Fishing for genetic signals

Fish are messy inhabitants of their freshwater homes. As they swim, mate, and bump up against obstacles, they leave behind tiny clues pointing to their presence long after they swim away. These sloughed-off cells, waste, and tissue combined with free DNA, algae, and microscopic organisms make up a genetic soup of environmental DNA (eDNA). Sampling, preserving, and analyzing this eDNA is like finding nature’s fingerprint at a crime scene and using it as a tool for smarter freshwater management.

In most cases, when managers want to know how many individuals of a certain species are present in a river or stream, they have to go to the site to count them by hand. Besides the inconvenience of sending staff out to a site at regular intervals, this process easily misses those species that are rare or infrequent in the system—you have to see it to know it was there.

eDNA monitoring is a boon to managers looking to more efficiently, frequently, and broadly monitor freshwater systems. Chris Scholin, President and CEO of MBARI, incepted the idea for an autonomous platform that could sample and analyze eDNA while a postdoctoral researcher at MBARI. The concept ultimately led to the development of MBARI’s Environmental Sample Processor (ESP), which samples and archives eDNA so that researchers can see a series of biological snapshots from an aquatic system.

eDNA degrades over time as it is exposed to UV radiation and other factors in the environment. Regular autonomous sampling enables managers to monitor rare and infrequent targets that would otherwise be missed by traditional sampling methods. Illustration: Fiona Martin © 2020 MBARI

Multiple factors primed the Scott Creek freshwater stream, which lies just north of Santa Cruz, as an optimal location for testing the application of eDNA monitoring. The creek is one of the southernmost habitats for endangered coho salmon and other species of interest like steelhead trout. The area is also at risk for the arrival of non-native New Zealand mudsnails and striped bass. The National Oceanic and Atmospheric Administration (NOAA) has documented fish counts of coho salmon for decades at the site, providing a consistent historical dataset to compare against eDNA samples.

The project was led by Jim Birch, director of the Sensors: Underwater Research of the Future (SURF) Center at MBARI, MBARI’s ESP team, and collaborators at Monterey Bay Aquarium, NOAA, and California State Polytechnic University, San Luis Obispo. Researchers at MBARI have been honing autonomous eDNA sampling capabilities with the ESP in various contexts, but this experiment was designed to answer questions about applying ESP technology as a tool for monitoring freshwater health.

  • How frequently would managers need to sample to see fluctuations in the eDNA signal?
  • Could you account for and subtract out the higher signal from nearby hatcheries?
  • What is the relationship between the eDNA signal and population abundance?

A second-generation ESP (2G ESP) was installed at a shelter next to the weir, where NOAA fish counts are regularly collected. Equipped with additional solar panels and telecommunications, the 2G ESP was deployed at the site from April 2019 to 2020.

A third-generation ESP sits on a platform near Scott Creek. Regular autonomous sampling by the ESP enables managers to monitor rare and infrequent targets that would otherwise be missed by traditional sampling. Image: Todd Walsh © 2019 MBARI

The instrument collected more than 700 samples during the year-long experiment by sampling as frequently as three times a day. This incredible volume of samples demonstrates that the ESP is an invaluable tool for the type of high-frequency monitoring necessary to catch anomalies before they become management problems.

One of the many benefits of MBARI’s engagement in public-private partnerships is tapping into existing resources to support technology transfer for broader applications. The Scott Creek experiment’s success emphasizes that ESPs could ultimately be installed with relative ease at USGS streamgage sites around the country.

These streamgage sites are often equipped with physical infrastructures like shelters or buildings, access to power, and telecommunications like satellite or radio. Additionally, they regularly monitor and update key streamflow data like temperature, salinity, and flow rate, which add helpful context to the eDNA samples.

The region is also facing a resurgence of grass carp, which decimate native vegetation and are notoriously difficult to eradicate once they gather to reproduce. Researchers are exploring how eDNA monitoring could be used as a reproductive blockade to identify their presence early and intervene.

Alex Hay, a researcher with the NOAA Southwest Fisheries Science Center, and Kevan Yamahara, an ESP specialist at MBARI, observe a rainbow trout retrieved from the downstream weir at Scott Creek. NOAA regularly conducts manual counts of fish in Scott Creek, which are a useful baseline for comparison with the ESP data. Image: Todd Walsh © 2019 MBARI

Although eDNA monitoring is not a silver bullet for freshwater management, it is an efficient and less invasive monitoring addition to the management toolkit. In streams like Scott Creek, eDNA can both indicate the presence of non-native species like mudsnails that pose a threat to the ecosystem and track the success of native species like coho salmon.

NOAA continues to test MBARI’s ESP as a tool for monitoring harmful algal blooms in the Great Lakes. These blooms typically appear in the summer and early fall when warm, nutrient-rich water prompts small blue-green algae (cyanobacteria) to produce a highly toxic compound called microcystin.

A long-range autonomous underwater vehicle (LRAUV) equipped with an ESP enables researchers to observe changes in the system on the fly. Whereas satellite monitoring is foiled by cloud cover, an LRAUV navigating the lake’s shallow waters can autonomously collect samples any time of day, rain or shine.

One of MBARI’s LRAUVs makes its way through the green, algae-rich waters of Lake Erie. Image: Ben Yair Raanan © 2019 MBARI

Maintaining a persistent presence in these systems leads to informed, proactive solutions. Monitoring harmful algal blooms in real-time in the Great Lakes region would enable managers to make smarter decisions about city water supplies.

With more evidence pointing to eDNA analysis as a breakthrough in monitoring aquatic systems, MBARI’s ESP technology is poised as the vehicle that will bring it to broad applications. Its ability to maintain a persistent presence in a system with minimal in-person maintenance and resources makes it a valuable long-term tool.

The ESP is not without some limitations. All eDNA studies require the simple act of acquiring samples; high-resolution sampling conducted by the ESP can lead to backlogs of samples waiting to be processed in the lab. A complete sample-to-analyses result will be required to fully recognize the full potential of ESP for eDNA management applications. The on-board ESP analytics, such as probe arrays and qPCR, are designed as targeted tools that could miss surprising observations. Samples that are archived within the instrument still have to be processed in a lab for broad-spectrum sequencing.

The ESP is a versatile and economical tool for monitoring key changes in aquatic health. This monitorial might include tracking the presence of native and non-native species, identifying harmful algal blooms, tracking pollution in our nation’s waterways, and studying ocean microbes. Illustration: Fiona Martin © 2020 MBARI

Yet, this technology offers the first real pathway for developing a kind of genomic weather map—a network of autonomous platforms providing a consistent and reliable stream of data for aquatic management and research. MBARI is leading the charge toward a more sustainable aquatic future by addressing the existing barriers to broad applications and leaning into valuable partnerships.

Monitoring eDNA at Scott Creek from MBARI on Vimeo.

Scott Creek, just north of Santa Cruz, California, is an optimal location for testing the application of eDNA monitoring in a freshwater stream. The creek is one of the southernmost habitats for endangered coho salmon and other species of interest like steelhead trout. The area is also at risk for the arrival of non-native New Zealand mudsnails and striped bass. NOAA has documented fish counts of coho salmon for decades at the site, providing a consistent historical dataset to compare against eDNA samples.

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