Data

A quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities

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=https://apps.aims.gov.au/metadata/view/d0a90c49-9799-4891-95ce-1e014a05d63b&rft.title=A quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities&rft.identifier=https://apps.aims.gov.au/metadata/view/d0a90c49-9799-4891-95ce-1e014a05d63b&rft.publisher=Australian Institute of Marine Science (AIMS)&rft.description=This data collection consists of microbial count data from seawater microbiomes based on both flow cytometry and 16S rRNA copy numbers from droplet digital PCR (ddPCR) that were used to validate a framework for quantifying absolute abundance of microbial communities for use in downstream ecotoxicology modelling. Seawater was collected from the AIMS jetty (19°16′38.4”S, 147°03′32.1”E) and the relationship between cell counts and absolute 16S rRNA gene copy numbers was determined by preparing varying proportions of natural seawater and artificial seawater suspensions (natural seawater proportions of 100, 80, 60, 40, 20, and 0% of a total 500 mL sample, with ASW making up the remaining proportion).For full methodological details please refer to the full research publication, Thomas et al. 2025 (https://doi.org/10.1186/s40793-025-00741-2) its supplementary materials and the associated GitHub repository (GitHub - MarieCThomas/Quantitative-PMA-16S-rRNA-Gene-Sequencing-Workflow). Additionally, raw sequencing data can be found in the NCBI Sequence Read Archives under BioProject number PRJNA1176196.Maintenance and Update Frequency: asNeeded&rft.creator=Australian Institute of Marine Science (AIMS) &rft.date=2026&rft.coverage=westlimit=147.0587128400803; southlimit=-19.277124223216084; eastlimit=147.0587128400803; northlimit=-19.277124223216084&rft.coverage=westlimit=147.0587128400803; southlimit=-19.277124223216084; eastlimit=147.0587128400803; northlimit=-19.277124223216084&rft_rights=Creative Commons Attribution-NonCommercial 3.0 Australia License http://creativecommons.org/licenses/by-nc/3.0/au/&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). (2025). A quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities. https://apps.aims.gov.au/metadata/view/d0a90c49-9799-4891-95ce-1e014a05d63b, accessed[date-of-access].&rft_subject=oceans&rft.type=dataset&rft.language=English Access the data
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Creative Commons Attribution-NonCommercial 3.0 Australia License
http://creativecommons.org/licenses/by-nc/3.0/au/

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). (2025). A quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities. https://apps.aims.gov.au/metadata/view/d0a90c49-9799-4891-95ce-1e014a05d63b, accessed[date-of-access]".

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This data collection consists of microbial count data from seawater microbiomes based on both flow cytometry and 16S rRNA copy numbers from droplet digital PCR (ddPCR) that were used to validate a framework for quantifying absolute abundance of microbial communities for use in downstream ecotoxicology modelling. Seawater was collected from the AIMS jetty (19°16′38.4”S, 147°03′32.1”E) and the relationship between cell counts and absolute 16S rRNA gene copy numbers was determined by preparing varying proportions of natural seawater and artificial seawater suspensions (natural seawater proportions of 100, 80, 60, 40, 20, and 0% of a total 500 mL sample, with ASW making up the remaining proportion).


For full methodological details please refer to the full research publication, Thomas et al. 2025 (https://doi.org/10.1186/s40793-025-00741-2) its supplementary materials and the associated GitHub repository (GitHub - MarieCThomas/Quantitative-PMA-16S-rRNA-Gene-Sequencing-Workflow). Additionally, raw sequencing data can be found in the NCBI Sequence Read Archives under BioProject number PRJNA1176196.

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Maintenance and Update Frequency: asNeeded

Modified: 18 09 2026

This dataset is part of a larger collection

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147.05871,-19.27712

147.05871284008,-19.277124223216

text: westlimit=147.0587128400803; southlimit=-19.277124223216084; eastlimit=147.0587128400803; northlimit=-19.277124223216084

Subjects
oceans |

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Other Information
Thomas, M.C., Waugh, G., Damjanovic, K. et al. Development of a quantitative PMA-16S rRNA gene sequencing workflow for absolute abundance measurements of seawater microbial communities. Environmental Microbiome 20, 81 (2025). https://doi.org/10.1186/s40793-025-00741-2

doi : https://doi.org/10.1186/s40793-025-00741-2

Microbial count data for varying proportions of natural and artificial seawater

url : https://api.aims.gov.au/data-v2.0/d0a90c49-9799-4891-95ce-1e014a05d63b/files/count_data.csv

Raw sequence reads

url : https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1176196

Microbial data used to correlate flow cytometry and ddPCR counts

url : https://api.aims.gov.au/data-v2.0/d0a90c49-9799-4891-95ce-1e014a05d63b/files/correlation_data.csv

R scripts

url : https://github.com/MarieCThomas/Quantitative-PMA-16S-rRNA-Gene-Sequencing-Workflow

Identifiers
  • global : d0a90c49-9799-4891-95ce-1e014a05d63b
ACN 633 798 857