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Microbial Ecology

, Volume 64, Issue 1, pp 105–116 | Cite as

Pyrosequencing Reveals Diverse and Distinct Sponge-Specific Microbial Communities in Sponges from a Single Geographical Location in Irish Waters

  • Stephen A. Jackson
  • Jonathan Kennedy
  • John P. Morrissey
  • Fergal O’Gara
  • Alan D. W. Dobson
Environmental Microbiology

Abstract

Marine sponges are host to numerically vast and phylogenetically diverse bacterial communities, with 26 major phyla to date having been found in close association with sponge species worldwide. Analyses of these microbial communities have revealed many sponge-specific novel genera and species. These endosymbiotic microbes are believed to play significant roles in sponge physiology including the production of an array of bioactive secondary metabolites. Here, we report on the use of culture-based and culture-independent (pyrosequencing) techniques to elucidate the bacterial community profiles associated with the marine sponges Raspailia ramosa and Stelligera stuposa sampled from a single geographical location in Irish waters and with ambient seawater. To date, little is known about the microbial ecology of sponges of these genera. Culture isolation grossly underestimated sponge-associated bacterial diversity. Four bacterial phyla (Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria) were represented amongst ~200 isolates, compared with ten phyla found using pyrosequencing. Long average read lengths of ~430 bp (V1–V3 region of 16S rRNA gene) allowed for robust resolution of sequences to genus level. Bacterial OTUs (2,109 total), at 95% sequence similarity, from ten bacterial phyla were recovered from R. ramosa, 349 OTUs were identified in S. stuposa representing eight phyla, while 533 OTUs from six phyla were found in surrounding seawater. Bacterial communities differed significantly between sponge species and the seawater. Analysis of the data for sponge-specific taxa revealed that 2.8% of classified reads from the sponge R. ramosa can be defined as sponge-specific, while 26% of S. stuposa sequences represent sponge-specific bacteria. Novel sponge-specific clusters were identified, whereas the majority of previously reported sponge-specific clusters (e.g. Poribacteria) were absent from these sponge species. This deep and robust analysis provides further evidence that the microbial communities associated with marine sponge species are highly diverse and divergent from one another and appear to be host-selected through as yet unknown processes.

Keywords

Sponge Proteobacteria Actinobacteria Firmicutes Bacteroidetes 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

This work was funded by the Beaufort Marine Research Award, part of the Sea Change Strategy and the Strategy for Science Technology and Innovation (2006–2012), with the support of The Marine Institute under the Marine Research Sub-Programme of the National Development Plan 2007–2013. We wish to thank Bernard Picton from the National Museums of Northern Ireland and Christine Morrow of Queens University Belfast for sponge collection and identification. We are also grateful to Mike Taylor for providing 16S rRNA datasets used in his sponge-specific cluster analysis.

Supplementary material

248_2011_2_MOESM1_ESM.doc (36 kb)
Fig. S1 Maximum likelihood phylogenetic tree of bacteria from the phylum Cyanobacteria including a cluster (four sequences) derived from the marine sponge R. ramosa (Rrc388—R. ramosa cluster 388) forming a monophyletic novel sponge-specific cluster (DOC 35 kb)
248_2011_2_MOESM2_ESM.doc (28 kb)
Fig. S2 Maximum likelihood phylogenetic tree of bacteria from the phylum Nitrospira including 18 clusters (3,166 sequences) derived from the marine sponge S. stuposa recruiting to sponge cluster 23 according to the numbering system of Webster et al. [54] (DOC 28 kb)
248_2011_2_MOESM3_ESM.doc (902 kb)
Fig. S3 Maximum likelihood phylogenetic tree of bacteria from the α class of Proteobacteria including 16 clusters (391 sequences) derived from the marine sponge R. ramosa forming a monophyletic novel sponge-specific cluster (DOC 902 kb)
248_2011_2_MOESM4_ESM.doc (406 kb)
Table S1 Relative abundance (by percentage) of 16S V1–V3 454 tag sequence reads from marine sponges and seawater at all taxonomic levels to genus level (DOC 406 kb)

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Stephen A. Jackson
    • 1
  • Jonathan Kennedy
    • 1
  • John P. Morrissey
    • 1
    • 2
  • Fergal O’Gara
    • 1
    • 2
    • 3
  • Alan D. W. Dobson
    • 1
    • 2
  1. 1.Marine Biotechnology Centre, Environmental Research InstituteUniversity College CorkCorkIreland
  2. 2.Department of MicrobiologyUniversity College CorkCorkIreland
  3. 3.BIOMERIT Research CentreUniversity College CorkCorkIreland

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