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Novel primers for 1...
Novel primers for 16S rRNA-based archaeal community analyses in environmental samples
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- Gantner, S (författare)
- Uppsala universitet,Limnologi
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- Andersson, Anders F. (författare)
- Uppsala universitet,KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,Limnologi
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- Alonso-Saez, Laura (författare)
- Uppsala universitet,Limnologi
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- Bertilsson, Stefan (författare)
- Uppsala universitet,Limnologi
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(creator_code:org_t)
- Elsevier BV, 2011
- 2011
- Engelska.
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Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 84:1, s. 12-18
- Relaterad länk:
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Next generation sequencing technologies for in depth analyses of complex microbial communities rely on rational primer design based on up-to-date reference databases. Most of the 16S rRNA-gene based analyses of environmental Archaea community composition use PCR primers developed from small data sets several years ago, making an update long overdue. Here we present a new set of archaeal primers targeting the 16S rRNA gene designed from 8500 aligned archaeal sequences in the SILVA database. The primers 340F-1000R showed a high archaeal specificity (<1% bacteria amplification) covering 93 and 97% of available sequences for Crenarchaeota and Euryarchaeota respectively. In silico tests of the primers revealed at least 38% higher coverage for Archaea compared to other commonly used primers. Empirical tests with clone libraries confirmed the high specificity of the primer pair to Archaea in three biomes: surface waters in the Arctic Ocean, the pelagic zone of a temperate lake and a methanogenic bioreactor. The clone libraries featured both Euryarchaeota and Crenarchaeota in variable proportions and revealed dramatic differences in the archaeal community composition and minimal phylogenetic overlap between samples.
Ämnesord
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
Nyckelord
- *Biodiversity
- *Environmental Microbiology
- Archaea/*classification/*genetics
- Computational Biology
- DNA Primers/*genetics
- DNA
- Archaeal/chemistry/genetics
- High-Throughput Nucleotide Sequencing/methods
- Metagenomics/*methods
- Molecular Sequence Data
- Polymerase Chain Reaction/methods
- RNA
- Archaeal/genetics
- RNA
- Ribosomal
- 16S/*genetics
- Sensitivity and Specificity
- Freshwater ecology
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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