Diversity of Bacteria in the Marine Sponge Aplysina fulva in Brazilian Coastal Waters

Abstract

Microorganisms can account for up to 60% of the fresh weight of marine sponges. Marine sponges have been hypothesized to serve as accumulation spots of particular microbial communities, but it is unknown to what extent these communities are directed by the organism or the site or occur randomly. To address this question, we assessed the composition of specific bacterial communities associated with Aplysina fulva, one of the prevalent sponge species inhabiting Brazilian waters. Specimens of A. fulva and surrounding seawater were collected in triplicate in shallow water at two sites, Caboclo Island and Tartaruga beach, Búzios, Brazil. Total community DNA was extracted from the samples using "direct" and "indirect" approaches. 16S rRNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analyses of the total bacterial community and of specific bacterial groups-Pseudomonas and Actinobacteria-revealed that the structure of these assemblages in A. fulva differed drastically from that observed in seawater. The DNA extraction methodology and sampling site were determinative for the composition of actinobacterial communities in A. fulva. However, no such effects could be gleaned from total bacterial and Pseudomonas PCR-DGGE profiles. Bacterial 16S rRNA gene clone libraries constructed from directly and indirectly extracted DNA did not differ significantly with respect to diversity and composition. Altogether, the libraries encompassed 15 bacterial phyla and the candidate division TM7. Clone sequences affiliated with the Cyanobacteria, Chloroflexi, Gamma-and Alphaproteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were, in this order, most abundant. The bacterial communities associated with the A. fulva specimens were distinct and differed from those described in studies of spongeassociated microbiota performed with other sponge species.

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

“…PCR-DGGE patterns of highly ranked bacterial taxa (i.e., Bacteria and Actinobacteria) revealed lower diversities and the selection of particular ribotypes in E. fluviatilis as compared to bulk water samples. Similar effects have been registered in 16S rRNA gene based PCR-DGGE studies of marine sponges [9,14]. Regardless of phylum classification, clone library analysis confirmed the diversity trends determined by PCR-DGGE fingerprinting, demonstrating that the structure of the E. fluviatilis associated bacterial community stood in sharp contrast to that of the bacterioplankton.…”

“…16S rRNA gene amplicons were applied onto polyacrylamide gels containing a 46.5-65 % gradient of denaturants (100 % denaturants defined as 7 M urea and 40 % formamide) and a 6-9 % gradient of acrylamide [9]. Mixtures of PCR products from five bacterial species (Arthrobacter sp., Burkholderia sp., Enterobacter sp., Listeria sp.…”

“…The obtained homogenates were centrifuged for 2 min at 500×g, transferred into new centrifuge tubes and subjected to a final centrifugation step of 30 min at 10,000×g. The resulting cell pellets were used for DNA extraction with the Fast DNA® Spin Kit for Soil (Bio101, Q-Biogene, Heidelberg, Germany) with a slight modification to the supplier`s protocol [9]. Each water DNA sample was derived from 500 ml of lake water filtered through a sterile 0.2-μm nitrocellulose membrane filter (Carl Roth GmbH, Karlsruhe, Germany; 47 mm) using a vacuum pump.…”

“…In marine sponges, microbial associates may comprise up to 38 % of the sponge body weight [7] with densities reaching 10 8 -10 10 bacteria per g of sponge wet weight [1], 2-4 orders of magnitude higher than those typical for seawater. In the last 10 years or so, the 16S rRNA gene database from marine sponges has grown continuously (see [8] for a review), revealing sponge-associated bacterial communities to stand in sharp contrast to those of their environmental surroundings [9,10]. The marine sponge microbiome has been shown to encompass a number of bacterial lineages referred to as "sponge-specific" [8,[11][12][13][14][15], suggesting a selective process favouring particular bacteria.…”

Diversity and Bioactivity of Marine Bacteria Associated with the Sponges Candidaspongia flabellata and Rhopaloeides odorabile from the Great Barrier Reef in Australia

“…The genera that prevailed among the sponge samples from C. flabellata were Pseudovibrio, Ruegeria and Bacilli and from R. odorabile, Pseudovibrio, Vibrio and Bacilli suggesting a similar diversity between the two Great Barrier Reef sponge species even though the cultivable community isolate numbers from R. odorabile was considerably lower than that of C. flabellata. The fact that these bacterial species have also been found to be associated with other sponge species from different reef locations around the world [8,18,[70][71][72][73] suggests that these symbiotic bacterial classes may be common associates of marine sponges, even in the distantly related ones.…”