Ammonia Oxidizer

14,000,000 Leading Edge Experts on the ideXlab platform

Scan Science and Technology

Contact Leading Edge Experts & Companies

Scan Science and Technology

Contact Leading Edge Experts & Companies

The Experts below are selected from a list of 14670 Experts worldwide ranked by ideXlab platform

James I Prosser - One of the best experts on this subject based on the ideXlab platform.

  • Abiotic Conversion of Extracellular NH2OH Contributes to N2O Emission during Ammonia Oxidation
    2017
    Co-Authors: Shurong Liu, Michael Wagner, James I Prosser, Ping Han, Linda Hink, Nicolas Brüggemann
    Abstract:

    Abiotic processes involving the reactive Ammonia-oxidation intermediates nitric oxide (NO) or hydroxylamine (NH2OH) for N2O production have been indicated recently. The latter process would require the availability of substantial amounts of free NH2OH for chemical reactions during Ammonia (NH3) oxidation, but little is known about extracellular NH2OH formation by the different clades of Ammonia-oxidizing microbes. Here we determined extracellular NH2OH concentrations in culture media of several Ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as one complete Ammonia Oxidizer (comammox) enrichment (Ca. Nitrospira inopinata) during incubation under standard cultivation conditions. NH2OH was measurable in the incubation media of Nitrosomonas europaea, Nitrosospira multiformis, Nitrososphaera gargensis, and Ca. Nitrosotenuis uzonensis, but not in media of the other tested AOB and AOA. NH2OH was also formed by the comammox enrichment during NH3 oxidation. This enrichment exhibited the largest NH2OH:final product ratio (1.92%), followed by N. multiformis (0.56%) and N. gargensis (0.46%). The maximum proportions of NH4+ converted to N2O via extracellular NH2OH during incubation, estimated on the basis of NH2OH abiotic conversion rates, were 0.12%, 0.08%, and 0.14% for AOB, AOA, and Ca. Nitrospira inopinata, respectively, and were consistent with published NH4+:N2O conversion ratios for AOB and AOA

  • cultivation of an obligate acidophilic Ammonia Oxidizer from a nitrifying acid soil
    Proceedings of the National Academy of Sciences of the United States of America, 2011
    Co-Authors: Laura E Lehtovirtamorley, James I Prosser, Kilian Stoecker, Andreas Vilcinskas, Graeme W Nicol
    Abstract:

    Nitrification is a fundamental component of the global nitrogen cycle and leads to significant fertilizer loss and atmospheric and groundwater pollution. Nitrification rates in acidic soils (pH < 5.5), which comprise 30% of the world's soils, equal or exceed those of neutral soils. Paradoxically, autotrophic Ammonia oxidizing bacteria and archaea, which perform the first stage in nitrification, demonstrate little or no growth in suspended liquid culture below pH 6.5, at which Ammonia availability is reduced by ionization. Here we report the discovery and cultivation of a chemolithotrophic, obligately acidophilic thaumarchaeal Ammonia Oxidizer, "Candidatus Nitrosotalea devanaterra," from an acidic agricultural soil. Phylogenetic analysis places the organism within a previously uncultivated thaumarchaeal lineage that has been observed in acidic soils. Growth of the organism is optimal in the pH range 4 to 5 and is restricted to the pH range 4 to 5.5, unlike all previously cultivated Ammonia Oxidizers. Growth of this organism and associated Ammonia oxidation and autotrophy also occur during nitrification in soil at pH 4.5. The discovery of Nitrosotalea devanaterra provides a previously unsuspected explanation for high rates of nitrification in acidic soils, and confirms the vital role that thaumarchaea play in terrestrial nitrogen cycling. Growth at extremely low Ammonia concentration (0.18 nM) also challenges accepted views on Ammonia uptake and metabolism and indicates novel mechanisms for Ammonia oxidation at low pH.

  • Growth of Ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene
    FEMS microbiology ecology, 2009
    Co-Authors: Pierre Offre, James I Prosser, Graeme W Nicol
    Abstract:

    Autotrophic Ammonia-oxidizing bacteria were considered to be responsible for the majority of Ammonia oxidation in soil until the recent discovery of the autotrophic Ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal Ammonia Oxidizers to soil Ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 degrees C, and the effect of an inhibitor of Ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial Ammonia Oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are Ammonia Oxidizers. Growth of only archaeal but not bacterial Ammonia Oxidizers occurred in microcosms with active nitrification, indicating that Ammonia oxidation was mostly due to archaea in the conditions of the present study.

  • pcr profiling of Ammonia Oxidizer communities in acidic soils subjected to nitrogen and sulphur deposition
    FEMS Microbiology Ecology, 2007
    Co-Authors: C S Schmidt, Kristine A Hultman, David Robinson, Ken Killham, James I Prosser
    Abstract:

    Communities of Ammonia-oxidizing bacteria (AOB) were characterized in two acidic soil sites experimentally subjected to varying levels of nitrogen and sulphur deposition. The sites were an acidic spruce forest soil in Deepsyke, Southern Scotland, with low background deposition, and a nitrogen-saturated upland grass heath in Pwllpeiran, North Wales. Betaproteobacterial Ammonia-Oxidizer 16S rRNA and Ammonia monooxygenase (amoA) genes were analysed by cloning, sequencing and denaturing gradient gel electrophoresis (DGGE). DGGE profiles of amoA and 16S rRNA gene fragments from Deepsyke soil in 2002 indicated no effect of nitrogen deposition on AOB communities, which contained both Nitrosomonas europaea and Nitrosospira. In 2003, only Nitrosospira could be detected, and no amoA sequences could be retrieved. These results indicate a decrease in the relative abundance of AOB from the year 2002 to 2003 in Deepsyke soil, which may be the result of the exceptionally low rainfall in spring 2003. Nitrosospira-related sequences from Deepsyke soil grouped in all clusters, including cluster 1, which typically contains only sequences from marine environments. In Pwllpeiran soil, 16S rRNA gene libraries were dominated by nonAmmonia Oxidizers and no amoA sequences were detectable. This indicates that autotrophic AOB play only a minor role in these soils even at high nitrogen deposition.

  • comparison of pcr primer based strategies for characterization of Ammonia Oxidizer communities in environmental samples
    FEMS Microbiology Ecology, 2006
    Co-Authors: Shahid Mahmood, Thomas E Freitag, James I Prosser
    Abstract:

    PCR-based techniques are commonly used to characterize microbial communities, but are subject to bias that is difficult to assess. This study aimed to evaluate bias of several PCR primer-based strategies used to study diversity of autotrophic Ammonia Oxidizers. 16S rRNA genes from soil- or sediment-DNA were amplified using primers considered either selective or specific for betaproteobacterial Ammonia Oxidizers. Five approaches were assessed: (a) amplification with primers βAMO143f-βAMO1315r; (b) amplification with primers CTO189f-CTO654r; (c) nested amplification with βAMO143f-βAMO1315r followed by CTO189f-CTO654r primers; (d) nested amplification with βAMO143f-βAMO1315r and CTO189f-Pf1053r primers; (e) nested amplification with 27f-1492r and CTO189f-CTO654r primers. Amplification products were characterized by denaturing gradient gel electrophoresis (DGGE) analysis after further amplification with 357f-GC-518r primers. DGGE profiles of soil communities were heterogeneous and depended on the approach followed. Ammonia Oxidizer diversity was higher using approaches (b), (c) and (e) than using (a) and (d), where sequences of the most prominent bands showed similarities to nonAmmonia Oxidizers. Profiles from marine sediments were more consistent, regardless of the approach adopted, and sequence analysis of excised bands indicated that these consisted of Ammonia Oxidizers only. The study demonstrates the importance of choice of primer, of screening for sequences of nontarget organisms and use of several approaches when characterizing microbial communities in natural environments.

Huaiying Yao - One of the best experts on this subject based on the ideXlab platform.

  • Biological nitrification inhibition by sorghum root exudates impacts Ammonia-oxidizing bacteria but not Ammonia-oxidizing archaea
    Biology and Fertility of Soils, 2021
    Co-Authors: Yang Zhang, Stephen Chapman, Huaiying Yao
    Abstract:

    Sorghum has a great capacity to release biological nitrification inhibitors (BNIs), but the inhibitory effect on nitrification and Ammonia Oxidizer populations under planted soil conditions is unclear. A pot experiment with three nitrogen (N) application rates (0, 50, and 200 mg N kg−1) was set up to detect the influence of sorghum growth on soil nitrification and investigate the function of blocking the activity of Ammonia Oxidizers. A 15N-labeled experiment was also conducted to detect the N form absorbed by sorghum. Sorghum root exudates were collected at 30 days after transplanting to hydroponic culture and added into cultured soil to determine the shifts in the populations of nitrifiers. The 15N labeling experiment showed that the uptake rate by sorghum of ammonium N fertilizer was 24% and that of nitrate N fertilizer was 9%, indicating that sorghum was an ammonium using plant. Compared with unplanted soil, sorghum planting had a significant inhibitory effect on the nitrification process even at the high-N fertilizer rates. Autotrophic nitrification was the prevailing process, and sorghum root exudation inhibited this process as much as dicyandiamide (DCD, 10 mg kg−1). Root exudates had a significant inhibitory effect on Ammonia-oxidizing bacteria (AOB) but had no effect on Ammonia-oxidizing archaea (AOA).

  • nitrous oxide flux Ammonia Oxidizer and denitrifier abundance and activity across three different landfill cover soils in ningbo china
    Journal of Cleaner Production, 2018
    Co-Authors: Xi-en Long, Huaiying Yao, Ying Huang, Haifeng Chi, Naseer Ahmad
    Abstract:

    Abstract Nitrous oxide (N 2 O) is an important greenhouse gas, whose production from landfill sites has not been given adequate attention yet. Municipal solid waste disposal site could be a potential contributor to N 2 O emissions. Here, we conducted a transect study to determine N 2 O flux and the abundance and activity of nitrifiers and denitrifiers across three different landfill sites (Ninghai: NH, Xiangshan: XS, and Fenghua: FH). Microbial abundance and community structure were determined using quantitative polymerase chain reaction, terminal-restriction fragment length polymorphism (T-RFLP), and clone library. The highest mean N 2 O flux (3.44 mg m −2 h −1 ) and global warming potential (1025.12 eq-CO 2 m −2 h −1 ) were detected at the XS and NH sites, respectively. Soil nutrients (dissolved organic C, dissolved organic N, and total organic C), C:N ratio, and the abundance and activity of nitrifiers and denitrifiers determined the flux of N 2 O across the three landfill cover soils. Nitrification and denitrification made comparable contribution to N 2 O production in the soils. Nitrososphaera -associated archaeal amoA gene accounted for 99% of Ammonia-oxidizing archaea (AOA) sequences at the XS site, whereas soil/sediment cluster I of AOA dominated (>50%) at the NH and FH sites. The predominant Ammonia-oxidizing bacteria sequences (>75%) of the FH site were affiliated with the Nitrosomonas lineage and more than half the sequences belonged to cluster 3b at the XS and NH sites. The nirK sequences affiliated with Alpha-proteobacteria ( Phyllobacteriaceae , Rhizobiaceae and Bradyrhizobiaceae ) (>78%) and nirS sequences affiliated with Beta-proteobacteria (>45%) governed the denitrifiers in the soils. Heavy metals (Cu and Cr), C:N ratio, and C sources (total C and dissolved organic C) determined the distribution of the nitrifier and denitrifier communities. In conclusion, the condition of the landfill sites contributed significantly to the N 2 O emissions, and AOA and nirK-type denitrifiers dominated the leachate-affected cover soils.

  • MOESM1 of pH rather than nitrification and urease inhibitors determines the community of Ammonia Oxidizers in a vegetable soil
    2017
    Co-Authors: Xi-en Long, Sha Huang, Huaiying Yao
    Abstract:

    Additional file 1: Table S1. Primers of AOA and AOB used for molecular analyses. Table S2. Pearson correlation between pH and the relative abundance of archaeal Ammonia Oxidizer TRFs. Table S3. Pearson correlation between pH and the relative abundance of bacterial Ammonia Oxidizer TRFs. Table S4. Genotype patterns based on the clone libraries of amoA genes. Figure S1. Log number of AOA and AOB amoA copies in four different treatments (control; urea; urea+nitrapyrin; urea+NBPT) at different pH levels. Error bars indicate standard errors of three replicates, different capital letters indicate the significant difference within different treatments at same pH level (P 

  • pH rather than nitrification and urease inhibitors determines the community of Ammonia Oxidizers in a vegetable soil
    SpringerOpen, 2017
    Co-Authors: Xi-en Long, Sha Huang, Huaiying Yao
    Abstract:

    Abstract Nitrification inhibitors and urease inhibitors, such as nitrapyrin and N-(n-butyl) thiophosphoric triamide (NBPT), can improve the efficiencies of nitrogen fertilizers in cropland. However, their effects on Ammonia-oxidizing archaea (AOA) and Ammonia-oxidizing bacteria (AOB) across different soil pH levels are still unclear. In the present work, vegetable soils at four pH levels were tested to determine the impacts of nitrification and urease inhibitors on the nitrification activities, abundances and diversities of Ammonia Oxidizers at different pHs by real-time PCR, terminal restriction fragment length polymorphism (T-RFLP) and clone sequence analysis. The analyses of the abundance of Ammonia Oxidizers and net nitrification rate suggested that AOA was the dominate Ammonia Oxidizer and the key driver of nitrification in acidic soil. The relationships between pH and Ammonia Oxidizer abundance indicated that soil pH dominantly controlled the abundance of AOA but not that of AOB. The T-RFLP results suggested that soil pH could significantly affect the AOA and AOB community structure. Nitrapyrin decreased the net nitrification rate and inhibited the abundance of bacterial amoA genes in this vegetable soil, but exhibited no effect on that of the archaeal amoA genes. In contrast, NBPT just lagged the hydrolysis of urea and kept low NH4 +-N levels in the soil at the early stage. It exhibited no or slight effects on the abundance and community structure of Ammonia Oxidizers. These results indicated that soil pH, rather than the application of urea, nitrapyrin and NBPT, was a critical factor influencing the abundance and community structure of AOA and AOB

  • multi factorial drivers of Ammonia Oxidizer communities evidence from a national soil survey
    Environmental Microbiology, 2013
    Co-Authors: Graeme W Nicol, Huaiying Yao, Thomas E Freitag, Colin D Campbell, Stephen Chapman, Brajesh K Singh
    Abstract:

    Summary The factors driving the abundance and community composition of soil microbial communities provide fundamental knowledge on the maintenance of biodiversity and the ecosystem services they underpin. Several studies have suggested that microbial communities are spatially organized, including functional groups and much of the observed variation is explained by geographical location or soil pH. Soil Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are excellent models for such study due to their functional, agronomic and environmental importance and their relative ease of characterization. To identify the dominant drivers of different Ammonia Oxidizers, we used samples (n = 713) from the National Soil Inventory of Scotland (NSIS). Our results indicate that 40–45% of the variance in community compositions can be explained by 71 environmental variables. Soil pH and substrate, which have been regarded as the two main drivers, only explained 13–16% of the total variance. We provide strong evidence of multi-factorial drivers (land use, soil type, climate and N deposition) of Ammonia-oxidizing communities, all of which play a significant role in the creation of specific niches that are occupied by unique phylotypes. For example, one AOA phylotype was strongly linked to woodland/semi-natural grassland, rainfall and N deposition. Some soil typologies, namely regosols, have a novel AOA community composition indicating typology as one of the factors which defines this ecological niche. AOA abundance was high and strongly linked the rate of potential nitrification in the highly acidic soils supporting the argument that AOA are main Ammonia Oxidizers in acidic soils. However, for AOB, soil pH and substrate (Ammonia) were the main drivers for abundance and community composition. These results highlight the importance of multiple drivers of microbial niche formation and their impact on microbial biogeography that have significant consequences for ecosystem functioning.

David C White - One of the best experts on this subject based on the ideXlab platform.

  • impact of herbicides on the abundance and structure of indigenous β subgroup Ammonia Oxidizer communities in soil microcosms
    Environmental Toxicology and Chemistry, 2001
    Co-Authors: Yunjuan Chang, A Anwar K M Hussain, John R Stephen, Michael D Mullen, David C White, Aaron D Peacock
    Abstract:

    In this study, mixtures of five herbicide-formulated products (atrazine, dicamba, fluometuron, metolachlor, and sulfentrazone) were applied to soil microcosm columns in increasing concentrations. The toxic impact of herbicides on the indigenous β-subclass Proteobacteria autotrophic Ammonia-Oxidizer (β-AAO) community was assessed. The β-AAO population abundances were estimated by competitive polymerase chain reaction (PCR) targeting the gene amoA, encoding the α-subunit of Ammonia monooxygenase. Community structure was examined by PCR and denaturing gradient gel electrophoresis targeting 16S rDNA with band excision and sequence analysis, and by analysis of amoA gene fragment clone libraries. The 16S rDNA analyses showed that a single ribotype of Nitrosospira cluster 3 was the dominant β-AAO in all treatments. At a finer scale, amoA clone library analysis suggested a shift in community structure corresponding to the 100-ppm application. Competitive PCR indicated significant differences between treatments. The control exhibited relatively stable population abundance over the time period examined. The 10-ppm treatment induced a population increase, but a significant decrease was induced by the 100-ppm application. At 1,000 ppm, the Ammonia-Oxidizer population dropped below the method detection limit by the first sampling point. An impact on Ammonia Oxidizers resulting from the application of herbicides was observed, both in abundance and community structure.

  • effect of toxic metals on indigenous soil β subgroup proteobacterium Ammonia Oxidizer community structure and protection against toxicity by inoculated metal resistant bacteria
    Applied and Environmental Microbiology, 1999
    Co-Authors: John R Stephen, Yunjuan Chang, David C White, George A Kowalchuk, Sarah J Macnaughton, Kam T Leung, Cissy A Flemming
    Abstract:

    Contamination of soils with toxic metals is a major problem on military, industrial, and mining sites worldwide. Of particular interest to the field of bioremediation is the selection of biological markers for the end point of remediation. In this microcosm study, we focus on the effect of addition of a mixture of toxic metals (cadmium, cobalt, cesium, and strontium as chlorides) to soil on the population structure and size of the Ammonia Oxidizers that are members of the beta subgroup of the Proteobacteria (beta-subgroup Ammonia Oxidizers). In a parallel experiment, the soils were also treated by the addition of five strains of metal-resistant heterotrophic bacteria. Effects on nitrogen cycling were measured by monitoring the NH3 and NH4+ levels in soil samples. The gene encoding the alpha-subunit of Ammonia monooxygenase (amoA) was selected as a functional molecular marker for the beta-subgroup Ammonia oxidizing bacteria. Community structure comparisons were performed with clone libraries of PCR-amplified fragments of amoA recovered from contaminated and control microcosms for 8 weeks. Analysis was performed by restriction digestion and sequence comparison. The abundance of Ammonia Oxidizers in these microcosms was also monitored by competitive PCR. All amoA gene fragments recovered grouped with sequences derived from cultured Nitrosospira. These comprised four novel sequence clusters and a single unique clone. Specific changes in the community structure of beta-subgroup Ammonia Oxidizers were associated with the addition of metals. These changes were not seen in the presence of the inoculated metal-resistant bacteria. Neither treatment significantly altered the total number of beta-subgroup Ammonia-oxidizing cells per gram of soil compared to untreated controls. Following an initial decrease in concentration, Ammonia began to accumulate in metal-treated soils toward the end of the experiment.

John R Stephen - One of the best experts on this subject based on the ideXlab platform.

  • impact of herbicides on the abundance and structure of indigenous β subgroup Ammonia Oxidizer communities in soil microcosms
    Environmental Toxicology and Chemistry, 2001
    Co-Authors: Yunjuan Chang, A Anwar K M Hussain, John R Stephen, Michael D Mullen, David C White, Aaron D Peacock
    Abstract:

    In this study, mixtures of five herbicide-formulated products (atrazine, dicamba, fluometuron, metolachlor, and sulfentrazone) were applied to soil microcosm columns in increasing concentrations. The toxic impact of herbicides on the indigenous β-subclass Proteobacteria autotrophic Ammonia-Oxidizer (β-AAO) community was assessed. The β-AAO population abundances were estimated by competitive polymerase chain reaction (PCR) targeting the gene amoA, encoding the α-subunit of Ammonia monooxygenase. Community structure was examined by PCR and denaturing gradient gel electrophoresis targeting 16S rDNA with band excision and sequence analysis, and by analysis of amoA gene fragment clone libraries. The 16S rDNA analyses showed that a single ribotype of Nitrosospira cluster 3 was the dominant β-AAO in all treatments. At a finer scale, amoA clone library analysis suggested a shift in community structure corresponding to the 100-ppm application. Competitive PCR indicated significant differences between treatments. The control exhibited relatively stable population abundance over the time period examined. The 10-ppm treatment induced a population increase, but a significant decrease was induced by the 100-ppm application. At 1,000 ppm, the Ammonia-Oxidizer population dropped below the method detection limit by the first sampling point. An impact on Ammonia Oxidizers resulting from the application of herbicides was observed, both in abundance and community structure.

  • comparative diversity of Ammonia Oxidizer 16s rrna gene sequences in native tilled and successional soils
    Applied and Environmental Microbiology, 1999
    Co-Authors: Mary Ann Bruns, James I Prosser, John R Stephen, George A Kowalchuk, E A Paul
    Abstract:

    Autotrophic Ammonia Oxidizer (AAO) populations in soils from native, tilled, and successional treatments at the Kellogg Biological Station Long-Term Ecological Research site in southwestern Michigan were compared to assess effects of disturbance on these bacteria. N fertilization effects on AAO populations were also evaluated with soils from fertilized microplots within the successional treatments. Population structures were characterized by PCR amplification of microbial community DNA with group-specific 16S rRNA gene (rDNA) primers, cloning of PCR products and clone hybridizations with group-specific probes, phylogenetic analysis of partial 16S rDNA sequences, and denaturing gradient gel electrophoresis (DGGE) analysis. Population sizes were estimated by using most-probable-number (MPN) media containing varied concentrations of ammonium sulfate. Tilled soils contained higher numbers than did native soils of culturable AAOs that were less sensitive to different ammonium concentrations in MPN media. Compared to sequences from native soils, partial 16S rDNA sequences from tilled soils were less diverse and grouped exclusively within Nitrosospira cluster 3. Native soils yielded sequences representing three different AAO clusters. Probes for Nitrosospira cluster 3 hybridized with DGGE blots from tilled and fertilized successional soils but not with blots from native or unfertilized successional soils. Hybridization results thus suggested a positive association between the Nitrosospira cluster 3 subgroup and soils amended with inorganic N. DGGE patterns for soils sampled from replicated plots of each treatment were nearly identical for tilled and native soils in both sampling years, indicating spatial and temporal reproducibility based on treatment.

  • effect of toxic metals on indigenous soil β subgroup proteobacterium Ammonia Oxidizer community structure and protection against toxicity by inoculated metal resistant bacteria
    Applied and Environmental Microbiology, 1999
    Co-Authors: John R Stephen, Yunjuan Chang, David C White, George A Kowalchuk, Sarah J Macnaughton, Kam T Leung, Cissy A Flemming
    Abstract:

    Contamination of soils with toxic metals is a major problem on military, industrial, and mining sites worldwide. Of particular interest to the field of bioremediation is the selection of biological markers for the end point of remediation. In this microcosm study, we focus on the effect of addition of a mixture of toxic metals (cadmium, cobalt, cesium, and strontium as chlorides) to soil on the population structure and size of the Ammonia Oxidizers that are members of the beta subgroup of the Proteobacteria (beta-subgroup Ammonia Oxidizers). In a parallel experiment, the soils were also treated by the addition of five strains of metal-resistant heterotrophic bacteria. Effects on nitrogen cycling were measured by monitoring the NH3 and NH4+ levels in soil samples. The gene encoding the alpha-subunit of Ammonia monooxygenase (amoA) was selected as a functional molecular marker for the beta-subgroup Ammonia oxidizing bacteria. Community structure comparisons were performed with clone libraries of PCR-amplified fragments of amoA recovered from contaminated and control microcosms for 8 weeks. Analysis was performed by restriction digestion and sequence comparison. The abundance of Ammonia Oxidizers in these microcosms was also monitored by competitive PCR. All amoA gene fragments recovered grouped with sequences derived from cultured Nitrosospira. These comprised four novel sequence clusters and a single unique clone. Specific changes in the community structure of beta-subgroup Ammonia Oxidizers were associated with the addition of metals. These changes were not seen in the presence of the inoculated metal-resistant bacteria. Neither treatment significantly altered the total number of beta-subgroup Ammonia-oxidizing cells per gram of soil compared to untreated controls. Following an initial decrease in concentration, Ammonia began to accumulate in metal-treated soils toward the end of the experiment.

  • analysis of β subgroup proteobacterial Ammonia Oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing
    Applied and Environmental Microbiology, 1998
    Co-Authors: John R Stephen, Mary Ann Bruns, George A Kowalchuk, A E Mccaig, C J Phillips, T M Embley, James I Prosser
    Abstract:

    A combination of denaturing gradient gel electrophoresis (DGGE) and oligonucleotide probing was used to investigate the influence of soil pH on the compositions of natural populations of autotrophic beta-subgroup proteobacterial Ammonia Oxidizers. PCR primers specific to this group were used to amplify 16S ribosomal DNA (rDNA) from soils maintained for 36 years at a range of pH values, and PCR products were analyzed by DGGE. Genus- and cluster-specific probes were designed to bind to sequences within the region amplified by these primers. A sequence specific to all beta-subgroup Ammonia Oxidizers could not be identified, but probes specific for Nitrosospira clusters 1 to 4 and Nitrosomonas clusters 6 and 7 (J. R. Stephen, A. E. McCaig, Z. Smith, J. I. Prosser, and T. M. Embley, Appl. Environ. Microbiol. 62:4147-4154, 1996) were designed. Elution profiles of probes against target sequences and closely related nontarget sequences indicated a requirement for high-stringency hybridization conditions to distinguish between different clusters. DGGE banding patterns suggested the presence of Nitrosomonas cluster 6a and Nitrosospira clusters 2, 3, and 4 in all soil plots, but results were ambiguous because of overlapping banding patterns. Unambiguous band identification of the same clusters was achieved by combined DGGE and probing of blots with the cluster-specific radiolabelled probes. The relative intensities of hybridization signals provided information on the apparent selection of different Nitrosospira genotypes in samples of soil of different pHs. The signal from the Nitrosospira cluster 3 probe decreased significantly, relative to an internal control probe, with decreasing soil pH in the range of 6.6 to 3.9, while Nitrosospira cluster 2 hybridization signals increased with increasing soil acidity. Signals from Nitrosospira cluster 4 were greatest at pH 5.5, decreasing at lower and higher values, while Nitrosomonas cluster 6a signals did not vary significantly with pH. These findings are in agreement with a previous molecular study (J. R. Stephen, A. E. McCaig, Z. Smith, J. I. Prosser, and T. M. Embley, Appl. Environ. Microbiol 62:4147-4154, 1996) of the same sites, which demonstrated the presence of the same four clusters of Ammonia Oxidizers and indicated that selection might be occurring for clusters 2 and 3 at acid and neutral pHs, respectively. The two studies used different sets of PCR primers for amplification of 16S rDNA sequences from soil, and the similar findings suggest that PCR bias was unlikely to be a significant factor. The present study demonstrates the value of DGGE and probing for rapid analysis of natural soil communities of beta-subgroup proteobacterial Ammonia Oxidizers, indicates significant pH-associated differences in Nitrosospira populations, and suggests that Nitrosospira cluster 2 may be of significance for Ammonia-oxidizing activity in acid soils.

Michael Wagner - One of the best experts on this subject based on the ideXlab platform.

  • Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland
    Frontiers Media S.A., 2018
    Co-Authors: Anne Daebeler, Holger Daims, Christopher J. Sedlacek, Craig W. Herbold, Julia Vierheilig, Petra Pjevac, Mads Albertsen, Rasmus H. Kirkegaard, José R. De La Torre, Michael Wagner
    Abstract:

    Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic Ammonia Oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one§ enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as “Candidatus Nitrosocaldus islandicus,” is an obligately thermophilic, aerobic chemolithoautotrophic Ammonia Oxidizer, which stoichiometrically converts Ammonia to nitrite at temperatures between 50 and 70°C. “Ca. N. islandicus” encodes the expected repertoire of enzymes proposed to be required for archaeal Ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation§. Nevertheless, Ammonia oxidation by this AOA appears to be NO-dependent as “Ca. N. islandicus” is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that “Ca. N. islandicus” has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic Ammonia Oxidizer is the absence of DNA polymerase D genes§ – one of the predominant replicative DNA polymerases in all other Ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA

  • Abiotic Conversion of Extracellular NH2OH Contributes to N2O Emission during Ammonia Oxidation
    2017
    Co-Authors: Shurong Liu, Michael Wagner, James I Prosser, Ping Han, Linda Hink, Nicolas Brüggemann
    Abstract:

    Abiotic processes involving the reactive Ammonia-oxidation intermediates nitric oxide (NO) or hydroxylamine (NH2OH) for N2O production have been indicated recently. The latter process would require the availability of substantial amounts of free NH2OH for chemical reactions during Ammonia (NH3) oxidation, but little is known about extracellular NH2OH formation by the different clades of Ammonia-oxidizing microbes. Here we determined extracellular NH2OH concentrations in culture media of several Ammonia-oxidizing bacteria (AOB) and archaea (AOA), as well as one complete Ammonia Oxidizer (comammox) enrichment (Ca. Nitrospira inopinata) during incubation under standard cultivation conditions. NH2OH was measurable in the incubation media of Nitrosomonas europaea, Nitrosospira multiformis, Nitrososphaera gargensis, and Ca. Nitrosotenuis uzonensis, but not in media of the other tested AOB and AOA. NH2OH was also formed by the comammox enrichment during NH3 oxidation. This enrichment exhibited the largest NH2OH:final product ratio (1.92%), followed by N. multiformis (0.56%) and N. gargensis (0.46%). The maximum proportions of NH4+ converted to N2O via extracellular NH2OH during incubation, estimated on the basis of NH2OH abiotic conversion rates, were 0.12%, 0.08%, and 0.14% for AOB, AOA, and Ca. Nitrospira inopinata, respectively, and were consistent with published NH4+:N2O conversion ratios for AOB and AOA

  • distinct gene set in two different lineages of Ammonia oxidizing archaea supports the phylum thaumarchaeota
    Trends in Microbiology, 2010
    Co-Authors: Anja Spang, Roland Hatzenpichler, Patrick Tischler, Thomas Rattei, Celine Brochierarmanet, Wolfgang R Streit, Eva Spieck, David A Stahl, Michael Wagner
    Abstract:

    Globally distributed archaea comprising Ammonia Oxidizers of moderate terrestrial and marine environments are considered the most abundant archaeal organisms on Earth. Based on 16S rRNA phylogeny, initial assignment of these archaea was to the Crenarchaeota. By contrast, features of the first genome sequence from a member of this group suggested that they belong to a novel phylum, the Thaumarchaeota. Here, we re-investigate the Thaumarchaeota hypothesis by including two newly available genomes, that of the marine Ammonia Oxidizer Nitrosopumilus maritimus and that of Nitrososphaera gargensis, a representative of another evolutionary lineage within this group predominantly detected in terrestrial environments. Phylogenetic studies based on r-proteins and other core genes, as well as comparative genomics, confirm the assignment of these organisms to a separate phylum and reveal a Thaumarchaeota-specific set of core informational processing genes, as well as potentially ancestral features of the archaea.