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Fig. S1. Phylogenetic placement of Cytophaga/Flavo-bacterium/Bacteroides 16S rRNA bacterial sequences from T. benedii tail ends based on ML analyses (sequences from this study in red, in parentheses the number of sequences with > 99.0% to the given sequence). Scale bar = 0.10 estimated substitutions per site. Numbers next to nodes correspond to bootstrap values based on 100 ML replicates (only values above 60% are shown).

Fig. S2. Phylogenetic placement of deltaproteobacterial 16S rRNA sequences from T. benedii tail ends based on ML analyses (sequences from this study in red, in parentheses the number of sequences with > 99.0% to the given sequence). Five sphingobacterial sequences were used as an outgroup (arrow). Scale bar = 0.10 estimated substitutions per site. Numbers next to nodes correspond to bootstrap values based on 100 ML replicates (only values above 60% are shown).

Fig. S3. CARD-FISH images of epibacteria on T. benedii tail ends. A. Cross section through the tail end showing the thick layer of bacteria covering the surface of the worm (eubacterial probe EUBI-III). B. The general gammaproteobacterial probe (GAM42a, red) hybridized with rods and cocci in the mucus membrane, while the Gamma 1 ectosymbionts hybridized with specific probes (shown in green: TbGAM1-138) but not with the GAM42a probe. C. The T. benedii Gamma 2 ectobionts (hybridized with the specific probe TbGAM2-447, green) were cocci-shaped and found occasionally in the mucous membrane. D.-E. Deltaproteobacteria (probe DELTA495a, red) and Bacteroidetes (probe CF319a, green) populated the worm's mucous layer. Deltaproteobacteria occurred singly as rods in groups of coccoid or oval shaped cells. Bacteroidetes mostly occurred in patches within the mucus and were often rod-shaped, and sometimes elongated or filamentous.

Table S1. Additional oligonucleotide probes used in this study that did not result in reproducible clear signals.

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