Relationships between Sphaerulina musiva Infection and the Populus Microbiome and Metabolome

Abstract

Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.

Keywords: 16S rRNA; ITS; Septoria; metabolomics; microbial ecology; phyllosphere; plant endosphere; plant-microbe interactions; rhizosphere.

FIG 1

Mean (and standard error) Sphaerulina musiva abundance among genotypes (A) and levels of infection (B) across sample types. Populus trichocarpa resistance to S. musiva is classified as in reference .

FIG 2

Significant (P_adj < 0.05) log₂ fold differences in leaf metabolites between infected (red) and noninfected (gray) Populus trichocarpa trees.

FIG 3

Spearman rho (and 95% confidence intervals) of correlations between Sphaerulina musiva abundance and α-diversity in Hill numbers (q = 0 is analogous to richness, q = 1 is analogous to Shannon diversity, and q = 2 is analogous to Simpson diversity) across plant-associated habitats for Archaea and Bacteria (A) and Fungi (B).

FIG 4

Spearman rho (and 95% confidence intervals) of correlations between Archaea and Bacteria α-diversity (q = 0, i.e., richness) in the leaf endosphere and leaf metabolite concentrations. Only significant (P_adj < 0.05) values are shown.

FIG 5

Coefficients (and standard errors) of significant correlations (P_adj < 0.05) between the relative abundance of microbial phyla and S. musiva abundance across plant endosphere habitats (A) and plant surface habitats (B). Also shown is the relative abundance of microbial genera and stearic acid in the leaf endosphere of P. trichocarpa (C) determined by ANCOM-BC.