Soil Bacteria Vie for a Plant Partner

March 02, 2018

Teasing apart the partnership between nitrogen-fixing bacteria and their plant hosts in a natural setting is now possible, thanks to a novel new approach.



A single handful of soil is easily home to millions of bacteria. Some plants – like beans, clover, and alfalfa — form a partnership with common soil bacteria — known as rhizobia. The bacteria can “fix nitrogen,” or convert nitrogen from a gas into a compound the roots can absorb. Both parties benefit since the bacteria gains carbon and the plant gains nitrogen.

These give-and-take relationships are extremely common in nature, yet scientists struggle to disentangle the complex web between the players. Isolating bacteria from soil is no easy feat. Since nitrogen-fixing bacteria are common, the majority of them float freely in the soil without a plant host. This begs the question, why do some bacteria end up in a partnership with a plant while the majority remain unattached?

In a recent article published in Proceedings of the National Academy of Sciences, a team of University of Minnesota researchers describe a novel approach to tackle this question, examining the genetic diversity of hundreds of bacterial strains from the same species simultaneously.

This relationship between plants and nitrogen-fixing bacteria has long interested Peter Tiffin, a professor in the College of Biological Sciences. For nearly a decade, Tiffin worked with colleagues — most notably Michael Sadowsky and Nevin Young — to study this relationship from the plant’s perspective. Since a plant benefits immensely from this partnership, it makes sense that they select specific bacterial strains.

When Liana Burghardt arrived as a post-doc in the Tiffin Lab in 2015, she brought new expertise and energy. “These bacteria are doing something really amazing,” says Burghardt. “Not only are they inhabiting different host environments each growing season, but they also have to survive in a soil environment that’s very different from the host.”

These bacteria compete amongst each other for a plant to set up shop, something that was missed when researchers studied strains individually. New methods allowed them to tease apart how the communities changed over time in response to competition among strains. It is important to not only consider what bacterial strain is the best partner for a plant, but also whether that bacteria will outcompete its neighbors to form that partnership. Even if the strain is preferred by the plant, if it loses in a head-to-head match with another strain, it will continue to float freely in the soil.

This has significant implications for the agricultural sector. This partnership — or symbiosis — between rhizobia and plants is critical and seeds are often coated with nitrogen-fixing bacteria before planting. However, these bacterial strains might lose out to other bacterial strains in the soil if they are poor competitors. Agricultural fields are loaded with microbes that don’t necessarily benefit the plant. Imagine if a strain of nitrogen-fixing bacteria could be optimized for the plant’s benefit while simultaneously beating out its competitors. “If that symbiosis can be improved even a little bit,” Tiffin says, “it could have significant impacts on agricultural yields, particularly in low-input systems”

One of the most exciting implications of this work is the potential to pinpoint which bacterial strains not only result in the greatest plant benefit, but also remain competitive in the soil. For the Tiffin Lab, this manuscript serves as a launching pad for a slew of ecological and evolutionary experiments. “We are now enabled and empowered with this tool to ask these new questions,” says Burghardt.

Equipped with the ability to isolate bacterial strains in the soil, Tiffin and his team are looking forward to taking the experiments out of the greenhouse and into field. The novel method will allow researchers in other study systems to ask similar questions and promises to provide new insights into complex bacterial communities surround us.  –Claire Wilson