The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions

Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases. Relatedness of all model systems studied, and the five most abundant archaeal genera found in each system. Abundant genera are based on relative abundances in the amplicon data. Gray circles indicate the absence of detectable archaea. Red circles on the hosts identify sampled sites. Hosts are ordered using an unscaled phylogenetic tree based on species divergence times of a molecular time tree available through TimeTree5 and visualized in iTOL. Asterisks indicate branches where the tree is based on approximation through a close relative. The single Cand. Nitrosotalea or Haloferaceae found in D. melanogaster and H. vulgaris, respectively, were excluded as they could not be replicated. Where divergent from phylum names in the SILVA database, current names from the GTDB database were added.