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19 pages, 6 figures, 3 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmars.2021.673171/full#supplementary-material ; Understanding the factors that modulate prokaryotic assemblages and their niche partitioning in marine environments is a longstanding challenge in marine microbial ecology. This study analyzes amplicon sequence variant (ASV) diversity and co-occurrence of prokaryotic (Archaea and Bacteria) communities through coastal-oceanic gradients in the NW Iberian upwelling system and adjacent open-ocean (Atlantic Ocean). Biogeographic patterns were investigated in relation with environmental conditions, mainly focusing on the optical signature of the dissolved organic matter (DOM). Alpha- and beta-diversity were horizontally homogeneous [with the only exception of Archaea (∼1700 m depth), attributed to the influence of Mediterranean water, MW], while beta-diversity was significantly vertically stratified. Prokaryotic communities were structured in four clusters (upper subsurface, lower subsurface, intermediate, and deep clusters). Deep (>2000 m) archaeal and bacterial assemblages, and intermediate (500-2000 m) Bacteria (mainly SAR202 and SAR406), were significantly related to humic-like DOM (FDOM-M), while intermediate Archaea were additionally related to biogeochemical attributes of the high-salinity signature of MW. Lower subsurface (100-500 m) Archaea (particularly one ASV belonging to the genus Candidatus Nitrosopelagicus) were mainly related to the imprint of high-salinity MW, while upper subsurface (≤100 m) archaeal assemblages (particularly some ASVs belonging to Marine Group II) were linked to protein-like DOM (aCDOM254). Conversely, both upper and lower subsurface bacterial assemblages were mainly linked to aCDOM254 (particularly ASVs belonging to Rhodobacteraceae, Cyanobacteria, and Flavobacteriaceae) and nitrite concentration (mainly members of Planctomycetes). Most importantly, our analysis unveiled depth-ecotypes, such as the ASVs MarG.II_1 belonging to the archaeal deep cluster (linked to FDOM-M) and MarG.II_2 belonging to the upper subsurface cluster (related to FDOM-T and aCDOM254). This result strongly suggests DOM-mediated vertical niche differentiation, with further implications for ecosystem functioning. Similarly, positive and negative co-occurrence relationships also suggested niche partitioning (e.g., between the closely related ASVs Thaum._Nit._Nit._Nit._1 and _2) and competitive exclusion (e.g., between Thaum._Nit._Nit._Nit._4 and _5), supporting the finding of non-randomly, vertically structured prokaryotic communities. Overall, differences between Archaea and Bacteria and among closely related ASVs were revealed in their preferential relationship with compositional changes in the DOM pool and environmental forcing. Our results provide new insights on the ecological processes shaping prokaryotic assembly and biogeography ; Funding for sampling and analysis was provided by the projects "Fuentes de materia orgánica y diversidad funcional del microplancton en las aguas profundas del Atlántico Norte" (MODUPLAN, Ref. CTM2011-24008-MAR, 2012-2015, Plan Nacional I+D+i), and "Deep Standard Oceanographic Sections monitoring program RADIALES-PRODUNDOS," funded by the Instituto Español de Oceanografía (IEO). This work was partly funded by European Union Atlantic Area Interreg project iFADO (EAPA/165_2016) and from the Axencia Galega de Innovación (GAIN, Xunta de Galicia, Spain). TR-R was supported by the MICINN program "Personal Técnico de Apoyo a la Investigación" (PTA, Ref. PTA2015-10948-I) and the project iFADO. MN-C was funded by the projects HOTMIX and FERMIO (MINECO, CTM2011–30010–C02 MAR and CTM2014-57334-JIN, respectively), both co-financed with FEDER funds. AA was funded by grant REMEI (CTM2015-70340-R) from the Spanish Ministry of Economy, Industry and Competitiveness, and Grant 2017SGR/1568 from the CIRIT-Generalitat de Catalunya to Consolidated Research Groups ; With the institutional support of the 'Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S) ; Peer reviewed

The effect of inorganic nutrients on planktonic assemblages has traditionally relied on concentrations rather than estimates of nutrient supply. We combined a novel dataset of hydrographic properties, turbulent mixing, nutrient concentration, and picoplankton community composition with the aims of (i) quantifying the role of temperature, light, and nitrate fluxes as factors controlling the distribution of autotrophic and heterotrophic picoplankton subgroups, as determined by flow cytometry, and (ii) describing the ecological niches of the various components of the picoplankton community. Data were collected at 97 stations in the Atlantic Ocean, including tropical and subtropical open-ocean waters, the northwestern Mediterranean Sea, and the Galician coastal upwelling system of the northwest Iberian Peninsula. A generalized additive model (GAM) approach was used to predict depth-integrated biomass of each picoplankton subgroup based on three niche predictors: sea surface temperature, averaged daily surface irradiance, and the transport of nitrate into the euphotic zone, through both diffusion and advection. In addition, niche overlap among different picoplankton subgroups was computed using nonparametric kernel density functions. Temperature and nitrate supply were more relevant than light in predicting the biomass of most picoplankton subgroups, except for Prochlorococcus and low-nucleic-acid (LNA) prokaryotes, for which irradiance also played a significant role. Nitrate supply was the only factor that allowed the distinction among the ecological niches of all autotrophic and heterotrophic picoplankton subgroups. Prochlorococcus and LNA prokaryotes were more abundant in warmer waters (> 20°C) where the nitrate fluxes were low, whereas Synechococcus and high-nucleic-acid (HNA) prokaryotes prevailed mainly in cooler environments characterized by intermediate or high levels of nitrate supply. Finally, the niche of picoeukaryotes was defined by low temperatures and high nitrate supply. These results support the key role of nitrate supply, as it not only promotes the growth of large phytoplankton, but it also controls the structure of marine picoplankton communities. ; We thank the officers and crew of the research vessels Hespérides, Sarmiento de Gamboa, Mytilus, Ramon Margalef and Lura for their help during the cruises. We are also very grateful to Fátima Eiroa for the flow cytometry analysis in the NICANOR, HERCULES1, HERCULES2, HERCULES3, and ASIMUTH cruises. Finally, we would like to thank Julia Uitz and the two anonymous reviewers for their valuable comments on the paper. This research was supported by the Spanish Ministry of Economy and Competitiveness (MINECO) through projects CTM2012-30680 to Beatriz Mouriño, CTM2008-0626I-C03-01 to Mikel Latasa, REN2003-09532-C03-01 to Ramiro Varela Benvenuto, CTM2004-05174-C02 to Emilio Marañón, and CTM2011-25035 to Pedro Cermeño; by the Galician government through grants 09MMA027604PR to Manuel Ruiz Villareal and EM2013/021 to Beatriz Mouriño; by the Instituto Español de Oceanografia (IEO) through the time series project RADIALES coordinated by Antonio Bode and by the 7th Framework Programme of the European Commission through grant FP7 SPACE.2010.1.1-01 261860 to Manuel Ruiz Villareal. Jose Luis Otero Ferrer acknowledges the receipt of a FPI contract from MINECO (CTM2012-30680) and Bieito Fernádez Castro a Juan de La Cierva Formación fellowship (FJCI-641 2015-25712, Ministerio de Economía y Competitividad, Spanish government).

22 pages, 4 tables, 5 figures ; The effect of inorganic nutrients on planktonic assemblages has traditionally relied on concentrations rather than estimates of nutrient supply. We combined a novel dataset of hydrographic properties, turbulent mixing, nutrient concentration, and picoplankton community composition with the aims of (i) quantifying the role of temperature, light, and nitrate fluxes as factors controlling the distribution of autotrophic and heterotrophic picoplankton subgroups, as determined by flow cytometry, and (ii) describing the ecological niches of the various components of the picoplankton community. Data were collected at 97 stations in the Atlantic Ocean, including tropical and subtropical open-ocean waters, the northwestern Mediterranean Sea, and the Galician coastal upwelling system of the northwest Iberian Peninsula. A generalized additive model (GAM) approach was used to predict depth-integrated biomass of each picoplankton subgroup based on three niche predictors: sea surface temperature, averaged daily surface irradiance, and the transport of nitrate into the euphotic zone, through both diffusion and advection. In addition, niche overlap among different picoplankton subgroups was computed using nonparametric kernel density functions. Temperature and nitrate supply were more relevant than light in predicting the biomass of most picoplankton subgroups, except for Prochlorococcus and lownucleic- acid (LNA) prokaryotes, for which irradiance also played a significant role. Nitrate supply was the only factor that allowed the distinction among the ecological niches of all autotrophic and heterotrophic picoplankton subgroups. Prochlorococcus and LNA prokaryotes were more abundant in warmer waters ( > 20 C) where the nitrate fluxes were low, whereas Synechococcus and high-nucleic-acid (HNA) prokaryotes prevailed mainly in cooler environments characterized by intermediate or high levels of nitrate supply. Finally, the niche of picoeukaryotes was defined by low temperatures and high nitrate supply. These results support the key role of nitrate supply, as it not only promotes the growth of large phytoplankton, but it also controls the structure of marine picoplankton communities ; This research was supported by the Spanish Ministry of Economy and Competitiveness (MINECO) through projects CTM2012-30680 to Beatriz Mouriño, CTM2008-0626I-C03-01 to Mikel Latasa, REN2003-09532-C03-01 to Ramiro Varela Benvenuto, CTM2004-05174-C02 to Emilio Marañón, and CTM2011- 25035 to Pedro Cermeño; by the Galician government through grants 09MMA027604PR to Manuel Ruiz Villareal and EM2013/021 to Beatriz Mouriño; by the Instituto Español de Oceanografia (IEO) through the time series project RADIALES coordinated by Antonio Bode and by the 7th Framework Programme of the European Commission through grant FP7 SPACE.2010.1.1- 01 261860 to Manuel Ruiz Villareal. Jose Luis Otero Ferrer acknowledges the receipt of a FPI contract from MINECO (CTM2012-30680) and Bieito Fernádez Castro a Juan de La Cierva Formación fellowship (FJCI-641 2015-25712, Ministerio de Economía y Competitividad, Spanish government) ; Peer reviewed