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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 Ammoniaoxidation 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, Kilian Stoecker, James I Prosser, 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.

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-protproteobacteria ( Phyllobacteriaceae , Rhizobiaceae and Bradyrhizobiaceae ) (>78%) and nirS sequences affiliated with Beta-protproteobacteria (>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 

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 AmmoniaOxidizer (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 AmmoniaOxidizer 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 AmmoniaOxidizer (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 AmmoniaOxidizer 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.

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 aminamino 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 polypolymerase 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, Eva Spieck, Celine Brochierarmanet, Thomas Rattei, Patrick Tischler, Wolfgang R Streit, 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.