Chelsea Smith
The University of Alabama
| Subject Areas: | Aquatic Ecology |
Recent Activity
ABSTRACT:
This study was conducted in the Shambley Creek research watershed (outlet location: 32.98410915, -88.01334337) on privately owned property in Greene County (AL, USA). The watershed drains a non-perennial unnamed tributary to Shambley Creek, and contains 0.70 km^2 of coniferous forest managed for silviculture in the East Gulf Coastal Plain physiographic section. Located near Eutaw, AL, the watershed spans an elevation range from 63 to 94 m above sea level, and is a tributary to the Sipsey River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 7.3°C and 27.4°C respectively, and mean annual precipitation of 1,350 mm/yr.
Samples were filtered with a 0.45um PES filter and frozen until analysis. Aqueous concentrations of anions were determined using an IC-3000 IC system (Dionex, Sunnyvale, CA) equipped with Dionex AERS 500 suppressor (2 mm, Thermo Scientific) and Dionex AS auto-sampler (Thermo Scientific). A Dionex IonPac AS15 column (2 mm × 50 mm, Thermo Scientific) with a guard column Dionex IonPac AG15 (2 mm × 50 mm, Thermo Scientific) was used to separate anions using a mobile phase of 38 mM KOH and a flow rate of 0.3 mL/min. The column temperature is 30 °C. Chromeleon software 7.1 is used for system control. Final data tab shows average of triplicates collected in the field and st dev of triplicates. Any NO3 values below 0.01 mg/L are below the lowest standard used in lab analysis and should be interpreted with caution.
The final data tab includes QA/QC’d averaged data for fluoride, chloride, nitrite, bromide, nitrate, phosphate, and sulfate in ppm with standard deviations. If the sample is below detection (BD), it is denoted as that and highlighted pink. Average NAs indicate analytes were not run or that samples were missing. NA’s in the standard deviations columns could indicate that those samples were not run or that only replicate was able to be analyzed.
ABSTRACT:
This study was conducted in the Talladega research watershed (outlet location: 33.76219799, -85.59550775) in the Talladega National Forest (Cleburne County, AL, USA). The watershed drains a non-perennial unnamed tributary of Pendergrass Creek, and contains 0.92 km^2 of mixed coniferous and deciduous forest in the Piedmont Upland physiographic section. Located near Anniston, AL, the watershed spans an elevation range from 345 to 456 m above sea level and is a tributary to the Coosa River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 5.3°C and 25.3°C respectively, and mean annual precipitation of 1,400 mm/yr.
Samples were filtered with a 0.45um PES filter and frozen until analysis. Aqueous concentrations of anions were determined using an IC-3000 IC system (Dionex, Sunnyvale, CA) equipped with Dionex AERS 500 suppressor (2 mm, Thermo Scientific) and Dionex AS auto-sampler (Thermo Scientific). A Dionex IonPac AS15 column (2 mm × 50 mm, Thermo Scientific) with a guard column Dionex IonPac AG15 (2 mm × 50 mm, Thermo Scientific) was used to separate anions using a mobile phase of 38 mM KOH and a flow rate of 0.3 mL/min. The column temperature is 30 °C. Chromeleon software 7.1 is used for system control. Final data tab shows average of triplicates collected
The final data tab includes QA/QC’d averaged data for fluoride, chloride, nitrite, bromide, nitrate, phosphate, and sulfate in ppm with standard deviations. If the sample is below detection (BD), it is denoted as that and highlighted pink. Average NAs indicate analytes were not run or that samples were missing. NA’s in the standard deviations columns could indicate that those samples were not run or that only replicate was able to be analyzed.
ABSTRACT:
This study was conducted in the Paint Rock research watershed (outlet location: 34.96861724, -86.16501705) on privately owned property in Jackson County (AL, USA). The watershed drains a non-perennial unnamed tributary to Burks Creek, and contains 2.97 km^2 of deciduous forest in the Cumberland Plateau physiographic section. Located near Estillfork, AL, the watershed spans an elevation range from 211 to 550 m above sea level, and is a tributary to the Paint Rock River (within the larger Tennessee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 4.4°C and 25.4°C respectively, and mean annual precipitation of 1,390 mm/yr.
Samples were filtered with a 0.45um PES filter and frozen until analysis. Aqueous concentrations of anions were determined using an IC-3000 IC system (Dionex, Sunnyvale, CA) equipped with Dionex AERS 500 suppressor (2 mm, Thermo Scientific) and Dionex AS auto-sampler (Thermo Scientific). A Dionex IonPac AS15 column (2 mm × 50 mm, Thermo Scientific) with a guard column Dionex IonPac AG15 (2 mm × 50 mm, Thermo Scientific) was used to separate anions using a mobile phase of 38 mM KOH and a flow rate of 0.3 mL/min. The column temperature is 30 °C. Chromeleon software 7.1 is used for system control. Final data tab shows average of triplicates collected in the field and st dev of triplicates. Any NO3 values below 0.01 mg/L are below the lowest standard used in lab analysis and should be interpreted with caution.
ABSTRACT:
These data were collected in support of the sampling goals of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) Project. This study took place in Shane’s Creek (434 ha) at the Konza Prairie Biological Station, a long term ecological research station that has been in operation since 1980. Shane’s Creek is annually cattle-grazed and burned every three years. Konza is located in the Flint Hills of northern Kansas. In 2023, the outlet of the stream wet up in March and dried down in July; in 2024, the outlet of the stream wet up in March and dried down in September. Average annual precipitation for this site is 35.62 inches.
We constructed a wooden stream diversion structure halfway down a 380m reach containing four pools and three riffles above and below the structure. The structure had 4 1-foot diameter holes installed with PVC couplers. Four 130m corrugated flexible tubes were laid out from the diversion structure to the bottom of the impact reach. We deployed 20 STICs throughout the control and impact reach to quantify the extent of drying using rebar. Construction and preparation occurred in February and March, when the stream was dry, to minimize construction-related disturbances to the experimental sampling. Prior to experimental dry down, water was able to flow from upstream (control reach) to downstream (impact reach) through the holes. We obtained pre-dry down sampling to collect a reference point for both the control and impact reaches. These “pre-dry week X” samples were collected from April to mid-July due to multiple flooding events (April 25th, June 26th, and July 3rd) that disrupted the experimental setup and required redeployment of experimental structures and equipment. During the experimental dry down (“dry week X” samples), we attached the tubes to the couplers in the diversion structure. Flow was diverted around the impact reach into the downstream watershed for five weeks, during which we collected weekly samples. Following the final forced drying sampling, tubes were cut from their couplers to allow flow to resume in the impact reach (“re-wet week X” samples). After 6 hours, we performed day 0 re-wet sampling. Twenty four hours later, we performed day 1 re-wet sampling. One week later, the stream began to naturally dry down in both the control and impact reaches, and collected weekly natural dry down samples for two weeks (“natural dry down week X” samples).
We collected triplicate water samples for soluble reactive phosphorus (SRP; µg/L) and ammonia (NH4-N, µg/L) on each sampling occasion with a subset of samples also analyzed for nitrate/nitrite (NO3-N, NO2-N, µg/L). We collected samples at the specified location when water was present using a syringe in a well-mixed area of the stream. We then filtered water through sterile PVDF 0.45 µm syringe filters (VWR) into clean bottles following the AIMS Surface Water Chemistry SOP (Burgin 2024). For all analytes, we froze samples until analysis in the lab using colorimetric methods on an AQ300 Discrete Analyzer (SEAL Analytical, Mequon, Wisconsin, USA). We prepared and applied reagents to samples and standards of known concentrations. For SRP, reagents react to form a blue complex, the absorbance of which is measured at 880nm. Known standards were used to create calibration curves ranging from 0 μg/L to 75 μg/L with check standards run every 10. Detection limits were set at 6 μg/L. We used the phenol method for NH4-N with known standards used to create calibration curves ranging from 0 μg/L to 500 μg/L and check standards run every 10 samples. Detection limits were set at 11 μg/L. To determine NOx-N, we analyzed samples with and without cadmium reduction with known standards used to create calibration curves ranging from 0 µg/L to 1000 µg/L for NOx-N and 0 µg/L to 750 µg/L for NO2-N with detection limits set at 20 µg/L NO3-N. Differences between NOx-N and NO2-N were used to calculate NO3-N. Triplicates were inspected for outliers with mean and standard deviation reported in data.
ABSTRACT:
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 generally used a surber sampler, though if water was too deep, a D-net was used to scrub a similar area (0.09 m2) or when channels became too constrained a mini surber was employed (0.02 m2). 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). Additional habitat data can be found on HydroShare.
TAL- This study was conducted in the Talladega research watershed (outlet location: 33.76219799, -85.59550775) in the Talladega National Forest (Cleburne County, AL, USA). The watershed drains a non-perennial unnamed tributary of Pendergrass Creek, and contains 0.92 km^2 of mixed coniferous and deciduous forest in the Piedmont Upland physiographic section. Located near Anniston, AL, the watershed spans an elevation range from 345 to 456 m above sea level and is a tributary to the Coosa River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 5.3°C and 25.3°C respectively, and mean annual precipitation of 1,400 mm/yr.
WHR-This study was conducted in the Shambley Creek research watershed (outlet location: 32.98410915, -88.01334337) on privately owned property in Greene County (AL, USA). The watershed drains a non-perennial unnamed tributary to Shambley Creek, and contains 0.70 km^2 of coniferous forest managed for silviculture in the East Gulf Coastal Plain physiographic section. Located near Eutaw, AL, the watershed spans an elevation range from 63 to 94 m above sea level, and is a tributary to the Sipsey River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 7.3°C and 27.4°C respectively, and mean annual precipitation of 1,350 mm/yr.
PRF-This study was conducted in the Paint Rock research watershed (outlet location: 34.96861724, -86.16501705) on privately owned property in Jackson County (AL, USA). The watershed drains a non-perennial unnamed tributary to Burks Creek, and contains 2.97 km^2 of deciduous forest in the Cumberland Plateau physiographic section. Located near Estillfork, AL, the watershed spans an elevation range from 211 to 550 m above sea level, and is a tributary to the Paint Rock River (within the larger Tennessee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 4.4°C and 25.4°C respectively, and mean annual precipitation of 1,390 mm/yr.
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Created: April 15, 2025, 11:45 p.m.
Authors: Smith, Chelsea · Carla L. Atkinson · Speir, Shannon · Wolford, Michelle · Taylor Layman · Plont, Stephen
ABSTRACT:
This study was conducted in the Talladega research watershed (outlet location: 33.76219799, -85.59550775) in the Talladega National Forest (Cleburne County, AL, USA) as part of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) project, an NSF EPSCoR funded project (OIA 2019603). The project sought to explore the impacts of stream drying on downstream water quality across Kansas, Oklahoma, Alabama, and Idaho, integrating datasets on hydrology, microbiomes, macroinvertebrates, and biogeochemistry. The Talladega watershed drains a non-perennial unnamed tributary of Pendergrass Creek and contains 0.92 km2 of mixed coniferous and deciduous forest in the Piedmont Upland physiographic section. Located near Anniston, AL, the watershed spans an elevation range from 345 to 456 m above sea level and is a tributary to the Coosa River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 5.3°C and 25.3°C respectively, and mean annual precipitation of 1,400 mm/yr.
We collected samples every ~3 weeks from October 7, 2021, to October 3, 2024, at the outlet of our watershed (TLM01, approach 1), seasonally at seven distributed sites (approach 2) and across 39 spatially distributed sites on June 9, 2022- June 10, 2022 (approach 3). We collected triplicate water samples for soluble reactive phosphorus (SRP; µg/L) and ammonia (NH4-N, µg/L) on each sampling occasion with a subset of samples also analyzed for nitrate/nitrite (NO3-N, NO2-N, µg/L). We collected samples at the specified location when water was present using a syringe in a well-mixed area of the stream. We then filtered water through sterile PVDF 0.45 µm syringe filters (VWR) into clean bottles following the AIMS Surface Water Chemistry SOP (Burgin 2024). For all analytes, we froze samples until analysis in the lab using colorimetric methods (APHA 2017) on an AQ300 Discrete Analyzer (SEAL Analytical, Mequon, Wisconsin, USA). We prepared and applied reagents to samples and standards of known concentrations. For SRP, reagents react to form a blue complex, the absorbance of which is measured at 880nm. Known standards were used to create calibration curves ranging from 0 μg/L to 75 μg/L with check standards run every 10. Detection limits were set at 6 μg/L. We used the phenol method for NH4-N with known standards used to create calibration curves ranging from 0 μg/L to 500 μg/L and check standards run every 10 samples. Detection limits were set at 11 μg/L. To determine NOx-N, we analyzed samples with and without cadmium reduction with known standards used to create calibration curves ranging from 0 µg/L to 1000 µg/L for NOx-N and 0 µg/L to 750 µg/L for NO2-N with detection limits set at 20 µg/L NO3-N. Differences between NOx-N and NO2-N were used to calculate NO3-N. Triplicates were inspected for outliers with mean and standard deviation reported in data.
Created: April 16, 2025, 12:21 a.m.
Authors: Smith, Chelsea · Carla L. Atkinson · Plont, Stephen · Wolford, Michelle · Speir, Shannon · Taylor Layman
ABSTRACT:
This study was conducted in the Shambley Creek research watershed (outlet location: 32.98410915, -88.01334337) on privately owned property in Greene County (AL, USA) as part of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) project, an NSF EPSCoR funded project (OIA 2019603). The project sought to explore the impacts of stream drying on downstream water quality across Kansas, Oklahoma, Alabama, and Idaho, integrating datasets on hydrology, microbiomes, macroinvertebrates, and biogeochemistry. The watershed drains a non-perennial unnamed tributary to Shambley Creek and contains 0.70 km2 of coniferous forest managed for silviculture in the East Gulf Coastal Plain physiographic section. Located near Eutaw, AL, the watershed spans an elevation range from 63 to 94 m above sea level and is a tributary to the Sipsey River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 7.3°C and 27.4°C respectively, and mean annual precipitation of 1,350 mm/yr.
We collected samples every ~3 weeks from October 14, 2021, to October 1, 2024, at the outlet of our watershed (WHM01, approach 1) and seasonally at seven distributed sites (approach 2). We collected triplicate water samples for soluble reactive phosphorus (SRP; µg/L) and ammonia (NH4-N, µg/L) on each sampling occasion with a subset of samples also analyzed for nitrate/nitrite (NO3-N, NO2-N, µg/L). We collected samples at the specified location when water was present using a syringe in a well-mixed area of the stream. We then filtered water through sterile PVDF 0.45 µm syringe filters (VWR) into clean bottles following the AIMS Surface Water Chemistry SOP (Burgin 2024). For all analytes, we froze samples until analysis in the lab using colorimetric methods (APHA 2017) on an AQ300 Discrete Analyzer (SEAL Analytical, Mequon, Wisconsin, USA). We prepared and applied reagents to samples and standards of known concentrations. For SRP, reagents react to form a blue complex, the absorbance of which is measured at 880nm. Known standards were used to create calibration curves ranging from 0 μg/L to 75 μg/L with check standards run every 10. Detection limits were set at 6 μg/L. We used the phenol method for NH4-N with known standards used to create calibration curves ranging from 0 μg/L to 500 μg/L and check standards run every 10 samples. Detection limits were set at 11 μg/L. To determine NOx-N, we analyzed samples with and without cadmium reduction with known standards used to create calibration curves ranging from 0 µg/L to 1000 µg/L for NOx-N and 0 µg/L to 750 µg/L for NO2-N with detection limits set at 20 µg/L NO3-N. Differences between NOx-N and NO2-N were used to calculate NO3-N. Triplicates were inspected for outliers with mean and standard deviation reported in data.
Created: April 16, 2025, 12:59 a.m.
Authors: Smith, Chelsea · Carla L. Atkinson · Plont, Stephen · Wolford, Michelle · Speir, Shannon · Taylor Layman · Claudia Dorantes
ABSTRACT:
This study was conducted in the Paint Rock research watershed (outlet location: 34.96861724, -86.16501705) on privately owned property in Jackson County (AL, USA) as part of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) project, an NSF EPSCoR funded project (OIA 2019603). The project sought to explore the impacts of stream drying on downstream water quality across Kansas, Oklahoma, Alabama, and Idaho, integrating datasets on hydrology, microbiomes, macroinvertebrates, and biogeochemistry. The watershed drains a non-perennial unnamed tributary to Burks Creek and contains 2.97 km2 of deciduous forest in the Cumberland Plateau physiographic section. Located near Estillfork, AL, the watershed spans an elevation range from 211 to 550 m above sea level and is a tributary to the Paint Rock River (within the larger Tennessee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 4.4°C and 25.4°C respectively, and mean annual precipitation of 1,390 mm/yr.
We collected samples every ~3 weeks from October 13, 2021, to October 1, 2024, at the outlet of our watershed (PRM01, approach 1) and seasonally at seven distributed sites (approach 2). We collected triplicate water samples for soluble reactive phosphorus (SRP; µg/L) and ammonia (NH4-N, µg/L) on each sampling occasion with a subset of samples also analyzed for nitrate/nitrite (NO3-N, NO2-N, µg/L). We collected samples at the specified location when water was present using a syringe in a well-mixed area of the stream . We then filtered water through sterile PVDF 0.45 µm syringe filters (VWR) into clean bottles following the AIMS Surface Water Chemistry SOP (Burgin 2024). For all analytes, we froze samples until analysis in the lab using colorimetric methods (APHA 2017) on an AQ300 Discrete Analyzer (SEAL Analytical, Mequon, Wisconsin, USA). We prepared and applied reagents to samples and standards of known concentrations. For SRP, reagents react to form a blue complex, the absorbance of which is measured at 880nm. Known standards were used to create calibration curves ranging from 0 μg/L to 75 μg/L with check standards run every 10. Detection limits were set at 6 μg/L. We used the phenol method for NH4-N with known standards used to create calibration curves ranging from 0 μg/L to 500 μg/L and check standards run every 10 samples. Detection limits were set at 11 μg/L. To determine NOx-N, we analyzed samples with and without cadmium reduction with known standards used to create calibration curves ranging from 0 µg/L to 1000 µg/L for NOx-N and 0 µg/L to 750 µg/L for NO2-N with detection limits set at 20 µg/L NO3-N. Differences between NOx-N and NO2-N were used to calculate NO3-N. Triplicates were inspected for outliers with mean and standard deviation reported in data.
Created: June 12, 2025, 5:21 p.m.
Authors: Smith, Chelsea · Carla Atkinson · Daniel Allen
ABSTRACT:
This study was conducted in the Talladega research watershed (outlet location: 33.76219799, -85.59550775) in the Talladega National Forest (Cleburne County, AL, USA) as part of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) project, an NSF EPSCoR funded project (OIA 2019603). The project sought to explore the impacts of stream drying on downstream water quality across Kansas, Oklahoma, Alabama, and Idaho, integrating datasets on hydrology, microbiomes, macroinvertebrates, and biogeochemistry. The Talladega watershed drains a non-perennial unnamed tributary of Pendergrass Creek and contains 0.92 km2 of mixed coniferous and deciduous forest in the Piedmont Upland physiographic section. Located near Anniston, AL, the watershed spans an elevation range from 345 to 456 m above sea level and is a tributary to the Coosa River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 5.3°C and 25.3°C respectively, and mean annual precipitation of 1,400 mm/yr.
We collected samples every ~3 weeks from November 27, 2021, to January 31, 2023, at the outlet of our watershed (TLM01, approach 1). This data resource characterizes non-perennial stream sites and other metadata for macroinvertebrate samples collected as part of the NSF-funded project AIMS (Aquatic Intermittency Effects on Microbiomes in Streams), including Approach 1 (maintenance sampling'), Approach 2 ('seasonal sampling') across 7 distributed sites and Approach 3 (spatiialy intense synoptic across 28 sites). Characterization of sampling sites follow the AIMS Macroinvertebrate Field Sampling SOP (Allen & Busch, 2024). Briefly, 100 m transects were marked, with AIMS STIC centers at 50m. Samples were collected at 0, 20, 40, 60, 80, and 100 m and compiled into a single macroinvertebrate sample. Field data was collected at each transect depending on whether the sampling crew observed surface water in the stream channel at the time of sampling ('WetDry'), a visual estimation of benthic sediment and algae cover percentage, percent canopy cover (estimated via densiometer), the wetted width of the stream at each sampling location where possible, and if the full 100m reach was connected and flowing. Some measurements are missing from sites due to logistical/human errors, and are recorded as NAs. Wetted width could only be collected when surface water was present, so NAs associated with dry sites are flagged ('WW_flag' variable) for convenience. In addition, substrate estimates, canopy cover, habitat classifcation, habitat isolation, and depth were not recorded for dry sites.
Created: June 12, 2025, 5:27 p.m.
Authors: Smith, Chelsea · Carla Atkinson · Daniel Allen
ABSTRACT:
This study was conducted in the Shambley Creek research watershed (outlet location: 32.98410915, -88.01334337) on privately owned property in Greene County (AL, USA) as part of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) project, an NSF EPSCoR funded project (OIA 2019603). The project sought to explore the impacts of stream drying on downstream water quality across Kansas, Oklahoma, Alabama, and Idaho, integrating datasets on hydrology, microbiomes, macroinvertebrates, and biogeochemistry. The watershed drains a non-perennial unnamed tributary to Shambley Creek and contains 0.70 km2 of coniferous forest managed for silviculture in the East Gulf Coastal Plain physiographic section. Located near Eutaw, AL, the watershed spans an elevation range from 63 to 94 m above sea level and is a tributary to the Sipsey River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 7.3°C and 27.4°C respectively, and mean annual precipitation of 1,350 mm/yr.
We collected samples every ~3 weeks from November 4, 2021, to JFebruary 9, 2023, at the outlet of our watershed (WHM01, approach 1). This data resource characterizes non-perennial stream sites and other metadata for macroinvertebrate samples collected as part of the NSF-funded project AIMS (Aquatic Intermittency Effects on Microbiomes in Streams), including Approach 1 (maintenance sampling') and Approach 2 ('seasonal sampling') across 7 distributed sites. Characterization of sampling sites follow the AIMS Macroinvertebrate Field Sampling SOP (Allen & Busch, 2024). Briefly, 100 m transects were marked, with AIMS STIC centers at 50m. Samples were collected at 0, 20, 40, 60, 80, and 100 m and compiled into a single macroinvertebrate sample. Field data was collected at each transect depending on whether the sampling crew observed surface water in the stream channel at the time of sampling ('WetDry'), a visual estimation of benthic sediment and algae cover percentage, percent canopy cover (estimated via densiometer), the wetted width of the stream at each sampling location where possible, and if the full 100m reach was connected and flowing. Some measurements are missing from sites due to logistical/human errors, and are recorded as NAs. Wetted width could only be collected when surface water was present, so NAs associated with dry sites are flagged ('WW_flag' variable) for convenience. In addition, substrate estimates, canopy cover, habitat classifcation, habitat isolation, and depth were not recorded for dry sites.
Created: June 12, 2025, 5:32 p.m.
Authors: Smith, Chelsea · Carla Atkinson · Daniel Allen
ABSTRACT:
This study was conducted in the Paint Rock research watershed (outlet location: 34.96861724, -86.16501705) on privately owned property in Jackson County (AL, USA) as part of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) project, an NSF EPSCoR funded project (OIA 2019603). The project sought to explore the impacts of stream drying on downstream water quality across Kansas, Oklahoma, Alabama, and Idaho, integrating datasets on hydrology, microbiomes, macroinvertebrates, and biogeochemistry. The watershed drains a non-perennial unnamed tributary to Burks Creek and contains 2.97 km2 of deciduous forest in the Cumberland Plateau physiographic section. Located near Estillfork, AL, the watershed spans an elevation range from 211 to 550 m above sea level and is a tributary to the Paint Rock River (within the larger Tennessee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 4.4°C and 25.4°C respectively, and mean annual precipitation of 1,390 mm/yr.
We collected samples every ~3 weeks from November 3, 2021, to January 11, 2023, at the outlet of our watershed (PRM01, approach 1). This data resource characterizes non-perennial stream sites and other metadata for macroinvertebrate samples collected as part of the NSF-funded project AIMS (Aquatic Intermittency Effects on Microbiomes in Streams), including Approach 1 (maintenance sampling'). Characterization of sampling sites follow the AIMS Macroinvertebrate Field Sampling SOP (Allen & Busch, 2024). Briefly, 100 m transects were marked, with AIMS STIC centers at 50m. Samples were collected at 0, 20, 40, 60, 80, and 100 m and compiled into a single macroinvertebrate sample. Field data was collected at each transect depending on whether the sampling crew observed surface water in the stream channel at the time of sampling ('WetDry'), a visual estimation of benthic sediment and algae cover percentage, percent canopy cover (estimated via densiometer), the wetted width of the stream at each sampling location where possible, and if the full 100m reach was connected and flowing. Some measurements are missing from sites due to logistical/human errors, and are recorded as NAs. Wetted width could only be collected when surface water was present, so NAs associated with dry sites are flagged ('WW_flag' variable) for convenience. In addition, substrate estimates, canopy cover, habitat classification, habitat isolation, and depth were not recorded for dry sites. For a periods of sampling, four equally spaced water depths were collected across the transect.
Created: July 2, 2025, 8:32 p.m.
Authors: Smith, Chelsea · Daniel Allen · Carla Atksinson
ABSTRACT:
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 generally used a surber sampler, though if water was too deep, a D-net was used to scrub a similar area (0.09 m2) or when channels became too constrained a mini surber was employed (0.02 m2). 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). Additional habitat data can be found on HydroShare.
TAL- This study was conducted in the Talladega research watershed (outlet location: 33.76219799, -85.59550775) in the Talladega National Forest (Cleburne County, AL, USA). The watershed drains a non-perennial unnamed tributary of Pendergrass Creek, and contains 0.92 km^2 of mixed coniferous and deciduous forest in the Piedmont Upland physiographic section. Located near Anniston, AL, the watershed spans an elevation range from 345 to 456 m above sea level and is a tributary to the Coosa River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 5.3°C and 25.3°C respectively, and mean annual precipitation of 1,400 mm/yr.
WHR-This study was conducted in the Shambley Creek research watershed (outlet location: 32.98410915, -88.01334337) on privately owned property in Greene County (AL, USA). The watershed drains a non-perennial unnamed tributary to Shambley Creek, and contains 0.70 km^2 of coniferous forest managed for silviculture in the East Gulf Coastal Plain physiographic section. Located near Eutaw, AL, the watershed spans an elevation range from 63 to 94 m above sea level, and is a tributary to the Sipsey River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 7.3°C and 27.4°C respectively, and mean annual precipitation of 1,350 mm/yr.
PRF-This study was conducted in the Paint Rock research watershed (outlet location: 34.96861724, -86.16501705) on privately owned property in Jackson County (AL, USA). The watershed drains a non-perennial unnamed tributary to Burks Creek, and contains 2.97 km^2 of deciduous forest in the Cumberland Plateau physiographic section. Located near Estillfork, AL, the watershed spans an elevation range from 211 to 550 m above sea level, and is a tributary to the Paint Rock River (within the larger Tennessee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 4.4°C and 25.4°C respectively, and mean annual precipitation of 1,390 mm/yr.
Created: July 3, 2025, 3:05 p.m.
Authors: Smith, Chelsea · Busch, Michelle · Flynn, Sarah · Brown, Connor L. · Burgin, Amy · Carla Atksinson · Talylor Layman · Claudia Dorantes · Utzman, Claire · Sommerville, Alexi · Wilhelm, Jessica
ABSTRACT:
These data were collected in support of the sampling goals of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) Project. This study took place in Shane’s Creek (434 ha) at the Konza Prairie Biological Station, a long term ecological research station that has been in operation since 1980. Shane’s Creek is annually cattle-grazed and burned every three years. Konza is located in the Flint Hills of northern Kansas. In 2023, the outlet of the stream wet up in March and dried down in July; in 2024, the outlet of the stream wet up in March and dried down in September. Average annual precipitation for this site is 35.62 inches.
We constructed a wooden stream diversion structure halfway down a 380m reach containing four pools and three riffles above and below the structure. The structure had 4 1-foot diameter holes installed with PVC couplers. Four 130m corrugated flexible tubes were laid out from the diversion structure to the bottom of the impact reach. We deployed 20 STICs throughout the control and impact reach to quantify the extent of drying using rebar. Construction and preparation occurred in February and March, when the stream was dry, to minimize construction-related disturbances to the experimental sampling. Prior to experimental dry down, water was able to flow from upstream (control reach) to downstream (impact reach) through the holes. We obtained pre-dry down sampling to collect a reference point for both the control and impact reaches. These “pre-dry week X” samples were collected from April to mid-July due to multiple flooding events (April 25th, June 26th, and July 3rd) that disrupted the experimental setup and required redeployment of experimental structures and equipment. During the experimental dry down (“dry week X” samples), we attached the tubes to the couplers in the diversion structure. Flow was diverted around the impact reach into the downstream watershed for five weeks, during which we collected weekly samples. Following the final forced drying sampling, tubes were cut from their couplers to allow flow to resume in the impact reach (“re-wet week X” samples). After 6 hours, we performed day 0 re-wet sampling. Twenty four hours later, we performed day 1 re-wet sampling. One week later, the stream began to naturally dry down in both the control and impact reaches, and collected weekly natural dry down samples for two weeks (“natural dry down week X” samples).
We collected triplicate water samples for soluble reactive phosphorus (SRP; µg/L) and ammonia (NH4-N, µg/L) on each sampling occasion with a subset of samples also analyzed for nitrate/nitrite (NO3-N, NO2-N, µg/L). We collected samples at the specified location when water was present using a syringe in a well-mixed area of the stream. We then filtered water through sterile PVDF 0.45 µm syringe filters (VWR) into clean bottles following the AIMS Surface Water Chemistry SOP (Burgin 2024). For all analytes, we froze samples until analysis in the lab using colorimetric methods on an AQ300 Discrete Analyzer (SEAL Analytical, Mequon, Wisconsin, USA). We prepared and applied reagents to samples and standards of known concentrations. For SRP, reagents react to form a blue complex, the absorbance of which is measured at 880nm. Known standards were used to create calibration curves ranging from 0 μg/L to 75 μg/L with check standards run every 10. Detection limits were set at 6 μg/L. We used the phenol method for NH4-N with known standards used to create calibration curves ranging from 0 μg/L to 500 μg/L and check standards run every 10 samples. Detection limits were set at 11 μg/L. To determine NOx-N, we analyzed samples with and without cadmium reduction with known standards used to create calibration curves ranging from 0 µg/L to 1000 µg/L for NOx-N and 0 µg/L to 750 µg/L for NO2-N with detection limits set at 20 µg/L NO3-N. Differences between NOx-N and NO2-N were used to calculate NO3-N. Triplicates were inspected for outliers with mean and standard deviation reported in data.
Created: Sept. 3, 2025, 7:23 p.m.
Authors: Arial J. Shogren · Seybold, Erin · Smith, Chelsea · Plont, Stephen · Zarek, Kaci · Carla L. Atkinson · Busch, Michelle
ABSTRACT:
This study was conducted in the Paint Rock research watershed (outlet location: 34.96861724, -86.16501705) on privately owned property in Jackson County (AL, USA). The watershed drains a non-perennial unnamed tributary to Burks Creek, and contains 2.97 km^2 of deciduous forest in the Cumberland Plateau physiographic section. Located near Estillfork, AL, the watershed spans an elevation range from 211 to 550 m above sea level, and is a tributary to the Paint Rock River (within the larger Tennessee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 4.4°C and 25.4°C respectively, and mean annual precipitation of 1,390 mm/yr.
Samples were filtered with a 0.45um PES filter and frozen until analysis. Aqueous concentrations of anions were determined using an IC-3000 IC system (Dionex, Sunnyvale, CA) equipped with Dionex AERS 500 suppressor (2 mm, Thermo Scientific) and Dionex AS auto-sampler (Thermo Scientific). A Dionex IonPac AS15 column (2 mm × 50 mm, Thermo Scientific) with a guard column Dionex IonPac AG15 (2 mm × 50 mm, Thermo Scientific) was used to separate anions using a mobile phase of 38 mM KOH and a flow rate of 0.3 mL/min. The column temperature is 30 °C. Chromeleon software 7.1 is used for system control. Final data tab shows average of triplicates collected in the field and st dev of triplicates. Any NO3 values below 0.01 mg/L are below the lowest standard used in lab analysis and should be interpreted with caution.
Created: Sept. 3, 2025, 7:40 p.m.
Authors: Seybold, Erin · Arial J. Shogren · Smith, Chelsea · Plont, Stephen · Zarek, Kaci · Carla L. Atkinson · Busch, Michelle
ABSTRACT:
This study was conducted in the Talladega research watershed (outlet location: 33.76219799, -85.59550775) in the Talladega National Forest (Cleburne County, AL, USA). The watershed drains a non-perennial unnamed tributary of Pendergrass Creek, and contains 0.92 km^2 of mixed coniferous and deciduous forest in the Piedmont Upland physiographic section. Located near Anniston, AL, the watershed spans an elevation range from 345 to 456 m above sea level and is a tributary to the Coosa River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 5.3°C and 25.3°C respectively, and mean annual precipitation of 1,400 mm/yr.
Samples were filtered with a 0.45um PES filter and frozen until analysis. Aqueous concentrations of anions were determined using an IC-3000 IC system (Dionex, Sunnyvale, CA) equipped with Dionex AERS 500 suppressor (2 mm, Thermo Scientific) and Dionex AS auto-sampler (Thermo Scientific). A Dionex IonPac AS15 column (2 mm × 50 mm, Thermo Scientific) with a guard column Dionex IonPac AG15 (2 mm × 50 mm, Thermo Scientific) was used to separate anions using a mobile phase of 38 mM KOH and a flow rate of 0.3 mL/min. The column temperature is 30 °C. Chromeleon software 7.1 is used for system control. Final data tab shows average of triplicates collected
The final data tab includes QA/QC’d averaged data for fluoride, chloride, nitrite, bromide, nitrate, phosphate, and sulfate in ppm with standard deviations. If the sample is below detection (BD), it is denoted as that and highlighted pink. Average NAs indicate analytes were not run or that samples were missing. NA’s in the standard deviations columns could indicate that those samples were not run or that only replicate was able to be analyzed.
Created: Sept. 3, 2025, 8:01 p.m.
Authors: Arial J. Shogren · Seybold, Erin · Smith, Chelsea · Plont, Stephen · Zarek, Kaci · Carla L. Atkinson · Busch, Michelle
ABSTRACT:
This study was conducted in the Shambley Creek research watershed (outlet location: 32.98410915, -88.01334337) on privately owned property in Greene County (AL, USA). The watershed drains a non-perennial unnamed tributary to Shambley Creek, and contains 0.70 km^2 of coniferous forest managed for silviculture in the East Gulf Coastal Plain physiographic section. Located near Eutaw, AL, the watershed spans an elevation range from 63 to 94 m above sea level, and is a tributary to the Sipsey River (within the larger Mobile-Tombigbee basin). The region has a humid subtropical climate, with mean daily January and July air temperatures of 7.3°C and 27.4°C respectively, and mean annual precipitation of 1,350 mm/yr.
Samples were filtered with a 0.45um PES filter and frozen until analysis. Aqueous concentrations of anions were determined using an IC-3000 IC system (Dionex, Sunnyvale, CA) equipped with Dionex AERS 500 suppressor (2 mm, Thermo Scientific) and Dionex AS auto-sampler (Thermo Scientific). A Dionex IonPac AS15 column (2 mm × 50 mm, Thermo Scientific) with a guard column Dionex IonPac AG15 (2 mm × 50 mm, Thermo Scientific) was used to separate anions using a mobile phase of 38 mM KOH and a flow rate of 0.3 mL/min. The column temperature is 30 °C. Chromeleon software 7.1 is used for system control. Final data tab shows average of triplicates collected in the field and st dev of triplicates. Any NO3 values below 0.01 mg/L are below the lowest standard used in lab analysis and should be interpreted with caution.
The final data tab includes QA/QC’d averaged data for fluoride, chloride, nitrite, bromide, nitrate, phosphate, and sulfate in ppm with standard deviations. If the sample is below detection (BD), it is denoted as that and highlighted pink. Average NAs indicate analytes were not run or that samples were missing. NA’s in the standard deviations columns could indicate that those samples were not run or that only replicate was able to be analyzed.