Here we provide optimised vertical eddy diffusivity estimates for the PeECE III and KOSMOS 2013 mesocosm experiment, obtained from a model-based reanalysis. These diffusivities are derived from the observed temperature and salinity profiles that have been published in Schulz et al., 2008.

Furthermore, we make our model code available, providing an adjustable tool to simulate vertical mixing in any other pelagic mesocosm.
We also provide the interpolated and regridded temperature and salinity profiles of the PeECE III experiment as well as the density profiles which we calculated from the temperature and salinity profiles using the R package seacarb (Lavigne et al., 2011). These data files are required as input to run simulations of the PeECE III experiment with the 1D mesocosm mixing model.

The columns of the environmental files (required input files for the model) from left to right are: Experiment year, month, day, Julian day, photosynthetically active radiation (PAR) [W/m^2], temperature [C], salinity [PSU], CO2 concentration [ppm], wind speed [m/s]. The rows list the respective value of each hour of the experiment. Temperature and salinity in this table are hourly interpolated values of the daily measurements published by the PeECE III team (2005). PAR has been calculated from global radiation data of Bergen provided by Olseth et al., 2005.

In the temperature, salinity and density files, the rows indicate the depth (0.5 m resolution, the first row is the surface, the last row is the bottom), whereas the columns indicate the experiment time at an hourly resolution

Dietze, Heiner

Getzlaff, Julia

Mathesius, Sabine

Oschlies, Andreas

Schartau, Markus

Controlled manipulation of environmental conditions within large enclosures in the ocean, so-called pelagic mesocosms, has become a standard method to explore potential responses of marine plankton communities to anthropogenic change. Among the challenges of interpreting mesocosm data is the often uncertain role of vertical mixing, which usually is not observed directly. To account for mixing nonetheless, two pragmatic assumptions are common: either that the water column is homogeneously mixed or that it is divided into two water bodies with a horizontal barrier inhibiting turbulent exchange. In this study, we present a model-based reanalysis of vertical turbulent diffusion in the mesocosm experiments PeECE III and KOSMOS 2013. Our diffusivity estimates indicate intermittent mixing events along with stagnating periods and yield simulated temperature and salinity profiles that are consistent with the observations. Here, we provide the respective diffusivities as a comprehensive data product in the Network Common Data Format (NetCDF). This data product will help to guide forthcoming model studies that aim at deepening our understanding of biogeochemical processes in the PeECE III and KOSMOS 2013 mesocosms, such as the CO2-related changes in marine carbon export. In addition, we make our model code available, providing an adjustable tool to simulate vertical mixing in any other pelagic mesocosm. The data product and the model code are available at https://doi.org/10.1594/PANGAEA.905311 (Mathesius et al., 2019)

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– Supplementary Information –Reanalysis of vertical mixing in mesocosm experiments:PeECE III and KOSMOS 2013Sabine Mathesius1, Julia Getzlaff1, Heiner Dietze1,2, Andreas Oschlies1,2, and Markus Schartau11GEOMAR Helmholtz Centre for Ocean Research Kiel2Kiel University (CAU)Correspondence to: Sabine Mathesius (smathesius@geomar.de)112II2 Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experimentsdaysdepth [m]1 5 10 15 2086420Temperaturedaysdepth [m]1 5 10 15 2086420Salinity Diffusivitydaysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420m2 s−1PSU ° C9 10 11 12 13 30.0 30.5 31.0 31.5 32.0 1e−06 1e−05 1e−04 0.001 0.01 0.1Figure 1. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #1 of PeECE III. The first row shows observedtemperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation (secondrow), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experiments 3daysdepth [m]1 5 10 15 2086420Temperaturedaysdepth [m]1 5 10 15 2086420Salinity Diffusivitydaysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420m2 s−1PSU ° C9 10 11 12 13 31.0 31.5 32.0 1e−06 1e−05 1e−04 0.001 0.01 0.1Figure 2. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #2 of PeECE III. The first row shows observedtemperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation (secondrow), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).4 Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experimentsdaysdepth [m]1 5 10 15 2086420Temperaturedaysdepth [m]1 5 10 15 2086420Salinity Diffusivitydaysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420m2 s−1PSU ° C9 10 11 12 13 30.0 30.5 31.0 31.5 32.0 1e−06 1e−05 1e−04 0.001 0.01 0.1Figure 3. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #3 of PeECE III. The first row shows observedtemperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation (secondrow), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experiments 5daysdepth [m]1 5 10 15 2086420Temperaturedaysdepth [m]1 5 10 15 2086420Salinity Diffusivitydaysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420m2 s−1PSU ° C9 10 11 12 13 14 15 30.0 30.5 31.0 31.5 32.0 1e−06 1e−05 1e−04 0.001 0.01 0.1Figure 4. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #4 of PeECE III. The first row shows observedtemperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation (secondrow), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).6 Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experimentsdaysdepth [m]1 5 10 15 2086420Temperaturedaysdepth [m]1 5 10 15 2086420Salinity Diffusivitydaysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420m2 s−1PSU ° C9 10 11 12 30.5 31.0 31.5 32.0 1e−06 1e−05 1e−04 0.001 0.01 0.1Figure 5. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #5 of PeECE III. The first row shows observedtemperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation (secondrow), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experiments 7daysdepth [m]1 5 10 15 2086420Temperaturedaysdepth [m]1 5 10 15 2086420Salinity Diffusivitydaysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420m2 s−1PSU ° C9 10 11 12 13 30.5 31.0 31.5 32.0 1e−06 1e−05 1e−04 0.001 0.01 0.1Figure 6. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #6 of PeECE III. The first row shows observedtemperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation (secondrow), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).8 Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experimentsdaysdepth [m]1 5 10 15 2086420Temperaturedaysdepth [m]1 5 10 15 2086420Salinity Diffusivitydaysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420m2 s−1PSU ° C9 10 11 12 13 14 30.5 31.0 31.5 32.0 1e−06 1e−05 1e−04 0.001 0.01 0.1Figure 7. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #7 of PeECE III. The first row shows observedtemperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation (secondrow), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experiments 9daysdepth [m]1 5 10 15 2086420Temperaturedaysdepth [m]1 5 10 15 2086420Salinity Diffusivitydaysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420m2 s−1PSU ° C9 10 11 12 13 30.5 31.0 31.5 32.0 1e−06 1e−05 1e−04 0.001 0.01 0.1Figure 8. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #8 of PeECE III. The first row shows observedtemperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation (secondrow), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).10 Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experimentsdaysdepth [m]1 5 10 15 2086420Temperaturedaysdepth [m]1 5 10 15 2086420Salinity Diffusivitydaysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420daysdepth [m]1 5 10 15 2086420m2 s−1PSU ° C9 10 11 12 13 14 30.5 31.0 31.5 32.0 1e−06 1e−05 1e−04 0.001 0.01 0.1Figure 9. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #9 of PeECE III. The first row shows observedtemperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation (secondrow), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experiments 11Figure 10. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #1 of KOSMOS 2013. The first row showsobserved temperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation(second row), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).12 Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experimentsFigure 11. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #2 of KOSMOS 2013. The first row showsobserved temperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation(second row), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experiments 13Figure 12. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #3 of KOSMOS 2013. The first row showsobserved temperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation(second row), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).14 Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experimentsFigure 13. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #4 of KOSMOS 2013. The first row showsobserved temperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation(second row), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experiments 15Figure 14. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #5 of KOSMOS 2013. The first row showsobserved temperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation(second row), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).16 Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experimentsFigure 15. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #6 of KOSMOS 2013. The first row showsobserved temperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation(second row), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experiments 17Figure 16. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #7 of KOSMOS 2013. The first row showsobserved temperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation(second row), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).18 Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experimentsFigure 17. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #8 of KOSMOS 2013. The first row showsobserved temperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation(second row), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experiments 19Figure 18. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #9 of KOSMOS 2013. The first row showsobserved temperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation(second row), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).20 Mathesius et al.: SI: Reanalysis of vertical mixing in mesocosm experimentsFigure 19. Temporal evolution of temperature, salinity, and diffusivity profiles in mesocosm #10 of KOSMOS 2013. The first row showsobserved temperature and salinity; the following rows show simulated temperature, salinity, and diffusivity for a) the salinity optimisation(second row), b) the temperature optimisation (third row), and c) the optimisation that depends on both temperature and salinity (fourth row).

Reanalysis of vertical mixing in mesocosm experiments: PeECE III and KOSMOS 2013

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http://oceanrep.geomar.de/48195/2/essd-2019-166-supplement.pdf

Reanalysis of vertical mixing in mesocosm experiments: PeECE III and KOSMOS 2013

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