Diversity and spatiotemporal dynamics of bacterial communities: physicochemical and other drivers along an acid mine drainage
Aurélie Volant
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorCorresponding Author
Odile Bruneel
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Correspondence: Odile Bruneel, Laboratoire HydroSciences Montpellier, UMR5569, Université Montpellier 2, Place E. Bataillon, CC MSE, 34095 Montpellier, France. Tel.: (+33)4 67 14 36 59; fax: (+33)4 67 14 47 74; e-mail: [email protected]Search for more papers by this authorAngélique Desoeuvre
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorMarina Héry
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorCorinne Casiot
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorNoëlle Bru
Laboratoire de Mathématiques et de leurs Applications, UMR 5142 (CNRS), Université de Pau et des Pays de l'Adour, Pau, France
Search for more papers by this authorSophie Delpoux
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorAnne Fahy
Équipe Environnement et Microbiologie, EEM, UMR 5254 (IPREM, CNRS), Université de Pau et des Pays de l'Adour, Pau, France
Search for more papers by this authorFabien Javerliat
Équipe Environnement et Microbiologie, EEM, UMR 5254 (IPREM, CNRS), Université de Pau et des Pays de l'Adour, Pau, France
Search for more papers by this authorOlivier Bouchez
INRA Auzeville, Plateforme Génomique Chemin de Borde Rouge, Castanet-Tolosan, France
Search for more papers by this authorRobert Duran
Équipe Environnement et Microbiologie, EEM, UMR 5254 (IPREM, CNRS), Université de Pau et des Pays de l'Adour, Pau, France
Search for more papers by this authorPhilippe N. Bertin
Département Microorganismes, Génomes, Environnement, Laboratoire de Génétique Moléculaire, Génomique, Microbiologie, GMGM, UMR 7156 (Université de Strasbourg, CNRS), Strasbourg, France
Search for more papers by this authorFrançoise Elbaz-Poulichet
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorBéatrice Lauga
Équipe Environnement et Microbiologie, EEM, UMR 5254 (IPREM, CNRS), Université de Pau et des Pays de l'Adour, Pau, France
Search for more papers by this authorAurélie Volant
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorCorresponding Author
Odile Bruneel
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Correspondence: Odile Bruneel, Laboratoire HydroSciences Montpellier, UMR5569, Université Montpellier 2, Place E. Bataillon, CC MSE, 34095 Montpellier, France. Tel.: (+33)4 67 14 36 59; fax: (+33)4 67 14 47 74; e-mail: [email protected]Search for more papers by this authorAngélique Desoeuvre
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorMarina Héry
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorCorinne Casiot
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorNoëlle Bru
Laboratoire de Mathématiques et de leurs Applications, UMR 5142 (CNRS), Université de Pau et des Pays de l'Adour, Pau, France
Search for more papers by this authorSophie Delpoux
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorAnne Fahy
Équipe Environnement et Microbiologie, EEM, UMR 5254 (IPREM, CNRS), Université de Pau et des Pays de l'Adour, Pau, France
Search for more papers by this authorFabien Javerliat
Équipe Environnement et Microbiologie, EEM, UMR 5254 (IPREM, CNRS), Université de Pau et des Pays de l'Adour, Pau, France
Search for more papers by this authorOlivier Bouchez
INRA Auzeville, Plateforme Génomique Chemin de Borde Rouge, Castanet-Tolosan, France
Search for more papers by this authorRobert Duran
Équipe Environnement et Microbiologie, EEM, UMR 5254 (IPREM, CNRS), Université de Pau et des Pays de l'Adour, Pau, France
Search for more papers by this authorPhilippe N. Bertin
Département Microorganismes, Génomes, Environnement, Laboratoire de Génétique Moléculaire, Génomique, Microbiologie, GMGM, UMR 7156 (Université de Strasbourg, CNRS), Strasbourg, France
Search for more papers by this authorFrançoise Elbaz-Poulichet
Laboratoire HydroSciences Montpellier, HSM, UMR 5569 (IRD, CNRS, Universités Montpellier 1 et 2), Université Montpellier 2, Montpellier, France
Search for more papers by this authorBéatrice Lauga
Équipe Environnement et Microbiologie, EEM, UMR 5254 (IPREM, CNRS), Université de Pau et des Pays de l'Adour, Pau, France
Search for more papers by this authorAbstract
Deciphering the biotic and abiotic factors that control microbial community structure over time and along an environmental gradient is a pivotal question in microbial ecology. Carnoulès mine (France), which is characterized by acid waters and very high concentrations of arsenic, iron, and sulfate, provides an excellent opportunity to study these factors along the pollution gradient of Reigous Creek. To this end, biodiversity and spatiotemporal distribution of bacterial communities were characterized using T-RFLP fingerprinting and high-throughput sequencing. Patterns of spatial and temporal variations in bacterial community composition linked to changes in the physicochemical conditions suggested that species-sorting processes were at work in the acid mine drainage. Arsenic, temperature, and sulfate appeared to be the most important factors that drove the composition of bacterial communities along this continuum. Time series investigation along the pollution gradient also highlighted habitat specialization for some major members of the community (Acidithiobacillus and Thiomonas), dispersal for Acidithiobacillus, and evidence of extinction/re-thriving processes for Gallionella. Finally, pyrosequencing revealed a broader phylogenetic range of taxa than previous clone library-based diversity. Overall, our findings suggest that in addition to environmental filtering processes, additional forces (dispersal, birth/death events) could operate in AMD community.
Supporting Information
| Filename | Description |
|---|---|
| fem12394-sup-0001-FigS1.tifimage/tif, 3.4 MB | Fig. S1. Composition of different phyla based on classification of 16S rRNA gene sequences of bacteria from each sample using RDP Classifier: (a) Proteobacteria orders, (b) Actinobacteria orders, (c) Firmicutes orders, and (d) Acidobacteria orders. |
| fem12394-sup-0002-FigS2.tifimage/tif, 595.2 KB | Fig. S2. Histogram of the relative abundance of dominant OTUs at the Carnoulès sampling sites (G. ferruginea subsp. capsiferriformans ES-2: NC_014394; A. ferrooxidans strain HL1: JF815535; Thiobacillus sp. ML2-16: DQ145970; Pseudomonas migulae: AY605698; A. ferrivorans SS3: NR_074660; Actinobacterium BGR 105: GU168008; Acidobacteriaceae bacterium CH1: DQ355184; Ferrimicrobium sp. Py-F2: KC208496; Metallibacterium sp. ×11: HE858262; Alicyclobacillaceae bacterium Feo-D4-16-CH: FN870323; Acidisphaera sp. nju-AMDS1: FJ915153; Betaproteobacterium OYT1: AB720115. |
| fem12394-sup-0003-FigS3.tifimage/tif, 30.7 MB | Fig. S3. Nonmetric multidimensional scaling analysis of the composition of the bacterial community estimated by (a) T-RFLP and (b) 454 pyrosequencing based on 16S rRNA genes. |
| fem12394-sup-0004-FigS4.tifimage/tif, 68.2 MB | Fig. S4. (a) Ordination plot of CCA based on pyrosequencing data showing OTUs with relative abundance >5%. (b) Abundant OTUs and their correlation with environmental variables and phylogenetic affiliation determined by blast search. |
| fem12394-sup-0005-TableS1.docxWord document, 38 KB | Table S1. Physicochemical characteristics of the water at each sampling site and sampling date. |
| fem12394-sup-0006-TableS2.docxWord document, 32.9 KB | Table S2. Relative abundance (in %) of total sequences of bacterial 16S rRNA genes from each sample assigned to different phyla. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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