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• 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]

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]

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]

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]

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]

Urine patches in grazed systems are hotspots for nitrogen (N) cycling and losses to the wider environment. Retention and subsequent recycling of urinary-N is key to minimise losses and increase ecosystem nitrogen use efficiency. Biosynthesis into the microbial organic N pool is an important N pathway but this has not been directly quantified in a urine patch. Herein, we present the results of a time course experiment using soil mesocosms sown with perennial ryegrass (Lolium perenne L.) and treated with 15N-labelled sheep urine to determine partitioning of the applied N between plant, soil biomass pools and leaching losses following simulated rainfall events. 15N-tracing used bulk and compound-specific 15N-stable isotope probing (SIP) to determine the fate of urinary N. Initial high leaching losses (233 kg N ha−1) were comprised of native soil N, ammonium and nitrate derived from urine by urea hydrolysis and nitrification, respectively. Leaching subsequently decreased whilst uptake into plant biomass and microbial biosynthesis increased during periods of low rainfall. Uptake into above and belowground plant biomass was the largest fate of urinary-15N after 94 d (42%), although assimilation into microbial biomass dominated for ca. 1 month after urine deposition (34%). Compound-specific 15N–SIP of amino acids and amino sugars revealed immobilisation of urinary-N following mineralisation was the dominant pathway for biosynthesis, with incorporation into bacterial organic N pools more rapid than into the fungal biomass. There was also intact utilisation of glycine derived from urine. This study provides clear evidence that direct assimilation of urine-derived N into microbial organic N pools is an important process for retaining N in a urine patch, which will subsequently support plant N supply during microbial turnover. [Display omitted] • 15N-labelled urine was traced into plant, microbial and leaching pools in a grassland mesocosm. • Leaching losses were reduced, and plant uptake increased during periods of low rainfall. • Microbial uptake of urinary-N occurred via mineralisation-immobilisation and intact pathways. • Microbial assimilation was dominated by bacteria over fungi. [ABSTRACT FROM AUTHOR]

Efficient fertiliser nitrogen (N) management is critical to global food production and ecosystem health. Considering sheep grazing systems as whole ecosystems, and quantifying key ecosystem services provided by the soil microbial community, including plant N supply and N pollution mitigation, is essential in assessments of N use efficiency (NUE). Using a systems approach, we disassembled a low-intensity sheep (>5 ewe ha−1) grazed grassland, dominated by Lolium perenne , into a series of interlinked 15N-tracer experiments in North Wales during a summer growing season to assess fertiliser-N partitioning. 15N was traced into soil microbial protein-N via compound-specific amino acid 15N-stable isotope probing, with subsequent integration to provide a whole-system perspective. Retention of feed-N into sheep was low (11 %), despite high grass 15N-fertiliser uptake (58 %). The majority of grazed-N re-entered the soil N-cycle as excreta (47 % of total 15N) during the peak growing season. Quantifying 15N-assimilation into soil microbial protein (0–15 cm) demonstrated the central role soil microbes occupy in capturing excess fertiliser (16 %) and urinary-N (8 %) of the total 15N-fertiliser applied, thereby reducing N losses and subsequently supporting plant N supply. This approach emphasises how future management of moderate intensity grazing systems should target sheep NUE, alongside the role of the soil microbial community to retain, and later recycle N, for plant supply, optimising essential ecosystem service provisioning. • Interlinked whole ecosystem 15N tracing study for holistic approach • Mass balance of N cycle through grazing system revealed importance of soil retention to reduce losses. • Microbial assimilation of fertiliser and urine is a major fate of applied 15N. [ABSTRACT FROM AUTHOR]

Cysteine (Cys) and methionine (Met) are unique amino acids that contain not only nitrogen (N) but also sulfur (S); thus, they are a source of S for plants under low-soil-SO 4 2- conditions. However, whether low-molecular-weight organic N and S can be utilised by plants or contribute to plant growth remains unknown. Therefore, this study aimed to examine the uptake of organic and inorganic N and S by plants and the role of microbial decomposition under monocropping and intercropping based on 13C, 15N, 14C, and 35S quad labelling. As indicated by the 13C/14C uptake, clover, millet, and ryegrass utilised 0.24–1.68% of the added Cys and Met within 6 h and encountered considerable competition from soil microorganisms. The added Met and Cys were rapidly utilised by microorganisms, and part of the N was subsequently released as inorganic N, which was taken up by plants (15N-Cys: 9.3–15.2%; 15N-Met: 5.9–13.4%) within 6 h. Six hours after addition, 57.8–78.5% of the 35S-Met and 26.2–56.0% of the 35S-Cys were retained in the microbial biomass, while more 35S-Cys was mineralised to SO 4 2−. Plants took up 5.5–12.4% of 35S-Cys and only 3.4–6.0% of 35S-Met, and 35S uptake was dominated by inorganic S after the mineralisation of Cys and Met. N uptake from Cys and Met accounted for less than 1% of the total N uptake from the soil, while S uptake from Cys and Met accounted for 9.3–27.0% and 2.8–11.8% of the total S uptake from the soil, respectively. Additionally, Cys was more rapidly mineralised to SO 4 2− by soil microbes than Met; the produced SO 4 2− was further utilised by plant roots. The contributions of Cys and Met to the total N and S uptake were the highest in millet monocropping while intercropping altered the relative contributions of organic and inorganic N and S. Overall, soil soluble Cys and Met played a limited role in plant N uptake but were an important source of plant S uptake. • Clover, millet, and ryegrass captured only 0.24–1.68% of intact Cys and Met within 6 h. • The inorganic N and S derived from Cys and Met mineralisation were captured by plants. • Soil soluble Cys and Met were an important source of plant S nutrition. • Intercropping of plants altered the uptake of organic and inorganic N and S. [ABSTRACT FROM AUTHOR]

• Statistical relationships of pasture N 2 O, CO 2 & CH 4 fluxes & environmental data. • Extensive site N 2 O flux predictors consistent with controls & literature. • Use of a spatial regression changed predictors for Intensive site N 2 O fluxes. • Significant predictors of GHG fluxes are site- & GHG-specific. • Missing predictors or more complex (e.g. non-stationary) relationships. Greenhouse gas (GHG) fluxes from livestock grazed pasture soils are highly variable in both space and time but the quantitative importance of the factors regulating this variation remain poorly understood. Our aim was to explore this variability on contrasting extensively (low input) and intensively managed sheep-grazed 'case-study' pastures. We quantified (through standard and spatially-informed regressions) the statistical relationships between GHG fluxes (nitrous oxide (N 2 O), carbon dioxide (CO 2) and methane (CH 4)) and a range of soil, field and management characteristics. Fluxes of these three GHGs at two study sites were highly variable, but spatial structure (i.e. autocorrelation) was only observed in the variability of N 2 O fluxes across the intensive site and CO 2 fluxes across the extensive site. The regression analyses identified significant GHG predictor variables for the extensive site as: NO 3 − (p < 0.001) and vegetation-type (p < 0.01) for N 2 O (R 2 = 0.57; p = 0.000); NH 4 + (p < 0.05), slope (p < 0.05) and elevation (p < 0.01) for CO 2 (R 2 = 0.34; p = 0.000); and NO 3 − (p < 0.01), NH 4 + (p < 0.05) and soil moisture (p < 0.05) for CH 4 (R 2 = 0.25; p = 0.005). Significant GHG predictor variables for the intensive site were soil moisture (p < 0.01) and bulk density (p < 0.01) for N 2 O (R 2 = 0.27; p = 0.005); soil moisture (p < 0.001) for CO 2 (R 2 = 0.31; p = 0.001); while none were found for CH 4 (R 2 = 0.10; p = 0.655). Key factors driving GHG variation were both site- and GHG-specific, with fluxes controlled by local conditions leading to differences in limiting factors (possibly even at the within-site scale). Our statistical analyses suggest a larger range of driving variables (e.g. air and soil temperature or other soil chemical properties such as total extractable N) may be required to more fully capture the observed variability in the GHG processes considered here, and that it may also be fruitful for future analyses to consider non-linear, non-stationary and interacting relationships across space- and time-scales. Adequacies of each site's sample design also played a key interpretive role in the GHG processes, requiring further evaluation through additional sampling campaigns. [ABSTRACT FROM AUTHOR]

Understanding the change in function of the biological community under different soil conditions is key to effective soil quality monitoring and mitigation of soil degradation. Current measures of biological soil quality suffer from drawbacks with most techniques having high expense, low throughput or a narrow focus on one component of the community. The aim of this study was to assess the use of volatilomics as a method to profile the soil microbial community and compare the technique to phospholipid fatty acid (PLFA) profiling as a measure of biological soil quality. An agricultural grassland soil (Eutric Cambisol) was subjected to a range of stresses in replicate laboratory mesocosms. Treatments included the imposition of hypoxia/anoxia by flooding with freshwater or saltwater in the presence or absence of plant residues. The volatile organic compound (VOC) and PLFA profile of each treatment was then compared to unamended mesocosms. We hypothesized that the VOC fingerprint of soil would be highly responsive to changes in microbial metabolic status/functioning and thus provide a complementary approach to PLFAs for evaluating soil biological health. We also hypothesized that the VOC profile would have greater discriminatory power than PLFAs for determining differences between soil treatments. A headspace solid phase microextraction (HSSPME) method coupled with gas chromatography quadrupole-time of flight mass spectrometry (GC/Q-TOFMS) was used to analyse the broad spectrum of VOCs produced by each soil. Across all soil treatments 514 unique VOC peaks were detected. Overall, VOCs showed greater sensitivity than the PLFA analysis in separating soil quality treatments. Eighteen individual VOCs were identified which were primarily responsible for this separation (e.g. indole, α-ionone, isophorone, 3-octanone, p -cresol, 2-ethyl-phenol). Anaerobic soils amended with residues showed the greatest separation from other treatments, with most of this differentiation associated with ten individual VOCs. The anaerobic soils also showed a significant reduction in the number of VOCs emitted but an increase in total VOC emissions. In conclusion, our findings provide evidence that soil VOCs rapidly respond to changes in soil quality and therefore hold great potential as a novel functionally relevant diagnostic measure of biological soil quality. • GC-MS profiling of VOCs in soil using headspace SPME. • Identification of compounds driving treatment differences in soil quality. • Substrate availability is key in the production and emission of VOCs. • Critical comparison of VOCs and PLFAs as soil quality indicators. • VOCs show potential as rapid, sensitive and functional indicators of soil quality. [ABSTRACT FROM AUTHOR]