The smallest creatures can have some of the biggest impacts on the planet. You can get a sense of how healthy a given environment is by taking a census of the types of microorganisms that call it home. Now researchers at Berkeley Lab have developed a new way to get a larger snapshot of what’s going on, by looking specifically at the genes bacteria pass around to help each other adapt to a changing world.

While most species pass genes down “vertically” from parent to child, bacteria have the ability to share them “horizontally,” swapping DNA packages called plasmids to essentially teach each other new tricks. This sneaky skill-swapping is how bacteria are quickly becoming resistant to antibiotics.

Since they’re shared so widely, studying these plasmids can give scientists a window into the environment as a whole, by looking at what kind of pressures the organisms there are facing. If, for example, a pond is particularly salty, you might find a high level of plasmids that help bacteria survive saltiness.

“When you want to learn about a microbial community, focusing specifically on their plasmids allows you to get a sense of the suite of capabilities that a community wants to keep mobile perhaps because they are needed periodically,” says Aindrila Mukhopadhyay, lead researcher on the study. “Studying plasmids is like looking inside someone’s backpack to see what they’re keeping handy to use themselves and potentially share with another person. Say you look inside and find an umbrella. It may not be raining at the time, but the umbrella suggests that it rains from time to time.”

This overall network of plasmids is known as the plasmidome. While this isn’t the first time scientists have studied it, the team developed and refined a new method to help separate it from the wider pool of chromosomal DNA in a sample. The new method lets scientists detect different-sized plasmids even in environments with relatively few bacteria.

Lead researcher Aindrila Mukhopadhyay, left, and lead author of the paper, Ankita Kothari, right

The team tested the technique in samples of groundwater from several wells at the Oak Ridge Field Research Center, an environment that’s laden with heavy metals. Hundreds of different plasmids were found, and similar ones showed up in different samples regardless of the variety of bacteria species present.

The most common plasmids found were those that gave bacteria resistance to mercury, but interestingly, the team didn’t detect any mercury in the water. The fact that these genes had spread around so widely indicated that the water must have been contaminated by mercury in the past, and the microbial community is still hanging onto the resistance in case it happens again.

Knowing these kinds of things can give scientists a snapshot of the past and present of a site and the organisms that live there, as well as a glimpse at how well they might be able to adapt to certain changes in future. On top of that, the study might help uncover new plasmids that could be put to work cleaning up the environment, for example, or treating sewage.

“These mobile genetic packages present a way to manipulate these organisms naturally,” says Ankita Kothari, lead author of the study. “So, if you want to go examine an ecosystem at a molecular level and you need genetic tools to do that, the answer could be in the plasmidome already.”

The research was published in the journal mBio.

Source: Berkeley Lab

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