RT Journal Article SR Electronic T1 Lotus japonicus symbiosis genes impact microbial interactions between symbionts and multikingdom commensal communities JF bioRxiv FD Cold Spring Harbor Laboratory SP 547687 DO 10.1101/547687 A1 Thorsten Thiergart A1 Rafal Zgadzaj A1 Zoltán Bozsóki A1 Ruben Garrido-Oter A1 Simona Radutoiu A1 Paul Schulze-Lefert YR 2019 UL http://biorxiv.org/content/early/2019/07/11/547687.abstract AB The legume Lotus japonicus engages in mutualistic symbiotic relationships with arbuscular mycorrhiza (AM) fungi and nitrogen-fixing rhizobia. Using plants grown in natural soil and community profiling of bacterial 16S rRNA genes and fungal internal transcribed spacers (ITS), we examined the role of the Lotus symbiosis genes RAM1, NFR5, SYMRK, and CCaMK in structuring bacterial and fungal root-associated communities. We found host genotype-dependent community shifts in the root and rhizosphere compartments that were confined to bacteria in nfr5 or fungi in ram1 mutants, whilst symrk and ccamk plants displayed changes across both microbial kingdoms. We observed in all AM mutant roots an almost complete depletion of Glomeromycota taxa that was accompanied by a concomitant enrichment of Helotiales and Nectriaceae fungi, suggesting compensatory niche replacement within the fungal community. A subset of Glomeromycota whose colonization is strictly dependent on the common symbiosis pathway was retained in ram1 mutants, indicating that RAM1 is dispensable for intraradical colonization by some Glomeromycoyta fungi. However, intraradical colonization by bacteria belonging to the Burkholderiaceae and Anaeroplasmataceae is dependent on AM root infection, revealing a microbial interkingdom interaction. Despite an overall robustness of the bacterial root microbiota against changes in the composition of root-associated fungal assemblages, bacterial and fungal co-occurrence network analysis demonstrates that simultaneous disruption of AM and rhizobia symbiosis increases the connectivity among taxa of the bacterial root microbiota. Our findings imply a broad role for Lotus symbiosis genes in structuring the root microbiota and identify unexpected microbial interkingdom interactions between root symbionts and commensal communities.Importance Studies on symbiosis genes in plants typically focus on binary interactions between roots and soil-borne nitrogen-fixing rhizobia or mycorrhizal fungi in laboratory environments. We utilized wild-type and symbiosis mutants of a model legume, grown in natural soil, in which the bacterial or fungal or both symbioses are impaired to examine potential interactions between the symbionts and commensal microorganisms of the root microbiota when grown in natural soil. This revealed microbial interkingdom interactions between the root symbionts and fungal as well as bacterial commensal communities. Nevertheless, the bacterial root microbiota remains largely robust when the fungal symbiosis is impaired. Our work implies a broad role for host symbiosis genes in structuring the root microbiota of legumes.