Abstract
Environmental DNA (eDNA) can be used to identify macroorganisms and describe biodiversity, and thus has promise to supplement biological monitoring in marine ecosystems. Despite this promise, scaling sample acquisition to the size and temporal scales needed for effective monitoring would require prohibitively large investments in time and human resources. To improve upon these problems, here we test the efficacy of an autonomous eDNA sampling system and compare results obtained to traditional eDNA sampling methods. The autonomous sampling instrument consisted of the Environmental Sample Processor, (ESP) coupled to an autonomous underwater vehicle (AUV). We tested equivalency between the ESP and traditional eDNA sampling methods by comparing the quantification of eDNA across a broad range of taxa, from microbes (SAR11), phytoplankton (Pseudo-nitzschia spp.), invertebrates (krill: Euphausia pacifica) to vertebrates (anchovy: Engraulis mordax). No significant differences in eDNA densities were observed between the sample collection and filtration methods. eDNA filters collected by the ESP were preserved and stable for 21 days, the typical deployment length of the instrumentation. Finally, we demonstrated the unique capabilities of an autonomous, mobile ESP during a deployment near Monterey Bay, CA, by remotely and repeatedly sampling a water mass over 12 hours. The development of a mobile ESP reveals the promise of utilizing eDNA measurements to observe complex biological processes.
Highlights
Management and conservation efforts aimed at protecting marine organisms and ecosystem function require observing species assemblages over long periods of time and over large areas (Pereira et al, 2013; Miloslavich et al, 2018; Muller-Karger et al, 2018)
In this study we addressed this need by (1) comparing gene abundances of target organisms collected robotically and traditionally from both experimental and native samples, and (2) evaluating the stability of preserved environmental DNA (eDNA) samples collected by the 3G Environmental Sample Processor (ESP) since there is a lag between in situ sample collections and their return to a laboratory. qPCR was utilized in this study to provide a quantitative measurement for making comparison between methods
We report the results of the indirect comparisons for completeness. eDNA concentrations of the taxa recovered using the LRAUVESP during field operations compared to those recovered using ship-based CTD Niskin sample collections that employed a benchtop-ESP and traditional methods are shown in Figure 3. eDNA concentrations recovered for anchovy (HKW = 0.19, pKW = 0.91), Pseudo-nitzschia (HKW = 1.85, pKW = 0.39), krill (HKW = 0.12, pKW = 0.95), and SAR11 (HKW = 1.07, pKW = 0.58) were similar using the three different sample collection and processing methods (n = 4)
Summary
Management and conservation efforts aimed at protecting marine organisms and ecosystem function require observing species assemblages over long periods of time and over large areas (Pereira et al, 2013; Miloslavich et al, 2018; Muller-Karger et al, 2018). Traditional monitoring approaches are often reliant on ships, human observers, and combinations of direct sampling (water, nets, fishing) and tagging of individual animals. Active surveillance has been utilized for monitoring invasive species or rare organisms of conservation concern with quantitative or digital PCR, such as white sharks (Lafferty et al, 2018), killer whales (Baker et al, 2018), and seastars (Uthicke et al, 2018). Most eDNA analytical procedures require a human presence to collect and process samples, which inherently limits where and how frequently collections can be made – especially when sampling sites cannot be accessed
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