AtlantECO Deliverable - D04.4 - Handbook of Standards and Best Practices

The present deliverable (D4.4) reports on AtlantECO’s Handbook of Standards and Best Practices. It was developed throughout the project, and its content is presented in three deliverables (D4.1, D4.2 & D4.4), which are all publicly accessible under a single DOI (https://doi.org/10.5281/zenodo.4897860) and also available via UNESCO’s Ocean Best Practices. AtlantECO generated new observations as part of the project’s sampling activities in synergy with other European and International projects (see deliverable D4.7). The Handbook provides a set of Standard Operating Procedures (SOPs) for methodologies used across these activities to study the Ocean microbiome. These SOPs also constitute a basis for comparing protocols and aggregating results from different observation programmes. The SOPs are generic and describe key methodological concepts, materials and procedural steps, which gives the different observation programmes enough flexibility to adopt the standards and best practices and adapt the SOPs to their specific context. The Handbook includes in deliverable D4.1 (https://doi.org/10.5281/zenodo.4897861): Guiding principles for the design of AtlantECO's Standards & Best Practices A filtration kit for key genomics, proteomics and metabolomics protocols An imaging kit for key phenomics protocols The Handbook includes in deliverable D4.2 (https://doi.org/10.5281/zenodo.6956974) a collection of fivedownloadable packages: Sampling protocols from Mission Microbiomes AtlantECO Sampling protocols from AtlantECO’s Brazil-South-Africa line of the Continuous Plankton Recorder Analysis protocols for metabarcoding, metagenomics and metatranscriptomics Analysis protocols for imaging Access and Benefits Sharing protocols The Handbook includes in deliverable D4.4 (https://doi.org/10.5281/zenodo.18801151): Revised guiding principles for the design of AtlantECO's Standards & Best Practices A revised System of Biological Entities composing the Ocean Microbiome Ocean Microbiome - Standard Operating Procedures published on protocols.io 62 one-pager protocols from Mission Microbiomes AtlantECO, also published on protocols.io The most significant impact and legacy of AtlantECO’s Handbook of Standards and Best Practices is the publication of the Ocean Microbiome - Standard Operating Procedures (OM-SOPs) at protocols.io, an online platform widely used in research to cite, share, discover and use reproducible methods. Each OM-SOP is published as a collection that can branch into many equivalent or derived protocols. These branches can be established with already existing protocols, such as those from project Tara Oceans, or can be created new as we did for Mission Microbiomes AtlantECO. As a legacy, EMBL-EBI will continue to curate the OM-SOPs at protocols.io, and to invite and help other projects to branch in their own protocols into the OM-SOPs, including EMBRC’s EMO-BON, EMBL’s TRaversing the European Coastline (TREC) and EC|BIOcean5D.