a comprehensive evaluation of pcr primers to amplify the nifh gene of nitrogenase综合评价pcr引物来扩增nifh固氮酶基因.pdfVIP

A Comprehensive Evaluation of PCR Primers to Amplify the nifH Gene of Nitrogenase John Christian Gaby, Daniel H. Buckley* Department of Crop and Soil Sciences, Cornell University, Ithaca, New York, United States of America Abstract The nifH gene is the most widely sequenced marker gene used to identify nitrogen-fixing Bacteria and Archaea. Numerous PCR primers have been designed to amplify nifH, but a comprehensive evaluation of nifH PCR primers has not been performed. We performed an in silico analysis of the specificity and coverage of 51 universal and 35 group-specific nifH primers by using an aligned database of 23,847 nifH sequences. We found that there are 15 universal nifH primers that target 90% or more of nitrogen fixers, but that there are also 23 nifH primers that target less than 50% of nifH sequences. The nifH primers we evaluated vary in their phylogenetic bias and their ability to recover sequences from commonly sampled environments. In addition, many of these primers will amplify genes that do not mediate nitrogen fixation, and thus it would be advisable for researchers to screen their sequencing results for the presence of non-target genes before analysis. Universal primers that performed well in silico were tested empirically with soil samples and with genomic DNA from a phylogenetically diverse set of nitrogen-fixing strains. This analysis will be of great utility to those engaged in molecular analysis of nifH genes from isolates and environmental samples. Citation: Gaby JC, Buckley DH (2012) A Comprehensive Evaluation of PCR Primers to Amplify the nifH Gene of Nitrogenase. PLoS ONE 7(7): e42149. doi:10.1371/ journal.pone.0042149 Editor: Jose Luis Balcazar, Catalan Institute for Water Research (ICRA), Spain Received March 27, 2012; Accepted July 2, 2012; Published July 25, 2012 Copyr