Quantitative metatranscriptomics and biogeochemical rate measurements reveal microbial pathways driving carbon and nitrogen cycles in an Arctic coastal lagoon

Abstract Microbial communities in Arctic coastal lagoons mediate nitrogen and carbon cycling at the terrestrial–marine interface of these rapidly changing ecosystems. To investigate these microbial processes, we measured gene expression, nitrification, and inorganic carbon assimilation in waters of Elson Lagoon on the Beaufort Sea coast under ice cover (April), during spring break‐up (July), and in open water (August). Quantitative metatranscriptomics with internal controls quantified per‐liter transcript abundances alongside in situ light and dark 15 N‐ammonium, 15 N‐urea, and 13 C‐bicarbonate stable isotope tracer incubations. Nitrification was only detectable during ice cover, showing high rates for Arctic coastal systems and evidence of light inhibition. Although carbon assimilation was relatively low during ice cover, dark carbon assimilation accounted for nearly half of total uptake, matching estimates of chemoautotrophic potential based on nitrification. Microbial gene expression also shifted seasonally in abundance and function. Transcripts for nitrification peaked during ice cover when genes for ammonia oxidation and 3‐HP/4‐HB carbon fixation were primarily expressed by archaeal genus Nitrosopumilus , while those for nitrite oxidation and reverse TCA carbon fixation were expressed by bacterial phylum Nitrospinota. During break‐up and open water, expression shifted toward urea metabolism, nitrogen assimilation, Calvin Cycle carbon fixation, and anaplerotic pathways. These shifts highlight the seasonality of microbial metabolic strategies and reveal distinct functional shifts across the Arctic lagoon seasonal cycle. The findings suggest that ongoing warming and declining ice cover may reduce chemoautotrophic activity and alter nitrogen and carbon cycling under future conditions, with implications for nutrient dynamics and primary production in Arctic coastal ecosystems.