Toward a global public repository of community protocols to encourage best practices in biomolecular ocean observing and research

Biomolecular ocean observing and research is a rapidly evolving field that uses omics approaches to describe biodiversity at its foundational level, giving insight into the structure and function of marine ecosystems over time and space. It is an especially effective approach for investigating the marine microbiome. To mature marine microbiome research and operations within a global ocean biomolecular observing network (OBON) for the UN Decade of Ocean Science for Sustainable Development and beyond, research groups will need a system to effectively share, discover, and compare “omic” practices and protocols. While numerous informatic tools and standards exist, there is currently no global, publicly-supported platform specifically designed for sharing marine omics [or any omics] protocols across the entire value-chain from initiating a study to the publication and use of its results. Toward that goal, we propose the development of the Minimum Information for an Omic Protocol (MIOP), a community-developed guide of curated, standardized metadata tags and categories that will orient protocols in the value-chain for the facilitated, structured, and user-driven discovery of suitable protocol suites on the Ocean Best Practices System. Users can annotate their protocols with these tags, or use them as search criteria to find appropriate protocols. Implementing such a curated repository is an essential step toward establishing best practices. Sharing protocols and encouraging comparisons through this repository will be the first steps toward designing a decision tree to guide users to community endorsed best practices.

eDNA, metadata, methods, ocean best practices, ocean observations, omics, protocol management

10.3389/fmars.2021.758694

2296-7745

Samuel, Robyn, Mairin

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Meyer, Raissa

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Buttigieg, Pier Luigi

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Davies, Neil

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Jeffery, Nicholas

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Meyer, Christopher

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Pavloudi, Christina

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Pitz, Kathleen

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Sweetlove, Maxime

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Theroux, Susanna

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van de Kamp, Jodie

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Watts, Alison

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11 October 2021

Samuel, Robyn, Mairin

0ee6bcf6-9278-439c-ab49-9d349813f692

Meyer, Raissa

d0d46483-0ea2-44ad-b2a9-eebe07c014c3

Buttigieg, Pier Luigi

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Davies, Neil

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Jeffery, Nicholas

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Meyer, Christopher

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Pavloudi, Christina

b6d4e189-9e73-4993-8cdf-e4f951e72061

Pitz, Kathleen

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Sweetlove, Maxime

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Theroux, Susanna

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van de Kamp, Jodie

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Watts, Alison

01be8570-09ef-4a35-bc6a-8e524310e47a

Samuel, Robyn, Mairin, Meyer, Raissa, Buttigieg, Pier Luigi, Davies, Neil, Jeffery, Nicholas, Meyer, Christopher, Pavloudi, Christina, Pitz, Kathleen, Sweetlove, Maxime, Theroux, Susanna, van de Kamp, Jodie and Watts, Alison (2021) Toward a global public repository of community protocols to encourage best practices in biomolecular ocean observing and research. Frontiers in Marine Science, 8, [758694]. (doi:10.3389/fmars.2021.758694).

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Accepted/In Press date: 21 September 2021

Published date: 11 October 2021

Additional Information: Funding Information: RS was supported by the Natural Environment Research Council (NERC) NEXUSS Studentship (grant number NE/N012070/1). RM’s contributions were supported by the European Union’s Horizon 2020 Research and Innovation Programmes under grant agreement N◦ 862923, project AtlantECO (Atlantic ECOsystem assessment, forecasting and sustainability), and grant agreement N◦ 862626, project EuroSea (Improving and Integrating European Ocean Observing and Forecasting Systems for Sustainable use of the Oceans). NJ was supported by the Fisheries and Oceans Canada Marine Conservation Targets programme. CP was supported by BIOIMAGING-GR (MIS 5002755) implemented under “Action for Strengthening Research and Innovation Infrastructures” funded by the Operational Programme “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and co-financed by Greece and the European Union (European Regional Development Fund), ECCO (project ID 343) funded by the 1st call for the support of Post-doctoral Researchers by the Hellenic Foundation for Research and Innovation (HFRI) and FutureMARES (grant agreement N◦ 869300) funded by the European Union’s Horizon 2020 Research and Innovation Programme. In addition, CP’s research is co-financed by Greece and the European Union (European Social Fund-ESF) through the Operational Programme «Human Resources Development, Education and Lifelong Learning» in the context of the project “Reinforcement of Postdoctoral Researchers—2nd Cycle” (MIS-5033021), implemented by the State Scholarships Foundation (IKY). JK was supported by the CSIRO Environomics Future Science Platform and the Australian Microbiome Initiative. The Australian Microbiome initiative was supported by funding from Parks Australia through the Bush Blitz program funded by the Australian Government and BHP, Bioplatforms Australia and the Integrated Marine Observing Publisher Copyright: © Copyright © 2021 Samuel, Meyer, Buttigieg, Davies, Jeffery, Meyer, Pavloudi, Pitz, Sweetlove, Theroux, van de Kamp and Watts.

Keywords: eDNA, metadata, methods, ocean best practices, ocean observations, omics, protocol management

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