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

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.

Two distinct microbial communities revealed in the sponge Cinachyrella

“…In the sponges Raspailia ramosa and Stelligera stuposa , 32 and 17% of the Proteobacteria sequences, respectively, were unclassified as opposed to only 1% in the seawater (Jackson et al, 2012). Further exploration suggests that many of our unclassified Proteobacteria OTUs are sponge-specific and the presence of large clusters of sponge-specific and sponge- and coral-specific bacteria in the invertebrates have been described (Simister et al, 2012).…”

Description of Endozoicomonas euniceicola sp. nov. and Endozoicomonas gorgoniicola sp. nov., bacteria isolated from the octocorals Eunicea fusca and Plexaura sp., and an emended description of the genus Endozoicomonas

“…Numerous cultureindependent studies of marine invertebrates have shown similar dominance of members of Endozoicomonas (often incorrectly referred to as the uncharacterized genus 'Spongiobacter' or simply referred to as gammaproteobacteria clones) (e.g. Bellantuono et al, 2012;Bourne & Munn, 2005;Bourne et al, 2008;Cooney et al, 2002;Hansson et al, 2009;Jackson et al, 2012;Kennedy et al, 2008;Kvennefors et al, 2010;Lee et al, 2012;Littman et al, 2009;Lopez et al, 2008;Menezes et al, 2010;Morrow et al, 2012;Pike et al, 2012;Rohwer et al, 2001;Schuett et al, 2007;Zurel et al, 2011). Previous studies have demonstrated that coralassociated Endozoicomonas strains probably contribute to the degradation of sulfur compounds [e.g.…”

Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene

“…Molecular approaches, such as 16S ribosomal RNA (rRNA) clone libraries (Eichler et al 2006;Gihring et al 2012;Zhang et al 2013a) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) (Garrido et al 2014;González-Arenzana et al 2013;Sun et al 2013;Zhang et al 2013b), have greatly increased our comprehension of microbial communities, although these methods poorly represent the rare bacterial groups. In recent years, 454 pyrosequencing has been introduced as a next-generation sequencing method for revealing relatively detailed profiles of microbial communities (Beloshapka et al 2013;Jackson et al 2012). The main advantages of 454 pyrosequencing are a much lower cost per base, the omission of a plasmid cloning step, a large amount of sequence data per run, and long read lengths with an average of up to 400 bps (Glenn 2011;Margulies et al 2005).…”