RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots

Abstract

Herbaspirillum seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize plants, wheat seedlings growing hydroponically in Hoagland's medium were inoculated with H. seropedicae and incubated for 3 days. Total mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of root attached and planktonic bacteria revealed extensive metabolic adaptations to the epiphytic life style. These adaptations include expression of specific adhesins and cell wall re-modeling to attach to the root. Additionally, the metabolism was adapted to the microxic environment and nitrogen-fixation genes were expressed. Polyhydroxybutyrate (PHB) synthesis was activated, and PHB granules were stored as observed by microscopy. Genes related to plant growth promotion, such as auxin production were expressed. Many ABC transporter genes were regulated in the bacteria attached to the roots. The results provide new insights into the adaptation of H. seropedicae to the interaction with the plant.

Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing

“…seropedicae was attached to wheat roots but downregulated when H. seropedicae was attached to maize roots (12, 13), suggesting that this gene may be involved in host specificity. Six of the genes described in Table S3 were found to be essential only in H.…”

“…seropedicae with different plant hosts (12–14). In addition, comparative genomics and metagenomics studies have shown that certain functions, e.g., nutrient transport systems, type IV conjugal DNA-protein transfer secretion systems, plant growth promotion genes, and iron uptake systems, are overrepresented in the genomes of bacterial endophytes, compared to rhizospheric or soil bacteria (4, 15–17).…”

Bacterial Endophyte Colonization and Distribution within Plants

“…The process of adherence of Rhizobia on legume roots, plant pathogenic bacteria on plant leaf or root surfaces, and Agrobacterium on roots of the host plant has been thoroughly studied in the past [ 84 , 85 , 86 ]. However, the mechanisms by which bacterial endophytes attach on plant surfaces remain relatively unexplored [ 87 ].…”

RNA-Seq analysis of gene expression for floral development in crested wheatgrass (Agropyron cristatum L.)

“…Recently, next-generation deep-sequencing technologies such as Solexa/Illumina RNA-sequencing (RNA-Seq) have provided new approaches to study global transcriptome profiles for species without reference genomes. RNA-Seq can study transcripts of a certain trait in a given developmental stage and has been used to investigate the transcriptomic profiles in some grass species [15,16]. Zhang et al [17] performed de novo transcriptome sequencing of tetraploid crested wheatgrass to develop genomic resources for wheat genetic improvement.…”