Uncovering the core microbiome and distributions of palmerolide inSynoicum adareanumacross the Anvers Island archipelago, Antarctica

Abstract

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Discovery of an Antarctic ascidian-associated uncultivated Verrucomicrobia with antimelanoma palmerolide biosynthetic potential

“…Neither the semiquantitative measure of ASV copies nor the real time PCR abundance estimates of the three biosynthetic gene targets correlated with the mass-normalized levels of palmerolide A present in the same samples. As discussed (27), this is likely a result of bioaccumulation in the ascidian tissues. This result provided strong support that the genetic capacity for palmerolide A production was associated with a novel member of the Opitutaceae, a taxonomic family with representatives found across diverse host-associated and free-living ecosystems.…”

“…The three BGC gene targets co-varied across all samples (r 2 > 0.7 for all pairs), with the NRPS gene copy levels slightly lower overall (mean: 0.66 and 0.59 copies per ng host tissue for NRPS:AT1 and NRPS:HCS respectively, n=63). We investigated the relationship between BGC gene copies per ng host tissue for each sample and palmerolide A levels determined for the same samples using mass spectrometry, however no correlation was found (R<0.03, n=63; (27)). We then assessed the semi-quantitative relationship between the occurrence of SSU rRNA amplicon sequence variants (ASV, n=461; (27)) and the abundance of the three palmerolide A BGC gene targets.…”

“…We investigated the relationship between BGC gene copies per ng host tissue for each sample and palmerolide A levels determined for the same samples using mass spectrometry, however no correlation was found (R<0.03, n=63; (27)). We then assessed the semi-quantitative relationship between the occurrence of SSU rRNA amplicon sequence variants (ASV, n=461; (27)) and the abundance of the three palmerolide A BGC gene targets. Here, we found a robust correlation (R=0.83 -0.99) between all 3 gene targets and a single amplicon sequence variant (ASV15) in the core microbiome (SI Appendix, Fig.…”

“…However, this does appear to be the case, and novel natural products have been discovered across algae, sponges, corals, nudibranchs, echinoderms, bryozoans, ascidians, and increasingly amongst microorganisms (16) for which the ecological roles have been deduced in a number of cases (13,17). Studies of Antarctic benthic invertebrate-microbe associations however, pale in comparison to studies at lower latitudes, yet the few studies that have been reported suggest these associations (i) harbor an untapped reservoir of biological diversity (18)(19)(20)(21) including fungi (22), (ii) are host species-specific (23,24), (iii) provide the host with sources of nitrogen and fixed carbon (25) and (iv) have biosynthetic functional potential (26,27).…”

“…The core microbiome of the palmerolide A-producing ascidian S. adareanum in samples collected across the Anvers Island archipelago (n=63 samples; (27)) is comprised of five bacterial phyla including Proteobacteria (dominating the microbiome), Bacteroidetes, Nitrospirae, Actinobacteria and Verrucomicrobia. A few candidate taxa in particular, were suggested to be likely palmerolide A producers based on relative abundance and biosynthetic potential determined by analysis of lineage-targeted biosynthetic capability (genera: Microbulbifer, Pseudovibrio, Hoeflea, and the family Opitutaceae (27). This motivated interrogation of the S. adarenum microbiome metagenome, with the goals of determining the metagenome-encoded biosynthetic potential, identifying candidate palmerolide A biosynthetic gene cluster (BGC)(s) and establishing the identity of the palmerolide A producing organism.…”