COI amplicon sequences from river sediments and surface waters of the Bronx River Estuary, New York City
COI sequences were amplified the primers mlCOIintF (GGWACWGGWTGAACWGTWTAYCCYCC) and jgHCO2198 (TANACYTCNGGRTGNCCRAARAAYCA) using the Qiagen HotStarTaq Plus Master Mix Kit (Qiagen, USA) under standard conditions. After agarose gel checks, PCR products were purified with calibrated Ampure XP beads (Agencourt Bioscience, USA). DADA2 was used as a QIIME2 plugin to denoise and quality filter the sequences, assign amplicon sequence variants (ASVs), and generate a feature table of ASVs (features) and metadata (Callahan et al. 2016). Primers and low-quality base calls were trimmed at the ends of each single-end sequence during the DADA2 step. The decontam program was then run on the feature table to remove potential contaminants  (Davis et al. 2018).  Once taxonomic classification was completed using a custom database, the ASV feature table, taxonomy, and sample metadata were exported for analysis in R.