Microbial plankton in southern Hudson Bay and James Bay in late summer

Hudson Bay and James Bay, on the southern margin of the Arctic, are warming and freshening as river discharge increases and surrounding permafrost thaws, yet their microbial plankton remain poorly described, and James Bay and the waters around the Belcher Islands have never been surveyed with environmental DNA. We conducted the first dedicated DNA-based survey of eukaryotic and prokaryotic plankton in southern Hudson Bay and James Bay, sequencing 18S rRNA (V9) and 16S rRNA (V4) gene amplicons from 72 samples collected at 51 stations in August 2022 and 2023. Hierarchical clustering resolved nine distinct communities; the primary division separated surface James Bay from Hudson Bay, with further structuring by year, distance to coast, depth, and riverine influence. Temperature, salinity, depth, and distance to coast together explained 31% of community variation (distance-based redundancy analysis), and threshold indicator taxa analysis placed an abrupt community-level change in offshore surface waters at 55.3 N and a salinity of ~24.5. Across this boundary, primary producers shifted from large Chaetoceros diatoms in Hudson Bay to the picoplanktonic green alga Picochlorum and the cyanobacterium Cyanobium in James Bay, while large Gyrodinium dinoflagellates and Calanus copepods gave way to Gymnodinium, Pseudocalanus, and small cercozoans and ciliates. Heterotrophic bacteria in Hudson Bay were dominated by Proteobacteria, Bacteroidota, and Verrucomicrobiota, likely using diatom- and dinoflagellate-derived organic matter, whereas Actinomycetota and Planctomycetota dominated James Bay, likely using cyanobacterial and terrestrial dissolved organic matter. Prokaryotic diversity was highest in riverine, estuarine, and James Bay waters and declined northward and seaward. We also report the first strong presence of marine Synechococcus CC9902 in Hudson Bay and identify cosmopolitan bacteria that provide a baseline for future monitoring. These results suggest that continued freshening of the Hudson Bay Complex will favour smaller primary producers and a stronger microbial loop, and that ecosystem shifts may occur abruptly once surface waters cross a salinity threshold.