AndreaBozzo/ceres-open-data-index huggingface dataset:
Data from: Crop- and weather-dependent yield and wind erosion benefits from a conservation practices system

<p>This dataset records several responses in a large-scale field south of Mandan, ND to two agricultural management systems, aspirational (ASP; cover crops, and retained wheat straw) and business-as-usual (BAU; no cover crops, wheat straw harvested). Measurements were collected over one full cropping sequence corn-soybean-spring wheat from 2020-2022. Measurements included sediment mass flux, grain yield, grain crop aboveground biomass, grain crop harvest index, and cover crop biomass.</p>
<p>Full details about the data files including variable definitions are provided in the Read Me file.</p>

Tags: corn, cover-crops, maize, sediment-mass-flux, soybean, spring-wheat
Organization: Department of Agriculture
PhenoCam images from JERNORT site, Jornada Experimental Range, New Mexico, USA since 2014

<p>This data set consists of repeat digital imagery from the tower-mounted digital cameras (hereafter, PhenoCams) at the Jornada Experimental Range. JER is a member of the PhenoCam network, which has as its mission to serve as a long-term, continental-scale, phenological observatory. Imagery is uploaded to the PhenoCam server every 30 minutes. The archived images provide a permanent record that can be visually-inspected to determine the phenological state of the vegetation at any point in time. Vegetation greenness metrics (e.g., GCC) derived from the ratio of the green color band to sum of red, green, and blue color bands serve as proxies for vegetation greenness.  Greenness metrics can be extracted from the images using simple image processing methods in 1-day or 3-day increments.
This dataset is available to the public and may be freely downloaded. Please keep the designated Contact person informed of any plans to use the dataset. Consultation or collaboration with the original investigators is strongly encouraged. Publications and data products that make use of the dataset must include proper acknowledgement.
The development of PhenoCam has been supported by multiple entities. Those include the Northeastern States Research Cooperative, NSF’s Macrosystems Biology program (award EF-1065029), DOE’s Regional and Global Climate Modeling program (award DE-SC0016011), the US National Park Service Inventory and Monitoring Program, the USA National Phenology Network (grant number G10AP00129 from the United States Geological Survey), and is currently supported by the Department of Agriculture (USDA) Agricultural Research Service.
This research is a contribution from the Long-Term Agroecosystem Research (LTAR) network. LTAR and the Jornada Experimental Range are supported by the United States Department of Agriculture (USDA) Agricultural Research Service. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: PhenoCam images from JERNORT.</p> <p>File Name: Web Page, url: <a href="https://phenocam.sr.unh.edu/webcam/sites/jernort/">https://phenocam.sr.unh.edu/webcam/sites/jernort/</a> </p></li></ul><p></p>

Tags: ars, data-gov, digital-image, long-term-monitoring-sites, ltar, new-mexico, np216, phenocam, phenology, primary-productivity
Organization: Department of Agriculture
Data from: Diversified grain rotations can be highly and reliably productive in unstable climates

<p dir="ltr">Data and analysis from: </p><p dir="ltr">Ewing, P. M., Chim, B. K., Lehman, R. M., & Osborne, S. L. (2024). Diversified grain rotations can be highly and reliably productive in unstable climates. <i>Field Crops Research</i>, <i>310</i>, 109361.</p><p dir="ltr">Data was collected from the "Alternative Rotation" managed by Dr. Shannon Osborne at the USDA-ARS North Central Agricultural Research Laboratory in Brookings, SD USA. The study was established in 2000 and is a randomized complete block comparing the corn-soybean rotation with some regionally relevant, diversified rotations. It is still being conducted at the Eastern South Dakota Soil and Water Research Farm, also in Brookings. The presented data covers 2001-2016 and is the yield of eight crops grown in 6 rotations of 2-4 crops and years per rotation. Weather data is included.</p><p dir="ltr">Analyses in this repository tested whether diversified rotations could a) match the productivity (grain yield) of simplified rotations while b) stabilizing productivity against variable weather in the western Corn Belt. Follow-up analyses look at mechanisms behind observed productivity-stability patterns at the rotation scale.</p><p dir="ltr">This is an R repository. See README.md for use instructions. A full and possibly easier-to-use version of this repository is on github: https://github.com/PatrickEwing-USDA/NCARL_altrot_yield</p>

Tags: crop-rotation-and-succession, diversity-productivity-relationship, diversity-stability-relationship, long-term-research, niche-complementarity-effect, overyielding
Organization: Department of Agriculture
Nebraska Prairie Study for Agricultural Antibiotic Resistance in Lincoln, Nebraska

<p>Nebraska Prairie Study for Agricultural Antibiotic Resistance in Lincoln, Nebraska
The inherent spatial heterogeneity and complexity of antibiotic resistant bacteria and antibiotic resistance (AR) genes in manureaffected soils makes it difficult to sort out resistance that can be attributed to human antibiotic use from resistance that occurs naturally in the soil. This study characterizes native Nebraska prairie soils that have not been affected by human or food-animal waste products to provide data on background levels of resistance in southeastern Nebraskan soils. Soil samples were collected from 20 sites enumerated on tetracycline and cefotaxime media; screened for tetracycline-, sulfonamide-, b-lactamase–, and macrolide-resistance genes; and characterized for soil physical and chemical parameters. All prairies contained tetracyclineand cefotaxime-resistant bacteria, and 48% of isolates collected were resistant to two or more antibiotics. Most (98%) of the soil samples and all 20 prairies had at least one tetracycline gene. Most frequently detected were tet(D), tet(A) tet(O), tet(L), and tet(B). Sulfonamide genes, which are  considered a marker of human or animal activity, were detected in 91% of the samples, despite the lack of human inputs at these sites. No correlations were found between either phenotypic or genotypic resistance and soil physical or chemical parameters. Heterogeneity was observed in AR within and between prairies. Therefore, multiple samples are necessary to overcome heterogeneity and to accurately assess AR. Conclusions regarding AR depend on the gene target measured. To determine the impacts of food-animal antibiotic use on resistance, it is essential that background and/or baseline levels be considered, and where appropriate subtracted out, when evaluating AR in agroecosystems.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: GeoData catalog record.</p> <p>File Name: Web Page, url: <a href="https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/196aa7cb-1880-49ad-a4a3-a220be105dbb" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/196aa7cb-1880-49ad-a4a3-a220be105dbb</a> </p></li></ul>

Tags: antibiotic-resistance, ars, data-gov, environment, farming, np211, np212, prairie, soil
Organization: Department of Agriculture
Data from: Pre-inoculation water deficit effects on grapevine physiology, Xylella fastidiosa titers and Pierce's disease progression

<p>Data are from three experimental trials examining pre-existing water stress on Xylella fastidiosa infections and possible associated shifts in host chemistry, including free sugar, amino acid, and phenolic compound measurements. Trials A and B were utilized in the manuscript, whereas Trial C was data from an experiment whereby the water stress treatment was not significant enough to affect plant physiology or bacterial progression (but included for completeness). Predawn water potentials and photosynthesis were provided for trial B to show methodology worked (and for trial C to show the failure to reach water stress).</p>
<div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Pre-infection water stress effects on Xylella fastidiosa progression and grapevine chemistry.</p> <p>File Name: Preinfection Water Stress Effects on Xf Data.xlsx</p><p>Resource Description: Data represent affects of water stress on Xylella titers and Pierce's disease progression, as well as changes in grapevine stem amino acid, sugar, or phenolic compounds. Data were from three trials. Two of these were deemed from successful experiments with water stress obtained (Trials A and B), but the last trial (Trial C) did not appear to have induced water stress, based on pre-dawn water potentials. Data were summarized in a manuscript submitted for publication.</p></li></ul><p></p>

Tags: amino-acids, ars, data-gov, drought-stress, grapevine, np303, phenolics, sugars, xylella-fastidiosa-subsp-fastidiosa
Organization: Department of Agriculture
Data from: Long-term compost use and high frequency low concentration fertigation reduce N<sub>2</sub>O emissions from a California almond orchard

<p dir="ltr">Using compost as an agricultural amendment offers a means to reduce organic waste, as mandated by California State Bill 1383. Compost application, through the addition of soil organic matter, leads to improvements in soil physical characteristics and soil organic carbon content. Effects of compost application (7-year duration; 38-dry tonnes ha<sup>-1</sup>) on soil nitrous oxide (N<sub>2</sub>O), inorganic nitrogen pools, soil temperature and water content, bulk density and total carbon and N content were examined. Soils were also measured for soil pH, electrical conductivity, and total C and N. These findings were compared to the control, which had not received compost application.</p><p dir="ltr">The research site was located ∼8 km west of Modesto, California (37˚37′38.17“ N 121˚5′21.57”W), on a 10.5-ha almond orchard (Prunus <i>dulcis</i>, 270 m by 395 m). The orchard was replanted in 2012 with Nonpareil cultivars and interplanted with Aldrich and Carmel cultivars, all grafted on Nemaguard peach rootstock [<i>Prunus persica </i>(L.) Bratsch]. Trees were 4.3 m apart along the row, with 6.4 m between rows, and irrigated by surface drip hose with embedded emitters every 3.7 m (0.07 L min<sup>−1</sup>).</p><p dir="ltr">The two treatments, No Compost and Compost (n=3 replicates per treatment), were studied in the growing season (December 2018–August 2019). All other management was consistent between treatments, representing standard practices for the almond industry in this region. The orchard began HFLC nutrient management in 2018, and the total amounts of fertilizer N and irrigation were adjusted in response to anticipated tree demand as determined by the grower. In 2019, orchard received ∼195 kg N ha<sup>−1</sup> over 14 fertigation events (March–July, 2019) through a drip irrigation system using HFLC. These 14 fertilization events ranged from 4.5 kg N ha<sup>−1</sup> to 28.0 kg ha<sup>−1</sup>.</p><p dir="ltr">Findings were compared graphically against other data from 5 other studies examining the effects of irrigation and fertigation practices on N<sub>2</sub>O. Total cumulative emissions were calculated by date and treatment over the growing season. The effects of sampling date, treatment and area spanning the drip zone were analyzed for N<sub>2</sub>O, soil temperature and water content, water-filled pore space, ammonium and nitrate.</p>

Tags: almonds, california, compost, fertigation, greenhouse-gas-emissions, nitrous-oxide
Organization: Department of Agriculture
Data from: Effect of cricket protein powders on dough functionality and bread quality

<p>Data collected from duplicate laboratory analysis of the functional properties of wheat flour dough mixed with cricket protein powders. Dough properties were evaluated for dough strength and elasticity. Breads were baked from all flour treatments and bread quality evaluated from image analysis of crumb structure, loaf volume, and texture analysis.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: Water absorption data
File Name: Water Absorption Data.csv
Resource Description: Water absorption for control wheat flours (CF), with added cricket protein powder (E = Entomo Farms; G=GrioPro) at 0 to 20% addition levels.</p>
</li>
<li>
<p>Resource Title: Kieffer ratio data
File Name: Kieffer analysis R to E ratio.csv
Resource Description: Kieffer data on wheat flour dough with 0 to 20% cricket protein powder added. All terms defined in the included dataset.</p>
</li>
<li>
<p>Resource Title: Kieffer force and distance data
File Name: Kieffer force and distance.csv
Resource Description: Kieffer force and distance data for wheat flour with cricket protein powder added at 0 to 20% levels. All terms defined in attached data set.</p>
</li>
<li>
<p>Dough mixing properties
File Name: mixing properties.csv
Resource Description: Dough mixing properties of wheat flour with cricket protein powder added to 0 to 20% (all terms defined in attached data set).</p>
</li>
<li>
<p>Resource Title: Texture profile analysis
File Name: Texture Profile analysis over time.csv
Resource Description: Texture profile analysis of bread made from wheat flour with cricket protein powder added at 0 to 20% levels. All terms defined in attached data set.</p>
</li>
</ul>

Tags: ars, bread, cricket-protein-powder, data-gov, dough, np306, protein, wheat-flour
Organization: Department of Agriculture
De novo transcriptome assembly of Schizaphis gramium Biotype I feeding on wheat

<p>Transcriptome was generated from pooled adult aphids that were fed on wheat plants containing the Dn4 and DN7 resistance gene as well as Yuma plants containing no resistant genes (Dn0).  The assembly was generated using Trinity.  All assembled transcripts, including those that were not predicted to encode ORFs, are included along with their corresponding functional annotations from Trinotate.   </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: De novo transcriptome assembly of Schizaphis graminum Biotype I.</p> <p>File Name: Trinity.fasta_.txt</p><p>Resource Description: Reads were assembled using Trinity version 2.3.2.  All transcripts greater than 200 nt were retained in this version of the assembly.  </p><p>Resource Software Recommended: Notepad++,url: <a href="https://notepad-plus-plus.org/">https://notepad-plus-plus.org/</a> </p></li><br><li><p>Resource Title: Filtered Transcriptome Assembly of Schizaphis graminum.</p> <p>File Name: Greenbug<em>FilteredTrinity.transdecoder.mRNA</em>.fasta_.txt</p><p>Resource Description: Only transcripts with transcripts per million mapped reads values (TPM) >=0.05 and transcripts whose expression levels represented >=10% of their dominant isoform were retained for differential expression.   </p><p>Resource Software Recommended: Notepad++,url: <a href="https://notepad-plus-plus.org/">https://notepad-plus-plus.org/</a> </p></li><br><li><p>Resource Title: Trinotate results for Schizaphis graminum transcriptome assembly.</p> <p>File Name: Greenbug_trinotate_annotation_report.xls</p><p>Resource Description: Trinotate was used to obtain highest scoring blastp matches to annotated proteins curated in the swiss-prot, detect Pfam domains, obtain gene ontology annotations, and obtain KEGG annotations.  </p><p>Resource Software Recommended: Microsoft Excel,url: <a href="https://products.office.com/en-us/excel">https://products.office.com/en-us/excel</a> </p></li><br><li><p>Resource Title: Protein coding translations of Schizaphis graminum assembly.</p> <p>File Name: Greenbug_FilteredTrinityfasta<em>fromTrial6.sh</em>.o2516954.fasta<em>.transdecoder.pep</em>.txt</p><p>Resource Description: TransDecoder was used to predict open reading frames in the final transcriptome assembly.  </p><p>Resource Software Recommended: Notepad++,url: <a href="https://notepad-plus-plus.org/">https://notepad-plus-plus.org/</a> </p></li></ul><p></p>

Tags: ars, data-gov, de-novo-transcriptome, rna-de-novo-assembly, rna-seq
Organization: Department of Agriculture
Data from: Fructooligosaccharides (FOS) differentially modifies the in vitro gut microbiota in an age-dependent manner

<p>A 24-h in vitro culturing method was used to determine whether fructooligosaccharide (FOS) treatment effects on the human gut microbiome has a differential effect by age, using fecal samples  from 18 adults in 3 age groups with 6 individuals for each group, young adult (25–35 years of age), adult (36–50 years of age), and older adult (51–70 years of age). Data collected include: amplicon sequencing of the V1-V2 regions of the 16S rRNA gene (available in the NCBI Sequence Read Archive associated with BioProject PRJNA883714: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA883714">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA883714</a>), total bacterial qPCR, Bifidobacterium genus specific q-PCR, and short chain fatty acid concentrations. </p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: Sample metadata
File Name: FOS_sample_attributes.csv</p>
</li>
<li>
<p>Resource Title: Short Chain Fatty Acid concentrations
File Name: FOS_SCFA_data.csv</p>
</li>
<li>
<p>Resource Title: Total bacterial and Bifidobacterium genus qPCR
File Name: total_bacteria_and_Bifidobacterium_specific_qPCR.csv</p>
</li>
</ul>

Tags: 16s-rrna-sequence-data, ars, bifidobacteria, data-gov, fructooligosaccharides, np306, prebiotics, short-chain-fatty-acids
Organization: Department of Agriculture
Diverse Rotations Improve Valuable Ecosystem Services (DRIVES) Database

<p dir="ltr">The DRIVES database combines of historical data from long-term agricultural field experiments throughout North America. Currently, the database contains crop yield, weather, agronomic management, and experimental metadata for 21 long-term experimental sites in the US, Canada, and Mexico. For details on DRIVES research and participating sites, visit <a href="https://www.drives-network.org/" target="_blank">https://www.drives-network.org/</a>.</p><p dir="ltr">As of May 2025, 17 sites have agreed to release the first round of data to the public on two conditions. First, users must complete a data request form to be granted access: <a href="https://www.drives-network.org/data-request" rel="noreferrer" target="_blank">https://www.drives-network.org/data-request</a>. Second, any publications or products must adequately acknowledge the DRIVES data by citing this repository and acknowledging the Ontario Agri-Food Innovation Alliance for Canadian sites.</p><p dir="ltr">After completing the <a href="https://www.drives-network.org/" rel="noreferrer" target="_blank">data request form</a>, you will receive an email with instructions for logging into the database. Canadian sites require a separate data request form emailed to <a href="mailto:acorrend@uoguelph.ca" target="_blank">acorrend@uoguelph.ca</a> (Elora) and <a href="mailto:dhooker@uoguelph.ca" target="_blank">dhooker@uoguelph.ca</a> (Ridgetown). A partially filled form is included in this repository and at <a href="https://www.drives-network.org/data-request" target="_blank">https://www.drives-network.org/data-request</a>. Users can download and harmonize database tables using the <a href="https://drives-project.github.io/drivesR/" rel="noreferrer" target="_blank">drivesR package</a>, which can be installed from <a href="https://github.com/DRIVES-Project/drivesR." rel="noreferrer" target="_blank">github.com/DRIVES-Project/drivesR</a>. Instructions for installing and using the package can be found on our github page: <a href="https://drives-project.github.io/drivesR/" rel="noreferrer" target="_blank">drives-project.github.io/drivesR/</a></p><p dir="ltr">This repository contains metadata tables, dictionaries, and inventories of DRIVES data. Detailed descriptions of each resource can be found in the README file.</p>

Tags: agronomic-management, crop-diversity, crop-rotation, crop-yields, long-term-experiments, north-america, sustainable-agriculture, weather-station-data
Organization: Department of Agriculture
2014 Naive Broiler CAFO Study for Agricultural Antibiotic Resistance in Mississippi State, Mississippi

<p>2014 Naive Broiler CAFO Study for Agricultural Antibiotic Resistance in Mississippi State, Mississippi
Conventional commercial broiler production involves the rearing of more than 20,000 broilers in a single confined space, atop bedding material such as pine shavings or rice hulls, for approximately 6.5 weeks. This environment is known for harboring pathogens and antibiotic resistant bacteria, but studies have focused on previously established houses. A concerted effort by the broiler industry has involved the scaling back of antibiotic use on-farm, but this has only been a recent occurrence. In the current study, a set of three naïve houses were followed from inception through 11 broiler flocks and monitored for ambient climatic conditions, bacterial pathogens, and antibiotic resistance. Within the first 3 weeks of the first flock cycle, 100% of litter samples were positive for Salmonella and Listeria while Campylobacter was culture negative. In all likelihood, given that pre flock bedding and soil levels were negative for pathogens and 4-5 orders of magnitude lower for other indicators, chicks most likely provided the colonizing bacteria. The influence of intra-house location was minor with only watering lines and side walls influencing some pathogen and indicator levels. Most bacterial groups experienced the typical cyclical pattern of litter contamination seen in other studies. This study represents a first of its kind view into the time required for bacterial pathogens and antibiotic resistance to colonize and establish in naïve broiler houses.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: GeoData catalog record.</p> <p>File Name: Web Page, url: <a href="https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/83c91004-f234-441f-9616-2bd33149f42b" target="_blank">https://geodata.nal.usda.gov/geonetwork/srv/eng/catalog.search#/metadata/83c91004-f234-441f-9616-2bd33149f42b</a> </p></li></ul>

Tags: antibiotic-resistance, antibiotic-resistance-genes, ars, broiler-poultry, data-gov, environment, farming, litter, np211, np212, poultry, tetracycline
Organization: Department of Agriculture