New York Harbor environmental DNA detection of fish, 12 month update
33 additional water samples (109 total) were collected from August through December 2016, extending the original six-month study to twelve months.
Samples were analyzed as described in the original study. Briefly, one-liter water samples were filtered through a 0.45μM nylon filter, DNA was isolated using MoBio PowerSoil kit, amplified with broad-range vertebrate 12S primers, indexed with Nextera tags, and submitted to GENEWIZ for 2x150bp MiSeq sequencing. Fastq files were analyzed using DADA2 and unique sequences were submitted to GenBank using BLAST. Sequences matching fish species were selected for further analysis. The complete set of fastq files and associated data are deposited together with original dataset in NCBI Sequence Read Archive under BioProject ID PRJNA358446.
New findings include 1) fall decrease in species per sample; 2) seasonal species counts roughly paralleled water temperature in the estuary; and 3) six additional species detected (Fig. 1). The fall decrease in species counts strengthens the original finding, namely, eDNA detectability is coincident with known seasonal movements of fish populations in and out of the lower Hudson estuary. The complete data set further supports eDNA localization within the estuary: nearshore marine species eDNAs were more common in East River (Atlantic silverside, cunner, rock gunnel, scup, seaboard goby), and brackish estuary species eDNAs were more common in the Hudson River (American eel, hogchoker, naked goby) (Fig. 1).
At both sites, rarefaction analysis, new to this update, revealed a relatively small proportion of species produced the great majority of eDNA reads (Fig. 2). In particular, about 20% of species accounted for about 90% of reads at both sites; the predominant species differed by site consistent with known habitat preferences.
Table 1. Fish amplicon reads by sample.
Table 2. Fish 12s amplicon sequences.