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Endozoicomonas montiporae (FJ347758); S1 (J:20)(S:18)(JD:9)(SD:12); S2 (J:5)(S:6)(D:4); S3 (J:9)(S:3)(D:1)

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87 S3 (J:1) S1 (S:1) 65 Eunicella cavolini bacteria (u) (JQ691564); S1 (S:1)(JD:3); S2 (S:4); S3 (J:1)(D:1) 74 Gammaproteobacteria (u) (HQ242533); S1 (SD:3) 98 Pseudomonas stutzeri (JN644606); S1 (JD:1) 99 Gammaproteobacteria (u) (GU061297) 56 Bacteria (u) (JX016311); S3 (D:1) 93 S1 (J:1) 75 Eunicella cavolini bacteria (u) (JQ691580); S1 (J:1)(S:2)(JD:4); S2 (J:1)(S:4); S3 (J:4)(S:3) 45 Gammaproteobacteria (GU230329); W (J:1) 99 Gammaproteobacteria (u) (GU230302); W (J:1) 98 99 51 Enterobacter sp. (JX566614); S1 (JD:1) 97 S2 (D:1) Gammaproteobacteria Shewanella sp. (EU697087) 99 Gammaproteobacteria (u) (AY354850) W (S:1) 43 Gammaproteobacteria (u) (AY627370); W (S:1) 99 S3 (D:1) 95 Legionella feeleii (NR 026117) S3 (D:1) 91 Gammaproteobacteria (u) (GU230348) S2 (D:1) 98 Thiothrix sp. (u) (AY426613) 43 88 S2 (D:1) Gammaproteobacteria (AJ620496) S3 (D:1) Gammaproteobacteria (u) (JN662223) 74 Gammaproteobacteria (u) (FJ205341); W (S:1) 95 98 S3 (D:1) Gammaproteobacteria (u) (AB544415) Gammaproteobacteria (u) (JF344011) 79 Bacteria (u) (JQ347341) 85 S1 (SD:2) 88 99 Delftia sp. (EF426439); S2 (D:1) 99 93 Achromobacter sp. (EU696789); S1 (J:1) 99 40 Ralstonia solanacearum (FJ984435); S3 (J:1) Betaproteobacteria 71 Betaproteobacteria (HM057710); W (J:1) 99 99 40 Deltaproteobacteria (u) (JF344336); S3 (D:1)

70 Bacteria (u) (HQ121247) 97 S3 (D:1) 38 Myxococcales sp. (u) (EU437528) Deltaproteobacteria Deltaproteobacteria (u) (AB189349) 96 S3 (S:1) 59 Bacteria (u) (JQ041458) 90 99 S3 (J:1)(S:3)(D:1) 43 Rickettsiales sp. (u) (EF667892) Bacteria (u) (GU118428); S3 (S:1) 99 W (S:1) 72 SAR11 (u) (HQ22641); S3 (S:1); W (J:1) 99 SAR11 (u) (JN591854); W (J:2) 7399 59 Alphaproteobacteria (u) (HM057778); W (J:1)(S:1) Rhodospirillales sp. (u) (JN591815); W (J:1) 99 99 Sphingomonas sp. (AY162145); S2 (S:1); S3 (J:1)(S:1) 99 Stappia alba (AJ889010); S1 (JD:2) 42 Alphaproteobacteria (u) (GQ337284) S2 (D:1) 45 S2 (S:1) 79 Rhodospirillaceae sp. (KC545306) S3 (D:1) 82 Kordiimonas aquimaris (GU289640) Alphaproteobacteria Alphaproteobacteria (u) (DQ269053) 93 Bacteria (u) (JF769569) 45 W (J:1) 99 Roseobacter sp. (u). (AF245635); W (J:2) 53 S3 (D:1) 53 98 Bacteria (u) (EU799773) 83 Rhodobacteraceae sp. (u) (HQ242427); W (J:3) 34 69 Alphaproteobacteria (u) (AY499668) 47 S1 (JD:1) 92 47 Loktanella sp. (FJ889559); S1 (SD:1) 66 S1 (JD:1) 89 Roseobacter sp. (AY576690); S3 (D:1) 96 Roseovarius sp. (FR693292); S1 (JD:1); S3 (D:1)

42 Marinosulfonomas methylotropha (AY771769) 67 Rhodobacteraceae sp. (KC416645); S3 (D:3) 75 99 W (J:1) 35 Bacteria (u) (HQ821690) 43 S3 (S:1) 75 Cyanobacteria (u) (GU170744) Cyanobacteria (u) (HQ821789); W (J:1)(S:1) 80 W (S:1) 92 74 Cyanobacteria (u) (JF344552) Cyanobacteria (u) (JF344394) 46 S2 (D:1) 96 S3 (J:1) Cyanobacteria 60 Cyanobacteria (u) (HQ821848) 91 Cyanobacteria (u) (HQ821622); W (J:1) 93 63 Cyanobacteria (u) (JN038984); S1 (S:1) 99 99 Bacteria (u) (HQ821727); W (J:1) 51 S3 (J:1) 51 Synechococcus sp. (AY172800) 99 S3 (D:1) Synechococcus sp. (AY172834) 63 Verrucomicrobia (u) (AF424512); S2 (D:2); S3 (D:1); W (J:1) 96 Verrucomicrobia (u) (DQ302112) 99 W (S:1) 99 Verrucomicrobia W (S:3) 55 Bacteria (u) (JN874141); W (S:1) 99 S3 (D:1) Chloroflexi 99 Chloroflexi bacteria (u) (DQ811857) 70 W (S:1) 30 99 Planctomycetes (u) (HM799084) Planctomycetes W (S:1) 99 S1 (SD:1) 42 Deep-sea bacteria (u) (AM997941) 99 81 Bacteroidetes (u) (EF016484); W(J:1) 93 Bacteroidetes (u) (JQ580433); W (J:1) 97 99 56 Bacteroidetes (u) (AY354780); W (J:1)

75 Bacteroidetes (u) (AY354779); W (S:1) 96 99 54 S1 (SD:1); S2 (D:3) Bacteroidetes (u) (EF471466) 37 97 S1 (SD:1) Bacteroidetes (u) (AY500022) 91 98 S1 (SD:2) Maribacter sp. (FR821175) Bacteroidetes (u) (AY500037); S3 (D:1) 93 Flavobacteria (u) (FN433401); W (S:1) 88 98 W (J:1) 97 Bacteroidetes (u) (HM057802) 86 Flavobacteriaceae sp. (u) (EU394574); W (J:1)(S:1) S1 (SD:1) 33 98 S1 (SD:1) Bacteroidetes Polaribacter sp. (AB681442)

41 W (J:1) 54 W (J:1) 74 Bacteroidetes (u) (EF016473) 85 Cytophaga sp. (AB017046) S2 (D:1) 95 Aquimarina macrocephali (AB517144); S1 (JD:3); W (S:1) 33 97 Flavobacteria (u) (AM279187); W (S:1) 43 W (J:1) 92 Bacteroidetes (u) (EF016482) W (J:1) 63 Flavobacteria (u) (JN233039) 40 54 S1 (JD:1) W (S:1) 33 Flaviramulus sp. (JQ687104) S3 (D:1) 89 S3 (D:1) 0.05 36 Olleya marilimosa (JN175350)

Figure 3b. Phylogenetic tree of reverse partial 16S rRNA gene sequences of clone libraries derived from sea water samples (W) and Eunicella verrucosa samples collected at sites 1 (S1), 2 (S2) and 3 (S3) in June (J), September (S), and when diseased (D). Numbers in brackets relate to number of clones from each library. Reference sequences include closest NCBI affiliations, which include bacteria previously isolated from corals and other marine invertebrates. The tree was calculated using the Maximum Likelihood method and Tamura-nei model as implemented in MEGA 5.1. Bootstrap values (500 replicates) are indicated on the branches. The scale bar corresponds to 0.05 substitutions per nucleotide position.