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MBE Advance Access originally published online on July 8, 2008
Molecular Biology and Evolution 2008 25(9):1955-1966; doi:10.1093/molbev/msn146
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Phylogenetic Analysis of Nitrite, Nitric Oxide, and Nitrous Oxide Respiratory Enzymes Reveal a Complex Evolutionary History for Denitrification

Christopher M. Jones*, Blaz Stres{dagger}, Magnus Rosenquist{ddagger} and Sara Hallin*

* Department of Microbiology, Swedish Agricultural University, Uppsala, Sweden
{dagger} Zootechnical Department, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
{ddagger} Department of Radiology, Oncology, and Clinical Immunology, Uppsala University Hospital, Uppsala, Sweden

E-mail: Chris.Jones{at}mikrob.slu.se.

Accepted for publication June 25, 2008.

Denitrification is a facultative respiratory pathway in which nitrite (NO2–), nitric oxide (NO), and nitrous oxide (N2O) are successively reduced to nitrogen gas (N2), effectively closing the nitrogen cycle. The ability to denitrify is widely dispersed among prokaryotes, and this polyphyletic distribution has raised the possibility of horizontal gene transfer (HGT) having a substantial role in the evolution of denitrification. Comparisons of 16S rRNA and denitrification gene phylogenies in recent studies support this possibility; however, these results remain speculative as they are based on visual comparisons of phylogenies from partial sequences. We reanalyzed publicly available nirS, nirK, norB, and nosZ partial sequences using Bayesian and maximum likelihood phylogenetic inference. Concomitant analysis of denitrification genes with 16S rRNA sequences from the same organisms showed substantial differences between the trees, which were supported by examining the posterior probability of monophyletic constraints at different taxonomic levels. Although these differences suggest HGT of denitrification genes, the presence of structural variants for nirK, norB, and nosZ makes it difficult to determine HGT from other evolutionary events. Additional analysis using phylogenetic networks and likelihood ratio tests of phylogenies based on full-length sequences retrieved from genomes also revealed significant differences in tree topologies among denitrification and 16S rRNA gene phylogenies, with the exception of the nosZ gene phylogeny within the data set of the nirK-harboring genomes. However, inspection of codon usage and G + C content plots from complete genomes gave no evidence for recent HGT. Instead, the close proximity of denitrification gene copies in the genomes of several denitrifying bacteria suggests duplication. Although HGT cannot be ruled out as a factor in the evolution of denitrification genes, our analysis suggests that other phenomena, such gene duplication/divergence and lineage sorting, may have differently influenced the evolution of each denitrification gene.

Key Words: denitrification • phylogeny • nirK • nirS • norB • nosZ

Jennifer Wernegreen, Associate Editor


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