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Pre- and Post- Hurricane Maria Dry Soil Collection (GUAN, LAJA) (repackaging of occurrences published by the NEON Biorepository Data Portal)

These samples from Soil Collection (Distributed Periodic) (NEON-SOIC-DP) were collected at NEON GUAN and LAJA sites in Puerto Rico before (July and November 2017) and after (July 2018) Hurricane Maria, a Category 5 storm that affected the Carribean and occurred September 16, 2017 – October 2, 2017.

NEON Biorepository Aquatic Microalgae Collection (Chemical Preservation) (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains subsamples of aquatic microalgae preserved in either glutaraldehyde or a high-iodine Lugol's solution (NEON sample class: ptx_taxonomy_in.preserved). Periphyton and phytoplankton samples are collected three times per year at wadeable stream, river, and lake sites during aquatic biology bout windows, roughly in spring, summer, and fall. Benthic samples are collected using the most appropriate sampler for the habitat and substratum type, including rock scrubs, grab samples, and epiphyton. In wadeable streams, periphyton samples are collected in the two most dominant benthic habitat types (e.g. riffles, runs, pools, step pools), and seston samples were collected from the water column near the S2 sensor (seston samples were discontinued in 2018). In lakes, water-column phytoplankton samples are collected near the buoy and littoral sensors using a Kemmerer sampler, and in littoral areas using the best benthic sampling method for the dominant substratum type. In rivers, phytoplankton samples are collected near the buoy and two other deep-water locations using a Kemmerer or Van Dorn sampler, and in littoral areas using the best benthic sampling method for the dominant substratum type. All field-collected samples are split into subsamples in the domain support facility, preserved, and shipped to a contracting taxonomy laboratory where samples are further subsampled for analysis and archiving. All samples are archived in 20 mL glass scintillation vials and stored in a temperature (17-18°C) and humidity controlled environment. Phytoplankton and seston samples are preserved in a 2% high-iodine Lugol's solution from 2014-2020 and 0.5% glutaraldehyde starting in 2021. Periphyton samples are preserved in 0.5% glutaraldehyde. See related links below for protocols and NEON related data products.

NEON Biorepository Aquatic Microalgae Collection (Freeze-dried) (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains freeze-dried subsamples of aquatic microalgae (NEON sample class: ptx_taxonomy_in.freezeDried). Periphyton and phytoplankton samples are collected three times per year at wadeable stream, river, and lake sites during aquatic biology bout windows, roughly in spring, summer, and fall. Benthic samples are collected using the most appropriate sampler for the habitat and substratum type, including rock scrubs, grab samples, and epiphyton. In wadeable streams, periphyton samples are collected in the two most dominant benthic habitat types (e.g. riffles, runs, pools, step pools), and seston samples were collected from the water column near the S2 sensor (seston samples were discontinued in 2018). In lakes, water-column phytoplankton samples are collected near the buoy and littoral sensors using a Kemmerer sampler, and in littoral areas using the best benthic sampling method for the dominant substratum type. In rivers, phytoplankton samples are collected near the buoy and two other deep-water locations using a Kemmerer or Van Dorn sampler, and in littoral areas using the best benthic sampling method for the dominant substratum type. All field-collected samples are split into subsamples in the domain support facility, preserved, and shipped to a contracting taxonomy laboratory where samples are further subsampled for analysis and archiving. Freeze dried subsamples contained cleaned, freeze dried diatoms. Samples are archived in 20 mL glass scintillation vials and stored at room temperature. See related links below for protocols and NEON related data products.

NEON Biorepository Aquatic Microalgae Collection (Microscope Slides) (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains slide-mounted subsamples of aquatic microalgae (NEON sample class: ptx_taxonomy_in.slideID). Periphyton and phytoplankton samples are collected three times per year at wadeable stream, river, and lake sites during aquatic biology bout windows, roughly in spring, summer, and fall. Benthic samples are collected using the most appropriate sampler for the habitat and substratum type, including rock scrubs, grab samples, and epiphyton. In wadeable streams, periphyton samples are collected in the two most dominant benthic habitat types (e.g. riffles, runs, pools, step pools), and seston samples were collected from the water column near the S2 sensor (seston samples were discontinued in 2018). In lakes, water-column phytoplankton samples are collected near the buoy and littoral sensors using a Kemmerer sampler, and in littoral areas using the best benthic sampling method for the dominant substratum type. In rivers, phytoplankton samples are collected near the buoy and two other deep-water locations using a Kemmerer or Van Dorn sampler, and in littoral areas using the best benthic sampling method for the dominant substratum type. All field-collected samples are split into subsamples in the domain support facility, preserved, and shipped to a contracting taxonomy laboratory where samples are further subsampled for analysis and archiving. Algae specimens in this collection contain cleaned diatom subsamples that have been mounted on glass microscope slides and are archived at room temperature. See related links below for protocols and NEON related data products.

NEON Biorepository Benthic Microbe Collection (Sterivex Filters) (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains benthic biofilm samples collected on 67 mm long, 1.7 cm diameter, 0.22 um Sterivex capsule filters (NEON sample class: amb_fieldParent_in.archiveID). Benthic biofilm samples are collected 3 times per year at the same time and location as periphyton (microalgae) samples and microbe samples sent for sequencing analysis, three times per year in wadeable streams during aquatic biology bout windows, roughly in spring, summer, and fall. Benthic biofilms are not collected in lakes and rivers. Samples are collected from rock and wood scrubs using field-sterile methods, and filtered through a 0.22 um Sterivex SVGP capsule filters. In wadeable streams, periphyton samples are collected in the two most dominant benthic habitat types (e.g. riffles, runs, pools, step pools). Sterivex filters are capped and flash-frozen in the field and then shipped to the Biorepository to be archived at -80 degrees Celsius. See related links below for protocols and NEON related data products.

NEON HQ Soil Archive (Megapit) (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains soil samples collected from the megapit at each terrestrial site (NEON sample class: mgp_perarchivesample). During the construction of all 47 terrestrial field sites, "Megapit" soils were collected from multiple horizons at a single soil pit that was up to 2m deep. These samples serve as a reference of soil physical and chemical conditions at the time the NEON site was constructed. The Megapit Archive is curated at the NEON program headquarters in Boulder, CO. Megapit soil samples are available upon request (https://www.neonscience.org/samples/soil-archive).

NEON Biorepository Particulate Mass Filter Collection (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains quartz microfiber particulate mass filters (NEON sample class: dpm_fieldData_in.sampleID and dpm_filterBlank_in.sampleID). Particulate mass sampling is executed at six of NEON's terrestrial sites, located in Domains 10, 13, and 15. The subset of sites included for sampling are those in the Basin and Range, Eastern and Western slopes of the Rocky Mountains, and the Eastern plains of Colorado. This selection of sites enables focus on transportation of particulate matter from the Great Basin and the Colorado Plateau by prevailing westerly winds over the Colorado Rocky Mountains, to receptor sites in the Rockies and Great Plains. Samples are collected by an automated assembly that pulls air through a quartz microfiber filter with a porosity of 10 micrometers, to collect PM10. Filters are weighed at high precision pre- and post-deployment at the Colorado Department of Public Health and Environment Air Resources Laboratory to determine dust deposition mass. Filters are then shipped to the Biorepository to be archived at 4 degrees Celsius in air-tight plastic sleeves. Subsamples of the filters are available to the science community upon request to enable the assessment of chemical and nutrient inputs in the region. Additionally, 5 filter blanks from each box of filters are archived and available upon request. See related links below for protocols and NEON related data products.

NEON Biorepository Soil Collection (Distributed Periodic) (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains air-dried soil samples collected during periodic soil sampling at NEON terrestrial sites (NEON sample class: sls_bgcSubsampling_in.bgcArchiveID). Soil biogeochemical samples are collected once every 5 years, with three unique sampling locations per plot and ten plots per site. Soil sampling is conducted to a maximum depth of 30 ± 1 cm where possible. When organic (O) and mineral (M) horizons are present within a single profile they are separated prior to analysis and archiving. However, other sub-horizons are not separated. Soil from the O horizon is homogenized and non-soil material is removed by hand (no sieving), whereas soil from the M horizon is homogenized and sieved to 2 mm. Prior to archiving, all soil samples are air-dried, then placed into glass jars and stored at room temperature. See links below for NEON data products that provide various physical, chemical, and biological measurements (pH, moisture, carbon and nitrogen content and stable isotopes, inorganic nitrogen pools and net transformation rates, microbial community composition and biomass) for these same soils. In addition, a more detailed characterization of the dominant soil types at each site, including taxonomy, texture, bulk density, and geochemical properties, occurred during the construction period of NEON through two projects. These data are available in NEON data products Soil physical and chemical properties, distributed initial characterization (DP1.10047.001) and Soil physical and chemical properties, Megapit (DP1.00096.001).

NEON Biorepository Soil Microbe Collection (Bulk Subsamples) (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains samples collected during periodic soil sampling and frozen at ultra-low temperatures in order to provide material for microbial sequencing or other microbial analyses (NEON sample classes: sls_soilCoreCollection_in.geneticArchiveSample1ID, sls_soilCoreCollection_in.geneticArchiveSample2ID, sls_soilCoreCollection_in.geneticArchiveSample3ID, sls_soilCoreCollection_in.geneticArchiveSample4ID, sls_soilCoreCollection_in.geneticArchiveSample5ID,sls_metagenomicsPooling_in.compositeSampleID). Archive samples are collected during each soil sampling bout and are promptly frozen. Three unique locations are sampled per plot, with ten plots per site. Bouts occur three times per year in order to capture the prevailing conditions at the site during different seasons, except in Alaska where only 1 bout is possible. Soil sampling is conducted to a maximum depth of 30 ± 1 cm, and when organic (O) and mineral (M) horizons are present within a single profile, they are separated prior to analysis and archiving. However, other sub-horizons are not separated. During the majority of bouts, only the top horizon (O if present, else M) is collected and archived. Soils are homogenized and non-soil material is removed by hand in the field, then subsamples are immediately frozen on dry ice. They are maintained in ultra-low temperature freezers until shipment to the Biorepository. See links below for NEON data products that provide physical, chemical, and biological measurements for these same soils (soil pH and moisture are always measured; chemical properties as well as microbial community composition and biomass are determined only for a subset of collection bouts). In addition, a more detailed characterization of the dominant soil types at each site, including taxonomy, texture, bulk density, and geochemical properties, occurred during the construction period of NEON through two projects. These data are available in NEON data products Soil physical and chemical

NEON Biorepository Soil Microbe Collection (DNA Extracts ) (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains genetic extracts from soil microbes collected during periodic soil sampling at NEON terrestrial sites (NEON sample class: mic_dnaExtraction_in.soilDnaSampleID). Three unique locations are sampled per plot with ten soil plots per site. Bouts occur three times per year in order to capture the prevailing conditions at the site during different seasons, except in Alaska where there only 1 bout is possible. However, the frequency of genetic analysis and thus DNA archiving varies by site type. Soil sampling is conducted to a maximum depth of 30 ± 1 cm, and when organic (O) and mineral (M) horizons are present within a single profile, they are separated prior to analysis and archiving. However, other sub-horizons are not separated. During the majority of bouts, only the top horizon (O if present, else M) is analyzed for genetic content. Soils are homogenized and non-soil material is removed by hand in the field, then subsamples are immediately frozen on dry ice. They are maintained in ultra-low temperature freezers until they are shipped to an analytical facility for DNA extraction, sample preparation and sequencing. During peak greenness bouts, subsamples from each of the 3 sampling locations per plot are combined to form a plot-level composite that is used for metagenomics analysis. Laboratory metadata are delivered to NEON for QC testing and acceptance, and then formatted for upload to public sequence repositories. Genetic extracts are shipped from the analytical facility in 96-well plates to the NEON Biorepository to be archived at -80 degrees Celsius. See links below for NEON data products that provide physical, chemical, and biological measurements for these same soils (soil pH, moisture, and microbial properties are always measured; chemical properties are determined only for a subset of collection bouts). The metabarcoding protocol used by Battelle Applied Genomics is available in the NEON document library (https://data.neonscience.org/docu

NEON Biorepository Surface Water Microbe Collection (Sterivex Filters) (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains surface water microbe samples collected on 67 mm long, 1.7 cm diameter, 0.22 um Sterivex capsule filters (NEON sample class: amc_fieldCellCounts_in.archiveID). Surface water microbe samples are collected at the same time and location as surface water cell count samples and surface water chemistry samples once per month in wadeable streams (12 times per year) and every-other month in lakes and rivers (6 times per year). Details on sampling locations and timing are provided in the NEON document titled Surface Water Chemistry Sampling in Aquatic Habitats (https://data.neonscience.org/documents). In wadeable streams, surface water microbe samples are collected near the downstream S2 sensor location. In lakes, microbial samples are collected near the the 'buoy', 'littoral 1', and 'littoral 2' sensors, and sampling depth(s) is dependent on lake stratification. In rivers, microbial samples are collected near the buoy sensor. Water samples are filtered on 0.22 um Sterivex capsule filters, capped and flash-frozen in the field. Sterivex filters are archived at the NEON Biorepository at -80 degrees Celsius. See related links below for protocol.

NEON Biorepository Wet Deposition Collection (repackaging of occurrences published by the NEON Biorepository Data Portal)

This collection contains wet deposition samples collected during precipitation events at NEON terrestrial and aquatic sites (NEON sample class: wdp_collection_in.chemSubsampleID). Samples are collected in a climate controlled wet deposition collector located at the tower top of terrestrial sites, and at the meteorologic tower of select aquatic sites. The automated assembly detects precipitation with an optical sensor and opens to collect wet deposition during all rain events. This allows for all types of precipitation to enter the glass collection bottles located within the enclosure. Once precipitation has ceased (as detected by the optical precipitation detector), the retractable lid closes until the next precipitation event is detected. Every two weeks samples are retrieved. A portion of the sample is filtered and sent to an analytical facility for analysis of major ions, pH, and conductivity. The remaining (unused) portion of the sample is not filtered and archived at 4 degrees Celsius for five years. Samples are stored in plastic Nalgene bottles, either PP or HDPE. See related links below for protocols and NEON related data products. Please note that associated datasets include important remarks and notes from the analysis laboratory about the condition of each sample (for example, if debris or contaminants were observed in the sample).

Ayres 2019: Quantitative Guidelines for Establishing and Operating Soil Archives (repackaging of occurrences published by the NEON Biorepository Data Portal)

Ayres, E. 2019. Quantitative Guidelines for Establishing and Operating Soil Archives. Soil Science Society of America Journal, 83(4): 973-981. https://doi.org/10.2136/sssaj2019.02.0050  

opencc-by-4.0Mar 2020View details →

Model outputs for occurrence and hunting data‐based models of wild boar distribution and abundance, July 2019 update

These maps  are wild boar habitat suitability outputs based on newly available data of wild boar, and models for predicting wild boar relative abundance using hunting yields. Objectives: - Validation of previously produced hunting yield maps and new ones - Downscaling to 10x10 km grid - Downscaling to 2x2 km grid Model settings and predictors:     - Model from ENETWILD report August 2019 - Assuming cells as municipality in 10x10 km grid downscaling - Assuming cells as hunting grounds in 2x2 km grid downscaling     Conclusions guiding future methodological steps - To update wild boar hunting yield data for some specific regions; - To increase hunting yield data resolution; - To explore model independent parametrization for each bioregion. Files: August_2019_HY_nut00_10x10        >> Model outputs based on hunting yield GLM analyses August_2019_occurrences_bioclim   >> Model outputs based on Bioclim analyses August_2019_occurrences_glm         >> Model outputs based on Generalised linear model August_2019_occurrences_ksvm      >> Model outputs based on Support vector Machine analyses August_2019_occurrences_maxent   >> Model outputs based on Maxent analyses August_2019_occurrences_randomForest>> Model outputs based on Random Forest analyses --------------------------------------------------------------------------------------------------------------------------------------------------------- These maps are models obtained in intermediate phases of the ENETWILD project based on available information.  There are frequent updates in order to improve the results. For methodological approach and details check the paper:  ENETWILD‐consortium, P. Acevedo, S .Croft, G C Smith, J. A. Blanco-Aguiar, J. Fernandez-Lopez, M. Scandura, M. Apollonio, E.Ferroglio, Oliver Keuling, M. Sange, S. Zanet, F. Brivio, T. Podgórski, K.Petrović, G. Body, A.  Cohen, R. Soriguer, J. Vicente (2019). ENETwild modelling of wild boar distribution and abundance: update of occurrence and hunting data‐based models. EFSA Supporting Publications, 16(8), 1674E. <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fefsa.onlinelibrary.wiley.com%2Fdoi%2Fabs%2F10.2903%2Fsp.efsa.2019.EN-1674&data=02%7C01%7C%7Ca8ad922eefde42f5cb5208d7c5054851%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C637194498792136402&sdata=fqdiYEOqYIlHaDbp5a7kVdGQ6FWuFEydJNhSWOghH%2FQ%3D&reserved=0">https://efsa.onlinelibrary.wiley.com/doi/abs/10.2903/sp.efsa.2019.EN-1674</a> . Permission for reuse occurrence  outputs records is granted under the terms of a CC-BY-NC license. Permission for reuse hunting yield outputs is granted under the terms indicated by EFSA.

opencc-by-4.0May 2020View details →

Model outputs for update of occurrence and hunting yield-based data models for wild boar at European scale: new approach to handle the bioregion effect, May 2020 update

These maps are models obtained in intermediate phases of the ENETWILD project based on available information. There are frequent updates in order to improve the results. Objectives: - Incorporate additional data to provide new maps of wild boar suitability with a resolution of 2x2 km >>> file 3_June_2020_suitability_2x2.tif - New model based on hunting yield with different approaches to handle the biorregion effect >>> files 1_June_2020_HY_nut01_10x10_twostep.tif  &  2_June_2020_HY_nut01_10x10_pca.tif Model settings and predictors:     - Hunting yield modeling including biorregion effect as bioclimatic PCA scores - Hunting yield addressing biorregion effect in a two-step procedure with independent parametrization for each bioregion Conclusions guiding future methodological steps: - For wild boar suitability maps at 2x2 km, additional data on survey effort is critical in the southern bioregion - Hunting yield model predictions at 10x10 km grids overestimated the hunting bag numbers obtained from the external datasets - HY model with independent parametrization for each bioregion performed better that previous and new strategies For further details and methodological approach see the paper: ENETWILD-consortium, P. Acevedo, S .Croft, G C Smith, J. A. Blanco-Aguiar, J. Fernandez-Lopez, M. Scandura, M. Apollonio, E.Ferroglio, Oliver Keuling, M. Sange, S. Zanet, F. Brivio, T. Podgórski, K.Petrović, Soriguer, J. Vicente (2020) update of occurrence and hunting yield-based data models for wild boar at European scale: new approach to handle the bioregion effect. EFSA supporting publication 2020 TO BE COMPLETED Permission for reuse hunting yield outputs is granted under the terms indicated  by EFSA.

opencc-by-4.0Nov 2020View details →

Data and code for the manuscript: "Varying richness need not imply non-random species co-occurrence: implications for specifying null models"

Data and R code for the manuscript "Varying richness need not imply non-random species co-occurrence: implications for specifying null models".

opencc-by-4.0Oct 2024View details →

Data from: Area of habitat maps and validated occurrences for neotropical birds of conservation concern

Understanding species distributions is essential for advancing bird conservation, especially in the rapidly changing landscapes of the Neotropics, where habitat loss and degradation are accelerating. Area of Habitat (AOH) maps offer valuable spatial tools for illustrating species distributions by highlighting potentially suitable habitats within their geographic range. In this study, we generated AOH maps for 713 neotropical bird species of conservation concern, which includes species listed as globally or nationally threatened, endemic, or with restricted ranges. Using primary biodiversity data and a structured geospatial workflow, we refined approximately 2.5 million occurrence records through a flagging process and validated 50,743 records manually. This unparalleled effort led to the creation of high-quality AOH maps, along with altitude-corrected Extent of Occurrence (EOO-DEM) and Inverse Distance Weighted (IDW) range maps.  Our AOH maps significantly improved species distribution predictions for 82% of species, over EOO-DEM maps. The validated occurrences and AOH maps produced in this study have wide-ranging applications, providing a valuable basis for the development of new species distribution models and for evaluating species’ natural history, extinction risk, and habitat threats. They also support the identification of priority areas for strategic conservation investments. Importantly, these maps played a key role in systematic conservation planning analyses for the Conserva Aves initiative, which is facilitating the creation of more than 80 new protected areas across Latin America, safeguarding 2 million hectares and improving the management of an additional 2 million hectares (<a href="https://conserva-aves.org/">https://conserva-aves.org/</a>).