Genomic blueprints of sponge- prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria

ABSTRACT Marine sponges are early-branching, filter-feeding metazoans that usually host complex microbiomes comprised of several, currently uncultivatable symbiotic lineages. Here, we use a low-carbon based strategy to cultivate low-abundance bacteria from Spongia officinalis. This approach favoured the growth of Alphaproteobacteria strains in the genera Anderseniella, Erythrobacter, Labrenzia, Loktanella, Ruegeria, Sphingorhabdus, Tateyamaria and Pseudovibrio, besides two likely new genera in the Rhodobacteraceae family. Mapping of complete genomes against the metagenomes of S. officinalis, seawater, and sediments confirmed the rare status of all the above-mentioned lineages in the marine realm. Remarkably, this community of low-abundance Alphaproteobacteria possesses several genomic attributes common to dominant, presently uncultivatable sponge symbionts, potentially contributing to host fitness through detoxification mechanisms (e.g. heavy metal and metabolic waste removal, degradation of aromatic compounds), provision of essential vitamins (e.g. B6 and B12 biosynthesis), nutritional exchange (especially regarding the processing of organic sulphur and nitrogen) and chemical defence (e.g. polyketide and terpenoid biosynthesis). None of the studied taxa displayed signs of genome reduction, indicative of obligate mutualism. Instead, versatile nutrient metabolisms along with motility, chemotaxis, and tight-adherence capacities - also known to confer environmental hardiness – were inferred, underlying dual host-associated and free-living life strategies adopted by these diverse sponge-associated Alphaproteobacteria.ACKNOWLEDGEMENTS The authors would like to thank Telma Franco for her help during sample processing and bacterial DNA extractions, Marta Valente for Sanger-sequencing of16S rRNA genes, and Martin T. Jahn for providing insights into data analysis. We thank Jochen Blom for his assistance with the software package EDGAR. This work was supported by the Portuguese Foundation for Science and Technology (FCT) through the research grants PTDC/BIA-MIC/3865/2012 and PTDC/MAR-BIO/1547/2014 [conceded to RC] and a full PhD scholarship from the Erasmus Mundus Programme/SALAM EMA2 lot7/SALA1206422 [conceded to EK]. CONTRIBUTIONS R.C., U.N.d.R. and E.K. planned the research; E.K. performed laboratory experiments; R.C. and U.H. provided reagents and materials; E.K., T.K.C., B.M.S., C.J.C. and R.C. analysed the data; E.K. and R.C. wrote the first draft of the manuscript and prepared figures and tables. E.K. and R.C. wrote the final manuscript text; All authors reviewed the manuscript. ETHICS DECLARATIONS Competing Interests The authors declare no competing interests