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Diatoms are one of the major primary producers in the ocean, responsible annually for ~20% of photosynthetically fixed CO 2 on Earth. In oceanic models, they are typically represented as large (>20 µm) microphytoplankton. However, many diatoms belong to the nanophytoplankton (2–20 µm) and a few species even overlap with the picoplanktonic size-class (<2 µm). Due to their minute size and difficulty of detection they are poorly characterized. Here we describe a massive spring bloom of the smallest known diatom ( Minidiscus ) in the northwestern Mediterranean Sea. Analysis of Tara Oceans data, together with literature review, reveal a general oversight of the significance of these small diatoms at the global scale. We further evidence that they can reach the seafloor at high sinking rates, implying the need to revise our classical binary vision of pico- and nanoplanktonic cells fueling the microbial loop, while only microphytoplankton sustain secondary trophic levels and carbon export. Diatoms are major oceanic primary producers, but some species belonging to the nano- and even picoplankton size are poorly characterized. Here the authors describe a massive spring bloom of the smallest known diatom in the Mediterranean Sea and reveal their general oversight at the global scale.

Water safety is a major concern for public health and for natural environment preservation. We propose to use bacteriophages to develop biosensor tools able to detect human and animal pathogens present in water. For this purpose, we take advantage of the highly discriminating properties of the bacteriophages, which specifically infect their bacterial hosts. The challenge is to use a fluorescent reporter protein that will be synthesized, and thus detected, only once the specific recognition step between a genetically modified temperate bacteriophage and its bacterial host has occurred. To ensure the accuracy and the execution speed of our system, we developed a test that does not require bacterial growth, since a simple 1-hour infection step is required. To ensure a high sensitivity of our tool and in order to detect up to a single bacterium, fluorescence is measured using a portable flow cytometer, also allowing on-site detection. In this study, we have constructed and characterized several \"phagosensor\" prototypes using the HK620 bacteriophage and its host Escherichia coli TD2158 and we successfully adapted this method to Salmonella detection. We show that the method is fast, robust and sensitive, allowing the detection of as few as 10 bacteria per ml with no concentration nor enrichment step. Moreover, the test is functional in sea water and allows the detection of alive bacteria. Further development will aim to develop phagosensors adapted on demand to the detection of any human or animal pathogen that may be present in water.

Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30–50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2 to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteria Prochlorococcus spp. Free O2 levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2 production and consumption by aerobic processes under apparent anoxic conditions. Transcrip-tomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2 production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.

Nitrogen is essential for life but is often a major limiting nutrient for growth in the ocean. Biological dinitrogen fixation is a major source of new nitrogen to surface waters and promotes marine productivity. Yet the fate of diazotroph-derived nitrogen (DDN) in marine ecosystems has been poorly studied, and its transfer to auto- and heterotrophic plankton has not been measured. Here, we use high-resolution nanometer scale secondary ion mass spectrometry (nanoSIMS) coupled with 15N₂ isotopic labelling and flow cytometry cell sorting to examine the DDN transfer to specific groups of natural phytoplankton and bacteria during three diazotroph blooms dominated by the cyanobacterium Trichodesmium spp. in the South West Pacific. During these experiments, 13%±2% to 48%±5% of the fixed 15N₂ was released into the dissolved pool and 6%±1% to 8%±2% of this DDN was transferred to non-diazotrophic plankton after 48 h. The primary beneficiaries of this DDN were diatoms (45%±4% to 61%±38%) and bacteria (22%±27% to 38%±12%), followed by pico-phytoplankton (3%±1% to 21%±14%). The DDN was quickly converted to non-diazotrophic plankton biomass, in particular that of diatoms, which increased in abundance by a factor of 1.4–15 over the course of the three experiments. The single-cell approach we used enabled quantification of the actual transfer of DDN to specific groups of autotrophic and heterotrophic plankton in the surface ocean, revealing a previously unseen level of complexity in the pathways that occur between N₂ fixation and the eventual export of DDN from the photic zone.

Numerical simulations have shown that finescale structures such as fronts are often suitable places for the generation of vertical velocities, transporting subsurface nutrients to the euphotic zone and thus modulating phytoplankton abundance and community structure. In these structures, direct in situ estimations of the phytoplankton growth rates are rare; although difficult to obtain, they provide precious information on the ecosystem functioning. Here, we consider the case of a front separating two water masses characterized by several phytoplankton groups with different abundances in the southwestern Mediterranean Sea. In order to estimate possible differences in growth rates, we measured the phytoplankton diurnal cycle in these two water masses as identified by an adaptive and Lagrangian sampling strategy. A size-structured population model was then applied to these data to estimate the growth and loss rates for each phytoplankton group identified by flow cytometry, showing that these two population parameters are significantly different on the two sides of the front and consistent with the relative abundances. Our results introduce a general method for estimating growth rates at frontal systems, paving the way for in situ exploration of finescale biophysical interactions.

Marine virioplankton, the most abundant biological entities in the ocean, play essential roles in microbial ecology and biogeochemical cycling. This study investigates their biogeography in the Northwest Pacific using enhanced‐resolution flow cytometry and phenotypic diversity analyses. By resolving four consistent viral subclusters across oceanic and coastal waters and detecting a fifth subcluster in the Yellow Sea, we revealed previously unrecognized patterns of viral community structures. Viral abundances ranged from 3.69 × 10⁶ to 17.09 × 10⁶ particles/mL, showing clear coastal‐oceanic differentiation. Environmental gradients, particularly temperature, chlorophyll, and picoplankton abundance, emerged as the primary drivers of virioplankton community structure. These findings underscored the tight coupling between viral populations and their microbial hosts across contrasting marine environments. Phenotypic diversity analysis revealed distinct viral communities in the Luzon Strait, despite comparable abundance patterns to adjacent regions, demonstrating the method's sensitivity in detecting subtle community shifts. This study advances understanding of marine viral biogeography and introduces a robust framework for investigating viral community dynamics. The approach enables high‐throughput screening across large spatial scales while maintaining sensitivity to fine‐scale community variations, offering new possibilities for monitoring viral responses to environmental change in marine ecosystems. Enhanced‐resolution flow cytometry combined with phenotypic diversity analysis reveals four consistent viral subclusters and a fifth restricted to the Yellow Sea across the Northwest Pacific. These results identify a cryptic diversity hotspot in the Luzon Strait and demonstrate how environmental and biological gradients shape large‐scale patterns in marine viral biogeography.

Ciliates are important components in planktonic food webs, but our understanding of their community structures in different oceanic water masses is limited. We report pelagic ciliate community characteristics in three seas: the tropical West Pacific, the Bering Sea and the Arctic Ocean. Planktonic ciliate abundance had “bimodal-peak”, “surface-peak” and “DCM (deep chlorophyll a maximum layer)-peak” vertical distribution patterns in the tropical West Pacific, the Bering Sea and the Arctic Ocean, respectively. The abundance proportion of tintinnid to total ciliate in the Bering Sea (42.6%) was higher than both the tropical West Pacific (7.8%) and the Arctic Ocean (2.0%). The abundance proportion of small aloricate ciliates (10–20 µm size-fraction) in the tropical West Pacific was highest in these three seas. The Arctic Ocean had higher abundance proportion of tintinnids in larger LOD (lorica oral diameter) size-class. Proportion of redundant species increased from the Arctic Ocean to the tropical West Pacific. Our result provided useful data to further understand ecology roles of planktonic ciliates in different marine habitats.

Model simulations and remote sensing observations show that ocean dynamics at fine scales (1–100 km in space, day–weeks in time) strongly influence the distribution of phytoplankton. However, only a few in situ-based studies at fine scales have been performed, and most of them concern western boundary currents which may not be representative of less energetic regions. The PROTEVSMED-SWOT cruise took place in the moderately energetic waters of the western Mediterranean Sea (WMS), in the region south of the Balearic Islands. Taking advantage of near-real-time satellite information, we defined a sampling strategy in order to cross a frontal zone separating different water masses. Multi-parametric in situ sensors mounted on the research vessel, on a towed vehicle and on an ocean glider were used to sample physical and biogeochemical variables at a high spatial resolution. Particular attention was given to adapting the sampling route in order to estimate the vertical velocities in the frontal area also. This strategy was successful in sampling quasi-synoptically an oceanic area characterized by the presence of a narrow front with an associated vertical circulation. A multiparametric statistical analysis of the collected data identifies two water masses characterized by different abundances of several phytoplankton cytometric functional groups, as well as different concentrations of chlorophyll a and O2. Here, we focus on moderately energetic fronts induced by fine-scale circulation. Moreover, we explore physical–biological coupling in an oligotrophic region. Our results show that the fronts induced by the fine-scale circulation, even if weaker than the fronts occurring in energetic and nutrient-rich boundary current systems, maintain nevertheless a strong structuring effect on the phytoplankton community by segregating different groups at the surface. Since oligotrophic and moderately energetic regions are representative of a very large part of the world ocean, our results may have global significance when extrapolated.

After the exponential growth phase, variability in the scattering efficiency of phytoplankton cells over their complete life cycle is not well characterised. Bulk measurements are impacted by senescent cells and detritrus. Thus the analysis of the evolution of the optical properties thanks to their morphological and/or intra-cellular variations remains poorly studied. Using the Cytosense flow cytometer (CytoBuoy b.v., NL), the temporal course of the forward and sideward efficiencies of two phytoplankton species (Thalassiosira pseudonana and Chlamydomonas concordia) were analyzed during a complete life-cycle. These two species differ considerably from a morphological point of view. Over the whole experiment, the forward and sideward efficiencies of Thalassiosira pseudonana were, on average, respectively 2.2 and 1.6 times higher than the efficiencies of Chlamydomonas concordia. Large intra-species variability of the efficiencies were observed over the life cycle of the considered species. It highlights the importance of considering the optical properties of phytoplankton cells as a function of the population growth stage of the considered species. Furthermore, flow cytometry measurements were combined with radiative transfer simulations and biogeochemical and optical measurements. Results showed that the real refractive index of the chloroplast is a key parameter driving the sideward signal and that a simplistic two-layered model (cytoplasm-chloroplast) seems particularly appropriate to represent the phytoplankton cells.

Trait structure is increasingly used in plankton ecology to understand diversity and biogeography. However, our knowledge of microzooplankton (e.g. planktonic ciliates) trait structure and its variation with hydrography is limited. In this study, we analyzed planktonic ciliate trait structure in waters with different hydrography and deep Chlorophyll a maximum (DCM) layers over three seamounts: Yap, Mariana, and Caroline seamounts. Mariana seamount had a lower surface temperature than the Yap and Caroline seamounts. DCM layers over Mariana and Caroline seamounts were deeper than Yap seamount. There was a weak upwelling in upper 50 m around top of Mariana seamount. The ciliate distribution showed bimodal pattern (high abundance appeared in the surface and DCM layers) over three seamounts. At surface layer, the large size-fraction (>30 µm) abundance proportion to aloricate ciliate over Yap seamount (44.4%) was higher than Mariana (32.8%) and Caroline (36.1%) seamounts. For tintinnid abundance proportion to total ciliate, Mariana (12.0%) and Caroline (11.5%) seamounts at about 100-m depth were higher than that of Yap seamount (6.4%). Vertically, tintinnid could be divided into 4 groups over the three seamounts. At 30-m depth, group I (species occurring from surface to 100 m only) was dominant component over Yap and Caroline seamounts, while group IV (species occurring at every depth) changed into dominant component over Mariana seamount, the weak upwelling might be the reason. Salpingella faurei was the top dominant species, which corresponded to deeper DCM layers over Mariana and Caroline seamounts. Our results showed that the upwelling and the deeper DCM could influence the planktonic ciliate trait structure.