Rapid cell turnover rates accompanied by extensive detritus production are likely a means of avoiding permanent, stress-induced damage to the sponge ( De Goeij et al., 2009 Alexander et al., 2014). By filtering extensive volumes of seawater-up to thousands of liters per kg sponge daily ( Reiswig, 1974)-they take in food bacteria, but also potential pathogens, toxins and physical stress factors ( De Goeij et al., 2009). Marine sponges (Porifera) are evolutionary ancient metazoans dating back to Precambrian times ( Li et al., 1998 Love et al., 2009). This study characterizes the genomic repertoire of sponge symbionts at an unprecedented resolution and it provides greater insights into the molecular mechanisms underlying microbial-sponge symbiosis. A third guild of symbionts may be viewed as nutritional generalists that perform largely the same metabolic pathways but lack such extraordinary numbers of the relevant genes. A within-symbionts genome comparison revealed a nutritional specialization of at least two symbiont guilds, where one appears to metabolize carnitine and the other sulfated polysaccharides, both of which are abundant molecules in the sponge extracellular matrix. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities.

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