Portable method lets scientists identify plant DNA out in the field

At the Vaud botanical gardens in Lausanne, a group of students gathers around a specimen of Hedera colchica, more commonly known as Persian ivy. They’re examining how the plant responds to tiny beige patches placed on its emerald leaves. The patches, developed under the GenoRobotics project, are made of a hydrogel and contain a matrix of 11x11 microneedles measuring just 800 microns high.

“Microneedle patches were initially developed to inject substances like vaccines,” says Nicolas Adam, GenoRobotics coordinator. “When we started our project six years ago, we were the among the first to use these kinds of patches to extract information. As far as I know, we’re still the only research group to employ them to extract host DNA from plants. This form of extraction is simple and fast, and cuts the cost by a factor of ten relative to the conventional method.”

Positive impact on biodiversity

Around 50 students are involved in GenoRobotics, which is part of EPFL’s MAKE initiative. Their goal is to facilitate the process of categorizing plant species to gain a better understanding of how the ecosystems work, thus helping to protect biodiversity. The team has designed a portable DNA identification method that’s both inexpensive and robust. It can be employed out in the field to conduct on-site analyses: scientists would no longer need to carry samples back to a lab, for example, and could determine the name of a species right away. And should they stumble across a new species, scientists can collect a wealth of information immediately.

“Our portable approach can identify plant DNA – including the extraction, amplification and sequencing steps – in record time and at a much lower cost than the standard process, which must be conducted in a lab,” says Adam. The research group has made their results available in open source, for the benefit of the entire scientific community.

Ramping up for Madagascar

The students are developing their protocol in association with the Lausanne Botanical Garden, which is part of the Naturéum museum. The Garden agreed to make some of its 5,000 species available for testing. The GenoRobotics team is aiming to have the protocol ready by this fall, when an expedition is planned to the Madagascar rainforests – home to a number of indigenous species. “If we want to preserve the Earth’s biodiversity effectively, we’ve got to first have a clear picture of all it includes,” says Patrice Descombes, curator in chief of the Naturéum botanical gardens. “EPFL’s GenoRobotics project is designed to make a significant step in this direction, which is why we’ve decided to support it through our role as a research organization. Working with the students has also given us fresh ideas and helps us showcase our collections of plant species.”

The opportunity to take concrete steps towards protecting biodiversity is what prompted Ghali Jaidi, a second-year Bachelor’s student in life-science engineering, to join the project. “I was frustrated by the lack of hands-on experience in my coursework,” he explains. “But GenoRobotics gave me an opportunity to apply the theory I learned in class to a concrete problem. It’s expanded my skillset and made me more comfortable using the lab equipment.” Jaidi’s tasks include testing different liquid buffers to determine which one can keep the DNA fragments intact for as long as possible between the extraction and amplification steps.

Samuel Goodchild, a third-year Bachelor’s student in life-science engineering, is working specifically on the amplification step. “We decided to use a recombinase polymerase method with enzymes, since it can be carried out at temperatures between 37°C and 40°C,” he says. This method uses much less energy than the conventional PCR method and can be carried out in the field, in around 40 minutes instead of two or three hours.

The GenoRobotics protocol was tested during a 2023 outing to the Jorat Natural Park, and proved to be reliable. Descombes, also a seasoned botanist, took part in that exercise. The team compared their results with those from the standard process. As it turned out, the two datasets lined up.

“Our method can currently generate an average of two DNA barcodes, which is usually enough to distinguish different species,” says Adam. “But we’d ideally like to obtain four barcodes since that would give us a lot more information, especially for new species. We plan to further improve our extraction procedure so that it can collect more DNA and be less sensitive to factors like seasonality” – since the procedure requires green leaves – “as well as to the type of plant and the presence of contaminants such as proteins and sugars that inhibit DNA amplification.”

Saving time and money

Another goal for the project team is to reduce the cost of DNA sequencing, mainly by shortening the amount of time required. The students have chosen to use the sequencer developed by Oxford Nanopore Technologies – the only portable one currently on the market. They’ve created an algorithm that can construct DNA sequences in real-time as the sequencing is taking place, and then compare them to an existing database. “That means we can stop the sequencing process as soon as we obtain DNA sequences that are of good enough quality and let us identify a plant with enough accuracy,” says Adam. “And of course, our algorithm is capable of running offline for use in remote areas.”

The GenoRobotics project is inherently cross-disciplinary, as it draws on a broad range of skills: computer science, biology, engineering and more. “In addition to the project’s goal of protecting biodiversity, what drew me was the way it combines biology and engineering,” says Charlotte Alers, a Master’s student in Neuro-X and the head of the GenoRobotics expedition unit. “Each team member brings their own specialized knowledge, so we really get to learn from each other. I’m also getting experience with training students on the analysis procedures, which is making me look at the basics from a different perspective.” As she waits to head off on the Madagascar expedition this fall, Alers is doing dry runs with her group through the local botanical gardens, uncovering some of the still-hidden secrets of plant DNA.