Supplementary information provided with Murray et al.: Discovery of an Antarctic ascidian-associated uncultivated Verrucomicrobia with antimelanoma palmerolide biosynthetic potential

The Antarctic marine ecosystem harbors a wealth of biological and chemical
innovation that has risen in concert over millennia since the isolation of
the continent and formation of the Antarctic circumpolar current.
Scientific inquiry into the novelty of marine natural products produced by
Antarctic benthic invertebrates led to the discovery of a bioactive
macrolide, palmerolide A, that has specific activity against melanoma and
holds considerable promise as an anticancer therapeutic. While this
compound was isolated from the Antarctic ascidian Synoicum adareanum, its
biosynthesis has since been hypothesized to be microbially mediated, given
structural similarities to microbially-produced hybrid non-ribosomal
peptide-polyketide macrolides. Here, we describe a metagenome-enabled
investigation aimed at identifying the biosynthetic gene cluster (BGC) and
palmerolide A-producing organism. A 74 Kbp candidate BGC encoding the
multi-modular enzymatic machinery (hybrid Type I-trans-AT polyketide
synthase-non-ribosomal peptide synthetase and tailoring functional
domains) was identified and found to harbor key features predicted as
necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome
samples targeting the candidate BGC revealed a high correlation between
palmerolide-gene targets and a single 16S rRNA gene variant (R=0.83 –
0.99). Through repeated rounds of metagenome sequencing followed by
binning contigs into metagenome-assembled genomes, we were able to
retrieve a near-complete genome (10 contigs) of the BGC-producing
organism, a novel verrucomicrobium within the Opitutaceae family that we
propose here as Candidatus Synoicihabitans palmerolidicus. The refined
genome assembly harbors five highly similar BGC copies, along with
structural and functional features that shed light on the host-associated
nature of this unique bacterium.