Abstract
Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments. In order to better understand the molecular mechanisms of bacteria-plant symbiosis, we have systematically analyzed the primary transcriptome of strain FZB42 grown under rhizosphere-mimicking conditions using differential RNA sequencing (dRNA-seq). Our analysis revealed 4,877 transcription start sites for protein-coding genes, identified genes differentially expressed under different growth conditions, and corrected many previously mis-annotated genes. We also identified a large number of riboswitches and cis-encoded antisense RNAs, as well as trans-encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus. Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.
Highlights
Rhizobacteria are a heterogeneous group of bacteria directly colonizing or living in the vicinity of plant roots
B. amyloliquefaciens FZB42 was cultured under four conditions [43]: i) in 1CM medium (1% peptone, 0.05% yeast extract, 0.5% NaCl); ii) 1CM medium supplemented with maize root exudates (RE) of 0.25 mg/ml; iii) 1CM medium supplemented with 10% soil extract (SE) prepared from soil collected from the farmland in Wuerzburg, Germany; iv) 1CM medium supplemented with both the maize root exudates (0.25 mg/ml) and the soil extract (10%)
Since we wanted to identify genes affected by RE at a similar growth stage, two additional samples were further collected at middle stationary phase (MSP) under SE and RS conditions, resulting in six bacterial samples in total
Summary
Rhizobacteria are a heterogeneous group of bacteria directly colonizing or living in the vicinity of plant roots. Many rhizobacteria are beneficial to plants as they stimulate plant growth and/ or protect plants from phytopathogens. Rhizobacteria have been developed as microbial fertilizer and biocontrol agents. Understanding the symbiotic relationship between rhizobacteria and their host plants has been a longstanding research interest in environmental microbiology. Among a large variety of plant inhabitants, the Gram-positive rhizobacterium B. amyloliquefaciens subsp. Plantarum FZB42 was extensively used as a model of plant-growth-promoting organisms to study the mechanisms of rhizobacterial biocontrol activity [1,2,3,4,5,6].
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