Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives

Systematic and Applied Microbiology
C X Restrepo-OrtizEmilio O Casamayor

Abstract

The Thaumarchaeota SAGMCG-1 group and, in particular, members of the genus Nitrosotalea have high occurrence in acidic soils, the rhizosphere, groundwater and oligotrophic lakes, and play a potential role in nitrogen cycling. In this study, the specific oligonucleotide fluorescence in situ hybridization probe SAG357 was designed for this Thaumarchaeota group based on the available 16S rRNA gene sequences in databases, and included the ammonia-oxidizing species Nitrosotalea devanaterra. Cell permeabilization for catalyzed reporter deposition fluorescence in situ detection and the hybridization conditions were optimized on enrichment cultures of the target species N. devanaterra, as well as the non-target ammonia-oxidizing archaeon Nitrosopumilus maritimus. Probe specificity was improved with a competitor oligonucleotide, and fluorescence intensity and cell visualization were enhanced by the design and application of two adjacent helpers. Probe performance was tested in soil samples along a pH gradient, and counting results matched the expected in situ distributions. Probe SAG357 and the CARD-FISH protocol developed in the present study will help to improve the current understanding of the ecology and physiology of N. devanaterra...Continue Reading

References

Sep 5, 1976·Journal of Molecular Biology·A Braithwaite
Mar 12, 1992·Nature·J A FuhrmanA A Davis
Jun 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·E F DeLong
Dec 20, 1989·Journal of Immunological Methods·M N BobrowG J Litt
Jan 1, 1980·Applied and Environmental Microbiology·B M Chassy, A Giuffrida
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jun 1, 2002·Applied and Environmental Microbiology·Annelie PernthalerRudolf Amann
May 7, 2003·Applied and Environmental Microbiology·Raju SekarRudolf Amann
Feb 27, 2004·Nucleic Acids Research·Wolfgang LudwigKarl-Heinz Schleifer
Sep 4, 2004·Applied and Environmental Microbiology·Annelie Pernthaler, Rudolf Amann
Jul 15, 2005·Pest Management Science·Anna Barra CaraccioloCarlo Cremisini
Sep 1, 1994·Applied and Environmental Microbiology·K TrebesiusK H Schleifer
Jul 18, 2006·Nucleic Acids Research·T Z DeSantisG L Andersen
Nov 14, 2006·Nucleic Acids Research·Alexander LoyMatthias Horn
Jan 25, 2008·Environmental Microbiology·Jean-Christophe Auguet, Emilio O Casamayor
Feb 16, 2008·Nature Reviews. Microbiology·Céline Brochier-ArmanetPatrick Forterre
Apr 17, 2008·Nature Reviews. Microbiology·Rudolf Amann, Bernhard M Fuchs
May 21, 2009·FEMS Microbiology Reviews·Tuba H ErguderWilly Verstraete
Sep 8, 2009·FEMS Microbiology Ecology·Laura E LehtovirtaGraeme W Nicol
Jan 18, 2011·Applied and Environmental Microbiology·Jean-Christophe AuguetEmilio O Casamayor
May 7, 2011·Current Opinion in Microbiology·Michael PesterMichael Wagner
Sep 8, 2011·Proceedings of the National Academy of Sciences of the United States of America·Laura E Lehtovirta-MorleyGraeme W Nicol
Sep 21, 2011·Proceedings of the National Academy of Sciences of the United States of America·Marc MussmannIan M Head
Oct 12, 2012·PloS One·Antoni Fernàndez-Guerra, Emilio O Casamayor
Nov 28, 2012·FEMS Microbiology Ecology·Jean-Christophe Auguet, Emilio O Casamayor

❮ Previous
Next ❯

Citations

Oct 10, 2020·The Science of the Total Environment·Jingjing LiuTian C Zhang

❮ Previous
Next ❯

Related Concepts

Related Feeds

Archaeogenetics

Recent advances in genomic sequencing has led to the discovery of new strains of Archaea and shed light on their evolutionary history. Discover the latest research on Archaeogenetics here.