Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling

Abstract

Environmental DNA (eDNA) is an emerging and powerful method for use in marine research, conservation, and management, yet time‐ and resource‐intensive protocols limit the scale of implementation. Long‐range autonomous underwater vehicles equipped with autonomous environmental sample processors (LRAUV‐ESPs) provide a new means for scaling up marine eDNA sample collection and processing. Here, we used eDNA metabarcoding of four marker genes (mitochondrial 12S rRNA, bacterial and archaeal 16S rRNA, nuclear 18S rRNA, and mitochondrial COI), which encompass the diversity of marine species from microbes to vertebrates, to demonstrate the efficacy of an LRAUV‐ESP in sampling eDNA and assessing community structure in the Monterey Bay National Marine Sanctuary. The sequencing results from samples that were autonomously collected were comparable with those collected from a ship at similar locations, times, and depths, supporting previous results that found no significant differences using targeted qPCR. This study demonstrates the potential of equipping autonomous underwater vehicles with ESPs to greatly expand the scale of eDNA sample collection and processing and provide much needed information regarding the changing spatial and temporal patterns of marine biodiversity, especially in many data‐poor regions of the world's oceans.

Analysis of the Persistence and Particle Size Distributional Shift of Sperm-Derived Environmental DNA to Monitor Jack Mackerel Spawning Activity

“…On the other hand, when targeting species with unknown or variable spawning times of day, knowledge of the spawning time of day may be revealed by collecting a series of temporal samples across the spawning window and examining changes in the ratio. Although collecting a series of temporal samples over a long period of time is strongly limited by time and effort, several studies on eDNA monitoring using autosamplers have been reported in recent years, and further technological developments will hopefully solve this problem in the future. − …”

Lake Erie field trials to advance autonomous monitoring of cyanobacterial harmful algal blooms

“…Despite the environmental conditions and potential to sample different water masses, qPCR and sequencing results did not differ significantly between manual and autonomous sampling for all (12) parameters tested (Table 1). Ultimately, these Great Lakes field trials increased the range of environments in which the LRAUV-3G ESP has been successfully deployed, as previous demonstrations with qPCR (Yamahara et al, 2019) and amplicon data (Truelove et al, 2022) were restricted to openocean systems. Overall, the extensive agreement observed between sample collection methods (Table 1) supports the use of the LRAUV-3G Normalized abundance of sequence reads from genes of the full mcy operon (mcyA-J) versus only the mcyE gene based on the metagenomic data for samples collected in 2018 (grey) and 2019 (black).…”

“…Archive cartridges concentrated particles in the sample water via filtration through two stacked 25-mm diameter Durapore filters (EMD Millipore, Burlington, MA, USA) consisting of a 5-mm filter sitting directly on top of a 0.22-mm filter. Once filtration completed, the sample volume was recorded and ~1.6 mL of RNALater ® Stabilization Solution (Invitrogen, Carlsbad, CA, USA) was added to preserve the particulate samples for subsequent laboratory analyses (Pargett et al, 2015;Yamahara et al, 2019;Truelove et al, 2022). For lysis Den Uyl et al 10.3389/fmars.2022.1021952 cartridges, the concentration of particle-associated microcystin in the resulting lysate was measured onboard the LRAUV in near-real-time using a surface plasmon resonance instrument employing a competitive ELISA assay (Ussler et al, 2019).…”

“…Mission commands can be sent whether the vehicle is nearby, underwater, or in the middle of a mission and are received and implemented by the vehicle upon receiving incoming communications when surfacing. In prior open ocean deployments, the LRAUV-3G ESP has been used successfully to collect and preserve nucleic acid samples near Monterey Bay, CA and north of Oahu, HI (Yamahara et al, 2019;Zhang et al, 2019;Zhang et al, 2021;Truelove et al, 2022) .…”

Impact of preservation method and storage period on ribosomal metabarcoding of marine microbes: Implications for remote automated samplings

“…There is a growing toolbox and increasing application of automated water and particle sampling approaches ( Supplementary Table S1 ). As in situ molecular analysis is still an emerging technology ( Moore et al, 2021 ) and beyond the resource capacity of many observing programs, automated samplers mostly perform in situ preservation of sample material ( Yamahara et al, 2019 ; Lindsay, 2021 ; Truelove et al, 2022 ). In situ preservation intends to minimize signal modification over the extended duration of device deployment and laboratory processing.…”