Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates

Abstract

BackgroundBacillus amyloliquefaciens SQR9 is a plant growth-promoting rhizobacteria (PGPR) with outstanding abilities to enhance plant growth and to control soil-borne diseases. Root exudates is known to play important roles in plant-microbe interactions. To explore the rhizosphere interactions and plant-beneficial characteristics of SQR9, the complete genome sequence as well as the transcriptome in response to maize root exudates under biofilm-forming conditions were elucidated.ResultsMaize root exudates stimulated SQR9 biofilm formation in liquid culture, which is known to be positively correlated with enhanced root colonization. Transcriptional profiling via RNA-sequencing of SQR9 under static conditions indicated that, at 24 h post-inoculation, root exudates stimulated the expression of metabolism-relevant genes, while at 48 h post-inoculation, genes related to extracellular matrix production (tapA-sipW-tasA operon) were activated by root exudates. The individual components in maize root exudates that stimulated biofilm formation included glucose, citric acid, and fumaric acid, which either promoted the growth of SQR9 cells or activated extracellular matrix production. In addition, numerous groups of genes involved in rhizosphere adaptation and in plant-beneficial traits, including plant polysaccharide utilization, cell motility and chemotaxis, secondary antibiotics synthesis clusters, and plant growth promotion-relevant, were identified in the SQR9 genome. These genes also appeared to be induced by the maize root exudates.ConclusionsEnhanced biofilm formation of B. amyloliquefaciens SQR9 by maize root exudates could mainly be attributed to promoting cell growth and to inducing extracellular matrix production. The genomic analysis also highlighted the elements involved in the strain’s potential as a PGPR. This study provides useful information for understanding plant-rhizobacteria interactions and hence for promoting the agricultural applications of this strain.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1825-5) contains supplementary material, which is available to authorized users.

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“…Recently, the transcriptome analysis of B. amyloliquefaciens SQR9 was reported (a member of the BA-PA that also isolated by our laboratory) incubated with maize root exudates [which partially mimicked the presence of a rhizosphere (Zhang et al, 2015)]. Thirteen genes that belong to PA-specific core genome and were gained through HGT at the divergence event between PA and nPA (BA-PA branch), were observed to be induced by root exudates (Tables S3, S8, S10), including mtlA (GP102111, mannitol transporter) and glnQ/M (GP102791/GP102793, glutamine transporters) involved in transport of important compounds in root exudates (Badri and Vivanco, 2009).…”