Robot samples environmental DNA to monitor ocean health

Most of the ocean’s biodiversity is still unknown, with up to 2,000 new species being described every year. In order to obtain some more clues regarding the biological diversity in the world’s oceans, scientists have turned to robots.

As they move around the ocean, aquatic species leave behind tiny parts of genetic material. A research team from Monterey Bay Aquarium Research Institute (MBARI) is using autonomous underwater robots to obtain these samples, known as environmental DNA (eDNA) and learn more about biodiversity changes in sensitive areas, the presence of rare or endangered species, and the spread of invasive species - all critical to understanding, promoting and maintaining a healthy ocean.

“We know that eDNA is an incredibly powerful tool for studying ocean communities, but we’ve been limited by what we can accomplish using crewed research vessels," said Kobun Truelove, the lead author of the paper. "Now, autonomous technology is helping us make better use of our time and resources to study new parts of the ocean.” 

For the study, researchers combined two novel autonomous platforms developed by MBARI: the long-range autonomous underwater vehicle (LRAUV) and the Environmental Sample Processor (ESP). The LRAUV is a nimble robot that can travel to remote areas of the ocean for extended periods of time. The ESP is a robotic 'laboratory-in-a-can' that filters seawater and preserves eDNA for future study.

Technology innovations like this are revolution¡sing ocean conservation efforts. Currently, the sampling of eDNA in the ocean requires weeks on an expensive research vessel limited to a localised area. Instead, by equipping an LRAUV with ESP technology, the MBARI researchers can expand the scale of ocean monitoring over time and space, and monitor changes in sensitive ecosystems in ways that were not possible previously.

“Organisms move as conditions change in our oceans and Great Lakes, affecting the people and economies that rely on those species,” said Kelly Goodwin, a co-author of the study. “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 that were called for in the NOAA's 'Omics Strategic Plan. For this research, MBARI collaborated with researchers at the NOAA Atlantic Oceanographic and Meteorological Laboratory and the University of Washington to complete 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.

In the study, the ship-based team lowered bottles to a specific depth to collect and preserve water samples. Meanwhile, an LRAUV equipped with an ESP autonomously sampled and preserved eDNA at similar locations and depths. The eDNA samples were returned to the lab for in-depth sequencing.

In order to analyse the eDNA samples, the researchers used a technique known as metabarcoding. This method looks for short DNA excerpts and provides a breakdown of the groups present in the sample. The researchers analysed four different types of gene markers, each representing a slightly different level of the food web. Together, the results yielded revealed similar patterns of biodiversity. 

The findings from the study mark an exciting step forward for the monitoring of marine ecosystems.

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

The findings of the study have been published in Environmental DNA.

E&T looked at the problems of how scientists are tackling the world’s dead oceans in our recent issue.