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Background  Diazotrophic (nitrogen-fixing) Gram-positive and endospore-formed  Paenibacillus  spp. have potential uses as a bacterial fertilizer in agriculture. The transcriptional analysis of nitrogen fixation in  Paenibacillus  is lacking, although regulation mechanisms of nitrogen fixation have been well studied in Gram-negative diazotrophs.    Results  Here we report a global transcriptional profiling analysis of nitrogen fixation in  Paenibacillus  sp. WLY78 cultured under N 2 -fixing condition (without O 2  and NH 4  + ) and non-N 2 -fixing condition (air and 100 mM NH 4  + ). The  nif  (nitrogen fixation) gene operon composed of 9 genes ( nifBHDKENXhesAnifV ) in this bacterium was significantly up-regulated in N 2 -fixing condition compared to non-N 2 -fixing condition, indicating that  nif  gene transcription is strictly controlled by NH 4  +  and O 2 . qRT-PCR confirmed that these  nif  genes were differently expressed. Non- nif  genes specifically required in nitrogen fixation, such as  mod ,  feoAB  and  cys  encoding transporters of Mo, Fe and S atoms, were coordinately transcribed with  nif  genes in N 2 -fixing condition. The transcript abundance of  suf  operon specific for synthesis of Fe-S cluster was up-regulated in N 2 -fixing condition, suggesting that Sul system, which takes place of  nifS  and  nifU , plays important role in the synthesis of nitrogenase. We discover potential specific electron transporters which might provide electron from Fe protein to MoFe protein of nitrogenase. The  glnR  whose predicted protein might mediate  nif  transcription regulation by NH 4  +  is significantly up-regulated in N 2 -fixing condition. The transcription levels of nitrogen metabolism and anaerobic respiration were also analyzed.    Conclusions  The  nif  gene operon ( nifBHDKENXhesAnifV ) in  Paenibacillus  sp. WLY78 is significantly up-regulated in N 2 -fixing condition compared to non-N 2 -fixing condition. Non- nif  genes specifically required in nitrogen fixation were also significantly up-regulated in N 2 -fixing condition. Fur and Fnr which are involved in anaerobic regulation and GlnR which might mediate  nif  gene transcription regulation by NH 4  +  were significantly up-regulated in N 2 -fixing condition. This study provides valuable insights into nitrogen fixation process and regulation in Gram-positive firmicutes.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-016-0642-6) contains supplementary material, which is available to authorized users.

Genome-wide transcriptome profiling of nitrogen fixation in Paenibacillus sp. WLY78