Researchers developed a new eDNA collection system to look at biodiversity in tropical rainforests.
Introduction
Have you ever climbed a tree in your backyard? You would have seen some leaves and maybe some bugs, a bird, or a squirrel. But what else was hiding up there out of sight?
All these organisms make up the biodiversity of your tree. A healthy ecosystem contains a wide range of living things. Biodiverse ecosystems provide important functions for humans. This could be providing food or clean water. When humans do things like cut down trees or pollute the air, it can harm biodiversity.
Tropical rainforests are special because they have high biodiversity. Unfortunately, many tropical rainforests are hard to get to. This makes it difficult for researchers to study them. This is especially true for the rainforest canopy. To climb up and explore this special place, people have needed to build tall towers or special walkways. Some researchers have even hired specialized climbers who use ropes – like jungle adventurers!
Scientists can use environmental DNA (eDNA) to detect species that are hard to find or measure. All living things have DNA, and they leave behind traces of it in their environment. This could be from skin, pee, poop, or hair. We can then compare the DNA we collect to DNA databases. This can help us figure out what organisms the DNA came from. A bit like how detectives use DNA to identify who was at a crime scene!
We wondered if it was possible to collect eDNA from organisms in the rainforest canopy. We hypothesized that DNA from organisms living in the tree tops would wash down through the leaves when it rained. We wanted to use this eDNA to look at biodiversity. We also wanted to see if we could detect differences in biodiversity based on human activity.
Methods
We collected rainwash from forests in French Guiana, South America. We built a rainwash collector using an upside-down umbrella (Figure 1). Then we attached a plastic bottle to the bottom. We placed a filter below the plastic bottle to capture eDNA. Using this setup, we compared two areas. One was an old-growth tropical rainforest. The other was a former rubber tree plantation.
We performed two different experiments.
Over time. We randomly placed 5 collectors in each area. We took eDNA samples after 1, 5, 10, 20, and 40 days. We then used this data to figure out how long to leave our collectors in the rainforest. Our goal was to pick up the most biodiversity.
Over space. We placed rainwash collectors 20 meters apart in each area. We left them for 40 days before collecting the eDNA samples.
We then extracted the DNA from each sample. We compared specific sections of DNA to several databases. This identified the taxa (categories of organisms) living in rainforest canopies. Then we calculated a number to represent the biodiversity of the ecosystem.
Results
We identified 562 different taxa using our eDNA samples. We found organisms like ferns and mosses, amphibians and birds, and flies and beetles. We also identified a few mammals, such as bats and monkeys. We found that the old-growth rainforest had 1.3 to 1.9 times higher biodiversity than the plantation. We saw this pattern for plants, vertebrates, and insects (see Figure 2 on p.3).
We found that leaving collectors out for 8–20 days gathered the most biodiversity. Also, the biodiversity we detected was very localized to an area.
Discussion
We used eDNA in rainwash to detect high biodiversity in the rainforest canopy. We saw that there was less biodiversity in areas with high human activity. Our data can help us understand these hard-to-sample ecosystems. It can also show us how humans might be impacting biodiversity.
Conservation management relies on good information about biodiversity. To help with this goal, our new method of collecting eDNA has several benefits.
Our collectors are made from common and cheap materials. Anyone can create, install, and use them.
They sample the rainforest canopy passively. This means we won’t disturb organisms that live there. And we don’t have to climb into the trees!
They can stay out in the rainforest for 8–20 days at a time without anyone needing to check them.
They can collect DNA from very localized areas.
Unfortunately, we could not match some of our eDNA sequences with species in the DNA databases. This is because many tropical taxa are missing in DNA databases. Hopefully people will add more organisms to these databases in the future. This will make eDNA a more powerful tool to assess rainforest biodiversity.
Conclusion
We developed a new way to look at biodiversity in the tropical rainforest. We knew it was challenging to go up to the canopy to see what was there. So we came up with the idea that rainwash would bring that information down to us.
Scientists often need to think outside the box to get information that is difficult to see. They also need to be careful about how they spend their research money. We used old umbrellas, rather than fancy scientific equipment, to collect the rainwater. What everyday problems can you solve in creative ways?
