The Herschel-PACS photometer calibration

This paper provides an overview of the PACS photometer flux calibration concept, in particular for the principal observation mode, the scan map. The absolute flux calibration is tied to the photospheric models of five fiducial stellar standards (α Boo, α Cet, α Tau, β And, γ Dra). The data processing steps to arrive at a consistent and homogeneous calibration are outlined. In the current state the relative photometric accuracy is ～2 % in all bands. Starting from the present calibration status, the characterization and correction for instrumental effects affecting the relative calibration accuracy is described and an outlook for the final achievable calibration numbers is given. After including all the correction for the instrumental effects, the relative photometric calibration accuracy (repeatability) will be as good as 0.5 % in the blue and green band and 2 % in the red band. This excellent calibration starts to reveal possible inconsistencies between the models of the K-type and the M-type stellar calibrators. The absolute calibration accuracy is therefore mainly limited by the 5 % uncertainty of the celestial standard models in all three bands. The PACS bolometer response was extremely stable over the entire Herschel mission and a single, time-independent response calibration file is sufficient for the processing and calibration of the science observations. The dedicated measurements of the internal calibration sources were needed only to characterize secondary effects. No aging effects of the bolometer or the filters have been found. Also, we found no signs of filter leaks. The PACS photometric system is very well characterized with a constant energy spectrum νF _ν = λF _λ = const as a reference. Colour corrections for a wide range of sources SEDs are determined and tabulated.     

Internal catchment process simulation in a snow‐dominated basin: performance evaluation with spatiotemporally variable runoff generation and groundwater dynamics

Hydrologic models have increasingly been used in forest hydrology to overcome the limitations of paired watershed experiments, where vegetative recovery and natural variability obscure the inferences and conclusions that can be drawn from such studies. Models are also plagued by uncertainty, however, and parameter equifinality is a common concern. Physically‐based, spatially‐distributed hydrologic models must therefore be tested with high‐quality experimental data describing a multitude of concurrent internal catchment processes under a range of hydrologic regimes. This study takes a novel approach by not only examining the ability of a pre‐calibrated model to realistically simulate watershed outlet flows over a four year period, but a multitude of spatially‐extensive, internal catchment process observations not previously evaluated, including: continuous groundwater dynamics, instantaneous stream and road network flows, and accumulation and melt period spatial snow distributions. Many hydrologic model evaluations are only on the comparison of predicted and observed discharge at a catchment outlet and remain in the ‘infant stage’ in terms of model testing. This study, on the other hand, tests the internal spatial predictions of a distributed model with a range of field observations over a wide range of hydroclimatic conditions. Nash‐Sutcliffe model efficiency was improved over prior evaluations due to continuing efforts in improving the quality of meteorological data collection. Road and stream network flows were generally well simulated for a range of hydrologic conditions, and snowpack spatial distributions were well simulated for one of two years examined. The spatial variability of groundwater dynamics was effectively simulated, except at locations where strong stream–groundwater interactions exist. Model simulations overall were quite successful in realistically simulating the spatiotemporal variability of internal catchment processes in the watershed, but the premature onset of simulated snowmelt for one of the simulation years has prompted further work in model development. Copyright © 2011 John Wiley & Sons, Ltd.     

Seasonal and depth-related dynamics of prokaryotes and viruses in surface and deep waters of the northwestern Mediterranean Sea

The study site located in the northwestern Mediterranean Sea was visited nine times in 2005–2006 to collect water samples from the epi- (5 m), meso- (200, 600 m), and bathypelagic (1000, 2000 m) zone. Total abundance of prokaryotes and viruses was determined by flow cytometry (FCM). Prokaryotic abundance in the epi-, meso-, and bathypelagic varied between 0.9 and 15.9×10⁵, 0.6 and 2.1×10⁵, and 0.3 and 1.3×10⁵ ml⁻¹, respectively. Variation of viral abundance in the epi-, meso-, and bathypelagic was between 1.2 and 57.5×10⁶, 0.5 and 3.5×10⁶, and 0.4 and 1.3×10⁶ ml⁻¹, respectively. The fraction of low (LNA) and high (HNA) nucleic acid prokaryotes averaged 42.9% and 57.1% throughout the water column and did not differ between depth layers. Throughout the water column the fraction of low, medium, and high fluorescent viruses (Vir-LF, Vir-MF, Vir-HF) averaged 66.3%, 30.2%, and 3.5%. Vir-LF and Vir-MF did not differ between depth layers; however, Vir-HF showed a preference for surface waters. The fraction of LNA cells decreased in the epi- and increased in the bathypelagic with decreasing stratification. The fraction of Vir-LF viruses increased in the epipelagic and decreased in the bathypelagic with increasing prokaryotic abundance. Also, the relationship between viral abundance and the bacterial community was different in surface and deep waters. The data suggest that different mechanisms of interaction between viruses and their prokaryotic hosts prevail at the surface and in deep waters.     

Effects of different closures for thickness diffusivity

The effects of spatial variations of the thickness diffusivity (K) appropriate to the parameterisation of [Gent, P.R. and McWilliams, J.C., 1990. Isopycnal mixing in ocean circulation models. J. Phys. Oceanogr., 20, 150–155.] are assessed in a coarse resolution global ocean general circulation model. Simulations using three closures yielding different lateral and/or vertical variations in K are compared with a simulation using a constant value. Although the effects of changing K are in general small and all simulations remain biased compared to observations, we find systematic local sensitivities of the simulated circulation on K. In particular, increasing K near the surface in the tropical ocean lifts the depth of the equatorial thermocline, the strength of the Antarctic Circumpolar Current decreases while the subpolar and subtropical gyre transports in the North Atlantic increase by increasing K locally. We also find that the lateral and vertical structure of K given by a recently proposed closure reduces the negative temperature biases in the western North Atlantic by adjusting the pathways of the Gulf Stream and the North Atlantic Current to a more realistic position.     

Validation of the three-dimensional ECOHAM model in the German Bight for 2004 including population dynamics of Pseudocalanus elongatus

A three-dimensional ecosystem model for the North Sea which includes competition between Pseudocalanus elongatus and the rest of the zooplankton biomass was applied to describe the seasonal cycle of zooplankton in 2003–2004. The paper presents the comparison of simulated stage-resolved abundances with copepod counts at several stations in the German Bight during the GLOBEC-Germany project from February to October 2004. A validation of influential state variables gives confidence that the model is able to calculate reliably the stage development and abundances of P. elongatus as well as the range of bulk zooplankton biomass, and thus the ratio of population biomass to total biomass. In the German Bight, the population is below 20% in spring. The ratio increases up to 50% during summer. The number of generations was estimated from peaks in egg abundance to about 4–8 generations of P. elongatus in the southern North Sea. A mean of four generations per year were estimated in the central North Sea, six to eight generations northwest of the Dogger Bank (tails end) and five generations in the German Bight.     

Functional composition, but not richness, affected the performance of sessile suspension-feeding assemblages

The efficiency by which communities capture limiting resources may be related to the number of species or functional types competing therein. This is because species use different resources (i.e. complementarity effect) or because species-rich communities include species with extreme functional traits (positive selection effect). We conducted two manipulative studies to separate the effects of functional richness and functional identity on the feeding efficiency (i.e. filtration rate) of suspension-feeding invertebrates growing on vertical surfaces. In addition, one experiment tested whether the density of organisms influences the effect of functional diversity. Monocultures and complete mixtures of functional types were fed with a solution of microalgae of different sizes (6 μm–40 μm). Experiments conducted at two locations, Helgoland and Plymouth, showed that functional identity had far larger effects on filtration rate than richness. Mixtures did not outperform the average monoculture or the best-performing monoculture and this pattern was independent on density. The high efficiency of one of the functional types in consuming most microalgae could have minimised the resource complementarity. The loss or gain of particular species may therefore have a stronger impact on the functioning of epibenthic communities than richness per se.     

Widespread rocky reef occurrence in the central English Channel and the implications for predictive habitat mapping

Reefs are one of the marine habitats listed in Annex I of the European Union's Habitats Directive, which aims to establish a coherent European ecological network of Special Areas of Conservation. EU Member States are required to prepare and propose a national list of sites for evaluation under the scheme, but currently the occurrence of reefs in the United Kingdom's nearshore and offshore areas is not well documented. Here we report on our search for rocky reefs in the central English Channel, which unexpectedly revealed an extensive reef system covering an area of 1100 km². Prior to our work, it was generally perceived that the seabed in this area comprised mostly gravel, with a few isolated rock outcrops.Our approach to determining the location, extent and character of these reefs incorporated broad, medium and fine-scale analyses over a 3200 km² area of seabed, using single- and multi-beam acoustic data, ground-truthed by underwater video and stills imagery. A benthic terrain model was developed in ArcGIS to map topographic features at the broad and medium scales. Biotope assignments were made at the fine scale through detailed analysis of video footage obtained from 30 sampling stations. The study area has a complex geological history and lies at the centre of a major bedload-parting zone. Together, these strongly influence the seabed character and the distribution of biotopes. An integrated assessment of the physical and biological features was used to map the study area to level 4 of the EUNIS habitat classification system.Similar physical conditions exist in other areas of the UK continental shelf, raising the prospect of predicting where other rocky reef systems might occur. In the absence of a co-ordinated national seabed survey programme, such predictions, coupled with interpretation of existing single-beam bathymetry data, can help prioritise areas where limited survey resources could be most effectively deployed.     

Observational and numerical modeling methods for quantifying coastal ocean turbulence and mixing

In this review paper, state-of-the-art observational and numerical modeling methods for small scale turbulence and mixing with applications to coastal oceans are presented in one context. Unresolved dynamics and remaining problems of field observations and numerical simulations are reviewed on the basis of the approach that modern process-oriented studies should be based on both observations and models. First of all, the basic dynamics of surface and bottom boundary layers as well as intermediate stratified regimes including the interaction of turbulence and internal waves are briefly discussed. Then, an overview is given on just established or recently emerging mechanical, acoustic and optical observational techniques. Microstructure shear probes although developed already in the 1970s have only recently become reliable commercial products. Specifically under surface waves turbulence measurements are difficult due to the necessary decomposition of waves and turbulence. The methods to apply Acoustic Doppler Current Profilers (ADCPs) for estimations of Reynolds stresses, turbulence kinetic energy and dissipation rates are under further development. Finally, applications of well-established turbulence resolving particle image velocimetry (PIV) to the dynamics of the bottom boundary layer are presented. As counterpart to the field methods the state-of-the-art in numerical modeling in coastal seas is presented. This includes the application of the Large Eddy Simulation (LES) method to shallow water Langmuir Circulation (LC) and to stratified flow over a topographic obstacle. Furthermore, statistical turbulence closure methods as well as empirical turbulence parameterizations and their applicability to coastal ocean turbulence and mixing are discussed. Specific problems related to the combined wave-current bottom boundary layer are discussed. Finally, two coastal modeling sensitivity studies are presented as applications, a two-dimensional study of upwelling and downwelling and a three-dimensional study for a marginal sea scenario (Baltic Sea). It is concluded that the discussed methods need further refinements specifically to account for the complex dynamics associated with the presence of surface and internal waves.     

Grain size and depositional environment as predictors of permeability in coastal marine sands

More than half of the surface sediments covering the continental shelves are sandy, which may permit substantial sub-seafloor pore water advection. Knowledge of sediment permeability is required for quantifying advection and associated solute transport, but studies of marine sediments typically report grain size analyses rather than permeability. Here data from 23 studies were examined to determine the range in permeabilities reported for sublittoral marine sands and to assess the utility of permeability–grain size relationships in this setting. In the resulting database, the permeability of small (∼30 cm) undisturbed cores collected from the sea floor all fell between 2 × 10⁻¹² and 4 × 10⁻¹⁰ m², a range where advective transport induced by wave and current action should be pervasive. The range in grain size was very similar for near-shore (<10 m water depth) and continental shelf samples (>10 m water depth), but the permeability of the continental shelf samples was consistently lower for the same median grain size. Empirical permeability–grain size relationships generated a poor fit (r² = 0.35) for the aggregate data, but separate relationships for near-shore and continental shelf samples were significantly better, r² = 0.66 and 0.77, respectively. Permeability–grain size relationships thus may be useful for sublittoral sands, but a larger database needs to be accumulated before reliable fit parameters and variability can be predicted. Thus it is recommended that permeability be routinely determined when characterizing sedimentological properties of marine sand deposits. Concurrent determinations of sediment bulk density and porosity may further improve estimates of permeability.     

Modeling of mesoscale coupled ocean–atmosphere interaction and its feedback to ocean in the western Arabian Sea

Observations of the western Arabian Sea over the last decade have revealed a rich filamentary eddy structure, with large horizontal SST gradients in the ocean, developing in response to the southwest monsoon winds. This summertime oceanic condition triggers an intense mesoscale coupled interaction, whose overall influence on the longer-term properties of this ocean remains uncertain. In this study, a high-resolution regional coupled model is employed to explore this feedback effect on the long-term dynamical and thermodynamical structure of the ocean.The observed relationship between the near-surface winds and mesoscale SSTs generate Ekman pumping velocities at the scale of the cold filaments, whose magnitude is the order of 1 m/day in both the model and observations. This additional Ekman-driven velocity, induced by the wind-eddy interaction, accounts for approximately 10–20% of oceanic vertical velocity of the cold filaments. This implies that Ekman pumping arising from the mesoscale coupled feedback makes a non-trivial contribution to the vertical structure of the upper ocean and the evolution of mesoscale eddies, with obvious implications for marine ecosystem and biogeochemical variability.Furthermore, SST features associated with cold filaments substantially reduce the latent heat loss. The long-term latent heat flux change due to eddies in the model is approximately 10–15 W/m² over the cold filaments, which is consistent with previous estimates based on short-term in situ measurements. Given the shallow mixed layer, this additional surface heat flux warms the cold filament at the rate of 0.3–0.4 °C/month over a season with strong eddy activity, and 0.1–0.2 °C/month over the 12-year mean, rendering overall low-frequency modulation of SST feasible. This long-term mixed layer heating by the surface flux is approximately ±10% of the lateral heat flux by the eddies, yet it can be comparable to the vertical heat flux. Potential dynamic and thermodynamic impacts of this observed air–sea interaction on the monsoons and regional climate are yet to be quantified given the strong correlation between the Somalia upwelling SST and the Indian summer monsoons.