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Scientists are using autonomous underwater robots to sample eDNA

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Environmental DNA (eDNA) is an emerging and robust method for use in marine research, conservation, and management, yet time- and resource-intensive protocols limit the scale of implementation. The tool detected organisms from all domains of life in the environment without visual or auditory observations.

In a significant step forward for monitoring the biodiversity of marine systems, a new study by MBARI scientists is using autonomous underwater robots to sample environmental DNA (eDNA). They combined two novel independent platforms: the long-range autonomous underwater vehicle (LRAUV) and the Environmental Sample Processor (ESP).

The LRAUV is a little robot that can go to far-flung ocean parts and stay there for long periods. The ESP is a robotic “laboratory-in-a-can” that filters seawater while preserving eDNA for future research.

By combining both technologies, scientists can expand the scale of ocean monitoring over time and space. Technology innovations like this are revolutionizing ocean conservation efforts. Both technologies allowed scientists to maintain a persistent presence in the ocean and monitor changes in sensitive ecosystems in ways that were not possible previously.

Kelly Goodwin, a co-author of the study and collaborator at the National Oceanic and Atmospheric Administration (NOAA), said, “Organisms move as conditions change in our oceans and Great Lakes, affecting the people and economies that rely on those species. We need cheaper and more nimble approaches to monitor biodiversity on a large scale. This study provides the synergistic development of eDNA and uncrewed technologies we need in direct response to priorities laid out in the NOAA Omics Strategic Plan.”

In collaboration with the NOAA Atlantic Oceanographic and Meteorological Laboratory and the University of Washington, scientists completed three expeditions in the Monterey Bay National Marine Sanctuary. The team coordinated sample collection between MBARI’s three research vessels, the NOAA Fisheries ship Reuben Lasker, and a fleet of MBARI’s LRAUVs.

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Scientists lowered bottles to a certain depth to gather and preserve water samples to collect and preserve water samples. In the meantime, an LRAUV equipped with an ESP sampled and preserved eDNA at similar depths and locations. The eDNA samples were sent back to the lab for further analysis.

Using a technique called metabarcoding, scientists analyzed eDNA samples and translated the data into a measure of biodiversity. They found four different types of gene markers, each representing a slightly different level of the food web.

The combined data provided a more comprehensive picture of community composition. Similar biodiversity patterns were seen in samples taken from research ships and autonomous vehicles.

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Kobun Truelove, a biological oceanographer at MBARI, said, “The findings from the study mark an exciting step forward for monitoring marine ecosystems. This work is all about increasing the scale of eDNA research. Instead of looking at an individual species, we can start to characterize biological community structure in the ocean more broadly.”

Francisco Chavez, MBARI Senior Scientist and a co-author of the study, said, “Good data are the bedrock of sustainable ocean management. Regular environmental DNA monitoring tells us who is there and what changes over time. When it comes to an understanding of the impacts of climate change—one of the biggest threats to ocean health—this information is essential.”

Filling in these data gaps is critical to strengthening global ocean health. Ship-based research will continue to play an essential role in oceanographic studies, but adding new autonomous technology to the toolkit will expand the capacity for research, monitoring, and resource management.

Journal Reference:

  1. Truelove, N.K., N.V. Patin, M. Min, K.J. Pitz, C.M. Preston, K.M. Yamahara, Y. Zhang, B. Raanan, B. Kieft, B. Hobson, L.R. Thompson, K.D. Goodwin, and F.P. Chavez (2022). Expanding the temporal and spatial scales of environmental DNA research with autonomous sampling. Environmental DNA. DOI: 10.1002/edn3.299

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