Soft sediment ecology of Lough Hyne Marine Reserve - spatial and temporal patterns

Distribution of soft sediment benthic fauna and the environmental factors affecting them were studied, to investigate changes across spatial and temporal scales. Investigations took place at Lough Hyne Marine Reserve using a range of methods. Data on the sedimentation rates of organic and inorganic matter were collected at monthly intervals for one year at a number of sites around the Lough, by use of vertical midwater-column sediment traps. Sedimentation of these two fractions were not coupled; inorganic matter sedimentation depended on hydrodynamic and weather factors, while the organic matter sedimentation was more complex, being dependent on biological and chemical processes in the water column. The effects of regular hypoxic episodes on benthic fauna due to a natural seasonal thermocline were studied in the deep Western Trough, using camera-equipped remotely-operated vehicle to follow transects, on a three-monthly basis over one year. In late summer, the area below the thermocline of the Western Trough was devoid of visible fauna. Decapod crustaceans were the first taxon to make use of ameliorating oxygen conditions in autumn, by darting below the thermocline depth, most likely to scavenge. This was indicated by tracks that they left on the surface of the Trough floor. Some species, most noticeably Fries’ goby Lesueurigobius friesii, migrated below the thermocline depth when conditions were normoxic and established semi-permanent burrows. Their population encompassed all size classes, indicating that this habitat was not limited to juveniles of this territorial species. Recolonisation by macrofauna and burrowing megafauna was studied during normoxic conditions, from November 2009 to May 2010. Macrofauna displayed a typical post-disturbance pattern of recolonisation with one species, the polychaete Scalibregma inflatum, occurring at high abundance levels in March 2010. In May, this population had become significantly reduced and a more diverse community was established. The abundance of burrowing infauna comprising decapods crabs and Fries’ gobies, was estimated by identifying and counting their distinctive burrow structures. While above the summer thermocline depth, burrow abundance increased in a linear fashion, below the thermocline depth a slight reduction of burrow abundance occurred in May, when oxygen conditions deteriorated again. The majority of the burrows occurring in May were made by Fries’ gobies, which are thought to encounter low oxygen concentrations in their burrows. Reduction in burrow abundance of burrowing shrimps Calocaris macandreae and Callianassa subterranea (based on descriptions of burrow structures from the literature), from March to May, might be related to their reduced activity in hypoxia, leading to loss of structural burrow maintenance. Spatial and temporal changes to macrofaunal assemblage structures were studied seasonally for one year across 5 sites in the Lough and subject to multivariate statistical analysis. Assemblage structures were significantly correlated with organic matter levels in the sediment, the amounts of organic matter settling out of the water column one month before macrofaunal sampling took place as well as current speed and temperature. This study was the first to investigate patterns and processes in the Lough soft sediment ecology across all 3 basins on a temporal and spatial scale. An investigation into the oceanographic aspects of the development, behaviour and break-down of the summer thermocline of Lough Hyne was performed in collaboration with researchers from other Irish institutions.

Variability in north temperate dung beetle assemblages at different spatial and temporal scales

This study examined the spatial and temporal variability of dung beetle assemblages across a variety of scales e.g. from the between-pad scale (examining the effects of dung size and type) to larger spatial scales encompassing southern Ireland. Dung beetle assemblage structure as sampled by dung pad cohort samples and dung baited pitfall trapping were compared. Generally, the rank order of abundance of dung beetle species was significantly correlated between pitfall catches and cohort pad samples. Across different dung sizes, in both pitfall catches and cohort pad samples, the relative abundance of species was frequently significantly different, but the rank order of abundance of dung beetle was usually significantly correlated. Considerable variations in pitfall catches at temporal scales of a few days appeared to be closely related to weather conditions and rotational grazing. However, despite considerable variation in absolute abundances between consecutive days of sampling, assemblage structure typically remained very similar. The relationship between dung pad size and dung beetle colonisation was investigated. In field experiments in which pads of different sizes (0.25 L, 0.5 L, 1.0 L and 1.5 L) were artificially deposited, there was a positive relationship between pad size and both biomass and number of beetles colonising dung pads and pitfall traps. In addition, with one exception, the field experiments indicated a general positive relationship between dung pad size and biomass density (dung beetle biomass per unit dung volume). A laboratory experiment indicated that pat residence times of A. rufipes were significantly correlated with dung pad size. Investigation of naturally-deposited cow dung pads in the field also indicated that both larval numbers and densities were significantly correlated with dung pad size. These results were discussed in the context of theory related to aggregation and coexistence of species, and resource utilisation by organisms in ephemeral, patchy resources. The colonisation by dung beetles of dung types from native herbivores (sheep, horse and cow) was investigated in field experiments. There were significant differences between the dung types in the chemical parameters measured, and there were significant differences in abundances of dung beetles colonising the dung types. Sheep dung was typically the preferred dung type. Data from these field experiments, and from published literature, indicated that dung beetle species can display dung type preferences, in terms of comparisons of both absolute and relative abundances. In addition, data from laboratory experiments indicate that both Aphodius larval production and pat residence times tended to be higher in those dung types which were preferred by adult Aphodius in the colonisation experiments. Data from dung-baited pitfall trapping (from this and another study) at several sites (up to 180 km distant) and over a number of years (between 1991 and 1996) were used to investigate spatial and temporal variation in dung beetle assemblage structure and composition (Aphodius, Sphaeridium and Geotrupes) across a range of scales in southern Ireland. Species richness levels, species composition and rank order of abundances were very similar between the assemblages. The temporal variability between seasons within any year exceeded temporal variability between years. DCA ordinations indicated that there was a similar level of variability between assemblage structure from the between-field (~1km) to regional (~180 km) spatial scales, and between year (6 years) temporal scales. At the biogeographical spatial scale, analysis of data from the literature indicated that there was considerable variability at this scale, largely due to species turnover.

Biodiversity change in the Irish uplands - the effects of grazing management

As a prominent form of land use across much of upland Europe, extensive livestock grazing may hold the key to the sustainable management of these landscapes. Recent agricultural policy reform, however, has resulted in a decline in upland sheep numbers, prompting concern for the biodiversity value of these areas. This study quantifies the effects of varying levels of grazing management on plant, ground beetle and breeding bird diversity and assemblage in the uplands and lowlands of hill sheep farms in County Kerry, Ireland. Farms represent a continuum of light to heavy grazing, measured using a series of field indicators across several habitats, such as the internationally important blanket bog, home to the ground beetle, Carabus clatratus. Linear mixed effects modelling and non-metric multidimensional scaling are employed to disentangle the most influential management and environmental factors. Grazing state may be determined by the presence of Molinia caerulea or Nardus stricta, and variables such as % traditional ewes, % vegetation litter and % scrub prove valuable indicators of diversity. Measures of ecosystem functioning, e.g. plant biomass (nutrient cycling) and % vegetation cover (erosion rates) are influenced by plant diversity, which is influenced by grazing management. Levels of the ecosystem service, soil organic carbon, vary with ground beetle abundance and diversity, potentially influencing carbon sequestration and thereby climate change. The majority of species from all three taxa are found in the lowlands, with the exception of birds such as meadow pipit and skylark. The scale of measurement should be determined by the size and mobility of the species in question. The challenge is to manage these high nature value landscapes using agri-environment schemes which enhance biodiversity by maintaining structural heterogeneity across a range of scales, altitudes and habitats whilst integrating the decisions of people living and working in these marginal areas.

Presenting SAPUSS: solving aerosol problem by using synergistic strategies in Barcelona, Spain

This paper presents the summary of the key objectives, instrumentation and logistic details, goals, and initial scientific findings of the European Marie Curie Action SAPUSS project carried out in the western Mediterranean Basin (WMB) during September-October in autumn 2010. The key SAPUSS objective is to deduce aerosol source characteristics and to understand the atmospheric processes responsible for their generations and transformations - both horizontally and vertically in the Mediterranean urban environment. In order to achieve so, the unique approach of SAPUSS is the concurrent measurements of aerosols with multiple techniques occurring simultaneously in six monitoring sites around the city of Barcelona (NE Spain): a main road traffic site, two urban background sites, a regional background site and two urban tower sites (150 m and 545 m above sea level, 150 m and 80 m above ground, respectively). SAPUSS allows us to advance our knowledge sensibly of the atmospheric chemistry and physics of the urban Mediterranean environment. This is well achieved only because of both the three dimensional spatial scale and the high sampling time resolution used. During SAPUSS different meteorological regimes were encountered, including warm Saharan, cold Atlantic, wet European and stagnant regional ones. The different meteorology of such regimes is herein described. Additionally, we report the trends of the parameters regulated by air quality purposes (both gaseous and aerosol mass concentrations); and we also compare the six monitoring sites. High levels of traffic-related gaseous pollutants were measured at the urban ground level monitoring sites, whereas layers of tropospheric ozone were recorded at tower levels. Particularly, tower level night-time average ozone concentrations (80 +/- 25 mu g m(-3)) were up to double compared to ground level ones. The examination of the vertical profiles clearly shows the predominant influence of NOx on ozone concentrations, and a source of ozone aloft. Analysis of the particulate matter (PM) mass concentrations shows an enhancement of coarse particles (PM2.5-10) at the urban ground level (+64 %, average 11.7 mu g m(-3)) but of fine ones (PM1) at urban tower level (+28 %, average 14.4 mu g m(-3)). These results show complex dynamics of the size-resolved PM mass at both horizontal and vertical levels of the study area. Preliminary modelling findings reveal an underestimation of the fine accumulation aerosols. In summary, this paper lays the foundation of SAPUSS, an integrated study of relevance to many other similar urban Mediterranean coastal environment sites.

Evaluating the spatial transferability and temporal repeatability of remote-sensing-based lake water quality retrieval algorithms at the European scale: a meta-analysis approach

Many studies have shown the considerable potential for the application of remote-sensing-based methods for deriving estimates of lake water quality. However, the reliable application of these methods across time and space is complicated by the diversity of lake types, sensor configuration, and the multitude of different algorithms proposed. This study tested one operational and 46 empirical algorithms sourced from the peer-reviewed literature that have individually shown potential for estimating lake water quality properties in the form of chlorophyll-a (algal biomass) and Secchi disc depth (SDD) (water transparency) in independent studies. Nearly half (19) of the algorithms were unsuitable for use with the remote-sensing data available for this study. The remaining 28 were assessed using the Terra/Aqua satellite archive to identify the best performing algorithms in terms of accuracy and transferability within the period 2001–2004 in four test lakes, namely Vänern, Vättern, Geneva, and Balaton. These lakes represent the broad continuum of large European lake types, varying in terms of eco-region (latitude/longitude and altitude), morphology, mixing regime, and trophic status. All algorithms were tested for each lake separately and combined to assess the degree of their applicability in ecologically different sites. None of the algorithms assessed in this study exhibited promise when all four lakes were combined into a single data set and most algorithms performed poorly even for specific lake types. A chlorophyll-a retrieval algorithm originally developed for eutrophic lakes showed the most promising results (R2 = 0.59) in oligotrophic lakes. Two SDD retrieval algorithms, one originally developed for turbid lakes and the other for lakes with various characteristics, exhibited promising results in relatively less turbid lakes (R2 = 0.62 and 0.76, respectively). The results presented here highlight the complexity associated with remotely sensed lake water quality estimates and the high degree of uncertainty due to various limitations, including the lake water optical properties and the choice of methods.

Genome-scale analyses of health-promoting bacteria: probiogenomics

The human body is colonized by an enormous population of bacteria (microbiota) that provides the host with coding capacity and metabolic activities. Among the human gut microbiota are health-promoting indigenous species (probiotic bacteria) that are commonly consumed as live dietary supplements. Recent genomics-based studies (probiogenomics) are starting to provide insights into how probiotic bacteria sense and adapt to the gastrointestinal tract environment. In this Review, we discuss the application of probiogenomics in the elucidation of the molecular basis of probiosis using the well-recognized model probiotic bacteria genera Bifidobacterium and Lactobacillus as examples.

The broad-scale distribution and abundance of Scyphomedusae in Irish waters

Scyphomedusae are receiving increasing recognition as key components of marine ecosystems. However, information on their distribution and abundance beyond coastal waters is generally lacking. Organising access to such data is critical to effectively transpose findings from laboratory, mesocosm and small scale studies to the scale of ecological processes. These data are also required to identify the risks of detrimental impacts of jellyfish blooms on human activities. In Ireland, such risks raise concerns among the public, but foremost amongst the professionals of the aquaculture and fishing sectors. The present work looked at the opportunity to get access to new information on the distribution of jellyfish around Ireland mostly by using existing infrastructures and programmes. The analysis of bycatch data collected during the Irish groundfish surveys provided new insights into the distribution of Pelagia noctiluca over an area >160 000 km2, a scale never reached before in a region of the Northeast Atlantic (140 sampling stations). Similarly, 4 years of data collected during the Irish Sea juvenile gadoid fish survey provided the first spatially, explicit, information on the abundance of Aurelia aurita and Cyanea spp. (Cyanea capillata and Cyanea lamarckii) throughout the Irish Sea (> 200 sampling events). In addition, the use of ships of opportunity allowed repeated samplings (N = 37) of an >100 km long transect between Dublin (Ireland) and Holyhead (Wales, UK), therefore providing two years of seasonal monitoring of the occurrence of scyphomedusae in that region. Finally, in order to inform the movements of C. capillata in an area where many negative interactions with bathers occur, the horizontal and vertical movements of 5 individual C. capillata were investigated through acoustic tracking.

Multi-scale modelling of atomic layer deposition

High-permittivity ("high-k") dielectric materials are used in the transistor gate stack in integrated circuits. As the thickness of silicon oxide dielectric reduces below 2 nm with continued downscaling, the leakage current because of tunnelling increases, leading to high power consumption and reduced device reliability. Hence, research concentrates on finding materials with high dielectric constant that can be easily integrated into a manufacturing process and show the desired properties as a thin film. Atomic layer deposition (ALD) is used practically to deposit high-k materials like HfO2, ZrO2, and Al2O3 as gate oxides. ALD is a technique for producing conformal layers of material with nanometer-scale thickness, used commercially in non-planar electronics and increasingly in other areas of science and technology. ALD is a type of chemical vapor deposition that depends on self-limiting surface chemistry. In ALD, gaseous precursors are allowed individually into the reactor chamber in alternating pulses. Between each pulse, inert gas is admitted to prevent gas phase reactions. This thesis provides a profound understanding of the ALD of oxides such as HfO2, showing how the chemistry affects the properties of the deposited film. Using multi-scale modelling of ALD, the kinetics of reactions at the growing surface is connected to experimental data. In this thesis, we use density functional theory (DFT) method to simulate more realistic models for the growth of HfO2 from Hf(N(CH3)2)4/H2O and HfCl4/H2O and for Al2O3 from Al(CH3)3/H2O.Three major breakthroughs are discovered. First, a new reaction pathway, ’multiple proton diffusion’, is proposed for the growth of HfO2 from Hf(N(CH3)2)4/H2O.1 As a second major breakthrough, a ’cooperative’ action between adsorbed precursors is shown to play an important role in ALD. By this we mean that previously-inert fragments can become reactive once sufficient molecules adsorb in their neighbourhood during either precursor pulse. As a third breakthrough, the ALD of HfO2 from Hf(N(CH3)2)4 and H2O is implemented for the first time into 3D on-lattice kinetic Monte-Carlo (KMC).2 In this integrated approach (DFT+KMC), retaining the accuracy of the atomistic model in the higher-scale model leads to remarkable breakthroughs in our understanding. The resulting atomistic model allows direct comparison with experimental techniques such as X-ray photoelectron spectroscopy and quartz crystal microbalance.