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Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

  • Microbiology of Aquatic Systems
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Abstract

The microbial community composition in meromictic Lake Kivu, with one of the largest CH4 reservoirs, was studied using 16S rDNA and ribosomal RNA (rRNA) pyrosequencing during the dry and rainy seasons. Highly abundant taxa were shared in a high percentage between bulk (DNA-based) and active (RNA-based) bacterial communities, whereas a high proportion of rare species was detected only in either an active or bulk community, indicating the existence of a potentially active rare biosphere and the possible underestimation of diversity detected when using only one nucleic acid pool. Most taxa identified as generalists were abundant, and those identified as specialists were more likely to be rare in the bulk community. The overall number of environmental parameters that could explain the variation was higher for abundant taxa in comparison to rare taxa. Clustering analysis based on operational taxonomic units (OTUs at 0.03 cutoff) level revealed significant and systematic microbial community composition shifts with depth. In the oxic zone, Actinobacteria were found highly dominant in the bulk community but not in the metabolically active community. In the oxic–anoxic transition zone, highly abundant potentially active Nitrospira and Methylococcales were observed. The co-occurrence of potentially active sulfur-oxidizing and sulfate-reducing bacteria in the anoxic zone may suggest the presence of an active yet cryptic sulfur cycle.

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Acknowledgments

In addition to the authors of this paper, the Lake Kivu consortium includes the following individuals: S. Bouillon (KatholiekeUniversiteit Leuven), M.-V. Commarieu, F. A. E. Roland (Université de Liège), B. Leporcq, K. de Saedeleer (Université de Namur), A. Anzil, S. Vanderschueren, C. Michiels (UniversitéLibre de Bruxelles), and G. Alunga (DR Congo team). The consortium gratefully acknowledges the Rwanda Energy Company and Michel Halbwachs for free access to their industrial platform off Gisenyi. R. Trias (Institut de Physique du Globe de Paris, France) is acknowledged for supplying some of the qPCR-positive controls. This work was funded by the Fonds National de la RechercheScientifique (FNRS) under the MICKI (Microbial diversity and processes in Lake Kivu) project and the Belgian Federal Science Policy Office EAGLES (East African Great Lake Ecosystem Sensitivity to changes, SD/AR/02A) project, and contributes the European Research Council starting grant project AFRIVAL (African river basins: Catchment-scale carbon fluxes and transformations, 240002).

Conflict of Interest

The authors declare no conflict of interest.

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Author notes

  1. Marc Llirós

    Present address: Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Spain

Authors and Affiliations

  1. Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussel, Belgium

    Özgul İnceoğlu, Tamara García-Armisen & Pierre Servais

  2. Laboratory of Freshwater Ecology, Université de Namur, Namur, Belgium

    Marc Llirós & Jean-Pierre Descy

  3. Departments of Microbiology and Immunology, and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada

    Sean A. Crowe

  4. Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven, Leuven, Belgium

    Cedric Morana

  5. Chemical Oceanography Unit, Université de Liège, Liège, Belgium

    François Darchambeau & Alberto V. Borges

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Correspondence to Özgul İnceoğlu.

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Table S1

Diversity indices for bacterial OTUs in the analyzed water column. (DOC 87 kb)

Table S2

Diversity indices for archaeal OTUs in the analyzed water column. (DOC 88 kb)

Figure S1

Rank-abundance plots based on present and active bacterial OTUs at a dissimilarity level of 3 % at depths of 10 and 100 m during September 2012. (PDF 121 kb)

Figure S2

Vertical depth profiles of different DNA- and RNA-based bacterial taxa related to different biogeochemical processes from September 2012 water samples: (a) Actinobacteria, (a) Cyanobacteria, (c) Planctomycetes, (d) Nitrospira, (e) Methylococcales, (f) Desulfobacterales and Desulfuromonadales, (g) Epsilonproteobacteria, (h) Dehalococcoidaceae (i) Chlorobi, (j) Methanomicrobia and Methanobacteria. The transition zone is indicated with a gray shade. (PDF 33 kb)

Figure S3

Hierarchical clustering of Bray-Curtis similarities of the archaeal community composition at OTU level retrieved by pyrosequencing of both DNA (black symbols) and RNA (grey symbols) nucleic acid pools in (A) February and (B) September. Samples were grouped according to oxygen content as: oxic (triangles), transition (dots), and anoxic (squares). (PDF 14 kb)

Figure S4

Network analyses of co-occurring shared bacterial (circles) and archaeal (squares) OTUs in the anoxic zone basedon correlation analyses. A connection stands for a strong (Pearson r >0.8) and significant (p-value 0.01) correlation. The size of each node is proportional to the number of connections (i.e., degree). (PDF 20 kb)

Figure S5

Relationship between occupancy (i.e., niche breadth) and relative abundance of (a) DNA-based and (b) RNA-based bacterial communitiesin the water column of Lake Kivu.High niche breadth values are indicative for habitat generalists whereas low values can be assigned to habitat specialists. (PDF 197 kb)

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İnceoğlu, Ö., Llirós, M., Crowe, S.A. et al. Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu. Microb Ecol 70, 596–611 (2015). https://doi.org/10.1007/s00248-015-0612-9

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  • DOI: https://doi.org/10.1007/s00248-015-0612-9

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