“Root-Microbiota Communications”

Plants in nature are heavily colonized by a wide range of microbes, consituting the plant microbiota.

We aim to understand the molecular dialogue between roots and microbiota that ultimately dictates root growth and immunity, as well as the structure and function of root microbiota. We are particularly interested in secreted signals that can operate at a distance.

Our research is funded by the German Research Foundation (DFG) under the scheme of the Priority Programme “Deconstruction and Reconstruction of Plant Microbiota” (DECRyPT).

Project ID: 402201269; GEPRIS description can be found here.

Research projects

Root Growth Promotion by
Rhizobiales commensal bacteria

Root-associated commensal bacteria that belong to the order Rhizobiales are capable of promoting A. thaliana primary root growth (Garrido-Oter*, Nakano*, Dombrowski* et al., 2018, Cell Host & Microbe). This root growth promotion (RGP) activity is mediated by the host sulfated pathway (Hucklenbroich et al., 2021, bioRxiv). We are working on further dissecting the molecular mechanisms by which Rhizobiales commensals interfere with host root developmental processes.

root growth-defence coordination

Plant growth and defence are coordinated with each other to maximize overall plant fitness in complex natural environments. We showed that root-associated bacteria, constituting the root microbiota, interfere with this process and suppress immunity-triggered root growth inhibition (Garrido-Oter*, Nakano*, Dombrowski* et al., 2018, Cell Host & Microbe). We aim to decipher the molecular mechanisms by which root microbiota interfere with host growth-defence coordination and whether and how such microbial interference influences overall plant physiology.

Transcriptional response of plants to microbiota, and vice versa

Plants respond to microbes, but how plants discriminate between pathogens and non-pathogens, including microbiota members, remains unclear. Our recent RNAseq meta-analysis revealed that the root transcriptional responses triggered by microbial inoculations were clearly different between roots inoculated with pathogens and non-pathogens while remarkably similar among non-pathogen inoculated roots, irrespective of whether they were inoculated with bacteria, fungi, or a mixture of them (Hucklenbroich et al., 2021, bioRxiv). We aim to understand the relevance of such a common response (the cause or a consequence of commensalism?).

ER body-mediate assembly
of root-associated microbiota
Collaboration with Kenji Yamada @ Jagiellonian University

Plants in the family Brassicaceae develop a unique, spindle-shaped ER-derived organelle called the ER body (the bright structures in the right picture; Nakano* and Yamada* et al., 2014, Frontiers in Plant Science). We previously showed that PYK10, the predominant constituent of root ER bodies in A. thaliana, harbours myrosinase activity (Nakano et al., 2017, The Plant Journal). Myrosinases hydrolyze glucosinolates, a class of sulfur-containing specialized metabolites, to produce bioactive compounds that are responsible for defence against herbivores and microbial pathogens. We recently identified a role for root ER bodies in modulating root microbiota assembly, partially via contributing to the secretion of Trp-derived specialized metabolites and their catabolites to the rhizosphere (Basak et al., 2022, bioRxiv).

Specialized metabolite-mediated interaction between tobacco roots and Arthorbacter bacteria commensals
Collaboration with Akifumi Sugiyama @ Kyoto University

Tobacco roots produce nicotine and santhopine, the specialized metabolites uniquely found in this plant lineage. We show that tobacco root microbiota is characterized by an enrichment of a bacterial genus Arthobacter (Shimasaki et al., 2021, mBio). We are now working on the molecular mechanisms underlying this enrichment.