AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Evaluating the Long-Term Efficacy of Four Active Ingredients against <i>Rhyzopertha dominica </i>(F.) (Coleoptera: Bostrichidae) and <i>Sitophilus oryzae </i>(L.) (Coleoptera: Curculionidae) on Stored Sorghum

<p dir="ltr">The objective of this study was to determine the residual efficacy of four commercially available grain protectants, Gravista<sup>®</sup> (deltamethrin + methoprene + PBO), Diacon<sup>®</sup> IGR (methoprene), Sensat™ (spinosad), and EverGreen<sup>®</sup> (pyrethrin), applied to sorghum and held for each of eight storage periods spanning 28 weeks, against <i>Rhyzopertha dominica</i> and <i>Sitophilus oryzae</i>. Subsamples were collected every 4 weeks (up to 28 post grain protectant application) and infested with 10 adults of either <i>R. dominica</i> or <i>S. oryzae.</i> The initial adult mortality was assessed 7 d post-exposure to the treated grain. After adult mortality was determined, the sorghum was held for 8 weeks and adult progeny were counted. Additionally the amount of frass and insect damaged kernels were also evaluated. </p>

Tags: grain-protectants, integrated-pest-managment, long-term-efficacy, postharvest-storage, sorghum, stored-product-pests
Organization: Department of Agriculture
Data from: A whole-genome assembly of St. Augustine grass and visualizing diversity within the species

<p dir="ltr">Variant data in the format of a variant call format file (.vcf) produced from 79 diverse diploid St. Augustine grass accessions producing 760,159 variants from the article 'A whole-genome assembly of St. Augustine grass and visualizing diversity within the species'.</p><p dir="ltr">St. Augustine grass leaf samples were obtained in the greenhouse, then utilized for sequencing. Reads were utilized for variant calling to produce the variant call format file (VCF) made available here. Additional details are provided in the manuscript.</p>

Tags: ars, data-gov, genotypes, st-augustinegrass, stenotaphrum-secundatum
Organization: Department of Agriculture
Data from: Organic production reduces subsurface nitrate leaching and maintains crop yields in US Mollisol

<p dir="ltr">Organic production aims to diversify crop rotation and use organic fertilizer sources to build soil fertility and improve soil health indicators. This data evaluates the impact of organic farming on water quality in artificially drained midwestern Mollisols of central Iowa. This 7-year study compares tile nitrate loss and yields under three cropping systems: (1) conventional corn (<i>Zea mays</i> L)-soybean (<i>Glycine max</i> L.), (2) organic corn–soybean–oat (<i>Avena sativa</i> L.)/alfalfa (<i>Medicago sativa</i> L)–alfalfa, and (3) organic perennial pasture. Nitrogen (N) fertilization consisted of sidedress urea ammonium nitrate for conventional corn (168 kg N ha<sup>−1</sup>) and spring-applied composted manure for organic corn (168 kg N ha<sup>−1</sup>) and oats (56 kg N ha<sup>−1</sup>). The dataset comprises of monthly values of subsurface drainage discharge, flow weighted nitrate concentrations, and the mass of nitrate-nitrogen (NO3-N) in drainage discharge for each of 30 corresponding experimental plots from 2014 to 2020. Dataset also includes annual harvested grain yields corrected to standard moisture content and above-ground biomass yields (excluding grain).</p><p dir="ltr">Resources in this dataset:</p><ul><li>Resource Title: Field Operations.xlsx. Metadata information describing management practices and operations for each crop each year.</li><li>Resource Title: NitrateLoad_SubsurfaceDrainage_FWNC.csv. This dataset provides monthly values of Nitrate-N load, subsurface drainage discharge, and flow weighted nitrate concentrations from 2014 to 2020.</li><li>Resource Title Set: Yield_Alfalfa.csv, Yield_ConvCorn.csv, Yield_ConvSoybean.csv, Yield_Oat.csv, Yield_OrgCorn.csv, and Yield_OrgSoybean.csv. These datasets provide biomass and grain yields of conventional soybean and corn, organic soybean, corn, oats and alfalfa from 2014-2020.</li><li>Resource Title: Precipitation.csv. Cumulative monthly precipitation for the study location, 2014-2020. Monthly values were calculated from daily values from the Iowa Environmental Mesonet (<a href="https://gcc02.safelinks.protection.outlook.com/?url=https://mesonet.agron.iastate.edu/request/coop/fe.phtml&data=05|02|Andrew.McLaughlin@usda.gov|337be1ea0e1a4ce5b3e208de7941047e|ed5b36e701ee4ebc867ee03cfa0d4697|1|0|639081517313761125|Unknown|TWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ==|0|||&sdata=sYlh8F3XAnxvphOMd7eBeR6NyC4+YYvWtxBVqab9CYM=&reserved=0" target="_blank">https://mesonet.agron.iastate.edu/request/coop/fe.phtml</a>).</li></ul><p><br></p>

Tags: alfalfa, corn, drainage-water, grain-yields, iowa, nitrate, nitrogen, oats, organic-farming, pasture, soybean, subsurface-drainage
Organization: Department of Agriculture
Data from: Assessing permethrin susceptibility of field-collected biting midges (Diptera: Ceratopogonidae) in Florida and evidence for resistance evolution using laboratory selections

<p dir="ltr">Biting midges (<i>Culicoides</i> spp.) are small blood-feeding insects that pose a significant threat to livestock and wildlife due to their role in transmitting serious viral diseases such as bluetongue virus, epizootic hemorrhagic disease virus, and vesicular stomatitis virus. Control of these pests has relied heavily on insecticide treatments which are applied directly to animals, around premises, or to barriers like mesh or fabric. However, little is known about how effective specific insecticides are against local midge species or how likely these insects are to develop resistance. To address this gap, we tested the efficacy of permethrin, a commonly used insecticide, on both lab-reared and wild midges in Florida. Results showed that lab-reared midges were significantly more tolerant than their wild counterparts, and wild midges were more susceptible than mosquitoes to permethrin sprayed from the ground. However, many midge species occupy forest canopies, which likely limits exposure to ground-level applications. Importantly, the study found that biting midges can develop significant resistance to permethrin in just two generations, raising concerns about long-term reliance on this control strategy. These findings mark the first documented evidence of potential insecticide resistance in <i>Culicoides</i> spp., underscoring the need for targeted, species-specific management strategies to better control midge populations and reduce disease transmission risks.</p>

Tags: culicoides-midges, deer, insecticide, pyrethroid, sheep
Organization: Department of Agriculture
Managing juniper encroachment in eastern Montana rangelands

<p dir="ltr">Beginning in 2024, ARS scientists began documenting effects of juniper encroachment in open mixed-grass prairie and the effects of mechanical juniper removal. This work is focused on public grazing allotments administered by the US Bureau of Land Management in eastern Montana. The research focuses on the structure, composition, and herbaceous productivity of rangeland ecosystems, with a focus on invasive species dynamics and forage availability for livestock grazing. </p>

Tags: conifer-management, juniper-encroachment, rangeland-management, rangeland-restoration, woody-plant-removal
Organization: Department of Agriculture
Data from: Gravel transport from impact plates in Goodwin Creek Experimental Watershed, Panola County, Mississippi, USA

<p dir="ltr">Gravel transport is difficult to measure in streams and rivers, but it is needed for assessing the impact of dam removal on river systems, for studies of streambed ecology, for stream restoration, and for engineering design of in-channel structures. The measurement of gravel transport is particularly challenging because it is both temporally and spatially heterogenous, it must sometimes be measured at remote locations, and it is labor-intensive and time consuming. Steel plates equipped with accelerometers that are installed in a channel bed can be used for automated measurement of gravel transport by detecting the impacts of gravel particles being transported in the channel. In this study, two accelerometer-equipped stainless-steel impact plates were installed in the Goodwin Creek Experimental Watershed near Batesville, Mississippi, USA. Flow and transport rates from 30 flow events are presented here to show the efficacy of the system and to study gravel bedload in Goodwin Creek. It was found that flow events typically produced clockwise transport rate hysteresis, likely indicating supply-limited conditions for gravel on the falling limbs of hydrographs.</p>

Tags: bedload, impact-plates, sediment-transport
Organization: Department of Agriculture
Code for: Sensitivity of soil nutrient pools, but stability of microbial processes, under reduced rainfall and altered grazing management in northern mixed-grass prairie

<p dir="ltr">Nutrient cycling is a key ecosystem service provided by soils, which may be impacted by global change-induced droughts and alterations to grazing pressure. While the belowground abiotic and biotic responses to drought are increasingly studied, linkages among plant, animal, and microbial responses to drought remain poorly understood. Here we used an innovative experimental approach to enable understanding the relative importance of rainfall reduction, bovine grazing, and their interplay on soil nutrient pools and processes during and after treatments. Specifically, we experimentally imposed a two-year drought of varying intensity (five levels) at two northern mixed-grass prairie sites in Montana and Wyoming. Crossed with this drought treatment, we also imposed a gradient of bovine grazing pressure during the two drought years and three years of recovery following the drought. We found that rainfall reductions at both sites resulted in reductions in soil available P and micronutrients during treatment application. Conversely, rainfall reductions caused both immediate and persistent increases in soil NO<sub>3</sub><sup>-</sup>. Soil nutrients were generally unaffected by grazing treatments. In contrast, biotic soil properties including the activities of six extracellular enzymes and bacterial and fungal community compositions were relatively resistant to rainfall reduction treatments. However, grazing treatments appeared to have a greater effect on extracellular enzyme activity potentials and soil microbial community composition. Overall, our results highlight the relative stability of belowground processes in semi-arid rangelands in the face of drought and land management strategies.</p><p dir="ltr">The article utilizing this dataset is at <a href="https://doi.org/10.1016/j.soilbio.2025.110071" rel="noreferrer noopener" target="_blank">https://doi.org/10.1016/j.soilbio.2025.110071</a>.</p>

Tags: cattle, drought, extracellular-enzyme-activity-eea, fort-keogh, grassland, micronutrients, nitrogen, northern-mixed-grass-prairie-soil, phosphorus, soil-compaction, soil-microbial-community, thunder-basin-ecoregion
Organization: Department of Agriculture
Data from: Chromosome-level genome assembly of Osmia taurus Smith (Hymenoptera: Megachilidae), an invasive bee species in North America

<p dir="ltr">Supplementary files for "Chromosome-level genome assembly of <i>Osmia taurus</i> Smith (Hymenoptera: Megachilidae), an invasive bee species in North America" Authors: Stephania Sandoval-Arango, Rena M. Schweizer, Michael G. Branstetter, Margarita M. Lopez-Uribe, Sheina B. Sim, Scott M. Geib, Jay D. Evans1</p><p dir="ltr">The mason bee, <i>Osmia taurus</i> (Hymenoptera: Megachilidae), is native to Asia and was accidentally introduced to North America. This introduced species is now widespread and considered invasive due to negative impacts on native <i>Osmia </i>species. The number of introductions, invasion pathways, and mechanisms by which <i>O. taurus</i> has been able to establish and spread are currently unknown. Here, we present a high-quality genome assembly of <i>O. taurus</i> that will serve as a resource to study the genomic basis of its successful establishment in North America. We combined PacBio HiFi long-read sequencing, Hi-C short-read sequencing, and RNAseq data to assemble and annotate the genome. The genome of <i>O. taurus</i> is 536 Mb and represents one of the largest genomes sequenced in Megachilidae. About 70% of its genome is composed of repetitive elements. The supplementary data in this repository corresponds to annotation files generated during gene annotation with EGAPx, repeat annotation with RepeatModeler + RepeatMasker and Earlgrey, and the mitochondrial genome annotation. Additionally, we provide the complete phylogenetic tree generated using Ultraconserved elements extracted from the genomes of 16 megachilids, which was used to build Fig. 4. The analyses were performed on the United States Department of Agriculture (USDA) - SCINet/Mississippi State University High Performance Computing Cluster (HPC) Atlas.</p><p dir="ltr">These resources are meant to allow for future comparisons with additional related species and resquencing efforts for <i>Osmia taurus</i>, a bee species that is expanding its range across eastern North America.</p><p><br></p>

Tags: bee, beenome100, genome, i5k, pollinator
Organization: Department of Agriculture
Data and Code: Increasing global risk of khapra beetle invasion forecasted under diverse environmental conditions

<p dir="ltr">The khapra beetle, <i>Trogoderma granarium, </i>is a stored product pest of global concern. The pest is readily transported with cargo and has been reported in over 60 countries, several of which have spent millions in USD to eradicate populations. Despite the profound risk to stored grain commodities, nothing is known about the influence of climate change on the potential future distribution of species. We utilize MaxEnt and two datasets representing 1) only the historical range and 2) all global locations where it currently is or was established even if it was later eradicated to model areas of suitability under current climatic conditions and project to the future with the accumulated data under low (SSP126) and high (SSP585) climate change scenarios at close (2040) and distant (2080) time points. The potential distribution using historical data was much reduced compared to the combined model; consequently, all established localities, even if eradicated, change model outcomes and thus are important when building models. An increase of high potential suitability (>75% suitable) is projected with greater time and climatic scenarios, primarily in North America and Europe, which have previously eradicated <i>T. granarium</i>. These areas need greater surveillance for early detection and eradication to prevent expansion of <i>T. granarium </i>inland toward areas of high grain production.</p><p dir="ltr">The dataset provided includes all occurrence data points used in the manuscript "Increasing global risk of khapra beetle invasion forecasted under diverse environmental conditions" including longitude and latitude and the reference or repository where the data point was obtained. The code provided is the backbone of the MaxEnt modeling procedure used to make distribution predictions for current and future climate change predictions. </p>

Tags: habitat-suitability, khapra-beetle, maxent-suitability-model, stored-product-insects, temperature
Organization: Department of Agriculture
Metadata from: Mob and rotational grazing influence pasture biomass, nutritive value, and species composition

<p>This is digital research metadata corresponding to a published manuscript in Agronomy Journal, "Mob and rotational grazing influence pasture biomass, nutritive value, and species composition", Vol. 112 p. 2866-2878. Dataset may be accessed via the included link at the Dryad data repository. </p>
<p>Mob grazing, which uses very high stocking densities for short durations followed by a relatively long rest period, was designed to mimic bison (Bison bison) grazing in western U.S. grassland. This project assessed the suitability of mob grazing for livestock production in the Northeast. Objectives were to compare the effects of mob and rotational grazing on dry matter (DM) mass, nutritive value, and botanical composition across four grazing seasons. Eight, 0.10‐ha paddocks were established in 2014 as a randomized complete block with four replications, and seeded with alfalfa (Medicago sativa L.), white clover (Trifolium repens L.), orchardgrass (Dactylis glomerata L.), narrowleaf plantain (Plantago lanceolata L.), and tall fescue [Schedonorus arundinaceus (Schreb.) Dumort]. Mob‐grazed (MOB) paddocks were grazed by yearling beef cattle twice each year, (70–90–day interval), and rotationally grazed (ROT) paddocks were grazed four to six times each year (when sward height reached 25 cm). </p>
<p>Methods are described in the manuscript <a href="https://doi.org/10.1002/agj2.20215">https://doi.org/10.1002/agj2.20215</a>. Descriptions corresponding to each figure and table in the manuscript are placed on separate tabs in the Excel file to clarify abbreviations and summarize the data headings and units. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Link to Mob and Rotational Study dataset at Datadryad.org.</p> <p>File Name: Web Page, url: <a href="https://doi.org/10.5061/dryad.79cnp5ht4">https://doi.org/10.5061/dryad.79cnp5ht4</a> </p><p>Data set one: weather data (precipitation and temperature), pasture height, forage removal, cumulative and per harvest forage mass, botanical composition, and nutritive values of forage material subjected to mob and rotational grazing over a 4-year period (2015-2018) in central Pennsylvania.</p></li></ul><p></p>

Tags: ars, data-gov, forage-production, mob-grazing, np215, range-management-grazing, rotational-grazing, species-mixture
Organization: Department of Agriculture
Data from: Time-lapse ensemble-based electrical resistivity tomography to monitor water flow from managed aquifer recharge operations

<p dir="ltr">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.</p>

Tags: central-valley-of-california-usa, drywell, geostatistics, managed-aquifer-recharge-mar, model-ensemble-study, source-code, time-lapse-electrical-resistivity-tomography
Organization: Department of Agriculture
Delta Produce Sources Study

<p>The Delta Produce Sources Study was an observational study designed to measure and compare food environments of farmers markets (n=3) and grocery stores (n=12) in 5 rural towns located in the Lower Mississippi Delta region of Mississippi. Data were collected via electronic surveys from June 2019 to March 2020 using a modified version of the Nutrition Environment Measures Survey (NEMS) Farmers Market Audit tool. The tool was modified to collect information pertaining to source of fresh produce and also for use with both farmers markets and grocery stores.  Availability, source, quality, and price information were collected and compared between farmers markets and grocery stores for 13 fresh fruits and 32 fresh vegetables via SAS software programming.  Because the towns were not randomly selected and the sample sizes are relatively small, the data may not be generalizable to all rural towns in the Lower Mississippi Delta region of Mississippi. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Delta Produce Sources Study dataset .</p> <p>File Name: DPS Data Public.csv</p><p>Resource Description: The dataset contains variables corresponding to availability, source (country, state and town if country is the United States), quality, and price (by weight or volume) of 13 fresh fruits and 32 fresh vegetables sold in farmers markets and grocery stores located in 5 Lower Mississippi Delta towns.</p><p>Resource Software Recommended: Microsoft Excel,url: <a href="https://www.microsoft.com/en-us/microsoft-365/excel">https://www.microsoft.com/en-us/microsoft-365/excel</a> </p></li><br><li><p>Resource Title: Delta Produce Sources Study data dictionary.</p> <p>File Name: DPS Data Dictionary Public.csv</p><p>Resource Description: This file is the data dictionary corresponding to the Delta Produce Sources Study dataset.</p><p>Resource Software Recommended: Microsoft Excel,url: <a href="https://www.microsoft.com/en-us/microsoft-365/excel">https://www.microsoft.com/en-us/microsoft-365/excel</a> </p></li></ul><p></p>

Tags: ars, data-gov, farmers-markets, food-environment, fruits-and-vegetables, grocery-stores, locally-sourced-produce, np107
Organization: Department of Agriculture