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1. Projected 21st-century changes in marine heterotrophic bacteria under climate change

   https://doi.org/10.3389/fmicb.2023.1049579  

   Kim, Heather H; Laufkötter, Charlotte; Lovato, Tomas; Doney, Scott C; Ducklow, Hugh W (February 2023, Frontiers in Microbiology)

   Marine heterotrophicBacteria(or referred to as bacteria) play an important role in the ocean carbon cycle by utilizing, respiring, and remineralizing organic matter exported from the surface to deep ocean. Here, we investigate the responses of bacteria to climate change using a three-dimensional coupled ocean biogeochemical model with explicit bacterial dynamics as part of the Coupled Model Intercomparison Project Phase 6. First, we assess the credibility of the century-scale projections (2015–2099) of bacterial carbon stock and rates in the upper 100 m layer using skill scores and compilations of the measurements for the contemporary period (1988–2011). Second, we demonstrate that across different climate scenarios, the simulated bacterial biomass trends (2076–2099) are sensitive to the regional trends in temperature and organic carbon stocks. Bacterial carbon biomass declines by 5–10% globally, while it increases by 3–5% in the Southern Ocean where semi-labile dissolved organic carbon (DOC) stocks are relatively low and particle-attached bacteria dominate. While a full analysis of drivers underpinning the simulated changes in all bacterial stock and rates is not possible due to data constraints, we investigate the mechanisms of the changes in DOC uptake rates of free-living bacteria using the first-order Taylor decomposition. The results demonstrate that the increase in semi-labile DOC stocks drives the increase in DOC uptake rates in the Southern Ocean, while the increase in temperature drives the increase in DOC uptake rates in the northern high and low latitudes. Our study provides a systematic analysis of bacteria at global scale and a critical step toward a better understanding of how bacteria affect the functioning of the biological carbon pump and partitioning of organic carbon pools between surface and deep layers. 

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2. What Is Refractory Organic Matter in the Ocean?

   https://doi.org/10.3389/fmars.2021.642637  

   Baltar, Federico; Alvarez-Salgado, Xosé A.; Arístegui, Javier; Benner, Ronald; Hansell, Dennis A.; Herndl, Gerhard J.; Lønborg, Christian (April 2021, Frontiers in Marine Science)

   null (Ed.)

   About 20% of the organic carbon produced in the sunlit surface ocean is transported into the ocean’s interior as dissolved, suspended and sinking particles to be mineralized and sequestered as dissolved inorganic carbon (DIC), sedimentary particulate organic carbon (POC) or “refractory” dissolved organic carbon (rDOC). Recently, the physical and biological mechanisms associated with the particle pumps have been revisited, suggesting that accepted fluxes might be severely underestimated ( Boyd et al., 2019 ; Buesseler et al., 2020 ). Perhaps even more poorly understood are the mechanisms driving rDOC production and its potential accumulation in the ocean. On the basis of recent conflicting evidence about the relevance of DOC degradation in the deep ocean, we revisit the concept of rDOC in terms of its “refractory” nature in order to understand its role in the global carbon cycle. Here, we address the problem of various definitions and approaches used to characterize rDOC (such as turnover time in relation to the ocean transit time, molecule abundance, chemical composition and structure). We propose that rDOC should be operationally defined. However, we recognize there are multiple ways to operationally define rDOC; thus the main focus for unifying future studies should be to explicitly state how rDOC is being defined and the analytical window used for measuring rDOC, rather than adhering to a single operational definition. We also conclude, based on recent evidence, that the persistence of rDOC is fundamentally dependent on both intrinsic (chemical composition and structure, e.g., molecular properties), and extrinsic properties (amount or external factors, e.g., molecular concentrations, ecosystem properties). Finally, we suggest specific research questions aimed at stimulating research on the nature, dynamics, and role of rDOC in Carbon sequestration now and in future scenarios of climate change. 

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3. Dynamic reworking of marine diatom endometabolomes in response to temperature and a model bacterium

   https://doi.org/10.1128/msystems.01036-25  

   Olofsson, Malin; Uchimiya, Mario; Ferrer-González, Frank X; Schreier, Jeremy E; Powers, McKenzie A; Smith, Christa B; Edison, Arthur S; Moran, Mary Ann (January 2026, mSystems)

   Makhalanyane, Thulani P (Ed.)

   ABSTRACT A large annual carbon flux occurs through the surface ocean’s labile dissolved organic carbon (DOC) pool, with influx dominated by phytoplankton-derived metabolites and outflux by heterotrophic bacterioplankton uptake. We addressed the dynamics of this carbon flow between microbial primary and secondary producers through analysis of theThalassiosira pseudonanaCCMP1335 endometabolome, a proxy for the labile DOC released upon phytoplankton lysis, as temperature and bacterial presence were altered. Diatom strains acclimated at one of three different temperatures (14°C, 20°C, or 28°C) were cultured either axenically or with the bacteriumRuegeria pomeroyiDSS-3, and their endometabolites analyzed by NMR. Median concentration variation between conditions was ~1.5-fold across all identified endometabolites. Those with roles as osmolytes varied most, exhibiting concentration differences up to 170-fold across conditions with the largest variations triggered by the presence/absence of the heterotrophic bacterium. Differential expression observed for diatom metabolite synthesis pathways suggested changes in synthesis rates as a mechanism for endometabolome remodeling. Consistent with expectations of high turnover by heterotrophic bacteria, endometabolite mean lifetimes in a DOC pool were <2 h to 12 h. IMPORTANCEThe role of labile DOC in the transfer of marine carbon between phytoplankton and heterotrophic bacteria was first recognized 40 years ago, yet the identity and dynamics of phytoplankton metabolites entering the labile DOC pool are still poorly known. Using metabolome and transcriptome profiling, we found highly variable composition and concentration of diatom endometabolites, depending on growth conditions and arising over time frames as short as a single growth cycle. This strong response to external conditions, both biotic and abiotic, suggests that the chemical composition of phytoplankton intracellular pools released during lysis shift with ocean conditions. As phytoplankton cell lysis is one of the largest sources of labile dissolved compounds in the ocean, dynamic compositional changes in the metabolites released to heterotrophic bacteria have implications for the fate of surface ocean carbon. 

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4. Hydrothermally Induced Refractory DOC Sinks in the Deep Pacific Ocean

   https://doi.org/10.1029/2025gb008659  

   Hansell, D A; German, C R; Carlson, C A; Druffel, E_R M; Jenkins, W J; Lang, S Q; Toner, B M (September 2025, Global Biogeochemical Cycles)

   Dissolved organic carbon (DOC) constitutes the largest pool of reduced carbon in the global ocean, with important contributions from both recently formed and aged, biologically refractory DOC (RDOC). The mechanisms regulating RDOC transformation and removal remain uncertain though hydrothermal vents have been identified as sources and sinks. This study examines RDOC sinks in the deep Pacific Ocean, highlighting the role of submarine hydrothermal systems. Geochemical survey data from GO‐SHIP and GEOTRACES projects, alongside specific investigations of Pacific hydrothermal systems, suggest that particulate iron introduced by hydrothermal systems plays a key role in scavenging DOC and delivering it to the seafloor, leaving a deficit in the RDOC of the deep ocean. Dilution of the oceanic water column by hydrothermal fluids exhibiting low DOC concentrations likely plays a secondary role. 

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5. Marine heatwaves and disease alter community metabolism and DOC fluxes on a widespread habitat-forming seagrass species (Zostera marina)

   https://doi.org/10.1016/j.scitotenv.2024.177820  

   Egea, Luis G; Jiménez-Ramos, Rocío; English, Mary K; Tomas, Fiona; Mueller, Ryan S (December 2024, Science of The Total Environment)

   Climate change and disease are two major threats to maintaining healthy seagrass habitats. Seagrasses, and the ecosystems they support, play a critical ecological role in global carbon (C) cycles, providing key ecosystem services, such as blue carbon storage. Zostera marina (eelgrass), the most widespread seagrass species globally, is increasingly affected by warming and is also regularly infected by the endophytic pathogen Labyrinthula zosterae. Both stressors negatively impact plant physiology and population distributions, yet the effects of these stressors on C cycling, and particularly on C metabolism and dissolved organic carbon (DOC) fluxes in eelgrass, remain largely unexplored. Through a mesocosm experiment simulating a marine heatwave (MHW) followed by pathogen challenge with L. zosterae, it was observed that the simulated MHW initially decreased daily community DOC fluxes and Net Production Rates (NPR), while not changing Respiration Rates. DOC released into the water column at the end of the MHW also was less bioavailable than DOC from the control treatment. Importantly, community NPR recovered to control levels after the simulated MHW was over, demonstrating the community's resilience to warming. On the other hand, plants challenged with L. zosterae, which caused a significant decrease in aboveground biomass, exhibited significant decreases in DOC and NPR up to 20 days after the infection. These results have important implications in blue carbon processes, given that both stressors significantly impact the quantity and quality of DOC produced by Z. marina communities. These findings also highlight the differing levels of resilience of C cycling in this system by showing that the impacts of the simulated heat wave may be more transient when compared to the effects of disease. 

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