nirS-type Denitrifiers Research Articles

Nitrogen and phosphorus additions alter soil N transformations in a Metasequoia glyptostroboides plantation.

Nitrogen (N) and phosphorus (P) enrichment due to anthropogenic activities can significantly affect soil N transformations in forest ecosystems. However, the effects of N and P additions on nitrification and denitrification processes in Metasequoia glyptostroboides plantations, and economically important forest type in China, remain poorly understood. This study investigated the responses of soil nitrification and denitrification rates, as well as the abundances of nitrifiers and denitrifiers, to different levels of N and P additions in a 6-year nutrient addition experiment in a M. glyptostroboides plantation. Stepwise multiple regression analysis was used to identify the main predictors of nitrification and denitrification rates. The results showed that moderate N addition (N2 treatment, 2.4 mol·m-2) stimulated nitrification rates and abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB), while excessive N and P additions inhibited denitrification rates and reduced the abundance of nirS-type denitrifiers. AOB abundance was the main predictor of nitrification rates under N additions, whereas microbial biomass carbon and nirS gene abundance were the key factors controlling denitrification rates. Under P additions, tree growth parameters (diameter at breast height and crown base height) and AOB abundance were the primary predictors of nitrification and denitrification rates. Our study reveals complex interactions among nutrient inputs, plant growth, soil properties, and microbial communities in regulating soil N transformations in plantation forests. This study also offers valuable insights for formulating effective nutrient management strategies to enhance the growth and health of M. glyptostroboides plantations under scenarios of increasing elevated nutrient deposition.

Response Characteristics and Community Assembly Mechanisms of nirS-Type Denitrifiers in the Alpine Wetland under Simulated Precipitation Conditions.

The nitrogen cycling process in alpine wetlands is profoundly affected by precipitation changes, yet the dynamic response mechanism of denitrifiers to long-term precipitation shifts in the alpine wetland of the Qinghai-Tibet Plateau remains enigmatic. Utilizing high-throughput sequencing analysis of nirS-type functional genes, this study delved into the dynamic response mechanism of nirS-type denitrifiers to precipitation changes in the alpine wetland of Qinghai Lake. The findings revealed that nirS-type denitrifiers in the alpine wetland of Qinghai Lake were primarily Proteobacteria, and Alpha diversity exhibited a negative correlation with the precipitation gradient, with deterministic processes predominating in the community assembly of denitrifying microbes. A 50% increase in rainfall shifted the community assembly process of denitrifiers from deterministic to stochastic. Dominant microflora at the genus level responded significantly to precipitation changes, with aerobic bacteria comprising the majority of differentially abundant taxa (55.56%). As precipitation increased, the complexity of the microbial interaction network decreased, and a 25% reduction in precipitation notably elevated the relative abundance of three key functional groups: chemoheterotrophic, aerobic chemoheterotrophic, and nitrogen fixation. Precipitation notably emerged as the primary regulator of nirS-type denitrifiers in the alpine wetland of Qinghai Lake, accounting for 51% of the variation in community composition. In summary, this study offers a fresh perspective for investigating the ecological processes of nitrogen cycling in alpine ecosystems by examining the diversity and community composition of nirS-type denitrifiers in response to precipitation changes.

Nanoplastics enhance the denitrification process and microbial interaction network in wetland soils

With the widespread presence of plastic waste in ecosystems, it is imperative to understand the response of natural processes to micro- and nanoplastic pollution pressures. However, the effects of nanoplastics on biogeochemical cycles are still overlooked and controversial. This study investigated the effects of three particle sizes (100 μm, 7 μm, and 80 nm) of polystyrene (PS) micro/nanoplastics (0.08 % of mass concentration) on denitrification processes and nirS/nirK denitrifying bacterial communities in wetland soils. The results indicated that PS nanoplastics were found to significantly enhance denitrification rates from 21.30 to 54.73 μmol N2·h−1·kg−1, increasing by 1.57 times compared to the control. Exposure to nanoplastics caused shifts in the composition and structure of the nirS-type denitrifier community. LEfSe analysis, random forest, and Mantel tests revealed that nirS denitrifying bacteria, especially Sideroxydans, played a pivotal role in driving denitrification rates (Mantel's R = 0.24, p = 0.002), likely due to the faster release of organic substrates from nanoplastics. Microbial co-occurrence networks demonstrated that nanoplastic amendments fostered a denser denitrifier network and led to shifts in keystone species. Sideroxydans appeared more likely to cooperate with other bacteria, such as Burkholderiales, to complete denitrification processes. This study suggests that nanoplastics are a potentially stronger driver of denitrification than microplastics, providing insight into the impact of plastic pollutants on biogeochemical cycling in natural wetland ecosystems. Given the widespread distribution of wetlands, the potential increase in gaseous nitrogen emissions due to nanoplastics pollution warrants attention.

Acidification Offset Warming-Induced Increase in N2O Production in Estuarine and Coastal Sediments.

Global warming and acidification, induced by a substantial increase in anthropogenic CO2 emissions, are expected to have profound impacts on biogeochemical cycles. However, underlying mechanisms of nitrous oxide (N2O) production in estuarine and coastal sediments remain rarely constrained under warming and acidification. Here, the responses of sediment N2O production pathways to warming and acidification were examined using a series of anoxic incubation experiments. Denitrification and N2O production were largely stimulated by the warming, while N2O production decreased under the acidification as well as the denitrification rate and electron transfer efficiency. Compared to warming alone, the combination of warming and acidification decreased N2O production by 26 ± 4%, which was mainly attributed to the decline of the N2O yield by fungal denitrification. Fungal denitrification was mainly responsible for N2O production under the warming condition, while bacterial denitrification predominated N2O production under the acidification condition. The reduced site preference of N2O under acidification reflects that the dominant pathways of N2O production were likely shifted from fungal to bacterial denitrification. In addition, acidification decreased the diversity and abundance of nirS-type denitrifiers, which were the keystone taxa mediating the low N2O production. Collectively, acidification can decrease sediment N2O yield through shifting the responsible production pathways, partly counteracting the warming-induced increase in N2O emissions, further reducing the positive climate warming feedback loop.

Relationship between Nitrogen Dynamics and Key Microbial Nitrogen-Cycling Genes in an Intensive Freshwater Aquaculture Pond.

Intensive aquaculture in high-density hybrid snakehead [Channa maculata (♀) × Channa argus (♂)] fishponds can lead to toxic conditions for fish. This study investigated nitrogen migration and transformation in these fishponds during different cultivation periods. Using qPCR technology, we analyzed the abundance variation of nitrogen-cycling microorganisms in water and sediment to reveal the nitrogen metabolism characteristics of hybrid snakehead fishponds. The results showed that fish biomass significantly impacts suspended particulate matter (SPM) flux. At the sediment-water interface, inorganic nitrogen fluxes showed predominant NO3--N absorption by sediments and NH4+-N and NO2--N release, especially in later cultivation stages. Sediments were rich in nirS and AMX 16S rRNA genes (ranging from 4.04 × 109 to 1.01 × 1010 and 1.19 × 108 to 2.62 × 108 copies/g, respectively) with nirS-type denitrifiers potentially dominating the denitrification process. Ammonia-oxidizing bacteria (AOB) were found to dominate the ammonia oxidation process over ammonia-oxidizing archaea (AOA) in both water and sediment. Redundancy analysis revealed a positive correlation between SPM flux, Chlorophyll a (Chl-a), and denitrification genes in the water, and between nitrogen-cycling genes and NH4+/NO2- fluxes at the interface. These findings provide a scientific basis for nitrogen control in hybrid snakehead fishponds.

Changes of Soil Nitrogen Fractions and nirS-Type Denitrifier Microbial Community in Response to N Fertilizer in the Semi-Arid Area of Northeast China

The denitrification process is one of the important processes in the soil nitrogen (N) cycle, and is closely related to the loss of soil N fertilizer. Five treatments were included in this study: N0 (control, no N application); N90 (N application rate 90 kg ha−1); N150 (N application rate 150 kg ha−1); N210 (N application rate 210 kg ha−1); and N270 (N application rate 270 kg ha−1), to study the effect of different N application rates on the soil nirS-type denitrifying bacterial community structure, the influence of key enzyme activities during the denitrification process, and the main environmental factors affecting the variation of the denitrifying bacterial community in maize field soil under the mulched fertigation system in the semi-arid region of Northeast China. The results showed that increasing N fertilizer application significantly increased the contents of soil inorganic N and acid-hydrolyzable organic N, but significantly decreased pH. N fertilizer significantly increased nitrate reductase (NAR) activity and nitrite reductase (NIR) activity. Excessive application of N fertilizer significantly increased the nirS gene copy numbers, and, at the same time, significantly decreased the diversity of nirS-type soil denitrifying bacteria. Proteobacteria was the dominant denitrifying phylum in all treatments, and N application promoted the growth of Bradyrhizobium belonging to this phylum. The application of N fertilizer significantly changed the community structure of nirS denitrifying bacteria, and the NO3−-N content was the most important factor for this observation. Soil organic matter (SOM) and non-hydrolyzable N (NHN) indirectly affected the denitrifying bacterial community structure through NAR activity and NIR activity, while soil total N (TN) and nitrate N (NO3−-N) indirectly affected yield through denitrifying bacterial community structure. Although increasing N fertilizer was beneficial in increasing soil nutrients, the community structure of nirS-type denitrifying bacteria changed significantly. This is attributed to the increase in soil NO3−-N accumulation caused by a large amount of N application. The results of this research provide an important scientific basis for further research on the response mechanism of farmland soil denitrifying microorganisms to different N fertilizer managements under the mulched fertigation system in the semi-arid region of Northeast China.

Combined pot experiments and subsequent DNA-SIP incubations reveal a core microbiota involved in modulating crop nitrogen uptake derived from soil

Revealing the biological mechanisms of the amount of crop nitrogen (N) uptake derived from soil (NDS) is crucial for the prediction of eco-friendly and cost-effective N fertilizer management; however, there is a dearth of studies on this topic, especially on the comprehensive comparison under N-amended and non-amended conditions. Here, we conducted a pot experiment using soils with soil organic matter (SOM) gradients under 15N-labeled urea amended (+N) or non-amended (−N) to explore whether NDS was mediated by a group of core taxa or by individual keystone species. Our results showed that NDS increased with SOM, regardless of N input or not. In addition, NDS under −N conditions was 11.1 %–56.8 % higher than that under +N conditions. We revealed that in addition to SOM and nirS gene, a group of highly interactive core microbes connecting keystone species and some specific taxa made major contributions to NDS variations, though the composition of the core microbes under −N conditions differed from that under +N conditions. These interactive core microbes were considered as core microbiota, which was derived from one module of soil network and contained nirS-type denitrifier, further suggesting their important role in mediating the NDS. Combined with the results from stable isotope probing incubations, it was found that under −N conditions, NDS was negatively correlated with unclassified Rhodobacterales and RB41, both of which showed positive correlations with the unclassified Solibacterales, one of the keystone species identified by network analysis; under +N conditions, NDS was positively correlated with keystone species Skermanella identified by network analysis, and NDS and Skermanella were both positively correlated with Gaiellaceae, Bradyrhizobiaceae, and Solirubrobacter. Our results provide new insights into the factors driving NDS variations, and suggest that the core microbiota connecting keystone species and some specific taxa should be considered as a key factor in N fertilizer management strategies targeting the enhancement of N-use efficiency and agricultural sustainability.

Irrigation rather than fertilization drives the abundance, community structure and assembly process of soil denitrifiers

Fertilization and irrigation have significant impacts on soil nitrogen cycling and associated microbes, yet we have limited understanding on community structure and assembly process of soil denitrifiers. Here, we examined the abundance, diversity, composition, and assembly process of soil denitrifier communities harboring the nirS, nirK, and nosZ genes in soils under long-term (11 years) fertilization and irrigation managements. Our results indicated that irrigation significantly increased the abundance of nirS, nirK, and nosZ genes by 6.10–18.85, 2.36–2.85, and 4.85–6.16 times in the chemical fertilizer (NPK) treatments and by 1.02–13.68, 0.95–1.45, and 1.49–2.28 times in the manure (M) treatments compared to the corresponding control without irrigation (I0), respectively. Principal co-ordinates analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) showed that fertilization had a more important role in altering the nosZ-type denitrifier community structure, while irrigation dominated in influencing the nirS- and nirK-type. Regardless of fertilization, irrigation shifted community assembly of the nirS-type denitrifier from deterministic process to stochastic process, while driving the nosZ-type from stochastic process to deterministic process. The nirK-type denitrifier was determined by stochastic process and was neither affected by fertilization nor irrigation. Network co-occurrence analysis showed that irrigation differently affected the community network complexity under NPK and M. One irrigation (I1) and two irrigations (I2) increased and decreased the network complexity, respectively, in the NPK treatments, while opposite results were found in M. Additionally, soil moisture and pH significantly (p < 0.05) correlated with the gene abundance, community structure, and assembly process of the denitrifiers. Overall, irrigation rather than fertilization greatly induced the changes in abundance, community structure, network structure, and assembly process of the denitrifiers via soil moisture and pH, highlighting the importance of irrigation in regulating soil denitrification associated microbes.

Arbuscular mycorrhizal fungi reduce N2O emissions from degraded residue patches

Nitrous oxide (N2O) is a potent greenhouse gas, and agricultural soils represent a major anthropogenic source. Crop residues provide nutrients for plants but also act as hotspots of N2O production. The hyphae of arbuscular mycorrhizal fungi (AMF) could proliferate in organic patches, utilize released N from the organic patches, and potentially mitigate N2O emissions. However, the effect of AMF on N2O emissions in degraded residue patches and the possible microbial mechanism remain uncertain. Here, a mesocosm experiment was conducted to investigate the impact of AMF (Funneliformis mosseae) inoculation on N2O emissions, availabilities of carbon and nitrogen, extracellular enzyme activities, and the abundance of key N-cycling genes in degraded residue patches. Our results showed that AMF hyphae significantly reduced N2O emissions from degraded residue patches. Quantitative PCR analysis of key functional genes involved in N2O production (amoA, nirK, nirS) and consumption (nosZ) showed that AMF significantly reduced the abundance of the bacterial amoA and nirS genes. NH4+, NO3−, total dissolved nitrogen (TDN), total nitrogen (TN), and dissolved organic carbon (DOC) contents decreased drastically in the presence of AMF. In addition, the activities of all tested extracellular enzymes were significantly decreased by AMF and positively correlated with DOC content. Multiple stepwise regression analysis demonstrated that the abundance of the nirS gene primarily influenced N2O emissions and was positively correlated with DOC content in degraded residue patches. Our findings indicate that AMF suppressed N2O producers, particularly nirS-type denitrifiers, by slowing down the release of C and N from degraded residues, thereby leading to a cascade effect on the decrease of N2O emissions. This study provides a promising approach to mitigate N2O emissions by enhancing AMF in the agroecosystems.

Decreased soil pH weakens the positive rhizosphere effect on denitrification capacity

The stimulating effect of rhizosphere on denitrification is considered to be an unavoidable loss of soil nitrogen (N) and detrimental to crop N use efficiency, which is regulated by crop growth and soil properties. Soil acidification, occurring rapidly in many intensive farming lands, affects both crop growth and soil properties, thereby altering rhizosphere effect on denitrification. However, the mechanism by which soil acidification regulates rhizosphere denitrification still remains unclear. Here, we determined the denitrification capacity (DC) and associated community compositions of nirK- and nirS-type denitrifiers in maize rhizosphere and bulk soils at four acidity gradients (pH = 6.8, 6.1, 5.2, and 4.2). Results showed that the stimulating effect of rhizosphere on DC strongly depended on soil pH. Compared to bulk soil, rhizosphere soil had significantly higher DC at pH ≥ 5.2, but not at pH of 4.2. With increasing soil acidity, the stimulation of rhizosphere on DC (calculated as the difference in DC between rhizosphere and bulk soils) decreased from 8.01 to 0.01 mg N kg-1 d-1. Moreover, soil acidification significantly reduced the differences in dissolved organic carbon (DOC) and abundance of key nirK-type denitrifier taxa between rhizosphere and bulk soils, both of which were positively related to the stimulation of rhizosphere on DC. These findings demonstrated that soil acidification could weaken the positive rhizosphere effect on denitrification via regulated C availability and associated nirK-type denitrifier community, potentially reducing N loss risk in rhizosphere soil. The independent role of soil pH should be fully considered when modelling N behaviour in plant-soil systems.

Effects of grazing prohibition on nirK- and nirS-type denitrifier communities in salt marshes.

Grazing prohibition is an effective management practice to restore salt marsh functioning. However, the effects of grazing exclusion on denitrifying microbial communities and their controlling factors in salt marshes remain unclear. In this study, we surveyed soil physicochemical properties and above- and below-ground biomass and using quantitative polymerase chain reaction and Illumina MiSeq high-throughput sequencing technology to determine the relative abundance, composition, and diversity of nitrite reductase nirS- and nirK-type denitrifying bacterial communities associated with grazing prohibition treatments and elevations. The abundance of nirS-type denitrifiers increased with grazing prohibition time, whereas the abundance of nirK-type denitrifiers remained unaltered. Moreover, nirS-type denitrifiers were more abundant and diverse than nirK-type denitrifiers in all treatments. Grazing prohibition significantly altered the operational taxonomic unit richness, abundance-based coverage estimator, and Chao1 indices of the nirS-type denitrifying bacterial communities, whereas it only minimally affected the structure of the nirK-type denitrifying bacterial community. The results imply that the nirS community, rather than nirK, should be the first candidate for use as an indicator in the process of salt marsh restoration after grazing prohibition. Substances of concern, total nitrogen, and salinity were the key environmental factors affecting the abundance and community composition of nirS and nirK denitrifiers. The findings of this study provide novel insights into the influence of the length of grazing prohibition and elevation on nirS- and nirK-type denitrifying bacterial community composition in salt marshes.

Sub-surface drip irrigation reduced N2O emissions via inhibiting denitrification pathways in northern China

Water-saving irrigation has become an important method for alleviating water scarcity in semi-arid regions. However, the lack of knowledge about the effects of different water-saving irrigation techniques on soil nitrogen conversion limits the understanding of the underlying mechanisms involved in soil N2O emissions. To determine the effects of different irrigation methods on N2O emissions, we conducted a two-season experiment under four different irrigation methods (DI, surface drip irrigation; SDI, sub-surface drip irrigation; PRI, partial rootzone irrigation; FP, flood irrigation). Also, we studied the dynamics of nitrifier and denitrifier community structures and compositions and their associations and effects on N2O emissions. The results showed that seasonal N2O emissions were affected by irrigation practices and significantly correlated with the amount of irrigation and soil moisture. Drip irrigation significantly reduced N2O emissions, with 38–45 % (DI), 51–59 % (SDI), and 64–68 % (PRI) decreases compared to FP treatment. Under SDI, the copy numbers of ammonia-oxidizing archaea amoA significantly decreased and nirK displayed an increase compared to FP. The abundance of unclassified_Proteobacteria dominant among nirK-type denitrifiers under FP was observed to be strongly and positively correlated with N2O emissions, and the dominant bacteria shifted to Bosea under drip irrigation. Irrigation practices had a strong effect on the Shannon and ACE indexes of five key genes. PRI showed a similar effect under SDI treatment on nitrifier and denitrifier community structures. Furthermore, PRI, with only a 38 % reduction of irrigation water consumption, produced a 4.4–11.3 % lower yield than SDI. Therefore, SDI treatment can inhibit the denitrification process led by nirS-type denitrifiers and reduce the abundance of the dominant genus of nirK and promote nosZ abundance, thus decreasing N2O emissions. Our findings indicate that (i) drip irrigation increased ammonia-oxidizing bacteria amoA abundance and diversity but decreased nirS abundance, which led to N2O mitigation and (ii) SDI might be the best method for maintaining high crop yield with lower N2O emissions in intensively farmed fields.

Ecological interactions and the underlying mechanism of anammox and denitrification across the anammox enrichment with eutrophic lake sediments

BackgroundIncreasing attention has recently been devoted to the anaerobic ammonium oxidation (anammox) in eutrophic lakes due to its potential key functions in nitrogen (N) removal for eutrophication control. However, successful enrichment of anammox bacteria from lake sediments is still challenging, partly due to the ecological interactions between anammox and denitrifying bacteria across such enrichment with lake sediments remain unclear.ResultsThis study thus designed to fill such knowledge gaps using bioreactors to enrich anammox bacteria with eutrophic lake sediments for more than 365 days. We continuously monitored the influent and effluent water, measured the anammox and denitrification efficiencies, quantified the anammox and denitrifying bacteria, as well as the related N cycling genes. We found that the maximum removal efficiencies of NH4+ and NO2− reached up to 85.92% and 95.34%, respectively. Accordingly, the diversity of anammox and denitrifying bacteria decreased significantly across the enrichment, and the relative dominant anammox (e.g., Candidatus Jettenia) and denitrifying bacteria (e.g., Thauera, Afipia) shifted considerably. The ecological cooperation between anammox and denitrifying bacteria tended to increase the microbial community stability, indicating a potential coupling between anammox and denitrifying bacteria. Moreover, the nirS-type denitrifiers showed stronger coupling with anammox bacteria than that of nirK-type denitrifiers during the enrichment. Functional potentials as depicted by metagenome sequencing confirmed the ecological interactions between anammox and denitrification. Metagenome-assembled genomes-based ecological model indicated that the most dominant denitrifiers could provide various materials such as amino acid, cofactors, and vitamin for anammox bacteria. Cross-feeding in anammox and denitrifying bacteria highlights the importance of microbial interactions for increasing the anammox N removal in eutrophic lakes.ConclusionsThis study greatly expands our understanding of cooperation mechanisms among anammox and denitrifying bacteria during the anammox enrichment with eutrophic lake sediments, which sheds new insights into N removal for controlling lake eutrophication.CVCoauCFapAiN4c5Sdx-EeVideo

Shifts in composition and function of bacterial communities reveal the effect of small barriers on nitrous oxide and methane accumulation in fragmented rivers.

Rivers are often blocked by barriers to form different habitats, but it is not clear whether this change will affect the accumulation of N2O and CH4 in rivers. Here, low barriers (less than 2 m, LB) increased N2O concentration by 1.13 times and CH4 decreased by 0.118 times, while high barriers (higher than 2 m, less than 5 m high, HB) increased N2O concentration by 1.19 times and CH4 by 2.76 times. Co-occurrence network analysis indicated LB and HB can promote the enrichment of Cyanobium and Chloroflexi, further limiting complete denitrification and increasing N2O accumulation. The LB promotes methanotrophs (Methylocystis, Methylophilus, and Methylotenera) to compete with denitrifiers (Pseudomonas) in water, and reduce CH4 accumulation. While the HB can promote the methanotrophs to compete with nitrifiers (Nitrosospira) in sediment, thus reducing the consumption of CH4. LB and HB reduce river velocity, increase water depth, and reduce dissolved oxygen (DO), leading to enrichment of nirS-type denitrifiers and the increase of N2O concentration in water. Moreover, the HB reduces DO concentration and pmoA gene abundance in water, which can increase the accumulation of CH4. In light of the changes in the microbial community and variation in N2O and CH4 accumulation, the impact of fragmented rivers on global greenhouse gas emissions merits further study.

Characteristics of soil N2O emission and N2O-producing microbial communities in paddy fields under elevated CO2 concentrations

The effects of elevated carbon dioxide (CO2) concentration (e[CO2]) on nitrous oxide (N2O) emissions from paddy fields and the microbial processes involved in N2O emissions have recently received much attention. Ammonia-oxidizing microorganisms and denitrifying bacteria dominate the production of N2O in paddy soils. To better understand the dynamics of N2O production under e[CO2], a field experiment was conducted after five years of CO2 fumigation based on three treatments: CK (ambient atmospheric CO2), T1 (CK + increase of 40 ppm per year until 200 ppm), and T2 (CK + 200 ppm). N2O fluxes, soil physicochemical properties, and N2O production potential were quantified during the rice-growth period. The functional gene abundance and community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed using quantitative polymerase chain reaction (qPCR) and those of ammonia-denitrifying bacteria (nirS- and nirK-type) were analyzed using Illumina MiSeq sequencing. N2O emissions decreased by 173% and 41% under the two e[CO2] treatments during grain filling and milk ripening, respectively (P < 0.05). N2O emissions increased by 279% and 172% in the T2 treatment compared with T1 during the tillering and milk-ripening stages, respectively (P < 0.05). Furthermore, the N2O production potential was significantly higher in the CK treatment than in T1 and T2 during the elongation stage. The N2O production potential and abundance of AOA amoA genes in T1 treatment were significantly lower than those in CK treatment during the high N2O emission phase caused by mid-season drainage (P < 0.05). Although nirK- and nirS-type denitrifying bacteria community structure and diversity did not respond significantly (P > 0.05) to e[CO2], the abundance of nirK-type denitrifying bacteria significantly affected the N2O flux (P < 0.05). Linear regression analysis showed that the N2O production potential, AOA amoA gene abundance, and nirK gene abundance explained 47.2% of the variation in N2O emissions. In addition, soil nitrogen (N) significantly affected the nirK- and nirS-type denitrifier communities. Overall, our results revealed that e[CO2] suppressed N2O emissions, which was closely associated with the abundance of AOA amoA and nirK genes (P < 0.05).

Soil CO2 and N2O emissions and microbial abundances altered by temperature rise and nitrogen addition in active-layer soils of permafrost peatland.

Changes in soil CO2 and N2O emissions due to climate change and nitrogen input will result in increased levels of atmospheric CO2 and N2O, thereby feeding back into Earth's climate. Understanding the responses of soil carbon and nitrogen emissions mediated by microbe from permafrost peatland to temperature rising is important for modeling the regional carbon and nitrogen balance. This study conducted a laboratory incubation experiment at 15 and 20°C to observe the impact of increasing temperature on soil CO2 and N2O emissions and soil microbial abundances in permafrost peatland. An NH4NO3 solution was added to soil at a concentration of 50 mg N kg-1 to investigate the effect of nitrogen addition. The results indicated that elevated temperature, available nitrogen, and their combined effects significantly increased CO2 and N2O emissions in permafrost peatland. However, the temperature sensitivities of soil CO2 and N2O emissions were not affected by nitrogen addition. Warming significantly increased the abundances of methanogens, methanotrophs, and nirK-type denitrifiers, and the contents of soil dissolved organic carbon (DOC) and ammonia nitrogen, whereas nirS-type denitrifiers, β-1,4-glucosidase (βG), cellobiohydrolase (CBH), and acid phosphatase (AP) activities significantly decreased. Nitrogen addition significantly increased soil nirS-type denitrifiers abundances, β-1,4-N- acetylglucosaminidase (NAG) activities, and ammonia nitrogen and nitrate nitrogen contents, but significantly reduced bacterial, methanogen abundances, CBH, and AP activities. A rising temperature and nitrogen addition had synergistic effects on soil fungal and methanotroph abundances, NAG activities, and DOC and DON contents. Soil CO2 emissions showed a significantly positive correlation with soil fungal abundances, NAG activities, and ammonia nitrogen and nitrate nitrogen contents. Soil N2O emissions showed positive correlations with soil fungal, methanotroph, and nirK-type denitrifiers abundances, and DOC, ammonia nitrogen, and nitrate contents. These results demonstrate the importance of soil microbes, labile carbon, and nitrogen for regulating soil carbon and nitrogen emissions. The results of this study can assist simulating the effects of global climate change on carbon and nitrogen cycling in permafrost peatlands.

Differential responses of soil nirS- and nirK-type denitrifying microbial communities to long-term application of biogas slurry in a paddy soil

Biogas slurry (BS) has been widely used as an organic fertilizer in rice paddy fields in China, with potential impacts on the diversity and activity of many biogeochemically important microbial communities. Among these communities, denitrifiers play a significant role in nitrogen (N) transformation and loss in such ecosystems. Here, we examined the abundance, diversity, and community composition of nirS- and nirK-type denitrifiers in paddy soils after long-term application of BS with different N contents using quantitative PCR and high-throughput sequencing. The experiment included four treatments: 1) mineral fertilizer with 270 kg N ha−1; 2) BS with 270 kg N ha−1; 3) BS with 405 kg N ha−1; and 4) BS with 540 kg N ha−1. Our results showed that BS application increased the soil nitrite reductase (NIR) activity by 5.9–27.5 % compared to mineral fertilizer application. Higher nirS gene abundance was observed in BS fertilized soils with increasing N content and was significantly correlated with NIR activity, but nirK gene abundance did not change with different fertilization intensities. Biogas slurry as a substitute for mineral fertilizer significantly decreased the alpha-diversity of only nirS-type denitrifiers at low application rate, but such negative effect was offset by increasing BS fertilization intensity. The community compositions of both nirS- and nirK-type denitrifiers shifted following changes in fertilizer type or intensity, and were significantly influenced by soil organic carbon (SOC), available phosphorus (AP), zinc (for both groups), and copper (for only nirK-type denitrifiers). The structural equation model indicated that the differences in soil NIR activity were mainly explained by SOC, AP, Zn, and the nirS-type denitrifier communities. Sulfurifustis, Thiobaclillus, Microvirgula and Duganella appeared to be the main genera governing NIR activity in the studied paddy fields. In conclusion, increasing BS application intensity can greatly alter the abundance and structure of the nirS-type denitrifying communities, and to a lesser extent, those of the nirK-type denitrifiers in paddy soils.

Stable nitrogen-cycling capacity in relation to fertilization and intercropping in a sub-boreal grassland

Grasslands are important in sub-boreal climate agricultural systems and are managed with various combinations of N fertilization and plant species. Ammonia-oxidizing and denitrifying microorganisms are key players in determining the fate of nitrogen (N) and thereby also the yield in grassland systems and their impact on gaseous N losses and leaching. We established a three-year field study in southern Finland with fertilizer treatment as a main-plot factor, including organic and synthetic fertilizers and plant species and mixtures thereof as the sub-plot factor. We quantified six genes encoding key N-cycling enzymes by quantitative PCR to determine the abundance of the communities involved in N-transformation processes and also included previously published data on crop yield, soil properties and the overall bacterial community composition. With the exception of ammonia oxidizing bacteria (AOB), which were primarily affected by fertilization, the abundances of all other N-cycling communities changed over time with either an increase or decrease from summer to autumn. Differences in gene abundances between plant species treatments and in fertilizer by plant species interactions were detected mainly in the beginning of the cropping season during the first year. The nirS-type denitrifiers and nosZII nitrous oxide reducers responded more to changes in soil properties than their functional counterpart nirK and nosZI communities. Using structural equation modeling, we show that the overall microbial community composition and diversity played an important role in mediating the management effects on crop yield, genetic potential for N retention and N2O sink capacity. However, a trade-off between the genetic potential for N retention and N2O sink capacity was detected, indicating the challenges in managing grasslands in a sustainable way.

Diverse nirS-type Denitrifying Bacteria Contribute to Vital Nitrogen Loss in Natural Acidic Red Soils.

Denitrifying bacteria, playing a key role in nitrogen removal in ecosystem, are highly diverse and complex in their community composition. However, there were few reports on the abundance, community composition, and the contribution to nitrogen loss of denitrifiers in natural acidic red soils. In this study, we investigated the structure and function of nirS-type denitrifying bacteria in ten natural red soil samples collected from nine provinces in southern China, based on quantitative polymerase chain reaction (qPCR) and high-throughput sequencing techniques. Nitrogen loss from microbial denitrification in red soils of southern China was estimated up to 9.86 Tg N per year based on 15N isotope tracing method. The abundance of nirS-type denitrifiers varied from 8.41 × 105 to 2.55 × 109 copies per gram of dry weight. The community of nirS-type denitrifying bacterial was revealed, which contained 50 dominant OTUs assigned to 9 clusters phylogenetically related to Marinobacter, Rhodobacter, and other uncultured species. pH was the key factor affecting both denitrification rates and community composition. Our results demonstrate that nirS-type denitrifying bacteria have higher abundance, diversity, and contribution to the nitrogen loss in natural acidic red soils of southern China.

Distinctive Microbial Processes and Controlling Factors Related to Indirect N2O Emission from Agricultural and Urban Rivers in Taihu Watershed.

Inland rivers are hotspots of anthropogenic indirect nitrous oxide (N2O) emissions, but the underlying microbial processes remain poorly understood. This study measured N2O fluxes from agricultural and urban rivers in Taihu watershed and investigated the microbial processes driving N2O production and consumption. The N2O fluxes were significantly higher in agricultural rivers (140.1 ± 89.1 μmol m-2 d-1) than in urban rivers (25.1 ± 27.0 μmol m-2 d-1) (p < 0.001). All wind-based models significantly underestimated N2O flux in urban rivers (p < 0.05) when using the Intergovernmental Panel on Climate Change method because they underestimated the N2O emission factor (EF5r). Wind speed and nitrate were the key factors affecting N2O fluxes in agricultural and urban rivers, respectively. NirK-type denitrifiers produced N2O in urban river water, while nirS-type denitrifiers consumed N2O in the sediments of all rivers. Co-occurrence network analysis indicated organics from Microcystis served as electron donors for denitrifiers (dominated by Flavobacterium) in water, while direct interspecies electron transfer between Thiobacillus and methanogens and between Dechloromonas and sulfate-reducing bacteria enhanced N2O reduction in sediments. This study advances our knowledge on the distinctive microbial processes that determine N2O emissions in inland rivers and illustrates the need to revise EF5r for N2O estimation in urban rivers.