Environmental distribution of two widespread uncultured freshwater Euryarchaeota clades unveiled by specific primers and quantitative PCR
Article first published online: 18 AUG 2013
© 2013 John Wiley & Sons Ltd and Society for Applied Microbiology
Environmental Microbiology Reports
Volume 5, Issue 6, pages 861–867, December 2013
How to Cite
Restrepo-Ortiz, C. X. and Casamayor, E. O. (2013), Environmental distribution of two widespread uncultured freshwater Euryarchaeota clades unveiled by specific primers and quantitative PCR. Environmental Microbiology Reports, 5: 861–867. doi: 10.1111/1758-2229.12088
- Issue published online: 14 NOV 2013
- Article first published online: 18 AUG 2013
- Accepted manuscript online: 25 JUL 2013 04:41AM EST
- Manuscript Accepted: 19 JUL 2013
- Manuscript Received: 28 APR 2013
- Spanish Office of Science (MINECO). Grant Numbers: CGL2009-13318, CGL2012-32747
Fig. S1. Phylogenetic context for the 16S rRNA gene of the Euryarchaeota DHVE and MEG targeted by specific primers in this study (SILVA ribosomal database 111 RefNR, July 2012). The clades are highlighted and equivalent clade nomenclature has been added following Durbin and Teske (2011; 2012). Scale bar, 10% estimated divergence.
Fig. S2. Specificity level (number of bands observed in an agarose gel) observed for the newly designed primers at different PCR annealing temperatures. Averaged values and error range for PCR products obtained from lakes Bergús, Llebreta and Muntanyó d'Arreu. The primers set MEG 93f-392r (expected PCR product size ∼ 296 bp) and DSEG 510f-725r (∼ 216 bp) showed the best performance and specificity.
Fig. S3. Maximum-likelihood phylogenetic tree for the 16S rRNA gene of the Euryarchaeota clade MEG (Miscellaneous Euryarchaeota Group comprising the clades pMC2A384 and VALII/Eury4; Durbin and Teske, 2012) targeted by the specific primers set designed in this study. Scale bar, 10% estimated divergence.
Fig. S4. Maximum-likelihood phylogenetic tree for the 16S rRNA gene of the Euryarchaeota clade DSEG (Deep-Sea Euryarchaeotal Groups, targeting the cluster named VALIII comprising the DHVE-3/DSEG, BC07-2A-27/DSEG-3 and DSEG-2 groups; Durbin and Teske, 2011; 2012) targeted by the specific primer set designed in this study. Scale bar, 10% estimated divergence.
Table S1. NCBI accession numbers of the 16S rRNA gene sequences used to design the new and specific primers for Euryarchaeotal clades MEG and DSEG in combination with the Pyrenean 16S rRNA gene dataset.
Table S2. Specific primers set designed in this study for qPCR analysis of the euryarchaeotal clades MEG and DSEG. The primer sets MEG 93f-392r, and DSEG 510f-725r showed the best performance and specificity, respectively (see Fig S2).
Table S3. Environmental parameters of the different lakes analysed in this study and specific 16S rRNA gene abundances for the Euryarchaeota DSEG and MEG, and Thaumarchaeota SAGMGC populations. Standard deviations < 10% applies for all the qPCR data. N/A not available; N/D not detected.
Table S4. Environmental parameters for the different dates and depths analysed in Lake Redon and specific 16S rRNA gene abundances for the Euryarchaeota DSEG and MEG, and Thaumarchaeota SAGMGC populations. Standard deviations < 10% applies for all the qPCR data. N/A not available; N/D not detected.
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