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Supplementary information TABLE 2. PCR primers used during this study. The reverse
transcription was done with the AMV reverse transcriptase followed by the quantitative PCR
by Tfl DNA-Polymerase. Both enzymes are included in the used Access One-Step-RT-PCR
Kit (Promega). The iCycler iQ RT PCR detection system (Bio-Rad) was used for
amplification of a serial dilution of (a) RNA in duplicates. An equal initial amount of RNA
and determination of PCR efficiency and threshold cycle at identical fluorescence signal is the
basic for detection differences in gene expression.
Primer system
Primer sequence
Reference
Annealing
temperature
16S rRNA
amoA
recA
519f
5’-CAGCMGCCGCGGTAANWC-3’
907r
5’-CCGTCAATTCMTTTRAGTT-3’
AOA-amoA-f
5’-CTGAYTGGGCYTGGACATC-3’
AOA-amoA-r
5’-TTCTTCTTTGTTGCCCAGTA-3’
GD1-recA-f614
5’-CTCCGGAGACACACTGGT-3’
GD1-recA-r822
5’-TAGCTCGCCCTCTTTTGAGA-3’
(3, 4)
52 °C
(1)
58.5°C
this work*
54 °C
*
Primer design based on recA sequence information of Sulfurimonas sp. GD1 (key player of
pelagic redoxclines of the central Baltic Sea (2)).
References
1.
Coolen, M. J. L., B. Abbas, J. van Bleijswijk, E. C. Hopmans, M. M. M. Kuypers,
S. G. Wakeham, and J. S. Sinninghe Damste. 2007. Putative ammonia-oxidizing
Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using
16S ribosomal and functional genes and membrane lipids. Environ. Microbiol.
9:1001-1016.
2.
Grote, J. 2009. Physiology, ecology, and genomics of facultative chemoautotrophic
Epsilonproteobacteria in marine pelagic redoxclines. PhD thesis, University of
Rostock, Germany.
3.
Lane, D. J. 1991. 16S/23S rRNA sequencing. John Wiley and Sons, Chichester.
4.
Stubner, S. 2002. Enumeration of 16S rDNA of Desulfotomaculum lineage 1 in rice
field soil by real-time PCR with SybrGreen detection. J. Microbiol. Meth. 50:155-164.