• Energy Research

As climate change continues to increase air temperature in high-altitude ecosystems, it has become critical to understand the controls and scales of aquatic habitat vulnerability to warming. Here we used a nested array of high-frequency sensors, and advances in time-series models, to examine spatiotemporal variation in thermal vulnerability in a model Sierra Nevada watershed. Stream thermal sensitivity to atmospheric warming fluctuated strongly over the year and peaked in spring and summer—when hot days threaten invertebrate communities most. The reach scale (~50 m) best captured variation in summer thermal regimes. Elevation, discharge, and conductivity were important correlates of summer water temperature across reaches, but upstream water temperature was the paramount driver—supporting that cascading warming occurs downstream in the network. Finally, we used our estimated summer thermal sensitivity and downscaled projections of summer air temperature to forecast end-of-the-century stream warming, when extreme drought years like 2020-2021 become the norm. We found that 25.5% of cold-water habitat may be lost under business-as-usual RCP 8.5 (or 7.9% under mitigated RCP 4.5). This estimated reduction suggests that 27.2% of stream macroinvertebrate biodiversity (11.9% under the mitigated scenario) will be stressed or threatened in what was previously cold‑water habitat. Our quantitative approach is transferrable to other watersheds with spatially‑replicated time series and illustrates the importance of considering variation in the vulnerability of mountain streams to warming over both space and time. This approach may inform watershed conservation efforts by helping identify, and potentially mitigate, sites and time windows of peak vulnerability. Please see the README.md document. Please see the README.md document.

Climate change is affecting the phenology of organisms and ecosystem processes across a wide range of environments. However, the links between organismal and ecosystem process change in complex communities remain uncertain. In snow-dominated watersheds, snowmelt in the spring and early summer, followed by a long low-flow period, characterizes the natural flow regime of streams and rivers. Here, we examined how earlier snowmelt will alter the phenology of mountain stream organisms and ecosystem processes via an outdoor mesocosm experiment in stream channels in the Eastern Sierra Nevada, California. The low-flow treatment, simulating a 3- to 6-wk earlier return to summer baseflow conditions projected under climate change scenarios in the region, increased water temperature and reduced biofilm production to respiration ratios by 32%. Additionally, most of the invertebrate species explaining community change (56% and 67% of the benthic and emergent taxa, respectively), changed in phenology as a consequence of the low-flow treatment. Further, emergent flux pulses of the dominant insect group (Chironomidae) almost doubled in magnitude, benefitting a generalist riparian predator. Changes in both invertebrate community structure (composition) and functioning (production) were mostly fine-scale, and response diversity at the community level stabilized seasonally aggregated responses. Our study illustrates how climate change in vulnerable mountain streams at the rain-to-snow transition is poised to alter the dynamics of stream food webs via fine-scale changes in phenology—leading to novel predator–prey “matches” or “mismatches” even when community structure and ecosystem processes appear stable at the annual scale.

Time frame: Begin date 4/21/2019 - End date 8/25/2019. General study design- We subjected nine large-scale, flow-through outdoor stream mesocosms in California’s Sierra Nevada to three flow regime treatments: a flow regime based on historic average conditions (current treatment), a mitigated climate change scenario where low flow begins three weeks earlier than currently (3-week treatment), and an unmitigated climate change scenario where low flow begins six weeks earlier than currently (6-week treatment). Over the course of a season, we regularly measured primary production; community composition, production, and emergence of benthic and emergent stream invertebrates; and Brewer’s Blackbird (Euphagus cyanocephalus) feeding activity. We tested for immediate vs. delayed effects of advanced low flows by combining the period of the study (i.e., start, middle, and end) with the treatment, creating a variable that captures both timing and treatment effects (i.e., period-treatment). We ran a piecewise structural equation model to elucidate and compare mechanisms driving low-flow effects on stream invertebrate production and emergence. Methods description- We used nine channels that are 50 m long by 1 m wide, consist of six pools connected by long riffle sections in a meandering fashion, and are fed by the adjacent Convict Creek. We assigned each channel to one of three treatments (with three replicate channels each) in a block design. The three treatments were: (1) current hydrologic conditions based on the historic (long-term) hydrograph at Convict Creek (based on US Geological Survey gage 10265200), with a flow regime that reaches baseflow conditions around August 3rd (i.e., current treatment); (2) hydrologic conditions under a mitigated climate change scenario, where the stream would return to baseflow conditions three weeks earlier than it currently does (i.e., 3-week treatment); and (3) hydrologic conditions under unmitigated climate change, where the stream would return to baseflow six weeks earlier than it currently does (i.e., 6-week treatment). We regulated discharge by controlling sluice gates at the head of each channel. Flows in the channels differed by one order of magnitude between high-flow and low-flow conditions (i.e., 15 L/s and 1.5 L/s, respectively), following a typical Sierra Nevada stream hydrograph for a small stream. Channels were inspected and maintained daily, were heavily instrumented (see next section), and were monitored and sampled for several responses: primary production, secondary production, benthic and emerging stream invertebrates (composition and abundance), and visitation by riparian birds. The three periods we designated in the study are start (5/11/2019 - 6/10/2019), middle (6/11/2019 - 8/2/2019), and end (8/3/2019 - 8/21/2019). We measured water depth and water temperature every five minutes throughout the experiment (4/21/2019–8/25/2019) with replicated pressure transducers (HOBO U20L-04, Onset). We placed a pressure transducer in the fifth pool downstream in each channel and two emerged sensors on land to correct data for fluctuations in atmospheric pressure, and thus calculate water level (i.e., pool depth). Water level series were subsequently transformed into discharge series via channel-specific rating curves. Rating curves were developed for each channel by estimating discharge manually using channel depth and velocity measurements taken with a Marsh-McBirney Flo-Mate 2000 current meter throughout the summer (17-26 repeated estimates per channel). We measured water temperature using the same HOBO U20L-04 sensors that recorded data every five minutes in pools. We averaged discharge and water temperature to hourly values, which we then used to calculate daily metrics (e.g., daily mean, minimum, maximum, and diel range). We estimated epilithic biofilm primary production using the light/dark bottle method at each channel, once every three weeks. We calculated epilithic biofilm respiration (ER), net primary production (NPP), and the sum of their absolute values–gross primary production (GPP). We used three representative cobbles from the streambed for each sample and measured their surface area using aluminum foil to correct for differences in surface area. All primary production measurements were taken during peak sunlight hours between 10 am and 2 pm using two 90-minute incubation periods for light, followed by dark measurements. Benthic stream invertebrates were removed from rocks prior to incubation. We conducted three replicates for each channel at each sampling date (n = 162). Daily epilithic biofilm GPP per channel was estimated by multiplying the channel average hourly rate by the number of sunlight hours at each date (n = 54). We estimated daily epilithic biofilm ER per channel by multiplying the channel average hourly rate by 24 hours at each date (n = 54). Daily primary production was then estimated for the interval between each sampling date by averaging the bookend interval values. We multiplied the average interval value by the number of days in the interval and finally summed these values to generate cumulative seasonal channel estimates (n = 9). We sampled benthic stream invertebrates using a 500-micron Surber sampler at six visit dates three weeks apart throughout the experiment. Each sample was a composite of three subsamples (two riffles and one pool sample for 0.279 m^2 total) to represent the overall stream community. We took benthic samples for the current and 6-week treatment channels (n = 36) and stored them in 70% ethanol. We then subsampled the composite samples using a rotating-drum splitter in the laboratory to sort and identify at least 500 individuals from each composite sample under a stereomicroscope. All subsamples were completely processed to avoid bias regarding the size of individuals picked and identified. Benthic stream invertebrates were identified to the highest resolution possible, typically genus or species level, and all intact specimens were measured. Benthic stream invertebrate biomass was then estimated using published taxon-specific length-mass relationships. The subsampled community was multiplied by the inverse of the fraction of the total sample that was identified (e.g., if ¼ of the sample was identified to get a count over 500 individuals, then the abundance of each taxon was multiplied by 4). We assigned length values to these extrapolated individuals (and individuals that could be identified but not measured due to damage) using the length values from randomly selected individuals of the same taxon in the sample. We sampled emergent stream invertebrates using emergence traps, each deployed for 72 hours every three weeks during the experiment. We sampled emergence four additional times halfway between the three-week intervals for every sample visit after the second one when flows began to differ between treatments (n = 90 overall). We deployed emergence traps at the tail of riffles (to capture the influence of both riffle and pool habitat) next to HOBO sensors. We identified emergent insects to genus or family level (depending on taxa), and measured the length of intact specimens. Emergence traps were tent-shaped, covered 0.33 m2 of the stream, and had 2 mm white mesh. We noticed Brewer's Blackbirds (Euphagus cyanocephalus) feeding in channels at the onset of low flow in the 6-week treatment channels (June 22, 2019). We recorded the feeding behavior of Brewer’s Blackbirds shortly thereafter by observing the time duration that any bird of this species occupied the benthos of the channels over a 30-minute period periodically throughout the remainder of the experiment. We observed all channels every few days initially but switched to weekly observations once Brewer’s Blackbirds fledged and moved to meadow habitat. Laboratory, field, or other analytical methods- We estimated benthic stream invertebrate secondary production via a combination of three methods. We used the size-frequency method for taxa that were abundant throughout the experiment (i.e., >1% of total abundance) and had known generation times, excluding Chironomidae, Oligochaeta, Turbellaria, and Muscidae. For Chironomids, we used the instantaneous growth rate method. Production was calculated using regression equations for non-Tanypodinae chironomids, which incorporate mean temperature into growth estimates for small, medium, and large chironomids. Finally, we used the production-to-biomass ratio method (P/B) for the remaining taxa, including Tanypodinae, by multiplying seasonal biomass by known P/B ratios in the literature of the closest related taxa possible. Uncertainty in production from P/B ratios is unlikely to affect our results, as taxa in this group comprised <1% of the total assemblage production. We estimated emergent insect biomass using published, taxon-specific length-mass relationships. *Quality control- Data was recorded in hard copies and digitally to reduce the risk of mistyped data. Data was plotted visually for outliers that were erroneous and paper copies were referenced to ensure values were correct. # Climate change is poised to alter mountain stream ecosystem processes via organismal phenological shifts ## Description of the Data and file structure [https://doi.org/10.6078/D10712](https://doi.org/10.6078/D10712) ### Details for: Discharge\_dryad.csv * Dataset description: The dataset includes the average discharge of each channel on each day of the experiment taken with U20 Onset sensors recording every 15 minutes. Sensors were located in pools near the downstream end of channels and secured to cinder blocks at the streambed. Variables * Date: Date with day, month, and year. The format is month/day/year and the year is 2019. * Channel: Channel number beginning at the upstream channel closest to Convict Creek as #1 and ending with the downstream channel farthest from Convict Creek being #9 * Treatment: The treatment of the channel as described above in methods * Discharge_Av_Chan_L_s: Average daily discharge (L/s). Raw water depth data is collected from sensors and transformed using rating curves created for each channel using 22 measuring dates throughout the experiment. Rating curves are not perfect estimates, however. Discharge values estimated above 30 L/s by the rating curve were set to 30 L/s because flows were unlikely to be any higher based on manual discharge estimates and channel capacity. Discharge estimated below 0 L/s were set to 0 L/s, although no channels actually dried. ### Details for: Water\_Temperature\_dryad.csv * Dataset description: The dataset includes daily mean, minimum, and maximum water temperatures of each channel taken with U20 Onset sensors recording every 15 minutes. Variables * day: Date with day, month, and year. Format is month/day/year where the year is 2019. * Channel: Channel number beginning at the upstream channel closest to Convict Creek as #1 and ending with the downstream channel farthest from Convict Creek being #9 * Treatment: The treatment of the channel as described above in methods * Temp_Av_Daily_C: Mean daily temperature of a channel in degrees Celsius. * Temp_Max_Daily_C: Maximum daily temperature of a channel in degrees Celsius. * Temp_Min_Daily_C: Minimum daily temperature of a channel in degrees Celsius. ### Details for: Benthic\_Macroinvertebrates\_dryad.csv * Dataset description: The dataset includes the lowest taxonomic identification and size of all benthic macroinvertebrates in the study. Variables * Date: Date with day, month, and year. Format is month/day/year where the year is 2019. * Channel: Channel number beginning at the upstream channel closest to Convict Creek as #1 and ending with the downstream channel farthest from Convict Creek being #9 * Treatment: The treatment of the channel as described above in methods * Order: The order of the organism * Family: The family of the organism * Lowest: The lowest taxonomic identification possible for the organism, typically genus. * Corrected_Size_mm: The length of the organism measured from its head to the end of its abdomen in most cases. Organisms without a head such as Pisidium or snails had the widest cross-section measured as their length. ### Details for: Primary\_production\_dryad.csv * Dataset description: The dataset includes primary production data taken using the light dark bottle method. Primary production values are corrected by the surface area of cobbles used. A YSI dissolved oxygen meter was used for measurements. Variables * Date: Date with day, month, and year. Format is month/day/year where the year is 2019. * Channel: Channel number beginning at the upstream channel closest to Convict Creek as #1 and ending with the downstream channel farthest from Convict Creek being #9 * Treatment: The treatment of the channel as described above in methods * Section: The riffle that the substrate originated from. Each channel had three sections measured at each measuring date. Sections are numbered from one-seven with one being the riffle section farthest upstream. * GPP_C_mg_m2: Gross primary production (GPP) measured in mg carbon per m^2. * NPP_C_mg_m2: Net primary production (NPP) measured in mg carbon per m^2. * ER_C_mg_m2: Ecosystem respiration (ER) measured in mg carbon per m^2. * Light hours: the hours of sunlight for the date. This is used to calculate daily values of GPP, NPP, and ER. * GPP_ER_Ratio: The ratio between GPP and ER which indicates if carbon sequestration occurs from primary production. ### Details for: Emergent\_macroinvertebrates\_dryad.csv * Dataset description: The dataset includes the lowest taxonomic identification and size of all emergent macroinvertebrates in the study. Variables * Date: Date with day, month, and year. Format is month/day/year where the year is 2019. * Channel: Channel number beginning at the upstream channel closest to Convict Creek as #1 and ending with the downstream channel farthest from Convict Creek being #9 * Treatment: The treatment of the channel as described above in methods * Order: The order of the organism * Family: The family of the organism * Subfamily: The subfamily of the organism * lowest: The lowest taxonomic identification possible for the organism, typically family, tribe, or genus. * Size_mm: The length of the organism measured from its head to the end of its abdomen. * Sex: The sex of the organism, when detectible. M = male, F = female ### Details for: BrewersBlackbird\_dryad.csv * Date: Date with day, month, and year. Format is month/day/year where the year is 2019. * Time: The time when the 30 minute observation period began. PM and AM are listed with hour and minute. * Channel: Channel number beginning at the upstream channel closest to Convict Creek as #1 and ending with the downstream channel farthest from Convict Creek being #9 * Riparian_time_s: The time in seconds that a bird was observed along the side of a channel. * Benthic_time_s: The time in seconds that a bird was observed within a channel in the channel bed. * Number_individuals: The total number of individual birds observed during the period. * Treatment: The treatment of the channel as described above in methods ## Code/Software Leathers_2024_PNAS_Code.R contains the code used to process, analyze, and plot data. Questions about the code can be addressed to Kyle Leathers - [kyle_leathers@berkeley.edu](mailto:kyle_leathers@berkeley.edu) ## Sharing/access Information Suggested Citation: Leathers, K., Herbst, D., de Mendoza, G., Doerschlag, G., Ruhi, A. (2024), Data for: Climate change is poised to alter mountain stream ecosystem processes via organismal phenological shifts, Dryad, Dataset, [https://doi.org/10.6078/D10712](https://doi.org/10.6078/D10712) Climate change is affecting the phenology of organisms and ecosystem processes across a wide range of environments. However, the mechanisms linking organismal to ecosystem process change in complex communities are uncertain. Here we examined how earlier snowmelt will alter the phenology of stream organisms and ecosystem processes, via a large-scale field experiment in outdoor stream channels. Extended low flows increased water temperature, reducing production-to-respiration ratios by 32%. The stream invertebrate community shifted due to phenological shifts in two-thirds of the taxa, and emergent flux pulses of the dominant insect group (Chironomidae) almost doubled, benefitting a generalist riparian predator. Our study shows that climate change in mountain streams is poised to alter the dynamics of stream food webs via fine-scale changes in phenology—leading to novel predator-prey ‘matches’ or 'mismatches’ even when community structure and ecosystem processes appear stable at the annual scale.

Time frame: Begin date 4/21/2019 - End date 8/25/2019. General study design- We subjected nine large-scale, flow-through outdoor stream mesocosms in California's Sierra Nevada to three flow regime treatments: a flow regime based on historic average conditions (current treatment), a mitigated climate change scenario where low flow begins three weeks earlier than currently (3-week treatment), and an unmitigated climate change scenario where low flow begins six weeks earlier than currently (6-week treatment). Over the course of a season, we regularly measured primary production; community composition, production, and emergence of benthic and emergent stream invertebrates; and Brewer's Blackbird (Euphagus cyanocephalus) feeding activity. We tested for immediate vs. delayed effects of advanced low flows by combining the period of the study (i.e., start, middle, and end) with the treatment, creating a variable that captures both timing and treatment effects (i.e., period-treatment). We ran a piecewise structural equation model to elucidate and compare mechanisms driving low-flow effects on stream invertebrate production and emergence. Methods description- We used nine channels that are 50 m long by 1 m wide, consist of six pools connected by long riffle sections in a meandering fashion, and are fed by the adjacent Convict Creek. We assigned each channel to one of three treatments (with three replicate channels each) in a block design. The three treatments were: (1) current hydrologic conditions based on the historic (long-term) hydrograph at Convict Creek (based on US Geological Survey gage 10265200), with a flow regime that reaches baseflow conditions around August 3rd (i.e., current treatment); (2) hydrologic conditions under a mitigated climate change scenario, where the stream would return to baseflow conditions three weeks earlier than it currently does (i.e., 3-week treatment); and (3) hydrologic conditions under unmitigated climate change, where the stream would return to baseflow six weeks earlier than it currently does (i.e., 6-week treatment). We regulated discharge by controlling sluice gates at the head of each channel. Flows in the channels differed by one order of magnitude between high-flow and low-flow conditions (i.e., 15 L/s and 1.5 L/s, respectively), following a typical Sierra Nevada stream hydrograph for a small stream. Channels were inspected and maintained daily, were heavily instrumented (see next section), and were monitored and sampled for several responses: primary production, secondary production, benthic and emerging stream invertebrates (composition and abundance), and visitation by riparian birds. The three periods we designated in the study are start (5/11/2019 - 6/10/2019), middle (6/11/2019 - 8/2/2019), and end (8/3/2019 - 8/21/2019). We measured water depth and water temperature every five minutes throughout the experiment (4/21/2019–8/25/2019) with replicated pressure transducers (HOBO U20L-04, Onset). We placed a pressure transducer in the fifth pool downstream in each channel and two emerged sensors on land to correct data for fluctuations in atmospheric pressure, and thus calculate water level (i.e., pool depth). Water level series were subsequently transformed into discharge series via channel-specific rating curves. Rating curves were developed for each channel by estimating discharge manually using channel depth and velocity measurements taken with a Marsh-McBirney Flo-Mate 2000 current meter throughout the summer (17-26 repeated estimates per channel). We measured water temperature using the same HOBO U20L-04 sensors that recorded data every five minutes in pools. We averaged discharge and water temperature to hourly values, which we then used to calculate daily metrics (e.g., daily mean, minimum, maximum, and diel range). We estimated epilithic biofilm primary production using the light/dark bottle method at each channel, once every three weeks. We calculated epilithic biofilm respiration (ER), net primary production (NPP), and the sum of their absolute values–gross primary production (GPP). We used three representative cobbles from the streambed for each sample and measured their surface area using aluminum foil to correct for differences in surface area. All primary production measurements were taken during peak sunlight hours between 10 am and 2 pm using two 90-minute incubation periods for light, followed by dark measurements. Benthic stream invertebrates were removed from rocks prior to incubation. We conducted three replicates for each channel at each sampling date (n = 162). Daily epilithic biofilm GPP per channel was estimated by multiplying the channel average hourly rate by the number of sunlight hours at each date (n = 54). We estimated daily epilithic biofilm ER per channel by multiplying the channel average hourly rate by 24 hours at each date (n = 54). Daily primary production was then estimated for the interval between each sampling date by averaging the bookend interval values. We multiplied the average interval value by the number of days in the interval and finally summed these values to generate cumulative seasonal channel estimates (n = 9). We sampled benthic stream invertebrates using a 500-micron Surber sampler at six visit dates three weeks apart throughout the experiment. Each sample was a composite of three subsamples (two riffles and one pool sample for 0.279 m^2 total) to represent the overall stream community. We took benthic samples for the current and 6-week treatment channels (n = 36) and stored them in 70% ethanol. We then subsampled the composite samples using a rotating-drum splitter in the laboratory to sort and identify at least 500 individuals from each composite sample under a stereomicroscope. All subsamples were completely processed to avoid bias regarding the size of individuals picked and identified. Benthic stream invertebrates were identified to the highest resolution possible, typically genus or species level, and all intact specimens were measured. Benthic stream invertebrate biomass was then estimated using published taxon-specific length-mass relationships. The subsampled community was multiplied by the inverse of the fraction of the total sample that was identified (e.g., if ¼ of the sample was identified to get a count over 500 individuals, then the abundance of each taxon was multiplied by 4). We assigned length values to these extrapolated individuals (and individuals that could be identified but not measured due to damage) using the length values from randomly selected individuals of the same taxon in the sample. We sampled emergent stream invertebrates using emergence traps, each deployed for 72 hours every three weeks during the experiment. We sampled emergence four additional times halfway between the three-week intervals for every sample visit after the second one when flows began to differ between treatments (n = 90 overall). We deployed emergence traps at the tail of riffles (to capture the influence of both riffle and pool habitat) next to HOBO sensors. We identified emergent insects to genus or family level (depending on taxa), and measured the length of intact specimens. Emergence traps were tent-shaped, covered 0.33 m2 of the stream, and had 2 mm white mesh. We noticed Brewer's Blackbirds (Euphagus cyanocephalus) feeding in channels at the onset of low flow in the 6-week treatment channels (June 22, 2019). We recorded the feeding behavior of Brewer's Blackbirds shortly thereafter by observing the time duration that any bird of this species occupied the benthos of the channels over a 30-minute period periodically throughout the remainder of the experiment. We observed all channels every few days initially but switched to weekly observations once Brewer's Blackbirds fledged and moved to meadow habitat. Laboratory, field, or other analytical methods- We estimated benthic stream invertebrate secondary production via a combination of three methods. We used the size-frequency method for taxa that were abundant throughout the experiment (i.e., >1% of total abundance) and had known generation times, excluding Chironomidae, Oligochaeta, Turbellaria, and Muscidae. For Chironomids, we used the instantaneous growth rate method. Production was calculated using regression equations for non-Tanypodinae chironomids, which incorporate mean temperature into growth estimates for small, medium, and large chironomids. Finally, we used the production-to-biomass ratio method (P/B) for the remaining taxa, including Tanypodinae, by multiplying seasonal biomass by known P/B ratios in the literature of the closest related taxa possible. Uncertainty in production from P/B ratios is unlikely to affect our results, as taxa in this group comprised <1% of the total assemblage production. We estimated emergent insect biomass using published, taxon-specific length-mass relationships. *Quality control- Data was recorded in hard copies and digitally to reduce the risk of mistyped data. Data was plotted visually for outliers that were erroneous and paper copies were referenced to ensure values were correct. Climate change is affecting the phenology of organisms and ecosystem processes across a wide range of environments. However, the mechanisms linking organismal to ecosystem process change in complex communities are uncertain. Here we examined how earlier snowmelt will alter the phenology of stream organisms and ecosystem processes, via a large-scale field experiment in outdoor stream channels. Extended low flows increased water temperature, reducing production-to-respiration ratios by 32%. The stream invertebrate community shifted due to phenological shifts in two-thirds of the taxa, and emergent flux pulses of the dominant insect group (Chironomidae) almost doubled, benefitting a generalist riparian predator. Our study shows that climate change in mountain streams is poised to alter the dynamics of stream food webs via fine-scale changes in phenology—leading to novel predator-prey 'matches' or 'mismatches' even when community structure and ecosystem processes appear stable at the annual scale. Funding provided by: Sequoia Parks Conservancy*Crossref Funder Registry ID: Award Number: Funding provided by: University of California SystemCrossref Funder Registry ID: https://ror.org/00pjdza24Award Number: Funding provided by: Margaret C. Walker Fund*Crossref Funder Registry ID: Award Number: Funding provided by: University of California, BerkeleyCrossref Funder Registry ID: https://ror.org/01an7q238Award Number: