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

BMC Genomics
Nan ZhangRuifu Zhang

Abstract

Bacillus 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. Maize 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 adaptatio...Continue Reading

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Methods Mentioned

BETA
RNA-Seq
PCR
phosphotransferase
Illumina sequencing
fluorescence microscopy

Software Mentioned

Glimmer
Prodigal
Circos
Roche 454 suite
tRNAscan
RPS
PHAST
SE
FASTX
Python

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