Fig. S1. Parsimony network of O. mucofloris COI haplotypes (69 individuals from 3 whale-falls, with 28 individuals from this study and 41 individuals from previous studies including Glover et al., 2005). COI haplotype numbers correspond to those shown in Table 4. Each circle shows a unique COI haplotype; circle size shows the number of individuals that share the haplotype. Lines connecting circles represent 1 nucleotide difference between haplotypes, open circles on lines represent unsampled theoretical haplotypes, dashed lines show alternative connections between haplotypes. Colours represent endosymbiont clusters A–H; the proportion of a colour within a circle shows the number of host individuals that had the endosymbiont cluster. Unknown: endosymbionts that hybridized with the general Osedax endosymbiont probe but not with probes specific to clusters A–H. nd: Endosymbiont identity not determined.

Fig. S2. Phylogeny of bacteria from the (A) Alphaproteobacteria and Bacteroidetes, and (B) Epsilonproteobacteria associated with O. mucofloris. Only 16S rRNA sequences > 1200 bp were used in maximum likelihood (phyML) analyses with 100 bootstraps (values > 70% to the left of a given node). Shorter sequences were added afterwards without changing the tree topology using the arb parsimony add function. Sequences from this study in bold. Scale bars = 0.10 estimated substitutions per site.

Fig. S3.O. mucofloris epibiotic bacteria.A. Fluorescence in situ hybridization. Epifluorescence micrograph of cross section through the root tissues of Individual Omu 16 showing abundant Bacteriodetes (arrow) in the mucus layer covering the worm (shown in green with probe CF319a) and endosymbionts (arrowhead) (shown in yellow with probe EUBI-III) in the epithelial cells (e). Host nuclei stained blue with DAPI.B. Scanning electron micrograph of epibiotic bacteria on the trunk surface of O. mucofloris. Such a dense covering of epibiotic bacteria was not observed on other worm species prepared in the same way. Specimens were critical point dryed, coated in gold and imaged using a Phillips XL30 SEM. Scale bars: (A) = 20 μm and (B) = 10 μm.

Table S1. Clone library 16S rRNA sequences. Oceanospirillales symbiont sequences were grouped in a cluster if they had at least 99.5% sequence identity. For Epsilonproteobacteria, Alphaproteobacteria and Bacteroidetes sequences, only those found in several host individuals are shown, all other sequences are grouped under ‘others’. Number of nearly full-length sequences shown in parentheses (both strands were sequenced).

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