Soil Microbe Collection (DNA Extracts) (NEON-SOMC-DNA)

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). Archived extracts range from about 20 to 100 uL. See related links below for protocols and NEON related data products, which include information on the concentration of the DNA. The DNA extraction and sequencing protocols used by Battelle Applied Genomics are available in the NEON document library (https://data.neonscience.org/documents).

"Microbial"Microbial

Contacts: NEON Biorepository, biorepo@asu.edu
Collection Manager: Azhar Husain, azhar.husain@asu.edu
NEON Soil physical and chemical properties, periodic: https://data.neonscience.org/data-products/DP1.10086.001
NEON Soil microbe marker gene sequences: https://data.neonscience.org/data-products/DP1.10108.001
NEON Soil microbe metagenome sequences: https://data.neonscience.org/data-products/DP1.10107.001
NEON Soil microbe community composition: https://data.neonscience.org/data-products/DP1.10081.001
Collection Type: Preserved Specimens
Management: Live Data managed directly within data portal
Global Unique Identifier: 240b1266-5618-4b82-8be2-14cf9d2f6eb6
Digital Metadata: EML File
EDI Dataset page: https://www.doi.org/10.6073/pasta/0e289d3991e3cf3ac6a1844384a9d0aa
Cite this collection:
NEON Biorepository Data Portal. 2024. Soil Microbe Collection (DNA Extracts) (repackaging of occurrences published by the NEON Biorepository Data Portal) Environmental Data Initiative. https://doi.org/10.6073/pasta/0e289d3991e3cf3ac6a1844384a9d0aa (Accessed via the NEON Biorepository Data Portal, https://biorepo.neonscience.org/, 2024-06-18).
Collection Statistics
  • 14,467 specimen records
  • 14,467 (100%) georeferenced
  • 3,571 publication references
Extra Statistics
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Geographic Distribution - United States
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