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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]

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]

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]

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]

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]

Urine patches contribute greatly to greenhouse gas emissions within livestock grazed ecosystems. The effective area of a ruminant urine patch comprises the wetted area, the diffusional area and the pasture response area. This study specifically assesses the importance of considering the diffusional area for monitoring urine patch N2O emissions. Spatial and temporal changes in N2O emissions and potential drivers of emissions (soil pH, EC, redox potential, dissolved organic carbon and nitrogen, NO- 3 and NH+ 4) were measured in sheep urine amended Eutric Cambisol mesocosms, maintained at 50% or 70% waterfilled pore space (WFPS). At 70% WFPS, over 10 weeks, the emission factor (EF) was greater when considering the wetted area plus a 9 cm diffusional area (EF = 2.75 ± 0.72% of applied N) than when considering the wetted area alone (EF = 1.44 ± 0.30% of applied N); differences were not statistically significant at 50% WFPS. Redox potential, total extractable N and WFPS contributed significantly to the observed variation in daily N2O fluxes from the urine patch. We conclude that the urine patch diffusional area is an extremely important source of emissions from urine patches. This has implications when measuring EFs, as the lateral diffusion of solutes may be restricted by chamber walls resulting in an underestimate of N2O emissions, particularly at higher soil moisture contents. Site-specific assessments of the urine patch diffusional area should be made, and accounted for, prior to monitoring emissions and calculating emission factors from urine patches applied within chambers. [ABSTRACT FROM AUTHOR]

The effects of long-term N and P fertilisation on soil organic nitrogen (SON) turnover are unclear. We sampled soils fertilised by N and/or P since 1843 at Rothamsted Research to investigate the effects of long-term N and P fertilisation on high- or low-molecular-weight SON decomposition and gross N mineralisation. Short-term assays with added 14C-labelled proteins, peptides, and amino acids and gross organic N mineralisation were measured, and the microbial communities and functions were also assessed in parallel. Long-term N fertilisation increased the contents of soil extractable organic N and peptides but decreased organic N-hydrolysing enzyme activities (N-acetyl-β-D-glucosaminidase and leucine aminopeptidase). Fertilisation with P and N accelerated and reduced the decomposition of 14C-labelled organic N compounds, respectively. The decomposition of peptides and amino acids, as labile SON components, was mainly regulated by soil P content because microbial biomass and activity were more sensitive to P fertilisation than to N fertilisation. Gross NH 4 +/NO 3 − production and consumption were accelerated by 41%–60% under N fertilisation but remained unchanged under P fertilisation compared to the unfertilised treatment. Metagenomic sequencing showed that N fertilisation increased microbial diversity and enriched functional genes associated with organic N decomposition, compared to the unfertilised treatment. P fertilisation had no effect on the abundance of these functional genes. In agricultural practices, it is essential to comprehensively consider the interaction between N and P fertilisation to optimise the cycling and utilisation of SON. [Display omitted] • Effects of N and P fertilisation on soil N in the Rothamsted Experiment were tested. • Added N regulated soluble protein decomposition. • Added P regulated peptide and amino acid decomposition. • Long-term N fertilisation enriched genes involved in soil organic N decomposition. • Gross N mineralisation was accelerated by N fertilisation but not by P fertilisation. [ABSTRACT FROM AUTHOR]

The application of lime and mineral fertiliser is known to mitigate soil acidification and improve soil quality in improved grasslands. However, the long-term effect of simultaneous lime and fertiliser amendments on soil carbon (C) and sulphur (S) cycling is still poorly understood. To examine if soil pH or nutrient availability are the dominant factors regulating C and S cycling, we evaluated the biodegradation of methionine (organic S), gross S transformation, and microbial S utilisation using 35S and 14C dual-labelling. Soil samples (0–10 cm) were collected from one unfertilised control and five annual limed (Ca) treatments with or without nitrogen (N), phosphorus (P), potassium (K) and sulphur (S) fertilisers (Ca, CaN, CaNP, CaNPKCl, CaNPK 2 SO 4) in an 82-year-old upland grassland experiment in Rengen, Germany. Long-term lime application increased soil pH values but significantly (p < 0.05) decreased soil organic C content. Fertilisation had no significant effect on microbial utilisation of 35S-labelled methionine, while microbial immobilisation of 35SO 4 2− in the limed soils was significantly reduced compared to the control. This is attributed to either the increased soil pH or decreased C availability after liming. Microbial carbon use efficiency (CUE) was significantly higher in soils with applied P fertiliser (i.e., CaNP: 0.66 ± 0.02, CaNPKCl: 0.68 ± 0.02, CaNPK 2 SO 4 : 0.65 ± 0.01) compared to the CaN treatment (0.58 ± 0.01). Moreover, compared to CaN, CaNP and CaNPKCl treatments significantly increased gross S turnover, while no significant effects were observed in the CaNPK 2 SO 4 treatment. Soil P deficits decreased microbial CUE and S bioavailability. Although P fertiliser addition alleviated microbial P limitation when N fertiliser was added, S fertiliser (CaNPK 2 SO 4) present constrained S transformation rates. Overall, the importance of P availability for global S cycling in grasslands is shown, especially under N-enrichment conditions. However, the subsequent potential for C loss from long-term liming should be carefully considered in grassland management. Long-term lime plus mineral nutrients fertilisers have a negative effect on microbial inorganic S immobilisation, this is attributed to either the decreased C availability or the increased soil pH from lime addition. While the effects of long-term lime plus mineral nutrients fertilisers on gross S fluxes and carbon use efficiency (CUE) depend on how the mineral nutrient is applied, long-term lime with imbalanced nutrient (e.g. sole N) resulted in the decrease of CUE and gross S transformation because of the low P availability. Long-term lime with both N and P nutrients leads to the increase of CUE and gross S transformation, which is mainly due to high P availability. [Display omitted] • Long-term lime application significantly decreased soil organic carbon content. • Lime plus N (CaN) decreased microbial carbon use efficiency significantly and had lower gross S flux rates. • Microbes are subject to intensive P limitation under treatment CaN. • Microbial inorganic 35S immobilisation decreased with lime input. • S fertiliser (CaNPK 2 SO 4) potentially constrained S transformation rates. [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]

Soils support a wide range of ecosystem services that underpin Earth system functioning. It is therefore essential that we have robust approaches to evaluate how anthropogenic perturbation affects soil quality and the delivery of these services. Metabolomics, the large-scale study of low molecular weight organic compounds in soil, offers one potential approach to characterise soils and evaluate the metabolic status of the soil biological community. The aims of the present study were to 1) characterise the soil metabolome across a contrasting range of soil types, 2) understand the relationships between common chemical and physical soil quality indicators and its metabolome, and 3) evaluate the discriminatory power of soil metabolomics and its potential use as a soil quality indicator. Nine different topsoils with 5 replications were collected along an altitudinal primary productivity gradient encompassing a wide range of soil types and land uses. Metabolites were extracted from soil using 3:3:2 (v/v/v) acetonitrile:isopropanol:water and individual compounds identified using a gas chromatography-mass spectrometry (GC-MS) platform. Overall, 405 individual compounds were detected, of which 146 were positively identified, including sugars, amino acids, organic acids, nucleobases, sugar alcohols, lipids and a range of secondary metabolites. The concentration and profile of metabolites was found to vary greatly between the soil types. Further, the soils' metabolomic fingerprints correlated to a number of environmental factors, including pH, land-use, moisture and salinity. We also tentatively attributed soil-specific metabolites to potential functional pathways, although complementary proteomic, genomic and transcriptomic approaches would be needed to provide definitive supporting evidence. In conclusion, soil metabolomics offers the potential to reveal the complex molecular networks and metabolic pathways operating in the soil microbial community and a means of evaluating soil function. Further work is now required to benchmark soil metabolomes under a wide range of management regimes so that they can be used for the quantitative assessment of soil quality. Image 1 • Soil metabolites were extracted using acetonitrile, isopropanol and water. • Metabolites with contrasting chemical properties were detected using GC-MS. • Soils could be categorized into 4 distinct groups based on metabolite profiles. • Soil metabolomic fingerprints correlated to several environmental factors. • Potential functional pathways were indicated for exploration. [ABSTRACT FROM AUTHOR]

Abstract The return of agricultural crop residues are vital to maintain or even enhance soil fertility. However, the influence of application rate of crop residues on denitrification and its related gaseous N emissions is not fully understood. We conducted a fully robotized continuous flow incubation experiment using a Helium/Oxygen atmosphere over 30 days to examine the effect of maize straw application rate on: i) the rate of denitrification, ii) denitrification product stoichiometry N 2 O/(N 2 O+N 2), and iii) the contribution of fungal denitrification to N 2 O fluxes. Five treatments were established using sieved, repacked sandy textured soil; i) non-amended control, ii) nitrate only, iii) low rate of straw + nitrate, iv) medium rate of straw + nitrate, and iv) high rate of straw + nitrate (n = 3). We simultaneously measured NO, N 2 O as well as direct N 2 emissions and used the N 2 O 15N site preference signatures of soil-emitted N 2 O to distinguish N 2 O production from fungal and bacterial denitrification. Uniquely, soil NO 3 − measurements were also made throughout the incubation. Emissions of N 2 O during the initial phase of the experiment (0–13 days) increased almost linearly with increasing rate of straw incorporation and with (almost) no N 2 production. However, the rate of straw amendment was negatively correlated with N 2 O, but positively correlated with N 2 fluxes later in the experimental period (13–30 days). Soil NO 3 − content, in all treatments, was identified as the main factor responsible for the shift from N 2 O production to N 2 O reduction. Straw amendment immediately lowered the proportion of N 2 O from bacterial denitrification, thus implying that more of the N 2 O emitted was derived from fungi (18 ± 0.7% in control and up to 40 ± 3.0% in high straw treatments during the first 13 days). However, after day 15 when soil NO 3 − content decreased to <40 mg NO 3 −-N kg−1 soil, the N 2 O 15N site preference values of the N 2 O produced in the medium straw rate treatment showed a sharp declining trend 15 days after onset of experiment thereby indicating a clear shift towards a more dominant bacterial source of N 2 O. Our study singularly highlights the complex interrelationship between soil NO 3 − kinetics, crop residue incorporation, fungal denitrification and N 2 O/(N 2 O + N 2) ratio. Overall we found that the effect of crop residue applications on soil N 2 O and N 2 emissions depends mainly on soil NO 3 − content, as NO 3 − was the primary regulator of the N 2 O/(N 2 O + N 2) product ratio of denitrification. Furthermore, the application of straw residue enhanced fungal denitrification, but only when the soil NO 3 − content was sufficient to supply enough electron acceptors to the denitrifiers. Highlights • Straw application rate does not directly affect N 2 O/(N 2 O+N 2) ratio. • N 2 O emission following straw application is controlled by soil NO 3 − content. • Straw addition increases fungal N 2 O. [ABSTRACT FROM AUTHOR]

Fertilizer regime affects plant growth and soil microbial community composition, however, its impact on organic nitrogen (N) uptake by plants remains poorly understood. To address this, we undertook an in-situ, short-term uptake experiment based on 13 C, 15 N labelling, and 13 C-PLFA analysis at two long-term (6 year) fertilizer trial sites (Jintan and Changshu). Each site had five treatments: a control without fertilizers, NPK fertilizers, 50% NPK fertilizer +6 t/ha pig manure, 100% NPK fertilizer + cereal straw, and 50% NPK fertilizer +6 t/ha pig manure and cereal straw. Overall, we found that 6–21% and 6–11% of the added 13 C- 15 N-glycine was taken up intact by wheat, while 18–35% and 8–20% was captured by soil microorganisms in Jintan and Changshu locations, respectively. These results indicate that wheat has an appreciable capacity to utilize organic N, even in fertile agricultural soils. Organic N uptake by wheat correlated positively with ammonium and nitrate soil contents, indicating that inorganic N may enhance organic N capture by increasing plant biomass. The 13 C: 15 N ratio in the microbial biomass showed that 32–71% and 13–71% of the 15 N was absorbed through a direct uptake route in Jintan and Changshu soils. Chemical fertilizer reduced microbial biomass and increased the proportion of intact glycine uptake by wheat. Gram-positive bacteria accounted for 18–23%, and 13–15% of the total 13 C labelled PLFA in Jintan and Changshu, respectively, while Gram-negative bacteria accounted for 43–48% and 66–72% indicating that they are the dominant competitors with plants for soil nutrients. Total 15 N uptake by wheat and microorganisms was highest in the 50% NPK fertilizer + pig manure and cereal straw treatment at both sites, indicating that it represents the best fertilizer practice for sustainable food production, as it not only reduced chemical fertilizer application, improved wheat growth and microbial biomass, but also increased wheat utilization of soil organic N. [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]

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]

Due to their substantial volume, subsoils contain more of the total soil carbon (C) pool than topsoils. Much of this C is thousands of years old, suggesting that subsoils offer considerable potential for long-term C sequestration. However, knowledge of subsoil C behaviour and manageability remains incomplete, and subsoil C storage potential has yet to be realised at a large scale, particularly in agricultural systems. A range of biological (e.g. deep-rooting), chemical (e.g. biochar burial) and physical (e.g. deep ploughing) C sequestration strategies have been proposed, but are yet to be assessed. In this review, we identify the main factors that regulate subsoil C cycling and critically evaluate the evidence and mechanistic basis of subsoil strategies designed to promote greater C storage, with particular emphasis on agroecosystems. We assess the barriers and opportunities for the implementation of strategies to enhance subsoil C sequestration and identify 5 key current gaps in scientific understanding. We conclude that subsoils, while highly heterogeneous, are in many cases more suited to long-term C sequestration than topsoils. The proposed strategies may also bring other tangible benefits to cropping systems (e.g. enhanced water holding capacity and nutrient use efficiency). Furthermore, while the subsoil C sequestration strategies we reviewed have large potential, more long-term studies are needed across a diverse range of soils and climates, in conjunction with chronosequence and space-for-time substitutions. Also, it is vital that subsoils are more consistently included in modelled estimations of soil C stocks and C sequestration potential, and that subsoil-explicit C models are developed to specifically reflect subsoil processes. Finally, further mapping of subsoil C is needed in specific regions (e.g. in the Middle East, Eastern Europe, South and Central America, South Asia and Africa). Conducting both immediate and long-term subsoil C studies will fill the knowledge gaps to devise appropriate soil C sequestration strategies and policies to help in the global fight against climate change and decline in soil quality. In conclusion, our evidence-based analysis reveals that subsoils offer an untapped potential to enhance global C storage in terrestrial ecosystems. • Agricultural subsoils may be more suited to long-term C sequestration than topsoils. • Sequestration strategies have variable effects on C stocks, depending on soil type. • Enhanced subsoil C storage can bring ancillary tangible benefits to cropping systems. • Subsoil sampling and incorporation in models and maps is essential. • Policies are needed for C sequestration in the whole soil profile, not just topsoils. [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]

Although S deficiency has been reported in plants worldwide, the belowground biogeochemical cycling of S is not well known. The combined use of mineral fertiliser and manure is regarded as a suitable fertilisation strategy to maintain agricultural soil productivity. A long-term (1964–2018) field experiment was selected to determine how manure application affects soil gross S mineralisation and immobilisation, and plant-derived organic S, cysteine (Cys), and methionine (Met) biological decomposition by 35S, 14C, and 15N labelling. High organic manure application did not increase organic S content in the topsoil owing to the high mineralisation rate, but it increased the organic S content in subsoil where mineralisation rates were relatively lower. S immobilisation dominated gross S fluxes, and the highest SO 4 2− immobilisation rates were recorded under medium manure application. Most plant-derived protein S was decomposed to SO 4 2− after 15 min, and only approximately 30% was retained in the microbial biomass. Protein bioavailability may have a more dominant role in soil S mineralisation than soil S-containing amino acids, owing to its higher concentration. The immobilisation of SO 4 2− was considerably slower than that of proteins and amino acids, which indicates that the microorganisms preferred organic S over inorganic S and that the use is driven by C demand rather than S demand. Moreover, the microbial community released SO 4 2− and NH 4 + after taking up Cys and Met, and the imbalance of elements between substrates and microbes played a dominant role in soil S cycling. This process was strongly regulated by the nature of the substrate; less SO 4 2− was released from Met than from Cys. Among the three important processes for organic S decomposition—the uptake by microorganisms, SO 4 2− release, and SO 4 2− reuse—manure application had a greater effect on SO 4 2− release during organic S decomposition. Overall, manure application increased S bioavailability owing to high S fluxes, and high- and low-molecular weight organic S could be rapidly decomposed to SO 4 2−. • High manure application increased organic S content in subsoil, not in topsoil • The highest S immobilisation rate was recorded under medium manure application • SO 4 2− immobilisation was slower than protein and amino acid immobilisation • More SO 4 2− was generated from Cys than from Met owing to metabolic differences • SO 4 2− release but not microorganisms uptake of Cys and Met was affected by manure [ABSTRACT FROM AUTHOR]

Nitrogen (N) and sulphur (S) are essential nutrients for plant growth. A pot experiment was conducted to verify whether maize and soybean under monoculture and intercropping could utilise N- and S-containing amino acids when competing with soil microorganisms. Maize and soybean were able to utilise methionine (Met; 1.9–2.2% of total addition) and cysteine (Cys; 0.6–1.6% of total addition) as N and S sources, however they faced competition with soil microorganisms. Six hours after microbial uptake, 45.3–64.0% of the S from Met was retained in the microbial biomass, while there was much lower retention from Cys (16.8–34.5%), and 32.5–44.1% of the S from Cys and 15.6–33.3% of that from Met was transformed to SO 4 2−. Cys was a superior S source for plants compared to Met, as higher SO 4 2− release from Cys could support plant growth. Both maize and soybean plants took up NH 4 + (98–99% of total N uptake) and SO 4 2− (85–90%) as their main N and S sources from soil. The N from Cys and Met accounted for only ~1% of total N uptake from soil, and organic Cys and Met accounted for only ~0.2% of the total N uptake, indicating that these two amino acids have limited effects on plant N nutrition, due to the high inorganic N content in agricultural soil. However, the Cys and Met contribution (i.e., organic S uptake and mineral S uptake originating from Cys and Met) to total S uptake (10–15%) was an order of magnitude higher than their N contributions, suggesting that Cys and Met play an important role in soil S nutrition. Intercropping altered the uptake but not the preference for N and S forms in maize and soybean. Overall, the results suggest that S-containing amino acids are important S sources for plant growth even at a lower concentration in soil, but that they play a limited role in plant N nutrition due to a larger inorganic N pool in agricultural soil. • Maize and soybean can use methionine and cysteine as N and S sources. • Plant utilisation of inorganic S derived from cysteine was more than from methionine. • Higher S from cysteine was transformed to SO 4 2− than methionine. • Soil microorganisms mineralised inorganic S originating from methionine and cysteine that were later captured by plant. • Intercropping altered the uptake but not the preference for N and S forms in maize and soybean. [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]

In soils, cysteine and methionine represent the predominant constituents of the low molecular weight organic S, but their role in plant nutrition and soil S cycling is unclear. Cysteine and methionine uptake by pot-cultivated wheat and oilseed rape and their cycling were evaluated using 14C and 35S labelling. About 0.16%–0.30% of 14C from cysteine and methionine was absorbed by the plants after 6 h, indicating that the plants could utilise organic S, with oilseed rape showing higher ability than wheat to take up intact organic S and its derivative inorganic S. Plants utilised organic S with much lower efficiency than inorganic S because most organic S was decomposed by microorganisms. Nitrogen (N) addition enhanced plant S uptake, as high N uptake stimulates S immobilization. About 28%–33% and 67–71% of 14C from cysteine and methionine, respectively, were retained in the microbial biomass (MB), a much higher proportion of 14C from cysteine was released as 14CO 2 from the soil than from methionine. Further, 16%–25% and 61%–72% of 35S from cysteine and methionine, respectively, were retained in the MB, and 35%–42% and 5%–9% were released from it as SO 4 2−. Microbial carbon (C) and S use efficiency for cysteine was lower than for methionine, whereas plants utilised higher amounts of cysteine-derived S as sulphate. The higher microbial utilisation rate of methionine by soil microorganisms, compared with cysteine, may reduce the bioavailability of this compound in the soil solution, and, consequently, its uptake by plants. • Oilseed rape took up more intact organic S and SO 4 2− derived from organic S than wheat. • Microbial utilisation of methionine by soil microorganisms was higher than cysteine. • 35%–42% of cysteine and 5%–9% of methionine were released as SO 4 2− after 4 h. [ABSTRACT FROM AUTHOR]

Plant sulphur (S) deficiency is a worldwide concern. However, the mechanisms controlling the immobilization and mineralization of low-molecular weight organic S by soil microorganisms remain unclear. Therefore, we investigated the assimilation of carbon (C) and S by soil microorganisms using uniformly 14C- or 35S-labelled cysteine and methionine. The decomposition of cysteine and methionine in the soil occurred in three steps. First, the microbial biomass (MB) rapidly immobilised the added cysteine-S (55%–63%) and methionine-S (81%–84%) in less than 30 min. Subsequently, S in the MB was released as 35S-sulphate (release of S into the soil peaked at 1 h [21.4%] and 24 h [17.3%] after adding cysteine and methionine, respectively). Lastly, the released 35SO 4 2− was reutilised by microorganisms. The amount of 14CO 2 and 35SO 4 2− released from methionine was much lower than that from cysteine. The addition of excess glucose-C or inorganic nitrogen and S had little effect on cysteine and methionine uptake rate, but had a major effect on microbial C use efficiency (CUE) and internal S partitioning and the subsequent release of SO 4 2−. We conclude that the microbial community cycles S-containing amino acids at a high rate, irrespective of soil S and N status with a large proportion of the C used in catabolic processes. • S-containing amino acid (cysteine, methionine) uptake from soil was rapid. • Microbial CO 2 and SO 4 2− release was lower from methionine than from cysteine. • Glucose or inorganic S or N had little effect on cysteine and methionine uptake. • Glucose or inorganic S addition greatly affected microbial S and C use efficiency. [ABSTRACT FROM AUTHOR]

Maintaining an adequate phosphorus (P) supply for plants and microorganisms is central to agricultural production; however, the long-term effects of organic manure and inorganic fertilizer application on soil P cycling remain unclear. Organic P cycling in a sandy loam soil receiving medium and high rates of farmyard manure (FYM) with and without mineral fertilisers was studied in a long-term field experiment with 14C/33P isotope labelling and metagenomic shotgun sequencing. FYM application alone negatively affected soil total P and organic P (P o) accumulation by enhancing crop offtake, enhancing P o mineralisation and stimulating P loss from the topsoil by reducing its P sorption potential. The P mineralisation/immobilisation rates detected by the 33P pool dilution method were significantly correlated with the abundance of microbial P cycling genes. Soil available C and N concentrations were related to gross P mineralisation/immobilisation rates and the abundance of P uptake/scavenging genes. Microbial genes related to P uptake and metabolism were more abundant than P scavenging genes, while P scavenging genes may work efficiently as both of them can sustain similar P mineralisation and immobilisation rates. The addition of FYM also promoted phosphatase activity reflecting the increased supply of P o in these soils. Our study demonstrates that long-term FYM application alters soil P o stocks and cycling, and that microbial functional gene abundance was coupled with P cycling rates. Image 1 • Farmyard manure application alone negatively affected total P and organic P accumulation. • Cycling rates were significantly related to the abundance of microbial P cycling genes. • Soil available C and N content regulate biological P cycling. [ABSTRACT FROM AUTHOR]

Despite plastics providing great benefits to our daily life, plastics accumulating in the environment, especially microplastics (MPs; defined as particles <5 mm), can lead to a range of problems and potential loss of ecosystem services. Current research has demonstrated the significant impact of MPs on aquatic systems, but little is known about their effects on the terrestrial environment, especially within agroecosystems. Hereby, we investigated the effect of MPs type and amount on plant growth, soil microorganisms, and photoassimilate carbon (C) allocation. MPs had a negative, dose-dependent impact on plant growth affecting both above- and below-ground productivity (−22.9% and −8.4%). MPs also influenced assimilated 14C allocation in soil (+70.6%) and CO 2 emission (+43.9%). Although the activity of β-glucosidase was suppressed by MPs, other C- and N-cycling related enzyme activities were not affected. The type and amount of MPs in soil greatly altered C flow through the plant-soil system, highlighting that MPs negatively affect a range of C-dependent soil functions. Moreover, MPs increased the soil microbial biomass (+43.6%; indicated by PLFAs), and changed the structure and metabolic status of the microbial community. The evidence presented here suggests that MPs can have a significant impact on key pools and fluxes within the terrestrial C cycle with the response being both dose-dependent and MPs specific. We conclude that MPs in soil are not benign and therefore every step should be made to minimise their entry into the soil ecosystem and potential to transfer into the food chain. Image 1 • Microplastics (MPs) had a negative, dose-dependent impact on plant growth. • MPs altered C flow through the plant-soil system and C-dependent soil functions. • MPs increased microbial biomass and changed the structure of the community. • MPs stimulated microbial CUE but had little effect on exoenzyme activity. [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]