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The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers

Kim Heylen, Dirk Gevers (UGent), Bram Vanparys (UGent), Lieven Wittebolle (UGent), Joke Geets, Nico Boon (UGent) and Paul De Vos (UGent)
(2006) ENVIRONMENTAL MICROBIOLOGY. 8(11). p.2012-2021
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Abstract
Gene sequence analysis of nirS and nirK, both encoding nitrite reductases, was performed on cultivated denitrifiers to assess their incidence in different bacterial taxa and their taxonomical value. Almost half of the 227 investigated denitrifying strains did not render an nir amplicon with any of five previously described primers. NirK and nirS were found to be prevalent in Alphaproteobacteria and Betaproteobacteria, respectively, nirK was detected in the Firmicutes and Bacteroidetes and nirS and nirK with equal frequency in the Gammaproteobacteria. These observations deviated from the hitherto reported incidence of nir genes in bacterial taxa. NirS gene phylogeny was congruent with the 16S rRNA gene phylogeny on family or genus level, although some strains did group within clusters of other bacterial classes. Phylogenetic nirK gene sequence analysis was incongruent with the 16S rRNA gene phylogeny. NirK sequences were also found to be significantly more similar to nirK sequences from the same habitat than to nirK sequences retrieved from highly related taxa. This study supports the hypothesis that horizontal gene transfer events of denitrification genes have occurred and underlines that denitrification genes should not be linked with organism diversity of denitrifiers in cultivation-independent studies.
Keywords
BACTERIA, NITRITE REDUCTASE GENES, DIVERSITY, IDENTIFICATION, FRAGMENTS, EVOLUTION, ALIGNMENT, SYSTEMS

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Chicago
Heylen, Kim, Dirk Gevers, Bram Vanparys, Lieven Wittebolle, Joke Geets, Nico Boon, and Paul De Vos. 2006. “The Incidence of nirS and nirK and Their Genetic Heterogeneity in Cultivated Denitrifiers.” Environmental Microbiology 8 (11): 2012–2021.
APA
Heylen, Kim, Gevers, D., Vanparys, B., Wittebolle, L., Geets, J., Boon, N., & De Vos, P. (2006). The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. ENVIRONMENTAL MICROBIOLOGY, 8(11), 2012–2021.
Vancouver
1.
Heylen K, Gevers D, Vanparys B, Wittebolle L, Geets J, Boon N, et al. The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. ENVIRONMENTAL MICROBIOLOGY. 2006;8(11):2012–21.
MLA
Heylen, Kim, Dirk Gevers, Bram Vanparys, et al. “The Incidence of nirS and nirK and Their Genetic Heterogeneity in Cultivated Denitrifiers.” ENVIRONMENTAL MICROBIOLOGY 8.11 (2006): 2012–2021. Print.
@article{351385,
  abstract     = {Gene sequence analysis of nirS and nirK, both encoding nitrite reductases, was performed on cultivated denitrifiers to assess their incidence in different bacterial taxa and their taxonomical value. Almost half of the 227 investigated denitrifying strains did not render an nir amplicon with any of five previously described primers. NirK and nirS were found to be prevalent in Alphaproteobacteria and Betaproteobacteria, respectively, nirK was detected in the Firmicutes and Bacteroidetes and nirS and nirK with equal frequency in the Gammaproteobacteria. These observations deviated from the hitherto reported incidence of nir genes in bacterial taxa. NirS gene phylogeny was congruent with the 16S rRNA gene phylogeny on family or genus level, although some strains did group within clusters of other bacterial classes. Phylogenetic nirK gene sequence analysis was incongruent with the 16S rRNA gene phylogeny. NirK sequences were also found to be significantly more similar to nirK sequences from the same habitat than to nirK sequences retrieved from highly related taxa. This study supports the hypothesis that horizontal gene transfer events of denitrification genes have occurred and underlines that denitrification genes should not be linked with organism diversity of denitrifiers in cultivation-independent studies.},
  author       = {Heylen, Kim and Gevers, Dirk and Vanparys, Bram and Wittebolle, Lieven and Geets, Joke and Boon, Nico and De Vos, Paul},
  issn         = {1462-2912},
  journal      = {ENVIRONMENTAL MICROBIOLOGY},
  keyword      = {BACTERIA,NITRITE REDUCTASE GENES,DIVERSITY,IDENTIFICATION,FRAGMENTS,EVOLUTION,ALIGNMENT,SYSTEMS},
  language     = {eng},
  number       = {11},
  pages        = {2012--2021},
  title        = {The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers},
  url          = {http://dx.doi.org/10.1111/j.1462-2920.2006.01081.x},
  volume       = {8},
  year         = {2006},
}

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