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Ammonia oxidizers are key players in the global nitrogen cycle and are responsible for the oxidation of ammonia to nitrite, which is further oxidized to nitrate by other microorganisms. Their activity can lead to adverse effects on some human-impacted environments, including water pollution through leaching of nitrate and emissions of the greenhouse gas nitrous oxide (N2O). Ammonia monooxygenase (AMO) is the key enzyme in microbial ammonia oxidation and shared by all groups of aerobic ammonia oxidizers. The AMO has not been purified in an active form, and much of what is known about its potential structure and function comes from studies on its interactions with inhibitors. The archaeal AMO is less well studied as ammonia oxidizing archaea were discovered much more recently than their bacterial counterparts. The inhibition of ammonia oxidation by aliphatic alcohols (C1-C8) using the model terrestrial ammonia oxidizing archaeon ' Candidatus Nitrosocosmicus franklandus' C13 and the ammonia oxidizing bacterium Nitrosomonas europaea was examined in order to expand knowledge about the range of inhibitors of ammonia oxidizers. Methanol was the most potent specific inhibitor of the AMO in both ammonia oxidizers, with half-maximal inhibitory concentrations (IC50) of 0.19 and 0.31 mM, respectively. The inhibition was AMO-specific in ' Ca. N. franklandus' C13 in the presence of C1-C2 alcohols, and in N. europaea in the presence of C1-C3 alcohols. Higher chain-length alcohols caused non-specific inhibition and also inhibited hydroxylamine oxidation. Ethanol was tolerated by ' Ca. N. franklandus' C13 at a higher threshold concentration than other chain-length alcohols, with 80 mM ethanol being required for complete inhibition of ammonia oxidation. [ABSTRACT FROM AUTHOR]

[Display omitted] • A microelectrolysis-enhanced membrane-aerated biofilm reactor was developed. • The removal performance of NH 4 +-N and sulfamethoxazole (SMX) was enhanced. • The expression of ammonia monooxygenase (AMO) was up-regulated (0.92 log 2). • AMO exposed additional binding sites for NH 4 +-N and SMX. • Up-regulated antibiotic resistance genes were eliminated by 90%. A self-corrosion microelectrolysis (SME)-enhanced membrane-aerated biofilm reactor (eMABR) was developed for the removal of pollutants and reduction of antibiotic resistance genes (ARGs). Fe2+ and Fe3+ formed iron oxides on the biofilm, which enhanced the adsorption and redox process. SME can induce microorganisms to secrete more extracellular proteins and up-regulate the expression of ammonia monooxygenase (AMO) (0.92 log 2). AMO exposed extra binding sites (ASP-69) for antibiotics, weakening the competition between NH 4 +-N and sulfamethoxazole (SMX). The NH 4 +-N removal efficiency in the S-eMABR (adding SMX and IC) increased by 44.87 % compared to the S-MABR (adding SMX). SME increased the removal performance of SMX by approximately 1.45 times, down-regulated the expressions of sul 1 (−1.69 log 2) and sul 2 (−1.30 log 2) genes, and controlled their transfer within the genus. This study provides a novel strategy for synergistic reduction of antibiotics and ARGs, and elucidates the corresponding mechanism based on metatranscriptomic and molecular docking analyses. [ABSTRACT FROM AUTHOR]

• 4-CP biodegradation was enhanced with reduced volatilization in nitrifying MABR. • Cometabolism pathway of 4-CP in nitrifying MABR was proposed. • Mechanism involved in AMO-mediated cometabolism of 4-CP was elucidated. • MD approaches helped to explain the reactive sites of 4-CP metabolism. • DFT calculation can well elucidate the biotransformation product of 4-CP. Ammonia monooxygenase (AMO)-mediated cometabolism of organic pollutants has been widely observed in biological nitrogen removal process. However, its molecular mechanism remains unclear, hindering its practical application. Furthermore, conventional nitrification systems encounter significant challenges such as air pollution and the loss of ammonia-oxidizing bacteria, when dealing with wastewater containing volatile organic pollutants. This study developed a nitrifying membrane-aerated biofilm reactor (MABR) to enhance the biodegradation of volatile 4-chlorophenol (4-CP). Results showed that 4-CP was primarily removed via Nitrosomonas nitrosa -mediated cometabolism in the presence of NH 4 +-N, supported by the increased nicotinamide adenine dinucleotide (NADH) and adenosine triphosphate (ATP) content, AMO activity and the related genes abundance. Hydroquinone, detected for the first time and produced via oxidative dechlorination, as well as 4-chlorocatechol was primary transformation products of 4-CP. Nitrosomonas nitrosa AMO structural model was constructed for the first time using homology modeling. Molecular dynamics simulation suggested that the ortho -carbon in the benzene ring of 4-CP was more prone to metabolismcompared to the ipso -carbon. Density functional theory calculation revealed that 4-CP was metabolized by AMO via H-abstraction-OH-rebound reaction, with a significantly higher rebound barrier at the ipso -carbon (16.37 kcal·mol-1) as compared to the ortho -carbon (6.7 kcal·mol-1). This study fills the knowledge gap on the molecular mechanism of AMO-mediated cometabolism of organic pollutants, providing practical and theoretical foundations for improving volatile organic pollutants removal through nitrifying MABR. [Display omitted] [ABSTRACT FROM AUTHOR]

• Bacterial ammonia monooxygenase genes and host were decreased after COVID-19 exposure. • The disturbance of ammonia oxidation recovered in the post-pandemic period. • Disinfectants destroy cell structure and cause oxidative stress of Nitrosomonas. • Sodium hypochlorite induce the downregulation of ammonia monooxygenase genes. • Sodium hypochlorite destroy the structure of ammonia monooxygenase protein. Anthropogenic activities significantly impact the elemental cycles in aquatic ecosystems, with the N-cycling playing a critical role in potential nutrient turnover and substance cycling. We hypothesized that measures to prevent COVID-19 transmission profoundly altered the nitrogen cycle in riverine ecosystems. To investigate this, we re-analyzed metagenomic data and identified 60 N-cycling genes and 21 host metagenomes from four urban reaches (one upstream city, Wuhan, and two downstream cities) along the Yangtze River. Our analyses revealed a marked decrease in the abundance of bacterial ammonia monooxygenase genes, as well as in the host, ammonia-oxidizing autotrophic Nitrosomonas , followed by a substantial recovery post-pandemic. We posited that discharge of sodium hypochlorite (NaOCl) disinfectant may be a primary factor in the reduction of N-cycling process. To test this hypothesis, we exposed pure cultures of Nitrosomonas europaea to NaOCl to explore the microbial stress response. Results indicated that NaOCl exposure rapidly compromised the cell structure and inhibited ammonia oxidation of N. europaea , likely due to oxidative stress damage and reduced expression of nitrogen metabolism-related ammonia monooxygenase. Using the functional tagging technique, we determined that NaOCl directly destroyed the ammonia monooxygenase protein and DNA structure. This study highlights the negative impacts of chlorine disinfectants on the function of aquatic ecosystems and elucidates potential mechanisms of action. [Display omitted] [ABSTRACT FROM AUTHOR]

The abundance and taxonomic composition of ammonia‐oxidizing archaea (AOA) were assessed in paddy soils that had received more than 50 years of fertilization with and without inorganic N. The inorganic N fertilized treatments were: NPK and NPK + CO (nitrogen (N), phosphorus (P), potassium (K) and compost (CO)). The treatments without inorganic N were: CO, PK and control (unfertilized soils). Quantitative PCR (qPCR) analysis of the archaeal amoA gene showed no significant changes in AOA abundance following the long‐term application of inorganic N fertilizers. However, subsequent analysis of amoA gene sequencing data showed that inorganic N application significantly changed the AOA community composition and alpha diversity indices. Edge principal components analysis (PCA) showed varying contributions of distinct AOA lineages in separating samples according to the fertilization treatment. Addition of inorganic N favoured an increase in the abundance of AOA lineages belonging to Nitrososphaera, and the treatments without inorganic N additions formed a separate cluster dominated by Nitrosotalea lineage. The distinct response of the two AOA lineages points towards different community organization of soil AOA and strongly supports the concept of habitat partitioning in paddy soil ecosystems. Highlights: Lineages of AOA responded differently to different N management practices.Long‐term N fertilization selectively enriched AOA lineages, with C:N ratio a factor associated with such changesInorganic N favoured Nitrososphaera lineage abundanceRegardless of fertilizer status, Nitrosotalea lineage was dominant in the absence of inorganic N fertilization. [ABSTRACT FROM AUTHOR]

To date, little is known about the ecological significance of Comammox (COMplete AMMonia OXidizers) Nitrospira in the water column of freshwater lakes. Water samples collected along depth profiles were used to investigate the distribution of Comammox in 13 lakes characterized by a wide range of physicochemical properties. Several published primers, which target the α-subunit of the ammonia monooxygenase, generated non-specific PCR products or did not amplify target genes from lake water and other habitats. Therefore, a new primer set has been designed for specific detection of Comammox in lakes. The high specificity of the PCR assay was confirmed by sequencing analysis. Quantification of Comammox amoA genes in lake water samples based on droplet digital PCR (ddPCR) revealed very low abundances (not exceeding 85 amoA copies ml−1), which suggest that Comammox is of minor importance for the nitrification process in the water column of the study sites. Surprisingly, samples taken from the sediment/water-interface along an oxygen gradient in dimictic Piburger See showed Comammox abundances three to four magnitudes higher than in the pelagic realm of the lake, which indicates a preference of Comammox to a particle-attached lifestyle. [ABSTRACT FROM AUTHOR]

Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD. [ABSTRACT FROM AUTHOR]

Ammonia monooxygenase (AMO) is a key nitrogen transforming enzyme belonging to the same copper-dependent membrane monooxygenase family (CuMMO) as the particulate methane monooxygenase (pMMO). The AMO from ammonia oxidising archaea (AOA) is very divergent from both the AMO of ammonia oxidising bacteria (AOB) and the pMMO from methanotrophs and little is known about the structure or substrate range of the archaeal AMO. This study compares inhibition by C2-C8 linear 1-alkynes of AMO from two phylogenetically distinct strains of AOA, "Candidatus Nitrosocosmicus franklandus" C13 and "Candidatus Nitrosotalea sinensis" Nd2, with AMO from Nitrosomonas europaea and pMMO from Methylococcus capsulatus (Bath). An increased sensitivity of the archaeal AMO to short-chain32 length alkynes (=C5) appeared to be conserved across AOA lineages. Similarities in C2-C8 alkyne inhibition profiles between AMO from AOA and pMMO from M. capsulatus suggested that the archaeal AMO has a narrower substrate range compared to that of N. europaea AMO. Inhibition of AMO from "Ca. Nitrosocosmicus franklandus" and N. europaea by the aromatic alkyne phenylacetylene was also investigated. Kinetic data revealed that the mechanism by which phenylacetylene inhibits "Ca. Nitrosocosmicus franklandus" and N. europaea is different, indicating differences in the AMO active site between AOA and AOB. Phenylacetylene was found to be a specific and irreversible inhibitor of AMO from "Ca. Nitrosocosmicus franklandus" which does not compete with NH3 for binding at the active site. [ABSTRACT FROM AUTHOR]

Approximately two percent of the world's energy is consumed in the production of ammonia from hydrogen and nitrogen gas. Ammonia is used as a fertilizer ingredient for agriculture and distributed in the environment on an enormous scale to promote crop growth in intensive farming. Only 30–50 % of the nitrogen applied is assimilated by crop plants; the remaining 50–70 % goes into biological processes such as nitrification by microbial metabolism in the soil. This leads to an imbalance in the global nitrogen cycle and higher nitrous oxide emissions (a potent and significant greenhouse gas) as well as contamination of ground and surface waters by nitrate from the nitrogen‐fertilized farmland. This Review gives a critical overview of the current knowledge of soil microbes involved in the chemistry of ammonia nitrification, the structures and mechanisms of the enzymes involved, and phytochemicals capable of inhibiting ammonia nitrification. [ABSTRACT FROM AUTHOR]

To mitigate the toxicity of ammonia in aquaculture systems, marine and brackish water ammoniaoxidizing bacterial consortia have been developed and are used for activation of nitrifying bioreactors integrated to recirculating aquaculture systems. To shed more light on to these biological entities, diversity of both the consortia were analyzed based on random cloning of 16S rRNA gene and ammonia-oxidizing bacterial specific amoA gene sequences. The dendrograms of representative clones on the basis of amplified ribosomal DNA restriction analysis generated 22 and 19 clusters for marine and brackish water nitrifying consortia, respectively. Phylogenetic analysis demonstrated the presence of various autotrophic nitrifiers belonging to α-, β- and γ-Proteobacteria, anaerobic ammonia oxidizers, heterotrophic denitrifiers, Bacteroidetes, and Actinobacteria. Distribution patterns of the organisms within the two consortia were determined using the software Geneious and diversity indices were investigated using Mega 5.0, VITCOMIC and Primer 7. The abundance of ammonia oxidizers was found in the order of 2.21±0.25 x 109 copies/g wet weight of marine consortium and 6.20±0.23 x 107 copies/g of brackish water consortium. Besides, marine ammoniaoxidizing consortium exhibited higher mean population diversity and Shannon Wiener diversity than the brackish water counterparts. [ABSTRACT FROM AUTHOR]

Abstract Although the adverse impacts of emerging nanoparticles (NPs) on the biological nitrogen removal (BNR) process have been broadly reported, the adaptive responses of NP-impaired nitrifiers and the related mechanisms have seldom been addressed to date. Here, we systematically explored the adaption and recovery capacities of the ammonia oxidizer Nitrosomonas europae a under chronic TiO 2 NP exposure and different dissolved oxygen (DO) conditions at the physiological and transcriptional levels in a chemostat reactor. N. europae a cells adapted to 50 mg/L TiO 2 NP exposure after 40-d incubation and the inhibited cell growth, membrane integrity, nitritation rate, and ammonia monooxygenase activity all recovered regardless of the DO concentrations. Transmission electron microscope imaging indicated the remission of the membrane distortion after the cells' 40-d adaption to the NP exposure. The microarray results further suggested that the metabolic processes associated with the membrane repair were pivotal for cellular adaption/recovery, such as the membrane efflux for toxicant exclusion, the structural preservation or stabilization, and the osmotic equilibrium adjustment. In addition, diverse metabolic and stress-defense pathways, including aminoacyl-tRNA biosynthesis, respiratory chain, ATP production, toxin-antitoxin 'stress-fighting', and DNA repair were activated for the cellular adaption coupled with the metabolic activity recovery, probably via recovering the energy production/conversion efficiency and mediating the non-photooxidative stress. Finally, low DO (0.5 mg/L) incubated cells were more susceptible to TiO 2 NP exposure and required more time to adapt to and recover from the stress, which was probably due to the stimulation limitation of the oxygen-dependent energy metabolism with a lower oxygen supply. The findings of this study provide new insights into NP contamination control and management adjustments during the BNR process. Graphical abstract Image 1 Highlights • Cells adapted to chronic NP stress and all the metabolic activities recovered. • Membrane repair associated regulations were pivotal for cellular adaption. • Diverse metabolic and stress-defense pathways were activated for cell recovery. • Low DO condition compromised NP impaired cells' resistance and adaption capacities. • Stimulation limitation of respiratory chain accounted for the compromised capacity. [ABSTRACT FROM AUTHOR]

The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDPPCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems. IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification. [ABSTRACT FROM AUTHOR]

17α-ethinylestradiol (EE2) has received increasing attention as an emerging and difficult-to-remove emerging contaminant in recent years. Ammonia-oxidizing bacteria (AOB) have been reported to be effective in EE2 removal, and ammonia monooxygenase (AMO) is considered as the primary enzyme for EE2 removal. However, the molecular mechanism underlying the transformation of EE2 by AOB and AMO is still unclear. This study investigated the molecular mechanism of EE2 degradation using a combination of experimental and computational simulation methods. The results revealed that ammonia nitrogen was essential for the co-metabolism of EE2 by AOB, and that NH 3 bound with Cu C (one active site of AMO) to induce a conformational change in AMO, allowing EE2 to bind with the other active site (Cu B), and then EE2 underwent biological transformation. These results provide a theoretical basis and a novel research perspective on the removal of ammonia nitrogen and emerging contaminants (e.g., EE2) in wastewater treatment. [Display omitted] • The molecular mechanism underlying the transformation of EE2 by AMO was revealed. • Ammonia nitrogen was essential for the co-metabolism of EE2 by AMO. • NH 3 bound with Cu C in AMO and induced a conformational change of AMO. • EE2 bound with Cu B in AMO and underwent biotransformation after NH 3 binding. [ABSTRACT FROM AUTHOR]

Abstract Ionic liquids (ILs) were widely applied because of their excellent properties. The present investigation studied the toxicity of the IL 1-octyl-3-methylimidazolium hexafluorophosphate ([Omim]PF 6) to the soil microbial population and community diversity with dose (1.0, 2.0, 4.0, 6.0, and 8.0 mg kg−1) and exposure time (7, 10, and 13 d). The results show the IL was stable during the entire experimental period. The Biolog-ECO plate results indicated that the average well color development (AWCD) in the 6.0 and 8.0 mg kg−1 treatments was lower than these in the other treatments. The diversity indices of the Biolog analysis were significantly reduced. The abundance of the ammonia-oxidizing archaea (AOA-) and the ammonia-oxidizing bacteria (AOB-) ammonia monooxygenase (amoA) genes was measured by the real-time polymerase chain reaction (RT-PCR). In the treatments of 4.0, 6.0 and 8.0 mg kg−1, the abundance of amoA genes of the AOA- and AOB- were inhibited by IL [Omim]PF 6. Graphical abstract Image Highlights • The levels of amoA genes was used to study the toxicity of [Omim]PF 6 in brown soil. • Functional diversity of soil microbes was used to study the toxicity of [Omim]PF 6. • The concentrations of investigated IL in soil relatively maintained stable. • The investigated IL has potential risks if they were released to soil by accident. [ABSTRACT FROM AUTHOR]

The extensive release of cerium dioxide nanoparticles (CeO 2 NPs) causes increasing potential health and environmental risks. In this study, acute and chronic responses of macrophyte and microorganisms were evaluated following exposure to CeO 2 NPs in constructed wetlands (CWs). It was found that most of the CeO 2 NPs were retained in the CW substrate, with minor amounts accumulated in plant tissues. Photosynthetic activity experiment indicated that environmentally relevant concentration (1 mg/L) of CeO 2 NPs enhanced the net photosynthesis rate of plants, while chronic exposure to a high concentration (50 mg/L) of CeO 2 NPs inhibited photosynthesis. The variations of the malondialdehyde (MDA) content and antioxidant enzyme activities in plant tissues revealed that acute exposure to CeO 2 NPs induced oxidative stress to plants, while there was no obvious chronic effect. Moreover, the biomass increased marginally under exposure to 1 mg/L CeO 2 NPs, whereas exposure to 50 mg/L CeO 2 NPs reduced the total biomass of plants by 29%. The release of lactate dehydrogenase (LDH) suggested that chronic exposure to CeO 2 NPs inhibited microbial viability. Metagenome and enzymatic activities analyses further revealed that CeO 2 NPs significantly changed the microbial community structure and inhibited the activities of dehydrogenase, urease, ammonia monooxygenase, and phosphatase. This resulted in the decline of contaminant removal efficiency. Overall, acute and chronic exposure to CeO 2 NPs had multiple effects on macrophyte and microorganisms in CWs, which significantly impacted the treatment performance of the ecological system. [ABSTRACT FROM AUTHOR]

Planktonic archaea are thought to play an important role in ammonia oxidation in marine environments. Data on the distribution, abundance, and diversity of ammonia oxidizers in the coastal sea-surface microlayer (SML) are lacking, despite previous reports of high abundance of Thaumarchaeota in the SML of estuaries and freshwater lakes. Here, we failed to detect the presence of ammonia-oxidizing bacteria in any of our samples taken from a semi-enclosed marine inlet in Japan. Therefore, we shifted our focus to examine the archaeal community composition as well as the Thaumarchaeota marine group I (MG-I) and ammonia monooxygenase subunit A (amoA) gene copy numbers and composition in the SML and corresponding underlying water (UW, 20 cm). amoA gene copy numbers obtained by quantitative PCR were consistent with the typical values observed in the surface waters of oceanic and coastal environments where nitrification activity has been detected, but the copy numbers were two- to three-fold less than those reported from the surface layers and UW of high mountain lakes. Both amoA and MG-I 16S rRNA gene copy numbers were significantly negatively correlated with chlorophyll-a and transparent exopolymer particle concentrations in the SML. Communities of archaea and ammonia-oxidizing archaea in SML samples collected during low wind conditions (≤5 m s–1) differed the most from those in UW samples, whereas the communities in SML samples collected during high wind conditions were similar to the UW communities. In the SML, low ratios of amoA to MG-I 16S rRNA genes were observed, implying that most of the SML Thaumarchaeota lacked amoA. To our knowledge, our results provide the first comparison of ammonia-oxidizing communities in the coastal SML with those in the UW. [ABSTRACT FROM AUTHOR]

Forest ecosystems have great ecological values in mitigation of climate change and protection of biodiversity of flora and fauna; re-forestry is commonly used to enhance the sequestration of atmospheric CO2 into forest storage biomass. Therefore, seasonal and spatial dynamics of the major microbial players in nitrification, ammonia-oxidizing archaea (AOA) and bacteria (AOB), in acidic soils of young and matured revegetated forests were investigated to elucidate the changes of microbial communities during forest restoration, and compared to delineate the patterns of community shifts under the influences of environmental factors. AOA were more abundant than AOB in both young and matured revegetated forest soils in both summer and winter seasons. In summer, however, the abundance of amoA-AOA decreased remarkably (p < 0.01), ranging from 1.90 (± 0.07) × 108 copies per gram dry soil in matured forest to 5.04 (± 0.43) × 108 copies per gram dry soil in young forest, and amoA-AOB was below detection limits to obtain any meaningful values. Moreover, exchangeable Al3+ and organic matter were found to regulate the physiologically functional nitrifiers, especially AOA abundance in acidic forest soils. AOB community in winter showed stronger correlation with the restoration status of revegetated forests and AOA community dominated by Nitrosotalea devanaterra, in contrast, was more sensitive to the seasonal and spatial variations of environmental factors. These results enrich the current knowledge of nitrification during re-forestry and provide valuable information to developmental status of revegetated forests for management through microbial analysis. [ABSTRACT FROM AUTHOR]

Summary: Thaumarchaea are ubiquitous in marine habitats where they participate in carbon and nitrogen cycling. Although metatranscriptomes suggest thaumarchaea are active microbes in marine waters, we understand little about how thaumarchaeal gene expression patterns relate to substrate utilization and activity. Here, we report the global transcriptional response of the marine ammonia‐oxidizing thaumarchaeon ‘Candidatus Nitrosopelagicus brevis’ str. CN25 to ammonia limitation using RNA‐Seq. We further describe the genome and transcriptome of Ca. N. brevis str. U25, a new strain capable of urea utilization. Ammonia limitation in CN25 resulted in reduced expression of transcripts coding for ammonia oxidation proteins, and increased expression of a gene coding an Hsp20‐like chaperone. Despite significantly different transcript abundances across treatments, two ammonia monooxygenase subunits (amoAB), a nitrite reductase (nirK) and both ammonium transporter genes were always among the most abundant transcripts, regardless of growth state. Ca. N. brevis str. U25 cells expressed a urea transporter 139‐fold more than the urease catalytic subunit ureC. Gene coexpression networks derived from culture transcriptomes and 10 thaumarchaea‐enriched metatranscriptomes revealed a high degree of correlated gene expression across disparate environmental conditions and identified a module of coexpressed genes, including amoABC and nirK, that we hypothesize to represent the core ammonia oxidation machinery. [ABSTRACT FROM AUTHOR]

The toxicity of ionic liquids (ILs) on soil organisms has aroused wide attention due to their high-solubility. The present investigation focused on the toxicity of 1-octyl-3-methylimidazolium nitrate ([C 8 mim]NO 3 ) on the microbial populations (bacteria, fungi, and actinomycetes), soil enzyme (urease, dehydrogenase, acid phosphatase, and β-glucosidase) activities, microbial community diversity using terminal restriction fragment length polymorphism (T-RFLP), and abundance of the ammonia monooxygenase (amoA) genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) using quantitative real-time polymerase chain reaction (q-PCR) in brown soil at each trial with doses of 0, 1.0, 5.0, and 10.0 mg/kg on days 10, 20, 30, and 40. The contents of [C 8 mim]NO 3 in soil were measured using high performance liquid chromatography with recoveries of 84.3% to 85.2%, and changed less than 10% during the experimental period. A significant decrease was observed from the bacteria, fungi and actinomycetes populations at 10.0 mg/kg, at which the urease activity was inhibited and the β-glucosidase activity was stimulated on days 20, 30, and 40. In addition, [C 8 mim]NO 3 inhibited the dehydrogenase activity at 10 mg/kg on days 30 and 40 and the acid phosphatase activity on day 20. The diversity of the soil microbial community and the gene abundance of AOA- and AOB- amoA were also inhibited. Furthermore, the present investigation provided more scientific information for the toxicity evaluation of ILs in soil. [ABSTRACT FROM AUTHOR]

With the phase-out of persistent, bioaccumalative, and toxic perfluoroalkyl carboxylic acids (PFCAs), it is needed to explore the potential release of PFCAs from precursors being emitted into the environment. Biotransformation of fluorotelomer alcohols (FTOHs) via biological processes in wastewater treatment plants (WWTPs) leads to discharge of PFCAs into receiving waters. However, the commonly existed microbial activity that can impact on FTOHs biodegradation in WWTPs remains unclear. The objective of present research was to explore the relationship between ammonia-oxidation process and the enhanced PFCAs generation from FTOHs biodegradation under aerobic activated sludge. The obtained results indicate that the cometabolism process performed by nitrifying microorganisms (NMs) was responsible for enhanced PFCAs generation. Among NMs, the ammonia-oxidation bacteria that can express non-specific enzyme of ammonia monooxygenases resulted in the enhanced PFCAs generation from FTOHs. Meanwhile, the different addition amount of ammonia contributed to different defluorination efficiency of FTOHs. The present study further correlated the enhanced PFCAs generation from FTOHs biodegradation with ammonia-oxidation process, which can provide practical information on effective management of PFCAs generation in WWTPs. [ABSTRACT FROM AUTHOR]

Microbial nitrification is a key process in the nitrogen cycle in the continental shelf ecosystems. The genotype compositions and abundance of the ammonia monooxygenase gene, amoA, derived from ammonia-oxidizing archaea (AOA) and bacteria (AOB) in two size fractions (2–10 and 0.2–2 µm), were investigated in the East China Sea (ECS) in May 2008 using PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR). Four sites were selected across the continental shelf edge: continental shelf water (CSW), Kuroshio branch water (KBW), transition between CSW and KBW (TCSKB) and coastal KBW (CKBW). The gene copy numbers of AOA-amoA were higher than those of AOB-amoA in ECS. The relative abundance of amoA to the total 16S rRNA gene level reached approximately 15% in KBW and CKBW for the free-living fraction of AOA, whereas the level was less than 0.01% throughout ECS for the AOB. A cluster analysis of the AOA-amoA-DGGE band pattern showed distinct genotype compositions in CSW in both the size fractions and in the surface of the TCSKB and KBW. Sequences of the DGGE bands were assigned to two clades. One of the clades exclusively consisted of sequences derived from the 2–10-µm fraction. This study revealed that AOA-amoA abundance dominated over AOB-amoA throughout the ECS, whereas the genotype composition of AOA-amoA were distributed heterogeneously across the water masses. Additionally, this is the first report showing the distribution of AOA-amoA genotypes characteristic to particle-associated AOA in the offshore of the East China Sea. [ABSTRACT FROM AUTHOR]

Simultaneous nitrification and denitrification (SND) is a promising single-reactor biological nitrogen-removal method. Activated sludge with and without iron scrap supplementation (Sludge-Fe and Sludge-C, respectively) was acclimated under aerobic condition. The total nitrogen (TN) content of Sludge-Fe substantially decreased from 25.0 ± 1.0 to 11.2 ± 0.4 mg/L, but Sludge-C did not show the TN-removal capacity. Further investigations excluded a chemical reduction of NO3–-N by iron and a decrease of NH4+-N by microbial assimilation, and the contribution of SND was verified. Moreover, the amount of aerobic denitrifiers, such as bacteria belonging to the genera Thauera, Thermomonas, Rhodobacter, and Hyphomicrobium, was considerably enhanced, as observed through Miseq Illumina sequencing method. The activities of the key enzymes ammonia monooxygenase (AMO) and nitrite oxidoreductase (NXR), which are associated with nitrification, and periplasmic nitrate reductase (NAP) and nitrite reductase (NIR), which are related to denitrification, in Sludge-Fe were 1.23-, 1.53-, 3.60-, and 1.55-fold higher than those in Sludge-C, respectively. In Sludge-Fe, the quantity of the functional gene NapA encoding enzyme NAP, which is essential for aerobic denitrification, was significantly promoted. The findings indicate that SND is the primary mechanism underlying the removal of TN and that iron scrap can robustly stimulate SND under aerobic environment. [ABSTRACT FROM AUTHOR]

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH/NH equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al. Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils. [ABSTRACT FROM AUTHOR]

Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically relevant ammonia oxidizers is unfortunately extremely limited. Here, we discuss the challenges and opportunities for examining the ecology of ammonia-oxidizing organisms, particularly uncultivated Thaumarchaeota, through (meta)genome-driven structural biology of the enzymes ammonia monooxygenase (AMO) and nitrite reductase (NirK). [ABSTRACT FROM AUTHOR]

Ammonia-oxidizing marine archaea (mAOA) have been divided into two groups based on ammonia monooxygenase subunit A gene (amoA) phylogeny and they link to preferred habitat (depth in the water column); one is the Shallow Marine Clade (SMC) and the other is the Deep Marine Clade (DMC). Several determinative factors have been proposed to account for their depth-dependent distributions, including light intensity, ammonia concentration, water temperature, and dissolved oxygen concentration. Here, we report the change in abundance of SMC and DMC mAOA in response to nitrogen source and water temperature in a long-term incubation experiment using natural seawaters obtained from mesopelagic and bathypelagic layers. The abundance of each type of mAOA was determined by Q-PCR assay targeting amoA. We found that the abundance of SMC after 266 days of incubation increased at all three incubation temperatures (4, 10, 20°C), whereas the abundance of DMC was stable at low temperatures (4°C and sometimes 10°C) or decreased to below the detection limit at high temperatures (20°C and sometimes 10°C). The SMC abundance was higher in seawater cultures supplied with ammonium than in those supplied with nitrite, although DMC abundance was not responsive to ammonium concentration. These results imply that water temperature and ammonia concentration are significant factors in determining the vertical distribution of the SMC and DMC ecotypes of mAOA in the water column. [ABSTRACT FROM AUTHOR]

Ammonia-oxidizing bacteria (AOB) play an important role in nitrification in estuaries. The aim of this study was to examine the spatial abundance, diversity, and activity of AOB in coastal sediments of the Liaohe Estuary using quantitative PCR, high-throughput sequencing of the amoA gene coding the ammonia monooxygenase enzyme active subunit, and sediment slurry incubation experiments. AOB abundance ranged from 8.54 × 10 to 5.85 × 10 copies g of wet sediment weight and exhibited an increasing trend from the Liaohe Estuary to the open coastal zone. Potential nitrification rates (PNRs) ranged from 0.1 to 336.8 nmol N g day along the estuary to the coastal zone. Log AOB abundance and PNRs were significantly positively correlated. AOB richness decreased from the estuary to the coastal zone. High-throughput sequencing analysis indicated that the majority of amoA gene sequences fell within the Nitrosomonas and Nitrosomonas-like clade, and only a few sequences were clustered within the Nitrosospira clade. This finding indicates that the Nitrosomonas-related lineage may be more adaptable to the specific conditions in this estuary than the Nitrosospira lineage. Sites with high nitrification rates were located in the southern open region and were dominated by the Nitrosomonas-like lineage, whereas the Nitrosospira lineage was found primarily in the northern estuary mouth sites with low nitrification rates. Thus, nitrification potentials in Liaohe estuarine sediments in the southern open region were greater than those in the northern estuary mouth, and the Nitrosomonas-related lineage might play a more important role than the Nitrosospira lineage in nitrification in this estuary. [ABSTRACT FROM AUTHOR]

We performed a 18-month experiment on 0.496 m 3 pots filled with a sandy soil in which 1-year old nectarine trees were grown. With four replicates, the following amendment strategies were compared: a) unamended control; b) biochar (20 g fw kg −1 ); c) compost (76.8 g fw kg −1 ) and d) biocompost (mixing biochar and compost at the same rates of the previous two strategies). Amendments were applied at planting and only unamended and merely biochar-amended soils were fertilized with mineral inputs. Soil mineral N availability was regularly measured and at the end of the experiment, we determined total C and N concentration of soils and aged biochar fragments. Total soil respiration (R TOT ) was separated into soil organic-C derived (R SOC ) and rhizosphere (R R ) respiration by the trenching method. Total soil DNA was extracted from samples collected after 6 and 18 months and bacterial community analysis was carried out by denaturing gradient gel electrophoresis (DGGE). Expression of nitrification key genes of ammonia monooxygenase (AMO) and nitrite oxidoreductase (NOR) and the relative abundance of specific bacterial community ( Nitrosomonas spp. and Nitrobacter spp.) were determined by Real Time PCR on soil samples collected at 6, 12, 15, 16 and 18 months since amendments incorporation. The addition of compost significantly promoted soil mineral N, bacterial diversity and the relative expression of nitrification process related key genes. Furthermore, compost enhanced R SOC likely due to the stimulation of the microbial community by providing labile C sources. Conversely, changes due to the mere addition of biochar were negligible. However, biochar had no detrimental effects, rather it promoted gene expression involved in the nitrification process. A synergic effect between the two amendments emerged in the total soil C and N concentration and in the R SOC , leading to a significantly higher cumulative CO 2 . Although the source of the additional CO 2 rate remains uncertain, a priming effect induced by biochar on the labile compost-derived C-fractions is hypothesized. Compost reduced the relative richness of Arthrobacter spp. in soil, while Actinomadura flavalba , Saccharomonospora viridis , Thermosporomyces composti and Enterobacter spp. were peculiar of the biocompost profile which increased band richness. Biocompost significantly increased the relative abundance of Nitrosomonas spp. and Nitrobacter spp. and both AMO and NOR key genes expression levels. The mixture of biochar and compost seems effective to induce agronomical benefits, although environmental concerns (e.g. additional CO 2 emissions) require further investigations. [ABSTRACT FROM AUTHOR]

The ZnO nanoparticle (NP) effects on typical ammonia-oxidizing bacteria, Nitrosomonas europaea in a chemostat bioreactor, and the cells' toxicity adaptation and recovery potentials were explored. Hardly any inhibition was observed when the NP concentration was high up to 10 mg/L. The cells exposed to 50 mg/L ZnO NPs displayed time-dependent impairment and recovery potentials in terms of cell density, membrane integrity, nitrite production rate, and ammonia monooxygenase activity. The 6-h NP stress impaired cells were nearly completely restored during a 12-h recovery incubation, while the longer exposure time would cause irretrievable cell damage. Microarray analysis further indicated the transcriptional adaptation of N. europaea to NP stress. The regulations of genes encoding for membrane permeability or osmoprotectant, membrane integrity preservation, and inorganic ion transport during NP exposure and cell recovery revealed the importance of membrane fixation and the associated metabolisms for cells' self-protection and the following recovery from NP stress. The oxidative phosphorylation, carbon assimilation, and tricarboxylic acid (TCA) cycling pathways involved in the cells' antitoxicity activities and would promote the energy production/conversion efficiency for cell recovery. The heavy metal resistance, histidine metabolism, toxin-antitoxin defense, glycolysis, and sulfate reduction pathways were also suggested to participate in the cell detoxication and recovery processes. All these findings provided valuable insights into the mechanisms of cell-mediated ZnO NP cytotoxicity and their potential impacts on wastewater nitrogen removal system. [ABSTRACT FROM AUTHOR]

We used soils from a 33-year fertilizer experiment and performed high-throughput pyrosequencing analyses targeting the ammonia monooxygenase alpha subunit ( amoA ) gene (also qPCR and terminal restricted fragment length polymorphism (T-RFLP)) to determine whether and how the composition and structure of ammonia-oxidizing microbes in different particle-size fractions (>2000, 2000–200, 200–63, 63–2 and 2–0.1 μm) have changed in response to chronic inorganic (NPK) and organic (NPKM) fertilizer additions under a rice-wheat rotation. We found fertilization and particle-size fractions had strong effects on abundance and structure of ammonia-oxidizers and potential nitrification activity (PNA) ( P < 0.05) which was significantly enhanced under NPKM across all soil fractions. PNA was higher in clay fraction and lowest in silt fraction which was largely correlated to total N and C:N ratio. Aggregated boosted tree emphasized the role that total N and C:N ratio play on ammonia oxidizer abundance. Pyrosequencing data revealed that the Nitrososphaera and Nitrosospira were the dominant clusters of ammonia-oxidizing archaea (AOA) and bacteria (AOB), respectively. Even though AOA population was hundreds of times greater than AOB, it seemed AOB responded more sensitively to ambient shifts which was convinced by NMDS analyses based on Bray-Curtis distance of TRFs and also of OTUs from 454 pyrosequencing. [ABSTRACT FROM AUTHOR]

Many countries have begun to mandate the replacement of fossil fuels with biofuels. However, the impact of crop residue removal for biofuel feedstock on greenhouse gas emissions is poorly studied, particularly in terms of linkages to soil microorganisms. If soils from which residues are removed for biofuel feedstock produce additional N 2 O, this lessens the advantages of reduced carbon dioxide production from use of biofuels. Our first objective was to determine if there are relationships between residue removal, altered N 2 O emissions, physicochemical soil characteristics (ammonium and nitrate levels, dissolved organic carbon (DOC) and gravimetric water content), and the community composition of four different bacterial nitrifier/denitrifier genes. Our second objective was to use indicator species analysis to identify bacterial gene sequences (clustered into operational taxonomic units, or OTUs) that were most responsible for any observed shifts in measured nitrifier or denitrifier gene community composition. We chose to study two conventionally tilled fields of the same soil type that are situated adjacent to each other, which had been under contrasting corn-soybean residue management for two years prior to our study. We monitored field-scale soil nitrous oxide (N 2 O) emissions using micro-meterological techniques, and the community structures of soil bacteria carrying nitrifying/denitrifying genes (ammonia monooxygenase, amoA , nitrite reductases, nirS and nirK , and typical nitrous oxide reductase nosZ )using next-generation sequencing (NGS). Two years of corn or soybean residue removal (R−) in this system resulted in significantly higher levels of field-scale N 2 O emissions as well as contrasting edaphic conditions to residue retention (R+) over the seven month period evaluated, with significantly lower dissolved organic carbon (DOC), lower ammonia (NH 4 + -N) and higher nitrate (NO 3 -N) in the R− field. In addition, the community structure of the nitrification ( amoA ) and denitrification genes ( nirS/nirK and nosZ ) present in soil microoganisms was significantly different in each field and varied as ammonium levels (R+) or DOC or water content (R−) varied (all relationships were positive). Indicator species analysis found sequences (clustered into operational taxonomic units, or OTUs) that drive community shifts between fields or sampling times. Such indicator OTUs varied phylogenetically between R+ and R− fields and some were positively (0% amoA , 11% nirK , 11% nirS , 17% nosZ ) or negatively (22% amoA , 4% nirK , 4% nirS , 4% nosZ ) correlated with levels of N 2 O flux. Our work demonstrates that bacterial nitrifier/denitrifier community structure is important in the extent of in situ N 2 O release from agricultural soils, and that the relative abundances of specific OTUs may be more informative than overall diversity or richness when evaluating community functioning. [ABSTRACT FROM AUTHOR]

Microbial nitrification in soils is a major contributor to nitrogen (N) loss in agricultural systems. Some plants can secrete organic substances that act as biological nitrification inhibitors ( BNIs), and a small number of BNIs have been identified and characterized. However, virtually no research has focused on the important food crop, rice ( Oryza sativa)., Here, 19 rice varieties were explored for BNI potential on the key nitrifying bacterium Nitrosomonas europaea. Exudates from both indica and japonica genotypes were found to possess strong BNI potential. Older seedlings had higher BNI abilities than younger ones; Zhongjiu25 ( ZJ25) and Wuyunjing7 ( WYJ7) were the most effective genotypes among indica and japonica varieties, respectively., A new nitrification inhibitor, 1,9-decanediol, was identified, shown to block the ammonia monooxygenase ( AMO) pathway of ammonia oxidation and to possess an 80% effective dose ( ED80) of 90 ng μl−1. Plant N-use efficiency ( NUE) was determined using a 15N-labeling method. Correlation analyses indicated that both BNI abilities and 1,9-decanediol amounts of root exudates were positively correlated with plant ammonium-use efficiency and ammonium preference., These findings provide important new insights into the plant-bacterial interactions involved in the soil N cycle, and improve our understanding of the BNI capacity of rice in the context of NUE. [ABSTRACT FROM AUTHOR]

To investigate the nitrification potential of phyllospheric microbes, we incubated throughfall samples collected under the canopies of Japanese cedar ( Cryptomeria japonica) and analyzed the transformation of inorganic nitrogen in the samples. Nitrate concentration increased in the unfiltered throughfall after 4 weeks of incubation, but remained nearly constant in the filtered samples (pore size: 0.2 and 0.4 µm). In the unfiltered samples, δO and δN values of nitrate decreased during incubation. In addition, archaeal ammonia monooxygenase subunit A ( amoA) genes, which participate in the oxidation of ammonia, were found in the throughfall samples, although betaproteobacterial amoA genes were not detected. The amoA genes recovered from the leaf surface of C. japonica were also from archaea. Conversely, nitrate production, decreased isotope ratios of nitrate, and the presence of amoA genes was not observed in rainfall samples collected from an open area. Thus, the microbial nitrification that occurred in the incubated throughfall is likely due to ammonia-oxidizing archaea that were washed off the tree canopy by precipitation. [ABSTRACT FROM AUTHOR]

In biofilm systems for wastewater treatment (e.g., moving bed biofilms reactors--MBBRs) biofilm thickness is typically not under direct control. Nevertheless, biofilm thickness is likely to have a profound effect on the microbial diversity and activity, as a result of diffusion limitation and thus substrate penetration in the biofilm. In this study, we investigated the impact of biofilm thickness on nitrification and on the removal of more than 20 organic micropollutants in laboratory-scale nitrifying MBBRs. We used novel carriers (Z-carriers, AnoxKaldnes) that allowed controlling biofilm thickness at 50, 200, 300, 400, and 500 pm. The impact of biofilm thickness on microbial community was assessed via 16S rRNA gene amplicon sequencing and ammonia monooxygenase (amoA) abundance quantification through quantitative PCR (qPCR). Results from batch experiments and microbial analysis showed that (i) the thickest biofilm (500 μm) presented the highest specific biotransformation rate constants (κbio, L g-1 d-1) for 14 out of 22 micropollutants; (ii) biofilm thickness positively associated with biodiversity, which was suggested as the main factor for the observed enhancement of κbio, (iii) the thinnest biofilm (50 μm) exhibited the highest nitrification rate (gN d-1 g-1), amoA gene abundance and κbio values for some of the most recalcitrant micropollutants (i.e., diclofenac and targeted sulfonamides). Although thin biofilms favored nitrification activity and the removal of some micropollutants, treatment systems based on thicker biofilms should be considered to enhance the elimination of a broad spectrum of micropollutants. [ABSTRACT FROM AUTHOR]

Forest canopy structure controls the timing, amount, and chemical character of precipitation supply to soils through interception and drainage along crown surfaces (primarily as throughfall). Yet, few studies have examined forest canopy structural connections to soil microbial communities, and none have measured how throughfall affects microbial nitrogen (N) functions. Maritime Quercus virginiana Mill. (southern live oak) forests on St Catherine’s Island (GA, USA) provide an ideal venue to study this interaction as its throughfall patterns are spatially heterogeneous due to the arboreal epiphyte, Tillandsia usneoides L. (Spanish moss), and its edaphic conditions are relatively homogeneous. To test the hypothesis that throughfall patterns alter soil microbial community N-function, we examined soil microbial community N-functional (ammonia oxidizing and chitinolytic) genes, soil chemistry/texture, and throughfall amounts/chemistry for points along a canopy coverage continuum: large canopy gaps (0%), bare Q . virginiana canopy (50–60%), and Q . virginiana canopy hosting heavy T . usneoides (>=85%) over a typical growing season (Mar–Sep 2014). Denaturing Gradient Gel Electrophoresis (DGGE) and quantitative Polymerase Chain Reaction (qPCR) analyses were used to assess changes in the diversity and abundance, respectively, of soil chitinolytic bacterial and ammonia oxidizing archaeal genes. Significant differences in throughfall water and solute delivery (Na + , Cl − , PO 4 3− , SO 4 2− , K + , Ca 2+ , NO 3 − , NH 4 + ) were found to alter soil sodicity and salinity. Diversity of chitinolytic bacterial and ammonia oxidizing archaeal communities significantly differed across cover classes and negatively correlated to soil salinity, soil Na + concentration, and throughfall Cl − , SO 4 2− , and PO 4 3- concentrations. Results suggest throughfall can alter patterns in the soil microbial community’s N-functional gene diversity. [ABSTRACT FROM AUTHOR]

Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments. [ABSTRACT FROM AUTHOR]

Metagenomic sequencing was used to investigate the microbial structures, functional potentials, and biofouling-related genes in a membrane bioreactor (MBR). The results showed that the microbial community in the MBR was highly diverse. Notably, function analysis of the dominant genera indicated that common genes from different phylotypes were identified for important functional potentials with the observation of variation of abundances of genes in a certain taxon (e.g., Dechloromonas). Despite maintaining similar metabolic functional potentials with a parallel full-scale conventional activated sludge (CAS) system due to treating the identical wastewater, the MBR had more abundant nitrification-related bacteria and coding genes of ammonia monooxygenase, which could well explain its excellent ammonia removal in the low-temperature period. Furthermore, according to quantification of the genes involved in exopolysaccharide and extracellular polymeric substance (EPS) protein metabolism, the MBR did not show a much different potential in producing EPS compared to the CAS system, and bacteria from the membrane biofilm had lower abundances of genes associated with EPS biosynthesis and transport compared to the activated sludge in the MBR. [ABSTRACT FROM AUTHOR]

Nitrosomonas europaea is a chemolithoautotrophic bacterium that oxidizes ammonia (NH3) to obtain energy for growth on carbon dioxide (CO2) and can also produce nitrous oxide (N2O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses of N. europaea to conditions of replete (>5.2 mM) and limited inorganic carbon (IC) provided by either 1.0mMor 0.2mMsodium carbonate (Na2CO3) supplemented with atmospheric CO2. IC-limited cultures oxidized 25 to 58% of available NH3 to nitrite, depending on the dilution rate and Na2CO3 concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to those for NH3-limited cultures. Rates of N2O production increased 2.5- and 6.3-fold under the two IC-limited conditions, increasing the percentage of oxidized NH3-N that was transformed to N2O-N from 0.5% (replete) up to 4.4% (0.2 mM Na2CO3). Transcriptome analysis showed differential expression (P < 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in a decreased expression of ammonium/ ammonia transporter and ammonia monooxygenase subunits and increased the expression of genes involved in C1 metabolism, including the genes for RuBisCO (cbb gene cluster), carbonic anhydrase, folate-linked metabolism of C1 moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924 to NE0927) correlated with increased production of N2O. Together, these data suggest that N. europaea adapts physiologically during IC-limited steady-state growth, which leads to the uncoupling of NH3 oxidation from growth and increased N2O production. [ABSTRACT FROM AUTHOR]

Microbes are abundant in nature and often highly adapted to local conditions. While great progress has been made in understanding the ecological factors driving their distribution in complex environments, the underpinning molecular-evolutionary mechanisms are rarely dissected. Therefore, we scrutinized the coupling of environmental and molecular adaptation in Thaumarchaeota, an abundant archaeal phylum with a key role in ammonia oxidation. These microbes are adapted to a diverse spectrum of environmental conditions, with pH being a key factor shaping their contemporary distribution and evolutionary diversification. We integrated high-throughput sequencing data spanning a broad representation of ammonia-oxidizing terrestrial lineages with codon modelling analyses, testing the hypothesis that ammonia monooxygenase subunit A (AmoA) - a highly conserved membrane protein crucial for ammonia oxidation and classical marker in microbial ecology - underwent adaptation during specialization to extreme pH environments. While purifying selection has been an important factor limiting AmoA evolution, we identified episodic shifts in selective pressure at the base of two phylogenetically distant lineages that independently adapted to acidic conditions and subsequently gained lasting ecological success. This involved nonconvergent selective mechanisms (positive selection vs. selection acting on variants fixed during an episode of relaxed selection) leading to unique sets of amino acid substitutions that remained fixed across the radiation of both acidophilic lineages, highlighting persistent adaptive value in acidic environments. Our data demonstrates distinct trajectories of AmoA evolution despite convergent phenotypic adaptation, suggesting that microbial environmental specialization can be associated with diverse signals of molecular adaptation, even for marker genes employed routinely by microbial ecologists. [ABSTRACT FROM AUTHOR]

Community composition and abundance of ammonia-oxidizing archaea (AOA) were investigated using ammonia monooxygenase α subunit (amoA) in sediments from the Changjiang estuary and its adjacent area in the East China Sea (ECS). Real-time quantitative polymerase chain reaction (qPCR), clone libraries and sequencing were performed to characterize the AOA community. Clone libraries analysis showed that the majority ofamoAsequences fell within theNitrosopumiluscluster. Correlation analysis showed that AOA diversity was closely related to the nitrite concentration, which was consistent with the canonical correspondence analysis (CCA) where a significant association between nitrite and AOA community composition was observed. The qPCR results were found to be significantly correlated with the environmental parameters. In the gravity cores, a significant positive correlation was found between ammonium concentrations andamoAgene copy numbers from different sediment depths at station S31. At station S33, however, ammonium concentration had a negative correlation and nitrite concentration had a positive correlation withamoAgene copy numbers. In the surface sediments, chlorophyllaconcentration had a negative correlation and nitrate concentration had a positive correlation withamoAgene copy numbers. ComparedamoAgene copy numbers from AOA with those from ammonia-oxidizing β-proteobacteria (β-AOB) in the same studied areas, theamoAgene copy ratio of β-AOB to AOA was negatively correlated with the phosphate concentration and dissolved oxygen concentration, but was not significantly correlated with either ammonium concentrations or salinity. Our data provided valuable information to achieve a better understanding of the potential role of ammonia oxidizers at the interface between terrestrial and marine environments. [ABSTRACT FROM PUBLISHER]

Nitrosomonas europaea is an aerobic nitrifying bacterium that oxidizes ammonia (NH3) to nitrite (NO2-) through the sequential activities of ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase (HAO). Many alkynes are mechanismbased inactivators of AMO, and here we describe an activity-based protein profiling method for this enzyme using 1,7-octadiyne (17OD) as a probe. Inactivation of NH4+-dependent O2 uptake by N. europaea by 17OD was time- and concentration-dependent. The effects of 17OD were specific for ammonia-oxidizing activity, and de novo protein synthesis was required to reestablish this activity after cells were exposed to 17OD. Cells were reacted with Alexa Fluor 647 azide using a copper-catalyzed azidealkyne cycloaddition (CuAAC) (click) reaction, solubilized, and analyzed by SDS-PAGE and infrared (IR) scanning. A fluorescent 28-kDa polypeptide was observed for cells previously exposed to 17OD but not for cells treated with either allylthiourea or acetylene prior to exposure to 17OD or for cells not previously exposed to 17OD. The fluorescent polypeptide was membrane associated and aggregated when heated with β-mercaptoethanol and SDS. The fluorescent polypeptide was also detected in cells pretreated with other diynes, but not in cells pretreated with structural homologs containing a single ethynyl functional group. The membrane fraction from 17OD-treated cells was conjugated with biotin-azide and solubilized in SDS. Streptavidin affinity-purified polypeptides were on-bead trypsin-digested, and amino acid sequences of the peptide fragments were determined by liquid chromatography-mass spectrometry (LC-MS) analysis. Peptide fragments from AmoA were the predominant peptides detected in 17OD-treated samples. In-gel digestion and matrix-assisted laser desorption ionization-tandem time of flight (MALDI-TOF/TOF) analyses also confirmed that the fluorescent 28-kDa polypeptide was AmoA. [ABSTRACT FROM AUTHOR]

Ammonia-oxidizing microorganisms are partly responsible for the production of N 2 O, a potent greenhouse gas. Rice paddies provide a habitat where ammonia oxidizing microorganisms can be active. The influence of different agricultural practices on these microorganisms, particularly on archaeal ammonia oxidizers, is an active field of research. In this work, we conducted two greenhouse experiments where we analyzed the influence of two soil types with different organic matter contents, two rice cultivars and water management on both archaeal (AOA) and bacterial (AOB) ammonia oxidizers. We determined the AOA and AOB abundance and population structure by q-PCR and T-RFLP, respectively. The archaeal and bacterial ammonia monooxygenase subunit A gene was used as the PCR target. The AOA and AOB copy numbers were affected by sampling time in both experiments. AOA abundance was also influenced by the time of flooding. The population structure of AOA was more variable than that of AOB and was strongly determined by soil type. Changes in AOB population structure were observed mainly according to sampling time. [ABSTRACT FROM AUTHOR]

Nitrifying wastewater treatment plants (WWTPs) are more efficient than non-nitrifying WWTPs to remove several micropollutants such as pharmaceuticals and pesticides. This may be related to the activity of nitrifying organisms, such as ammonia-oxidizing bacteria (AOBs), which could possibly co-metabolically oxidize micropollutants with their ammonia monooxygenase (AMO). The role of AOBs in micropollutant removal was investigated with aerobic granular sludge (AGS), a promising technology for municipal WWTPs. Two identical laboratory-scale AGS sequencing batch reactors (AGS-SBRs) were operated with or without nitrification (inhibition of AMOs) to assess their potential for micropollutant removal. Of the 36 micropollutants studied at 1 µg l-1 in synthetic wastewater, nine were over 80% removed, but 17 were eliminated by less than 20%. Five substances (bisphenol A, naproxen, irgarol, terbutryn and iohexol) were removed better in the reactor with nitrification, probably due to co-oxidation catalysed by AMOs. However, for the removal of all other micropollutants, AOBs did not seem to play a significant role. Many compounds were better removed in aerobic condition, suggesting that aerobic heterotrophic organisms were involved in the degradation. As the AGS-SBRs did not favour the growth of such organisms, their potential for micropollutant removal appeared to be lower than that of conventional nitrifying WWTPs. [ABSTRACT FROM AUTHOR]

The effect of nitrification, nitratation and heterotrophic conditions on the biotransformation of several pharmaceuticals in a highly enriched nitrifying activated sludge was evaluated in this study by selective activation of ammonia oxidizing bacteria (AOB), nitrite oxidizing bacteria (NOB) and heterotrophic bacteria. Nitrifiers displayed a noticeable capacity to process ibuprofen due to hydroxylation by ammonia monooxygenase (AMO) to produce 2-hydroxy-ibuprofen. Naproxen was also biotransformed under nitrifying conditions. On the other hand, heterotrophic bacteria present in the nitrifying activated sludge (NAS) biotransformed sulfamethoxazole. In contrast, both nitrifying and heterotrophic activities were ineffective against diclofenac, diazepam, carbamazepine and trimethoprim. Similar biotransformation rates of erythromycin, roxithromycin and fluoxetine were observed under all conditions tested. Overall, results from this study give more evidence on the role of the different microbial communities present in activated sludge reactors on the biological removal of pharmaceuticals. [ABSTRACT FROM AUTHOR]

Oxygen is considered as a limiting factor for nitrification in rice paddy soil. However, little is known about how the nitrifying microbial community responds to different oxygen concentrations at community and transcript level. In this study, soil and roots were harvested from 50-day-old rice microcosms and were incubated for up to 45 days under two oxygen concentrations: 2 % O and 20 % O (ambient air). Nitrification rates were measured from the accumulation of nitrite plus nitrate. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was determined from the abundance (using quantitative PCR (qPCR)) and composition (using terminal restriction fragment length polymorphism and cloning/sequencing) of their amoA genes, that of nitrite oxidizers (NOB) by quantifying the nxrA gene of Nitrobacter spp. and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by quantifying the copy numbers of amoA and nxrA transcripts (using RT-qPCR). Different oxygen concentrations did not affect the community compositions of AOB, AOA, and NOB, which however were different between surface soil, bottom soil, and rice roots. However, nitrification rates were higher under ambient air than 2 % O, and abundance and transcript activities of AOB, but not of AOA, were also higher. Abundance and transcript copy numbers of Nitrobacter were also higher at ambient air. These results indicate that AOB and NOB, but not AOA, were sensitive to oxygen availability. [ABSTRACT FROM AUTHOR]

The distribution of isoprenoid glycerol dialkyl glycerol tetraethers ( GDGT) lipids synthesized by Thaumarchaeota has been shown to be temperature-dependent in world oceans. Depth-related differences in the ammonia monooxygenase ( amo A) of Thaumarchaeota have led to the classification of 'shallow' and 'deep water' clusters, potentially affecting GDGT distributions. Here, we investigate if this classification is also reflected in a key gene of the thaumarchaeotal lipid biosynthetic pathway coding for geranylgeranylglyceryl phosphate ( GGGP) synthase. We investigated metagenomic databases, suspended particulate matter and surface sediment of the Arabian Sea oxygen minimum zone. These revealed significant differences in amo A and GGGP synthase between 'shallow' and 'deep water' Thaumarchaeota. Intriguingly, amo A and GGGP synthase sequences of benthic Thaumarchaeota clustered with the 'shallow water' rather than with 'deep water' Thaumarchaeota. This suggests that pressure and temperature are unlikely factors that drive the differentiation, and suggests an important role of ammonia concentration that is higher in benthic and 'shallow water' niches. Analysis of the relative abundance of GDGTs in the Arabian Sea and in globally distributed surface sediments showed differences in GDGT distributions from subsurface to deep waters that may be explained by differences in the GGGP synthase, suggesting a genetic control on GDGT distributions. [ABSTRACT FROM AUTHOR]

Backgrounds and aims: Nitrogen (N) cycling in agro-ecosystems is likely to change under elevated O (eO) as a result of changes in plant material inputs to soils. The objective of this study was to understand how eO could change key N cycling processes in soils. Methods: Rhizosphere soils were collected from sensitive and tolerant wheat cultivars following a 5-year fumigation of O at 60 ppb (eO) and at ambient 40 ppb (aO) in a free-air ozone enrichment platform. Soil nitrifying and denitrifying enzyme activity (NEA and DEA), abundance of ammonia monooxygenase( amoA) and denitrifying bacteria genes( nirS and nirK), and other related properties were quantified. Results: Soil NEA, DEA, NH and NO were higher under eO than under aO, whereas microbial biomass N (MBN) decreased under eO, especially with the O-sensitive cultivar. No clear eO effect was observed on the abundance of amoA and nirS and nirK. Grain yield and shoot to root ratios decreased as a result of eO in the O-sensitive cultivar. Conclusions: eO stimulates soil N availability, but suppresses grain yields after 5 years, especially for the O-sensitive cultivar. Adaptive strategies should focus more on cultivar selection to retain N in soil and to assure the resilience of crop production in the future. [ABSTRACT FROM AUTHOR]

In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to compete with many different organisms for ammonium and are often exposed to long periods of ammonium starvation. We investigated the effect of ammonium starvation on ammonia-oxidizing archaea (AOA) and bacteria (AOB) enriched from freshwater lake sediments. Both AOA and AOB were able to recover even after almost two months of starvation; however, the recovery time differed. AOA and AOB retained their 16S rRNA (ribosomes) throughout the complete starvation period. The AOA retained also a small portion of the mRNA of the ammonia monooxygenase subunit A (amoA) for the complete starvation period. However, after 10 days, no amoA mRNA was detected anymore in the AOB. These results indicate that AOA and AOB are able to survive longer periods of starvation, but might utilize different strategies. [ABSTRACT FROM AUTHOR]

Sediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of < 10 μM in oligotrophic abyssal plain sediments near the South Atlantic Gyre compared with ammonium concentrations of > 700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities ( AOA and AOB) along a transect of seven sediment stations across the Namibian shelf by analysing their respective ammonia monooxygenase genes ( amoA). The relative abundance of archaeal and bacterial amoA (g−1 DNA) decreased with increasing ammonium concentrations, and bacterial amoA frequently outnumbered archaeal amoA at the sediment-water interface [0-1 cm below seafloor (cmbsf)]. In contrast, AOA were apparently as abundant as AOB or dominated in several deeper (> 10 cmbsf), anoxic sediment layers. Phylogenetic analyses showed a change within the AOA community along the transect, from two clusters without cultured representatives at the gyre to N itrososphaera and N itrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the N itrosospira cluster 1. Our results suggest that this predominantly marine AOB lineage without cultured representatives can thrive at low ammonium concentrations and is active in the marine nitrogen cycle. [ABSTRACT FROM AUTHOR]

Ammonia-oxidizing archaea ( AOA) and bacteria ( AOB) fill key roles in the nitrogen cycle. Thus, well-vetted methods for characterizing their distribution are essential for framing studies of their significance in natural and managed systems. Quantification of the gene coding for one subunit of the ammonia monooxygenase ( amoA) by polymerase chain reaction is frequently employed to enumerate the two groups. However, variable amplification of sequence variants comprising this conserved genetic marker for ammonia oxidizers potentially compromises within- and between-system comparisons. We compared the performance of newly designed non-degenerate quantitative polymerase chain reaction primer sets to existing primer sets commonly used to quantify the amoA of AOA and AOB using a collection of plasmids and soil DNA samples. The new AOA primer set provided improved quantification of model mixtures of different amoA sequence variants and increased detection of amoA in DNA recovered from soils. Although both primer sets for the AOB provided similar results for many comparisons, the new primers demonstrated increased detection in environmental application. Thus, the new primer sets should provide a useful complement to primers now commonly used to characterize the environmental distribution of AOA and AOB. [ABSTRACT FROM AUTHOR]

In drinking water, monochloramine may promote ammonia–oxidizing bacteria (AOB) growth because of concurrent ammonia presence. AOB use (i) ammonia monooxygenase for biological ammonia oxidation to hydroxylamine and (ii) hydroxylamine oxidoreductase for biological hydroxylamine oxidation to nitrite. In addition, monochloramine and hydroxylamine abiotically react, providing AOB a potential benefit by removing the disinfectant (monochloramine) and releasing growth substrate (ammonia). Alternatively and because biological hydroxylamine oxidation supplies the electrons (reductant) required for biological ammonia oxidation, the monochloramine/hydroxylamine abiotic reaction represents a possible inactivation mechanism by consuming hydroxylamine and inhibiting reductant generation. To investigate the abiotic monochloramine and hydroxylamine reaction's impact on AOB activity, the current study used batch experiments with Nitrosomonas europaea (AOB pure culture), ammonia, monochloramine, and hydroxylamine addition. To decipher whether hydroxylamine addition benefitted N. europaea activity by (i) removing monochloramine and releasing free ammonia or (ii) providing an additional effect (possibly the aforementioned reductant source), a previously developed cometabolism model was coupled with an abiotic monochloramine and hydroxylamine model for data interpretation. N. europaea maintained ammonia oxidizing activity when hydroxylamine was added before complete ammonia oxidation cessation. The impact could not be accounted for by monochloramine removal and free ammonia release alone and was concentration dependent for both monochloramine and hydroxylamine. In addition, a preferential negative impact occurred for ammonia versus hydroxylamine oxidation. These results suggest an additional benefit of exogenous hydroxylamine addition beyond monochloramine removal and free ammonia release, possibly providing reductant generation. [ABSTRACT FROM AUTHOR]