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

Restrepo-Ortiz, C. X.; Merbt, S. N.; Barrero-Canossa, Jimena; Fuchs, Bernhard M.; Casamayor, E. O.

doi:10.1016/j.syapm.2018.04.003

Item

ITEM ACTIONSEXPORT

Add to Basket

Local TagsRelease HistoryDetailsSummary

Released

Journal Article

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

MPS-Authors

/persons/resource/persons256952

Barrero-Canossa, Jimena
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

/persons/resource/persons210389

Fuchs, Bernhard M.
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

External Resource

No external resources are shared

Fulltext (restricted access)

There are currently no full texts shared for your IP range.

Fulltext (public)

There are no public fulltexts stored in PuRe

Supplementary Material (public)

There is no public supplementary material available

Citation

Restrepo-Ortiz, C. X., Merbt, S. N., Barrero-Canossa, J., Fuchs, B. M., & Casamayor, E. O. (2018). 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, 41(4), 408-413. doi:10.1016/j.syapm.2018.04.003.

Cite as: https://hdl.handle.net/21.11116/0000-0003-B855-E

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 and its relatives in natural environments. (C) 2018 Elsevier GmbH. All rights reserved.