Genome-derived criteria for assigning environmental narG and nosZ sequences to operational taxonomic units of nitrate reducers.
Ninety percent of cultured bacterial nitrate reducers with a 16S rRNA gene similarity of > or =97% had a narG or nosZ similarity of > or =67% or > or =80%, respectively, suggesting that 67% and 80% could be used as standardized, conservative threshold similarity values for narG and nosZ, respectively (i.e., any two sequences that are less similar than the threshold similarity value have a very high probability of belonging to different species), for estimating species-level operational taxonomic units. Genus-level tree topologies of narG and nosZ were generally similar to those of the corresponding 16S rRNA genes. Although some genomes contained multiple copies of narG, recent horizontal gene transfer of narG was not apparent.
Palmer
Katharina
K
Department of Ecological Microbiology, University of Bayreuth, Germany.
Drake
Harold L
HL
Horn
Marcus A
MA
D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D004275:DNA, Ribosomal / Q000235:genetics; D004783:Environmental Microbiology; D050901:Nitrate Reductase / Q000235:genetics*; D010088:Oxidoreductases / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid
D001426:Bacterial Proteins; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; C022763:nitrous oxide reductase; D050901:Nitrate Reductase