Host-microbe symbiosis in the marine sponge Halichondria panicea

Sponges (phylum Porifera) are considered one of the oldest extant lineages of the animal kingdom. Their close association with microorganism makes them suitable for studying early animal-microbe symbiosis and expanding our understanding of host-microbe interactions through conserved mechanisms. Moreover, many sponges and spongeassociated microorganisms produce bioactive compounds, making them highly relevant for the biotechnology and pharmaceutical industry. So far, however, it has not been possible to grow biotechnologically relevant sponge species or isolate their obligate microbial symbionts for these purposes. The marine sponge Halichondria panicea inhabits coastal areas worldwide, which makes the sponge easily accessible, and has therefore been a widely studied sponge species in terms of its biology and ecophysiology. However, the stability of its associated microbial community and the functional role of its permanent members has so far remained elusive. Despite previous studies showing bioactive properties of H. panicea, it is yet unknown if these are produced by the sponge itself or by microorganisms found in its body. In this study, the microbial diversity of H. panicea from Icelandic waters was analysed through marker gene sequencing, genomics and bacterial cultivation. We showed that H. panicea from Icelandic water hosts a dominant bacterial symbiont across geographical locations and seasons whereas other bacteria are geographically and temporally transient. Functional genomic analysis of the dominant symbiont, for which we propose a candidate status with the name “Candidatus Halichondribacter symbioticus”, showed a lack of regulatory genes in line with its obligate symbiotic lifestyle. In addition, it is enriched in sponge symbiont specific gene families related to host-symbiont interactions and defence. Despite the presence of a putative bacteriocin gene cluster, “Ca. H. symbioticus” does not appear to be the source of other bioactive secondary metabolites in this sponge. A comparison of different methods for ex situ cultivation of H. panicea showed that, while different cultivation set-ups allowed for successful maintenance of the sponge itself, only certain conditions also maintained “Ca. H. symbioticus” at a high relative abundance in the sponge body. Based on these results a novel method for sponge-microbe co-cultivation was demonstrated which increases the enriched bacterial diversity compared to standard plating methods. Although “Ca. H. symbioticus” remains un-isolated, other selected isolated bacteria from H. panicea were subjected to antimicrobial activity assays, genome sequencing and strain characterisation leading to the description of two novel species of marine bacteria and one novel putative host-associated bacterium. Due to the presence of a dominant bacterial symbiont and the amenability of H. panicea towards laboratory cultivation, the H. panicea – “Ca. H. symbioticus” system represents a promising model for studying early animal-microbe symbiosis. The results from this study lay the ground work for future studies exploring the interactions between H. panicea and “Ca. H. symbioticus”.