16S rRNA amplicon sequences from river sediments and waters of the Bronx River Estuary, New York City
DNA sequences were amplified with primers 515F-Y and R806 (515F: GTGYCAGCMGCCGCGGTAA + an identifier barcode; 806R: GGACTACNVGGGTWTCTAAT) using the Qiagen HotStarTaq Plus Master Mix Kit (Qiagen, USA) under standard conditions. After agarose gel checks, samples were purified with calibrated Ampure XP beads (Agencourt Bioscience, USA). Reads were processed using QIIME2 (v. 2019.10). First, the DADA2 plugin was used to quality filter, denoise, and join paired-end reads. Next, to taxonomically classify reads, the nave Bayesian q2-classifier as implemented in QIIME2 was used to compare reads to the SILVA 16S rRNA classifier trained on the 515f/806r priming region. Once taxonomic classification was complete, the data were exported for analysis in R.