Table 1.
A curated Spotify Playlist with songs at or near 160 bpm, the required shaking rate for FloppE-Dip samples (https://open.spotify.com/playlist/4L8gu97y0w6dzvLa3hRcLn?si=92c791f833ca4714).
Fig 1.
An overview of the FloppE-Dip protocol workflow.
Resealable baggies each containing a single membrane are prepared in advance of field work in a laminar flow hood to avoid contamination. Each sample is collected with fresh materials (refer to Figure 4). As Sample collection is done with fresh cups and bottled water with clean hands or wearing nitrile gloves. Take particular care not to touch the membrane or inside of the cup or baggie with bare or contaminated hands at any point. In the field, 180 mL of sediment and 180 mL fresh bottled water (using a 90 mL paper cup twice for each) are added to a resealable baggie containing a 3 x 3 cm2 piece of membrane, the baggie shaken for 30 s at 160 bpm, allowed to settle for 10 min, and the membrane transferred to a manilla coin envelope using clean forceps. Users are encouraged to wear nitrile gloves when transferring the membrane to the coin envelope. The envelope is then put into a small resealable baggie containing silica beads and stored in a manual defrost freezer (-20°C) until the DNA is extracted.
Table 2.
The sampling protocol for the FloppE-Dip samples (FD 1-4 and FD Blank) as well as the filtration samples (F1 and F Blank) showing the shake time and settling or contact times. Four replicates of each sediment sample were collected and two replicates of each blank.
Fig 2.
A field site map showing the locations where sediment samples for conventional filtration and FloppE-Dip samples were collected from beaches along the Salish Sea, British Columbia, for eDNA analysis.
Latitude and longitude are indicated on the x and y axes.\ The map lines delineate study areas and do not necessarily depict accepted national boundaries.
Table 3.
The average estimated copy number (copies/L) and corresponding standard error (SE) for sediment samples spiked in American bullfrog tissue slurry collected via the FloppE-Dip method (FD) or conventional filtration (F). The FD membranes had a contact time with the spiked sediment in water for either 0, 5, 10, or 20 min and the F sample was filtered for 30 min. All samples were collected in quadruplicate.
Table 4.
The average estimated copy number and corresponding standard errors (copies/L) for each intertidal sand sample ran on the IntegritE-DNA® and the eAMPE5 qPCR assays in the Field Application experiment.
Fig 3.
A box plot of the two data sets obtained from the filter samples and FloppE-Dip samples collected from beaches along the Salish Sea, British Columbia.
The copy number (copies/L) distribution and variability within each sample type and between the sample types is shown. A) IntegritE-DNA® and B) eAMPE5 qPCR assays. Significant differences between pairwise comparisons using the Wilcoxon test are indicated by “*”.
Fig 4.
Comparison of time and monetary costs of conventional filtration versus the FloppE-Dip method.
The basic equipment and consumables needed for each method are shown and the overall cost estimates in USD are indicated in bold.