SCOR Working Group 170

Physiology and Rates in Microbial Oceanography (PRIMO)

Note, the WG was proposed under the name “NEw physiological Metrics for Oceanography from ‘Omics (NEMOO).”

The need to understand how ocean global change affects marine life has exposed gaps in our knowledge of fundamental principles. Although molecular biological techniques, particularly ‘omics (genomics to proteomics), now dominate research in biological oceanography, physiological research has stagnated, leading to the assumption that physiology is outmoded. However, biological rates and biogeochemical fluxes remain the main currencies in biogeochemistry (BGC) models in which microbes play a central role. The question we aim to address – with a focus on marine microbes – is how to translate ‘omicsbased information on physiological potential into quantifiable physiological rates, and ultimately into BGC processes that can be represented in Earth system models.

While ‘omics has revealed patterns in marine microbial diversity and metabolic pathways, it largely provides only static snapshots of physiological potential. Studies that weave ‘omics and physiological rates together provide greater insights and improved mechanistic understanding. But despite these advances, there is widespread frustration about the paucity of physiological metrics, as most of these metrics were devised before the molecular biology revolution. To improve our understanding of the roles of marine microbes in biogeochemical cycles, we need better tools to quantify physiological activity. Physiological rates quantify the integrated activity of proteins that drive marine BGC cycles and can bridge the gap between ‘omics and biogeochemistry. We propose the development of a community and framework for co-designing physiological metrics as currency converters to link ‘omics datasets and BGC models, a central aim of the international BioGeoSCAPES program.

Erin Bertrand (Canada), Robert Strzepek (Australia)
Other Full Members
Shady Amin (United Arab Emirates), Federico Baltar (Austria), Rachel Foster (Sweden), Naomi Levine (USA), Aditee Mitra (UK), Thomas Ryan-Keogh (South Africa), Koji Suzuki (Japan), Susanne Wilken (Netherlands)
Associate Members
Cecilia Alonso (Uruguay), Lars Behrendt (Sweden), Tom Bibby (UK), Chuan Ku (China-Taipei), Maite Maldonado (Canada), Jana Milucka (Germany), Yeala Shaked (Israel), Dalin Shi (China-Beijing), Peter von Dassow (Chile), Taichi Yokokawa (Japan), Kai Ziervogel (USA), Patrizia Ziveri (Spain)
Ilka Peeken
Terms of Reference
  1. Review current physiological metrics, identify the key gaps in our understanding of marine microbial metabolism as revealed by ‘omics that are candidates for the co-design of new physiological assays, and rank these candidate assays according to their likely success for development and their biogeochemical importance.

  2. Identify the physiological metrics of marine microbial metabolism best suited to convert between the currencies of ‘omics datasets and models, from cellular (fine scale) to BGC (coarse scale) models, using the WGs combined expertise in ‘omics, physiology and modeling, and the knowledge gained from ToR 1.

  3. Determine the pathways to implementation with respect to assay development (learning the design process from systems biology, ecotoxicology, and biomedical sciences), and in doing so develop a framework and toolset for discovering proxies of marine microbial physiological processes that can bridge ‘omics and models.

  4. As a proof of concept, identify a flagship physiological metric to develop, using the roadmap designed in ToR 3, and assess whether this can be made high throughput and integrated with new observational platforms to stimulate the co-measurement of marine microbe ‘omics, physiology, and the BGC processes.

October 2023
Financial Sponsors