Validation of a regional Indonesian seas model based on a comparison between model and INSTANT transports

The International Nusantara Stratification and Transport (INSTANT) program measured currents through multiple Indonesian Seas passages simultaneously over a three-year period (from January 2004 to December 2006). The Indonesian Seas region has presented numerous challenges for numerical modelers - the Indonesian Throughflow (ITF) must pass over shallow sills, into deep basins, and through narrow constrictions on its way from the Pacific to the Indian Ocean. As an important region in the global climate puzzle, a number of models have been used to try and best simulate this throughflow. In an attempt to validate our model, we present a comparison between the transports calculated from our model and those calculated from the INSTANT in situ measurements at five passages within the Indonesian Seas (Labani Channel, Lifamatola Passage, Lombok Strait, Ornbai Strait, and Timor Passage). Our Princeton Ocean Model (POM) based regional Indonesian Seas model was originally developed to analyze the influence of bottom topography on the temperature and salinity distributions in the Indonesian seas region, to disclose the path of the South Pacific Water from the continuation of the New Guinea Coastal Current entering the region of interest up to the Lifamatola Passage, and to assess the role of the pressure head in driving the ITF and in determining its total transport. Previous studies found that this model reasonably represents the general long-term flow (seasons) through this region. The INSTANT transports were compared to the results of this regional model over multiple timescales. Overall trends are somewhat represented but changes on timescales shorter than seasonal (three months) and longer than annual were not considered in our model. Normal velocities through each passage during every season are plotted. Daily volume transports and transport-weighted temperature and salinity are plotted and seasonal averages are tabulated.

Contaminants in surface water and sediments around the Tynagh Mine, Galway, Ireland.

A former silver mine in Tynagh, Co. Galway, Ireland is one of the most contaminated mine sites in Europe with maximum concentrations of Zn, As, Pb, Mn, Ni, Cu, and Cd far exceeding guideline values for water and sediment. The aims of this research were to 1) further assess the contamination, particularly metals, in surface water and sediment around the site, and 2) determine if the contamination has increased 10 years after the Environmental Protection Agency Ireland (EPAI) identified off-site contamination. Site pH is alkaline to neutral because CaCO3-rich sediment and rock material buffer the exposed acid generating sulphide-rich ore. When this study was compared to the previous EPAI study conducted 10 years earlier, it appeared that further weathering of exposed surface sediment had increased concentrations of As and other potentially toxic elements. Water samples from the tailings ponds and adjacent Barnacullia Stream had concentrations of Al, Cd, Mn, Zn and Pb above guideline values. Lead and Zn concentrations from the tailings pond sediment were 16 and 5 times higher, respectively, than concentrations reported 10 years earlier. Pb and Zn levels in most sediment samples exceeded the Expert Group (EGS) guidelines of 1000 and 5000 mg/kg, respectively. Arsenic concentrations were as high as 6238 mg/kg in the tailings ponds sediment, which is 62 and 862 times greater than the EGS and Canadian Soil Quality Guidelines (CSQG), respectively. Cadmium, Cu, Fe, Mn, Pb and Zn concentrations in water and sediment were above guideline values downstream of the site. Additionally, Fe, Mn and organic matter (OM) were strongly correlated and correlated to Zn, Pb, As, Cd, Cu and Ni in stream sediment. Therefore, the nearby Barnacullia Stream is also a significant pathway for contaminant transport to downstream areas. Further rehabilitation of the site may decrease the contamination around the area.

The Environmental Fate of polybrominated diphenyl ethers in western Taiwan and coastal waters: evaluation with a fugacity based model

The environmental fate of polybrominated diphenyl ethers (PBDEs), a group of flame retardants that are considered to be persistent organic pollutants (POPs), around the Zhuoshui River and Changhua County regions of Taiwan was assessed. An investigation into emissions, partitioning, and fate of selected PBDEs was conducted based on the equilibrium constant (EQC) fugacity model developed at Trent University, Canada. Emissions for congeners PBDE 47, PBDE 99, and PBDE 209 to air (4.9–92 × 10−3 kg/h), soil (0.91–17.4 × 10−3 kg/h), and water (0.21–4.04 × 10−3 kg/h), were estimated by modifying previous models on PBDE emission rates by considering both industrial and domestic rates. It was found that fugacity modeling can give a reasonable estimation of the behavior, partitioning, and concentrations of PBDE congeners in and around Taiwan. Results indicate that PBDE congeners have a high affinity for partitioning into sediments then soils. As congener number decreases, the PBDEs then partition more readily into air. As the degree of bromination increases, congeners more readily partition to sediments. Sediments may then act as a long-term source of PBDEs which can be released back into the water column due to resuspension during storm events.

A field and reactive transport model study of arsenic in a basaltic rock aquifer

The use of geothermal energy as a source for electricity and district heating has increased over recent decades. Dissolved As can be an important constituent of the geothermal fluids brought to the Earth's surface. Here the field application of laboratory measured adsorption coefficients of aqueous As species on basaltic glass surfaces is discussed. The mobility of As species in the basaltic aquifer in the Nesjavellir geothermal system, Iceland was modelled by the one-dimensional (1D) reactive transport model PHREEQC ver. 2, constrained by a long time series of field measurements with the chemical composition of geothermal effluent fluids, pH, Eh and, occasionally, Fe- and As-dissolved species measurements. Di-, tri- and tetrathioarsenic species (As(OH)S22-, AsS₃H^2-, AsS33- and As(SH)4-) were the dominant form of dissolved As in geothermal waters exiting the power plant (2.556μM total As) but converted to some extent to arsenite (H₃AsO₃) and arsenate HAsO42- oxyanions coinciding with rapid oxidation of S2- to S2O32- and finally to SO42- during surface runoff before feeding into a basaltic lava field with a total As concentration of 0.882μM following dilution with other surface waters. A continuous 25-a data set monitoring groundwater chemistry along a cross section of warm springs on the Lake Thingvallavatn shoreline allowed calibration of the 1D model. Furthermore, a series of ground water wells located in the basaltic lava field, provided access along the line of flow of the geothermal effluent waters towards the lake. The conservative ion Cl^- moved through the basaltic lava field (4100m) in less than10a but As was retarded considerably due to surface reactions and has entered a groundwater well 850m down the flow path as arsenate in accordance to the prediction of the 1D model. The 1D model predicted a complete breakthrough of arsenate in the year 2100. In a reduced system arsenite should be retained for about 1ka. © 2011 Elsevier Ltd.

Using geotechnical and LIDAR spatial monitoring to determine key environmental slope instability thresholds of a Jurassic coastal landslide: Straidkilly Point, Northern Ireland, UK.

The Antrim Coast Road stretching from the seaport of Larne in the East of Northern Ireland to the famous Giant’s Causeway in the North has a well-deserved reputation for being one of the most spectacular roads in Europe (Day, 2006). At various locations along the route, fluid interactions between the problematic geology, Jurassic Lias Clay and Triassic Mudstone overlain by Cretaceous Limestone and Tertiary Basalt, and environmental variables result in frequent instances of slope instability within the vadose zone. During such instances of instability, debris flows and composite mudflows encroach on the carriageway posing a hazard to road users. This paper examines the site investigative, geotechnical and spatial analysis techniques currently being implemented to monitor slope stability for one site at Straidkilly Point, Glenarm, Northern Ireland. An in-depth understanding of the geology was obtained via boreholes, resistivity surveys and laboratory testing. Environmental variables recorded by an on-site weather station were correlated with measured pore water pressure and soil moisture infiltration dynamic data.
Terrestrial LiDAR (TLS) was applied to the slope for the monitoring of failures, with surveys carried out on a bi-monthly basis. TLS monitoring allowed for the generation of Digital Elevation Models (DEMs) of difference, highlighting areas of recent movement, erosion and deposition. Morphology parameters were generated from the DEMs and include slope, curvature and multiple measures of roughness. Changes in the structure of the slope coupled with morphological parameters are characterised and linked to progressive failures from the temporal monitoring. In addition to TLS monitoring, Aerial LiDARi datasets were used for the spatio-morphological characterisation of the slope on a macro scale. Results from the geotechnical and environmental monitoring were compared with spatial data obtained through Terrestrial and Airborne LiDAR, providing a multi-faceted approach to slope stability characterization, which facilitates more informed management of geotechnical risk by the Northern Ireland Roads Service.

Geotechnical monitoring using a combination of LIDAR, real-time dGPS, and electrical tomography to assess geotechnical risk of a coastal landslide.

The Antrim Coast Road stretching from the seaport of Larne in the East of Northern Ireland has a well-deserved reputation for being one of the most spectacular roads in Europe (Day, 2006). However the problematic geology; Jurassic Lias Clay and Triassic Mudstone overlain by Cretaceous Limestone and Tertiary Basalt, and environmental variables result in frequent instances of slope instability manifested in both shallow debris flows and occasional massive rotational movements, creating a geotechnical risk to this highway. This paper describes how a variety of techniques are being used to both assess instability and monitor movement of these active slopes near one site at Straidkilly Point, Glenarm. An in-depth understanding of the geology was obtained via boreholes, resistivity surveys and laboratory testing. Environmental variables recorded by an on-site weather station were correlated with measured pore water pressure and soil moisture infiltration data. Terrestrial LiDAR (TLS), with surveys carried out on a bi-monthly basis allowed for the generation of Digital Elevation Models (DEMs) of difference, highlighting areas of recent movement, accumulation and depletion. Morphology parameters were generated from the DEMs and include slope, curvature and multiple measures of roughness. Changes in the structure of the slope coupled with morphological parameters were characterised and linked to progressive failures from the temporal monitoring. In addition to TLS monitoring, Aerial LiDAR datasets were used for the spatio-morphological characterisation of the slope on a macro scale. A Differential Global Positioning System (dGPS) was also deployed on site to provide a real-time warning system for gross movements, which were also correlated with environmental conditions. Frequent electrical resistivity tomography (ERT) surveys were also implemented to provide a better understanding of long-term changes in soil moisture and help to define the complex geology. The paper describes how the data obtained via a diverse range of methods has been combined to facilitate a more informed management regime of geotechnical risk by the Northern Ireland Roads Service.

Two-Year Monitoring of Water Samples from Dam of Iskar and the Black Sea, Bulgaria, by Molecular Analysis: Focus on Mycobacterium spp

The coast of the Bulgarian Black Sea is a popular summer holiday destination. The Dam of Iskar is the largest artificial dam in Bulgaria, with a capacity of 675 million m3. It is the main source of tap water for the capital Sofia and for irrigating the surrounding valley. There is a close relationship between the quality of aquatic ecosystems and human health as many infections are waterborne. Rapid molecular methods for the analysis of highly pathogenic bacteria have been developed for monitoring quality. Mycobacterial species can be isolated from waste, surface, recreational, ground and tap waters and human pathogenicity of nontuberculose mycobacteria (NTM) is well recognized. The objective of our study was to perform molecular analysis for key-pathogens, with a focus on mycobacteria, in water samples collected from the Black Sea and the Dam of Iskar. In a two year period, 38 water samples were collected-24 from the Dam of Iskar and 14 from the Black Sea coastal zone. Fifty liter water samples were concentrated by ultrafiltration. Molecular analysis for 15 pathogens, including all species of genus Mycobacterium was performed. Our results showed presence of Vibrio spp. in the Black Sea. Rotavirus A was also identified in four samples from the Dam of Iskar. Toxigenic Escherichia coli was present in both locations, based on markers for stx1 and stx2 genes. No detectable amounts of Cryptosporidium were detected in either location using immunomagnetic separation and fluorescence microscopy. Furthermore, mass spectrometry analyses did not detect key cyanobacterial toxins. On the basis of the results obtained we can conclude that for the period 2012-2014 no Mycobacterium species were present in the water samples. During the study period no cases of waterborne infections were reported.

Abundance and diversity of sedimentary bacterial communities in a coastal productive setting in the Western Irish Sea

The bacterial community composition and biomass abundance from a depositional mud belt in the western Irish Sea and regional sands were investigated by phospholipid ester-linked fatty acid profiling, denaturing gradient gel electrophoresis and barcoded pyrosequencing of 16S rRNA genes. The study area varied by water depth (12-111 m), organic carbon content (0.09-1.57% TOC), grain size, hydrographic regime (well-mixed vs. stratified), and water column phytodetrital input (represented by algal polyunsaturated PLFA). The relative abundance of bacterial-derived PLFA (sum of methyl-branched, cyclopropyl and odd-carbon number PLFA) was positively correlated with fine-grained sediment, and was highest in the depositional mud belt. A strong association between bacterial biomass and eukaryote primary production was suggested based on observed positive correlations with total nitrogen and algal polyunsaturated fatty acids. In addition, 16S rRNA genes affiliated to the classes Clostridia and Flavobacteria represented a major proportion of total 16S rRNA gene sequences. This suggests that benthic bacterial communities are also important degraders of phytodetrital organic matter and closely coupled to water column productivity in the western Irish Sea.

A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities

Seafloor massive sulfide (SMS) mining will likely occur at hydrothermal systems in the near future. Alongside their mineral wealth, SMS deposits also have considerable biological value. Active SMS deposits host endemic hydrothermal vent communities, whilst inactive deposits support communities of deep water corals and other suspension feeders. Mining activities are expected to remove all large organisms and suitable habitat in the immediate area, making vent endemic organisms particularly at risk from habitat loss and localised extinction. As part of environmental management strategies designed to mitigate the effects of mining, areas of seabed need to be protected to preserve biodiversity that is lost at the mine site and to preserve communities that support connectivity among populations of vent animals in the surrounding region. These "set-aside" areas need to be biologically similar to the mine site and be suitably connected, mostly by transport of larvae, to neighbouring sites to ensure exchange of genetic material among remaining populations. Establishing suitable set-asides can be a formidable task for environmental managers, however the application of genetic approaches can aid set-aside identification, suitability assessment and monitoring. There are many genetic tools available, including analysis of mitochondrial DNA (mtDNA) sequences (e.g. COI or other suitable mtDNA genes) and appropriate nuclear DNA markers (e.g. microsatellites, single nucleotide polymorphisms), environmental DNA (eDNA) techniques and microbial metagenomics. When used in concert with traditional biological survey techniques, these tools can help to identify species, assess the genetic connectivity among populations and assess the diversity of communities. How these techniques can be applied to set-aside decision making is discussed and recommendations are made for the genetic characteristics of set-aside sites. A checklist for environmental regulators forms a guide to aid decision making on the suitability of set-aside design and assessment using genetic tools. This non-technical primer document represents the views of participants in the VentBase 2014 workshop.

The influence of water motion on the growth rate of the kelp Laminaria digitata

The shallow water kelp Laminaria digitata, abundant in coastal zones of the North Atlantic, is exposed to a range of hydrodynamic environments that makes it ideal for assessing the role of water motion on their growth rate. Here we quantify the growth of L. digitata, as a factor of blade and stipe elongation, at sites adjacent to Strangford Lough, Northern Ireland under different hydrodynamic conditions over a one year period. A modelling approach was used to numerically determine both the temporal and spatial variability of the hydrodynamic environment. Ambient seawater nutrient concentrations, temperature and irradiance were measured as well as the internal nutrient status of the L. digitata populations. Kelp populations growing in the greatest and lowest water motion showed the lowest growth rates. Differences observed in growth rate could not be attributed to seawater nutrient availability, temperature or light. The internal nutrient status also suggested no influence on the observed differences in growth rate. Therefore if there are minimal differences in light, temperature and nutrients between sites, then populations of L. digitata exposed to different water motions are likely to exhibit different growth rates. It is suggested that the growth rate differences observed were a function of water motion with the possibility that, in response to the hydrodynamic forces experienced by the algal cells, L. digitata kelps in the high energy environments were putting more energy into strengthening cell walls rather than blade elongation

Appropriate complexity for the prediction of coastal and estuarine geomorphic behaviour at decadal to centennial scales

Coastal and estuarine landforms provide a physical template that not only accommodates diverse ecosystem functions and human activities, but also mediates flood and erosion risks that are expected to increase with climate change. In this paper, we explore some of the issues associated with the conceptualisation and modelling of coastal morphological change at time and space scales relevant to managers and policy makers. Firstly, we revisit the question of how to define the most appropriate scales at which to seek quantitative predictions of landform change within an age defined by human interference with natural sediment systems and by the prospect of significant changes in climate and ocean forcing. Secondly, we consider the theoretical bases and conceptual frameworks for determining which processes are most important at a given scale of interest and the related problem of how to translate this understanding into models that are computationally feasible, retain a sound physical basis and demonstrate useful predictive skill. In particular, we explore the limitations of a primary scale approach and the extent to which these can be resolved with reference to the concept of the coastal tract and application of systems theory. Thirdly, we consider the importance of different styles of landform change and the need to resolve not only incremental evolution of morphology but also changes in the qualitative dynamics of a system and/or its gross morphological configuration. The extreme complexity and spatially distributed nature of landform systems means that quantitative prediction of future changes must necessarily be approached through mechanistic modelling of some form or another. Geomorphology has increasingly embraced so-called ‘reduced complexity’ models as a means of moving from an essentially reductionist focus on the mechanics of sediment transport towards a more synthesist view of landform evolution. However, there is little consensus on exactly what constitutes a reduced complexity model and the term itself is both misleading and, arguably, unhelpful. Accordingly, we synthesise a set of requirements for what might be termed ‘appropriate complexity modelling’ of quantitative coastal morphological change at scales commensurate with contemporary management and policy-making requirements: 1) The system being studied must be bounded with reference to the time and space scales at which behaviours of interest emerge and/or scientific or management problems arise; 2) model complexity and comprehensiveness must be appropriate to the problem at hand; 3) modellers should seek a priori insights into what kind of behaviours are likely to be evident at the scale of interest and the extent to which the behavioural validity of a model may be constrained by its underlying assumptions and its comprehensiveness; 4) informed by qualitative insights into likely dynamic behaviour, models should then be formulated with a view to resolving critical state changes; and 5) meso-scale modelling of coastal morphological change should reflect critically on the role of modelling and its relation to the observable world.

Climate drives temporal replacement and nested‐resultant richness patterns of Scottish coastal vegetation

Beta diversity quantifies spatial and/or temporal variation in species composition. It is comprised of two distinct components, species replacement and nestedness, which derive from opposing ecological processes. Using Scotland as a case study and a β-diversity partitioning framework, we investigate temporal replacement and nestedness patterns of coastal grassland species over a 34-yr time period. We aim to 1) understand the influence of two potentially pivotal processes (climate and land-use changes) on landscape-scale (5 × 5 km) temporal replacement and nestedness patterns, and 2) investigate whether patterns from one β-diversity component can mask observable patterns in the other.

We summarised key aspects of climate driven macro-ecological variation as measures of variance, long-term trends, between-year similarity and extremes, for three important climatic predictors (minimum temperature, water-balance and growing degree-days). Shifts in landscape-scale heterogeneity, a proxy of land-use change, was summarised as a spatial multiple-site dissimilarity measure. Together, these climatic and spatial predictors were used in a multi-model inference framework to gauge the relative contribution of each on temporal replacement and nestedness patterns.

Temporal β-diversity patterns were reasonably well explained by climate change but weakly explained by changes in landscape-scale heterogeneity. Climate was shown to have a greater influence on temporal nestedness than replacement patterns over our study period, linking nestedness patterns, as a result of imbalanced gains and losses, to climatic warming and extremes respectively. Important climatic predictors (i.e. growing degree-days) of temporal β-diversity were also identified, and contrasting patterns between the two β-diversity components revealed.

Results suggest climate influences plant species recruitment and establishment processes of Scotland's coastal grasslands, and while species extinctions take time, they are likely to be facilitated by climatic perturbations. Our findings also highlight the importance of distinguishing between different components of β-diversity, disentangling contrasting patterns than can mask one another.