Elimination of contamination in the published 16S rRNA gene sequence ofRothia amaraetype strain J18Tduring phylogenetic studies of a bacterial isolate from a suspension cell culture ofArabidopsis thaliana(Heynh.)

Abstract

ABSTRACTIn our phylogenetic studies of a bacterial strain isolated from anArabidopsissuspension culture, we obtained convincing evidence for contamination of the published 16S rRNA gene sequence ofRothia amaraetype strain J18T(GenBankAY043359.1). 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 andR. amaraetype strain J18T(and more than a dozen otherR. amaraemembers) 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 familyMicrococcaceae(the generaRothia, KocuriaandArthrobacter). 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, toR. amaraemembers 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.