Organisms associated with siphonophores revealed by short-read whole-genome sequencing

Siphonophores are associated with prey, parasites, microbes, and other organisms in the open ocean, but little is known about these siphonophore cobionts. To learn more about them, we investigated molecular bycatch: their DNA captured during siphonophore genome sequencing. We reanalysed 213 specimens of Physalia, Nanomia, Bargmannia and other siphonophores sequenced in four previously published studies. We recovered 104 bacterial genomes forming 32 genome clusters, including recurrent Metamycoplasmataceae and diverse proteobacteria, groups also found with other cnidarians. Bacterial communities differed among Physalia species sampled in the southwestern Pacific. We identified non-siphonophore eukaryotes from ribosomal markers in 38 specimens, including fish and copepods consistent with prey, parasitic flatworms, and Perkinsela-like relatives of amoeba endosymbionts. Alfonsino (Beryx) sequences in one Hawaiian P. utriculus specimen are consistent with capture of pelagic young of deepwater fishes. Molecular bycatch reveals the diversity of siphonophore associates from specimens already collected for genome research.