New genus-specific primers for PCR identification of Rubrobacter strains.
Actinobacteria
Atacama desert
Genus-specific primers
Rubrobacter
Taxonomy
Journal
Antonie van Leeuwenhoek
ISSN: 1572-9699
Titre abrégé: Antonie Van Leeuwenhoek
Pays: Netherlands
ID NLM: 0372625
Informations de publication
Date de publication:
Dec 2019
Dec 2019
Historique:
received:
15
03
2019
accepted:
01
08
2019
pubmed:
14
8
2019
medline:
18
3
2020
entrez:
14
8
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 31407134
doi: 10.1007/s10482-019-01314-3
pii: 10.1007/s10482-019-01314-3
pmc: PMC6834744
doi:
Substances chimiques
DNA Primers
0
DNA, Bacterial
0
DNA, Ribosomal
0
RNA, Ribosomal, 16S
0
Types de publication
Evaluation Study
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1863-1874Références
Int J Syst Evol Microbiol. 2017 May;67(5):1613-1617
pubmed: 28005526
Syst Appl Microbiol. 2012 Jul;35(5):306-9
pubmed: 22776713
FEMS Microbiol Ecol. 2005 Jun 1;53(1):141-55
pubmed: 16329936
Sci Rep. 2017 Aug 21;7(1):8373
pubmed: 28827739
Appl Environ Microbiol. 1999 Apr;65(4):1721-30
pubmed: 10103273
Appl Environ Microbiol. 2003 Oct;69(10):6189-200
pubmed: 14532080
Appl Environ Microbiol. 2002 May;68(5):2391-6
pubmed: 11976113
Mol Syst Biol. 2011 Oct 11;7:539
pubmed: 21988835
Int J Syst Evol Microbiol. 2007 Jul;57(Pt 7):1453-5
pubmed: 17625174
Microbiome. 2013 Nov 20;1(1):28
pubmed: 24451153
Extremophiles. 1999 Nov;3(4):235-8
pubmed: 10591012
Arch Microbiol. 2001 Nov;176(5):347-54
pubmed: 11702076
Int J Syst Evol Microbiol. 2014 Mar;64(Pt 3):705-9
pubmed: 24170773
Extremophiles. 2012 May;16(3):553-66
pubmed: 22527047
Syst Appl Microbiol. 2014 Jun;37(4):235-43
pubmed: 24780859
Appl Environ Microbiol. 2003 Jul;69(7):3858-67
pubmed: 12839754
Int J Syst Evol Microbiol. 2003 Mar;53(Pt 2):485-90
pubmed: 12710617
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D34-8
pubmed: 15608212
Proc Natl Acad Sci U S A. 1978 Oct;75(10):4801-5
pubmed: 368799
Extremophiles. 2018 Jan;22(1):47-57
pubmed: 29101684
Nat Rev Microbiol. 2014 Sep;12(9):635-45
pubmed: 25118885
BMC Bioinformatics. 2013 Feb 21;14:60
pubmed: 23432962
Int J Syst Evol Microbiol. 2003 Mar;53(Pt 2):569-76
pubmed: 12710628
Int J Syst Evol Microbiol. 2018 Nov;68(11):3487-3493
pubmed: 30300120
Environ Microbiol. 2003 Oct;5(10):896-907
pubmed: 14510843
Environ Microbiol. 2002 Nov;4(11):654-66
pubmed: 12460273
Appl Environ Microbiol. 2006 Mar;72(3):1719-28
pubmed: 16517615
Int J Syst Evol Microbiol. 2012 Mar;62(Pt 3):563-8
pubmed: 21515709
Int J Syst Evol Microbiol. 2012 Oct;62(Pt 10):2400-4
pubmed: 22140169
BMC Bioinformatics. 2012 Jun 18;13:134
pubmed: 22708584
Appl Environ Microbiol. 2002 Mar;68(3):1265-79
pubmed: 11872477
Microbiology. 1996 Oct;142 ( Pt 10):2863-70
pubmed: 8885402
Microbiol Mol Biol Rev. 2012 Mar;76(1):66-112
pubmed: 22390973
Bioinformatics. 2009 May 1;25(9):1189-91
pubmed: 19151095
Int J Syst Evol Microbiol. 2004 Sep;54(Pt 5):1849-55
pubmed: 15388754
Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42
pubmed: 24288368
Antonie Van Leeuwenhoek. 2018 Aug;111(8):1315-1332
pubmed: 29721711
Int J Syst Evol Microbiol. 2011 Nov;61(Pt 11):2606-9
pubmed: 21148679
FEMS Microbiol Ecol. 2000 Aug 1;33(2):111-120
pubmed: 10967210
Syst Appl Microbiol. 2011 Dec;34(8):595-9
pubmed: 21899973
Int J Syst Evol Microbiol. 2017 Sep;67(9):3597-3602
pubmed: 28875901
Int J Syst Evol Microbiol. 2009 Jan;59(Pt 1):87-94
pubmed: 19126730
Int J Syst Evol Microbiol. 2006 Feb;56(Pt 2):401-6
pubmed: 16449447
Int J Syst Evol Microbiol. 2014 Mar;64(Pt 3):858-62
pubmed: 24254741
Stand Genomic Sci. 2014 Mar 29;9(3):1062-75
pubmed: 25197483
FEMS Microbiol Ecol. 2003 Feb 1;43(1):13-9
pubmed: 19719692
Antonie Van Leeuwenhoek. 2014 Aug;106(2):279-85
pubmed: 24846053
Int J Syst Evol Microbiol. 2009 Mar;59(Pt 3):589-608
pubmed: 19244447
Int J Syst Evol Microbiol. 2013 Jul;63(Pt 7):2588-93
pubmed: 23264500
Methods Mol Biol. 2000;132:115-30
pubmed: 10547834
Int J Syst Evol Microbiol. 2016 Feb;66(2):652-665
pubmed: 26582010
Environ Microbiol. 2007 Nov;9(11):2894-902
pubmed: 17922771
Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):547-9
pubmed: 15774623