Key Expoitable Results (KERs)

The Mississippi River (MR) is the largest source of freshwater and nutrients to the Gulf of Mexico (GoM), strongly influencing stratification, primary production, and plankton organization. The interaction between buoyant plume waters and denser shelf waters in the northern Gulf of Mexico (nGoM) generates sharp density gradients that can promote fine-scale biological aggregation. We investigated how hydrographic structure associated with the MR plume controls the vertical distribution of plankton during May 2017 using an integrated instrumentation suite that included an in situ digital holographic imaging system (HOLOCAM) coupled with CTD and optical sensors. Phytoplankton thin layers were repeatedly detected at plume-edge stations within or immediately above a compressed pycnocline formed by bottom-trapped saline wedges. These layers were 1.2–3.5 m thick and exhibited chlorophyll-a concentrations up to threefold higher than background levels. The assemblage was dominated by chain-forming diatoms, particularly Chaetoceros debilis and C. socialis, whose local abundance maxima coincided with chlorophyll peaks. In contrast, copepods, appendicularians, and other zooplankton were broadly distributed throughout the upper water column and rarely aggregated within the layers. Redundancy analysis indicated that chlorophyll concentration and stratification intensity were primary drivers of community structure across stations. Satellite imagery revealed rapid short-term variability in plume extent, helping explain differences in stratification and thin layer development among sampling days. Our results demonstrate that salt-wedge dynamics at the plume–shelf interface constitute a key physical mechanism governing transient phytoplankton thin layer formation in the nGoM, while zooplankton responses remain weakly coupled at the temporal scales resolved here.

Climate-induced distribution changes are particularly challenging for fisheries targeting fish populations shared between exclusive economic zones (EEZs) and the high seas, known as straddling stocks. Here, we combine multiple datasets and ecosystem modeling to identify the presence of straddling stocks worldwide and consider the management implications of climate change–driven shifts. We identify 347 straddling stocks across 67 species, including both highly migratory and less mobile species. Our results suggest that regardless of the climate change scenario, at least 37% and 54% of stocks are projected to shift between EEZs and the high seas, by 2030 and 2050, respectively. More stocks are expected to shift toward the high seas, and highly migratory stocks are projected to shift across Regional Fisheries Management Organizations (RFMOs). Coastal states and RFMOs require to revise governance frameworks to support sustainable and equitable adaptation to shifting stocks. Developing such strategies requires cooperation between management bodies within EEZs and the high seas.

Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15 339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached prokaryotes and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine prokaryotic evolution through HGT.

Tropicalisation and other climate-induced range shifts are rapidly restructuring global biodiversity patterns. The detection of range shifts is often complex and requires big-data approaches. Environmental DNA (eDNA) monitoring is emerging as a powerful method for assessing biodiversity changes at unprecedented spatial and temporal resolutions. While eDNA-based methodologies continue to evolve, the impacts of species traits and eDNA dynamics are rarely measured, though they likely affect our eDNA data interpretation. Here we combine diverse methodologies to better understand processes affecting eDNA data and to elucidate how eDNA dispersal influences the interpretation of eDNA results in a tropicalisation context.

Particles sinking from the surface to the deep ocean play a key role in the biological carbon pump, whose efficiency depends partly on sinking velocities. Over the last decade, in situ imaging has enabled critical advances in our understanding of particle dynamics in the ocean. Yet, in situ velocity measurements are scarce and often inferred only from the bulk population of particles. Here, we introduce the VisuTrap, a new tool to measure in situ velocities of marine particles. It consists of an Underwater Vision Profiler 6 (UVP6) camera inserted into different types of sediment traps, which isolate a volume of water. Continuous image acquisition during shortterm or long-term deployments enables reconstruction of particle tracks and estimation of their in situ vertical velocities. We detail the configuration and special UVP6 settings for this application, as well as the image processing and track analysis pipeline. Then, we present results from several experiments in the Mediterranean Sea to illustrate the VisuTrap's use as a new approach to understand the dynamical behavior of marine particles in situ. In light of the broad range of morphological data generated by the UVP6, we discuss technical additions to refine in situ velocity measurements and the possibility of integrating such data into carbon flux assessments.

Ocean biogeochemical models underpin projections of future marine ecosystem change, including anticipated shifts in the biological carbon pump (BCP) and broader biogeochemical cycles. However, their outputs remain highly sensitive to model complexity and parameterisation choices. Here, we evaluate five configurations of the Pelagic Interaction Scheme for Carbon and Ecosystem Studies (PISCES) to quantify intramodel variability in net primary productivity (NPP), carbon export (Cexp), and export efficiency (e-ratio) over the 21st century under the high emissions RCP8.5 scenario. The tested PISCES configurations differed from the standard model through distinct modifications to phytoplankton growth processes, but are forced by identical physical variables, representing an ensemble opportunity. All configurations resolve NPP and Cexp within the range of remote-sensing variability. The more complex Quota-based configurations produce 15–21 (10–18) Pg C yr−1 more NPP than the simpler Monod-quota models in the reference (future) period, but this increase, driven by elevated small phytoplankton biomass, does not enhance Cexp, yielding lower e-ratios (0.14–0.17) than in the Monod-quota configurations (∼0.25). The introduction of a picophytoplankton functional type (PFT) emerges as one of the most influential parameterisation choices. It drives opposing future NPP responses between 30–60° N/S, an increase in the Monod-quota configurations versus a decline in the Quota-based ones, as well as contrasting latitudinal trends in Cexp within the same region. Other parameterisations, such as a low-iron scheme, an added diazotroph PFT, and explicit manganese cycling, exert more modest, regionally confined effects under high emissions scenarios, influencing NPP and Cexp primarily at biome scales rather than driving large-scale divergence in model behaviour.

Ocean currents are a key driver of plankton dispersal across the oceanic basins. However, species specific temperature constraints may limit the plankton dispersal. We propose a methodology to estimate the connectivity pathways and timescales for plankton species with given constraints on temperature tolerances, by combining Lagrangian modeling with network theory. We demonstrate application of two types of temperature constraints: thermal niche and adaptation potential and compare it to the surface water connectivity between sample stations in the Atlantic Ocean. We find that non-constrained passive particles representative of a plankton species can connect all the stations within three years at the surface with pathways mostly along the major ocean currents. However, under thermal constraints, only a subset of stations can establish connectivity. Connectivity time increases marginally under these constraints, suggesting that plankton can keep within their favorable thermal conditions by advecting via slightly longer paths. Effect of advection depth on connectivity is observed to be sensitive to the width of the thermal constraints, along with decreasing flow speeds with depth and possible changes in pathways.

Sexual reproduction is a nearly universal characteristic of the eukaryotic life cycle, yet it is rarely observed in natural populations of micro-eukaryotes. Sex is particularly relevant for diatoms, a key group of marine and freshwater phytoplankton, where sexual reproduction counters a progressive cell size reduction due to cellular division. Here, we leveraged controlled sex transcriptome experiments of four diatom species to develop a robust method for in situ monitoring of sexual reproduction events. The resulting panel of conserved marker genes was validated for specificity and sensitivity using metatranscriptomic profiling of a natural estuarine community undergoing massive sexual reproduction of multiple species in response to increased salinity. Analysis of metatranscriptomic data linked with Metagenome-Assembled Genomes from the Tara Oceans expedition revealed widespread and coordinated expression of these markers across nine diatom genera, complemented by observations of sexual stages in automated imaging resources. Our results reveal that diatom sexual reproduction is more widespread in the global ocean than previously thought, encompassing both dominant bloom-forming species and rare taxa. Our panel of markers to detect sexual reproduction in natural environments paves the road to better understand the interplay between endogenous and environmental controls of this pivotal process, essential for the diatoms’ evolutionary success.