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Ammonia (NH3) in the atmosphere affects both the environment and human health. It is therefore increasingly recognised by policy makers as an important air pollutant that needs to be mitigated, though it still remains unregulated in many countries. In order to understand the effectiveness of abatement strategies, routine NH3 monitoring is required. Current reference protocols, first developed in the 1990s, use daily samplers with offline analysis; however, there have been a number of technologies developed since, which may be applicable for high time resolution routine monitoring of NH3 at ambient concentrations. The following study is a comprehensive field intercomparison held over an intensively managed grassland in southeastern Scotland using currently available methods that are reported to be suitable for routine monitoring of ambient NH3. In total, 13 instruments took part in the field study, including commercially available technologies, research prototype instruments, and legacy instruments. Assessments of the instruments' precision at low concentrations (< 10 ppb) and at elevated concentrations (maximum reported concentration of 282 ppb) were undertaken. At elevated concentrations, all instruments performed well and with precision (r2 > 0.75). At concentrations below 10 ppb, however, precision decreased, and instruments fell into two distinct groups, with duplicate instruments split across the two groups. It was found that duplicate instruments performed differently as a result of differences in instrument setup, inlet design, and operation of the instrument. New metrological standards were used to evaluate the accuracy in determining absolute concentrations in the field. A calibration-free CRDS optical gas standard (OGS, PTB, DE) served as an instrumental reference standard, and instrument operation was assessed against metrological calibration gases from (i) a permeation system (ReGaS1, METAS, CH) and (ii) primary standard gas mixtures (PSMs) prepared by gravimetry (NPL, UK). This study suggests that, although the OGS gives good performance with respect to sensitivity and linearity against the reference gas standards, this in itself is not enough for the OGS to be a field reference standard, because in field applications, a closed path spectrometer has limitations due to losses to surfaces in sampling NH3, which are not currently taken into account by the OGS. Overall, the instruments compared with the metrological standards performed well, but not every instrument could be compared to the reference gas standards due to incompatible inlet designs and limitations in the gas flow rates of the standards. This work provides evidence that, although NH3 instrumentation have greatly progressed in measurement precision, there is still further work required to quantify the accuracy of these systems under field conditions. It is the recommendation of this study that the use of instruments for routine monitoring of NH3 needs to be set out in standard operating protocols for inlet setup, calibration, and routine maintenance in order for datasets to be comparable.

A comprehensive European dataset on monthly atmospheric NH3, acid gases (HNO3, SO2, HCl), and aerosols (NH4+, NO3-, SO42-, Cl−, Na+, Ca2+, Mg2+) is presented and analysed. Speciated measurements were made with a low-volume denuder and filter pack method (DEnuder for Long-Term Atmospheric sampling, DELTA®) as part of the EU NitroEurope (NEU) integrated project. Altogether, there were 64 sites in 20 countries (2006–2010), coordinated between seven European laboratories. Bulk wet-deposition measurements were carried out at 16 co-located sites (2008–2010). Inter-comparisons of chemical analysis and DELTA® measurements allowed an assessment of comparability between laboratories. The form and concentrations of the different gas and aerosol components measured varied between individual sites and grouped sites according to country, European regions, and four main ecosystem types (crops, grassland, forests, and semi-natural). The smallest concentrations (with the exception of SO42- and Na+) were in northern Europe (Scandinavia), with broad elevations of all components across other regions. SO2 concentrations were highest in central and eastern Europe, with larger SO2 emissions, but particulate SO42- concentrations were more homogeneous between regions. Gas-phase NH3 was the most abundant single measured component at the majority of sites, with the largest variability in concentrations across the network. The largest concentrations of NH3, NH4+, and NO3- were at cropland sites in intensively managed agricultural areas (e.g. Borgo Cioffi in Italy), and the smallest were at remote semi-natural and forest sites (e.g. Lompolojänkkä, Finland), highlighting the potential for NH3 to drive the formation of both NH4+ and NO3- aerosol. In the aerosol phase, NH4+ was highly correlated with both NO3- and SO42-, with a near-1:1 relationship between the equivalent concentrations of NH4+ and sum (NO3-+ SO42-), of which around 60 % was as NH4NO3. Distinct seasonality was also observed in the data, influenced by changes in emissions, chemical interactions, and the influence of meteorology on partitioning between the main inorganic gases and aerosol species. Springtime maxima in NH3 were attributed to the main period of manure spreading, while the peak in summer and trough in winter were linked to the influence of temperature and rainfall on emissions, deposition, and gas–aerosol-phase equilibrium. Seasonality in SO2 was mainly driven by emissions (combustion), with concentrations peaking in winter, except in southern Europe, where the peak occurred in summer. Particulate SO42- showed large peaks in concentrations in summer in southern and eastern Europe, contrasting with much smaller peaks occurring in early spring in other regions. The peaks in particulate SO42- coincided with peaks in NH3 concentrations, attributed to the formation of the stable (NH4)2SO4. HNO3 concentrations were more complex, related to traffic and industrial emissions, photochemistry, and HNO3:NH4NO3 partitioning. While HNO3 concentrations were seen to peak in the summer in eastern and southern Europe (increased photochemistry), the absence of a spring peak in HNO3 in all regions may be explained by the depletion of HNO3 through reaction with surplus NH3 to form the semi-volatile aerosol NH4NO3. Cooler, wetter conditions in early spring favour the formation and persistence of NH4NO3 in the aerosol phase, consistent with the higher springtime concentrations of NH4+ and NO3-. The seasonal profile of NO3- was mirrored by NH4+, illustrating the influence of gas–aerosol partitioning of NH4NO3 in the seasonality of these components. Gas-phase NH3 and aerosol NH4NO3 were the dominant species in the total inorganic gas and aerosol species measured in the NEU network. With the current and projected trends in SO2, NOx, and NH3 emissions, concentrations of NH3 and NH4NO3 can be expected to continue to dominate the inorganic pollution load over the next decades, especially NH3, which is linked to substantial exceedances of ecological thresholds across Europe. The shift from (NH4)2SO4 to an atmosphere more abundant in NH4NO3 is expected to maintain a larger fraction of reactive N in the gas phase by partitioning to NH3 and HNO3 in warm weather, while NH4NO3 continues to contribute to exceedances of air quality limits for PM2.5.

The impact of atmospheric reactive nitrogen (Nr) deposition on carbon (C) sequestration in soils and biomass of unfertilized, natural, semi-natural and forest ecosystems has been much debated. Many previous results of this dC∕dN response were based on changes in carbon stocks from periodical soil and ecosystem inventories, associated with estimates of Nr deposition obtained from large-scale chemical transport models. This study and a companion paper (Flechard et al., 2020) strive to reduce uncertainties of N effects on C sequestration by linking multi-annual gross and net ecosystem productivity estimates from 40 eddy covariance flux towers across Europe to local measurement-based estimates of dry and wet Nr deposition from a dedicated collocated monitoring network. To identify possible ecological drivers and processes affecting the interplay between C and Nr inputs and losses, these data were also combined with in situ flux measurements of NO, N2O and CH4 fluxes; soil NO3- leaching sampling; and results of soil incubation experiments for N and greenhouse gas (GHG) emissions, as well as surveys of available data from online databases and from the literature, together with forest ecosystem (BASFOR) modelling. Multi-year averages of net ecosystem productivity (NEP) in forests ranged from −70 to 826 g C m−2 yr−1 at total wet + dry inorganic Nr deposition rates (Ndep) of 0.3 to 4.3 g N m−2 yr−1 and from −4 to 361 g C m−2 yr−1 at Ndep rates of 0.1 to 3.1 g N m−2 yr−1 in short semi-natural vegetation (moorlands, wetlands and unfertilized extensively managed grasslands). The GHG budgets of the forests were strongly dominated by CO2 exchange, while CH4 and N2O exchange comprised a larger proportion of the GHG balance in short semi-natural vegetation. Uncertainties in elemental budgets were much larger for nitrogen than carbon, especially at sites with elevated Ndep where Nr leaching losses were also very large, and compounded by the lack of reliable data on organic nitrogen and N2 losses by denitrification. Nitrogen losses in the form of NO, N2O and especially NO3- were on average 27 % (range 6 %–54 %) of Ndep at sites with Ndep −2 yr−1 versus 65 % (range 35 %–85 %) for Ndep > 3 g N m−2 yr−1. Such large levels of Nr loss likely indicate that different stages of N saturation occurred at a number of sites. The joint analysis of the C and N budgets provided further hints that N saturation could be detected in altered patterns of forest growth. Net ecosystem productivity increased with Nr deposition up to 2–2.5 g N m−2 yr−1, with large scatter associated with a wide range in carbon sequestration efficiency (CSE, defined as the NEP ∕ GPP ratio). At elevated Ndep levels (> 2.5 g N m−2 yr−1), where inorganic Nr losses were also increasingly large, NEP levelled off and then decreased. The apparent increase in NEP at low to intermediate Ndep levels was partly the result of geographical cross-correlations between Ndep and climate, indicating that the actual mean dC∕dN response at individual sites was significantly lower than would be suggested by a simple, straightforward regression of NEP vs. Ndep.

The UK Acid Gases and Aerosol Monitoring Network (AGANet) was established in 1999 (12 sites, increased to 30 sites from 2006), to provide long-term national monitoring of acid gases (HNO3, SO2, HCl) and aerosol components (NO3−, SO42−, Cl−, Na+, Ca2+, Mg2+). An extension of a low-cost denuder-filter pack system (DELTA) that is used to measure NH3 and NH4+ in the UK National Ammonia Monitoring Network (NAMN) provides additional monthly speciated measurements for the AGANet. A comparison of the monthly DELTA measurement with averaged daily results from an annular denuder system showed close agreement, while the sum of HNO3 and NO3− and the sum of NH3 and NH4+ from the DELTA are also consistent with previous filter pack determination of total inorganic nitrogen and total inorganic ammonium, respectively. With the exception of SO2 and SO42−, the AGANet provides, for the first time, the UK concentration fields and seasonal cycles for each of the other measured species. The largest concentrations of HNO3, SO2, and aerosol NO3− and SO42− are found in southern and eastern England and smallest in western Scotland and Northern Ireland, whereas HCl are highest in south-eastern, south-western, and central England, that may be attributed to dual contribution from anthropogenic (coal combustion) and marine sources (reaction of sea salt with acid gases to form HCl). Na+ and Cl− are spatially correlated, with largest concentrations at coastal sites, reflecting a contribution from sea salt. Temporally, peak concentrations in HNO3 occurred in late winter and early spring attributed to photochemical processes. NO3− and SO42− have a spring maxima that coincides with the peak in concentrations of NH3 and NH4+, and are therefore likely attributable to formation of NH4NO3 and (NH4)2SO4 from reaction with higher concentrations of NH3 in spring. By contrast, peak concentrations of SO2, Na+, and Cl− during winter are consistent with combustion sources for SO2 and marine sources in winter for sea salt aerosol. Key pollutant events were captured by the AGANet. In 2003, a spring episode with elevated concentrations of HNO3 and NO3− was driven by meteorology and transboundary transport of NH4NO3 from Europe. A second, but smaller episode occurred in September 2014, with elevated concentrations of SO2, HNO3, SO42−, NO3−, and NH4+ that was shown to be from the Icelandic Holuhraun volcanic eruptions. Since 1999, AGANet has shown substantial decrease in SO2 concentrations relative to HNO3 and NH3, consistent with estimated decline in UK emissions. At the same time, large reductions and changes in the aerosol components provide evidence of a shift in the particulate phase from (NH4)2SO4 to NH4NO3. The potential for NH4NO3 to release NH3 and HNO3 in warm weather, together with the surfeit of NH3 also means that a larger fraction of the reduced and oxidized N is remaining in the gas phase as NH3 and HNO3 as indicated by the increasing trend in ratios of NH3 : NH4+ and HNO3 : NO3− over the 16-year period. Due to different removal rates of the component species by wet and dry deposition, this change is expected to affect spatial patterns of pollutant deposition with consequences for sensitive habitats with exceedance of critical loads of acidity and eutrophication. The changes are also relevant for human health effects assessment, particularly in urban areas as NH4NO3 constitutes a significant fraction of fine particulate matter (

A unique long-term dataset from the UK National Ammonia Monitoring Network (NAMN) is used here to assess spatial, seasonal and long-term variability in atmospheric ammonia (NH3: 1998–2014) and particulate ammonium (NH4+: 1999–2014) across the UK. Extensive spatial heterogeneity in NH3 concentrations is observed, with lowest annual mean concentrations at remote sites (−3) and highest in the areas with intensive agriculture (up to 22 µg m−3), while NH4+ concentrations show less spatial variability (e.g. range of 0.14 to 1.8 µg m−3 annual mean in 2005). Temporally, NH3 concentrations are influenced by environmental conditions and local emission sources. In particular, peak NH3 concentrations are observed in summer at background sites (defined by 5 km grid average NH3 emissions −1 yr−1) and in areas dominated by sheep farming, driven by increased volatilization of NH3 in warmer summer temperatures. In areas where cattle, pig and poultry farming is dominant, the largest NH3 concentrations are in spring and autumn, matching periods of manure application to fields. By contrast, peak concentrations of NH4+ aerosol occur in spring, associated with long-range transboundary sources. An estimated decrease in NH3 emissions by 16 % between 1998 and 2014 was reported by the UK National Atmospheric Emissions Inventory. Annually averaged NH3 data from NAMN sites operational over the same period (n = 59) show an indicative downward trend, although the reduction in NH3 concentrations is smaller and non-significant: Mann–Kendall (MK), −6.3 %; linear regression (LR), −3.1 %. In areas dominated by pig and poultry farming, a significant reduction in NH3 concentrations between 1998 and 2014 (MK: −22 %; LR: −21 %, annually averaged NH3) is consistent with, but not as large as the decrease in estimated NH3 emissions from this sector over the same period (−39 %). By contrast, in cattle-dominated areas there is a slight upward trend (non-significant) in NH3 concentrations (MK: +12 %; LR: +3.6 %, annually averaged NH3), despite the estimated decline in NH3 emissions from this sector since 1998 (−11 %). At background and sheep-dominated sites, NH3 concentrations increased over the monitoring period. These increases (non-significant) at background (MK: +17 %; LR: +13 %, annually averaged data) and sheep-dominated sites (MK: +15 %; LR: +19 %, annually averaged data) would be consistent with the concomitant reduction in SO2 emissions over the same period, leading to a longer atmospheric lifetime of NH3, thereby increasing NH3 concentrations in remote areas. The observations for NH3 concentrations not decreasing as fast as estimated emission trends are consistent with a larger downward trend in annual particulate NH4+ concentrations (1999–2014: MK: −47 %; LR: −49 %, p n = 23), associated with a lower formation of particulate NH4+ in the atmosphere from gas phase NH3.

Intensively managed grazed grasslands in temperate climates are globally important environments for the exchange of the greenhouse gases (GHGs) carbon dioxide (CO2), nitrous oxide (N2O) and methane (CH4). We assessed the N and C budget of a mostly grazed and occasionally cut and fertilised grassland in SE Scotland by measuring or modelling all relevant imports and exports to the field as well as changes in soil C and N stocks over time. The N budget was dominated by import from inorganic and organic fertilisers (21.9 g N m−2 a−1) and losses from leaching (5.3 g N m−2 a−1), N2 emissions (2.9 g N m−2 a−1), and NOx and NH3 volatilisation (3.9 g N m−2 a−1), while N2O emission was only 0.6 g N m−2 a−1. The efficiency of N use by animal products (meat and wool) averaged 9.9 % of total N input over only-grazed years (2004–2010). On average over 9 years (2002–2010), the balance of N fluxes suggested that 6.0 ± 5.9 g N m−2 a−1 (mean ± confidence interval at p > 0.95) were stored in the soil. The largest component of the C budget was the net ecosystem exchange of CO2 (NEE), at an average uptake rate of 218 ± 155 g C m−2 a−1 over the 9 years. This sink strength was offset by carbon export from the field mainly as grass offtake for silage (48.9 g C m−2 a−1) and leaching (16.4 g C m−2 a−1). The other export terms, CH4 emissions from the soil, manure applications and enteric fermentation, were negligible and only contributed to 0.02–4.2 % of the total C losses. Only a small fraction of C was incorporated into the body of the grazing animals. Inclusion of these C losses in the budget resulted in a C sink strength of 163 ± 140 g C m−2 a−1. By contrast, soil stock measurements taken in May 2004 and May 2011 indicated that the grassland sequestered N in the 0–60 cm soil layer at 4.51 ± 2.64 g N m−2 a−1 and lost C at a rate of 29.08 ± 38.19 g C m−2 a−1. Potential reasons for the discrepancy between these estimates are probably an underestimation of C losses, especially from leaching fluxes as well as from animal respiration. The average greenhouse gas (GHG) balance of the grassland was −366 ± 601 g CO2 eq. m−2 yr−1 and was strongly affected by CH4 and N2O emissions. The GHG sink strength of the NEE was reduced by 54 % by CH4 and N2O emissions. Estimated enteric fermentation from ruminating sheep proved to be an important CH4 source, exceeding the contribution of N2O to the GHG budget in some years.

Volcanic emissions, specifically from Iceland, pose a pan-European risk and are on the UK National Risk Register due to potential impacts on aviation, public health, agriculture, the environment and the economy, from both effusive and explosive activity. During the 2014–2015 fissure eruption at Holuhraun in Iceland, the UK atmosphere was significantly perturbed. This study focuses one major incursion in September 2014, affecting the surface concentrations of both aerosols and gases across the UK, with sites in Scotland experiencing the highest sulfur dioxide (SO2) concentrations. The perturbation event observed was confirmed to originate from the fissure eruption using satellite data from GOME2B and the chemical transport model, EMEP4UK, which was used to establish the spatial distribution of the plume over the UK during the event of interest. At the two UK European Monitoring and Evaluation Program (EMEP) supersite observatories (Auchencorth Moss, SE Scotland, and Harwell, SE England) significant alterations in sulfate (SO42−) content of PM10 and PM2.5 during this event, concurrently with evidence of an increase in ultrafine aerosol most likely due to nucleation and growth of aerosol within the plume, were observed. At Auchencorth Moss, higher hydrochloric acid (HCl) concentrations during the September event (max = 1.21 µg m−3, cf. annual average 0.12 µg m−3 in 2013), were assessed to be due to acid displacement of chloride (Cl−) from sea salt (NaCl) to form HCl gas rather than due to primary emissions of HCl from Holuhraun. The gas and aerosol partitioning at Auchencorth Moss of inorganic species by thermodynamic modelling confirmed the observed partitioning of HCl. Using the data from the chemical thermodynamic model, ISORROPIA-II, there is evidence that the background aerosol, which is typically basic at this site, became acidic with an estimated pH of 3.8 during the peak of the event.Volcano plume episodes were periodically observed by the majority of the UK air quality monitoring networks during the first 4 months of the eruption (August–December 2014), at both hourly and monthly resolution. In the low-resolution networks, which provide monthly SO2 averages, concentrations were found to be significantly elevated at remote “clean” sites in NE Scotland and SW England, with record-high SO2 concentrations for some sites in September 2014. For sites which are regularly influenced by anthropogenic emissions, taking into account the underlying trends, the eruption led to statistically unremarkable SO2 concentrations (return probabilities > 0.1, ∼ 10 months). However, for a few sites, SO2 concentrations were clearly much higher than has been previously observed (return probability 3000 months). The Holuhraun Icelandic eruption has resulted in a unique study providing direct evidence of atmospheric chemistry perturbation of both gases and aerosols in the UK background atmosphere. The measurements can be used to both challenge and verify existing atmospheric chemistry of volcano plumes, especially those originating from effusive eruptions, which have been underexplored due to limited observations available in the literature. If all European data sets were collated this would allow improved model verification and risk assessments for future volcanic eruptions of this type.

Dissolved organic nitrogen (DON) contributes significantly to the overall nitrogen budget, but is not routinely measured in precipitation or stream water. In order to investigate the contribution of DON to the deposition and export of N, precipitation, stream and soil water samples were collected from an ombrotrophic peatland and analysed for DON over a 2-year period. In wet-only deposition DON contributed up to 10 % of the total dissolved nitrogen (TDN) and was the most dominant fraction in soil water (99 %) and stream water (75 %). NH4+ was the most dominate form of N in precipitation, with NO3− contributing the least to precipitation, soil water and stream water. Precipitation and stream DON were qualitatively analysed by a two-dimensional gas chromatograph coupled to a nitrogen chemiluminescence detector (GC × GC-NCD) after trapping onto C18 solid phase extraction (SPE) cartridges. Ten unique compounds were detected and five identified as pyrrole, benzonitrile, dodecylamine, N-nitrosodipropylamine and decylamine. Five compounds were present in both precipitation and stream samples: pyrrole, benzonitrile and three unidentified compounds. The SPE-extraction efficiency for DON was very low (11 %), but with improvements DON speciation could become a valuable tool to provide information on its sources and pathways and inform chemical transport models.

Limited availability of ammonia (NH3) observations is currently a barrier for effective monitoring of the nitrogen cycle. It prevents a full understanding of the atmospheric processes in which this trace gas is involved and therefore impedes determining its related budgets. Since the end of 2007, the Infrared Atmospheric Sounding Interferometer (IASI) satellite has been observing NH3 from space at a high spatio-temporal resolution. This valuable data set, already used by models, still needs validation. We present here a first attempt to validate IASI-NH3 measurements using existing independent ground-based and airborne data sets. The yearly distributions reveal similar patterns between ground-based and space-borne observations and highlight the scarcity of local NH3 measurements as well as their spatial heterogeneity and lack of representativity. By comparison with monthly resolved data sets in Europe, China and Africa, we show that IASI-NH3 observations are in fair agreement, but they are characterized by a smaller variation in concentrations. The use of hourly and airborne data sets to compare with IASI individual observations allows investigations of the impact of averaging as well as the representativity of independent observations for the satellite footprint. The importance of considering the latter and the added value of densely located airborne measurements at various altitudes to validate IASI-NH3 columns are discussed. Perspectives and guidelines for future validation work on NH3 satellite observations are presented.

Surface concentrations of secondary inorganic particle components over the UK have been analysed for 2001–2010 using the EMEP4UK regional atmospheric chemistry transport model and evaluated against measurements. Gas/particle partitioning in the EMEP4UK model simulations used a bulk approach, which may lead to uncertainties in simulated secondary inorganic aerosol. However, model simulations were able to accurately represent both the long-term decadal surface concentrations of particle sulfate and nitrate and an episode in early 2003 of substantially elevated nitrate measured across the UK by the AGANet network. The latter was identified as consisting of three separate episodes, each of less than 1 month duration, in February, March and April. The primary cause of the elevated nitrate levels across the UK was meteorological: a persistent high-pressure system, whose varying location impacted the relative importance of transboundary versus domestic emissions. Whilst long-range transport dominated the elevated nitrate in February, in contrast it was domestic emissions that mainly contributed to the March episode, and for the April episode both domestic emissions and long-range transport contributed. A prolonged episode such as the one in early 2003 can have substantial impact on annual average concentrations. The episode led to annual concentration differences at the regional scale of similar magnitude to those driven by long-term changes in precursor emissions over the full decade investigated here. The results demonstrate that a substantial part of the UK, particularly the south and southeast, may be close to or exceeding annual mean limit values because of import of inorganic aerosol components from continental Europe under specific conditions. The results reinforce the importance of employing multiple year simulations in the assessment of emissions reduction scenarios on particulate matter concentrations and the need for international agreements to address the transboundary component of air pollution.

Biogenic influences on the composition and characteristics of aerosol were investigated on Bird Island (54°00' S, 38°03' W) in the South Atlantic during November and December 2010. This remote marine environment is characterised by large seabird and seal colonies. The chemical composition of the submicron particles, measured by an aerosol mass spectrometer (AMS), was 21% non-sea-salt sulfate, 2% nitrate, 8% ammonium, 22% organics and 47% sea salt including sea salt sulfate. A new method to isolate the sea spray signature from the high-resolution AMS data was applied. Generally, the aerosol was found to be less acidic than in other marine environments due to the high availability of ammonia, from local fauna emissions. By positive matrix factorisation five different organic aerosol (OA) profiles could be isolated: an amino acid/amine factor (AA-OA, 18% of OA mass), a methanesulfonic acid OA factor (MSA-OA, 25%), a marine oxygenated OA factor (M-OOA, 41%), a sea spray OA fraction (SS-OA, 7%) and locally produced hydrocarbon-like OA (HOA, 9%). The AA-OA was dominant during the first two weeks of November and found to be related with the hatching of penguins in a nearby colony. This factor, rich in nitrogen (N : C ratio = 0.13), has implications for the biogeochemical cycling of nitrogen in the area as particulate matter is often transported over longer distances than gaseous N-rich compounds. The MSA-OA was mainly transported from more southerly latitudes where phytoplankton bloomed. The bloom was identified as one of three sources for particulate sulfate on Bird Island, next to sea salt sulfate and sulfate transported from South America. M-OOA was the dominant organic factor and found to be similar to marine OA observed at Mace Head, Ireland. An additional OA factor highly correlated with sea spray aerosol was identified (SS-OA). However, based on the available data the type of mixture, internal or external, could not be determined. Potassium was not associated with sea salt particles during 19% of the time, indicating the presence of biogenic particles in addition to the MSA-OA and AA-OA factors.

A comprehensive assessment of nitrogen (N) flows at the landscape scale is fundamental to understand spatial interactions in the N cascade and to inform the development of locally optimised N management strategies. To explore these interactions, complete N budgets were estimated for two contrasting hydrological catchments (dominated by agricultural grassland vs. semi-natural peat-dominated moorland), forming part of an intensively studied landscape in southern Scotland. Local scale atmospheric dispersion modelling and detailed farm and field inventories provided high resolution estimations of input fluxes. Direct agricultural inputs (i.e. grazing excreta, N2 fixation, organic and synthetic fertiliser) accounted for most of the catchment N inputs, representing 82% in the grassland and 62% in the moorland catchment, while atmospheric deposition made a significant contribution, particularly in the moorland catchment, contributing 38% of the N inputs. The estimated catchment N budgets highlighted areas of key uncertainty, particularly N2 exchange and stream N export. The resulting N balances suggest that the study catchments have a limited capacity to store N within soils, vegetation and groundwater. The "catchment N retention", i.e. the amount of N which is either stored within the catchment or lost through atmospheric emissions, was estimated to be 13% of the net anthropogenic input in the moorland and 61% in the grassland catchment. These values contrast with regional scale estimates: Catchment retentions of net anthropogenic input estimated within Europe at the regional scale range from 50% to 90%, with an average of 82% (Billen et al., 2011). This study emphasises the need for detailed budget analyses to identify the N status of European landscapes.

Measurements of total nitrogen and inorganic nitrogen in precipitation samples from NitroEurope sites across Europe permit the calculation of organic nitrogen concentrations and wet deposition, by difference. The contribution of organic N to total N in precipitation ranged from only a few % to around 40% across 18 sites from northern Finland to Italy, similar to results from previous individual studies. This paper presents the absolute and relative contributions of organic N to wet N deposition across Europe, and examines seasonal trends. There were only weak correlations with other solutes in precipitation. These simple statistics indicate that sources of organic N in precipitation vary across Europe, and that no single source is responsible. The organic N contributes to total N deposition, yet this input is rarely quantified in nitrogen budgets.

Nitrogen (N) has emerged in recent years as a key factor associated with global changes, with impacts on biodiversity, ecosystems functioning and human health. In order to ameliorate the effects of excessive N, safety thresholds such as critical loads (deposition fluxes) and levels (concentrations) can be established. Few studies have assessed these thresholds for semi-natural Mediterranean ecosystems. Our objective was therefore to determine the critical loads of N deposition and long-term critical levels of atmospheric ammonia for semi-natural Mediterranean evergreen woodlands. We have considered changes in epiphytic lichen communities, one of the most sensitive comunity indicators of excessive N in the atmosphere. Based on a classification of lichen species according to their tolerance to N we grouped species into response functional groups, which we used as a tool to determine the critical loads and levels. This was done for a Mediterranean climate in evergreen cork-oak woodlands, based on the relation between lichen functional diversity and modelled N deposition for critical loads and measured annual atmospheric ammonia concentrations for critical levels, evaluated downwind from a reduced N source (a cattle barn). Modelling the highly significant relationship between lichen functional groups and annual atmospheric ammonia concentration showed the critical level to be below 1.9 μg m−3, in agreement with recent studies for other ecosystems. Modelling the highly significant relationship between lichen functional groups and N deposition showed that the critical load was lower than 26 kg (N) ha−1 yr−1, which is within the upper range established for other semi-natural ecosystems. Taking into account the high sensitivity of lichen communities to excessive N, these values should aid development of policies to protect Mediterranean woodlands from the initial effects of excessive N.

Inferential models have long been used to determine pollutant dry deposition to ecosystems from measurements of air concentrations and as part of national and regional atmospheric chemistry and transport models, and yet models still suffer very large uncertainties. An inferential network of 55 sites throughout Europe for atmospheric reactive nitrogen (Nr) was established in 2007, providing ambient concentrations of gaseous NH3, NO2, HNO3 and HONO and aerosol NH4+ and NO3− as part of the NitroEurope Integrated Project. Network results providing modelled inorganic Nr dry deposition to the 55 monitoring sites are presented, using four existing dry deposition routines, revealing inter-model differences and providing ensemble average deposition estimates. Dry deposition is generally largest over forests in regions with large ambient NH3 concentrations, exceeding 30–40 kg N ha−1 yr−1 over parts of the Netherlands and Belgium, while some remote forests in Scandinavia receive less than 2 kg N ha−1 yr−1. Turbulent Nr deposition to short vegetation ecosystems is generally smaller than to forests due to reduced turbulent exchange, but also because NH3 inputs to fertilised, agricultural systems are limited by the presence of a substantial NH3 source in the vegetation, leading to periods of emission as well as deposition. Differences between models reach a factor 2–3 and are often greater than differences between monitoring sites. For soluble Nr gases such as NH3 and HNO3, the non-stomatal pathways are responsible for most of the annual uptake over many surfaces, especially the non-agricultural land uses, but parameterisations of the sink strength vary considerably among models. For aerosol NH4+ and NO3− discrepancies between theoretical models and field flux measurements lead to much uncertainty in dry deposition rates for fine particles (0.1–0.5 μm). The validation of inferential models at the ecosystem scale is best achieved by comparison with direct long-term micrometeorological Nr flux measurements, but too few such datasets are available, especially for HNO3 and aerosol NH4+ and NO3−.

Base cations exert a large impact on various geochemical and geophysical processes both in the atmosphere and at the Earth surface. One of the essential roles of these compounds is impact on surface pH causing an increase in alkalinity and neutralizing the effects of acidity generated by sulphur and nitrogen deposition. During recent years anthropogenic emissions of base cations in the UK have decreased substantially, by about 70%, 78%, 75% and 48% for Na+, Mg2+, Ca2+ and K+, respectively, over the period 1990–2006. For the island regions, such as the UK, the main source of base cation particles is the aerosol produced from the sea surface. Here, the sea salt aerosol (SSA) emissions are calculated with parameterisations proposed by Mårtensson et al. (2003) for ultra fine particles, Monahan et al. (1986) for fine particles and Smith and Harisson (1998) for coarse particles continuously with a 0.1 μm size step using WRF-modelled wind speed data at a 5 km × 5 km grid square resolution with a 3 h time step for two selected years 2003 and 2006. SSA production has been converted into base cation emissions, with the assumption that the chemical composition of the particle emitted from the sea surface is equal to the chemical composition of sea water, and used as input data in the Fine Resolution Atmospheric Multi-pollutant Exchange Model (FRAME). FRAME model annual mean concentrations and total wet deposition at a 5 km × 5 km grid resolution, are compared with concentrations in air and wet deposition from the National Monitoring Network and measurements based estimates of UK deposition budget. The correlation coefficient for wet deposition achieves high values (R = 0.8) for Na+ and Mg2+, whereas for Ca2+ the correlation is poor (R < 0.3). Base cation concentrations are also represented well, with some overestimations on the west coast and underestimations in the centre of the land.

Read alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for downstream analyses. However, recent studies have shown that published alignment tools have variable mapping sensitivity and do not necessarily align all the reads which should have been aligned, a problem we termed as the false-negative non-alignment problem. Here we present Scavenger, a python-based bioinformatics pipeline for recovering unaligned reads using a novel mechanism in which a putative alignment location is discovered based on sequence similarity between aligned and unaligned reads. We showed that Scavenger could recover unaligned reads in a range of simulated and real RNA-seq datasets, including single-cell RNA-seq data. We found that recovered reads tend to contain more genetic variants with respect to the reference genome compared to previously aligned reads, indicating that divergence between personal and reference genomes plays a role in the false-negative non-alignment problem. Even when the number of recovered reads is relatively small compared to the total number of reads, the addition of these recovered reads can impact downstream analyses, especially in terms of estimating the expression and differential expression of lowly expressed genes, such as pseudogenes.

Read alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for downstream analyses. However, recent studies have shown that published alignment tools have variable mapping sensitivity and do not necessarily align all the reads which should have been aligned, a problem we termed as the false-negative non-alignment problem. Here we present Scavenger, a python-based bioinformatics pipeline for recovering unaligned reads using a novel mechanism in which a putative alignment location is discovered based on sequence similarity between aligned and unaligned reads. We showed that Scavenger could recover unaligned reads in a range of simulated and real RNA-seq datasets, including single-cell RNA-seq data. We found that recovered reads tend to contain more genetic variants with respect to the reference genome compared to previously aligned reads, indicating that divergence between personal and reference genomes plays a role in the false-negative non-alignment problem. Even when the number of recovered reads is relatively small compared to the total number of reads, the addition of these recovered reads can impact downstream analyses, especially in terms of estimating the expression and differential expression of lowly expressed genes, such as pseudogenes.

Accurate assessment of kidney function by measurement of glomerular filtration rate (GFR) is essential to the risk assessment of prospective living kidney donors. We evaluated the performance of various estimating equations for creatinine clearance (Cockcroft-Gault), GFR (Modification of Diet in Renal Disease, Chronic Kidney Disease Epidemiology Collaboration), and 24-hour urine collections for creatinine clearance in obese potential kidney donors. We evaluated 164 potential kidney donors including 49 with a BMI of 30–35 and 32 with a BMI >35 that have completed a routine living donor evaluation with a measured GFR. All the estimating equations performed poorly in obese donors. While 24-hour urine collections performed better, only 15% had an adequate 24-hour urine collection. Since obese kidney donors may be at higher than average risk for kidney failure, accurate assessment of kidney function in these donors is crucial to ensure their long-term health postdonation.

Chronic Hepatitis C (HCV) infection is an important cause of morbidity and mortality in patients with end-stage renal disease. Renal transplantation confers a survival advantage in HCV-infected patients. Renal transplant candidates with serologic evidence of HCV infection should undergo a liver biopsy to assess for fibrosis and cirrhosis. Patients with Metavir fibrosis score ≤3 and compensated cirrhosis should be evaluated for interferon-based therapy. Achievement of sustained virological response (SVR) may reduce the risks for both posttransplantation hepatic and extrahepatic complications such as de novo or recurrent glomerulonephritis associated with HCV. Patients who cannot achieve SVR and have no live kidney donor may be considered for HCV-positive kidneys. Interferon should be avoided after kidney transplant except for treatment of life-threatening liver injury, such as fibrosing cholestatic hepatitis. Early detection, prevention, and treatment of complications due to chronic HCV infection may improve the outcomes of kidney transplant recipients with chronic HCV infection.