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We provide here a comparative genome analysis of 31 strains within the genus  Paenibacillus  including 11 new genomic sequences of N 2 -fixing strains. The heterogeneity of the 31 genomes (15 N 2 -fixing and 16 non-N 2 -fixing  Paenibacillus  strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact  nif  cluster comprising nine genes  nifB ,  nifH ,  nifD ,  nifK ,  nifE ,  nifN ,  nifX ,  hesA  and  nifV  encoding Mo-nitrogenase is conserved in the 15 N 2 -fixing strains. The  nif  cluster is under control of a σ 70 -depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe–S] cluster is highly conserved in N 2 -fixing and non-N 2 -fixing strains. Furthermore, we demonstrate that the  nif  cluster enabled  Escherichia coli  JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that  Paenibacillus  and  Frankia  are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral  Paenibacillus  did not fix nitrogen. The N 2 -fixing  Paenibacillus  strains were generated by acquiring the  nif  cluster via horizontal gene transfer (HGT) from a source related to  Frankia . During the history of evolution, the  nif  cluster was lost, producing some non-N 2 -fixing strains, and  vnf  encoding V-nitrogenase or  anf  encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N 2 -fixing strains have additional  nif  and  nif -like genes which may result from gene duplications. The evolution of nitrogen fixation in  Paenibacillus  involves a mix of gain, loss, HGT and duplication of  nif/anf/vnf  genes. This study not only reveals the organization and distribution of nitrogen fixation genes in  Paenibacillus , but also provides insight into the complex evolutionary history of nitrogen fixation.

Comparative Genomic Analysis of N2-Fixing and Non-N2-Fixing Paenibacillus spp.: Organization, Evolution and Expression of the Nitrogen Fixation Genes