Quantifying nitrogen assimilation in the deep ocean: urea is an important nitrogen source for bathypelagic microbial communities

Nitrogen is an essential element for life, and its availability can regulate microbial biomass production in the oceans. In particular, urea and ammonium have been described as important nitrogen sources sustaining marine microbial activity in the photic layer of the oceans. However, how these molecules influence cell activity in the deep ocean is unclear, and the variability in their uptake rates with depth is largely unknown. In this study, combining cell-specific ¹⁵N uptake using nanoscale Secondary Ion Mass Spectrometry (nanoSIMS) with network analysis of 16S rRNA sequencing, we tested the uptake rates of ¹⁵N-urea, -ammonium and -amino acids in water from two vertical transects (50 m to 3000 m and 50 m to 4000 m water depth) collected in the northeast Pacific Ocean. Our results show the uptake of amino acids and ammonium peak in the photic zone in both transects. On the contrary, urea uptake rates were more variable and showed high rates in deep waters, with rates up to 2.7 10^-3 fg N µm^-3, 9 times higher than that for ammonium at the same depth. Furthermore, urea derived N was incorporated by up to 70% of the cells in the deep-ocean, highlighting its importance fueling microbial activity in the bathypelagic zone. Interestingly, urea uptake was inversely related to in situ ammonium concentration (rates were consistently higher when ammonium concentrations were low), suggesting that urea may represent a more important microbial source of nitrogen when other N compounds are scarce. Network analysis of 16S rRNA and in situ nutrient concentration showed that Thaumarchaeota, Gammaproteobacteria and Marinimicrobia groups were strongly correlated with urea in situ concentrations. These results highlight the importance of urea as a nitrogen source, particularly in the deep ocean where the uptake and potential recycling of urea by groups such as Thaumarchaeota may be key to sustaining microbial activity.