Imprint of denitrifying bacteria on the global terrestrial biosphere

Biochar and peat amendments affect nitrogen retention, microbial capacity and nitrogen cycling microbial communities in a metal and polycyclic aromatic hydrocarbon contaminated urban soil

Soil contaminants may restrict soil functions. A promising soil remediation method is amendment with biochar, which has the potential to both adsorb contaminants and improve soil health. However, effects of biochar amendment on soil-plant nitrogen (N) dynamics and N cycling microbial guilds in contaminated soils are still poorly understood. Here, a metal- and polycyclic aromatic hydrocarbon (PAH) contaminated soil was amended with either biochar (0, 3, 6 % w/w) and/or peat (0, 1.5, 3 % w/w) in a full-factorial design and sown with perennial ryegrass in an outdoor field trial. After three months, N and the stable isotopic ratio δ15N was measured in soil, roots and leaves, along with microbial responses. Aboveground grass biomass decreased by 30 % and leaf N content by 20 % with biochar, while peat alone had no effect. Peat in particular, but also biochar, stimulated the abundance of microorganisms (measured as 16S rRNA gene copy number) and basal respiration. Microbial substrate utilization (MicroResp™) was altered differentially, as peat increased respiration of all carbon sources, while for biochar, respiration of carboxylic acids increased, sugars decreased, and was unaffected for amino acids. Biochar increased the abundance of ammonia oxidizing archaea, while peat stimulated ammonia oxidizing bacteria, Nitrobacter-type nitrite oxidizers and comB-type complete ammonia oxidizers. Biochar and peat also increased nitrous oxide reducing communities (nosZI and nosZII), while peat alone or combined with biochar also increased abundance of nirK-type denitrifiers. However, biochar and peat lowered leaf δ15N by 2-4 ‰, indicating that processes causing gaseous N losses, like denitrification and ammonia volatilization, were reduced compared to the untreated contaminated soil, probably an effect of biotic N immobilization. Overall, this study shows that in addition to contaminant stabilization, amendment with biochar and peat can increase N retention while improving microbial capacity to perform important soil functions.

Protists play important roles in the assembly and stability of denitrifying bacterial communities in copper-tailings drainage

Unraveling the drivers controlling the assembly and stability of functional communities is a central issue in ecology. Despite extensive research and data, relatively little attention has been paid on the importance of biotic factors and, in particular, on the trophic interaction for explaining the assembly of microbial community. Here, we examined the diversity, assembly, and stability of nirS-, nirK-, and nosZ-type denitrifying bacterial communities in copper-tailings drainages of the Shibahe tailings reservoir in Zhongtiao Mountain, China's. We found that components of nirS-, nirK-, and nosZ-type denitrifying bacterial community diversity, such as taxon relative abundance, richness, and copy number, were strongly correlated with protist community composition and diversity. Assembly of the nirK-type denitrifying bacterial community was governed by dispersal limitation, whereas those of nirS- and nosZ-type communities were controlled by homogeneous selection. The relative importance of protist diversity in the assembly of nirK- and nosZ-type denitrifying bacterial communities was greater than that in nirS-type assembly. In addition, protists reduced the stability of the co-occurrence network of the nosZ-type denitrifying bacterial community. Compared with eukaryotic algae, protozoa had a greater impact on the stability of denitrifying bacterial community co-occurrence networks. Generally, protists affected the assembly and community stability of denitrifying bacteria in copper-tailings drainages. Our findings thus emphasize the importance of protists on affecting the assembly and community stability of denitrifying bacteria in copper-tailings drainages and may be useful for predicting changes in the ecological functions of microorganisms.

Modeling denitrification nitrogen losses in China's rice fields based on multiscale field-experiment constraints

Denitrification plays a critical role in soil nitrogen (N) cycling, affecting N availability in agroecosystems. However, the challenges in direct measurement of denitrification products (NO, N2 O, and N2 ) hinder our understanding of denitrification N losses patterns across the spatial scale. To address this gap, we constructed a data-model fusion method to map the county-scale denitrification N losses from China's rice fields over the past decade. The estimated denitrification N losses as a percentage of N application from 2009 to 2018 were 11.8 ± 4.0% for single rice, 12.4 ± 3.7% for early rice, and 11.6 ± 3.1% for late rice. The model results showed that the spatial heterogeneity of denitrification N losses is primarily driven by edaphic and climatic factors rather than by management practices. In particular, diffusion and production rates emerged as key contributors to the variation of denitrification N losses. These findings humanize a 38.9 ± 4.8 kg N ha-1  N loss by denitrification and challenge the common hypothesis that substrate availability drives the pattern of N losses by denitrification in rice fields.

Soil δ15N spatial distribution is primarily shaped by climatic patterns in the semiarid Caatinga, Northeast Brazil

Soil nitrogen isotopic composition (δ15Nsoil) is an invaluable tool as it integrates nitrogen (N) transformations in soils. In addition to serving as a baseline to understand the N cycle, spatial representations of δ15Nsoil across landscapes (or isoscapes) is a multi-purpose tool useful to investigate, for example, plant-microbe interactions, animal migration and forensics. We investigate the climatic and edaphic controls of δ15Nsoil utilising data from 29 geographical locations sampled across the semiarid Brazilian Caatinga biome. The sampling covered a mean annual precipitation (PA) gradient ranging from 0.51 to 1.36 m a-1 and eight soil types originating from three different geological origins. Our data show that the combination of higher aridity and lower seasonality (ψ) leads to higher values of δ15Nsoil. Moreover, soil total carbon had a positive relationship with δ15Nsoil, appearing within the best-supported models according to the information-theoretic approach undertaken here. The contribution to the plant communities by the Fabaceae trees expressed as their basal area was not related to δ15Nsoil values, suggesting that the magnitude of biological N fixation in the Caatinga is not large enough to be reflected in the soil. In addition, considering PA in a categorical fashion, i.e., 'high' (> 0.8 m a-1) and 'low' PA (< 0.8 m a-1), we found that, within the wetter category, δ15Nsoil was positively related to several soil properties (i.e., clay content, effective cation exchange capacity, exchangeable calcium, silt content, pHH2O, total phosphorus and sum of bases) and negatively related to sand content. Our study provides new insights into the functioning of semiarid ecosystems from a pedo-isotopic perspective and contributes to the overall understanding of the N cycle in the Caatinga region, with the potential to support the development of new conceptualisation of biogeochemical process and testing of global models that simulate N and C cycles.

Overestimated nitrogen loss from denitrification for natural terrestrial ecosystems in CMIP6 Earth System Models

Denitrification and leaching nitrogen (N) losses are poorly constrained in Earth System Models (ESMs). Here, we produce a global map of natural soil ¹⁵N abundance and quantify soil denitrification N loss for global natural ecosystems using an isotope-benchmarking method. We show an overestimation of denitrification by almost two times in the 13 ESMs of the Sixth Phase Coupled Model Intercomparison Project (CMIP6, 73 ± 31 Tg N yr^-1), compared with our estimate of 38 ± 11 Tg N yr^-1, which is rooted in isotope mass balance. Moreover, we find a negative correlation between the sensitivity of plant production to rising carbon dioxide (CO₂) concentration and denitrification in boreal regions, revealing that overestimated denitrification in ESMs would translate to an exaggeration of N limitation on the responses of plant growth to elevated CO₂. Our study highlights the need of improving the representation of the denitrification in ESMs and better assessing the effects of terrestrial ecosystems on CO₂ mitigation.

Effect of increased carbon load on denitrification efficiency and nitrate isotope enrichment factors in subsurface wastewater infiltration system

Denitrification plays a dominant role in nitrate removal in subsurface wastewater infiltration system (SWIS). However, the effect of increased carbon (C) load on denitrification efficiency in the SWIS remain unclear. In this study, we used analyses of stable isotopes of nitrogen (N) and oxygen (O) in nitrate to investigate the N and O isotope enrichment factors (¹⁵ ε and ¹⁸ ε) and quantified N losses via denitrification in SWIS. The results demonstrated that an increase in C loads positively affected the pollutant removal performance of SWIS. The natural abundance of ¹⁵ N and ¹⁸ O increased with decreasing nitrate concentration from 12.5 to 7.3 mg/L, accompanied by increased ¹⁵ ε and ¹⁸ ε from -8.7‰ to -10.6‰ and -5.9‰ to -8.2‰, respectively, as the C load increased from 18 to 36 g/(m²  d). The contribution of denitrification to nitrate removal was 62%, 71%, and 77% when C loads were 18, 27, and 36 g/(m²  d), respectively, indicating that increased C loads could improve the nitrate removal through denitrification in SWIS. PRACTITIONER POINTS: Increasing C loads positively affected the nitrate removal performance of SWIS. N and O isotope enrichment factors of nitrate increased with the enhancement of influent C load. A C load of 36 g/(m²  d) is recommended in SWIS to improve the N removal performance and denitrification efficiency.

Divergent response and adaptation of specific leaf area to environmental change at different spatio-temporal scales jointly improve plant survival

Specific leaf area (SLA) is one of the most important plant functional traits. It integrates multiple functions and reflects strategies of plants to obtain resources. How plants employ different strategies (e.g., through SLA) to respond to dynamic environmental conditions remains poorly understood. This study aimed to explore the spatial variation in SLA and its divergent adaptation through the lens of biogeographic patterns, evolutionary history, and short-term responses. SLA data for 5424 plant species from 76 natural communities in China were systematically measured and integrated with meta-analysis of field experiments (i.e., global warming, drought, and nitrogen addition). The mean value of SLA across all species was 21.8 m²  kg^-1 , ranging from 0.9 to 110.2 m²  kg^-1 . SLA differed among different ecosystems, temperature zones, vegetation types, and functional groups. Phylogeny had a weak effect on SLA, but plant species evolved toward higher SLA. Furthermore, SLA responded nonlinearly to environmental change. Unexpectedly, radiation was one of the main factors determining the spatial variation in SLA on a large scale. Conversely, short-term manipulative experiments showed that SLA increased with increased resource availability and tended to stabilize with treatment duration. However, different species exhibited varying response patterns. Overall, variation in long-term adaptation of SLA to environmental gradients and its short-term response to resource pulses jointly improve plant adaptability to a changing environment. Overall SLA-environment relationships should be emphasized as a multidimensional strategy for elucidating environmental change in future research.

Impact of environmental factors on the ammonia-oxidizing and denitrifying microbial community and functional genes along soil profiles from different ecologically degraded areas in the Siding mine

Ammonia oxidizers (ammonia-oxidizing bacteria (AOB amoA) and ammonia-oxidizing archaea (AOA amoA)) and denitrifiers (encoded by nirS, nirK and nosZ) in the soil nitrogen cycle exist in a variety of natural ecosystems. However, little is known about the contribution of these five N-related functional genes to nitrification and denitrification in the soil profile in severely ecologically degraded areas. Therefore, in the present study, the abundance, diversity and community composition of AOA, AOB, nirS, nirK and nosZ were investigated in the soil profiles of different ecologically degraded areas in the Siding mine. The results indicated that, at the phylum level, the dominant archaea were Crenarchaeota and Thaumarchaeota and the dominant bacteria were Proteobacteria. Heavy metal contents had a great impact on AOA amoA, nirS and nirK gene abundances. AOA amoA contributed more during the ammonia oxidation process and was better adapted for survival in heavy metal-contaminated environments. In addition to heavy metals, the soil organic matter (SOM) content and C/N ratio had strong effects on the AOA and AOB community diversity and structure. In addition, variations in the net ammonification and nitrification rates were proportional to AOA amoA abundance along the soil profile. The soil C/N ratio, soil available phosphorus content and soil moisture influenced the denitrification process. Both soil available phosphorus and moisture were more strongly related to nosZ than to nirS and nirK. In addition, nosZ presented a higher correlation with the nosZ/(nirS + nirK) ratio. Moreover, nosZ/(nirS + nirK) was the key functional gene group that drove the major processes for NH₄⁺-N and NO₃^--N transformation. This study demonstrated the role and importance of soil property impacts on N-related microbes in the soil profile and provided a better understanding of the role and importance of N-related functional genes and their contribution to soil nitrification and denitrification processes in highly degraded areas in the Siding mine.

Multi-isotope zooarchaeological investigations at Abri du Maras: The paleoecological and paleoenvironmental context of Neanderthal subsistence strategies in the Rhône Valley during MIS 3

The exploitation of mid- and large-sized herbivores (ungulates) was central to hominin subsistence across Late Pleistocene Europe. Reconstructing the paleoecology of prey-taxa is key to better understanding procurement strategies, decisions and behaviors, and the isotope analysis of faunal bones and teeth found at archaeological sites represent a powerful means of accessing information about past faunal behaviors. These isotope zooarchaeological approaches also have a near-unique ability to reveal environmental conditions contemporary to the human activities that produced these remains. Here, we present the results of a multi-isotope, multitissue study of ungulate remains from the Middle Paleolithic site of Abri du Maras, southern France, providing new insights into the living landscapes of the Rhône Valley during MIS 3 (level 4.2 = 55 ± 2 to 42 ± 3 ka; level 4.1 = 46 ± 3 to 40 ± 3 ka). Isotope data (carbon, nitrogen) reveal the dietary niches of different ungulate taxa, including the now-extinct giant deer (Megaloceros). Oxygen isotope data are consistent with a mild seasonal climate during level 4.2, where horse (Equus), bison (Bison), and red deer (Cervus elaphus) were exploited year-round. Strontium and sulfur isotope analyses provide new evidence for behavioral plasticity in Late Pleistocene European reindeer (Rangifer) between level 4.2 and level 4.1, indicating a change from the migratory to the sedentary ecotype. In level 4.1, the strong seasonal nature of reindeer exploitation, combined with their nonmigratory behavior, is consistent with a seasonally restricted use of the site by Neanderthals at that time or the preferential hunting of reindeer when in peak physical condition during the autumn.

Global distribution and climate sensitivity of the tropical montane forest nitrogen cycle

Tropical forests are pivotal to global climate and biogeochemical cycles, yet the geographic distribution of nutrient limitation to plants and microbes across the biome is unresolved. One long-standing generalization is that tropical montane forests are nitrogen (N)-limited whereas lowland forests tend to be N-rich. However, empirical tests of this hypothesis have yielded equivocal results. Here we evaluate the topographic signature of the ecosystem-level tropical N cycle by examining climatic and geophysical controls of surface soil N content and stable isotopes (δ¹⁵N) from elevational gradients distributed across tropical mountains globally. We document steep increases in soil N concentration and declining δ¹⁵N with increasing elevation, consistent with decreased microbial N processing and lower gaseous N losses. Temperature explained much of the change in N, with an apparent temperature sensitivity (Q₁₀) of ~1.9. Although montane forests make up 11% of forested tropical land area, we estimate they account for >17% of the global tropical forest soil N pool. Our findings support the existence of widespread microbial N limitation across tropical montane forest ecosystems and high sensitivity to climate warming.

Climatic and edaphic controls over soil δ15N in temperate grassland of northern China: A PLS-PATH analysis

Identifying the impact path of climate and soil factors on soil δ15N is very crucial for better understanding the N turnover in soils and the integrated information about ecosystem N cycling. Many studies have showed that climate and soil variables influence the change of soil δ15N. However, most of the existing studies focused on the overall impact of factor on soil δ15N, without distinguishing between the direct and indirect effect. Although scholars have studied the relationships among temperature, precipitation, soil N, soil pH, and soil δ15N rather than estimating all the causal relationships simultaneously. To answer the above-mentioned questions, a regional-scale soil collection was conducted across a temperate grassland in northern China. Meanwhile, a PLS-PATH analysis was utilized to evaluate the direct and indirect effects of various factors on soil δ15N and to explore the causal relationships among variables. The results showed that along the transect, mean annual precipitation (MAP) and mean annual temperature (MAT) directly and significantly reduced soil δ15N, and indirectly affected soil δ15N through their effects on soil pH, soil clay, soil N and soil C/N. Soil C/N ratio has a significant direct impact on soil δ15N with a negative correlation. Soil clay, soil N content, and soil pH have a total positive effect on soil δ15N, but the total positive impact of soil pH is very weak because it has a negative indirect impact on soil δ15N by affecting soil clay, soil N and soil C/N ratio. The total influence is, in order, MAP > MAT > soil C/N > soil clay > soil N > soil pH (in absolute value). The above results will provide valuable information about ecosystem N cycle in temperate grassland of northern China.

Elevational shifts in foliar-soil δ15 N in the Hengduan Mountains and different potential mechanisms

The natural abundance of stable nitrogen isotopes (δ¹⁵ N) provides insights into the N dynamics of terrestrial ecosystems, the determination of which is considered an effective approach for gaining a better understanding ecosystem N cycling. However, there is currently little information available regarding the patterns and mechanisms underlying the variation in foliar-soil δ¹⁵ N among mountain ecosystems. In this study, we examined the determinants of foliar-soil δ¹⁵ N in association with N transportation rates along an elevational gradient in the Hengduan Mountains. Despite the relatively high levels of available N produced from high N fixation and mineralization, we detected the lowest levels of foliar δ¹⁵ N at 3500 m a.s.l., reflecting the stronger vegetation N limitation at medium high elevations. The enhanced vegetation N limitation was driven by the combined effects of higher microbial immobilization and inherent plant dynamic (the shifts of δ¹⁵ N in vegetation preference, including vegetation community) with changing climate along the elevational gradient. Unexpectedly, we established that soil δ¹⁵ N was characterized by an undulating rise and uncoupled correlation with foliar δ¹⁵ N with increasing elevation, thereby indicating that litter input might not be a prominent driver of soil δ¹⁵ N. Conversely, soil nitrification and denitrification were found to make a more pronounced contribution to the pattern of soil δ¹⁵ N along the elevational gradient. Collectively, our results serve to highlight the importance of microbial immobilization in soil N dynamics and provide novel insights that will contribute to enhancing our understanding of N cycling as indicated by foliar-soil δ¹⁵ N along elevational gradients.

Rising CO2 and warming reduce global canopy demand for nitrogen

Nitrogen (N) limitation has been considered as a constraint on terrestrial carbon uptake in response to rising CO₂ and climate change. By extension, it has been suggested that declining carboxylation capacity (V_cmax ) and leaf N content in enhanced-CO₂ experiments and satellite records signify increasing N limitation of primary production. We predicted V_cmax using the coordination hypothesis and estimated changes in leaf-level photosynthetic N for 1982-2016 assuming proportionality with leaf-level V_cmax at 25°C. The whole-canopy photosynthetic N was derived using satellite-based leaf area index (LAI) data and an empirical extinction coefficient for V_cmax , and converted to annual N demand using estimated leaf turnover times. The predicted spatial pattern of V_cmax shares key features with an independent reconstruction from remotely sensed leaf chlorophyll content. Predicted leaf photosynthetic N declined by 0.27% yr^-1 , while observed leaf (total) N declined by 0.2-0.25% yr^-1 . Predicted global canopy N (and N demand) declined from 1996 onwards, despite increasing LAI. Leaf-level responses to rising CO₂ , and to a lesser extent temperature, may have reduced the canopy requirement for N by more than rising LAI has increased it. This finding provides an alternative explanation for declining leaf N that does not depend on increasing N limitation.

Microbiogeochemical Traits to Identify Nitrogen Hotspots in Permafrost Regions

Permafrost-affected tundra soils are large carbon (C) and nitrogen (N) reservoirs. However, N is largely bound in soil organic matter (SOM), and ecosystems generally have low N availability. Therefore, microbial induced N-cycling processes and N losses were considered negligible. Recent studies show that microbial N processing rates, inorganic N availability, and lateral N losses from thawing permafrost increase when vegetation cover is disturbed, resulting in reduced N uptake or increased N input from thawing permafrost. In this review, we describe currently known N hotspots, particularly bare patches in permafrost peatland or permafrost soils affected by thermokarst, and their microbiogeochemical characteristics, and present evidence for previously unrecorded N hotspots in the tundra. We summarize the current understanding of microbial N cycling processes that promote the release of the potent greenhouse gas (GHG) nitrous oxide (N2O) and the translocation of inorganic N from terrestrial into aquatic ecosystems. We suggest that certain soil characteristics and microbial traits can be used as indicators of N availability and N losses. Identifying N hotspots in permafrost soils is key to assessing the potential for N release from permafrost-affected soils under global warming, as well as the impact of increased N availability on emissions of carbon-containing GHGs.

Enrichment of bacteria involved in the nitrogen cycle and plant growth promotion in soil by sclerotia of rice sheath blight fungus

Rice sheath blight pathogen, Rhizoctonia solani, produces numerous sclerotia to overwinter. As a rich source of nutrients in the soil, sclerotia may lead to the change of soil microbiota. For this purpose, we amended the sclerotia of R. solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points. At the phyla level, Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control. An increased abundance of ammonia-oxidizing bacterium (AOB) Nitrosospira and Nitrite oxidizing bacteria (NOB) i.e., Nitrospira was observed, where the latter is reportedly involved in the nitrifier denitrification. Moreover, Thiobacillus, Gemmatimonas, Anaeromyxobacter and Geobacter, the vital players in denitrification, N2O reduction and reductive nitrogen transformation, respectively, depicted enhanced abundance in R. solani sclerotia-amended samples. Furthermore, asymbiotic nitrogen-fixing bacteria, notably, Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control. Plant growth promoting bacteria, such as Kribbella, Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil. As per our knowledge, this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R. solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.

Warming and redistribution of nitrogen inputs drive an increase in terrestrial nitrous oxide emission factor

Anthropogenic nitrogen inputs cause major negative environmental impacts, including emissions of the important greenhouse gas N2O. Despite their importance, shifts in terrestrial N loss pathways driven by global change are highly uncertain. Here we present a coupled soil-atmosphere isotope model (IsoTONE) to quantify terrestrial N losses and N2O emission factors from 1850-2020. We find that N inputs from atmospheric deposition caused 51% of anthropogenic N2O emissions from soils in 2020. The mean effective global emission factor for N2O was 4.3 ± 0.3% in 2020 (weighted by N inputs), much higher than the surface area-weighted mean (1.1 ± 0.1%). Climate change and spatial redistribution of fertilisation N inputs have driven an increase in global emission factor over the past century, which accounts for 18% of the anthropogenic soil flux in 2020. Predicted increases in fertilisation in emerging economies will accelerate N2O-driven climate warming in coming decades, unless targeted mitigation measures are introduced.

Changes in forest nitrogen cycling across deposition gradient revealed by δ15N in tree rings

Tree rings provide valuable insight into past environmental changes. This study aimed to evaluate perturbations in tree ring width (TRW) and δ¹⁵N alongside soil acidity and nutrient availability gradients caused by the contrasting legacy of air pollution (nitrogen [N] and sulphur [S] deposition) and tree species (European beech, Silver fir and Norway spruce). We found consistent declines of tree ring δ¹⁵N, which were temporarily unrelated to the changes in the TRW. The rate of δ¹⁵N change in tree rings was related to the contemporary foliar carbon (C) to phosphorus (P) ratio. This observation suggested that the long-term accumulation of ¹⁵N depleted N in tree rings, likely mediated by retained N from deposition, was restricted primarily to stands with currently higher P availability. The shifts observed in tree-ring δ¹⁵N and TRW suggest that acidic air pollution rather than changes in stand productivity determined alteration of N and C cycles. Stable N isotopes in tree rings provided helpful information on the trajectory of the N cycle over the last century with direct consequences for a better understanding of future interactions among N, P and C cycles in terrestrial ecosystems.

Nitrification, denitrification, and competition for soil N: Evaluation of two Earth System Models against observations

Earth System Models (ESMs) have implemented nitrogen (N) cycles to account for N limitation on terrestrial carbon uptake. However, representing inputs, losses, and recycling of N in ESMs is challenging. Here, we use global rates and ratios of key soil N fluxes, including nitrification, denitrification, mineralization, leaching, immobilization, and plant uptake (both NH₄ ⁺ and NO₃ ^- ), from the literature to evaluate the N cycles in the land model components of two ESMs. The two land models evaluated here, E3SM Land Model version 1 (ELMv1)-ECA and CLM5.0, originated from a common model but have diverged in their representation of plant-microbe competition for soil N. The models predict similar global rates of gross primary productivity (GPP) but have approximately two-fold to three-fold differences in their underlying global mineralization, immobilization, plant N uptake, nitrification, and denitrification fluxes. Both models dramatically underestimate the immobilization of NO₃ ^- by soil bacteria compared with literature values and predict dominance of plant uptake by a single form of mineral nitrogen (NO₃ ^- for ELM, with regional exceptions, and NH₄ ⁺ for CLM5.0). CLM5.0 strongly underestimates the global ratio of gross nitrification:gross mineralization and both models are likely to substantially underestimate the ratio of nitrification:denitrification. Few experimental data exist to evaluate this last ratio, in part because nitrification and denitrification are quantified using different techniques and because denitrification fluxes are difficult to measure at all. More observational constraints on soil nitrogen fluxes such as nitrification and denitrification, as well as greater scrutiny of the functional impact of introducing separate NH₄ ⁺ and NO₃ ^- pools into ESMs, could help to improve confidence in present and future simulations of N limitation on the carbon cycle.

δ15N of Chironomidae: An index of nitrogen sources and processing within watersheds for national aquatic monitoring programs

Nitrogen (N) removal along flowpaths to aquatic ecosystems is an important regulating ecosystem service that can help reduce N pollution in the nation's waterways, but can be challenging to measure at large spatial scales. Measurements that integrate N processing within watersheds would be particularly useful for assessing the magnitude of this vital service. Because most N removal processes cause isotopic fractionation, δ¹⁵N from basal food-chain organisms in aquatic ecosystems can provide information on both N sources and the degree of watershed N processing. As part of EPA's National Aquatic Resource Surveys (NARS), we measured δ¹⁵N of Chironomidae collected from over 2000 lakes, rivers and streams across the continental USA. Using information on N inputs to watersheds and summer total N concentrations ([TN]) in the water column, we assessed where elevated chironomid δ¹⁵N would indicate N removal rather than possible enriched sources of N. Chironomid δ¹⁵N values ranged from -4 to +20‰, and were higher in rivers and streams than in lakes, indicating that N in rivers and streams underwent more processing and cycling that preferentially removes ¹⁴N than N in lakes. Chironomid δ¹⁵N increased with watershed size, N inputs, and water chemical components, and decreased as precipitation increased. In rivers and streams with high watershed N inputs, we found lower [TN] in streams with higher chironomid δ¹⁵N values, suggesting high rates of gaseous N loss such as denitrification. At low watershed N inputs, the pattern reversed; streams with elevated chironomid δ¹⁵N had higher [TN] than streams with lower chironomid δ¹⁵N, possibly indicating unknown sources elevated in δ¹⁵N such as legacy N, or waste from animals or humans. Chironomid δ¹⁵N values can be a valuable tool to assess integrated watershed-level N sources, input rates, and processing for water quality monitoring and assessment at large scales.

Chronic atmospheric reactive N deposition has breached the N sink capacity of a northern ombrotrophic peatbog increasing the gaseous and fluvial N losses

Peatlands play an important role in modulating the climate, mainly through sequestration of carbon dioxide into peat carbon, which depends on the availability of reactive nitrogen (Nr) to mosses. Atmospheric Nr deposition in the UK has been above the critical load for functional and structural changes to peatland mosses, thus threatening to accelerate their succession by vascular plants and increasing the possibility of Nr export to downstream ecosystems. The N balance of peatlands has received comparatively little attention, mainly due to the difficulty in measuring gaseous N losses as well as the Nr inputs due to biological nitrogen fixation (BNF). In this study we have estimated the mean annual N balance of an ombrotrophic bog (Migneint, North Wales) by measuring in situ N₂ + N₂O gaseous fluxes and also BNF in peat and mosses. Fluvial N export was monitored through a continuous record of DON flux, while atmospheric N deposition was modelled on a 5 × 5 km grid. The mean annual N mass balance was slightly positive (0.7 ± 4.1 kg N ha^-1 y^-1) and varied interannually indicating the fragile status of this bog ecosystem that has reached N saturation and is prone to becoming a net N source. Gaseous N losses were a major N output term accounting for 70% of the N inputs, mainly in the form of the inert N₂ gas, thus providing partial mitigation to the adverse effects of chronic Nr enrichment. BNF was suppressed by 69%, compared to rates in pristine bogs, but was still active, contributing ~2% of the N inputs. The long-term peat N storage rate (8.4 ± 0.8 kg N ha^-1 y^-1) cannot be met by the measured N mass balance, showing that the bog catchment is losing more N than it can store due its saturated status.

Ectomycorrhizal fungi are associated with reduced nitrogen cycling rates in temperate forest soils without corresponding trends in bacterial functional groups

Microbial processes play a central role in controlling the availability of N in temperate forests. While bacteria, archaea, and fungi account for major inputs, transformations, and exports of N in soil, relationships between microbial community structure and N cycle fluxes have been difficult to detect and characterize. Several studies have reported differences in N cycling based on mycorrhizal type in temperate forests, but associated differences in N cycling genes underlying these fluxes are not well-understood. We explored how rates of soil N cycle fluxes vary across gradients of mycorrhizal abundance (hereafter "mycorrhizal gradients") at four temperate forest sites in Massachusetts and Indiana, USA. We paired measurements of N-fixation, net nitrification, and denitrification rates with gene abundance data for specific bacterial functional groups associated with each process. We find that the availability of NO₃ and rates of N-fixation, net nitrification, and denitrification are reduced in stands dominated by trees associated with ECM fungi. On average, rates of N-fixation and denitrification in stands dominated by trees associated with arbuscular mycorrhizal fungi were more than double the corresponding rates in stands dominated by trees associated with ectomycorrhizal fungi. Despite the structuring of flux rates across the mycorrhizal gradients, we did not find concomitant shifts in the abundances of N-cycling bacterial genes, and gene abundances were not correlated with process rates. Given that AM-associating trees are replacing ECM-associating trees throughout much of the eastern US, our results suggest that shifts in mycorrhizal dominance may accelerate N cycling independent of changes in the relative abundance of N cycling bacteria, with consequences for forest productivity and N retention.

Predicting the Ratio of Nitrification to Immobilization to Reflect the Potential Risk of Nitrogen Loss Worldwide

Nitrification and immobilization compete for soil ammonium (NH₄⁺); the relative dominance of these two processes has been suggested to reflect the potential risk of nitrogen loss from soils. Here, we compiled a database and developed a stochastic gradient boosting model to predict the global potential risk of nitrogen loss based on the ratio of nitrification to immobilization (N/I). We then conducted a meta-analysis to evaluate the effects of common management practices on the N/I ratio. The results showed that the soil N/I ratio varied with climate zones and land use. Soil total carbon, total nitrogen, pH, fertilizer nitrogen application rate, mean annual temperature, and mean annual precipitation are important factors of soil N/I ratio. Meta-analysis indicated that biochar, straw, and nitrification inhibitor application reduced the soil N/I ratio by 67, 64, and 78%, respectively. Returning plantation to forest and cropland to grassland decreased the soil N/I ratio by 88 and 45%, respectively. However, fertilizer nitrogen application increased the soil N/I ratio by 92%. Our study showed that the soil N/I ratio and its associated risk level of nitrogen loss were highly related to long-term soil and environmental properties with high spatial heterogeneity.

Influences of irrigation and fertilization on soil N cycle and losses from wheat-maize cropping system in northern China

Excess of water irrigation and fertilizer consumption by crops has resulted in high soil nitrogen (N) losses and underground water contamination not only in China but worldwide. This study explored the effects of soil N input, soil N output, as well as the effect of different irrigation and N- fertilizer managements on residual N. For this, two consecutive years of winter wheat (Triticum aestivum L.) -summer maize (Zea mays L.) rotation was conducted with: N applied at 0 kg N ha^-1 yr^-1, 420 kg N ha^-1 yr^-1 and 600 kg N ha^-1 yr^-1 under fertigation (DN0, DN420, DN600), and N applied at 0 kg N ha^-1 yr^-1 and 600 kg N ha^-1 yr^-1 under flood irrigation (FN0, FN600). The results demonstrated that low irrigation water consumption resulted in a 57.2% lower of irrigation-N input (p < 0.05) in DN600 when compared to FN600, especially in a rainy year like 2015-2016. For N output, no significant difference was found with all N treatments. Soil gaseous N losses were highly correlated with fertilization (p < 0.001) and were reduced by 23.6%-41.7% when fertilizer N was decreased by 30%. Soil N leaching was highly affected by irrigation and a higher reduction was observed under saving irrigation (reduced by 33.9%-57.3%) than under optimized fertilization (reduced by 23.6%-50.7%). The net N surplus was significantly increased with N application rate but was not affected by irrigation treatments. Under the same N level (600 kg N ha^-1 yr^-1), fertigation increased the Total Nitrogen (TN) stock by 17.5% (0-100 cm) as compared to flood irrigation. These results highlighted the importance to further reduction of soil N losses under optimized fertilization and irrigation combined with N stabilizers or balanced- N fertilization for future agriculture development.

Hot spots and hot moments of nitrogen removal from hyporheic and riparian zones: A review

The Earth is experiencing excessive nitrogen (N) input to its various ecosystems due to human activities. How to effectively and efficiently remove N from ecosystems has been, is and will be at the center of attention in N research. Hyporheic and riparian zones are widely acknowledged for their buffering capacity to reduce contaminants (especially N) transport downstream. However, these zones are usually misunderstood that they can remove N at all spots and at any moments. Here pathways of N removal from hyporheic and riparian zones are reviewed and summarized with an emphasize on their hot spots and hot moments. N is biogeochemically removed by denitrification, anammox, nitrifier denitrification, denitrifying anaerobic methane oxidation, Feammox and Sulfammox. Hot moments of N removal are mainly triggered by precipitation, fire and snowmelt. Finally, some research needs are outlined and discussed, such as developing approaches for multiscale sampling and monitoring, quantifying the effects of hot spots and hot moments at hyporheic and riparian zones and evaluating the impacts of human activities on hot spots and hot moments, to inspire more research on hot spots and hot moments of N removal. By this review, we hope to bring awareness of the heterogeneity of hyporheic and riparian zones to catchment managers and policy makers when tackling N pollution problems.

Nitrogen and Oxygen Isotope Signatures of Nitrogen Compounds during Anammox in the Laboratory and a Wastewater Treatment Plant

Isotopic fractionation factors against ¹⁵N and ¹⁸O during anammox (anaerobic ammonia oxidization by nitrite) are critical for evaluating the importance of this process in natural environments. We performed batch incubation experiments with an anammox-dominated biomass to investigate nitrogen (N) and oxygen (O) isotopic fractionation factors during anammox and also examined apparent isotope fractionation factors during anammox in an actual wastewater treatment plant. We conducted one incubation experiment with high δ¹⁸O of water to investigate the effects of water δ¹⁸O. The N isotopic fractionation factors estimated from incubation experiments and the wastewater treatment plant were similar to previous values. We also found that the N isotopic effect (¹⁵ε_NXR of -77.8 to -65.9‰ and ¹⁵Δ_NXR of -31.3 to -30.4‰) and possibly O isotopic effect (¹⁸ε_NXR of -20.6‰) for anaerobic nitrite oxidation to nitrate were inverse. We applied the estimated isotopic fractionation factors to the ordinary differential equation model to clarify whether anammox induces deviations in the δ¹⁸O vs δ¹⁵N of nitrate from a linear trajectory of 1, similar to heterotrophic denitrification. Although this deviation has been attributed to nitrite oxidation, the O isotopic fractionation factor for anammox is crucial for obtaining a more detailed understanding of the mechanisms controlling this deviation. In our model, anammox induced the trajectory of the δ¹⁸O vs δ¹⁵N of nitrate during denitrification to less than one, which strongly indicates that this deviation is evidence of nitrite oxidation by anammox under denitrifying conditions.

Nitrate Respiration in Thermus thermophilus NAR1: from Horizontal Gene Transfer to Internal Evolution

Genes coding for enzymes of the denitrification pathway appear randomly distributed among isolates of the ancestral genus Thermus, but only in few strains of the species Thermus thermophilus has the pathway been studied to a certain detail. Here, we review the enzymes involved in this pathway present in T. thermophilus NAR1, a strain extensively employed as a model for nitrate respiration, in the light of its full sequence recently assembled through a combination of PacBio and Illumina technologies in order to counteract the systematic errors introduced by the former technique. The genome of this strain is divided in four replicons, a chromosome of 2,021,843 bp, two megaplasmids of 370,865 and 77,135 bp and a small plasmid of 9799 pb. Nitrate respiration is encoded in the largest megaplasmid, pTTHNP4, within a region that includes operons for O₂ and nitrate sensory systems, a nitrate reductase, nitrate and nitrite transporters and a nitrate specific NADH dehydrogenase, in addition to multiple insertion sequences (IS), suggesting its mobility-prone nature. Despite nitrite is the final product of nitrate respiration in this strain, the megaplasmid encodes two putative nitrite reductases of the cd1 and Cu-containing types, apparently inactivated by IS. No nitric oxide reductase genes have been found within this region, although the NorR sensory gene, needed for its expression, is found near the inactive nitrite respiration system. These data clearly support that partial denitrification in this strain is the consequence of recent deletions and IS insertions in genes involved in nitrite respiration. Based on these data, the capability of this strain to transfer or acquire denitrification clusters by horizontal gene transfer is discussed.

The greening of the Northern Great Plains and its biogeochemical precursors

Vegetation greenness has increased across much of the global land surface over recent decades. This trend is projected to continue-particularly in northern latitudes-but future greening may be constrained by nutrient availability needed for plant carbon (C) assimilation in response to CO₂ enrichment (eCO₂ ). eCO₂ impacts foliar chemistry and function, yet the relative strengths of these effects versus climate in driving patterns of vegetative greening remain uncertain. Here we combine satellite measurements of greening with a 135 year record of plant C and nitrogen (N) concentrations and stable isotope ratios (δ¹³ C and δ¹⁵ N) in the Northern Great Plains (NGP) of North America to examine N constraints on greening. We document significant greening over the past two decades with the highest proportional increases in net greening occurring in the dries and warmest areas. In contrast to the climate dependency of greening, we find spatially uniform increases in leaf-level intercellular CO₂ and intrinsic water use efficiency that track rising atmospheric CO₂ . Despite large spatial variation in greening, we find sustained and climate-independent declines in foliar N over the last century. Parallel declines in foliar δ¹⁵ N and increases in C:N ratios point to diminished N availability as the likely cause. The simultaneous increase in greening and decline in foliar N across our study area points to increased N use efficiency (NUE) over the last two decades. However, our results suggest that plant NUE responses are likely insufficient to sustain observed greening trends in NGP grasslands in the future.

Nitrogen Isotope Fractionation During Archaeal Ammonia Oxidation: Coupled Estimates From Measurements of Residual Ammonium and Accumulated Nitrite

The naturally occurring nitrogen (N) isotopes, 15N and 14N, exhibit different reaction rates during many microbial N transformation processes, which results in N isotope fractionation. Such isotope effects are critical parameters for interpreting natural stable isotope abundances as proxies for biological process rates in the environment across scales. The kinetic isotope effect of ammonia oxidation (AO) to nitrite (NO2 -), performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is generally ascribed to the enzyme ammonia monooxygenase (AMO), which catalyzes the first step in this process. However, the kinetic isotope effect of AMO, or ε A M O , has been typically determined based on isotope kinetics during product formation (cumulative product, NO2 -) alone, which may have overestimated ε A M O due to possible accumulation of chemical intermediates and alternative sinks of ammonia/ammonium (NH3/NH4 +). Here, we analyzed 15N isotope fractionation during archaeal ammonia oxidation based on both isotopic changes in residual substrate (RS, NH4 +) and cumulative product (CP, NO2 -) pools in pure cultures of the soil strain Nitrososphaera viennensis EN76 and in highly enriched cultures of the marine strain Nitrosopumilus adriaticus NF5, under non-limiting substrate conditions. We obtained ε A M O values of 31.9-33.1‰ for both strains based on RS (δ15NH4 +) and showed that estimates based on CP (δ15NO2 -) give larger isotope fractionation factors by 6-8‰. Complementary analyses showed that, at the end of the growth period, microbial biomass was 15N-enriched (10.1‰), whereas nitrous oxide (N2O) was highly 15N depleted (-38.1‰) relative to the initial substrate. Although we did not determine the isotope effect of NH4 + assimilation (biomass formation) and N2O production by AOA, our results nevertheless show that the discrepancy between ε A M O estimates based on RS and CP might have derived from the incorporation of 15N-enriched residual NH4 + after AMO reaction into microbial biomass and that N2O production did not affect isotope fractionation estimates significantly.

Progressive nitrogen limitation across the Tibetan alpine permafrost region

The ecosystem carbon (C) balance in permafrost regions, which has a global significance in understanding the terrestrial C-climate feedback, is significantly regulated by nitrogen (N) dynamics. However, our knowledge on temporal changes in vegetation N limitation (i.e., the supply of N relative to plant N demand) in permafrost ecosystems is still limited. Based on the combination of isotopic observations derived from a re-sampling campaign along a ~3000 km transect and simulations obtained from a process-based biogeochemical model, here we detect changes in ecosystem N cycle across the Tibetan alpine permafrost region over the past decade. We find that vegetation N limitation becomes stronger despite the increased available N production. The enhanced N limitation on vegetation growth is driven by the joint effects of elevated plant N demand and gaseous N loss. These findings suggest that N would constrain the future trajectory of ecosystem C cycle in this alpine permafrost region.

Levels and variations of soil organic carbon and total nitrogen among forests in a hotspot region of high nitrogen deposition

Human activities have distinctly enhanced the deposition levels of atmospheric nitrogen (N) pollutants into terrestrial ecosystems, but whether and to what extents soil carbon (C) and N status have been influenced by elevated N inputs remain poorly understood in the 'real' world given related knowledge has largely based on N-addition experiments. Here we reported soil organic C (OC) and total N (TN) for twenty-seven forests along a gradient of N deposition (22.4-112.9 kg N/ha/yr) in the Beijing-Tianjin-Hebei (BTH) region of northern China, a global hotspot of high N pollution. Levels of soil TN in forests of the BTH region have been elevated compared with investigations in past decades, suggesting that long-term N deposition might cause soil TN increases. Combining with major geographical and environmental factors among the study forests, we found unexpectedly that soil moisture and pH values rather than N deposition levels were major regulators of the observed spatial variations of soil OC and TN contents. As soil moisture and pH values increased with mean annual precipitation and temperature, respectively, soil C and N status in forests of the BTH region might be more responsive to climate change than to N pollution. These evidence suggests that both N deposition and climate differences should be considered into managing ecosystem functions of forest resources in regions with high N pollution.

The missing nitrogen pieces: A critical review on the distribution, transformation, and budget of nitrogen in the vadose zone-groundwater system

Intensive agriculture and urbanization have led to the excessive and repeated input of nitrogen (N) into soil and further increased the amount of nitrate (NO₃^-) leaching into groundwater, which has become an environmental problem of widespread concern. This review critically examines both the recent advances and remaining knowledge gaps with respect to the N cycle in the vadose zone-groundwater system. The key aspects regarding the N distribution, transformation, and budget in this system are summarized. Three major missing N pieces (N in dissolved organic form, N in the deep vadose zone, and N in the nonagricultural system), which are crucial for closing the N cycle yet has been previously assumed to be insignificant, are put forward and discussed. More work is anticipated to obtain accurate information on the chemical composition, transformation mechanism, and leaching flux of these missing N pieces in the vadose zone-groundwater system. These are essential to support the assessment of global N stocks and management of N contamination risks.

Leaf and Soil δ15N Patterns Along Elevational Gradients at Both Treelines and Shrublines in Three Different Climate Zones

The natural abundance of stable nitrogen (N) isotope (δ15N) in plants and soils can reflect N cycling processes in ecosystems. However, we still do not fully understand patterns of plant and soil δ15N at alpine treelines and shrublines in different climate zones. We measured δ15N and N concentration in leaves of trees and shrubs and also in soils along elevational gradients from lower altitudes to the upper limits of treelines and shrublines in subtropical, dry- and wet-temperate regions in China. The patterns of leaf δ15N in trees and shrubs in response to altitude changes were consistent, with lower values occurring at higher altitude in all three climate zones, but such patterns did not exist for leaf Δδ15N and soil δ15N. Average δ15N values of leaves (−1.2‰) and soils (5.6‰) in the subtropical region were significantly higher than those in the two temperate regions (−3.4‰ and 3.2‰, respectively). Significant higher δ15N values in subtro4pical forest compared with temperate forests prove that N cycles are more open in warm regions. The different responses of leaf and soil δ15N to altitude indicate complex mechanisms of soil biogeochemical process and N sources uptake with environmental variations.

Denitrification as a major regional nitrogen sink in subtropical forest catchments: Evidence from multi-site dual nitrate isotopes

Increasing nitrogen (N) deposition in subtropical forests in south China causes N saturation, associated with significant nitrate (NO₃^- ) leaching. Strong N attenuation may occur in groundwater discharge zones hydrologically connected to well-drained hillslopes, as has been shown for the subtropical headwater catchment "TieShanPing", where dual NO₃^- isotopes indicated that groundwater discharge zones act as an important N sink and hotspot for denitrification. Here, we present a regional study reporting inorganic N fluxes over two years together with dual NO₃^- isotope signatures obtained in two summer campaigns from seven forested catchments in China, representing a gradient in climate and atmospheric N input. In all catchments, fluxes of dissolved inorganic N indicated efficient conversion of NH₄⁺ to NO₃^- on well-drained hillslopes, and subsequent interflow of NO₃^- over the argic B-horizons to groundwater discharge zones. Depletion of ¹⁵ N- and ¹⁸ O-NO₃^- on hillslopes suggested nitrification as the main source of NO₃^- . In all catchments, except one of the northern sites, which had low N deposition rates, NO₃^- attenuation by denitrification occurred in groundwater discharge zones, as indicated by simultaneous ¹⁵ N and ¹⁸ O enrichment in residual NO₃^- . By contrast to the southern sites, the northern catchments lack continuous and well-developed groundwater discharge zones, explaining less efficient N removal. Using a model based on ¹⁵ NO₃^- signatures, we estimated denitrification fluxes from 2.4 to 21.7 kg N ha^-1 year^-1 for the southern sites, accounting for more than half of the observed N removal. Across the southern catchments, estimated denitrification scaled proportionally with N deposition. Together, this indicates that N removal by denitrification is an important component of the N budget of southern Chinese forests and that natural NO₃^- attenuation may increase with increasing N input, thus partly counteracting further aggravation of N contamination of surface waters in the region.

Control of the Nitrogen Isotope Composition of the Fungal Biomass: Evidence of Microbial Nitrogen Use Efficiency

Changes in 15N/14N in the soil microbial biomass during nitrogen (N) mineralization have been hypothesized to influence 15N/14N in soil organic matter among ecosystem sites. However, a direct experimental test of this mechanism has not yet been performed. To evaluate the potential control of microbial N mineralization on the natural N isotope composition, we cultured fungi (Aspergillus oryzae) in five types of media of varying C:N ratios of 5, 10, 30, 50, and 100 for 4 d, and tracked changes in δ15N in the microbial biomass, NH4+, and dissolved organic N (DON: glycine) over the course of the experiment. High rates of NH4+ excretion from A. oryzae were accompanied by an increase in δ15N in the microbial biomass in low C:N media (i.e., C/N<30). In contrast, NH4+ was strongly retained in higher C/N treatments with only minor (i.e., <1 ‰) changes being detected in δ15N in the microbial biomass. Differences in δ15N in the microbial biomass were attributed to the loss of low-δ15N NH4+ in low, but not high C/N substrates. We also detected a negative linear correlation between microbial nitrogen use efficiency (NUE) and Δ15N (δ15N-biomass-δ15N-glycine). These results suggest an isotope effect during NH4+ excretion in relatively N-repleted environments in which microbial NUE is low, which may explain the vertical patterns of organic matter δ15N in soil profiles.

Nitrogen-cycling microbial community functional potential and enzyme activities in cultured biofilms with response to inorganic nitrogen availability

Biofilms mediate crucial biochemical processes in aquatic ecosystems. It was hypothesized that eutrophication may promote the growth of biofilms, resulting in larger numbers of functional genes. However, the metabolic activity and the roles of biofilms in N cycling will be affected by ambient inorganic nitrogen availability, not by the abundance of functional genes. Biofilms were cultured either with replete inorganic nitrogen (N-rep) or without exogenous inorganic nitrogen supply (N-def) in a flow incubator, and the N-cycling gene abundances (nifH, N₂ fixation; amoA, ammonia oxidation, archaea and bacteria; nirS and nirK, denitrification) and enzyme activities (nitrogenase and nitrate reductase) were analyzed. The results showed that, comparing the N-def and N-rep biofilms, the former contained lower nifH gene abundance, but higher nitrogenase activity (NA), while the latter contained higher nifH gene abundance, but lower NA. Different patterns of NA diel variations corresponded to the dynamic microbial community composition and different stages of biofilm colonization. Ammonia oxidizing bacteria (AOB), detected only in N-def biofilms, were responsible for nitrification in biofilms. N-rep biofilms contained high nirS and nirK gene abundance and high denitrification enzyme activity, but N-def biofilms contained significantly lower denitrification gene abundance and activity. In general, the strong N₂ fixation in N-def biofilms and strong denitrification in N-rep biofilms assured the balance of aquatic ecosystems. The results suggested that evaluation of the functional processes of N cycling should not only focus on genetic potential, but also on the physiological activity of biofilms.

Geographical Patterns of nirS Gene Abundance and nirS-Type Denitrifying Bacterial Community Associated with Activated Sludge from Different Wastewater Treatment Plants

Denitrifying bacteria is a driver of nitrogen removal process in wastewater treatment ecosystem. However, the geographical characteristics of denitrifying bacterial communities associated with activated sludge from diverse wastewater treatment plants (WWTPs) are still unclear. Here, quantitative PCR and next-generation sequencing of the nirS gene were applied to characterize the abundance and denitrifying bacterial communities from 18 geographically distributed WWTPs. The results showed that the nirS abundance ranged from 4.6 × 10² to 2.4 × 10³ copies per ng DNA, while nirS-type denitrifying bacterial populations were diverse and distinct from activated sludge communities. Among WWTPs, total nitrogen removal efficiencies varied from 25.8 to 84%, which was positively correlated with diversity indices, whereas abundance-based coverage estimator index decreased with an increase in latitude. The dominant phyla across all samples were proteobacteria, accounting for 46.23% (ranging from 17.98 to 87.07%) of the sequences. Eight of the 22 genera detected were dominant: Thauera sp., Alicycliphilus sp., and Pseudomonas sp., etc. Based on network analysis, the coexistence and interaction between dominant genera may be vital for regulating the nitrogen and carbon removal behaviors. Multivariate statistical analysis revealed that both geographic location and wastewater factors concurrently govern the distribution patterns of nirS-type denitrifying bacterial community harbored in WWTPs. Taking together, these results from the present study provide novel insights into the nirS gene abundance and nirS-type denitrifying bacterial community composition in geographically distributed WWTPs. Moreover, the knowledge gained will improve the operation and management of WWTPs for nitrogen removal.

The role of conserved proteins DrpA and DrpB in nitrate respiration of Thermus thermophilus

In many Thermus thermophilus strains, nitrate respiration is encoded in mobile genetic regions, along with regulatory circuits that modulate its expression based on anoxia and nitrate presence. The oxygen-responsive system has been identified as the product of the dnrST (dnr) operon located immediately upstream of the nar operon (narCGHJIKT), which encodes the nitrate reductase (NR) and nitrate/nitrite transporters. In contrast, the nature of the nitrate sensory system is not known. Here, we analyse the putative nitrate-sensing role of the bicistronic drp operon (drpAB) present downstream of the nar operon in most denitrifying Thermus spp. Expression of drp was found to depend on the master regulator DnrT, whereas the absence of DrpA or DrpB increased the expression of both DnrS and DnrT and, concomitantly, of the NR. Absence of both proteins made expression from the dnr and nar operons independent of nitrate. Polyclonal antisera allowed us to identify DrpA as a periplasmic protein and DrpB as a membrane protein, with capacity to bind to the cytoplasmic membrane. Here, we propose a role for DrpA/DrpB as nitrate sensors during denitrification.

High nitrogen isotope fractionation of nitrate during denitrification in four forest soils and its implications for denitrification rate estimates

Denitrification is a major process contributing to the removal of nitrogen (N) from ecosystems, but its rate is difficult to quantify. The natural abundance of isotopes can be used to identify the occurrence of denitrification and has recently been used to quantify denitrification rates at the ecosystem level. However, the technique requires an understanding of the isotopic enrichment factor associated with denitrification, which few studies have investigated in forest soils. Here, soils collected from two tropical and two temperate forests in China were incubated under anaerobic or aerobic laboratory conditions for two weeks to determine the N and oxygen (O) isotope enrichment factors during denitrification. We found that at room temperature (20°C), NO₃^- was reduced at a rate of 0.17 to 0.35μgNg^-1h^-1, accompanied by the isotope fractionation of N (¹⁵ε) and O (¹⁸ε) of 31‰ to 65‰ (48.3±2.0‰ on average) and 11‰ to 39‰ (18.9±1.7‰ on average), respectively. The N isotope effects were, unexpectedly, much higher than reported in the literature for heterotrophic denitrification (typically ranging from 5‰ to 30‰) and in other environmental settings (e.g., groundwater, marine sediments and agricultural soils). In addition, the ratios of Δδ¹⁸O:Δδ¹⁵N ranged from 0.28 to 0.60 (0.38±0.02 on average), which were lower than the canonical ratios of 0.5 to 1 for denitrification reported in other terrestrial and freshwater systems. We suggest that the isotope effects of denitrification for soils may vary greatly among regions and soil types and that gaseous N losses may have been overestimated for terrestrial ecosystems in previous studies in which lower fractionation factors were applied.

The impact of post-fire salvage logging on microbial nitrogen cyclers in Mediterranean forest soil

Forest fires are a regular occurrence in the Mediterranean basin. High severity fires and post-fire management can affect biological, chemical and physical properties of soil, including the composition and abundance of soil microbial communities. Salvage logging is a post-fire management strategy, which involves the removal of burnt wood from land after a fire. The main objective of this work was to evaluate the impact of post-fire salvage logging and microaggregation on soil microbial communities, specifically on the abundance of nitrogen cyclers and, thus, the potential of the soil for microbial nitrogen cycling. The abundance of nitrogen cyclers was assessed by quantification of microbial nitrogen cycling genes in soil DNA, including nifH (involved in nitrogen fixation), nirS/K and nosZ (involved in denitrification), amoA-B and amoA-Arch (involved in bacterial and archaeal nitrification, respectively). It was demonstrated that salvage logging reduced bacterial load post-fire when compared to tree retention control and resulted in significant changes to the abundance of functional bacteria involved in nitrogen cycling. Microbial gene pools involved in various stages of the nitrogen cycle were larger in control soil than in soil subjected to post-fire salvage logging and were significantly correlated with organic matter, available phosphorous, nitrogen and aggregate stability. The microaggregate fraction of the soil, which has been associated with greater organic carbon, was shown to be a hotspot for nitrogen cyclers particularly under salvage logging. The impact of post-fire management strategies on soil microbial communities needs to be considered in relation to maintaining ecosystem productivity, resilience and potential impact on climate change.

Nitrogen isotopes suggest a change in nitrogen dynamics between the Late Pleistocene and modern time in Yukon, Canada

A magnificent repository of Late Pleistocene terrestrial megafauna fossils is contained in ice-rich loess deposits of Alaska and Yukon, collectively eastern Beringia. The stable carbon (δ13C) and nitrogen (δ15N) isotope compositions of bone collagen from these fossils are routinely used to determine paleodiet and reconstruct the paleoecosystem. This approach requires consideration of changes in C- and N-isotope dynamics over time and their effects on the terrestrial vegetation isotopic baseline. To test for such changes between the Late Pleistocene and modern time, we compared δ13C and δ15N for vegetation and bone collagen and structural carbonate of some modern, Yukon, arctic ground squirrels with vegetation and bones from Late Pleistocene fossil arctic ground squirrel nests preserved in Yukon loess deposits. The isotopic discrimination between arctic ground squirrel bone collagen and their diet was measured using modern samples, as were isotopic changes during plant decomposition; Over-wintering decomposition of typical vegetation following senescence resulted in a minor change (~0-1 ‰) in δ13C of modern Yukon grasses. A major change (~2-10 ‰) in δ15N was measured for decomposing Yukon grasses thinly covered by loess. As expected, the collagen-diet C-isotope discrimination measured for modern samples confirms that modern vegetation δ13C is a suitable proxy for the Late Pleistocene vegetation in Yukon Territory, after correction for the Suess effect. The N-isotope composition of vegetation from the fossil arctic ground squirrel nests, however, is determined to be ~2.8 ‰ higher than modern grasslands in the region, after correction for decomposition effects. This result suggests a change in N dynamics in this region between the Late Pleistocene and modern time.

Agriculture is a major source of NO x pollution in California

Nitrogen oxides (NO _x = NO + NO₂) are a primary component of air pollution-a leading cause of premature death in humans and biodiversity declines worldwide. Although regulatory policies in California have successfully limited transportation sources of NO _x pollution, several of the United States' worst-air quality districts remain in rural regions of the state. Site-based findings suggest that NO _x emissions from California's agricultural soils could contribute to air quality issues; however, a statewide estimate is hitherto lacking. We show that agricultural soils are a dominant source of NO _x pollution in California, with especially high soil NO _x emissions from the state's Central Valley region. We base our conclusion on two independent approaches: (i) a bottom-up spatial model of soil NO _x emissions and (ii) top-down airborne observations of atmospheric NO _x concentrations over the San Joaquin Valley. These approaches point to a large, overlooked NO _x source from cropland soil, which is estimated to increase the NO _x budget by 20 to 51%. These estimates are consistent with previous studies of point-scale measurements of NO _x emissions from the soil. Our results highlight opportunities to limit NO _x emissions from agriculture by investing in management practices that will bring co-benefits to the economy, ecosystems, and human health in rural areas of California.

Nitrogen and carbon isotopic dynamics of subarctic soils and plants in southern Yukon Territory and its implications for paleoecological and paleodietary studies

We examine here the carbon and nitrogen isotopic compositions of bulk soils (8 topsoil and 7 subsoils, including two soil profiles) and five different plant parts of 79 C3 plants from two main functional groups: herbs and shrubs/subshrubs, from 18 different locations in grasslands of southern Yukon Territory, Canada (eastern shoreline of Kluane Lake and Whitehorse area). The Kluane Lake region in particular has been identified previously as an analogue for Late Pleistocene eastern Beringia. All topsoils have higher average total nitrogen δ15N and organic carbon δ13C than plants from the same sites with a positive shift occurring with depth in two soil profiles analyzed. All plants analyzed have an average whole plant δ13C of -27.5 ± 1.2 ‰ and foliar δ13C of -28.0 ± 1.3 ‰, and average whole plant δ15N of -0.3 ± 2.2 ‰ and foliar δ15N of -0.6 ± 2.7 ‰. Plants analyzed here showed relatively smaller variability in δ13C than δ15N. Their average δ13C after suitable corrections for the Suess effect should be suitable as baseline for interpreting diets of Late Pleistocene herbivores that lived in eastern Beringia. Water availability, nitrogen availability, spacial differences and intra-plant variability are important controls on δ15N of herbaceous plants in the study area. The wider range of δ15N, the more numerous factors that affect nitrogen isotopic composition and their likely differences in the past, however, limit use of the modern N isotopic baseline for vegetation in paleodietary models for such ecosystems. That said, the positive correlation between foliar δ15N and N content shown for the modern plants could support use of plant δ15N as an index for plant N content and therefore forage quality. The modern N isotopic baseline cannot be applied directly to the past, but it is prerequisite to future efforts to detect shifts in N cycling and forage quality since the Late Pleistocene through comparison with fossil plants from the same region.

Coupled molecular and isotopic evidence for denitrifier controls over terrestrial nitrogen availability

Denitrification removes ecologically available nitrogen (N) from the biosphere and influences both the pace and magnitude of global climate change. Disagreements exist over the degree to which this microbial process influences N-availability patterns across Earth's ecosystems. We combine natural stable isotope methods with qPCR to investigate how denitrifier gene abundance is related to variations in nitrate (NO3-) pool sizes across diverse terrestrial biomes and conditions. We analyze NO3- isotope composition (15N/14N, 18O/16O) and denitrifier gene nirS in 52 soil samples from different California ecosystems, spanning desert, chaparral, oak-woodland/savanna and forest. δ15N-NO3- correlates positively with δ18O-NO3- (P⩽0.03) and nirS abundance (P=0.00002) across sites, revealing the widespread importance of isotopic discrimination by soil denitrifiers. Furthermore, NO3- concentrations correlate negatively to nirS (P=0.002) and δ15N-NO3- (P=0.003) across sites. We also observe these spatial relationships in short-term (7-day), in situ soil-incubation experiments; NO3--depletion strongly corresponds with increased nirS, nirS/16 rRNA, and enrichment of heavy NO3- isotopes over time. Overall, these findings suggest that microbial denitrification can consume plant-available NO3- to low levels at multiple time scales, contributing to N-limitation patterns across sites, particularly in moist, carbon-rich soils. Furthermore, our study provides a new approach for understanding the relationships between microbial gene abundance and terrestrial ecosystem functioning.