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The rhizosphere soil microbiome (RSM) plays an important role in the nutritional metabolism of the exotic weed  Ageratina adenophora . However, our understanding of the composition and metabolic activity of this microbiome is limited. We used high-throughput sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer fragments in combination with transcriptome analysis to compare the composition and metabolic features of the RSMs of  A. adenophora  and the native plant species  Artemisia indica  and  Imperata cylindrica .  A. indica  cohabitates with the weed and  I. cylindrica  grows in uninvaded soil areas. We found fungi belonging to the phyla Ascomycota and Basidiomycota and bacteria belonging to the phyla Proteobacteria, Acidobacteria and Bacteroidetes were highly abundant in the RSMs of  A. adenophora  and both native plant species. The RSM of  A. adenophora  differed to varying degrees in the relative abundances of bacterial and fungal phyla and genera, and in levels of expression of functional genes from those of both the native species. The RSM of  A. adenophora  was more metabolically active than both of these, as indicated by marked increases in the expression levels of genes associated with cell wall, membrane, and envelope biogenesis, energy production and conversion, and the transport and metabolism of carbohydrates, amino acids, coenzymes, nucleotides, and secondary metabolites. Ascomycota and Basidiomycota contributed most significantly to these differences. The composition and metabolic activities of  A. adenophora  RSM differed less to the RSM of  A. indica  than to the RSM of  I. cylindrica . Fungal communities contributed most to the metabolic genes in the RSM of  A. adenophora.  These included the arbuscular mycorrhizal fungi Glomeromycota. The different relative abundances in the RSMs of these three plant populations may explain why  A. adenophora  is more successful in colonizing soils than the two native populations.

Compositional and functional profiling of the rhizosphere microbiomes of the invasive weed Ageratina adenophora and native plants