DOI: 10.6078/d10712
title: Data for: Climate change is poised to alter mountain stream ecosystem processes via organismal phenological shifts

description: 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.
description: Time frame: Begin date 4/21/2019 - End date 8/25/2019.
 <strong>General study design</strong>- 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 (<em>Euphagus
 cyanocephalus</em>) 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. <strong>Methods
 description</strong>- 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
 (<em>Euphagus cyanocephalus</em>) 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.
 <strong>Laboratory, field, or other analytical
 methods</strong>- 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.,
 &gt;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 &lt;1% of the total
 assemblage production. We estimated emergent insect biomass using
 published, taxon-specific length-mass relationships.
 <strong>*Quality control</strong>- 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.
description: # 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)