Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the ecologically important tropical sponge Ianthella basta. Marine sponge Ianthella basta thaumarchaeal symbiont

Marine sponges are one of the few documented eukaryotes that ubiquitously harbor symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. Here we visualize and quantify the dominant thaumarchaeal symbiont of the marine sponge Ianthella basta, and demonstrate its active role in ammonia-oxidation coupled to inorganic carbon fixation based on incubation experiments measuring net and gross nitrification rates that were inhibited by the NO-scavenger PTIO. Moreover, using a metaproteogenomic approach we assembled a near-complete thaumarchaeal genome bin and document not only its expression of proteins involved in the ammonia-oxidation and inorganic carbon fixation pathways, but also of an extracellular protease, a high-affinity branched-chain ABC transporter, numerous expanded members of a well-documented thaumarchaeal s-layer family, as well as extraceullar immunoglobulin-like domain-containing proteins. Phylogenomic analyses indicate that “Candidatus Nitrosospongia bastadiensis” clusters with members of the Nitrosopumilus clade and separately from other sequenced sponge thaumarchaeotes, while sharing a similar repertoire of mobile genetic elements, the full branched-chain amino acid ABC transporter operon, and extracellular subtilisin-like proteases.