In situ Autonomous Acquisition and Preservation of Marine Environmental DNA Using an Autonomous Underwater Vehicle

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 spatial and temporal scales needed for effective monitoring would require prohibitively large investments in time and human resources. To address this challenge, we evaluated 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 techniques by comparing the quantification of eDNA across a broad range of taxa, from microbes (SAR11), phytoplankton (Pseudo-nitzschia spp.), and invertebrates (krill: Euphausia pacifica) to vertebrates (anchovy: Engraulis mordax). No significant differences in eDNA densities were observed between the two 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 h. The development of a mobile ESP demonstrates the promise of utilizing eDNA measurements to observe complex biological processes in the ocean absent a human presence.

MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples

“…However, to perform eDNA biodiversity monitoring on a scale comparable to that of physical attributes, several technical challenges are yet to be overcome. For example, it is essential to develop an autonomous sampling instrument, called an "environmental sample processor" (ESP) (Scholin et al 2017), which is a robotic device that can be programmed to automate water sample filtration and preservation of the captured material for immediate analyses in situ (Yamahara et al 2019;Fukuba et al 2019). Furthermore, such instrumentation should be cost-effective to be installed in large numbers over a wide area.…”

Quantitative PCR assays to detect humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge) in marine water samples

“…Biomonitoring for common murre, rockfish, and whales in the CCE is usually carried out using visual surveys. The assays we developed here, along with assays that have been previously developed for krill, sardines, anchovies, and mackerel [36,51] In addition to increased monitoring efforts on specific species, an important emerging use of such data sets in the CCE is understanding larger scale questions such as how global climate change is affecting food webs [52].…”

“…Samples for testing the humpback whale assay were collected from the surface of the water column using a 10 L 10% HCl-acid washed, autoclaved polypropylene carboy (Nalgene, Rochester, NY) aboard the R/V Paragon.The samples used to test the shortbelly rockfish assay were collected aboard the R/V Reuben Lasker at 40 m depth using a Niskin array during conductivity-temperature-depth (CTD) casts.One liter water samples were collected from the Diving Birds Exhibit at the Monterey Bay Aquarium for testing the common murre assay using a 10% HCl-acid washed bottle. Water samples collected from the R/V Paragon were filtered and preserved with the Environmental Sample Processor using 0.22 µm pore size 255 mm diameter durapore filters (Millipore, Burlington, MA)[36]. All other water samples were filtered through 0.22 µm pore size 47 mm diameter durapore filters using DNA-clean, sterilized vacuum filtration devices.…”

Autonomous and In Situ Ocean Environmental Monitoring on Optofluidic Platform

“…Although we emphasize the applications of optofluidic platforms for the monitoring of chemical parameters in ocean environment in this review, they could also find uses in biological monitoring in the marine ecosystem. For example, a variety of in situ bio/biochemical analyzers (e.g., adenosine triphosphate analyzer and gene analyzer) have been developed on optofluidic platforms, most of them have been evaluated in the real ocean environments including the deep sea [103,104].…”