Data

Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts

Australian Institute of Marine Science
Australian Institute of Marine Science (AIMS)
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ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=http://geo.aims.gov.au/geonetwork/geonetwork/srv/eng/search?uuid=290075a2-333c-4489-9a35-07ee2ec991e5&rft.title=Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts&rft.identifier=http://geo.aims.gov.au/geonetwork/geonetwork/srv/eng/search?uuid=290075a2-333c-4489-9a35-07ee2ec991e5&rft.publisher=Australian Institute of Marine Science (AIMS)&rft.description=Four species of marine sponges were collected from Davies Reef at 4 - 9m depths. Four biological replicates of each of Carteriospongia foliascens, Cliona orientalis, Coscinoderma matthewsi, Ircinia ramosa, Pericharax heteroaphis, and Stylissa flabelliformis were placed into separated plastic bags filled with seawater and brought to the surface. Following collection, part of the tissue from each specimen was immediately preserved in 70% ethanol for species classification and the remaining tissue was snap-frozen in liquid nitrogen. Following sample preparation the LC-MS/MS spectrometry data were processed and annotated following the EMP method Computational methods for Release 2 and the EMP Multi-omics project (EMP500). Available from: https://github.com/biocore/emp/blob/master/methods/methods_release2.md. The mass spectra and the spectral matching results are accessible with the Metabolomics USI interface using the GNPS job ID and the corresponding MF id (e.g., X4151 corresponds to the scan/cluster number 4151). The computational annotations of putative small peptides, which can be classified as level 2/3 annotation (putative/partial structure) based on MSI standards [59], were performed using the DEREPLICATOR algorithm v.1.2.8 Mass spectrometry data were deposited on the MassIVE public repository under the accession MSV000083475. See Zhang et al. 2022 for futher details.Maintenance and Update Frequency: asNeededStatement: Established methods for sponge collection were used see: Botté ES, Nielsen S, Abdul Wahab MA, Webster J, Robbins S, Thomas T, et al. Changes in the metabolic potential of the sponge microbiome under ocean acidification. Nat Commun. 2019;10:1–10. Sponge species were identified based on their morphological characters by taxonomic specialists at the Western Australian Museum (Perth, Australia). Samples were prepared and extracted following the Earth Microbiome Project (EMP) protocol Nothias LF. Earth Microbiome Project (EMP) protocol for the LC-MS/MS. Available from: https://github.com/biocore/emp/blob/master/protocols/MetabolomicsLC.md Results of the DEREPLICATOR workflow can be accessed at https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=31be4f1f9d2e46a99823811ddd0cfd70. Schymanski EL, Jeon J, Gulde R, Fenner K, Ruff M, Singer HP, et al. Identifying small molecules via high resolution mass spectrometry: communicating confidence. Environ Sci Technol. 2014;48:2097–8 QC files are available from MassIVE Repository. See Zhang et al. 2022 for futher details.&rft.creator=Australian Institute of Marine Science (AIMS) &rft.date=2024&rft.coverage=westlimit=147.6375; southlimit=-18.8225; eastlimit=147.6375; northlimit=-18.8225&rft.coverage=westlimit=147.6375; southlimit=-18.8225; eastlimit=147.6375; northlimit=-18.8225&rft_rights= http://creativecommons.org/licenses/by/3.0/au/&rft_rights=http://i.creativecommons.org/l/by/3.0/au/88x31.png&rft_rights=WWW:LINK-1.0-http--related&rft_rights=License Graphic&rft_rights=Creative Commons Attribution 3.0 Australia License&rft_rights=http://creativecommons.org/international/au/&rft_rights=WWW:LINK-1.0-http--related&rft_rights=WWW:LINK-1.0-http--related&rft_rights=License Text&rft_rights=Use Limitation: All AIMS data, products and services are provided as is and AIMS does not warrant their fitness for a particular purpose or non-infringement. While AIMS has made every reasonable effort to ensure high quality of the data, products and services, to the extent permitted by law the data, products and services are provided without any warranties of any kind, either expressed or implied, including without limitation any implied warranties of title, merchantability, and fitness for a particular purpose or non-infringement. AIMS make no representation or warranty that the data, products and services are accurate, complete, reliable or current. To the extent permitted by law, AIMS exclude all liability to any person arising directly or indirectly from the use of the data, products and services.&rft_rights=Attribution: Format for citation of metadata sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: Australian Institute of Marine Science (AIMS). (2022). Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts. https://apps.aims.gov.au/metadata/view/290075a2-333c-4489-9a35-07ee2ec991e5, accessed[date-of-access].&rft_rights=Creative Commons Attribution 3.0 Australia License http://creativecommons.org/licenses/by/3.0/au&rft_subject=oceans&rft.type=dataset&rft.language=English Access the data
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Use Limitation: All AIMS data, products and services are provided "as is" and AIMS does not warrant their fitness for a particular purpose or non-infringement. While AIMS has made every reasonable effort to ensure high quality of the data, products and services, to the extent permitted by law the data, products and services are provided without any warranties of any kind, either expressed or implied, including without limitation any implied warranties of title, merchantability, and fitness for a particular purpose or non-infringement. AIMS make no representation or warranty that the data, products and services are accurate, complete, reliable or current. To the extent permitted by law, AIMS exclude all liability to any person arising directly or indirectly from the use of the data, products and services.

Attribution: Format for citation of metadata sourced from Australian Institute of Marine Science (AIMS) in a list of reference is as follows: "Australian Institute of Marine Science (AIMS). (2022). Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts. https://apps.aims.gov.au/metadata/view/290075a2-333c-4489-9a35-07ee2ec991e5, accessed[date-of-access]".

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reception@aims.gov.au
adc@aims.gov.au

Brief description

Four species of marine sponges were collected from Davies Reef at 4 - 9m depths. Four biological replicates of each of Carteriospongia foliascens, Cliona orientalis, Coscinoderma matthewsi, Ircinia ramosa, Pericharax heteroaphis, and Stylissa flabelliformis were placed into separated plastic bags filled with seawater and brought to the surface. Following collection, part of the tissue from each specimen was immediately preserved in 70% ethanol for species classification and the remaining tissue was snap-frozen in liquid nitrogen.


Following sample preparation the LC-MS/MS spectrometry data were processed and annotated following the EMP method Computational methods for Release 2 and the EMP Multi-omics project (EMP500). Available from: https://github.com/biocore/emp/blob/master/methods/methods_release2.md.


The mass spectra and the spectral matching results are accessible with the Metabolomics USI interface using the GNPS job ID and the corresponding MF id (e.g., X4151 corresponds to the scan/cluster number 4151). The computational annotations of putative small peptides, which can be classified as level 2/3 annotation (putative/partial structure) based on MSI standards [59], were performed using the DEREPLICATOR algorithm v.1.2.8


Mass spectrometry data were deposited on the MassIVE public repository under the accession MSV000083475. See Zhang et al. 2022 for futher details.

Lineage

Maintenance and Update Frequency: asNeeded
Statement: Established methods for sponge collection were used see: Botté ES, Nielsen S, Abdul Wahab MA, Webster J, Robbins S, Thomas T, et al. Changes in the metabolic potential of the sponge microbiome under ocean acidification. Nat Commun. 2019;10:1–10.


Sponge species were identified based on their morphological characters by taxonomic specialists at the Western Australian Museum (Perth, Australia).


Samples were prepared and extracted following the Earth Microbiome Project (EMP) protocol Nothias LF. Earth Microbiome Project (EMP) protocol for the LC-MS/MS. Available from: https://github.com/biocore/emp/blob/master/protocols/MetabolomicsLC.md


Results of the DEREPLICATOR workflow can be accessed at https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=31be4f1f9d2e46a99823811ddd0cfd70.


Schymanski EL, Jeon J, Gulde R, Fenner K, Ruff M, Singer HP, et al. Identifying small molecules via high resolution mass spectrometry: communicating confidence. Environ Sci Technol. 2014;48:2097–8


QC files are available from MassIVE Repository. See Zhang et al. 2022 for futher details.

Notes

Credit
Couvillion, SP. Pacific Northwest Laboratory, Richland, WA, USA
Credit
Zhang, S. University of New South Wales (UNSW)
Credit
Song, W. (UNSW)
Credit
Webster, N. Australian Institute of Marine Science (AIMS) and University of Queensland (UQ)
Credit
Thomas, T. University of New South Wales (UNSW)
Credit
Nothias, LF. University of California San Diego, USA

Modified: 13 03 2024

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147.6375,-18.8225

147.6375,-18.8225

text: westlimit=147.6375; southlimit=-18.8225; eastlimit=147.6375; northlimit=-18.8225

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Other Information
Zhang, S., Song, W., Nothias, LF. et al. Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts. Microbiome 10, 22 (2022). https://doi.org/10.1186/s40168-021-01220-9

doi : https://doi.org/10.1186/s40168-021-01220-9

Identifiers
  • global : 290075a2-333c-4489-9a35-07ee2ec991e5
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