Effects of temperatures near the freezing point on N2O emissions, denitrification and on the abundance and structure of nitrifying and denitrifying soil communities

How does microorganism in different zones cooperatively promote N2O emissions from SWIS during freeze-thaw?

Subsurface wastewater infiltration systems (SWIS) are environmentally-friendly technologies for domestic wastewater treatment, where pollutants are removed by physical, chemical and biological reactions. However, SWIS also produce nitrous oxide (N2O), a potent greenhouse gas. Distribution of dissolved oxygen and nitrogen in SWIS determines denitrification process, which affects microbial activity and N2O release degree in different layers of system. Top layer of SWIS substrate is exposed to environmental factors such as freeze-thaw (FT), which changes microbial community structure in different substrates. Exact mechanisms of microbial-mediated N2O emissions in SWIS are still unclear despite extensive research. Therefore, this study simulated FT process using in-situ SWIS, to investigate how FT disturbance affects microbial community structure and N2O release in SWIS profiles. Results showed that after the ninth freeze-thaw cycle, FT stimulated anaerobic bacteria activities such as Euryarchaeota, accounting for 78.4 % of total Euryarchaeota population in middle (60 cm) and 33.97 % in the lower layer. Under low oxygen conditions, NO2--N accumulation in middle and lower layers provided a sufficient nitrogen source for Euryarchaeota. Canonical correlation analysis (CCA) showed Euryarchaeota was significantly correlated with N2O emissions in middle and lower layers during FT, contributing 31.68 %-32.01 % and 61.78 %-65.15 %, respectively. These results suggested that FT disturbance enhanced denitrification by anaerobic bacteria in middle and lower layers of SWIS, significantly increasing N2O emissions. However, specific pathways and mechanisms of N2O production by Euryarchaeota remain to be elucidated in future studies.

Metagenomics reveals taxon-specific responses of soil nitrogen cycling under different fertilization regimes in heavy metal contaminated soil

Soil deficiency, cyclic erosion, and heavy metal pollution have led to fertility loss and ecological function decline in mining areas. Fertilization is an important way to rapidly replenish soil nutrients, which have a major influence on the soil nitrogen cycling process, but different fertilization regimes have different impacts on soil properties and microbial functional potentials. Here, metagenomic sequencing was used to investigate the different responses of key functional genes of microbial nitrogen cycling to fertilization regimes and explore the potential effects of soil physicochemical properties on the key functional genes. The results indicated that AC-HH (ammonium chloride-high frequency and concentration) treatment significantly increased the gene abundance of norC (13.40-fold), nirK (5.46-fold), and napA (5.37-fold). U-HH (urea-high frequency and concentration) treatment significantly increased the gene abundance of hao (6.24-fold), pmoA-amoA (4.32-fold) norC (7.00-fold), nosZ (3.69-fold), and nirK (6.88-fold). Functional genes were distributed differently among the 10 dominant phyla. The nifH and nifK genes were distributed only in Proteobacteria. The hao gene was distributed in Gemmatimonadetes, Nitrospirae and Proteobacteria. Fertilization regimes caused changes in functional redundancy in soil, and nirK and nirB, which are involved in denitrification, were present in different genera. Fertilization regimes with high frequency and high concentration were more likely to increase the gene abundance at the genus level. In summary, this study provides insights into the taxon-specific response of soil nitrogen cycling under different fertilization regimes, where changes in fertilization regimes affect microbial nitrogen cycling by altering soil physicochemical properties in a complex dynamic environment.

Effect of nitrification inhibitor (DMPP) on nitrous oxide emissions from agricultural fields: Automated and manual measurements

Nitrogen fertilisation contributes significantly to the atmospheric increase of nitrous oxide (N₂O). Application of nitrification inhibitors (NIs) is a promising strategy to mitigate N₂O emissions and improve N-use efficiency in agricultural systems. This study investigated the effect of NI, 3,4-dimethylpyrazol phosphate (DMPP) on N₂O mitigation from spring barley and spring oilseed rape. Manual and automatic chamber methodologies were used to capture spatial and temporal variability in N₂O emissions. In a second experiment, we study the effect of N fertiliser levels without NI (0 %, 50 %, 100 %, 150 % and 200 % of recommended amount of N fertiliser), as well as 100 % of N with NI on N₂O emissions in spring barley. The automated chamber measurements showed dynamics of N₂O changes throughout the season, including positive and negative peaks that were unobservable with manual chambers due to low temporal resolution. Although not significant, application of NI tended to reduce N₂O emissions. The reduction was on average 16 % in spring barley and 58 % in spring oilseed rape in manual chamber measurements. However, N₂O reduction was 108 % in continuous automatic chamber measurements in spring barley. The N₂O EFs for the growing season were very low (0.025 % to 0.148 %), with a greater reduction in EF in spring oilseed rape (76 %) than in spring barley (32 %) with NI application. A positive correlation (R = 80 %) was observed between N fertiliser levels and N₂O emissions. Crop yield and crop N uptake were not significantly affected by the use of NI. This study highlighted that NI can reduce N₂O emissions, but the reduction effects are plot, crop and microclimate specific. Long-term experiments with continuous plot-scale measurements are needed to capture and optimise N₂O mitigation effect of NIs across wide variability in soils and microclimates in agroecosystems.

Contribution of the nongrowing season to annual N2O emissions from the permafrost wetland in Northeast China

Permafrost regions store large amounts of soil organic carbon and nitrogen, which are major sources of greenhouse gas. With climate warming, permafrost is thawing and releasing an abundance of greenhouse gases into the atmosphere and contributing to climate warming. Numerous studies have shown the mechanism of nitrous oxide (N₂O) emissions from the permafrost region during the growing season. However, little is known about the temporal pattern and drivers of nongrowing season N₂O emissions from the permafrost region. In this study, N₂O emissions from the permafrost region were investigated from June 2016 to June 2018 using the static opaque chamber method. We aimed to quantify the seasonal dynamics of nongrowing season N₂O emissions and their contribution to the annual budget. The results showed that the N₂O emissions ranged from - 35.75 to 74.16 μg m^-2 h^-1 with 0.89 to 1.44 kg ha^-1 being released into the atmosphere during the nongrowing season in the permafrost region. The permafrost wetland types had no significant influence on the nongrowing season N₂O emissions due to the nitrate content. The cumulative N₂O emissions during the nongrowing season contributed to 41.96-53.73% of the annual budget, accounting for almost half of the annual emissions in the permafrost region. The driving factors of N₂O emissions were different among the nongrowing season, growing season, and entire period. The N₂O emissions from the nongrowing season and total 2-year observation period were mainly affected by soil temperature, which could explain 3.01-9.54% and 6.07-14.48% of the temporal variation in N₂O emissions, respectively. In contrast, the N₂O emissions from the growing season were controlled by soil temperature, water table level, pH, NH₄⁺-N, NO₃^--N, total nitrogen, total organic carbon, and C/N ratio, which could explain 14.51-45.72% of the temporal variation of N₂O emissions. Nongrowing season N₂O emissions are an essential component of annual emissions and cannot be ignored in the permafrost region.

Roots and other residues from leys with or without red clover: Quality and effects on N2O emission factors in a partly frozen soil following autumn ploughing

Revised IPCC guidelines assume that a constant share of N in decomposing crop residues is directly emitted as N₂O (emission factor: EF_N2O), and calculate the amount of nitrogen (N) in non-removable residues of temporary grasslands proportionally to the average annual herbage yield. However, EF_N2O depends on the intrinsic quality of the residues and their interactions with environmental conditions. Only a few field studies on N₂O emissions from grassland renewal are available, and none have simultaneously quantified the N amount and quality of non-removable residues (roots and stubble). To gain insight into the effect of non-removable residue quality on EF_N2O, we studied the amount and quality of roots and stubble and their effect on EF_N2O following the ploughing of three-year-old swards. The measured amount of N in non-removable residues was approximately 20, 25, and 31 kg N per 1 Mg average annual dry matter yield in grass, red clover-grass, and red clover, and 70-83% of it was below ground. However, the EF_N2O of non-removable residues measured over 252 days was lower (0.24%, SE = 14% for grass and red clover-grass) than the IPCC default value (0.6%, CV: 50%) for wet regions, although within the uncertainty margin, and was significantly lower than the EF_N2O of incorporated herbage, which was related to differences in EF_CO2. We advocate for more specific studies that separate the effects of belowground and aboveground residues (AGR), considering the possibility of simplifying the accounting of N₂O emissions from belowground residues while improving that of non-removable AGR from temporary grasslands and other green crops. We observed the accumulation of N₂O in the frozen soil under snow, which was released during diurnal percolation of meltwater. N₂O emissions from frozen soil accounted for 30% or more of the total emissions.

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N₂O), a potent greenhouse gas.

How could simulated dewatering of slurry mitigate nitrous oxide emissions from fall and spring injections? - A modelling study in a Chernozem soil in Western Canada

Process-based ecosystem models, such as ecosys, can be useful tools to gain insights and accurately project nitrous oxide (N₂O) inventories in national, regional and global scales, and to explore potential emission reduction strategies. Our objectives are to investigate how the ecosys model simulate the effects of fall and spring slurry injections on N₂O production and if de-watering slurry could become a potential N₂O mitigation strategy for both fall and spring injections. The ecosys model was used to simulate hourly N₂O fluxes from 2014 to 2017 in a cropping system with and without slurry (fall and spring additions) in comparison with field measurements in Alberta, Canada. Furthermore, we performed simulations of de-watered fall and spring slurry applications in the same scenarios. Our results showed ecosys adequately simulated soil temperatures and moisture contents at 10 and 20 cm depths [correlation coefficients (r) ≥ 0.929 for temperatures; r ≥ 0.529 for moistures]. The divergences of modelled and measured soil water contents during spring thaws could be attributed to uncertainties in model inputs for soil hydrological parameters as well as uncertainties in field measurements. The model captured reasonably well the dynamics of N₂O fluxes from soils receiving fall and spring slurry (r = 0.356). However, the concurrent discrepancies of N₂O fluxes between modelled and measured values during the wetter spring thaw of 2017 might be a result of an unsatisfactory simulation of snowmelt infiltration and runoff. Compared to whole slurry, simulated de-watered slurry resulted in considerable reductions in cumulative N₂O emissions by 16-36 and 23-29% for fall and spring slurry injections, respectively. The model results indicate that de-watering slurry would potentially be an efficient emission mitigation strategy; however, there is still a paucity of studies addressing the feasibility of dewatering as a practice and further research can focus on this knowledge gap.

Warming Shapes nirS- and nosZ-Type Denitrifier Communities and Stimulates N2O Emission in Acidic Paddy Soil

Warming strongly stimulates soil nitrous oxide (N2O) emission, contributing to the global warming trend. Submerged paddy soils exhibit huge N2O emission potential; however, the N2O emission pathway and underlying mechanisms for warming are not clearly understood. We conducted an incubation experiment using 15N to investigate the dynamics of N2O emission at controlled temperatures (5, 15, 25, and 35°C) in 125% water-filled pore space. The community structures of nitrifiers and denitrifiers were determined via high-throughput sequencing of functional genes. Our results showed that elevated temperature sharply enhanced soil N2O emission from submerged paddy soil. Denitrification was the main contributor, accounting for more than 90% of total N2O emission at all treatment temperatures. N2O flux was coordinatively regulated by nirK-, nirS-, and nosZ-containing denitrifiers but not ammonia-oxidizing archaea or ammonia-oxidizing bacteria. The nirS-containing denitrifiers were more sensitive to temperature shifts, especially at a lower temperature range (5 to 25°C), and showed a stronger correlation with N2O flux than that of nirK-containing denitrifiers. In contrast, nosZ-containing denitrifiers exhibited substantial variation at higher temperatures (15 to 35°C), thereby playing an important role in N2O consumption. Certain taxa of nirS- and nosZ-containing denitrifiers regulated N2O flux, including nirS-containing denitrifiers affiliated with Rhodanobacter and Cupriavidus as well as nosZ-containing denitrifiers affiliated with Azoarcus and Azospirillum. Together, these findings suggest that elevated temperature can significantly increase N2O emission from denitrification in submerged paddy soils by shifting the overall community structures and enriching some indigenous taxa of nirS- and nosZ-containing denitrifiers. IMPORTANCE The interdependence between global warming and greenhouse gas N2O has always been the hot spot. However, information on factors contributing to N2O and temperature-dependent community structure changes is scarce. This study demonstrated high-temperature-induced N2O emission from submerged paddy soils, mainly via stimulating denitrification. Further, we speculate that key functional denitrifiers drive N2O emission. This study showed that denitrifiers were more sensitive to temperature rise than nitrifiers, and the temperature sensitivity differed among denitrifier communities. N2O-consuming denitrifiers (nosZ-containing denitrifiers) were more sensitive at a higher temperature range than N2O-producing denitrifiers (nirS-containing denitrifiers). This study's findings help predict N2O fluxes under different degrees of warming and develop strategies to mitigate N2O emissions from paddy fields based on microbial community regulation.

Depression of Groundwater Table and Reduced Nitrogen Application Jointly Regulate the Bacterial Composition of nirS-Type and nirK-Type Genes in Agricultural Soil

Despite the known influence of nitrogen fertilization and groundwater conditions on soil microbial communities, the effects of their interactions on bacterial composition of denitrifier communities have been rarely quantified. Therefore, a large lysimeter experiment was conducted to examine how and to what extent groundwater table changes and reduced nitrogen application would influence the bacterial composition of nirK-type and nirS-type genes. The bacterial composition of nirK-type and nirS-type genes were compared at two levels of N input and three groundwater table levels. Our results demonstrated that depression of groundwater table, reduced nitrogen application and their interactions would lead to drastic shifts in the bacterial composition of nirS-type and nirK-type genes. Structural equation models (SEMs) indicated that depression of groundwater table and reduced nitrogen application not only directly altered the species composition of denitrifier bacterial communities, but also indirectly influenced them through regulating soil nutrient and salinity. Furthermore, the variation in soil NO3−–N and electrical conductivity caused by depression of groundwater table and reduced nitrogen application played the most important role in altering the community composition of denitrifier bacterial communities. Together, our findings provide first-hand evidence that depression of groundwater table and reduced nitrogen application jointly regulate the species composition of denitrifier bacterial communities in agricultural soil. We highlight that local environmental conditions such as groundwater table and soil attributes should be taken into account to enrich our knowledge of the impact of nitrogen fertilization on soil denitrifier bacterial communities, or even biogeochemical cycles.

Comparison of Soil Greenhouse Gas Fluxes during the Spring Freeze–Thaw Period and the Growing Season in a Temperate Broadleaved Korean Pine Forest, Changbai Mountains, China

Soils in mid-high latitudes are under the great impact of freeze–thaw cycling. However, insufficient research on soil CO2, CH4, and N2O fluxes during the spring freeze–thaw (SFT) period has led to great uncertainties in estimating soil greenhouse gas (GHG) fluxes. The present study was conducted in a temperate broad-leaved Korean pine mixed forest in Northeastern China, where soils experience an apparent freeze–thaw effect in spring. The temporal variations and impact factors of soil GHG fluxes were measured during the SFT period and growing season (GS) using the static-chamber method. The results show that the soil acted as a source of atmospheric CO2 and N2O and a sink of atmospheric CH4 during the whole observation period. Soil CO2 emission and CH4 uptake were lower during the SFT period than those during the GS, whereas N2O emissions were more than six times higher during the SFT period than that during the GS. The responses of soil GHG fluxes to soil temperature (Ts) and soil moisture during the SFT and GS periods differed. During the SFT period, soil CO2 and CH4 fluxes were mainly affected by the volumetric water content (VWC) and Ts, respectively, whereas soil N2O flux was influenced jointly by Ts and VWC. The dominant controlling factor for CO2 was Ts during the GS, whereas CH4 and N2O were mainly regulated by VWC. Soil CO2 and N2O fluxes accounted for 97.3% and 3.1% of the total 100-year global warming potential (GWP100) respectively, with CH4 flux offsetting 0.4% of the total GWP100. The results highlight the importance of environmental variations to soil N2O pulse during the SFT period and the difference of soil GHG fluxes between the SFT and GS periods, which contribute to predicting the forest soil GHG fluxes and their global warming potential under global climate change.

Effects of short-term freezing on nitrous oxide emissions and enzyme activities in a grazed pasture soil after bovine-urine application

Nitrous oxide (N₂O) emissions from soils applied with livestock excreta have been widely reported previously. The highest N₂O emissions from soils are also often reported during thawing periods in cold regions where soil freezing is common. However, the combined effects of cow urine application and freeze-thaw events on N₂O emissions and the related enzyme activities are still not clear. Thus, we simulated a freeze-thaw event at -3 °C for 7 days, and then increased to 3 °C for 46 days using intact soil cores with cow urine (392 kg N ha^-1). We compared the factors influencing the magnitudes of N₂O emissions through soil microbial processes with and without the freeze-thaw event. Dicyandiamide (DCD), an inhibitor of nitrification, was added to investigate the significance of nitrification on N₂O emissions. The N₂O emission rates from the urine-applied soils peaked to approximately 1000 μg N₂O-N m^-2 h^-1 immediately after the soils thawed. Soil freezing with urine application was significantly higher cumulative N₂O emissions (537 mg N₂O-N m^-2), compared to non-frozen soils with urine (247 mg N₂O-N m^-2) during the incubation period (54 days). The effect of DCD application on N₂O emissions was not clear during the freeze-thaw event, although nitrate production rates were reduced. After the freezing event, soil moisture (water-filled pore space) was significantly higher in the non-frozen soils compared to the frozen soils, due to a 9% decline in bulk density of frozen soils. Additionally, the impact of thawing on urease and denitrification enzyme activities was influenced by the urine application. Urine application increased the urease activity, while the freezing event decreased the magnitudes. The physical changes in the soils were also important controlling factors of the N₂O emissions from cow urine-applied soils in cold regions.

Effect of increasing precipitation and warming on microbial community in Tibetan alpine steppe

Soil microorganisms play an important role in regulating the feedback of Alpine steppe ecosystems to future climate change. However, the interaction effect of warming and increasing precipitation on soil microorganisms remains unclear, in the face of an ongoing warmer and wetter climate on the Tibetan Plateau. In this study, we investigate the multi-factorial effects on soil microbial diversity, community structure, and microbial interactions in a three-year climate change experiment established in an Alpine steppe on the Tibetan Plateau, involving warming (+2 °C), +15% increasing precipitation and +30% increasing precipitation. Compared to warming, warming plus increasing precipitation alleviated the decrease in microbial diversity, and increased the dissimilarities in microbial community structures, largely influenced by water and substrate availability. We further observed differences in moisture increased the differences in microbial diversity and dissimilarities in microbial community structures across different precipitation levels under ambient temperature. Interestingly, warming plus increasing precipitation could create more ecological niches for microbial species to coexist but may lessen the strength of microbial interactions in contrast to increasing precipitation alone. Collectively, our findings indicate that microbial responses to future climate change in Alpine steppe soils will be more complex than those under single-climate-factor conditions.

Development of droplet digital PCR assays to quantify genes involved in nitrification and denitrification, comparison with quantitative real-time PCR and validation of assays in vineyard soil

Quantifying genes in soil is important to relate the abundance of soil bacteria to biogeochemical cycles. Quantitative real-time PCR is widely used for quantification, but its use with environmental samples is limited by poor reaction efficiencies or by PCR inhibition through co-purified soil substances. Droplet digital PCR (ddPCR) is a technology for absolute, sensitive quantification of genes. This study optimized eight ddPCR assays to quantify total bacteria and archaea as well as the nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide. Detection and quantification thresholds were compared with those of quantitative real-time PCR and were equal to, or improved, in ddPCR. To validate the assays using environmental samples, soil DNA was isolated from two vineyards in the Okanagan valley in British Columbia, Canada, over the 2017 growing season. Soil properties related to the observed gene abundances were determined. Total bacteria, nirK, and nosZII increased with time and the soil C/N ratio and NH₄⁺-N concentration affected total archaea and archaeal amoA negatively. The results, compared with those of other studies, showed that ddPCR is a valid alternative to qPCR to quantify genes involved in nitrification or denitrification.

Linking changes in snow cover with microbial nitrogen cycling functional gene abundance and expression in agricultural soil

In eastern Canada, climate change-related warming and increased precipitation may alter winter snow cover, with potential consequences for soil conditions, nitrogen (N) cycling, and microbes. We conducted a 2-year field study aimed at determining the influence of snow removal, snow accumulation, and ambient snow in a potato-barley crop system on the abundance and expression of denitrifier (nirS, nirK, nosZ) and nitrifier (ammonium oxidizing archaeal (AOA) and bacterial (AOB) amoA) genes. Denitrifier and nitrifier abundance and expression results were compared to N2O production, soil atmosphere accumulation, and surface fluxes. In the first winter, nirK abundance was lowest while AOB abundance was greatest in snow accumulation treatments. In the second winter, greatest abundances were observed in the ambient snow treatment, which had greatest N2O accumulation and spring thaw fluxes, suggesting a link between microbial populations and biogeochemical functioning. Treatment effects on gene expression were limited, but greatest AOA, AOB, and nosZ expression was measured near 0°C and above 15°C, indicating that activity was promoted by freeze-thaw conditions and at summer temperatures. Overall, effects of changing snow depth on denitrifier and nitrifier abundance were not solely due to change in soil temperature, but also to soil moisture and/or interactions between these parameters.

The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle

Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N₂O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.

Presence of spring-thaw N2O emissions are not linked to functional gene abundance in a drip-fertigated cropped soil in arid northwestern China

Spring-thaw represents a significant source for nitrous oxide (N₂O) emissions from fertilized croplands in temperate regions. In this study, we present surface N₂O fluxes, soil-profile N₂O concentrations at 5, 15, 30 and 60 cm depths along with the abundance of nitrifiers and denitrifiers over the winter and spring-thaw periods in an arid, drip- fertigated cotton field, which had received spring application of 240 kg N ha^-1 as urea alone (Urea), polymer-coated urea (ESN), and urea plus urease and nitrification inhibitors. Nitrous oxide emissions from December to April were generally unaffected by fertilizer treatments with a cumulative average of 186 g N ha^-1, accounting for 39% of the annual N₂O emissions. Emission peaks occurred at spring-thaw and coincided with increasing soil-profile N₂O concentrations at all depths, suggesting the burst in N₂O fluxes was due to new N₂O production, rather than a physical release of N₂O trapped in the soil profiles over winter. The abundance of nitrifier and denitrifier genes changed over the winter and spring-thaw periods but was not affected by fertilizer treatments from the previous spring, suggesting the abundance of N₂O-producing microorganism was more controlled by environmental conditions than N sources applied in the previous spring. The daily N₂O flux rate from December to April was positively correlated with soil temperature, water-filled pore space, and denitrifying enzyme activity, but not with the gene copy number of AOA, AOB, narG, nirS, nirK and nosZ, indicating that variation in the abundance of these genes was not contributing to the N₂O emissions. These results suggest that N₂O emissions in spring-thaw are substantial for drip-fertigated croplands in the arid regions and should be considered in the annual budgets. The environmental factors such as soil temperature and moisture are likely more important than the copy-numbers of N₂O-producing functional genes in driving the variability in spring-thaw emissions.

Niche Separation of Ammonia Oxidizers in Mudflat and Agricultural Soils Along the Yangtze River, China

Nitrification driven by ammonia oxidizers is a key step of nitrogen removal in estuarine environments. Spatial distribution characteristics of ammonia-oxidizers have been well understood in mudflats, but less studied in the agricultural soils next to mudflats, which also play an important role in nitrogen cycling of the estuarine ecosystem. In the present research, we investigated ammonia oxidizers' distributions along the Yangtze River estuary in Jiangsu Province, China, sampling soils right next to the estuary (mudflats) and the agricultural soils 100 m away. We determined the relationship between the abundance of amoA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and the potential nitrification rates of the mudflats and agricultural soils. We also identified the environmental variables that correlated with the composition of the ammonia oxidizers' communities by 16S rRNA gene pyrosequencing. Results indicated that agricultural soils have significantly higher potential nitrification rates as well as the AOA abundance, and resulted in strong phylogenetic clustering only in AOA communities. The ammonia oxidizers' community compositions differed dramatically among the mudflat and agricultural sites, and stochasticity played a dominant role. The AOA communities were dominated by the Group 1.1a cluster at the mudflat, whereas the 54D9 and 29i4 clusters were dominant in agriculture soils. The dominant AOB communities in the mudflat were closely related to the Nitrosospira lineage, whereas the agricultural soils were dominated by the Nitrosomonas lineage. Soil organic matter and salinity were correlated with the ammonia oxidizers' community compositions.

Contrasting Warming and Ozone Effects on Denitrifiers Dominate Soil N2O Emissions

Nitrous oxide (N₂O) in the atmosphere is a major greenhouse gas and reacts with volatile organic compounds to create ozone (an air pollutant) in the troposphere. Climate change factors such as warming and elevated ozone (eO₃) affect N₂O fluxes, but the direction and magnitude of these effects are uncertain and the underlying mechanisms remain unclear. We examined the impact of simulated warming (control + 3.6 °C) and eO₃ (control + 45 ppb) on soil N₂O fluxes in a soybean agroecosystem. Results obtained showed that warming significantly increased soil labile C, microbial biomass, and soil N mineralization, but eO₃ reduced these parameters. Warming enhanced N₂O-producing denitrifers ( nirS- and nirK-type), corresponding to increases in both the rate and sum of N₂O emissions. In contrast, eO₃ significantly reduced both N₂O-producing and N₂O-consuming ( nosZ-type) denitrifiers but had no impact on N₂O emissions. Further, eO₃ offsets the effects of warming on soil labile C, microbial biomass, and the population size of denitrifiers but still increased N₂O emissions, indicating a direct effect of temperature on N₂O emissions. Together, these findings suggest that warming may promote N₂O production through increasing both the abundance and activities of N₂O-producing microbes, positively feeding back to the ongoing climate change.

A urine-fuelled soil-based bioregenerative life support system for long-term and long-distance manned space missions

A soil-based cropping unit fuelled with human urine for long-term manned space missions was investigated with the aim to analyze whether a closed-loop nutrient cycle from human liquid wastes was achievable. Its ecohydrology and biogeochemistry were analysed in microgravity with the use of an advanced computational tool. Urine from the crew was used to supply primary (N, P, and K) and secondary (S, Ca and Mg) nutrients to wheat and soybean plants in the controlled cropping unit. Breakdown of urine compounds into primary and secondary nutrients as well as byproduct gases, adsorbed, and uptake fractions were tracked over a period of 20 years. Results suggested that human urine could satisfy the demand of at least 3 to 4 out of 6 nutrients with an offset in pH and salinity tolerable by plants. It was therefore inferred that a urine-fuelled life support system can introduce a number of advantages including: (1) recycling of liquids wastes and production of food; (2) forgiveness of neglect as compared to engineered electro-mechanical systems that may fail under unexpected or unplanned conditions; and (3) reduction of supply and waste loads during space missions.

Greenhouse gas fluxes over managed grasslands in Central Europe

Central European grasslands are characterized by a wide range of different management practices in close geographical proximity. Site-specific management strategies strongly affect the biosphere-atmosphere exchange of the three greenhouse gases (GHG) carbon dioxide (CO₂ ), nitrous oxide (N₂ O), and methane (CH₄ ). The evaluation of environmental impacts at site level is challenging, because most in situ measurements focus on the quantification of CO₂ exchange, while long-term N₂ O and CH₄ flux measurements at ecosystem scale remain scarce. Here, we synthesized ecosystem CO₂ , N₂ O, and CH₄ fluxes from 14 managed grassland sites, quantified by eddy covariance or chamber techniques. We found that grasslands were on average a CO₂ sink (-1,783 to -91 g CO₂  m^-2  year^-1 ), but a N₂ O source (18-638 g CO₂ -eq. m^-2  year^-1 ), and either a CH₄ sink or source (-9 to 488 g CO₂ -eq. m^-2  year^-1 ). The net GHG balance (NGB) of nine sites where measurements of all three GHGs were available was found between -2,761 and -58 g CO₂ -eq. m^-2  year^-1 , with N₂ O and CH₄ emissions offsetting concurrent CO₂ uptake by on average 21 ± 6% across sites. The only positive NGB was found for one site during a restoration year with ploughing. The predictive power of soil parameters for N₂ O and CH₄ fluxes was generally low and varied considerably within years. However, after site-specific data normalization, we identified environmental conditions that indicated enhanced GHG source/sink activity ("sweet spots") and gave a good prediction of normalized overall fluxes across sites. The application of animal slurry to grasslands increased N₂ O and CH₄ emissions. The N₂ O-N emission factor across sites was 1.8 ± 0.5%, but varied considerably at site level among the years (0.1%-8.6%). Although grassland management led to increased N₂ O and CH₄ emissions, the CO₂ sink strength was generally the most dominant component of the annual GHG budget.

In-situ atrazine biodegradation dynamics in wheat (Triticum) crops under variable hydrologic regime

A comprehensive biodegradation reaction network of atrazine (ATZ) and its 18 byproducts was coupled to the nitrogen cycle and integrated in a computational solver to assess the in-situ biodegradation effectiveness and leaching along a 5m deep soil cultivated with wheat in West Wyalong, New South Wales, Australia. Biodegradation removed 97.7% of 2kg/ha ATZ yearly applications in the root zone, but removal substantially decreased at increasing depths; dechlorination removed 79% of ATZ in aerobic conditions and 18% in anaerobic conditions, whereas deethylation and oxidation removed only 0.11% and 0.15% of ATZ, respectively. The residual Cl mass fraction in ATZ and 4 byproducts was 2.4% of the applied mass. ATZ half-life ranged from 150 to 247days in the soil surface. ATZ reached 5m soil depth within 200years and its concentration increased from 1×10^-6 to 4×10^-6mg/kg_dry-soil over time. The correlation between ATZ specific biomass degradation affinity Φ₀ and half-life t_1/2, although relatively uncertain for both hydrolyzing and oxidizing bacteria, suggested that microorganisms with high Φ₀ led to low ATZ t_1/2. Greater ATZ applications were balanced by small nonlinear increments of ATZ biodegraded fraction within the root zone and therefore less ATZ leached into the shallow aquifer.

Abnormal pH elevation in the Chaobai River, a reclaimed water intake area

The pH is a primary index reflecting water quality in rivers. The Jian River and Chaobai River are two reclaimed water intake areas which have elevated pH. This elevated pH has a marked effect on both the phytoplankton, species in water and vegetation on the shore. Understanding the main reasons causing pH elevation in river water has important implications for river ecosystem management and the improvement of water quality and can provide a theoretical basis for the direction of water quality improvement. For this reason, each biogeochemical and physical process influencing pH changes in water was quantified along the flow direction in the Wenyu to Chaobai reclaimed water diversion project, in which proton consumption and production by such processes were monitored and calculated at five monitoring sections. The calculations indicated that photosynthesis and denitrification were the primary reasons for the increase of pH in the Jian River and Chaobai River. Oppositely, carbonate precipitation and sediment decomposition restricted the increase of pH in both rivers. In addition, CO₂ emission to the air also promoted a increase of pH in the Jian River, while CO₂ absorption from the air restricted the increase of pH in the Chaobai River. NO₃^- nitrogen in reclaimed water was not efficiently removed and the reclaimed water flow condition in the intake area created favorable conditions for photosynthesis of algae breeding and denitrification by microorganisms. Therefore, biogeochemical and physical processes that promoted the increase of pH were greater than inhibiting processes and the pH gradually increased along the flow direction. The contribution rates of photosynthesis and denitrification for the increase of pH were 55.48 and 27.09%, respectively, in the Jian River and 78.08 and 21.92%, respectively, in the Chaobai River. In addition, CO₂ emission contributed 17.43% of the increase in pH in the Jian River.

Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment

Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.

Climate change amplifies gross nitrogen turnover in montane grasslands of Central Europe in both summer and winter seasons

The carbon- and nitrogen-rich soils of montane grasslands are exposed to above-average warming and to altered precipitation patterns as a result of global change. To investigate the consequences of climatic change for soil nitrogen turnover, we translocated intact plant-soil mesocosms along an elevational gradient, resulting in an increase of the mean annual temperature by approx. 2 °C while decreasing precipitation from approx. 1500 to 1000 mm. Following three years of equilibration, we monitored the dynamics of gross nitrogen turnover and ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soils over an entire year. Gross nitrogen turnover and gene levels of AOB and AOA showed pronounced seasonal dynamics. Both summer and winter periods equally contributed to cumulative annual N turnover. However, highest gross N turnover and abundance of ammonia oxidizers were observed in frozen soil of the climate change site, likely due to physical liberation of organic substrates and their rapid turnover in the unfrozen soil water film. This effect was not observed at the control site, where soil freezing did not occur due to a significant insulating snowpack. Climate change conditions accelerated gross nitrogen mineralization by 250% on average. Increased N mineralization significantly stimulated gross nitrification by AOB rather than by AOA. However, climate change impacts were restricted to the 2-6 cm topsoil and rarely occurred at 12-16 cm depth, where generally much lower N turnover was observed. Our study shows that significant mineralization pulses occur under changing climate, which is likely to result in soil organic matter losses with their associated negative impacts on key soil functions. We also show that N cycling processes in frozen soil can be hot moments for N turnover and thus are of paramount importance for understanding seasonal patterns, annual sum of N turnover and possible climate change feedbacks.

The subzero microbiome: microbial activity in frozen and thawing soils

Most of the Earth's biosphere is characterized by low temperatures (<5°C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and, in particular, thawing of frozen soils are not yet well understood, although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change.

Methane and nitrous oxide exchange over a managed hay meadow

The methane (CH4) and nitrous oxide (N2O) exchange of a temperate mountain grassland near Neustift, Austria, was measured during 2010-2012 over a time period of 22 months using the eddy covariance method. Exchange rates of both compounds at the site were low, with 97% of all half-hourly CH4 and N2O fluxes ranging between ±200 and ±50 ng m-2 s-1, respectively. The meadow acted as a sink for both compounds during certain time periods, but was a clear source of CH4 and N2O on an annual timescale. Therefore, both gases contributed to an increase of the global warming potential (GWP), effectively reducing the sink strength in terms of CO2 equivalents of the investigated grassland site. In 2011, our best guess estimate showed a net greenhouse gas (GHG) sink of -32 g CO2 equ. m-2 yr-1 for the meadow, whereby 55% of the CO2 sink strength of -71 g CO2m-2 yr-1 was offset by CH4 (N2O) emissions of 7 (32) g CO2 equ. m-2 yr-1. When all data were pooled, the ancillary parameters explained 27 (42)% of observed CH4 (N2O) flux variability, and up to 62 (76)% on shorter timescales in-between management dates. In the case of N2O fluxes, we found the highest emissions at intermediate soil water contents and at soil temperatures close to 0 or above 14 °C. In comparison to CO2, H2O and energy fluxes, the interpretation of CH4 and N2O exchange was challenging due to footprint heterogeneity regarding their sources and sinks, uncertainties regarding post-processing and quality control. Our results emphasize that CH4 and N2O fluxes over supposedly well-aerated and moderately fertilized soils cannot be neglected when evaluating the GHG impact of temperate managed grasslands.