Publisher Correction: Biodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome

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Biodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome

In the deep ocean symbioses between microbes and invertebrates are emerging as key drivers of ecosystem health and services. We present a large-scale analysis of microbial diversity in deep-sea sponges (Porifera) from scales of sponge individuals to ocean basins, covering 52 locations, 1077 host individuals translating into 169 sponge species (including understudied glass sponges), and 469 reference samples, collected anew during 21 ship-based expeditions. We demonstrate the impacts of the sponge microbial abundance status, geographic distance, sponge phylogeny, and the physical-biogeochemical environment as drivers of microbiome composition, in descending order of relevance. Our study further discloses that fundamental concepts of sponge microbiology apply robustly to sponges from the deep-sea across distances of >10,000 km. Deep-sea sponge microbiomes are less complex, yet more heterogeneous, than their shallow-water counterparts. Our analysis underscores the uniqueness of each deep-sea sponge ground based on which we provide critical knowledge for conservation of these vulnerable ecosystems

Zooming into the sponge microbiome in the omics era

Marine sponges represent an excellent example of host-microbe symbiosis. Yet, most sponge-associated microorganisms remain uncultured, hampering efforts in determining interactions with their sponge host. This project aimed at enhancing our understanding of the sponge-bacteria interplay, focusing on both cultured and yet-uncultured sponge-associated lineages. Several novel sponge-associated taxa were elucidated by resolving their phylogeny and reconstructing their primary and secondary metabolism. Genome-based predictions revealed that the sponge microbiome mediates the interactions of the holobiont via heterotrophy, potential metabolite exchange and chemical defense. Sponge symbionts also possessed an extended genomic repertoire of defense systems implying adaptation to host environment. Moreover, genome mining for biosynthetic gene clusters (BGCs) and bioactivity screening of sponge-associated strains detected many candidate BGCs potentially involved in observed anticancer and antibacterial activity. Altogether, this work shed light into novel sponge-associated phylotypes, features that point at a symbiotic lifestyle and a rich secondary metabolite biosynthesis arsenal with biotechnological potential

Bioactivity screening and gene-trait matching of sponge-associated bacteria

This dataset includes raw sequencing reads, draft genome assemblies and 16S rRNA gene sequences of bacteria isolated from different marine sponge species

Bioactivity Screening and Gene-Trait Matching across Marine Sponge-Associated Bacteria

Marine sponges harbor diverse microbial communities that represent a significant source of natural products. In the present study, extracts of 21 sponge-associated bacteria were screened for their antimicrobial and anticancer activity, and their genomes were mined for secondary metabolite biosynthetic gene clusters (BGCs). Phylogenetic analysis assigned the strains to four major phyla in the sponge microbiome, namely Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Bioassays identified one extract with anti-methicillin-resistant Staphylococcus aureus (MRSA) activity, and more than 70% of the total extracts had a moderate to high cytotoxicity. The most active extracts were derived from the Proteobacteria and Actinobacteria, prominent for producing bioactive substances. The strong bioactivity potential of the aforementioned strains was also evident in the abundance of BGCs, which encoded mainly beta-lactones, bacteriocins, non-ribosomal peptide synthetases (NRPS), terpenes, and siderophores. Gene-trait matching was performed for the most active strains, aiming at linking their biosynthetic potential with the experimental results. Genetic associations were established for the anti-MRSA and cytotoxic phenotypes based on the similarity of the detected BGCs with BGCs encoding natural products with known bioactivity. Overall, our study highlights the significance of combining in vitro and in silico approaches in the search of novel natural products of pharmaceutical interest

Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis

Background Members of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity. Results Comparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene- and genome-based phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes, often arranged in polysaccharide utilization loci (PULs), support the capacity of marine Flavobacteriaceae to utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studied Flavobacteriaceae in contrast to members of other phyla, highlighting the particular presence of this feature within the Bacteroidetes. Notably, not all bacteria predicted to glide formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal of Flavobacteriaceae with high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains. Conclusions Our study elucidates the functional repertoire of marine Flavobacteriaceae and highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential

Genome sequencing of Marine Flavobacteriaceae isolated from sponges

Genomic sequences of sponge-derived Flavobacteriaceae were generated. A comparative genomics analysis elucidated the functional repertoire of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade

Genome sequencing of Marine Flavobacteriaceae isolated from sponges

Genomic sequences of sponge-derived Flavobacteriaceae were generated. A comparative genomics analysis elucidated the functional repertoire of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade

Bioactivity screening and gene-trait matching of sponge-associated bacteria

This dataset includes raw sequencing reads, draft genome assemblies and 16S rRNA gene sequences of bacteria isolated from different marine sponge species

Comparative genomic analysis of Flavobacteriaceae : insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis

BACKGROUND: Members of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity. RESULTS: Comparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene- and genome-based phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes, often arranged in polysaccharide utilization loci (PULs), support the capacity of marine Flavobacteriaceae to utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studied Flavobacteriaceae in contrast to members of other phyla, highlighting the particular presence of this feature within the Bacteroidetes. Notably, not all bacteria predicted to glide formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal of Flavobacteriaceae with high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains. CONCLUSIONS: Our study elucidates the functional repertoire of marine Flavobacteriaceae and highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential