Compositional profiling of the rhizosphere microbiome of Canada thistle reveals consistent patterns across the United States northern Great Plains

Abstract

Canada thistle is a pervasive perennial weed, causing challenges to agricultural and natural ecosystems globally. Although research has focused on the phenology, genetics, and control of Canada thistle, little is known about the rhizosphere microbiome and the role plant-microbe interactions play in invasion success. This study investigated the rhizosphere microbiome of Canada thistle across diverse climates, soils, and crops in the U.S. northern Great Plains. Soil and rhizosphere samples were collected and bacterial 16S and fungal ITS2 sequencing were performed to characterize the core microbiome and identify potential factors contributing to invasion success. Amplicon sequencing revealed a stable core microbiome that was detected in the Canada thistle rhizosphere across all locations. The core microbiome was dominated by the bacterial phyla Actinobacteriota and Proteobacteria and fungal phyla Ascomycota and Basidiomycota. Differential abundance analysis showed rhizosphere fungal communities were enriched in pathogen-containing genera with a 1.7-fold greater abundance of Fusaria and a 2.6-fold greater abundance of Gibberella compared to bulk soil. Predictive functional profiling showed rhizosphere communities were enriched (p < 0.05, FDR corrected) in plant pathogen fungal guilds which represented 19% of the fungal community. The rhizosphere microbiome was similar in composition across environments, highlighting the stable association between Canada thistle and specific microbial taxa. This study characterized the core microbiome of Canada thistle, and the findings highlight plant-microbe interactions shaping invasive behavior. These findings are important for understanding the ecological impacts of plant invasion and soil-microbe ecological processes.

Keywords: Canada thistle; Invasive species; Rhizosphere microbiome; Weeds.

Figure 1

Bacterial and fungal alpha diversity comparison between Canada thistle rhizosphere and bulk soil across locations. Metrics used for microbial community diversity were coverage and species dominance (inverse Simpson’s). (a) Bacterial coverage, (b) bacterial Simpson’s dominance, (c) Fungal coverage, and (d) fungal Simpson’s dominance.

Figure 2

Relative abundance of rhizosphere bacterial phyla (a) and fungal phyla (b) and bacterial families (c) and fungal families (d) across locations. Bacterial taxa are faceted by cropping system (annual or perennial) where thistle rhizosphere samples were collected.

Figure 3

NMDS ordination plot of the Aitchison dissimilarity matrix at the genus level with differences in microbial community structure colored by location. (a) Bacterial community, (b) fungal community.

Figure 4

A high number of microbes were consistently detected in the Canada thistle rhizosphere across the US northern Great Plains. Abundance-occupancy distributions were used to identify core rhizosphere microbiome members for bacteria in annual (a) and perennial (b) cropping systems and fungi (c). Taxa unique to a location are colored by location and taxa shared across locations are white. The solid line represents the fit of the neutral model, and the dashed line is 95% confidence around the model prediction. Taxa detected in at least 80% of samples were considered members of the core. Relative abundance of core taxa are shown in box plots, color coded by phylum, and grouped by family. (d) rhizosphere bacteria from thistle sampled in annual cropping systems, (e) rhizosphere bacteria from thistle sampled in perennial cropping systems, and (f) fungi. Bar plots show the number of taxa within each family in the core microbiome.

Figure 5

Differential abundance between rhizosphere and bulk soil at the genus level based on ALDEx2 center log ratio transformed data with Kruskal–Wallis rank sum test and p values FDR corrected using Holm’s method. Only the 20 most abundant significant taxa (p < 0.05) are shown. (a) bacterial taxa from thistle sampled in annual cropping systems, (b) bacterial taxa from thistle sampled in perennial cropping systems, and (c) Fungi. Bacterial communities were analyzed separately from annual and perennial cropping systems due to differences in sequencing approaches.

Figure 6

Differential abundance analysis by ALDEx2 with center log ratio transformed data with Kruskal–Wallis rank sum test and p values FDR corrected using Holm’s method. Bacterial MetaCyc superclass 2 functions predicted by PICRUSt2 that were different between thistle rhizosphere and bulk soil from (a) thistle sampled in annual cropping systems, (b) thistle sampled in perennial cropping systems. (c) Fungal ecological guild predictions by FUNGuild. Only taxa with significant (p < 0.05, FDR corrected) differences are shown.

Figure 7

PCA ordination plots of predicted functions. (a) Center log ratio transformed bacterial PICRUSt2 predicted Metacyc functions at a rank of Superpathway1. (b) Center log ratio transformed FUNguild predicted fungal functional guilds. Ellipses show the 95% confidence intervals.