Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant-Bacteria Interactions.

Tongda Li,Timothy Sawbridge,German Spangenberg,Jatinder Kaur,Ross Mann

doi:10.3390/plants10091802

Tongda Li, Timothy Sawbridge + Show 3 more

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https://doi.org/10.3390/plants10091802

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Abstract

Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant–bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future enhancements of beneficial interactions. In this study, dual RNA-seq analyses were performed to provide insights into the early-stage interactions between barley seedlings and three novel bacterial strains (two Paenibacillus sp. strains and one Erwinia gerundensis strain) isolated from the perennial ryegrass seed microbiome. Differentially expressed bacterial and barley genes/transcripts involved in plant–bacteria interactions were identified, with varying species- and strain-specific responses. Overall, transcriptome profiles suggested that all three strains improved stress response, signal transduction, and nutrient uptake and metabolism of barley seedlings. Results also suggested potential improvements in seedling root growth via repressing ethylene biosynthesis in roots. Bacterial secondary metabolite gene clusters producing compounds that are potentially associated with interactions with the barley endophytic microbiome and associated with stress tolerance of plants under nutrient limiting conditions were also identified. The results of this study provided the molecular basis of plant growth-promoting activities of three novel bacterial strains in barley, laid a solid foundation for the future development of these three bacterial strains as biofertilisers, and identified key differences between bacterial strains of the same species in their responses to plants.

Highlights

Plants and bacteria can establish mutualistic beneficial interactions or undesirable pathogenic interactions [1], leading to great impacts on the performance of agriculturally important crops and pastures
Transcript quantification showed that 80–90% and 85–90% of reads from bacterial and plant samples were mapped to the corresponding transcriptome reference, including the transcriptome generated from Prokka [19] annotation for bacterial samples and a barley reference transcriptome BaRTv1.0 [20] for plant samples, respectively
Dual RNA-seq analyses of barley roots co-incubated with the three novel Plant growth-promoting (PGP) bacterial strains

Summary

Introduction

Plants and bacteria can establish mutualistic beneficial interactions or undesirable pathogenic interactions [1], leading to great impacts on the performance of agriculturally important crops and pastures. Recent work by Liu et al [15] demonstrated that interactions between P. polymyxa YC0136 and tobacco plants enhanced phytohormone transduction and systemic resistance against pathogens in the plant, as well as stimulated auxin biosynthesis in the bacterial strain. Such promising results suggest that dual RNA-seq analyses should be used to deepen our understandings of interactions between more plant species, especially agricultural crops, and other novel PGP bacteria including Paenibacillus spp. and E. gerundensis

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