A Streptomyces Consortium Contributes Distinct Microbial Interactions During Arabidopsis thaliana Microbiome Assembly

Although plant microbiome assembly involves a series of both plant-microbe and microbe-microbe interactions, the latter is less often directly tested. Here, we investigate a role for Streptomyces strains to influence assembly of other bacteria into root microbiomes through the use of two synthetic communities (SynComs): a 21-member community including four Streptomyces strains and a 17-member community lacking those Streptomyces strains. Following inoculation with these SynComs on wild-type Arabidopsis thaliana Col-0, differential abundance modeling on root endosphere 16S ribosomal RNA gene amplicon sequencing data revealed altered abundance of four diverse SynCom members: Arthrobacter sp. 131, Agrobacterium sp. 33, Burkholderia sp. CL11, and Ralstonia sp. CL21. Modeling results were tested by seedling coinoculation experiments with the four Streptomyces strains and differentially abundant members, which confirmed the predicted decreased abundance for Arthrobacter sp. 131, Agrobacterium sp. 33, and Ralstonia sp. CL21 when Streptomyces strains were present. We further characterized how the phytohormone salicylic acid (SA) mediates Streptomyces strains' influence over Agrobacterium sp. 33 and Burkholderia sp. CL11 seedling colonization. Although decreased colonization of Ralstonia sp. CL21 and Arthrobacter sp. 131 when Streptomyces spp. are present were not influenced by SA, direct antibiosis of Arthrobacter sp. 131 by Streptomyces was observed. These results highlight a role for Streptomyces-mediated microbial interactions during plant root microbiome assembly as well as distinct mechanisms that mediate them. Understanding the role of microbial interactions during microbiome assembly will inform the production of beneficial microbial treatments for use in agricultural fields.

Automated summary

This study investigates the influence of Streptomyces strains on the assembly of root microbiomes and reveals that they can significantly affect the abundance of other bacteria. The study also uncovers the mechanisms through which Streptomyces strains influence the colonization and growth of Agrobacterium and Burkholderia strains.