Uncovering the Microbial Diversity of Two Exotic Calcareous Sponges

Functional and Genomic Insights into the Biotechnological Potential of Vibrio spp. Isolated from Deeply Polluted and Pristine Environments

Vibrio spp. are remarkably diverse bacteria, being worthy of investigation not only for their antibiotic resistance and virulence, but also for their biotechnological potential. Indeed, there is increasing evidence that these bacteria display industrially relevant traits, particularly as producers of antimicrobial substances, tensioactive/emulsifying compounds, and enzymes. Here, our aim was to investigate the potential of Vibrio strains isolated from two different marine sources to produce such biotechnologically applicable substances. From the eighteen analyzed strains, five were isolated from plastic particles from a heavily polluted urban estuary and 13 from calcareous sponges inhabiting submarine caves in an isolated volcanic archipelago in the Atlantic Ocean. Enzymatic screening revealed that most strains were agarolytic and cellulolytic. Overall, six strains showed antimicrobial activity against Staphylococcus aureus ATCC 29,213, with four of them active towards Escherichia coli ATCC 25,922 as well. Additionally, eight strains were positive for the production of bioemulsifiers. Genomic analyses of four strains further revealed insights regarding the enzymatic arsenal, as shown by the detection of several key gene clusters pertaining to the chitin degradation pathway, and also encoding diverse classes of antimicrobial-active metabolites. Our findings highlight the biotechnological potential of Vibrio spp., evidencing their functional diversity and the need for continued and sustained prospecting of this bacterial genus to uncover its potential high-value-added bioproducts.

Marine Sponge Endosymbionts: Structural and Functional Specificity of the Microbiome within Euryspongia arenaria Cells

Sponge microbiomes are typically profiled by analyzing the community DNA of whole tissues, which does not distinguish the taxa residing within sponge cells from extracellular microbes. To uncover the endosymbiotic microbiome, we separated the sponge cells to enrich the intracellular microbes. The intracellular bacterial community of sponge Euryspongia arenaria was initially assessed by amplicon sequencing, which indicated that it hosts three unique phyla not found in the extracellular and bulk tissue microbiomes. These three phyla account for 66% of the taxonomically known genera in the intracellular microbiome. The shotgun metagenomic analysis extended the taxonomic coverage to viruses and eukaryotes, revealing the most abundant signature taxa specific to the intracellular microbiome. Functional KEGG pathway annotation demonstrated that the endosymbiotic microbiome hosted the greatest number of unique gene orthologs. The pathway profiles distinguished the intra- and extracellular microbiomes from the tissue and seawater microbiomes. Carbohydrate-active enzyme analysis further discriminated each microbiome based on their representative and dominant enzyme families. One pathway involved in digestion system and family esterase had a consistently higher level in intracellular microbiome and could statistically differentiate the intracellular microbiome from the others, suggesting that triacylglycerol lipases could be the key functional component peculiar to the endosymbionts. The identified higher abundance of lipase-related eggNOG categories further supported the lipid-hydrolyzing metabolism of endosymbiotic microbiota. Pseudomonas members, reported as lipase-producing bacteria, were only in the endosymbiotic microbiome, meanwhile Pseudomonas also showed a greater abundance intracellularly. Our study aided a comprehensive sponge microbiome that demonstrated the taxonomic and functional specificity of endosymbiotic microbiota.

IMPORTANCE Sponges host abundant microbial symbionts that can produce an impressive number of novel bioactive metabolites. However, knowledge on intracellular (endosymbiotic) microbiota is scarce. We characterize the composition and function of the endosymbiotic microbiome by separation of sponge cells and enrichment of intracellular microbes. We uncover a noteworthy number of taxa exclusively in the endosymbiotic microbiome. We unlock the unique pathways and enzymes of endosymbiotic taxa. This study achieves a more comprehensive sponge microbial community profile, which demonstrates the structural and functional specificity of the endosymbiotic microbiome. Our findings not only open the possibility to reveal the low abundant and the likely missed microbiota when directly sequencing the sponge bulk tissues, but also warrant future in-depth exploration within single sponge cells.