There is an increasing awareness of numerous beneficial interactions between microbes and animals. For example, gut microbes aid in digestion of complex organic matter and photosynthetic symbionts harness the power of the sun to fuel growth of corals and sponges. Sponges hosting photosynthetic symbionts represent up to 50% of the sponge community on the benthos, but can amount to nearly 90% of the communities in some tropical reefs. For several decades, eutrophication of reef environments has been linked to an increase in the heterotrophic sponge population, at the expense of phototrophic types, with impact on the nutrient balance of the ecosystem as a whole. The role the sponge microbiome plays in the fitness of holobiont in relation to environmental factors is just starting to be explored.

Our aim was to dissect out the biochemical and molecular basis of the ancient symbiosis between cyanobacteria and marine sponges of the class Demospongiae. A photosynthetic prokaryote symbiont of Phyllospongia sp. was isolated through flow cytometry sorting, the genetic material of the symbiont was then amplified and sequenced. The symbiont genome was reconstructed into contigs with a total of 2.1 Mb, comparable to the genome size of free-living marine cyanobacteria. Analysis of the symbiont genome demonstrates a near complete assembly of the defined cyanobacterial core gene set (96.5%). In comparison to the closely related free-living isolates the symbiont displays novel defence mechanisms, genes that promote/maintain interaction with the host, modified metabolic pathways as well as differences on nutrient requirements, regulation and transport capacity that reflect its adopted niche. This work provides insights into symbiosis maintenance and adaptation, and a better understanding of the genetic mechanisms underlying the biochemical fluxes between the host and symbiont.