Diazotrophs play a fundamental role in sustaining marine primary production in oligotrophic oceans by alleviating nitrogen limitation, thereby enhancing the Biological Carbon Pump and contributing to the export of carbon into the deep ocean. However, the short-term coupling between diazotroph dynamics, microbial communities and carbon export remains poorly understood because simultaneous high frequency observations thought the water column are scarce. This study investigated the temporal variability of diazotroph abundance, microbial community composition and particulate carbon export during a two-month period in the Western Tropical South Pacific. High frequency sampling of surface waters and mesopelagic marine snow collected at 175 and 500 m was combined with molecular analyses (qPCR and 18/16S rRNA sequencing) and biogeochemical measurements. Seasonal changes in the surface water column were associated with shifts in diazotroph communities and a Chlorophyll-a maximum. 13 days later, carbon export at 175 m increased by 113%. Throughout the 2 months, prokaryotic and eukaryotic communities displayed strong vertical structuring with significant difference between surface and mesopelagic samples. Eukaryotic assemblages suggested that grazing processes at the surface contributed to the microbial composition of sinking marine snow, whereas prokaryotic communities were influenced by the carbon export event, with decreasing diversity and the specialisation of specific taxa during the export event. These results demonstrate that carbon export and associated microbial communities can change over timescales of only a few days, emphasizing the importance of high-frequency, multi-depth observations for improving our understanding of the role of diazotrophs in the biological carbon pump and their future representation in ocean models.
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