Surface Water Microbe Collection (DNA Extracts) (NEON-SWMC-DNA)

This collection contains genetic extracts from surface water microbes collected during aquatic microbial sampling (NEON sample class: mic_dnaExtraction_in.amcDnaSampleID,mic_dnaExtraction_in.amcDnaOnlySampleID). Surface water metagenomic samples are collected at the same time and location as 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). In wadeable streams, samples are collected near the downstream S2 sensor location. In lakes, samples are collected near the the 'buoy', 'littoral 1', and 'littoral 2' sensors, and sampling depth(s) is dependent on lake stratification. In rivers, samples are collected near the buoy sensor. The filters are frozen on dry ice in the field, and later are shipped on dry ice to an analytical facility for DNA extraction, sample preparation, and shotgun metagenomic sequencing (only for samples collected during July or August), marker gene sequencing (and subsequent analysis of community composition), and microbial abundance (qPCR). Laboratory metadata are then delivered to NEON for QC testing and acceptance, and then are formatted for upload to public sequence repositories. Details on sampling locations and timing are provided in the NEON document Surface Water Chemistry Sampling in Aquatic Habitats (https://data.neonscience.org/documents). Genetic extracts in 96-well plates from Battelle Applied Genomics are archived in the NEON Biorepository at -80 degrees Celsius. 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
Surface water microbe metagenome sequences data product: https://data.neonscience.org/data-products/DP1.20281.001
Surface water microbe marker gene sequences data product: https://data.neonscience.org/data-products/DP1.20282.001
Surface water microbe group abundances data product: https://data.neonscience.org/data-products/DP1.20278.001
Surface water microbe community composition data product: https://data.neonscience.org/data-products/DP1.20141.001
Surface water microbe cell count data product: https://data.neonscience.org/data-products/DP1.20138.001
Collection Type: Preserved Specimens
Management: Live Data managed directly within data portal
Global Unique Identifier: a8259a78-67f6-4045-b006-4d67035549f6
Digital Metadata: EML File
Cite this collection:
Surface Water Microbe Collection (DNA Extracts). Occurrence dataset (ID: a8259a78-67f6-4045-b006-4d67035549f6) accessed via the NEON Biorepository Data Portal, https://biorepo.neonscience.org/, 2024-04-14).
Collection Statistics
  • 1,177 specimen records
  • 1,177 (100%) georeferenced
Extra Statistics
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