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rpoB gene as a novel molecular marker to infer phylogeny in Planctomycetales

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Abstract

The 16S rRNA gene has been used in the last decades as a gold standard for determining the phylogenetic position of bacteria and their taxonomy. It is a well conserved gene, with some variations, present in all bacteria and allows the reconstruction of genealogies of microorganisms. Nevertheless, this gene has its limitations when inferring phylogenetic relationships between closely related isolates. To overcome this problem, DNA–DNA hybridization appeared as a solution to clarify interspecies relationships when the sequence similarity of the 16S rRNA gene is above 97 %. However, this technique is time consuming, expensive and laborious and so, researchers developed other molecular markers such as sequencing of housekeeping or functional genes for accurate determination of bacterial phylogeny. One of these genes that have been used successfully, particularly in clinical microbiology, codes for the beta subunit of the RNA polymerase (rpoB). The rpoB gene is sufficiently conserved to be used as a molecular clock, it is present in all bacteria and it is a mono-copy gene. In this study, rpoB gene sequencing was applied to the phylum Planctomycetes. Based on the genomes of 19 planctomycetes it was possible to determine the correlation between the rpoB gene sequence and the phylogenetic position of the organisms at a 95–96 % sequence similarity threshold for a novel species. A 1200-bp fragment of the rpoB gene was amplified from several new planctomycetal isolates and their intra and inter-species relationships to other members of this group were determined based on a 96.3 % species border and 98.2 % for intraspecies resolution.

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Acknowledgments

This study was supported by Fundação para a Ciência e Tecnologia (FCT, PEst-C/MAR/LA0015/2011). The first author was financed by FCT (PhD Grant SFRH/BD/35933/2007) and a Marie Curie Early Stage Training Site MarMic EST MEST-CT-2004-007776.

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Authors and Affiliations

  1. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/nº, 4169-007, Porto, Portugal

    Joana Bondoso & Olga Maria Lage

  2. CIMAR/CIIMAR—Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123, Porto, Portugal

    Joana Bondoso & Olga Maria Lage

  3. Department of Microbiology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany

    Jens Harder

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  1. Joana Bondoso
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Correspondence to Joana Bondoso.

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Bondoso, J., Harder, J. & Lage, O.M. rpoB gene as a novel molecular marker to infer phylogeny in Planctomycetales . Antonie van Leeuwenhoek 104, 477–488 (2013). https://doi.org/10.1007/s10482-013-9980-7

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