NOT ALL GOOD BACTERIA GET ALONG

Just as the beneficial bacteria living in yogurt and sauerkraut are good for your gut, tiny organisms living in the soil help plants — by getting them nutrients, protecting them from drought, and fending off disease.

As modern agriculture races to produce more food and in a more sustainable way, intense research is underway on natural “probiotic” soil treatments containing living microorganisms. Developers of these products have been including multiple species of beneficial bacteria in their formulations, aiming to boost crop growth and yield. However, these selections must be made very carefully, according to new research from the University of Delaware, because not all good bacteria get along.

In a laboratory study with a relative of alfalfa and two species of beneficial bacteria, UD doctoral student Amanda Rosier and her adviser, Professor Harsh Bais, with Canadian colleague Pascale Beauregard from the Université de Sherbrooke, discovered that one species cuts off the communications signals from the other species, effectively cancelling out its benefits. The findings are reported in Frontiers in Microbiology, a peer-reviewed scientific journal.

Getting to the root of the matter

In her doctoral research, Rosier has been working to uncover how plants interact with the microbes living on and around their roots.

“When I talk to people about agriculture, I try to remind them how dependent we are on it and how fragile it is,” Rosier said. “Among all the global crises, how can we increase food production while mitigating harm to the environment? One way Professor Bais’s lab is doing this is by exploring this suite of microbes that help plants get nutrients, attack pathogens and increase crop yields. But how do bacteria do this? That is a fundamental question we are addressing.”

For the past decade, Bais’s laboratory has been focusing on understanding the biology and behavior of Bacillus subtilis, a bacterium that lives on the surface of plant roots and in the surrounding soil. He and his colleagues developed and patented a unique strain of the bacterium, called UD1022, which has been licensed by BASF and incorporated into four commercial products already in the market and sold in the U.S. and Canada.

Legumes, such as alfalfa, peas and beans, form symbiotic relationships with bacteria known as rhizobia, that live in bud-like nodules in the plant roots. These bacteria convert atmospheric nitrogen from the air into the nutrient that plants can use.

Rosier created a model system to study plant-microbe interactions using Medicago trunculata, a relative of alfalfa, and two different species of beneficial bacteria: Sinorhizobium meliloti (Rm8530), a plant symbiont, and Bacillus subtilis (UD1022), which lives on the plant root surface where it serves to promote plant growth in a myriad of ways.

As is the case in so many scientific studies, Rosier made an unexpected discovery along the way.

She was diligently growing the plants in sterile vessels for two months, painstakingly taking the plants out, counting the nodules on their roots, weighing the plants and then repeating the process three different times. But she just did not see the robust growth she anticipated.

“It really speaks to how specific these bacterial interactions are,” Rosier said. “They do different things and interact in different ways.”

‘Quorum quenching’ halts communications

Typically, the rhizobia (Rm8530) will form thick sugary coatings called biofilms, which are critical to forming their partnership with the plant. These bacteria form these biofilms through communicating intercellularly with each other through a process called “quorum sensing.”

Rosier conducted a series of genetic tests on the plants, which revealed that no biofilms were being produced by Sinorhizobium meliloti when grown together with Bacillus subtilis UD1022. Her further detective work revealed why. It turns out that Bacillus subtilis makes an enzyme — lactonase — that prevents the other bacterium from communicating with its kind. Scientists call this ability “quorum quenching.”

“These interactions between bacteria may be common and are critical to understand as we seek to develop new sustainable solutions in agriculture,” Bais said. “And for product developers, the moral of the story is that the bacteria that work for one system, won’t necessarily work in another. You have to proceed with caution.”

This finding also may shed light on human pathogens such as Pseudomonas, which relies on quorum sensing to communicate, Bais said. This antibiotic-resistant germ can cause pneumonia and infections in the blood and other parts of the body, particularly after surgery. Turning off its ability to communicate would offer a revolutionary new approach to treatment.

For now, Rosier is busy finishing her dissertation and looking forward to a career in academia to continue the research and teaching she loves.

“The power of the microbiome in agriculture is really untapped and we’re really on the cusp of what we can do with it,” Rosier said. “It’s really exciting to think about what lies ahead.”