Search

In an ocean reanalysis, historical observations are combined with ocean and biogeochemical general circulation models to produce a reconstruction of the oceanic properties in past decades. This is one possible method to better constrain the role of the ocean carbon cycle in the determination of the air–sea CO 2 flux. In this work, we investigate how the assimilation of physical variables and subsequently the combined assimilation of physical data and inorganic carbon variables – namely dissolved inorganic carbon (DIC) and alkalinity – affect the modelling of the marine carbonate system and the related air–sea CO 2 fluxes. The performance of the two assimilation exercises are quantitatively assessed against the assimilated DIC and alkalinity data and the independent ocean surface p CO 2 observations from global datasets. We obtain that the assimilation of physical observations has contrasting effects in different ocean basins when compared with the DIC and alkalinity data: it reduces the root-mean square error against the observed p CO 2 in the Atlantic and Southern oceans, while increases the model error in the North Pacific and Indian Oceans. In both cases the corrected evaporation rates are the major factor determining the changes in concentrations. The assimilation of inorganic carbon variables on top of the physical data gives a generalized improvement in the model error of inorganic carbon variables, also improving the annual mean and spatial distribution of air–sea fluxes in agreement with other published estimates. These results indicate that data assimilation of physical and inorganic carbon data does not guarantee the improvement of the simulated p CO 2 in all the oceanic regions; nevertheless, errors in p CO 2 are reduced by a factor corresponding to those associated with the air–sea flux formulations. [ABSTRACT FROM AUTHOR]

Abstract: The response of phytoplankton growth to iron supply and its modulation by large-scale circulation and tropical instability waves (TIWs) in the eastern equatorial Pacific has been investigated with an ocean biogeochemical model. This process study shows that iron can be efficiently advected from the New Guinea shelf through the Equatorial Undercurrent (EUC) to the eastern Pacific. The presence of a continental iron source is necessary for the maintenance of the observed subsurface iron maximum in the EUC core. In the eastern Pacific region, phytoplankton production is enhanced when additional iron is available in the EUC. Simulated phytoplankton variability is linked to TIWs activity, as revealed by a wavelet analysis of the total autotrophic carbon. The net local effect of the waves on phytoplankton can be either positive or negative depending on several factors. When the iron nutricline is sufficiently shallow to be reached by the wave vertical scale, the effect of the waves is to enhance iron availability in the euphotic zone leading to a net local increase of phytoplankton biomass. We therefore suggest that the local maxima of phytoplankton observed in moorings off the Equator in the eastern Pacific might be not only the result of concentration mechanisms, but also the result of an increase in local production sustained by advected iron. [Copyright &y& Elsevier]

In this paper results from the application of an ocean data assimilation (ODA) system, combining a multivariate reduced-order optimal interpolator (OI) scheme with a global ocean general circulation model (OGCM), are described. The present ODA system, designed to assimilate in situ temperature and salinity observations, has been used to produce ocean reanalyses for the 1962–2001 period. The impact of assimilating observed hydrographic data on the ocean mean state and temporal variability is evaluated. A special focus of this work is on the ODA system skill in reproducing a realistic ocean salinity state. Results from a hierarchy of different salinity reanalyses, using varying combinations of assimilated data and background error covariance structures, are described. The impact of the space and time resolution of the background error covariance parameterization on salinity is addressed. [ABSTRACT FROM AUTHOR]

Abstract: This paper presents a global ocean implementation of a multi-component model of marine pelagic biogeochemistry coupled on-line with an ocean general circulation model forced with climatological surface fields (PELAgic biogeochemistry for Global Ocean Simulations, PELAGOS). The final objective is the inclusion of this model as a component in an Earth System model for climate studies. The pelagic model is based on a functional stoichiometric representation of marine biogeochemical cycles and allows simulating the dynamics of C, N, P, Si, O and Fe taking into account the variation of their elemental ratios in the functional groups. The model also includes a parameterization of variable chlorophyll/carbon ratio in phytoplankton, carrying chl as a prognostic variable. The first part of the paper analyzes the contribution of non-local advective–diffusive terms and local vertical processes to the simulated chl distributions. The comparison of the three experiments shows that the mean chl distribution at higher latitudes is largely determined by mixing processes, while vertical advection controls the distribution in the equatorial upwelling regions. Horizontal advective and diffusive processes are necessary mechanisms for the shape of chl distribution in the sub-tropical Pacific. In the second part, the results have been compared with existing datasets of satellite-derived chlorophyll, surface nutrients, estimates of phytoplankton community composition and primary production data. The agreement is reasonable both in terms of the spatial distribution of annual means and of the seasonal variability in different dynamical oceanographic regions. Results indicate that some of the model biases in chl and surface nutrients distributions can be related to deficiencies in the simulation of physical processes such as advection and mixing. Other discrepancies are attributed to inadequate parameterizations of phytoplankton functional groups. The model has skill in reproducing the overall distribution of large and small phytoplankton but tends to underestimate diatoms in the northern higher latitudes and overestimate nanophytoplankton with respect to picoautotrophs in oligotrophic regions. The performance of the model is discussed in the context of its use in climate studies and an approach for improving the parameterization of functional groups in deterministic models is outlined. [Copyright &y& Elsevier]

Mucocutaneous leishmaniasis (MCL) in South and Central America is characterized by the dissemination (metastasis) of Leishmania Viannia subgenus parasites from a cutaneous lesion to nasopharyngeal tissues. Little is known about the pathogenesis of MCL, especially with regard to the virulence of the parasites and the process of metastatic dissemination. We previously examined the functional relationship between cytoplasmic peroxiredoxin and metastatic phenotype using highly, infrequently, and nonmetastatic clones isolated from an L. (V.) guyanensis strain previously shown to be highly metastatic in golden hamsters. Distinct forms of cytoplasmic peroxiredoxin were identified and found to be associated with the metastatic phenotype. We report here that peroxidase activity in the presence of hydrogen peroxide and infectivity differs between metastatic and nonmetastatic L. (V.) guyanensis clones. After hydrogen peroxide treatment or heat shock, peroxiredoxin was detected preferentially as dimers in metastatic L. (V.) guyanensis clones and in L. (V.) panamensis strains from patients with MCL, compared with nonmetastatic parasites. These data provide evidence that resistance to the first microbicidal response of the host cell by Leishmania promastigotes is linked to peroxiredoxin conformation and may be relevant to intracellular survival and persistence, which are prerequisites for the development of metastatic disease. Copyright © 2006 Infectious Diseases Society of America [ABSTRACT FROM AUTHOR]

An ocean analysis, assimilating both surface and subsurface hydrographic temperature data into a global ocean model, has been produced for the period 1958-2000, and used to study the time and space variations of North Atlantic upper ocean heat content (HC). Observational evidence is presented for interannual-to-decadal variability of upper ocean thermal fluctuations in the North Atlantic related to the North Atlantic Oscillation (NAO) variability over the last 40 years. The assimilation scheme used in the ocean analysis is a univariate, variational optimum interpolation of temperature. The first guess is produced by an eddy permitting global ocean general circulation forced by atmospheric reanalysis from the National Center for Environmental Prediction (NCEP). The validation of the ocean analysis has been done through the comparison with objectively analyzed observations and independent data sets. The method is able to compensate for the model systematic error to reproduce a realistic vertical thermal structure of the region and to improve consistently the model estimation of the time variability of the upper ocean temperature. Empirical orthogonal function (EOF) analysis shows that an important mode of variability of the wintertime upper ocean climate over the North Atlantic during the period of study is characterized by a tripole pattern both for SST and upper ocean HC. A similar mode is found for summer HC anomalies but not for summer SST. Over the whole period, HC variations in the subtropics show a general warming trend while the tropical and north eastern part of the basin have an opposite cooling tendency. Superimposed on this linear trend, the HC variability explained by the first EOF both in winter and summer conditions reveals quasi-decadal oscillations correlated with changes in the NAO index. On the other hand, there is no evidence of correlation in time between the NAO index and the upper ocean HC averaged over the whole North Atlantic which exhibits a substantial and monotonic warming trend during the last two decades of the analysis period. The maximum correlation is found between the leading principal component of winter HC anomalies and NAO index at 1 year lag with NAO leading. For SST anomalies significant correlation is found only for winter conditions. In contrast, for HC anomalies high correlations are found also in the summer suggesting that the summer HC keeps a memory of winter conditions. [ABSTRACT FROM AUTHOR]

This article introduces the second generation CMCC Earth System Model (CMCC‐ESM2) that extends a number of marine and terrestrial biogeochemical processes with respect to its CMIP5 predecessor. In particular, land biogeochemistry was extended to a wider set of carbon pools and plant functional types, along with a prognostic representation of the nitrogen cycle. The marine ecosystem representation was reshaped toward an intermediate complexity of lower trophic level interactions, including an interactive benthic compartment and a new formulation of heterotrophic bacterial population. Details are provided on the model setup and implementation for the different experiments performed as contribution to the sixth phase of the Coupled Model Intercomparison Project. CMCC‐ESM2 shows an equilibrium climate sensitivity of 3.57°C and a transient climate response of 1.97°C which are close to the CMIP5 and CMIP6 multi‐model averages. The evaluation of the coupled climate‐carbon response in the historical period against available observational datasets show a consistent representation of both physical and biogeochemical quantities. However, the land carbon sink is found to be weaker than the current global carbon estimates and the simulated marine primary production is slightly below the satellite‐based average over recent decades. Future projections coherently show a prominent global warming over the northern hemisphere with intensified precipitations at high latitudes. The expected ranges of variability for oceanic pH and oxygen, as well as land carbon and nitrogen soil storage, compare favorably with those assessed from other CMIP6 models. Plain Language Summary: Earth System Models integrate our knowledge on the underlying physical and biogeochemical mechanisms that drive or influence the global climate and the biosphere over the land and in the ocean. These models are used to provide realistic estimates of climate variability and its response to perturbations in the chemical constituents of the atmosphere and modifications of the terrestrial surface. This work describes the science at the base of the second generation Earth System Model developed at the Euro‐Mediterranean Centre on Climate Change and the major results obtained from the simulation of historical (from the pre‐industrial period until present) and different future scenarios up to 2100 in the context of the sixth Coupled Model Intercomparison Project. The model provides a solid representation of the present‐day physical climate and biosphere dynamics in comparison to available observations and data reconstruction of the recent past. The projected global warming signal and carbon accumulation within terrestrial and oceanic systems under future climate scenarios are comparable to the findings of other models involved in the sixth intercomparison project. Key Points: This work introduces the second generation CMCC Earth System Model (CMCC‐ESM2) and its configuration for CMIP6Estimated climate sensitivity and carbon‐climate feedbacks are similar to average of CMIP5 and locate in the lower end of CMIP6Both climate and biogeochemical dynamics are assessed through the comparison with observations and previous literature findings [ABSTRACT FROM AUTHOR]

We investigate the effects of realistic oceanic initial conditions on a set of decadal climate predictions performed with a state-of-the-art coupled ocean-atmosphere general circulation model. The decadal predictions are performed in both retrospective (hindcast) and forecast modes. Specifically, the full set of prediction experiments consists of 3-member ensembles of 30-year simulations, starting at 5-year intervals from 1960 to 2005, using historical radiative forcing conditions for the 1960-2005 period, followed by RCP4.5 scenario settings for the 2006-2035 period. The ocean initial states are provided by ocean reanalyses differing by assimilation methods and assimilated data, but obtained with the same ocean model. The use of alternative ocean reanalyses yields the required perturbation of the full three-dimensional ocean state aimed at generating the ensemble members spread. A full-value initialization technique is adopted. The predictive skill of the system appears to be driven to large extent by trends in the radiative forcing. However, after detrending, a residual skill over specific regions of the ocean emerges in the near-term. Specifically, natural fluctuations in the North Atlantic sea-surface temperature (SST) associated with large-scale multi-decadal variability modes are predictable in the 2-5 year range. This is consistent with significant predictive skill found in the Atlantic meridional overturning circulation over a similar timescale. The dependency of forecast skill on ocean initialization is analysed, revealing a strong impact of details of ocean data assimilation products on the system predictive skill. This points to the need of reducing the large uncertainties that currently affect global ocean reanalyses, in the perspective of providing reliable near-term climate predictions. [ABSTRACT FROM AUTHOR]

The effect of atmospheric horizontal resolution on tropical variability is investigated within the modified Scale Interaction Experiment (SINTEX) coupled model, SINTEX-Frontier (SINTEX-F), developed jointly at Istituto Nazionale di Geofisica e Vulcanologia (INGV), L’Institut Pierre-Simon Laplace (IPSL), and the Frontier Research System. The ocean resolution is not changed as the atmospheric model resolution is modified from spectral resolution 30 (T30) to spectral resolution 106 (T106). The horizontal resolutions of the atmospheric model T30 and T106 are investigated in terms of the coupling characteristics, frequency, and variability of the tropical ocean–atmosphere interactions. It appears that the T106 resolution is generally beneficial even if it does not eliminate all the major systematic errors of the coupled model. There is an excessive shift west of the cold tongue and ENSO variability, and high resolution also has a somewhat negative impact on the variability in the east Indian Ocean. A dominant 2-yr peak for the Niño-3 variability in the T30 model is moderated in the T106 as it shifts to a longer time scale. At high resolution, new processes come into play, such as the coupling of tropical instability waves, the resolution of coastal flows at the Pacific–Mexican coasts, and improved coastal forcing along the coast of South America. The delayed oscillator seems to be the main mechanism that generates the interannual variability in both models, but the models realize it in different ways. In the T30 model it is confined close to the equator, involving relatively fast equatorial and near-equatorial modes, and in the high-resolution model, it involves a wider latitudinal region and slower waves. It is speculated that the extent of the region that is involved in the interannual variability may be linked to the time scale of the variability itself. [ABSTRACT FROM AUTHOR]

Abstract: The protective capabilities of three Leishmania recombinant proteins – histone 1 (H1) and hydrophilic acylated surface protein B1 (HASPB1) immunized singly, or together as a protein cocktail vaccine with Montanide™, and the polyprotein MML immunized with MPL®-SE adjuvant – were assessed in beagle dogs. Clinical examination of the dogs was carried out periodically under blinded conditions and the condition of the dogs defined as asymptomatic or symptomatic. At the end of the trial, we were able to confirm that following infection with L. infantum promastigotes, five out of eight dogs immunized with H1 Montanide™, and four out of eight dogs immunized with either the combination of HASPB1 with Montanide™ or the combination of H1+HASPB1 with Montanide™, remained free of clinical signs, compared with two out of seven dogs immunized with the polyprotein MML and adjuvant MPL®-SE, and two out of eight dogs in the control group. The results demonstrate that HASPB1 and H1 antigens in combination with Montanide™ were able to induce partial protection against canine leishmaniasis, even under extreme experimental challenge conditions. [Copyright &y& Elsevier]

Abstract: The set of equations for global ocean biogeochemistry deterministic models have been formulated in a comprehensive and unified form in order to use them in numerical simulations of the marine ecosystem for climate change studies (PELAGOS, PELAgic biogeochemistry for Global Ocean Simulations). The fundamental approach stems from the representation of marine trophic interactions and major biogeochemical cycles introduced in the European Regional Seas Ecosystem Model (ERSEM). Our theoretical formulation revisits and generalizes the stoichiometric approach of ERSEM by defining the state variables as Chemical Functional Families (CFF). CFFs are further subdivided into living, non-living and inorganic components. Living CFFs are the basis for the definition of Living Functional Groups, the biomass-based functional prototype of the real organisms. Both CFFs and LFGs are theoretical constructs which allow us to relate measurable properties of marine biogeochemistry to the state variables used in deterministic models. This approach is sufficiently generic that may be used to describe other existing biomass-based ecosystem model. [Copyright &y& Elsevier]

Euro‐Mediterranean Centre on Climate Change coupled climate model (CMCC‐CM2) represents the new family of the global coupled climate models developed and used at CMCC. It is based on the atmospheric, land and sea ice components from the Community Earth System Model coupled with the global ocean model Nucleus for European Modeling of the Ocean. This study documents the model components, the coupling strategy, particularly for the oceanic, atmospheric, and sea ice components, and the overall model ability in reproducing the observed mean climate and main patterns of interannual variability. As a first step toward a more comprehensive, process‐oriented, validation of the model, this work analyzes a 200‐year simulation performed under constant forcing corresponding to present‐day climate conditions. In terms of mean climate, the model is able to realistically reproduce the main patterns of temperature, precipitation, and winds. Specifically, we report improvements in the representation of the sea surface temperature with respect to the previous version of the model. In terms of mean atmospheric circulation features, we notice a realistic simulation of upper tropospheric winds and midtroposphere geopotential eddies. The oceanic heat transport and the Atlantic meridional overturning circulation satisfactorily compare with present‐day observations and estimates from global ocean reanalyses. The sea ice patterns and associated seasonal variations are realistically reproduced in both hemispheres, with a better skill in winter. Main weaknesses of the simulated climate are related with the precipitation patterns, specifically in the tropical regions with large dry biases over the Amazon basin. Similarly, the seasonal precipitation associated with the monsoons, mostly over Asia, is weaker than observed. The main patterns of interannual variability in terms of dominant empirical orthogonal functions are faithfully reproduced, mostly in the Northern Hemisphere winter. In the tropics the main teleconnection patterns associated with El Niño–Southern Oscillation and with the Indian Ocean Dipole are also in good agreement with observations. Key Points: New CMCC climate model built coupling atmosphere and land components of NCAR model with NEMO ocean modelRealistic representation of mean climate and main patterns of variability, mostly for the Northern Hemisphere winterImprovements in some aspects of the SST pattern with respect to a previous version of CMCC model [ABSTRACT FROM AUTHOR]

Accurate knowledge of the location and magnitude of ocean heat content (OHC) variability and change is essential for understanding the processes that govern decadal variations in surface temperature, quantifying changes in the planetary energy budget, and developing constraints on the transient climate response to external forcings. We present an overview of the temporal and spatial characteristics of OHC variability and change as represented by an ensemble of dynamical and statistical ocean reanalyses (ORAs). Spatial maps of the 0-300 m layer show large regions of the Pacific and Indian Oceans where the interannual variability of the ensemble mean exceeds ensemble spread, indicating that OHC variations are well-constrained by the available observations over the period 1993-2009. At deeper levels, the ORAs are less well-constrained by observations with the largest differences across the ensemble mostly associated with areas of high eddy kinetic energy, such as the Southern Ocean and boundary current regions. Spatial patterns of OHC change for the period 1997-2009 show good agreement in the upper 300 m and are characterized by a strong dipole pattern in the Pacific Ocean. There is less agreement in the patterns of change at deeper levels, potentially linked to differences in the representation of ocean dynamics, such as water mass formation processes. However, the Atlantic and Southern Oceans are regions in which many ORAs show widespread warming below 700 m over the period 1997-2009. Annual time series of global and hemispheric OHC change for 0-700 m show the largest spread for the data sparse Southern Hemisphere and a number of ORAs seem to be subject to large initialization 'shock' over the first few years. In agreement with previous studies, a number of ORAs exhibit enhanced ocean heat uptake below 300 and 700 m during the mid-1990s or early 2000s. The ORA ensemble mean (±1 standard deviation) of rolling 5-year trends in full-depth OHC shows a relatively steady heat uptake of approximately 0.9 ± 0.8 W m (expressed relative to Earth's surface area) between 1995 and 2002, which reduces to about 0.2 ± 0.6 W m between 2004 and 2006, in qualitative agreement with recent analysis of Earth's energy imbalance. There is a marked reduction in the ensemble spread of OHC trends below 300 m as the Argo profiling float observations become available in the early 2000s. In general, we suggest that ORAs should be treated with caution when employed to understand past ocean warming trends-especially when considering the deeper ocean where there is little in the way of observational constraints. The current work emphasizes the need to better observe the deep ocean, both for providing observational constraints for future ocean state estimation efforts and also to develop improved models and data assimilation methods. [ABSTRACT FROM AUTHOR]

The present work aims at evaluating the scalability performance of a high-resolution global ocean biogeochemistry model (PELAGOS025) on massive parallel architectures and the benefits in terms of the time-to-solution reduction. PELAGOS025 is an on-line coupling between the physical ocean model NEMO and the BFM biogeochemical model. Both the models use a parallel domain decomposition along the horizontal dimension. The parallelisation is based on the message passing paradigm. The performance analysis has been done on two parallel architectures, an IBM BlueGene/Q at ALCF (Argonne Leadership Computing Facilities) and an IBM iDataPlex with Sandy Bridge processors at CMCC (Euro Mediterranean Center on Climate Change). The outcome of the analysis demonstrated that the lack of scalability is due to several factors such as the I/O operations, the memory contention, the load unbalancing due to the memory structure of the BFM component and, for the BlueGene/Q, the absence of a hybrid parallelisation approach. [ABSTRACT FROM AUTHOR]

We propose an improvement of an oceanographic three dimensional variational assimilation scheme (3D-VAR), named OceanVar, by introducing a recursive filter (RF) with the third order of accuracy (3rd-RF), instead of an RF with first order of accuracy (1st-RF), to approximate horizontal Gaussian covariances. An advantage of the proposed scheme is that the CPU's time can be substantially reduced with benefits on the large scale applications. Experiments estimating the impact of 3rd-RF are performed by assimilating oceanographic data in two realistic oceanographic applications. The results evince benefits in terms of assimilation process computational time, accuracy of the Gaussian correlation modeling, and show that the 3rd-RF is a suitable tool for operational data assimilation. [ABSTRACT FROM AUTHOR]

Abstract: A one-dimensional ecosystem numerical model is used to simulate the ecosystem changes that could have occurred in the open ocean areas of the Eastern Mediterranean Sea during the Climatic Optimum interval (9500–6000 B.P., Mercone et al. [Mercone, D., Thomson, J., Croudace, I.W., Siani, G., Paterne, M., Troelstra, S., 2000. Duration of S1, the most recent sapropel in the eastern Mediterranean Sea, as indicated by accelerator mass spectrometry radiocarbon and geochemical evidence. Paleoceanography 15, 336–347]). In this period the S1 sapropel was deposited. S1 is the most recent sapropel in the succession of organic carbon-rich layers intercalated in normal Neogene sedimentary sequences. Different theories have been invoked in order to explain the deposition of this peculiar layer. Our simulations seem to indicate that the modified thermohaline circulation, supplying oxygen only in the first 500 m of the water column, is responsible for the sapropel deposition when higher productivity is allowed in the euphotic zone. The model shows the importance in this process of bacteria that consume oxygen by decomposing the Particulate Organic Matter (POM) produced in the upper water column. The sinking velocity of POM partially regulates the timescale of the occurrence of anoxia at the bottom and in the whole water column, allowing the relatively rapid onset of sapropel deposition. [Copyright &y& Elsevier]

Ensemble experiments are performed with five coupled atmosphere–ocean models to investigate the potential for initial-value climate forecasts on interannual to decadal time scales. Experiments are started from similar model-generated initial states, and common diagnostics of predictability are used. We find that variations in the ocean meridional overturning circulation (MOC) are potentially predictable on interannual to decadal time scales, a more consistent picture of the surface temperature impact of decadal variations in the MOC is now apparent, and variations of surface air temperatures in the North Atlantic Ocean are also potentially predictable on interannual to decadal time scales, albeit with potential skill levels that are less than those seen for MOC variations. This intercomparison represents a step forward in assessing the robustness of model estimates of potential skill and is a prerequisite for the development of any operational forecasting system. [ABSTRACT FROM AUTHOR]

The interannual variability in the tropical Indian Ocean, and in particular the Indian Ocean dipole mode (IODM), is investigated using both observations and a multi-decadal simulations performed by the coupled atmosphere–ocean general circulation model SINTEX. Overall, the characteristics of the simulated IODM are close to the features of the observed mode. Evidence of significant correlations between sea level pressure anomalies in the southeastern Indian Ocean and sea surface temperature anomalies in the tropical Indian and Pacific Oceans have been found both in observations and a multi-decadal simulation. In particular, a positive SLP anomaly in the southeastern part of the basin seems to produce favorable conditions for the development of an IODM event. The role played by the ocean dynamics both in the developing and closing phases of the IODM events is also investigated. Our results suggest that, during the developing phase, the heat content and SST variability associated with the IODM are influenced by a local response of the ocean to the winds, and a remote response with the excitation of Kelvin and Rossby waves. Ocean wave dynamics appear to be important also during the dying phase of the IODM, when equatorial downwelling Kelvin waves transport positive heat content anomalies from the western to the eastern part of the basin, suppressing the zonal heat content anomaly gradient. The results obtained from the model suggest a mechanism for the IODM. This mechanism is generally consistent with the characteristics of the observed IODM. Furthermore, it might give some clue in understanding the correlation between IODM and ENSO activity found both in the model and in the observations. [ABSTRACT FROM AUTHOR]