Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists

Abstract

SummaryBelow ground, microbe‐associated molecular patterns (MAMPs) of root‐associated microbiota can trigger costly defenses at the expense of plant growth. However, beneficial rhizobacteria, such as Pseudomonas simiae WCS417, promote plant growth and induce systemic resistance without being warded off by local root immune responses. To investigate early root responses that facilitate WCS417 to exert its plant‐beneficial functions, we performed time series RNA‐Seq of Arabidopsis roots in response to live WCS417 and compared it with MAMPs flg22417 (from WCS417), flg22Pa (from pathogenic Pseudomonas aeruginosa) and fungal chitin. The MAMP transcriptional responses differed in timing, but displayed a large overlap in gene identity. MAMP‐upregulated genes are enriched for genes with functions in immunity, while downregulated genes are enriched for genes related to growth and development. Although 74% of the transcriptional changes inflicted by live WCS417 overlapped with the flg22417 profile, WCS417 actively suppressed more than half of the MAMP‐triggered transcriptional responses, possibly to allow the establishment of a mutually beneficial interaction with the host root. Interestingly, the sector of the flg22417‐repressed transcriptional network that is not affected by WCS417 has a strong auxin signature. Using auxin response mutant tir1afb2afb3, we demonstrate a dual role for auxin signaling in finely balancing growth‐promoting and defense‐eliciting activities of beneficial microbes in plant roots.

Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism

“…b), in later interaction stages of the interaction, when Rhizophagus colonized the roots, the AM fungus activates plant defenses, implying that it is ultimately recognized as an unwanted invader. Activation of root defenses can lead to growth–defense tradeoffs, resulting in inhibition of growth (Gomez‐Gomez et al ., ; Stringlis et al ., ), which could, at least in part, explain the growth reduction observed in Arabidopsis plants after colonization of the roots by Rhizophagus .…”

“…Total RNA was extracted from A. thaliana Col‐0 and M. truncatula A17 roots as previously described (Stringlis et al ., ). RNA‐seq library preparation and sequencing were performed by KeyGene (Wageningen, the Netherlands).…”

“…Total RNA isolation from roots, cDNA synthesis and real‐time quantitative reverse transcription polymerase chain reaction were performed as described previously (Stringlis et al ., ) and using the gene‐specific primers described in Table S1. Relative quantification of specific mRNA levels was performed using the comparative method of Livak & Schmittgen ().…”

Expression of the Arabidopsis thaliana immune receptor EFR in Medicago truncatula reduces infection by a root pathogenic bacterium, but not nitrogen‐fixing rhizobial symbiosis

“…These results suggest that rhizobia have active mechanisms to suppress PTI. Consistent with this, it has recently been shown that the plant‐growth promoting rhizobacterium Pseudomonas simiae WCS417 actively suppresses many transcriptional changes induced by the PAMP flg22 (Stringlis et al ., ). Plant pathogenic bacteria can suppress host immunity by secretion of effectors, many of which interfere with the canonical PTI pathway at different stages (Pfeilmeier et al ., ).…”

Existing and Potential Statistical and Computational Approaches for the Analysis of 3D CT Images of Plant Roots

“…Important influences on root development may come from abiotic stressors such as drought, salinity, and extreme temperature [13,14] not to mention biotic stressors such as pathogens [15][16][17][18]. One important biotic stressor-or helper-of particular recent interest is the rhizosphere and root-rhizosphere interactions [19][20][21]. The study of such interactions is enabled by non-destructive phenotyping technologies that can examine the phenotypic impacts of such interactions in soil during the stages of growth [22].…”