Synoicum_adareanum_microbiome

Latest version published by SCAR - Microbial Antarctic Resource System on Feb 19, 2020 SCAR - Microbial Antarctic Resource System

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. Microbiome composition investigations were conducted to describe the microbiome structure and composition of the Antarctic ascidian, Synoicum adareanum. Metadata sets include (1) ascidian sample collections (63 samples) from the Anvers Island archipelago and associated 16S rRNA gene Illumina tag sequence data sets (V3-V4); palmerolide chemistry data was determined for the same set of 63 samples, and is included with the metadata;(2) bacterioplankton sample collections (14 samples) from the Anvers Island archipelago and associated 16S rRNA gene Illumina tag sequence data sets (V3); (3) bacterial isolate 16S rRNA gene sequences (16 isolates, nearly full length 16S RNA gene), cultivated from Synoicum adareanum homogenates.

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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.

GBIF Registration

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

Who created the resource:

Alison Murray
Research Professor
Desert Research Institute 2215 Raggio Parkway 89512 Reno NV US 775-673-7361
https://www.dri.edu/alison-murray-research
Bill Baker
Professor
University of South Florida US

Who can answer questions about the resource:

Alison Murray
Research Professor
Desert Research Institute 2215 Raggio Parkway 89512 Reno NV US 775-673-7361
https://www.dri.edu/alison-murray-research
Bill Baker
Professor
University of South Florida

Who filled in the metadata:

Alison Murray
Research Professor
Desert Research Institute 2215 Raggio Parkway 89512 Reno NV US 775-673-7361
https://www.dri.edu/alison-murray-research
Bill Baker
Professor
University of South Florida

Geographic Coverage

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

Bounding Coordinates South West [-64.926, -64.383], North East [-64.421, -62.889]

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.

Title Synoicum adareanum microbiome from the Anvers Island archipelago, Antarctica
Funding National Institute of Health (CA205932) National Science Foundation (OPP-0442857, ANT-0838776, PLR-1341339, 0632389) Joint Genome Institute’s Community Sequencing Program (JGI-634)
Study Area Description Anvers Island archipelago, Antarctica
Design Description We designed a study to investigate the potential that there is a core microbiome that persists with palmerolide A producing S. adareanum holobionts. We conducted a spatial survey of S. adareanum in which we studied coordinated specimen-level detection and quantitation of palmerolide A along with the host-associated microbiome diversity and community structure across the Anvers Island archipelago on the Antarctic Peninsula. This work aims to help identify potential palmerolide A producing microorganisms, and motivates metagenome sequencing which could then provide information on PalA biosynthesis. This is required to reach the ultimate goal of this research which is development of a potential therapeutic agent to fight melanoma.

The personnel involved in the project:

Principal Investigator
Alison Murray
Principal Investigator
Bill Baker

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.

Study Extent Samples were collected in Anvers Island Archipelago, Gerlache Strait, Palmer Deep and LaPeyrere Bay.
Quality Control NA

Method step description:

  1. NA

Additional Metadata

Alternative Identifiers https://ipt.biodiversity.aq/resource?r=synoicum_adareanum_microbiome