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DEEPEND Team Taking eDNA Samples at Sea

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Greetings, fellow deep-sea enthusiasts! I'm Pedro A. Peres, a postdoc at Florida International University, and I'm back with my second post on the blog. Today, I want to talk about an exciting new technique that is revolutionizing the way we study deep-sea environments: environmental DNA (eDNA).


Traditionally, to analyze the DNA of marine animals, we would collect and extract tissue samples directly from the animal. But what if we could get DNA samples without even seeing or sampling the animal? This is where eDNA comes in. Every living creature in nature releases DNA molecules in the environment through various means like skin, mucus, feces, and more. Scientists have discovered that we can extract and sequence these DNA fragments to detect specific species or assess community composition, all without ever having to interact with the animals directly.

In DEEPEND|RESTORE, Dr. Bracken-Grissom and I are working with Jonah Ventures ( to use this amazing technique focusing on deep-sea environments. The main challenge is that eDNA is a relatively new method but even newer for deep-sea environments. Many of the references available investigate freshwater or shallow waters, which have different features than the deep sea. This means that replicating their sampling method might not be ideal for the deep sea. For instance, animals in the deep sea are more spread out than in other environments, so should we filter more water to have a fair representation of the community we are investigating? Can we use acoustics to guide where to fire the CTD to collect water? And many other questions that we are thrilled to investigate!

On this cruise, PhD candidate Stormie Collins is in charge of filtering the water, preserving the filters, and logging the CTD data so we can analyze everything later. She and I assembled a cool eDNA setup provided by Jonah Ventures, and Dr. Kevin Boswell and PhD student Haley Glasmann are helping with the CTD. Teamwork! I’m excited to see our findings and what eDNA can reveal to us about deep waters.

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Dr. Heather Judkins is an associate professor in the Integrative Biology Department at the University of South Florida St. Petersburg. She received a Bachelors degree in Marine Affairs from the University of Rhode Island, Masters degree in Science Education from Nova Southeastern University and her PhD in Biological Oceanography from the University of South Florida. Her research focuses on understanding the evolution, ecology, and biogeography of cephalopods with a main focus currently in the Wider Caribbean. Her role in this project includes the identification of deep-sea cephalopods, examining genetic diversity, and analysis of cephalopod ecology and distribution in the water column.
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Guest Wednesday, 19 June 2024