Symbiotic Adaptation Drives Genome Streamlining of the Cyanobacterial Sponge Symbiont “Candidatus Synechococcus

ABSTRACT “Candidatus Synechococcus spongiarum ” is a cyanobacterial symbiont widely distributed in sponges, but its func-tions at the genome level remain unknown. Here, we obtained the draft genome (1.66 Mbp, 90 % estimated genome recovery) of “Ca. Synechococcus spongiarum ” strain SH4 inhabiting the Red Sea sponge Carteriospongia foliascens. Phylogenomic analysis revealed a high dissimilarity between SH4 and free-living cyanobacterial strains. Essential functions, such as photosynthesis, the citric acid cycle, and DNA replication, were detected in SH4. Eukaryoticlike domains that play important roles in sponge-symbiont interactions were identified exclusively in the symbiont. However, SH4 could not biosynthesize methionine and poly-amines and had lost partial genes encoding low-molecular-weight peptides of the photosynthesis complex, antioxidant enzymes, DNA repair enzymes, and proteins involved in resistance to environmental toxins and in biosynthesis of capsular and extracellu-lar polysaccharides. These genetic modifications imply that “Ca. Synechococcus spongiarum ” SH4 represents a low-light-adapted cyanobacterial symbiont and has undergone genome streamlining to adapt to the sponge’s mild intercellular environ-ment. IMPORTANCE Although the diversity of sponge-associated microbes has been widely studied, genome-level research on spong