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11 pages, 8 figures, supplementary material https://doi.org/10.3389/fmicb.2017.02360 ; A major challenge in microbial ecology is linking diversity and function to determine which microbes are actively contributing to processes occurring in situ. Bioorthogonal non-canonical amino acid tagging (BONCAT) is a promising technique for detecting and quantifying translationally active bacteria in the environment. This technique consists of incubating a bacterial sample with an analog of methionine and using click-chemistry to identify the cells that have incorporated the substrate. Here, we established an optimized protocol for the visualization of protein-synthesizing cells in oligotrophic waters that can be coupled with taxonomic identification using Catalyzed Reporter Deposition Fluorescent in Situ Hybridization. We also evaluated the use of this technique to track shifts in translational activity by comparing it with leucine incorporation, and used it to monitor temporal changes in both cultures and natural samples. Finally, we determined the optimal concentration and incubation time for substrate incorporation during BONCAT incubations at an oligotrophic site. Our results demonstrate that BONCAT is a fast and powerful semi-quantitative approach to explore the physiological status of marine bacteria ; This work was supported by grants EcoRARE (CTM2014-60467-JIN), funded by the Spanish Government and the European Regional Development Fund (ERDF), and REMEI (CTM2015-70340-R) funded by the Spanish Government ; Peer Reviewed

12 pages, 6 figures, supplemental material https://www.frontiersin.org/articles/10.3389/fmicb.2019.00760/full#supplementary-material ; Experiments with bacteria in culture have shown that they often display "feast and famine" strategies that allow them to respond with fast growth upon pulses in resource availability, and enter a growth-arrest state when resources are limiting. Although feast responses have been observed in natural communities upon enrichment, it is unknown whether this blooming ability is maintained after long periods of starvation, particularly in systems that are energy limited like the bathypelagic ocean. Here we combined bulk and single-cell activity measurements with 16S rRNA gene amplicon sequencing to explore the response of a bathypelagic community, that had been starved for 1.6 years, to a sudden organic carbon supply. We observed a dramatic change in activity within 30 h, with leucine incorporation rates increasing over two orders of magnitude and the number of translationally active cells (mostly Gammaproteobacteria) increasing 4-fold. The feast response was driven by a single operational taxonomic unit (OTU) affiliated with the Marinobacter genus, which had remained rare during 7 months of starvation. Our work suggests that bathypelagic communities harbor a seed bank of highly persistent and resourceful "feast and famine" strategists that might disproportionally contribute to carbon fluxes through fast responses to occasional pulses of organic matter ; This work was supported by grants DIFUMIC (2017SGR/1568, Generalitat de Catalunya), DOREMI (CTM2012-34294), HOTMIX (CTM2011-30010/MAR), REMEI (CTM2015-70340-R), and ANIMA (CTM2015-65720-R) funded by the Spanish Government, and EcoRARE (CTM2014-60467-JIN), funded by the Spanish Government and the European Regional Development Fund (ERDF). CRG was supported by a Juan de la Cierva contract (IJCI-2015-23505) and MS by a Viera y Clavijo contract funded by the ACIISI and the ULPGC ; Peer Reviewed

Special issue on Oxygen Minimum Zone Microbiology.-- 11 pages, 5 figures, 3 tables, supporting information https://doi.org/10.1111/1462-2920.15504.-- This is the pre-peer reviewed version of the following article: Yaiza M. Castillo, Irene Forn, Sheree Yau, Xosé Anxelu G. Morán, Laura Alonso-Sáez, Néstor Arandia-Gorostidi, Dolors Vaqué, Marta Sebastián; Seasonal dynamics of natural Ostreococcus viral infection at the single cell level using VirusFISH; Environmental Microbiology 23(6): 3009-3019 (2021), which has been published in final form at https://doi.org/10.1111/1462-2920.15504. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions ; Ostreococcus is a cosmopolitan marine genus of phytoplankton found in mesotrophic and oligotrophic waters, and the smallest free-living eukaryotes known to date, with a cell diameter close to 1 μm. Ostreococcus has been extensively studied as a model system to investigate viral–host dynamics in culture, yet the impact of viruses in naturally occurring populations is largely unknown. Here, we used Virus Fluorescence in situ Hybridization (VirusFISH) to visualize and quantify viral-host dynamics in natural populations of Ostreococcus during a seasonal cycle in the central Cantabrian Sea (Southern Bay of Biscay). Ostreococcus were predominantly found during summer and autumn at surface and 50 m depth, in coastal, mid-shelf and shelf waters, representing up to 21% of the picoeukaryotic communities. Viral infection was only detected in surface waters, and its impact was variable but highest from May to July and November to December, when up to half of the population was infected. Metatranscriptomic data available from the mid-shelf station unveiled that the Ostreococcus population was dominated by the species O. lucimarinus. This work represents a proof of concept that the VirusFISH technique can be used to quantify the impact of viruses on targeted populations of key microbes from complex natural communities ; This work was supported by the Spanish projects MEFISTO (CTM2013-43767-P, MINECO) and ALLFLAGS (CTM2016-75083-R, MINECO). YMC was supported by a FPI Spanish fellowship (BES-2014-067849), SY was supported by a Juan de la Cierva fellowship (IJCI-2017-34245) and LAS was supported by a Juan de la Cierva and Ramon y Cajal contract (RYC-2012-11404). MS was supported by a Viera y Clavijo contract funded by the ACIISI and the ULPGC. NAG was supported by Basque Government's PhD-program fellowship ; With the funding support of the 'Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI) ; Peer reviewed