Data assimilation for marine monitoring and prediction: The MERCATOR operational assimilation systems and the MERSEA developments

During the past 15 years, a number of initiatives have been undertaken at national level to develop ocean forecasting systems operating at regional and/or global scales. The co-ordination between these efforts has been organized internationally through the Global Ocean Data Assimilation Experiment (GODAE). The French MERCATOR project is one of the leading participants in GODAE. The MERCATOR systems routinely assimilate a variety of observations such as multi-satellite altimeter data, sea-surface temperature and in situ temperature and salinity profiles, focusing on high-resolution scales of the ocean dynamics. The assimilation strategy in MERCATOR is based on a hierarchy of methods of increasing sophistication including optimal interpolation, Kalman filtering and variational methods, which are progressively deployed through the Syst`eme d’Assimilation MERCATOR (SAM) series. SAM-1 is based on a reduced-order optimal interpolation which can be operated using ‘altimetry-only’ or ‘multi-data’ set-ups; it relies on the concept of separability, assuming that the correlations can be separated into a product of horizontal and vertical contributions. The second release, SAM-2, is being developed to include new features from the singular evolutive extended Kalman (SEEK) filter, such as three-dimensional, multivariate error modes and adaptivity schemes. The third one, SAM-3, considers variational methods such as the incremental four-dimensional variational algorithm. Most operational forecasting systems evaluated during GODAE are based on least-squares statistical estimation assuming Gaussian errors. In the framework of the EU MERSEA (Marine EnviRonment and Security for the European Area) project, research is being conducted to prepare the next-generation operational ocean monitoring and forecasting systems. The research effort will explore nonlinear assimilation formulations to overcome limitations of the current systems. This paper provides an overview of the developments conducted in MERSEA with the SEEK filter, the Ensemble Kalman filter and the sequential importance re-sampling filter.

Categorisation of synoptic environments associated with mesoscale convective systems over the UK

Mesoscale convective systems (MCSs) are relatively rare events in the UK but, when they do occur, can be associated with weather that is considered extreme with respect to climatology (as indicated by the number of such events that have been analysed as case studies). These case studies usually associate UK MCSs with a synoptic environment known as the Spanish plume. Here a previously published 17 year climatology of UK MCS events is extended to the present day (from 1998 to 2008) and these events classified according to the synoptic environment in which they form. Three distinct synoptic environments have been identified, here termed the classical Spanish plume, modified Spanish plume, and European easterly plume. Detailed case studies of the two latter, newly defined, environments are presented. Composites produced for each environment further reveal the differences between them. The classical Spanish plume is associated with an eastward propagating baroclinic cyclone that evolves according to idealised life cycle 1. Conditional instability is released from a warm moist plume of air advected northeastwards from Iberia that is capped by warmer, but very dry air, from the Spanish plateau. The modified Spanish plume is associated with a slowly moving mature frontal system associated with a forward tilting trough (and possibly cut-off low) at 500 hPa that evolves according to idealised life cycle 2. As in the classical Spanish plume, conditional instability is released from a warm plume of air advected northwards from Iberia. The less frequent European easterly plume is associated with an omega block centred over Scandinavia at upper levels. Conditional instability is released from a warm plume of air advected westwards across northern continental Europe. Unlike the Spanish plume environments, the European easterly plume is not a warm sector phenomena associated with a baroclinic cyclone. However, in all environments the organisation of convection is associated with the interaction of an upper-level disturbance with a low-level region of warm advection.

Pea-barley intercropping for efficient symbiotic N-2-fixation, soil N acquisition and use of other nutrients in European organic cropping systems

Complementarity in acquisition of nitrogen (N) from soil and N-2-fixation within pea and barley intercrops was studied in organic field experiments across Western Europe (Denmark, United Kingdom, France, Germany and Italy). Spring pea and barley were sown either as sole crops, at the recommended plant density (P100 and B100, respectively) or in replacement (P50B50) or additive (P100B50) intercropping designs, in each of three cropping seasons (2003-2005). Irrespective of site and intercrop design, Land Equivalent Ratios (LER) between 1.4 at flowering and 1.3 at maturity showed that total N recovery was greater in the pea-barley intercrops than in the sole Crops Suggesting a high degree of complementarity over a wide range of growing conditions. Complementarity was partly attributed to greater soil mineral N acquisition by barley, forcing pea to rely more on N-2-fixation. At all sites the proportion of total aboveground pea N that was derived from N-2-fixation was greater when intercropped with barley than when grown as a sole crop. No consistent differences were found between the two intercropping designs. Simultaneously, the accumulation Of Phosphorous (P), potassium (K) and sulphur (S) in Danish and German experiments was 20% higher in the intercrop (P50B50) than in the respective sole crops, possibly influencing general crop yields and thereby competitive ability for other resources. Comparing all sites and seasons, the benefits of organic pea-barley intercropping for N acquisition were highly resilient. It is concluded that pea-barley intercropping is a relevant cropping strategy to adopt when trying to optimize N-2-fixation inputs to the cropping system. (C) 2009 Elsevier B.V. All rights reserved.

Pea-barley intercropping and short-term subsequent crop effects across European organic cropping conditions

Grain legumes are known to increase the soil mineral nitrogen (N) content, reduce the infection pressure of soil borne pathogens, and hence enhance subsequent cereals yields. Replicated field experiments were performed throughout W. Europe (Denmark, United Kingdom, France, Germany and Italy) to asses the effect of intercropping pea and barley on the N supply to subsequent wheat in organic cropping systems. Pea and barley were grown either as sole crops at the recommended plant density (P100 and B100, respectively) or in replacement (P50B50) or additive (P100B50) intercropping designs. In the replacement design the total relative plant density is kept constant, while the additive design uses the optimal sole crop density for pea supplementing with 'extra' barley plants. The pea and barley crops were followed by winter wheat with and without N application. Additional experiments in Denmark and the United Kingdom included subsequent spring wheat with grass-clover as catch crops. The experiment was repeated over the three cropping seasons of 2003, 2004 and 2005. Irrespective of sites and intercrop design pea-barley intercropping improved the plant resource utilization (water, light, nutrients) to grain N yield with 25-30% using the Land Equivalent ratio. In terms of absolute quantities, sole cropped pea accumulated more N in the grains as compared to the additive design followed by the replacement design and then sole cropped barley. The post harvest soil mineral N content was unaffected by the preceding crops. Under the following winter wheat, the lowest mineral N content was generally found in early spring. Variation in soil mineral N content under the winter wheat between sites and seasons indicated a greater influence of regional climatic conditions and long-term cropping history than annual preceding crop and residue quality. Just as with the soil mineral N, the subsequent crop response to preceding crop was negligible. Soil N balances showed general negative values in the 2-year period, indicating depletion of N independent of preceding crop and cropping strategy. It is recommended to develop more rotational approaches to determine subsequent crop effects in organic cropping systems, since preceding crop effects, especially when including legumes, can occur over several years of cropping.

Role of nesting resources in organising diverse bee communities in a Mediterranean landscape

1. The habitat components determining the structure of bee communities are well known when considering foraging resources; however, there is little data with respect to the role of nesting resources. 2. As a model system this study uses 21 diverse bee communities in a Mediterranean landscape comprising a variety of habitats regenerating after fire. The findings clearly demonstrate that a variety of nesting substrates and nest building materials have key roles in organising the composition of bee communities. 3. The availability of bare ground and potential nesting cavities were the two primary factors influencing the structure of the entire bee community, the composition of guilds, and also the relative abundance of the dominant species. Other nesting resources shown to be important include availability of steep and sloping ground, abundance of plant species providing pithy stems, and the occurrence of pre-existing burrows. 4. Nesting resource availability and guild structure varied markedly across habitats in different stages of post-fire regeneration; however, in all cases, nest sites and nesting resources were important determinants of bee community structure.

Inter-laboratory variation of in vitro cumulative gas production profiles of feeds using manual and automated methods

A study was conducted to estimate variation among laboratories and between manual and automated techniques of measuring pressure on the resulting gas production profiles (GPP). Eight feeds (molassed sugarbeet feed, grass silage, maize silage, soyabean hulls, maize gluten feed, whole crop wheat silage, wheat, glucose) were milled to pass a I mm screen and sent to three laboratories (ADAS Nutritional Sciences Research Unit, UK; Institute of Grassland and Environmental Research (IGER), UK; Wageningen University, The Netherlands). Each laboratory measured GPP over 144 h using standardised procedures with manual pressure transducers (MPT) and automated pressure systems (APS). The APS at ADAS used a pressure transducer and bottles in a shaking water bath, while the APS at Wageningen and IGER used a pressure sensor and bottles held in a stationary rack. Apparent dry matter degradability (ADDM) was estimated at the end of the incubation. GPP were fitted to a modified Michaelis-Menten model assuming a single phase of gas production, and GPP were described in terms of the asymptotic volume of gas produced (A), the time to half A (B), the time of maximum gas production rate (t(RM) (gas)) and maximum gas production rate (R-M (gas)). There were effects (P<0.001) of substrate on all parameters. However, MPT produced more (P<0.001) gas, but with longer (P<0.001) B and t(RM gas) (P<0.05) and lower (P<0.001) R-M gas compared to APS. There was no difference between apparatus in ADDM estimates. Interactions occurred between substrate and apparatus, substrate and laboratory, and laboratory and apparatus. However, when mean values for MPT were regressed from the individual laboratories, relationships were good (i.e., adjusted R-2 = 0.827 or higher). Good relationships were also observed with APS, although they were weaker than for MPT (i.e., adjusted R-2 = 0.723 or higher). The relationships between mean MPT and mean APS data were also good (i.e., adjusted R 2 = 0. 844 or higher). Data suggest that, although laboratory and method of measuring pressure are sources of variation in GPP estimation, it should be possible using appropriate mathematical models to standardise data among laboratories so that data from one laboratory could be extrapolated to others. This would allow development of a database of GPP data from many diverse feeds. (c) 2005 Published by Elsevier B.V.

The value of sown grass margins for enhancing soil macrofaunal biodiversity in arable systems

The presence of a grass strip was found to be beneficial to soil macrofauna, increasing the species densities and abundances of earthworms, woodlice and staphylinid beetles. The biodiversity of the three main feeding groups - predators, soil ingesters and litter consumers - was also significantly higher in the grass strips than in the field edges without strips, indicating that establishment of grassy margins in arable fields may enhance ecosystem services such as soil fertility and pest control. The grass strip habitat contained a large number of species of soil macrofauna, being second only to hedgerow habitat, with 10% of the total species list for the farm found only within the margins. Of the rare species recorded on the farm, five of the nine were from the grass strips, four of which were found only there. This study shows that establishing grassy strips in the margins of arable fields increases the biodiversity of the soil macrofauna, both within fields (alpha diversity) and across the farm (beta diversity). (C) 2008 Elsevier B.V. All rights reserved.

Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna

Background: Ibuprofen and other nonsteroidal anti-inflammatory drugs have been designed to interrupt eicosanoid metabolism in mammals, but little is known of how they affect nontarget organisms. Here we report a systems biology study that simultaneously describes the transcriptomic and phenotypic stress responses of the model crustacean Daphnia magna after exposure to ibuprofen. Results: Our findings reveal intriguing similarities in the mode of action of ibuprofen between vertebrates and invertebrates, and they suggest that ibuprofen has a targeted impact on reproduction at the molecular, organismal, and population level in daphnids. Microarray expression and temporal real-time quantitative PCR profiles of key genes suggest early ibuprofen interruption of crustacean eicosanoid metabolism, which appears to disrupt signal transduction affecting juvenile hormone metabolism and oogenesis. Conclusion: Combining molecular and organismal stress responses provides a guide to possible chronic consequences of environmental stress for population health. This could improve current environmental risk assessment by providing an early indication of the need for higher tier testing. Our study demonstrates the advantages of a systems approach to stress ecology, in which Daphnia will probably play a major role.

In vitro fermentation of carbohydrates by porcine faecal inocula and their influence on Salmonella Typhimurium growth in batch culture systems

The aim of this study was to evaluate in vitro the influence of fermentable carbohydrates on the activity of porcine microbiota and survival of Salmonella Typhimurium in a batch culture system simulating the porcine hindgut. The carbohydrates tested were xylooligosaccharides, a mixture of fructooligosaccharides/inulin (FIN), fructooligosaccharides (FOS), gentiooligosaccharides (GEO) and lactulose (LAC). These ingredients stimulated the growth of selected Bifidobacterium and Lactobacillus species in pure cultures. In batch cultures, the carbohydrates influenced some fermentation parameters. For example, GEO and FIN significantly increased lactic acids compared with the control (no added carbohydrate). With the exception of LAC, the test carbohydrates increased the production of short-chain fatty acid (SCFA) and modified SCFA profiles. Quantitative analysis of bacterial populations by FISH revealed increased counts of the Bifidobacterium group compared with control and, with exception of FOS, increased Lactobacillus, Leuconostoc and Weissella spp. counts. Salmonella numbers were the lowest during the fermentation of LAC. This work has looked at carbohydrate metabolism by porcine microbiota in a pH-controlled batch fermentation system. It provides an initial model to analyse interactions with pathogens.

Closely coupled behaviour in networked robot systems

Multiple cooperating robot systems may be required to take up a closely coupled configuration in order to perform a task. An example is extended baseline stereo (EBS), requiring that two robots must establish and maintain for a certain period of time a constrained kinematic relationship to each other. In this paper we report on the development of a networked robotics framework for modular, distributed robot systems that supports the creation of such configurations. The framework incorporates a query mechanism to locate modules distributed across the two robot systems. The work presented in this paper introduces special mechanisms to model the kinematic constraint and its instantiation. The EBS configuration is used as a case study and experimental implementation to demonstrate the approach.

Multiple-scattering in radar systems: a review

Although extensively studied within the lidar community, the multiple scattering phenomenon has always been considered a rare curiosity by radar meteorologists. Up to few years ago its appearance has only been associated with two- or three-body-scattering features (e.g. hail flares and mirror images) involving highly reflective surfaces. Recent atmospheric research aimed at better understanding of the water cycle and the role played by clouds and precipitation in affecting the Earth's climate has driven the deployment of high frequency radars in space. Examples are the TRMM 13.5 GHz, the CloudSat 94 GHz, the upcoming EarthCARE 94 GHz, and the GPM dual 13-35 GHz radars. These systems are able to detect the vertical distribution of hydrometeors and thus provide crucial feedbacks for radiation and climate studies. The shift towards higher frequencies increases the sensitivity to hydrometeors, improves the spatial resolution and reduces the size and weight of the radar systems. On the other hand, higher frequency radars are affected by stronger extinction, especially in the presence of large precipitating particles (e.g. raindrops or hail particles), which may eventually drive the signal below the minimum detection threshold. In such circumstances the interpretation of the radar equation via the single scattering approximation may be problematic. Errors will be large when the radiation emitted from the radar after interacting more than once with the medium still contributes substantially to the received power. This is the case if the transport mean-free-path becomes comparable with the instrument footprint (determined by the antenna beam-width and the platform altitude). This situation resembles to what has already been experienced in lidar observations, but with a predominance of wide- versus small-angle scattering events. At millimeter wavelengths, hydrometeors diffuse radiation rather isotropically compared to the visible or near infrared region where scattering is predominantly in the forward direction. A complete understanding of radiation transport modeling and data analysis methods under wide-angle multiple scattering conditions is mandatory for a correct interpretation of echoes observed by space-borne millimeter radars. This paper reviews the status of research in this field. Different numerical techniques currently implemented to account for higher order scattering are reviewed and their weaknesses and strengths highlighted. Examples of simulated radar backscattering profiles are provided with particular emphasis given to situations in which the multiple scattering contributions become comparable or overwhelm the single scattering signal. We show evidences of multiple scattering effects from air-borne and from CloudSat observations, i.e. unique signatures which cannot be explained by single scattering theory. Ideas how to identify and tackle the multiple scattering effects are discussed. Finally perspectives and suggestions for future work are outlined. This work represents a reference-guide for studies focused at modeling the radiation transport and at interpreting data from high frequency space-borne radar systems that probe highly opaque scattering media such as thick ice clouds or precipitating clouds.

A comparison of stratosphere-troposphere transport in convection-permitting and convection-parameterizing simulations of three mesoscale convective systems

The transport of stratospheric air into the troposphere within deep convection was investigated using the Met Office Unified Model version 6.1. Three cases were simulated in which convective systems formed over the UK in the summer of 2005. For each of these three cases, simulations were performed on a grid having 4 km horizontal grid spacing in which the convection was parameterized and on a grid having 1 km horizontal grid spacing, which permitted explicit representation of the largest energy-containing scales of deep convection. Cross-tropopause transport was diagnosed using passive tracers that were initialized above the dynamically defined tropopause (2 potential vorticity unit surface) with a mixing ratio of 1. Although the synoptic-scale environment and triggering mechanisms varied between the cases, the total simulated transport was similar in all three cases. The total stratosphere-to-troposphere transport over the lifetime of the convective systems ranged from 25 to 100 kg/m2 across the simulated convective systems and resolutions, which corresponds to ∼5–20% of the total mass located within a stratospheric column extending 2 km above the tropopause. In all simulations, the transport into the lower troposphere (defined as below 3.5 km elevation) accounted for ∼1% of the total transport across the tropopause. In the 4 km runs most of the transport was due to parameterized convection, whereas in the 1 km runs the transport was due to explicitly resolved convection. The largest difference between the simulations with different resolutions occurred in the one case of midlevel convection considered, in which the total transport in the 1 km grid spacing simulation with explicit convection was 4 times that in the 4 km grid spacing simulation with parameterized convection. Although the total cross-tropopause transport was similar, stratospheric tracer was deposited more deeply to near-surface elevations in the convection-parameterizing simulations than in convection-permitting simulations.

Some physical drivers of changes in the winter storm tracks over the North Atlantic and Mediterranean during the Holocene

The winter climate of Europe and the Mediterranean is dominated by the weather systems of the mid-latitude storm tracks. The behaviour of the storm tracks is highly variable, particularly in the eastern North Atlantic, and has a profound impact on the hydroclimate of the Mediterranean region. A deeper understanding of the storm tracks and the factors that drive them is therefore crucial for interpreting past changes in Mediterranean climate and the civilizations it has supported over the last 12 000 years (broadly the Holocene period). This paper presents a discussion of how changes in climate forcing (e.g. orbital variations, greenhouse gases, ice sheet cover) may have impacted on the ‘basic ingredients’ controlling the mid-latitude storm tracks over the North Atlantic and the Mediterranean on intermillennial time scales. Idealized simulations using the HadAM3 atmospheric general circulation model (GCM) are used to explore the basic processes, while a series of timeslice simulations from a similar atmospheric GCM coupled to a thermodynamic slab ocean (HadSM3) are examined to identify the impact these drivers have on the storm track during the Holocene. The results suggest that the North Atlantic storm track has moved northward and strengthened with time since the Early to Mid-Holocene. In contrast, the Mediterranean storm track may have weakened over the same period. It is, however, emphasized that much remains still to be understood about the evolution of the North Atlantic and Mediterranean storm tracks during the Holocene period.

Learning across business sectors: context, embeddedness and conceptual chasms

While the construction industry is frequently encouraged to learn from other business sectors, the difficulties of transferring knowledge from one context to another are rarely acknowledged. The problematic nature of knowledge is addressed with particular emphasis on the concept of contextual embeddedness. From this point of view, the process of 'knowledge transfer' depends upon a prolonged process of socialization between actors from both the 'receiving' and 'sending' contexts networking. It is contended that a significant conceptual chasm exists between the exhortations of industry leaders to learn from other sectors and the theoretical complexities associated with knowledge transfer. An ongoing research project is described that seeks to facilitate knowledge sharing between construction and aerospace. A novel approach to knowledge sharing based upon soft systems methodology (SSM) (Mode 2) is described and justified. Initial findings from the first cycle of the research are discussed and used to highlight the importance of context in the implementation of supply chain management.

Using learning networks to understand complex systems: a case study of biological, geophysical and social research in the Amazon

Developing high-quality scientific research will be most effective if research communities with diverse skills and interests are able to share information and knowledge, are aware of the major challenges across disciplines, and can exploit economies of scale to provide robust answers and better inform policy. We evaluate opportunities and challenges facing the development of a more interactive research environment by developing an interdisciplinary synthesis of research on a single geographic region. We focus on the Amazon as it is of enormous regional and global environmental importance and faces a highly uncertain future. To take stock of existing knowledge and provide a framework for analysis we present a set of mini-reviews from fourteen different areas of research, encompassing taxonomy, biodiversity, biogeography, vegetation dynamics, landscape ecology, earth-atmosphere interactions, ecosystem processes, fire, deforestation dynamics, hydrology, hunting, conservation planning, livelihoods, and payments for ecosystem services. Each review highlights the current state of knowledge and identifies research priorities, including major challenges and opportunities. We show that while substantial progress is being made across many areas of scientific research, our understanding of specific issues is often dependent on knowledge from other disciplines. Accelerating the acquisition of reliable and contextualized knowledge about the fate of complex pristine and modified ecosystems is partly dependent on our ability to exploit economies of scale in shared resources and technical expertise, recognise and make explicit interconnections and feedbacks among sub-disciplines, increase the temporal and spatial scale of existing studies, and improve the dissemination of scientific findings to policy makers and society at large. Enhancing interaction among research efforts is vital if we are to make the most of limited funds and overcome the challenges posed by addressing large-scale interdisciplinary questions. Bringing together a diverse scientific community with a single geographic focus can help increase awareness of research questions both within and among disciplines, and reveal the opportunities that may exist for advancing acquisition of reliable knowledge. This approach could be useful for a variety of globally important scientific questions.