Bacteria living within plants can change them in unpredictable ways

Endophytic bacteria, microbes living in plant tissue, can change how a plant grows. But experiments with microbe communities shows that it's not in a predictable way.

Some organisms that shape plant growth actually live within the plant. Jeremiah Henning and colleagues have been examining if they can predict how endophytic bacteria affect the plants they live in. To do this they ran two experiments. “In the first study, we inoculated a single genotype of Populus deltoides with individual root endophytic bacteria and measured plant phenotype,” Henning and colleagues wrote in the American Journal of Botany. “Next, data from this single inoculation were used to predict phenotypic traits after mixed three‐strain community inoculations, which we tested in the second experiment.”

Populus deltoides after the National Resources Conservation Service / Wikipedia.

Henning and colleagues refer back to an earlier paper by Grime on the mass ratio hypothesis. This argues that a species’s effect on an ecosystem is proportional to its abundance. While it’s a popular hypothesis, Grime notes: “It is important to specify that the mass ratio hypothesis is restricted in application to the role of autotrophs in ecosystem processes. When attention is turned to other trophic elements, such as parasites, herbivores, predators and symbionts, the possibility arises for ecosystem impacts that are less predictably related to abundance.”

That means that there is the possibility that the mass ratio hypothesis does not apply to bacteria living within a plant.

Sure enough, this is what Henning and colleagues have found. Despite Burkholderia BT03 being up to 99% of the population of bacteria, the team found it had little effect on the phenotype of Populus deltoides. Yet plants with a mixture of closely related Pseudomonas strains allocated mass in different ways to leaves, stems and roots. Crucially, the effects were non-additive making them unpredictable. “We were unable to predict plant biomass allocation or chlorophyll content based on relative‐abundance‐weighted microbial composition or assuming each microbe has equal effect on plant phenotype regardless of relative abundance,” said the authors.

The interactivity between microbe species is the key point of the paper. In the discussion, the authors shows a number of ways that simple -omics approaches miss key elements of how the bacterial community is working.

“Our results emphasize the need to incorporate community dynamics and species interactions in plant-microbe studies. Nevertheless, the recent flurry of papers that have demonstrated the ability of plant endophytes to control plant gene expression, immune response, and overall functioning were conducted in single‐microbe systems and ignored the role of species interactions in diverse communities. ” said Henning and colleagues in the paper. “Our study highlights a potential direction to investigate the linkage between phylogenetic relatedness and function in microbial communities.”

“The application of trait‐based approaches to understand the ecology and evolution of microbiome communities provides an exciting opportunity to transition from describing variation in diversity patterns within and among individuals to finally understanding the consequences of microbiome diversity and predicting shifts in the functioning of microbiome communities.”