Transcriptome Profiling of the Endophyte Burkholderia phytofirmans PsJN Indicates Sensing of the Plant Environment and Drought Stress

Abstract

It is widely accepted that bacterial endophytes actively colonize plants, interact with their host, and frequently show beneficial effects on plant growth and health. However, the mechanisms of plant-endophyte communication and bacterial adaption to the plant environment are still poorly understood. Here, whole-transcriptome sequencing of B. phytofirmans PsJN colonizing potato (Solanum tuberosum L.) plants was used to analyze in planta gene activity and the response of strain PsJN to plant stress. The transcriptome of PsJN colonizing in vitro potato plants showed a broad array of functionalities encoded in the genome of strain PsJN. Transcripts upregulated in response to plant drought stress were mainly involved in transcriptional regulation, cellular homeostasis, and the detoxification of reactive oxygen species, indicating an oxidative stress response in PsJN. Genes with modulated expression included genes for extracytoplasmatic function (ECF) group IV sigma factors. These cell surface signaling elements allow bacteria to sense changing environmental conditions and to adjust their metabolism accordingly. TaqMan quantitative PCR (TaqMan-qPCR) was performed to identify ECF sigma factors in PsJN that were activated in response to plant stress. Six ECF sigma factor genes were expressed in PsJN colonizing potato plants. The expression of one ECF sigma factor was upregulated whereas that of another one was downregulated in a plant genotype-specific manner when the plants were stressed. Collectively, our study results indicate that endophytic B. phytofirmans PsJN cells are active inside plants. Moreover, the activity of strain PsJN is affected by plant drought stress; it senses plant stress signals and adjusts its gene expression accordingly.

A New Approach to Modify Plant Microbiomes and Traits by Introducing Beneficial Bacteria at Flowering into Progeny Seeds

“…The probe and primers were designed in a previous study (Sheibani-Tezerji et al, 2015) to match the gene for transcription termination factor rho (Bphyt_1824) in the genome of strain PsJN. qPCR reactions contained (10 μl total volume): 1x SsoFast Probes, 0.5 μM of each primer, 0.35 μM probe, and 5–100 ng DNA.…”

“…The bacterium itself is also active inside plant. More than 60% of all genes encoded on the genome were expressed in P. phytofirmans PsJN during endophytic colonization of potato plants and gene expression pattern changed in response to host plant drought stress (Sheibani-Tezerji et al, 2015). In shoots of Arabidopsis thaliana strain PsJN expresses genes related to iron storage and transport, which resulted in enhanced iron uptake and accumulation in the host plant (Zhao et al, 2016).…”

The Plant Microbiota: Systems-Level Insights and Perspectives

“…This indicates that individual taxa have evolved specific strategies to successfully move to favorable locations and persist in these environments. However, transcripts related to motility were underrepresented in a Burkholderia strain endophytic in potato plants, indicating that motility might no longer be needed once cells have attached to or entered a plant tissue (117). Similarly, analysis of the transcriptome of a leaf-pathogenic Pseudomonas strain revealed high expression of genes related to motility during epiphytic growth, whereas expression was strongly reduced when the bacteria were colonizing the apoplast (153).…”

“…Indeed, stress response was identified as a significantly enriched functional category in grapevine rhizosphere metagenomes compared with surrounding bulk soil (157). Furthermore, transcriptional profiling of endophytic Burkholderia of potato plants exposed to drought stress indicated that endophytes are affected by environmental influences, and upregulation of several extracytoplasmic function (ECF) sigma factors potentially involved in stress resistance was observed (117). Besides abiotic stresses, plant microbiota are exposed to biotic stresses and antimicrobial compounds of both plant and microbial origin.…”

A glimpse of the endophytic bacterial diversity in roots of blackberry plants (Rubus fruticosus)

“…These three genera have also been detected as endophytes in the roots of Mexican husk tomato plants (Physalis ixocarpa Brot.) by Márquez-Santacruz et al (2010), and as regular microbiota in many other plant hosts (Li et al, 2015;Ludwig-Müller, 2015;Sheibani-Tezerji et al, 2015).…”