Diel and eddy driven changes in microbial gene expression and biogeochemistry in the oceanic chlorophyll maximum

Oceanic microorganisms can rapidly respond to environmental variability. Determining how physical and biological processes control microbial distributions, abundances, and metabolic dynamics is challenging. Here, we used autonomous underwater vehicles capable of Lagrangian feature tracking and in situ sampling, in combination with ship-based measurements, to examine diel to weekly scale changes in microbial transcription and biogeochemistry in the deep chlorophyll maximum (DCM) of a mesoscale cyclonic eddy. Nearly 20% of total transcript expression showed diel periodicity, highlighting the importance of the diurnal cycle on phytoplankton metabolism in the dim waters of the DCM. Eddy-induced isopycnal uplift increased nutrient concentrations and caused upward displacement of the DCM, driving increased picoeukaryotic cell abundances and transcriptional activity of nitrate-incorporating photoautotrophs. As the eddy weakened, the DCM deepened and transcriptional activity shifted towards chemolithoautotrophic ammonia-oxidizing archaea. The temporal dynamics observed demonstrate how plankton communities rapidly respond to both diel variation and stochastic mesoscale disturbances.