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New genus-specific primers for PCR identification of Rubrobacter strains

Lookup NU author(s): Dr Jean Franco Castro Figueroa, Dr Imen Nouioui, Professor Alan Bull, Professor Michael Goodfellow



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


© 2019, The Author(s).A set of oligonucleotide primers, Rubro223f and Rubro454r, were found to amplify a 267 nucleotide sequence of 16S rRNA genes of Rubrobacter type strains. The primers distinguished members of this genus from other deeply-rooted actinobacterial lineages corresponding to the genera Conexibacter, Gaiella, Parviterribacter, Patulibacter, Solirubrobacter and Thermoleophilum of the class Thermoleophilia. Amplification of DNA bands of about 267 nucleotides were generated from environmental DNA extracted from soil samples taken from two locations in the Atacama Desert. Sequencing of a DNA library prepared from the bands showed that all of the clones fell within the evolutionary radiation occupied by the genus Rubrobacter. Most of the clones were assigned to two lineages that were well separated from phyletic lines composed of Rubrobacter type strains. It can be concluded that primers Rubro223f and Rubro454r are specific for the genus Rubrobacter and can be used to detect the presence and abundance of members of this genus in the Atacama Desert and other biomes.

Publication metadata

Author(s): Castro JF, Nouioui I, Asenjo JA, Andrews B, Bull AT, Goodfellow M

Publication type: Article

Publication status: Published

Journal: Antonie van Leeuwenhoek

Year: 2019

Volume: 112

Pages: 1863-1874

Online publication date: 12/08/2019

Acceptance date: 01/08/2019

Date deposited: 30/08/2019

ISSN (print): 0003-6072

ISSN (electronic): 1572-9699

Publisher: Springer Netherlands


DOI: 10.1007/s10482-019-01314-3


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