Maximum Temperature Limits for Chinook, Coho, and Chum Salmon, and Steelhead Trout in the Pacific Northwest

Storing and managing water for the environment is more efficient than mimicking natural flows

Dams and reservoirs are often needed to provide environmental water and maintain suitable water temperatures for downstream ecosystems. Here, we evaluate if water allocated to the environment, with storage to manage it, might allow environmental water to more reliably meet ecosystem objectives than a proportion of natural flow. We use a priority-based water balance operations model and a reservoir temperature model to evaluate 1) pass-through of a portion of reservoir inflow versus 2) allocating a portion of storage capacity and inflow for downstream flow and stream temperature objectives. We compare trade-offs to other senior and junior priority water demands. In many months, pass-through flows exceed the volumes needed to meet environmental demands. Storage provides the ability to manage release timing to use water efficiently for environmental benefit, with a co-benefit of increasing reservoir storage to protect cold-water at depth in the reservoir.

Modeling instream temperature from solar insolation under varying timber harvesting intensities using RPAS laser scanning

Stream temperatures are influenced by the amount of solar insolation they receive. Increasing stream temperatures associated with climate warming pose detrimental health risks to freshwater ecosystems. In British Columbia (BC), Canada, timber harvesting along forested streams is managed using riparian buffer zones of varying widths and designations. Within buffer zones, depending on distance from the stream, selective thinning may be permitted or harvest may be forbidden. In this study, we used airborne laser scanning (ALS) point cloud data acquired via a remotely piloted aircraft system (RPAS) to derive forest canopy characteristics that were then used to estimate daily incoming summer and fall solar insolation for five stream reaches in coastal conifer-dominated temperate forests in Vancouver Island, BC, Canada. We then examined empirical relationships between estimated insolation and actual instream temperature measurements. Based on these empirical relationships, the potential effects of timber harvest on instream temperatures were simulated by comparing scenarios of different riparian forest harvest intensities. Our results indicated that modeled solar insolation explained 43-90 % of the variation in observed stream reach temperatures, and furthermore, when a single cold-water stream reach was excluded explained an overall 81 % of variation. Simulated harvesting scenarios generally projected increases in maximum stream reach temperatures 1-2 °C in summer and early fall months. However, in a full clearcut scenario (i.e. where all trees were removed), maximum stream reach temperatures increased as much as 5.8 °C. Our results emphasize the importance of retaining riparian vegetation for the maintenance of habitable temperatures for freshwater-reliant fish with thermal restrictions. In addition, we demonstrate the feasibility of RPAS-based monitoring of stream reach shading and canopy cover, enabling detailed assessment of environmental stressors faced by fish populations under climate warming.

Closing the gap between science and management of cold-water refuges in rivers and streams

Human activities and climate change threaten coldwater organisms in freshwater ecosystems by causing rivers and streams to warm, increasing the intensity and frequency of warm temperature events, and reducing thermal heterogeneity. Cold-water refuges are discrete patches of relatively cool water that are used by coldwater organisms for thermal relief and short-term survival. Globally, cohesive management approaches are needed that consider interlinked physical, biological, and social factors of cold-water refuges. We review current understanding of cold-water refuges, identify gaps between science and management, and evaluate policies aimed at protecting thermally sensitive species. Existing policies include designating cold-water habitats, restricting fishing during warm periods, and implementing threshold temperature standards or guidelines. However, these policies are rare and uncoordinated across spatial scales and often do not consider input from Indigenous peoples. We propose that cold-water refuges be managed as distinct operational landscape units, which provide a social and ecological context that is relevant at the watershed scale. These operational landscape units provide the foundation for an integrated framework that links science and management by (1) mapping and characterizing cold-water refuges to prioritize management and conservation actions, (2) leveraging existing and new policies, (3) improving coordination across jurisdictions, and (4) implementing adaptive management practices across scales. Our findings show that while there are many opportunities for scientific advancement, the current state of the sciences is sufficient to inform policy and management. Our proposed framework provides a path forward for managing and protecting cold-water refuges using existing and new policies to protect coldwater organisms in the face of global change.

Temperature-associated virulence, species susceptibility and interspecies transmission of a Lactococcus petauri strain from rainbow trout

Lactococcus petauri is an important emergent aquaculture pathogen in the USA. To better understand environmental conditions conducive to piscine lactococcosis and the susceptibility of fish species, laboratory-controlled challenges were used as models of infection. Rainbow trout Oncorhynchus mykiss maintained at 13 or 18°C were challenged by intracoelomic (ICe) injection with 101, 103 or 105 colony-forming units per fish (CFU fish-1) and monitored for 21 d. At 13°C, trout experienced mortalities of 7, 7 and 0%, and bacterial persistence of 0, 20 and 0% in survivors, respectively. When exposed to the same bacterial doses, trout maintained at 18°C experienced mortalities of 59, 84 and 91%, and bacterial persistence of 60, 66 and 0% in survivors, confirming a significant role of temperature in the pathogenesis of lactococcosis. Additionally, the susceptibility of rainbow trout, Chinook salmon Oncorhynchus tshawytscha, white sturgeon Acipenser transmontanus, Nile tilapia Oreochromis niloticus, and koi Cyprinus carpio to infection by L. petauri was compared using ICe challenges at 18°C. Trout and salmon experienced 96 and 56% cumulative mortality, respectively, and 17% of surviving salmon remained persistently infected. There were no mortalities in the other fish species, and no culturable bacteria recovered at the end of the challenge. However, when surviving fish were used in further cohabitation trials, naïve trout housed with previously exposed tilapia exhibited 6% mortality, demonstrating that non-salmonids can become sub-clinical carriers of this pathogen. The data obtained provide useful information regarding temperature-associated virulence, fish species susceptibility, and potential carrier transmission of L. petauri that can be used in the development of better management practices to protect against piscine lactococcosis.

Adult spawners: A critical period for subarctic Chinook salmon in a changing climate

Concurrent, distribution-wide abundance declines of some Pacific salmon species, including Chinook salmon (Oncorhynchus tshawytscha), highlights the need to understand how vulnerability at different life stages to climate stressors affects population dynamics and fisheries sustainability. Yukon River Chinook salmon stocks are among the largest subarctic populations, near the northernmost extent of the species range. Existing research suggests that Yukon River Chinook salmon population dynamics are largely driven by factors occurring between the adult spawner life stage and their offspring's first summer at sea (second year post-hatching). However, specific mechanisms sustaining chronic poor productivity are unknown, and there is a tremendous sense of urgency to understand causes, as declines of these stocks have taken a serious toll on commercial, recreational, and indigenous subsistence fisheries. Therefore, we leveraged multiple existing datasets spanning parent and juvenile stages of life history in freshwater and marine habitats. We analyzed environmental data in association with the production of offspring that survive to the marine juvenile stage (juveniles per spawner). These analyses suggest more than 45% of the variability in the production of juvenile Chinook salmon is associated with river temperatures or water discharge levels during the parent spawning migration. Over the past two decades, parents that experienced warmer water temperatures and lower discharge in the mainstem Yukon River produced fewer juveniles per spawning adult. We propose the adult spawner life stage as a critical period regulating population dynamics. We also propose a conceptual model that can explain associations between population dynamics and climate stressors using independent data focused on marine nutrition and freshwater heat stress. It is sobering to consider that some of the northernmost Pacific salmon habitats may already be unfavorable to these cold-water species. Our findings have immediate implications, given the common assumption that northern ranges of Pacific salmon offer refugia from climate stressors.

Elodea mediates juvenile salmon growth by altering physical structure in freshwater habitats

Invasive species introductions in high latitudes are accelerating and elevating the need to address questions of their effects on Subarctic and Arctic ecosystems. As a driver of ecosystem function, submerged aquatic vegetation is one of the most deleterious biological invasions to aquatic food webs. The aquatic plant Elodea spp. has potential to be a widespread invader to Arctic and Subarctic ecosystems and is already established in 19 waterbodies in Alaska, USA. Elodea spp. has been found to alter ecosystem processes through multiple pathways; yet little is known about the impact of Elodea spp. on fish life history. A primary concern is the effect of Elodea spp. on juvenile Pacific salmon (Oncorhynchus spp.), because this invading plant can form dense stands in littoral zones, potentially impacting important freshwater rearing habitats used by juvenile fish for foraging and refuge from predators. We used a field experiment to test the effect of Elodea spp. on juvenile coho salmon (O. kisutch) growth in an infested lake near Cordova, Alaska, USA. We found that Elodea spp. stands result in reduced growth and a lower trophic position for juvenile coho salmon over the summer compared to habitats dominated by a native assemblage of aquatic plants. While infested sites were not associated with significant changes in water condition or primary productivity compared to sites dominated by native vegetation, zooplankton densities were reduced, and Elodea spp. height and vegetation richness increased macroinvertebrate densities. Combined, these results indicate that Elodea spp. may alter the flow of energy to juvenile salmon by restructuring space and affecting prey resources for rearing fish. Furthermore, these results suggest that widespread establishment of Elodea spp. may alter the quality of habitat for juvenile salmon and, by affecting juvenile fish growth, could lead to population-level impacts on salmon returns.

Population variability in thermal performance of pre-spawning adult Chinook salmon

Climate change is causing large declines in many Pacific salmon populations. In particular, warm rivers are associated with high levels of premature mortality in migrating adults. The Fraser River watershed in British Columbia, Canada, supports some of the largest Chinook salmon (Oncorhynchus tshawytscha) runs in the world. However, the Fraser River is warming at a rate that threatens these populations at critical freshwater life stages. A growing body of literature suggests salmonids are locally adapted to their thermal migratory experience, and thus, population-specific thermal performance information can aid in management decisions. We compared the thermal performance of pre-spawning adult Chinook salmon from two populations, a coastal fall-run from the Chilliwack River (125 km cooler migration) and an interior summer-run from the Shuswap River (565 km warmer migration). We acutely exposed fish to temperatures reflecting current (12°C, 18°C) and future projected temperatures (21°C, 24°C) in the Fraser River and assessed survival, aerobic capacity (resting and maximum metabolic rates, absolute aerobic scope (AAS), muscle and ventricle citrate synthase), anaerobic capacity (muscle and ventricle lactate dehydrogenase) and recovery capacity (post-exercise metabolism, blood physiology, tissue lactate). Chilliwack Chinook salmon performed worse at high temperatures, indicated by elevated mortality, reduced breadth in AAS, enhanced plasma lactate and potassium levels and elevated tissue lactate concentrations compared with Shuswap Chinook salmon. At water temperatures exceeding the upper pejus temperatures (T_pejus, defined here as 80% of maximum AAS) of Chilliwack (18.7°C) and Shuswap (20.2°C) Chinook salmon populations, physiological performance will decline and affect migration and survival to spawn. Our results reveal population differences in pre-spawning Chinook salmon performance across scales of biological organization at ecologically relevant temperatures. Given the rapid warming of rivers, we show that it is critical to consider the intra-specific variation in thermal physiology to assist in the conservation and management of Pacific salmon.

Tough places and safe spaces: Can refuges save salmon from a warming climate?

The importance of thermal refuges in a rapidly warming world is particularly evident for migratory species, where individuals encounter a wide range of conditions throughout their lives. In this study, we used a spatially explicit, individual-based simulation model to evaluate the buffering potential of cold-water thermal refuges for anadromous salmon and trout (Oncorhynchus spp.) migrating upstream through a warm river corridor that can expose individuals to physiologically stressful temperatures. We considered upstream migration in relation to migratory phenotypes that were defined in terms of migration timing, spawn timing, swim speed, and use of cold-water thermal refuges. Individuals with different migratory phenotypes migrated upstream through riverine corridors with variable availability of cold-water thermal refuges and mainstem temperatures. Use of cold-water refuges (CWRs) decreased accumulated sublethal exposures to physiologically stressful temperatures when measured in degree-days above 20, 21, and 22°C. The availability of CWRs was an order of magnitude more effective in lowering accumulated sublethal exposures under current and future mainstem temperatures for summer steelhead than fall Chinook Salmon. We considered two emergent model outcomes, survival and percent of available energy used, in relation to thermal heterogeneity and migratory phenotype. Mean percent energy loss attributed to future warmer mainstem temperatures was at least two times larger than the difference in energy used in simulations without CWRs for steelhead and salmon. We also found that loss of CWRs reduced the diversity of energy-conserving migratory phenotypes when we examined the variability in entry timing and travel time outside of CWRs in relation to energy loss. Energy-conserving phenotypic space contracted by 7%-23% when CWRs were unavailable under the current thermal regime. Our simulations suggest that, while CWRs do not entirely mitigate for stressful thermal exposures in mainstem rivers, these features are important for maintaining a diversity of migration phenotypes. Our study suggests that the maintenance of diverse portfolios of migratory phenotypes and cool- and cold-water refuges might be added to the suite of policies and management actions presently being deployed to improve the likelihood of Pacific salmonid persistence into a future characterized by climate change.

Spatiotemporal distribution of Ceratonova shasta in the lower Columbia River Basin and effects of exposure on survival of juvenile chum salmon Oncorhynchus keta

In the Columbia River Basin (CRB), USA, anthropogenic factors ranging from dam construction to land use changes have modified riverine flow and temperature regimes and degraded salmon habitat. These factors are directly implicated in native salmon and steelhead (Oncorhynchus species) population declines and also indirectly cause mortality by altering outcomes of ecological interactions. For example, attenuated flows and warmer water temperatures drive increased parasite densities and in turn, overwhelm salmonid resistance thresholds, resulting in high disease and mortality. Outcomes of interactions between the freshwater myxozoan parasite, Ceratonova shasta, and its salmonid hosts (e.g., coho O. kisutch and Chinook salmon O. tshawytscha) are well-described, but less is known about effects on chum salmon O. keta, which have a comparatively brief freshwater residency. The goal of this study was to describe the distribution of C. shasta relative to chum salmon habitat in the CRB and assess its potential to cause mortality in juvenile chum salmon (listed as threatened in the CRB under the U.S. Endangered Species Act). We measured C. shasta densities in water samples collected from chum salmon habitat throughout the lower CRB during the period of juvenile chum salmon outmigration, 2018–2020. In 2019, we exposed caged chum salmon fry from two hatchery stocks at three C. shasta-positive sites to assess infection prevalence and survival. Results demonstrated: (1) C. shasta was detected in spawning streams from which chum salmon have been extirpated but was not detected in contemporary spawning habitat while juvenile chum salmon were present, (2) spatiotemporal overlap occurs between C. shasta and juvenile chum salmon in the Columbia River mainstem, and (3) low densities of C. shasta caused lethal infection in chum salmon fry from both hatchery stocks. Collectively, our results suggest C. shasta may limit recovery of chum salmon now and in the future.

How riparian and floodplain restoration modify the effects of increasing temperature on adult salmon spawner abundance in the Chehalis River, WA

Stream temperatures in the Pacific Northwest are projected to increase with climate change, placing additional stress on cold-water salmonids. We modeled the potential impact of increased stream temperatures on four anadromous salmonid populations in the Chehalis River Basin (spring-run and fall-run Chinook salmon Oncorhynchus tshawytscha, coho salmon O. kisutch, and steelhead O. mykiss), as well as the potential for floodplain reconnection and stream shade restoration to offset the effects of future temperature increases. In the Chehalis River Basin, peak summer stream temperatures are predicted to increase by as much as 3°C by late-century, but restoration actions can locally decrease temperatures by as much as 6°C. On average, however, basin-wide average stream temperatures are expected to increase because most reaches have low temperature reduction potential for either restoration action relative to climate change. Results from the life cycle models indicated that, without restoration actions, increased summer temperatures are likely to produce significant declines in spawner abundance by late-century for coho (-29%), steelhead (-34%), and spring-run Chinook salmon (-95%), and smaller decreases for fall-run Chinook salmon (-17%). Restoration actions reduced these declines in all cases, although model results suggest that temperature restoration alone may not fully mitigate effects of future temperature increases. Notably, floodplain reconnection provided a greater benefit than riparian restoration for steelhead and both Chinook salmon populations, but riparian restoration provided a greater benefit for coho. This pattern emerged because coho salmon tend to spawn and rear in smaller streams where shade restoration has a larger effect on stream temperature, whereas Chinook and steelhead tend to occupy larger rivers where temperatures are more influenced by floodplain connectivity. Spring-run Chinook salmon are the only population for which peak temperatures affect adult prespawn survival in addition to rearing survival, making them the most sensitive species to increasing stream temperatures.

Assessing climate change impacts on Pacific salmon and trout using bioenergetics and spatiotemporal explicit river temperature predictions under varying riparian conditions

Pacific salmon and trout populations are affected by timber harvest, the removal and alteration of riparian vegetation, and the resulting physical changes to water quality, temperature, and associated delivery of high-quality terrestrial prey. Juvenile salmon and trout growth, a key predictor of survival, is poorly understood in the context of current and future (climate-change mediated) conditions, with resource managers needing information on how land use will impact future river conditions for these commercially and culturally important species. We used the Heat Source water temperature modeling framework to develop a spatiotemporal model to assess how riparian canopy and vegetation preservation and addition could influence river temperatures under future climate predictions in a coastal river fed by a moraine-dammed lake: the Quinault River in Washington State. The model predicted higher water temperatures under future carbon emission projections, representative concentration pathway (RCP) 4.5 and 8.5, with varying magnitude based on different riparian vegetation scenarios. We used the daily average temperature output from these scenarios to predict potential juvenile fish growth using the Wisconsin bioenergetics model. A combination of riparian vegetation removal and continued high carbon emissions resulted in a predicted seven-day average daily maximum temperature (7DADM) increase of 1.7°C in the lower river by 2080; increases in riparian shading mitigate this 7DADM increase to only 0.9°C. Under the current thermal regime, bioenergetics modeling predicts juvenile fish lose weight in the lower river; this loss of potential growth worsens by an average of 20–83% in the lower river by 2080, increasing with the loss of riparian shading. This study assess the impact of riparian vegetation management on future thermal habitat for Pacific salmon and trout under warming climates and provide a useful spatially explicit modeling framework that managers can use to make decisions regarding riparian vegetation management and its mechanistic impact to water temperature and rearing juvenile fish.

A process-based assessment of landscape change and salmon habitat losses in the Chehalis River basin, USA

Identifying necessary stream and watershed restoration actions requires quantifying natural potential habitat conditions to diagnose habitat change and evaluate restoration potential. We used three general methods of quantifying natural potential: historical maps and survey notes, contemporary reference sites, and models. Historical information was available only for the floodplain habitat analysis. We used contemporary reference sites to estimate natural potential habitat conditions for wood abundance, riparian shade, main channel length, and side channel length. For fine sediment, temperature, and beaver ponds we relied on models. We estimated a 90% loss of potential beaver pond area, 91% loss of side-channel length, and 92% loss or degradation of floodplain marshes and ponds. Spawning habitat area change due to wood loss ranged from -23% to -68% across subbasins. Other changes in habitat quantity or quality were smaller-either in magnitude or spatial extent-including rearing habitat areas, stream temperature, and accessible stream length. Historical floodplain habitat mapping provided the highest spatial resolution and certainty in locations and amounts of floodplain habitat lost or degraded, whereas use of the contemporary reference information provided less site specificity for wood abundance and side-channel length change. The models for fine sediment levels and beaver pond areas have the lowest reach-specific certainty, whereas the model of temperature change has higher certainty because it is based on a detailed riparian inventory. Despite uncertainties at the reach level, confidence in subbasin-level estimates of habitat change is moderate to high because accuracy increases as data are aggregated over multiple reaches. Our results show that the largest habitat losses were floodplain and beaver pond habitats, but use of these habitat change results in salmon life-cycle models can illustrate how the potential benefits of alternative habitat restoration actions varies among species with differing habitat preferences.

The heat shock response shows plasticity in embryonic lake whitefish (Coregonus clupeaformis) exposed to repeated thermal stress

We examined the impact of repeated thermal stress on the heat shock response (HSR) of thermally sensitive lake whitefish (Coregonus clupeaformis) embryos. Our treatments were designed to mimic temperature fluctuations in the vicinity of industrial thermal effluents. Embryos were either maintained at control temperatures (3 ^oC) or exposed to a repeated thermal stress (TS) of 3 or 6 ^oC above control temperature every 3 or 6 days throughout embryonic development. At 82 days post-fertilisation, repeated TS treatments were stopped and embryos received either a high level TS of 12, 15, or 18 ^oC above ambient temperature for 1 or 4 h, or no additional TS. These treatments were carried out after a 6 h recovery from the last repeated TS. Embryos in the no repeated TS group responded, as expected, with increases in hsp70 mRNA in response to 12, 15 and 18 ^oC high-level TS. However, exposure to repeated TS of 3 or 6 ⁰C every 6 days also resulted in a significant upregulation of hsp70 mRNA relative to the controls. Importantly, these repeated TS events and the associated elevations in hsp70 attenuated the upregulation of hsp70 in response to a 1 h, high-level TS of 12 ^oC above ambient, but not to either longer (4 h) or higher (15 or 18 ^oC) TS events. Conversely, hsp90α mRNA levels were not consistently elevated in the no repeated TS groups exposed to high-level TS. In some instances, hsp90α levels appeared to decrease in embryos exposed to repeated TS followed by a high-level TS. The observed attenuation of the HSR in lake whitefish embryos demonstrates that embryos of this species have plasticity in their HSR and repeated TS may protect against high-level TS, but the response differs based on repeated TS treatment, high-level TS temperature and duration, and the gene of interest.

Classifying California's stream thermal regimes for cold-water conservation

Stream temperature science and management is rapidly shifting from single-metric driven approaches to multi-metric, thermal regime characterizations of streamscapes. Given considerable investments in recovery of cold-water fisheries (e.g., Pacific salmon and other declining native species), understanding where cold water is likely to persist, and how cold-water thermal regimes vary, is critical for conservation. California’s unique position at the southern end of cold-water ecosystems in the northern hemisphere, variable geography and hydrology, and extensive flow regulation requires a systematic approach to thermal regime classification. We used publicly available, long-term (> 8 years) stream temperature data from 77 sites across California to model their thermal regimes, calculate three temperature metrics, and use the metrics to classify each regime with an agglomerative nesting algorithm. Then, we assessed the variation in each class and considered underlying physical or anthropogenic factors that could explain differences between classes. Finally, we considered how different classes might fit existing criteria for cool- or cold-water thermal regimes, and how those differences complicate efforts to manage stream temperature through regulation. Our results demonstrate that cool- and cold-water thermal regimes vary spatially across California. Several salient findings emerge from this study. Groundwater-dominated streams are a ubiquitous, but as yet, poorly explored class of thermal regimes. Further, flow regulation below dams imposes serial discontinuities, including artificial thermal regimes on downstream ecosystems. Finally, and contrary to what is often assumed, California reservoirs do not contain sufficient cold-water storage to replicate desirable, reach-scale thermal regimes. While barriers to cold-water conservation are considerable and the trajectory of cold-water species towards extinction is dire, protecting reaches that demonstrate resilience to climate warming remains worthwhile.

Uncoupling Thermotolerance and Growth Performance in Chinook Salmon: Blood Biochemistry and Immune Capacity

Ocean warming and extreme sea surface temperature anomalies are threatening wild and domesticated fish stocks in various regions. Understanding mechanisms for thermotolerance and processes associated with divergent growth performance is key to the future success of aquaculture and fisheries management. Herein, we exposed Chinook salmon (Oncorhynchus tshawytscha) to environmentally relevant water temperatures (19–20 °C) approaching their upper physiological limit for three months and sought to identify blood biomarkers associated with thermal stress and resilience. In parallel, blood biochemical associations with growth performance were also investigated. Temperature stress-activated leukocyte apoptosis induced a minor immune response, and influenced blood ion profiles indicative of osmoregulatory perturbation, regardless of how well fish grew. Conversely, fish displaying poor growth performance irrespective of temperature exhibited numerous biomarker shifts including haematology indices, cellular-based enzyme activities, and blood clinical chemistries associated with malnutrition and disturbances in energy metabolism, endocrine functioning, immunocompetence, redox status, and osmoregulation. Findings provide insight into mechanisms of stress tolerance and compromised growth potential. Biochemical phenotypes associated with growth performance and health can potentially be used to improve selective breeding strategies.

The effects of temperature and salinity on the endocrinology in two life stages of juvenile rainbow/steelhead trout (Oncorhynchus mykiss)

The San Francisco Bay Delta is experiencing seasonally warmer waters and saltwater intrusion into historically freshwater ecosystems due to climate change. Steelhead/rainbow trout (Oncorhynchus mykiss) are resident in the Bay-Delta from juvenile development through the smoltification process. Due to increases in sea level, premature seawater (SW) acclimation may co-occur with increased temperatures on pre-smolt juveniles. To evaluate the interactive effects of salinity and temperature on juvenile life stages of salmonids, rainbow trout alevin (3 days post-hatching) were exposed to 13, 16.4 and 19°C for 10 days and then challenged for 24 h to 18 parts per thousand SW. Similarly, fry (4 weeks post-hatching) were exposed to 13, 16.4 and 19°C for 2 weeks (14 days) and then challenged to SW. Estradiol-17β (E₂ ), cortisol, triiodothyronine (T₃ ) and thyroxine (T₄ ) were measured in whole animal homogenates and muscle tissue using enzyme-linked immunosorbent assays. Transcripts of gill Na⁺ /K⁺ ATPase β (NKAα1b), brain growth hormone I (gh1) and brain gonadotropin-releasing hormone receptor 2 (gnrh2) were also measured. Alevin exhibited a significant temperature-dependent decrease in survival, and fry showed a temperature-dependent decrease in condition factor. The gene expression of NKAα1b, gh1 and gnrh2 significantly decreased in all SW-challenged alevin, and a significant decrease in gnrh2 expression was observed in fry with temperature. Alevin T₃ and T₄ concentrations significantly increased with increasing temperature. There was a temperature-dependent increase in E₂ of fry but not of alevin. The results of this study demonstrate that increasing temperature and SW exposure may adversely affect the survival and SW acclimation of alevin and fry stages of salmonids and that the tolerances of younger juvenile stages should be considered when assessing the response of salmonid populations to climate change stressors.

Summer Is Coming! Tackling Ocean Warming in Atlantic Salmon Cage Farming

Atlantic salmon (Salmo salar) cage farming has traditionally been located at higher latitudes where cold seawater temperatures favor this practice. However, these regions can be impacted by ocean warming and heat waves that push seawater temperature beyond the thermo-tolerance limits of this species. As more mass mortality events are reported every year due to abnormal sea temperatures, the Atlantic salmon cage aquaculture industry acknowledges the need to adapt to a changing ocean. This paper reviews adult Atlantic salmon thermal tolerance limits, as well as the deleterious eco-physiological consequences of heat stress, with emphasis on how it negatively affects sea cage aquaculture production cycles. Biotechnological solutions targeting the phenotypic plasticity of Atlantic salmon and its genetic diversity, particularly that of its southernmost populations at the limit of its natural zoogeographic distribution, are discussed. Some of these solutions include selective breeding programs, which may play a key role in this quest for a more thermo-tolerant strain of Atlantic salmon that may help the cage aquaculture industry to adapt to climate uncertainties more rapidly, without compromising profitability. Omics technologies and precision breeding, along with cryopreservation breakthroughs, are also part of the available toolbox that includes other solutions that can allow cage farmers to continue to produce Atlantic salmon in the warmer waters of the oceans of tomorrow.

Not All Rivers Are Created Equal: The Importance of Spring-Fed Rivers under a Changing Climate

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.

Using Comprehensive Scenarios to Identify Social–Ecological Threats to Salmon in the Kenai River Watershed, Alaska

Environmental changes caused by climate change in Alaska pose a serious threat to the food, energy and water systems that support the culturally diverse communities statewide. The fishing industry, watershed managers and other stakeholders struggle with understanding and predicting the rates, magnitude and location of changes occurring in their regions primarily because of the significant range of uncertainty inherent in these changes. With the guidance of stakeholders, we demonstrate a scenario analysis methodology to elucidate the interactions among various components and uncertainties within the food, energy and water systems of the Kenai River Watershed. Alternative scenario analysis provided stakeholders with a venue and process to consider plausible futures in which rates of change in critical uncertainties were modeled to elucidate potential responses. Critical uncertainties ranged from climatic impacts on freshwater systems, to new energy development proposals, to changes in sport and personal use fisheries. Working together, stakeholders developed narratives that reflected different combinations of future uncertainty to guide potential management actions now and in the future. Five scenarios were developed by stakeholders that capture the complex interactions in the Kenai River Watershed as a social–ecological system. This process provides a way for managers and stakeholders to plan for the future in a richer way than extrapolating trends for obvious drivers of change. We present this framework as a platform for integrating climate, landscape and cultural change data into actionable decisions, crafted by stakeholders, to improve future food, energy and water resource management at the watershed scale.

Environmentally triggered shifts in steelhead migration behavior and consequences for survival in the mid-Columbia River

The majority of Columbia River summer-run steelhead encounter high river temperatures (near or > 20°C) during their spawning migration. While some steelhead pass through the mid-Columbia River in a matter of days, others use tributary habitats as temperature refuges for periods that can last months. Using PIT tag detection data from adult return years 2004-2016, we fit 3-component mixture models to differentiate between "fast", "slow", and "overwintering" migration behaviors in five aggregated population groups. Fast fish migrated straight through the reach on average in ~7-9 days while slow fish delayed their migration for weeks to months, and overwintering fish generally took ~150-250 days. We then fit covariate models to examine what factors contributed to the probability of migration delay during summer months (slow or overwintering behaviors), and to explore how migration delay related to mortality. Finally, to account for the impact of extended residence times in the reach for fish that delayed, we compared patterns in estimated average daily rates of mortality between migration behaviors and across population groups. Results suggest that migration delay was primarily triggered by high river temperatures but temperature thresholds for delay were lowest just before the seasonal peak in river temperatures. While all populations groups demonstrated these general patterns, we documented substantial variability in temperature thresholds and length of average delays across population groups. Although migration delay was related to higher reach mortality, it was also related to lower average daily mortality rates due to the proportional increase in reach passage duration being larger than the associated increase in mortality. Lower daily mortality rates suggest that migration delay could help mitigate the impacts of harsh migration conditions, presumably through the use of thermal refuges, despite prolonged exposure to local fisheries. Future studies tracking individual populations from their migration through reproduction could help illuminate the full extent of the tradeoffs between different migration behaviors.

Glacier recession alters stream water quality characteristics facilitating bloom formation in the benthic diatom Didymosphenia geminata

Glaciers provide cold, turbid runoff to many mountain streams in the late summer and buffer against years with low snowfall. The input of glacial meltwater to streams maintains unique habitats and support a diversity of stream flora and fauna. In western Canada, glaciers are anticipated to retreat by 60-80% by the end of the century, and this retreat will invoke widespread changes in mountain ecosystems. We used a space-for-time substitution along a gradient of glacierization in western Canada to develop insights into changes that may occur in glaciated regions over the coming decades. Here we report on observed changes in physical (temperature, turbidity), and chemical (dissolved and total nutrients) characteristics of mountain streams and the associated shifts in their diatom communities during de-glacierization. Shifts in habitat characteristics across gradients include changes in nutrient concentrations, light penetration, temperatures, and flow, all of which have led to distinct changes in diatom community composition. Importantly, glacial-fed rivers were 3-5 °C cooler than rivers without glacial contributions. Declines in glacial meltwater contribution to streams resulted in shifts in the timing of nutrient fluxes and lower concentrations of total phosphorus (TP), soluble reactive phosphorus (SRP), and higher dissolved inorganic nitrogen (DIN) and light penetration. The above set of conditions were linked to the overgrowth of the benthic diatom Didymosphenia geminata. These changes in stream condition and D. geminata colony development primarily occurred in streams with marginal (2-5%) to no glacier cover. Our data support a hypothesis that climate-induced changes in river hydrochemistry and physical condition lead to a phenological mismatch that favors D. geminata bloom development.

Integrating Metapopulation Dynamics into a Bayesian Network Relative Risk Model: Assessing Risk of Pesticides to Chinook Salmon (Oncorhynchus tshawytscha) in an Ecological Context

The population level is often the biological endpoint addressed in ecological risk assessments (ERAs). However, ERAs tend to ignore the metapopulation structure, which precludes an understanding of how population viability is affected by multiple stressors (e.g., toxicants and environmental conditions) at large spatial scales. Here we integrate metapopulation model simulations into a regional-scale, multiple stressors risk assessment (Bayesian network relative risk model [BN-RRM]) of organophosphate (OP) exposure, water temperature, and DO impacts on Chinook salmon (Oncorhynchus tshawytscha). A matrix metapopulation model was developed for spring Chinook salmon in the Yakima River Basin (YRB), Washington, USA, including 3 locally adapted subpopulations and hatchery fish that interact with those subpopulations. Three metapopulation models (an exponential model, a ceiling density-dependent model, and an exponential model without dispersal) were integrated into the BN-RRM to evaluate the effects of population model assumptions on risk calculations. Risk was defined as the percent probability that the abundance of a subpopulation would decline from their initial abundance (500 000). This definition of risk reflects the Puget Sound Partnership's management goal of achieving "no net loss" of Chinook abundance. The BN-RRM model results for projection year 20 showed that risk (in % probability) from OPs and environmental stressors was higher for the wild subpopulations-the American River (50.9%-97.7%) and Naches (39.8%-84.4%) spring Chinook-than for the hatchery population (CESRF 18.5%-46.5%) and the Upper Yakima subpopulation (21.5%-68.7%). Metapopulation risk was higher in summer (58.1%-68.7%) than in winter (33.6%-53.2%), and this seasonal risk pattern was conserved at the subpopulation level. To reach the management goal in the American River spring Chinook subpopulation, the water temperature conditions in the Lower Yakima River would need to decrease. We demonstrate that 1) relative risk can vary across a metapopulation's spatial range, 2) dispersal among patches impacts subpopulation abundance and risk, and 3) local adaptation within a salmon metapopulation can profoundly impact subpopulation responses to equivalent stressors. Integr Environ Assess Manag 2021;17:95-109. © 2020 SETAC.

Assessing contributions of cold-water refuges to reproductive migration corridor conditions for adult Chinook Salmon and steelhead trout in the Columbia River, USA

Diadromous fish populations face multiple challenges along their migratory routes. These challenges include suboptimal water quality, harvest, and barriers to longitudinal and lateral connectivity. Interactions among factors influencing migration success make it challenging to assess management options for improving migratory fish conditions along riverine migration corridors. We describe a spatially explicit simulation model that integrates complex individual behaviors of fall-run Chinook Salmon (Oncorhynchus tshawytscha) and summer-run steelhead trout (O. mykiss) during migration, responds to variable habitat conditions over a large extent of the Columbia River, and links migration corridor conditions to fish condition outcomes. The model is built around a mechanistic behavioral decision tree that drives individual interactions of fish within their simulated environments. By simulating several thermalscapes with alternative scenarios of thermal refuge availability, we examined how behavioral thermoregulation in cold-water refuges influenced migrating fish conditions. Outcomes of the migration corridor simulation model show that cold-water refuges can provide relief from exposure to high water temperatures, but do not substantially contribute to energy conservation by migrating adults. Simulated cooling of the Columbia River decreased reliance on cold-water refuges and there were slight reductions in migratory energy expenditure. This modeling of simulated thermalscapes provides a framework for assessing the contribution of cold-water refuges to the success of migrating fishes, but any final determination will depend on analyzing fish survival and health for their entire migration, water temperature management goals and species recovery targets.

An innovative bivariate approach to detect joint temporal trends in environmental conditions: Application to large French rivers and diadromous fish

Most key life-events of organisms are synchronized by complex interactions of several environmental cues to ensure optimal survival and growth of individuals and their offspring. However, global change is known to affect multiple components of ecosystems and cues at the same time. Therefore, detecting joint trends in covariate time series is a crucial challenge in global change ecology that has rarely been addressed so far. In this context, we designed an innovative combination of kernel density estimations and Mann-Kendall trend tests to detect joint temporal trends in a pair of environmental variables. This methodological framework was tested on >30 years (1976-2019) of water temperature and discharge data for 6 large French rivers (the Garonne, Dordogne, Rhône, Rhine, Loire and Vienne rivers). The implications of such trends in both temperature and discharge for diadromous species key life-cycle processes were then explored by checking if significant bivariate environmental changes occurred during seasons of upstream and downstream migration, and reproductive activities. Results were contrasted between rivers and seasons: many rivers displayed an increase in the number of days with high water temperature and low river discharge, but local discharge regulation measures could have mitigated the trend in discharge. Our findings showed that species migrating or spawning in spring were likely to be strongly impacted by the new environmental conditions in the Garonne, Loire and Rhône rivers, given the marked changes in water temperature and discharge associations detected by our new method. Conditions experienced by fall-running and spawning species have been strongly affected in all the rivers studied. This innovative methodology was implemented in a new R package, ChocR, for application to other environments and ecosystems.

Elevated incubation temperature improves later-life swimming endurance in juvenile Chinook salmon, Oncorhynchus tshawytscha

The effect of incubation and rearing temperature on muscle development and swimming endurance under a high-intensity swimming test was investigated in juvenile Chinook salmon (Oncorhynchus tshawytscha) in a hatchery experiment. After controlling for the effects of fork length (L_F ) and parental identity, times to fatigue of fish were higher when fish were incubated or reared at warmer temperatures. Significant differences among combinations of pre- and post-emergence temperatures conformed to 15-15°C > 15-9°C > 9-9°C > 7-9°C > 7-7°C in 2011 when swimming tests were conducted at 300 accumulated temperature units post-emergence and 15-9°C > (7-9°C = 7-7°C) in 2012 when swimming tests were conducted at an L_F of c. 40 mm. The combination of pre- and post-emergence temperatures also affected the number and size of muscle fibres, with differences among temperature treatments in mean fibre cross-sectional area persisting after controlling for L_F and parental effects. Nonetheless, neither fibre number nor fibre size accounted for significant variation in swimming endurance. Thus, thermal carryover effects on swimming endurance were not mediated by thermal imprinting of muscle structure. This is the first study to test how temperature, body size and muscle structure interact to affect swimming endurance during early development in salmon.

On the Ecology and Distribution of Steelhead (Oncorhynchus mykiss) in California's Eel River

The preservation of life history and other phenotypic complexity is central to the resilience of Pacific salmon stocks. Steelhead (Oncorhynchus mykiss) express a diversity of life-history strategies such as the propensity to migrate (anadromy/residency) and the timing and state of maturation upon return to freshwater (run-timing), providing an opportunity to study adaptive phenotypic complexity. Historically, the Eel River supported upwards of 1 million salmon and steelhead, but the past century has seen dramatic declines of all salmonids in the watershed. Here we investigate life-history variation in Eel River steelhead by using Rapture sequencing, on thousands of individuals, to genotype the region diagnostic for run-timing (GREB1L) and the region strongly associated with residency/anadromy (OMY5) in the Eel River and other locations, as well as determine patterns of overall genetic differentiation. Our results provide insight into many conservation-related issues. For example, we found that distinct segregation between winter and summer-run steelhead correlated with flow-dependent barriers in major forks of the Eel, that summer-run steelhead inhabited the upper Eel prior to construction of an impassable dam, and that both life history and overall genetic diversity have been maintained in the resident trout population above; and we found no evidence of the summer-run allele in the South Fork Eel, indicating that summer run-timing cannot be expected to arise from standing genetic variation in this and other populations that lack the summer-run phenotype. The results presented in this study provide valuable information for designing future restoration and management strategies for O. mykiss in Northern California and beyond.

Ecosystem response to earlier ice break-up date: Climate-driven changes to water temperature, lake-habitat-specific production, and trout habitat and resource use

Climate warming has yielded earlier ice break-up dates in recent decades for lakes leading to water temperature increases, altered habitat, and both increases and decreases to ecosystem productivity. Within lakes, the effect of climate warming on secondary production in littoral and pelagic habitats remains unclear. The intersection of changing habitat productivity and warming water temperatures on salmonids is important for understanding how climate warming will impact mountain ecosystems. We develop and test a conceptual model that expresses how earlier ice break-up dates influence within lake habitat production, water temperatures and the habitat utilized by, resources obtained and behavior of salmonids in a mountain lake. We measured zoobenthic and zooplankton production from the littoral and pelagic habitats, thermal conditions, and the habitat use, resource use, and fitness of Brook Trout (Salvelinus fontinalis). We show that earlier ice break-up conditions created a "resource-rich" littoral-benthic habitat with increases in zoobenthic production compared to the pelagic habitat which decreased in zooplankton production. Despite the increases in littoral-benthic food resources, trout did not utilize littoral habitat or zoobenthic resources due to longer durations of warm water temperatures in the littoral zone. In addition, 87% of their resources were supported by the pelagic habitat during periods with earlier ice break-up when pelagic resources were least abundant. The decreased reliance on littoral-benthic resources during earlier ice break-up caused reduced fitness (mean reduction of 12 g) to trout. Our data show that changes to ice break-up drive multi-directional results for resource production within lake habitats and increase the duration of warmer water temperatures in food-rich littoral habitats. The increased duration of warmer littoral water temperatures reduces the use of energetically efficient habitats culminating in decreased trout fitness.

A manipulative thermal challenge protocol for adult salmonids in remote field settings

Manipulative experiments provide stronger evidence for identifying cause-and-effect relationships than correlative studies, but protocols for implementing temperature manipulations are lacking for large species in remote settings. We developed an experimental protocol for holding adult Chinook salmon (Oncorhynchus tshawytscha) and exposing them to elevated temperature treatments. The goal of the experimental protocol was to validate heat stress biomarkers by increasing river water temperature from ambient (~14°C) to a treatment temperature of 18°C or 21°C and then maintain the treatment temperature over 4 hours within a range of ±1.0°C. Our protocol resulted in a mean rate of temperature rise of 3.71°C h-1 (SD = 1.31) to treatment temperatures and mean holding temperatures of 18.0°C (SD = 0.2) and 21.0°C (SD = 0.2) in the low- and high-heat treatments, respectively. Our work demonstrated that manipulative experiments with large, mobile study species can be successfully developed in remote locations to examine thermal stress.

Saviour A. Watershed-scale climate influences productivity of Chinook salmon populations across southcentral Alaska

The ecosystems supporting Pacific salmon (Oncorhynchus spp.) are changing rapidly as a result of climate change and habitat alteration. Understanding how-and how consistently-salmon populations respond to changes at regional and watershed scales has major implications for fisheries management and habitat conservation. Chinook salmon (O. tshawytscha) populations across Alaska have declined over the past decade, resulting in fisheries closures and prolonged impacts to local communities. These declines are associated with large-scale climate drivers, but uncertainty remains about the role of local conditions (e.g., precipitation, streamflow, and stream temperature) that vary among the watersheds where salmon spawn and rear. We estimated the effects of these and other environmental indicators on the productivity of 15 Chinook salmon populations in the Cook Inlet basin, southcentral Alaska, using a hierarchical Bayesian stock-recruitment model. Salmon spawning during 2003-2007 produced 57% fewer recruits than the previous long-term average, leading to declines in adult returns beginning in 2008. These declines were explained in part by density dependence, with reduced population productivity following years of high spawning abundance. Across all populations, productivity declined with increased precipitation during the fall spawning and early incubation period and increased with above-average precipitation during juvenile rearing. Above-average stream temperatures during spawning and rearing had variable effects, with negative relationships in many warmer streams and positive relationships in some colder streams. Productivity was also associated with regional indices of streamflow and ocean conditions, with high variability among populations. The cumulative effects of adverse conditions in freshwater, including high spawning abundance, heavy fall rains, and hot, dry summers may have contributed to the recent population declines across the region. Identifying both coherent and differential responses to environmental change underscores the importance of targeted, watershed-specific monitoring and conservation efforts for maintaining resilient salmon runs in a warming world.

Hatching and survival of the salmon 'gill maggot' Salmincola californiensis (Copepoda: Lernaeopodidae) reveals thermal dependence and undocumented naupliar stage

Salmincola californiensis is a Lernaeopodid copepod parasitizing Pacific salmon and trout of the genus Oncorhynchus. Salmincola californiensis is of increasing concern in both native and introduced ranges because of its potential fish health impacts and high infection prevalence and intensity in some systems. Discrepancies in the documented life history phenology of S. californiensis with the sister species Salmincola edwardsii, as well as our laboratory observations, led us to question the existing literature. We documented a naupliar stage, thought lost for S. californiensis. In addition, we found a high degree of thermal sensitivity in egg development, with eggs developing faster under warmer conditions. Survival of copepodids was also highly dependent on temperature, with warmer conditions reducing lifespan. The longest lived copepodid survived 18 days at 4°C in stark contrast to the generally accepted <48 h survival for that life stage. We also note a consistent relationship between egg sac size and the number of eggs contained. However, egg sac sizes were highly variable. Our findings demonstrate that revisiting old assumptions for S. californiensis and related taxa will be a necessary step to improving our knowledge of the parasite life history and development that will be critical to disease management.

A scientometric review of the research on the impacts of climate change on water quality during 1998-2018

Research on the impacts of climate change on water quality helps to better formulate water quality strategies under the challenge of an uncertain future, which is critical for human survival and development. As a result, in recent years, there has been growing attention given to research in the field, and the attention has led to an increasing number of publications, which is why a systematic literature review on this topic has been proposed in the current paper. This study reviewed 2998 related articles extracted from the Science Citation Index-Expanded (SCI-E) database from 1998 to 2018 to analyse and visualize historical trend evolution, current research hotspots, and promising ideas for future research by combining a traditional literature review, bibliometric analysis, and scientific knowledge mapping. The results revealed that the impacts of climate change on water quality mainly included the aggravation of eutrophication, changes in the flow, hydrological and thermal conditions, and the destruction of ecosystems and biodiversity. Further exploration of the influence mechanism of climate change on cyanobacteria is an emerging research topic. Additionally, the water quality conditions of shallow lakes and drinking water are promising future research objects. In the context of climate change, the general rules of water quality management and the scientific planning of land use are of great significance and need to be further studied. This study provides a practical and valuable reference for researchers to help with the selection of future research topics, which may contribute to further development in this field.

Glacier Retreat and Pacific Salmon

Glaciers have shaped past and present habitats for Pacific salmon (Oncorhynchus spp.) in North America. During the last glacial maximum, approximately 45% of the current North American range of Pacific salmon was covered in ice. Currently, most salmon habitat occurs in watersheds in which glacier ice is present and retreating. This synthesis examines the multiple ways that glacier retreat can influence aquatic ecosystems through the lens of Pacific salmon life cycles. We predict that the coming decades will result in areas in which salmon populations will be challenged by diminished water flows and elevated water temperatures, areas in which salmon productivity will be enhanced as downstream habitat suitability increases, and areas in which new river and lake habitat will be formed that can be colonized by anadromous salmon. Effective conservation and management of salmon habitat and populations should consider the impacts of glacier retreat and other sources of ecosystem change.

Mechanisms behind interactive effects of temperature and bifenthrin on the predator avoidance behaviors in parr of chinook salmon (Oncorhynchus tshawytscha)

Many coastal systems have been experiencing the effects of non-chemical and chemical anthropological stressors through respective increases in surface water temperatures and rainstorm-derived runoff events of pyrethroid pesticide movement into waterways such as the San Francisco Bay-Delta. Salmonid populations in the Bay-Delta have been dramatically declining in recent decades. Therefore, the aim of this study was to investigate the interactive effects of bifenthrin, a pyrethroid insecticide, and increasing water temperatures on targeted neuroendocrine and behavioral responses in Chinook salmon (Oncorhynchus tshawytscha) parr (10- month post-hatch). Parr were reared at 11 °C, 16.4 °C, or 19 °C for 14 days and, in the final 96 h of rearing, exposed to nominal concentrations of 0, 0.15, or 1.5 μg/L bifenthrin. A predatory avoidance Y-Maze behavioral assay was conducted immediately following exposures. Parr were presented a choice of clean or odorant zones, and locomotive behavior was recorded. Thyroid hormones (T3 and T4), estradiol, and testosterone were quantified within plasma using ELISAs, and the expression of brain hormone and dopamine receptor genes were also evaluated by qPCR. Brain dopamine levels were analyzed by LC/MS. No significant changes were observed in brain transcripts or plasma hormone concentrations with bifenthrin or increasing temperature. However, temperature did significantly lower brain dopamine levels in fish reared at 19 °C compared to 11 °C controls, but was unaltered by bifenthrin treatment. In contrast, parr reared at 11 °C and exposed to 1.5 μg/L bifenthrin spent significantly less time avoiding a predatory odorant compared to vehicle controls reared at 11 °C. The 16.4 °C and 1.5 μg/L-treated fish spent significantly more time in the neutral arm compared to the odorant and clean arms, as well as spending significantly less time in the clean arm compared to the 11 °C control fish. These results suggest that the interaction of temperature and bifenthrin may be adversely impacting predator-avoidance behavior, which may not be related to dopaminergic responses.

Spatiotemporal distribution of juvenile chum salmon in Otsuchi Bay, Iwate, Japan, inferred from environmental DNA

To understand the ecology of juvenile chum salmon during early marine life after their downstream migration, we developed a quantitative PCR-based environmental DNA (eDNA) method specific for chum salmon and investigated the spatiotemporal distribution of eDNA in Otsuchi Bay, Iwate, Japan. Indoor aquarium experiments demonstrated the following characteristics of chum salmon eDNA: (1) the eDNA shedding and degradation were time- and water temperature-dependent and the bacterial abundance could contribute to the eDNA decay, (2) fecal discharge may not be the main source of eDNA, and (3) a strong positive Pearson correlation was found between the number of juveniles and the eDNA amounts. As we discovered strong PCR inhibition from the seawater samples of the bay, we optimized the eDNA assay protocol for natural seawater samples by adding a further purification step and modification of PCR mixture. The intensive eDNA analysis in the spring of 2017 and 2018 indicated that juvenile chum salmon initially inhabited in shallow waters in the shorefront area and then spread over the bay from January to June. The eDNA data also pointed out that outmigration of juvenile chum salmon to open ocean temporarily suspended in April, possibly being associated with the dynamics of the Oyashio Current as suggested by a previous observation. The eDNA method thus enables us large-scale and comprehensive surveys without affecting populations to understand the spatiotemporal dynamics of juvenile chum salmon.

Modelling the impacts of climate change on riverine thermal regimes in western Canada's largest Pacific watershed

Quantification of climate change impacts on the thermal regimes of rivers in British Columbia (BC) is crucial given their importance to aquatic ecosystems. Using the Air2Stream model, we investigate the impact of both air temperature and streamflow changes on river water temperatures from 1950 to 2015 across BC’s 234,000 km² Fraser River Basin (FRB). Model results show the FRB’s summer water temperatures rose by nearly 1.0 °C during 1950–2015 with 0.47 °C spread across 17 river sites. For most of these sites, such increases in average summer water temperature have doubled the number of days exceeding 20 °C, the water temperature that, if exceeded, potentially increases the physiological stress of salmon during migration. Furthermore, river sites, especially those in the upper and middle FRB, show significant associations between Pacific Ocean teleconnections and regional water temperatures. A multivariate linear regression analysis reveals that air temperature primarily controls simulated water temperatures in the FRB by capturing ~80% of its explained variance with secondary impacts through river discharge. Given such increases in river water temperature, salmon returning to spawn in the Fraser River and its tributaries are facing continued and increasing physical challenges now and potentially into the future.

Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead (Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook (O. tshawytscha) in the California Central Valley, coho (O. kisutch) in California and southern Oregon, sockeye (O. nerka) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.

Warm, dry winters truncate timing and size distribution of seaward-migrating salmon across a large, regulated watershed

Ecologists are pressed to understand how climate constrains the timings of annual biological events (phenology). Climate influences on phenology are likely significant in estuarine watersheds because many watersheds provide seasonal fish nurseries where juvenile presence is synched with favorable conditions. While ecologists have long recognized that estuaries are generally important to juvenile fish, we incompletely understand the specific ecosystem dynamics that contribute to their nursery habitat value, limiting our ability to identify and protect vital habitat components. Here we examined the annual timing of juvenile coldwater fish migrating through a seasonally warm, hydrologically managed watershed. Our goal was to (1) understand how climate constrained the seasonal timing of water conditions necessary for juvenile fish to use nursery habitats and (2) inform management decisions about (a) mitigating climate-mediated stress on nursery habitat function and (b) conserving heat-constrained species in warming environments. Cool, wet winters deposited snow and cold water into mountains and reservoirs, which kept the lower watershed adequately cool for juveniles through the spring despite the region approaching its hot, dry summers. For every 1°C waters in April were colder, the juvenile fish population (1) inhabited the watershed 4-7 d longer and (2) entered marine waters, where survival is size selective, at maximum sizes 2.1 mm larger. Climate therefore appeared to constrain the nursery functions of this system by determining seasonal windows of tolerable rearing conditions, and cold water appeared to be a vital ecosystem component that promoted juvenile rearing. Fish in this system inhabit the southernmost extent of their range and already rear during the coolest part of the year, suggesting that a warming climate will truncate rather than shift their annual presence. Our findings are concerning for coldwater diadromous species in general because warming climates may constrain watershed use and diminish viability of life histories (e.g., late springtime rearing) and associated portfolio benefits over the long term. Lower watershed nurseries for coldwater fish in warming climates may be enhanced through allocating coldwater reservoir releases to prolong juvenile rearing periods downstream or restorations that facilitate colder conditions.

Avoiding Conflicts between Future Freshwater Algae Production and Water Scarcity in the United States at the Energy-Water Nexus

Sustainable production of algae will depend on understanding trade-offs at the energy-water nexus. Algal biofuels promise to improve the environmental sustainability profile of renewable energy along most dimensions. In this assessment of potential US freshwater production, we assumed sustainable production along the carbon dimension by simulating placement of open ponds away from high-carbon-stock lands (forest, grassland, and wetland) and near sources of waste CO 2 . Along the water dimension, we quantified trade-offs between water scarcity and production for an ‘upstream’ indicator (measuring minimum water supply) and a ‘downstream’ indicator (measuring impacts on rivers). For the upstream indicator, we developed a visualization tool to evaluate algae production for different thresholds for water surplus. We hypothesized that maintaining a minimum seasonal water surplus would also protect river habitat for aquatic biota. Our study confirmed that ensuring surplus water also reduced the duration of low-flow events, but only above a threshold. We also observed a trade-off between algal production and the duration of low-flow events in streams. These results can help to guide the choice of basin-specific sustainability targets to avoid conflicts with competing water users at this energy-water nexus. Where conflicts emerge, alternative water sources or enclosed photobioreactors may be needed for algae cultivation.

Development and application of a qPCR assay targeting Ichthyophthirius multifiliis in environmental water samples

Ichthyophthirius multifiliis (Ich) is a globally distributed, freshwater parasitic ciliate that infects wild and cultured fishes. It has a direct, temperature-dependent life cycle that enables rapid multiplication when hosts are plentiful and environmental conditions are favorable. Accurate detection is central to the control of Ich infections and prevention of host mortality, particularly in wild systems where chemical treatments are not feasible. In the Klamath River, California, USA, the parasite threatens pre-spawning adult salmon Oncorhynchus spp. Currently, Ich is monitored by lethal sampling of fish hosts and visual quantification of parasite load. This method is insensitive to light infections, contributes to pre-spawn mortality of wild salmon, and does not allow for population-level disease risk assessments. We developed and applied an alternate sampling method based on molecular analysis of water samples for parasite DNA. We sequenced the small subunit ribosomal DNA (ssrDNA) of Ich isolates collected from the Klamath River, and then developed and validated a novel qPCR assay (SYTO9) that targets Ich ssrDNA. Our assay has better specificity than previously published assays, with strong linearity, efficiency and repeatability. The limit of detection was 50 copies of ssrDNA, equivalent to ~2 theronts in a sample. We found that Ich abundance in environmental water samples collected from the lower Klamath River from July to October, 2014 through 2016, related to observed parasite load on salmon sampled concurrently, indicating that the qPCR assay could be a useful monitoring tool for Ich in the Klamath River, with applications beyond the region.

Individual Based Modelling of Fish Migration in a 2-D River System: Model Description and Case Study

CONTEXT

Diadromous fish populations in the Pacific Northwest face challenges along their migratory routes from declining habitat quality, harvest, and barriers to longitudinal connectivity. These stressors complicate the prioritization of proposed management actions intended to improve conditions for migratory fishes including anadromous salmon and trout.

OBJECTIVES

We describe a multi-scale hybrid mechanistic-probabilistic simulation model linking migration corridor conditions to fish fitness outcomes. We demonstrate the model's utility using a case study of salmon and steelhead adults in the Columbia River migration corridor exposed to spatially- and temporally-varying stressors.

METHODS

The migration corridor simulation model is based on a behavioral decision tree that governs individual interactions with the environment, and an energetic submodel that estimates the hourly costs of migration. Emergent properties of the migration corridor simulation model include passage time, energy use, and survival.

RESULTS

We observed that the simulated fishes' initial energy density, the migration corridor temperatures they experienced, and their history of behavioral thermoregulation were the primary determinants of their fitness outcomes. Insights gained from use of the model might be exploited to identify management interventions that increase successful migration outcomes.

CONCLUSIONS

This paper describes new methods that extend the suite of tools available to aquatic biologists and conservation practitioners. We have developed a 2-dimensional spatially-explicit behavioral and physiological model and illustrated how it can be used to simulate fish migration within a river system. Our model can be used to evaluate trade-offs between behavioral thermoregulation and fish fitness at population scales.

Subsurface biogeochemistry is a missing link between ecology and hydrology in dam-impacted river corridors

Global investment in hydropower is rapidly increasing, fueled by a need to manage water availability and by incentives promoting renewable energy sources. This expansion poses unrecognized risks to the world's vulnerable freshwater ecosystems. While many hydropower impacts have been investigated, dam-induced alterations to subsurface processes influence river corridor ecosystem health in ways that remain poorly understood. We advocate for a better understanding of dam impacts on subsurface biogeochemical activity, its connection to hydrology, and follow-on trophic cascades within the broader river corridor. We delineate an integrated view of hydropower impacts in which dam-induced changes to surface water flow regimes generate changes in surface-subsurface hydrologic exchange flows (HEFs) that subsequently (1) regulate resource availability for benthic microorganisms at the base of aquatic food webs and (2) impose kinetic constraints on biogeochemical reactions and organismal growth across a range of trophic levels. These HEF-driven effects on river corridor food webs, as mediated by subsurface biogeochemistry, are a key knowledge gap in our assessment of hydropower sustainability and putatively combine with other, more well-known dam impacts to result in significant changes to river corridor health. We suggest targeted laboratory and field-based studies to link hydrobiogeochemical models used to predict heat transport, biogeochemical rates, and hydrologic flow with ecological models that incorporate biomass changes in specific categories of organisms. Doing so will enable predictions of feedbacks among hydrology, temperature, biogeochemical rates, organismal abundances, and resource transfer across trophic levels. This understanding of dam impacts on subsurface hydrobiogeochemistry and its connection to the broader aquatic food web is fundamental to enabling mechanism-based decision making for sustainable hydropower operations.

Eye in the Sky: Using UAV Imagery of Seasonal Riverine Canopy Growth to Model Water Temperature

Until recently, stream temperature processes controlled by aquatic macrophyte shading (i.e., the riverine canopy) was an unrecognized phenomenon. This study aims to address the question of the temporal and spatial scale of monitoring and modeling that is needed to accurately simulate canopy-controlled thermal processes. We do this by using unmanned aerial vehicle (UAV) imagery to quantify the temporal and spatial variability of the riverine canopy and subsequently develop a relationship between its growth and time. Then we apply an existing hydrodynamic and water temperature model to test various time steps of canopy growth interpolation and explore the balance between monitoring and computational efficiencies versus model performance and utility for management decisions. The results show that riverine canopies modeled at a monthly timescale are sufficient to represent water temperature processes at a resolution necessary for reach-scale water management decisions, but not local-scale. As growth patterns were more frequently updated, negligible changes were produced by the model. Spatial configurations of the riverine canopy vary interannually; new data may need to be gathered for each growth season. However, the risks of inclement field conditions during the early growth period are a challenge for monitoring via UAVs at sites with access constraints.

Combined effects of warming and hypoxia on early life stage Chinook salmon physiology and development

Early life stages of salmonids are particularly vulnerable to warming and hypoxia, which are common stressors in hyporheic, gravel bed, rearing habitat (i.e. a 'redd'). With the progression of global climate change, high temperatures and hypoxia may co-occur more frequently within redds, particularly for salmonid species at their southern range limit. Warming and hypoxia have competing effects on energy supply and demand, which can be detrimental to energy-limited early life stages. We examined how elevated temperature and hypoxia as individual and combined stressors affected the survival, physiological performance, growth, and development of Chinook salmon (Oncorhynchus tshawytscha). We reared late fall-run Chinook salmon from fertilization to the fry stage in a fully factorial design of two temperatures [10°C (ambient) and 14°C (warm)] and two oxygen levels [normoxia (100% air saturation, 10 mg O₂/l) and hypoxia (50% saturation, 5.5 mg O₂/l)]. Rearing in hypoxia significantly reduced hatching success, especially in combination with warming. Both warming and hypoxia improved acute thermal tolerance. While rearing in hypoxia improved tolerance to acute hypoxia stress, warming reduced hypoxia tolerance. Hypoxia-reared fish were smaller at hatch, but were able to reach similar sizes to the normoxia-reared fish by the fry stage. High temperature and normoxia resulted in the fastest rate of development while low temperature and hypoxia resulted in the slowest rate of development. Despite improved physiological tolerance to acute heat and hypoxia stress, hypoxia-reared embryos had reduced survival and growth, which could have larger population-level effects. These results suggest that both warming and hypoxia are important factors to address in conservation strategies for Chinook salmon.

Temperature and depth profiles of Chinook salmon and the energetic costs of their long-distance homing migrations

River warming poses an existential threat to many Pacific salmon (Oncorhynchus spp) populations. However, temperature-mediated risks to salmon are often complex and addressing them requires species- and population-specific data collected over large spatial and temporal scales. In this study, we combined radiotelemetry with archival depth and temperature sensors to collect continuous thermal exposure histories of 21 adult spring- and summer-run Chinook salmon (O. tshawytscha) as they migrated hundreds of kilometers upstream in the Columbia River basin. Salmon thermal histories in impounded reaches of the Columbia and Snake rivers were characterized by low daily temperature variation but frequent and extensive vertical movements. Dives were associated with slightly cooler salmon body temperatures (~ 0.01 to 0.02 °C/m), but there was no evidence for use of cool-water thermal refuges deep in reservoirs or at tributary confluences along the migration route. In tributaries, salmon were constrained to relatively shallow water, and they experienced ~ 2-5 °C diel temperature fluctuations. Differences in migration timing and among route-specific thermal regimes resulted in substantial among-individual variation in migration temperature exposure. Bioenergetics models using the collected thermal histories and swim speeds ranging from 1.0 to 1.5 body-lengths/s predicted median energetic costs of ~ 24-40% (spring-run) and ~ 37-60% (summer-run) of initial reserves. Median declines in total mass were ~ 16-24% for spring-run salmon and ~ 19-29% for summer-run salmon. A simulated + 2 °C increase in water temperatures resulted in 4.0% (spring-run) and 6.3% (summer-run) more energy used per fish, on average. The biotelemetry data provided remarkable spatial and temporal resolution on thermal exposure. Nonetheless, substantial information gaps remain for the development of robust bioenergetics and climate effects models for adult Chinook salmon.