Monitoring ocean health with autonomous technology

The ocean plays a vital role in sustaining life on Earth, but its expansive waters can be challenging to study and monitor long term. Environmental DNA, or eDNA, collected and analyzed by autonomous robots may be changing this.

Scientists use eDNA to detect the presence of aquatic species from the tiny bits of genetic material organisms leave behind. This DNA soup offers clues 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.

By combining two novel platforms developed by MBARI—the long-range autonomous underwater vehicle (LRAUV) and the Environmental Sample Processor (ESP)—researchers can tap into the potential for eDNA to expand the monitoring of ocean health.

Aquatic organisms leave behind a trail of cells, skin, waste, and mucus. Just a few drops of water can contain this cellular material in addition to microscopic animals, algae, viruses, and free DNA. Known as environmental DNA, or eDNA, these genetic clues can help scientists identify a diverse cast of characters long after they have moved on. Video: © 2022 MBARI

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. By equipping an LRAUV with ESP technology, researchers can expand the scale of ocean monitoring over time and space. By comparison, traditional sampling of eDNA in the ocean requires weeks on an expensive research vessel limited to a localized area.

Technology innovations like the LRAUV are reshaping conservation efforts by allowing a more frequent and persistent presence in the world’s ocean, enhancing our capacity to evaluate marine biodiversity.

Marine biodiversity is a measure of the abundance of individuals and species in the ocean. This interconnected mosaic of organisms—from the smallest plankton to the largest whales—supports food webs, produces the air we breathe, and regulates our climate.

Autonomous underwater robots like MBARI’s long-range autonomous underwater vehicle (LRAUV) carry a groundbreaking “laboratory-in-a-can” to sample environmental DNA (eDNA) and expand monitoring of ocean health. Image: © 2021 MBARI/Monterey Bay Aquarium

Because of the importance of understanding marine biodiversity, it is imperative that new technological tools used to measure diversity perform at levels similar to or better than current tools. Thus, MBARI collaborated with researchers at the NOAA Atlantic Oceanographic and Meteorological Laboratory and the University of Washington to determine if new robotic tools were as effective at sampling marine biodiversity as traditional ship-based methods. To do this, 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 Monterey Bay National Marine Sanctuary in 2017 and 2018. A 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, essentially “fingerprinting” the sample to identify which organisms may have been present.

“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. Now, autonomous technology is helping us make better use of our time and resources to study new parts of the ocean.” —MBARI Senior Research Technician Kobun Truelove

Related organisms share certain DNA sequences in common. These sequences are known as gene markers. When researchers analyzed gene markers from eDNA samples—using a technique known as metabarcoding—the markers could be sorted into similar groups, providing a snapshot of the biological groups present and providing a measure of biodiversity. The researchers analyzed four different gene markers, each representing a slightly different level of the food web. Together, the results yielded a holistic picture of community composition, but most importantly, the samples collected from research ships and autonomous vehicles revealed similar patterns of biodiversity.

eDNA-detecting robots represent an exciting step forward for monitoring marine ecosystems. Now, instead of physically capturing each species, researchers can start to more broadly characterize biological community structure in the ocean by simply taking water samples in areas of interest.

Using technology to study biodiversity has further advantages. For instance, LRAUVs are not tied to ship schedules, and can travel for weeks at a time and hundreds of kilometers. They can enable more frequent sampling in areas of interest than traditional research vessels, which typically only visit remote sites infrequently. And they can be quickly and inexpensively turned around, remaining in areas far longer than traditional research vessels, despite the weather. Ship-based research will continue to play an important role in oceanographic studies, but adding new autonomous technology to the toolkit will expand the capacity for research, monitoring, and resource management. Ultimately, MBARI researchers envision deploying a fleet of LRAUVs equipped with ESP technology.

That autonomous future is already becoming a reality.

This past fall, MBARI took part in a unique expedition to explore the remote waters of Alaska with uncrewed technology.

The Aleutians Uncrewed Ocean Exploration expedition sought to collect ocean mapping and environmental data in unexplored waters around the Aleutian Islands.

NOAA Ocean Exploration and the Bureau of Ocean Energy Management were the primary sponsors of the Aleutians Uncrewed Ocean Exploration expedition, which was led and facilitated by NOAA Ocean Exploration Cooperative Institute and partners—the University of New Hampshire, Saildrone, and MBARI. Additional funding and support came from the National Oceanographic Partnership Program, NOAA Research, NOAA’s Office of Coast Survey, NOAA’s Deep Sea Coral Research and Technology Program, and the U.S. Geological Survey (USGS).

The expedition leveraged the Saildrone Surveyor, an advanced uncrewed surface vessel piloted remotely from shore and powered primarily by wind and solar energy.

The Saildrone Surveyor (right) in Alaska’s Dutch Harbor at the beginning of the Aleutians Uncrewed Ocean Exploration expedition. Image courtesy of Saildrone

The Surveyor carries a suite of instruments to collect acoustic, oceanographic, and meteorological data to support a wide range of research applications. During the expedition last fall, its primary research objective was to map several areas around the Aleutian Islands that had never been mapped with high resolution. The Surveyor also carried MBARI’s ESP technology to sample eDNA during its transit from Alameda, California, to Dutch Harbor, Alaska, and along its mapping route, crisscrossing the Aleutian Islands.

This partnership further underscored how MBARI technology can help researchers and resource managers to better understand the health of parts of the ocean that are not easily accessible with crewed research ships.

The work done at MBARI with LRAUVs, ESPs, and eDNA is contributing directly to national programs like MBON (Marine Biodiversity Observation Network), as well as international ones associated with the UN Decade of Sustainable Development like Marine Life 2030 and OBON (Ocean Biomolecular Observation Network).

A new partnership between MBARI and USGS is developing a portable robotic sampler to detect invasive species, pathogens, parasites, and other threats to our nation’s rivers and streams. Image: Jim Birch © 2018 MBARI

MBARI’s groundbreaking ESP technology is helping researchers study more than just ocean biodiversity and health—this innovative technology was noticed by water scientists at USGS, the agency responsible for the health and management of America’s waterways.

The USGS has successfully used eDNA methods as an early-detection strategy for biological threats to important aquatic systems. For example, the USGS has previously conducted eDNA surveys for invasive carp, dreissenid mussels, round gobies, and Burmese pythons in water basins across the country, but they have found that sample acquisition is still an expensive and time-consuming factor for their biological questions.

Several years ago, USGS scientists talked to MBARI scientists about the possibility of using an ESP as an automated sample-collection robot. Would that be possible? Not only possible but surprisingly successful!

Starting in 2018 and running for three summers, the USGS was able to collect at least one sample every day for more than two months, providing a window into whether certain invasive species were present in some of the most iconic western rivers in the United States.

MBARI’s ESP was designed for deployment in rugged marine environments. A new portable eDNA sampler will allow for nimble deployments of this technology in rivers and streams. Image courtesy of Devin Jones, USGS

Despite these successful demonstrations, there were drawbacks. The current ESP design was built to be a sturdy 181-kilogram (400-pound) machine for use in rugged marine environments. The ESP was also designed to do much more than simply acquire and preserve material, so half of the device was unused. The ESP was also difficult to install and move, and would not scale to large numbers of sites due to cost and complexity. Most importantly, scientists frequently expressed interest in simply collecting and preserving samples, leaving the processing for the laboratory once the instrument was collected. Such a device could thus be smaller, lighter, and less expensive.

It was from these proof-of-concept studies that a new cooperative agreement was signed in 2022 between MBARI and the USGS. This project, called the Rapid eDNA Assessment and Deployment Initiative and Network, or READI-Net, will develop portable robotic DNA samplers capable of independently acquiring and preserving eDNA samples. These devices will have a myriad of uses, from ship-board operations to autonomous monitoring of coastal and inland streams. This partnership will help advance the detection of invasive species, pathogens, and parasites that cause ecological and economic damage to aquatic systems, as well as provide aquatic biodiversity data.

As part of the new agreement, MBARI and USGS will design a new robotic eDNA sampler. This device will be smaller, lighter, and easy to carry—about the size of a microwave oven—with an easy-to-use computer to facilitate deployments and wireless connectivity so researchers can control sampling remotely. These new eDNA samplers will provide high-quality data for scientists, leading to effective monitoring for aquatic biological threats.

eDNA contains a snapshot of an ecosystem—genetic traces that animals, viruses, and microscopic organisms leave behind. MBARI researchers developed the Environmental Sample Processor (ESP) to autonomously collect, preserve, and analyze eDNA. Video: © 2022 MBARI

The eDNA robot will be programmed to take samples frequently, at any time of day, and will collect large amounts of data that must be managed and analyzed. The USGS READI-Net researchers will develop field and laboratory procedures to acquire high-quality data, produce analytical tools to process and validate large volumes of information, and create products for the public and decision-makers to easily visualize results.

Funding for this new partnership comes from President Biden’s Bipartisan Infrastructure Law, which includes a $510.7 million investment for the USGS.

eDNA has become a critical tool to study and steward the environment. MBARI is leading efforts to analyze eDNA samples remotely, complemented by deeper analysis in the lab. As MBARI continues to invest in research programs and technologies rooted in eDNA, we are upgrading our facilities to support this new, specialized field. A new eDNA laboratory is under construction at MBARI that will give our researchers and engineers the space they need to process eDNA samples and develop new robotic tools for expanding autonomous analysis in the field.

With a new lab and continued technological developments, MBARI innovation will transform the monitoring of aquatic environments that are so vital to humanity.

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