Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes

Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets

Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis

The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida) is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (∼150 Mb). Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi) were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia) and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas) compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST) indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome

Morphological description of six species of Suberitida (Porifera: Demospongiae) from the unexplored north-eastern coast of Brazil, with emphasis on two new species

International audienceThe Order Suberitida is defined as a group of marine sponges without an obvious cortex, a skeleton devoid of microscleres, and with a deletion of a small loop of 15 base pairs in the secondary structure of the 28S rDNA as a molecular synapomorphy. Suberitida comprises three families and 26 genera distributed worldwide, but mostly in temperate and polar waters. Twenty species were reported along the entire Brazilian coast, and although the Northeastern coast of Brazil seems to harbour a richest sponge fauna, our current knowledge is concentrated along the Southeastern Atlantic coast. A survey has been implemented along the northern coast of Brazil, and the collection allowed the identification of six species belonging to the Order Suberitida, two of them are considered new to science

The aromatic domain 66YWYWW70 of subunit VIII of the yeast ubiquinol-cytochrome c oxidoreductase is important for both assembly and activity of the enzyme

AbstractThe aromatic character of the region 66YWYWW70 of the 11-kDa subunit VIII of ubiquinol-cytochrome c oxidoreductase (bc1 complex) of the yeast Saccharomyces cerevisiae has previously been demonstrated to be important for assembly of a functional complex [Hemrika et al. (1994) FEBS Lett. 344, 15–19]. Especially the aromatic nature of residue 66 appeared to be relevant, as the very low level (5%) of bc1 complex in the mutant 66SASAA70 was restored to nearly 70% of the wild-type level in a phenotypic revertant with the sequence 66FASAA70. In the present study, three other site-directed mutants (66SAYAA70, 66SASAW70 and 66SWYWW70) were constructed and analysed. The data indicate that the presence of one aromatic residue is enough for a substantial level of assembly and that its position modulates the level of both assembly and electron transfer activity. The results also confirm the relevance of this region of subunit VIII for the formation of the Qout reaction domain, as reported by Hemrika et al. [(1993) Eur. J. Biochem. 215, 601–609]. It is further shown that the lowered specific activity of the mutant described by these authors is not due to the introduction of a cysteine in the sequence of subunit VIII

Effect of Mussel`s Gender and Size on a Stress Response Biomarker

In mussels, stress signals such as heat, osmotic shock and hypoxia lead to the activation of the phosphorylated p38 mitogen activated protein kinase (pp38-MAPK). This stress activated protein has been efficiently used as a biomarker to several natural and anthropogenic stresses. However, what has not been tested is whether differences in gender or size can affect the response of this biomarker. The present study tested whether there was variation in the expression of pp38-MAPK in mussels Perna perna of different gender and size classes when exposed to natural stress conditions, such as air exposure. The results show that gender does not affect the expression of pp38-MAPK. However, size does have an effect, where mussels smaller than 6.5 cm displayed significantly (p < 0.05) lower levels of pp38-MAPK when compared to those larger than 7 cm. Mussels are one of the most used bioindicator species and the use of biomarkers to determine the health status of an ecosystem has been greatly increasing over the years. The present study highlights the importance of using mussels of similar size classes when performing experiments using stress-related biomarkers.`CNPq/Programas Ciencias do Mar Brazil/Germany`[59004/2005-0]Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

How a collaborative integrated taxonomic effort has trained new spongiologists and improved knowledge of Martinique Island (French Antilles, eastern Caribbean Sea) marine biodiversity.

Although sponges are important components of benthic ecosystems of the Caribbean Sea, their diversity remained poorly investigated in the Lesser Antilles. By organizing a training course in Martinique, we wanted both to promote taxonomy and to provide a first inventory of the sponge diversity on this island. The course was like a naturalist expedition, with a field laboratory and a classroom nearby. Early-career scientists and environmental managers were trained in sponge taxonomy. We gathered unpublished data and conducted an inventory at 13 coastal sites. We explored only shallow water habitats (0-30 m), such as mangroves, reefs or rocky bottoms and underwater caves. According to this study, the sponge fauna of Martinique is currently represented by a minimum of 191 species, 134 of which we could assign species names. One third of the remaining non-identified sponge species we consider to be new to science. Martinique appears very remarkable because of its littoral marine fauna harboring sponge aggregations with high biomass and species diversity dominating over coral species. In mangroves, sponges cover about 10% of the surface of subtidal roots. Several submarine caves are true reservoirs of hidden and insufficiently described sponge diversity. Thanks to this new collaborative effort, the Eastern Caribbean has gained a significant increase of knowledge, with sponge diversity of this area potentially representing 40% of the total in the Caribbean Sea. We thus demonstrated the importance of developing exploratory and educational research in areas historically devoid of biodiversity inventories and systematics studies. Finally, we believe in the necessity to consider not only the number of species but their distribution in space to evaluate their putative contribution to ecosystem services and our willingness to preserve them

Relative functional contributions that differed significantly between the dominant proteobacterial groups.

<p>The first column shows each pair of organisms (e.g., <i>Alpha</i>- and <i>Gammaproteobacteria</i>) that differed significantly (p-value <0.05) for a subsystem (e.g., “metabolism of aromatic compounds”), detected using ANOVA for multiple groups. The percentage bars were colored as follows: <i>Alphaproteobacteria</i> (blue); <i>Gammaproteobacteria</i> (orange); <i>Betaproteobacteria</i> (green), <i>Burkholderiales</i> (purple); bacteria (light blue); and total species (red). The second column shows the detected differences with the 90% confidence interval, as calculated using the Tukey-Kramer post-hoc test.</p

Bacterial orders that were significantly overrepresented in sponge or seawater metagenomes.

<p>Organismal classifications differing significantly (p-value <0.00001) were indicated by direct Poisson model-based comparisons of the two groups of metagenomes.</p

Relative abundances of bacterial phyla and proteobacterial classes (<i>inset</i>) in the sponge and seawater organismal classifications.

<p>Asterisks indicate organisms differing significantly (p-value <0.00001) between groups based on direct Poisson model-based comparisons.</p