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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  

openCC0Aug 2024View details →

Mapping EDI, NEON and DataONE units to the QUDT ontology, 2022

In the metadata of digital environmental datasets, automated processing is hindered by the wide variety of representations for unit that may be human-readable, but may not be unambiguous or machine-interpretable, (e.g., grams per square meter, gm/m2, g/m2, gm-2, g/m^2, g.m-2, g m-2 and gramPerMeterSquared). Matching disparate representations of the same unit into a single unit concept from an ontology assists with interpretation and reuse by providing a linkage to a complete unit definitions with label, description, dimensions. Datasets with shared units can be identified during searches, and are more suitable for automating analyses and potential transformation. This dataset contains data and code associated with a project to map units in ecological metadata collected between 2013 and 2022 by DataONE, the Environmental Data Initiative and the U.S. National Ecological Observatory Network to the QUDT ontology using successive string transformations. Data entities include a) raw metadata as received (355,057 unit instances) b) integrated raw data c) substitution tables for string transformations d) resulting lookup table for 896 distinct units matched to QUDT units e) associated R code used for QUDT matching plus a web service and R functions for adding annotation elements to Ecological Metadata Language metadata documents. Using these substitutions and code, 91% of unit instances in the raw metadata could be matched to QUDT. Data and results are discussed in “Porter JH, M O’Brien, M Frants, S Earl, M Martin, C Laney. (in review) Using a Units Ontology to Annotate Pre-Existing Metadata. Submitted to Scientific Data.

opencc-by-4.0Nov 2019View details →

Fig. 1 in Glyphosate commercial formulation effects on preoptic area and hypothalamus of Cardinal Neon Paracheirodon axelrodi (Characiformes: Characidae)

Fig. 1. Cross-section of preoptic area (AP) and posterior diencephalic region (PDR) of Paracheirodon axelrodi showing its different neuronal nuclei. a. Panoramic view of AP showing different neuronal nuclei. b. Panoramic view of PDR, including HT neuronal nuclei. Technique: high resolution optical microscopy (HROM) Bar 100 μm.

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R_JAGS code for estimation and analysis of species-area-relationship (SAR) parameters from NEON (National Ecological Observatory Network) data on plant surveys

Invasive species science is heavily geared toward the invasive agent. However, management to protect native species also requires a proactive approach focused on understanding the features affecting community vulnerability to invasion impacts. Vulnerability is likely the result of factors acting across spatial scales, from local to regional, and it is the combined effects of these factors that will determine the magnitude of vulnerability. We introduce an analytical framework that quantifies the scale-dependent impact of biological invasions from the shape of the native species-area-relationship (SAR). We leverage newly available, biogeographically extensive vegetation data from the US National Ecological Observatory Network to assess plant community vulnerability to invasion impact as a function of factors acting across scales. We analyzed more than 1000 SARs widely distributed across the USA along environmental gradients and under different levels of invasion. Results show that a decrease in native richness is consistently associated with invasive species cover, but it is only at relatively high levels of invasion that native richness is compromised. After accounting for variation in baseline ecosystem diversity, net primary productivity, and human modification, ecoregions that are colder and wetter seem to be most vulnerable to losses of native plant species at the local level, while warmer and wetter areas seem most susceptible at the landscape level. We also document how the combined effects of cross-scale factors result in a heterogenous spatial pattern of vulnerability. This pattern cannot be predicted by analyses at any single scale, underscoring the importance of accounting for factors acting across scales. Simultaneously assessing differences in vulnerability between distinct plant communities at local, landscape and regional scales provided outputs that can be used to inform policy and management aimed at reducing vulnerability to the impact of plant invasions.

opencc-zeroApr 2022View details →

opencc-zeroJun 2024View details →

Dataset: Neonode Inc. (NEON) Stock Performance

This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.

Linked collectors and determiners for: NEON Biorepository Invertebrate Bycatch Collection (Archive Pooling).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Invertebrate Bycatch Collection (Archive Pooling)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb">https://bionomia.net/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb">https://gbif.org/dataset/596bde6d-0df5-46cb-8eef-92dc3f169ceb</a>. Formatted as a Frictionless Data package.

opencc-by-4.0Jun 2020View details →

FIGURE 1 in Phylogenetic relationships of the neon tetras Paracheirodon spp. (Characiformes: Characidae: Stethaprioninae), including comments on Petitella georgiae and Hemigrammus bleheri

FIGURE 1 | Maximum Likelihood phylogenetic reconstruction of Stethaprioninae sensu Mirande (2018) using 16S ribosomal RNA and cytochrome C oxidase subunit I concatenated dataset after inclusion of Paracheirodon simulans and Petitella georgiae. Bootstrap values (≥ 75%) are shown near the nodes. Neon tetras are highlighted in red, and rummy-nose tetras are highlighted in blue.

Linked collectors and determiners for: NEON Biorepository Mammal Collection (Vouchers [Standard Sampling]).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Mammal Collection (Vouchers [Standard Sampling])". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/f28219f3-49cd-4b55-99ad-39f3ced87ddd">https://bionomia.net/dataset/f28219f3-49cd-4b55-99ad-39f3ced87ddd</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/f28219f3-49cd-4b55-99ad-39f3ced87ddd">https://gbif.org/dataset/f28219f3-49cd-4b55-99ad-39f3ced87ddd</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: NEON Biorepository Mammal Collection (Vouchers [Outside of Standard Sampling]).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Mammal Collection (Vouchers [Outside of Standard Sampling])". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/9f5e2bfa-8ea0-46c5-bc6b-909a82f67af4">https://bionomia.net/dataset/9f5e2bfa-8ea0-46c5-bc6b-909a82f67af4</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/9f5e2bfa-8ea0-46c5-bc6b-909a82f67af4">https://gbif.org/dataset/9f5e2bfa-8ea0-46c5-bc6b-909a82f67af4</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: NEON Biorepository Mammal Collection (Ear Tissue).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Mammal Collection (Ear Tissue)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/f3ca3b02-8e8b-4909-9628-abbe50cd44f1">https://bionomia.net/dataset/f3ca3b02-8e8b-4909-9628-abbe50cd44f1</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/f3ca3b02-8e8b-4909-9628-abbe50cd44f1">https://gbif.org/dataset/f3ca3b02-8e8b-4909-9628-abbe50cd44f1</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: NEON Biorepository Mammal Collection (Fecal Samples).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Mammal Collection (Fecal Samples)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/973879fb-3e36-49ca-ab09-01b87bea0deb">https://bionomia.net/dataset/973879fb-3e36-49ca-ab09-01b87bea0deb</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/973879fb-3e36-49ca-ab09-01b87bea0deb">https://gbif.org/dataset/973879fb-3e36-49ca-ab09-01b87bea0deb</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: NEON Biorepository Mammal Collection (Hair Samples).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Mammal Collection (Hair Samples)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/26b8da97-b067-4220-8335-7c267726ba41">https://bionomia.net/dataset/26b8da97-b067-4220-8335-7c267726ba41</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/26b8da97-b067-4220-8335-7c267726ba41">https://gbif.org/dataset/26b8da97-b067-4220-8335-7c267726ba41</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: NEON Biorepository Fish Collection (Vouchers).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Fish Collection (Vouchers)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/0c0258d8-e503-4d57-9734-92aad4072dd2">https://bionomia.net/dataset/0c0258d8-e503-4d57-9734-92aad4072dd2</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/0c0258d8-e503-4d57-9734-92aad4072dd2">https://gbif.org/dataset/0c0258d8-e503-4d57-9734-92aad4072dd2</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: NEON Biorepository Mammal Collection (Blood Samples).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Mammal Collection (Blood Samples)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/5ab197be-317f-438f-b1a6-daa2e9381cb2">https://bionomia.net/dataset/5ab197be-317f-438f-b1a6-daa2e9381cb2</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/5ab197be-317f-438f-b1a6-daa2e9381cb2">https://gbif.org/dataset/5ab197be-317f-438f-b1a6-daa2e9381cb2</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: NEON Biorepository Carabid Collection (Trap Sorting).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Carabid Collection (Trap Sorting)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/2564e9e2-0248-4a3b-8344-24fc0956ed73">https://bionomia.net/dataset/2564e9e2-0248-4a3b-8344-24fc0956ed73</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/2564e9e2-0248-4a3b-8344-24fc0956ed73">https://gbif.org/dataset/2564e9e2-0248-4a3b-8344-24fc0956ed73</a>. Formatted as a Frictionless Data package.

Linked collectors and determiners for: NEON Biorepository Carabid Collection (Pinned Vouchers).

Natural history specimen data linked to collectors and determiners held within, "NEON Biorepository Carabid Collection (Pinned Vouchers)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/8cb7c449-ba11-4464-865e-8029b8d772e8">https://bionomia.net/dataset/8cb7c449-ba11-4464-865e-8029b8d772e8</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/8cb7c449-ba11-4464-865e-8029b8d772e8">https://gbif.org/dataset/8cb7c449-ba11-4464-865e-8029b8d772e8</a>. Formatted as a Frictionless Data package.