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High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling

  • Microbiology of Aquatic Systems
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Abstract

Microbial communities growing under extreme low redox conditions are present in anoxic and sulfide-rich (euxinic) environments such as karstic lakes and experience limitation of electron acceptors. The fine natural chemical gradients and the large diversity of organic and inorganic compounds accumulated in bottom waters are impossible to mimic under laboratory conditions, and only a few groups have been cultured. We investigated the bacterial composition in the oxic-anoxic interface and in the deep waters of three sulfurous lakes from the Lake Banyoles karstic area (NE Spain) through 16S rRNA gene tag sequencing and identified the closest GenBank counterpart. High diversity indices were found in most of the samples with >15 phyla/classes and >45 bacterial orders. A higher proportion of operational taxonomic units (OTUs) of the “highest novelty” was found in the hypolimnia (38 % of total sequences) than in the metalimnia (17 %), whereas the percentage of OTUs closer to cultured counterparts (i.e., 97 % identity in the 16S rRNA gene) was 6 to 21 %, respectively. Elusimicrobia, Chloroflexi, Fibrobacteres, and Spirochaetes were the taxa with the highest proportion of novel sequences. Interestingly, tag sequencing results comparison with metagenomics data available from the same dataset, showed a systematic underestimation of sulfur-oxidizing Epsilonproteobacteria with the currently available 907R “universal” primer. Overall, despite the limitation of electron acceptors, a highly diverse and novel assemblage was present in dark and euxinic hypolimnetic freshwaters, unveiling a hotspot of microbial diversity with a remarkable gap with cultured counterparts.

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Acknowledgments

JC Auguet, M Llirós, and F Gich, are acknowledged for their field assistance. This research was funded by grants GOS-LAKES CGL2009-08523-E and DARKNESS CGL2012-32747 to EOC and ARCANOX CGL2009-13318-C02-02 to CBM from the Spanish Office of Science (MINECO) and from the financial support by the Beyster Family Fund of the San Diego Foundation and the Life Technologies Foundation to the J. Craig Venter Institute.

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Authors and Affiliations

  1. Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain

    Tomàs Llorens-Marès, Xavier Triadó-Margarit & Emilio O. Casamayor

  2. Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Girona, Spain

    Carles M. Borrego

  3. Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain

    Carles M. Borrego

  4. Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA

    Chris L. Dupont

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  1. Tomàs Llorens-Marès
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  2. Xavier Triadó-Margarit
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  3. Carles M. Borrego
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  4. Chris L. Dupont
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  5. Emilio O. Casamayor
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Correspondence to Emilio O. Casamayor.

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Llorens-Marès, T., Triadó-Margarit, X., Borrego, C.M. et al. High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling. Microb Ecol 71, 566–574 (2016). https://doi.org/10.1007/s00248-015-0696-2

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