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Many bacteria lend other species a helping hand

Beneficial interactions between bacterial species are more common than previously thought

by Celia Henry Arnaud
November 11, 2021

A chip with wells containing droplets.
Credit: Jared Kehe
Pairs of bacteria species, one fluorescently labeled and the other unlabeled, are cultured together in droplets. Fluorescence measurements are used to assess the growth of the labeled bacteria. Each well is about 140 µm wide.

Bacterial species help each other succeed more often than previously thought, according to a recent study (Sci. Adv. 2021, DOI: 10.1126/sciadv.abi7159). In the study, more than 35% of pairings between bacterial species enhanced growth for at least one of the two species. The findings could be used to guide improvements in bacterial growth in cultures through the pairing of compatible species, the authors say.

Previously, the common view was that competition ruled in interactions between microbes, says Jonathan Friedman of the Hebrew University of Jerusalem, who co-led the research with Paul C. Blainey of the Massachusetts Institute of Technology and the Broad Institute of MIT and Harvard. “It turns out that very often, actually, they help each other,” Friedman says.

The researchers tested 20 soil bacteria species growing in 40 nutrient conditions that differed in the amount and type of carbon source. To determine how bacteria species affect each other’s growth, the researchers cultured pairs of species, one fluorescently labeled and the other unlabeled. They used fluorescence measurements to track the growth of the labeled species with its pair and alone. They ran each pairing twice, swapping which species was labeled. The researchers measured more than 180,000 interactions.

If a pairing caused either species to grow faster than it did alone, the researchers considered it a positive interaction, even if the boosted species slowed growth of its partner. In such cases of parasitism, the weaker grower usually benefited at the expense of the stronger grower.

The researchers found that the relationship between any pair of species depended strongly on the culture conditions. Many species pairs were capable of different types of interaction depending on the carbon source. Predicting what will happen in one environment based on what happens in another often turns out to be wrong, Friedman says: “You change the environment, and the interaction can change qualitatively, not just quantitatively.”

Friedman says the study findings could be exploited in synthetic ecology or engineering. Promoting the growth of a microbe could be a matter of finding another microbe that grows well in that particular environment.

“The work is very significant,” says Sara Mitri, who studies microbial ecology at the University of Lausanne. The extent of beneficial interactions among bacteria “is a long-standing question and is difficult to test at such a large scale,” she says. The findings square with what Mitri says she has observed in her lab with similar species.

The researchers don’t yet know what’s driving the different bacterial interactions. “It’s the nature of the beast that if you study one particular interaction, then you can go in depth into the mechanism. If you study tens of thousands, then there’s no way,” Friedman says. “You sacrifice the mechanism for statistics or generality.” He and his collaborators believe that these beneficial interactions among bacteria may play an important role in shaping microbial ecosystems.

“I certainly hope that investigators who specialize in some of these organisms or metabolism of some of the specific carbon sources will take on some of that detailed mechanistic work,” Blainey says. “I hope we will get folks excited about doing detailed follow up.”


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