N-cycling Processes Research Articles

The long-acting herbicide mesosulfuron-methyl inhibits soil microbial community assembly mediating nitrogen cycling.

Mesosulfuron-methyl is a widely used herbicide in wheat fields. We previously reported that mesosulfuron-methyl alters the bacterial/fungal community structure in experimental indoor microcosms, ultimately affecting NO3--N and NH4+-N contents in soil nitrogen (N) cycling. However, how mesosulfuron-methyl application alter soil N cycling by changing microbial community assembly is unknown. Here, we designed an outdoor experiment comprising 2-month periods to investigate changes in soil N-cycle functional genes and structural shifts in the microbial community assembly in response to mesosulfuron-methyl applied at 11.25 and 112.5g a.i. hm-2. Results showed that high mesosulfuron-methyl input significantly decreased AOA amoA and nirK abundances within the initial 15 days, but increased AOB amoA on day 60. The nifH abundance displayed a stimulation-inhibition trend. Moreover, high mesosulfuron-methyl input decreased the network's complexity, and newly formed multiple network modules exhibited strong negative associations with nifH, AOB amoA, nirK and nirS. Further structural equation model demonstrated that mesosulfuron-methyl did reveal strong direct inhibition of nirK, and it indirectly affected nirK by changing nifH abundance and Planomicrobium. Thus mesosulfuron-methyl perturbs N-cycling processes by reshaping bacterial community assembly. Taken together, our study provides theoretical support for determining the microbiological mechanism by which mesosulfuron-methyl affects soil N cycling.

Regulation of denitrification/ammonia volatilization by periphyton in paddy fields and its promise in rice yield promotion.

Nitrogen (N) is the most limiting nutrient in rice production. N loss via denitrification and ammonia (NH3 ) volatilization decreases N utilization efficiency. The effect of periphyton (a widespread soil surface microbial aggregate in paddy soil) on N-cycling processes and rice growth in paddy soils remain unclear. The purpose of this study was to reveal the interactions of periphyton with the overlying water and sediment in paddy soils on denitrification/NH3 emissions and rice yield by combining pot experiments and path analysis modeling. The sediment exerted significant direct and positive effects on denitrification. The periphyton both directly and indirectly enhanced denitrification, mainly by regulating the ammonium (NH4 + )-N content in the sediment. The total contribution of periphyton to denitrification was stronger than that of the overlying water but smaller than that of the sediment. The pH in the overlying water and the NH4 + -N content in the sediment had a strong positive effect on NH3 volatilization. Although the periphyton biomass and chlorophylla directly prohibited NH3 emissions, this was counterbalanced by the indirect stimulation effects of the periphyton due to its positive alteration of the pH. Moreover, periphyton facilitated rice yield by 10.2% by releasing N. Although the periphyton may have driven N loss by regulating the NH4 + -N content in the sediment and the pH in the overlying water, our study also found that the periphyton was considered a temporary N sink and provided a sustained release of N for rice, thus increasing the rice yield. © 2022 Society of Chemical Industry.

Long-term N-addition alters the community structure of functionally important N-cycling soil microorganisms across global grasslands

Anthropogenic nitrogen (N) input is known to alter the soil microbiome, but how N enrichment influences the abundance, alpha-diversity and community structure of N-cycling functional microbial communities in grasslands remains poorly understood. Here, we collected soils from plant communities subjected to up to 9 years of annual N-addition (10 g N m−2 per year using urea as a N-source) and from unfertilized plots (control) in 30 grasslands worldwide spanning a large range of climatic and soil conditions. We focused on three key microbial groups responsible for two essential processes of the global N cycle: N2 fixation (soil diazotrophs) and nitrification (AOA: ammonia-oxidizing archaea and AOB: ammonia-oxidizing bacteria). We targeted soil diazotrophs, AOA and AOB using Illumina MiSeq sequencing and measured the abundance (gene copy numbers) using quantitative PCR. N-addition shifted the structure of the diazotrophic communities, although their alpha-diversity and abundance were not affected. AOA and AOB responded differently to N-addition. The abundance and alpha-diversity of AOB increased, and their community structure shifted with N-addition. In contrast, AOA were not affected by N-addition. AOA abundance outnumbered AOB in control plots under conditions of low N availability, whereas N-addition favoured copiotrophic AOB. Overall, N-addition showed a low impact on soil diazotrophs and AOA while effects for AOB communities were considerable. These results reveal that long-term N-addition has important ecological implications for key microbial groups involved in two critical soil N-cycling processes. Increased AOB abundance and community shifts following N-addition may change soil N-cycling, as larger population sizes may promote higher rates of ammonia oxidation and subsequently increase N loss via gaseous and soil N-leaching. These findings bring us a step closer to predicting the responses and feedbacks of microbial-mediated N-cycling processes to long-term anthropogenic N-addition in grasslands.

Deciphering the nitrate sources and processes in the Ganga river using dual isotopes of nitrate and Bayesian mixing model

The dual isotopes of dissolved NO3- (n = 43) has been used to delineate the nitrate sources and N-cycling processes in the Ganga river. The proportional contribution of nitrate from different sources has been estimated using the Bayesian mixing model. The seasonal NO3- concentration in the lower stretch of the river Ganga varied between 4.1 and 64.1 μM with higher concentration during monsoon and post-monsoon season and lower concentration during the pre-monsoon and winter season. The temporal variation in the isotopic values ranged between +0.0 and +9.6‰ for δ15NNO3- and −1.2 to +11.0‰ for δ18ONO3-. The spatial NO3- concentration during the post-monsoon season varied between 23.2 and 57.7 μM, with higher values from the middle and lower values from the lower stretch of the river Ganga. The isotopic ratio during the post-monsoon season varied between −1.0 and +11.3‰ for δ15NNO3- and −4.6 to +5.2‰ for δ18ONO3-. The temporal dataset from the lower stretch of the river Ganga showed the dominance of nitrate derived from the nitrification of soil organic matter (SOM) (average ∼53.4%). The nitrate contribution from synthetic fertilizers was observed to be higher during the post-monsoon season (34.7 ± 23.4%) compared to that in the monsoon (25.5 ± 19.5%) and pre-monsoon (22.2 ± 19.6%) season. No significant seasonal variations were observed in the nitrate input from manure/sewage (∼13.9%). Spatial samples collected during the post-monsoon season showed higher contribution of synthetic fertilizer in the lower stretch (34.6 ± 22.7%) compared to the middle stretch (21.1 ± 18.2%), which indicates greater influence of the agricultural activity in the lower stretch. The dual isotope study of dissolved NO3- established that the nitrate in the Ganga river water is mostly derived from the nitrification of incoming organic compounds and is subsequently removed via assimilatory nitrate uptake. The study also emphasises significant nitrification and assimilatory nitrate removal processes operating in the mixing zone of the Ganga river and Hooghly estuary.

Snow Exclusion Does Not Affect Soil Ammonia-Oxidizing Bacteria and Archaea Communities

Soil ammonia-oxidizing microorganisms play important roles in nitrogen (N) cycling in cold ecosystems, but how changes in snow cover will affect their distribution and associated functional characteristics remains unclear. A snow manipulation experiment was conducted to explore the effects of snow exclusion on soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities and functional characteristics in a spruce forest in the eastern Tibet Plateau. Results showed that the amoA gene abundance and community composition of AOA and AOB did not differ between snow regimes but varied among winter periods. AOA and AOB gene abundances showed a decreasing trend during the snow cover melting period. During the deep snow cover period, Thaumarchaeota and Crenarchaeota in the AOA community decreased significantly, while Proteobacteria and Nitrosospira in the AOB community increased significantly. The main factors affecting the changes in AOA and AOB community diversity and composition were soil MBN, nitrate nitrogen, and temperature, while AOA and AOB community diversity and composition were also significantly correlated with soil enzyme activities related to N cycling. These results recommend that the season-driven variations strongly affected soil ammonia-oxidizing community and functional characteristics more than momentary snow cover change. Such findings offer new insights into how soil N-cycling processes would respond to reduced snowfall in high-altitude regions.

Soil Microbial Co-Occurrence Patterns under Controlled-Release Urea and Fulvic Acid Applications.

The increasing amount of agricultural applications of controlled-release urea (CRU) and fulvic acids (FA) demands a better understanding of FA’s effects on microbially mediated nitrogen (N) nutrient cycling. Herein, a 0–60 day laboratory experiment and a consecutive pot experiment (2016–2018) were carried out to reveal the effects of using CRU on soil microbial N-cycling processes and soil fertility, with and without the application of FA. Compared to the CRU treatment, the CRU+FA treatment boosted wheat yield by 22.1%. To reveal the mechanism of CRU+FA affecting the soil fertility, soil nutrient supply and microbial community were assessed and contrasted in this research. From 0–60 days, compared with the CRU treatment, leaching NO3−-N content of CRU+FA was dramatically decreased by 12.7–84.2% in the 20 cm depth of soil column. Different fertilizers and the day of fertilization both have an impact on the soil microbiota. The most dominant bacterial phyla Actinobacteria and Proteobacteria were increased with CRU+FA treatment during 0–60 days. Network analysis revealed that microbial co-occurrence grew more intensive during the CRU+FA treatment, and the environmental change enhanced the microbial community. The CRU+FA treatment, in particular, significantly decreased the relative abundance of Sphingomonas, Lysobacter and Nitrospira associated with nitrification reactions, Nocardioides and Gaiella related to denitrification reactions. Meanwhile, the CRU+FA treatment grew the relative abundance of Ensifer, Blastococcus, and Pseudolabrys that function in N fixation, and then could reduce NH4+-N and NO3−-N leaching and improve the soil nutrient supply. In conclusion, the synergistic effects of slow nutrition release of CRU and growth promoting of FA could improve the soil microbial community of N cycle, reduce the loss of nutrients, and increase the wheat yield.

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.

The quality of organic amendments affects soil microbiome and nitrogen-cycling bacteria in an organic farming system

Organic amendments are applied in organic farming systems to provide nutrients for crop uptake and to improve soil health. Compost is often favored over fresh manure for food safety reasons, while fresh manure can be a valuable source of readily available nitrogen (N). However, the potential for fresh versus composted manure to differentially affect soil microbial and N-cycling functional communities over multiple seasons remains unknown. We compared the effect of composted vs. fresh cattle manure on soil microbial communities using taxonomic and functional approaches. Soils were collected from field plots with three organic N treatments: control (no amendment), composted manure (compost, 224 kg/ha total N), and fresh manure (manure, 224 kg/ha total N) in an organic production system. Illumina amplicon sequencing was used to comprehensively assess the bacterial community (16S rRNA genes), fungal community (ITS), ureolytic community (ureC), chitinolytic community (chiA), bacterial ammonia oxidizers (AOBamoA), and nitrite oxidizers (Nitrospira nxrB). The results showed that both compost and manure treatment significantly changed the soil microbial communities. Manure had a stronger effect than compost on soil bacterial and fungal community composition, as well as on the ureolytic and chitinolytic communities, while compost treated soils had higher microbial richness than manure treated soils. Both taxonomic and functional approaches showed that the microbial community was more responsive to fresh manure than to compost. Manure treated soil also had more complex microbial interactions than compost treated soil. The abundance and community composition of N-cycling functional groups often played more limited roles than soil chemical properties (soil organic carbon, extractable organic carbon, and pH) in driving N-cycling processes. Results from our study may guide strategies for the management of organic amendments in organic farming systems and provide insights into the linkages between soil microbial communities and soil function.

Closing the circle for urban food waste anaerobic digestion: The use of digestate and biochar on plant growth in potting soil

Food waste can be used via anaerobic digestion (AD) to produce biogas. The liquid by-product (digestate) contains nitrogen (mainly as ammonium) which is susceptible to N loss as a fertiliser and also faces logistical constraints for agricultural use. Biochar can adsorb and retain nutrients and alter microbial N-cycling processes. We investigated the use of digestate as a nutrient source and its interactions with biochar when applied to potting mix targeted for localised urban use. Tomato (Solanum lycopersicum L.) plants were grown for 45 days in potting mix amended with five rates of food-waste-derived digestate (0, 2, 4, 6, 8 and 10% v/v), with and without biochar (10% v/v). At harvest, plant growth parameters and potting soil characteristics were measured. The rhizosphere bacterial community was profiled by amplicon sequencing followed by an in-silico analysis of putative functional genes. Plant biomass and shoot N concentration increased with digestate addition in a typical nutrient dose-response curve. While growth lagged when digestate was combined with biochar, both treatments reached a similar maximum shoot yield. Biochar application decreased soil mineral N content and two putative ammonium nitrification cycling genes, AmoA and AmoB, which prevent the conversion of NO3- from NH4+. Rhizosphere bacteria beta-diversity separated into two distinct clusters, with and without biochar, at all levels of digestate. Addition of biochar with digestate decreased the availability of soil mineral N by decreasing the mineralisation of nitrogen which likely reduced the risk of N loss. The rhizosheath bacterial community mediated this effect. Further quantification of these processes may aid in optimising of the benefits for the environment and plant growth from the transformation of blended organic urban wastes into organic fertilisers for potting soils.

Slope aspect determines the abundance and composition of nitrogen‐cycling microbial communities in an alpine ecosystem

Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning.

Distinct soil microbial communities under Ageratina adenophora invasions.

Ageratina adenophora is one of the most hazardous invasive weeds in China. It can form a single species community quickly and cause extensive ecological harm. The belowground microbial community can participate in nutrient transformation in soil and plays an important role in the invasiveness of exotic plant species. We selected sampling sites with different invasion levels of A. adenophora. The soil property and soil biogeochemical activity were measured in both bulk and rhizosphere soil under the aggressive weed A. adenophora and under adjacent native plants. The composition of bacterial communities was investigated using high-throughput 16S rRNA gene sequencing. We found that the rhizosphere habitat selectively accumulated Sphingomonas and Steroidobacter and reduced the abundance of Gaiella and Gp6 regardless of plant host. The presence of A. adenophora caused a switch in microbial composition from Aeromicrobium and Marmoricola to Reyranella and Bradyrhizobium in the bulk soil, and from Gp4, Pirellula, Lysobacter and Aridibacterrae to Reyranella and Streptomyces in the rhizosphere soil. We also revealed specific microbes that closely related with N-cycling processes. In addition, soil pH was the main factor affecting microbial communities in both bulk and rhizosphere soil. Our study confirmed that the rhizosphere environment imposed homogenous microbial communities. The invasion of A. adenophora selected specialized bacterial communities in soils and specific microbes that potentially mediated soil nutrition cycling. Our findings provide ecological explanation to explain how the underground microbes help A. adenophora invasive.

Conversion of grassland to cropland altered soil nitrogen-related microbial communities at large scales

Land-use changes may dramatically disturb underground microbial biodiversity, especially in the fragile ecological areas. However, the impact of conversion of grassland to cropland on soil nitrogen (N)-related microbial communities is not fully understood in the farming-pastoral ecotone of northern China. Therefore, 24 paired grassland and cropland soil samples were collected in this region to investigate the community structure and assembly processes of soil N-related microorganisms via amplicon sequencing of nifH, archaeal and bacterial amoA, and nxrB genes. The results showed higher ammonia-oxidizing bacteria (AOB) alpha diversity but a lower nitrite-oxidizing bacteria (NOB) diversity in cropland soil compared to grassland soil. Non-metric multidimensional scaling ordinations revealed that diazotroph, AOB and NOB communities differed considerably between grassland and cropland soil. Soil microbial co-occurrence networks showed that conversion of grassland to cropland significantly lowered the average degree, average clustering coefficient, total nodes and links, resulting in less complex microbial networks in cropland soil. Land-use change altered AOB community assembly processes, resulting from a stochasticity-dominated process in grassland soil to a determinism-dominated process in cropland soil. In contrast, deterministic processes were dominant in diazotroph community assembly, whereas stochastic processes were dominant in constructing ammonia-oxidizing archaea and NOB communities in both grassland and cropland soil. These results provide novel evidence that the conversion of grassland to cropland altered the diversity and assembly processes of soil microbial communities involved in soil N-cycling processes, which has important implications for the potential changes in soil functions under land-use changes.

Emergent properties of microbial communities drive accelerated biogeochemical cycling in disturbed temperate forests.

Despite ever-increasing availability of detailed information about microbial community structure, relationships of microbial diversity with ecosystem functioning remain unclear. We investigated these relationships at the Coweeta Hydrologic Laboratory, where past forest disturbances (e.g., clear-cut) have altered both ecosystem processes (e.g., increased N export) and microbial communities (e.g., increased bacterial diversity). We sampled soils from disturbed and adjacent reference forests, characterized resident microbial communities, and measured several microbial C-cycle and N-cycle process rates. Microbial communities from historically disturbed soils exhibited altered ecosystem functioning, including generally higher rates of C- and N-cycle processes. Disturbed soil microbial communities also exhibited altered ecosystem multifunctionality, a composite variable consisting of all measured process rates as well as extracellular enzyme activities. Although we found few relationships between ecosystem functions and microbial alpha diversity, all functions were correlated with microbial community composition metrics, particularly r:K strategist ratios of bacterial phyla. Additionally, for both ecosystem multifunctionality and specific processes (i.e., C- and N-mineralization), microbial metrics significantly improved models seeking to explain variation in process rates. Our work sheds light on the links between microbial communities and ecosystem functioning and identifies specific microbial metrics important for modeling ecosystem responses to environmental change.

Fertilizer stabilizers reduce nitrous oxide emissions from agricultural soil by targeting microbial nitrogen transformations

Nitrous oxide (N2O) is a pollutant released from agriculture soils following N fertilizer application. N stabilizers, such as N-(n-butyl) thiophosphoric triamide (NBPT) and 3,4-dimethylpyrazole phosphate (DMPP) could mitigate these N2O emissions when applied with fertilizer. Here, field experiments were conducted to investigate the microbial mechanisms by which NBPT and DMPP mitigate N2O emissions following urea application. We determined dynamic N2O emissions and inorganic N concentrations for two wheat seasons and combined this with metagenomic sequencing. Application of NBPT, DMPP, and both NBPT and DMPP together with urea decreased mean N2O accumulative emissions by 77.8, 91.4 and 90.7%, respectively, compared with urea application alone, mainly via repressing the increase in NO2− concentration after N fertilization. Sequencing results indicated that urea application enriched microorganisms that were positively correlated with N2O production, whereas N stabilizers enriched microorganisms that were negatively correlated with N2O production. Furthermore, compared to urea application alone, NBPT with urea reduced the abundances of genes related to denitrification, including napA/nasA, nirS/nirK, and norBC, resulting in a higher soil NO3− pool. Conversely, DMPP application, either alone or together with NBPT, decreased the abundance of genes involved in ammonia oxidation and denitrification, including amoCAB, hao, napA/nasA, nirS/nirK, and norBC, and maintained a greater soil NH4+ pool. Both N stabilizers resulted in similar abundances of nirABD—which is related to NO2− reducers—as when no N fertilizer was applied, which could prevent NO2− accumulation, consequently mitigating N2O emissions. These findings suggest that the high effectiveness of N stabilizers on mitigating N2O emissions could be attributed to changes to soil microbial communities and N-cycling functional genes to control the by-product or intermediate products of microbial N-cycling processes in agricultural soils.

Dynamics of Soil Microbial N-Cycling Strategies in Response to Cadmium Stress.

Globally increasing trace metal contamination of soils requires a better mechanistic understanding of metal-stress impacts on microbially mediated nutrient cycling. Herein, a 5-month laboratory experiment was employed to assess the effects of cadmium (Cd) on soil microbial N-cycling processes and associated functional gene abundance, with and without urea amendment. In non-N-amended soils, Cd progressively stimulated microbial populations for N acquisition from initial dissolved organic N (DON) to later recalcitrant organic N. The acceleration of N catabolism was synchronously coupled with C catabolism resulting in increased CO2/N2O fluxes and adenosine triphosphate (ATP) contents. The abundance of microbes deemed inefficient in N catabolism was gradually repressed after an initial stimulation period. We posit that enhanced exergonic N processes diminished the need for endergonic activities as a survival strategy for N communities experiencing metal stress. With urea amendment, Cd exhibited an initial stimulation effect on soil nitrification and a later a promotion effect on mineralization, along with an increase in the associated microbial populations. In N-amended soils, Cd accelerated N/C transformation processes, but decreased N2O and CO2 fluxes by 19 and 14%, respectively. This implies that under eutrophic conditions, Cd synchronously altered microbial C/N metabolism from a dominance of catabolic to anabolic processes. These results infer a nutrient-based adjustment of microbial N-cycling strategies to enhance their metal resistance.

Thinning promotes the nitrogen and phosphorous cycling in forest soils

Thinning, a major practice of even-aged forest management, notably affects the stand structure and microclimates and thus in turn soil nitrogen (N) and phosphorous (P) cycling. However, the magnitude and direction of these effects remain uncertain. We performed a meta-analysis of 1228 observations from 115 studies worldwide to explore the effects of thinning on forest soil N and P processes. The results showed that thinning increased the concentrations of soil nitrate, total P, and available P by 11.7%, 6.1%, and 11.4%, respectively, but had no effect on the concentrations of soil total N and ammonium. Thinning stimulated soil microbial activities regulating soil N and P cycling, evidenced by the increased microbial biomass N and the activities of N- and P-acquiring extracellular enzymes. Thinning also increased net N mineralization and nitrification rates, but did not significantly affect N2O emission. However, these thinning effects varied with climates and forest biomes. The effect sizes of N-cycling processes were significantly correlated with mean annual precipitation or mean annual temperature, implying that these N fluxes are more sensitive to thinning in warm and humid regions. Collectively, our meta-analysis indicates that thinning promotes forest soil N and P cycling and increases the soil fertility, which are conducive to improving forest ecosystem functions.

Deepened snow enhances gross nitrogen cycling among Pan-Arctic tundra soils during both winter and summer

Many Arctic regions currently experience an increase in winter snowfall as a result of climate change. Deepened snow can enhance thermal insulation of the underlying soil during winter, resulting in warmer soil temperatures that promote soil microbial nitrogen (N)-cycle processes and the availability of N and other nutrients. We conducted an ex situ study comparing the effects of deepened snow (using snow fences that have been installed for 3–13 years) on microbial N-cycle processes in late summer (late growing season) and winter (late snow-covered season) among five tundra sites in three different geographic locations across the Arctic (Greenland (dry and wet tundra), Canada (mesic tundra), and Svalbard, Norway (heath and meadow tundra)). Soil gross N cycling rates (mineralization, nitrification, immobilization of ammonium (NH4+) and nitrate (NO3−), and denitrification) were determined using a15N pool dilution. Potential denitrification activity (PDA) and nitrous oxide reductase activity (N2OR) were measured to assess denitrifying enzyme activities.The deepened snow treatment across all sites had a significant effect of the potential soil capacity of accelerating N cycling rates in late winter, including quadrupled gross nitrification, tripled NO3−-N immobilization, and doubled denitrification as well as significantly enhanced late summer gross N mineralization, denitrification (two-fold) and NH4+-N availability. The increase in gross N mineralization and nitrification rates were primarily driven by the availability of dissolved organic carbon (DOC) and nitrogen (DON) across sites. The largest increases in winter DOC and DON concentrations due to deepened snow were observed at the two wetter sites (wet and mesic tundra), and N cycling rates were also more strongly affected by deepened snow at these two sites than at the three other drier sites. Together, these results suggest that the potential effects of deepened winter snow in stimulating microbial N-cycling activities will be most pronounced in relatively moist tundra ecosystems. Hence, this study provides support to prior observations that growing season biogeochemical cycles in the Arctic are sensitive to snow depth with altered nutrient availability for microorganisms and vegetation. It can be speculated that on the one hand growing season N availability will increase and promote plant growth, but on the other hand foster increased water- and gaseous (e.g. N2 and N2O) N-losses with implications for overall nutrient status.

Microbially facilitated nitrogen cycling in tropical corals

Tropical scleractinian corals support a diverse assemblage of microbial symbionts. This ‘microbiome’ possesses the requisite functional diversity to conduct a range of nitrogen (N) transformations including denitrification, nitrification, nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). Very little direct evidence has been presented to date verifying that these processes are active within tropical corals. Here we use a combination of stable isotope techniques, nutrient uptake calculations and captured metagenomics to quantify rates of nitrogen cycling processes in a selection of tropical scleractinian corals. Denitrification activity was detected in all species, albeit with very low rates, signifying limited importance in holobiont N removal. Relatively greater nitrogen fixation activity confirms that corals are net N importers to reef systems. Low net nitrification activity suggests limited N regeneration capacity; however substantial gross nitrification activity may be concealed through nitrate consumption. Based on nrfA gene abundance and measured inorganic N fluxes, we calculated significant DNRA activity in the studied corals, which has important implications for coral reef N cycling and warrants more targeted investigation. Through the quantification and characterisation of all relevant N-cycling processes, this study provides clarity on the subject of tropical coral-associated biogeochemical N-cycling.

Nitrogen cycling processes in sediments of the Pearl River Estuary: Spatial variations, controlling factors, and environmental implications

Numerous studies have unveiled the importance of nitrogen (N) transformation processes over the past decades, but comprehensive studies of key N-cycling processes are still rare in estuarine and coastal ecosystems. Here, we used isotope pairing, isotope-tracing, and isotope dilution techniques combined with quantitative polymerase chain reaction to investigate microbial N-cycling processes in surface sediments (0–5 cm) of the Pearl River Estuary. The average rates of denitrification, anammox, DNRA, N2 fixation, N mineralization, and NH4+ immobilization were 1.41 ± 0.89, 0.067 ± 0.033, 0.47 ± 0.28, 0.31 ± 0.30, 1.86 ± 1.09, and 1.30 ± 0.83 μg N g−1 dry d−1, respectively. Sediment grain size, organic matter, nutrients, and Fe2+/Fe3+ rather than gene abundances controlled these rates. The abundances of bacterial 16S rRNA, anammox 16S rRNA, nirS, nrfA, nifH, bacteria-amoA, and archaea-amoA genes were significantly correlated with organic matter, nutrients, and sediment grain size. In general, higher rates and gene abundance was occurred in outer than inner estuary. Among these pathways, denitrification contributed 41.83–90.13% of the total nitrate reduction, as compared to 0.94–8.58% for anammox and 8.55–54.56% for DNRA. The sediment N-loss fluxes caused by denitrification and anammox in our study area (1.5 × 1010 m2) was about 6.2 × 107 mol N d−1, accounting for ~42.1% of the riverine dissolved inorganic N fluxes, suggesting that the sediment of the Pearl River Estuary has great significance to the mitigation and controlling of N pollution in this ecosystem. Additionally, the net NH4+ production via sediment microbial pathways (N mineralization, N2 fixation, DNRA, NH4+ immobilization, and anammox) was estimated at ~ 5.5 × 107 mol N d−1, while the net NO3− consumption (denitrification, anammox, and DNRA) was ~8.3 × 107 mol N d−1. Overall, these results highlight the importance of complicated N-cycling processes in controlling the N budget in the Pearl River Estuary and improve the understanding of both the processes and associated controlling factors in estuarine and coastal ecosystems.

Different sexual impacts of dioecious Populus euphratica on microbial communities and nitrogen cycle processes in natural forests

Plant-soil microbe interactions are determined by plant characters. Sexual dimorphism in root development, nitrogen (N) assimilation and resource allocation have been studied in different environments. However, how dioecious plants affect soil microbial communities in natural forests, particularly in low precipitation regions, is still poorly known. In this study, natural Populus euphratica forests were investigated in three arid regions. We hypothesized that males and females impose sex-specific impacts on physiochemical traits of soil, microbial communities and N-cycling processes. We discovered only little sex effect on most physiochemical traits, and bacterial and fungal communities in top soil (0–20 cm) in the three studied forests. However, the sex effect was greater in deep soil. Compared with fungi, the structure and composition of bacterial communities were affected more by plant sex in the rhizosphere and bulk soil. Sex indirectly affected N-cycling processes through a negative impact on the soil water content. Expressions of AOA, AOB, nifH, nirS and nirK in the rhizosphere soil were significantly affected by sex, forest site and their interactions. Proteobacteria, Actinobacteria and Firmicutes in the rhizosphere and bulk soils of P. euphratica males showed more significant effects on ammoxidation, N fixation, denitrification and protease activities when compared to females. The results suggest that sexual differences in shaping bacterial communities and affecting N-cycling processes are greater when the soil becomes drier. Thus, low precipitation causes intense sex differences in the nitrogen uptake and use efficiency. Our study highlights the importance of sexual effects on shaping specific microbial communities and N-cycling processes.