Molecular Tools for the Detection of Nitrogen Cycling Archaea
Author
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-01-08
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic capacities, which sets them up for potentially major roles in the biogeochemistry of their ecosystems.
The detection, characterization, and quantification of archaeal functions in mixed communities require Archaea-specific primers or probes for the corresponding metabolic genes.
Five pairs of degenerate primers were designed to target archaeal genes encoding key enzymes of nitrogen cycling: nitrite reductases NirA and NirB, nitrous oxide reductase (NosZ), nitrogenase reductase (NifH), and nitrate reductases NapA/NarG.
Sensitivity towards their archaeal target gene, phylogenetic specificity, and gene specificity were evaluated in silico and in vitro.
Owing to their moderate sensitivity/coverage, the novel nirB-targeted primers are suitable for pure culture studies only.
The nirA-targeted primers showed sufficient sensitivity and phylogenetic specificity, but poor gene specificity.
The primers designed for amplification of archaeal nosZ performed well in all 3 criteria; their discrimination against bacterial homologs appears to be weakened when Archaea are strongly outnumbered by bacteria in a mixed community.
The novel nifH-targeted primers showed high sensitivity and gene specificity, but failed to discriminate against bacterial homologs.
Despite limitations, 4 of the new primer pairs are suitable tools in several molecular methods applied in archaeal ecology.
American Psychological Association (APA)
Rusch, Antje. 2013. Molecular Tools for the Detection of Nitrogen Cycling Archaea. Archaea،Vol. 2013, no. 2013, pp.1-10.
https://search.emarefa.net/detail/BIM-489677
Modern Language Association (MLA)
Rusch, Antje. Molecular Tools for the Detection of Nitrogen Cycling Archaea. Archaea No. 2013 (2013), pp.1-10.
https://search.emarefa.net/detail/BIM-489677
American Medical Association (AMA)
Rusch, Antje. Molecular Tools for the Detection of Nitrogen Cycling Archaea. Archaea. 2013. Vol. 2013, no. 2013, pp.1-10.
https://search.emarefa.net/detail/BIM-489677
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-489677