Plants with defects in some of these 24 genes are more susceptible to harmful bacteria, Vorholt's team has shown. And since other studies had noticed that some genes in the core set are also involved in plant responses to osmotic shock or fungal infestation, the ETH researchers infer that the 24 genes constitute a general defensive response. “It looks like an immune training, even though the bacteria we used aren’t pathogens, but rather partners in a natural community,” Vorholt says.
Bacterial community out of control
In the second study, Vorholt and her team explored how bacterial communities change when mutations cause a plant to be deficient in one or several genes. The team expected to see that genetic defects in receptors, which plants use to detect the presence of microbes, play a major role in the story.
What they didn’t expect was that another genetic defect would have the biggest effect: if the plants were deficient in a certain enzyme, an NADPH oxidase, the bacterial community was thrown off-kilter. Plants use this enzyme to produce highly reactive oxygen radicals, which have an antimicrobial effect. In the absence of this NADPH oxidase, microbes that under normal circumstances lived peacefully on the leaves developed into what are known as opportunistic pathogens.
Is the NADPH oxidase found among the core set of 24 genes responsible for general defensive response? “No, that would have been too good to be true,” says Sebastian Pfeilmeier, a member of Vorholt’s research group and lead author of the study. This is because the gene responsible for the NADPH oxidase is turned on prior to contact with microbes and because the enzyme is activated by chemical reactions governed by phosphorylation.
For Vorholt, the two studies show that synthetic microbiomes are a promising approach to investigating the complex interactions within different communities. “Since we can control and precisely engineer the communities, we can do much more than just observe what happens. In addition to simply determining cause and effect, we can understand them on a molecular level,” Vorholt says. An ideal microbiome protects plants from diseases while also making them more resilient to drought and salty conditions. This is why the agricultural industry is among those interested in the team’s results. They should help farmers harness the power of the microbiome in the future.