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Background: Continuous nitrogen (N) deposition interferes with soil N cycling in forests, which highly impacts soil nitrous oxide (N2O) emissions and accelerates global warming. Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is one of the most widely planted species in southern China, and is usually located in areas with high N deposition rates. However, the impact of N deposition on soil N2O emissions in subtropical Chinese fir plantations and the potential risk of increasing N input remain elusive. Methods: Here, we conducted an in situ study in a subtropical Chinese fir plantation at Fengyang Mountain Nature Reserve, China, from 2019 to 2020 with four N addition rates: control (CK: ambient N deposition), low-N (LN: 50 kg N ha−1 yr−1), medium-N (MN: 100 kg N ha−1 yr−1), and high-N (HN: 200 kg N ha−1 yr−1). Results: We found that soil N2O emission rates increased with N addition rates by 71%, 176%, and 241% under LN, MN, and HN treatment compared to CK, respectively, and reached a significant level only under HN. Soil moisture was significantly reduced together with increased leaf N concentrations under N addition. Meanwhile, the microbial biomass in the middle of the growing season was significantly lower than at the end of the growing season. These results may suggest that N deposition stimulated plants to take up more N and water, which intensified plant-microbe competition and therefore alleviated further increases in N2O emissions under N deposition, especially under low N inputs. N deposition enhanced the abundance of ammonia oxidizing archaea and bacteria and the accumulation of NO3−-N in the soil but did not affect the abundance of nitrate-reducing bacteria (nirS and nirK). The results likely support that nitrification processes act as the major source of enhanced N2O emissions under N fertilization. Conclusions: Our study advances our understanding of the impacts of N deposition on the soil N2O emissions in the Chinese fir plantations and highlights that plant N acquisition needs to be incorporated as an important explanatory variable when predicting N2O fluxes under global increases in N deposition. [ABSTRACT FROM AUTHOR]

On the Qinghai–Tibet Plateau, nitrogen (N) cycling, such as nitrification and denitrification, in the alpine meadow soils have been considerably affected by grazing, with possible consequences for nitrous oxide (N2O) emissions. However, there is a lack of understanding about how the potential nitrification activity (PNA) and the potential denitrification activity (PDA) might be affected by the grazing intensity. We collected the soil samples in alpine meadow in the east of the Qinghai–Tibet Plateau that was grazed at different intensities from 2015 in peak growing season 2021. We determined the soil physical and chemical properties, the functional gene abundances of nitrifiers and denitrifiers, and the soil PNA and PDA to explore the relationships between a range of abiotic and biotic factors and the PNA and PDA. We found that the PNA and the nitrifiers were significantly affected by the grazing intensity but that the PDA and the denitrifiers were not. The ammonia-oxidizing archaea (AOA) abundance was highest but the ammonia-oxidizing bacteria (AOB)abundance was lower than the control significantly at the highest grazing intensity. The AOA abundance and the soil NH4+-N explained most of the variation in the PNA. The pH was the main predictor of the PDA and controlled the nirS abundance but not the nirK and nosZ abundances. Overall, the PNA was more responsive to the grazing intensity than the PDA. These findings can improve estimations of the nitrification and denitrification process and N2O emissions in alpine meadow. [ABSTRACT FROM AUTHOR]

Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides newstrategies to further study their interactions among the four types of nitrifiers. [ABSTRACT FROM AUTHOR]

Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA1F/amoA2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB169F/nxrB638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO2−, and NO3−. Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. Key points: • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO2−, and NO3− are important shapers of nitrifier communities in mangroves. [ABSTRACT FROM AUTHOR]

Ammonia oxidation driven by ammonia-oxidizing archaea (AOA) and bacteria (AOB) plays a significant role in the nitrogen cycle, but the mechanism of this important action in reservoir sediments is unclear. In this study, based on quantitative PCR and Illumina high-throughput sequencing of the ammonia monooxygenase (AMO) gene, the abundance, diversity and community structure of AOA and AOB in Miyun Reservoir sediments were investigated. The key environmental factors for regulating community structure, as well as the response of AOA and AOB abundance and transcriptional activity to external ammonia and organic carbon, were also explored. The results showed that the diversity and abundance of AOB in the reservoir sediments were higher than those of AOA, and the community structure of AOA showed a different spatial distribution characteristics compared with those of AOB. AOA community structure was closely related to ammonia nitrogen concentration and water depth, while that of AOB were not significantly affected by environmental factors. AOB were more sensitive to concentration variations of ammonia nitrogen and organic carbon from exogenous sources. Therefore, in Miyun Reservoir sediments, AOA were more sensitive to the influence of environmental factors in the reservoir area, while AOB were more sensitive to the influence of exogenous sources. [ABSTRACT FROM AUTHOR]

A betaproteobacterial chemolithotrophic ammonia-oxidizing bacterium designated APG5T was isolated from supralittoral sand of the Edmonds City Beach, WA, USA. Growth was observed at 10–35 °C (optimum, 30 °C), pH 5–9 (optimum, pH 8) and ammonia concentrations as high as 100 mM (optimum, 1–30 mM NH4Cl). The strain grows optimally in a freshwater medium but tolerates up to 400 mM NaCl. It is most closely related to ‘Nitrosomonas ureae’ (96.7% 16S rRNA and 92.4% amoA sequence identity). The 3.75-Mbp of AGP5T draft genome contained a single rRNA operon and all necessary tRNA genes and has the lowest G+C content (43.5%) when compared to the previously reported genomes of reference strains in cluster 6 Nitrosomonas. Based on an average nucleotide identity of 82% with its closest relative (‘N. ureae’ Nm10T) and the suggested species boundary of 95–96%, a new species Nitrosomonas supralitoralis sp. nov. is proposed. The type strain of Nitrosomonas supralitoralis is APG5T (= NCIMB 14870T = ATCC TSD-116T). [ABSTRACT FROM AUTHOR]

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Landfill leachate, due to its recalcitrant nature and toxicity, poses a serious environmental threat, which requires the implementation of effective treatment processes. In this work, a full-scale treatment system consisting of two Sequencing Batch Reactors (SBRs) was used for the processing of landfill leachate of intermediate to mature age (BOD/COD ratio of 0.16). Biosystem operation resulted in BOD5, COD and TKN removal efficiencies of 81%, 39% and 76%, respectively, whereas the low residual NO3--N concentration in the effluent (4.01 ± 0.10 mg/L) was indicative of the efficient denitrification process. Assessment of hydrolytic potential of activated sludge revealed high endocellular and extracellular lipase activities, which reached values up to 206 and 141 U/g protein respectively, possibly as the consequence of plastics degradation during maturation process. Implementation of Illumina sequencing indicated the predominance of Alphaproteobacteria, accompanied by members of Bacteroidetes, Betaproteobacteria and Chloroflexi. Paracoccus was the predominant genus identified, followed by representatives of the genera Bellilinea, Flavobacterium, Thauera and Truepera. Nitrosomonas was the major ammonia-oxidizing bacterium (AOB), while nitrite oxidation was mainly achieved by the uncultured nitrite-oxidizing bacterium (NOB) Candidatus Nitrotoga. [ABSTRACT FROM AUTHOR]

Recirculating aquaculture systems (RAS) are important for water quality management in aquaculture facilities, and can help resume water consumption. However, information about the community structure of the micro-ecosystem existing in biofilters, especially the participation of the known nitrifying groups (i.e., AOA, AOB, NOB, and comammox Nitrospira), remains to be fully clarified. In this research, we compared the community structures in three RAS systems operated at different temperatures in a marine aquarium, through both amoA-targeted qPCR assay and 16S rRNA-targeted next-generation sequencing. As result, AOA was the primary nitrifier in the biofilters and was typically abundant and diverse in high-temperature samples (ca. 25 °C). NOB's relative abundance patterns were numerically similar to that of AOA, suggesting a cooperation relationship between AOA and NOB in the marine RAS system. AOB was at a comparable level with AOA in medium-temperature samples (ca. 19 °C), while their abundance sharply decreased in high-temperature samples. The number of observed OTUs of AOA in high-temperature samples was 1.9 and 1.5 times as much as that detected in low (ca. 10 °C) and medium temperature samples respectively, suggesting a much more diverse and predominant occurrence of AOA at high temperatures. Comammox Nitrospira was only detected at a low level in the biofilter samples, suggesting a negligible contribution to the nitrification process in such ammonia-limited, saline biofilms. Although comammox Nitrospira cannot be detected by 16S rRNA-based analysis, the high diversity and abundance of NOB that were detected in high-temperature samples indicated the prospective possibility of the occurrence of complete ammonia oxidation at high temperatures. [ABSTRACT FROM AUTHOR]

Soil ammonia-oxidizing microorganisms play important roles in nitrogen (N) cycling in cold ecosystems, but how changes in snow cover will affect their distribution and associated functional characteristics remains unclear. A snow manipulation experiment was conducted to explore the effects of snow exclusion on soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities and functional characteristics in a spruce forest in the eastern Tibet Plateau. Results showed that the amoA gene abundance and community composition of AOA and AOB did not differ between snow regimes but varied among winter periods. AOA and AOB gene abundances showed a decreasing trend during the snow cover melting period. During the deep snow cover period, Thaumarchaeota and Crenarchaeota in the AOA community decreased significantly, while Proteobacteria and Nitrosospira in the AOB community increased significantly. The main factors affecting the changes in AOA and AOB community diversity and composition were soil MBN, nitrate nitrogen, and temperature, while AOA and AOB community diversity and composition were also significantly correlated with soil enzyme activities related to N cycling. These results recommend that the season-driven variations strongly affected soil ammonia-oxidizing community and functional characteristics more than momentary snow cover change. Such findings offer new insights into how soil N-cycling processes would respond to reduced snowfall in high-altitude regions. [ABSTRACT FROM AUTHOR]

Ammonia oxidizing bacteria (AOB) play a key role in the biological oxidation of ammonia to nitrite and mark their significance in the biogeochemical nitrogen cycle. There has been significant development in harnessing the ammonia oxidizing potential of AOB in the past few decades. However, very little is known about the potential applications of AOB in the bioenergy sector. As alternate sources of energy represent a thrust area for environmental sustainability, the role of AOB in bioenergy production becomes a significant area of exploration. This review highlights the role of AOB in bioenergy production and emphasizes the understanding of the genetic make-up and key cellular biochemical reactions occurring in AOB, thereby leading to the exploration of its various functional aspects. Recent outcomes in novel ammonia/nitrite oxidation steps occurring in a model AOB – Nitrosomonas europaea propel us to explore several areas of environmental implementation. Here we present the significant role of AOB in microbial fuel cells (MFC) where Nitrosomonas sp. play both anodic and cathodic functions in the generation of bioelectricity. This review also presents the potential role of AOB in curbing fuel demand by producing alternative liquid fuel such as methanol and biodiesel. Herein, the multiple roles of AOB in bioenergy production namely: bioelectricity generation, bio-methanol, and biodiesel production have been presented. [ABSTRACT FROM AUTHOR]

To achieve energy-efficient shortcut nitrogen removal of wastewater in the future, selective elimination of nitrite-oxidizing bacteria (NOB) while enriching ammonia-oxidizing microorganisms is a crucial step. However, the underlying mechanisms of partial nitrification are still not well understood, especially the newly discovered ultrasound-based partial nitrification. To elucidate this issue, in this study two bioreactors were set up, with one established partial nitrification by ultrasonication while the other didn't. During the operation of both reactors, the taxonomic and functional composition of the microbial community were investigated through metagenomics analysis. The result showed that during ultrasonic partial nitrification, ammonia-oxidizing archaea (AOA), Nitrososphaerales, was enriched more than ammonia-oxidizing bacteria (AOB), Nitrosomonas. The enrichment of microorganisms in the community increased the abundance of genes involved in microbial energy generation from lipid and carbohydrates. On the other hand, the abundance of NOB, Nitrospira and Nitrolancea, and Comammox Nitrospira decreased. Selective inhibition of NOB was highly correlated with genes involved in signal transduction enzymes, such as encoding histidine kinase and serine/threonine kinase. These findings provided deep insight into partial nitrification and contributed to the development of shortcut nitrification in wastewater treatment plants. [ABSTRACT FROM AUTHOR]

An ex-situ 15 N–18O tracing experiment with soils collected from the valley and slope, respectively, of a subtropical secondary karst forest with three N addition levels, i.e., 0, 50, and 100 kg N ha−1 year−1 for each topographic position to investigate N2O production pathways. Autotrophic nitrification pathways (ammonia oxidation, nitrifier denitrification, and nitrification-coupled denitrification) accounted for > 70% of total N2O production, but denitrification pathways (heterotrophic denitrification and co-denitrification) were the minor source of N2O at both topographic positions. In the valley, chronic N addition stimulated ammonia oxidation-derived N2O, which was paralleled by increased ammonia-oxidizing archaea (AOA) amoA gene transcript abundance, but inhibited nitrifier denitrification- and nitrification-coupled denitrification–derived N2O along with suppressed ammonia-oxidizing bacteria (AOB) amoA gene transcript abundance and stimulated nosZII gene transcript abundance, respectively. On the slope, chronic N addition stimulated ammonia oxidation-derived N2O along with increased AOB amoA gene transcript abundance, and enhanced nitrifier denitrification-derived N2O congruent with increased AOB amoA and decreased nirK gene transcript abundances. In addition, chronic N addition reduced the relative contribution of heterotrophic denitrification to N2O production but had no significant influence on heterotrophic denitrification-derived N2O on the slope. Overall, our results provide a comprehensive view in terms of how topography-driven soil properties regulate N2O production and its pathways in a subtropical forest. [ABSTRACT FROM AUTHOR]

Nitrification has been widely applied in wastewater treatment, however gaining more insight into the nitrifiers' physiology and stress response is necessary for the optimization of nutrient removal and design of advanced processes. Since nitrification initiates with ammonia oxidation performed by ammonia-oxidizing bacteria (AOB), the purpose of this study was to investigate the effects of short-term ammonia starvation on nitrogen uptake and transformation efficiency, as well as the performance of starved nitrifiers under various initial substrate concentrations and pH values. Ammonium deprivation for 3 days resulted in fast ammonium/ammonia accumulation upon nitrogen availability, with a maximum uptake rate of 3.87 mmol gprotein−1 min−1. Furthermore, a delay in the production of nitrate was observed with increasing starvation periods, resulting in slower recovery and lower nitrification rate compared to non-starved cells. The maximum accumulation capacity observed was 8.51% (w/w) independently of the external nitrogen concentration, at a range of 250–750 mg N L−1, while pH significantly affected ammonia oxidizers' response, with alkaline values enhancing nitrogen uptake. In total, ammonia accumulation after short-term starvation might serve as an important strategy that helps AOB restore their activity, while concurrently it could be applied in wastewater treatment for effective nitrogen removal and subsequent biomass utilization. [ABSTRACT FROM AUTHOR]

The effectiveness of formic acid on partial nitrification in sequence batch reactor (SBR) is studied. In addition, the mechanism for achieving and maintaining stable partial nitrification by formic acid is also analyzed. The results of the long-term effect of formic acid on partial nitrification showed that when formic acid was not added, the effluent was primarily nitrate. After adding formic acid for 1 week, the partial nitrification operated stably, and the average ammonia conversion rate and nitrite accumulation rates were 99.25% and 89.41%, respectively, while the yield of nitrite was only 46.22%. After stopping formic acid dosing, the partial nitrification was maintained for ∼20 days, and during this period, the nitrite yield increased to 85.89%. The high-throughput analysis of the activated sludge samples showed that the ammonia oxidizing bacteria (AOB) Nitrosomonas and Sphingomonas only presented in the formic acid system. The denitrifiers Acidovorax, Bacillus, Comamonas, Flavobacterium, Lactococcus, Paracoccus, Terrimonas, and Thauera enriched when the formic acid was added. The long-term effect of formic acid on partial nitrification was consistent with the results of the molecular operating environment simulation analysis and the high-throughput sequencing analysis. Therefore, formic acid was considered to be responsible for the partial nitrification process in this study. By measuring the oxygen uptake rate, the activities of AOB and nitrite oxidizing bacteria (NOB) were analyzed, and the results indicated that formic acid dosing promoted AOB activity more than inhibiting NOB. [ABSTRACT FROM AUTHOR]

BACKGROUND: The combination of partial nitrification (PN) and anaerobic ammonium oxidation has been identified as a promising technology for the removal of nitrogenous contaminants from wastewater. The inhibition or wash‐out of nitrite‐oxidizing bacteria (NOB) while keeping the ammonia oxidizing bacteria (AOB) active is key for PN. Multiple strategies, including intermittent aeration, pH shocks and sulfide addition, were investigated in this study for the start‐up of PN and stable suppression of NOB. RESULTS: Intermittent aeration with a dissolved oxygen (DO) level of <5 mg L−1 effectively suppressed NOB activity and resulted in an average nitrite accumulation (NAR) of 93%, implying that the initial DO level during the aeration phase may influence the establishment of successful PN. Likewise, when the reactor was run at a low pH (5), both AOB and NOB activity was reduced. When the pH was raised to neutral pH (7.5), there was an increase in AOB activity with an average NAR of 84%; however, NOB activity remained suppressed. Likewise, when the reactor was fed with sulfide (≤25 mg L−1) without pH control, the average NAR increased from 63% to 85%. CONCLUSIONS: This study proposes a successful approach to achieving PN by controlling DO level in the aeration phase during intermittent aeration and pH control. The findings also show that the nitrite oxidation process is more sensitive to sulfide than the ammonium oxidation process. As a result, the findings of this study may contribute to a better understanding of establishing PN in a sequential batch system. © 2022 Society of Chemical Industry (SCI). [ABSTRACT FROM AUTHOR]

Soil microbial transformation of nitrogen (N) in nutrient-limited native C4 grasslands can be affected by N fertilization rate and C4 grass species. Here, we report in situ dynamics of the population size (gene copy abundances) and activity (transcript copy abundances) of five functional genes involved in soil N cycling (nifH, bacterial amoA, nirK, nirS, and nosZ) in a field experiment with two C4 grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) under three N fertilization rates (0, 67, and 202 kg N ha-1). Diazotroph (nifH) abundance and activity were not affected by N fertilization rate nor grass species. However, moderate and high N fertilization promoted population size and activity of ammonia oxidizing bacteria (AOB, quantified via amoA genes and transcripts) and nitrification potential. Moderate N fertilization increased abundances of nitrite-reducing bacterial genes (nirK and nirS) under switchgrass but decreased these genes under big bluestem. The activity of nitrous oxide reducing bacteria (nosZ transcripts) was also promoted by moderate N fertilization. In general, high N fertilization had a negative effect on N-cycling populations compared to moderate N addition. Compared to big bluestem, the soils planted with switchgrass had a greater population size of AOB and nitrite reducers. The significant interaction effects of sampling season, grass species, and N fertilization rate on N-cycling microbial community at genetic-level rather than transcriptional-level suggested the activity of N-cycling microbial communities may be driven by more complex environmental factors in native C4 grass systems, such as climatic and edaphic factors. [ABSTRACT FROM AUTHOR]

Purpose: Rapid nitrification leads to loss of nitrogen (N) fertilizer in agricultural systems. Plant produced/derived biological nitrification inhibitors (BNIs) are an effective eco-strategy to rein-in soil nitrification to improve crop-N uptake and nitrogen use efficiency (NUE) in production systems. Sorgoleone is the major component of hydrophobic-BNI-activity in sorghum roots. However, the role of genetic differences in sorgoleone production in reducing soil nitrification and N2O emissions are not established. Methods: Two genetic-stocks of sorghum with high-sorgoleone (HS), and two with low-sorgoleone (LS) production from roots were grown using hydroponics in a plant-growth chamber, in soil in pots in a glasshouse, and in a field experiment. Release of hydrophilic-BNI activity from roots of HS and LS genetic stocks, sorgoleone levels in rhizosphere soils, soil nitrification rates, soil-nitrifier activity and N2O emissions were measured to understand the interplay involving sorgoleone release, hydrophilic-BNI release from roots, soil nitrification, plant growth and N uptake. Results: HS-producing genetic-stocks showed higher hydrophilic-BNI-capacity compared to LS- producing genetic-stocks. Biomass production and N uptake were significantly higher in HS than in LS genetic-stocks. Glasshouse and field studies suggest that HS genetic stocks had stronger suppressive impact on soil-nitrifier-populations (ammonia-oxidizing archaea and ammonia-oxidizing bacteria), soil-nitrification, and soil-N2O emissions than in LS genetic-stocks. Conclusion: These results demonstrate that HS sorghum genetic-stocks suppress soil nitrifier activity and can potentially reduce N losses from NO3 − leaching and N2O emissions more effectively than LS genetic-stocks. [ABSTRACT FROM AUTHOR]

Purpose: The abundance of nitrogen (N)-cycling genes is frequently used to indicate N cycling and predict N2O emissions. However, it remains difficult to clearly define how soil N-cycling genes in different ecosystems respond to anthropogenic N additions. Methods: We applied a meta-analysis approach to examine data about N-cycling genes (nifH, ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), nirK, nirS, and nosZ) in different ecosystems from 119 peer-reviewed articles. Results: In the ecosystems examined, the patterns of change in the abundances of the target genes, apart from AOA, varied considerably. This variation reflects the distinctive soil characteristics of ecosystems that develop when different forms of N are applied at different rates and over different durations. The nifH abundance decreased significantly, by 32.79%, in forests but did not change in grasslands and croplands. The AOB abundance increased in all three ecosystems, by 193.06% in grasslands, 73.26% in forests, and 151.86% in croplands, respectively. The denitrification gene abundances, namely the nirK, nirS, and nosZ, in croplands also increased significantly, by 60.74%, 47.42%, and 69.54%, respectively. Conclusion: In general, climate factors and long-term applications of organic N at high rates had significant effects on the gene abundances in different ecosystems, through their influence on soil properties. An enhanced understanding of how N additions influence the abundance of other N-cycling functional genes can help us improve our ability to model the populations and activities of microbial functional communities and predict N fluxes. [ABSTRACT FROM AUTHOR]

Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2-), which can be further oxidized to nitrate (NO3-). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2- and NO3-, with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4+) and NO3---and NO2---dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils. [ABSTRACT FROM AUTHOR]

Rivers play a significant role in the global nitrous oxide (N 2 O) budget. However, the microbial sources and sinks of N 2 O in river systems are not well understood or quantified, resulting in the prolonged neglect of nitrification. This study investigated the isotopic signatures of N 2 O, thereby quantifying the microbial source of N 2 O production and the degree of N 2 O reduction in the Yellow River. Although denitrification has long been considered to be the dominant pathway of N 2 O production in rivers, our findings indicated that denitrification only accounted for 18.3% (8.2%–43.0%) of the total contribution to N 2 O production in the Yellow River, with 50.2%–80.2% being concurrently reduced. The denitrification contribution to N 2 O production (R2 = 0.44, p < 0.01) and N 2 O reduction degree (R2 = 0.70, p < 0.01) were positively related to the dissolved organic carbon (DOC) content. Similar to urban rivers and eutrophic lakes, denitrification was the primary process responsible for N 2 O production (43.0%) in certain reaches with high organic content (DOC = 5.29 mg/L). Nevertheless, the denitrification activity was generally constrained by the availability of electron donors (average DOC = 2.51 mg/L) throughout the Yellow River basin. Consequently, nitrification emerged as the primary contributor in the well-oxygenated Yellow River. Additionally, our findings further distinguished the respective contribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to N 2 O emissions. Although AOB dominated the N 2 O production in the Yellow River, the AOA specie abundance (AOA/(AOA + AOB)) contributed up to 32.6%, which resulted in 25.6% of the total nitrifier-produced N 2 O, suggesting a significant occurrence of AOA in the oligotrophic Yellow River. Overall, this study provided a non-invasive approach for quantifying the microbial sources and sinks to N 2 O emissions, and demonstrated the substantial role of nitrification in the large oligotrophic rivers. [Display omitted] • Nitrification was the primary contributor to N 2 O in the well-oxygenated Yellow River. • DOC content determined the denitrification activity and N 2 O reduction degree. • Denitrification was generally constrained by electron donors in the Yellow River. • 50.2%–80.2% N 2 O was reduced to N 2 in the Yellow River. The quantification of the microbial sources to N 2 O emissions highlights the important role of nitrification to N 2 O emission in large rivers. [ABSTRACT FROM AUTHOR]

The current challenge in wastewater denitrification lies in the treatment of low carbon to nitrogen ratio(C/N) wastewater. Integrating Anaerobic Ammonia Oxidation(Anammox) with a microbial fuel cell(MFC) enables simultaneous pollutant removal and electricity generation, leading to enhanced treatment efficiency and reduced energy consumption. However, achieving stable and effective treatment effects under high nitrogen concentration conditions remains a general research difficulty. The Anaerobic fluidized bed MFC(AFB-MFC) experiment successfully integrated Anammox ammonia oxidizing bacteria (AnAOB) into the anode and cathode chambers, resulting in a continuous operation for 258 days. The reactor successfully initiated operation within 48 days and maintained stable performance within an NLR range of 0.5–1.0 kgN/m3/d. The system performance was found to be influenced by DO and substrate concentration, demonstrating consistent high nitrogen removal ability across different HRT. Ultimately, the Anammox AFB-MFC achieved a nitrogen removal efficiency (NRE) of 96.89%, while its power generation performance gradually improved, yielding a final output voltage ranging from 370 to 420 mV. The microbial community within the reactor comprised diverse electricity-producing bacteria and AnAOB. This study highlights the excellent denitrification and power generation potential of Anammox AFB-MFC under low energy consumption conditions and provides theoretical groundwork for the practical implementation of Anammox. [Display omitted] • Successfully initiated and operated the Anammox AFB-MFC coupling system. • Demonstrated significant efficacy in denitrification and power generation. • The reactor demonstrated exceptional stability in denitrification performance. • The main microbial communities consist of AnAOB and electricity-producing bacteria. • The processes of Anammox and electricity generation mutually enhance each other. [ABSTRACT FROM AUTHOR]

Obtaining efficient autotrophic ammonia removal (aka partial nitritation-anammox, or PNA) requires a balanced microbiome with abundant aerobic and anaerobic ammonia oxidizing bacteria and scarce nitrite oxidizing bacteria. Here, we analyzed the microbiome of an efficient PNA process that was obtained by sequential feeding and periodic aeration. The genomes of the dominant community members were inferred from metagenomes obtained over a 6 month period. Three Brocadia spp. genomes and three Nitrosomonas spp. genomes dominated the autotrophic community; no NOB genomes were retrieved. Two of the Brocadia spp. genomes lacked the genomic potential for nitrite reduction. A diverse set of heterotrophic genomes was retrieved, each with genomic potential for only a fraction of the denitrification pathway. A mutual dependency in amino acid and vitamin synthesis was noted between autotrophic and heterotrophic community members. Our analysis suggests a highly-reticulated nitrogen cycle in the examined PNA microbiome with nitric oxide exchange between the heterotrophs and the anammox guild. [ABSTRACT FROM AUTHOR]

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 NHC4 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 NHC4 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. [ABSTRACT FROM AUTHOR]

In this study, effects of carbon to nitrogen (COD/TN) ratios of biogas slurry on shortcut nitrification-denitrification in a pilot-scale integrated fixed film activated sludge (IFAS) system were investigated. Lowering the COD/TN ratio from 11.7 to 6.2 exerted a negative impact on shortcut nitrification-denitrification performance. Accordingly, the NH3-N and TN removal rates decreased from 94.4 to 91.2% and 92.3 to 85.9%, respectively. The dynamics of microbial assembly was analyzed by MiSeq sequencing, and the denitrifying functional genes were quantified by qPCR. The results showed that ammonia oxidizing bacteria and amoA gene were more abundant on the biofilm of oxic tank, indicating they play a key role in NH3-N removal. Autotrophic, endogenous, and fast heterotrophic kinetics denitrifiers were coexisted and enriched in the IFAS system with a decreasing of COD/TN ratio. TN removal was mainly affected by denitrifiers (including Arenimonas, Acidovorax, and Thaurea) harboring narG and nirS genes. Canonical correspondence analysis proved that COD/TN ratio was the most critical factor driving the succession of microbial community. Dissolved oxygen (DO) and pH were found positively correlated with denitrifiers at low COD/TN ratio conditions. As a result, NH3-N and TN removal were effectively enhanced when the DO level in the oxic tank of IFAS system was increased to 1.0–3.0 mg/L. [ABSTRACT FROM AUTHOR]

Purpose Phosphorus (P) is one of the key elements in the agricultural sector, allowing improved production yields. Phosphate rock is a natural source of phosphorus; however, its low reactivity limits the release of P available to plants in the short term, conditioning its application in a direct way. Research was conducted to determine the effect of phosphate rock on a manure compost mix by measuring its availability of P and its microorganism activity. Method Cattle manure, equine manure, and poultry manure from three provinces of the department of Boyacá, Colombia, were moistened up to 60% with fermented mineralized liquid and composted with different proportions of phosphate rock. After 60 days of composting, the mineral content and microorganism activity were measured. Results This study revealed three notable results. First, the addition of phosphate rock led to an increase in total and available P and a decrease in water-soluble phosphorus and inhibitory effects of phosphatase activity. Second, composting with the three manures resulted in microorganism activity levels higher than 700*104 CFU, exceeding the NTC's definition of an inoculant fertilizer in the agricultural process. Third, a strong positive relationship was found between ammonia-oxidizing bacteria and PBII, a medium correlation was found between PSM and TP, and a negative correlation was found between pH and PT. Conclusion Composting manure with phosphoric rock could be a low-cost source of macronutrients, minerals, and microorganisms to promote soil health and crop yields. [ABSTRACT FROM AUTHOR]

Climate and litter chemistry are major factors influencing litter decay, a process mediated by microbes, such as fungi, nitrogen-fixing bacteria and ammonia-oxidizing bacteria. Increasing atmospheric CO2 concentrations can decrease nitrogen (N) and increase condensed tannin (CT) content in foliar litter, reducing litter quality and slowing decomposition. We hypothesized that reduced litter quality inhibits microbes and is the mechanism causing decomposition to slow. Litterbags of Douglas-fir needles and poplar leaves with a range of N (0.61–1.57%) and CT (2.1–29.1%) treatment and natural acid unhydrolyzable residue (35.3–41.5%) concentrations were placed along climatic gradients in mature Douglas-fir stands of coastal British Columbia rainshadow forests. The structure (diversity, richness and evenness) and composition of microbial communities were analyzed using DGGE profiles of 18S, NifH-universal and AmoA PCR amplicons in foliar litter after 7, 12, 24 and 43 months of decay. High CT and low N concentrations in leaf litter were associated with changes in microbial community composition, especially fungi. Contrary to our hypothesis, high CT and low N treatments did not inhibit microbial colonization or diversity. The joint effects of air temperature and soil moisture on microbial community composition at our sites were more important than the effects of initial litter chemistry. [ABSTRACT FROM AUTHOR]

Salinization is considered a threat to agricultural soil and decreases crop yield worldwide. Nitrification and denitrification are the core processes of soil N-cycle. However, the response of nitrifiers and denitrifiers to salinity in agricultural soils remains ambiguous. The study aimed to explore the effect of salinity on nitrifiers and denitrifiers communities in agricultural soils along a naturally occurring salinity gradient. The effects of salinity on the abundance, composition, and interactions of nitrifiers and denitrifiers in surface soils were investigated. The abundance of nitrifiers significantly decreased in response to the increase in salinity. Ammonia-oxidizing archaea (AOA) were more susceptible to salinity elevation than ammonia-oxidizing bacteria (AOB). Nitrospira and Nitrobacter showed a similar trend to the salinity gradient, but the relative abundance of Nitrobacter was increased in the saline soils. High salinity decreased the abundance of napA and nirK, but had no significant effect on other marker genes for denitrification. Besides electrical conductivity, total sulfur (TS)+available potassium (AK) and TN+TS+C/N+total phosphorus (TP)+AK significantly explained the variation in denitrifier and nitrifier communities. We also found that high salinity decreased the connections between different N functional genes. These results implied the alteration of the nitrogen cycling community by high salinity mainly through decreasing AOA, NOB, and some denitrifiers with nitrate or nitrite reduction potentials and weakening the connectivity between nitrogen cycling drivers. [ABSTRACT FROM AUTHOR]

Acquisition of stable nitritation and efficient anammox play a crucial role in partial nitritation (PN) combined with anammox for nitrogen removal from ammonium-rich wastewater. Due to the limitation of ammonia-oxidizing bacteria (AOB) enrichment and nitrite-oxidizing bacteria (NOB) control in traditional membrane biological reactor (MBR), it can result in a lower nitrite production rate (NPR) and unstable PN, eventually reducing the nitrogen removal rate (NRR) via PN-anammox. In this study, we developed a zeolite membrane biological reactor (ZMBR) to enhance the PN of iron oxide red wastewater (IORW), in which the biofilm derived from the zeolite surface can provide free ammonia (FA)-containing microenvironment for AOB enrichment and NOB inhibition. The results showed that ZMBR can tolerate a higher influent nitrogen loading rate (NLR) of 2.78 kg/(m3⋅day) in comparison to the traditional MBR [2.02 kg/(m3⋅day)] and the NPR in ZMBR and traditional MBR were 1.39 and 0.96 kg/(m3⋅day), respectively. The mass concentration ratio of NO 2 - -N/ NH 4 + -N ranged from 1.05 to 1.33 in ZMBR, suggesting a suitable condition for nitrogen removal via anammox. Subsequently, the domesticated granular sludge obtained from a paper-making wastewater treatment was used as the carrier of anammox bacteria to remove nitrogen. After 93 days of operation, the NRR was observed to be 2.33 kg/(m3⋅day) and high-throughput sequencing indicated that the relatively higher abundance (45.0%) of Candidatus Kuenenia stuttgartiensis was detected in the granular sludge of the bottom part of the reactor, which can produce more proteins and lipids, suggesting a good settleability. Overall, this study provides a high-efficient method to control PN and domesticate anammox for nitrogen removal from IORW. [ABSTRACT FROM AUTHOR]

The anaerobic/aerobic sequencing batch reactor (SBR) (A/O-SBR) system has been a major focus of recent research because of its high nitrogen (N) and phosphorus (P) removal efficiencies in wastewater treatment plants. The feasibility of using the A/O-SBR system in plateau regions (altitude 3,000 m) remains unclear. In this study, two A/O-SBR systems were established, and the effect of atmospheric pressure on nutrient removal performance was studied. High N and P removal efficiencies of 90.19%±3.96% and 98.83%±1.90% , respectively, were achieved in the A/O-SBR system under low atmospheric pressure (72 kPa, called R2). The A/O-SBR system under low atmospheric pressure had higher P-uptake activity (24 mg/L), indicating that P removal was higher in R2 than in the A/O-SBR system under normal atmospheric pressure (97 kPa, called R1). The 16S rDNA sequencing analysis showed that the abundance of denitrifying glycogen accumulating organisms was higher in R2 than in R1, which was opposite to the pattern of P-accumulating organisms (PAOs), denitrifying PAOs, and ammonia-oxidizing bacteria. Batch tests were consistent with the microbial community analysis. Therefore, efficient N and P removal performance was achieved under low atmospheric pressure, and the functional microbial abundance and microbial activities related to N and P removal were significantly affected. The results of this study have implications for removing pollutants during wastewater treatment in plateau regions. [ABSTRACT FROM AUTHOR]

Water ionization is an efficient physical water treatment technology, and crop water and nutrient use efficiencies can be improved using ionized water for irrigation. In order to explore the effect of ionized water on soil nitrification and nitrifying microorganisms, we conducted a laboratory soil incubation experiment with the addition of ionized water and ordinary water under different soil water contents (equal to 30%, 60%, 100% and 175% of the field capacity, θFC). During the soil incubation, we analyzed soil inorganic nitrogen transformation, ammonia oxidation gene abundances and nitrifying microbial community structure. The results showed that, no matter adding ordinary water or ionized water, the soil nitrification rate and the abundance of ammonia oxidizing bacteria in the 100%θFC treatment were significantly higher than those in other water conditions, while the abundance of ammonia oxidizing archaea was not affected by the soil water content. With the same soil water content, the nitrification rate of ionized water treatment was stronger than that of the ordinary water treatment. Although the absolute abundance of ammonia-oxidizing microorganisms in ionized water treatment was significantly lower than that of ordinary water (p < 0.05), the relative abundance of some dominant nitrifying microbial genera in the ionized water treatment was significantly higher (p < 0.05). The dominant genera may play a key role in the nitrification process. The results show that ionized water irrigation can significantly promote the nitrification of silt loam soil, especially under 100%θFC conditions, and may regulate soil nitrification by affecting some dominant nitrifying microorganisms. This study provides a theoretical basis for understanding the biological regulation mechanism of ionized water irrigation on soil nutrient transformation and for application of ionized water to field irrigation. [ABSTRACT FROM AUTHOR]

Soil aquifer treatment (SAT), as a gravity-based wastewater reuse process, is limited by oxygen availability to the microbial community in the soil. Using oxygen from enzymatic degradation of H2O2 to generate hyper-oxygen conditions can exceed solubility limitations associated with aeration, but little is known about the effect of hyper-oxygen conditions on the microbial community and the dominant bio-reactions. This study examined the impact of H2O2 addition on the community structure and process performance, along with SAT depth. Overall, two soil columns were incrementally fed synthetic secondary effluents to simulate infiltration through SAT. The experimental column received 14 mg/L hydrogen peroxide to double the level of natural oxygen available. The microbial kinetics of nitrifiers and heterotrophs were evaluated. We found that all of the H2O2 was degraded within the top 10 cm of the column, accompanied by a higher removal of COD (23 ± 0.25%) and ammonia (31 ± 3%) in comparison to the reference column. Higher nitrogen removal (23 ± 0.04%) was obtained for the whole process using H2O2. Analysis of nitrifiers indicated that ammonia-oxidizing bacteria were most influenced, obtaining higher concentration and abundance when exposed to H2O2. DNA sequencing analysis of samples exposed to H2O2 revealed significant community structure and diversity differences among heterotrophs. This study shows that not only aerobic, but also anoxic, microbial activity and process performance in a SAT system could be accelerated in existing infrastructure with H2O2, which could significantly decrease the associated environmental footprint. [ABSTRACT FROM AUTHOR]

The understanding of microbial compositions in different dimensions is essential to achieve the successful design and operation of the partial nitritation/anammox (PN/A) process. This study investigated the microbial communities of different sludge morphologies and spatial distribution in the one-stage PN/A process of treating real coal to ethylene glycol (CtEG) wastewater at a pilot-scale integrated fixed-film activated sludge (IFAS) reactor. The results showed that ammonia-oxidizing bacteria (AOB) was mainly distributed in flocs (13.56 ± 3.16%), whereas anammox bacteria (AnAOB) was dominated in the biofilms (17.88 ± 8.05%). Furthermore, the dominant AnAOB genus in biofilms among the first three chambers was Candidatus Brocadia (6.46 ± 2.14% to 11.82 ± 6.33%), whereas it was unexpectedly transformed to Candidatus Kuenenia (9.47 ± 1.70%) and Candidatus Anammoxoglobus (8.56 ± 4.69%) in the last chamber. This demonstrated that the niche differentiation resulting from morphological (dissolved oxygen) and spatial heterogeneity (gradient distribution of nutrients and toxins) was the main reason for dominant bacterial distribution. Overall, this study presents more comprehensive information on the heterogeneous distribution and transformation of communities in PN/A processes, providing a theoretical basis for targeted culture and selection of microbial communities in practical engineering. [ABSTRACT FROM AUTHOR]

This study aimed to elucidate the boundaries of ammonia and organic loading rates that allow for nitritation in continuous flow phosphorylated-polyvinyl alcohol entrapped cell reactors and to clarify the community structure of microorganisms involving nitrogen transformation in the gel bead matrices. At operating bulk dissolved oxygen concentration of 2 mg/L, nitritation was accomplished when the total ammonia nitrogen (TAN) loading rate was ≥ 0.3 kgN/m3/d. At TAN loading rates of ≤ 0.2 kgN/m3 /d, complete oxidation of ammonia to nitrate took place. Nitritation performance dropped with increased chemical oxygen demand (COD) loading rates indicating limitation of nitritation reactor operation at some COD loading conditions. 16S rRNA gene amplicon sequencing revealed that the uncultured Cytophagaceae bacterium, Arenimonas, Truepera, Nitrosomonas, Comamonas, unclassified Soil Crenarchaeotic Group, and uncultured Chitinophagaceae bacterium were highly abundant taxa in the reactors' gel bead matrices. qPCR with specific primers targeting amoA genes demonstrated the coexistence of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea, and Comammox in the gel bead matrices. AOB was likely the main functioning ammonia-oxidizing microorganisms due to the amoA gene being of highest abundance in most of the studied conditions. Nitrite-oxidizing microorganisms presented in less relative abundance than ammonia-oxidizing microorganisms, with Nitrobacter rather than Nitrospira dominating in the group. Results obtained from this study are expected to further the application of nitritation entrapped cell reactors to real wastewater treatment processes. [ABSTRACT FROM AUTHOR]

Organic material amendments have been proposed as an effective strategy to promote soil health by enhancing soil fertility and promoting nitrogen (N) cycling and N use efficiency (NUE). Thus, it is important to investigate the extent to which the structure and function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) differentially respond to the organic material amendments in field settings. Here, we conducted a 9-year field experiment to track the responses of AOA and AOB populations to the organic material amendments and measured the potential nitrification activity (PNA), plant productivity, and NUE in the plant rhizosphere interface. Our results revealed that the organic material amendments significantly enhanced the abundance and diversity of AOA and AOB populations. Further, significant differences were observed in the composition and co-occurrence network of AOA and AOB. A higher occurrence of potential competitive interactions between taxa and enumerated potential keystone taxa was observed in the AOA-AOB network. Moreover, we found that AOA was more important than AOB for PNA under the organic material amendments. Structural equation modeling suggested that the diversity of AOA and AOB populations induced by the potential competitive interactions with keystone taxa dynamically accelerated the rate of PNA, and positively affected plant productivity and NUE under the organic material amendments. Collectively, our study offers new insights into the ecology and functioning of ammonia oxidizers and highlights the positive effects of organic material amendments on nitrogen cycling dynamics. [ABSTRACT FROM AUTHOR]

Nitrification, a key pathway of nitrogen (N) loss from agricultural soils, is performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). We examined the seasonal dynamics (2 years) of ammonia oxidizer gene abundances across a gradient of soil carbon (C) and N in a semi-arid soil after 8 years of tillage and crop residue treatments. AOB was more dominant than AOA in the surface soil, as AOA were undetected in 96% of samples. Seasonal variation in AOB abundance was related to substrate availability; AOB gene copy numbers increased at the end of the growing season (during summer fallow) following higher concentrations in dissolved organic matter soil water. This suggests increased co-location between AOB and substrate resources in pores still filled with water as the soils dried. AOB was however not statistically related to soil ammonium concentrations, soil water content, rainfall or temperature. Organic matter inputs enhanced AOB abundance independent of seasonal variation. AOB abundance was greatest in autumn and immediately preceding the start of the growing season, and coincided with elevated soil nitrate concentrations. The growth of the AOB population is likely to contribute to increased risk of N loss through leaching and/or denitrification at the start of the crop growing season following summer fallow. [ABSTRACT FROM AUTHOR]

Anaerobic ammonium oxidation (anammox) has recently become of significant interest due to its capability for cost-effective nitrogen elimination from wastewater. However, anaerobic ammonia-oxidizing bacteria (AnAOB) are sensitive to environmental changes and toxic substances. In particular, the presence of antibiotics in wastewater, which is considered unfavorable to the anammox process, has become a growing concern. Therefore, it is necessary to evaluate the effects of these inhibitors to acquire information on the applicability of the anammox process. Hence, this review summarizes our knowledge of the effects of commonly detected antibiotics in water matrices, including fluoroquinolone, macrolide, β-lactam, chloramphenicol, tetracycline, sulfonamide, glycopeptide, and aminoglycoside, on the anammox process. According to the literature, the presence of antibiotics in wastewater could partially or completely inhibit anammox reactions, in which antibiotics targeting protein synthesis or DNA replication (excluding aminoglycoside) were the most effective against the AnAOB strains. [ABSTRACT FROM AUTHOR]

To decrease the cost of wastewater treatment at the plant, the Wuzhou Shenguan Protein Enteric Coating Production Plant designed and built an expanded granular sludge bed (EGSB)-ceramic membrane bioreactor reactor (CMBR) process for treating high-concentration organic wastewater with a capacity of 25 m3/d. The EGSB is divided into anaerobic and microaerobic sections. The purpose of the anaerobic section is to substantially degrade COD, and the main functions of the microaerobic section are to coordinate the relationship between hydrolytic acid-producing bacteria, methanogenic bacteria (MBP), and sulfate-reducing bacteria (SRB) and to mitigate the inhibitory effects between them to simultaneously remove COD and sulfate. Anaerobic ammonia-oxidizing bacteria were added to the CMBR reactor to remove both COD and ammonia nitrogen. The results of the operation showed that more than 99% of the COD was removed by the EGSB-CMBR process, while the removal rates of NH4+-N and SS were greater than 70% and 90%, respectively. In addition, the effluent met the requirements of the secondary standard of the Comprehensive Wastewater Discharge Standard (8978-1996). Economic and technical analyses showed that the modified EGSB-CMBR reactor has a high treatment efficiency, which greatly saves on the cost of the "commissioned treatment" of high-concentration organic waste liquid in the plant. Specifically, it can save more than 800,000 CNY for the plant annually. [ABSTRACT FROM AUTHOR]

Agronomic practices such as long-term use of plastic film mulching (PFM) and application of organic and inorganic fertilizers have profound effect on soil microbial community. However, there is limited information on the abundance and community structure of ammonia-oxidizers where these practices have been employed. In this study, we investigated soil ammonia oxidizers in a long-term application of fertilizer plots with or without PFM in two seasons of a maize-growing period. The fertilization treatments included: non-fertilizer control (CK), nitrogen fertilizer (N), organic manure (M), nitrogen fertilizer plus organic manure combined (MN). Real-time quantitative polymerase chain reaction (qPCR) of ammonia monooxygenase (amoA) genes revealed that the abundances of ammonia-oxidizing archaea (AOA) (1.0 x 107 to 2.0 × 1011 per copies g−1 dry soil weight) significantly (p < 0.05) out-numbered ammonia-oxidizing bacteria (AOB) (5.0 x 105 to 4.0 × 109 copies g−1 dry soil weight) abundances for June, July and October respectively. The phylogenetic analyses of denaturing gradient gel electrophoresis (DGGE) 16S rRNA gene revealed that AOB-uncultured Nitrosospira sp dominated bacterial ammonia oxidizers in fertilized and non-fertilized soils, regardless of PFM treatments for July and October. The non-fertilization treatment significantly increased bacterial richness (15.67 ± 0.33) under PFM treatment relative to fertilized treatments. [ABSTRACT FROM AUTHOR]

Purpose Nitrogen (N) fertilizer application in agricultural soil is a primary anthropogenic nitrous oxide (N2O) source. Currently, the effect of the N fertilizer type on N2O emissions from upland soil has been rarely reported. To this end, impacts of various types of N fertilizer on N2O emissions in purple caitai (Brassica campestris L. ssp. chinensis var. purpurea) fields are investigated in this work. The field experiment was carried out with four treatments, including inorganic N fertilization (I), organic N fertilization (O), integrated organic-inorganic N fertilization (I+O) and no fertilization (CK). The nitrifier/denitrifier abundance was determined using absolute real-time quantitative PCR. Compared with I and O, I+O significantly increased dissolved organic C content, microbial biomass C and microbial biomass N by 24–63%, 12–38% and 13–36% on average, respectively. Moreover, the seasonal cumulative N2O-N emissions and fertilizer-induced N2O emission factor under I+O were significantly lower than those under I and O by 17–29% and 23–39%, respectively. The results indicate that N fertilizer type significantly affects the N2O emissions, and the integrated organic-inorganic N fertilization can mitigate the N2O emissions primarily by inhibiting the nitrification mediated by ammonia-oxidizing bacteria in purple caitai fields. Integrated organic-inorganic N fertilization is an ideal N fertilization regime to enhance soil fertility and yield and reduce N2O emissions in the upland fields. [ABSTRACT FROM AUTHOR]

During the past decades, extensive nitrogen fertilization and acid deposition have greatly contributed to soil acidification in agroecosystems. Liming, the addition of calcium- and magnesium-rich material to soil, is an effective management strategy used to improve fertility and productivity of agricultural soils degraded by acidification. Nitrification plays a central role in nitrogen (N) availability in agroecosystems and contributes to soil acidification. However, little is known regarding the effects of liming on this process and microbial populations that drive it. Here, we investigated population dynamics and activity of ammonia oxidizers in response to a 2-year liming field trial in acidic soils received long-term fertilization with chemical N fertilizers and short-term lime amendment in microcosm incubations. Our results showed that activity, abundance and population structure of both ammonia-oxidizing archaea (AOA) and bacteria (AOB) were sensitive to liming in fertilized acidic soils. AOB abundance and potential nitrification rates increased in field plots subjected to liming, whereas the opposite was observed for AOA. In microcosm incubations, AOA abundance increased progressively over 60 days, namely under low CaO levels, whereas AOB abundance was greatly stimulated only during the first week under high CaO levels. 13CO2-SIP-DNA experiments further supported that AOA were the most active ammonia oxidizers in fertilized field soils. However, in N-fertilized soils freshly amended with CaO, only autotrophic growth of AOB was observed after seven days, but not after 30 days when growth of AOA was observed. Taken together, our results indicated that both AOA and AOB play a role in nitrification following liming in fertilized acidic soils, likely through selection of better adapted clades of organisms. Although AOA were likely the main drivers of nitrification in these soils in the long-term, liming stimulated AOB activity in the short-term.

Ammonia-oxidizing bacteria (AOB) are ubiquitous on the earth and have broad applications in bioremediation. However, the number of their species with standing in nomenclature and deposited in Microbial Culture Collections still remains low. Moreover, only a few novel species have been reported over the last decades. In this study, we sealed agar in serum bottles to develop a kind of solid agar plate with the oxygen concentration in the headspace maintained at low levels. By using these plates, eight AOB isolates including two novel species were obtained. When AOB cells were grown on the sealed solid agar plates, the time to form visible colonies was largely reduced and the maximum diameter of colonies reached 2 mm, which makes the process of AOB isolation rapid and efficient. Based on five AOB isolates, the headspace oxygen concentration had a significant influence on AOB growth either on solid plate or in liquid culture. Especially, when grown under 21 % O 2 , the number of colonies formed on solid agar plates was very low and sometimes no visible colony formed. Besides the application on AOB isolation, the sealed solid agar plate was also effective for the enumeration and preservation of AOB cells. When preserved under room temperature for more than ten months, the AOB colonies on the plate could still be recovered. This method provides a feasible way to isolate more novel AOB species from the environment and deposit more species in Microbial Culture Collections., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15 N-urea incubation has not been totally clarified. The 15 N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C 2 H 2 almost completely inhibited NO 3 - -N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15 N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15 N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15 N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different., (© 2024. The Author(s).)

Chloramination is an effective strategy for eliminating pathogens from drinking water and repressing their regrowth in water distribution systems. However, the inevitable release of NH 4 potentially promotes nitrification and associated ammonia-oxidizing bacteria (AOB) contamination. In this study, AOB (Nitrosomona eutropha) were isolated from environmental water and treated with two disinfection stages (chloramine disinfection and chloramine residues) to investigate the occurrence mechanisms of AOB in chloramination. The results showed that N. eutropha had considerable resistance to monochloramine compared to Escherichia coli, whose inactivation rate constant was 19.4-fold lower. The higher resistance was attributed to high levels of extracellular polymer substances (EPS) in AOB, which contribute to AOB surviving disinfection and entering the distribution system. In AOB response to the chloramine residues stage, the respiratory activity of N. eutropha remained at a high level after three days of continuous exposure to high chloramine residue concentrations (0.5-1.5 mg/L). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) suggested that the mechanism of N. eutropha tolerance involved a significantly high expression of the intracellular oxidative stress-regulating (sodB, txrA) and protein-related (NE1545, NE1546) genes. Additionally, this process enhanced EPS secretion and promoted biofilm formation. Adhesion predictions based on the XDLVO theory corroborated the trend of biofilm formation. Overall, the naturally higher resistance contributed to the survival of AOB in primary disinfection; the enhanced antioxidant response of surviving N. eutropha accompanied by biofilm formation was responsible for their increased resistance to the residual chloramines.+ potentially promotes nitrification and associated ammonia-oxidizing bacteria (AOB) contamination. In this study, AOB (Nitrosomona eutropha) were isolated from environmental water and treated with two disinfection stages (chloramine disinfection and chloramine residues) to investigate the occurrence mechanisms of AOB in chloramination. The results showed that N. eutropha had considerable resistance to monochloramine compared to Escherichia coli, whose inactivation rate constant was 19.4-fold lower. The higher resistance was attributed to high levels of extracellular polymer substances (EPS) in AOB, which contribute to AOB surviving disinfection and entering the distribution system. In AOB response to the chloramine residues stage, the respiratory activity of N. eutropha remained at a high level after three days of continuous exposure to high chloramine residue concentrations (0.5-1.5 mg/L). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) suggested that the mechanism of N. eutropha tolerance involved a significantly high expression of the intracellular oxidative stress-regulating (sodB, txrA) and protein-related (NE1545, NE1546) genes. Additionally, this process enhanced EPS secretion and promoted biofilm formation. Adhesion predictions based on the XDLVO theory corroborated the trend of biofilm formation. Overall, the naturally higher resistance contributed to the survival of AOB in primary disinfection; the enhanced antioxidant response of surviving N. eutropha accompanied by biofilm formation was responsible for their increased resistance to the residual chloramines., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Comammox Nitrospira and canonical ammonia-oxidizing bacteria (cAOB) generally coexist in activated sludge. In present study, the effect of comammox Nitrospira on N 2 O production during nitrification of activated sludge was investigated. Comammox Nitrospira and cAOB were separately enriched in two nitrifying reactors, with respective relative abundance of approximately 98% in ammonia oxidizer community. The N 2 O emission factor (EF) of nitrification in comammox Nitrospira dominated reactor was 0.35%, consistently lower than that (2.2%) in cAOB dominated reactor. When increasing the relative abundance of comammox Nitrospira in ammonia oxidizer community, the N 2 O EF of nitrification decreased exponentially, which suggested that comammox Nitrospira not only decreased N 2 O production directly but also might have reduced N 2 O yield by cAOB. When cAOB dominated the ammonia oxidizer community of sludge, decreasing pH to 6.3, lowering DO to less than 0.5 mg/L, and increasing nitrite concentration enhanced N 2 O EF dramatically. When comammox Nitrospira became the dominant ammonia oxidizer, however, the N 2 O EF correlated to nitrite insignificantly and a low DO of 0.2 mg/L and weakly acidic pH (6.3) decreased N 2 O EF by approximately 70% and 60%, respectively. These results imply that enhancing the relative abundance of comammox Nitrospira in sludge is an effective way to reducing N 2 O emissions and can also offset the promoting effects of acidic pH, low DO, and high nitrite concentration on N 2 O production during nitrification., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The discovery of Comammox bacteria (CMX) has changed our traditional concept towards nitrification, yet its role in constructed wetlands (CWs) remains unclear. This study investigated the contributions of CMX and two canonical ammonia-oxidizing microorganisms, ammonia-oxidizing bacteria (AOB) and archaea to nitrification in four regions (sediment, shoreside, adjacent soil, and water) of a typical CW using DNA-based stable isotope probing. The results revealed that CMX not only widely occurred in sediment and shoreside zones with high abundance (5.08 × 10 4 and 6.57 × 10 4 copies g -1 soil, respectively), but also actively participated in ammonia oxidation, achieving ammonia oxidation rates of 1.43 and 2.00 times that of AOB in sediment and shoreside, respectively. Phylogenetic analysis indicated that N. nitrosa was the dominant and active CMX species. These findings uncovered the crucial role of CMX in nitrification of sediment and shoreside, providing a new insight into nitrogen cycle of constructed wetlands., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Biochar is an important soil amendment that can enhance the biological properties of soil, as well as nitrogen (N) uptake and utilization in N-fertilized crops. However, few studies have characterized the effects of urea and biochar application on soil biochemical traits and its effect on paddy rice. Therefore, a field trial was conducted in the early and late seasons of 2020 in a randomized complete block design with two N levels (135 and 180 kg ha−1) and four levels of biochar (0, 10, 20, and 30 t ha−1). The treatment combinations were as follows: 135 kg N ha−1 + 0 t B ha−1 (T1), 135 kg N ha−1 + 10 t B ha−1 (T2), 135 kg N ha−1 + 20 t B ha−1 (T3), 135 kg N ha−1 + 30 t B ha−1 (T4), 180 kg N ha−1 + 0 t B ha−1 (T5), 180 kg N ha−1 + 10 t B ha−1 (T6), 180 kg N ha−1 + 20 t B ha−1 (T7) and 180 kg N ha−1 + 30 t B ha−1 (T8). The results showed that soil amended with biochar had higher soil pH, soil organic carbon content, total nitrogen content, and mineral nitrogen (NH4+-N and NO3−-N) than soil that had not been amended with biochar. In both seasons, the 20 t ha−1 and 30 t ha−1 biochar treatments had the highest an average concentrations of NO3–-N (10.54 mg kg−1 and 10.25 mg kg−1, respectively). In comparison to soil that had not been treated with biochar, the average activity of the enzymes urease, polyphenol oxidase, dehydrogenase, and chitinase was, respectively, 25.28%, 14.13%, 67.76%, and 22.26% greater; however, the activity of the enzyme catalase was 15.06% lower in both seasons. Application of biochar considerably increased the abundance of ammonia-oxidizing bacteria (AOB), which was 48% greater on average in biochar-amended soil than in unamended soil. However, there were no significant variations in the abundances of ammonia-oxidizing archaea (AOA) or nitrite-oxidizing bacteria (NOB) across treatments. In comparison to soil that had not been treated with biochar, the average N content was 24.46%, 20.47%, and 19.08% higher in the stem, leaves, and panicles, respectively. In general, adding biochar at a rate of 20 to 30 t ha−1 with low-dose urea (135 kg N ha−1) is a beneficial technique for improving the nutrient balance and biological processes of soil, as well as the N uptake and grain yield of rice plants.