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. 2021 Feb 26;9:57. doi: 10.1186/s40168-020-00966-y

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — A schematic model depicting the functional mechanism underlying the impacts on root microbiota by the dcl234 triple mutation. In the canonical RdDM pathway, Arabidopsis DCL2, DCL3, and DCL4 function in continuum to regulate the biogenesis of 21–24 nt siRNAs, whose precursors originate from Pol IV-dependent transcription. In wild-type Arabidopsis, the canonical RdDM pathway shows no connection with the assembly of root microbiota. In the dcl234 triple mutant, the disrupted sRNA homeostasis leads to multilayered alterations in several biological processes that are important for plant-microbe interactions, including defense-related gene expression, cell wall modifications, and root exudation of metabolites, which are concomitant with an altered root microbiota assembly. Dashed arrows indicate potential effects (see the main text for details). Besides the dcl234 triple mutant, the RdDM mutants (with the corresponding gene names in parentheses) investigated in this study include nrpd1-3 (Pol IV), nrpe1-11 (Pol V), rrp6l1-2 (RRP6L1), and ddc (DRM1, DRM2, CMT3). In addition to the examined factors, several other RdDM components are also shown [24], including CLSY1 (CLASSY 1), SHH1 (SAWADEE HOMEODOMAIN HOMOLOGUE 1), RDR2 (RNA-DEPENDENT RNA POLYMERASE 2), AGO4 (ARGONAUTE 4), and AGO6. For simplicity, not all known RdDM components are shown