This collection contains genetic extracts of benthic microbes collected during aquatic microbial sampling (NEON sample class: mic_dnaExtraction_in.ambDnaSampleID,mic_dnaExtraction_in.ambDnaOnlySampleID). Benthic microbe samples are collected at the same time and location as periphyton (microalgae) samples, three times per year in wadeable streams during aquatic biology bout windows, roughly in spring, summer, and fall. Samples are collected using field-sterile methods 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). Cobble scrubs are filtered on 0.22 um Sterivex capsule filters, capped and flash-frozen in the field. Grab samples of sediment (silt, sand) or plant material/epiphyton are collected when appropriate and flash frozen in the field. Frozen samples are shipped to an analytical facility for DNA extraction, sample preparation, and shotgun metagenomic sequencing (only for samples collected during the summer collection bout), marker gene sequencing (and subsequent analysis of community composition), and microbial abundance (qPCR). Laboratory metadata are delivered to NEON for QC testing and acceptance, and then are formatted for upload to public sequence repositories. Genetic extracts in 96-well plates are archived at -80 degrees Celsius. See related links below for protocols and NEON related data products. The DNA extraction and sequencing protocols used by Battelle Applied Genomics are available in the NEON document library (https://data.neonscience.org/documents).