• Thu. Jun 30th, 2022

Scientists use autonomous underwater robots to sample eDNA

ByRandall B. Phelps

May 24, 2022

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

In a significant advance 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 new independent platforms: the Long Range Autonomous Underwater Vehicle (LRAUV) and the Environmental Sample Processor (ESP).

The LRAUV is a small robot that can travel to distant ocean regions and stay there for long periods of time. ESP is a robotic “laboratory in a box” that filters seawater while preserving eDNA for future research.

By combining the two technologies, scientists can extend the scale of ocean monitoring in time and space. Technological innovations like this are revolutionizing ocean conservation efforts. Both technologies have enabled scientists to maintain a persistent presence in the ocean and monitor changes in sensitive ecosystems in ways not previously possible.

Kelly Goodwin, study co-author and National Oceanic and Atmospheric Administration (NOAA) collaborator, said: “Organisms are shifting as conditions change in our oceans and Great Lakes, affecting the people and economies that depend on these species. We need cheaper and more agile approaches to monitoring biodiversity at scale. This study provides the synergistic development of eDNA and unmanned technologies that we need in direct response to the priorities set out in the NOAA Omics Strategic Plan.

Working with NOAA’s Atlantic Oceanographic and Meteorological Laboratory and the University of Washington, scientists conducted three expeditions to the Monterey Bay National Marine Sanctuary. The team coordinated sample collection between MBARI’s three research vessels, NOAA fishing vessel Reuben Lasker, and a fleet of MBARI LRAUVs.

Scientists lowered the bottles to a certain depth to collect and store water samples to collect and store water samples. In the meantime, an ESP-equipped LRAUV sampled and stored eDNA at similar depths and locations. The eDNA samples were returned 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 genetic markers, each representing a slightly different level of the food web.

The combined data provided a more complete picture of community composition. Similar biodiversity patterns have been observed in samples taken from research vessels and self-driving vehicles.

Kobun Truelove, biological oceanographer at MBARI, said: “The results of the study mark an exciting step forward for the monitoring of marine ecosystems. This work aims to increase the scale of eDNA research. Instead of looking at an individual species, we can begin to characterize the biological community structure in the ocean more broadly.

Francisco Chavez, senior MBARI researcher and co-author of the study, said: “Good data is the foundation of sustainable ocean management. Regular monitoring of environmental DNA tells us who is there and what is changing over time. When it comes to understanding the impacts of climate change, one of the greatest threats to the health of the oceans, this information is essential.

Addressing these data gaps is critical to strengthening global ocean health. On-board research will continue to play a vital role in oceanographic studies, but the addition of new autonomous technology to the toolbox will expand research, monitoring and resource management capability.

Journal reference:

  1. Truelove, NK, NV Patin, M. Min, KJ Pitz, CM Preston, KM Yamahara, Y. Zhang, B. Raanan, B. Kieft, B. Hobson, LR Thompson, KD Goodwin and FP Chavez (2022). Expand the temporal and spatial scales of environmental DNA research with self-contained sampling. Environmental DNA. DO I: 10.1002/edn3.299