Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts

Abstract

Marine sponges contain complex bacterial communities of considerable ecological and biotechnological importance, with many of these organisms postulated to be specific to sponge hosts. Testing this hypothesis in light of the recent discovery of the rare microbial biosphere, we investigated three Australian sponges by massively parallel 16S rRNA gene tag pyrosequencing. Here we show bacterial diversity that is unparalleled in an invertebrate host, with more than 250 000 sponge-derived sequence tags being assigned to 23 bacterial phyla and revealing up to 2996 operational taxonomic units (95% sequence similarity) per sponge species. Of the 33 previously described ‘sponge-specific’ clusters that were detected in this study, 48% were found exclusively in adults and larvae – implying vertical transmission of these groups. The remaining taxa, including ‘Poribacteria’, were also found at very low abundance among the 135 000 tags retrieved from surrounding seawater. Thus, members of the rare seawater biosphere may serve as seed organisms for widely occurring symbiont populations in sponges and their host association might have evolved much more recently than previously thought.

Coral reef invertebrate microbiomes correlate with the presence of photosymbionts

“…Although present in all samples, the Cyanobacteria were particularly abundant (8-24% relative abundance) in Heterostegina depressa and in one Marginopora vertebralis sample (17% relative abundance). The composition of microbial communities associated with the sponge Rhopaloeides odorabile was different to those associated with other invertebrates, although this community pattern is consistent with a previous investigation (Webster et al, 2010).…”

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

“…Proteobacteria (the a-subdivision), Cyanobacteria and Euryarchaeota were the most dominant groups in all our seawater samples (Figures 5 and 6). Although these phyla also dominated other planktonic systems (Morris et al, 2002;Giovannoni and Stingl, 2005), the microbial diversity in our samples was low in comparison with that of other oceans (Venter et al, 2004;Sogin et al, 2006;Webster et al, 2010). All these contrasting results may suggest that the Red Sea is a very unique environment, different from other marine habitats.…”

“…Using this technology, Sogin et al have demonstrated that the previous molecular methods underestimated the true bacterial diversity by one to two orders of magnitude, and most of the observed phylogenetic diversity revealed by this new technique was represented by thousands of low-abundance populations (Sogin et al, 2006). Extremely high diversity of bacterial ribotypes in three sponge species from Australia's Great Barrier Reef and the vertical transmission of certain groups of 'spongespecific' members from sponge adults to larvae were also successfully revealed using this method (Webster et al, 2010). However, this technique has not been fully utilized to study the spatial variations of microbial communities in sponges, which may help to address the issue of stability and specificity of the microbial associates.…”

“…V5 and V6 regions of the recruited cluster sequences were split by recognizing the U789F and U1068R primers, and then aligned with the tag pyrosequence reads using MUSCLE (Edgar, 2004). Similarity matrix was calculated as mentioned above and a minimum of 75% sequence similarity threshold was applied for assigning the tag sequences into the cluster showing the highest similarity (Webster et al, 2010). The relative abundance and occurrence of tag assigned into sponge-specific clusters were visualized as a heatmap using JColorGrid (Joachimiak et al, 2006).…”

Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians

“…The advent of high-throughput, next-generation DNA sequencing platforms offers new opportunities for in-depth microbial diversity evaluation across large sample sets. Deep sequencing of microbial communities from soils, seawater and sponges has revealed diversity estimates over an order of magnitude higher than that recovered by traditional sequencing techniques (Huber et al, 2007;Roesch et al, 2007;Webster et al, 2010), including the detection of bacterial phyla not represented in firstgeneration sequencing datasets (e.g., Webster and Taylor, 2012). Similarly, the recent application of next generation sequencing to the ascidian microbiota has revealed a high diversity of symbiotic microbes and uncovered new ascidian-associated microbial lineages in the colonial host Lissoclinum patella and solitary host Styela plicata (Erwin et al, 2013), highlighting the depth of microbial biodiversity and unknown facultative and obligate symbiotic microbes awaiting discovery within ascidian hosts.…”