New York Harbor environmental DNA detection of fish, 12 month update

Updated dataset for "Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary (PLOS ONE 2017 e0175186).

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.