Bacillus amyloliquefaciens alters gene expression, ROS production and lignin synthesis in cotton seedling roots

Aims Previous research demonstrated that applying Bacillus amyloliquefaciens to cotton seeds promotes growth, alters root architecture and alleviates salt stress of cotton seedlings. This research was undertaken to further study the genetic responses elicited in cotton seedlings by this growth promoting bacterium. Methods and Results GeneChip microarrays and RT‐qPCR were used to detect changes in gene expression in seedling roots inoculated with B. amyloliquefaciens. Roots were stained with 3′3‐diaminobenzidine and phloroglucinol‐HCl to determine whether treated seedlings had a greater accumulation of reactive oxygen species and lignin. Two hundred and fifty‐two transcripts were differentially expressed in inoculated cotton seedling roots; 139 transcripts were up‐regulated and 113 were down‐regulated. Some up‐regulated transcripts were related to nitrate assimilation, cell growth, hormones, transport, transcription factors and antioxidants. Five genes identified to be up‐regulated using microarrays were determined to be up‐regulated using RT‐qPCR. Inoculated cotton seedling roots had a greater accumulation of reactive oxygen species and lignin. Conclusions The differential expression of genes associated with diverse functions supports that B. amyloliquefaciens elicits a complex genetic response in seedling roots. Significance and Impact of the Study This study demonstrated that beneficial bacteria can alter gene expression of cotton that leads to growth promotion.