Biology and Fertility of Soils

, Volume 49, Issue 7, pp 965–970 | Cite as

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

  • Richa Anand
  • Christopher Peter Chanway
Short Communication


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.


Paenibacillus polymyxa Endophyte nif genes Sequence 



We are grateful to S. Graham and D. Brooks for the assistance with phylogenetic analysis. Funding was provided by an NSERC Discovery Grant to CPC and an NSERC CGSD3 to RA.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Department of Forest SciencesUniversity of British ColumbiaVancouverCanada
  2. 2.IL-7BC Children’s HospitalVancouverCanada
  3. 3.Faculty of Land and Food SystemsUniversity of British ColumbiaVancouverCanada

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