Abstract:
Despite successful use of Plant Growth Promoting Rhizobacteria (PGPR) in agriculture, little is known about
specific mechanisms of gene regulation facilitating the effective communication between bacteria and plants during
plant colonization. Active PGPR strain B. atrophaeus UCMB-5137 was studied in this research. RNA sequencing
profiles were generated in experiments where root exudate stimulations were used to mimic interactions between
bacteria and plants. It was found that the gene regulation in B. atrophaeus UCMB-5137 in response to the root
exudate stimuli differed from the reported gene regulation at similar conditions in B. amyloliquefaciens FZB42,
which was considered as a paradigm PGPR. This difference was explained by hypersensitivity of UCMB-5137 to
the root exudate stimuli impelling it to a sessile root colonization behavior through the CcpA-CodY-AbrB
regulation. It was found that the transcriptional factor DegU also could play an important role in gene regulations
during plant colonization. A significant stress caused by the root exudates on in vitro cultivated B. atrophaeus
UCMB-5137 was noticed and discussed. Multiple cases of conflicted gene regulations showed scantiness of our
knowledge on the regulatory network in Bacillus. Some of these conflicted regulations could be explained by
interference of non-coding RNA (ncRNA). Search through differential expressed intergenic regions revealed 49
putative loci of ncRNA regulated by the root exudate stimuli. Possible target mRNA were predicted and a general
regulatory network of B. atrophaeus UCMB-5137 genome was designed.
