Synoicum_adareanum_microbiome

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How to cite

Researchers should cite this work as follows:

Baker BJ. 2020. Synoicum adareanum sampling u/w video Mar 2011 Palmer Station Antarctica doi:10.5061/dryad.gxd2547gw, Dryad Data.

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The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

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This resource has been registered with GBIF, and assigned the following GBIF UUID: a45749ef-2235-4869-94cd-f074bb2895e8.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Metadata; ascidian; microbiome; bacterioplankton; palmerolide; natural products; Synoicum; Antarctic Peninsula; 16s rRNA; marine

Contacts

Geographic Coverage

Samples were collected in Anvers Island Archipelago, Gerlache Strait, Palmer Deep and LaPeyrere Bay.

Project Data

The ascidian, S. adareanum, from the Antarctic Peninsula near Anvers Island, is known to produce a bioactive compound, palmerolide A (PalA) that has specific activity to melanoma, a particularly invasive and metastatic form of skin cancer. The combined non-ribosomal peptide-polyketide structure of PalA has similarities to microbially-produced macrolides which motivated this study utilizing culture-dependent and -independent investigations coupled with PalA detection to improve our understanding of the host-associated microbiome and relationship to PalA. Cultivation efforts yielded seven different bacteria, none of which produced PalA under the conditions tested. The genome sequence was mined for one of the most abundant members of the microbiome, Pseudovibrio sp. str. TunPSC04-5.I4, revealing eight biosynthetic gene clusters, none supporting the potential for PalA biosynthesis. PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples from each) sampled from seven sites across the Anvers Island archipelago. These 63 samples were used to assess microbiome composition (V3-4 16S rRNA gene sequence variants) which revealed a core suite of 21 bacteria, 20 of which were distinct from regional bacterioplankton. Co-occurrence analysis yielded several subsystems that may interact functionally and although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. Sequence variant relative abundance, and biosynthetic potential of related organisms pointed to a subset of the core membership as potential PalA producers which provides a gateway to identifying the producer of palmerolides in future work.

The personnel involved in the project:

Sampling Methods

A spatial survey of Synoicum adareanum was executed in which samples were collected by SCUBA in austral fall between 23 March and 3 April 2011. Seven sampling sites (depths 24.7 - 31 m) around the region accessible by Zodiac boat from Palmer Station were selected in which we sampled in a nested design where three multi-lobed colonies were selected from each site, and three lobes per colony were sampled. In total, 63 S. adareanum lobes were sampled (9 from each site). Samples were transported to Palmer Station on ice, and frozen at -80 °C until processing at DRI and USF. Frozen S. adareanum lobes were cut longitudinally in half for parallel processing through DNA and palmerolide detection pipelines. Reference seawater data set was represented by samples that had been collected in February-March 2008 (five samples) and in August-September 2008 (nine samples) from LTER Station B near Anvers Island (east of the Bonaparte Point dive site), and at a few other locations in the region. Seawater samples were collected by a submersible pump and acid washed silicone tubing at 10 m at Station B, and using a rosette equipped with 12 L Niskin bottles for the offshore samples at 10 m and 500 m (2 samples each depth). The February-March seawater samples were processed using in-line filtration with a 2.5 um filter (Polygard, Millipore) to screen larger organisms and bacterioplankton were concentrated using a tangential flow filtration system and the cells were harvested on 25 mm 0.2 um Supor filters (Millipore). The August-September seawater samples were processed using inline filtration with a 3.0 um filter (Versapor, Millipore), and then bacterioplankton was collected onto 0.2 um Sterivex (Millipore) filters using a multichannel peristaltic pump (Masterflex). All filters were immersed in sucrose lysis buffer(68) and stored frozen at -80 °C until extraction. S. adareanum samples collected by SCUBA in 2004 and 2007 were used for cultivation. The 2004 specimen were archived in 20% glycerol at -80 °C until processing by manual homogenization using sterilized mortar and pestle prior to plating a suspension onto marine agar 2216 plates in 2006. The 2007 samples were homogenized immediately following collection using sterilized mortar and pestle, and suspensions were prepared in 1X marine broth or filter-sterilized seawater then transferred at 4 °C.

Method step description:

1. NA

Additional Metadata