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 process...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2022-07-01
|
| Series: | Environmental DNA |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/edn3.299 |
| _version_ | 1818015788314918912 |
|---|---|
| author | Nathan K. Truelove Nastassia V. Patin Markus Min Kathleen J. Pitz Chris M. Preston Kevan M. Yamahara Yanwu Zhang Ben Y. Raanan Brian Kieft Brett Hobson Luke R. Thompson Kelly D. Goodwin Francisco P. Chavez |
| author_facet | Nathan K. Truelove Nastassia V. Patin Markus Min Kathleen J. Pitz Chris M. Preston Kevan M. Yamahara Yanwu Zhang Ben Y. Raanan Brian Kieft Brett Hobson Luke R. Thompson Kelly D. Goodwin Francisco P. Chavez |
| author_sort | Nathan K. Truelove |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-14T07:03:15Z |
| format | Article |
| id | doaj.art-1afaa0b13b87459e8b65c10d168d5127 |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-04-14T07:03:15Z |
| publishDate | 2022-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-1afaa0b13b87459e8b65c10d168d51272022-12-22T02:06:40ZengWileyEnvironmental DNA2637-49432022-07-014497298410.1002/edn3.299Expanding the temporal and spatial scales of environmental DNA research with autonomous samplingNathan K. Truelove0Nastassia V. Patin1Markus Min2Kathleen J. Pitz3Chris M. Preston4Kevan M. Yamahara5Yanwu Zhang6Ben Y. Raanan7Brian Kieft8Brett Hobson9Luke R. Thompson10Kelly D. Goodwin11Francisco P. Chavez12Monterey Bay Aquarium Research Institute Moss Landing California USAOcean Chemistry and Ecosystems Division Atlantic Oceanographic and Meteorological Laboratory National Oceanic and Atmospheric Administration Miami Florida USAMonterey Bay Aquarium Research Institute Moss Landing California USAMonterey Bay Aquarium Research Institute Moss Landing California USAMonterey Bay Aquarium Research Institute Moss Landing California USAMonterey Bay Aquarium Research Institute Moss Landing California USAMonterey Bay Aquarium Research Institute Moss Landing California USAMonterey Bay Aquarium Research Institute Moss Landing California USAMonterey Bay Aquarium Research Institute Moss Landing California USAMonterey Bay Aquarium Research Institute Moss Landing California USAOcean Chemistry and Ecosystems Division Atlantic Oceanographic and Meteorological Laboratory National Oceanic and Atmospheric Administration Miami Florida USAOcean Chemistry and Ecosystems Division Atlantic Oceanographic and Meteorological Laboratory National Oceanic and Atmospheric Administration Miami Florida USAMonterey Bay Aquarium Research Institute Moss Landing California USAAbstract 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.https://doi.org/10.1002/edn3.299biodiversitybiomonitoringenvironmental DNAmarine protected areas |
| spellingShingle | Nathan K. Truelove Nastassia V. Patin Markus Min Kathleen J. Pitz Chris M. Preston Kevan M. Yamahara Yanwu Zhang Ben Y. Raanan Brian Kieft Brett Hobson Luke R. Thompson Kelly D. Goodwin Francisco P. Chavez Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling Environmental DNA biodiversity biomonitoring environmental DNA marine protected areas |
| title | Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling |
| title_full | Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling |
| title_fullStr | Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling |
| title_full_unstemmed | Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling |
| title_short | Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling |
| title_sort | expanding the temporal and spatial scales of environmental dna research with autonomous sampling |
| topic | biodiversity biomonitoring environmental DNA marine protected areas |
| url | https://doi.org/10.1002/edn3.299 |
| work_keys_str_mv | AT nathanktruelove expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT nastassiavpatin expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT markusmin expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT kathleenjpitz expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT chrismpreston expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT kevanmyamahara expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT yanwuzhang expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT benyraanan expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT briankieft expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT bretthobson expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT lukerthompson expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT kellydgoodwin expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling AT franciscopchavez expandingthetemporalandspatialscalesofenvironmentaldnaresearchwithautonomoussampling |