Towards a planetary-scale observing system for marine microbes: enhancing the interoperability and legacy of marine microbial data and metadata through a transparent, accessible, and coordinated network of omics data

Abstract

Marine microbes are vital to ocean ecosystems, driving nutrient cycling, primary production, and climate regulation. Omics-enabled microbial observations are crucial for understanding, predicting, and sustainably managing these dynamic systems. By analyzing DNA, organisms can be identified, and their functions predicted, offering a unified approach to biological observation across all life forms. Complementing established methods, omics observations provide insights into ocean health, establish baselines for change, fuel discoveries, and inform policy decisions. However, advances in microbiome research are often not scaled or sustained globally, and digital outputs frequently fail to translate into integrated awareness and discovery.

This thesis builds the basis for an interoperable observing system for marine microbes so that innovation and discovery contribute towards a FAIR digital commons that is operationally sound and coordinated across regions and research domains. Chapters II and VI focus on global coordination by establishing key networks that unify stakeholders through a common vision, laying the groundwork for a cohesive observing system. Chapter III enhances interoperability of (meta)data across different platforms by building a sustainable translation layer between the main metadata standards in omics biodiversity data, while Chapter V advances the standardization and accessibility of observational methods, improving method comparability and data integration. Chapter VII assesses the current state of metadata in public archives, identifying gaps and suggesting improvements, and Chapter VIII introduces an omics data paper type to incentivise better metadata management practices. Chapter IV tests the feasibility of integrating metagenomics data across observatories, providing analysis-ready metadata and a reproducible workflow. Further, it synthesizes a perspective on maximizing current and future opportunities in marine microbial observing and research.