Phylogenetic inference of the Irciniidae family based on the cytochrome oxidase gene, subunit 1.

<p>The Maximum Likelihood tree (-ln likelihood: 1383.921591) is shown, with sequences retrieved in this study highlighted in bold. Numbers at tree nodes are bootstrap values and posterior probabilities calculated in Maximum Likelihood and MCMC Bayesian analyses, respectively, and values above 70/0.95 are shown.</p

PCR-DGGE fingerprints and canonical analyses.

<p>PCR-DGGE 16S rRNA gene fingerprints of <i>S. spinosulus</i>, <i>I. variabilis</i> and seawater DNA samples generated with “total-community” bacterial primers (A) and specific primer systems for <i>Actinobacteria</i> (C) and <i>Alphaproteobacteria</i> (E). The arrows indicate bands that were excised from DG-gels and sequenced. Corresponding ordination biplots of PCR-DGGE fingerprints and qualitative environmental variables are shown in panels B, D, F. Symbols: ▴ <i>S. spinosulus</i>, ▪ <i>I. variabilis</i> and • Seawater. Labels displayed on the diagram axes refer to the percentage variations of PCR-DGGE ribotypes - environment correlation accounted for the respective axis. The “star” symbols represent the centroid positions of the environmental variables in the diagram. Variables that significantly (<i>p</i><0.05) influence the bacterial community composition are indicated by an asterisk.</p

Taxonomic affiliation of the bioactive bacteria isolated from <i>E. discophorus</i>.

<p>Taxonomic affiliation of the bioactive bacteria isolated from <i>E. discophorus</i>.</p

Closest 16S rRNA gene relatives of seawater-derived and “cosmopolitan” PCR-DGGE bands.

1<p>Closest 16S rRNA gene relative using the “sequence match” tool of the Ribosomal Database Project (RDP).</p>2<p>Closest 16S rRNA gene relatives as determined by the blast-n search in the National Center for Biotechnology Information (NCBI) database.</p

Results of bioactivity by genera and screening method (<i>Janus</i> and Duetz systems) obtained against <i>Bacillus subtilis</i>, <i>Staphylococcus aureus</i> MRSA, <i>Aliivibrio fisheri</i> and <i>Vibrio harveyi.</i>

<p>Results of bioactivity by genera and screening method (<i>Janus</i> and Duetz systems) obtained against <i>Bacillus subtilis</i>, <i>Staphylococcus aureus</i> MRSA, <i>Aliivibrio fisheri</i> and <i>Vibrio harveyi.</i></p

Phylogenetic inference of <i>Chloroflexi</i> 16S rRNA genes.

<p>Tree construction procedure was as described for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053029#pone-0053029-g004" target="_blank">Figure 4</a>, except that sequences from SC46 were selected along with sequences from SC47, which were used as outgroup <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053029#pone.0053029-Simister1" target="_blank">[34]</a>. The Maximum Likelihood tree is shown (-ln likelihood: 3791,095).</p

Epifluorescence counts.

<p>Microscopy pictures taken from <i>S. spinosulus</i> (A), <i>I. variabilis</i> (B) and Seawater (C) are shown. Arrows exemplify counted bacterial cells. Values in panel (D) are expressed as means ± standard errors of log-transformed total cell numbers (TCN).</p

Phylogenetic inference of <i>Actinobacteria</i> 16S rRNA genes.

<p>The modified ARB database generated by Simister et al., <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053029#pone.0053029-Simister1" target="_blank">[34]</a> used long sequences (≥1200 bp) to infer the phylogeny and shorter sequences were added using the ARB parsimony interactive tool. Sequences from the sponge-specific cluster 22 (SC22) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053029#pone.0053029-Simister1" target="_blank">[34]</a> along with sequences closely related to band 1 and outgroup sequences were selected for further phylogenetic analysis. The Maximum Likelihood tree (-ln likelihood: 4501,317092) is shown, with sequences retrieved in this study highlighted in bold. Numbers at tree nodes are bootstrap values and posterior probabilities calculated in Maximum Likelihood and MCMC Bayesian analyses, respectively, and values above 70/0.95 are shown.</p

Phylogenetic inference of <i>Gammaproteobacteria</i> 16S rRNA genes.

<p>Tree construction procedure was as described for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053029#pone-0053029-g004" target="_blank">Figure 4</a>, except that sequences closely related to band 2 were selected as well as sequences from SC155 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053029#pone.0053029-Simister1" target="_blank">[34]</a>, which were used as outgroup. The Maximum Likelihood tree is shown (-ln likelihood: 2696,593494).</p