Draft Genome Sequence of Vibrio sp. Strain Vb278, an Antagonistic Bacterium Isolated from the Marine Sponge Sarcotragus spinosulus

Draft Genome Sequence of Vibrio jasicida 20LP, an Opportunistic Bacterium Isolated from Fish Larvae

We present the genome sequence of Vibrio jasicida 20LP, a bacterial strain retrieved from larvae of gilthead seabream (Sparus aurata), a highly valuable, model fish species in land-based aquaculture. Annotation of the V. jasicida 20LP genome reveals multiple genomic features potentially underpinning opportunistic associations with diverse marine animals.

Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis

Although the Mediterranean Sea covers approximately a 0.7% of the world's ocean area, it represents a major reservoir of marine and coastal biodiversity. Among marine organisms, sponges (Porifera) are a key component of the deep-sea benthos, widely recognized as the dominant taxon in terms of species richness, spatial coverage, and biomass. Sponges are evolutionarily ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. In the present work, we firstly aimed at exploring the biodiversity of marine sponges from four different areas of the Mediterranean: Faro Lake in Sicily and "Porto Paone", "Secca delle fumose", "Punta San Pancrazio" in the Gulf of Naples. Eight sponge species were collected from these sites and identified by morphological analysis and amplification of several conserved molecular markers (18S and 28S RNA ribosomal genes, mitochondrial cytochrome oxidase subunit 1 and internal transcribed spacer). In order to analyze the bacterial diversity of symbiotic communities among these different sampling sites, we also performed a metataxonomic analysis through an Illumina MiSeq platform, identifying more than 1500 bacterial taxa. Amplicon Sequence Variants (ASVs) analysis revealed a great variability of the host-specific microbial communities. Our data highlight the occurrence of dominant and locally enriched microbes in the Mediterranean, together with the biotechnological potential of these sponges and their associated bacteria as sources of bioactive natural compounds.

Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes

BACKGROUND

Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater.

RESULTS

We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates.

CONCLUSIONS

Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.

Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea

Marine sponges are excellent examples of invertebrate-microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.

Draft Genome Sequence of Labrenzia sp. Strain EL143, a Coral-Associated Alphaproteobacterium with Versatile Symbiotic Living Capability and Strong Halogen Degradation Potential

We report here the genome sequence of Labrenzia sp. EL143, an alphaproteobacterium isolated from the gorgonian coral Eunicella labiata that possesses various genes involved in halogen and aromatic compound degradation, as well as polyketide synthesis. The strain also maintains multiple genes that confer resistance to toxic compounds such as heavy metals and antibiotics.

Draft Genome Sequence of Sphingorhabdus sp. Strain EL138, a Metabolically Versatile Alphaproteobacterium Isolated from the Gorgonian Coral Eunicella labiata

Here, we report the draft genome sequence of Sphingorhabdus sp. strain EL138, an alphaproteobacterium that shows potential to degrade polycyclic aromatic compounds and to cope with various heavy metals and antibiotics. Moreover, the strain, isolated from the gorgonian coral Eunicella labiata, possesses several genes involved in the biosynthesis of polyphosphates, polyketides, and terpenoids.

Genomic Insights into Aquimarina sp. Strain EL33, a Bacterial Symbiont of the Gorgonian Coral Eunicella labiata

To address the metabolic potential of symbiotic Aquimarina spp., we report here the genome sequence of Aquimarina sp. strain EL33, a bacterium isolated from the gorgonian coral Eunicella labiata This first-described (to our knowledge) animal-associated Aquimarina genome possesses a sophisticated repertoire of genes involved in drug/antibiotic resistance and biosynthesis.

Draft Genome Sequence of Vibrio sp. Strain Evh12, a Bacterium Retrieved from the Gorgonian Coral Eunicella verrucosa

To shed light on the associations established between Vibrio species and soft corals in coastal ecosystems, we report here the draft genome sequence of Vibrio sp. strain Evh12, a bacterium that has been isolated from the gorgonian coral Eunicella verrucosa and that shows antagonistic activity against Escherichia coli.