AtlantECO-KER-AM-2

The Southern Ocean hosts a high degree of endemic plants and animals, yet the genetic diversity, function and evolutionary relationships of microbial communities remains unexplored, particularly in the aphotic “dark ocean,” where microbes play critical roles in local and global food webs. Here, we performed a metagenomic analysis of 44 aphotic seawater samples collected from multiple depths across the Southern Ocean to characterize the functional gene repertoire of these microbial communities. Of the 11,896,546 species-level unigenes1 identified, ~ 87% appear specific to the Southern Ocean and are distinct from other major ocean datasets. We reconstructed 502 bacterial and 108 archaeal metagenome-assembled genomes (MAGs), revealing widespread capacities for inorganic carbon fixation via the Calvin cycle, the hydroxypropionate-hydroxybutyrate cycle, and the 3-hydroxypropionate bi-cycle. Metapangenomic analyses indicated that several genes involved in the oxidation of reduced nutrients including ammonia, nitrite, and thiosulfate, are shared across the aphotic water column through horizontal gene transfer. MAGs belonging to Acidimicrobia, Gammaproteobacteria, and SAR324 were abundant throughout the dark Southern Ocean and showed potential for both chemolithoautotrophy and carbohydrate degradation, suggesting mixotrophy as a key metabolic strategy. Together, these findings reveal the unique functional and genomic diversity of deep Southern Ocean microbiomes and provide insights into their roles in carbon cycling within one of Earth’s most important marine carbon sinks.

Marine plankton are key drivers of ocean productivity and global carbon cycling, yet their quantitative biogeography remains poorly characterized. Environmental genomic datasets are inherently compositional, restricting analyses to relative abundances and limiting their integration into ecological and biogeochemical models. Here we combine DNA mass measurements, filtered seawater volumes, and metagenomic relative abundances to generate absolute estimates of cell concentrations and carbon biomass of plankton across the global ocean. Leveraging thousands of samples, this approach provides quantitative estimates for hundreds of eukaryotic and thousands of prokaryotic environmental genomes, unveiling ecological associations not captured by compositional data. Using the psbO marker gene, we reconstruct quantitative biogeographies of photosynthetic lineages and, through global-scale modeling, project their distributions to generate quantitative maps of phytoplankton communities across the world’s ocean. By bridging genomic data with biogeochemical metrics, this study provides novel resources for integrating plankton at genomic resolution into next-generation biogeochemical models.

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.