MBARI has long been a leader in developing cutting-edge technology that allows researchers to study ecosystem health in novel ways. MBARI engineers are leveraging advances in sensing, computing, and communications to create innovative instruments for monitoring aquatic environments. We design, test, and iterate technologies that can then be broadly adopted by the scientific, resource management, and conservation communities.
MBARI’s Environmental Sample Processor (ESP) enables scientists and resource managers to monitor the health of remote aquatic environments. Equipped with advanced biological sensors and a wireless data connection, this “lab in a can” transmits real-time data about the health of rivers, lakes, and marine habitats and preserves samples for further study.
With its ESP, MBARI is revolutionizing monitoring of the ocean and our nation’s waterways. The ESP autonomously conducts analyses without constant human oversight, making it an efficient and cost-effective alternative to traditional sampling. This unique instrument helps scientists detect harmful organisms and toxins and assess water quality. The ESP can also collect environmental DNA (eDNA), the genetic material left behind by aquatic organisms. eDNA is a powerful tool for assessing and monitoring biodiversity.
The ESP represents more than two decades of engineering innovation from the MBARI team. Our researchers currently deploy two versions of the ESP. The second-generation (2G) ESP conducts stationary, autonomous sampling, real-time algal toxin detection, and eDNA collection and preservation. The third-generation (3G) ESP incorporates many of the same functions but is a highly portable system that can be carried by autonomous robots, including MBARI’s long-range autonomous underwater vehicle (LRAUV), making it suitable for more complex oceanographic studies.
In 2024, MBARI partnered with a wide range of collaborators, from federal resource managers to local communities, to leverage 2G- and 3G-ESP technology to study and protect freshwater and ocean ecosystem health.
Monitoring ocean-based climate solutions
Renewable energy is integral to addressing the climate crisis, but resource managers and policymakers need to know technologies like offshore wind turbines are safe for ocean ecosystems. Offshore wind farms introduce new challenges in biomonitoring. For example, Denmark’s Jutland Peninsula has 13 wind farms, with five more planned for construction. The Danish government uses ship-based surveys to monitor the impact of installing hundreds of wind turbines in shallow waters across this region. Ship-based sampling is expensive and requires substantial resources. Resource managers are increasingly looking to autonomous systems to conduct these biological surveys and grow their capacity to monitor ocean environments in space and time.
With funding from the Velux Foundation and the Independent Research Fund Denmark, MBARI partnered with researchers from the Danish Technical University (DTU) to deploy a pair of 3G-ESP LRAUVs in June 2024 to survey the biological community around a wind farm.
MBARI’s LRAUV is a nimble robot that can travel to remote areas of the ocean for extended periods. Outfitting the LRAUV with the 3G ESP enhances the vehicle’s capabilities by allowing resource managers to tap into the potential for eDNA—a measure of biological community health—to expand ocean health monitoring. The 3G ESP has cartridges mounted in a rotating carousel that can filter up to 60 individual water samples during a single deployment. In the lab, these filters are subjected to in-depth sequencing of collected DNA in order to identify which organisms may have been present. By deploying multiple vehicles, researchers can take a snapshot of ocean biodiversity over a large area. Repeated surveys can reveal changes in the community over time.
During the Denmark deployment, each vehicle surveyed around the same wind farm—one inside and one outside of the farm—gathering approximately 120 eDNA samples to compare the biological communities and thereby measure the wind farm's impact on the biology in the area. DTU researchers have since analyzed these samples to inform a year-long study to determine whether wind turbines affect marine biodiversity, and are now considering how this technology can be applied in other efforts, such as coastal resiliency.
Expanding surveying capacity with autonomous robots will enable resource managers to scale up biological monitoring of wind farms and other offshore infrastructure. The data collected by MBARI technology can potentially be used for future environmental impact assessments of wind turbines to ensure that offshore wind energy development is safe for marine life and communities.
In summer 2024, MBARI LRAUVs equipped with 3G-ESP instruments conducted biological surveys around a wind farm off the coast of Denmark to understand the potential impacts of offshore wind energy development on marine ecosystems. Image: Chris Preston © 2024 MBARI
Tracking toxic algae in the Great Lakes
Cyanobacteria, or blue-green algae, are microscopic bacteria naturally found in aquatic environments. Occasionally, these cyanobacteria produce harmful toxins during blooms. Blooms of toxic cyanobacteria—known as CHABs (cyanobacterial harmful algal blooms)—risk the health of humans, pets, and livestock and can devastate communities around the Great Lakes.
Lake Erie is a vital drinking water source for more than 2 million people along the Ohio and Michigan coasts and a vibrant economic hub for tourism. Millions of people flock to its shores yearly to enjoy swimming, fishing, and boating during the summer. However, its shallow depth, warm waters, and nutrient runoff from agriculture and urban areas make Lake Erie particularly vulnerable to CHABs, which have become increasingly prevalent in the lake in recent decades.
Since 2017, NOAA’s Great Lakes Environmental Research Laboratory (GLERL) has used a trio of 2G-ESP instruments to monitor Lake Erie water quality, providing near real-time toxin data about cyanobacteria blooms. The development of 3G-ESP technology offered an opportunity to expand monitoring capabilities. Since 2018, MBARI researchers and our NOAA collaborators have deployed a 3G-ESP LRAUV in Lake Erie, helping resource managers develop detailed toxicity warning systems and forecasts for lake communities. Advanced algorithms developed by MBARI software engineers were used to detect blooms and target water sample collections. The presence and prevalence of cyanobacterial toxins can be assessed immediately using surface plasmon resonance (SPR) technology, with results sent to shore in real time.
In 2023 and 2024, MBARI and NOAA researchers expanded their fieldwork into shallower areas of the lake by installing a 3G ESP on an uncrewed autonomous surface vehicle (ASV) that can survey waters the LRAUV system cannot access.
MBARI’s ESP technology in the Great Lakes offers continuous, real-time measurements of cyanobacterial toxins, overcoming limitations like cloud cover and satellite constraints that hinder traditional surveys. Capable of assessing bloom biomass and toxin levels, ESP technology has been routinely employed to support informed decision-making to protect public health and local economies.
To study CHABs in the shallowest parts of Lake Erie, during the 2024 fieldwork season, NOAA researchers outfitted an autonomous surface vehicle with MBARI’s 3G ESP. Image courtesy of Reagan Errera/NOAA GLERL
Empowering communities for wildlife conservation
The California Department of Fish and Wildlife has been monitoring declining returns of endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) in Northern California. Multiple groups have developed plans to help restore salmon populations in the McCloud River, an upper tributary of the Sacramento River.
The winter-run Chinook salmon are uniquely adapted to the cold, stable, spring-fed waters of the McCloud River, making them the only Chinook in the world that spawn in the summer. With the Shasta Dam blocking access to their historical habitat and droughts projected to intensify in California’s future, returning these salmon to their cold-water refuge—where they can be stewarded again by the Winnemem Wintu tribe—is essential for ensuring their survival and enhancing climate resilience.
MBARI partnered with the University of California, Davis, NOAA’s Southwest Fisheries Science Center, and the Winnemem Wintu tribe to deploy a 2G ESP in the McCloud River. This technology detects the genetic markers of Chinook salmon and monitors their downstream movements during times of the year when physical monitoring and fish collection are not possible. Since much of the river is inaccessible, the ESP provides critical insights into the salmon’s habitat use and migration timing, providing information that would otherwise remain unknown. This collaboration also involves members of the Winnemem Wintu tribe, dedicated to restoring Chinook salmon populations and preserving the tribe’s ancestral lands from Buliyum Puyuuk (Mount Shasta) down the Winnemem Waywaket (McCloud River) watershed.
If salmon fry are present, MBARI’s 2G ESP can noninvasively collect eDNA samples, helping resource managers track whether the fry have successfully made their way downstream. This summer, the team tested this concept by installing a 2G ESP on the McCloud River and collecting 130 eDNA samples that researchers at UC Davis and NOAA are analyzing to assess salmon fry's presence and relative abundance.
MBARI researchers navigated unexpected challenges from deploying the 2G ESP in a remote location, including protecting the device from curious bears and other local wildlife and weatherproofing its sensitive instrumentation from the intense summer heat. By leveraging the tribe's knowledge and the ingenuity of MBARI engineers, the team adapted the ESP to continue operating successfully throughout the summer survey.
Next year, the team will deploy a second 2G ESP to expand salmon monitoring. eDNA is a promising tool for studying salmon migration and detecting pathogens and predators that could impact the success of salmon reintroduction efforts.
MBARI’s 2G ESP is helping communities in Northern California evaluate salmon conservation strategies. Installing the instrument in this remote location required design modifications to protect it from curious wildlife and extreme summer heat. Image: © 2024 MBARI
Developing new nimble technology
Invasive species, pathogens, and parasites can damage aquatic systems ecologically and economically. They threaten commercial and recreational fishing industries and increase the risk of spreading diseases that can impact human health. The U.S. Geological Survey (USGS) has successfully used eDNA as an early detection strategy for biological threats in aquatic systems. However, sample acquisition is expensive and time-consuming.
In 2017, USGS researchers began using MBARI’s 2G ESP for eDNA monitoring. This pilot project identified the need for an instrument with a smaller footprint and streamlined functionality that could be produced in large numbers and deployed in diverse environments. In 2022, MBARI partnered with the USGS to develop a new portable robotic DNA sampler that can collect eDNA on filters for up to 144 individual sample events.
As part of a USGS program called the Rapid eDNA Assessment and Deployment Initiative and Network, or READI-Net, MBARI engineers adapted and streamlined our ESP technology and created a scalable, cost-effective DNA sampler. Named FIDO—the Filtering Instrument for DNA Observations sampler—this device was developed in record time and will enhance early detection and rapid-response methods to help resource managers contain and control aquatic biological threats.
In February, MBARI engineers installed the FIDO sampler on our dock in Moss Landing, California, for a two-week test of the instrument’s basic engineering functionality. Resource managers were invited to “test-drive” the FIDO sampler via their cell phones to assess its remote operation capabilities. This deployment provided insight into how resource managers can use FIDO to detect and respond to environmental changes.
Collaborations like READI-Net make MBARI’s engineering innovation more accessible to our peers. MBARI is committed to expanding access to our advanced research tools by prioritizing affordability and scalability and developing partnerships to transfer our technology to third parties for commercial production, opening up new possibilities for our work to have an even broader impact.
Building capacity for eDNA technology
In June 2024, the White House Office of Science, Technology, and Policy published the National Aquatic eDNA Strategy, part of a larger effort to advance sustainable management of marine and freshwater resources. Members of the MBARI team lent their expertise to help advance and inform this strategy. This plan elevates eDNA as an important tool for mapping and monitoring biodiversity and calls for increased collaboration among public and private agencies to improve and advance eDNA research and operations.
Expanding eDNA technology for monitoring and protecting aquatic ecosystems is critical to this strategy. The strategy aims to standardize eDNA practices, improve data sharing, and set performance metrics for reliable, consistent agency use. Through collaborative research and national standards, this strategy supports U.S. conservation goals by offering a science-driven, cost-effective approach to managing and safeguarding aquatic resources.
In November, MBARI teamed up with our education and conservation partner, the Monterey Bay Aquarium, to host an experiment for our peers in the eDNA technology field to test and validate autonomous eDNA sampling technologies. The Aquarium’s Animal Care team keeps a detailed record of the fishes, invertebrates, and algae that live in their Kelp Forest exhibit, making it an ideal model to assess instruments’ ability to detect genetic markers from a diverse community of marine life.
The experiment gathered data from MBARI’s 2G ESP, 3G ESP, and FIDO instruments, Cawthron Institute’s TorpeDNA passive sampler being tested through the Synchro research collaboration hosted at MBARI, and instruments commercially available from Aquatic Labs, Dartmouth Oceans Technologies, Inc., McLane Research Laboratories, Inc., Ocean Diagnostics, and Smith-Root.
The nine devices processed water samples from the Kelp Forest exhibit while researchers manually collected and tested water samples for comparison. Findings from this experiment will help the eDNA research community create standardized performance benchmarks that ensure data collected across a range of technologies are consistent. This will improve the scientific community’s ability to share data from biodiversity assessments and enhance decision-making for aquatic environments.
“Partnerships with scientists, resource managers, and community leaders are expanding access to MBARI technology to help guide decision-making about aquatic environments.”
—SURF Center Director James Birch
Looking toward the future
The ESP is a versatile and cost-effective tool to provide detailed, real-time information about aquatic ecosystems, transforming how we monitor the health of our ocean, lakes, and rivers. The application of ESP technology in diverse projects—from tracking harmful algal blooms in the Great Lakes to aiding salmon conservation efforts in Northern California—demonstrates its vast potential to support ecological research, improve environmental response strategies, and advance biodiversity monitoring.
MBARI engineering innovation has transformed how we study life around Monterey Bay. Our partnerships with NOAA, USGS, and others allow us to share MBARI technology with scientists, resource managers, decision-makers, and communities across the country and overseas. MBARI and our collaborators continue to find new ways to grow the ESP tech ecosystem, and we cannot wait to see what new science and conservation opportunities the future will bring.
Research Publications:
Kelly, R.P., D.M. Lodge, K.N. Lee, S. Theroux, A.J. Sepulveda, C.A. Scholin, J.M. Craine, E.A. Allan, K.M. Nichols, K.M. Parsons, K.D. Goodwin, Z. Gold, F.P. Chavez, R.T. Noble, C.L. Abbott, M.R. Baerwald, A.M. Naaum, P.M. Thielen, A.L. Simons, C.L. Jerde, J.J. Duda, M.E. Hunter, J.A. Hagan, R.S. Meyer, J.A. Steele, M.Y. Stoeckle, H.M. Bik, C.P. Meyer, E. Stein, K.E. James, A.C. Thomas, E. Demir-Hilton, M.A. Timmers, J.F. Griffith, M.J. Weise, and S.B. Weisberg. 2024. Toward a national eDNA strategy for the United States. Environmental DNA, 6(1): e432. https://doi.org/10.1002/edn3.432
Preston, C., K. Yamahara, D. Pargett, C. Weinstock, J. Birch, B. Roman, S. Jensen, B. Connon, R. Jenkins, J. Ryan, and C. Scholin. 2024. Autonomous eDNA collection using an uncrewed surface vessel over a 4200-km transect of the eastern Pacific Ocean. Environmental DNA, 6(1): e468. https://doi.org/10.1002/edn3.468
Ussler, W., G.J. Doucette, C.M. Preston, C. Weinstock, N. Allaf, B. Roman, S. Jensen, K. Yamahara, L.A. Lingerfelt, C.M. Mikulski, B.W. Hobson, B. Kieft, B.-Y. Raanan, Y. Zhang, R.M. Errera, S.A. Ruberg, P.A. Den Uyl, K.D. Goodwin, S.D. Soelberg, C.E. Furlong, J.M. Birch, and C.A. Scholin. 2024. Underway measurement of cyanobacterial microcystins using a surface plasmon resonance sensor on an autonomous underwater vehicle. Limnology and Oceanography Methods, 22: 681–699. https://doi.org/10.1002/lom3.10627
Zhang, Y., B. Kieft, B.W. Hobson, B.-Y. Raanan, W. Ussler, C.M. Preston, R.M. Errera, P.A. Den Uyl, A.V. Woude, G.J. Doucette, S.A. Ruberg, K.D. Goodwin, J.M. Birch, and C.A. Scholin. 2024. Using a long-range autonomous underwater vehicle to find and sample harmful algal blooms in Lake Erie. Limnology and Oceanography Methods, 22: 473–483. https://doi.org/10.1002/lom3.10621