Bacterial communities associated with Microcystis colonies differ from free-living communities living in the same ecosystem
Version of Record online: 13 JUN 2013
© 2013 John Wiley & Sons Ltd and Society for Applied Microbiology
Environmental Microbiology Reports
Volume 5, Issue 5, pages 716–724, October 2013
How to Cite
Parveen, B., Ravet, V., Djediat, C., Mary, I., Quiblier, C., Debroas, D. and Humbert, J.-F. (2013), Bacterial communities associated with Microcystis colonies differ from free-living communities living in the same ecosystem. Environmental Microbiology Reports, 5: 716–724. doi: 10.1111/1758-2229.12071
- Issue online: 2 OCT 2013
- Version of Record online: 13 JUN 2013
- Accepted manuscript online: 21 MAY 2013 06:28AM EST
- Manuscript Accepted: 15 MAY 2013
- Manuscript Received: 27 JAN 2013
- INSU. Grant Number: EC2CO
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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