.8 %, n = 12), black (13.6 %, n = 11), green (6.2 %, n = 5), transparent (4.9 %, n = 4), pink, grey and brown (2.5 %, n = 2, each) and orange (1.2 %, n = 1). No significant correlation was observed between the number of plastic particles and the body size. Eight types of polymers were identified in the plastic particles analyzed using 2D FTIR Imaging. The most frequent polymer was artificial cellulose fiber. This is the first report of plastic ingestion by freshwater elasmobranchs in the world. Plastic waste has become an emerging problem in aquatic ecosystems globally and our results provide an important datapoint for freshwater stingrays in the Neotropics.

The authors declare no conflicts of interest. Data (Lusardi, 2022) are available in Figshare at https://doi.org/10.6084/m9.figshare.20737975.v2.

We used compound-specific isotope analysis of carbon isotopes in amino acids (AAs) to determine the biosynthetic source of AAs in fish from major tributaries to California's Sacramento-San Joaquin river delta (i.e., the Sacramento, Cosumnes and Mokelumne rivers). Using samples collected in winter and spring between 2016 and 2019, we confirmed that algae are a critical component of floodplain food webs in California's Central Valley. Results from bulk stable isotope analysis of carbon and nitrogen in producers and consumers were adequate to characterize a general trophic structure and identify potential upstream and downstream migration into our study site by American shad Alosa sapidissima and rainbow trout Oncorhynchus mykiss, respectively. However, owing to overlap and variability in source isotope compositions, our bulk data were unsuitable for conventional bulk isotope mixing models. Our results from compound-specific carbon isotope analysis of AAs clearly indicate that algae are important sources of organic matter to fish of conservation concern, such as Chinook salmon Oncorhynchus tshawytscha in California's Central Valley. However, algae were not the exclusive source of energy to metazoan food webs. We also revealed that other sources of AAs, such as bacteria, fungi and higher plants, contributed to fish as well. While consistent with the well-supported notion that algae are critical to aquatic food webs, our results highlight the possibility that detrital subsidies might intermittently support metazoan food webs.

Floodplains are highly productive environments that provide critical rearing habitat and increased growth for diverse native fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Yet, stranding during the flood recession is a potential negative outcome in restored ecosystems where environmental cues are not always present as they were under historical conditions. Outmigration cues of native and non-native fishes from a restored floodplain were evaluated along the Cosumnes River, CA, USA. This river is the only remaining major unregulated river in the Sierra Nevada that flows into the Central Valley. It remains unclear how native and non-native fishes utilize spatiotemporally heterogeneous habitats in the Cosumnes River; however, a better understanding of these dynamics could yield insight into how degraded river ecosystems in the region could be rehabilitated to benefit native fishes. In 2018 and 2019, daily fyke net surveys of fish assemblages were conducted within the floodplain and in outmigration corridors, along with the collection of environmental data to identify possible cues. Bayesian modeling showed that temperature increases, along with the rate of floodplain drawdown and the average flow over a rolling seven-day period, were important triggers for cuing native fishes to exit the floodplain. We conclude that the numerous benefits to the aquatic food web and growth of native fishes justify the risk of stranding that floodplain restoration poses, particularly when supplemented with outmigration cues.

Context Cross-boundary subsidies create important growth opportunities for a range of taxa. In modified river systems, remnant patches of floodplain and flood bypasses become ephemeral hotspots of zooplankton production, however, the extent to which these prey items are (or could be) transported downstream is unclear. Objectives We investigated the diet of juvenile salmon under varying hydroclimatic conditions to assess the importance of floodplain-produced prey subsidies in an otherwise food-scarce region. Methods Juvenile salmon (n = 3033) and zooplankton were sampled across the California Central Valley Sacramento-San Joaquin River Delta in 2014–2018, incorporating a range of climatic conditions including drought and flood. Salmon stomach fullness and diet composition, and ambient zooplankton densities were used to assess spatiotemporal patterns in prey production and consumption. Results Floodplain-produced cladocerans provided ephemeral food pulses to juvenile salmon in downstream riverine habitats. Salmon had the fullest stomachs in wetter years (2016–2017) and the emptiest stomachs in the final year of a multi-year drought (2015). Cladoceran abundances in the water column and salmon diets were highest during wet periods and below floodplains, and decreased with increasing distance downstream, consistent with flow-mediated trophic subsidies. Conclusions These data emphasize the importance of maintaining diverse, interconnected habitats to support resilient fish populations and the potential for managing floodplains to boost prey production and delivery. Here, the inundation of a flood bypass (or lack of) played a pivotal role shaping the juvenile salmon foodscape. As freshwater ecosystems are increasingly transformed by large-scale engineering, it is important to coordinate infrastructure, habitat and flow modifications to maximize climate resilience and trophic benefits to target species.

Riverine ecosystems in their natural state are complex mosaics of habitats whose conditions vary across space and time as landscape features filter prevailing hydrologic forcing. Yet, through anthropogenic alteration many large river systems have become simplified through the construction of levees and dams that reduce lateral connectivity and flow variability. The extent to which shifts in habitat mosaics create conditions that support different trophic responses that manifest in differences in fish growth across the landscape remains largely untested. This is primarily due to limitations in linking habitat features, dynamic physical processes, and trophic transfer of energy to higher taxa at the landscape scale. Here, we conducted large-scale enclosure experiments across varying habitats on a fluvial floodplain as a model system to measure factors that influence habitat-specific growth rates in multiple Chinook Salmon (Oncorhynchus tshawytscha) stocks important to fisheries and of conservation concern. Using an ecosystem approach, we reveal that landscape context, water residence time, and habitat type (agricultural, wetland, river channel) result in different hot-spots of primary and secondary food production. This variation in the aquatic foodscape resulted in significant variation in salmon growth rates and ultimate size and morphology across the landscape. Floodplain habitats generally exhibited higher water residence times as highlighted by higher specific conductance, salinity, and chlorophyll-a values. Pelagic invertebrate abundance was 10 to 100 times more abundant in the off-channel habitats compared to the river channels. The average daily growth rates of the juvenile Chinook Salmon ranged from 0.15 mm day−1 and 0.01 g day−1 in the riverine habitat to 0.55 mm day−1 and 0.07 g day−1 in the off-channel habitat. These data were used to build mixed effects models that showed the influence of chlorophyll-a concentration, water temperature and pelagic invertebrate composition on fish growth across locations throughout the experiment. As landscapes become increasingly simplified there is increased risk of losing the mosaic of habitats necessary to achieve enhanced fish growth and phenotypically diverse and sustainable salmon populations. This in-situ experimental and modeling approach can be applied to other systems to develop ecosystem indicators such as habitat-specific fish growth rates to manage landscapes and processes to support resilient fish populations.

Tracking habitat use and dietary shifts in migratory species is vital to conservation and management. Yet, conventional animal tracking often precludes tracking small juveniles at critical life stages where recruitment bottlenecks often manifest. Stable isotope analysis (SIA) in consecutive laminae in eye lenses, a protein‐rich depositional tissue, has emerged as a promising tool in fishes to develop long‐term interpretive records of dietary histories using a single archival tissue. Currently, studies using fish eye lenses to study SIA in diets have primarily been conducted in marine environments using δ 13 C and δ 15 N to identify resource partitioning, ontogenetic shifts and lifelong trophic histories. To date, no studies have examined freshwater taxa nor used δ 34 S isotopes. We placed juvenile (Chinook Salmon) Oncorhynchus tshawytscha in experimental enclosures in three different freshwater habitats (hatchery, river and seasonal floodplain), each with isotopically distinct and well‐characterized food webs. This experimental approach allowed us to directly measure diets and quantify tissue turnover rates in eye lenses as well as the isotopic fractionation among fish tissues (fin and muscle tissue) in distinct habitat types using stable isotopes δ 13 C, δ 15 N and δ 34 S. Bulk eye‐lens stable isotope measurements were analysed for juvenile salmon lenses and were found to be consistent with the isotopic values of rearing habitats. Slight additional isotopic fractionation was only found in δ 13 C. We then successfully applied the method to a larger, reproductively mature adult salmon captured in freshwater and inferred juvenile habitat use. SIA in eye lenses using three dietary isotopes (δ 13 C, δ 15 N and δ 34 S) has significant potential for answering critical questions about migration, diet, foraging ecology and life history of migratory aquatic animals on Earth. Such information would have immediate application towards conservation management of diverse species and habitats at multiple scales.

In the Western United States, volcanic spring-fed rivers are anticipated to become increasingly more important for salmonids and other native fishes, as these rivers will retain coldwater habitats as the climate warms. Despite this, little is known about the hydro-biogeochemical interactions within these ecosystems. A review of existing literature on spring-fed rivers, coupled with a decade of research on volcanic spring-fed rivers of northern California, finds that these systems are exceptionally productive and exhibit stable environmental conditions. These unique conditions stem from hydrogeologic processes typical of young volcanic terrains. Aquatic macrophytes, common to some nutrient-rich spring-fed systems, play a disproportionate role in hydrologic and geomorphic processes by facilitating ecological interactions and velocity conditions that improve juvenile salmonid growth. We find that volcanic spring-fed rivers are also resilient to climate change, due not only to their ability to dampen water temperature changes through deep groundwater flow but also because of their nutrient-driven high ecosystem productivity, which may enable coldwater species to metabolically compensate for marginal increases in water temperature. Understanding the fundamental geomorphic and ecological differences between these rare ecosystems and their numerically dominant runoff rivers is essential for developing long-term conservation strategies for coldwater species under a rapidly changing climate.