Physiology and Rates in Microbial Oceanography (PRIMO)
ToR1
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.
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To address ToR1, we will undertake 3 activities.
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1.1: review the literature for existing physiological metrics, including those from other relevant research fields (e.g., freshwater science, ecotoxicology, gut microbiome) and from other SCOR WGs (e.g., 156, 165, 166). This review will cover classic physiological metrics routinely used in biological oceanography, as well as novel metrics that are being developed to determine physiological rates at a cellular and community level (e.g., click chemistry, nano-SIMS and SIP, quantitative metaproteomics).
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1.2: identify knowledge gaps of key metabolic pathways, as revealed by the global ‘omics datasets, due to the lack of physiological measurements.
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1.3: combine the outcomes from Activities 1.1 and 1.2 to create a ranked list of the key metabolic pathways to focus on. Activity 1.3 will include a detailed assessment of i) the best approach for each physiological process (e.g., targeted assays vs. measuring substrates), ii) our ability to design such metrics, and iii) their highest-value insight into marine microbial dynamics and biogeochemical cycling.
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ToR2
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.
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To address ToR 2, we will undertake 2 activities that build on the ToR 1 deliverables.
2.1: identify improvements needed in our ability to couple ‘omics to physiological rate proxies. This will enhance the skill of cellular-scale models that predict physiological rates, perhaps through the leveraging of ‘omics data directly (e.g., McCain et al., 2021). This work will focus on physiological rate proxies that are relevant to, and can be easily incorporated into, ocean scale models (e.g., nutrient uptake, organic carbon production). WG member Levine will lead this effort, as their group develops innovative, interdisciplinary numerical models that provide insight into how cell dynamics impact large- scale processes (e.g., rates of global carbon cycling). The WG will discuss how to best link observations and laboratory data to coarser grained biogeochemical models (e.g., NPZD or trait-based models), exploring the use of proteome allocation, quota, and metabolic models. We will also work to identify the best ways to leverage output from cell-scale models into ocean scale models (e.g., DARWIN).
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2.2: collaborate with ocean scale modelers (see PRIMO net, described below) to identify critical physiological proxies to parameterize in their models. For the desired proxies, we can then determine the candidate assays we need to quantify to target those proxies. In this way, we propose to ‘reverse engineer’ physiological metrics from ‘omics with input from modelers. Ultimately, Activity 2.1 and 2.2 will allow us to create a ranked list of the priority co-designed physiological proxies to target for method development.
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ToR3
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.
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To address ToR 3, we will develop a framework and toolset to design and implement the physiological proxies identified in ToR 2.
WG members with expertise in novel physiological techniques (e.g., nano- SIMS and SIP, quantitative metaproteomics) will lead the effort. We will draw on our WG members’ knowledge of isotope and tracer labeling (e.g., Maldonado), in situ stable isotope probing techniques to tease apart individual contributions of different taxa to community physiological rates (e.g., Wilkin), and novel methods’ development for physiological rate determinations in marine phytoplankton (e.g., Behrendt), as well as insights from researchers in other disciplines (e.g., systems biology, ecotoxicology, and biomedical sciences) that our WG members collaborate with.
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ToR4
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.
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To address ToR 4, we will undertake 2 activities.
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4.1: identify a flagship physiological metric to develop, using the roadmap designed in activity 3.1. This WG has the capability to conduct concomitant in situ community-based rate measurements, single-cell physiological rate determinations, and ‘omics research. Furthermore, WG and PRIMO net members (e.g., Bertrand, Crowe and Maldonado) have developed a novel autonomous submersible profiling and incubation system (BioApnea) to investigate in situ microbial activity and function. This system can i) collect samples for microbial ‘omics studies, and for dissolved and particulate trace metal and nutrient analyses, and ii) determine in situ metabolic rates with minimal perturbation and high temporal and spatial resolution. These combined multi-disciplinary approaches will be used to validate this flagship physiological metric as a proxy bridging ‘omics and models.
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4.2: explore whether our flagship physiological metric can be made high-throughput and scalable. Can this assay be conducted using existing, low-cost instruments and accessible reagents? Such efforts would enable unprecedented spatial and temporal resolution and accessibility to research communities lacking complex instrumentation. Such accessibility could provide inspiration for our research community in future assay co-design efforts.
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