Mean dynamic topography and oceanographic parameters estimated from an inverse model and satellite geodesy, with link to model result in one single NetCDF file (392 MB), including the inverse data error covariance

Geostrophic surface velocities can be derived from the gradients of the mean dynamic topography-the difference between the mean sea surface and the geoid. Therefore, independently observed mean dynamic topography data are valuable input parameters and constraints for ocean circulation models. For a successful fit to observational dynamic topography data, not only the mean dynamic topography on the particular ocean model grid is required, but also information about its inverse covariance matrix. The calculation of the mean dynamic topography from satellite-based gravity field models and altimetric sea surface height measurements, however, is not straightforward. For this purpose, we previously developed an integrated approach to combining these two different observation groups in a consistent way without using the common filter approaches (Becker et al. in J Geodyn 59(60):99-110, 2012, doi:10.1016/j.jog.2011.07.0069; Becker in Konsistente Kombination von Schwerefeld, Altimetrie und hydrographischen Daten zur Modellierung der dynamischen Ozeantopographie, 2012, http://nbn-resolving.de/nbn:de:hbz:5n-29199). Within this combination method, the full spectral range of the observations is considered. Further, it allows the direct determination of the normal equations (i.e., the inverse of the error covariance matrix) of the mean dynamic topography on arbitrary grids, which is one of the requirements for ocean data assimilation. In this paper, we report progress through selection and improved processing of altimetric data sets. We focus on the preprocessing steps of along-track altimetry data from Jason-1 and Envisat to obtain a mean sea surface profile. During this procedure, a rigorous variance propagation is accomplished, so that, for the first time, the full covariance matrix of the mean sea surface is available. The combination of the mean profile and a combined GRACE/GOCE gravity field model yields a mean dynamic topography model for the North Atlantic Ocean that is characterized by a defined set of assumptions. We show that including the geodetically derived mean dynamic topography with the full error structure in a 3D stationary inverse ocean model improves modeled oceanographic features over previous estimates.

Altered neurotransmitter function in CO2-exposed stickleback (Gasterosteus aculeatus): a temperate model species for ocean acidification research

Studies on the consequences of ocean acidification for the marine ecosystem have revealed behavioural changes in coral reef fishes exposed to sustained near-future CO2 levels. The changes have been linked to altered function of GABAergic neurotransmitter systems, because the behavioural alterations can be reversed rapidly by treatment with the GABAA receptor antagonist gabazine. Characterization of the molecular mechanisms involved would be greatly aided if these can be examined in a well-characterized model organism with a sequenced genome. It was recently shown that CO2-induced behavioural alterations are not confined to tropical species, but also affect the three-spined stickleback, although an involvement of the GABAA receptor was not examined. Here, we show that loss of lateralization in the stickleback can be restored rapidly and completely by gabazine treatment. This points towards a worrying universality of disturbed GABAA function after high-CO2 exposure in fishes from tropical to temperate marine habitats. Importantly, the stickleback is a model species with a sequenced and annotated genome, which greatly facilitates future studies on underlying molecular mechanisms.

Age model for ODP Leg 175 sites

Upwelling along the western coast of Africa south of the equator may be partitioned into three major areas, each having its own dynamics and history: (1) the eastern equatorial region, comprising the Congo Fan and the area of Mid-Angola; (2) the Namibia upwelling system, extending from the Walvis Ridge to Lüderitz; and (3) the Cape Province region, where upwelling is subdued. The highest nutrient contents in thermocline waters are in the northern region, the lowest in the southern one. Wind effects are at a maximum near the southern end of the Namibia upwelling system, and maximum productivity occurs near Walvis Bay, where the product between upwelling rate and nutrient content of upwelled waters is at a maximum. In the Congo/Angola region, opal tends to follow organic carbon quite closely in the Quaternary record. However, organic carbon has a strong precessional component, while opal does not. Despite relatively low opal content, sediments off Angola show the same patterns as those off the Congo; thus, they are part of the same regime. The spectrum shows nonlinear interference patterns between high- and low-latitude forcing, presumably tied to thermocline fertility and wind. On Walvis Ridge, as in the Congo-Angola region, the organic matter record behaves normally; that is, supply is high during glacial periods. In contrast, interglacial periods are favorable for opal deposition. The pattern suggests reduction in silicate content of the thermocline during glacial periods. The reversed phase (opal abundant during interglacials) persists during the entire Pleistocene and can be demonstrated deep into the Pliocene, not just on Walvis Ridge but all the way to the Oranje River and off the Cape Province. From comparison with other regions, it appears that silicate is diminished in the global thermocline, on average, whenever winds become strong enough to substantially shorten the residence time of silicate in upper waters (Walvis Hypothesis, solving the Walvis Paradox of reversed phase in opal deposition). The central discovery during Leg 175 was the documentation of a late Pliocene opal maximum for the entire Namibia upwelling system (early Matuyama Diatom Maximum [MDM]). The maximum is centered on the period between the end of the Gauss Chron and the beginning of the Olduvai Chron. A rather sharp increase in both organic matter deposition and opal deposition occurs near 3 Ma in the middle of the Gauss Chron, in association with a series of major cooling steps. As concerns organic matter, high production persists at least to 1 Ma, when there are large changes in variability, heralding subsequent pulsed production periods. From 3 to 2 Ma, organic matter and opal deposition run more or less parallel, but after 2 Ma opal goes out of phase with organic matter. Apparently, this is the point when silicate becomes limiting to opal production. Thus, the MDM conundrum is solved by linking planetary cooling to increased mixing and upwelling (ramping up to the MDM) and a general removal of silicate from the upper ocean through excess precipitation over global supply (ramping down from the MDM). The hypothesis concerning the origin of the Namibia opal acme or MDM is fundamentally the same as the Walvis Hypothesis, stating that glacial conditions result in removal of silicate from the thermocline (and quite likely from the ocean as a whole, given enough time). The Namibia opal acme, and other opal maxima in the latest Neogene in other regions of the ocean, marks the interval when a cooling ocean selectively removes the abundant silicate inherited from a warm ocean. When the excess silicate is removed, the process ceases. According to the data gathered during Leg 175, major upwelling started in the late part of the late Miocene. Presumably, this process contributed to the drawing down of carbon dioxide from the atmosphere, helping to prepare the way for Northern Hemisphere glaciation.

Light-modulated responses of growth and photosynthetic performance to ocean acidification in the model diatom Phaeodactylum tricornutum

Ocean acidification (OA) due to atmospheric CO2 rise is expected to influence marine primary productivity. In order to investigate the interactive effects of OA and light changes on diatoms, we grew Phaeodactylum tricornutum, under ambient (390 ppmv; LC) and elevated CO2 (1000 ppmv; HC) conditions for 80 generations, and measured its physiological performance under different light levels (60 µmol/m**2/s, LL; 200 µmol/m**2/s, ML; 460 µmol/m**2/s, HL) for another 25 generations. The specific growth rate of the HC-grown cells was higher (about 12-18%) than that of the LC-grown ones, with the highest under the ML level. With increasing light levels, the effective photochemical yield of PSII (Fv'/Fm') decreased, but was enhanced by the elevated CO2, especially under the HL level. The cells acclimated to the HC condition showed a higher recovery rate of their photochemical yield of PSII compared to the LC-grown cells. For the HC-grown cells, dissolved inorganic carbon or CO2 levels for half saturation of photosynthesis (K1/2 DIC or K1/2 CO2) increased by 11, 55 and 32%, under the LL, ML and HL levels, reflecting a light dependent down-regulation of carbon concentrating mechanisms (CCMs). The linkage between higher level of the CCMs down-regulation and higher growth rate at ML under OA supports the theory that the saved energy from CCMs down-regulation adds on to enhance the growth of the diatom.

The photo-physiological response of a model cnidarian-dinoflagellate symbiosis to CO2-induced acidification at the cellular level

We measured the relationship between CO2-induced seawater acidification, photo-physiological performance and intracellular pH (pHi) in a model cnidarian-dinoflagellate symbiosis - the sea anemone Aiptasia sp. -under ambient (289.94 ± 12.54 µatm), intermediate (687.40 ± 25.10 µatm) and high (1459.92 ± 65.51 µatm) CO2 conditions. These treatments represented current CO2 levels, in addition to CO2 stabilisation scenarios IV and VI provided by the Intergovernmental Panel on Climate Change (IPCC). Anemones were exposed to each treatment for two months and sampled at regular intervals. At each time-point we measured a series of physiological responses: maximum dark-adapted fluorescent yield of PSII (Fv/Fm), gross photosynthetic rate, respiration rate, symbiont population density, and light-adapted pHi of both the dinoflagellate symbiont and isolated host anemone cell. We observed increases in all but one photo-physiological parameter (Pgross:R ratio). At the cellular level, increases in light-adapted symbiont pHi were observed under both intermediate and high CO2 treatments, relative to control conditions (pHi 7.35 and 7.46 versus pHi 7.25, respectively). The response of light-adapted host pHi was more complex, however, with no change observed under the intermediate CO2 treatment, but a 0.3 pH-unit increase under the high CO2 treatment (pHi 7.19 and 7.48, respectively). This difference is likely a result of a disproportionate increase in photosynthesis relative to respiration at the higher CO2 concentration. Our results suggest that, rather than causing cellular acidosis, the addition of CO2 will enhance photosynthetic performance, enabling both the symbiont and host cell to withstand predicted ocean acidification scenarios.

Digital elevation model (DEM), surveyed stream network (SSN), mask and stream sampling points (SSP)

These data are provided to allow users for reproducibility of an open source tool entitled 'automated Accumulation Threshold computation and RIparian Corridor delineation (ATRIC)'

Towards convection-resolving, global atmospheric simulations with the Model for Prediction Across Scales (MPAS) v3.1: an extreme scaling experiment, links to sourcecode of model and grides

The Model for Prediction Across Scales (MPAS) is a novel set of Earth system simulation components and consists of an atmospheric model, an ocean model and a land-ice model. Its distinct features are the use of unstructured Voronoi meshes and C-grid discretisation to address shortcomings of global models on regular grids and the use of limited area models nested in a forcing data set, with respect to parallel scalability, numerical accuracy and physical consistency. This concept allows one to include the feedback of regional land use information on weather and climate at local and global scales in a consistent way, which is impossible to achieve with traditional limited area modelling approaches. Here, we present an in-depth evaluation of MPAS with regards to technical aspects of performing model runs and scalability for three medium-size meshes on four different high-performance computing (HPC) sites with different architectures and compilers. We uncover model limitations and identify new aspects for the model optimisation that are introduced by the use of unstructured Voronoi meshes. We further demonstrate the model performance of MPAS in terms of its capability to reproduce the dynamics of the West African monsoon (WAM) and its associated precipitation in a pilot study. Constrained by available computational resources, we compare 11-month runs for two meshes with observations and a reference simulation from the Weather Research and Forecasting (WRF) model. We show that MPAS can reproduce the atmospheric dynamics on global and local scales in this experiment, but identify a precipitation excess for the West African region. Finally, we conduct extreme scaling tests on a global 3?km mesh with more than 65 million horizontal grid cells on up to half a million cores. We discuss necessary modifications of the model code to improve its parallel performance in general and specific to the HPC environment. We confirm good scaling (70?% parallel efficiency or better) of the MPAS model and provide numbers on the computational requirements for experiments with the 3?km mesh. In doing so, we show that global, convection-resolving atmospheric simulations with MPAS are within reach of current and next generations of high-end computing facilities.