Elimination of contamination in the published 16S rRNA gene sequence of Rothia amarae type strain J18T during phylogenetic studies of a bacterial isolate from a suspension cell culture of Arabidopsis thaliana (Heynh.)

Abstract

In our phylogenetic studies of a bacterial strain isolated from an Arabidopsis suspension culture, we obtained convincing evidence for contamination of the published 16S rRNA gene sequence of Rothia amarae type strain J18T (GenBank AY043359.1). Correction of this sequence by deleting the contamination region eliminated contradictions in bioinformatic results that included comparisons of the small-subunit (SSU) rRNA secondary structures. Further, correction of the contaminated sequence yielded sequence identity values for the 16S rRNA genes of the isolate and R. amarae type strain J18T (and more than a dozen other R. amarae members) above the threshold for species demarcation. The phylogram of the 16S rRNA gene sequences of the type strains closely related to the isolate under study (interspecies sequence identity values, 96-98.7%) united members of the family Micrococcaceae (the genera Rothia, Kocuria and Arthrobacter). A great diversity of habitat conditions was noted for these bacteria, isolated from animals, soil, aqueous media, plant tissues and other sources. This applies, in particular, to R. amarae members that are most closely related to the isolate under study by the 16S rRNA gene sequence criterion (sequence identity, near 100%) and belong to four ecotypes: Antarctic, aquatic, soil and endophytic.