Yamada, N., Fukuda, H., Ogawa, H., Saito, H. & Suzumura, M. Heterotrophic bacterial production and extracellular enzymatic activity in sinking particulate matter in the western North Pacific Ocean. Front. Microbiol. 3, 379. https://doi.org/10.3389/fmicb.2012.00379 (2012).
Google Scholar
del Giorgio, P., Cole, J. & Cimbleris, A. Respiration rates in bacteria exceed phytoplankton production in unproductive aquatic systems. Nature 385, 148–151 (1997).
Google Scholar
Teira, E. et al. Sample dilution and bacterial community composition influence empirical leucine-to-carbon conversion factors in surface waters of the world’s oceans. Appl. Environ. Microbiol. 81, 8224–8232 (2015).
Google Scholar
Dobal-Amador, V. et al. Vertical stratification of bacterial communities driven by multiple environmental factors in the waters (0–5000 m) off the Galician coast (NW Iberian margin). Deep-Sea Res. I(114), 1–11 (2016).
Kirchman, D., Ducklow, H. W. & Mitchell, R. Estimates of bacterial growth from changes in uptake rates and biomass. Appl. Environ. Microbiol. 44, 1296–1307 (1982).
Google Scholar
Simon, M. & Azam, F. Protein content and protein synthesis rates of planktonic marine bacteria. Mar. Ecol. Prog. Ser. 51, 201–213 (1989).
Google Scholar
Ducklow, H. Bacterial production and biomass in the ocean. In Microbial Ecology of the Oceans (ed. Kirchman, D.) 85–120 (Wiley, 2000).
Varela, M. M., Bode, A., Morán, X. A. G. & Valencia, J. Dissolved organic nitrogen (DON) release and bacterial activity in the upper layers of the Atlantic Ocean. Microb. Ecol. 51, 487–500 (2006).
Google Scholar
Calvo-Díaz, A. & Morán, X. A. G. Empirical leucine-to-carbon conversion factors for estimating heterotrophic bacterial production: Seasonality and predictability in a temperate coastal ecosystem. Appl. Environ. Microbiol. 75, 3216–3221 (2009).
Google Scholar
Alonso-Sáez, L., Pinhassi, J., Pernthaler, J. & Gasol, J. M. Leucine-to-carbon empirical conversion factor experiments: Does bacterial community structure have an influence?. Environ. Microbiol. 12, 2988–2997 (2010).
Google Scholar
Gasol, J. M. et al. Mesopelagic prokaryotic bulk and single-cell heterotrophic activity and community composition in the NW Africa-Canary Islands coastal-transition zone. Prog. Oceanogr. 83, 189–196 (2009).
Google Scholar
Baltar, F., Aristegui, J., Gasol, J. M. & Herndl, G. Prokaryotic carbon utilization in the dark ocean: Growth efficiency, leucine-to-carbon conversion factors, and their relation. Aquat. Microb. Ecol. 60, 227–232 (2010).
Varela, M. M., Rodríguez-Ramos, T., Guerrero-Feijóo, E. & Nieto-Cid, M. Changes in activity and community composition shape bacterial responses to size-fractionated marine DOM. Front. Microbiol. 11, 586148. https://doi.org/10.3389/fmicb.2020.586148 (2020).
Google Scholar
Sarmento, H., Morana, C. & Gasol, J. M. Bacterioplankton niche partitioning in the use of phytoplankton-derived dissolved organic carbon: Quantity is more important than quality. ISME J. 10, 2582–2592 (2016).
Google Scholar
Guerrero-Feijóo, E. et al. Optical properties of dissolved organic matter relate to different depth-specific patterns of archaeal and bacterial community structure in the North Atlantic Ocean. FEMS Microbiol. Ecol. 93, 1–14 (2017).
Helms, J. R. et al. Absorption spectral slopes and slope ratios as indicators of molecular weight, source and photobleaching of chromophoric dissolved organic matter. Limnol. Oceanogr. 51, 2170–2180 (2008).
Stedmon, C. A. & Nelson, N. B. The optical properties of DOM in the ocean. In Biogeochemistry of Marine Dissolved Organic Matter (eds Hansell, D. A. & Carlson, C. A.) 481–508 (Academic Press, 2015).
Nieto-Cid, M., Álvarez-Salgado, X. A. & Pérez, F. F. Microbial and photochemical reactivity of fluorescent dissolved organic matter in a coastal upwelling system. Limnol. Oceanogr. 51, 1391–1400 (2006).
Google Scholar
Rodríguez-Ramos, T., Nieto-Cid, M., Auladell, A., Guerrero-Feijóo, E. & Varela, M. M. Vertical niche partitioning of archaea and bacteria linked to shifts in dissolved organic matter quality and hydrography in North Atlantic waters. Front. Mar. Sci. 8, 673171. https://doi.org/10.3389/fmars.2021.673171 (2021).
Google Scholar
Bode, A., Álvarez-Osorio, M. T., Cabanas, J. M., Miranda, A. & Varela, M. Recent trends in plankton and upwelling intensity off Galicia (NW Spain). Prog. Oceanogr. 83, 342–350 (2009).
Google Scholar
Teira, E. et al. Plankton carbon budget in a coastal wind-driven upwelling station off A Coruña (NW Iberian Peninsula). Mar. Ecol. Prog. Ser. 265, 31–43 (2003).
Google Scholar
Ruiz-Villarreal, M. et al. Oceanographic conditions in North and Northwest Iberia and their influence on the Prestige oil spill. Mar. Pollut. Bull. 53, 220–238 (2006).
Google Scholar
Lavin, A. et al. The Bay of Biscay: The encountering of the ocean and the shelf. In The Sea, Volume 14B: The Global Coastal Ocean (eds Robinson, A. & Brink, K.) 993–1001 (Harvard University Press, 2006).
Pedrós-Alió, C., Calderón-Paz, J. I., Guixa-Boixereu, N., Estrada, M. & Gasol, J. M. Bacterioplankton and phytoplankton biomass and production during summer stratification in the northwestern Mediterranean Sea. Deep-Sea Res. I(46), 985–1019 (1999).
Barbosa, A. B. et al. Short-term variability of heterotrophic bacterioplankton during upwelling off the NW Iberian margin. Prog. Oceanogr. 51, 339–359 (2001).
Google Scholar
Morán, X. A., Gasol, J. M., Pedrós-Alió, C. & Estrada, M. Partitioning of phytoplankton organic carbon production and bacterial production along a coastal-offshore gradient in the NE Atlantic during different hydrographic regimes. Aquat. Microb. Ecol. 29, 239–252 (2002).
Martínez-García, S. et al. Differential responses of phytoplankton and heterotrophic bacteria to organic and inorganic nutrient additions in coastal waters off the NW Iberian Peninsula. Mar. Ecol. Prog. Ser. 416, 17–33 (2010).
Google Scholar
Li, X., Xu, J., Shi, Z., Li, Q. & Li, R. Variability in the empirical leucine-to-carbon conversion factors along an environmental gradient. Acta Oceanol. Sin. 37, 77–82 (2018).
Doval, M. D., Nogueira, E. & Pérez, F. F. Spatio-temporal variability of the thermohaline and biogeochemical properties and dissolved organic carbon in a coastal embayment affected by upwelling: The Ría de Vigo (NW Spain). J. Mar. Sys. 14, 135–150 (1998).
Valencia, J. et al. Variations in planktonic bacterial biomass and production, and phytoplankton blooms off A Coruña (NW Spain). Sci. Mar. 67, 143–157 (2003).
Bode, A., Álvarez-Osorio, M. T. & Varela, M. Phytoplankton and macrophyte contributions to littoral food webs in the Galician upwelling estimated from stable isotopes. Mar. Ecol. Prog. Ser. 318, 89–102 (2006).
Google Scholar
Bode, A., Varela, M., Canle, M. & González, N. Dissolved and particulate organic nitrogen in shelf waters of northern Spain during spring. Mar. Ecol. Prog. Ser. 214, 43–54 (2001).
Google Scholar
Lønborg, C. & Álvarez-Salgado, X. A. Tracing dissolved organic matter cycling in the eastern boundary of the temperate North Atlantic using absorption and fluorescence spectroscopy. Deep Res. Part I 85, 35–46 (2014).
Lønborg, C., Yokokawa, T., Herndl, G. & Álvarez-Salgado, X. A. Production and degradation of fluorescent dissolved organic matter in surface waters of the eastern North Atlantic Ocean. Deep Res. Part I(96), 28–37 (2015).
Lønborg, C., Davidson, K., Álvarez-Salgado, X. A. & Miller, A. E. J. Bioavailability 904 and bacterial degradation rates of dissolved organic matter in a temperate coastal area 905 during an annual cycle. Mar. Chem. 113, 219–226 (2009).
Teira, E. et al. Plankton carbon budget in a coastal wind-driven upwelling station off A Coruna (NW Iberian Peninsula). Mar. Ecol. Prog. Ser. 265, 31–43 (2003).
Google Scholar
Álvarez-Salgado, X. A., Arístegui, J., Barton, E. D. & Hansell, D. A. Contribution of upwelling filaments to offshore carbon export in the subtropical Northeast Atlantic Ocean. Limnol. Oceanogr. 52, 1287–1292 (2007).
Google Scholar
Álvarez-Salgado, X. A. et al. Off-shelf fluxes of labile materials by an upwelling filament in the NW Iberian Upwelling System. Prog. Oceanogr. 51, 321–337 (2001).
Google Scholar
del Giorgio, P. A. et al. Coherent patterns in bacterial growth, growth efficiency, and leucine metabolism along a northeastern Pacific inshore-offshore transect. Limnol. Oceanogr. 56, 1–16 (2011).
Google Scholar
Aristegui, J., Gasol, J. M., Duarte, C. M. & Herndl, G. J. Microbial oceanography of the dark ocean’s pelagic realm. Limnol. Oceanogr. 54, 1501–1529 (2009).
Google Scholar
Herndl, G. J. & Reinthaler, T. Microbial control of the dark end of the biological pump. Nat. Geosci. 6, 718–724 (2013).
Google Scholar
Landry, Z., Swan, B. K., Herndl, G. J., Stepanauskas, R. & Giovannoni, S. J. SAR202 genomes from the dark ocean predict pathways for the oxidation of recalcitrant dissolved organic matter. MBio 8, e00413-17. https://doi.org/10.1128/mBio.00413-17 (2017).
Google Scholar
Catalá, T. et al. Dissolved Organic Matter (DOM) in the open Mediterranean Sea. I. Basin–wide distribution and drivers of chromophoric DOM. Prog. Oceanogr. 165, 35–51 (2018).
Google Scholar
Bjørnsen, P. K. & Kuparinen, J. Determination of bacterioplankton biomass, net production and growth efficiency in the Southern Ocean. Mar. Ecol. Prog. Ser. 71, 185–194 (1991).
Google Scholar
Weinbauer, M. G. et al. Synergistic and antagonistic effects of viral lysis and protistan grazing on bacterial biomass, production and diversity. Environ. Microbiol. 9(3), 777–788 (2007).
Google Scholar
Evans, C. et al. Shift from carbon flow through the microbial loop to the viral shunt in coastal Antarctic waters during austral summer. Microorganisms 9, 460 (2021).
Google Scholar
Gasol, J. M., Zweifel, U., Peters, F., Fuhrman, J. D. & Hagström, H. Significance of size and nucleic acid content heterogeneity as measured by flow cytometry in Natural Planktonic Bacteria. Appl. Environ. Microbiol. 65, 104475–104483 (1999).
Google Scholar
Calvo-Díaz, A. & Morán, X. A. G. Seasonal dynamics of picoplankton in shelf waters of the southern Bay of Biscay. Aquat. Microb. Ecol. 42, 159–174 (2006).
Norland, S. The relationship between biomass and volume of bacteria. In Handbook of Methods in Aquatic Microbial Ecology (eds Kemp, P. F. et al.) 303–307 (CRC Press, 1993).
Kirchman, D., Knees, E. & Hodson, R. Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl. Environ. Microbiol. 49, 599–607 (1985).
Google Scholar
Smith, D. C. & Azam, F. A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine. Mar. Microb. Food Webs 6, 107–114 (1992).
Massana, R. et al. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 63, 50–56 (1997).
Google Scholar
Herlemann, D. P. et al. Transitions in bacterial communities along the 2000km salinity gradient of the Baltic Sea. ISME J. 5, 1571–1579 (2011).
Google Scholar
Callahan, B. J., McMurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643 (2017).
Google Scholar
R Core Team. R: A language and environment for statistical computing http://www.r-project.org (2018).
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
Google Scholar
Huse, S. M., Welch, D. M., Morrison, H. G. & Sogin, M. L. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12, 1889–1898 (2010).
Google Scholar
Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.4–6 http://www.CRAN.R-project.org/package=vegan (2018).
Álvarez-Salgado, X. A. & Miller, A. E. J. Simultaneous determination of dissolved organic carbon and total dissolved nitrogen in seawater by high temperature catalytic oxidation: Conditions for precise shipboard measurements. Mar. Chem. 62, 325–333 (1998).
Green, S. A. & Blough, N. V. Optical absorption and fluorescence properties of chromophoric dissolved organic matter in natural waters. Limnol. Oceanogr. 29, 1903–1916 (1994).
Google Scholar
Shapiro, S. S. & Wilk, M. B. An analysis of variance test for normality (complete samples). Biometrika 52, 591–611 (1965).
Google Scholar
Pearson, K. Notes on the history of correlation. Biometrika 13, 25–45 (1920).
Addinsoft XLSTAT statistical and data analysis solution http://www.xlstat.com (2020).
Burnham, K. & Anderson, D. Information and Likelihood Theory: A Basis for Model Selection and Inference in Model Selection and Inference: A Practical Information-Theoretic Approach 60–64 (Springer, 2002).
Clarke, K. Nonparametric multivariate analyses of changes in community structure. Austral Ecol. 18, 117–143 (1993).
Quinn, T. P. et al. A field guide for the compositional analysis of any-omics data. GigaScience 8, giz107. https://doi.org/10.1093/gigascience/giz107 (2019).
Google Scholar
Source: Ecology - nature.com
