RNAseq analysis of the transcriptomic response of 6 Burkholderia strains to rice root exudates

In this study we monitored the RNAseq response of 3 Burkholderia (B. vietnamiensis LMG10929, B. reimsis ABIP441, B. servocepacia ABIP444) and 3 Paraburkholderia (P. kururiensis M130, P. sabiae ABIP630, Paraburkholderia sp. ABIP659) strains originating from rice roots, to an exposure of rice root exudates. The control condition was a broth culture of bacteria in VSG medium (Vincent Succinate Glutamate), while the exudates condition was VSG + Nipponbare rice root exudates. Rice root exudates were recovered from plants grown in a 6 times diluted Hoagland solution in hydroponic condition, after 3 days of plant growth. These were lyophilised and concetrated, and used at 1X to stimulate bacteria. Bacteria were exposed to exudates at OD 0.075 in VSG and bacterial cells were sampled at mid-log exponential phase of growth.