Dehalogenating Desulfoluna spp. are ubiquitous in host-specific sponge microbiomes of the Great Barrier Reef.

Marine sponge holobionts are important contributors to numerous biogeochemical cycles, including the natural organohalogen cycle. Sponges produce diverse brominated secondary metabolites, which select for a population of anaerobic debrominating bacteria within the sponge body. Sponge microbiomes can be host-specific, but the selection and host-specificity of debrominating bacteria are unknown currently. In this study, we used nanopore long-read sequencing of nearly full-length ribosomal RNA operons to evaluate host-specificity of the Great Barrier Reef sponge microbiomes at the strain level and to determine if host specificity extends to sponge-associated dehalogenating bacteria. Reductive debromination activity was observed in anaerobic enrichment cultures established from all Great Barrier Reef sponges. Even though other bacterial symbionts of interest, including Nitrospira spp. and Ca. Synechococcus spp. demonstrated strong host-specificity, Desulfoluna spp., a key sponge-associated dehalogenating bacterium showed no evidence of host-specificity. This suggests different modes of transmission and/or retention of different members of the sponge microbiome residing within the same host species. These findings expand our understanding of how sponge microbiomes are assembled and the relationship between the host and individual bacterial strains.