MBARI’s new robotic sampler aims to transform monitoring of aquatic ecosystems

Developed in partnership with USGS READI-Net, FIDO uses DNA to detect threats like invasive species, pathogens, and parasites.

Why It Matters

A new low-cost autonomous robot expands access to MBARI’s engineering innovation, providing resource managers, decision-makers, and communities a tool for monitoring aquatic environments and mitigating the ecological and economic impacts of biological threats.

Invasive species, pathogens, and parasites can have serious ecological consequences for aquatic ecosystems and also put human health and economies at risk. Early detection of these biological threats is vital for mitigating their impact.

A scientific instrument sits in a research lab. The instrument has an orange handle, a bright blue plastic basket, and a square blue metal frame printed with the instrument’s name FIDO Filtering Instrument for DNA Observation, and logos for FIDO, USGS, and MBARI. Four additional instruments are lined up in a row in the background. In the foreground are several clear round plastic pucks with black rubber seals. In the background are a window and the white walls of a research lab. — With MBARI’s cutting-edge ESP technology at its core, FIDO aims to make autonomous eDNA sampling more accessible. Image: Marike Pinsonneault © 2026 MBARI

FIDO—the Filtering Instrument for DNA Observation—is a next-generation autonomous robot capable of sampling environmental DNA (eDNA) to detect harmful organisms in aquatic environments. Developed by MBARI engineers in partnership with USGS and the Rapid eDNA Assessment and Deployment Initiative and Network (READI-Net), FIDO is a vital new tool resource managers can use to monitor lakes, rivers, and streams.

“MBARI technology is transforming monitoring of aquatic ecosystems. We’ve applied our engineering innovation to a new robotic DNA sampler designed with affordability, reliability, and scalability in mind to detect the pathogens, parasites, and invasive species threatening waterways across the country,” said Jim Birch, director of MBARI’s SURF Center.

DNA detectives

Environmental DNA (eDNA) is any genetic material that organisms leave behind in their aquatic habitat. A trail of shed cells, skin, waste, and mucus allows scientists to identify organisms even when they are not physically observed or collected. Just a few drops of water contain cellular material in addition to microscopic animals, algae, viruses, and free DNA.

Scientists can use these genetic clues like a fingerprint to assess and monitor biodiversity, look for rare or endangered species, and track the spread of invasive species—all critical to understanding, promoting, and maintaining ecosystem health.

Building on MBARI innovation

MBARI’s Environmental Sample Processor (ESP) is a powerful robot for monitoring aquatic environments. Originally designed for the marine environment, the ESP can collect and process samples autonomously, leveraging advances in robotics and biological sensors to detect harmful organisms and toxins, assess water quality, and collect and preserve eDNA samples. The ESP can transmit data back to managers, providing near-real-time information on the health of rivers, lakes, and marine habitats. The ESP represents more than two decades of engineering innovation from the MBARI team.

Its use in the marine environment required the ESP to be sturdy, resulting in a 181-kilogram (400-pound) machine capable of operations up to 50 meters (164 feet) underwater. In 2017, USGS researchers were intrigued by the robotic sampling capabilities for long-term sample collection, particularly the collection of eDNA. Several demonstration deployments identified the need for an instrument that was smaller, lighter, and had streamlined functionality, that could be produced in large numbers and deployed in diverse environments.

Early detection and rapid response

An engineer with shaggy blond hair wearing a black sweatshirt and blue jeans prepares a scientific instrument in a lab. He is adjusting the instrument’s blue metal frame. In the foreground is another instrument with a square blue metal frame printed with the name FIDO Filtering Instrument for DNA Observation and logos for FIDO, USGS, and MBARI. In the background are benches, shelves, and cabinets of assorted engineering equipment. — MBARI engineers constructed a fleet of portable FIDO samplers that USGS researchers can deploy in remote locations to detect pathogens, parasites, and invasive species. Image: Marike Pinsonneault © 2026 MBARI

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. USGS has successfully used eDNA as an early-detection strategy for biological threats in aquatic environments, so resource managers and communities can mitigate their impact by taking effective and economical management actions.

READI-Net develops cutting-edge autonomous eDNA sampling robots, sampling protocols, and analytical tools enabling managers and scientists to design early-detection programs to address their specific needs.

In November 2022, MBARI partnered with the USGS to develop new portable robotic DNA samplers tailored to monitoring the health of rivers and streams and detecting biological threats. Over the past three years, MBARI engineers have been working to adapt core components of the ESP for use in a smaller and lighter device.

Combining the use of eDNA with an autonomous autosampler allows biosurveillance to occur any time of day or night, regardless of personnel schedules, human safety concerns, and adverse weather. Enhanced early detection will enable managers to rapidly respond to biological threats, increasing the chances for targeted, effective, and cost-effective management actions, and provides the opportunity to eliminate target species before they can become established in new habitats, spread, and cause ecological and economic harm.

Nimble new technology

A tray of dozens of clear, round plastic pucks with black rubber rings waits for inspection. — FIDO uses a carousel of pucks to collect and preserve eDNA that contains the genetic “fingerprints” of aquatic organisms. Image: Marike Pinsonneault © 2026 MBARI

FIDO is a new and innovative eDNA sampling technology designed to become the “best friend” of managers, scientists, and READI-Net partners tasked with aquatic biosurveillance and biomonitoring.

The instrument can collect and preserve up to 144 samples. Weighing just 22 kilograms (50 pounds), it is small enough to be carried into the field by a single person. The system filters environmental water through standard 47-millimeter (1.8-inch) filters housed in reusable filter pucks, and preserves the collected material for later analysis. Multiple FIDO instruments can be controlled from a single cloud web interface, allowing researchers to efficiently monitor networks of instruments.

FIDO was also designed to be produced at relatively low cost, making it accessible to as wide a range of users as possible.

Expanding access

In December, MBARI engineers hosted a two-day workshop to train USGS READI-Net project members and collaborators on the use of FIDO, which included the deployment of two FIDO instruments in Moss Landing harbor adjacent to MBARI’s research facilities. Workshop participants also worked with MBARI staff to prepare a user manual for FIDO.

Members of the USGS READI-Net team will conduct further testing of FIDO in the lab this winter. In the summer, they will begin field testing the instrument in a variety of environments, including USGS stream gages, research vessels, and invasive species corridors.

FIDO will advance READI-Net’s ability to support its partners conducting aquatic biosurveillance and biomonitoring by providing technology that is more affordable, capable of doing more work, and provides the user flexibility on when, where, and how to use it. Having affordable, technologically advanced, and well-tested tools that quickly detect novel biological threats enables managers to rapidly respond and protect the ecosystems, recreation opportunities, and local and regional economies.

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.

This work is supported by the Infrastructure Investment and Jobs Act (IIJA) to advance a National Early Detection and Rapid Response (EDRR) Framework with additional funding from the David and Lucile Packard Foundation.

Story by Senior Science Communication and Media Relations Specialist Raúl Nava

For additional information or images relating to this article, please email pressroom@mbari.org.

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