What the Hell is On My Plant: A Botanist’s Guide to Metagenomics

Image Credit: Mislav Marohnić, CC BY 2.0, Image Cropped

If you’re unlucky, you already know that humans possess a skin microbiome. It sounds gross, but it’s simply an entire ecosystem of  microbes like bacteria living on our skin (maybe it is gross). Some of them help us, others might make us sick, for example when they enter open wounds. Plants have a similar set-up, hosting different ecosystems of bacteria on their leaves.

Hopefully, at this point I’ve made your skin crawl (because as you now know, it is literally crawling). But that microbiome can actually tell us some fascinating things about the animal or plant we’re looking at. So today, I’ll go through exactly what metagenomics is, and some of the information we can glean from a plant’s surface (I am a botanist after all).

Whenever you take a leaf and extract DNA to look at the genetics of that plant, you usually also get the DNA of those microbes. This is called the metagenome of the plant. And if you have several samples from different places, you can check where in the world those microbes are from. This might be of special interest when you look at invasive plants – alien (non-native) plants with negative effects on the native species. Not all alien plants become invasive, and figuring out what makes a species likely to be invasive is one of THE big questions in invasion biology. One theory states that they might expand quickly and outcompete natives because in their new territory, they’re able to escape enemies like herbivores or pathogens. That means that figuring out whether or not pathogens are present in both the new and native ranges of a species can be extremely helpful. This is complicated further, as just because we can find a common pathogen on the plant in its invasive range today, does not mean it was there from the start. It might have been introduced later when the plant was already established. This is where herbarium specimens can be really helpful.

Herbarium specimens are pressed and dried plants. Some of them were collected up to 400 years ago. And for some plants, you have pretty good time series, showing how they first spread throughout a new region. So not only is this perfect to check whether an invasive plant brought its native pathogens with it or not, it can also tell us how the use of pesticides that became common in the 1940s influences the metagenomic composition of plants. But, does DNA of those microbes actually survive on herbarium specimens?

Related: The Revolutionary Headache of Ancient DNA

I’ve spent a lot of the last few years looking at herbarium and modern samples from two different species (Arabidopsis thaliana and Ambrosia artemisiifolia) to check if we can find the same microbes. Even if I’m really only interested in one species, I need to use two different species to make sure that the microbes I find on herbarium specimens are actually those that naturally occur on the plants. Herbarium specimens are dried painfully slowly, and have been since the 1600s. Unfortunately, this means that fungus can grow on the samples. Additionally, since these samples are studied all the time, so potentially some careless Homo sapien could infect the plant with their own microbiome. So we need a second species to compare and ensure that microbes are naturally occurring and not a product of our handling of the specimens.

We did indeed find a couple of microbe species in almost all herbarium specimens of the two plant species we looked at. Those species were (nearly) absent in the modern samples. And as we looked at two very different plant species, we would not really expect them to have such a similar metagenomic composition. We therefore think that those microbes are actually “herbarium contamination”. And we found them in samples from 10 different herbaria. The most common of those, the fungus Alternaria alternata, made up up to 7 % of the sequencing reads, which is quite a lot.

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The Common Ragweed, an invasive plant to Europe originally from North America, can cause immense despair for hayfever sufferers and local vegetation. But did it bring some of its own pathogens with it? (Image Credit: Harry Rose, CC BY 2.0)

Now that sounds irritating, but it can be quite helpful. The reads of this fungus had ancient DNA damage (read more about it in The Revolutionary Headache of Ancient DNA) similar to that of the host plant. This indicates that the fungus was either already on the plant or infected the specimen shortly afterwards. Once we better understand when the specimens get infected, it can help to better preserve the herbarium specimens we already have and those that will be prepared in the future. That means they’re still useful for scientists in the future. But the good news is, that by excluding those microbes that are most likely “herbarium contaminants”, the metagenomic composition of modern and herbarium specimens of the same plant species looked more similar. So by knowing which microbes we need to exclude from the analysis, we can look for changes over time. And we actually found that one bacterium is quite common in Am. artemisiifolia herbarium samples from North America, but we didn’t find it in Europe. This is pretty cool as Am. artemisiifolia (the Common Ragweed, which you can read more about at the link below) is native to North America and invasive to Europe. It indicates the plant did indeed escape some pathogens when it colonized Europe. We actually don’t know yet what the bacterium does, so we can’t be sure yet. As always in science, more work is necessary.

Related: The Common Ragweed

This study (you can access a link to the full version here) shows that the millions of herbarium specimens around the world can be a good resource for yet another study field. So we need to make sure to preserve this treasure as good as we can for future generations to use (see also article on type specimens). Who knows what other types of analysis are possible in a few years that we can’t even imagine yet.

So that’s your crash course to metagenomics in plant life, and the value of herbarium specimens. Next time you’re at a museum, remember that there’s probably a room somewhere in that building teeming with microscopic ecosystems dancing around the skin of a plant.

Just as there is one dancing on your skin right now. Sleep well.

Vanessia Bieker is a PhD candidate at the Norwegian University of Science and Technology. She studies Ambrosia artemisiifolia, an annual weed that is native to North America and became invasive upon introduction to Europe. She uses historic herbarium samples and modern samples from the native as well as the invasive range to study changes over time. Check out her previous articles at her Ecology for the Masses profile.

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