amoA Gene Abundance Research Articles

Exogenous C6-HSL enhanced the cometabolic removal of sulfadiazine by an enriched ammonia oxidizing bacteria culture.

The removal of antibiotics in wastewater treatment plants (WWTPs) is generally insufficient. Studies have proved that ammonia-oxidizing bacteria (AOB) are capable of degrading antibiotics through cometabolism. However, the actual operating conditions in WWTPs are generally unfavorable for AOB to fully reach its cometabolic potential. Studies have demonstrated that exogenous N-acyl homoserine lactones (AHLs) can enhance the treatment efficiency of wastewater treatment microorganisms by regulating their quorum sensing system. However, few studies have reported the effect of exogenous AHLs on the cometabolic removal of antibiotics by AOB. In this study, a typical AHL, N-hexanoyl-L-homoserine lactone (C6-HSL), was selected to explore its effects on the cometabolic removal of a typical antibiotic, sulfadiazine (SDZ), by an enriched AOB culture and the microbial responses of the culture during the process. The results showed that the exposure to SDZ (0.1-10mg/L) led to the decrease in ammonia oxidation rate, the concentrations of intracellular adenosine triphosphate and ammonia oxygenase (AMO) and the abundances of amoA gene and AOB, while more extracellular polymeric substances (EPS) were secreted to resist the adverse effects brought by SDZ. With the simultaneous addition of SDZ (1 and 10mg/L) and exogenous C6-HSL (1μM), it was found that C6-HSL significantly enhanced the removal efficiency and rate of SDZ by the enriched AOB culture. By promoting EPS secretion, strengthening energy metabolism, promoting AMO synthesis, increasing AOB and amoA gene abundances and altering microbial community structure, C6-HSL restored the microbial activity and alleviated the pressure on microorganisms induced by SDZ. It is expected that this study could provide a new strategy for enhancing antibiotics removal in wastewater.

Niche Partitioning and Intraspecific Variation of Thaumarchaeota in Deep Ocean Sediments.

Deep-sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, their ecology and evolutionary adaptations are not well understood. Metagenomic analyses were conducted on samples from various depths of a 750-cm sediment core collected from the Mariana Trench Challenger Deep. The abundance of Thaumarchaeota and archaeal amoA generally decreased with depth, except for an unexpected peak midway through the core. The thaumarchaeotal metagenome-assembled genomes were classified into diverse phylogenetic clusters associated with amoA-NP-γ, amoA-NP-θ, and amoA-NP-δ of ammonia-oxidising Thaumarchaeota and non-ammonia-oxidising lineages. The most abundant group was within amoA-NP-γ, which is usually found in coastal and shallow habitats, indicating potential niche expansion from marine shallow to hadal environments. This benthic group showed within-species genomic variations compared to the previously identified Hadal water group, suggesting microdiversification of hadal Thaumarchaeota along with niche separation between benthic and pelagic environments. Evolutionary adaptations associated with the benthic-to-pelagic transition included reduced genome size, loss of motility/cell adhesion, altered energy metabolism, and different mechanisms for substrate acquisition and regulation (e.g., ammonium). These findings offer new insights into the evolution of hadal Thaumarchaeota and demonstrate, for the first time, intraspecies-level genomic variation in Thaumarchaeota related to the benthic-versus-pelagic niche partitioning in the deep ocean.

Impacts of Legacy and Contemporary Nitrogen Inputs on N2O and CO2 Emissions in Miscanthus and Maize Cultivated Soils

ABSTRACTNutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteus (M×g) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N2O) and carbon dioxide (CO2) emissions, as well as key N cycling genes in soils where M×g and maize were grown. A 150‐day soil incubation experiment was conducted using soils from a long‐term M×g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha−1 year−1) and a contemporary amendment (60 mg N kg−1) with negative control (0 mg N kg−1). We observed significant increases in cumulative N2O emissions in Mxg soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amoA gene abundance, which plays a significant role in nitrification in nutrient‐rich soils, also increased with higher legacy fertilization rates in M×g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N2O emissions, but cumulative CO2 emissions and amoA gene abundance significantly increased. The abundances of norB genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N2O emissions, particularly for perennial bioenergy crops.

Enhanced electron transfer for the improvement of nitrogen removal efficiency and N2O reduction at low temperatures.

Low temperature generally restricts biological activity, slowing down electron transfer in biogeochemical cycles and causing a series of environmental problems such as nitrogen pollution. We present a strategy to boost electron transfer in microbial cell at low temperatures via stimulation with low current. It is demonstrated by establishing a constructed wetland system coupled with solar powered microbial electrolysis cell, which enhances microbial activity through external micro currents (18.9 ± 5.5 μA) for removing nitrogen pollution in winter (average temperature from -6.6 to 4.5 °C). We investigated the efficiency of pollutants removal, microbial activity, N2O production and its mechanisms using complexes activity detection, RT-qPCR, incubation, and 15N-18O dual-isotope labeling techniques. The activity of complexes I, II, III, and IV collectively represent the microbial electron transfer rate. Results indicated that the microcurrents increased the activity of complexes II, III and IV by 96 %, 172 %, and 313 %, respectively. The transcription abundance of amoA genes in ammonia oxidation and nirS/K genes in denitrification by 263 % and 51 %, respectively. Consequently, NH4+-N removal efficiency improved from 23 % to 35 %, and NO3--N removal efficiency from 21 % to 31 %. Moreover, microcurrents reduced N2O emission by 44 %. However, external microcurrent stimulation did not alter the microbial production pathway of N2O as determined by the 15N-18O dual isotope labeling technique. The relative abundance of the nitrifying bacteria Nitrosomonas, Nitrosospira, and Nitrospira, as well as the denitrifying bacteria Methylotenera, significantly increased due to microcurrent stimulation. Specifically, Nitrospira exhibited the highest increase of 156 %. Our findings provide a novel way to enhance N removal efficiency and simultaneously reduce N2O emission of biological system like constructed wetlands in winter conditions.

Phenacetin enhanced the inorganic nitrogen removal performance of anammox bacteria naturally in-situ enriched system

Among the earliest synthetic antipyretic drugs, phenacetin (PNCT) could be used as the novel partial nitrification (PN) inhibitor to effectively inhibit nitrite-oxidizing bacteria (NOB). In practical application, the rapidly starting of PN could provide stable source of nitrite for anaerobic ammonium oxidation (anammox) process. However, impact of PNCT on anaerobic ammonia oxidizing bacteria (AnAOB) and its underlying mechanisms were not clear. In this research, totally 14 times of PNCT aerobic soaking treatment were performed in the AnAOB naturally enrichment system to improve total inorganic nitrogen removal efficiency (TINRE). After once of PNCT treatment, TINRE rose from 61.89 % to 79.93 %. After 14 times of PNCT treatment, NOB Nitrospira relative abundance decreased from 9.82 % to 0.71 %, though Candidatus Brocadia relative abundance also declined, it might gradually adjust to PNCT by converting the leading oligotype species. The activity and relative abundances of NOB were reduced by PNCT via decreasing the abundances of genes amoA and nxrB, enzymes NxrA and NxrB. Moreover, Candidatus Jettenia and Ca. Brocadia might be the potential host of qacH-01 and they played the crucial role in the shaping profile of antibiotic resistance genes (ARGs). The explosive propagation or transmission of ARGs might not take place after PNCT treatment.

Long-term effects of film mulching and fertilization regimes on gross N transformations in calcareous dryland soils

Plastic film mulching (PM) and nitrogen (N) fertilization regimes significantly affect crop yield, N supply capacity, and N losses. However, the long-term effects and the underlying mechanisms, like the belowground N transformations, call for in-depth investigation. Here, a 15N tracing study was conducted to quantify the gross N transformation rates of the calcareous soil subjected to 12 years of PM and various fertilization regimes. We found that autotrophic nitrification (ONH4) and mineralization (M) were the predominant soil N conversion processes, while dissimilatory nitrate reduction to ammonium (DNRA) and nitrate immobilization (INO3) were negligible in the calcareous soil, leading to the accumulation of nitrate. Long-term PM significantly decreased the rates of M, recalcitrant organic-N mineralization (MNrec), ONH4, and NH4+ immobilization to labile organic-N (INH4_Nlab) due to the negative effect on the abundances of fungi and ammonia-oxidizing bacteria (AOB) amoA gene compared to control soil. Relative to no N control, different fertilization regimes significantly increased the AOB amoA gene abundance, decreased fungal abundance and ITS:16S ratio, thus increasing ONH4 and M, decreasing NH4+ immobilization rates to labile and recalcitrant organic-N. Compared to normal N rate (F225), high N rate (F380) and normal N plus manure (F225+M) markedly increased ONH4 and INO3. Regression analyses revealed that M and AOB amoA gene abundance affected ONH4, and in turn N2O production. The findings provide an improved understanding of the long-term effects of PM and N managements on soil N supply capacity and potential N losses based on internal N cycling and molecular biology.

Impact of Drying–Wetting Cycles on Nitrification Inhibitors (DMPP and DMPSA) in a Greenhouse Experiment with Two Contrasting Mediterranean Soils

Studies of the impact of nitrification inhibitors (NIs), specifically DMPP and DMPSA, on N2O emissions during “hot moments” have produced conflicting results regarding their effectiveness after rewetting. This study aimed to clarify the effectiveness of NIs in reducing N2O emissions by assessing residual DMP concentration and its influence on ammonia-oxidizing bacteria (AOB) in two pot experiments using calcareous (Soil C, Calcic Haploxerept) and acidic soils (Soil A, Dystric Xerochrepts). Fertilizer treatments included urea (U), DMPP, and DMPSA. The experiments were divided into Phase I (water application to dry period, 44 days) and Phase II (rewetting from days 101 to 121). In both phases for Soil C, total N2O emissions were reduced by 88% and 90% for DMPP and DMPSA, respectively, compared with U alone. While in Phase I, the efficacy of NIs was linked to the regulation of AOB populations, in Phase II this group was not affected by NIs, suggesting that nitrification may not be the predominant process after rewetting. In Soil A, higher concentrations of DMP from DMPP were maintained compared to Soil C at the end of each phase. Despite this, NIs had no significant effect due to low nitrification rates and limited amoA gene abundance, indicating unfavorable conditions for nitrifiers. The study highlights the need to optimize NIs to reduce N2O emissions and improve nitrogen efficiency, while understanding their interactions with the soil. This knowledge is necessary in order to design fertilization strategies that improve the sustainability of agriculture under climate change.

Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere.

Plastic marine debris is known to harbor a unique microbiome (termed the "plastisphere") that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52ng N2O N g-1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.

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.

Combined metabolomic and microbial community analyses reveal that biochar and organic manure alter soil C-N metabolism and greenhouse gas emissions

The use of biochar to reduce the gas emissions from paddy soils is a promising approach. However, the manner in which biochar and soil microbial communities interact to affect CO2, CH4, and N2O emissions is not clearly understood, particularly when compared with other amendments. In this study, high-throughput sequencing, soil metabolomics, and quantitative real-time PCR were utilized to compare the effects of biochar (BC) and organic manure (OM) on soil microbial community structure, metabolomic profiles and functional genes, and ultimately CO2, CH4, and N2O emissions. Results indicated that BC and OM had opposite effects on soil CO2 and N2O emissions, with BC resulting in lower emissions and OM resulting in higher emissions, whereas BC, OM, and their combined amendments increased cumulative CH4 emissions by 19.5 %, 31.6 %, and 49.1 %, respectively. BC amendment increased the abundance of methanogens (Methanobacterium and Methanocella) and denitrifying bacteria (Anaerolinea and Gemmatimonas), resulting in an increase in the abundance of mcrA, amoA, amoB, and nosZ genes and the secretion of a flavonoid (chrysosplenetin), which caused the generation of CH4 and the reduction of N2O to N2, thereby accelerating CH4 emissions while reducing N2O emissions. Simultaneously, OM amendment increased the abundance of the methanogen Caldicoprobacter and denitrifying Acinetobacter, resulting in increased abundance of mcrA, amoA, amoB, nirK, and nirS genes and the catabolism of carbohydrates [maltotriose, D-(+)-melezitose, D-(+)-cellobiose, and maltotetraose], thereby enhancing CH4 and N2O emissions. Moreover, puerarin produced by Bacillus metabolism may contribute to the reduction in CO2 emissions by BC amendment, but increase in CO2 emissions by OM amendment. These findings reveal how BC and OM affect greenhouse gas emissions by modulating soil microbial communities, functional genes, and metabolomic profiles.

Pilot-scale investigation of an advanced biofloc technology for treating Pacific white shrimp effluent: Performance and insight mechanisms

Biofloc technology (BFT) is extensively used in the treatment of water quality in intensive shrimp aquaculture systems. However, the rapid accumulation of biofloc in middle-to-late culture stages poses challenges for system management, impacting the economic yield of aquaculture operations. To address this issue, an advanced biofloc system (A-BS) that integrates a moving bed biofilm reactor (MBBR) with BFT was constructed, and the biofloc system (BS) was used as a control group. During a 100-day pilot-scale operation, the A-BS group effectively regulated water quality and enhanced the growth rate of Pacific white shrimp (Litopenaeus vannamei). In the A-BS group, the average concentrations of ammonia, nitrite, chemical oxygen demand, and mixed liquor suspended solids were substantially reduced compared to those in the BS group, measuring 0.19, 0.55, 36.36, and 229 mg/L, respectively, across the middle-to-late culture stages. Notably, the final stocking density and survival rate of shrimp in the A-BS group, reached 7.04 kg/m3 and 81.22 %, surpassing those in the BFT group. Furthermore, microbial community and functional gene analyses revealed more in-depth insights into the related mechanisms. Bacterial abundance and diversity, as well as the presence of denitrification genes such as Unclassified_f_Rhodobacteraceae and Paracoccus, were markedly higher in the A-BS group than in the BS group. The integration of MBBR into A-BS significantly increased the abundance of amoA and nirK genes, which are crucial for water quality stability during later culture stages. This proof-of-concept investigation confirms that the MBBR–BFT coupling process in A-BS holds promise for advancing sustainable aquaculture practice and provides strategic guidance for the modernization of the industry.

Impact of nitrogen and phosphorus amendments on nitrogen‐cycling microbial abundances and potentials: A meta‐analysis

AbstractThe rapid increase in nitrogen (N) and phosphorus (P) availabilities in terrestrial ecosystems has led to sustained shifts in soil microbial communities and microbially‐mediated N‐cycling. However, the specific effects of N and P amendments on N‐cycling microbes are poorly understood. This meta‐analysis synthesizes the effects of N and/or P amendments on the abundances and functional potentials of N‐cycling genes involved in N₂ fixation, organic N mineralization, nitrification, and denitrification across natural ecosystems and diverse soil conditions in China. Our findings indicate that ammonia‐oxidizing bacteria (AOB) showed greater responsiveness to N amendment than ammonia‐oxidizing archaea (AOA), and AOB amoA abundance increased while AOA amoA abundance decreased with P amendments. Additionally, the abundance of nirS declined, while nirK abundance remained unresponsive to both N and P amendments. These findings highlight the distinct ecological niches occupied by microbial groups with equivalent functions in response to N and P amendments. Moreover, our findings indicate that soil N and P availabilities, along with soil acidification induced by N additions and microbial biomass carbon content, are key factors regulating N‐cycling gene abundances and potentials. The driving mechanisms for N‐cycling genes and their corresponding potentials appear to be distinct, with gene abundance showing only a limited influence on functional potentials. This suggests that factors such as soil properties and microbial community compositions may be more critical determinants of N‐cycling processes than functional gene abundances with regard to scenarios of increasing N and P deposition.

The Effects of Mixed Robinia pseudoacacia and Quercus variabilis Plantation on Soil Bacterial Community Structure and Nitrogen-Cycling Gene Abundance in the Southern Taihang Mountain Foothills.

Mixed forests often increase their stability and species richness in comparison to pure stands. However, a comprehensive understanding of the effects of mixed forests on soil properties, bacterial community diversity, and soil nitrogen cycling remains elusive. This study investigated soil samples from pure Robinia pseudoacacia stands, pure Quercus variabilis stands, and mixed stands of both species in the southern foothills of the Taihang Mountains. Utilizing high-throughput sequencing and real-time fluorescence quantitative PCR, this study analyzed the bacterial community structure and the abundance of nitrogen-cycling functional genes within soils from different stands. The results demonstrated that Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacterial groups across all three forest soil types. The mixed-forest soil exhibited a higher relative abundance of Firmicutes and Bacteroidetes, while Nitrospirae and Crenarchaeota were most abundant in the pure R. pseudoacacia stand soils. Employing FAPROTAX for predictive bacterial function analysis in various soil layers, this study found that nitrogen-cycling processes such as nitrification and denitrification were most prominent in pure R. pseudoacacia soils. Whether in surface or deeper soil layers, the abundance of AOB amoA, nirS, and nirK genes was typically highest in pure R. pseudoacacia stand soils. In conclusion, the mixed forest of R. pseudoacacia and Q. variabilis can moderate the intensity of nitrification and denitrification processes, consequently reducing soil nitrogen loss.

Vermicompost and flue gas desulfurization gypsum addition to saline-alkali soil decreases nitrogen losses and enhances nitrogen storage capacity by lowering sodium concentration and alkalinity

Saline-alkali soils have poor N storage capacity, high N loss and inadequate nutrient supply potential, which are the main limiting factors for crop yields. Vermicompost can increase organic nutrient content, improve soil structure, and enhance microbial activity and function, and the Ca2+ in flue gas desulfurization (FGD) gypsum can replace Na+ and neutralize alkalinity in saline-alkali soils though chemical improvement. This study aimed to determine if vermicompost and FGD gypsum addition could improve the N storage capacity through decreasing NH3 volatilization and 15N/NO3− leaching from saline-alkali soils. The results indicate that the combined application of vermicompost and FGD gypsum led to the displacement and leaching Na+ in the upper soil layer (0–10 cm), as well as the neutralization of HCO3− by the reaction with Ca2+. This treatment also improved soil organic matter content and macroaggregate structure. Also, these amendments significantly increased the abundance of nifH and amoA genes, while concurrently decreasing the abundance of nirK gene. The structural improvements and the lowering of Na + concentration in and alkalinity decreased cumulative NH3 volatilization, and leaching of 15N and NO3− to the deep soil layer (20–30 cm). FGD gypsum increased the 15N stocks and inorganic N stocks of saline-alkali soil, whereas vermicompost not only increased the 15N and inorganic N stocks, but also increased the total N stocks, the combination of vermicompost and FGD gypsum can not only increase the available N storage capacity, but also enhance the potential for N supply. Therefore, vermicompost and FGD gypsum decrease N loss and increase N storage capacity through structural improvement, and lowering of Na+ concentration and alkalinity, which is crucial for improving the productivity of saline-alkali soil.

Performances of full-scale biological nitrogen pre-treatment process for drinking water source: Seasonal variations and microbial community

This study investigated the performance of the full-scale unit over a two-year period to enhance nitrification efficiency and provide operational strategies. Results indicated that raw water quality from Donggan River was notably influenced by seasonal variations, particularly during dry and wet seasons, impacting the nitrification efficiency of the biological pretreatment process. Factors such as influent concentrations of ammonia and total Kjeldahl nitrogen were found to have significant effects on nitrification, with temperature and conductivity also showing correlations. The specific rate of ammonia removal was calculated to be approximately 0.1 kg-N/m3/d under the existing operational setup. Moreover, elevating dissolved oxygen levels above 4 mg/L was proposed to potentially boost ammonia oxidation based on findings from experiments conducted in lab-scale bioreactors. In times of increased influent ammonia levels, the elimination of about 1–3 mg-N/L of total nitrogen signified the activation of denitrification processes. This observation was corroborated by results from next-generation sequencing techniques, verifying the existence of denitrifying microorganisms. The real-time PCR analysis results indicated that the abundance of comammox amoA gene was comparable with the abundance of the AOB amoA gene, indicating the presence of comammox Nitrospira and their potential role on nitrification in the system.

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.

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 superiority of hydrophilic polyurethane in comammox-dominant ammonia oxidation during low-strength wastewater treatment

Carriers have been extensively employed to enhance nitrification performance during low-strength wastewater treatment by retaining slow-growing ammonia oxidizing microorganisms (AOMs). Still, there is a dearth of systematic understanding of biofilm properties and microbial community structure formed on different carriers. In this study, hydrophilic polyurethane foam (PUF) carriers were prepared and compared with five widely used commercial carriers, namely Kaldness 3, Biochip, activated carbon, volcanic rock, and zeolite. The results indicated that the biofilms formed on carriers enhanced microbial ammonia oxidation activity. Additionally, the biofilm developed on the PUF demonstrated the most superior performance among all selected carriers, not only exhibiting the highest abundant and the most active AOMs, with amoA gene abundance of 1.41 × 1013 copies/m3 and specific ammonia oxidation rate of 9.84 g NH4+-N/(m3 × h), but also possessing a compact structure, with 3.41 kg VSS/m3 and 46.83 mg extracellular polymeric substances/g VSS. The high-throughput sequencing analysis revealed that the comammox (CMX) Nitrospira dominated on biofilm due to the intrinsically low apparent half-saturation constant for substrate. A unique ecological community structure was established on PUF, characterized by low species diversity and high homogeneity in alignment with community characteristics of CMX. The biofilms on PUF contributed to the proliferation of CMX Nitrospira dominated by Nitrospira nitrosa, achieving the highest proportion among colonial three AOMs at 86.58 %. The appropriate average pore size, superior hydrophilicity, and large specific surface area of PUF carriers provided a robust foundation for the exceptional ammonia oxidation performance of the formed biofilms.

Effects of Three Antibiotics on Nitrogen-Cycling Bacteria in Sediment of Aquaculture Water

Antibiotics are commonly used to prevent and control aquaculture diseases. However, long-term overuse of antibiotics not only leaves residues but also leads to changes in the nitrogen cycle in water, which threatens the survival of aquaculture organisms. The current results showed that sulfamethoxazole had no significant effect on the nitrogen cycle process in the actual aquaculture concentration. The inhibitory effect of 1.05 mg/L norfloxacin on ammonia-oxidizing bacteria was significantly greater than that on ammonia-oxidizing archaea, and the gene abundance of AOB amoA on the 14th day increased by 2.48 times compared with the 7th day. Under the influence of 3.9 mg/L oxytetracycline, the gene abundance of AOB amoA decreased significantly, while the number of AOA amoA genes increased, suggesting that there may be functional redundancy between AOA and AOB. At the genus level in the norfloxacin group, the relative abundance of Sva0485 increased by 14.0% on the 7th day compared with the control group but decreased 12.77% in the addition group. The relative abundance of Firmicutes, another dominant species in the oxytetracycline group, was 25.9%. This study shows that the addition of antibiotics may have a negative effect on the nitrogen-cycling microorganisms in aquaculture water.

Diversity and abundance of archaeal amoA genes in the permanent and temporary oxygen minimum zones of Indian Ocean

Oxygen minimum zones are results of oxygen consumption exceeding the oxygen availability in stratified water columns of the marine environment. We compared the ammonia monooxygenase subunit A (amoA) gene abundance and the diversity of ammonia-oxidising archaea (AOA) in the Arabian Sea (AS) with those of the Bay of Bengal (BoB). Three primer pairs targeting amoA genes of water column A (WCA), water column B (WCB) and total AOA (amoAt) captured different densities of gene copy numbers in both marginal seas. Water column A (WCA) ecotypes were more abundant in the AS than in the BoB. Core-OMZ depths of the BoB contained 10 times lower amoA copy numbers than those of the AS. Along with sampling depth, concentration of ammonia shapes the WCA/WCB ecotypes in AS/BoB. Among the total AOA populations, WCB ecotypes were more abundant. The amoA gene sequences were either of Nitrosopumilales or Ca. Nitrosotaleales members and belonged to NP-γ, NP-δ, NS-β, NS-γ and NS-ε sub-clades. Pairwise distance and nucleotide diversity index analysis reveals that BoB nurtures two times more diverse amoA sequences than the AS. The core OMZ region of the BoB contains a two-fold higher diversity of amoA gene sequences compared to the AS, whereas the AS contains 13 times more abundant amoA copies than the BoB.