Current nifH Sequence Database
We have developed an annotated nifH sequence database for use in studies of nitrogenase diversity and ecology as described in Gaby & Buckley (2014). The database is in ARB format and contains 32,954 aligned nifH sequences with associated metadata. The sequences are organized phylogenetically and a guide tree is available for navigation. The database also contains full length nifH, nifD, nifK, and 16S rRNA gene sequences extracted from the genomes of 185 nitrogen fixing organisms.
The full ARB database can be downloaded here nifH_database_2012.arb.
A fasta version contining only aligned nifH sequences is also available nifH_database_2012.fasta.
Gaby, J. C., D. H. Buckley (2014) A comprehensive, aligned nifH gene database: a multi-purpose tool for studies of nitrogen-fixing bacteria. Database. 2014:bauoo1. doi: 10.1093/database/bau001
Evaluation of nifH PCR Primers
Using an earlier version of the nifH database (nifH_database_2010_07_14.arb) we performed a systematic evaluation of PCR primers that target the nifH gene to determine their utility for the study of diazotroph diversity and ecology (Gaby & Buckley, 2012).
Gaby, J. C., D. H. Buckley (2012) A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase . PloS ONE. 7:e42149. doi:10.1371/journal.pone.0042149
Evaluation of nifH Diversity
Using an earlier version of the nifH database (nifH_database_2_4_09.arb) we performed a systematic evaluation of nifH sequence diversity as a function of sequence phylogeny and environmental origin (Gaby & Buckley, 2011)
Gaby, J. C., D. H. Buckley (2011) A global census of diazotroph diversity. Environmental Microbiology. 13:1790. doi:10.1111/j.1462-2920.2011.02488.x
Other Papers on Nitrogen-Fixing Microorganisms
Gaby, J. C. and Buckley, D. H. (2017) The use of degenerate primers in qPCR analysis of functional genes can cause dramatic quantification bias as revealed by investigation of nifH primer performance. Microbial Ecology. 74:701-708. doi: 10.1007/s00248-017-0968-0
Pepe-Ranney, C., Koechli, C., Potrafka, R., Andam, C., Eggleston, E., Garcia-Pichel, F., Buckley, D.H. (2016) Non-cyanobacterial diazotrophs dominate dinitrogen fixation in biological soil crusts at the early stage of crust formation. International Society for Microbial Ecology Journal. 10:287–298. doi:10.1038/ismej.2015.106
Gaby, J. C. and D. H. Buckley (2014) Assessment of nitrogenase diversity in the environment. In F. J. de Bruijn (ed.). Biological Nitrogen Fixation . Wiley/Blackwell, New York.
Hsu, S. and D. H. Buckley (2009) Correspondence between diazotroph diversity and rates of nitrogen fixation in soil. International Society for Microbial Ecology Journal. 3:124-136.
Noar, J. and D. H. Buckley (2009) Ideonella azotifigens sp. nov., an aerobic diazotroph of the Betaproteobacteria isolated from grass rhizosphere soil, and emended description of the genus Ideonella. International Journal of Systematic and Evolutionary Microbiology. 59 :1941-1946.
Buckley, D. H ., V. Huangyutitham , S-F. Hsu, T. A. Nelson (2008) 15N2 -DNA-Stable isotope probing of diazotrophic methanotrophs in soil. Soil Biology and Biochemistry. 40:1272-1283.
Buckley, D. H., V. Huangyutitham, S-F. Hsu, and T. A. Nelson. (2007) Stable isotope probing with 15 N achieved by disentangling the effects of genome G + C content and isotope enrichment on DNA density. Applied and Environmental Microbiology. 73:3189-3195.
Buckley, D. H., V. Huangyutitham, S-F. Hsu, and T. A. Nelson. (2007) Stable isotope probing with 15N2 reveals novel non-cultivated diazotrophs in soil. Applied and Environmental Microbiology. 73:3196-3204.