Dissecting the co-transcriptome landscape of plants and microbiota members

Abstract

Interactions between plants and each neighboring microbial species are fundamental building blocks that collectively determine the structure and function of the plant microbiota, but the molecular basis of such interactions is poorly characterized. Here, we monocolonized Arabidopsis leaves with nine plant-associated bacteria from all major phyla of the plant microbiota and profiled co-transcriptomes of plants and bacteria. These strains elicited quantitatively different plant transcriptional responses including typical pattern-triggered immunity responses. Genes of non-pathogenic bacteria involved in general metabolism and energy production were commonly suppressed in planta in contrast to a virulent pathogen. Various nutrient acquisition pathways that are frequently encoded in the genomes of plant-associated bacteria were induced in planta in a strain-specific manner, shedding light on bacterial adaptation to the plant environment and identifying a potential driving force of niche separation. Integrative analyses of plant and bacterial transcriptomes suggested that the transcriptional reprogramming of plants is largely uncoupled from that of bacteria at an early stage of interactions. This study provides insights into how plants discriminate among bacterial strains and sets the foundation for in-depth mechanistic dissection of plant-microbiota interactions.

Shared in planta population and transcriptomic features of nonpathogenic members of endophytic phyllosphere microbiota

“…( 27 )] in the genes up-regulated inside plants when compared to the inoculum. This appears to be inconsistent with what has recently been observed for eight microbiota strains ( 38 ). However, if we compare in vitro planktonic populations grown in liquid media to those of populations grown inside plants for Pst ΔhrcCΔCFA , we do observe enrichment of up-regulated PA genes ( SI Appendix , Table S9 ).…”

“…The inoculum used for our transcriptome analysis was grown in solid agar plates while the inoculum for the Nobori et al. ( 38 ) study was grown in liquid media. Perhaps, solid agar mimics more closely the cues for the up-regulation of PA genes inside the leaf apoplast.…”

Network organization of the plant immune system: from pathogen perception to robust defense induction

“…Moreover, microbiota can help plants cope with biotic or abiotic stress (Cheng et al, 2019;Muller et al, 2016), with 'beneficial' microbiota extending the defense response to various diseases (Vannier et al, 2019). It becomes possible to describe microbial consortia through metagenomic analyses, to perform their functional characterization, and to elucidate modulated plant immune networks (Nobori et al, 2021). In addition, GWA mapping methods have demonstrated their power in identifying genes underlying QDR to many pathogens and competitive plant-plant interactions (Bartoli and Roux, 2017;Frachon et al, 2019) and should be used more widely.…”

Cross-feeding niches among commensal leaf bacteria are shaped by the interaction of strain-level diversity and resource availability

“…Microbial taxonomic diversity in plant tissues generally follows a gradient from high in roots to lower in leaves, with relatively few taxa that further colonize the leaf apoplastic space as endophytes [1,9,10]. This limitation is due to strong constraints on microbial life in the apoplast, including the tight regulation of nutrient resources imposed by plants, presumably in part to limit microbial growth [11][12][13]. Bacterial survival requires at least basic nutrients like carbon and nitrogen.…”