environmental DNA – Concepts and applications for biodiversity monitoring

The escalating loss of biodiversity demands effective and accessible monitoring methods. Environmental DNA (eDNA) monitoring is a promising solution due to its speed, scalability, and cost-efficiency. Despite the growing literature, ETH’s curriculum lacked coverage on this crucial topic until the introduction of our Massive Open Online Course (MOOC). Our goal was to share the expertise of research groups at ETH Zürich and WSL to registered students using a flipped-classroom course together with connecting with students all over the world to spread the application of the methods.

This MOOC aimed to educate a diverse audience, including students, scientists, practitioners, and policy makers, about the practical aspects of eDNA sample collection and analyses. As initially planned, we have structured the course into modules, progressing across the critical step toward gathering biodiversity data, and including the sampling design, sample collection, laboratory analyses, bioinformatics, data analyses, ecological interpretation and decision making for policy. To illustrate these steps, the registered students could select specific case studies and datasets focusing on soil, freshwater, and marine environments.

By the end of the course, we aimed for participants to have acquired a practical understanding of eDNA monitoring’s potential and be equipped to apply learned techniques in real-world scenarios. The emphasis on best practices ensures that the knowledge gained is both theoretical and applicable, fostering a collective commitment to preserving global biodiversity.

This course was offered both as an online participation MOOC on the edX platform (open to everybody) and as in-person classes and practicals for the ETH students. Out of the total of 13 sessions (of 2 x 45 minutes) throughout the semester, 7 sessions were in-person sessions which took place every 2 weeks (the students working on a MOOC Module every other week). During the in-person sessions, we used the time to consolidate their theoretical knowledge learned the week before on the MOOC platform and reinforce their practical experience.
The first in-person session gave the students a general introduction, introducing them to the topic of environmental DNA and detailing the course logistics. It was asked that the students register on the edX platform and complete the module 1 of the MOOC course (introduction).
In the second in-person session, an excursion to the ETH Waldlabor was organized, where the students engaged to learn about different eDNA sampling techniques, which were demonstrated by the lecturers. Working in small groups and provided with a map of the area, the students engaged in an exercise to develop an experimental sampling design in a designated sampling area. Each group then applied all the sampling methods according to their sampling design and collected eDNA samples from soil, stream water and the surface of tree leaves.
In the next in-person session, we brought the students into the lab to demonstrate how to process the collected samples. In small groups, every 20 minutes, they rotated to different demonstrations to observe the entire lab process and gained hands-on experience with different steps of the eDNA analysis workflow.
After the lab, the students met in class for a hands-on exercise with bioinformatic to process sequenced reads and create eDNA datasets. The students were given a set of sequences to process using a R-based pipeline on their own computer. Each step of the pipeline was explained and discussed in class.
In the next session, the student learned how to compute biodiversity indicators from eDNA datasets. The students were provided with a tutorial to characterize the taxonomic, functional, and phylogenetic components of the diversities of fish along the French coast of Brittany.
The two final sessions were dedicated to ecological interpretation and reporting. The students needed to write a 5-page report on an assigned topic related to the planning of a study involving eDNA sampling.

Our project aimed to deliver the first MOOC course on the topic of using environmental DNA surveys for biodiversity covering the full workflow from field to data interpretation. We planned to achieve this in two pillars. The goal of the first pillar was to learn the theoretical background of eDNA. We used a mix of video lectures, video interviews with leading experts, quizzes and interactive simulations to ensure a variety of methods and active learning. The second pillar contained different case studies that focus on applying the methods learned in the first pillar to real-life problems in different ecosystems around the world.

Overall, we are happy to report for the first offering with only a little bit of outreach through the networks of those involved and some advertisement by ETH social media channels, the course had a very successful first run with 907 students registered from 86 countries. We received excellent feedback and the average satisfaction rating was 4.2/5, range 2-5). Of those that ranked it low in satisfaction commented that they had expectations for more advanced training, so we can likely improve the description that this course is for beginners with not much experience in the methods. As the discipline of environmental DNA draws on many skill sets the feedback was mixed as to who rated some aspects positive and negative. Even experts in the topic are not typically a master of all the steps, so it was to be expected that depending on how much background one might have different elements will have been too basic for some or too detailed for the level. An example was the laboratory module was assessed as too complicated for many students with limited background in laboratory. Thus, one solution could be to improve the provided material at different levels of background knowledge. In the future, it would also be interesting to try to bring some practical exercise to the MOOC for students as well, or offer more advanced bioinformatic exercises for the students with more advanced abilities. Another aim is to also increase the number and variety of the case studies so that a broad set of topics can be used to learn about eDNA. This could be sourced from the global community to also have a larger contribution and credibility for the course.

• eDNA MOOC Trailer