Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota
Original Publication
Wippel, K., Tao, K., Niu, Y. et al. Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. Nat Microbiol 6, 1150–1162 (2021). https://doi.org/10.1038/s41564-021-00941-9
Abstract
Roots of different plant species are colonized by bacterial communities, that are distinct even when hosts share the same habitat. It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species. To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics. We analysed taxonomically paired synthetic communities from L. japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host. Our findings show that host preference in commensal bacteria from diverse taxonomic groups is associated with their invasiveness into standing root-associated communities.
Data Availability
The strains of the Lj-SPHERE collection will be deposited at and will be available on request from the Leibniz Institute DSMZ in Braunschweig, Germany. Raw 16S rRNA amplicon reads have been deposited in the European Nucleotide Archive under the accession number PRJEB37695. Similarly, sequencing reads and genome assemblies of the Lj-SPHERE core collection have been uploaded to the same database with the accession number PRJEB37696. Source data are provided with this paper.
Code availability
The scripts used for the computational analyses described in this study are available at http://www.github.com/garridoo/ljsphere, to ensure replicability and reproducibility of these results.
License
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