Introducing… Environmental DNA Analysis and Applications

This semester, the BIT Program will be offering a new course to introduce students to the concept of “environmental DNA,” or eDNA, which is essentially free-floating DNA or DNA from free-floating cells in an environment. It will be taught by Dr. Hasley, who joined the Program last spring. “It’s not really a field of research, but [eDNA] is a really useful tool, so I want to take this opportunity to show students some potential applications of modern biotechnology to ecology and environmental science problems,” he said.

 I want to take this opportunity to show students some potential applications of modern biotechnology to ecology and environmental science problems

Dr. Hasley

The course lectures will be structured around a set of broad topics surrounding the applicability of eDNA, including biodiversity assessment and metagenomics. “Biodiversity assessment is just a way of asking, ‘who’s there,’ for a particular environment,” Dr. Hasley said. This includes metabarcoding, in which researchers compare genomic material from an environmental sample to a database of known barcode sequences, in order to tell which species are represented in the sample. Metagenomics is a similar concept, but “researchers sequence all of the genomic material, rather than just a region.” This allows them to assemble individual genomes or create gene models, which can then be used to identify species and sort them into taxa. From there, he plans to get into more specific topics, such as endangered species tracking and invasive species detection.

The lab portion of the course will allow students to apply some of these concepts to their very own research projects. Dr. Hasley hopes that students will be able to go out to a nearby body of water – likely the stream that runs through campus – to collect their own samples for the lab portion of the class. Students would be able to follow the process all the way through: from collection, to DNA extraction and sequencing, to using software tools for analysis. Though students will be doing a lot of bioinformatics work, especially toward the end of the module, Dr. Hasley wants to make sure that the course is accessible to everyone, even if they don’t have a strong coding background. “I’m trying to make it approachable, so while it’s definitely not introductory biology, I’m not expecting students to know the tools and everything going in,” he said. And he’s also designed the course to be easily translated into an online format if classes are forced online again due to COVID-19. He has pre-extracted samples ready to go if students aren’t able to do the collection and extraction themselves, and most of the rest of the course can be completed online. 

In addition to planning for and around the possibility of COVID-related issues with classes, Dr. Hasley is trying to incorporate universal design for learning (UDL) into the course as much as possible. Mainly, that means he’ll be doing his best to expand options for students when it comes to project submission and reading content. “Students will be able to choose the format they use for their final project submission,” he said, “so that may be a paper, or a video walking me through what they’ve done.” He’s also providing students with both primary and secondary sources, because different students will get different things out of each source. “I want to provide multiple ways of accessing the content and thinking about it,” he said. Beyond improving accessibility for students, he wants to make sure the class structure encourages participation from students. This means that he’s setting it up to function similar to a seminar-style course, where students can discuss and ask questions freely. “I don’t expect everyone to be obsessed with eDNA,” he said, “but I hope everyone is ready to engage with the content, and that everyone gets something out of it.”

Dr. Hasley is hoping to increase his work with eDNA, which is a tool that has exploded in popularity in recent years. “Environmental DNA is gaining traction in research communities, whether they be state or federal agencies, diversity research agencies, or invasive species research,” he said. While he’s still formulating his research question and interests in the field, he’s interested in applying it to biodiversity and conservation research, which exists at the intersection of the ecology and molecular biology fields. And if students have different research interests, working with eDNA does produce a lot of transferable skills that could be helpful in other research contexts. For example, “handling DNA, troubleshooting, and working with computers and web-based tools to do data analysis and interpretation.” These can all be easily applied to other fields, such as forensics or customs enforcement, where eDNA samples could be helpful in identifying multiple DNA sources in an environment.

Environmental DNA is gaining traction in research communities, whether they be state or federal agencies, diversity research agencies, or invasive species research

Dr. Hasley

The course, which will be offered in Session II this semester, has been designed for students who are interested in continuing to develop their computational analysis, wet lab, and field biology skills. “It’s for students who are interested in applying biotechnology to ecological and environmental science questions,” Dr. Hasley said. The unique mix of experiences this class offers will allow students to see the many ways in which they can pursue eDNA and its applications further.