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Studying environmental DNA and ocean currents to locate fish aggregations in Puerto Rico

Marine scientists in Puerto Rico are investigating if water samples can be used to determine what types of fish and other organisms are present in an ocean ecosystem, and how ocean currents play a role in detecting the presence of these organisms. This research on environmental DNA and fish aggregations, using an ADCP from Nortek, helps us understand our underwater world in a unique and previously unobtainable way.

Isla Mar Research Expeditions is a field-based marine education and research company founded and led by two fish biologists in Puerto Rico whose primary investigative focus is fisheries management.

Their mission is to provide marine science education, field-based research training and experience and public outreach in ocean conservation throughout Puerto Rico and other parts of the Caribbean.


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A calm day for eDNA sampling as the team heads offshore to the underwater research sites.

We had a chat with Fish Biologist Dr. Chelsea Harms-Tuohy about how the group has been using Nortek’s AWAC ADCP as part of their research.

The project, funded by NOAA’s Saltonstall-Kennedy grant program, is a pilot project that investigates the possibility of using eDNA – that is, environmental DNA, which is DNA of organisms that can be extracted from environmental samples – as a means for locating elusive fish spawning aggregations.


Early morning heading out to dive for the eDNA research project, which included deployment of an ADCP from Nortek.

These aggregations are generally difficult to locate, as doing so requires the observer to be present at exactly the right time and place. Thus, in an attempt to alleviate some of the traditionally field-intensive search-and-locate methodology, Isla Mar Research Expeditions scientists are piloting a method of collecting water samples at known fish spawning aggregation sites in Puerto Rico to see if they can detect the presence of their target fish.

What was the main focus of your eDNA sampling and fish aggregation research project, where you used a Nortek ADCP?

“This project was our response to the call to locate new fish spawning aggregations in Puerto Rico, with the goal of being able to monitor these aggregations for the future.

“This is no simple task, as locating aggregations requires cooperation with fishers, hours of diving and being in ‘the right place at the right time’, and can be equipment intensive (using passive acoustic devices to monitor for courtship-associated sounds, audible mating sounds that some fish produce that would indicate the potential presence of the target fish). Our research could provide fisheries management (both locally and nationally) with critical information about the timing and duration that a fish spawning aggregation remains in a particular (both spatially and temporally predictable) site. Our goal is to help sustain and replenish our fisheries in Puerto Rico.”


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The AWAC unit deployed on Isla Mar Research Expeditions’ home-made anchoring platform.

Pardon the ignorance, but what is eDNA sampling?

“eDNA is environmental DNA, or basically DNA that can be detected and obtained from an environmental sample. That sample can be soil, water, air ... DNA of all organisms in that sample can be extracted, or you can just extract DNA from target organisms – which can be a little tricky. In our case, we are searching for a needle in the haystack of targeting one particular fish species in our water samples, but we’re increasing the chances of detecting that target species by sampling during a time that fish is in a greater-than-normal abundance at the sample site.”

Why is your research on eDNA and fish aggregation beneficial for greater society and the advancement of science?

“This is an innovative tool that allows for more rapid assessment and less dive-intensive sampling for our field of fisheries science.

“The ability to detect the presence of fish at a site without actually having to verify that the fish is there is a way for us to rapidly search for unknown spawning aggregation sites. But this is essentially a pilot project, and the verdict is still out on whether this method will work as we hypothesize.

“In the past, we would need to see (or hear, with passive acoustics) the actual fish to know if it was at the spawning site. With eDNA we should be able to detect it was there with or without a visual or auditory record.”

Why did you choose to include Nortek’s ADCP in this research on eDNA sampling and fish aggregation?

“We contacted Nortek to use the AWAC ADCP because we did not have a unit ourselves and were trying to find someone willing to work with us on our budget and provide rental of a unit. A colleague suggested contacting Nortek directly to inquire about this, and they were extremely fair in their rental price and worked with us to meet our needs. This was critical because use of this unit allowed us to address certain questions that would help us understand our results.”


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Sending the AWAC ADCP unit back to the surface using lift bags.

How does this ADCP provide value in this research? What challenges did this instrumentation help you resolve?

“We needed to understand how eDNA could move within and around our ocean environment.

“The ocean being a dynamic system means there are many factors completely outside of our control that can significantly influence our ability to detect the presence of DNA in the water.

“For example, the speed and direction of the current will determine if we should be upstream or downstream from the fish aggregation at the time that we sample. The AWAC unit was used to tell us what was happening with the current speed and direction at the exact time and place that we collected our water samples at the aggregation site.

“This will help inform us about eDNA residency time in the water and could help us explain reasons for if we detect or cannot detect the presence of DNA in the samples. The ocean is a new environment for eDNA research, and some of these questions are posed by the scientific community, so we hoped to be able to answer those with this project and use of the AWAC ADCP.”


The team prepares to deploy the AWAC ADCP from the vessel, lowering it down slowly with a rope and then following up with a dive to confirm its location and placement on the seafloor.

Can you explain how the AWAC functions when deployed in the field?

“The unit is programmed to sample the current direction, current speed and water temperature at set intervals and for a set duration of time. That information is recorded on a memory card in the unit, which is extracted and used to develop visualizations of this information.”

How have Nortek’s staff worked together with you on this project? Any challenges you had to overcome together?

“Nortek worked with us to find something that truly allowed us to achieve what we needed, with the funds we had available. Without Nortek, this part of the project would absolutely not have been possible.”

How did the AWAC ADCP perform? Have you got any data that are particularly interesting, useful or outstanding?

“We had no issues with the AWAC unit while it was deployed and we developed a simple and easy way to deploy and retrieve the unit from our vessel. As for the results, we were able to get a very nice visual on what the currents were doing at our sites. This allowed us to detect when the currents were the strongest and if that occurred while we were sampling. In some areas, this was exactly the case.


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An example of one of the visualizations produced using the data collected by the AWAC. This figure shows the speed and direction of the ocean currents at the seafloor (just a couple meters above the AWAC) at one of the project’s sampling locations.

“Despite our efforts to control for sampling during slack tides, slow currents or good weather, we still encountered strong currents at one of our sites which I hypothesize will influence our ability to detect our target fish species in our samples – but that is what we are working on now! Overall, it was advantageous to be able to see exactly what the ocean was doing at the exact time we were in the water sampling. This will be very helpful in constructing the full story for this project.”


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The AWAC ADCP deployed on the seafloor at one of the eDNA sampling locations.

What does the future hold for eDNA research in marine biology and ocean science?

“The future is really open for eDNA application, especially in regard to how it is used in the ocean systems. We plan to use the tool to further explore questions about fish spawning timing and duration, to locate shark mating aggregations and perhaps even to investigate its application for detecting illegal fishing.”


The team prepares for a dive to sample water and sediment for DNA extraction to search for the presence of a particular fish species at a specific location.

Aggregation of black margates (Anisotremus surinamensis) perhaps for the purpose of spawning, but this video shows an example of a “larger than normal” abundance of fish at a single location. This is an example of what researchers in the Isla Mar Research Expeditions team are looking for to determine presence of a spawning aggregation (a site used for reproduction).

Also check out this ECO Magazine article on how researchers from the National Institute for Environmental Studies, Tohoku University, Shimane University, Kyoto University, Hokkaido University and Kobe University have studied a method for estimating population abundance of fish species by means of measuring concentration of environmental DNA in the water.

In this video from OCEARCH you’ll see researchers using a similar technique to search for the presence of Great White sharks in their eDNA samples.


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