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Fig. S1. Principal coordinate analysis performed on the relative proportions of phyla and classes in the four samples of the attached and free-living bacterial communities.

Fig. S2. Frequency distribution of the OTUs identified among all the sequences retrieved in the attached and free-living fractions, and a cumulative curve constructed from this frequency distribution. Operational taxonomic units (OTUs) were defined by using MOTHUR (Schloss et al., 2009) with a 98% cut-off threshold.

Fig. S3. Parsimony phylogenetic trees of partial 16S rRNA sequences obtained from attached and free-living bacterial communities using the arb software. All the sequences were added to a backbone tree built with the sequences of the main bacterial phyla found in aquatic ecosystems and of typical freshwater clades previously defined (Zwart et al., 2002; Newton et al., 2011). Two methods were used for the phylogenetic reconstruction (parsimony and neighbour-joining). New putative clades were identified based on the following criteria: (i) each contained sequences from at least two different sampling dates; (ii) each was a monophyletic group supported by the two tree constructions; and (iii) the bootstrap values were greater than 60%. Using these criteria, the percentage similarity between environmental sequences belonging to the same cluster was always greater than 90%.

A. 16S rRNA phylogenetic tree of partial sequences for Betaproteobacteria showing representative OTUs in the proposed clusters. (A) betaI (B) betaI (C) betaI (D) betaIV, beta-Vill-2 (E) lbVII, LiUU-11–179. 2 (betV), betaII (F) lbVI, beta-Vill-1, betaIII, lbV, and LiUU-5–131 (betVI). Lake Limmaren clone; AY509464 and Lake Vallentunasjon clone; AY509484 were used as outgroup.

B. 16S rRNA phylogenetic tree of partial sequences for Gammaproteobacteria showing representative OTUs in the proposed clusters. (A) Legionella group, gam-Vill-2, M. psychrophilus (gamI) and LiUU-3–334.2. (B) gamIV, gam-Vill-1, LiUU-9–113 (C) gamIII. Nitrosococcus halophilus str. Nc4; AF287298 were used as outgroup.

C. 16S rRNA phylogenetic tree of partial sequences for Alphaproteobacteria showing representative OTUs in the proposed clusters. (A) CR-FL11, alpha-Vill-1, B. intermedia (alphaII), LiUU-9–115, LiUU-9–283.2, A0904 (B) GOBB3-C201, N. subacrtica (alphaIV), GKS2-124, alpha-Vill-3, alpha-Vill-2 and LD-12 (alphaV). Rickettsia bellii str.; U11014.1 and Orientia tsutsugamushi str. Karp; D38623.1 were used as outgroup.

D. 16S rRNA phylogenetic tree of partial sequences for Bacteroidetes showing representative OTUs in the proposed clusters. (A) B88 (bacII-A), IRD18A11 (B) B99 (bacV), bac-Vill-4, IRD18G07 (C) PRD18D09, FukuN47 (D) LD1, LD2 (cfIV), PRD01a001B (cfIII), bac-Vill-3, bac-Vill-2, bac-Vill-1, CL500-6 and IRD18D04. Clones, 02D2Z08; DQ397339 and SSM-NB17; AB187001 were used as outgroup.

E. 16S rRNA phylogenetic tree of partial sequences for Deinococcus-Thermus showing representative OTUs in the proposed clusters, Deinococcus group. Deinococcus radiophilus str. DSM 20551T; Y11333.1 was used as outgroup.

F. 16S rRNA phylogenetic tree of partial sequences for Actinobacteria showing representative OTUs in the proposed clusters. (A) ACK-M1(acI-A), CL120-6 (acI-A), STA2- 30(acI-B) (B) acII, Micrococcus group, acSTL and acIV. Lake Fuchskuhle clone FukuN22; AJ289994.1 was used as outgroup.

G. 16S rRNA phylogenetic tree of partial sequences for Verrucomicrobia showing representative OTUs in the proposed clusters; LiUU-9–243.2, FukuS27, FukuN18 and CLO-14(CL120-10). Desulfurobacterium thermolithotrophum; AJ001049.1 was used as outgroup.

For all trees, the sequences obtained in this study are depicted in the form ‘AB/FL_sn_n’, where AB stands for attached bacteria, FL for free- living, sn for sampling number and n for the name of the clone.

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