N-cycling Functional Genes Research Articles

Unveiling the Hidden Responses: Metagenomic Insights into Dwarf Bamboo (Fargesia denudata) Rhizosphere under Drought and Nitrogen Challenges.

Dwarf bamboo (Fargesia denudata) is a crucial food source for the giant pandas. With its shallow root system and rapid growth, dwarf bamboo is highly sensitive to drought stress and nitrogen deposition, both major concerns of global climate change affecting plant growth and rhizosphere environments. However, few reports address the response mechanisms of the dwarf bamboo rhizosphere environment to these two factors. Therefore, this study investigated the effects of drought stress and nitrogen deposition on the physicochemical properties and microbial community composition of the arrow bamboo rhizosphere soil, using metagenomic sequencing to analyze functional genes involved in carbon and nitrogen cycles. Both drought stress and nitrogen deposition significantly altered the soil nutrient content, but their combination had no significant impact on these indicators. Nitrogen deposition increased the relative abundance of the microbial functional gene nrfA, while decreasing the abundances of nirK, nosZ, norB, and nifH. Drought stress inhibited the functional genes of key microbial enzymes involved in starch and sucrose metabolism, but promoted those involved in galactose metabolism, inositol phosphate metabolism, and hemicellulose degradation. NO3--N showed the highest correlation with N-cycling functional genes (p < 0.01). Total C and total N had the greatest impact on the relative abundance of key enzyme functional genes involved in carbon degradation. This research provides theoretical and technical references for the sustainable management and conservation of dwarf bamboo forests in giant panda habitats under global climate change.

Changes in nitrogen functional genes and microbial populations in soil profiles of a peatland under different burning regimes

Microbes in peatlands provide key ecosystem services and are essential for their role in biogeochemical cycling. Prescribed burning is a common aspect of peatland management but the practice has been criticized for being ecologically damaging due to its effect on the biological, chemical and physical properties of the soil. It is poorly understood how burning affects soil N cycling and previous studies have focused predominantly on the topsoil whilst giving less attention to changes with soil depth. This study investigated the changes of microbial abundance (bacterial 16S rRNA and fungal 18S rRNA) and the abundance of N-cycle functional genes involved in archaeal and bacterial ammonia oxidation (amoA-AOA and amoA-AOB), denitrification (nirK and nirS), N fixation (nifH) and organic N decomposition (chiA) in soil profiles across three burn treatments on a managed peatland landscape (a ‘non-burn’ since 1954 control, 20 years burn interval, and 10 years burn interval). Our results indicate the abundance of bacterial 16S rRNA and fungal 18 s rRNA was affected by burn treatment, soil depth and their interaction and were greater in the non-burn control plots. The abundances of amoA-AOA, amoA-AOB, and nifH were significantly higher in the topsoil of the non-burn control plots while the abundance of nirK was higher in plots subject to short rotation and long rotation burn regimes but also decreased significantly with soil depth. The abundance of nirS was not affected by burn treatment or soil depth. ChiA abundance was affected by burn treatment, soil depth and their interaction. N-cycle functional gene abundance responded differently to environmental factors associated with prescribed burning and varied with soil depth. These findings suggest that the practice of burning affects microbial N turnover potential and provides an important insight into the soil N-cycling potential of peatlands under different burning regimes.

Seasonal changes in N-cycling functional genes in sediments and their influencing factors in a typical eutrophic shallow lake, China.

N-cycling processes mediated by microorganisms are directly linked to the eutrophication of lakes and ecosystem health. Exploring the variation and influencing factors of N-cycling-related genes is of great significance for controlling the eutrophication of lakes. However, seasonal dynamics of genomic information encoding nitrogen (N) cycling in sediments of eutrophic lakes have not yet been clearly addressed. We collected sediments in the Baiyangdian (BYD) Lake in four seasons to explore the dynamic variation of N-cycling functional genes based on a shotgun metagenome sequencing approach and to reveal their key influencing factors. Our results showed that dissimilatory nitrate reduction (DNRA), assimilatory nitrate reduction (ANRA), and denitrification were the dominant N-cycling processes, and the abundance of nirS and amoC were higher than other functional genes by at least one order of magnitude. Functional genes, such as nirS, nirK and amoC, generally showed a consistent decreasing trend from the warming season (i.e., spring, summer, fall) to the cold season (i.e., winter). Furthermore, a significantly higher abundance of nitrification functional genes (e.g., amoB, amoC and hao) in spring and denitrification functional genes (e.g., nirS, norC and nosZ) in fall were observed. N-cycling processes in four seasons were influenced by different dominant environmental factors. Generally, dissolved organic carbon (DOC) or sediment organic matter (SOM), water temperature (T) and antibiotics (e.g., Norfloxacin and ofloxacin) were significantly correlated with N-cycling processes. The findings imply that sediment organic carbon and antibiotics may be potentially key factors influencing N-cycling processes in lake ecosystems, which will provide a reference for nitrogen management in eutrophic lakes.

氮磷添加下典型温带、亚热带森林土壤氮循环功能基因丰度和微生物群落属性数据集

Nitrogen (N) and phosphorus (P) are essential nutrients for soil microbial growth and activities. There are notable differences in the concentrations of N and P and the characteristics of microbial communities observed between temperate and subtropical forests soils, and this is also true for soil vertical profiles. As a consequence of the rise in global atmospheric N deposition, soil nutrient imbalances and P limitation are increasingly aggravated in eastern China. However, there is a lack of systematic dataset showing how N deposition and P addition affect soil N cycling microbes and soil physicochemical properties in eastern China; hence a comprehensive dataset is needed to a better understanding of the impact of N deposition and P addition on soil nitrogen cycle. This dataset is constructed based on the field experimental setup in the forests of Chinese Ecosystem Research Network (CERN). To obtain a systematic dataset on N-cycling microbial communities, we conducted measurements and collected data of soil N-cycling functional genes abundance, N-cycling microbial community diversities and compositions and enzyme activities in three typical forests with N and/or P additions. We collected 0-10 cm top soils from a temperate forest (Changbai Mountain) and two subtropical forests (Qianyanzhou and Dinghu Mountain) with field N and/or P additions, and the soils along 0-80 cm vertical profiles without nutrient additions. The N-cycling functional genes involved in the datasets cover ammonia oxidizing archaea amoA, ammonia oxidizing bacteria amoA, nirK, nirS, nosZ, qnorB, narG, nir, nifH and chiA. The potential activities included in the datasets cover nitrification activity, denitrification activity, nitrogen fixation activity and organic nitrogen decomposition enzyme activity. The datasets also include soil physiochemical properties, including soil pH, moisture content, N2O emission, net nitrification rate and the concentrations of organic carbon, NH4+ , NO3− , available phosphorus, total nitrogen, total carbon, total phosphorus and dissolved organic carbon. The creation and sharing of the datasets can provide data and support for understanding the microbial mechanisms of soil N-cycling and the modelling processes under the scenario of aggravated N deposition and P addition. The datasets will also provide support for forest management efforts with regard to greenhouse gas N2O emission, N and nutrient loss in forest ecosystems.

The Long-Term Application of Controlled-Release Nitrogen Fertilizer Maintains a More Stable Bacterial Community and Nitrogen Cycling Functions Than Common Urea in Fluvo-Aquic Soil

Controlled-release nitrogen fertilizer (CRNF) has been proven to surpass common urea by mitigating nutrient losses, enhancing soil quality, and improving crop productivity. However, the long-term effects of CRNF on soil biological properties are not well understood. Here, a 12-year field experiment was conducted with five treatments: no N fertilizer (PK); the split application of urea at the farmer’s practice rate (FP) and the optimal rate (OPT); the one-time application of CRNF at the same rate as the OPT (CRNF); and a 20% reduced rate of the OPT (0.8CRNF). Soil samples were collected during the maize tasseling and filling stages; high-throughput sequencing and the PICRUSt2 method were employed to determine the bacterial community and its functional potential. The results showed that CRNF significantly increased alkaline hydrolysis N by 14.10% and 9.45% compared to OPT during the tasseling and filling stages, respectively. This increase in soil available N resulted in a significant increase in bacterial diversity of 2.09% and 2.35% compared with the FP and OPT, respectively. The bacterial community in the FP and OPT changed markedly between the tasseling and filling stages, with many bacterial species at the ASV and genus levels showing variations in relative abundance. In contrast, CRNF and 0.8CRNF exhibited stable N-cycling functions, as indicated by the lower variations in nitrate reductase and predicted N-cycling functional genes between the tasseling and filling stages. The obtained results suggest that CRNF application can enhance soil N supply, promote the formation of stable bacterial communities, and maintain stable N-cycling functions.

The connection between the antibiotic resistome and nitrogen-cycling microorganisms in paddy soil is enhanced by application of chemical and plant-derived organic fertilizers

Antibiotic resistant genes (ARGs) present significant risks to environments and public health. In particular, there is increasing awareness of the role of soil nitrogen in ARG dissemination. Here, we investigated the connections between antibiotic resistome and nitrogen-cycling microbes in paddy soil by performing five-year field experiments with the treatments of no nitrogen fertilization (CK), reduced chemical nitrogen fertilization (LN), conventional chemical nitrogen fertilization (CN) and plant-derived organic nitrogen fertilization (ON). Compared with CK treatment, CN and ON treatments significantly increased soil NH4+ and TN concentrations by 25.4%–56.5% and 10.4%–20.1%, respectively. Redundancy analysis revealed significantly positive correlation of NH4+ with most ARGs, including tetA, macB and barA. Correspondingly, CN and ON treatments enhanced ARG abundances by 21.9%–23.2%. Moreover, CN and ON treatments promoted nitrate/nitrite-reducing bacteria and linked the corresponding N-cycling functional genes (narG, narH, nirK and nrfA) with most ARGs. Metagenomic binning was performed and identified Gemmatimonadaceae, Caulobacteraceae, Ilumatobacteraceae and Anaerolineaceae as hosts for both ARGs and nitrate/nitrite reduction genes that were enriched by CN and ON treatments. Soil resistome risk score analysis indicated that, although there was increased relation of ARG to nitrogen-cycling microorganisms with nitrogen fertilizer application, the environmental risk of ARGs was not increased due to the lower distribution of ARGs in pathogens. This study contributed to a deeper understanding of the role of soil nitrogen in shaping ARG profiles and controlling soil resistome risk.

Effects of Different Manures in Combination with Fulvic Acid on the Abundance of N-Cycling Functional Genes in Greenhouse Soils

To investigate the effects of different manures in combination with fulvic acid on the abundance of N-cycling functional genes in greenhouse soils, Chinese cabbage was planted for three growing seasons. A total of six treatments—pig manure (P), pig manure + fulvic acid (PH), chicken manure (C), chicken manure + fulvic acid (CH), sheep manure (S), sheep manure + fulvic acid (SH) and no fertilization (CK)—were set up. The abundance of 13 soil N-cycling functional genes (gdhA, amoA-1, amoA-2, amoB, narG, nirK-1, nirK-2, nirK-3, nirS-1, nirS-2, nirS-3, nosZ and nifH) were investigated after the harvest of the third growing season using a gene chip approach. The results showed that fertilization treatments increased the abundance of most N-cycling functional genes in the soil, such as nitrification genes amoA-2 and amoB as well as denitrification genes narG, nirK-1, nirS-1 and nirS-2, with the stronger influence of sheep and pig manure than chicken manure. Fortunately, the additional fulvic acid reduced the increasing effect resulting from pig, chicken and sheep manure application. The abundance of functional genes for nitrogen cycling in soil was positively correlated with the content of soil organic matter, available phosphorus and NO3−-N, and negatively correlated with electrical conductivity. Overall, fertilization treatments increased soil nitrification and denitrification genes abundance, with a risk of increasing soil nitrogen loss, but the supplementary fulvic acid could limit the increase. In this study, it was concluded that the sheep manure (31.3 t/ha) + fulvic acid (7.5 kg/ha) treatment was more powerful in regulating the abundance of N-cycling functional genes in soil.

Excessive manure application stimulates nitrogen cycling but only weakly promotes crop yields in an acidic Ultisol: Results from a 20-year field experiment

Population growth and growing demand for livestock products produce large amounts of manure, which can be harnessed to maintain soil sustainability and crop productivity. However, the impacts of excessive manure application on crop yields, nitrogen (N)-cycling processes and microorganisms remain unknown. Here, we explored the effects of 20-year of excessive rates (18 and 27 Mg ha–1 yr–1) of pig manure application on peanut crop yields, soil nutrient contents, N-cycling processes and the abundance of N-cycling microorganisms in an acidic Ultisol in summer and winter, compared with none and a regular rate (9 Mg ha–1 yr–1) of pig manure application. Long-term excessive pig manure application, especially at the high-rate, significantly increased soil nutrient contents, the abundance of N-cycling functional genes, potential nitrification and denitrification activity, while it had a weaker effect on peanut yield and plant biomass. Compared with manure application, seasonality had a much weaker effect on N-cycling gene abundance. Random forest analysis showed that available phosphorus (AP) content was the primary predictor for N-cycling gene abundance, with significant and positive associations with all tested N-cycling genes. Our study clearly illustrated that excessive manure application would increase N-cycling gene abundance and potential N loss with relatively weak promotion of crop yields, providing significant implications for sustainable agriculture in the acidic Ultisols.

Effect of Tubifex tubifex on the purification function of saturated vertical flow constructed wetlands for effluents with varying C/N ratios

The improvement effect of Tubifex tubifex on the pollutant removal efficiencies (REs) of vertical flow constructed wetlands (VF-CWs) treating wastewater with various C/N ratios was explored. The experiment was conducted in pilot-scale saturated VF-CWs, being added different densities of T. tubifex and fed synthetic wastewater with successive C/N ratios of 0.5, 1.5, 3.0 and 6.0. The results suggest that T. tubifex addition and the influent C/N ratio had an interactive effect, i.e., T. tubifex addition improved NOx−-N, NH4+-N, TN and COD REs by 36.7%, 56.5%, 22.6%, and 10.0%, respectively, under low C/N ratios, while high C/N ratios inhibited this improvement. Low-density T. tubifex addition significantly increased substrate dissolved oxygen (DO) by retarding excessive soil organic matter (OM) accumulation. With T. tubifex addition, an improvement in bacterial diversity, the relative abundance of N-cycle and fermentative bacteria, and N-cycle functional genes was only observed in substrates under low C/N ratios. T. tubifex can improve the purification function of saturated VF-CWs, but this strategy strongly depends on both the influent C/N ratio and density of T. tubifex addition.

Synergistic benefits of lime and 3,4-dimethylpyrazole phosphate application to mitigate the nitrous oxide emissions from acidic soils

Acidic soils cover approximately 50 % of the arable land with high N2O emission potential. 3,4-dimethylpyrazole phosphate (DMPP) inhibits N2O emission from soils; however, its efficiency is affected by acidity. Liming is used for soil conditioning to ameliorate the effects of acidity. In the present study, we investigated the effects of liming on the efficiency of DMPP in inhibiting N2O emission in acidic soils and the mechanisms involved. We evaluated the impact of liming, DMPP, and combined application and its microbial responses in two acidic soils from Zengcheng (ZC) and Shaoguan (SG) City, Guangdong Province, China. Soils were subjected to four treatments: un-limed soil (low soil pH) + urea (LU), un-limed soil + urea + DMPP (LD), limed soil (high soil pH) + urea (HU), and limed soil + urea + DMPP (HD) for analyses of the mineral N, N2O emissions, and full-length 16S and metagenome sequencing. The results revealed that, HU significantly decreased and increased the N2O emission by 17.8 % and 235.0 % in ZC and SG, respectively, compared with LU. This was caused by a trade-off between N2O production and consumption after liming, where microbial communities and N-cycling functional genes show various compositions in different acidic soils. LD reduced N2O emission by 23.5 % in ZC, whereas decreased 1.5 % was observed in SG. Interestingly, DMPP efficiency considerably improved after liming in two acidic soils. Compared with LU, HD significantly reduced N2O emissions by 61.2 % and 48.5 % in ZC and SG, respectively. Synergy of mitigation efficiency was observed by lime and DMPP application, which was attributed to the changes in the dominant nitrifiers and the increase in N2O consumption by denitrifiers. The combined application of lime and DMPP is a high-efficiency strategy for N2O mitigation can ensure agricultural sustainability in acidic arable soils with minimal environmental damage.

Differential Responses of Soil Microbial N-Cycling Functional Genes to 35 yr Applications of Chemical Fertilizer and Organic Manure in Wheat Field Soil on Loess Plateau

Fertilization changes nitrogen (N)-cycling processes and associated microbial communities in agricultural ecosystems. However, the long-term responses of N-cycling potential and microbial functional genes to different fertilization sources remain unclear. Soil samples were collected to a depth of 20 cm under winter wheat applied annually with N fertilizer (NF), organic manure (OM), N fertilizer plus organic manure (NM), and a control without fertilization (CK) for 35 yr, and they were analyzed for microbial functional genes involved in soil N cycling using metagenome sequencing in the Loess Plateau of China. Soil N fractions were greater with OM and NM than NF and CK. The total abundances of N-cycling genes were 9.3% (p &lt; 0.05) greater with NM than CK, and 8.2% (p &lt; 0.05) and 12.2% (p &lt; 0.01) higher with OM and NM than NF, respectively. Compared to CK, OM and NM increased the abundance of genes associated with nitrification, denitrification, dissimilatory nitrate reduction, and assimilatory nitrate reduction, but decreased the abundance of genes related to organic N metabolism. However, NF increased the abundance of genes involved in nitrification. Both OM and NM also enhanced the relative abundance of Proteobacteria carrying N-cycling genes but reduced those of Firmicutes and Cyanobacteria. Soil organic carbon, total N, and potential carbon mineralization were the dominant factors affecting the abundances of N-cycling genes. Long-term application of OM and NM can promote N cycling by enhancing gene abundance due to increased soil organic matter and microbial biomass compared to NF and CK.

Different Cropping Patterns to Restore Saline-Alkali Soils in Northeast China Affect the Abundance of Functional Genes in the Soil Nitrogen Cycle

Considerable attention has been paid to the establishment of an appropriate cropping patterns for the restoration of saline-alkali lands. This study’s goal was to explore changes in nitrogen-cycling (N-cycling) gene (nitrogen fixation: nifH; nitrification: AOA, AOB, and nxrB; denitrification: narG, norB, and nosZ) abundance of three cropping patterns at two soil depths in saline-alkali soils. Results showed that rotation and mixture promoted soil nutrients. N-cycling functional genes were significantly influenced by soil depths and cropping patterns. Compared with monoculture, rotation decreased the abundance of nifH, AOA, narG, and nosZ and increased the abundance of AOB; mixture decreased the abundance of AOA, narG, and nosZ and increased the abundance of AOB and nxrB in the 0–15 cm soil depth. Rotation increased all genes abundance; mixture increased nosZ abundance and decreased nxrB abundance in 15–30 cm soil depth. Soil protease, cellulase, nitrate reductase, pH, AK (available potassium), and AP (available phosphorus) were important factors influencing N-cycling gene abundance. In conclusion, rotation and mixture not only reduced soil salinity but also improved soil fertility and nitrogen cycling. These findings can provide some theories for the sustainable development of N-cycling during the restoration of saline-alkali soils.

Positive and negative effects of recirculating aquaculture water advanced oxidation: O3 and O3/UV treatments improved water quality but increased antibiotic resistance genes

Recirculating aquaculture systems (RASs) can be efficiently used for aquaculture, and oxidation treatment is commonly used to improve water quality. However, the effects of oxidation treatments on aquaculture water safety and fish yield in RASs are poorly understood. In this study, we tested the effects of O3 and O3/UV treatments on aquaculture water quality and safety during culture of crucian carp. O3 and O3/UV treatments reduced the dissolved organic carbon (DOC) concentration by ∼40% and destroyed the refractory organic lignin-like features. There was enrichment of ammonia oxidizing (Nitrospira, Nitrosomonas, and Nitrosospira) and denitrifying (Pelomonas, Methyloversatilis, and Sphingomonas) bacteria, and N-cycling functional genes were enriched by 23% and 48%, respectively, after O3 and O3/UV treatments. Treatment with O3 and O3/UV reduced NH4+-N and NO2–-N in RASs. O3/UV treatment increased fish length and weight as well as probiotics in fish intestine. However, high saturated intermediates and tannin-like features induced antibiotic resistance genes (ARGs) in O3 and O3/UV treatments, by 52% and ∼28%, respectively, and also enhanced horizontal transfer of ARGs. Overall, the application of O3/UV achieved better effects. However, understanding the potential biological risks posed by ARGs in RASs and determining the most efficient water treatment strategies to mitigate these risks should be goals of future work.

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.

Effects of biochar addition and deficit irrigation with brackish water on yield-scaled N2O emissions under drip irrigation with mulching

Biochar has been proven to have great potential for mitigating greenhouse gas emissions and improving crop growth. However, the effects of biochar addition on yield-scaled N2O emissions in a mulched and drip-irrigated maize field using different irrigation water qualities and quantities remain unclear. A two-year field experiment was conducted to examine the effects of biochar addition, irrigation level and water salinity on soil N2O emissions, maize yield and grain N uptake in Northwest China. Eight treatments in total included the combination of two biochar addition rates of 0 t/ha (B0) and 60 t/ha (B1), two irrigation levels of full (W1) and deficit irrigation (W2, W2 = 1/2 W1) and two water salinity levels of freshwater (S0, 0.71 g/L) and brackish water (S1, 4 g/L). The soil properties, N2O emission fluxes, maize yield and grain N uptake, along with the abundances of N-cycle functional marker genes were measured during the two growing seasons. Soil water-filled pore space (WFPS), soil NH4+-N and NO3--N contents accounted for the majority of the variation in the dynamic changes of N2O fluxes. Deficit irrigation had lower N2O emissions compared with full irrigation, which was more pronounced in the second year. Relative to freshwater irrigation, brackish water irrigation increased N2O emissions under W1, but freshwater and brackish water irrigation had similar N2O emissions under W2 in both years. Biochar addition effectively mitigated N2O emissions by 29.4–31.0% and 17.9–29.2% under different irrigation treatments in 2020 and 2021, respectively. The continuous drought induced by deficit irrigation weakened the effectiveness of biochar in reducing N2O emissions. The differences in N-cycle functional marker genes could not reflect the variation in cumulative N2O emissions among treatments. Under all irrigation treatments excluding W2S1, biochar addition improved the total maize yield and grain N uptake over the two-year period by 4.06–10.74% and 5.57–8.63%, respectively. Brackish water and deficit irrigation increased grain and grain N yield-scaled N2O emissions, whereas biochar addition reduced both of them. Overall, these findings suggest that biochar addition can effectively reduce N2O emissions and increase yield and grain N uptake under brackish water and deficit drip irrigation with mulching in a maize field system, and thus adding biochar can help with achieving the sustainability of agricultural production in areas with limited freshwater resources.

Long-term manure amendment reduces nitrous oxide emissions through decreasing the abundance ratio of amoA and nosZ genes in an Ultisol

Organic fertilizers are frequently applied to soils to improve soil multifunctionality and maintain crop productivity in agricultural practices. However, how organic fertilizations influence soil nitrous oxide (N2O) emissions remains ambiguous, especially considering their linkage with the abundance of nitrogen (N)-cycling microorganisms. Here, we conducted an incubation experiment to examine the effect of partial replacement of mineral fertilizers with organic fertilizers on the abundance of N-cycling functional genes and N2O emissions at 60 % and 100 % water-filled pore space (WFPS) in an acidic Ultisol. Soil samples were collected from 32-year fertilization trials, including four treatments of control (no fertilizer), mineral NPK fertilizer (NPK), NPK + Peanut Straw (NPKS), and NPK + Pig Manure (NPKM). The N2O emissions from soils incubated at 100 % WFPS were significantly higher than those at 60 % WFPS in all treatments. Compared with NPK, NPKS and NPKM reduced N2O emissions, with a more pronounced effect in NPKM. The N2O flux was positively associated with the abundance of AOA and AOB amoA genes, and the abundance ratio of amoA/nosZ (i.e., the ratio of AOA amoA plus AOB amoA and nosZ І plus nosZ ІІ) when the peak N2O flux appeared. Random forest analysis showed that the abundance ratio of amoA/nosZ was the best predictor for N2O emissions. Compared with NPK, NPKM increased soil pH but reduced the abundance ratio of amoA/nosZ, which might be the key factor in reducing N2O emissions. Together, our findings suggested that long-term manure application reduced N2O emissions by decreasing the abundance ratio of amoA/nosZ and provided novel insights into the impact of organic fertilizers on N2O emissions in acidic agricultural soils.

Diffusive nitrous oxide (N2O) fluxes across the sediment-water-atmosphere interfaces in aquaculture shrimp ponds in a subtropical estuary: Implications for climate warming

Emissions of the potent greenhouse gas nitrous oxide (N2O) from aquaculture remain a large knowledge gap in the global N2O budget. The water column and the sediment of aquaculture ponds present very different environmental conditions, but their relative contributions to N2O production and emission are poorly resolved. We sampled three aquaculture ponds in the Min River Estuary in southeastern China monthly throughout the farming season. Based on the dissolved N2O concentrations within the water column and in sediment porewater, we calculated the diffusive N2O fluxes across the water-atmosphere interface (WAI) and sediment-water interface (SWI). The diffusive N2O flux averaged 216.9 nmol m−2 h−1 across WAI and 16.0 nmol m−2 h−1 across SWI. The estimated N2O production rate under steady-state condition was 0.13 nmol L−1 h−1 in the water column and 1.07 nmol L−1 h−1 in sediment porewater. Hence, the water column compartment and the sediment compartment of the aquaculture ponds played different roles in N2O dynamics. Based on our data, it is calculated that China’s coastal aquacultural ponds would emit 0.2 Gg N2O yr−1, or less than 1% of all aquaculture N2O emission in China. Therefore, coastal shrimp aquaculture has a relative minor climate impact compared to other aquaculture operations. Future studies should examine the role of N-cycling functional genes on N2O production and the mechanisms regulating N2O emission from aquaculture ecosystems.

The active functional microbes contribute differently to soil nitrification and denitrification potential under long-term fertilizer regimes in North-East China.

Nitrogen (N) cycling microorganisms mediate soil nitrogen transformation processes, thereby affecting agricultural production and environment quality. However, it is not fully understood how active N-cycling microbial community in soil respond to long-term fertilization, as well as which microorganisms regulate soil nitrogen cycling in agricultural ecosystem. Here, we collected the soils from different depths and seasons at a 29-year fertilization experimental field (organic/chemical fertilizer), and investigated the transcriptions of N-cycling functional genes and their contribution to potential nitrification and denitrification. We found that long-term fertilization exerted significant impacts on the transcript abundances of nitrifiers (AOA amoA, AOB amoA and hao) and denitrifiers (narG and nosZ), which was also notably influenced by season variation. The transcriptions of AOA amoA, hao, and narG genes were lowest in autumn, and AOB amoA and nosZ transcript abundances were highest in autumn. Compared to no fertilization, soil potential nitrification rate (PNR) was reduced in fertilization treatments, while soil potential denitrification rate (PDR) was significantly enhanced in organic combined chemical fertilizer treatment. Both PNR and PDR were highest in 0–20 cm among the tested soil depths. Path model indicated active nitrifiers and denitrifiers had significant impact on soil PNR and PDR, respectively. The transcriptions of AOA amoA and nxr genes were significantly correlated with soil PNR (Pearson correlation, r > 0.174, p < 0.05). Significant correlation of napA and nosZ transcriptions with soil PDR (Pearson correlation, r > 0.234, p < 0.05) was also revealed. Random forest analysis showed that SOC content and soil pH were the important factors explaining the total variance of active nitrifers and denitrifiers, respectively. Taken together, long-term fertilization regimes reduced soil PNR and enhanced PDR, which could be attributed to the different responses of active N-cycling microorganisms to soil environment variations. This work provides new insight into the nitrogen cycle, particularly microbial indicators in nitrification and denitrification of long-term fertilized agricultural ecosystems.

Annual Nitrogen Removal Efficiency and Change in Abundance of Nitrogen Cycling Microorganisms in Swine Wastewater Treated by Crop Straw Materials

Based on previous research, using straw material to treat swine wastewater can effectively reduce the concentration of nitrogen (N); however, the annual N-removal efficiency and change in the abundance of N-cycling functional genes remain unclear. In this study, four treatments (wheat straw, rice straw, corn stalk, and CK) were set up, with the aim of studying the annual N-removal efficiency and change in the abundance of functional genes. Our results showed that:① the total nitrogen (TN) removal and NH4+-N removal efficiency were the best in the first six months and were significantly reduced in the following six months. In addition, the TN removal and NH4+-N efficiency in straw and wheat straw were better than those in corn straw. The TN-removal efficiency in straw and wheat straw were 32.81%±11.34% and 32.99%±9.60%, respectively. The NH4+-N removal efficiency in straw and wheat straw were 35.3%±13.23% and 34.97%±12.00%, respectively. ② The abundance of N-cycling functional genes significantly increased by the addition of straw materials, compared with that of the CK (P<0.05). The average abundances of nirK, nirS, and hzsB were 6.45×109 copies·L-1, 6.18×109 copies·L-1, and 2.31×109 copies·L-1, respectively. The average abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were 6.12×1010 copies·L-1 and 4.93×109 copies·L-1, respectively. The average hzsB gene abundance was 2.31×109 copies·L-1. The average abundance of 16S rRNA in the treatment was 8.90×1010 copies·L-1. The abundances of hzsB and nirS genes in the straw and wheat straw were higher than those in the other treatment, indicating that the activities of anaerobic ammonia oxidation and denitrifying microorganisms were significantly increased by the addition of straw and wheat straw (P<0.05). In addition, the abundance of AOA and AOB genes were increased in wheat straw, suggesting that wheat straw could promote nitrification. The results provided data supporting the molecular mechanism of nitrogen removal in swine wastewater treatment with straw materials.

Successions and interactions of phyllospheric microbiome in response to NH3 exposure.

Phyllosphere and numerous phyllospheric microbiomes present a huge potential for air pollution mitigation. Despite research investigating the microbial compositions in the phyllosphere, the successions and interactions of the phyllospheric microbiome under ammonia gas (NH3) stress remain poorly understood. Herein, we performed 16S rDNA, the internal transcribed spacer (ITS) profiling and a quantitative microbial element cycling (QMEC) method to reveal successions, co-occurrence, and N-cycling functions changes of phyllospheric bacteria and fungi during NH3 exposure. The NH3 input mainly elevated ammonium (NH4+-N) and total nitrogen (TN) levels on the leaf surface. The exposure in the phyllosphere decreased fungal concentration with a homogeneity increase while enhanced bacterial concentration with a noticeable richness drop. Both short-term (2-week) and long-term (6-week) exposure induced significant changes in microbial compositions. Bacterial genera (Nocardioides, Pseudonocardia) and fungal genera (Alternaria, Acremonium) dominated throughout the exposure. Intensive microbial interactions compared to that in the natural phyllosphere were observed via network analysis. Our results showed that N-cycling functional genes were largely stimulated by the exposure and might, in turn contribute to NH3 pollution buffer and alleviation via microbial metabolism. This study extended the knowledge on microbial responses to NH3 exposure in the phyllosphere and enlightened phylloremediation on NH3 through the microbial role.