Nif gene sequence and arrangement in the endophytic diazotroph Paenibacillus polymyxa strain P2b-2R

Abstract

We characterized nif gene structure of Paenibacillus polymyxa strain P2b-2R, an endophytic diazotroph that can provide up to 79 % of foliar N in lodgepole pine through biological nitrogen fixation. We amplified a 388-bp internal nifH gene fragment from P2b-2R using the single specific primer–polymerase chain reaction (SSP-PCR) and performed a Southern blot analysis of Pst I/HindIII-digested genomic DNA to evaluate the sequence, copy number, and location in the nif gene operon. This strain was found to possess a single copy of the nifH gene with nifB located directly upstream of nifH and D. Phylogenetic analyses of the full nifH, partial nifB, and nifD, and 16s rDNA (rrs) gene sequences indicated that P2b-2R was part of a monophyletic cluster with other members of the genus Paenibacillus and suggest that nifH is transmitted horizontally while nifD is transmitted vertically. Our results provide the first full nifH sequence from a P. polymyxa strain and indicate that arrangement of genes in the P2b-2R nif operon is consistent with those observed in other species of the genus Paenibacillus.