Synechococcus are the most abundant and widely distributed picocyanobacteria in the ocean. The salt-wedge type of estuary possesses the complete horizontal and vertical gradient of salinity together with other physical and chemical parameters. In order to reveal whether such a complex environmental gradient harbors a high diversity of Synechococcus, we investigated the abundance, taxonomic composition and pigment genetic diversity of Synechococcus in surface and bottom waters across the salinity gradient in a salt-wedge estuary by flow cytometric analysis and pyrosequencing of the rpoC1 gene and cpcBA operon (encoding phycocyanin). Synechococcus were ubiquitously distributed in the studied region, with clear spatial variations both horizontally and vertically. The abundance and diversity of Synechococcus were low in the freshwater-dominated low salinity waters. By pyrosequencing of the rpoC1 gene, we have shown that with the increase of salinity, the dominant Synechococcus shifted from the freshwater Synechococcus to the combination of phylogenetic subcluster 5.2 and freshwater Synechococcus, and then the strictly marine subcluster 5.1 clade III. Besides, the composition of Synechococcus assemblage in the deep layer was markedly different from the surface in the stratified waters (dissimilarities: 40.32%-95.97%, SIMPER analysis). High abundance of clade III Synechococcus found in the brackish waters may revise our previous understanding that strains of this clade prefers oligotrophic environment. Our data also suggested that both the phylogenetic subcluster 5.3 Synechococcus, a lineage that was not well understood, and subcluster 5.1 clade I, a typical cold water lineage, were widely distributed in the bottom layer of the estuary. Clade I detected in the studied region was mainly contributed by subclade IG. Analysis of the cpcBA operon sequences revealed niche partitioning between type 1 and type 3 Synechococcus, with type 2 distributed broadly across the whole environmental gradients. Our results suggest that the salt wedge estuary provides various niches for different lineages of Synechococcus, making it an environment with high Synechococcus diversity compared with adjacent freshwater and shelf sea environments.

Phytoplankton are diverse and abundant as primary producers in the ocean, with diversity and community compositions varying spatially. How fundamental processes (e.g., selection, dispersal, and drift) regulate their global biogeography remains to be comprehensively explored.

Biological nitrogen fixation is increasingly recognized as an important source of new nitrogen in a warming ocean. However, the basin‐scale spatiotemporal distribution of nitrogen‐fixing organisms (diazotrophs) in the ocean and its controlling environmental factors remain unclear. Here we examined the basin‐scale seasonal distribution patterns of major diazotrophs (filamentous cyanobacterial Trichodesmium, unicellular cyanobacterial UCYN‐A1, and proteobacterial Gamma‐A) in surface waters of the North Pacific from 2014 to 2016 with unprecedented coverage and resolution. In general, UCYN‐A1, Trichodesmium, and Gamma‐A were abundant during spring‐autumn, summer‐autumn, and spring respectively. Regarding latitudinal patterns of abundance, UCYN‐A1 showed dome shape; Trichodesmium was gradually decreasing from low‐ to high‐latitude regions; and Gamma‐A did not show a clear pattern, which were coincident with the distinct correlations between the diazotrophs and temperature. All three diazotrophs were abundant (reached 10⁶–10⁷ nifH gene copy number L⁻¹) in the North Pacific transition zone and subtropical gyre, where the cyanobacterial diazotrophs were more abundant in both the western and eastern North Pacific than in the central North Pacific. The diazotroph abundance in the western North Pacific was positively correlated with eddy kinetic energy and sea surface height anomaly, which implies an enhancement of diazotrophs in mesoscale eddies associated with the western boundary current Kuroshio and its extension. The cyanobacterial diazotrophs were positively correlated with wind stress curl, a measurable parameter of wind‐driven upwelling, in the eastern North Pacific. Our study refines the biogeography of three major diazotrophs and highlights the importance of physical forcing in mediating their dynamics.

Marine phytoplankton is one of the most important nodes in global biogeochemical cycle. Deciphering temperature-associated marine phytoplankton cell stoichiometric changes and the underlying molecular mechanisms are therefore of great ecological concerns.

Recognizing the prokaryotic community and its functions in hypoxic (>5 to ≤60 μM O ₂ ) environments before further expansion of OMZs is critical. We demonstrate the prokaryotic community and its potential functions in nitrogen metabolism in the Bay of Bengal (BoB), where oxygen concentration is barely above suboxic level.

In this study, we used miTAG approach to analyze the distributional pattern and fine‐scale genetic diversity of the ammonia oxidizing archaea (AOA) lineages in the global oceans with the metagenomics data sets of the Tara Oceans global expedition (2009–2013). Using the ammonium monooxygenase alpha subunit gene as a biomarker, the AOA communities in the global oceans were recovered with highly diverse operational taxonomic units that affiliated to previously defined clades, including water column A (WCA), water column B (WCB), and SCM1‐like clades. In general, the AOA communities were obviously segregated with depth (except the upwelling regions), and the communities in the euphotic zones were more heterogeneous than in the mesopelagic zones (MPZs). The WCA distributed more evenly and widely in the euphotic zone and MPZs, while WCB and SCM1‐like clade mainly distributed in MPZ and high‐latitude waters, respectively. At fine‐scale genetic diversity, SCM1‐like and 2 WCA subclades showed distinctive niche separations of distributional pattern. We further divided the AOA subclades into ecological significant taxonomic units (ESTUs), which were delineated from the distribution pattern of their corresponding subclades. For example, ESTUs of WCA have different correlations with depth, nitrate to silicate ratio, and salinity; SCM1‐like A was negatively correlated with irradiation, whereas other SCM1‐like ESTUs preferred low‐temperature and high‐nutrient conditions. Our result showed that the previously defined AOA clades and ecotypes consist of highly diverse sublineages, whose diversity might be overlooked in the past. The distribution patterns of different ESTUs imply their ecophysiological characteristics and potential roles in biogeochemical cycling.