Abstract: Coastal ecosystems are among the most human-impacted habitats globally, and their management is often critically linked to recovery of declining native species. In the San Francisco Estuary, the Delta Smelt (Hypomesus transpacificus) is an endemic, endangered fish strongly tied to Californian conservation planning. The complex life history of Delta Smelt combined with dynamic seasonal and spatial abiotic conditions result in dissimilar environments experienced among ontogenetic stages, which may yield stage-specific susceptibility to abiotic stressors. Climate change is forecasted to increase San Francisco Estuary water temperature and salinity; therefore, understanding the influences of ontogeny and phenotypic plasticity on tolerance to these critical environmental parameters is particularly important for Delta Smelt and other San Francisco Estuary fishes. We assessed thermal and salinity limits in several ontogenetic stages and acclimation states of Delta Smelt, and paired these data with environmental data to evaluate sensitivity to climate-change stressors. Thermal tolerance decreased among successive stages, with larval fish exhibiting the highest tolerance and post-spawning adults having the lowest. Delta Smelt had limited capacity to increase tolerance through thermal acclimation, and comparisons with field temperature data revealed that juvenile tolerance limits are the closest to current environmental conditions, which may make this stage especially susceptible to future climate warming. Maximal water temperatures observed in situ exceeded tolerance limits of juveniles and adults. Although these temperature events are currently rare, if they increase in frequency as predicted, it could result in habitat loss at these locations despite other favourable conditions for Delta Smelt. In contrast, Delta Smelt tolerated salinities spanning the range of expected environmental conditions for each ontogenetic stage, but salinity did impact survival in juvenile and adult stages in exposures over acute time scales. Our results underscore the importance of considering ontogeny and phenotypic plasticity in assessing the impacts of climate change, particularly for species adapted to spatially and temporally heterogeneous environments.

Komoroske et al., 2014
Abstract: In 2004 the grant and contract work of the High Seas Salmon Research Program, Fisheries Research Institute (FRI), School of Aquatic and Fishery Sciences (SAFS), University of Washington, included five projects: (1) “North Pacific Anadromous Fish Commission (NPAFC) Research Coordination,” (2) “Migration Studies of Salmon in the Bering Sea,” (3) “Diet Overlap and Potential Feeding Competition Between Yukon River Chum Salmon and Hatchery Salmon in the Gulf of Alaska in Summer,” (4) “Estimates of the Bycatch of Yukon River Chinook Salmon in U.S. Groundfish Fisheries in the Eastern Berng Sea, 1997-1999,” and (5) “Global Ocean Ecosystems Dynamics (GLOBEC) 2000: Feeding, Growth, Condition, and Energetics of Juvenile Pink Salmon in the Northern Gulf of Alaska.” This final report for 2004 includes reports on specific tasks as described in the Statement of Work for “NPAFC Research Coordination” (National Oceanic and Atmospheric Administration (NOAA) Contract No. 50ABNF-1-0002), as well as related tasks funded by the other grants and contracts.

Strange, 2004
Abstract: This collaborative project uses temperature sensitive radio transmitters to track the movements and monitor the internal body temperatures of adult spring chinook during upriver migration in the Klamath River Basin, California. Salmon are tagged throughout the run in or near the Klamath River estuary and tracked to their respective holding areas or natal tributaries. Combined with data from automated listening stations, external archival temperature tags, river temperature monitoring, and snorkel surveys of thermal refugia the results of this study will provide valuable information on thermal refugia use, thermal experience, migration behavior, and stock specific run timing for adult spring chinook. This project is a critical step towards understanding the role of thermal refugia in mitigating stress and mortality from elevated temperatures during upriver migration.

Myers et al. 2005
Abstract: Basking activity of western pond turtles (Clemmys marmorata) was studied on two forks of the Trinity River in northern California, the dammed Mainstem Trinity River and the undammed South Fork Trinity River. The thermal regime between these two riverine systems is extreme due to the hypolimnetic release from the Lewiston Dam on the Mainstem Trinity River. Turtles studied on the Mainstem Trinity River were exposed to summer water temperatures that are >10°C lower than the control population on the South Fork Trinity River. We tested the null hypothesis that there would be no difference in thermal regulatory behavior times between the two populations of C. marmorata. However, there was a significant difference between the two population’s thermal regulatory behavior, with the Mainstem Trinity River population of C. marmorata spending more time seeking aquatic thermal refugia and basking than the South Fork Trinity River population (Yates chi-square value = 2368.07, P = 0.0000, and t-value = -3.4048, P = 0.0078) when compared to the river maximum water temperatures. Individual turtles from the undammed South Fork Trinity River tended to bask for shorter periods of time per day and also utilized aquatic basking behaviors compared to the turtles from the Mainstem Trinity River population. The artificially colder thermal regime created by the hypolimnetic releases from the Lewiston Dam may be influencing the turtles thermoregulatory behavior on the Mainstem Trinity River and having these animals seeking alternative aquatic thermal refugia.

Bettaso et al., 2005
Fisheries and Ocean Canada, Institute Maurice-Lamontagne

Abstract: An annual high-seas research cruise to investigate the stock condition of Pacific salmon was conducted in the central North Pacific Ocean and the Bering Sea from 9 June to 21 July 2004 onboard the Japanese research vessel Wakatake maru. Research cruise activities included the collection of data on oceanography, primary production, zooplankton, salmonid fishes, and other organisms. A total of 6,510 salmonids was caught by longline and gillnet: 685 fishes in the central North Pacific Ocean and 5,825 fishes in the central Bering Sea. In the North Pacific Ocean, coho and chum salmon were the most abundant species (40.4% and 39.6%, respectively), followed by pink salmon (9.6%), sockeye salmon (4.2%), steelhead trout (3.9%), and chinook salmon (2.2%). In the Bering Sea, chum salmon was the most abundant species (76.4%), followed by pink (9.9%), sockeye (9.7%), chinook (3.7%), and coho salmon (0.3%). A total of 872 samples of salmonid stomach contents was examined onboard the research vessel. Brain, pituitary, and blood samples were obtained from 100 chum salmon for endocrine studies. There were 717 salmon (30 sockeye, 573 chum, 31 pink, 50 coho, and 33 chinook salmon) tagged with disk tags and released in the North Pacific Ocean and the Bering Sea. From among fish released with disk-tags, 22 sockeye, 85 chum, 19 pink, and 32 chinook salmon were released carrying one of three different archival tags.

Morita et al., 2004
Abstract: Adult sockeye salmon, Oncorhynchus nerka (Walbaum in Artedi, 1792), return to Lake Washington several months prior to spawning, spending the warmest months of the year in the lake. We proposed that the fish selected a temperature range ideal for final sexual maturation and energy conservation prior to swimming upstream to spawn. The temperature preferences of the adult sockeye salmon in Lake Washington are attributable to physiological factors, as they are not avoiding predators or seeking prey and are not limited by dissolved oxygen. At the Hiram M. Chittenden Locks, 257 sockeye salmon were tagged with temperature loggers in the summer of 2003, and 38 tags with readable data were recovered. The fish spent an average of 6 days swimming through the ship canal’s warm water (ca. 18 °C) and then experienced a drop to temperatures of 13 °C or lower when they entered the lake and descended below the thermocline. Fish remained in the lake for an average of 83 days before migrating upstream to spawn, as indicated by a sudden increase in recorded temperature. Approximately 92% of temperature records in the lake were 9–11 °C, corresponding to depths of 18–30 m. The salmon rarely occupied the cooler and warmer waters available to them. Finally, the apparent thermal preference decreased over the summer, perhaps as a function of sexual maturation.

Newell & Quinn, 2005
Abstract: Data storage tags (DSTs) were applied to Atlantic salmon (Salmo salar L.) smolts during their seaward migration in the spring of 2002 at a fish counting fence on Campbellton River, Newfoundland. Our objectives were to discover whether or not salmon smolts could carry DSTs and survive, whether or not useful data on thermal habitat could be obtained and interpreted, and whether or not salmon smolts moved vertically in the water column. Data were downloaded from 15 of the recovered tags and revealed the hourly water temperatures experienced by the fish for periods of 3 to 71 days. The data on the DSTs were analyzed for temperature patterns in relation to migration behavior and diurnal movement of the fish. While in the sea, the DSTs recorded night temperatures of 12.5°C, which were higher than day temperatures of 11.6°C; the record from moored recorders, however, indicated that sea temperatures actually declined at night. It is hypothesized that posts-molts avoid avian predators during daylight hours by positioning themselves deeper in the water column and that they were pursuing prey during the deeper vertical descents or ascents noted during the periods of more rapid changes in temperature.

Reddin et al., 2005
Abstract: Bats are among the most thermo-labile of all mammals. Many species and individuals regulate their rate of energy expenditure by adjusting body temperature in response to either the immediate size of their on-board fat reserves or to past or future foraging success. For this reason, monitoring body temperature can tell us much about foraging success and the energetic challenges that individuals face. This is particularly true for hibernating bats, most of which must survive for up to 8 months on a fixed energy reserve. Hibernating bats may adjust the depth of torpor in response to the size of their fat stores by selecting specific microclimates. They may also adjust the frequency and duration of winter arousals. Torpor parameters are difficult to study by direct observation because hibernating bats are sensitive to human disturbance. Here, we present a new self-contained datalogger that now allows the measurement of body temperature for bats as small as 10g.

Pitre et al.
Abstract: 1. Many endotherms employ torpor during periods of resource scarcity, but this state of substantially reduced body temperature and metabolism appears to impose significant physiological costs. Accordingly, individuals can be expected to vary the expression of torpor according to the size of their energy reserves. 2. Although dietary polyunsaturated fatty acids (PUFAs) are important for maintaining the fluidity of membrane phospholipids and depot fats at low body temperatures, they are also prone to autoxidation, which can result in significant somatic damage. Dietary PUFA may thus influence the depth and duration of torpor during hibernation. 3. We evaluated the hypothesis that both an increase in the size of the burrow food hoard and an elevation of its PUFA composition can cause chipmunks to reduce their use of torpor both by reducing the time spent torpid and by maintaining higher body temperature during torpor. 4. We provided individual chipmunks with equicaloric natural-PUFA and high-PUFA supplements 10 days prior to autumn immergence. We measured seven parameters that characterize the depth and duration of torpor used by hibernating chipmunks using temperature-sensitive data loggers mounted on neck collars. We compared torpor patterns for the natural-PUFA, high-PUFA and control groups at a study site in southern Quebec, Canada. We also compared control animals from Quebec with unsupplemented controls from a more southerly site in Pennsylvania, USA characterized by higher food availability and less severe winters. 5. Chipmunks provided …

Munro et al., 2005
Department of Animal Physiology, Nicolas Copernicus University

Jefimow et al.
Abstract: First evidence of bat white-nose syndrome (WNS) was documented in a photograph taken at Howes Cave, 52 km west of Albany, New York on February 16, 2006. Since emerging in the northeastern United States, WNS has been confirmed by gross and histologic examinations of bats at 33 sites in Connecticut, Massachusetts, New York, and Vermont…

Blehert et al., 2008
Abstract: Free-ranging, juvenile thirteen-lined ground squirrels (Ictidomys tridecemlineatus) in southwestern Michigan were fitted in late summer or fall with external skin-temperature loggers. Data were obtained the following spring for five males and three females. During the heterothermal period, all squirrels exhibited 11–22 prolonged (x 5 9.4 d) torpor bouts punctuated by typically brief (x 5 14.3 h) arousal bouts, with mean monthly torpor bouts becoming longer and deeper until Feb. and reversing thereafter. Torporbout duration increased as minimum skin and soil temperatures decreased. On average, males initiated the first torpor bout later in fall, terminated the last torpor bout significantly earlier in spring and thus spent less time in the heterothermal period than did females. Three males displayed relatively short torpor bouts and long arousal bouts as they approached the end of hibernation. Squirrels gained weight variably in fall and spring, and one female lost 39% of body mass during hibernation.

Kisser & Goodwin, 2012
The biogeochemical changes that occur in the hyporheic zone are highly dependent on the time solutes are in contact with riverbed sediments. To gain a better understanding of physical controls on nitrogen reactions, a two-dimensional longitudinal flow and solute transport model was developed to estimate the spatial distribution of mean residence time (MRT) in the hyporheic zone along a riffle-pool sequence. A physically distributed flow and transport model was necessary to estimate spatially distributed mean residence times. The approach used in this investigation accounts for the mixing of hyporheic water of different ages given advection and dispersion (Goode, 1996). Uncertainty of flow and transport parameters was evaluated using standard Monte-Carlo (MC) analysis and the generalized likelihood uncertainty estimation (GLUE) method.

Naranjo et al., 2013
Measuring vertically nested temperatures at the streambed interface poses practical challenges that are addressed here with a new discrete subsurface temperature profiling probe. We describe a new temperature probe and its application for heat as a tracer investigations to demonstrate the probe’s utility. Accuracy and response time of temperature measurements made at six discrete depths in the probe were analyzed in the laboratory using temperature bath experiments. We find the temperature probe to be an accurate and robust instrument that allows for easily installation and long-term monitoring in highly variable environments. Because the probe is inexpensive and versatile, it is useful for many environmental applications that require temperature data collection for periods of several months in environments that are difficult to access or require minimal disturbance.

Naranjo et al., 2015
The Walker River is an important source of water for western Nevada. The river provides water for agriculture and recharge to local aquifers used by several communities. Farmers began diverting water from the Walker River in the 1860s to support growing agricultural development. Over time, the reduced inflows into Walker Lake from upstream reservoirs and diversions have resulted in 170 feet of lake level decline and increased dissolved-solids concentrations to levels that threaten aquatic ecosystems, including survival of Lahonton cutthroat trout, a native species listed in the Endangered Species Act. Investigations of the water-budget components in the Walker River Basin have revealed uncertainty in the recharge to aquifers from irrigation canals. To address this need, the U.S. Geological Survey conducted an extensive field study from March 2012 through October 2013 to quantify seepage losses in selected canals in the Smith Valley, Mason Valley, and Walker Lake Valley irrigation areas.
The seepage rates estimated for the 2012 and 2013 irrigation seasons in the Smith Valley transect sites (Saroni and Plymouth canals) ranged between 0.01 to 2.5 feet per day (ft/d) (0.01 to 0.68 cubic feet per second per mile [ft3/s-mi]). From 2012 to 2013, the average number of days the canals had flowing water decreased from 190 to 125 due to drier climate and lack of water available for diversion from the Walker River. The nearly 50-percent reductions in volumetric loss rates between 2012 and 2013 were associated with less than average diversions into canals from the Walker River and reductions in infiltration rates following routine canal maintenance.
Models developed for the Saroni canal in 2012 were recalibrated in 2013 to evaluate changes in seepage as a result of siltation. Just prior to the 2012 irrigation season, nearly the entire length of the canal was cleared of vegetation and debris to improve flow conveyance. In 2013, following the first year of maintenance, a 90-percent reduction in seepage was observed at one of the transect sites. The removal of sediment-clogged layers during canal maintenance may have more profound effects on seepage rates beyond what was observed at the transect sites. The seepage rates for the Saroni canal in 2012 ranged from 0.02 to 1.6 ft/d (0.03 to 0.4 ft3/s-mi). The total seepage loss in the Saroni canal for the 2012 and 2013 irrigation seasons was estimated to be 1,100 and 590 acre-feet (acre-ft), respectively.
Seepage rates on the Plymouth canal in Smith Valley in 2012 were among the lowest, ranging from 0.01 to 0.2 ft/d (0.01 to 0.1 ft3/s-mi). In 2013, the seepage rate on the Plymouth canal was similar to 2012; however, the volumetric loss was reduced by 50 percent due to the 50-percent reduction in number of canal flow days. Lower rates of seepage on the Plymouth canal for the 2012 and 2013 irrigation seasons were estimated to be 210 and 130 acre-ft, respectively.
The seepage rates estimated for the 2012 and 2013 irrigation seasons in the Mason Valley transect sites (Fox, Mickey, and Campbell ditches) ranged from 0.1 to 3.3 ft/d (0.2 to 1.3 ft3/s-mi). The influence of water-table declines on seepage was observed at the Mickey and Campbell ditches. In 2012, the estimated seepage on the Mickey ditch was 1.6 ft/d during a period when the water-table altitude was at or above the canal altitude. Following extensive declines in the water table, the hydraulic gradient increased between the canal and the shallow aquifer, thereby increasing the seepage rates to 3.2 ft/d in 2013. During the period of hydraulic disconnection, seepage rates increased to 9.5 ft/d during intermittent periods of canal flow. For the Mickey ditch, the seepage loss in 2013 was 1.5 times the rate estimated in 2012 despite the canal having 45 days less flow. Similarly, the Campbell ditch seepage loss increased slightly from 660 to 700 acre-ft, a factor of 1.1, with 49 days less flow. The seepage loss for the Fox ditch did not exhibit significant year to year variability. The annual seepage loss estimated for 2012 and 2013 in the Fox ditch was 2,100 and 2,200 acre-ft, respectively.
The seepage rates estimated for the 2013 irrigation season in the Walker Lake Valley transect sites (Schurz Lateral Canals 1A and 2A, and Canal 2) ranged from 0.7 to 0.9 ft/d (0.4 to 1.3 ft3/s-mi). In Walker Lake Valley, diversions into Lateral Canals 1A and 2A during the 2013 irrigation season were highly intermittent, a characteristic common of lateral diversions. The annual estimated seepage loss in Walker Lake Valley ranged between 50 and 725 acre-ft among the transect sites.

Naranjo et al., 2016

Groundwater-flow models are often calibrated using a limited number of observations relative to the unknown inputs required for the model. This is especially true for models that simulate groundwater–surface water interactions. In this case, subsurface temperature sensors can be
an efficient means for collecting long-term data that capture the transient nature of physical processes, such as seepage losses. Continuous and spatially dense network of diverse observation data can be used to improve knowledge of important physical drivers, conceptualize, and
calibrate variably saturated groundwater flow models. An example is presented for which the results of such analysis were used to help guide irrigation districts and water management decisions on costly upgrades to conveyance systems to improve water usage, farm productivity, and
restoration efforts to improve downstream water quality and ecosystems.

Naranjo et al., 2017

This document provides a brief method overview on the deployment and removal of the temperature profiling probe developed by the U.S. Geological Survey (USGS) in 2015 and referred to as SensorRod or temperature rod (TROD). The TROD is suitable for short- to long-term deployments (days to years) for evaluating thermal gradients in soils and sediments beneath surface water. Applications include evaluating exchange between groundwater and surface water, seepage losses in agricultural canals, infiltration on hillslopes, and timing of snowmelt and runoff. The temperature sensors inside the TROD are iButtons and are meant to be replaceable when needed. The housing is water tight and is made of schedule 80 PVC pipe. Sensor intervals are flexible and can be built to specific applications.
A joint patent (U.S 10/180,360.) and license agreement between the USGS and Alpha Mach for the TROD design was obtained in 2019, and a paper in Water Resource Research describes the design and testing (Naranjo and Turcotte, 2015).