Supplementary Methods text
Sediment sampling at SPG 11 and SPG 12. Freshly retrieved multicores containing
sediment and overlying water were removed to a 4° C cold room for subsampling. Two
50-mL Falcon tubes of supernatant were collected from the overlying water of the
multicore, and subsequently frozen at -80°C. SPG11 multicore sediments were sampled
using three autoclaved 60mL syringes with the tip cones cut off. To sample sediments,
the core liner was pulled down so that it was nearly flush with the sediment surface.
Syringes were then pushed into the sediment, taking care to avoid sampling within ~1cm
of the core liner. Pulling the core liner down further to just above the bottom of the cutoff
syringe, the syringes were pulled laterally out of the core. The sediment was then
extruded from the syringe and rounds of sediment were sliced off at specific intervals
using a flame-sterilized scraper. Sampling intervals were 1 cm for 0-20 cm depth, 2 cm
for 20-30 cm depth, and 5 cm for 30-40 cm depth. Samples from the same interval were
pooled in a sterile Whirl-Pak bag and then frozen at -80°C. The sampling horizon was
reestablished after each syringe sampling by using a flame-sterilized scraper to smooth
the sediment flush with the syringe depressions.
SPG12 sediments used in this study were collected via gravity coring, with a total
recovery of 401 cm. Cores were split into approximately 1m-long sections, and further
sectioned into ~30 cm rounds. Cores were sampled by pushing autoclaved cut-off 60 mL
syringes into the core cross-section, avoiding an approximately 1-2 cm margin inside the
core liner, and then extruding the sample 1 cm at a time while slicing off subsamples
using a flame-sterilized spatula. Subsamples were stored in sterile Whirl-Pak bags or
sterile 50-mL Falcon tubes (BD Biosciences) and frozen at -80°C until analysis.
Statistical analyses of sequence diversity. SONS (Schloss and Handelsman
2006a) estimated the Chao1 (Chao 1984) species diversity of each depth, and crosscomparied community structure using abundance-based Jaccard (Smith et al. 1996, Yue
et al. 2001) and Theta (Yue and Clayton 2005) diversity indices. Both individual
community Chao1 estimates and estimates of the Chao1 diversity shared between two
communities (shared Chao1) were calculated. The abundance-based Jaccard index
measures the intersection of the combined assemblage of phylotypes, and can be
considered the probability that given a phylotype present in one assemblage, it is present
in both assemblages (Schloss and Handelsman 2006a). By contrast, ThetaYC corrects for
the differences in relative abundance of phylotypes in each assemblage, taking into
account both the incidence of shared phylotypes and the similarity of their relative
abundances in each assemblage. Thus, it can be considered a percentile measure of the
similarity of community structures.
Treeclimber (Schloss and Handelsman 2006b) was used to test the hypothesis that the
overall structure of two communities is statistically the same. P values indicate the
probability that a similar association between phylogeny and sample origin would occur
by chance.
Taq error correction. The number of unique OTUs was plotted versus distance,
based on a collector’s curve using all SPG11 and SPG12 MG-I sequences as calculated in
DOTUR, and corrected for the contribution of Taq error to divergence according to
Acinas et al. (2004), based on an error rate of 2x10-5 per site per duplication (Klepac-
Ceraj et al. 2004) and an average amplicon length of 1400 base pairs, yielding an average
of 1.6 errors per 16S rDNA sequence, or ~0.11%.
Supplement references:
Acinas, S.G., Klepac-Ceraj, V., Hunt, D.E., Pharino, C., Ceraj, I., Distel, D.L., and Polz,
M.F. (2004) Fine-scale phylogenetic architecture of a complex bacterial community.
Nature 430:551-554.
Klepac-Ceraj, V., Bahr, M., Crump, B.C., Teske, A.P., Hobbie, J.E., and Polz, M.F.
(2004) High overall diversity and dominance of microdiverse relationships in salt marsh
sulfate-reducing bacteria. Environ Microbiol 6: 686-698.
Schloss, P.D., and Handelsman, J. (2006a) Introducing SONS, a tool for operational
taxonomic unit-based comparisons of microbial community memberships and structures.
Appl Environ Microbiol 72: 6773-6779.
Schloss, P.D., and Handelsman, J. (2006b) Introducing TreeClimber, a test to compare
microbial community structures. Appl Environ Microbiol 72: 2379-2384.
Smith, W., Solow, A.R., and Preston, P.E. (1996) An estimator of species overlap using a
modified beta-binomial model. Biometrics 52: 1472-1477.
Yue, J.C., Clayton, M.K., and Lin, F.C (2001) A nonparametric estimator of species
overlap. Biometrics 57: 743-749.
Yue, J.C., and Clayton, M.K. (2005) A similarity measure based on species proportions.
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