Abundance Of Ammonia-oxidizing Bacteria amoA Gene Research Articles

Maize–peanut intercropping and N fertilization changed the potential nitrification rate by regulating the ratio of AOB to AOA in soils

Maize–peanut intercropping could potentially mitigate nitrogen (N) loss from the soil, a process primarily governed by the net nitrification rate. However, the impact of maize–peanut intercropping on the potential nitrification rate (PNR) and its relationships with key players, such as ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), are not well understood. Herein, we conducted a field experiment involving two management systems and two crops, namely, maize (MPm) and peanut (MPp) intercropping, maize monoculture (MM), and peanut monoculture (PM), under three N fertilization rates (no N fertilization, 150 kg N ha−1, and 300 kg N ha−1). Under intercropping (MPm and MPp), the abundance of AOA amoA gene increased by 64.8% and 60.3% and the abundance of AOB amoA gene increased by 63.2% and 68.2% compared to the MM and PM monoculture systems, respectively. Furthermore, the abundances of AOA and AOB decreased in MPp and MM, while AOB increased in MPm and PM across the N fertilization gradient. The PNR increased corresponding to the N fertilization rates, with intercropping enhancing the PNR in peanut-planted soil but reducing the PNR in maize-planted soil compared to monocropping. Notably, no significant positive relationship between the abundances of AOA or AOB and the PNR. Random forest analysis indicated that the AOB/AOA ratio was an important predictor of the PNR. N fertilization and intercropping regulated the AOB/AOA ratio mainly through controlling the ammonia content and the soil C/N, respectively. These findings highlight the substantial impacts of N fertilization and intercropping on PNR, with the AOB/AOA ratio emerging as a valuable predictive indicator for the PNR.

Polyaspartic calcium improved soil quality and altered nitrification process in saline‐sodic paddy soils

AbstractSaline‐sodic paddy soils in the Songnen Plain suffer from nitrogen loss due to nitrification. The purpose of the study is to explore soil saline improvement and nitrification mitigation effects of polyaspartic calcium (PASP‐Ca) by evaluating changes of soil quality, nitrification, and microbial communities. Four PASP‐Ca application treatments (additions of 0, 500, 1000, and 1500 kg hm−2) were studied in an experiment in saline‐sodic paddy soils of the Songnen Plain, China. Results showed that PASP‐Ca application significantly decreased soil pH, electrical conductivity (EC), and water‐soluble salt ions, and significantly increased soil total carbon (TC), total nitrogen (TN), urease activity (UA), and sucrase activity (SA). PASP‐Ca application significantly slowed down soil nitrification, which was manifested in a significant increase in ammonium nitrogen () and a significant decrease in nitrate nitrogen () and ammonia monooxygenase activity (AMO). The composition and distribution of soil nitrifying microbial communities were affected by soil salinity, nutrient, and enzyme activities. Ammonia‐oxidizing bacteria (AOB) plays an important role in the nitrification process of saline‐sodic paddy soils, while PASP‐Ca application significantly inhibited nitrification by suppressing AOB amoA gene abundance. This study shows that PASP‐Ca, as an effective amendment, can improve soil salinization and slow down nitrification, which has an important role and significance in improving nitrogen utilization and reducing nitrogen loss of saline‐sodic soils.

Mechanisms of mitigating nitrous oxide emission during composting by biochar and calcium carbonate addition

To investigate the mechanisms underlying effects of biochar and calcium carbonate (CaCO3) addition on nitrous oxide (N2O) emissions during composting, this paper conducted a systematic study on mineral nitrogen (N), dissolved organic carbon (C) and N, sources of N2O, and functional genes. Biochar and CaCO3 addition decreased N2O emissions by 26.5–47.8% (9.5–96.9 mg N kg−1 dw) and 13.9–37.4% (12.0–121.0 mg N kg−1 dw) compared to the control (14.3–179.7 mg N kg−1 dw), respectively. The mitigation of N2O emission was caused by decreased contribution of ammonia-oxidizing bacteria (AOB) and fungi to N2O production due to diminished AOB amoA, fungal nirK and P450 gene abundances, or by stimulated N2O reduction to N2 owing to increased abundances of nosZⅠ and nosZⅠⅠ genes under biochar and CaCO3 addition. The findings suggest that the addition of biochar or CaCO3 is effective in mitigating N2O emission during composting.

Nitrogen fertilization rate affects communities of ammonia-oxidizing archaea and bacteria in paddy soils across different climatic zones of China

Nitrogen fertilization has important effects on nitrification. However, how the rate of nitrogen fertilization affects nitrification potential, as well as the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), remains unclear. We performed a large-scale investigation of nitrification potential and ammonia-oxidizer communities in Chinese paddy fields at different nitrogen fertilization rates across different climatic zones. It was found that the nitrification potential at the high nitrogen fertilization rate (≥150 kg−1 N ha−1) was 23.35 % higher than that at the intermediate rate (100–150 kg−1 N ha−1) and 20.77 % higher than that at the low rate (< 100 kg−1 N ha−1). The nitrification potential showed no significant variation among different nitrogen fertilization rates across climatic zones. Furthermore, the AOA and AOB amoA gene abundance at the high nitrogen fertilization rate was 481.67 % and 292.74 % higher (p < 0.05) than that at the intermediate rate, respectively. Correlation analysis demonstrated a significant positive correlation between AOB abundance and nitrification potential. AOA and AOB community composition differed significantly among nitrogen fertilization rates. Moreover, soil NH4+ content, pH, water content, bulk density, and annual average temperature were regarded as key environmental factors influencing the community structure of ammonia-oxidizers. Taken together, the nitrogen fertilization rate had a significant impact on the communities of AOA and AOB but did not significantly alter the nitrification potential. Our findings provide new insights into the impact of nitrogen fertilization management on nitrification in rice paddy fields.

Accelerated nitrification and altered community structure of ammonia-oxidizing microorganisms in the saline-alkali tolerant rice rhizosphere of coastal solonchaks

Plantations of saline-alkali tolerant rice in coastal areas are proposed as a strategy to improve rice yield and ensure global food security. The soil nitrification process driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is an integral part of the soil nitrogen cycle and correlates with the quality of coastal solonchak. However, little is known about the effects of saline-alkali tolerant rice cultivation on the soil nitrification process in coastal solonchaks. In this study, we investigated the community structures of AOA/AOB and the nitrification rate in the rice rhizosphere along salinity gradients. The abundance and nitrification rates of AOA and AOB declined with increasing salinity. Saline-alkali-tolerant rice cultivation significantly increased the abundance of AOA and AOB amoA genes from (3.09–11.5) × 106 and (7.76–52.0) × 105 copies g−1 in soils to (16.2–50.9) × 106 and (69.2–423) × 105 copies g−1 in the rhizosphere, respectively. Compared with bulk soils, the nitrification rate of AOA and AOB in the rhizosphere increased significantly with salinity. Saline-alkali-tolerant rice cultivation enhanced the nitrification process of saline-alkali tolerant soil by increasing the nitrification contribution of AOB. Our findings offer new clues on the accelerated nitrification process in the saline-alkali tolerant rice rhizosphere in coastal solonchaks and reveal its roles in shaping AOA/AOB communities, providing suggestions for saline-alkali tolerant rice plantations in coastal solonchaks.

DMPP mitigates N2O and NO productions by inhibiting ammonia-oxidizing bacteria in an intensified vegetable field under different temperature and moisture regimes

Vegetable soils with high nitrogen input are major sources of nitrous oxide (N2O) and nitric oxide (NO), and incorporation of the nitrification inhibitor 3, 4-dimethylpyrazole phosphate (DMPP) into soils has been documented to effectively reduce emissions. However, the efficiency of DMPP in terms of soil N2O and NO mitigations varies greatly depending on soil temperature and moisture levels. Thus, further evaluations of DMPP efficiency in diverse environments are required to encourage widespread application. A laboratory incubation study (28 d) was established to investigate the interactive effects of DMPP, temperature (15, 25, and 35 °C), and soil moisture (55% and 80% of water-holding capacity (WHC)) on net nitrification rate, N2O and NO productions, and gene abundances of nitrifiers and denitrifiers in an intensive vegetable soil. Results showed that incubating soil with 1% DMPP led to partial inhibition of the net nitrification rate and N2O and NO productions, and the reduction percentage of N2O production was higher than that of NO production (69.3% vs. 38.2%) regardless of temperature and soil moisture conditions. The increased temperatures promoted the net nitrification rate but decreased soil N2O and NO productions. Soil moisture influenced NO production more than N2O production, decreasing with the increased moisture level (80%). The inhibitory effect of DMPP on cumulative N2O and NO productions decreased with increased temperatures at 55% WHC. Conversely, the inhibitory effect of DMPP on cumulative N2O production increased with increased temperatures at 80% WHC. Based on the correlation analyses and automatic linear modeling, the mitigation of both N2O and NO productions from the soil induced by DMPP was attributed to the decreases in ammonia-oxidizing bacteria (AOB) amoA gene abundance and NO2--N concentration. Overall, our study indicated that DMPP reduced both N2O and NO productions by regulating the associated AOB amoA gene abundance and NO2--N concentration. These findings improve our insights regarding the implications of DMPP for N2O and NO mitigations in vegetable soils under various climate scenarios.

Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China.

The newly identified complete ammonia oxidizer (comammox) that converts ammonia directly into nitrate has redefined the long-held paradigm of two-step nitrification mediated by two distinct groups of nitrifiers. However, exploration of the niche differentiation of canonical nitrifiers and comammox Nitrospira and their ecological importance in agroecosystems is still limited. Here, we adopted quantitative PCR (qPCR) and Illumina MiSeq sequencing to investigate the effects of five long-term fertilization regimes in the variations of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira abundances and comammox community composition in two soil layers (0-20 cm, topsoil; 20-40 cm, subsoil) in an Alfisol in Northeast China. The fertilization treatments included no fertilizer (CK); chemical nitrogen (N) fertilizer; chemical N; phosphorus (P) and potassium (K) fertilizers (NPK); recycled organic manure (M) and chemical N, P, K plus recycled manure (MNPK). Compared with CK, manure and/or chemical fertilizer significantly increased the AOB amoA gene abundance. Long-term recycled manure increased soil organic matter (SOM) contents and maintained the soil pH, but decreased the NH4 +-N concentrations, which markedly promoted the nxrA and nxrB gene abundances of NOB and the amoA gene abundances of comammox Nitrospira clade A and AOA. Although the comammox Nitrospira clade B abundance tended to decrease after fertilization, the structural equation modeling analysis showed that comammox clade B had direct positive impacts on soil potential ammonia oxidation (PAO; λ = 0.59, p < 0.001). The long-term fertilization regime altered the community composition of comammox Nitrospira. Additionally, comammox Nitrospira clades A and B had individual response patterns to the soil layer. The relative abundance of clade A was predominant in the topsoil in the N (86.5%) and MNPK (76.4%) treatments, while clade B appeared to be dominant in the subsoil (from 78.7 to 88.1%) with lower ammonium contents, implying niche separation between these clades. Soil pH, NH4 +-N and SOM content were crucial factors shaping the soil nitrifying microbial abundances and the comammox Nitrospira community. Together, these findings expand the current understanding of the niche specialization and the important role of comammox Nitrospira in terrestrial ecosystems.

A meta-analysis to examine whether nitrification inhibitors work through selectively inhibiting ammonia-oxidizing bacteria.

Nitrification inhibitor (NI) is often claimed to be efficient in mitigating nitrogen (N) losses from agricultural production systems by slowing down nitrification. Increasing evidence suggests that ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) have the genetic potential to produce nitrous oxide (N2O) and perform the first step of nitrification, but their contribution to N2O and nitrification remains unclear. Furthermore, both AOA and AOB are probably targets for NIs, but a quantitative synthesis is lacking to identify the “indicator microbe” as the best predictor of NI efficiency under different environmental conditions. In this present study, a meta-analysis to assess the response characteristics of AOB and AOA to NI application was conducted and the relationship between NI efficiency and the AOA and AOB amoA genes response under different conditions was evaluated. The dataset consisted of 48 papers (214 observations). This study showed that NIs on average reduced 58.1% of N2O emissions and increased 71.4% of soil concentrations, respectively. When 3, 4-dimethylpyrazole phosphate (DMPP) was applied with both organic and inorganic fertilizers in alkaline medium soils, it had higher efficacy of decreasing N2O emissions than in acidic soils. The abundance of AOB amoA genes was dramatically reduced by about 50% with NI application in most soil types. Decrease in N2O emissions with NI addition was significantly correlated with AOB changes (R2 = 0.135, n = 110, P < 0.01) rather than changes in AOA, and there was an obvious correlation between the changes in concentration and AOB amoA gene abundance after NI application (R2 = 0.037, n = 136, P = 0.014). The results indicated the principal role of AOB in nitrification, furthermore, AOB would be the best predictor of NI efficiency.

Di-(2-ethylhexyl) phthalate (DEHP) exposure suppressed the community diversity and abundance of ammonia-oxidizers and mitigated N2O emissions in an alkaline soil

Phthalic acid esters (PAEs) pollution has become an increasing issue worldwide, but little is known about its effects on ammonia-oxidizers and nitrous oxide (N2O) in the soil environment. Here, a 50-day soil microcosm experiment was conducted using low and high doses bis (2-Ethylhexyl) phthalate (DEHP) to estimate the effect of DEHP exposure on soil N2O emissions and the nitrifying community in calcareous soil. The results showed that DEHP exposure at 10 and 100 mg kg-1 doses significantly reduced N2O by 67.5% and 73.6%, respectively, relative to the DEHP absent treatment. The microbial biomass carbon and nitrogen (MBC and MBN) were consistently and significantly decreased with DEHP exposure at 5, 22, and 50 days after incubation, especially with high-dose. The bipartite association networks showed that DEHP exposure changed the compositions of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. Moreover, the AOA and AOB amoA gene abundances were significantly decreased by DEHP addition to the soil (P < 0.05). Random forest modeling showed that the AOB Shannon index and pH were the most important biotic and abiotic factors affecting N2O emissions in the soil with DEHP exposure, respectively. Partial least squares path modeling (PLS-PM) demonstrated that the reduction of N2O emissions due to DEHP exposure was mainly ascribed to the changes of the AOB community. The results from this study highlight the toxicity of DEHP on the ammonia oxidizers, and its mitigating effect on N2O emissions in the soil where ammonia-oxidation is largely driven by AOB.

PH and ammonium concentration are dominant predictors of the abundance and community composition of comammox bacteria in long-term fertilized Mollisol

The newly-discovered complete ammonia-oxidizing bacteria (comammox) doubts our inherent understanding of nitrification. Herein, we study communities of comammox, ammonia-oxidizing bacteria (AOB) and archaea (AOA) in Mollisol after a 30-year fertilization history with four treatments: chemical nitrogen (N) and potassium (K) fertilizers (NK); chemical N, phosphorus (P), and K fertilizers (NPK); chemical NPK fertilizers plus organic manure (NPKM); and a control without fertilizers (CK). Compared with CK, chemical fertilizer treatments (NK and NPK) significantly reduced AOA amoA gene abundance and increased AOB and comammox amoA gene abundances. The highest values of AOA and AOB amoA gene abundances were found in the NPKM treatment and the highest value of comammox amoA gene abundance was observed in the NK treatment. The application of combined NPK and organic manure (NPKM) significantly increased AOA, AOB, and comammox amoA gene abundances compared to CK. Long-term chemical fertilization decreased the diversity of comammox community; whereas, the application of combined NPK with organic manure (NPKM) restored it to levels comparable to CK. Long-term fertilization management altered the community structure of comammox based on principal coordinate analysis (PCoA). Soil pH and NH4+-N concentration were the key factors affecting soil abundance and community structure of comammox. This study demonstrates the different responses of comammox community and canonical ammonia oxidizers to long-term fertilization practices in Mollisol.

Molecular analysis of microbial nitrogen transformation and removal potential in mangrove wetlands under anthropogenic nitrogen input

Mangrove ecosystems are natural nitrogen removal systems that are primarily mediated by nitrogen cycle microorganisms, but their relative contributions to nitrogen transformation and removal in mangrove sediments under anthropogenic nitrogen input needs further resolution and characterization. Here, we investigated the responses and the relative contributions of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), anaerobic ammonium oxidizing (anammox) bacteria and denitrifying bacteria after spiking urea into mangrove sediments incubated in a laboratory microcosm experiment for four weeks. During incubation, the diversity, abundances and transcription levels of the hzo genes for anammox bacteria, amoA genes for AOA and AOB, and nirS genes for denitrifying bacteria were monitored using targeted gene clone library analyses and quantitative PCR assays at the DNA and RNA levels. The results showed that mangrove sediments harbour habitat-specific anammox bacteria which related to Candidatus Scalindua and Candidatus Kuenenia clades. Mangrove specific AOA related to deep branched clades within Candidatus Nitrososphaera and Candidatus Nitrosotalea, and AOB related to Nitrosomonas and Nitrosospira were also detected in the collected sediment samples. Growth and activity of AOA were detected at all levels of amendment of nitrogen input, whereas AOB growth was detectable only at the high-level nitrogen input (1.5 mg urea per gram of dry sediment) with no amoA transcripts and lower abundance than AOA. The abundance and transcription levels of the nirS gene were higher (~1000 times) than those of the hzo gene in all groups. Pearson correlation analysis demonstrated that the abundance of both AOA and AOB amoA genes had a significant positive correlation with the nirS gene (p < 0.01). These results indicated that nitrification (primarily mediated by the AOA)-denitrification process played the most important role in nitrogen removal from the amendment of nitrogen short-term input in the mangrove sediments.

Abundance and community structure of ammonium monooxygenase (amoA) genes in the wet season of liaohe estuary sediments

Ammonia oxidation is an important part of the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are important players in the ammoxidation process. In this study, 13 sediment samples from the Liaohe estuary were collected in the wet season. The abundances of 16S rRNA and amoA genes were detected by real-time fluorescence quantitative PCR. The diversity and community structure of AOA and AOB were investigated by constructing clone libraries. The AOA and AOB amoA gene abundances ranged from 3.10 × 106–2.85 × 107 and 6.59 × 105–1.20 × 107 copies/g wet deposit, respectively. At all sites, AOA abundance was greater than AOB (AOA: AOB = 2.2–86.5). The ratio of AOA: archaeal 16S rRNA gene abundances and AOB: bacterial 16S rRNA gene abundances were 4.6 × 10−3–1.5 × 10−2 and 1.5 × 10−6–1.0 × 10−4. Phylogenetic analysis showed that the AOA amoA sequences were mainly Nitrosophaera and Nitrosopumilus, and most of the AOB amoA sequences belong to unclassified bacteria, which mainly were detected in estuarine sediments and wetland soils. AOA and AOB community had an obvious spatial heterogeneity. In addition, canonical correspondence analysis showed that the salinity, ammonia, total phosphorus, total organic carbon, sand, and silt content were the main driven factors of AOA and AOB community structure, in which the sand and silt content had a significant contribution.

Ammonia oxidizers in river sediments of the Qinghai-Tibet Plateau and their adaptations to high-elevation conditions

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) as well as complete ammonia oxidizers (comammox) aerobically catalyze ammonia oxidation which plays essential roles in riverine nitrogen cycle. However, performances of these ammonia oxidizers in high-elevation river sediments have rarely been documented. This study investigated the abundance, community, and activity of ammonia oxidizers in five high-elevation rivers of the Qinghai-Tibet Plateau (QTP). Comammox were dominant ammonia oxidizers in 23% of studied samples and the clade B was principal comammox type. amoA gene abundances of AOA and AOB in these high-elevation rivers were comparable to those in low-elevation rivers. However, in contrast to most studied low-elevation rivers, AOB amoA gene abundance outnumbered AOA in 92% samples, which might be caused by the lower temperature and more intense solar radiation of the QTP. Potential nitrification rates (PNRs) ranged from 0.02 to 2.95 nmol-N h−1 g−1 dry sediment. Ammonia concentration was the limiting factor to PNRs at some sites, and when ammonia was not limiting, the PNR: ammonia ratio was greater at higher temperatures. There was no apparent variation in ammonia oxidizer community compositions along the elevation gradient due to the high elevation (2687 to 4223 m) of our entire study area. However, compared with low-elevation rivers, the lower temperature, huge diurnal temperature change, and lower nutrient conditions in the QTP rivers shaped distinctive communities for ammonia oxidizers; the unique community characteristics were significantly correlated to PNRs. These results suggest that ammonia oxidizers in the five high-elevation rivers have adapted to high-elevation conditions; more research should be conducted to study their adaptation mechanisms and their roles in riverine nitrogen cycle.

Ammonia-oxidizing bacterial and archaeal communities in tropical bioaugmented zero water exchange shrimp production systems

Ammonia oxidation is an important process in the removal of ammonia generated from feed and metabolic wastes in aquaculture systems. Considering the biogeochemical importance of ammonia oxidation in bioaugmented zero water exchange aquaculture systems, the diversity and abundance of bacterial and archaeal ammonia-oxidizing communities were analyzed in three selected ponds at different time intervals during the culture period, to unravel the key environmental factors influencing their distribution in the system. The diversity and abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in three tropical bioaugmented zero water exchange (ZWE) shrimp culture systems were analyzed using ammonia monooxygenase A (amoA) gene from the sediment metagenome during different phases of culture. The environmental factors associated with the variability in bacterial and archaeal amoA gene abundance and diversity were elucidated using RDA and Pearson correlation analysis. Ammonia-oxidizing archaea (AOA), Nitrosopumilus sp., Nitrosospharea sp., and ammonia-oxidizing bacteria (AOB), Nitrosomonas sp., were the dominant ammonia-oxidizing communities in the ZWE ponds studied. AOA shared 41 OTUs, and the maximum distribution was influenced by dissolved oxygen in the system, whereas AOB shared 4 OTUs. The copy numbers amoA gene determined using qPCR showed that the AOA amoA gene was 10- to 100-fold abundant than AOB amoA gene. Gene abundance of AOA was positively related to total organic carbon (TOC) and salinity of sediments, and the temperature had a negative impact on bacterial amoA gene abundance. The dissolved oxygen and TOC had a negative and redox potential a positive impact on the diversity of AOA, whereas pH had a negative impact on the diversity of AOB. The ammonia-oxidizing archaeal communities dominated the bioaugmented zero water exchange aquaculture systems compared to bacteria based on the abundance and diversity analysis using amoA gene sequence-based OTU analysis and gene copy numbers. Dissolved oxygen, total organic carbon, and Eh of the sediments contributed to the distribution and abundance of AOA group in the ZWE ponds. This study points to the importance of environmental management in these culture systems for maintaining ammonia-oxidizing populations for optimal ammonia removal. The relative contribution of the archaea and bacteria to ammonia oxidation in these systems is to be further resolved along with that of anammox and comammox bacteria, which would help to develop appropriate biostimulation or bioaugmentation strategies for the management of these sustainable aquaculture production systems.

Shifts in the Community Dynamics and Activity of Ammonia‐Oxidizing Prokaryotes Along the Yangtze Estuarine Salinity Gradient

AbstractAmmonia oxidation, the first and rate‐limiting step in nitrification, plays a critical role in the nitrogen cycle. However, the links between the dynamics of ammonia‐oxidizing communities and ecosystem processes along the estuarine salinity gradient remain uncertain. In this study, we examined the diversity, abundance, and community structure of ammonia‐oxidizing prokaryotes, and the potential nitrification rates along the Yangtze estuarine salinity gradient. Phylogenetic analysis showed that the predominant ammonia‐oxidizing bacteria (AOB) and ammonia‐oxidizing archaea (AOA) fell within the Nitrosospira and Nitrosopumilus clusters, respectively. The AOB amoA gene abundance (4.67 × 105 to 3.90 × 107 copies per gram of dry sediment) outnumbered AOA (5.14 × 104 to 8.88 × 106 copies per gram of dry sediment). The potential nitrification rates varied between 0.13 and 0.63 μg N·g−1·day−1 and related only to AOA amoA gene abundance. Salinity had significant effects on AOA amoA gene abundance, nitrification rates, and the community structure of ammonia‐oxidizing prokaryotes. Principal coordinate analysis showed that the AOB amoA gene clones derived from the middle‐ and high‐salinity regions behaved as a cohesive group, while all the low‐salinity clone libraries were grouped together. Moreover, the distribution of AOA communities showed a distinct salinity differentiation. Overall, this study improves the understanding of the dynamic shifts in ammonia‐oxidizing microorganisms in the Yangtze Estuary.

Niche separation of comammox Nitrospira and canonical ammonia oxidizers in an acidic subtropical forest soil under long-term nitrogen deposition

The recent discovery of comammox Nitrospira capable of converting ammonia to nitrate in a single organism radically challenged our century-long perception of the classic two-step nitrification performed by ammonia oxidizers and nitrite oxidizers. However, our understanding of the niche separation of comammox Nitrospira and canonical nitrifiers in forest ecosystems remains limited, especially under a global scenario of elevated nitrogen (N) deposition. Here we evaluated the impacts of six-year N deposition on the dynamics of comammox Nitrospira, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a subtropical forest soil. Soil inorganic N concentrations significantly increased under the six-year simulation of N deposition, while soil pH, available phosphorus, total carbon (C), C/N ratio and microbial biomass significantly decreased. Quantitative PCR showed that the amoA gene abundances of comammox Nitrospira clade B and AOA substantially increased under the increasing rates of N deposition. By contrast, the AOB amoA gene abundance significantly decreased with the higher levels of N deposition (100 and 150 kg N ha−1 yr−1). Increased 13CO2 incorporation into the AOA communities, rather than comammox Nitrospira or AOB, was demonstrated in a DNA-stable isotope probing microcosm, indicative of the capacity of AOA to assimilate 13CO2 through autotrophic nitrification in the investigated subtropical forest soil under long-term N deposition. Phylogenetic analysis revealed that the autotrophic AOA assemblages belonged to the Nitrosotalea cluster, and their capacity for assimilating CO2 through autotrophic nitrification was not affected by the long-term N deposition. Taken together, we provided new evidence for the niche separation of comammox Nitrospira and canonical ammonia oxidizers in soil nitrification under the long-term N deposition in the acidic subtropical forest soil.

Abundance of ammonia-oxidizing bacteria and archaea under different ventilation strategies during cattle manure composting

Composting of cattle manure was conducted under four ventilation strategies, i.e., no-aeration (A-00), continuous aeration (B-44), non-aeration for 14 d and then aeration for 42 d (C-04), aeration for 14 d and then no-aeration for 42 d (D-40). Physicochemical parameters and potential ammonia oxidation (PAO) indicated that continuous and intermittent ventilation provide favourable conditions for ammonia-oxidizing bacteria (AOB) and archaea (AOA) to oxidize ammonia. Quantitative PCR (qPCR) analysis showed AOB amoA gene abundance of all treatments on every sampling day ranged from 2.25 × 105 to 2.76 × 109copies/g, was significantly lower than that of archaeal amoA gene from 2.71 × 108 to 9.05 × 1011copies/g. There was also a significantly positive relationship between PAO rates and AOB (r2 ≥ 0.066, p < 0.05) and AOA (r2 ≥ 0.300, p < 0.05) abundance. These data suggested that ammonia oxidation is driven by both AOA and AOB in cattle manure composting.

Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments

Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1–100 mg kg−1) and copper (Cu, 50–500 mg kg−1) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg−1 BDE 209 with a 100 mg kg−1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments.

Comparison of lime- and biochar-mediated pH changes in nitrification and ammonia oxidizers in degraded acid soil

Ca-amendments are recommended for soil fertility enhancement in acid soils. Biochar (Bc) can be used as an alternative for the same purpose. Biochar additions have been reported to alter microbial communities in soils and biogeochemical processes including nitrogen (N) cycling. In a microcosm experiment, we investigated the interactive effects of soil pH, the type of soil amendment (lime or biochar), and the NH4 + supply on net N mineralization and nitrification in degraded acid soil and on the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Soil was incubated under native pH and CaCO3 or biochar-manipulated pH to reach pH 6.2 and 6.8 in the presence or absence of added ammonium for 70 days. Our results showed that Bc had a longer-lasting effect on soil pH than CaCO3, suggesting that Bc could be a preferable liming agent. Increased pH stimulated microbial activity and led to increased N mineralization, which was higher when CaCO3 was applied. Although pH increase and NH4 +-N addition had no immediate effect on nitrification, they synergically enhanced nitrification at the end of the experiment. The amoA gene of AOA consistently outnumbered that of AOB, whereas only AOB amoA gene abundance number was significantly correlated with nitrification and their abundance followed similar trend as NO3 −-N during the incubation. In acid soils where AOB could play a significant role in nitrification, biochar could result in more pronounced changes in N cycle than lime application which could be of especially high interest in intensively managed soils with high N inputs.

Wheat straw-derived biochar amendment stimulated N2O emissions from rice paddy soils by regulating the amoA genes of ammonia-oxidizing bacteria

Biochar amendment of upland soil has been generally accepted to mitigate nitrous oxide (N2O) emissions. However, this is not always the case in rice paddy soil, and the underlying mechanisms are not well understood. To evaluate how biochar amendment affects N2O production and emissions in paddy soil, an incubation experiment was designed including six treatments: wheat straw-derived biochar (slow pyrolyzed at 400 °C) amendment at rates of 0% (Control), 1% and 4% soil mass (w/w), inorganic nitrogen (N) fertilizer amendment (with urea), and N fertilizer plus 1% biochar and 4% biochar. The application of 4% biochar significantly increased N2O emissions from N-unfertilized and fertilized soils during the 45-day incubation, by 291% and 256%, respectively, while 1% biochar amendment significantly increased soil N2O emissions when accompanied by N fertilizer addition. On day 14, when the N2O emission peaks occurred, N2O flux was significantly correlated with soil pH in all treatments. Biochar addition also enhanced the abundance of ammonia-oxidizing bacteria (AOB) amoA genes, which was significantly related to soil pH. Among all detected N2O-forming and reducing microbial genes, the abundance of AOB amoA genes was most closely related to N2O flux. On biochar addition, the AOB community structure shifted from Nitrosospira-dominated toward Nitrosomonas, and the diversity of AOB was significantly increased. Compared with the control, biochar amendment decreased, albeit not significantly, the abundance of the nitrous oxide reductase encoding gene nosZ, but did not alter the abundance of nitrite reductase encoding genes nirK and nirS. Our study suggests that wheat straw-derived biochar amendment of paddy soils increased soil pH, which in turn increased the abundance and diversity of AOB and N2O emissions.