cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15482/usda.adc/28705052.v1
title: Survivorship and gut microbial community of <i>Bombus vosnesenskii </i>exposed to an herbicide, a fungicide, an insecticide, or the combination of all three chemicals

description: We investigated site-level differences in survival and microbiome structure of wild bumble bees exposed to multiple pesticides, both individually and in combination. We collected wild <i>Bombus vosnesenskii</i> foragers (<i>N</i> = 175) from an alpine meadow, a valley lake shoreline, and a suburban park and maintained them on a diet containing an herbicide (glyphosate), a fungicide (tebuconazole), an insecticide (imidacloprid), or a combination of these chemicals. The herbicide treatment was 30 ppm of glyphosate (Sigma-Aldrich, USA), the fungicide treatment was 30 ppb of tebuconazole (Sigma-Aldrich, USA), and the insecticide treatment was 30 ppb of imidacloprid (Sigma-Aldrich, USA). These chemicals were selected because they had the highest estimated use for each chemical class (insecticide, herbicide, fungicide) in our region (Washoe county, Nevada, (Wieben 2019)). These concentrations of imidacloprid and tebuconazole approximate the median of those detected in nectar (Zioga et al. 2020). The concentration we chose for glyphosate is within the range of field-realistic exposure from treated plants (Herbert et al. 2014, Thompson et al. 2022, Helander et al. 2023b) although is likely higher than bees would experience foraging from <i>non</i>-target plants (Zioga et al. 2023). We monitored survival daily for 20 days. Every 3 days, we replaced feeders with a clean feeder with 1000 mL of solution. We continued the experiment until bees died or at day 20 (whichever came first) at which point we weighed the bees, measured their intertegular (IT) span to estimate body size (Cane 1987) and dissected out the midgut and hindgut (hereafter ‘gut’) for DNA extractions and 16s sequencing (see below).<br><br>
DOI: 10.3886/e240528
title: HIFLD OPEN US Army Corps of Engineers (USACE) Military Districts

description: USACE Military District boundaries. Polygons were derived from National Atlas states and/or from data provided by the district.
description: Archived from the HIFLD Open GIS data repository, which was deactivated on August 26, 2025.
DOI: 10.15482/usda.adc/28704857
title: Pollinator visitation, floral microbes, and seed set of <i>Penstemon strictus</i> treated with a fungicide, an insecticide, and both chemicals

description: Rocky Mountain Penstemon (<i>Penstemon</i><i> strictus</i>; <i>N </i>= 126), were transplanted into 11.35-liter plastic pots. Plants were assigned to one of three experimental treatments (fungicide, insecticide, or their combination) or to a water control. Treatment assignments were randomized within phenological stage (flowering, budding, or vegetative) and each treatment was replicated 32 times in a randomized block design (except block 32 which only had an insecticide and control plant). The insecticide was applied directly to the soil as the product “Bioadvanced Fruit, Citrus & Vegetable Insect Protection” (SBM Company, McClellan Park, CA) which contains 0.235% of the neonicotinoid imidacloprid as an active ingredient. The fungicide was applied as a foliar spray as the product “Bioadvanced Disease Control for Roses, Flowers, & Shrubs” which contains 2.9% tebuconazole as an active ingredient. These chemicals were applied according to the manufacturer’s protocols and two water controls (soil application and/or foliar spray) were also applied such that each plant received a soil application and foliar spray of some type. We recorded flowering date, number of flowers per plant, plant height, and herbivory damage weekly. Herbivory damage was visually estimated as percent damage across the entire plant; this was later converted to a binary (yes/no) survey of presence of herbivory damage to account for observer bias. At the conclusion of the experiment, we collected and dissected all fruits so that seeds could be counted and weighed.
DOI: 10.15482/usda.adc/28704857.v1
title: Pollinator visitation, floral microbes, and seed set of <i>Penstemon strictus</i> treated with a fungicide, an insecticide, and both chemicals

description: Rocky Mountain Penstemon (<i>Penstemon</i><i> strictus</i>; <i>N </i>= 126), were transplanted into 11.35-liter plastic pots. Plants were assigned to one of three experimental treatments (fungicide, insecticide, or their combination) or to a water control. Treatment assignments were randomized within phenological stage (flowering, budding, or vegetative) and each treatment was replicated 32 times in a randomized block design (except block 32 which only had an insecticide and control plant). The insecticide was applied directly to the soil as the product “Bioadvanced Fruit, Citrus & Vegetable Insect Protection” (SBM Company, McClellan Park, CA) which contains 0.235% of the neonicotinoid imidacloprid as an active ingredient. The fungicide was applied as a foliar spray as the product “Bioadvanced Disease Control for Roses, Flowers, & Shrubs” which contains 2.9% tebuconazole as an active ingredient. These chemicals were applied according to the manufacturer’s protocols and two water controls (soil application and/or foliar spray) were also applied such that each plant received a soil application and foliar spray of some type. We recorded flowering date, number of flowers per plant, plant height, and herbivory damage weekly. Herbivory damage was visually estimated as percent damage across the entire plant; this was later converted to a binary (yes/no) survey of presence of herbivory damage to account for observer bias. At the conclusion of the experiment, we collected and dissected all fruits so that seeds could be counted and weighed.
DOI: 10.3886/e240528v1
title: HIFLD OPEN US Army Corps of Engineers (USACE) Military Districts

description: USACE Military District boundaries. Polygons were derived from National Atlas states and/or from data provided by the district.
description: Archived from the HIFLD Open GIS data repository, which was deactivated on August 26, 2025.
DOI: 10.15482/usda.adc/28899146
title: Dataset from: Significant mortality of old trees across a dry forest landscape, Oregon, USA

description: This dataset consists of an unbiased sample of tree species and tree ages from 11 randomly located sites across unlogged roadless areas combined with a targeted sample of the older age classes of trees present at each site. This network of 1,617 trees on the Malheur National Forest was originally part of two separate research projects conducted in 2012-2013 and each tree was revisited in 2022-2023 to examine mortality rates of old and mature trees. Four of the sites experienced wildfire in 2014, 2015, or 2021.During initial data collection in 2012-2013 we extracted a 5.15 mm diameter core from each tree containing the pith or within five rings of the pith allowing us to determine the age of each tree. All tree cores collected in the field were sanded with progressively finer grits of sandpaper, crossdated, and measured to 0.001 mm precision. We verified the accuracy of crossdating using COFECHA software and adjusted dating as necessary (Holmes 1983).This data set contains tree information including locations, status, species, diameter at breast height, age, tree height, scaled basal area increment for 5, 10, 25, and 50 years prior to initial measurement; site information including potential vegetation type, competition metrics such as basal area and stems per hectare; and environmental variables including VPD, temperature, precipitation, net primary productivity, heat load, slope, and aspect. For more detailed information see manuscript and supplemental online materials.We investigated recent forest mortality dynamics by revisiting a network of 1,617 trees in unlogged roadless areas in the Blue Mountains of eastern Oregon for which we have precise age and growth data. There was extensive mortality of the oldest trees in stands—a quarter of trees ≥300 years of age died over a ten-year period. Trees with below average basal area increment were more likely to die in stands that have not experienced wildfire in the last 130 years. Smaller trees were more likely to die in stands that experienced wildfire during the ten-year observation period. Douglas-fir and western juniper experienced a lower rate of mortality than ponderosa pine, western larch, or grand fir in sites that have not experienced wildfire. There was little evidence for a difference in mortality between species in sites that experienced wildfire. We describe a novel simulation model which demonstrated that succession of young trees is unlikely to replace recent losses of old trees. The confluence of a rare insect defoliator outbreak, drought, and past management decisions that increased competitive stress and fuel connectivity is the most likely explanation for the elevated mortality we observed. The protected areas where we collected data are not achieving old tree conservation objectives. Active management to reduce forest competition outside of protected areas is the most realistic pathway for old tree conservation in dry forests.Model and code are available on github: https://github.com/AmandaBrackett/Malheur-OldTree-Mort
DOI: 10.15482/usda.adc/28899146.v1
title: Dataset from: Significant mortality of old trees across a dry forest landscape, Oregon, USA

description: This dataset consists of an unbiased sample of tree species and tree ages from 11 randomly located sites across unlogged roadless areas combined with a targeted sample of the older age classes of trees present at each site. This network of 1,617 trees on the Malheur National Forest was originally part of two separate research projects conducted in 2012-2013 and each tree was revisited in 2022-2023 to examine mortality rates of old and mature trees. Four of the sites experienced wildfire in 2014, 2015, or 2021.During initial data collection in 2012-2013 we extracted a 5.15 mm diameter core from each tree containing the pith or within five rings of the pith allowing us to determine the age of each tree. All tree cores collected in the field were sanded with progressively finer grits of sandpaper, crossdated, and measured to 0.001 mm precision. We verified the accuracy of crossdating using COFECHA software and adjusted dating as necessary (Holmes 1983).This data set contains tree information including locations, status, species, diameter at breast height, age, tree height, scaled basal area increment for 5, 10, 25, and 50 years prior to initial measurement; site information including potential vegetation type, competition metrics such as basal area and stems per hectare; and environmental variables including VPD, temperature, precipitation, net primary productivity, heat load, slope, and aspect. For more detailed information see manuscript and supplemental online materials.We investigated recent forest mortality dynamics by revisiting a network of 1,617 trees in unlogged roadless areas in the Blue Mountains of eastern Oregon for which we have precise age and growth data. There was extensive mortality of the oldest trees in stands—a quarter of trees ≥300 years of age died over a ten-year period. Trees with below average basal area increment were more likely to die in stands that have not experienced wildfire in the last 130 years. Smaller trees were more likely to die in stands that experienced wildfire during the ten-year observation period. Douglas-fir and western juniper experienced a lower rate of mortality than ponderosa pine, western larch, or grand fir in sites that have not experienced wildfire. There was little evidence for a difference in mortality between species in sites that experienced wildfire. We describe a novel simulation model which demonstrated that succession of young trees is unlikely to replace recent losses of old trees. The confluence of a rare insect defoliator outbreak, drought, and past management decisions that increased competitive stress and fuel connectivity is the most likely explanation for the elevated mortality we observed. The protected areas where we collected data are not achieving old tree conservation objectives. Active management to reduce forest competition outside of protected areas is the most realistic pathway for old tree conservation in dry forests.Model and code are available on github: https://github.com/AmandaBrackett/Malheur-OldTree-Mort
DOI: 10.15482/usda.adc/29042780
title: Data from: Time-lapse ensemble-based electrical resistivity tomography to monitor water flow from managed aquifer recharge operations

description: Various managed aquifer recharge strategies, such as drywells, are being used in the California Central Valley (CCV) to replenish groundwater resources that have been depleted by over-pumping, especially during droughts. Drywell technology allows recharge water to bypass shallow impermeable layers and possible contaminated soils near the land surface. Understanding water flow in the vadose zone is crucial for assessing the performance of drywells regarding the amount of water that reaches the groundwater table and the fate of solutes. In this study, we demonstrate the applicability of time-lapse electrical resistivity tomography (TL-ERT) for imaging the water flow and subsequent aquifer recharge at a drywell site in the CCV with a thick (67–72 meters) vadose zone. Additionally, TL-ERT results were compared to point-scale observations from a collocated monitoring well. To invert our TL-ERT data sets, geostatistical constraints were applied to favor layered models as expected due to the alluvial deposits in the study area. By considering different correlation lengths, an ensemble of resistivity model solutions was generated per time-step instead of a single model solution (as typically performed). Model differences between the mean model of the baseline data set and the models from the subsequent time steps allowed us to image the wetting front development until reaching the regional aquifer, a perched water table, and flush of salts that were otherwise not visible or blurred when using single model solutions from standard deterministic TL-ERT inversion approaches.
DOI: 10.15482/usda.adc/29042780.v1
title: Data from: Time-lapse ensemble-based electrical resistivity tomography to monitor water flow from managed aquifer recharge operations

description: Various managed aquifer recharge strategies, such as drywells, are being used in the California Central Valley (CCV) to replenish groundwater resources that have been depleted by over-pumping, especially during droughts. Drywell technology allows recharge water to bypass shallow impermeable layers and possible contaminated soils near the land surface. Understanding water flow in the vadose zone is crucial for assessing the performance of drywells regarding the amount of water that reaches the groundwater table and the fate of solutes. In this study, we demonstrate the applicability of time-lapse electrical resistivity tomography (TL-ERT) for imaging the water flow and subsequent aquifer recharge at a drywell site in the CCV with a thick (67–72 meters) vadose zone. Additionally, TL-ERT results were compared to point-scale observations from a collocated monitoring well. To invert our TL-ERT data sets, geostatistical constraints were applied to favor layered models as expected due to the alluvial deposits in the study area. By considering different correlation lengths, an ensemble of resistivity model solutions was generated per time-step instead of a single model solution (as typically performed). Model differences between the mean model of the baseline data set and the models from the subsequent time steps allowed us to image the wetting front development until reaching the regional aquifer, a perched water table, and flush of salts that were otherwise not visible or blurred when using single model solutions from standard deterministic TL-ERT inversion approaches.
DOI: 10.15482/usda.adc/29175224
title: Data from: Five-year timeseries of sap-flux-scaled transpiration reveals inter-annual variation between tree water use and precipitation in a pinyon and juniper woodland

description: The USDA-ARS conducted a five-year study of transpirational water use of single-leaf pinyon (<i>Pinus monopylla</i>) and Utah juniper (<i>Juniperus osteosperma</i>) at the Porter Canyon Experimental Watershed (PCEW) in the Great Basin of Nevada, USA. A total of 29 pinyon and 16 juniper trees that were representative of the natural size-class variation within the PCEW were selected for long-term sap flow measurements. All trees were instrumented with two sets of 2 cm Granier-style thermal dissipation sap flow probes, as tree core measurements obtained in late 2011 indicated that sapwood depth was greater than 2 cm on average for all trees. Two sets of probes were installed radially into the xylem at approximately north-south orientation, depending on branch architecture, and spaced 15 cm axially with the top probe approximately 50 cm above the ground. This dataset is comprised of nine .CSV files covering the five-year period. The five-year period encompassed five water years from October 1st, 2013 to September 30th, 2018. The dataset includes measurements of mean daily vapor pressure deficit, solar radiation, and volumetric water content at 20 cm. The data set also includes mean daily sap flux density, mean daily whole tree volumetric water use, mean daily water use per basal area, and scaled daily site water use. Lastly, the dataset includes the relationship of mean daytime sap flux density to mean daytime vapor pressure deficit for days within the growing season time periods when: 1) soil volumetric water content was not a sap flux-limiting factor and 2) soil volumetric water content was a sap flux-limiting factor.
DOI: 10.15482/usda.adc/29175224.v1
title: Data from: Five-year timeseries of sap-flux-scaled transpiration reveals inter-annual variation between tree water use and precipitation in a pinyon and juniper woodland

description: The USDA-ARS conducted a five-year study of transpirational water use of single-leaf pinyon (<i>Pinus monopylla</i>) and Utah juniper (<i>Juniperus osteosperma</i>) at the Porter Canyon Experimental Watershed (PCEW) in the Great Basin of Nevada, USA. A total of 29 pinyon and 16 juniper trees that were representative of the natural size-class variation within the PCEW were selected for long-term sap flow measurements. All trees were instrumented with two sets of 2 cm Granier-style thermal dissipation sap flow probes, as tree core measurements obtained in late 2011 indicated that sapwood depth was greater than 2 cm on average for all trees. Two sets of probes were installed radially into the xylem at approximately north-south orientation, depending on branch architecture, and spaced 15 cm axially with the top probe approximately 50 cm above the ground. This dataset is comprised of nine .CSV files covering the five-year period. The five-year period encompassed five water years from October 1st, 2013 to September 30th, 2018. The dataset includes measurements of mean daily vapor pressure deficit, solar radiation, and volumetric water content at 20 cm. The data set also includes mean daily sap flux density, mean daily whole tree volumetric water use, mean daily water use per basal area, and scaled daily site water use. Lastly, the dataset includes the relationship of mean daytime sap flux density to mean daytime vapor pressure deficit for days within the growing season time periods when: 1) soil volumetric water content was not a sap flux-limiting factor and 2) soil volumetric water content was a sap flux-limiting factor.
DOI: 10.15482/usda.adc/29212463
title: Database of USDA ARS JETs on channel boundary materials

description: This dataset contains 1253 jet erosion tests (JETs) conducted <i>in situ</i> on stream-related materials by staff of the USDA-ARS National Sedimentation Laboratory, Oxford, MS, across the contiguous U.S. between 1997 and 2023. For each JET, its location in the channel cross section (e.g., bed, bank toe, and bank face), type of jet test device used, and time series of scour hole depth and associated pressure head are provided. The JET is comprehensively described by Hanson and Cook (2004). The JET is used to measure the erosion resistance of soils. A submerged jet formed by forcing pressurized flow through a nozzle is used to exert a shear stress on an erodible soil surface. The rate at which the soil surface erodes is measured over time. Erosion rate and applied shear stress can be calculated from the time series of scour hole depth and pressure head provided for each JET in this dataset. The relation between erosion rate and shear stress, termed erosion function, is then used to describe soil erosion resistance. The ARS post-processing tools for JETs (PP-JET) are available from GitHub (Langendoen, 2025). The derived erosion functions can be used for developing improved JET post-processing methods, evaluating the influence of different jet test devices, developing new mechanistic descriptions of the erosion of channel boundary materials, and as information required to assess best management practices for river management.
DOI: 10.15482/usda.adc/29212463.v1
title: Database of USDA ARS JETs on channel boundary materials

description: This dataset contains 1253 jet erosion tests (JETs) conducted <i>in situ</i> on stream-related materials by staff of the USDA-ARS National Sedimentation Laboratory, Oxford, MS, across the contiguous U.S. between 1997 and 2023. For each JET, its location in the channel cross section (e.g., bed, bank toe, and bank face), type of jet test device used, and time series of scour hole depth and associated pressure head are provided. The JET is comprehensively described by Hanson and Cook (2004). The JET is used to measure the erosion resistance of soils. A submerged jet formed by forcing pressurized flow through a nozzle is used to exert a shear stress on an erodible soil surface. The rate at which the soil surface erodes is measured over time. Erosion rate and applied shear stress can be calculated from the time series of scour hole depth and pressure head provided for each JET in this dataset. The relation between erosion rate and shear stress, termed erosion function, is then used to describe soil erosion resistance. The ARS post-processing tools for JETs (PP-JET) are available from GitHub (Langendoen, 2025). The derived erosion functions can be used for developing improved JET post-processing methods, evaluating the influence of different jet test devices, developing new mechanistic descriptions of the erosion of channel boundary materials, and as information required to assess best management practices for river management.