Supplemental Figures 1 through 3. Denaturing gradient gel images of bacterial 16S rDNA (Supplemental
Figure 1), pmoA (Supplemental Figure 2), and archaeal 16S rDNA (Supplemental Figure 3) PCR products
with DNA recovered from density fractions from 12C-CH4 (left) and 13C-CH4 (right) incubations from
Chicago Bog and Michigan Hollow fen. Measured densitites in g ml-1 are written vertically at the top of each
lane. Arrows point to bands present in heavier fractions of the 13C samples that were absent from 12C
controls and that were excised for further analysis. The 3 bands present in every sample lane of the 4
bacterial 16S rDNA gels in Supplemental Figure 1 were determined to originate from bacterial or bacterial
DNA contamination of the “molecular grade” glycogen (Fisher Scientific, Fair Lawn, NJ, USA) used to
precipitate and purify DNA; a problem common to nearly all brands of commercially available moleculargrade glycogen from North American suppliers (c.f. Bantram et al. 2009, Nucleic acid contamination of glycogen
used in nucleic acid precipitation and assessment of linear polyacrylamide as an alternative co-precipitant. BioTechniques
47:1019-1022). An X over lanes on the bacterial 16S rDNA gels was from a last, least dense 11 th fraction
recovered from a much smaller volume of CsCl2 than the first 10 densest fractions that was not included in
the other PCRs or DGGE gels.
marker
marker
X
1.708
X
empty lane
1.710
1.688
1.721
1.727
1.741
1.746
1.747
1.757
1.758
empty lane
1.713
Michigan Hollow 13-C 16s rDNA
1.701
1.706
1.725
1.731
1.738
1.750
1.767
1.770
1.770
Michigan Hollow 12-C 16s rDNA
marker
marker
X
1.678
1.687
1.702
1.711
1.730
1.737
Chicago Bog 12-C bacterial 16s rDNA
marker
marker
empty lane
X
1.697
1.704
1.716
1.722
1.726
1.739
1.749
1.752
1.762
empty lane
marker
C2 16s rRNA
1.731
1.749
1.752
1.759
1.794
marker
Supplemental Figure 1.
Chicago Bog 13-C bacterial 16s rDNA
Marker
1.688
1.701
1.706
1.725
1.731
1.738
1.750
1.767
1.770
1.770
Michigan Hollow 12-C pmoA
Marker
1.708
1.710
1.713
1.721
1.727
1.741
marker
1.746
1.747
1.757
1.758
marker
marker
1.678
1.687
1.702
1.711
1.730
marker
1.737
1.739
1.749
1.752
1.762
marker
Chicago Bog 12-C pmoA
marker
1.697
marker
1.704
1.716
1.722
1.726
1.731
1.749
1.752
1.759
1.794
marker
Supplemental Figure 2.
Chicago Bog 13-C pmoA
Michigan Hollow 13-C pmoA
Supplemental Figure 3.
Supplemental Figure 4. Phylogenetic tree illustrating the relatedness of a single archaeal 16S rDNA
sequence detected in a higher density fraction of the 13C Chicago Bog DNA but not the 12C controls (see
Supplemental Figure 3). Other sequences are 16S rDNA of isolates and other uncultivated archaea from
environmental samples retrieved from GenBank.