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Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R2 values averaged 0.62±0.11 , and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models. [ABSTRACT FROM AUTHOR]

Iron (Fe) is a key limiting nutrient for Southern Ocean phytoplankton. Input of Fe into the Southern Ocean is projected to change due to global warming, yet the combined effects of a concurrent increase in temperature with dissolved Fe (dFe) addition on phytoplankton growth and community composition have not been extensively studied. To improve our understanding of how Antarctic phytoplankton communities respond to Fe and enhanced temperature, we performed four full factorial onboard bioassays under trace-metal-clean conditions with phytoplankton communities from different regions of the Weddell Sea and the Amundsen Sea in the Southern Ocean. Treatments consisted of 2 nM Fe addition with 2 °C warming (TF), Fe addition at in situ temperature (F) + 2 °C warming with no Fe addition (T) and a control at in situ temperature with no Fe addition (control, C). Temperature had a limited effect by itself but boosted the positive response of the phytoplankton to Fe addition. Photosynthetic efficiency, phytoplankton abundances and chlorophyll a concentrations typically increased (significantly) with Fe addition (F and/or TF treatment), and the phytoplankton community generally shifted from haptophytes to diatoms upon Fe addition. The < 20 µ m phytoplankton fraction displayed population-specific growth responses, resulting in a pronounced shift in community composition and size distribution (mainly towards larger-sized phytoplankton) for the F and TF treatments. Such a distinct enhanced impact of dFe supply with warming on Antarctic phytoplankton size, growth and composition will likely affect trophic transfer efficiency and ecosystem structure, with potential significance for the biological carbon pump. [ABSTRACT FROM AUTHOR]

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-Series Study in the North Atlantic Ocean collected by in situ pumps and the AUV Clio were distributed with a paired metagenome, and one-dimensional liquid chromatographic data dependent acquisition mass spectrometry analyses was stipulated. Analysis of mass spectra from seven laboratories through a common informatic pipeline identified a shared set of 1056 proteins from 1395 shared peptides constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R² values ranging from 0.43 to 0.83, and a Sørensen similarity analysis of the top 1,000 proteins revealed 70-80% similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. An informatic intercomparison study, involving 10 laboratories using 8 software packages successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research including integration into global scale ocean surveys and ocean biogeochemical models. [ABSTRACT FROM AUTHOR]

Oxidative stress plays a role in many aspects of cellular metabolism, and as a result, antioxidants have the potential to impact cellular stoichiometry and biogeochemical cycles. We reviewed how antioxidant systems influence macronutrient and micronutrient stoichiometry in marine phytoplankton and identified that antioxidant systems have important implications for micronutrient stoichiometry. By leveraging diatom proteomic data, we empirically estimated the level of micronutrient quota variation that can be attributed to antioxidant systems. Fe‐containing antioxidant expression may contribute to 3.3–10 μmol : mol variation in Fe : C, and superoxide dismutases appear to be important contributors to variation in Mn, Ni, Zn, and Cu quotas in phytoplankton. Critical next steps for the study of phytoplankton antioxidant systems are to (1) distinguish between oxidative stress and redox‐based gene regulation and (2) determine how antioxidants influence variation or consistency in micronutrient quotas under various environmental conditions. [ABSTRACT FROM AUTHOR]

Marine phytoplankton vary widely in size across taxa, and in cell suspension densities across habitats and growth states. Cell suspension density and total biovolume determine the bulk influence of a phytoplankton community upon its environment. Cell suspension density also determines the intercellular spacings separating phytoplankton cells from each other, or from co-occurring bacterioplankton. Intercellular spacing then determines the mean diffusion paths for exchanges of solutes among co-occurring cells. Marine phytoplankton and bacterioplankton both produce and scavenge reactive oxygen species (ROS), to maintain intracellular ROS homeostasis to support their cellular processes, while limiting damaging reactions. Among ROS, hydrogen peroxide (H2O2) has relatively low reactivity, long intracellular and extracellular lifetimes, and readily crosses cell membranes. Our objective was to quantify how cells can influence other cells via diffusional interactions, using H2O2 as a case study. To visualize and constrain potentials for cell-to-cell exchanges of H2O2, we simulated the decrease of [H2O2] outwards from representative phytoplankton taxa maintaining internal [H2O2] above representative seawater [H2O2]. [H2O2] gradients outwards from static cell surfaces were dominated by volumetric dilution, with only a negligible influence from decay. The simulated [H2O2] fell to background [H2O2] within ~3.1 µm from a Prochlorococcus cell surface, but extended outwards 90 µm from a diatom cell surface. More rapid decays of other, less stable ROS, would lower these threshold distances. Bacterioplankton lowered simulated local [H2O2] below background only out to 1.2 µm from the surface of a static cell, even though bacterioplankton collectively act to influence seawater ROS. These small diffusional spheres around cells mean that direct cell-to-cell exchange of H2O2 is unlikely in oligotrophic habits with widely spaced, small cells; moderate in eutrophic habits with shorter cell-to-cell spacing; but extensive within phytoplankton colonies. [ABSTRACT FROM AUTHOR]

The collapse of the Northwest Atlantic cod (Gadus morhua) stocks in the early 1990s led to widespread ecological changes offshore. Changes in coastal fish communities are less known, largely due to the lack of historical records and long-term, standardized research surveys in coastal ecosystems. We aimed to overcome this with a unique dataset known as the Fleming survey. From 1959 to 1964, a systematic beach-seine survey was conducted to examine juvenile cod abundance in 84 bays (42 of which were consistently sampled and therefore analysed) along the east coast of Newfoundland. In addition to cod, all other fish collected in the seines were recorded. These surveys were repeated from 1992 to 1996 after the cod collapse, and document a substantial reduction in a dominant inshore species—juvenile Atlantic cod. Weshowthat total fish abundance declined significantly with the decrease of cod, whereas Shannon diversity and species evenness significantly increased. Species richness increased in some regions but decreased in others. We also found significant changes in the composition of the fish community likely due to a combination of release from predation from fewer large cod feeding in inshore areas as well as a release from competition from fewer juvenile cod occupying the coastal habitat. Region and the presence of vegetated habitats also significantly influenced the fish community. This study shows a strong reorganization of coastal fish communities after a large-scale fisheries collapse with implications for ecosystem-based and cross-ecosystem management. [ABSTRACT FROM AUTHOR]

Microbes transform their environments using diverse enzymatic reactions. However, it remains challenging to measure microbial reaction rates in natural environments. Despite advances in global quantification of enzyme abundances, the individual relationships between enzyme abundances and their reaction rates have not been systematically examined. Using matched proteomic and reaction rate data from microbial cultures, we show that enzyme abundance is often insufficient to predict its corresponding reaction rate. However, we discovered that global proteomic measurements can be used to make accurate rate predictions of individual reaction rates (median R2 = 0.78). Accurate rate predictions required only a small number of proteins and they did not need explicit prior mechanistic knowledge or environmental context. These results indicate that proteomes are encoders of cellular reaction rates, potentially enabling proteomic measurements in situ to estimate the rates of microbially mediated reactions in natural systems., (© The Author(s) 2025. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Microbes transform their environments using diverse enzymatic reactions. However, it remains challenging to measure microbial reaction rates in natural environments. Despite advances in global quantification of enzyme abundances, the individual relationships between enzyme abundances and their reaction rates have not been systematically examined. Using matched proteomic and reaction rate data from microbial cultures, we show that enzyme abundance is often insufficient to predict its corresponding reaction rate. However, we discovered that global proteomic measurements can be used to make accurate rate predictions of individual reaction rates (median R 2 = 0.78). Accurate rate predictions required only a small number of proteins and they did not need explicit prior mechanistic knowledge or environmental context. These results indicate that proteomes are encoders of cellular reaction rates, potentially enabling proteomic measurements in situ to estimate the rates of microbially mediated reactions in natural systems.