High contribution of dark dissolved inorganic carbon uptake to microbial carbon cycling in a shallow Mediterranean basin

Dissolved inorganic carbon (DIC) fixation is arguably the most relevant process for Earth’s biogeochemistry. Photoautotrophs dwelling in the sunlit ocean are responsible for 50% of the planetary primary production. Alongside, chemoautotrophic DIC fixation occurs throughout the water column, yielding a carbon flux doubling the organic carbon advected by the world’s rivers into the ocean. Among the vast array of chemoautotrophic metabolic pathways, nitrification has important biogeochemical implications, driving nitrogen cycling and chemosynthesis throughout the water column. Nonetheless, DIC fixation fueling heterotrophic processes represents a significant yet underappreciated CO2 flux in marine carbon cycling. Virtually all heterotrophs express various carboxylases catalysing the incorporation of CO2 into organic molecules. Among these pathways, anaplerotic processes are often prevalent, contributing to 1%–8% of the cell carbon biomass. Aiming to decipher the relevance of dark DIC (dDIC) fixation in shallow temperate waters, we explored its interannual patterns in natural microbial communities of the northern Adriatic Sea for 2.5 years at monthly intervals, complementing rate measurements with microbial community dynamics through 16S rRNA gene amplicon sequencing. Furthermore, we quantified the abundance of the archaeal ammonia monooxygenase α-subunit (amoA) to assess the role of chemoautotrophic processes. Biogeochemical contextualisation of our data showed that most of the measured dDIC uptake was fuelling heterotrophic processes, especially during summer, possibly linked to i) an enhanced metabolic effort towards the degradation of refractory organic matter and ii) photoheterotrophy-mediated DIC uptake. Nonetheless, back-calculations of ammonia oxidation and nitrite accumulation rates showed that the contribution of nitrification to total dDIC fixation, ranged between 7.87% ± 2.85% and 22.50% ± 10.75% in surface and bottom samples, respectively. Therefore, a considerable fraction of wintertime dDIC uptake rates was potentially due to autotrophic processes fuelled by ammonia oxidation putatively performed by the archaeon Candidatus Nitrosopumilus. Our time-series approach highlighted possible seasonal differences in autotrophic vs. heterotrophic DIC uptake in shallow temperate waters. While heterotrophic processes likely prevail during summer in a mixture of anaplerotic and photoheterotrophic pathways, ammonia oxidation-mediated chemoautotrophy appears to be relatively important during winter, fuelling a non-negligible fraction of the bulk dDIC uptake and determining a recurrent nitrite accumulation impacting shallow temperate waters' biogeochemistry.