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As the UK leaves the European Union, the Common Agricultural Policy (CAP), which for decades has dictated how and when farming support is delivered, will be replaced with a new UK agricultural policy which will see UK farmers, especially upland livestock farmers, facing a more challenging economic environment and a significant change to the way in which farming support is delivered. This study used a series of interviews with UK farmers across differing locations and categories to ascertain how levels of social capital may hinder or enhance a farmer's willingness to embrace future agricultural policy. We found that more conventional farmers who have never participated in agri-environment schemes and those currently in government-run schemes display high levels of bonding capital and low levels of bridging and linking capital which may hinder their ability to adapt to change. In contrast, farmers who embrace a pubic goods approach to land management displayed high bridging and linking capital and are more likely to work with government officials to adapt to policy change. Communities are more likely to become sustainable if they have access to government support and advice, and if relationships with other community members and stakeholders with an interest in rural communities, the natural environment and land management are encouraged and maintained. • Conventional farmers access high levels of bonding social capital. • High Nature Value Farmers access high levels of bridging and linking social capital. • As farmers' community roles diminish, community co-operative action reduces. • The government must shift from controller and provider to catalyst and facilitator. [ABSTRACT FROM AUTHOR]

Globally, progress in reducing greenhouse gas (GHG) emissions from livestock agricultural systems has been slow. Attention has focussed on implementation science: understanding barriers to the uptake of GHG emissions mitigation measures and identifying solutions. Here, solutions presented by stakeholders associated with the Welsh sheep, beef and dairy sectors were used to create a typology of implementation strategies providing insights for improving uptake of GHG emissions mitigation measures in these sectors globally. A grounded theory approach identified themes and underlying categories of solutions in data gathered from stakeholders, through semi-structured interviews and facilitated workshops. Four categories were identified, underlying 25 themes coded from the data: Basis for change (relating to the knowledge, skills and resources of those involved), Levels of change (working around, overcoming or altering challenges), Approaches to change (accommodating, controlling or empowering) and Types of change (specific practical solutions or capacity-building). Basis for change and Approaches to change determine responsibility for change from practical (who has the capacity) and subjective (who should be responsible) perspectives. The typology is discussed in the context of previously identified challenges and examples of current implementation strategies. Findings provide a framework of solutions to support policymakers, and researchers engaged in implementation science. [ABSTRACT FROM AUTHOR]

Peatlands drained for agriculture are among the most intensive sources of greenhouse gas (GHG) emissions from the land-use sector. Policy decisions on the most effective strategies to reduce GHG emissions in line with Paris Agreement goals, alongside strategies that can halt any ongoing soil and biodiversity losses, are hindered by a lack of understanding on how proposed mitigation measures are likely to be received by the farming sector. Research has identified effective GHG reduction measures, but successful on-farm adoption of these measures is contingent upon farmer perceptions of the relative practicality of implementing the measures, and the economic impact that adoption will have on the farm business. In this study, Best–Worst Scaling, a discrete choice survey method, was utilised to elicit expert (climate change, policy and biodiversity) and farmer opinion on the relative effectiveness, practicality and level of economic cost of mitigation measures that can reduce GHG emissions at the farm level. The method enabled individual mitigation measures to be ranked by effectiveness (expert opinion), practicality and economic cost (farmer opinions). There were no measures ranked as both effective and practical, or effective with low cost, but there were measures ranked by farmers as practical and low cost to implement. These included: more effective nutrient management, reduced or no tillage, the installation of buffer zones, increased fossil fuel efficiency and the optimisation of irrigation systems. The strong divergence of 'effective' measures on the one hand, and 'practical' and 'economic' measures on the other, highlights the major challenges involved in reducing high GHG emissions from agricultural organic soils. Resolving these challenges will require a combination of financial mechanisms to compensate farmers for higher costs and/or reduced yields, engagement and advice to support farmers in adopting changes in management practice, and agricultural innovation and adaptation to maintain overall food production and economic viability. If these challenges are overcome, more sustainable landscape management on agricultural lowland peat could make significant contributions to achieve national and international climate change targets. • Agricultural peatlands have high carbon emissions because of drainage practices. • Expert and farmer perceptions on emission reduction mitigation measures was captured. • Wetter farming measures were identified as essential for emission reductions. • No measures explored ranked as both effective and practical, or effective with low cost. [ABSTRACT FROM AUTHOR]

• Extreme winter flooding negatively altered soil physical, chemical and biological indicators. • Soil available P was reduced by 42% in the flooded areas after the flood event. • Plant biomass in arable fields was reduced by 19–34% in flooded areas. • Total soil microbial biomass increased by 60% after flooding. • Grassland soils were more resilient than other crops. Evidence suggests that climate change is increasing the frequency of extreme weather events (e.g. excessive rainfall, heat, wind). The winter of 2013-14 saw exceptional levels of rainfall across the UK leading to extreme and prolonged flooding (up to 3 months with floodwater depths up to 3 m) in several low-lying agricultural areas (e.g. Somerset Levels, Thames Valley). The impact of extreme flooding and the speed of ecosystem recovery at the field-scale, however, remain poorly understood. The main objectives of this study were therefore to: (1) assess the effect of this extreme winter flooding event on a range of soil physical, chemical and biological quality indicators at 15 flood-affected sites (arable and grassland), (2) determine if these changes in soil health were reversible in the short term (< 1 year), and (3) to evaluate the effectiveness of different mechanical interventions (sward-lifting, subsoiling, slot-seeding and aerating) to accelerate the amelioration of the damage caused by winter flooding at 2 of the 15 sites. Once the floodwater had receded (April 2014), we found that several of the measured soil quality indicators were negatively affected in the flooded areas in comparison with non-flooded areas. This included a decrease in soil bulk density (by 19%), soil pH (by 0.4 units), and available P (by up to 42%). Flooding increased soil microbial biomass (60%), induced a shift in soil microbial community structure and reduced earthworm numbers. After 8 months of recovery, only soil pH remained significantly reduced (by 0.3 units) in the flooded areas in comparison to the unflooded areas. Flooding had a negative impact on the overlying vegetation at the arable sites (biomass production was reduced by between 19 and 34%) but had no major impact at the grassland sites in the long-term. In the flood amelioration experiment, the subsoiled plots produced grass with a higher nutrient content (e.g. N - up to 35%, Ca - up to 19% and Mg - up to 58%). However, the four different interventions appeared to have little positive impact on most of the soil quality indicators measured. In conclusion, extreme winter flooding was found to induce short-term alterations in key soil quality indicators and to destroy winter crops, although these effects did not persist in the longer term. Our results therefore indicate that the temperate agroecosystems evaluated here were highly resilient to winter flood stress and that recovery to a pre-flood state could be achieved within 1 year. Improved management strategies are still needed to speed up the rate of recovery after flood events to facilitate a faster return to agricultural production. [ABSTRACT FROM AUTHOR]

Abstract The frequency and intensity of extreme weather events (e.g. flood, drought) are predicted to increase for the foreseeable future and it is expected that these will negatively impact upon agroecosystem functioning. Our understanding of how grassland ecosystems respond to extreme weather events occurring at different times of the year, however, is lacking. To better understand the seasonal response of grassland to flooding, we subjected an agricultural grassland to an 8-week extreme flood event at three different temperatures (5 °C-winter, 15 °C-spring/autumn and 25°C-summer) and then followed its subsequent recovery for 9 weeks after floodwater removal. We focused on key indicators of ecosystem functioning including primary production, nutrient cycling, greenhouse gas (GHG) emissions, ammonia (NH 3) volatilization, and soil microbial communities. The experiment used intact soil mesocosms (1 kg) with indigenous vegetation collected from a grassland with no previous history of flooding. Flooding reduced biomass production by 18% at 5 °C, 50% at 15 °C and 95% at 25 °C. Flooding also significantly disrupted elemental cycling (nitrogen, phosphorus and carbon) as evidenced by an increased release of P, Fe and NH 4 + into the soil and overlying floodwater and large amounts of CH 4 and NH 3 released to the atmosphere (mainly during the flooding). These effects were more pronounced at higher temperatures (e.g. 45–700 kg CH 4 C ha−1 and 1–5 kg NH 3 N ha−1 at 15 and 25 °C, respectively). In addition, after floodwater removal this NH 4 + was rapidly nitrified leading to large losses of N 2 O (1.0–14.2 kg N 2 O N ha−1 at 5–25 °C, respectively). Especially at higher temperatures, flooding resulted in a reduction in soil microbial biomass (more than 58% of the equivalent unflooded treatment at 25 °C) and changes in microbial community structure (assessed by PLFAs). Further, some of these changes persisted after flood removal including a loss of actinomycetes, arbuscular mycorrhizal fungi and fungi. Overall, we conclude that ecosystem responses to extreme weather events are critically dependent on temperature with those occurring at higher temperatures having a greater negative impact than those at the lowest temperature (5 °C). The large potential release of CH 4 and N 2 O also suggests that flood events should be considered as a potential source of GHGs when comparing top-down and bottom-up calculations of national inventories, and that further work is needed to better refine GHG emission estimates for these events. Highlights • Flooding induced a rapid release of nutrients, especially at higher temperatures. • 700 kg CH 4 C ha−1 and 5 kg NH 3 N ha−1 were released in the flood phase at 25 °C. • During soil recovery, nitrification led to 1.0–14.2 kg N 2 O N ha−1 losses at 5–25 °C. • Flooding reduced soil microbial biomass, actinomycetes and arbuscular mycorrhiza. • Flooding reduced biomass production by 18% at 5 °C, 50% at 15 °C and 95% at 25 °C. [ABSTRACT FROM AUTHOR]

Abstract Soils around the world are being exposed to weather events which are unprecedented in recent history. To maintain the delivery of soil-related ecosystem services and to promote greater soil resilience it is essential to understand how plant-soil systems respond to these extreme events. In this study we replicated a recent period of extreme rainfall and prolonged spring flooding in a temperate grassland which had no previous history of flooding. Intact soil mesocosms (Eutric Cambisol) 1 kg weight were subjected to a simulated long-term spring flood (15 °C, 2 months) and maintained in the light with above ground indigenous vegetation (Lolium perenne L.) or dark with and without indigenous vegetation to simulate different flood typologies. In comparison to a no-flood control treatment, nutrient cycling, water quality, air quality (greenhouse gas emissions), habitat provision and biological population regulation shifts were evaluated. Flooding induced a rapid release of nutrients into the soil solution and overlying floodwater, resulting in potential nutrient losses up to 15 mg Fe, 16 mg NH 4 +, 360 mg DOC and 28 mg DON, per mesocosm. The presence of plants increased the rate of nutrient release (especially P), with the effects magnified when light transmission through the floodwater was restricted (1.3 mg P vs 0.2 mg P, per mesocosm). Flooding induced a rapid decline in redox potential and subsequent production of CH 4 , especially in the darkened treatments (10 and between 11 and 16 times higher than the control, without and with light restrictions, respectively). Upon removal of the floodwater, the accumulated NH 4 + was nitrified leading to a shift in greenhouse gas emissions, from CH 4 to N 2 O emissions. N 2 O was only significantly produced in the mesocosms kept under light restrictions (13 times higher than in other two treatments). Flooding eliminated earthworms, reduced grass production after soil recovery (from 28 g for control mesocosms to 11 g and <1 g for flooded mesocosms without and with light restrictions, respectively). Soil microbial biomass was also reduced (up to a 22–27% of the total PLFAs) and flooding induced shifts in microbial community structure, particularly a loss of soil fungi. The soil fungi content quickly recovered (4 weeks) when light was not restricted during the flood period, however, no such recovery was seen in the darkened treatments. Overall, we conclude that extreme flood events cause rapid and profound changes in soil function. Both the impact of the flooding and the time to recover is exacerbated when light is restricted (e.g. in sediment laden floodwater). In addition, our results suggest that the presence of flood-resilient plants can mitigate against some of the negative impacts of flooding on soil functioning. Highlights • Flooding eliminated earthworms and altered soil microbial community structure. • Flooding reduced the size of the microbial biomass and fungal content. • Vegetation played a vital role in preserving soil quality during flooding. • Decomposition of vegetation induced P loss in light restricted floodwater. • Impact of flooding was greater under light restricted floodwater conditions. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Challenges identified to implementing GHG mitigation measures in livestock systems. • Practical, knowledge and cognitive limitations interact with interests. • Cognitive limitations and critical perspectives of change highlighted. • Conceptual model for policymakers links main types of challenge. Abstract Livestock agriculture is a significant global emitter of greenhouse gases (GHG) and the sector is under pressure to reduce its environmental footprint. Dairy, sheep and beef production are major contributors to emissions. Here, a study of the barriers to implementing GHG mitigation measures on sheep, beef and dairy farms in Wales provides insights into challenges for these sectors globally. Data were gathered from 18 stakeholder organisations and farmers using semi-structured interviews and facilitated workshops. Participants were asked about the challenges to implementing measures associated with different parts of the farming system. Data were analysed using a grounded theory approach. Identified themes covered the range of challenges to the implementation of climate-friendly agricultural practice described in a global review. A conceptual model linking categories of challenge (Practical limitations, Knowledge limitations, Cognitive limitations and Interests) was developed from the data. Comparing the findings with existing work on behavioural change revealed two major differences: i) The concept of Cognitive limitations highlighted the importance of cognitive processes recognised in social psychology to the implementation of change in livestock agriculture. It differentiated specific cognitive biases incorporated in behavioural models from constraints affecting the thought processes in which these biases develop and which they affect, ii) Critical elements such as power relationships and conflicting stakeholder interests were highlighted as important factors outside the scope of behavioural change models. The conceptual model developed can support policymakers in understanding and tackling challenges to change in livestock agricultural systems. [ABSTRACT FROM AUTHOR]

Due to climate change, the frequency and duration of flood events are predicted to increase in many regions of the world. This is expected to cause large changes in soil functioning and to a progressive decline in soil quality such as reduced rates of nutrient cycling, enhanced greenhouse gas emissions and loss of soil biodiversity. There is a knowledge gap, however, on how temperate agricultural soils under different management practices (e.g. manure application) respond to prolonged river or coastal flooding. The main objective of this work was to determine the effects of a simulated prolonged flooding with saline and freshwater on soil N cycling, following application of a low C:N organic amendment (broiler litter) at two temperatures, representative of a winter and a spring flood event. Using laboratory mesocosms we simulated prolonged winter (6 °C) and spring (14 °C) flooding of soil amended with broiler litter. We also compared the effects of inundation with either river (freshwater) or coastal (saline) water. An agricultural grassland soil (Eutric Cambisol) was subjected to different combinations of treatments (flood with fresh or saline water, winter vs spring temperatures, with/without poultry manure). The impact of these treatments on soil solution N dynamics, greenhouse gas emissions (CO 2 , CH 4 , N 2 O) and microbial community structure (by PLFA analysis) were evaluated over an 11 week simulated flood event followed by an 8 week soil recovery period (without flood). Overall, potential losses of NH 4 + and cumulative GHG emissions were increased by flooding and the presence of manure. CH 4 emissions were found to dominate under freshwater flooding conditions and N 2 O under saline flooding. Significant releases of GHG occurred during both flooding and after floodwater removal. Temperature was less influential on regulating GHG under the different treatments. These releases in GHG were associated with disruption in N cycling and changes in soil microbial composition and these changes persisted after floodwater removal. Extreme flooding negatively impacts soil functioning, however, the magnitude of any changes remain critically dependent on flood duration and source of flood water, and management conditions. Further work is required at the field scale to understand the molecular basis of the responses observed in this study. [ABSTRACT FROM AUTHOR]

Terrestrial soil denitrification is of great importance for closing the nitrogen (N) cycle, yet the current understanding of soil denitrification response to N fertilization remains uncertain. While there has been a focus on factors controlling N 2 O fluxes from agricultural soils because of its global warming effect, much less is known about factors controlling total denitrification losses, yet these can be sufficiently large to affect N use efficiency. Here, we collated 353 observations from 74 papers and conducted a global-scale meta-analysis to explore the effects of N fertilization on agricultural soil denitrification (N 2 O + N 2 ) where the acetylene inhibition technique was used. Relative to the control, N fertilization significantly increased soil denitrification by an average of 174%, although the magnitude of this increase differed significantly across environmental and soil conditions. Soil denitrification was more responsive to N fertilization in grasslands than in croplands. The changes in soil denitrification increased exponentially when the rates of synthetic N fertilizer application ≤ 250 kg N ha − 1 , but above this threshold, there were no further increases. The responses of soil denitrification to N fertilization were negatively correlated with soil clay content, C:N ratio, and bulk density. The comparable responses of soil N 2 O emissions (165%) and denitrification to N fertilization resulted in a small insignificant decrease of the N 2 O:N 2 ratio. Organic fertilizer applied with and without synthetic N fertilizer can contribute to lower N 2 O emissions probably by facilitating the last step of soil denitrification to N 2 production. Taken together, we conclude that these findings can provide important insights on regulating soil denitrification, which might contribute to improvement of N use efficiency and elimination of its negative impacts in agro-ecosystems. [ABSTRACT FROM AUTHOR]

Thyroid nodules are common, and a frequent reason for referral to secondary care. Clinical assessment and investigation should aim to address: functional status of the thyroid; exclusion of malignancy; and the presence of other symptoms (e.g. tracheal or oesophageal compression). A combination of neck ultrasound and fine-needle aspiration cytology (FNAC) can usually help establish a plan of management, allowing conservative management of most patients, and surgical treatment for those with suspected or confirmed thyroid cancer. The limitations of FNAC include a relatively high rate of inadequate/non-diagnostic samples, and the inability of cytology to distinguish between benign and malignant follicular neoplasms. Surgery may therefore be required to establish the diagnosis in patients with indeterminate nodules, in addition to its role in treatment for compressive symptoms or thyrotoxicosis. [ABSTRACT FROM AUTHOR]

Cysteine (Cys) and methionine (Met) are central to terrestrial S cycling because they are sources of carbon (C), nitrogen (N), and sulphur (S) for plant nutrition and microbial growth. However, soil microorganisms are expected to compete for the C, N and S in these S-amino acids. We hypothesized that microbial competition would be greater in soils with low plant productivity due to lower C inputs from plants. Here we added 14C-labelled Cys and Met to 5 soils collected from an altitude-driven primary grassland productivity gradient, we then measured microbial uptake with a centrifugal drainage procedure over 60 min, and the subsequent mineralization with NaOH traps over 48 h. Our results revealed that both Cys and Met were rapidly assimilated by soil microbes, with half-lives ranging from 0.34 to 2.14 min, which is an order of magnitude (or more) faster than when determined from measurement of 14CO 2 evolution. This considerable delay between microbial 14C removal from soil solution and subsequent 14CO 2 evolution indicates that the degradation of Cys and Met in grassland soils occurred mainly through biological processes. Soil microbial uptake of Cys and Met was dominated by a high-affinity transport system (0.01–0.1 mM), while a lower affinity transport system became more important at higher substrate concentrations (1–100 mM). In addition, microbial uptake and mineralization rates of Cys and Met declined in less productive, higher elevation sites, suggesting that the turnover of organic N and S, and subsequent availability for plant uptake is likely to be controlled by soil fertility. We conclude that although Cys and Met may represent a minor component of DON and DOS pools in soil, their importance for soil microbes and plant nutrition may have been underestimated due to their fast turnover and replenishment rates in grassland soils. • Cystine and methionine turned over faster in soils from low altitude sites. • Methionine showed a lower mineralization rate than cysteine. • < 20% of amino acid-14C was retained in soil solution within 10 min. • Degradation of cysteine or methionine occurred mainly through biological processes. [ABSTRACT FROM AUTHOR]

Wood represents the single most important source of renewable energy worldwide and depending on the mechanism of energy production can lead to the production of by-products with vastly different properties (i.e. wood ash (WA) from incineration and biochar (BC) from pyrolysis). These are typically applied to land, however, a critical comparison of their impact on soil quality and carbon (C) cycling is lacking. To address this, we generated biochar (450 °C) and wood ash (870 °C) from the same mixed hardwood feedstock and added it to an agricultural grassland at comparable rates under both laboratory and field conditions (10 t ha −1 and 571 kg ha −1 for BC and WA, respectively). We hypothesized that alkaline, nutrient-rich wood ash would stimulate microbial activity, resulting in the loss of soil organic matter (SOM), while biochar which is recalcitrant to microbial attack would promote the stabilization of native SOM. The effects on the soil microbial community and soil C and N cycling were determined over 1 year. Overall, biochar promoted soil quality by enhancing nutrient availability (P and K), moisture retention and increasing soil C content. However, it was also associated with an increase in below-ground CO 2 loss. As plant productivity was unaffected and laboratory incubations of biochar with 14 C-labelled SOM showed no indication of priming, we deduce that this CO 2 originates from the biochar itself. This is supported by the lack of effect of biochar on soil N cycling, microbial biomass and community structure. Wood ash had almost no effect on either soil quality or vegetation quality (yield and foliar nutrient content) under field conditions but did induce negative SOM priming under both laboratory and field conditions. We conclude that when applied at field-relevant rates, neither amendment had a detrimental effect on native SOM cycling. While wood ash promotes the retention of native SOM, biochar may be a better strategy for enhancing SOM levels because of its intrinsic recalcitrant character, however, this needs to be offset against the reduced amount of energy derived from pyrolysis in comparison to incineration. [ABSTRACT FROM AUTHOR]

Sulphur-containing amino acids (i.e. Cysteine (Cys) and methionine (Met)) constitute an important proportion of the soil organic sulphur. However, detailed information regarding the microbial transformation of Cys and Met at a molecular level remain poorly characterized. To trace the fate of carbon (C) and sulphur (S) derived from Cys and Met in an agricultural grassland soil, a14C and 35S dual-isotopic labelling approach was adopted. We also investigated whether their mineralization was affected by manipulating C (added as glucose), nitrogen (N), phosphorus (P) and S (added as NH 4 NO 3 , KH 2 PO 4 and K 2 SO 4) availability in soil solution. Our results showed that over a 7-day incubation period, 67.2–89.2% of the 14C derived from Cys and Met was respired as 14CO 2 , 2.7–19.5% had been immobilized in the soil microbial biomass; while the recovery of 35S in soil solution ranged from 6.4 to 9.9%, with the reminder retained in the soil microbial biomass. Overall, our results indicated that soil microbial communities possess a high capacity to utilize Cys and Met. Furthermore, using the 14C and 35S dual-labelling technique, we found that C and S derived from Cys and Met were microbially mineralized and immobilized at different rates, indicating that the cycles of these two elements were temporally decoupled at the molecular level. The addition of glucose-C increased 14CO 2 respiration from Cys and Met after 7 d, while in comparison inorganic N, P and S addition had less effect on 14C and 35S partitioning. Schematic presentation of carbon, nitrogen and sulphur partitioning from two S-containing amino acids in grassland soils after 7-d incubation. a: labelled amino acid uptake into soil microbial biomass; b: subsequent microbial mineralization. (35S FE : (35S in the 0.01 M CaCl 2 extract of fumigated soils - 35S uf) × 100/0.35/35S O (%)). [Display omitted] • 67.2–89.2% of 14C derived from Cys and Met were respired as 14CO 2 in 168 h. • 92.2–93.6% of 35S derived from Cys and Met retained in soil microbial biomass. • N from Cys and Met was firstly released as NH 4 +, then rapidly converted to NO 3 −. • Glucose addition led to significant increase in 14CO 2 respiration from Cys and Met. [ABSTRACT FROM AUTHOR]

The cycling of soil organic matter (SOM) and carbon (C) within the soil is governed by the presence of key macronutrients, particularly nitrogen (N) and phosphorus (P). The relative ratio of these nutrients has a direct effect on the potential rates of microbial growth and nutrient processing in soil and thus is fundamental to ecosystem functioning. However, the effect of changing soil nutrient stoichiometry on the small organic molecule (i.e., metabolite) composition and cycling by the microbial community remains poorly understood. Here, we aimed to disentangle the effect of stoichiometrically balanced nutrient addition on the soil metabolomic profile and apparent microbial carbon use efficiency (CUE) by adding a labile C source (glucose) in combination with N and/or P. After incorporation of the added glucose into the microbial biomass (48 h), metabolite profiling was undertaken by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). 494 metabolites were identified across all treatments mainly consisting of lipids (n = 199), amino acids (n = 118) and carbohydrates (n = 43), >97% of which showed significant changes in concentration between at least one treatment. Overall, glucose-C addition generally increased the synthesis of other carbohydrates in soil, while addition of C and N together increased peptide synthesis, indicative of protein formation and turnover. The combination of C and P significantly increased the number of fatty acids synthesised. There was no significant change in the PLFA-derived microbial community structure or microbial biomass following C, N and P addition. Further, N addition led to an increase in glucose-C partitioning into anabolic processes (i.e., increased CUE), suggesting the microbial community was N, but not P limited. Based on the metabolomic profiles observed here, we conclude that inorganic nutrient enrichment causes substantial shifts in both primary and secondary metabolism within the microbial community, leading to changes in resource flow and thus soil functioning, however, the microbial community illustrated significant metabolic flexibility. • Metabolomics reveal fundamental metabolite synthesis with changing stoichiometry. • C + N addition increased carbohydrates and peptides and increased substrate usage. • N limitation had the greatest impact on the soil's metabolic profile. • C + P addition significantly increased fatty acid synthesis and accumulation. [ABSTRACT FROM AUTHOR]

Arbuscular mycorrhizal fungi (AMF) form symbioses with most plants, potentially improving their growth and nutrient assimilation activities. Cysteine (Cys) and methionine (Met) are nitrogen (N)- and sulphur (S)-containing amino acids. Compared with phosphate and N, limited attention has been paid to the role of AMF in low molecular weight organic S acquisition. To explore the uptake and relative contributions of organic and inorganic N and S to plants, and the role of AMF in S uptake, a pot study was conducted based on 14C, 35S, 13C, and 15N quad labelling (6-h labelling test after adding the labelled solution to the soil–plant system) using a mutant tomato genotype with highly decreased AMF symbiosis capacity. Tomato roots can uptake limited amounts of added Met and Cys (<1.77%) within 6 h, as indicated by the 14C and 13C labelling results, and most of them were utilised by soil microorganisms. After uptake for 6 h, 10.0–14.8% of N and 1.4–6.1% of S derived from added Cys and Met were utilised by plants, mainly in inorganic N and S forms derived from Cys and Met decomposition. Met and Cys could be important S sources (Met: 3.0–9.8%, Cys: 8.8–22.0%) for plants, however have negligible roles in N nutrition (∼1%), as most N uptake by plants was derived from soil inorganic N. The tomato uptake of inorganic S derived from Cys decomposition was much higher than that derived from Met, as higher ratios of S-Cys were released as SO 4 2− from microorganisms during the 6-h testing periods. Even with the artificial addition of AMF, most of the added Met and Cys were utilised by Gram-negative bacteria, as indicated by 13C-PLFA biomarkers. AMF reduced host plant uptake of organic N and S, but stimulated plant N uptake from Met and Cys, which was mainly inorganic N following mineralisation. AMF not only utilise organic carbon from host plants but also capture soil organic matter to satisfy their energy demands. In the spaces where both root and AMF occur, AMF colonisation decreased tomato 35S uptake from Cys, Met, and SO 4 2− by 24.6%, 20.6%, and 11.0% within the 6-h uptake period, respectively, when compared with that in the mutant genotype with reduced colonisation capacity; in contrast, AMF colonisation increased 35S-Cys uptake by 118.7% from areas that roots could not reach. Overall, AMF enhanced host plant N uptake but reduced organic N uptake under competition with plant roots for S in the rhizosphere, but stimulated plant S uptake by extraradical mycelia, based on this short-term pulse-chase test. • Limited Met and Cys was absorbed by tomato under competition with microorganisms. • Inorganic S uptake by tomato from Cys decomposition higher than that from Met. • Met and Cys could be key S sources for plants, with negligible roles in N nutrition. • AMF reduce plant organic N/S uptake but stimulate plant N uptake from Met and Cys. • AMF colonisation increased 35S-Cys uptake from areas roots could not reach. [ABSTRACT FROM AUTHOR]

Summary Objectives To observe the long term response to first-line antiretroviral therapy (ART) in HIV and hepatitis B virus (HBV) co-infected patients in Ghana and explore predictors of poor clinical outcomes. Methods Retrospective cohort study of hepatitis B surface antigen (HBsAg) positive and negative patients receiving predominantly NNRTI-based ART with lamivudine plus either zidovudine or stavudine for up to seven years. Cox proportional hazards and Kaplan Meier survival analyses compared clinical outcomes and identified baseline characteristics predictive of poor outcomes. A mixed effects model compared changes in CD4 counts. Results A total of 299 HBsAg-positive and 1869 HBsAg-negative patients started ART between 2004 and 2008. Over a median 35 months of follow-up, HBsAg-positive patients were more likely to die or default care than HBsAg-negative patients, aHR 1.36 (95% CI, 1.03–1.80). HBsAg-positive patients were also more likely to develop Grade 3/4 hepatotoxicity than HBsAg-negative patients, HR 1.99 (1.16–3.40) on survival analysis. There was no significant difference in CD4 responses between HBsAg-positive and HBsAg-negative patients. Conclusions HBsAg-positive patients are at significantly increased risk of adverse clinical outcomes after starting ART. Further studies are warranted to evaluate whether these risks remain now that tenofovir is becoming routinely available in Ghana. [ABSTRACT FROM AUTHOR]

Plastics are now widespread in the natural environment. Due to their size, microplastics (MPs; defined as particles <5 mm) in particular, have the potential to cause damage and harm to organisms and may lead to a potential loss of ecosystem services. Research has demonstrated the significant impact of MPs on aquatic systems; however, little is known about their effects on the terrestrial environment, particularly within agroecosystems, the cornerstone of global food production. Soil biology is highly responsive to environmental perturbation and change. Hereby, we investigated the effect of pure low-density polyethylene (LDPE) MP loading (0, 100, 1000, or 10000 kg ha−1) on soil and plant biological health in a field environment over a cropping season. Our results showed that MP loading had no significant effect (p > 0.05) on the soil bacterial community diversity (as measured by amplicon sequencing of bacterial 16S rRNA gene), the size and structure of the PLFA-derived soil microbial community, or the abundance and biomass of earthworms. In addition, metabolomic profiling revealed no dose-dependent effect of MP loading on soil biogenic amine concentrations. The growth and yield of wheat plants (Triticum aestivum L., cv. Mulika) were also unaffected by MP dose, even at extremely high (≥1000 kg ha−1) loading levels. Nitrogen (N) cycling gene abundance before and after N fertiliser application on the MP loaded experimental plots showed relatively little change, although further experimentation is suggested, with similar trends evident for soil nitrous oxide (N 2 O) flux. Overall, we illustrate that MPs themselves may not pose a significant problem in the short term (days to months), due to their recalcitrant nature. We also emphasise that most MPs in the environment are not pure or uncontaminated, containing additives (e.g. plasticisers, pigments and stabilisers) that are generally not chemically bound to the plastic polymer and may be prone to leaching into the soil matrix. Understanding the effect of additives on soil biology as well as the longer-term (years to decades) impact of MPs on soil biological and ecological health in the field environment is recommended. • Pure microplastic (MP) loading had no effect on the soil microbial community. • Wheat crop growth and yield were unaffected by MP loading compared to control. • Nitrogen cycling (gene abundance and N 2 O flux) showed little change with MP loading. • There was no MP dose-dependent impact on soil biological health. [ABSTRACT FROM AUTHOR]

Summary: Objectives: To determine the prevalence of HIV-associated renal dysfunction (RD), identify risk factors for RD and explore the association between baseline renal function and mortality in an HIV-infected population in Ghana. Methods: Creatinine clearance (CrCl) or estimated glomerular filtration rate (eGFR) was calculated in patients attending an HIV clinic between 2004 and 2011 using Cockcroft-Gault, MDRD and CKD-EPI formulae. Logistic regression analysis was used to identify risk factors associated with RD and Kaplan–Meier/Cox proportional regression analyses to explore associations between baseline CrCl/eGFR and subsequent mortality. Results: In 3137 patients starting antiretroviral therapy (ART) the frequency (95%-CI) of RD, defined by CrCl <60 ml/min/1.73 m2 using Cockroft-Gault formula was 38.8% (37.1–40.5%). RD prevalence in a sub-population of 238 patients, including proteinuria in the definition, was 15.3% (10.3–22.1%) in ART-treated and 43.6% (34.0–53.7%) in ART-naïve patients. RD at baseline was associated with increasing age, low CD4 counts, advanced WHO stage and female gender. Cox proportional hazard analysis identified an increased hazard of death with decreasing CrCl, HR 1.46 (1.31–1.63) for each tertile lower than CrCl of 90 ml/min/1.73 m2. Conclusions: RD is very common in HIV-infected ART-naïve Ghanaians, and associated with increased risk of mortality. Screening and monitoring of RD is important in this setting, particularly as tenofovir use increases. [Copyright &y& Elsevier]

Abstract: Mineralisation rates provide valuable information concerning the overall cycling of soil organic N; however, detailed information regarding the pathways preceding the mineralisation of organic substrates remains elusive. We have adopted a molecular approach to open the ‘black box’ of organic N cycling in soil. Stable isotope probing employing compound-specific isotopic analysis was used to trace the fate of N and C within metabolites central to organic N cycling. In time course experiments, 15N and 13C from two dual-labelled amino acid (AA) substrates (U-13C,15N-glutamate and U-13C,15N-glycine) were followed into AAs biosynthesised de novo. In the majority of cases, highly significant differences (P <0.01) were revealed in the magnitude and rate of N and C transfer from the AA substrates to products of central metabolic pathways prior to their loss from the AA pool. By applying linear and non-linear regressions, several important parameters were derived, namely rate constants, magnitude of fluxes and measures of biosynthetic proximity, which describe the rate and magnitude of N and C flux through primary metabolic processes. The significant differences in N and C processing demonstrate a decoupling of the N and C cycles at the molecular level, i.e. after 32days the magnitude of N flux into newly biosynthesised AAs was twofold greater than that of C from both substrates. We anticipate that the parameters derived will have potential for use in developing detailed models of soil organic N and C processing, the construction of which is founded on the connectivity of the processes fundamental to life. [ABSTRACT FROM AUTHOR]

Climate change is expected to increase the frequency and severity of droughts in many regions of the world. Soil health is likely to be negatively impacted by these extreme events. It is therefore important to understand the impact of drought on soil functioning and the delivery of soil-related ecosystem services. This study aimed to assess the resilience and change in physiological status of the microbial community under extreme moisture stress conditions using novel metabolic profiling approaches, namely complex lipids and untargeted primary metabolites. In addition, we used phospholipid fatty acid (PLFA) profiling to identify changes in microbial community structure. Soil samples were collected during a natural, extreme drought event and post-drought from replicated grassland split plots, planted with either deep-rooting Festulolium (cv. AberNiche) or Lolium perenne L. (cv. AberEcho), receiving nitrogen (N) fertiliser loading rates at either 0 or 300 kg N ha−1 yr−1. These plots were split at the start of the drought period, and half of each subplot was irrigated with water throughout the drought period at a rate of 50 mm week−1 to alleviate moisture stress. PLFA analysis revealed a distinct shift in microbial community between drought and post-drought conditions, primarily driven by N loading and water deficit. Complex lipid analysis identified 239 compounds and untargeted analysis of primary metabolites identified 155 compounds. Both soil complex lipids and primary metabolites showed significant changes under drought conditions. Additionally, the irrigated 'reference' plots had a significantly higher cumulative greenhouse gas (CO 2 and N 2 O) flux over the period of sampling. Recovery of the microbial lipidome and metabolome to reference plot levels post-drought was rapid (within days). Considerable changes in soil primary metabolomic and lipidomic concentrations shown in this study demonstrate that while soil metabolism was strongly affected by moisture stress, the system (plant and soil) was highly resilient to an intense drought. • Novel exploration of soil complex lipids and metabolites during natural drought. • Identification of bioindicator compounds associated with drought and N fertilisation. • Drought rather than N loading rate had the greatest effect on the soil metabolome. • Use of a drought-resistant grass variety had no major effect on the metabolome. • The system (plant and soil) was shown to be highly resilient to drought. [ABSTRACT FROM AUTHOR]

• Evaluating the extent of reliance upon Pillar 1 payments in UK/Welsh farms. • Approximately 34% of Welsh farm holdings face serious financial difficulties. • 44% of agricultural land in Wales is vulnerable to land use change or abandonment. • There are social and ecological risks associated with land use change. • A balanced approach keeps farmers on the land and delivers quality 'Public Goods'. On the 23rd June 2016, the UK referendum on European Union (EU) membership resulted in a vote to leave the EU. This departure, should it occur, would see the implementation of a new agricultural policy within the UK which will most likely see the removal of direct financial support to farmers. In this study, we use combined agricultural survey and rural payments data to evaluate the extent of reliance upon Pillar 1 payments, based on a sample of 24,492 (i.e. 70%) of farm holdings in Wales. This approach eliminates some of the variation found in the Farm Business Survey through the delivery of a more comprehensive picture on the numbers and types of farm holding potentially facing economic hardship and the quantities of land and livestock associated with those holdings. We estimate ˜34% of our sampled Welsh farm holdings face serious financial difficulties and show ˜44% of agricultural land on sampled farm holdings in Wales being vulnerable to land use change or abandonment. Based on our results, we consider the potential social and ecological impacts that the removal of direct payments may have on land use in Wales. We also discuss the use of a more balanced approach to land management that could support governmental visions to keep farmers on the land, improve productivity and deliver high quality 'Public Goods'. [ABSTRACT FROM AUTHOR]

Soil carbon (C) sequestration is often viewed as a nature-based solution to help mitigate climate change. Key to realising this potential is a better understanding of which C inputs promote greater long-term C storage. The priming effect (PE) is the change in rates of microbial soil organic matter (SOM) decomposition caused by the addition of organic or mineral amendments to soil. The apparent PE (changes in CO 2 from microbial biomass turnover) of substrates is often studied as a confounding factor, however, the real PE (decomposition of native SOM) is rarely measured due to uncertainties in C pool differentiation. Here, we used a 50-day mesocosm study to compare the effect of various common soil amendments (wood biochar and ash, protein, amino acids, glucose, cellulose, cattle farmyard manure (FYM), cattle slurry, inorganic N fertiliser, and different ratios of wheat straw:shoot mixes) on the real and apparent PEs of soil, using 5-year old quasi-stable 14C-labelled SOM and 14C-labelled active microbial biomass, respectively. Our results show that there are often significant differences in the real and apparent PE, for the same amendment, with variance in magnitude and, in some case, direction. We identified few consistent drivers of PE across the two assays, however, there was a negative relationship between the initial C:N ratio of the treatment and PEs, suggesting that while the nutrient stoichiometry of the C amendment is important, the usability and quality of the substrate for the microbial community are key to determining its priming response. Equally, context is important for interpretation, as treatments that elicit positive priming may still be replenishing or increasing soil C stocks. • The priming effect (PE) is a key regulator of the net C balance of agroecosystems. • We compared the impact of a diverse range of C substrates on real and apparent PEs. • Real and apparent PEs varied in magnitude and, in some cases, direction. • Care should be taken when interpreting real and apparent PEs. • Substrate quality, stoichiometry and accessibility were key PE drivers. [ABSTRACT FROM AUTHOR]

Growing evidence suggests that tropospheric ozone has widespread effects on vegetation, which can contribute to alter ecosystem carbon (C) dynamics and belowground processes. In this study, we used intact soil mesocosms from a semi-improved grassland and investigated the effects of elevated ozone, alone and in combination with nitrogen (N) fertilization on soil-borne greenhouse gas emissions and ecosystem C fluxes. Ozone exposure under fully open-air field conditions was occurred during the growing season. Across a one-year period, soil methane (CH 4) and nitrous oxide (N 2 O) emissions did not differ between treatments, but elevated ozone significantly depressed soil CH 4 uptake by 14% during the growing season irrespective of N fertilization. Elevated ozone resulted in a 15% reduction of net ecosystem exchange of carbon dioxide, while N fertilization significantly increased ecosystem respiration during the growing season. Aboveground biomass was unaffected by elevated ozone during the growing season but significantly decreased by 17% during the non-growing season. At the end of the experiment, soil mineral N content, net N mineralization and extracellular enzyme activities (i.e., cellobiohydrolase and leucine aminopeptidase) were higher under elevated ozone than ambient ozone. The short-term effect of single application of N fertilizer was primarily responsible for the lack of the interaction between elevated ozone and N fertilization. Therefore, results of our short-term study suggest that ozone exposure may have negative impacts on soil CH 4 uptake and C sequestration and contribute to accelerated rates of soil N-cycling. • Temperate grassland mesocosms were exposed to ozone with or without N fertilizer. • Elevated ozone had negative effects on soil CH 4 uptake and net ecosystem CO 2 exchange. • Aboveground biomass was reduced during the non-growing but not the growing season. • A positive feedback of soil N-cycling to ozone exposure was detected. [ABSTRACT FROM AUTHOR]