WPS orchestration using the Taverna workbench: The eScience approach

eScience is an umbrella concept which covers internet technologies, such as web service orchestration that involves manipulation and processing of high volumes of data, using simple and efficient methodologies. This concept is normally associated with bioinformatics, but nothing prevents the use of an identical approach for geoinfomatics and OGC (Open Geospatial Consortium) web services like WPS (Web Processing Service). In this paper we present an extended WPS implementation based on the PyWPS framework using an automatically generated WSDL (Web Service Description Language) XML document that replicates the WPS input/output document structure used during an Execute request to a server. Services are accessed using a modified SOAP (Simple Object Access Protocol) interface provided by PyWPS, that uses service and input/outputs identifiers as element names. The WSDL XML document is dynamically generated by applying XSLT (Extensible Stylesheet Language Transformation) to the getCapabilities XML document that is generated by PyWPS. The availability of the SOAP interface and WSDL description allows WPS instances to be accessible to workflow development software like Taverna, enabling users to build complex workflows using web services represented by interconnecting graphics. Taverna will transform the visual representation of the workflow into a SCUFL (Simple Conceptual Unified Flow Language) based XML document that can be run internally or sent to a Taverna orchestration server. SCUFL uses a dataflow-centric orchestration model as opposed to the more commonly used orchestration language BPEL (Business Process Execution Language) which is process-centric.

Shore height and differentials between macrobenthic assemblages in vegetated and unvegetated areas of an intertidal sandflat

Intertidal macrobenthic faunal assemblages of a dual seagrass/callianassid-structured sandflat system were investigated in subtropical Moreton Bay, Queensland. Consistently across all 20 stations, the gastropod-dominated seagrass supported greater abundance (2.5×) and species richness (2×) than the amphipod-dominated sandflat. There was no evidence of along-shore or up-shore variation in the overall assemblage properties such as total abundance, species richness or diversity within either habitat type, except for variation in sandflat abundance between sites. But seagrass and sandflat assemblages both varied significantly in composition from site to site, and seagrass assemblage composition also varied with shore height. Shore height and site, however, only accounted for ≤41% of total variation. The two faunal assemblages showed a Bray–Curtis dissimilarity of 97.7% and within-habitat similarities of <20%. There was no consistency in distribution of greater diversity, dominance or evenness. No differential between any assemblage features in adjacent sandflat and seagrass samples changed with shore height, supporting hypotheses that such differentials are not maintained by predation. Macrofaunal species richness and diversity were closely coupled within sandflat stations but were uncoupled within seagrass ones, questioning the value of diversity as a comparative measure.

Iron organic speciation determination in rainwater using cathodic stripping voltammetry

A sensitive method using Competitive Ligand Exchange-Adsorptive Cathodic Stripping Voltammetry (CLE-ACSV) has been developed to determine for the first time iron (Fe) organic speciation in rainwater over the typical natural range of pH. We have adapted techniques previously developed in other natural waters to rainwater samples, using the competing ligand 1-nitroso-2-naphthol (NN). The blank was equal to 0.17 ± 0.05 nM (n = 14) and the detection limit (DL) for labile Fe was 0.15 nM which is 10–70 times lower than that of previously published methods. The conditional stability constant for NN under rainwater conditions was calibrated over the pH range 5.52–6.20 through competition with ethylenediaminetetraacetic acid (EDTA). The calculated value of the logarithm of β′Fe3+3(NN)β′Fe3+(NN)3 increased linearly with increasing pH according to log β′Fe3+3(NN)=2.4±0.6×pH+11.9±3.5log β′Fe3+(NN)3=2.4±0.6×pH+11.9±3.5 (salinity = 2.9, T = 20 °C). The validation of the method was carried out using desferrioxamine mesylate B (DFOB) as a natural model ligand for Fe. Adequate detection windows were defined to detect this class of ligands in rainwater with 40 μM of NN from pH 5.52 to 6.20. The concentration of Fe-complexing natural ligands was determined for the first time in three unfiltered and one filtered rainwater samples. Organic Fe-complexing ligand concentrations varied from 104.2 ± 4.1 nM equivalent of Fe(III) to 336.2 ± 19.0 nM equivalent of Fe(III) and the logarithm of the conditional stability constants, with respect to Fe3+, varied from 21.1 ± 0.2 to 22.8 ± 0.3. This method will provide important data for improving our understanding of the role of wet deposition in the biogeochemical cycling of iron.

A mechanistic explanation of the Sargasso Sea DMS summer paradox

In the Sargasso Sea, maximum dimethylsulfide (DMS) accumulation occurs in summer, concomitant with the minimum of chlorophyll and 2 months later than its precursor, dimethylsulfoniopropionate (DMSP). This phenomenon is often referred to as the DMS "summer paradox". It has been previously suggested that the main agent triggering this pattern is increasing irradiance leading to light stress-induced DMS release from phytoplankton cells. We have developed a new model describing DMS(P) dynamics in the water column and used it to investigate how and to what extent processes other than light induced DMS exudation from phytoplankton, may contribute to the DMS summer paradox. To do this, we have conceptually divided the DMS "summer paradox" into two components: (1) the temporal decoupling between chlorophyll and DMSP and (2) the temporal decoupling between DMSP and DMS. Our results suggest that it is possible to explain the above cited patterns by means of two different dynamics, respectively: (1) a succession of phytoplankton types in the surface water and (2) the bacterially mediated DMSP(d) to DMS conversion, seasonally varying as a function of nutrient limitation. This work differs from previous modelling studies in that the presented model suggests that phytoplankton light-stress induced processes may only partially explain the summer paradox, not being able to explain the decoupling between DMSP and DMS, which is possibly the more challenging aspect of this phenomenon. Our study, therefore, provides an "alternative" explanation to the summer paradox further underlining the major role that bacteria potentially play in DMS production and fate.

The co-location of offshore windfarms and decapod fisheries in the UK: Constraints and opportunities

The offshore wind sector in the UK is expanding rapidly and is set to occupy significant areas of the coastal zone, making it necessary to explore the potential for co-location with other economic activities. The presence of turbine foundations introduces hard substrates into areas previously dominated by soft sediments, implying that artificial reef effects may occur, with potential benefits for fisheries. This review focuses on the possibilities for locating fisheries for two commercially important decapods, the brown crab Cancer pagurus and the European lobster Homarus gammarus, within offshore wind farms. Existing understanding of habitat use by C pagurus and H. gammarus suggests that turbine foundations have the potential to act as artificial reefs, although the responses of these species to noise and electromagnetic fields are poorly understood. Offshore wind farm monitoring programmes provide very limited information, but do suggest that adult C pagurus associate with turbine foundations, which may also serve as nursery areas. There was insufficient deployment and monitoring of rock armouring to draw conclusions about the association of H. gammarus with offshore wind farm foundations. The limited information currently available demonstrates the need for further research into the ecological and socioeconomic issues surrounding fishery co-location potential.

The influence of ocean acidification on nitrogen regeneration and nitrous oxide production in the North-West European shelf sea

The assimilation and regeneration of dissolved inorganic nitrogen, and the concentration of N2O, was investigated at stations located in the NW European shelf sea during June/July 2011. These observational measurements within the photic zone demonstrated the simultaneous regeneration and assimilation of NH4+, NO2− and NO3−. NH4+ was assimilated at 1.82–49.12 nmol N L−1 h−1 and regenerated at 3.46–14.60 nmol N L−1 h−1; NO2− was assimilated at 0–2.08 nmol N L−1 h−1 and regenerated at 0.01–1.85 nmol N L−1 h−1; NO3− was assimilated at 0.67–18.75 nmol N L−1 h−1 and regenerated at 0.05–28.97 nmol N L−1 h−1. Observations implied that these processes were closely coupled at the regional scale and nitrogen recycling played an important role in sustaining phytoplankton growth during the summer. The [N2O], measured in water column profiles, was 10.13 ± 1.11 nmol L−1 and did not strongly diverge from atmospheric equilibrium indicating that sampled marine regions where neither a strong source nor sink of N2O to the atmosphere. Multivariate analysis of data describing water column biogeochemistry and its links to N-cycling activity failed to explain the observed variance in rates of N-regeneration and N-assimilation, possibly due to the limited number of process rate observations. In the surface waters of 5 further stations, Ocean Acidification (OA) bioassay experiments were conducted to investigate the response of NH4+ oxidising and regenerating organisms to simulated OA conditions, including the implications for [N2O]. Multivariate analysis was undertaken which considered the complete bioassay dataset of measured variables describing changes in N-regeneration rate, [N2O] and the biogeochemical composition of seawater. While anticipating biogeochemical differences between locations, we aimed to test the hypothesis that the underlying mechanism through which pelagic N-regeneration responded to simulated OA conditions was independent of location and that a mechanistic understanding of how NH4+ oxidation, NH4+ regeneration and N2O production responded to OA could be developed. Results indicated that N-regeneration process responses to OA treatments were location specific; no mechanistic understanding of how N-regeneration processes respond to OA in the surface ocean of the NW European shelf sea could be developed.

Investigating the inter-relationships between water attenuated irradiance, primary production and DMS(P)

Both solar irradiance and primary production have been proposed as independent controls on seawater dimethyl sulphide (DMS) and dimethylsulphoniopropionate (DMSP) concentrations. However, irradiance also drives photosynthesis, and thus influences a complex set of inter-related processes that modulate marine DMS. We investigate the potential inter-relationships between the rate of primary production (carbon assimilation), water-attenuated irradiance and DMS/DMSP dynamics by applying correlation analysis to a high resolution, concurrently sampled in situ data set from a range of latitudes covering multiple biogeochemical provinces from 3 of the 4 Longhurst biogeochemical domains. The combination of primary production (PP) and underwater irradiance (Iz) within a multivariate regression model is able to explain 55% of the variance in DMS concentrations from all depths within the euphotic zone and 66% of the variance in surface DMS concentrations. Contrary to some previous studies we find a variable representing biological processes is necessary to better account for the variance in DMS. We find that the inclusion of Iz accounts for variance in DMS that is independent from the variance explained by PP. This suggests an important role for solar irradiance (beyond the influence of irradiance upon primary production) in mediating the relationship between the productivity of the ecosystem, DMS/DMSP production and ambient seawater DMS concentrations.

Sardine cycles, krill declines, and locust plagues: revisiting ‘wasp-waist’ food webs

‘Wasp-waist’ systems are dominated by a mid trophic-level species that is thought to exert top-down control on its food and bottom-up control on its predators. Sardines, anchovy, and Antarctic krill are suggested examples, and here we use locusts to explore whether the wasp-waist concept also applies on land. These examples also display the traits of mobile aggregations and dietary diversity, which help to reduce the foraging footprint from their large, localised biomasses. This suggests that top-down control on their food operates at local aggregation scales and not at wider scales suggested by the original definition of wasp-waist. With this modification, the wasp-waist framework can cross-fertilise marine and terrestrial approaches, revealing how seemingly disparate but economically important systems operate.