Abundance Of Ammonia-oxidizing Bacteria Research Articles

The cooperative interaction of AOB and comammox clade A drives nitrification and N2O emissions in a long-term organic fertilized paddy soil

The newly discovered complete ammonia oxidizer (comammox Nitrospira) is able to single-step nitrification capability, and increased our understanding of soil nitrogen cycling. However, the response of comammox and ammonia-oxidizing bacteria (AOB) and archaea (AOA) to long-term fertilization and rhizosphere effects in paddy soils and their relative contribution to the nitrification-derived N2O emissions is still unclear. Here, we collected rhizosphere and bulk soils with thirty years of different fertilization strategies, i.e., non-fertilization (CK), chemical N, P, and K application (NPK), and NPK plus pig manure application (NPKM), respectively, to test changes in nitrification potential rate (PNR), N2O emission fluxes, abundance of ammonia oxidizers and their significant drivers. The result showed that NPKM significantly increased soil C and N levels, the proportion of soil middle-size particles (40.35–148.00 μm class), and soil PNR, but decreased soil N2O emissions, especially in the drying time of paddy (P < 0.05), compared to NPK fertilization. NPKM had the highest values of AOA, AOB, and comammox clade A amoA gene copy numbers (P < 0.05), but clade B was increased by the NPK in the rhizosphere soil. Furthermore, fertilization showed greater effects on ammonia oxidizers (except for clade B) than the rhizosphere effect. Mantel test showed that SOM, TP, pH, NH4+, and NO3− were main abiotic factors causing the niche separation among ammonia oxidizers. Linear regression analysis and structural equation model (SEM) showed that both PNR and N2O emission fluxes were significantly associated with the abundance of AOB and comammox clade A (P < 0.05). Therefore, our results underline the importance of AOB together with comammox clade A in nitrification and N2O production in long-term organic fertilized paddy fields, which could provide new ideas for the mitigation of N2O emission by adopting organic fertilization scenarios in Chinese paddy fields.

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil.

Through the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study. The soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing. The results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities.

The different responses of AOA and AOB communities to irrigation systems in the semi-arid region of Northeast China.

Ammonia oxidation is the rate-limiting step in nitrification and the key step in the nitrogen (N) cycle. Most soil nutrients and biological indicators are extremely sensitive to irrigation systems, from the perspective of improving soil fertility and soil ecological environment, the evaluation of different irrigation systems and suitability of selection, promote crop production and soil quality, study the influence of the soil microenvironment contribute to accurate evaluation of irrigation farmland soil health. Based on the amoA gene, the abundance and community diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and their responses to soil physicochemical factors and enzyme activities were studied in semi-arid areas of Northeast China. The study consisted of three irrigation systems: flood irrigation (FP), shallow buried drip irrigation (DI), and mulched drip irrigation (MF). The results showed that DI and MF significantly increased the contents of alkaline hydrolyzed nitrogen (AN), nitrate nitrogen (NO3--N), soil moisture, and the activities of ammonia monooxygenase (AMO) and hydroxylamine oxidase (HAO). Compared with FP, DI significantly increased the abundance of soil AOA and AOB, while MF significantly increased the abundance of soil AOB. Irrigation systems significantly affected the community composition of ammonia-oxidizing microorganisms (AOM). Also, AN and soil moisture had the greatest influence on the community composition of AOA and AOB, respectively. The AOB community had better stability and stress resistance. Moreover, the symbiotic network of AOB in the three irrigation systems was more complex than that of AOA. Compared with FP, the AOA community under treatment DI had higher complexity and stability, maintaining the versatility and sustainability of the ecosystem, while the AOB community under treatment MF had higher transfer efficiency in terms of matter and energy. In conclusion, DI and MF were more conducive to the propagation of soil AOM in the semi-arid area of Northeast China, which can provide a scientific basis for rational irrigation and N regulation from the perspective of microbiology.

Wheat straw and microbial inoculants have an additive effect on N2O emissions by changing microbial functional groups

AbstractStraw‐decomposing microbial inoculants (MIs) have been increasingly applied to straw‐amended soils. However, the interactive effects and underlying microbial mechanisms of straw and decomposing MIs on nitrous oxide (N2O) emissions remain unclear. Here, a pot experiment with an Aquic Inceptisol was conducted to determine soil N2O emissions and the abundance and composition of microbial functional genes under six amendments: wheat straw (W), Bacillus subtilis MI (B), Streptomyces rochei MI (S), a combination of straw and B. subtilis MI (WB), a combination of straw and S. rochei MI (WS), and a control without wheat straw or MI (C). Compared with the control, the amendments of straw, decomposing MIs, and their combinations decreased soil N2O emissions by 43%, 22–30%, and 46–60%, respectively. Mechanistically, the positive relationship between ammonia‐oxidizing bacteria (AOB) and soil potential nitrification rate (PNR), along with decreased AOB abundance (−36%) following straw and decomposing MI amendments, further suggested that AOB predominated soil nitrification and was responsible for the suppressed nitrification. In addition, straw amendment increased nirK gene abundance (by 48%) and potential denitrification rate (by 11%), while the increase in nosZI gene abundance (+25%) involved in N2O consumption contributed to the decrease in N2O emissions. Overall, the additive effect of straw and decomposing MIs on soil N2O emissions was associated with two amendment‐induced changes in the abundance and composition of AOB and straw‐stimulated the abundance of the nosZI gene. Our results revealed the potential for mitigating N2O emissions following the amendments of straw and MI by influencing soil N2O‐related microbial groups.

Distinguished denitrifying phosphorus removal in the high-rate anoxic/microaerobic system for sewage treatment

This study re-evaluated the role of anoxic and anaerobic zones during the enhanced biological phosphorus (P) removal process by investigating the potential effect of introducing an anoxic zone into a high-rate microaerobic activated sludge (MAS) system (1.60–1.70 kg chemical oxygen demand (COD) m−3 d−1), i.e., a high-rate anoxic/microaerobic (A/M) system for sewage treatment. In the absence of a pre-anaerobic zone, introducing an anoxic zone considerably reduced effluent NOx−-N concentrations (7.2 vs. 1.5 mg L−1) and remarkably enhanced total nitrogen (75% vs. 89%) and total P (18% vs. 60%) removal and sludge P content (1.48% vs. 1.77% (dry weight)) due to further anoxic denitrifying P removal in the anoxic zone (besides simultaneous nitrification and denitrification in the microaerobic zone). High-throughput pyrosequencing demonstrated the niche differentiation of different polyphosphate accumulating organism (PAO) clades (including denitrifying PAO [DPAO] and non-DPAO) in both systems. Introducing an anoxic zone considerably reduced the total PAO abundance in sludge samples by 42% and modified the PAO community structure, including 17–19 detected genera. The change was solely confined to non-DPAOs, as no obvious change in total abundance or community structure of DPAOs including 7 detected genera was observed. Additionally, introducing an anoxic zone increased the abundance of ammonia-oxidizing bacteria by 39%. The high-rate A/M process provided less aeration, higher treatment capacity, a lower COD requirement, and a 75% decrease in the production of waste sludge than the conventional biological nutrient removal process.

Urban and agricultural land use led to niche differentiation of AOA, AOB and comammox along the Beiyun River continuum

River ecological health has been severely threatened by anthropogenic land-use pressures. Here, by combining remote sensing and molecular biology methods, we evaluated the impact of land-use activities on nitrification, a fundamental ecological process in rivers, which is conducted by ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB), or the newly discovered complete ammonia oxidisers (comammox). We explored the relationships of the abundance, activity, and diversity of AOA, AOB, and comammox in river sediments with land-use pressure by proposing a quantitative land use pattern index (LPI) over a 184 km continuum along the Beiyun River in North China. We found that comammox dominated nitrification in the forestry upstream (67.07 % in summer, 56.40 % in winter), while AOB became the major player in the urban middle (56.51 % in summer, 53.08 % in winter) and agricultural downstream reaches (62.98 % in summer, 50.74 % in winter). In addition, urban and agricultural land use lowered the α diversity of AOA and comammox, as well as simplified their co-occurrence networks, but promoted AOB diversity and complicated their networks. The structural equation model illustrated that the key drivers affecting the key taxa and activities were ammonia, and C/N for AOB, and total organic matter, and pH for comammox. We thus conclude that watershed urban and agricultural land use drive the niche differentiation of AOA, AOB, and comammox, specifically leading to a robust AOB community but weakened AOA and comammox communities. Our study connects the macro and micro worlds and provides a new paradigm for studying the variation in microbial communities as well as the potential ecological consequences under the increased anthropogenic land-use pressures in the Anthropocene.

Effects of 3-year biochar application on carbon sequestration, nitrogen retention and nitrate leaching of fluvo-aquic soil profiles in vegetable rotation fields

The impacts of biochar application on the carbon (C) and nitrogen (N) cycles in soil profiles in vegetable fields have rarely been reported. A three-year field experiment (CK, control; BC, biochar; N, nitrogen fertilizer; BCN, biochar and nitrogen fertilizer) was conducted in fluvo-aquic soil with a wild cabbage-Chinese cabbage rotation to investigate biochar effects on soil organic carbon (SOC) sequestration, N retention, and nitrate (NO3−) leaching in the soil profile (topsoil, 0–20 cm; subsoil, 20–50 cm; third-layer soil, 50–100 cm). The results showed that the biochar-induced increase in topsoil SOC under N fertilization was greater for Chinese cabbage season than for wild cabbage season. Excluding biochar-N, biochar application caused an extra increase in topsoil total nitrogen (TN) under N fertilization. Biochar decreased the NO3−-N concentration of third-layer soil solution, particularly under N fertilization, indicating that biochar reduced the potential source of NO3− leaching. Under N fertilization, biochar reduced the abundances of carbon-degrading bacteria (Streptomyces, Bacillus, Mycobacterium, and Sphingomonas) and genes (sga, xylA, lig, and pgu) in the topsoil, as well as the abundances of ammonia-oxidizing bacteria (Nitrosospira and Nitrosomonas) and gene (amoA) in the third-layer soil. However, biochar increased the abundance of ammonia-assimilating bacteria (Rhodococcus) and gene (glnA) in the topsoil. Biochar inhibited the microbial function associated with C degradation by affecting soil TN, thus enhancing topsoil SOC sequestration. Biochar promoted the soil microbial function related to ammonia assimilation by affecting dissolved organic carbon (DOC), subsequently enhancing ammonia assimilation. Moreover, biochar initially inhibited ammonia oxidation in the third-layer soil by increasing soil DOC, subsequently affecting nitrite oxidation and ultimately reducing soil NO3− leaching. Biochar significantly increased the N use efficiency of vegetables in the last two years. This study provides insights into biochar effects on the changes in soil microbial function, which promoted SOC sequestration, enhanced N retention and mitigated nitrate leaching in a vegetable rotation field.

Mitigation of N2O emissions in water-saving paddy fields: Evaluating organic fertilizer substitution and microbial mechanisms

Water-saving irrigation strategies can successfully alleviate methane emissions from rice fields, but significantly stimulate nitrous oxide (N2O) emissions because of variations in soil oxygen level and redox potential. However, the relationship linking soil N2O emissions to nitrogen (N) functional genes during various fertilization treatments in water-saving paddy fields has rarely been investigated. Furthermore, the mitigation potential of organic fertilizer substitution on N2O emissions and the microbial mechanism in rice fields must be further elucidated. Our study examined how soil N2O emissions were affected by related functional microorganisms [ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), nirS, nirK and nosZ] to various fertilization treatments in a rice field in southeast China over two years. In this study, three fertilization regimes were applied to rice cultivation: a no nitrogen (N) (Control), an inorganic N (Ni), and an inorganic N with partial N substitution with organic manure (Ni+No). Over two rice-growing seasons, cumulative N2O emissions averaged 0.47, 4.62 and 4.08 kg ha−1 for the Control, Ni and Ni+No treatments, respectively. In comparison to the Ni treatment, the Ni+No fertilization regime considerably reduced soil N2O emissions by 11.6% while maintaining rice yield, with a lower N2O emission factor from fertilizer N (EF) of 0.95%. Nitrogen fertilization considerably raised the AOB, nirS, nirK and nosZ gene abundances, in comparison to the Control treatment. Moreover, the substitution of organic manure for inorganic N fertilizer significantly decreased AOB and nirS gene abundances and increased nosZ gene abundance. The AOB responded to N fertilization more sensitively than the AOA. Total N2O emissions significantly correlated positively with AOB and nirS gene abundances while having a negative correlation with nosZ gene abundance and the nosZ/nirS ratio across N-fertilized plots. In summary, we conclude that organic manure substitution for inorganic N fertilizer decreased soil N2O emissions primarily by changing the soil NO3−-N, pH and DOC levels, thus inhibiting the activities of ammonia oxidation in nitrification and nitrite reduction in denitrification, and strengthening N2O reduction in denitrification from water-saving rice paddies.

The addition of discrimination inhibitors stimulations discrimination potential and N2O emissions were linked to predation among microorganisms in long term nitrogen application and straw returning systems.

Ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) have been proven to be key microorganisms driving the ammonia oxidation process. However, under different fertilization practices, there is a lack of research on the impact of interaction between predators and AOA or AOB on nitrogen cycling at the multi-trophic level. In this study, a network-oriented microscopic culture experiment was established based on four different long-term fertilization practices soils. We used the nitrification inhibitors 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxide-3-oxyl (PTIO) and 3, 4-Dimethylpyrazole phosphate (DMPP) inhibited AOA and AOB, respectively, to explore the impact of interaction between protists and AOA or AOB on nitrogen transformation. The results showed that long-term nitrogen application promoted the potential nitrification rate (PNR) and nitrous oxide (N2O) emission, and significantly increased the gene abundance of AOB, but had no obvious effect on AOA gene abundance. DMPP significantly reduced N2O emission and PNR, while PTIO had no obvious effect on them. Accordingly, in the multi-trophic microbial network, Cercozoa and Proteobacteria were identified as keystone taxa of protists and AOB, respectively, and were significantly positively correlated with N2O, PNR and nitrate nitrogen. However, Nitrososphaerota archaeon as the keystone species of AOA, had an obvious negative linkage to these indicators. The structural equation model (SEM) showed that AOA and AOB may be competitors to each other. Protists may promote AOB diversity through direct trophic interaction with AOA. The interaction pattern between protists and ammonia-oxidizing microorganisms significantly affects potential nitrification rate and N2O emission, which has important implications for soil nitrogen cycle.

High efficiency and stable partial nitration achieved via gel immobilization

Long-term high efficiency and stable partial nitrification (PN) performance was achieved using gel-immobilized partial nitrifying bacteria. The PN characteristics of the filler under high and low ammonia nitrogen concentrations and low temperature were comprehensively studied and the rapid reactivation was achieved after reactor breakdown or long stagnation period. The results showed that the maximum ammonia oxidation rate was 66.8 mg•(L•h)−1 and the nitrite accumulation rate was above 95 % for the filler. Efficient and stable PN performance depends on the high abundance of ammonia-oxidizing bacteria (AOB) inside the filler and dynamically microbial community. In addition, the oxygen-limited zone and competition between the microorganisms inside the filler effectively inhibited the growth of nitrite oxidizing bacteria, and the sludge outside the filler assisted in this process, which supported the dominant position of AOB in fillers. This study provides a reliable technology for the practical application of the PN nitrogen removal process.

Assessing the effectiveness of 3, 4-dimethylpyrazole phosphate (DMPP) inhibitor in mitigating N2O emissions from contrasting Cd-contaminated soils

Improving nitrogen use efficiency of chemical fertilizers is essential to mitigate the negative environmental impacts of nitrogen. Nitrification, the conversion of ammonium to nitrate via nitrite by soil microbes, is a prominent source of nitrogen loss in soil systems. The effectiveness of nitrification inhibitors in reducing nitrogen loss through inhibition of nitrification is well-documented, however, their efficacy in heavy metals-contaminated soils needs thorough investigations. The current study assessed the efficacy of nitrification inhibitor 3, 4-dimethylpyrazole phosphate (DMPP) in reducing nitrous oxide (N2O) emissions in cadmium (Cd) contaminated paddy and red soils under lab-controlled environment. Obtained results indicated the substantial reduction in N2O emissions with DMPP in paddy and red soil by 48 and 35 %, respectively. However, Cd contamination resulted in reduced efficacy of DMPP, thus decreased the N2O emissions by 36 and 25 % in paddy and red soil, respectively. It was found that addition of DMPP had a significant effect on the abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA). Notably, the reduction in N2O emissions by DMPP varied with the abundance of AOB. Moreover, Cd pollution resulted in a significant (P < 0.05) reduction in the abundance of archaeal and bacterial amoA genes, as well as bacterial nirK, nirS, and nosZ genes. The combined treatment of Cd and DMPP had a detrimental impact on denitrifiers, thereby influencing the overall efficiency of DMPP. These findings provide novel insights into the application of DMPP to mitigate nitrification and its potential role in reducing N2O emissions in contaminated soils.

Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments

The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3−-N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.

Bioremediation of rapid sand filters for removal of organic micropollutants during drinking water production

Rapid sand filtration (RSF) is used during drinking water production for removal of particles, possible harmful microorganisms, organic material and inorganic compounds such as iron, manganese, ammonium and methane. However, RSF can also be used for removal of certain organic micropollutants (OMPs). In this study, it was investigated if OMP removal in columns packed with sand from full scale RSFs could be stimulated by bioaugmentation (i.e. inoculating RSFs with sand from another RSF) and/or biostimulation (i.e. addition of nutrients, vitamins and trace-elements that stimulate microbial growth). The results showed that removal of PFOA, carbamazepine, 1-H benzotriazole, amidotrizoate and iopamidol in the columns was low (< 20 %). Propranolol and diclofenac removal was higher (50–60 %) and propranolol removal likely occurred via sorption processes, whereas for diclofenac it was unclear if removal was a combination of physical-chemical and biological processes. Moreover, bioaugmentation and biostimulation resulted in 99 % removal of gabapentin and metoprolol after 38 days and 99 % removal of acesulfame after 52 days of incubation. The bioaugmented column without biostimulation showed 99 % removal for gabapentin and metoprolol after 52 days, and for acesulfame after 80 days. In contrast, the non-bioaugmented column did not remove gabapentin, removed < 40 % metoprolol and showed 99 % removal of acesulfame only after 80 days of incubation. Removal of these OMPs was negatively correlated with ammonium oxidation and the absolute abundance of ammonia-oxidizing bacteria. 16S rRNA gene sequencing showed that OMP removal of acesulfame, gabapentin and metoprolol was positively correlated to the relative abundance of specific bacterial genera that harbor species with a heterotrophic and aerobic or denitrifying metabolism. These results show that bioaugmentation of RSF can be successful for OMP removal, where biostimulation can accelerate this removal.

How does biochar influence soil nitrification and nitrification-induced N2O emissions?

Nitrification is a major pathway of N2O production, especially in aerobic soils. The amendment of soils with biochar has been suggested as a promising solution to regulate soil N cycle and reduce N2O emissions. However, there is a lack of comprehensive and quantitative understanding of biochar impacts on soil nitrification and nitrification-induced N2O emissions. In this study, a meta-analysis was conducted using data compiled across 95 peer-reviewed studies. Results showed that biochar in general significantly increased soil nitrification rate by 56 %, with overall no significant effect on nitrification-induced N2O emissions, suggesting that biochar likely restricted the fraction of nitrified N emitted as N2O emissions. The abundance of ammonia-oxidizing bacteria (AOB) was significantly increased by 37 % following biochar addition, but that of ammonia-oxidizing archaea (AOA) did not change significantly, indicating that the impact of biochar on AOB rather than AOA may play an important role in soil nitrification. The impacts of biochar on soil nitrification processes were heterogeneous depending on soil properties. Biochar increased soil nitrification rate and AOB abundance to a larger extent in poorly pH-buffered soils such as those with acidic pH (<5), low organic carbon (<10 g kg−1), or poor texture (rich in either sand or clay), which may be attributed to the liming and structural effects of biochar that regulate soil pH and water-air status. The overall no significant effect of biochar on nitrification-induced N2O emissions was due to a positive effect in acidic soils, a negative effect in alkaline soils, and little effect in neutral soils. This study provides a comprehensive insight into how different factors mediate the response of soil nitrification processes to biochar amendment, which contributes to a new understanding of biochar function in regulating soil N2O emissions, and can assist in designing biochar projects that would benefit soil N cycle while minimizing undesirable side effects.

Impacts of aboveground litter and belowground roots on soil greenhouse gas emissions: Evidence from a DIRT experiment in a pine plantation

Plant detritus alteration may influence soil greenhouse gas emissions, but the direction, extent and mechanisms remain uncertain. Here we conducted a DIRT (Detritus Input and Removal Treatment) experiment in a Pinus sylvestris var. mongolica plantation in Saihanba (Hebei Province, China), manipulating aboveground litter (L-: litter removal, L: normal litter, L+: litter doubling) and belowground roots (R-: root removal, R: with root) resulting in six treatments. We measured CO2, N2O, and CH4 fluxes during 2019 and 2020 growing seasons, along with soil physicochemical, enzymatic and microbial variables. Our findings revealed that soil CO2 and N2O emissions increased with litter input, while CH4 uptake decreased. The absence of roots decreased soil CO2 emission and CH4 uptake but increased N2O emission. Aboveground litter enhanced the carbon cycling variables, such as extractable organic carbon (EOC), the ratio of soil extractable organic carbon to extractable total nitrogen (EOC:ETN), soil carbon mineralization rate (Cmin), and peroxidase activity (PER), resulting in increased CO2 emission. In contrast, the absence of roots increased the nitrogen cycling variables, such as soil extractable total nitrogen (ETN), nitrate nitrogen content (NO3−-N), the ratio of soil extractable organic carbon to extractable total nitrogen (EOC:ETN), soil net nitrogen mineralization rate (Nmin), and the abundance of ammonia-oxidizing bacteria (AOB), leading to increased N2O emission. Moreover, soil CH4 uptake was mainly influenced by soil microclimate: aboveground litter input reduced CH4 uptake by lowering soil temperature, while belowground roots benefited CH4 uptake via reducing soil moisture by water uptake. Taken together, our study suggests that soil CO2, N2O, and CH4 emissions (or uptake) are influenced by both aboveground and belowground plant inputs through various pathways. While aboveground litter input promotes the emissions of greenhouse gasses, the mitigating effect of belowground roots on N2O and CH4 partially offsets the increment of CO2 emission in this plantation.

Tree species richness and functional composition drive soil nitrification through ammonia-oxidizing archaea in subtropical forests

Understanding the links between plant diversity and functional microbiota is crucial for unraveling the mechanisms by which plant communities regulate ecosystem functions. However, the underlying mechanism of how tree diversity influences soil nitrification remains elusive in forest ecosystems. Here we investigated the impacts of tree species richness and their functional composition (including functional identity and functional trait diversity) on the dynamics of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and arbuscular mycorrhizal (AM) fungi using a tree diversity experiment established with 32 native tree species in a subtropical forest biome. Our study revealed that tree species richness had a positive concave-down relationship with the abundance of AOA. Furthermore, the community-weighted mean of leaf nitrogen and specific root length were significant positive factors for the abundances of AOA and AOB, respectively. By contrast, functional trait diversity of specific root length was negatively associated with the biomass of AM fungi. Regression analysis showed that the abundance of AOA was positively correlated with soil net nitrification rates, while the biomass of AM fungi was negatively correlated with soil net nitrification rates. The structural equation model showed that the positive effect of leaf nitrogen on nitrification was driven by the increase in AOA. By contrast, the functional trait diversity of specific root length indirectly increased soil nitrification via a negative impact on the biomass of AM fungi. Taken together, our findings demonstrate that both tree species richness and tree functional composition promoted soil nitrification by increasing the AOA abundance, and emphasize the key role of the interplay between tree diversity and functional microbiota in predicting ecosystem functions.

Comparative biotic and abiotic effects on greenhouse gas emissions from agricultural ecosystems: application of straw or biochar?

Farmland has become a significant contributor to greenhouse gas (GHG) emissions, and research has shown that the addition of straw or biochar may be a viable method for mitigating these emissions. However, there is a lack of understanding regarding the comparative biotic and abiotic effects of straw and biochar amendments on GHG emissions. To address this knowledge gap, we conducted a meta-analysis of 100 published papers to quantify the impact of straw and biochar application on GHG emissions. Our findings indicate that straw application significantly increased CO2 and CH4 emissions from agricultural ecosystems by 46.2% and 113.5%, respectively, but did not have a significant effect on N2O emissions. Conversely, biochar amendment significantly reduced CO2, CH4, and N2O emissions by an average of 11.0%, 31.7%, and 22.8%, respectively. We also found that straw and biochar amendments increased soil pH, soil organic carbon (SOC), and C/N ratio, and there were significant differences between them. Moreover, straw application significantly increased the microbial biomass carbon (MBC) content and microbial quotient by 37.1% and 20.1%, respectively, while biochar application increased the MBC content by 25.0% without a significant effect on the microbial quotient. Furthermore, both straw and biochar applications promoted the nitrification process and increased the abundance of ammonia-oxidizing bacteria (AOB) by 50.7% with straw and by 57.5% and 75.1% with biochar for ammonia-oxidizing archaea (AOA) and AOB, respectively. The denitrification process was also stimulated by straw or biochar amendment, resulting in an increase in the abundance of nirK by 22.9% and 16.8%, respectively. Biochar amendment additionally increased the abundance of nosZ by 29.4%, indicating that the main reason for reducing N2O emissions through biochar application is the conversion of NO3--N to N2. Thus, compared to straw application, biochar application is a more effective method for reducing greenhouse gas emissions.

Full substitution of chemical fertilizer by organic manure decreases soil N2 O emissions driven by ammonia oxidizers and gross nitrogen transformations.

Replacing synthetic fertilizer by organic manure has been shown to reduce emissions of nitrous oxide (N2 O), but the specific roles of ammonia oxidizing microorganisms and gross nitrogen (N) transformation in regulating N2 O remain unclear. Here, we examined the effect of completely replacing chemical fertilizer with organic manure on N2 O emissions, ammonia oxidizers, gross N transformation rates using a 13-year field manipulation experiment. Our results showed that organic manure reduced cumulative N2 O emissions by 16.3%-210.3% compared to chemical fertilizer. The abundance of ammonia oxidizing bacteria (AOB) was significantly lower in organic manure compared with chemical fertilizer during three growth stages of maize. Organic manure also significantly decreased AOB alpha diversity and changed their community structure. However, organic manure substitution increased the abundance of ammonia oxidizing archaea and the alpha diversity of comammox Nitrospira compared to chemical fertilizer. Interestingly, organic manure decreased organic N mineralization by 23.2%-32.9%, and autotrophic nitrification rate by 10.5%-45.4%, when compared with chemical fertilizer. This study also found a positive correlation between AOB abundance, organic N mineralization and gross autotrophic nitrification rate with N2 O emission, and their contribution to N2 O emission was supported by random forest analysis. Our study highlights the key roles of ammonia oxidizers and N transformation rates in predicting cropland N2 O.

Nitrification in the water column of Lake Erie: Seasonal patterns, community dynamics, and competition with cyanobacterial harmful algal blooms

Abstract This study reports directly measured nitrification rates in the water column of western Lake Erie, which is affected by annual cyanobacterial harmful algal blooms, and across all three Lake Erie basins. Over three field seasons, 15NH4+ stable isotope tracers were employed to quantify nitrification rates, and relative abundances of ammonia-oxidizing bacteria and ammonia-oxidizing archaea were determined via qPCR. Nitrification rates ranged from undetectable to 1,270 nmol L-1 d-1 and were generally greatest in the western basin near the Maumee River mouth (a major nutrient source). Nitrification rates were highest in early summer, and often lowest during peak cyanobacterial harmful algal blooms months (August and September), before increasing again in October. In the western basin, nitrification was negatively correlated with cyanobacterial biomass. There were no consistent differences in nitrification rates between the three Lake Erie basins. Over the three years in western Lake Erie, ammonia-oxidizing bacteria and ammonia-oxidizing archaea were often present in high and similar abundances, but overall, ammonia-oxidizing bacteria exceeded ammonia-oxidizing archaea, particularly in 2017. No relationships were observed between nitrification rates and ammonia-oxidizing bacteria and ammonia-oxidizing archaea abundances. Thus, despite abundant ammonia-oxidizer DNA, lower nitrification rates during cyanobacterial harmful algal blooms suggest that nitrifiers were poor competitors for regenerated and available NH4+ during these blooms, as also observed in similar systems. Low nitrification rates during cyanobacterial harmful algal blooms could limit system nitrogen removal via denitrification, a natural pathway for its removal and a valuable ecosystem service. Lower denitrification rates allow more bioavailable nitrogen to remain in the system and support biomass and microcystin production; therefore, these results help explain how non-nitrogen-fixing cyanobacterial harmful algal blooms persist, despite low bioavailable nitrogen concentrations during these blooms, and support management efforts to reduce external nitrogen loading to eutrophic systems.

Comammox plays a functionally important role in the nitrification of rice paddy soil with different nitrogen fertilization levels

Chemoautotrophic ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizers (comammox) catalyze ammonia oxidation; however, quantifying their individual gross ammonia oxidation activities in complex soil ecosystems remains elusive. In this study, we investigated the nitrifying population and community dynamics in response to fertilization in paddy soil under long-term treatment with different urea concentrations (0, 100, 200, and 300 kg N ha−1; designated N0, N100, N200, and N300, respectively). The community structure of nitrifiers, including comammox, was changed by long-term N fertilizers input, which also enhanced AOB abundance and comammox clade A/B abundance ratio, whereas it did not affect AOA abundance. Nevertheless, the microbial population sizes and community compositions remained largely similar following short-term fertilization throughout one rice-growing season. Furthermore, by employing a 15NO3− pool dilution technique in combination with chlorate and 1-octyne inhibition, we conducted a soil microcosm incubation without substrate supplementation to distinguish the relative contribution of comammox to gross ammonia oxidation from those of AOA and AOB. Comammox exhibited higher nitrification activity in soils treated with more N fertilizers, with the contribution increasing from 34 % (N0) to 75 % (N300), although its abundance was not dominant. This could be attributed to the repeated N-based fertilization, which reduced the soil pH, thereby decreasing the soil-free ammonia concentration. In contrast, the contribution of AOA declined from 57 % (N0) to 19 % (N300), while that of AOB only accounted for a minor fraction (<25 %) despite being in high abundance. Altogether, our findings provide evidence that the activity of nitrifying guilds is more valuable than their abundance and provide insights into the potential functional significance of comammox in the nitrification process in rice paddy systems.