Water aging and the quality of organic carbon sources drive niche partitioning of the active bathypelagic prokaryotic microbiome Sebastián, Marta Sánchez Fernández, Pablo Salazar, Guillem Álvarez Salgado, Xosé Antón Reche Cañabate, Isabel G. Morán, Xosé Anxelu Sala, Maria Montserrat Duarte, Carlos Acinas, Silvia G. Gasol Piqué, Josep María Due to the scarcity of organic matter (OM) sources in the bathypelagic (1000–4000 m depth), prokaryotic metabolism is believed to be concentrated on particles originating from the surface. However, the structure of active bathypelagic prokaryotic communities and how it changes across environmental gradients remains unexplored. Using a combination of 16S rRNA gene and transcripts sequencing, metagenomics, and substrate uptake potential measurements, here we aimed to explore how water masses aging and the quality of OM influence the structure of the active microbiome, and the potential implications for community function. We found that the relative contribution of taxa with a free-living lifestyle to the active microbiome increased in older water masses that were enriched in recalcitrant OM, suggesting that these prokaryotes may also play a substantial role in the bathypelagic metabolism of vast areas of the ocean. In comparison to particle-associated prokaryotes, free-living prokaryotes exhibited lower potential metabolic rates, and harbored a limited number of twocomponent sensory systems, suggesting they have less ability to sense and respond to environmental cues. In contrast, particle-associated prokaryotes carried genes for particle colonization and carbohydrate utilization that were absent in prokaryotes with a free-living lifestyle. Consistently, we observed that prokaryotic communities inhabiting older waters displayed reduced abilities to colonize particles, and higher capabilities to use complex carbon sources, compared to communities in waters with a higher proportion of labile OM. Our results provide evidence of regionalization of the bathypelagic active prokaryotic microbiome, unveiling a niche partitioning based on the quality of OM. 2024-04-26T08:45:22Z 2024-04-26T08:45:22Z 2023-02-03 journal article Sebastián, M., Sánchez, P., Salazar, G., Álvarez-Salgado, X.A., Reche, I., Morán, X.A.G., Sala, M.M., Duarte, C.M., Acinas, S.G. and Gasol, J.M. (2024), Water aging and the quality of organic carbon sources drive niche partitioning of the active bathypelagic prokaryotic microbiome. Limnol Oceanogr, 69: 562-575. https://doi.org/10.1002/lno.12505 https://hdl.handle.net/10481/91176 10.1002/lno.12505 eng http://creativecommons.org/licenses/by-nc/4.0/ open access Atribución-NoComercial 4.0 Internacional John Wiley & Sons