Hybrid Genome Assemblies of Marine Bacteria Isolated from the Sponge Sycon capricorn

Sponges have complex relationships with bacteria, the roles of which include food, important components of the holobiont, pathogens, and accidentally accumulated elements of the environment. Consequently, sponges are reservoirs of microbial genomes and novel compounds. Therefore, we isolated and sequenced the whole genomes of bacterial species from the calcareous sponge Sycon capricorn .

Fast transcriptional activation of developmental signalling pathways during wound healing of the calcareous sponge Sycon ciliatum

Background: The ability to regenerate lost or damaged body parts is an ancient animal characteristic with a wide yet variable distribution across all phyla. Sponges, likely the sister group to all other animals, have remarkable regenerative abilities including whole body regeneration and re-development from dissociated cells. The calcareous sponge Sycon ciliatum has been subject to various regeneration studies since the beginning of the last century. However, the early steps of wound healing of S. ciliatum have not been addressed from the molecular perspective. Results: In this study, we combined electron microscopy with gene expression analysis to investigate wound healing after transverse sectioning of S. ciliatum. Microscopic analysis revealed massive transdifferentiation and collective migration behaviour of choanocytes and pinacocytes early upon injury (6-12h) as the main mechanisms for quick closure of the wound surface. RNA-sequencing identified upregulation of components of the conserved metazoan Wnt and TGFβ signalling pathways within 3h, preceding morphologically detectable wound healing events. De novo upregulation after a decline in expression coincides with morphologically visible polarity establishment. Moreover, by integrating the new wound healing data set with previously published data derived from intact sponge, we demonstrate similarity between gene activity during early wound healing and osculum maintenance. Whole mount in situ hybridisation of the TGFβ signalling pathway ligand SciTGFβU and signal transducer SciSmadRa show that the early activation of both is initially encompassing a large area surrounding the cut surface with gradual restriction to the edge of the forming regenerative membrane as wound healing progresses. While SciTGFβU transcripts are localised to exo- and endopinacocytes, SciSmadRa expression appears across all cell types. Using an EdU cell proliferation assay, we found that a global increase in cell proliferation is not visible before 12h into wound healing. Hence, the initial stages to cover the injury site including cell transdifferentiation and migration seem to be executed by cells remaining after injury. Gene expression clustering coupled with GO term enrichment analysis confirmed that expression of genes involved in processes related to cell proliferation, DNA repair as well as apoptotic processes at 3 and 6h of wound healing was not upregulated. On the other hand, genes associated with positive regulation of transcription, signal transduction, actin filament and chromatin organisation, as well as the Wnt signalling pathway are upregulated at early wound healing stages. Conclusion: We have analysed wound healing in the calcareous sponge Sycon ciliatum using microscopic and genomic methods. This study highlights a remarkable mechanism of interplay between cell transdifferentiation and collective migration we hypothesise to be regulated by conserved metazoan developmental pathways and numerous taxonomically restricted genes. Expression of these genes in regenerating and intact sponges sheds light on the long-standing question whether embryonic developmental pathways are redeployed in regeneration.

Assessing skeleton and microbiome responses of a calcareous sponge under thermal and pH stresses

Ocean higher temperature and acidity levels affect its carbonate chemistry, and calcifying organisms that depend on the calcium carbonate saturation state (ΩCaCO3) to build their skeleton may be vulnerable to these changes. Despite their important roles in the marine environment, little is known about the vulnerability of calcareous sponges under these stressors. We performed an acute short-term experiment (9 days) with thermal and pH stresses to explore their effects on the skeleton and microbiome of the calcareous sponge Sycettusa hastifera. We observed that sponge spicules showed no corrosion and no Mg/Ca ratio variation when exposed to stress conditions. However, the outermost spicules were smaller in low pH treatment, although these effects were often diminished when higher temperatures were also applied. In general, the sponges synthesized normally shaped spicules under stress conditions, but the proportion of deformed spicules increased significantly in elevated temperature. In addition, we observed a stable host–microbiome association in which there is microbiome flexibility under thermal and pH stresses with a significantly increase in abundance of some associated bacteria. Our results suggest that S. hastifera has low vulnerability under the future ocean conditions here designed, since it showed indications of resistance that could help them adapt and survive.

Cultivation-Independent Analysis of the Bacterial Community Associated With the Calcareous Sponge Clathrina clathrus and Isolation of Poriferisphaera corsica Gen. Nov., Sp. Nov., Belonging to the Barely Studied Class Phycisphaerae in the Phylum Planctomycetes

Marine ecosystems serve as global carbon sinks and nutrient source or breeding ground for aquatic animals. Sponges are ancient parts of these important ecosystems and can be found in caves, the deep-sea, clear waters, or more turbid environments. Here, we studied the bacterial community composition of the calcareous sponge Clathrina clathrus sampled close to the island Corsica in the Mediterranean Sea with an emphasis on planctomycetes. We show that the phylum Planctomycetes accounts for 9% of the C. clathrus-associated bacterial community, a 5-fold enrichment compared to the surrounding seawater. Indeed, the use of C. clathrus as a yet untapped source of novel planctomycetal strains led to the isolation of strain KS4T. The strain represents a novel genus and species within the class Phycisphaerae in the phylum Planctomycetes and displays interesting cell biological features, such as formation of outer membrane vesicles and an unexpected mode of cell division.

A new species of Ernstia (Porifera: Calcarea) described from marine aquarium

A new species of calcareous sponge, Ernstia pyrum sp. nov. (Calcarea, Calcinea, Clathrinida, Clathrinidae) is described from marine reef aquarium. It is assumed that its type locality is Indonesia. Molecular data render this species as a member of the genus Ernstia, although its morphology deviates in significant points from the original definition of the genus. In particular Ernstia pyrum sp. nov. has a clear atrial cavity not lined with choanocytes (true atrium), a feature not reported before for this genus.

A new genus of calcareous sponge discovered in the Caribbean Sea: Bidderia gen. nov. (Porifera, Calcarea, Calcinea)

Calcareous sponges from the Lesser Antilles were recently inventoried and several specimens morphologically resembling species of the genus Ascoleucetta were collected. Morphological and molecular (C-LSU and ITS) analyses indicated that these specimens from the Lesser Antilles constituted a new genus. They lack the conspicuous and very characteristic ornamentation of the inhalant apertures found in two out of three species of Ascoleucetta, including the type species A. compressa. In the molecular analyses, the specimens clustered as an independent lineage, distant from the clade of A. compressa. Based on these results, we decided to erect a new genus, Bidderia gen. nov., whose type species is Bidderia bicolora gen. nov. sp. nov. Considering this new discovery, we are proposing to transfer the species A. amitsba to the genus Bidderia gen. nov. and to rediagnose Ascoleucetta.