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Continuous application of organic fertilizers can cause accumulation of organic phosphorus (P) in soil, especially in the low-molecular-weight organic phosphorus (LMWOP) forms. This organic P pool represents a potentially important source of P for both plants and microorganisms. To understand the effect of long-term fertilization (30 years) (P-rich soil) vs. fallowing (P-poor soil) on the bioavailability and fate of LMWOP in subtropical paddy soils, we determined the sorption and mineralization of 14C-labeled adenosine, adenosine monophosphate (AMP), adenosine diphosphate (ADP), and adenosine triphosphate (ATP) in each soil. The contents of carbon, nitrogen, and P in the P-rich soil were more than two times greater than those in the P-poor soil. The mineralization rates of the LMWOP compounds were faster in the P-rich soil compared to the P-poor soil, and followed the order AMP>ADP>ATP. Using sterilized soil, all forms of adenosine-P were strongly sorbed to the solid phase and reached saturation in a short time, with the adsorbance increasing with the number of phosphate groups. We concluded that the mineralization of LMWOP compounds was repressed slightly by sorption to the solid phase, but only in the short term. Thus, LMWOP compounds serve as readily available sources of C for microorganisms, making P available for themselves as well as for the plants. However, P accumulation and the progressive saturation of the P sorption sites in highly fertile soils may increase the potential risk of P runoff.

Plant S deficiency is common, but the role of S-containing amino acids such as cysteine in plant S uptake is unknown. We applied 14C-, 35S-, 13C-, and 15N-labelled cysteine to wheat and oilseed rape rhizospheres and traced the plants’ elemental uptake. Both plants absorbed 0.37–0.81% of intact cysteine after 6 h with no further increase after 24 h. They absorbed 1.6–11.5% 35S and 12.3–7.6% 15N from cysteine after 24 h and utilised SO42− as their main S source (75.5–86.4%). Added and naturally occurring cysteine-S contributed 5.6 and 1.1% of total S uptake by wheat and oilseed rape, respectively. Cysteine and inorganic S derived from cysteine contributed 24.5 and 13.6% of uptake for wheat and oilseed rape, respectively, after 24 h. Oilseed rape absorbed ~10-fold more S from cysteine and SO42− than did wheat. The highest absorption of free cysteine should be in the organic-rich soil patches. Soil microorganisms rapidly decomposed cysteine (t1/2 = 1.37 h), and roots absorbed mineralised inorganic N and S. After 15 min, 11.7–14.3% of the 35S-cysteine was retained in the microbial biomass, while 30.2–36.7% of the SO42− was released, suggesting that rapid microbial S immobilisation occurs after cysteine addition. Plants acquire N and S from cysteine via unidirectional soil-to-root nutrient flow, and cysteine is an important S source for plants.

Soil soluble nitrogen (N) is crucial to the N nutrition and productivity of plants. Consequently, understanding the factors that affect its pool size and composition is of considerable importance. Here, six typical forest types in northeast China were investigated to determine the dynamics of soil soluble N across seasons and plant communities, and the potential drivers. Soil free amino acids, NH4+, NO3−, dissolved organic N (DON) and a variety of soil characteristics were measured over the growing season (from May to September). Seasonality showed a stronger effect on the availability of soil inorganic N and free amino acids than vegetation. The coefficients of variation of soil inorganic N, amino acid-N and the potential drivers (moisture and DON) appeared to be greater for season, and the concentrations of these available N sources tended to be higher at the beginning than at the height of growing season. Potential soil drivers (e.g. moisture, microbial biomass-N and DON) and plant phenology together drove the seasonal dynamics of inorganic N and amino acid-N. Arginine, histidine, serine, leucine, aspartic acid, glycine, glutamic acid and proline composed the dominant soil amino acid pool in the temperate forest soils. The basic amino acids (arginine and histidine) were consistently dominant irrespective of vegetation and season, suggesting that selective sorption by the soil solid phase could play an important role in regulating the cycling of amino acid-N in these temperate forest ecosystems. This research indicates that changes in local soil properties, and plant phenology caused by seasonality, exert a powerful influence on the characteristics of plant-soil N cycling.

Soils in temperate agroecosystems are frequently exposed to extremes of moisture and temperature during which time soil functioning may be negatively affected. The aim of this study was to directly compare the effects of a single dry-wet or freeze-thaw (−5 °C or −20 °C) cycle on extracellular enzyme activity and soil organic matter turnover. We measured the activity of six enzymes before and after imposing the freeze-thaw or dry-rewet events. Our results showed that drying had a much greater impact on total enzyme activity than a −20 °C freezing event (38 vs. 10% reduction, respectively), while freezing at −5 °C had no appreciable effect. Enzyme activity recovered back to control levels relatively quickly which we ascribe to de novo exoenzyme production (within 3 d for the −20 °C freeze-thaw treatment and 14 d for the dry-wet treatment). We added 14C-labelled plant residues to the soil prior to imposing the same thermal or moisture stress events. Monitoring residue decomposition before and after imposing the treatments indicated that none of the stress regimes greatly affected organic matter turnover rates. Our results did reveal, however, a pulse of 14CO2 which was produced during the drying and freezing events themselves. We ascribe this to a shift in microbial metabolism and the production of stress avoidance metabolites (e.g. osmo- and cryo-protectants, membrane lipids). Our work highlights that extreme weather events may affect exoenzyme activity, however, these responses are transitory and are unlikely to greatly affect soil organic matter cycling unless they occur at high frequency.

Protein hotspots in soil, such as those associated with decaying soil fauna or plant litter, may produce ephemeral patches of disproportionately high soil nutrients. These hotspots may occur at the macro- and microscale in close proximity to plant roots, however, the likely concentration of soluble products produced in these hotspots remains poorly understood. To address this, we buried two contrasting biomass residues in soil, namely earthworm (Lumbricus terrestris) and clover (Trifolium repens). Their transformation to amino acids, NH4+ and NO3− were monitored continually over 6 days using microdialysis. All treatments showed greater soluble nitrogen (N) concentrations compared to the unamended controls. The highest concentrations of both amino acids (12.9 mM after 12 h) and NH4+ (45.3 mM after 6 h) were generated in the vicinity of decomposing earthworm. In comparison, dried clover residues yielded 2.7 mM of amino acids at 6 h. After 12 h, amino acid and NH4+ concentrations in both earthworm and dried clover treatments showed a steep decline, returning close to background levels (

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 NH4+, 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 CH4, 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 NH4+ was nitrified leading to a shift in greenhouse gas emissions, from CH4 to N2O emissions. N2O 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

Global plant sulphur (S) deficiency is increasing because of a reduction in sulphate-based fertiliser application combined with continuous S withdrawal during harvest. Here, we applied (13)C, (15)N, (14)C, and (35)S quad labelling of the S-containing amino acids cysteine (Cys) and methionine (Met) to understand S cycling and microbial S transformations in the soil. The soil microorganisms absorbed the applied Cys and Met within minutes and released SO(4)(2−) within hours. The SO(4)(2−) was reutilised by the MB within days. The initial microbial utilisation and SO(4)(2−) release were determined by amino acid structure. Met released 2.5-fold less SO(4)(2−) than Cys. The microbial biomass retained comparatively more C and S from Met than Cys. The microorganisms decomposed Cys to pyruvate and H(2)S whereas they converted Met to α-ketobutyrate and S-CH(3). The microbial stoichiometries of C, N, and S derived from Cys and Met were balanced after 4 d by Cys-derived SO(4)(2−) uptake and Met-derived CO(2) release. The microbial C:N:S ratio dynamics showed rapid C utilisation and loss, stable N levels, and S accumulation. Thus, short-term organic S utilisation by soil microorganisms is determined by amino acid structure whilst long-term organic S utilisation by soil microorganisms is determined by microbially controlled stoichiometry.

Generally, the physical, chemical and biological attributes of a soil combined with abiotic factors (e.g. climate and topography) drive pedogenesis. However, biological indicators of soil quality play no direct role in traditional soil classification and surveys. To support their inclusion in classification schemes, previous studies have shown that soil type is a key factor determining microbial community composition in arable soils. This suggests that soil type could be used as proxy for soil biological function and vice versa. In this study we assessed the relationship between soil biological indicators with either vegetation cover or soil type. A wide range of soil attributes were measured on soils from across the UK to investigate whether; (1) appropriate soil quality factors (SQFs) and indicators (SQIs) can be identified, (2) soil classification can predict SQIs; (3) which soil quality indicators were more effectively predicted by soil types, and (4) to what extent do soil types and/ or aggregate vegetation classes (AVCs) act as major regulators of SQIs. Factor analysis was used to group 20 soil attributes into six SQFs namely; Soil organic matter, Organic matter humification, Soluble nitrogen, Microbial biomass, Reduced nitrogen and Soil humification index. Of these, Soil organic matter was identified as the most important SQF in the discrimination of both soil types and AVCs. Among the measured soil attributes constituting the Soil organic matter factor were, microbial quotient and bulk density were the most important attributes for the discrimination of both individual soil types and AVCs. The Soil organic matter factor discriminated three soil type groupings and four aggregate vegetation class groupings. Only the Peat soil and Heath and bog AVC were distinctly discriminated from other groups. All other groups overlapped with one another, making it practically impossible to define reference values for each soil type or AVC. We conclude that conventionally classified soil types cannot predict the SQIs (or SQFs), but can be used in conjunction with the conventional soil classifications to characterise the soil types. The two-way ANOVA showed that the AVCs were a better regulator of the SQIs than the soil types and that they (AVCs) presented a significant effect on the soil type differences in the measured soil attributes.

Protein represents a major input of organic matter to soil and is an important source of carbon (C) and nitrogen (N) for microorganisms. Therefore, determining which soil properties influence protein mineralisation in soil is key to understanding and modelling soil C and N cycling. However, the effect of different soil properties on protein mineralisation, and especially the interactions between soil properties, are poorly understood. We investigated how topsoil and subsoil properties affect protein mineralisation along a grassland altitudinal (catena) sequence that contained a gradient in soil type and primary productivity. We devised a schematic diagram to test the key edaphic factors that may influence protein mineralisation in soil (e.g. pH, microbial biomass, inorganic and organic N availability, enzyme activity and sorption). We then measured the mineralisation rate of 14C-labelled soluble plant-derived protein and amino acids in soil over a two-month period. Correlation analysis was used to determine the associations between rates of protein mineralisation and soil properties. Contrary to expectation, we found that protein mineralisation rate was nearly as fast as for amino acid turnover. We ascribe this rapid protein turnover to the low levels of protein used here, its soluble nature, a high degree of functional redundancy in the microbial community and microbial enzyme adaptation to their ecological niche. Unlike other key soil N processes (e.g. nitrification, denitrification), protease activity was not regulated by a small range of factors, but rather appeared to be affected by a wide range of interacting factors whose importance was dependent on altitude and soil depth [e.g. above-ground net primary productivity (NPP), soil pH, nitrate, cation exchange capacity (CEC), C:N ratio]. Based on our results, we hypothesise that differences in soil N cycling and the generation of ammonium are more related to the rate of protein supply rather than limitations in protease activity and protein turnover per se.

Aims The capacity of plant roots to directly acquire organic nitrogen (N) in the form of oligopeptides and amino acids from soil is well established. However, plants have poor access to protein, the central reservoir of soil organic N. Our question is: do plants actively secrete proteases to enhance the breakdown of soil protein or are they functionally reliant on soil microorganisms to undertake this role? Methods Growing maize and wheat under sterile hydroponic conditions with and without inorganic N, we measured protease activity on the root surface (root-bound proteases) or exogenously in the solution (free proteases). We compared root protease activities to the rhizosphere microbial community to estimate the ecological significance of root-derived proteases. Results We found little evidence for the secretion of free proteases, with almost all protease activity associated with the root surface. Root protease activity was not stimulated under N deficiency. Our findings suggest that cereal roots contribute one-fifth of rhizosphere protease activity. Conclusions Our results indicate that plant N uptake is only functionally significant when soil protein is in direct contact with root surfaces. The lack of protease upregulation under N deficiency suggests that root protease activity is unrelated to enhanced soil N capture.

Application of biochar into soils has commonly been used as a strategy for sequestering carbon in soils, for improving soil fertility and remediating soil pollution. However, the implications of biochar amendments on pesticide decomposition has a potential risk in the agricultural soil. In this study, the experiment including four treatments, control (no biochar and no Arbuscular mycorrhizal fungi (AMF), biochar (biochar without AMF), AMF (AMF without biochar), biochar +AMF was performed for evaluating the influence of AMF combined with biochar on simazine fate including the sorption, leaching and biodegradation. Compared with the control, biochar application inhibited simazine decomposition and AMF inoculation alleviated the inhibition when host plant was symbiosised and no influence without symbiosis. However, the simazine decomposition in AMF was different with that in control with symbiosis and decreased without symbiosis, which indicated AMF has a potential to increase the simazine decomposition with symbiosis. In addition, biochar application and AMF inoculation both decreased simazine uptake by plant; biochar application significantly decreased simazine content in the leachate and AMF strengthened this function. However, AMF inoculation has no effect on simazine leaching. These phenomens was attributed to the soil adsorption capacity variation due to biochar application or AMF inoculation. Overall, biochar application combined AMF inoculation can mitigate simazine accumulation in the soil surface and decrease the concentration. However, the comprehensive understanding about biochar application influence on AMF, AMF inoculation affect biochar or soil native organic matter decomposition need further and systematic research for evaluation this method is feasible or not.

Amyris is a fermentation product company that leverages synthetic biology and has been bringing novel fermentation products to the market since 2009. Driven by breakthroughs in genome editing, strain construction and testing, analytics, automation, data science, and process development, Amyris has commercialized nine separate fermentation products over the last decade. This has been accomplished by partnering with the teams at 17 different manufacturing sites around the world. This paper begins with the technology that drives Amyris, describes some key lessons learned from early scale-up experiences, and summarizes the technology transfer procedures and systems that have been built to enable moving more products to market faster. Finally, the breadth of the Amyris product portfolio continues to expand; thus the steps being taken to overcome current challenges (e.g. automated strain engineering can now outpace the rest of the product commercialization timeline) are described.

The impact of global warming on the metabolic state of a species may be examined by either measuring physiological rates across a latitudinal gradient or by assessing short-term responses under experimentally controlled temperature regimes. The combination of the two approaches is seldom used but it provides valuable information on an organism's responses to temperature at broader temporal and spatial scales while allowing the isolation of temperature effects from other environmental variables. Here we used both approaches to assess the warming effects on the total acquisition of dissolved inorganic nitrogen (DIN; nitrate, ammonium) and organic N (DON; amino acids, peptides) by the globally widespread seagrass Zostera marina. DIN and DON uptake rates were measured in plants from three sites covering the species latitudinal distribution in Europe (Iceland, UK and Portugal). The responses of DIN and DON uptake rates of plants from the middle latitude (UK) to a latitudinal range of temperatures (8, 12 and 17 degrees C) were also measured. We further examined the microbial uptake of DON along the latitudinal distribution and whether temperature is the main driver of that uptake. Our results showed that warming greatly increased the total N uptake by Z. marina and also the relative contribution of DON to total N acquisition. The microbial uptake of DON increased towards warmer latitudes, and temperature was the main driver of these observations. Ocean warming will increase the nitrogen demand of Z. marina and this demand may be met by an increasing uptake of organic nitrogen forms. This indicates that Z. marina, and probably other seagrass species, can be winners under global change as nitrogen uptake capacity will not limit growth driven by increased photosynthetic assimilation of CO2. DL 57/2016/CP1361/CT0001, UID/Multi/04326/2019 info:eu-repo/semantics/publishedVersion

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 NH4+ and NO3− 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 NO3− production and assimilation. Rates of protein, peptide, and amino acid processing rate were 169–248, 87–147, and 85–305 mg N kgDWsoil−1 d−1, respectively, gross NH4+ and NO3− production and consumption were 1.8–5.8 mg N kgDWsoil−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 CO2 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.

There is ample experimental evidence for shifts in plant community composition under climate warming. To date, however, the underlying mechanisms driving these compositional shifts remain poorly understood. The amount and form of nitrogen (N) available to plants are among the primary factors limiting productivity and plant coexistence in terrestrial ecosystems. We conducted a short-term 15N tracer experiment in a ten-year warming and grazing experiment in an alpine grassland to investigate the effects of warming and grazing on plant uptake of NO3−-N, NH4+-N, and glycine-N. Four dominant plant species (Kobresia humilis, Potentilla anseria, Elymus nutans, Poa annua) were selected. Results We found that 10-years of warming decreased plant uptake of inorganic N by up to 80% in all species. In contrast, warming increased the uptake of organic N in K. humilis, P. anseria, and E. nutans but not in P. annua. Results showed that plant relative biomass increased hyperbolically with the ratio of the plant species total uptake of available N and plant community uptake of available N. And a significant positive correlation between plant species uptake of soil glycine-N and the uptake of total available N. The stable relative biomass of plant species is largely dependent on organic N uptake by plants. We conclude that plant organic N uptake maintains species dominance under long-term warming.

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 13C, 15N labelling, and 13C-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 13C-15N-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 13C:15N ratio in the microbial biomass showed that 32–71% and 13–71% of the 15N 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 13C 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 15N 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.

Despite considerable attention over the last 25 yr, the importance of early protein breakdown products to plant nitrogen (N) nutrition remains uncertain. We used rhizosphere injection of 15 N-, 13 C- and 14 C-labelled inorganic N and amino acid (l-alanine), with chase periods from 1 min to 24 h, to investigate the duration of competition for amino acid between roots (Triticum aestivum) and soil microorganisms. We further investigated how microbial modification of l-alanine influenced plant carbon (C) and N recovery. From recovery of C isotopes, intact alanine uptake was 0.2-1.3% of added. Soil microbes appeared to remove alanine from soil solution within 1 min and release enough NH4 + to account for all plant 15 N recovery (over 24 h) within 5 min. Microbially generated inorganic or keto acid C accounted for 24 h, indicating that long chase periods bias outcomes and fail to accurately simulate soil processes.

In contrast to the situation in plants inhabiting most of the world’s ecosystems, mycorrhizal fungi are usually absent from roots of the only two native vascular plant species of maritime Antarctica, Deschampsia antarctica and Colobanthus quitensis. Instead, a range of ascomycete fungi, termed dark septate endophytes (DSEs), frequently colonise the roots of these plant species. We demonstrate that colonisation of Antarctic vascular plants by DSEs facilitates not only the acquisition of organic nitrogen as early protein breakdown products, but also as non‐proteinaceous d‐amino acids and their short peptides, accumulated in slowly‐decomposing organic matter, such as moss peat. Our findings suggest that, in a warming maritime Antarctic, this symbiosis has a key role in accelerating the replacement of formerly dominant moss communities by vascular plants, and in increasing the rate at which ancient carbon stores laid down as moss peat over centuries or millennia are returned to the atmosphere as CO2., In contrast to the situation in plants inhabiting most of the world's ecosystems, mycorrhizal fungi are usually absent from roots of the only two native vascular plant species of maritime Antarctica, Deschampsia antarctica and Colobanthus quitensis. Instead, a range of ascomycete fungi, termed dark septate endophytes (DSEs), frequently colonise the roots of these plant species. We demonstrate that colonisation of Antarctic vascular plants by DSEs facilitates not only the acquisition of organic nitrogen as early protein breakdown products, but also as non‐proteinaceous D‐amino acids and their short peptides, accumulated in slowly‐decomposing organic matter, such as moss peat.

Carbon use efficiency (CUE) describes the relative partitioning of carbon (C) between anabolic and catabolic processes within the soil microbial community. Further, it represents a major factor regulating the amount of C cascading through the trophic levels of the soil food web. How CUE relates to C supply, however, remains poorly understood. The primary aim of this study was to determine how CUE varies across a range of spatial scales as a function of C substrate supply. Our secondary aim was to understand how variations in substrate CUE influences the interpretation of community level physiological profiles (CLPP). Using 16 different 14C-labelled substrates (including amino acids, sugars, organic acids and amino sugars) and soils collected at the field, regional and continental scale, we measured the rate of substrate uptake and mineralization from which we calculated CUE. Across all soils (n = 114) and substrates (n = 16), the average CUE for the microbial community was 0.568 ± 0.004 (range 0.492–0.794). While the partitioning of substrate-C within the biomass (immobilization/mineralization) over 72 h was highly conserved for some substrates (e.g. glucose), others showed a wide variability in CUE across the samples (e.g. valine). In the context of the CLPP methodology, we showed that individual sites could be statistically separated from each other, irrespective of whether the statistical analysis was based on microbial substrate uptake rate or mineralization rate. However, our results do suggest that caution is needed when ascribing observed CLPP differences to the importance of individual C pathways operating in soil due to the wide variation of CUE between substrates. In conclusion, we present new mechanistic evidence to support the paradigm that variation in ecosystem CUE may in part reflect differences in the types of C supplied to the microbial biomass.

Due to climate change, the frequency and duration of flood events are predicted to increase in many regions of the world. This is expected to cause large changes in soil functioning and to a progressive decline in soil quality such as reduced rates of nutrient cycling, enhanced greenhouse gas emissions and loss of soil biodiversity. There is a knowledge gap, however, on how temperate agricultural soils under different management practices (e.g. manure application) respond to prolonged river or coastal flooding. The main objective of this work was to determine the effects of a simulated prolonged flooding with saline and freshwater on soil N cycling, following application of a low C:N organic amendment (broiler litter) at two temperatures, representative of a winter and a spring flood event. Using laboratory mesocosms we simulated prolonged winter (6 °C) and spring (14 °C) flooding of soil amended with broiler litter. We also compared the effects of inundation with either river (freshwater) or coastal (saline) water. An agricultural grassland soil (Eutric Cambisol) was subjected to different combinations of treatments (flood with fresh or saline water, winter vs spring temperatures, with/without poultry manure). The impact of these treatments on soil solution N dynamics, greenhouse gas emissions (CO2, CH4, N2O) and microbial community structure (by PLFA analysis) were evaluated over an 11 week simulated flood event followed by an 8 week soil recovery period (without flood). Overall, potential losses of NH4+ and cumulative GHG emissions were increased by flooding and the presence of manure. CH4 emissions were found to dominate under freshwater flooding conditions and N2O under saline flooding. Significant releases of GHG occurred during both flooding and after floodwater removal. Temperature was less influential on regulating GHG under the different treatments. These releases in GHG were associated with disruption in N cycling and changes in soil microbial composition and these changes persisted after floodwater removal. Extreme flooding negatively impacts soil functioning, however, the magnitude of any changes remain critically dependent on flood duration and source of flood water, and management conditions. Further work is required at the field scale to understand the molecular basis of the responses observed in this study.

Due to their extreme aridity, high rate of UV irradiation and low soil carbon (C) content, the soils of the Atacama Desert represent one of the world's most hostile environments for microbial life and its survival. Although infrequent, climatic conditions may, however, prevail which temporarily remove these stresses and allow life to briefly flourish. In this study we investigated the response of soil microbial communities to water and C availability across an aridity gradient (semi-arid, arid, hyper-arid) within the Atacama Desert. We simulated the impact of hyper-dry spells, humid fogs and precipitation events on the activation of the microbial community and the subsequent mineralization of low (glucose) and high (plant residues) molecular weight C substrates. Our results showed that mineralization rate followed the trend: semi-arid > arid > hyper-arid. Some glucose mineralization was apparent under hyper-arid conditions (water activity, aw = 0.05), although this was 10-fold slower than under humid conditions and ca. 200-fold slower than under wet conditions. A lag phase in CO2 production after glucose-C addition in the hyper-arid soils suggested that mineralization was limited by the low microbial biomass in these soils. No lag phase was apparent in the corresponding semi-arid or arid soils. In contrast, the breakdown of the plant residues was initially much slower than for glucose and involved a much longer lag phase in all soils, suggesting that mineralization was limited by low exoenzyme activity, particularly in the humid and hyper-dry soils. Our results also showed that microbial C use efficiency followed the trend: hyper-arid > arid > semi-arid. In conclusion, we have shown that even under hyper-arid conditions, very low levels of microbial activity and C turnover do occur. Further, the microbial communities are capable of rapidly responding to available C once water becomes more abundant, however, this response is both biomass and metabolically limited in hyper-arid soils.

Most studies on plant nutrition tend to focus on the topsoil (plough layer) and frequently neglect subsoil processes. However, cereal roots can potentially acquire nutrients including organic and inorganic nitrogen (N) from deep in the soil profile. Greater knowledge on the interaction of plants and microbes in subsoil environments is required to evaluate whether deep rooting traits in cereals will achieve greater nutrient use efficiency and greater soil carbon (C) storage in cropping systems. This study aimed to evaluate the relationship between root distribution, organic and inorganic N availability and potential N supply at the critical growth period during the wheat cropping cycle in a sand textured Eutric Cambisol. Our results provide evidence of significant microbial capacity in the subsoil. The rate of plant residue turnover and the mineralization of organic C and N substrates (glucose, amino acids, peptides, protein) declined slightly with increasing soil depth; however, these rates were not correlated with basal soil respiration, microbial biomass or community structure. This suggests that the microbial population in subsoil is more C limited but that its activity can be readily stimulated upon C substrate addition. A significant potential for organic and inorganic N turnover was also demonstrated at depth with a similar abundance of ammonifiers and ammonia oxidizing bacteria (AOB) and archaea (AOA) throughout the soil profile. Again, N mineralization in subsoils appears to be substrate limited. Root density declined rapidly down the soil profile with few roots present past 50 cm; suggesting that this is the major factor limiting C recharge of soil organic matter and microbial activity in subsoils. Greater root proliferation at depth could allow greater capture of water and the recapture of N lost by leaching; however, our results suggest that plant-microbial competition for C and N is as intense in the subsoil as in the topsoil. We conclude that while deeper rooting may improve nutrient and water use efficiency it may not lead to much greater C sequestration in subsoils, at least in the short term.

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 SO42−. Cys was a superior S source for plants compared to Met, as higher SO42− release from Cys could support plant growth. Both maize and soybean plants took up NH4+ (98–99% of total N uptake) and SO42− (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.

Biochar application has been received much attention because biochar can improve the fertilizer utilization efficiency of soil. However, the effect of biochar produced at different temperature on t...

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.

Extreme flood events are predicted to have a negative impact on soil quality. Currently, there is a lack of information about the effect of agricultural practices on soil functioning and microbial processes under these events. We hypothesized that the impact of flooding on soil quality will be exacerbated when crop residues are present in the soil as they will induce more extreme anaerobicity. A spring extreme flood event (10 °C, 9 weeks) was simulated in mesocosms containing an arable sandy-loam soil low in nutrients. The main treatments were (1) with and without flooding and (2) with and without maize residue addition (8 Mg ha−1). We monitored changes in soil chemical quality indicators (e.g. pH, salinity, Fe3+, P, C, NH4 +, NO3 − and organic N), greenhouse gas (GHG) emissions (CO2, CH4, N2O) and soil microbial community composition (PLFAs) during a prolonged flood period (9 weeks) and an 8-week “recovery” period after flooding. In comparison to the other treatments, flooding in the presence of crop residues resulted in a dramatic drop in soil redox potential. This was associated with the enhanced release of Fe and C into solution and an increase in CH4 emissions. In contrast, maize residues reduced potential nitrate losses and N2O emissions, possibly due to complete denitrification and microbial N immobilization. Both flooding and maize residues stimulated microbial growth and promoted a shift in microbial community composition. Following floodwater removal, most of the soil quality indicators returned to the levels of the control treatment within 5 weeks. After this short recovery phase, no major impact of flooding could be observed on plant growth (maize pot-grown). Overall, we conclude that both extreme flooding and management regime negatively impact upon a range of soil quality indicators (e.g. redox, GHG emissions); however, the soil showed high resilience and recovered quickly after floodwater removal. Further work is required to investigate the impact of repeated extreme flood events on soil quality and function over longer timescales. Electronic supplementary material The online version of this article (doi:10.1007/s00374-017-1214-0) contains supplementary material, which is available to authorized users.

Dissolved organic nitrogen (DON) represents an important soluble nutrient pool in soil, however, little is known about the dynamics of DON in the litter and topsoil of Brazilian sugarcane (Saccharum spp.) fields, particularly those that are harvested mechanically, without burning. Therefore, the aim of this study was to determine the microbial mineralisation and sorption affinity of DON compounds in litter and soil from the litter-soil transition zone of two sugarcane plantations located in southeastern Brazil. We directly measured the C mineralisation of 14C-labelled amino acids (mix of 17 amino acids), peptides ( l -dialanine and l -trialanine), urea, and protein (isolated from tobacco leaves) by capturing 14CO2 evolved from the litter and soil over 168 h. A sorption assay was performed using the same treatments. We found differences in the organic and mineral N pools of the litter and soil, as well as in microbial community composition. Except for protein in the soil, the DON compounds were taken up rapidly by microbes. However, the C use efficiency was higher for the amino acid mix than for the peptides and urea, indicating more rapid post-uptake catabolism (with subsequent mineralisation as 14CO2) of both compounds. In addition, protein had the highest sorption affinity, especially in soil, and the weak sorption affinity of the amino acids, peptides, and urea indicates moderate bioavailability of these fractions to microbes and plants. We conclude that strong sorption of protein to the solid phase limits its bioavailability and represents a rate limiting step in DON turnover.

Grasslands cover more than 70% of the world's agricultural land playing a pivotal role in global food security, economy, and ecology due to their flexibility and functionality. Climate change, characterized by changes in temperature and precipitation patterns, and by increased levels of greenhouse gases in the atmosphere, is anticipated to increase both the frequency and severity of extreme weather events, such as drought, heat waves, and flooding. Potentially, climate change could severely compromise future forage crop production and should be considered a direct threat to food security. This review aimed to summarize our current understanding of the physiological and metabolic responses of temperate grasses to those abiotic stresses associated with climate change. Primarily, substantial decreases in photosynthetic rates of cool‐season grasses occur as a result of high temperatures, water‐deficit or water‐excess, and elevated ozone, but not CO2 concentrations. Those decreases are usually attributed to stomatal and non‐stomatal limitations. Additionally, while membrane instability and reactive oxygen species production was a common feature of the abiotic stress response, total antioxidant capacity showed a stress‐specific response. Furthermore, climate change‐related stresses altered carbohydrate partitioning, with implications for biomass production. While water‐deficit stress, increased CO2, and ozone concentrations resulted in higher carbohydrate content, the opposite occurred under conditions of heat stress and flooding. The extent of damage is greatly dependent on location, as well as the type and intensity of stress. Fortunately, temperate forage grass species are highly heterogeneous. Consequently, through intra‐ and in particular inter‐specific plant hybridization (e.g., Festuca x Lolium hybrids) new opportunities are available to harness, within single genotypes, gene combinations capable of combating climate change.

Biochar application has been receiving much attention as pesticide pollution mitigator because it reduces harmful chemicals. However, direct comparisons between the effect of biochar and straw on the simazine fate in soils remain poorly understood. We explored the impact of biochars and straw on the simazine behavior in a soil using a 14C labeling approach. Biochar was produced by the thermal treatment of wheat straw at four contrasting temperatures (250, 350, 450 and 550°C) and was incorporated into a sandy loam soil. The sorption of simazine in the biochar soil from 83.9% to 87.5% was significantly higher than 43.0% in the unamended soil and 35.7% in the soil amended with unprocessed straw, thus resulting in low samizine leaching from 21.8% to 42.6% in the biochar soil. However, biochar application suppressed the simazine decomposition, which is contrast in the straw soil. Furthermore, the biogeochemical behavior of simazine varied with the pyrolysis temperature. These results indicate biochar a...

In Brazil, N fertilisers are applied onto the surface of the sugarcane (Saccharum spp.) litter layer, which represents a large portion of the C stored in the agroecosystem. However, little is known about the influence of mineral N on decomposition of organic C compounds and mineral N transformations in the litter-soil transition zone. This investigation determined the effect of mineral N forms (NH4+ and NO3−) on glucose mineralisation and N dynamics in litter and topsoil from two sugarcane fields located in the state of Sao Paulo, Brazil. Carbon mineralisation and N availability were measured using 14C-labelled glucose, applied alone (glucose) or combined with NH4+ [as (NH4)2SO4] (glucose + ammonium) or NO3− (as KNO3) (glucose + nitrate) in litter and soil from the litter-soil transition zone. The 14C immobilised after 168 h had the following trend for the litter of both sites: glucose > glucose + ammonium > glucose + nitrate, while no differences among treatments were found for the soils. Higher immobilisation (increased by 165%, on average) occurred for NH4+ (glucose + ammonium) compared to NO3− (glucose + nitrate), primarily in the sugarcane litter. Carbon mineralisation in litter was N-limited, and the addition of mineral N accelerated the return of C to the atmosphere. Lower immobilisation of NO3− may increase N availability to plants relative to NH4+ in the short term, but also may lead to reduced C storage and larger greenhouse gas emissions due to faster mineralisation of labile carbohydrate through the NO3− reduction process.

Incorporating crop residues and biochar have received increasing attention as tools to mitigate atmospheric carbon dioxide (CO2) emissions and promote soil carbon (C) sequestration. However, direct comparisons between biochar, torrefied biomass and straw on both labile and recalcitrant soil organic matter (SOM) remains poorly understood. In this study, we explored the impact of biochars produced at different temperatures and torrefied biomass on the simple C substrates (glucose, amino acids), plant residues (Lolium perenne L.) and native SOM breakdown in soil using a 14C labeling approach. Torrefied biomass and biochars produced from wheat straw at four contrasting pyrolysis temperatures (250, 350, 450 and 550 °C) were incorporated into a sandy loam soil and their impact on C turnover compared to an un-amended soil or one amended with unprocessed straw. Biochar, torrefied biomass and straw application induced a shift in the soil microbial community size, activity and structure with the greatest effects in the straw-amended soil. In addition they also resulted in changes in microbial carbon use efficiency (CUE) leading to more substrate-C being partitioned into catabolic processes. While overall the biochar, torrefied biomass and straw addition increased soil respiration, it reduced the turnover rate of the simple C substrates, plant residues and native SOM and had no appreciable effect on the turnover rate of the microbial biomass. The negative SOM priming was positively correlated with biochar production temperature. We therefore ascribe the increase in soil CO2 efflux to biochar-derived C rather than that originating from SOM. In conclusion, the SOM priming magnitude is strongly influenced by both the soil organic C quality and the biochar properties. In comparison to straw, biochar has the greatest potential to promote soil C storage. However, straw and torrefied biomass may have other co-benefits which may make them more suitable as a CO2 abatement strategy. This article is protected by copyright. All rights reserved.

Dissolved organic matter (DOM) in soil solution represents a complex mixture of organic molecules and plays a central role in carbon and nitrogen cycling in plant–microbial–soil systems. We tested whether excitation–emission matrix (EEM) fluorescence spectroscopy can be used to characterize DOM and support previous findings that the majority of DOM is of high molecular weight (MW). EEM fluorescence spectroscopy was used in conjunction with MW fractionation to characterize DOM in soil solution from a grassland soil land management gradient in North Wales, UK. Data analysis suggested that three distinct fluorescence components could be separated and identified from the EEM data. These components were identified as being of humic-like or fulvic-like origin. Contrary to expectations, the majority of the fluorescence signal occurred in the small MW (

Shrublands cover a large proportion of the world’s land surface, yet they remain poorly studied in comparison to other ecosystems. Within shrublands, soil organic matter (SOM) is replenished from inputs of both above- and below-ground plant litter, however, their relative importance depends on their respective turnover rates. To critically address this, we measured the biodegradation rates of the soluble and insoluble components of 14 C-labelled above- and below-ground plant litter in soil. During the 150 day incubation, the amount of plant-derived soluble-C lost as 14 CO 2 was similar for the different plant parts being 64.7 ± 2.3% for roots, 72.1 ± 7.4% for stems, and 72.4 ± 1.8% for leaves. In comparison, the turnover of the insoluble fraction was much slower. However, again little difference in mineralisation was seen for the different plant parts with the total losses being 21.1 ± 0.9% for roots, 19.5 ± 1.6% for stems, and 19.6 ± 1% for leaves. A double exponential first order kinetic model fitted well to the experimental data. It also allowed the partitioning of C between microbial anabolic and catabolic processes for the soluble C component. Using this model, we deduced that the soluble fraction turns over ca. 40 times annually, whereas it takes ca. 2.5 years to turnover the insoluble fraction. For the soluble plant component, the overall microbial carbon use efficiency (CUE) was estimated to be greater for root-derived C in comparison to that derived from aboveground (no difference was observed for the insoluble component). From this, we tentatively suggest that C sourced from belowground plant components may persist longer in soil than C derived from aboveground plant components.

Cycling of low molecular weight dissolved organic nitrogen compounds constitutes an important component of soil organic matter turnover in soils. We determined how rapidly grassland soils can cycle urea, compared to the amino acid l-alanine, and the peptide l-trialanine. Using naturally occurring concentrations of 14C-labelled compounds the rates of removal from soil solution and subsequent mineralisation were measured. Biotic removal of all three compounds and subsequent mineralisation to CO2 occurred within minutes. This research has demonstrated, for the first time, the potential for rapid removal of urea at low concentrations by the soil microbial biomass.

The flow of carbon (C) through soil is inherently complex due to the many thousands of different chemical transformations occurring simultaneously within the soil microbial community. The accurate modelling of this C flow therefore represents a major challenge. In response to this, isotopic tracers (e.g. 13 C, 14 C) are commonly used to experimentally parameterise models describing the fate and residence time of individual C compounds within soil. In this study, we critically evaluated the combined use of experimental 14 C labelling and mathematical modelling to estimate C turnover times in soil. We applied 14 C-labelled alanine and glucose to an agricultural soil and simultaneously measured their loss from soil solution alongside the rate of microbial C immobilization and mineralization. Our results revealed that chloroform fumigation-extraction (CFE) cannot be used to reliably quantify the amount of isotopically labelled 13 C/ 14 C immobilised by the microbial biomass. This is due to uncertainty in the extraction efficiency values ( k ec ) within the CFE methodology which are both substrate and incubation time dependent. Further, the traditional mineralization approach (i.e. measuring 14/13 CO 2 evolution) provided a poor estimate of substrate loss from soil solution and mainly reflected rates of internal microbial C metabolism after substrate uptake from the soil. Therefore, while isotope addition provides a simple mechanism for labelling the microbial biomass it provides limited information on the behaviour of the substrate itself. We used our experimental data to construct a new empirical model to describe the simultaneous flow of substrate-C between key C pools in soil. This model provided a superior estimate of microbial substrate use and microbial respiration flux in comparison to traditional first order kinetic modelling approaches. We also identify a range of fundamental problems associated with the modelling of isotopic-C in soil, including issues with variation in C partitioning within the community, model pool connectivity and variation in isotopic pool dilution, which make interpretation of any C isotopic flux data difficult. We conclude that while convenient, the use of isotopic data ( 13 C, 14 C, 15 N) has many potential pitfalls necessitating a critical evaluation of both past and future studies.

Urine patches within pasture soils are hotspots for nitrogen (N) cycling and losses, where nitrification inhibitors (NI) offer a means of reducing such losses. Within urine influenced soil, more research has been conducted for dicyandiamide (DCD) than 3,4-dimethylpyrazole phosphate (DMPP). Differences in the efficacy of these NI are often ascribed to a greater mobility of DCD, which may lead to spatial separation from NH4 + and nitrifying microorganisms. We tested the mobility of 14C-labelled DCD and DMPP relative to sheep urine-derived NH4 + in soil columns of contrasting texture and organic matter content, following simulated rainfall. We also assessed factors influencing the vertical mobility of these NI in soils, including solubility, sorption/desorption processes and microbial degradation and uptake. Following 40-mm rainfall, without the presence of sheep urine, the distribution of both NI were similar in the soil columns; however, there was a greater retention of DCD compared to DMPP in the top 1 cm. Both NI appeared to co-locate well with urine-derived NH4 +, and the presence of sheep urine altered the leaching profile of the NI (compared to rainfall application alone), but this effect was inhibitor and soil-type dependent. A greater sorption to the soil matrix was observed for DCD in comparison to DMPP in all three studied soils, and the presence of urine generally increased desorption processes. Of the NI applied to the soil columns, 18–66 % was taken up within 30 min by the microbial community. However, only small amounts (

Peatlands export significant amounts of dissolved organic carbon (DOC) to freshwaters, but the quantity of DOC reaching marine environments is typically less than the input to the fluvial system due to processing within the water column. Key removal processes include photo-chemical degradation, and heterotrophic bacterial respiration. In this study we examined these processes using 14C-labelled DOC to quantify the extent of DOC breakdown and to determine its fate following irradiation under controlled laboratory conditions. We examined the influence of microbial processes occurring within the water column, the potential role of stream-bed biofilms, and the possible modifying effects of downstream mixing, as DOC in water from the peatland encounters runoff from upland mineral soils (“Mountain”), nutrient-rich runoff from agricultural soils, and seawater in an estuary. Our results demonstrated conservative mixing of DOC from Peatland and Mountain waters but interactive effects when Peatland water was mixed with Agricultural and Estuary waters and exposed to solar radiation. The mixing of Peatland and Agricultural waters led to net DOC production, suggesting that DOC was only partially degraded by solar radiation and that the products of this might have fuelled autotrophic microbial growth in the samples. The mixing of Peatland water with saline estuary water resulted in net DOC loss following irradiation, suggesting a role for sunlight in enhancing the flocculation of DOC to particulate organic carbon (POC) in saline environments.

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 14CO2 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 SO42−. 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.

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 35SO42− was reutilised by microorganisms. The amount of 14CO2 and 35SO42− 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 SO42−. 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.

Freeze-thaw and dry-wet cycles are common phenomena in temperate regions. Such events may have a significant influence on the functioning of the soil microbial community. Using non-targeted metabolomics, we compared the effects of a single freeze-thaw or dry-wet event on microbial metabolism in an agricultural soil with and without plants. We showed that a dry-wet cycle had a greater impact on solute and metabolite concentrations in the unplanted soil than a freeze-thaw cycle. Drying or freezing caused increases in dissolved organic C, sugars and polyols, suggesting enhanced microbial production to alleviate temperature or moisture stress. Increased nucleobase concentration in the unplanted soil after a dry-wet cycle, and increased amino acids following both stresses, suggested a breakdown of microbial DNA and proteins released from damaged cells. The impacts of stress on metabolites in the planted soil were less than in the unplanted soil. In conclusion, our findings indicate that the soil microbial community responds quickly to stress events by accumulating osmotic solutes (e.g. sugars and polyols) and that a freeze-thaw event causes less disruption than dry-rewetting, and that plants have a key role in the mitigation of the freezing or drying effects on soil microbial communities.

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.

The uptake of different soil nitrogen (N) forms by co-existing plant species is ecologically crucial, but in situ studies conducted to investigate this phenomenon across forest ecosystems are still limited. Here, stable isotope tracer techniques (13C and 15N) were used in the field, examining the uptake of inorganic and organic N by co-existing plant species, plasticity in N preference, and difference in the N uptake between layers of forest in temperate and cold-temperate forests in northeast China. Amino acid-N composed an important part (29% avg.) in the pool of available soil N (inorganic N and amino acid-N). The vegetation could take up glycine-derived N (intact uptake from 48% to 99%). With variation in habitat, Betula platyphylla and Sphagnum palustre modified their competitive abilities for uptake of intact glycine and apparent N preferences, illustrating the plasticity in the N preferences of plants. Due to the plasticity, the co-existing species appeared to show various N preference strategies in these forests. Canopy trees took up more glycine-derived N than understory plants, and vice versa for the inorganic N, which may be related to differences in the intensity of photosynthesis. This study indicates that soil amino acids are a potentially important N source, and various choices for N nutrition may alleviate inter-species competition and contribute to species co-existence in forest ecosystems in northeast China. Plasticity in N preference could underlie N source partitioning among the co-existing species. With ongoing N deposition in these and many other forest ecosystems, this research helps to clarify how soil–plant N cycling varies between canopy layers and the feedbacks that are taking place.