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Evidence for Selective Bacterial Community Structuring in the Freshwater Sponge Ephydatia fluviatilis

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Abstract

To understand the functioning of sponges, knowledge of the structure of their associated microbial communities is necessary. However, our perception of sponge-associated microbiomes remains mainly restricted to marine ecosystems. Here, we report on the molecular diversity and composition of bacteria in the freshwater sponge Ephydatia fluviatilis inhabiting the artificial lake Vinkeveense Plassen, Utrecht, The Netherlands. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints revealed that the apparent diversities within the domain Bacteria and the phylum Actinobacteria were lower in E. fluviatilis than in bulk water. Enrichment of specific PCR-DGGE bands in E. fluviatilis was detected. Furthermore, sponge- and bulk water-derived bacterial clone libraries differed with respect to bacterial community composition at the phylum level. E. fluviatilis-derived sequences were affiliated with six recognized phyla, i.e., Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, Chlamydiae and Verrucomicrobia, in order of relative abundance; next to the uncultured candidate phylum TM7 and one deeply rooted bacterial lineage of undefined taxonomy (BLUT). Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in the freshwater clone library whereas sequences affiliated with Planctomycetes, Verrucomicrobia, Acidobacteria and Armatimonadetes were found at lower frequencies. Fine-tuned phylogenetic inference showed no or negligible overlaps between the E. fluviatilis and water-derived phylotypes within bacterial taxa such as Alphaproteobacteria, Bacteroidetes and Actinobacteria. We also ascertained the status of two alphaproteobacterial lineages as freshwater sponge-specific phylogenetic clusters, and report on high distinctiveness of other E. fluviatilis specific phylotypes, especially within the Bacteroidetes, Planctomycetes and Chlamydia taxa. This study supports the contention that the composition and diversity of bacteria in E. fluviatilis is partially driven by the host organism.

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Acknowledgements

R. Costa was supported by the Soil Biotechnology Foundation and by the Portuguese Foundation of Science and Technology (FCT). T. Keller-Costa received a research fellowship from the Federation of European Microbiological Societies (FEMS) to perform this work. We thank Dr. Joana B.T. Xavier for the identification of the sponge specimens collected in this study. We are grateful to the late Niels Cox and Albert Ellens for their assistance during sampling.

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Authors and Affiliations

  1. Microbial Ecology and Evolution Research Group, Centre of Marine Sciences (CCMAR-CIMAR), University of Algarve, Gambelas, 8005-139, Faro, Portugal

    Rodrigo Costa

  2. Centre of Marine Sciences (CCMAR-CIMAR), University of Algarve, Gambelas, 8005-139, Faro, Portugal

    Tina Keller-Costa

  3. CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal

    Newton C. M. Gomes

  4. Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, MS-70A-3317, Berkeley, CA, 94720, USA

    Ulisses Nunes da Rocha

  5. Plant Research International, PO Box 16, Wageningen, The Netherlands

    Leo van Overbeek

  6. Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands

    Jan Dirk van Elsas

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  1. Rodrigo Costa
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  2. Tina Keller-Costa
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  3. Newton C. M. Gomes
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  4. Ulisses Nunes da Rocha
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Correspondence to Rodrigo Costa.

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Fig. S1

Location (arrow in a) and satellite image (b), and limnological parameters (c) of the Vinkeveense Plassen lake Utrecht, The Netherlands, measured on sampling day at 8 m depth. The arrow in b shows the E. fluviatilis sampling location (DOCX 589 kb)

Figure S2

Phylogenetic inference of Planctomycetes 16S rRNA gene sequences by Maximum Likelihood (ML), with sequences retrieved in this study highlighted in bold. Values in brackets give the number of clone sequences from this study, if more than one, in each tree leaf. Closest relatives to all E. fluviatilis and lake water sequences have been included in the analysis. Numbers at tree nodes are bootstrap values calculated in ML analysis, and values ≥70% are shown. Scale bar: number of nucleotide substitutions per site (GIF 51 kb)

High resolution image (EPS 185 kb)

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Costa, R., Keller-Costa, T., Gomes, N.C.M. et al. Evidence for Selective Bacterial Community Structuring in the Freshwater Sponge Ephydatia fluviatilis . Microb Ecol 65, 232–244 (2013). https://doi.org/10.1007/s00248-012-0102-2

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