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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]

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]

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]

Increasing tropospheric ozone poses a potential threat to both above- and belowground components of the terrestrial biosphere. Microorganisms are the main drivers of soil ecological processes, however, the link between soil microbial communities and ecological functions under elevated ozone remains poorly understood. In this study, we assessed the responses of three crop seedlings (i.e., soybean, maize, and wheat) growth and soil microbial communities to elevated ozone (40 ppb O 3 above ambient air) in a pot experiment in the solardomes. Results showed that elevated ozone adversely affected ecosystem multifunctionality by reducing crop biomass, inhibiting soil extracellular enzyme activities, and altering nutrient availability. Elevated ozone increased bacterial and fungal co-occurrence network complexity, negatively correlated with ecosystem multifunctionality. Changes in the relative abundance of some specific bacteria and fungi were associated with multiple ecosystem functioning. In addition, elevated ozone significantly affected fungal community composition but not bacterial community composition and microbial alpha-diversity. Crop type played a key role in determining bacterial alpha-diversity and microbial community composition. In conclusion, our findings suggest that short-term elevated ozone could lead to a decrease in ecosystem multifunctionality associated with changes in the complexity of microbial networks in soils. • Elevated ozone reduced ecosystem multifunctionality. • Changes in microbial community composition were linked to ecosystem functioning. • Elevated ozone negatively affected crop seedling growth and soil microbial activity. • Crop type shaped soil microbial community composition. [ABSTRACT FROM AUTHOR]

Improving phosphorus (P) use efficiency is key to improving the productivity and sustainability of cropping systems and slowing the exploitation rate of mineral P resources required for fertilizer production. At present, large amounts of added P in fertilizers and manure each year are retained in the soil and are not used by the crop. This 'legacy P' progressively accumulates in soil and represents an untapped P resource in tropical soils while in temperate soils it contributes to eutrophication. In the context of legacy P, the aim of this study was to quantify changes in soil P pools of contrasting bioavailability (determined using conventional chemical extraction procedures) during 12 successive brachiaria (Urochloa ruziziensis) cropping cycles in which no additional P was added. The study was undertaken in the greenhouse with 10 tropical (Brazil) and 6 temperate (UK) agricultural topsoils. Above-ground dry matter yield (DM) and P offtake was measured at each harvest alongside operationally-defined measures of the labile, moderately-labile and non-labile P pools at the start and end of the experiment. Over twelve repeated cultivation cycles, brachiaria demonstrated an ability to efficiently mine legacy P from all measurable soil pools across both sets of soils. This included the depletion of up to 87 % of non-labile soil P in some soils from the UK and up to 66 % from soils in Brazil after one year. While the amounts of initial labile P showed the closest positive relationship with plant P export, contrary to expectation the non-labile P pool also clearly contributed to plant nutrition across all the soils. As a cover crop, brachiaria clearly possesses traits which enable both the solubilization and efficient capture of soil P that can be harnessed to actively recycle historically non recalcitrant soil P fractions. Incorporating brachiaria into crop rotations or intercropping systems therefore shows promise as a strategy to enhance the longer-term sustainability of soil P management. • Brachiaria extracted P from labile and recalcitrant non-labile P pools in soil. • Soil labile and non-labile P content regulates plant uptake of legacy P rather than P adsorption strength. • Organic P was shown to directly contribute to plant P supply, contrary to recalcitrance paradigms. • Brachiaria cover crops can enhance P use efficiency by solubilizing soil legacy P. [ABSTRACT FROM AUTHOR]

Soil is an extremely complex and dynamic matrix, in part, due to the wide diversity of organisms living within it. Soil organic matter (SOM) is the fundamental substrate on which the delivery of ecosystem services depends, providing the metabolic fuel to drive soil function. As such, studying the soil metabolome (the diversity and concentration of low molecular weight metabolites), as a subset of SOM, holds the potential to greatly expand our understanding of the behaviour, fate, interaction and functional significance of small organic molecules in soil. Encompassing a wide range of chemical classes (including amino acids, peptides, lipids and carbohydrates) and a large number of individual molecules (ca. n = 105 to 106), the metabolome is a resultant (indirect) output of several layers of a biological hierarchy, namely the metagenome, metatranscriptome and metaproteome. As such, it may also provide support and validation for these "multi-omics" datasets. We present a case for the increased use of untargeted metabolomics in soil biochemistry, particularly for furthering our fundamental understanding of the functions driving SOM composition and biogeochemical cycling. Further, we discuss the scale of the challenge in terms of metabolite extraction, analysis and interpretation in complex plant-soil-microbial systems. Lastly, we highlight key knowledge gaps which currently limit our use of metabolomic approaches to better understand soil processes, including: (i) interpretation of large untargeted metabolomic datasets; (ii) the source, emission and fate of soil-derived volatile organic compounds (VOCs), (iii) assessing temporal fluxes of metabolites, and (iv) monitoring ecological interactions in the rhizosphere. While the application of metabolomics in ecosystem science is still in its relative infancy, its importance in understanding the biochemical system in relation to regulation, management and underpinning the delivery of ecosystem services is key to further elucidating the complex links between organisms, as well as the fundamental ability of the biological community to process and cycle key nutrients. • Soil organic matter is the metabolic fuel that drives soil function. • Untargeted metabolomics offers rich and functional biochemical data. • Discussion of challenges in extraction and analysis of complex substrates. • Emphasis of key knowledge gaps in interpretation and monitoring of soil. [ABSTRACT FROM AUTHOR]

This chapter reviews contributions made to agricultural and environmental science and practice from research on temperate grassland carried out from 1982 to present at Rothamsted Research's North Wyke Research Station, Devon, UK. It describes the evolution of the research program and demonstrates the importance of sustained, interdisciplinary, and collaborative research. North Wyke has maintained a clear research focus, alongside an ability to adapt to changing grassland and environmental research needs and funding sources, and despite having changed affiliations on several occasions. The substantial contribution to agricultural and environmental science arising from the research station has influenced and continues to influence farm practice, research, and policy nationally and internationally. Some key topics have included nutrient cycling, farm waste management, gaseous emissions, biodiversity, grazing management, animal production (meat and milk), and forage quality. Currently, North Wyke Research Station is leading the way on taking increasingly holistic approaches to researching more efficient, sustainable approaches to grazing-livestock agricultural production. This involves the use of world-leading, facilities such as the North Wyke Farm Platform, comprising three farmlets, designed to test the productivity and environmental sustainability of contrasting temperate grassland beef and sheep systems. Future perspectives highlight key challenges facing the agricultural industry including climate change mitigation and adaptation, and the growing world population. Opportunities exist to tackle these challenges through technological advances, but also through increased integration of agricultural, environmental, economic and social research. North Wyke Research Station provides an example of a research facility where such challenges can be addressed. [ABSTRACT FROM AUTHOR]

Nitrification inhibitors (NIs) such as dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) provide an opportunity to reduce losses of reactive nitrogen (Nr) from agricultural ecosystems. To understand the fate and efficacy of these two inhibitors, laboratory-scale experiments were conducted with 14 C-labelled DCD and DMPP to determine the relative rates of mineralization, recovery in soil extracts and sorption in two agricultural soils with contrasting pH and organic matter content. Concurrently, the net production of soil ammonium and nitrate in soil were determined. Two months after NI addition to soil, significantly greater mineralization of 14 C-DMPP (15.3%) was observed, relative to that of 14 C-DCD (10.7%), and the mineralization of both NIs increased with temperature, regardless of NI and soil type. However, the mineralization of NIs did not appear to have a major influence on their inhibitory effect (as shown by the low mineralization rates and the divergent average half-lives for mineralization and nitrification, which were 454 and 37 days, respectively). The nitrification inhibition efficacy of DMPP was more dependent on soil type than that of DCD, although the efficacy of both inhibitors was lower in the more alkaline, low-organic matter soil. Although a greater proportion of DMPP becomes unavailable, possibly due to physico-chemical sorption to soil or microbial immobilization, our results demonstrate the potential of DMPP to achieve higher inhibition rates than DCD in grassland soils. Greater consideration of the interactions between NI type, soil and temperature is required to provide robust and cost-effective advice to farmers on NI use. [ABSTRACT FROM AUTHOR]

Organic manure is widely applied in agricultural systems to improve soil nutrient cycling and other physicochemical properties. However, the biotic and abiotic mechanisms that drive C, N, P, and S cycling following manure application are not completely understood. In this study, soil samples were collected from long-term experimental plots that had been amended with farmyard manure or mineral fertilisers since 1964. Isotope labelling with 15N, 33P, and 35S; metagenomics; and high-throughput sequencing were used to reveal the relationships between C, N, P, and S dynamics and microbial community composition and functions depending on fertilisation. A clear niche differentiation was observed between bacteria and fungi under mineral and manure regimes. A network analysis showed that long-term manure application reduced the complexity and stability of soil microbial network. Furthermore, a variation partitioning analysis based on redundancy analysis indicated that microbial community variation was mainly driven by soil Cand N contents. Dissolved organic C was the most important factor regulating microbial community structure. Soil C and N contents explained 43.5% of bacterial and 37.9% of fungal community variations. In contrast, soil P and S contents explained 29.9% of bacterial and 20.3% of fungal community variations. Long-term manure application increased the abundance of most functional genes related to C, N, P, and S cycling. This led to increased C and N cycling rates under manure application, which provided sufficient substrates for microbial growth. Partial least squares path modelling indicated that soil physicochemical properties, especially dissolved organic carbon, directly influenced C and S cycling, whereas the N and P cycles were indirectly affected by the changes in microbial community composition. These results provide a new perspective on both direct and indirect effects of organic manure and inorganic fertilisers on the soil nutrient cycling processes mediated by soil microbial community. [Display omitted] • Long-term manure application reduced microbial complexity. • Dissolved organic C was the most important factor driving microbial succession. • Functional genes were enriched under manure application. [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]

Fen peatlands represent a globally important carbon (C) store, while also providing highly productive agricultural land. Drainage of these organic soils is required to create conditions suitable for crop growth, but this results in substantial greenhouse gas (GHG) emissions. One potential GHG mitigation option is to raise the groundwater table to reduce the duration and volume of peat exposure to aerobic conditions. However, the trade-off between maintaining food production and securing ecosystem function under a high water table (WT) presents a serious challenge for both land managers and policy makers. Therefore, we conducted a controlled mesocosm experiment to investigate the effects of WT elevation (from −50 cm to −30 cm) under three contrasting scenarios: (i) WT raised throughout the year, (ii) WT raised in the winter only, and (iii) WT raised in the growing season only. We measured GHG emissions, nitrate, ammonium and dissolved organic C concentrations in soil solution, alongside the yield of a commercially important crop (lettuce). Raising the WT throughout the year reduced lettuce yields by 37% and reduced CO 2 emissions by 36% without changing the loss rates of N 2 O or CH 4. Raising the WT only in the winter did not significantly reduce crop yield, but still suppressed CO 2 emissions during the fallow period (by 30%). Raising the WT only in the growing season reduced root growth and CO 2 emissions (by 27%), but had no major effect on lettuce yield. In conclusion, the present study shows that raising the groundwater table in the non-growing season reduced GHG emissions without negatively affecting lettuce yields, and may therefore represent a viable GHG mitigation option for agricultural peatlands. Image 1 • We tested the impact of water table (WT) depth on lettuce yields and GHG emissions. • Annual high WT management reduced lettuce yields by 37% and CO 2 emissions by 36%. • Raising the WT only in winter did not affect crop yield but reduced GHG emissions. • Raising the WT in non-growing season may represent a viable GHG mitigation option. [ABSTRACT FROM AUTHOR]

Land application of farmyard manure (FYM) is a widespread agronomic practice used to enhance soil fertility, but its long-term effects on soil microbial carbon (C) and nitrogen (N) cycling have not been investigated in detail. Topsoils (0–23 cm) and subsoils (23–38 cm) were collected from a field trial on a sandy-textured soil where FYM had been applied at high (50–25 t ha−1 yr−1, 28 yr) and low rates (10 t ha−1 yr−1, 16 yr), and compared to soil treated only with synthetic NPK fertilisers. The turnover rate of key components of soil organic matter (SOM; proteins, peptides, amino acids, cellulose, and glucose) were evaluated by 14C labelling and measuring cellobiohydrolase, β-glucosidase, β-1,4-N-acetylglucosaminidase, L-leucine aminopeptidase, protease, and deaminase activities, whereas gross NH 4 + and NO 3 − production and consumption were determined by 15N-isotope pool dilution. Microbial communities were determined using phospholipid fatty acid (PLFA) profiling. Our results indicate that long-term FYM addition significantly enhanced the accumulation of soil C and N, soil organic N (SON) turnover, exoenzyme activity, and gross NO 3 − production and assimilation. Rates of protein, peptide, and amino acid processing rate were 169–248, 87–147, and 85–305 mg N kg DWsoil −1 d−1, respectively, gross NH 4 + and NO 3 − production and consumption were 1.8–5.8 mg N kg DWsoil −1 d−1, and the highest rates were shown under the high FYM treatment in topsoil and subsoil. The half-life of cellulose and glucose decomposition under the high FYM treatment were 16.4% and 31.0% lower than them in the synthetic NPK fertiliser treatment, respectively, indicating higher rates of C cycling under high manure application as also evidenced by the higher rate of CO 2 production. This was ascribed to an increase in microbial biomass rather than a change in microbial community structure. Based on the high pool sizes and high turnover rate, this suggests that peptides may represent one of the dominant forms of N taken up by soil microorganisms. We conclude that long-term FYM application builds SOM reserves and induces faster rates of nutrient cycling by boosting microbial biomass rather than by changing its community composition. • The influence of manure application on soil C/N cycling was evaluated. • 14C labeling and 15N-pool dilution techniques were used. • Manure application significantly affects C/N cycling in soil by boosting microbial biomass. • Peptides may be important for terrestrial cycling and supply of N. [ABSTRACT FROM AUTHOR]