ABSTRACT:

These data were collected in support of the sampling goals of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) Project. We sampled macroinvertebrates along a 100 m reach every 20 m alternating channel location from left, to center, to right for a total of six samples per reach. We compiled all six samples into a composite sample, removed debris and leaf matter via manual inspection of material and elutriation, and sieved the remaining sample through a 500 µm sieve. We then preserved the sample in 95% ethanol and returned it to the lab. In the lab, ethanol was refreshed before we froze the sample in a -20 ºC freezer. We shipped samples to a commercial lab (Jonah Ventures, Boulder, CO) for metabarcoding analysis of the invertebrate community. Briefly, Jonah Ventures homogenized community samples with a hand immersion blender and extracted DNA with a DNeasy Powersoil Kit following the manufacturer’s protocol. They then amplified samples using two primers from the CO1 gene (CO1 F230 fragment Hajibabaei et al. 2012; CO1 BE fragment Folmer et al. 1994, Gibson et al. 2015). They conducted PCRs with initial denaturation at 95 ºC for 5 min, followed by 40 cycles of 40s at 95 ºC, 1 min at 46 ºC, 30s at 72 ºC and a final elongation at 72 ºC for 10 min. They then cleaned samples using Exo1/SAP, and pooled, normalized and indexed. Samples were sent for sequencing at the CU Boulder BioFrontiers Sequencing Center where the Center used the v2 500-cycle kit with appropriate quality control measures. Jonah Ventures then demuliplexed sequenced samples using phigs v2.1.0 followed by removal of gene primers and merging read pairs. Read pairs were then clustered using unoise3 denoising algorithm in vsearch and with sequences with less than 8 reads discarded. Taxonomy was assigned using a custom best-hits algorithm with reference to NCBI Gen Bank to each Exact Sequence Variant (ESV) (See linked Jonah Venture documents for full methods).

JDR - Johnston Draw is a 1.8-km2 watershed in southwestern Idaho, USA (outlet location: 43.1226, -116.776) located within the Reynolds Creek Critical Zone Observatory in western Idaho, a research center with cattle grazing. Elevation ranges from approximately 1490m to 1850m. The mean annual precipitation in the watershed is 550 mm/yr with rainfall occurring at the lower elevations and snowfall, resulting in large drifts, at the higher elevations (Godsey et al., 2018). Mean annual temperatures range from 8.9C at the bottom of watershed and 4.7C near the top.
GBJ - Located near Pocatello, ID, Gibson Jack Creek (outlet location: 42.7853, -112.4446) drains 1620 ha of the US Forest Service Research Natural Area within the Caribou National Forest. Predominantly forested with deciduous trees, sub-apline fir, Douglas fir, and with woody shrubs, sagebrush, and grasses, Gibson Jack spans an elevation range of 1555-2130 m, and has an mean annual temperature and precipitation of 6.5°C and 614.5 mm/yr, respectively. Gibson Jack spans the rain to snow transition with rainfall occurring at the lower elevations and snowfall at the upper elevations. Gibson Jack Creek drains to the Portnuef River and is heavily recreated by the local community.
DRC - Con1W in Dry Creek Experimental Watershed (outlet location: 43.730136, -116.134807), run by Boise State University and located near Boise, ID, is predominantly forested by Ponderosa Pine and Douglas fir, with woody shrubs, sagebrush, and grasses. With elevations from 1295-1907 m, Con1W in Dry Creek spans the rain-snow transition with rainfall occurring at lower elevations and snowfall at the upper elevations in the semi-arid southwestern region of Idaho. Con1W in Dry Creek has mean annual temperatures of 8.3°C and mean annual precipitation at 648.8 mm/yr.

ABSTRACT:

These data were collected in support of the sampling goals of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) Project. We sampled macroinvertebrates along a 100 m reach every 20 m alternating channel location from left, to center, to right for a total of six samples per reach. We compiled all six samples into a composite sample, removed debris and leaf matter via manual inspection of material and elutriation, and sieved the remaining sample through a 500 µm sieve. We then preserved the sample in 95% ethanol and returned it to the lab. In the lab, ethanol was refreshed before we froze the sample in a -20 ºC freezer. We shipped samples to a commercial lab (Jonah Ventures, Boulder, CO) for metabarcoding analysis of the invertebrate community. Briefly, Jonah Ventures homogenized community samples with a hand immersion blender and extracted DNA with a DNeasy Powersoil Kit following the manufacturer’s protocol. They then amplified samples using two primers from the CO1 gene (CO1 F230 fragment Hajibabaei et al. 2012; CO1 BE fragment Folmer et al. 1994, Gibson et al. 2015). They conducted PCRs with initial denaturation at 95 ºC for 5 min, followed by 40 cycles of 40s at 95 ºC, 1 min at 46 ºC, 30s at 72 ºC and a final elongation at 72 ºC for 10 min. They then cleaned samples using Exo1/SAP, and pooled, normalized and indexed. Samples were sent for sequencing at the CU Boulder BioFrontiers Sequencing Center where the Center used the v2 500-cycle kit with appropriate quality control measures. Jonah Ventures then demuliplexed sequenced samples using phigs v2.1.0 followed by removal of gene primers and merging read pairs. Read pairs were then clustered using unoise3 denoising algorithm in vsearch and with sequences with less than 8 reads discarded. Taxonomy was assigned using a custom best-hits algorithm with reference to NCBI Gen Bank to each Exact Sequence Variant (ESV) (See linked Jonah Venture documents for full methods).

KNZ - This study was conducted on the South Fork of the Kings Creek research watershed (outlet location: 39.092281, -96.58719) within Konza Prairie Biological Station (KBPS) near Manhattan (KS, USA). At the USGS gage located on the mainstem (06879560; est. 1979), Kings Creek is a 5th order intermittent stream draining 1059-ha of tallgrass prairie that is actively managed using controlled buns at varying frequencies (1-20 year return intervals) and grazing by bison or cattle. Kings Creek ranges in elevation from 338 to 430 m above sea level and drains into the Kansas River. The region is within a midwestern continental climate, with temperatures ranging from 4 to 22°C and mean annual precipitation averaging about 780 mm/yr.

This site lies within the Flint Hills ecoregion of eastern KS and northeastern OK, has a mean annual temperature of 11.7ºC (1983-2020), and 811 mm annual precipitation (1983-2020) with high interannual variability and an estimated 75% of annual precipitation occurring during late spring and early summer (Hayden 1998, Sadayappan et al. 2023). The AIMS study catchment, the South Fork of Kings Creek, is grazed by bison year-round, and includes sub-catchments with variable prescribed burn history, but the entire study area was burned in early April 2021. The riparian vegetation is deciduous gallery forest and the highest portion of the landscape is tallgrass prairie (Dodds et al. 2004) dominated by warm-season grasses, though woody encroachment has occurred in most subwatersheds (Sadayappan et al. 2023)*. The underlying bedrock of the Flint Hills ecotone is characterized as limestone, mudstone, and shale with predominately silty clay loam soils that rest atop (Hayden 1998, Vero et al. 2018).

Dodds, W. K., et al. 2004. BioScience 54(3):205-216.
Hayden, B. P. 1998. Grassland dynamics: Long-term ecological research in tallgrass prairie. Oxford University Press, New York.
Vero, S., G. et al. 2018. Vadose Zone Journal 17(1):1-11.

YMR - Youngmeyer Ranch is located in Elk County, KS (outlet location: 37.56442, -96.49106) and managed by Witchita State University and owned by the Youngmeyer Trust. The ranch is roughly 1902 ha of grassland prairie used predominantly for cattle grazing and is burned every 1-2 years. A tributary of the Elk River, specifically the south branch of the Elk River headwaters, elevation at Youngmeyer ranges from 373-488 m with mean annual temperature of 13.7°C and mean annual precipitation of 979mm. This site is geologically constructed of Permian age limestone and shale with layers of chert below silty clay loam soils (Houseman et al. 2016). This site is predominantly grassland composed of the same dominant grasses as Konza Prairie, with scattered black oaks (Q. veluntina) along the creeks (Houseman et al. 2016).

Houseman, G. R., M. S. Kraushar, and C. M. Rogers. 2016. Transactions of the Kansas Academy of Science 119(1):27-32.

ABSTRACT:

Located near Pocatello, ID, Gibson Jack Creek (outlet location: 42.7853, -112.4446) drains 1620 ha of the US Forest Service Research Natural Area within the Caribou National Forest. Predominantly forested with deciduous trees, sub-apline fir, Douglas fir, and with woody shrubs, sagebrush, and grasses, Gibson Jack spans an elevation range of 1555-2130 m, and has an mean annual temperature and precipitation of 6.5°C and 614.5 mm/yr, respectively. Gibson Jack spans the rain to snow transition with rainfall occurring at the lower elevations and snowfall at the upper elevations. Gibson Jack Creek drains to the Portnuef River and is heavily recreated by the local community.

These data were collected in support of the sampling goals of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) Project. These sensors were set to collect temperature and conductivity data every 15 minutes. Each .csv file is associated with a single site for a single year.

Naming convention
Guide to interpreting file names using STIC_MW_GBJ_STIC65_HS_2024.csv as an example:
- "STIC_MW_GBJ_" = same for all sites, indicating it is STIC data from the Mountian West region and the Gibson Jack watershed.
- "STIC65" = site code, corresponding to the location of the STIC within the watershed
- "HS" = sublocation, corresponding to the placement of the STIC at that site. All data in this resource was collected from sensors with a "HS" sublocation, meaning the STIC was placed at a high spot in the stream thalweg, and a wet reading is interpreted as an indicator of flowing surface water connection within the stream network.
- "2024" = year of STIC data included in file.

Methodological details:
STIC sensors were deployed in 2021 following the methods described here: http://www.hydroshare.org/resource/c82a87a6c63445029d35131260241386
STIC sensors were calibrated following the methods described here: http://www.hydroshare.org/resource/9f2027c779d64149be32bdb9eede54f2
A detailed description of the processing and classification workflow is available in Zipper et al: https://eartharxiv.org/repository/view/4909/

Due to data logger errors, maintenance, etc. there are not data for all sites at all timesteps.

Further information for all data fields can be found in the "Data Types" tab of this ReadME. Sensors recorded relative conductivity (here, condUncal) and used in conjunction with multi-point lab calibration curves to calculate wetdry and SpC fields. The lowest point on the standard curve was water with an SpC of 0, which represented the lowest possible condUncal that would yield a "wet" value. This zero was used as a threshold, and wetdry was calculated such that anything below this threshold was "dry" (wetdry = 0) and anything above was "wet" (wetdry = 1). Additionally, the rest of the standard curve was used to build a relationship between condUncal and SpC, and this linear model was applied to the condUncal to calculate SpC.

The qual_rating flags are (Details in Zipper et al):
Excellent: STIC was (1) calibrated prior to deployment, and (2) stayed operational throughout 95% of the download period, and (3) was not displaced from streambed (i.e., the external electrodes were within 1 cm from stream bed at the time of download indicating minimal erosion/deposition), and (4) data from sensor roughly agree with field observations of wet/dry (i.e., >1000 Lux sensor reading on day of removal corresponds to field observations of water at STIC).
Good: (1) STIC stayed operational throughout the entire download period, and (2) the external electrodes were within 1 cm from stream bed at the time of download, and (3) data from sensor roughly agree with field observations of wet/dry, but (4) the STIC was not calibrated prior to deployment.
Fair: (1) STIC stayed operational throughout 75% or more of the download period, and (2) data roughly agree with field observations, and/or (3) the external electrodes were between 1-3 cm from streambed at the time of download.
Poor: (1) STIC stayed operational throughout less than 75% of the download period, and/or (2) the external electrodes were >3 cm from streambed at the time of download, and/or (3) data does NOT agree with field observations.
The QAQC flags are denoted as follows; if multiple flags were generated, they were concatenated:
NA : no flags, data passes checks
C : calibration curve yielded a negative value for SpC, changed to a value of 0 manually
O : SpC value is higher than the highest measured Calibration point, and is therefore off the calibration curve
D : wetdry reading flagged as a potential anomaly (i.e., short period of dry surrounded by long period of wet, calculated using a moving window z-score of condUncal values)
T : wetdry reading interpreted from temperature data

ABSTRACT:

Johnston Draw is a 1.8-km2 watershed in southwestern Idaho, USA (outlet location: 43.1226, -116.776) located within the Reynolds Creek Critical Zone Observatory in western Idaho, a research center with cattle grazing. Elevation ranges from approximately 1490m to 1850m. The mean annual precipitation in the watershed is 550 mm/yr with rainfall occurring at the lower elevations and snowfall, resulting in large drifts, at the higher elevations (Godsey et al., 2018). Mean annual temperatures range from 8.9C at the bottom of watershed and 4.7C near the top.

These data were collected in support of the sampling goals of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) Project. These sensors were set to collect temperature and conductivity data every 15 minutes. Each .csv file is associated with a single site for a single year.

Naming convention
Guide to interpreting file names using STIC_MW_JDR_JDR28_HS_.2023csv as an example:
- "STIC_MW_JDR_" = same for all sites, indicating it is STIC data from the Mountian West region and the Johnston Draw watershed.
- "JDR28" = site code, corresponding to the location of the STIC within the watershed
- "HS" = sublocation, corresponding to the placement of the STIC at that site. All data in this resource was collected from sensors with a "HS" sublocation, meaning the STIC was placed at a high spot in the stream thalweg, and a wet reading is interpreted as an indicator of flowing surface water connection within the stream network.
- "2023" = year of STIC data included in file.

Methodological details:
STIC sensors were deployed in 2021 following the methods described here: http://www.hydroshare.org/resource/c82a87a6c63445029d35131260241386
STIC sensors were calibrated following the methods described here: http://www.hydroshare.org/resource/9f2027c779d64149be32bdb9eede54f2
A detailed description of the processing and classification workflow is available in Zipper et al: https://eartharxiv.org/repository/view/4909/

Due to data logger errors, maintenance, etc. there are not data for all sites at all timesteps.

Further information for all data fields can be found in the "Data Types" tab of this ReadME. Sensors recorded relative conductivity (here, condUncal) and used in conjunction with multi-point lab calibration curves to calculate wetdry and SpC fields. The lowest point on the standard curve was water with an SpC of 0, which represented the lowest possible condUncal that would yield a "wet" value. This zero was used as a threshold, and wetdry was calculated such that anything below this threshold was "dry" (wetdry = 0) and anything above was "wet" (wetdry = 1). Additionally, the rest of the standard curve was used to build a relationship between condUncal and SpC, and this linear model was applied to the condUncal to calculate SpC.

The qual_rating flags are (Details in Zipper et al):
Excellent: STIC was (1) calibrated prior to deployment, and (2) stayed operational throughout 95% of the download period, and (3) was not displaced from streambed (i.e., the external electrodes were within 1 cm from stream bed at the time of download indicating minimal erosion/deposition), and (4) data from sensor roughly agree with field observations of wet/dry (i.e., >1000 Lux sensor reading on day of removal corresponds to field observations of water at STIC).
Good: (1) STIC stayed operational throughout the entire download period, and (2) the external electrodes were within 1 cm from stream bed at the time of download, and (3) data from sensor roughly agree with field observations of wet/dry, but (4) the STIC was not calibrated prior to deployment.
Fair: (1) STIC stayed operational throughout 75% or more of the download period, and (2) data roughly agree with field observations, and/or (3) the external electrodes were between 1-3 cm from streambed at the time of download.
Poor: (1) STIC stayed operational throughout less than 75% of the download period, and/or (2) the external electrodes were >3 cm from streambed at the time of download, and/or (3) data does NOT agree with field observations.
The QAQC flags are denoted as follows; if multiple flags were generated, they were concatenated:
NA : no flags, data passes checks
C : calibration curve yielded a negative value for SpC, changed to a value of 0 manually
O : SpC value is higher than the highest measured Calibration point, and is therefore off the calibration curve
D : wetdry reading flagged as a potential anomaly (i.e., short period of dry surrounded by long period of wet, calculated using a moving window z-score of condUncal values)
T : wetdry reading interpreted from temperature data