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Sample records for aerobic ammonia oxidation

  1. Role of ammonia-oxidizing bacteria in micropollutant removal from wastewater with aerobic granular sludge.

    PubMed

    Margot, Jonas; Lochmatter, Samuel; Barry, D A; Holliger, Christof

    2016-01-01

    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. PMID:26877039

  2. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation.

    PubMed

    Könneke, Martin; Schubert, Daniel M; Brown, Philip C; Hügler, Michael; Standfest, Sonja; Schwander, Thomas; Schada von Borzyskowski, Lennart; Erb, Tobias J; Stahl, David A; Berg, Ivan A

    2014-06-01

    Archaea of the phylum Thaumarchaeota are among the most abundant prokaryotes on Earth and are widely distributed in marine, terrestrial, and geothermal environments. All studied Thaumarchaeota couple the oxidation of ammonia at extremely low concentrations with carbon fixation. As the predominant nitrifiers in the ocean and in various soils, ammonia-oxidizing archaea contribute significantly to the global nitrogen and carbon cycles. Here we provide biochemical evidence that thaumarchaeal ammonia oxidizers assimilate inorganic carbon via a modified version of the autotrophic hydroxypropionate/hydroxybutyrate cycle of Crenarchaeota that is far more energy efficient than any other aerobic autotrophic pathway. The identified genes of this cycle were found in the genomes of all sequenced representatives of the phylum Thaumarchaeota, indicating the environmental significance of this efficient CO2-fixation pathway. Comparative phylogenetic analysis of proteins of this pathway suggests that the hydroxypropionate/hydroxybutyrate cycle emerged independently in Crenarchaeota and Thaumarchaeota, thus supporting the hypothesis of an early evolutionary separation of both archaeal phyla. We conclude that high efficiency of anabolism exemplified by this autotrophic cycle perfectly suits the lifestyle of ammonia-oxidizing archaea, which thrive at a constantly low energy supply, thus offering a biochemical explanation for their ecological success in nutrient-limited environments. PMID:24843170

  3. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

    PubMed Central

    Könneke, Martin; Schubert, Daniel M.; Brown, Philip C.; Hügler, Michael; Standfest, Sonja; Schwander, Thomas; Schada von Borzyskowski, Lennart; Erb, Tobias J.; Stahl, David A.; Berg, Ivan A.

    2014-01-01

    Archaea of the phylum Thaumarchaeota are among the most abundant prokaryotes on Earth and are widely distributed in marine, terrestrial, and geothermal environments. All studied Thaumarchaeota couple the oxidation of ammonia at extremely low concentrations with carbon fixation. As the predominant nitrifiers in the ocean and in various soils, ammonia-oxidizing archaea contribute significantly to the global nitrogen and carbon cycles. Here we provide biochemical evidence that thaumarchaeal ammonia oxidizers assimilate inorganic carbon via a modified version of the autotrophic hydroxypropionate/hydroxybutyrate cycle of Crenarchaeota that is far more energy efficient than any other aerobic autotrophic pathway. The identified genes of this cycle were found in the genomes of all sequenced representatives of the phylum Thaumarchaeota, indicating the environmental significance of this efficient CO2-fixation pathway. Comparative phylogenetic analysis of proteins of this pathway suggests that the hydroxypropionate/hydroxybutyrate cycle emerged independently in Crenarchaeota and Thaumarchaeota, thus supporting the hypothesis of an early evolutionary separation of both archaeal phyla. We conclude that high efficiency of anabolism exemplified by this autotrophic cycle perfectly suits the lifestyle of ammonia-oxidizing archaea, which thrive at a constantly low energy supply, thus offering a biochemical explanation for their ecological success in nutrient-limited environments. PMID:24843170

  4. Aerobic nitrous oxide production through N-nitrosating hybrid formation in ammonia-oxidizing archaea.

    PubMed

    Stieglmeier, Michaela; Mooshammer, Maria; Kitzler, Barbara; Wanek, Wolfgang; Zechmeister-Boltenstern, Sophie; Richter, Andreas; Schleper, Christa

    2014-05-01

    Soil emissions are largely responsible for the increase of the potent greenhouse gas nitrous oxide (N2O) in the atmosphere and are generally attributed to the activity of nitrifying and denitrifying bacteria. However, the contribution of the recently discovered ammonia-oxidizing archaea (AOA) to N2O production from soil is unclear as is the mechanism by which they produce it. Here we investigate the potential of Nitrososphaera viennensis, the first pure culture of AOA from soil, to produce N2O and compare its activity with that of a marine AOA and an ammonia-oxidizing bacterium (AOB) from soil. N. viennensis produced N2O at a maximum yield of 0.09% N2O per molecule of nitrite under oxic growth conditions. N2O production rates of 4.6±0.6 amol N2O cell(-1) h(-1) and nitrification rates of 2.6±0.5 fmol NO2(-) cell(-1) h(-1) were in the same range as those of the AOB Nitrosospira multiformis and the marine AOA Nitrosopumilus maritimus grown under comparable conditions. In contrast to AOB, however, N2O production of the two archaeal strains did not increase when the oxygen concentration was reduced, suggesting that they are not capable of denitrification. In (15)N-labeling experiments we provide evidence that both ammonium and nitrite contribute equally via hybrid N2O formation to the N2O produced by N. viennensis under all conditions tested. Our results suggest that archaea may contribute to N2O production in terrestrial ecosystems, however, they are not capable of nitrifier-denitrification and thus do not produce increasing amounts of the greenhouse gas when oxygen becomes limiting. PMID:24401864

  5. Inhibiting Wet Oxidation of Ammonia

    NASA Technical Reports Server (NTRS)

    Onisko, D. B. L.

    1985-01-01

    Simple modification of wet-oxidation process for treating organicwaste reduces loss of fixed nitrogen, potentially valuable byproduct of process. Addition of sufficient sulfuric acid to maintain reaction pH below 3 greatly reduces oxidation of ammonia to free nitrogen. No equipment modification required.

  6. Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria.

    PubMed

    Sauder, Laura A; Ross, Ashley A; Neufeld, Josh D

    2016-04-01

    Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested onNitrosopumilus maritimus, two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representativeNitrosomonas europaea All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway. PMID:26946536

  7. Diversity, Physiology, and Niche Differentiation of Ammonia-Oxidizing Archaea

    PubMed Central

    2012-01-01

    Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, has been suggested to have been a central part of the global biogeochemical nitrogen cycle since the oxygenation of Earth. The cultivation of several ammonia-oxidizing archaea (AOA) as well as the discovery that archaeal ammonia monooxygenase (amo)-like gene sequences are nearly ubiquitously distributed in the environment and outnumber their bacterial counterparts in many habitats fundamentally revised our understanding of nitrification. Surprising insights into the physiological distinctiveness of AOA are mirrored by the recognition of the phylogenetic uniqueness of these microbes, which fall within a novel archaeal phylum now known as Thaumarchaeota. The relative importance of AOA in nitrification, compared to ammonia-oxidizing bacteria (AOB), is still under debate. This minireview provides a synopsis of our current knowledge of the diversity and physiology of AOA, the factors controlling their ecology, and their role in carbon cycling as well as their potential involvement in the production of the greenhouse gas nitrous oxide. It emphasizes the importance of activity-based analyses in AOA studies and formulates priorities for future research. PMID:22923400

  8. Controlling the catalytic aerobic oxidation of phenols.

    PubMed

    Esguerra, Kenneth Virgel N; Fall, Yacoub; Petitjean, Laurène; Lumb, Jean-Philip

    2014-05-28

    The oxidation of phenols is the subject of extensive investigation, but there are few catalytic aerobic examples that are chemo- and regioselective. Here we describe conditions for the ortho-oxygenation or oxidative coupling of phenols under copper (Cu)-catalyzed aerobic conditions that give rise to ortho-quinones, biphenols or benzoxepines. We demonstrate that each product class can be accessed selectively by the appropriate choice of Cu(I) salt, amine ligand, desiccant and reaction temperature. In addition, we evaluate the effects of substituents on the phenol and demonstrate their influence on selectivity between ortho-oxygenation and oxidative coupling pathways. These results create an important precedent of catalyst control in the catalytic aerobic oxidation of phenols and set the stage for future development of catalytic systems and mechanistic investigations. PMID:24784319

  9. Ammonia release method for depositing metal oxides

    DOEpatents

    Silver, Gary L.; Martin, Frank S.

    1994-12-13

    A method of depositing metal oxides on substrates which is indifferent to the electrochemical properties of the substrates and which comprises forming ammine complexes containing metal ions and thereafter effecting removal of ammonia from the ammine complexes so as to permit slow precipitation and deposition of metal oxide on the substrates.

  10. Ammonia release method for depositing metal oxides

    DOEpatents

    Silver, G.L.; Martin, F.S.

    1994-12-13

    A method is described for depositing metal oxides on substrates which is indifferent to the electrochemical properties of the substrates and which comprises forming ammine complexes containing metal ions and thereafter effecting removal of ammonia from the ammine complexes so as to permit slow precipitation and deposition of metal oxide on the substrates. 1 figure.

  11. Oxidation of ammonia and methane in an alkaline, saline lake

    USGS Publications Warehouse

    Joye, S.B.; Connell, T.L.; Miller, L.G.; Oremland, R.S.; Jellison, R.S.

    1999-01-01

    The oxidation of ammonia (NH3) and methane (CH4) was investigated in an alkaline saline lake, Mono Lake, California (U.S.A.). Ammonia oxidation was examined in April and July 1995 by comparing dark 14CO2 fixation rates in the presence or absence of methyl fluoride (MeF), an inhibitor of NH3 oxidation. Ammonia oxidizer-mediated dark 14CO2 fixation rates were similar in surface (5-7 m) and oxycline (11-15 m) waters, ranging between 70-340 and 89-186 nM d-1, respectively, or 1-7% of primary production by phytoplankton. Ammonia oxidation rates ranged between 580-2,830 nM d-1 in surface waters and 732-1,548 nM d-1 in oxycline waters. Methane oxidation was examined using a 14CH4 tracer technique in July 1994, April 1995, and July 1995. Methane oxidation rates were consistently higher in July, and rates in oxycline and anaerobic bottom waters (0.5-37 and 7-48 nM d-1, respectively) were 10-fold higher than those in aerobic surface waters (0.04-3.8 nM d-1). The majority of CH4 oxidation, in terms of integrated activity, occurred within anoxic bottom waters. Water column oxidation reduced the potential lake-atmosphere CH4 flux by a factor of two to three. Measured oxidation rates and water column concentrations were used to estimate the biological turnover times of NH3 and CH4. The NH3 pool turns over rapidly, on time scales of 0.8 d in surface waters and 10 d within the oxycline, while CH4 is cycled on 103-d time scales in surface waters and 102-d time scales within oxycline and bottom waters. Our data suggest an important role for NH3 oxidation in alkaline, saline lakes since the process converts volatile NH3 to soluble NO2-, thereby reducing loss via lake-atmosphere exchange and maintaining nitrogen in a form that is readily available to phytoplankton.

  12. Ammonia and nitrite oxidation in the Eastern Tropical North Pacific

    NASA Astrophysics Data System (ADS)

    Peng, Xuefeng; Fuchsman, Clara A.; Jayakumar, Amal; Oleynik, Sergey; Martens-Habbena, Willm; Devol, Allan H.; Ward, Bess B.

    2015-12-01

    Nitrification plays a key role in the marine nitrogen (N) cycle, including in oceanic oxygen minimum zones (OMZs), which are hot spots for denitrification and anaerobic ammonia oxidation (anammox). Recent evidence suggests that nitrification links the source (remineralized organic matter) and sink (denitrification and anammox) of fixed N directly in the steep oxycline in the OMZs. We performed shipboard incubations with 15N tracers to characterize the depth distribution of nitrification in the Eastern Tropical North Pacific (ETNP). Additional experiments were conducted to investigate photoinhibition. Allylthiourea (ATU) was used to distinguish the contribution of archaeal and bacterial ammonia oxidation. The abundance of archaeal and β-proteobacterial ammonia monooxygenase gene subunit A (amoA) was determined by quantitative polymerase chain reaction. The rates of ammonia and nitrite oxidation showed distinct subsurface maxima, with the latter slightly deeper than the former. The ammonia oxidation maximum coincided with the primary nitrite concentration maximum, archaeal amoA gene maximum, and the subsurface nitrous oxide maximum. Negligible rates of ammonia oxidation were found at anoxic depths, where high rates of nitrite oxidation were measured. Archaeal amoA gene abundance was generally 1 to 2 orders of magnitude higher than bacterial amoA gene abundance, and inhibition of ammonia-oxidizing bacteria with 10 μM ATU did not affect ammonia oxidation rates, indicating the dominance of archaea in ammonia oxidation. These results depict highly dynamic activities of ammonia and nitrite oxidation in the oxycline of the ETNP OMZ.

  13. Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota.

    PubMed

    Kozlowski, Jessica A; Stieglmeier, Michaela; Schleper, Christa; Klotz, Martin G; Stein, Lisa Y

    2016-08-01

    Chemolithotrophic ammonia-oxidizing bacteria and Thaumarchaeota are central players in the global nitrogen cycle. Obligate ammonia chemolithotrophy has been characterized for bacteria; however, large gaps remain in the Thaumarchaeotal pathway. Using batch growth experiments and instantaneous microrespirometry measurements of resting biomass, we show that the terrestrial Thaumarchaeon Nitrososphaera viennensis EN76(T) exhibits tight control over production and consumption of nitric oxide (NO) during ammonia catabolism, unlike the ammonia-oxidizing bacterium Nitrosospira multiformis ATCC 25196(T). In particular, pulses of hydroxylamine into a microelectrode chamber as the sole substrate for N. viennensis resulted in iterative production and consumption of NO followed by conversion of hydroxylamine to nitrite. In support of these observations, oxidation of ammonia in growing cultures of N. viennensis, but not of N. multiformis, was inhibited by the NO-scavenger PTIO. When based on the marginal nitrous oxide (N2O) levels detected in cell-free media controls, the higher levels produced by N. multiformis were explained by enzyme activity, whereas N2O in N. viennensis cultures was attributed to abiotic reactions of released N-oxide intermediates with media components. Our results are conceptualized in a pathway for ammonia-dependent chemolithotrophy in Thaumarchaea, which identifies NO as an essential intermediate in the pathway and implements known biochemistry to be executed by a proposed but still elusive copper enzyme. Taken together, this work identifies differences in ammonia-dependent chemolithotrophy between bacteria and the Thaumarchaeota, advances a central catabolic role of NO only in the Thaumarchaeotal pathway and reveals stark differences in how the two microbial cohorts contribute to N2O emissions. PMID:26882267

  14. Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils

    PubMed Central

    Wang, Baozhan; Zhao, Jun; Guo, Zhiying; Ma, Jing; Xu, Hua; Jia, Zhongjun

    2015-01-01

    Rice paddy fields are characterized by regular flooding and nitrogen fertilization, but the functional importance of aerobic ammonia oxidizers and nitrite oxidizers under unique agricultural management is poorly understood. In this study, we report the differential contributions of ammonia-oxidizing archaea (AOA), bacteria (AOB) and nitrite-oxidizing bacteria (NOB) to nitrification in four paddy soils from different geographic regions (Zi-Yang (ZY), Jiang-Du (JD), Lei-Zhou (LZ) and Jia-Xing (JX)) that are representative of the rice ecosystems in China. In urea-amended microcosms, nitrification activity varied greatly with 11.9, 9.46, 3.03 and 1.43 μg NO3−-N g−1 dry weight of soil per day in the ZY, JD, LZ and JX soils, respectively, over the course of a 56-day incubation period. Real-time quantitative PCR of amoA genes and pyrosequencing of 16S rRNA genes revealed significant increases in the AOA population to various extents, suggesting that their relative contributions to ammonia oxidation activity decreased from ZY to JD to LZ. The opposite trend was observed for AOB, and the JX soil stimulated only the AOB populations. DNA-based stable-isotope probing further demonstrated that active AOA numerically outcompeted their bacterial counterparts by 37.0-, 10.5- and 1.91-fold in 13C-DNA from ZY, JD and LZ soils, respectively, whereas AOB, but not AOA, were labeled in the JX soil during active nitrification. NOB were labeled to a much greater extent than AOA and AOB, and the addition of acetylene completely abolished the assimilation of 13CO2 by nitrifying populations. Phylogenetic analysis suggested that archaeal ammonia oxidation was predominantly catalyzed by soil fosmid 29i4-related AOA within the soil group 1.1b lineage. Nitrosospira cluster 3-like AOB performed most bacterial ammonia oxidation in the ZY, LZ and JX soils, whereas the majority of the 13C-AOB in the JD soil was affiliated with the Nitrosomona communis lineage. The 13C-NOB was overwhelmingly

  15. Sanitising black water by auto-thermal aerobic digestion (ATAD) combined with ammonia treatment.

    PubMed

    Nordin, Annika C; Vinnerås, Björn

    2015-01-01

    The effect of a two-step process on the concentration of pathogens and indicator microorganisms in black water (0.9-1% total solids) was studied. The treatment combined auto-thermal aerobic digestion (ATAD) and ammonia sanitisation. First, the temperature of the black water was increased through ATAD and when a targeted temperature was reached (33, 41 and 45.5 °C studied), urea was added to a 0.5% concentration (total ammonia nitrogen >2.9 g L⁻¹). Escherichia coli and Salmonella spp. were reduced to non-detectable levels within 3 days following urea addition at temperatures above 40 °C, whereas when urea was added at 33 °C E. coli was still present after 8 days. By adding urea at temperatures of 40 °C and above, a 5 log10 reduction in Enterococcus spp. and a 3 log10 reduction in Ascaris suum eggs was achieved 1 week after the addition. With combined ATAD and ammonia treatment using 0.5% ww urea added at an aerobic digestion temperature >40 °C, black water was sanitised regarding the pathogens studied in 2 weeks of total treatment time. PMID:26675998

  16. Surface Structure of Aerobically Oxidized Diamond Nanocrystals

    PubMed Central

    2015-01-01

    We investigate the aerobic oxidation of high-pressure, high-temperature nanodiamonds (5–50 nm dimensions) using a combination of carbon and oxygen K-edge X-ray absorption, wavelength-dependent X-ray photoelectron, and vibrational spectroscopies. Oxidation at 575 °C for 2 h eliminates graphitic carbon contamination (>98%) and produces nanocrystals with hydroxyl functionalized surfaces as well as a minor component (<5%) of carboxylic anhydrides. The low graphitic carbon content and the high crystallinity of HPHT are evident from Raman spectra acquired using visible wavelength excitation (λexcit = 633 nm) as well as carbon K-edge X-ray absorption spectra where the signature of a core–hole exciton is observed. Both spectroscopic features are similar to those of chemical vapor deposited (CVD) diamond but differ significantly from the spectra of detonation nanodiamond. The importance of these findings to the functionalization of nanodiamond surfaces for biological labeling applications is discussed. PMID:25436035

  17. Specific inhibitors of ammonia oxidation in Nitrosomonas.

    PubMed

    Hooper, A B; Terry, K R

    1973-08-01

    The following compounds or treatments have been shown to inhibit the oxidation of ammonia, but not the oxidation of hydroxylamine in cells of Nitrosomonas: (i) metal-binding agents such as allylthiourea or potassium cyanide; (ii) compounds such as SKF 525 which interact with cytochrome P-450 of mammalian microsomes; (iii) carbon monoxide; (iv) inhibitors of catalase, peroxidase, and amine oxidases such as thiosemicarbazide, ethylxanthate, and iproniazid, respectively; (v) uncouplers of oxidative phosphorylation such as m-chlorocarbonylcyanidephenylhydrazone; (vi) electron acceptors such as phenazine methosulfate; (vii) compounds such as methanol or N(2)O which react with free radicals; and (viii) illumination with 420 lux (5,000 foot candles) of light. PMID:4725614

  18. Specific Inhibitors of Ammonia Oxidation in Nitrosomonas

    PubMed Central

    Hooper, Alan B.; Terry, Kathleen R.

    1973-01-01

    The following compounds or treatments have been shown to inhibit the oxidation of ammonia, but not the oxidation of hydroxylamine in cells of Nitrosomonas: (i) metal-binding agents such as allylthiourea or potassium cyanide; (ii) compounds such as SKF 525 which interact with cytochrome P-450 of mammalian microsomes; (iii) carbon monoxide; (iv) inhibitors of catalase, peroxidase, and amine oxidases such as thiosemicarbazide, ethylxanthate, and iproniazid, respectively; (v) uncouplers of oxidative phosphorylation such as m-chlorocarbonylcyanidephenylhydrazone; (vi) electron acceptors such as phenazine methosulfate; (vii) compounds such as methanol or N2O which react with free radicals; and (viii) illumination with 420 lux (5,000 foot candles) of light. PMID:4725614

  19. Development of a simultaneous partial nitrification, anaerobic ammonia oxidation and denitrification (SNAD) bench scale process for removal of ammonia from effluent of a fertilizer industry.

    PubMed

    Keluskar, Radhika; Nerurkar, Anuradha; Desai, Anjana

    2013-02-01

    A simultaneous partial nitrification, anammox and denitrification (SNAD) process was developed for the treatment of ammonia laden effluent of a fertilizer industry. Autotrophic aerobic and anaerobic ammonia oxidizing biomass was enriched and their ammonia removal ability was confirmed in synthetic effluent system. Seed consortium developed from these was applied in the treatment of effluent in an oxygen limited bench scale SNAD type (1L) reactor run at ambient temperature (∼30°C). Around 98.9% ammonia removal was achieved with ammonia loading rate 0.35kgNH(4)(+)-N/m(3)day in the presence of 46.6mg/L COD at 2.31days hydraulic retention time. Qualitative and quantitative analysis of the biomass from upper and lower zone of the reactor revealed presence of autotrophic ammonia oxidizing bacteria (AOB), Planctomycetes and denitrifiers as the dominant bacteria carrying out anoxic oxidation of ammonia in the reactor. Physiological and molecular studies strongly indicate presence of anammox bacteria in the anoxic zone of the SNAD reactor. PMID:23313684

  20. Surface Structure of Aerobically Oxidized Diamond Nanocrystals

    DOE PAGESBeta

    Wolcott, Abraham; Schiros, Theanne; Trusheim, Matthew E.; Chen, Edward H.; Nordlund, Dennis; Diaz, Rosa E.; Gaaton, Ophir; Englund, Dirk; Owen, Jonathan S.

    2014-10-27

    Here we investigate the aerobic oxidation of high-pressure, high-temperature nanodiamonds (5–50 nm dimensions) using a combination of carbon and oxygen K-edge X-ray absorption, wavelength-dependent X-ray photoelectron, and vibrational spectroscopies. Oxidation at 575 °C for 2 h eliminates graphitic carbon contamination (>98%) and produces nanocrystals with hydroxyl functionalized surfaces as well as a minor component (<5%) of carboxylic anhydrides. The low graphitic carbon content and the high crystallinity of HPHT are evident from Raman spectra acquired using visible wavelength excitation (λexcit = 633 nm) as well as carbon K-edge X-ray absorption spectra where the signature of a core–hole exciton is observed.more » Both spectroscopic features are similar to those of chemical vapor deposited (CVD) diamond but differ significantly from the spectra of detonation nanodiamond. Lastly, we discuss the importance of these findings to the functionalization of nanodiamond surfaces for biological labeling applications.« less

  1. Surface Structure of Aerobically Oxidized Diamond Nanocrystals

    SciTech Connect

    Wolcott, Abraham; Schiros, Theanne; Trusheim, Matthew E.; Chen, Edward H.; Nordlund, Dennis; Diaz, Rosa E.; Gaaton, Ophir; Englund, Dirk; Owen, Jonathan S.

    2014-10-27

    Here we investigate the aerobic oxidation of high-pressure, high-temperature nanodiamonds (5–50 nm dimensions) using a combination of carbon and oxygen K-edge X-ray absorption, wavelength-dependent X-ray photoelectron, and vibrational spectroscopies. Oxidation at 575 °C for 2 h eliminates graphitic carbon contamination (>98%) and produces nanocrystals with hydroxyl functionalized surfaces as well as a minor component (<5%) of carboxylic anhydrides. The low graphitic carbon content and the high crystallinity of HPHT are evident from Raman spectra acquired using visible wavelength excitation (λexcit = 633 nm) as well as carbon K-edge X-ray absorption spectra where the signature of a core–hole exciton is observed. Both spectroscopic features are similar to those of chemical vapor deposited (CVD) diamond but differ significantly from the spectra of detonation nanodiamond. Lastly, we discuss the importance of these findings to the functionalization of nanodiamond surfaces for biological labeling applications.

  2. Ammonia Oxidizing Bacteria Community Dynamics in a Pilot-Scale Wastewater Treatment Plant

    PubMed Central

    Wang, Xiaohui; Wen, Xianghua; Xia, Yu; Hu, Ma; Zhao, Fang; Ding, Kun

    2012-01-01

    Background Chemoautotrophic ammonia oxidizing bacteria (AOB) have the metabolic ability to oxidize ammonia to nitrite aerobically. This metabolic feature has been widely used, in combination with denitrification, to remove nitrogen from wastewater in wastewater treatment plants (WWTPs). However, the relative influence of specific deterministic environmental factors to AOB community dynamics in WWTP is uncertain. The ecological principles underlying AOB community dynamics and nitrification stability and how they are related are also poorly understood. Methodology/Principal Findings The community dynamics of ammonia oxidizing bacteria (AOB) in a pilot-scale WWTP were monitored over a one-year period by Terminal Restriction Fragment Length Polymorphism (T-RFLP). During the study period, the effluent ammonia concentrations were almost below 2 mg/L, except for the first 60 days, indicting stable nitrification. T-RFLP results showed that, during the test period with stable nitrification, the AOB community structures were not stable, and the average change rate (every 15 days) of AOB community structures was 10%±8%. The correlations between T-RFLP profiles and 10 operational and environmental parameters were tested by Canonical Correlation Analysis (CCA) and Mantel test. The results indicated that the dynamics of AOB community correlated most strongly with Dissolved Oxygen (DO), effluent ammonia, effluent Biochemical Oxygen Demand (BOD) and temperature. Conclusions/Significance This study suggests that nitrification stability is not necessarily accompanied by a stable AOB community, and provides insight into parameters controlling the AOB community dynamics within bioreactors with stable nitrification. PMID:22558415

  3. Evaluation of methyl fluoride and dimethyl ether as inhibitors of aerobic methane oxidation

    USGS Publications Warehouse

    Oremland, R.S.; Culbertson, C.W.

    1992-01-01

    Methyl fluoride (MF) and dimethyl ether (DME) were effective inhibitors of aerobic methanotrophy in a variety of soils. MF and DME blocked consumption of CH4 as well as the oxidation of 14CH4 to 14CO2, but neither MF nor DME affected the oxidation of [14C]methanol or [14C]formate to 14CO2. Cooxidation of ethane and propane by methane-oxidizing soils was also inhibited by MF. Nitrification (ammonia oxidation) in soils was inhibited by both MF and DME. Production of N2O via nitrification was inhibited by MF; however, MF did not affect N2O production associated with denitrification. Methanogenesis was partially inhibited by MF but not by DME. Methane oxidation was ~100-fold more sensitive to MF than was methanogenesis, indicating that an optimum concentration could be employed to selectively block methanotrophy. MF inhibited methane oxidation by cell suspensions of Methylococcus capsulatus; however, DME was a much less effective inhibitor.

  4. Formation of aerobic granular sludge under adverse conditions: low DO and high ammonia.

    PubMed

    Zhang, Sheng-Hua; Zhang, Xiao-Hu; Lv, Lu; Wang, Qing; Jiang, Qipei

    2013-04-01

    In this study, two adverse environments: low dissolved oxygen (DO) and high ammonia concentration, were employed to investigate the morphology, interspecies quorum sensing, extracellular polymers (EPS) characterization and microbial communities in the formation of aerobic granular sludge. Results showed that low DO could promote filamentous bacterial outgrowth. Under high ammonia concentration aerobic granular sludge (AGS) could still be cultivated, although it was looser and lighter than the control group. During the early stage of the AGS cultivation process, Al-2 activity reached a peak value in all three reactors, and ultrasonic pre-treatment was not beneficial to the release of Al-2. During AGS formation, the production of polysaccharide exhibited increases from 12.2% to 40.3%, 49.6%, and 29.3%. And PS in R2 was the highest as the result of sludge bulking. PS/PN was 1.5 to approximately 8 in the three reactors. Three-dimensional EEM fuorescence spectroscopy variation indicated the change of protein in EPS, and the highest intensity of Peak T1 was obtained. The location shift of Peak T1 was not obvious, and Peaks A, C, and T2 shifted toward longer wavelengths (red shift) of 5 to approximately 60 nm, or shorter wavelengths (blue shift) of 10 to approximately 25 nm on the emission scale and/or excitation scale in all three reactors. This provided spectral information on the chemical structure changes. Bacteria in R3 had the highest species diversity, and all bacteria in beta-Proteobacteria were identified as genus Thauera, which suggested that simultaneous nitrification and denitrification occurred in R3. The filamentous bacteria in seed sludge and R2 were species-richer. There was a low abundance of filamentous bacteria in R1 and R3, which contributed to the granule structure stability. PMID:24620612

  5. Effect of ammonia plasma treatment on graphene oxide LB monolayers

    SciTech Connect

    Singh, Gulbagh; Botcha, V. Divakar; Narayanam, Pavan K.; Sutar, D. S.; Talwar, S. S.; Major, S. S.; Srinivasa, R. S.

    2013-02-05

    Graphene oxide monolayer sheets were transferred on Si and SiO{sub 2}/Si substrates by Langmuir-Blodgett technique and were exposed to ammonia plasma at room temperature. The monolayer character of both graphene oxide and plasma treated graphene oxide sheets were ascertained by atomic force microscopy. X-ray photoelectron spectroscopy and Raman spectroscopy revealed that ammonia plasma treatment results in enhancement of graphitic carbon content along with the incorporation of nitrogen. The conductivity of graphene oxide monolayers, which was in the range of 10{sup -6}-10{sup -7} S/cm, increased to 10{sup -2}-10{sup -3} S/cm after the ammonia plasma treatment. These results indicate that the graphene oxide was simultaneously reduced and N-doped during ammonia plasma treatment, without affecting the morphological stability of sheets.

  6. Ammonia and ethylene oxide permeation through selected protective clothing.

    PubMed

    Berardinelli, S P; Moyer, E S; Hall, R C

    1990-11-01

    An automated permeation test system was developed to collect permeation data. Three test specimens were evaluated simultaneously versus a challenge gas. The study evaluated chemical protective clothing garment materials for use by emergency response personnel confronted by ammonia or ethylene oxide in the gas phase. A total of 13 encapsulating suit materials and 2 glove materials were tested. Surgical latex material is not recommended for use in handling ammonia or ethylene oxide; other materials offer much greater protection. PMID:2085165

  7. OXIDATION OF NITROPYRIN TO 6-CHOLORPICOLINIC ACID BY THE AMMONIA-OXIDIZING BACTERIUM NOSTROSOMAS EUROPAEA

    EPA Science Inventory

    Suspensions of Nitrosomonas europaea catalyzed the oxidation of the commercial nitrification inhibitor nitrapyrin [2-chloro-6-(trichloromethyl)-pyridine]. apid oxidation of nitrapyrin (at a concentration of 10 uM) required the concomitant oxidation of ammonia, hydroxylamine, or h...

  8. SOIL NITROUS OXIDE, NITRIC OXIDE, AND AMMONIA EMISSIONS FROM A RECOVERING RIPARIAN ECOSYSTEM IN SOUTHERN APPALACHIA

    EPA Science Inventory

    The paper presents two years of seasonal nitric oxide, ammonia, and nitrous oxide trace gas fluxes measured in a recovering riparian zone with cattle excluded and in an adjacent riparian zone grazed by cattle. In the recovering riparian zone, average nitric oxide, ammonia, and ni...

  9. Impact resistance of different factors on ammonia removal by heterotrophic nitrification-aerobic denitrification bacterium Aeromonas sp. HN-02.

    PubMed

    Chen, Maoxia; Wang, Wenchao; Feng, Ye; Zhu, Xiaohua; Zhou, Houzhen; Tan, Zhouliang; Li, Xudong

    2014-09-01

    To give reference for the application of heterotrophic nitrification-aerobic denitrification bacteria in actual wastewater treatment, the impact resistance of extreme pH, low temperature, heavy metals and high salinity on ammonia removal by a typical heterotrophic nitrifying-aerobic denitrifying bacterium Aeromonas sp. HN-02 was investigated. The results showed that HN-02 demonstrated strong acid- and alkali-resistance. In addition, it remained active at 5°C, and the removal rates of ammonia and COD were 0.90 mg L(-1)h(-1) and 22.34 mg L(-1)h(-1), respectively. Under the same extent of immediate temperature drop, the temperature correction coefficients of ammonia, COD removal rates and cell growth rate were close. Moreover, HN-02 could survive in the solution containing 0.5 mg L(-1) Cu(2+) or 8 mg L(-1) Zn(2+), or 0.5 mg L(-1) of equivalent Cu(2+)-Zn(2+). Furthermore, efficient ammonia removal was retained at salinity below 20 g L(-1), thus it could be identified as a halotolerant bacterium. At last, stronger stress resulted in higher ΔCOD/ΔTN ratio. PMID:25006021

  10. Ammonia-oxidizing archaea have better adaptability in oxygenated/hypoxic alternant conditions compared to ammonia-oxidizing bacteria.

    PubMed

    Liu, Shuai; Hu, Baolan; He, Zhanfei; Zhang, Bin; Tian, Guangming; Zheng, Ping; Fang, Fang

    2015-10-01

    Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Few studies compared the adaptability of AOA and AOB for oxygenated/hypoxic alternant conditions in water-level-fluctuating zones. Here, using qPCR and 454 high-throughput sequencing of functional amoA genes of AOA and AOB, we examined the changes of abundances, diversities, and community structures of AOA and AOB in periodically flooded soils compared to the non-flooded soils in Three Gorges Reservoir. The increased AOA operational taxonomic unit (OTU) numbers and the higher ratios of abundance (AOA:AOB) in the periodically flooded soils suggested AOA have better adaptability for oxygenated/hypoxic alternant conditions in the water-level-fluctuating zones in the Three Gorges Reservoir and probably responsible for the ammonia oxidation there. Canonical correspondence analysis (CCA) showed that oxidation-reduction potential (ORP) had the most significant effect on the community distribution of AOA (p < 0.01). Pearson analysis also indicated that ORP was the most important factor influencing the abundances and diversities of ammonia-oxidizing microbes. ORP was significantly negatively correlated with AOA OTU numbers (p < 0.05), ratio of OTU numbers (AOA:AOB) (p < 0.01), and ratio of amoA gene abundances (AOA:AOB) (p < 0.05). ORP was also significantly positively correlated with AOB abundance (p < 0.05). PMID:26099334

  11. Aerobic sulfur-oxidizing bacteria: Environmental selection and diversification

    NASA Technical Reports Server (NTRS)

    Caldwell, D.

    1985-01-01

    Sulfur-oxidizing bacteria oxidize reduced inorganic compounds to sulfuric acid. Lithotrophic sulfur oxidizer use the energy obtained from oxidation for microbial growth. Heterotrophic sulfur oxidizers obtain energy from the oxidation of organic compounds. In sulfur-oxidizing mixotrophs energy are derived either from the oxidation of inorganic or organic compounds. Sulfur-oxidizing bacteria are usually located within the sulfide/oxygen interfaces of springs, sediments, soil microenvironments, and the hypolimnion. Colonization of the interface is necessary since sulfide auto-oxidizes and because both oxygen and sulfide are needed for growth. The environmental stresses associated with the colonization of these interfaces resulted in the evolution of morphologically diverse and unique aerobic sulfur oxidizers.

  12. Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China

    PubMed Central

    Zhang, Qiufang; Tang, Fangyuan; Zhou, Yangjing; Xu, Jirong; Chen, Heping; Wang, Mingkuang; Laanbroek, Hendrikus J.

    2015-01-01

    Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira. PMID:26579089

  13. Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China.

    PubMed

    Zhang, Qiufang; Tang, Fangyuan; Zhou, Yangjing; Xu, Jirong; Chen, Heping; Wang, Mingkuang; Laanbroek, Hendrikus J

    2015-01-01

    Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira. PMID:26579089

  14. Physiological plasticity of the thermophilic ammonia oxidizing archaeon Nitrosocaldus yellowstonii in response to a changing environment

    NASA Astrophysics Data System (ADS)

    Jewell, T.; Johnson, A.; Gelsinger, D.; de la Torre, J. R.

    2012-12-01

    Our understanding of nitrogen biogeochemical cycling in high temperature environments underwent a dramatic revision with the discovery of ammonia oxidizing archaea (AOA). The importance of AOA to the global nitrogen cycle came to light when recent studies of marine AOA demonstrated the dominance of these organisms in the ocean microbiome and their role as producers of the greenhouse gas nitrous oxide (N2O). Understanding how AOA respond to fluctuating environments is crucial to fully comprehending their contribution to global biogeochemical cycling and climate change. In this study we use the thermophilic AOA Nitrosocaldus yellowstonii strain HL72 to explore the physiological plasticity of energy metabolism in these organisms. Previous studies have shown that HL72 grows autotrophically by aerobically oxidizing ammonia (NH3) to nitrite (NO2-). Unlike studies of marine AOA, we find that HL72 can grow over a wide ammonia concentration range (0.25 - 10 mM NH4Cl) with comparable generation times when in the presence of 0.25 to 4 mM NH4Cl. However, preliminary data indicate that amoA, the alpha subunit of ammonia monooxygenase (AMO), is upregulated at low ammonia concentrations (<50 μM) compared to growth at 1 mM. Although the ammonia oxidation pathway has not been fully elucidated, we have shown that nitric oxide (NO) appears to be a key intermediate: exponentially growing HL72 produces significant NO and the removal of NO using a scavenger reversibly inhibits growth. In addition to AMO, the HL72 genome also contains sequences for a urease encoded by subunits ureABC and an active urea transporter. Urea ((NH2)2CO) is an organic compound ubiquitous to aquatic and soil habitats that, when hydrolyzed, forms NH3 and CO2. We examined urea as an alternate source of ammonia for the ammonia oxidation pathway. HL72 grows over a wide range of urea concentrations (0.25 - 10 mM) at rates comparable to growth on ammonia. In a substrate competition experiment HL72 preferentially

  15. Identification of Bacteria Responsible for Ammonia Oxidation in Freshwater Aquaria

    PubMed Central

    Burrell, Paul C.; Phalen, Carol M.; Hovanec, Timothy A.

    2001-01-01

    Culture enrichments and culture-independent molecular methods were employed to identify and confirm the presence of novel ammonia-oxidizing bacteria (AOB) in nitrifying freshwater aquaria. Reactors were seeded with biomass from freshwater nitrifying systems and enriched for AOB under various conditions of ammonia concentration. Surveys of cloned rRNA genes from the enrichments revealed four major strains of AOB which were phylogenetically related to the Nitrosomonas marina cluster, the Nitrosospira cluster, or the Nitrosomonas europaea-Nitrosococcus mobilis cluster of the β subdivision of the class Proteobacteria. Ammonia concentration in the reactors determined which AOB strain dominated in an enrichment. Oligonucleotide probes and PCR primer sets specific for the four AOB strains were developed and used to confirm the presence of the AOB strains in the enrichments. Enrichments of the AOB strains were added to newly established aquaria to determine their ability to accelerate the establishment of ammonia oxidation. Enrichments containing the Nitrosomonas marina-like AOB strain were most efficient at accelerating ammonia oxidation in newly established aquaria. Furthermore, if the Nitrosomonas marina-like AOB strain was present in the original enrichment, even one with other AOB, only the Nitrosomonas marina-like AOB strain was present in aquaria after nitrification was established. Nitrosomonas marina-like AOB were 2% or less of the cells detected by fluorescence in situ hybridization analysis in aquaria in which nitrification was well established. PMID:11722936

  16. Toxicity of ammonia to algae in sewage oxidation ponds.

    PubMed Central

    Abeliovich, A; Azov, Y

    1976-01-01

    Ammonia, at concentrations over 2.0 mM and at pH values over 8.0, inhibits photosynthesis and growth of Scenedesmus obliquus, a dominant species in high-rate sewage oxidation ponds. Photosynthesis of Chlorella pyrenoidosa, Anacystis nidulans, and Plectonema boryanum is also susceptible to ammonia inhibition. Dark respiration and cell morphology were unaffected by any combination of pH and ammonia concentrations tested, thus limiting the apparent effect to inhibition of the normal function of the chloroplasts. Methylamine had the same effect as ammonia, and its penetration into the cells was found to be pH dependent. Therefore, the dependence of toxicity of amines to algae on pH apparently results from the inability to penetrate the cell membrane in the ionized form. When operated at 120-h detention time of raw wastewater, the high-rate oxidation pond maintained a steady state with respect to algal growth and oxygen concentration, and the concentration of ammonia did not exceed 1.0 mM. Shifting the pond to 48-h detention time caused an increase in ammonia concentration in the pond water to 2.5 mM, and the pond gradually turned anaerobic. Photosynthesis, which usually elevates the pH of the pond water to 9.0 to 10.0, could not proceed beyond pH 7.9 because of the high concentration of ammonia, and the algal population was washed out and reduced to a concentration that could maintain a doubling time of 48 h without photosynthesis bringing the pH to inhibitory levels. Under these conditions, the pH of the bond becomes a factor that limits the operational efficiency of the oxidation pond. PMID:7192

  17. Aerobic Denitrifying Bacteria That Produce Low Levels of Nitrous Oxide

    PubMed Central

    Takaya, Naoki; Catalan-Sakairi, Maria Antonina B.; Sakaguchi, Yasushi; Kato, Isao; Zhou, Zhemin; Shoun, Hirofumi

    2003-01-01

    Most denitrifiers produce nitrous oxide (N2O) instead of dinitrogen (N2) under aerobic conditions. We isolated and characterized novel aerobic denitrifiers that produce low levels of N2O under aerobic conditions. We monitored the denitrification activities of two of the isolates, strains TR2 and K50, in batch and continuous cultures. Both strains reduced nitrate (NO3−) to N2 at rates of 0.9 and 0.03 μmol min−1 unit of optical density at 540 nm−1 at dissolved oxygen (O2) (DO) concentrations of 39 and 38 μmol liter−1, respectively. At the same DO level, the typical denitrifier Pseudomonas stutzeri and the previously described aerobic denitrifier Paracoccus denitrificans did not produce N2 but evolved more than 10-fold more N2O than strains TR2 and K50 evolved. The isolates denitrified NO3− with concomitant consumption of O2. These results indicated that strains TR2 and K50 are aerobic denitrifiers. These two isolates were taxonomically placed in the β subclass of the class Proteobacteria and were identified as P. stutzeri TR2 and Pseudomonas sp. strain K50. These strains should be useful for future investigations of the mechanisms of denitrifying bacteria that regulate N2O emission, the single-stage process for nitrogen removal, and microbial N2O emission into the ecosystem. PMID:12788710

  18. The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger.

    PubMed

    Martens-Habbena, Willm; Qin, Wei; Horak, Rachel E A; Urakawa, Hidetoshi; Schauer, Andrew J; Moffett, James W; Armbrust, E Virginia; Ingalls, Anitra E; Devol, Allan H; Stahl, David A

    2015-07-01

    Nitrification is a critical process for the balance of reduced and oxidized nitrogen pools in nature, linking mineralization to the nitrogen loss processes of denitrification and anammox. Recent studies indicate a significant contribution of ammonia-oxidizing archaea (AOA) to nitrification. However, quantification of the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to in situ ammonia oxidation remains challenging. We show here the production of nitric oxide (NO) by Nitrosopumilus maritimus SCM1. Activity of SCM1 was always associated with the release of NO with quasi-steady state concentrations between 0.05 and 0.08 μM. NO production and metabolic activity were inhibited by the nitrogen free radical scavenger 2-phenyl-4,4,5,5,-tetramethylimidazoline-1-oxyl-3-oxide (PTIO). Comparison of marine and terrestrial AOB strains with SCM1 and the recently isolated marine AOA strain HCA1 demonstrated a differential sensitivity of AOB and AOA to PTIO and allylthiourea (ATU). Similar to the investigated AOA strains, bulk water column nitrification at coastal and open ocean sites with sub-micromolar ammonia/ammonium concentrations was inhibited by PTIO and insensitive to ATU. These experiments support predictions from kinetic, molecular and biogeochemical studies, indicating that marine nitrification at low ammonia/ammonium concentrations is largely driven by archaea and suggest an important role of NO in the archaeal metabolism. PMID:25420929

  19. Ammonia oxidation rates and nitrification in the Arabian Sea

    NASA Astrophysics Data System (ADS)

    Newell, Silvia E.; Babbin, Andrew R.; Jayakumar, Amal; Ward, Bess B.

    2011-12-01

    Nitrification rates, as well as the relationships between rates and ammonia oxidizer abundance (both archaeal and bacterial), were investigated in the Arabian Sea. Ammonia oxidation rates were measured directly using 15N-NH4+stable isotope additions in gas-impermeable, trace metal clean trilaminate bags (500 mL) at in situ temperature. Tracer incubations were performed at three stations at depths above, below, and within the oxycline of the open-ocean oxygen minimum zone (OMZ). Ammonia oxidation rates were similar to previous open-ocean measurements, ranging from undetectable to 21.6 ± 0.1 nmol L-1 d-1. The highest rates at each station occurred at the primary nitrite maximum (above the OMZ), and rates were very low at depths greater than 900 m. The abundances of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were estimated using theamoA gene by quantitative polymerase chain reaction (qPCR). Both AOA and AOB amoA were detected above, within, and below the OMZ, although the AOA were always more abundant than the AOB, by a factor of 35-216. Nitrification rates were not directly correlated to AOA or AOB amoA abundance. These rates offer new insight into the role of nitrification in the mesopelagic zone. The abundance of AOA amoA genes at 1000 m suggests that ˜50% of the microbial biomass could be autotrophic. Additionally, the integrated nitrification rate at depth implies that nitrification could consume most of the ammonium produced by the flux of organic carbon in the mesopelagic zone.

  20. Aerobic Methane Oxidation in Alaskan Lakes Along a Latitudinal Transect

    NASA Astrophysics Data System (ADS)

    Martinez-Cruz, K. C.; Sepulveda-Jauregui, A.; Walter Anthony, K. M.; Anthony, P.; Thalasso, F.

    2013-12-01

    Karla Martinez-Cruz* **, Armando Sepulveda-Jauregui*, Katey M. Walter Anthony*, Peter Anthony*, and Frederic Thalasso**. * Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, Fairbanks, Alaska. ** Biotechnology and Bioengineering Department, Cinvestav, Mexico city, D. F., Mexico. Methane (CH4) is the third most important greenhouse gas in the atmosphere, after carbon dioxide and water vapor. Boreal lakes play an important role in the current global warming by contributing as much as 6% of global atmospheric CH4 sources annually. On the other hand, aerobic methane oxidation (methanotrophy) in lake water is a fundamental process in global methane cycling that reduces the amount of CH4 emissions to the atmosphere. Several environmental factors affect aerobic methane oxidation in the water column both directly and indirectly, including concentration of CH4 and O2, temperature and carbon budgets of lakes. We analyzed the potential of aerobic methane oxidation (PMO) rates in incubations of water collected from 30 Alaskan lakes along a north-south transect during winter and summer 2011. Our findings showed an effect of CH4 and O2 concentrations, temperature and yedoma thawing permafrost on PMO activity in the lake water. The highest PMO rates were observed in summer by lakes situated on thawing yedoma permafrost, most of them located in the interior of Alaska. We also estimated that 60-80% of all CH4 produced in Alaskan lakes could be taken up by methanotrophs in the lake water column, showing the significant influence of aerobic methane oxidation of boreal lakes to the global CH4 budget.

  1. Ammonia modification of oxide-free Si(111) surfaces

    NASA Astrophysics Data System (ADS)

    Chopra, Tatiana Peixoto; Longo, Roberto C.; Cho, Kyeongjae; Chabal, Yves J.

    2016-08-01

    Amination of surfaces is useful in a variety of fields, ranging from device manufacturing to biological applications. Previous studies of ammonia reaction on silicon surfaces have concentrated on vapor phase rather than wet chemical processes, and mostly on clean Si surfaces. In this work, the interaction of liquid and vapor-phase ammonia is examined on three types of oxide-free surfaces - passivated by hydrogen, fluorine (1/3 monolayer) or chlorine - combining infrared absorption spectroscopy, X-ray photoelectron spectroscopy, and first-principles calculations. The resulting chemical composition highly depends on the starting surface; there is a stronger reaction on both F- and Cl-terminated than on the H-terminated Si surfaces, as evidenced by the formation of Si-NH2. Side reactions can also occur, such as solvent reaction with surfaces, formation of ammonium salt by-products (in the case of 0.2 M ammonia in dioxane solution), and nitridation of silicon (in the case of neat and gas-phase ammonia reactions for instance). Unexpectedly, there is formation of Si-H bonds on hydrogen-free Cl-terminated Si(111) surfaces in all cases, whether vapor phase of neat liquid ammonia is used. The first-principles modeling of this complex system suggests that step-edge surface defects may play a key role in enabling the reaction under certain circumstances, despite the endothermic nature for Si-H bond formation.

  2. Aerobic Oxidation of an Osmium(III) N-Hydroxyguanidine Complex To Give Nitric Oxide.

    PubMed

    Xiang, Jing; Wang, Qian; Yiu, Shek-Man; Man, Wai-Lun; Kwong, Hoi-Ki; Lau, Tai-Chu

    2016-05-16

    The aerobic oxidation of the N-hydroxyguanidinum moiety of N-hydroxyarginine to NO is a key step in the biosynthesis of NO by the enzyme nitric oxide synthase (NOS). So far, there is no chemical system that can efficiently carry out similar aerobic oxidation to give NO. We report here the synthesis and X-ray crystal structure of an osmium(III) N-hydroxyguanidine complex, mer-[Os(III){NH═C(NH2)(NHOH)}(L)(CN)3](-) (OsGOH, HL = 2-(2-hydroxyphenyl)benzoxazole), which to the best of our knowledge is the first example of a transition metal N-hydroxyguanidine complex. More significantly, this complex readily undergoes aerobic oxidation at ambient conditions to generate NO. The oxidation is pH-dependent; at pH 6.8, fac-[Os(NO)(L)(CN)3](-) is formed in which the NO produced is bound to the osmium center. On the other hand, at pH 12, aerobic oxidation of OsGOH results in the formation of the ureato complex [Os(III)(NHCONH2)(L)(CN)3](2-) and free NO. Mechanisms for this aerobic oxidation at different pH values are proposed. PMID:27135258

  3. EXAMINING THE TEMPORAL VARIABILITY OF AMMONIA AND NITRIC OXIDE EMISSIONS FROM AGRICULTURAL PROCESSES

    EPA Science Inventory

    This paper examines the temporal variability of airborne emissions of ammonia from livestock operations and fertilizer application and nitric oxide from soils. In the United States, the livestock operations and fertilizer categories comprise the majority of the ammonia emissions...

  4. Enhanced abundance and diversity of ammonia-oxidizing Archaea in the Pearl River estuary

    NASA Astrophysics Data System (ADS)

    Xie, W.; Zhang, C. L.; Wang, P.; Zhou, X.; Guo, W.

    2014-12-01

    Thaumarchaeota are recently recognized as an important group of Archaea that can perform aerobic oxidation of ammonia in a wide range of environments. The goal of this study was to evaluate changes in abundance and diversity of planktonic ammonia-oxidizing Archaea (e.g., Thaumarchaeota) along a salinity gradient from the lower Pearl River to the northern South China Sea. Quantitative PCR and sequencing of total archaeal 16S rRNA gene and the archaeal amoA gene were performed on suspended particulate organic matter collected in different seasons from the freshwater to the ocean water. Total amoA gene copies and relative abundance of Thaumarchaeota all peaked in the estuary where salinity ranged between 4.5‰ and 26.7‰. The diversity of archaeal amoA gene was also highest in the estuary. Seasonality and SiO32- appear to be two major factors affecting the distribution of subclusters of archaeal amoA genes. For example, Nitrosopumilus subcluster 7.1 was most abundant in winter in fresh water, whereas Nitrososphaera were more abundant in summer. Samples collected from the area around Wanshan Island, which is located at the outermost part of the Pearl River estuary, had high abundance of unclassified archaeal amoA genes, suggesting some new groups of Thaumarchaeota might inhabit this water body. Overall, the high abundance and diversity of Thaumarchaeota in the Pearl River estuary may indicate enhanced role of AOA in nitrogen cycle in this dynamic ecosystem.

  5. Bacteria dominate the ammonia-oxidizing community in a hydrothermal vent site at the Mid-Atlantic Ridge of the South Atlantic Ocean.

    PubMed

    Xu, Wei; Li, Meng; Ding, Jie-Fei; Gu, Ji-Dong; Luo, Zhu-Hua

    2014-09-01

    Ammonia oxidation is the first and rate-limiting step of nitrification, which is carried out by two groups of microorganisms: ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). In this study, diversity and abundance of AOB and AOA were investigated in five rock samples from a deep-sea hydrothermal vent site at the Mid-Atlantic Ridge (MAR) of the South Atlantic Ocean. Both bacterial and archaeal ammonia monooxygenase subunit A (amoA) gene sequences obtained in this study were closely related to the sequences retrieved from deep-sea environments, indicating that AOB and AOA in this hydrothermal vent site showed typical deep ocean features. AOA were more diverse but less abundant than AOB. The ratios of AOA/AOB amoA gene abundance ranged from 1/3893 to 1/242 in all investigate samples, indicating that bacteria may be the major members responding to the aerobic ammonia oxidation in this hydrothermal vent site. Furthermore, diversity and abundance of AOA and AOB were significantly correlated with the contents of total nitrogen and total sulfur in investigated samples, suggesting that these two environmental factors exert strong influences on distribution of ammonia oxidizers in deep-sea hydrothermal vent environment. PMID:24893665

  6. Mechanism of copper(I)/TEMPO-catalyzed aerobic alcohol oxidation.

    PubMed

    Hoover, Jessica M; Ryland, Bradford L; Stahl, Shannon S

    2013-02-13

    Homogeneous Cu/TEMPO catalyst systems (TEMPO = 2,2,6,6-tetramethylpiperidine-N-oxyl) have emerged as some of the most versatile and practical catalysts for aerobic alcohol oxidation. Recently, we disclosed a (bpy)Cu(I)/TEMPO/NMI catalyst system (NMI = N-methylimidazole) that exhibits fast rates and high selectivities, even with unactivated aliphatic alcohols. Here, we present a mechanistic investigation of this catalyst system, in which we compare the reactivity of benzylic and aliphatic alcohols. This work includes analysis of catalytic rates by gas-uptake and in situ IR kinetic methods and characterization of the catalyst speciation during the reaction by EPR and UV-visible spectroscopic methods. The data support a two-stage catalytic mechanism consisting of (1) "catalyst oxidation" in which Cu(I) and TEMPO-H are oxidized by O(2) via a binuclear Cu(2)O(2) intermediate and (2) "substrate oxidation" mediated by Cu(II) and the nitroxyl radical of TEMPO via a Cu(II)-alkoxide intermediate. Catalytic rate laws, kinetic isotope effects, and spectroscopic data show that reactions of benzylic and aliphatic alcohols have different turnover-limiting steps. Catalyst oxidation by O(2) is turnover limiting with benzylic alcohols, while numerous steps contribute to the turnover rate in the oxidation of aliphatic alcohols. PMID:23317450

  7. Impact of TiO₂ and ZnO nanoparticles at predicted environmentally relevant concentrations on ammonia-oxidizing bacteria cultures under ammonia oxidation.

    PubMed

    Luo, Zhuanxi; Qiu, Zhaozheng; Chen, Zheng; Du Laing, Gijs; Liu, Aifen; Yan, Changzhou

    2015-02-01

    Increased application of titanium dioxide and zinc oxide nanoparticles (nano-TiO2 and nano-ZnO) raises concerns related to their environmental impacts. The effects that such nanoparticles have on environmental processes and the bacteria that carry them out are largely unknown. In this study, ammonia-oxidizing bacteria (AOB) enrichment cultures, grown from surface sediments taken from an estuary wetland in Fujian Province, China, were spiked with nano-TiO2 and nano-ZnO (with an average size of 32 and 43 nm, respectively) at predicted environmentally relevant concentrations (≤2 mg L(-1)) to determine their impacts on ammonia oxidation and the mechanisms involved. Results showed that higher nano-TiO2 concentrations significantly inhibited ammonia oxidation in enrichment cultures. It is noteworthy that the average ammonia oxidation rate was significantly correlated to the Shannon index, the Simpson's index, and AOB abundance. This suggested that ammonia oxidation inhibition primarily resulted from a reduction of AOB biodiversity and abundance. However, AOB biodiversity and abundance as well as the average ammonia oxidation rate were not inhibited by nano-ZnO at predicted environmentally relevant concentrations. Accordingly, an insignificant correlation was established between biodiversity and abundance of the AOB amoA gene and the average ammonia oxidation rate under nano-ZnO treatments. AOB present in samples belonged to the β-Proteobacteria class with an affinity close to Nitrosospira and Nitrosomonas genera. This suggested that identified impacts of nano-TiO2 and nano-ZnO on ammonia oxidation processes can be extrapolated to some extent to natural aquatic environments. Complex impacts on AOB may result from different nanomaterials present in aquatic environments at various ambient conditions. Further investigation on how and to what extent different nanomaterials influence AOB diversity and abundance and their subsequent ammonia oxidation processes is therefore

  8. Oxovanadium complex-catalyzed aerobic oxidation of propargylic alcohols.

    PubMed

    Maeda, Yasunari; Kakiuchi, Nobuyuki; Matsumura, Satoshi; Nishimura, Takahiro; Kawamura, Takashi; Uemura, Sakae

    2002-09-20

    A catalytic system consisting of vanadium oxyacetylacetonate [VO(acac)(2)] and 3 A molecular sieves (MS3A) in acetonitrile works effectively for the aerobic oxidation of propargylic alcohols [R(1)CH(OH)Ctbd1;CR(2)] to the corresponding carbonyl compounds under an atmospheric pressure of molecular oxygen. Although the reactivity of alpha-acetylenic alkanols (R(1) = alkyl) is lower compared to that of the alcohols of R(1) = aryl, alkenyl, and alkynyl, the use of VO(hfac)(2) as a catalyst and the addition of hexafluoroacetylacetone improve the product yield in these cases. A catalytic cycle involving a vanadium(V) alcoholate species and beta-hydrogen elimination from it has been proposed for this oxidation. PMID:12227802

  9. Amperometric detection and electrochemical oxidation of aliphatic amines and ammonia on silver-lead oxide thin-film electrodes

    SciTech Connect

    Ge, Jisheng

    1996-01-08

    This thesis comprises three parts: Electrocatalysis of anodic oxygen-transfer reactions: aliphatic amines at mixed Ag-Pb oxide thin-film electrodes; oxidation of ammonia at anodized Ag-Pb eutectic alloy electrodes; and temperature effects on oxidation of ethylamine, alanine, and aquated ammonia.

  10. Ammonia

    Integrated Risk Information System (IRIS)

    Ammonia ; CASRN 7664 - 41 - 7 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Effects

  11. Drivers of archaeal ammonia-oxidizing communities in soil.

    PubMed

    Zhalnina, Kateryna; de Quadros, Patrícia Dörr; Camargo, Flavio A O; Triplett, Eric W

    2012-01-01

    Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA. PMID:22715335

  12. Drivers of archaeal ammonia-oxidizing communities in soil

    PubMed Central

    Zhalnina, Kateryna; de Quadros, Patrícia Dörr; Camargo, Flavio A. O.; Triplett, Eric W.

    2012-01-01

    Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA. PMID:22715335

  13. Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea)

    PubMed Central

    Lipsewers, Yvonne A.; Bale, Nicole J.; Hopmans, Ellen C.; Schouten, Stefan; Sinninghe Damsté, Jaap S.; Villanueva, Laura

    2014-01-01

    Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria. PMID:25250020

  14. Toxic effects of butyl elastomers on aerobic methane oxidation

    NASA Astrophysics Data System (ADS)

    Niemann, Helge; Steinle, Lea I.; Blees, Jan H.; Krause, Stefan; Bussmann, Ingeborg; Lehmann, Moritz F.; Treude, Tina

    2013-04-01

    Large quantities of the potent greenhouse gas methane are liberated into the water column of marine and lacustrine environments where it may be consumed by aerobic methane oxidising bacteria before reaching the atmosphere.The reliable quantification of aerobic methane oxidation (MOx) rates is consequently of paramount importance for estimating methane budgets and to understand the controls on water column methane cycling. A widely used set of methods for measuring MOx rates is based on the incubation of water samples during which the consumption of methane is monitored, for instance with radio-tracer assays. Typically, incubation vessels are sealed with butyl rubber stoppers because these elastomers are essentially impermeable for gases at the relevant time scales. We tested the effect of different stopper materials (unmodified- and halogenated butyl rubber) on MOx activity in environmental samples and in cultures of methane oxidising bacteria. MOx rates in samples sealed with unmodified butyl rubber were > 75% lower compared to parallel incubations with halogenated butyl rubber seals, suggesting inhibiting/toxic effects associated with the use of unmodified butyl elastomers. To further explore the cause of these effects, we analysed aqueous extracts of the different stoppers. Halogenated butyl rubber stoppers appeared to bleed off comparably little amounts of organics. In stark contrast, extracts of unmodified butyl rubber were contaminated with various organic compounds including potential bactericides such as benzyltoluenes, phenylalkanes and benzuothiazoles. We also found tetramethylthiourea, a scavenger of active oxygen species, which may inhibit the MOx pathway.

  15. Mechanism of Copper(I)/TEMPO-Catalyzed Aerobic Alcohol Oxidation

    PubMed Central

    Hoover, Jessica M.; Ryland, Bradford L.; Stahl, Shannon S.

    2013-01-01

    Homogeneous Cu/TEMPO catalyst systems (TEMPO = 2,2,6,6-tetramethylpiperidine-N-oxyl) have emerged as some of the most versatile and practical catalysts for aerobic alcohol oxidation. Recently, we disclosed a (bpy)CuI/TEMPO/NMI catalyst system (NMI = N-methylimidazole) that exhibits fast rates and high selectivities, even with unactivated aliphatic alcohols. Here, we present a mechanistic investigation of this catalyst system, in which we compare the reactivity of benzylic and aliphatic alcohols. This work includes analysis of catalytic rates by gas-uptake and in situ IR kinetic methods and characterization of the catalyst speciation during the reaction by EPR and UV–visible spectroscopic methods. The data support a two-stage catalytic mechanism consisting of (1) “catalyst oxidation” in which CuI and TEMPO–H are oxidized by O2 via a binuclear Cu2O2 intermediate and (2) “substrate oxidation” mediated by CuII and the nitroxyl radical of TEMPO via a CuII-alkoxide intermediate. Catalytic rate laws, kinetic isotope effects, and spectroscopic data show that reactions of benzylic and aliphatic alcohols have different turnover-limiting steps. Catalyst oxidation by O2 is turnover limiting with benzylic alcohols, while numerous steps contribute to the turnover rate in the oxidation of aliphatic alcohols. PMID:23317450

  16. Comparative study on ammonia oxidation over Ni-based cermet anodes for solid oxide fuel cells

    NASA Astrophysics Data System (ADS)

    Molouk, Ahmed Fathi Salem; Yang, Jun; Okanishi, Takeou; Muroyama, Hiroki; Matsui, Toshiaki; Eguchi, Koichi

    2016-02-01

    In the current work, we investigate the performance of solid oxide fuel cells (SOFCs) with Ni‒yttria-stabilized zirconia (Ni-YSZ) and Ni‒gadolinia-dope ceria (Ni-GDC) cermet anodes fueled with H2 or NH3 in terms of the catalytic activity of ammonia decomposition. The cermet of Ni-GDC shows higher catalytic activity for ammonia decomposition than Ni-YSZ. In response to this, the performance of direct NH3-fueled SOFC improved by using Ni-GDC anode. Moreover, we observe further enhancement in the cell performance and the catalytic activity for ammonia decomposition with applying Ni-GDC anode synthesised by the glycine-nitrate combustion process. These results reveal that the high performance of Ni-GDC anode for the direct NH3-fueled SOFC results from its mixed ionic-electronic conductivity as well as high catalytic activity for ammonia decomposition.

  17. Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria

    PubMed Central

    Sonthiphand, Puntipar; Hall, Michael W.; Neufeld, Josh D.

    2014-01-01

    Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments. PMID:25147546

  18. Community Structure of Ammonia-Oxidizing Archaea and Ammonia-Oxidizing Bacteria in Soil Treated with the Insecticide Imidacloprid

    PubMed Central

    Cycoń, Mariusz; Piotrowska-Seget, Zofia

    2015-01-01

    The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil using the denaturing gradient gel electrophoresis (DGGE) approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S) and the Shannon-Wiener index (H) values for soil treated with the field rate (FR) dosage of imidacloprid (1 mg/kg soil) showed no changes in measured indices for the AOA and AOB community members. In turn, the 10∗FR dosage of insecticide (10 mg/kg soil) negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4+, known as the most important factor which determines the contribution of these microorganisms to soil nitrification. PMID:25705674

  19. Inhibition, Inactivation, and Recovery of Ammonia-Oxidizing Activity in Cometabolism of Trichloroethylene by Nitrosomonas europaea

    PubMed Central

    Hyman, M. R.; Russell, S. A.; Ely, R. L.; Williamson, K. J.; Arp, D. J.

    1995-01-01

    The kinetics of the cometabolism of trichloroethylene (TCE) by the ammonia-oxidizing soil bacterium Nitrosomonas europaea in short-term (<10-min) incubations were investigated. Three individual effects of TCE cometabolism on this bacterium were characterized. First, we observed that TCE is a potent competitive inhibitor of ammonia oxidation by N. europaea. The K(infi) value for TCE (30 (mu)M) is similar to the K(infm) for ammonia (40 (mu)M). Second, we examined the toxicity associated with TCE cometabolism by N. europaea. Stationary-phase cells of N. europaea oxidized approximately 60 nmol of TCE per mg of protein before ammonia-oxidizing activity was completely inactivated by reactive intermediates generated during TCE oxidation. At the TCE concentrations used in these experiments, ammonia did not provide significant protection against inactivation. Third, we have determined the ability of cells to recover ammonia-oxidizing activity after exposure to TCE. Cells recovering from TCE inactivation were compared with cells recovering from the specific inactivation of ammonia-oxidizing activity by light. The recovery kinetics were indistinguishable when 40% or less of the activity was inactivated. However, at increased levels of inactivation, TCE-inactivated cells did not recover as rapidly as light-inactivated cells. The kinetics of recovery appear to be dependent on both the extent of inactivation of ammonia-oxidizing activity and the degree of specificity of the inactivating treatment. PMID:16534997

  20. pH regulates ammonia-oxidizing bacteria and archaea in paddy soils in Southern China.

    PubMed

    Li, Hu; Weng, Bo-Sen; Huang, Fu-Yi; Su, Jian-Qiang; Yang, Xiao-Ru

    2015-07-01

    Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrogen cycling. However, the effects of environmental factors on the activity, abundance, and diversity of AOA and AOB and the relative contributions of these two groups to nitrification in paddy soils are not well explained. In this study, potential nitrification activity (PNA), abundance, and diversity of amoA genes from 12 paddy soils in Southern China were determined by potential nitrification assay, quantitative PCR, and cloning. The results showed that PNA was highly variable between paddy soils, ranging from 4.05 ± 0.21 to 9.81 ± 1.09 mg NOx-N kg(-1) dry soil day(-1), and no significant correlation with soil parameters was found. The abundance of AOA was predominant over AOB, indicating that AOA may be the major members in aerobic ammonia oxidation in these paddy soils. Community compositions of AOA and AOB were highly variable among samples, but the variations were best explained by pH. AOA sequences were affiliated to the Nitrosopumilus cluster and Nitrososphaera cluster, and AOB were classified into the lineages of Nitrosospira and Nitrosomonas, with Nitrosospira being predominant over Nitrosomonas, accounting for 83.6 % of the AOB community. Moreover, the majority of Nitrosomonas was determined in neutral soils. Canonical correspondence analysis (CCA) analysis further demonstrated that AOA and AOB community structures were significantly affected by pH, soil total organic carbon, total nitrogen, and C/N ratio, suggesting that these factors exert strong effects on the distribution of AOB and AOA in paddy soils in Southern China. In conclusion, our results imply that soil pH was a key explanatory variable for both AOA and AOB community structure and nitrification activity. PMID:25744648

  1. Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean.

    PubMed

    Luo, Zhu-Hua; Xu, Wei; Li, Meng; Gu, Ji-Dong; Zhong, Tian-Hua

    2015-08-01

    Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean. PMID:26014493

  2. [Element Sulfur Autotrophic Denitrification Combined Anaerobic Ammonia Oxidation].

    PubMed

    Zhou, Jian; Huang, Yong; Liu, Xin; Yuan, Yi; Li Xiang; Wangyan, De-qing; Ding, Liang; Shao, Jing-wei; Zhao, Rong

    2016-03-15

    A novel element sulfur autotrophic denitrification combined anaerobic ammonia oxidation process, reacted in CSTR, was used to investigate the sulfate production and alkalinity consumption during the whole process. The element sulfur dosage was 50 g · L⁻¹. The inoculation volume of ANAMMOX granular sludge was 100 g · L⁻¹. The agitation rate and environment reaction temperature of the CSTR were set to 120 r · min⁻¹ and 35°C ± 0.5°C, respectively. The pH of influent was maintained in range of 8. 0-8. 4. During the start-up stage of sulfur based autotrophic denitrification, the nitrogen removal loading rate could reach 0.56-0.71 kg · (m³ · d) ⁻¹ in the condition of 5.3 h hydrogen retention time and 200 mg · L⁻¹ nitrate nitrogen. After the addition of 60 mg · L⁻¹ ammonia nitrogen, Δn(SO₄²⁻):Δn(NO₃⁻) decreased from 1.21 ± 0.06 to 1.01 ± 0.10, Δ(IC): Δ(NO₃⁻-N) decreased from 0.72 ± 0.1 to 0.51 ± 0.11, and the effluent pH increased from 6.5 to 7.2. During the combined stage, the ammonia concentration of effluent was 10.1-19.2 mg · L⁻¹, and the nitrate-nitrogen removal loading rate could be maintained in range of 0.66-0.88 kg · (m³ · d)⁻¹. The Δn (NH₄⁺): Δn (NO₃⁻) ratio reached 0.43, and the NO₃⁻ removal rate was increased by 60% in the simultaneous ammonia and nitrate removal reaction under the condition of G(T) = 22-64 s⁻¹ and pH = 8.08, while improper conditions reduced the efficiency of simultaneous reaction. PMID:27337901

  3. Determination of Ammonia Oxidizing Bacteria and Nitrate Oxidizing Bacteria in Wastewater and Bioreactors

    NASA Technical Reports Server (NTRS)

    Francis, Somilez Asya

    2014-01-01

    The process of water purification has many different physical, chemical, and biological processes. One part of the biological process is the task of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB). Both play critical roles in the treatment of wastewater by oxidizing toxic compounds. The broad term is nitrification, a naturally occurring process that is carried out by AOB and NOB by using oxidation to convert ammonia to nitrite and nitrite to nitrate. To monitor this biological activity, bacterial staining was performed on wastewater contained in inoculum tanks and biofilm samples from bioreactors. Using microscopy and qPCR, the purpose of this experiment was to determine if the population of AOB and NOB in wastewater and membrane bioreactors changed depending on temperature and hibernation conditions to determine the optimal parameters for AOB/NOB culture to effectively clean wastewater.

  4. Molybdenum Catalyzed Ammonia Borane Dehydrogenation: Oxidation State Specific Mechanisms

    PubMed Central

    2015-01-01

    Though numerous catalysts for the dehydrogenation of ammonia borane (AB) are known, those that release >2 equiv of H2 are uncommon. Herein, we report the synthesis of Mo complexes supported by a para-terphenyl diphosphine ligand, 1, displaying metal–arene interactions. Both a Mo0 N2 complex, 5, and a MoII bis(acetonitrile) complex, 4, exhibit high levels of AB dehydrogenation, releasing over 2.0 equiv of H2. The reaction rate, extent of dehydrogenation, and reaction mechanism vary as a function of the precatalyst oxidation state. Several Mo hydrides (MoII(H)2, [MoII(H)]+, and [MoIV(H)3]+) relevant to AB chemistry were characterized. PMID:25034459

  5. FORMATION OF HYDROXYLAMINE ON DUST GRAINS VIA AMMONIA OXIDATION

    SciTech Connect

    He, Jiao; Vidali, Gianfranco; Lemaire, Jean-Louis; Garrod, Robin T.

    2015-01-20

    The quest to detect prebiotic molecules in space, notably amino acids, requires an understanding of the chemistry involving nitrogen atoms. Hydroxylamine (NH{sub 2}OH) is considered a precursor to the amino acid glycine. Although not yet detected, NH{sub 2}OH is considered a likely target of detection with ALMA. We report on an experimental investigation of the formation of hydroxylamine on an amorphous silicate surface via the oxidation of ammonia. The experimental data are then fed into a simulation of the formation of NH{sub 2}OH in dense cloud conditions. On ices at 14 K and with a modest activation energy barrier, NH{sub 2}OH is found to be formed with an abundance that never falls below a factor 10 with respect to NH{sub 3}. Suggestions of conditions for future observations are provided.

  6. Low-ammonia niche of ammonia-oxidizing archaea in rotating biological contactors of a municipal wastewater treatment plant

    PubMed Central

    Sauder, Laura A; Peterse, Francien; Schouten, Stefan; Neufeld, Josh D

    2012-01-01

    The first step of nitrification is catalysed by both ammonia-oxidizing bacteria (AOB) and archaea (AOA), but physicochemical controls on the relative abundance and function of these two groups are not yet fully understood, especially in freshwater environments. This study investigated ammonia-oxidizing populations in nitrifying rotating biological contactors (RBCs) from a municipal wastewater treatment plant. Individual RBC stages are arranged in series, with nitrification at each stage creating an ammonia gradient along the flowpath. This RBC system provides a valuable experimental system for testing the hypothesis that ammonia concentration determines the relative abundance of AOA and AOB. The results demonstrate that AOA increased as ammonium decreased across the RBC flowpath, as indicated by qPCR for thaumarchaeal amoA and 16S rRNA genes, and core lipid (CL) and intact polar lipid (IPL) crenarchaeol abundances. Overall, there was a negative logarithmic relationship (R2 = 0.51) between ammonium concentration and the relative abundance of AOA amoA genes. A single AOA population was detected in the RBC biofilms; this phylotype shared low amoA and 16S rRNA gene homology with existing AOA cultures and enrichments. These results provide evidence that ammonia availability influences the relative abundances of AOA and AOB, and that AOA are abundant in some municipal wastewater treatment systems. PMID:22639927

  7. Diversity and Abundance of Ammonia-Oxidizing Archaeal Nitrite Reductase (nirK) Genes in Estuarine Sediments of San Francisco Bay

    NASA Astrophysics Data System (ADS)

    Reji, L.; Lee, J. A.; Damashek, J.; Francis, C. A.

    2013-12-01

    Nitrification, the microbially-mediated aerobic oxidation of ammonia to nitrate via nitrite, is an integral component of the global biogeochemical nitrogen cycle. The first and rate-limiting step of nitrification, ammonia oxidation, is carried out by two distinct microbial groups: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Molecular ecological studies targeting the amoA gene have revealed the abundance and ubiquity of AOA in terrestrial as well as aquatic environments. In addition to the ammonia oxidation machinery that includes the amoA gene, AOA also encode a gene for copper-containing nitrite reductase (nirK). The distribution patterns and functional role of nirK in AOA remain mostly unknown; proposed functions include the indirect involvement in ammonia oxidation through the production of nitric oxide during nitrite reduction, and (2) nitrite detoxification. In the present study, the diversity and abundance of archaeal nirK genes in estuarine sediments were investigated using quantitative polymerase chain reaction, cloning and sequencing approaches. In sediment samples collected from the San Francisco Bay estuary, two archaeal nirK variants (AnirKa and AnirKb) were amplified using specific primer sets. Overall, AnirKa was observed to be significantly more abundant than AnirKb in the sediment samples, with variation in relative abundance spanning two to three orders of magnitude between sampling sites. Phylogenetic analysis revealed a number of unique archaeal nirK sequence types, as well as many that clustered with sequences from previous estuarine studies and cultured AOA isolates, such as Nitrosopumilus maritimus. This study yielded new insights into the diversity and abundance of archaeal nirK genes in estuarine sediments, and highlights the importance of further investigating the physiological role of this gene in AOA, as well as its suitability as a marker gene for studying AOA in the environment.

  8. Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments

    PubMed Central

    Li, Meng; Cao, Huiluo; Hong, Yiguo

    2010-01-01

    We investigated the diversity, spatial distribution, and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediment samples of different depths collected from a transect with different distances to mangrove forest in the territories of Hong Kong. Both the archaeal and bacterial amoA genes (encoding ammonia monooxygenase subunit A) from all samples supported distinct phylogenetic groups, indicating the presences of niche-specific AOA and AOB in mangrove sediments. The higher AOB abundances than AOA in mangrove sediments, especially in the vicinity of the mangrove trees, might indicate the more important role of AOB on nitrification. The spatial distribution showed that AOA had higher diversity and abundance in the surface layer sediments near the mangrove trees (0 and 10 m) but lower away from the mangrove trees (1,000 m), and communities of AOA could be clustered into surface and bottom sediment layer groups. In contrast, AOB showed a reverse distributed pattern, and its communities were grouped by the distances between sites and mangrove trees, indicating mangrove trees might have different influences on AOA and AOB community structures. Furthermore, the strong correlations among archaeal and bacterial amoA gene abundances and their ratio with NH4+, salinity, and pH of sediments indicated that these environmental factors have strong influences on AOA and AOB distributions in mangrove sediments. In addition, AOA diversity and abundances were significantly correlated with hzo gene abundances, which encodes the key enzyme for transformation of hydrazine into N2 in anaerobic ammonium-oxidizing (anammox) bacteria, indicating AOA and anammox bacteria may interact with each other or they are influenced by the same controlling factors, such as NH4+. The results provide a better understanding on using mangrove wetlands as biological treatment systems for removal of nutrients. Electronic supplementary material The online version of this

  9. Environmental control on aerobic methane oxidation in coastal waters

    NASA Astrophysics Data System (ADS)

    Steinle, Lea; Maltby, Johanna; Engbersen, Nadine; Zopfi, Jakob; Bange, Hermann; Elvert, Marcus; Hinrichs, Kai-Uwe; Kock, Annette; Lehmann, Moritz; Treude, Tina; Niemann, Helge

    2016-04-01

    Large quantities of methane are produced in anoxic sediments of continental margins and may be liberated to the overlying water column, where some of it is consumed by aerobic methane oxidizing bacteria (MOB). Aerobic methane oxidation (MOx) in the water column is consequently the final sink for methane before its release to the atmosphere, where it acts as a potent greenhouse gas. In the context of the ocean's contribution to atmospheric methane, coastal seas are particularly important accounting >75% of global methane emission from marine systems. Coastal oceans are highly dynamic, in particular with regard to the variability of methane and oxygen concentrations as well as temperature and salinity, all of which are potential key environmental factors controlling MOx. To determine important environmental controls on the activity of MOBs in coastal seas, we conducted a two-year time-series study with measurements of physicochemical water column parameters, MOx activity and the composition of the MOB community in a coastal inlet in the Baltic Sea (Boknis Eck Time Series Station, Eckernförde Bay - E-Bay). In addition, we investigated the influence of temperature and oxygen on MOx during controlled laboratory experiments. In E-Bay, hypoxia developed in bottom waters towards the end of the stratification period. Constant methane liberation from sediments resulted in bottom water methane accumulations and supersaturation (with respect to the atmospheric equilibrium) in surface waters. Here, we will discuss the factors impacting MOx the most, which were (i) perturbations of the water column (ii) temperature and (iii) oxygen concentration. (i) Perturbations of the water column caused by storm events or seasonal mixing led to a decrease in MOx, probably caused by replacement of stagnant water with a high standing stock of MOB by 'new' waters with a lower abundance of methanotrophs. b) An increase in temperature generally led to higher MOx rates. c) Even though methane was

  10. [Identification of a high ammonia nitrogen tolerant and heterotrophic nitrification-aerobic denitrification bacterial strain TN-14 and its nitrogen removal capabilities].

    PubMed

    Xin, Xin; Yao, Li; Lu, Lei; Leng, Lu; Zhou, Ying-Qin; Guo, Jun-Yuan

    2014-10-01

    A new strain of high ammonia nitrogen tolerant and heterotrophic nitrification-aerobic denitrification bacterium TN-14 was isolated from the environment. Its physiological and biochemical characteristics and molecular identification, performences of heterotrophic nitrification-aerobic, the abilities of resistance to ammonia nitrogen as well as the decontamination abilities were studied, respectively. It was preliminary identified as Acinetobacter sp. according to its physiological and biochemical characteristics and molecular identification results. In heterotrophic nitrification system, the ammonia nitrogen and total nitrogen removal rate of the bacterial strain TN-14 could reach 97.13% and 93.53% within 24 h. In nitrates denitrification system, the nitrate concentration could decline from 94.24 mg · L(-1) to 39.32 mg · L(-1) within 24 h, where the removal rate was 58.28% and the denitrification rate was 2.28 mg · (L · h)(-1); In nitrite denitrification systems, the initial concentration of nitrite could be declined from 97.78 mg · L(-1) to 21.30 mg x L(-1), with a nitrite nitrogen removal rate of 78.22%, and a denitrification rate of 2.55 mg · (L· h)(-1). Meanwhile, strain TN-14 had the capability of flocculant production, and the flocculating rate could reach 94.74% when its fermentation liquid was used to treat 0.4% kaolin suspension. Strain TN-14 could grow at an ammonia nitrogen concentration as high as 1200 mg · L(-1). In the aspect of actual piggery wastewater treatment by strain TN-14, the removal rate of COD, ammonia nitrogen, TN and TP cloud reached 85.30%, 65.72%, 64.86% and 79.41%, respectively. Strain TN-14 has a good application prospect in biological treatment of real high- ammonia wastewater. PMID:25693403

  11. Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon “Candidatus Nitrosotalea devanaterra”

    PubMed Central

    Sayavedra-Soto, Luis A.; Gallois, Nicolas; Schouten, Stefan; Stein, Lisa Y.; Prosser, James I.; Nicol, Graeme W.

    2016-01-01

    Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has been a long-standing paradox. While high rates of ammonia oxidation are frequently measured in acid soils, cultivated ammonia oxidizers grew only at near-neutral pH when grown in standard laboratory culture. Although a number of mechanisms have been demonstrated to enable neutrophilic AOB growth at low pH in the laboratory, these have not been demonstrated in soil, and the recent cultivation of the obligately acidophilic ammonia oxidizer “Candidatus Nitrosotalea devanaterra” provides a more parsimonious explanation for the observed high rates of activity. Analysis of the sequenced genome, transcriptional activity, and lipid content of “Ca. Nitrosotalea devanaterra” reveals that previously proposed mechanisms used by AOB for growth at low pH are not essential for archaeal ammonia oxidation in acidic environments. Instead, the genome indicates that “Ca. Nitrosotalea devanaterra” contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA. Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography–mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of “Ca. Nitrosotalea devanaterra” were not dominated by crenarchaeol, as found in neutrophilic AOA. This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization. PMID:26896134

  12. Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon "Candidatus Nitrosotalea devanaterra".

    PubMed

    Lehtovirta-Morley, Laura E; Sayavedra-Soto, Luis A; Gallois, Nicolas; Schouten, Stefan; Stein, Lisa Y; Prosser, James I; Nicol, Graeme W

    2016-05-01

    Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has been a long-standing paradox. While high rates of ammonia oxidation are frequently measured in acid soils, cultivated ammonia oxidizers grew only at near-neutral pH when grown in standard laboratory culture. Although a number of mechanisms have been demonstrated to enable neutrophilic AOB growth at low pH in the laboratory, these have not been demonstrated in soil, and the recent cultivation of the obligately acidophilic ammonia oxidizer "Candidatus Nitrosotalea devanaterra" provides a more parsimonious explanation for the observed high rates of activity. Analysis of the sequenced genome, transcriptional activity, and lipid content of "Ca Nitrosotalea devanaterra" reveals that previously proposed mechanisms used by AOB for growth at low pH are not essential for archaeal ammonia oxidation in acidic environments. Instead, the genome indicates that "Ca Nitrosotalea devanaterra" contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA. Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography-mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of "Ca Nitrosotalea devanaterra" were not dominated by crenarchaeol, as found in neutrophilic AOA. This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization. PMID:26896134

  13. Ammonia-oxidizing Archaea in laboratory-scale activated sludge systems for wastewater of low- or high-ammonium concentration.

    PubMed

    Oishi, Ryu; Hirooka, Kayako; Otawa, Kenichi; Tada, Chika; Nakai, Yutaka

    2012-07-01

    Ammonia-oxidizing bacteria (AOB) is known as ammonia-oxidizer in wastewater treatment systems. However, ammonia-oxidizing Archaea (AOA) is found from various environments, including wastewater treatment systems. In this study, to investigate the relationships between AOA population and ammonia concentration, AOA was monitored in two laboratory-scale reactors treating artificial wastewater of different ammonium concentrations by denaturing gradient gel electrophoresis targeting ammonia monooxygenase genes. At day 60 of the operation, AOA populations dominant in each reactor differed, suggesting the importance of influent ammonia concentration in dominant AOA selection. PMID:22776796

  14. Distribution of ammonia oxidizers in relation to vegetation characteristics in the Qilian Mountains, northwestern China

    NASA Astrophysics Data System (ADS)

    Tai, X. S.; Mao, W. L.; Liu, G. X.; Chen, T.; Zhang, W.; Wu, X. K.; Long, H. Z.; Zhang, B. G.; Gao, T. P.

    2014-04-01

    Nitrogen is the major limiting nutrient in cold environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in alpine meadow soils in northwestern China, namely those catalyzing the rate-limiting step of ammonia oxidation. In this study, ammonia-oxidizing communities in alpine meadow soils were characterized by real-time PCR and clone sequencing by targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. The results demonstrated that ammonia-oxidizing archaea (AOA) outnumbered ammonia-oxidizing bacteria (AOB) in the alpine meadow soils. Most of the AOA phylotypes detected in the study region fell within typical Group I.1b of Thaumarchaeota. Interestingly, a new ammonia-oxidizing archaeal group named "Kobresia meadow soil group" was found. Phylogenetic analysis of AOB communities exhibited a dominance of Nitrosospira-like sequences affiliated to beta-Proteobacteria. Compared with other alpine environments, Qilian Mountains had a great phylogenetic diversity of ammonia oxidizers. Principal Component Analysis (PCA) analysis showed that distinct AOA/AOB phylotype groups were attributed to different meadow types, reflecting an overall distribution of ammonia-oxidizing communities associated with meadow types. Redundancy Analysis (RDA) analysis showed that Axis 1 (90.9%) together with Axis 2 (9.1%) explained all the variables while Axis 1 exhibited a significant explanatory power. So that vegetation coverage mostly correlated to Axis 1 was the most powerful environmental factor in the study region. Characteristics of ammonia-oxidizing communities showed a close association with vegetation coverage.

  15. Prevalence of Nitrosomonas cluster 7 populations in the ammonia-oxidizing community of a submerged membrane bioreactor treating urban wastewater under different operation conditions.

    PubMed

    Cerrone, F; Poyatos, J M; Molina-Muñoz, M; Cortés-Lorenzo, C; González-López, J; Rodelas, B

    2013-07-01

    A pilot-scale ultrafiltration membrane bioreactor (MBR) was used for the aerobic treatment of urban wastewater in four experimental stages influenced by seasonal temperature and different sets of operation conditions. The structure of the ammonia-oxidizing bacteria (AOB) community was profiled by temperature gradient gel electrophoresis (TGGE), based on the amplification and separation of partial ammonia-monoxygenase subunit A (amoA) genes. Canonical correspondence analysis revealed that temperature, hydraulic retention time and percentage of ammonia removal had a significant effect on the fingerprints of AOB communities. Phylogenetic analysis conducted on amoA/AmoA sequences of reamplified TGGE bands showed, however, that closely related ammonia-oxidizing populations inhabited the sludge of the MBR in all experimental stages. Nitrosomonas cluster 7 populations (N. europaea-N. eutropha cluster) prevailed under all conditions tested, even when the MBR was operated under complete biomass retention or at low temperatures, suggesting that the high ammonia concentrations in the system were determinant to select r-strategist AOB. PMID:22976820

  16. Reduced graphene oxide supported Au nanoparticles as an efficient catalyst for aerobic oxidation of benzyl alcohol

    NASA Astrophysics Data System (ADS)

    Yu, Xianqin; Huo, Yujia; Yang, Jing; Chang, Sujie; Ma, Yunsheng; Huang, Weixin

    2013-09-01

    Various Au/C catalysts were prepared by Au nanoparticels supported on different carbonaceous supports including reduced graphene oxide (RGO), activated carbon (AC) and graphite (GC) using sol-immobilization method. Au/RGO shows a much higher activity than Au/AC and Au/GC in the liquid phase aerobic oxidation of benzyl alcohol. The superior catalytic performance of Au/RGO may be related to the presence of surface O-containing functional groups and moderate graphite character of RGO supports.

  17. Bacterial domination over archaea in ammonia oxidation in a monsoon-driven tropical estuary.

    PubMed

    Puthiya Veettil, Vipindas; Abdulaziz, Anas; Chekidhenkuzhiyil, Jasmin; Kalanthingal Ramkollath, Lallu; Karayadi Hamza, Fausia; Kizhakkepat Kalam, Balachandran; Kallungal Ravunnikutty, Muraleedharan; Nair, Shanta

    2015-04-01

    Autotrophic ammonia oxidizing microorganisms, which are responsible for the rate-limiting step of nitrification in most aquatic systems, have not been studied in tropical estuaries. Cochin estuary (CE) is one of the largest, productive, and monsoon-driven estuary in India opening into the southeast Arabian Sea. CE receives surplus quantities of ammonia through industrial and domestic discharges. The distribution of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia-oxidizing bacteria (anammox) were studied using fluorescence in situ hybridization (FISH) and their relative contribution to the process as well as the governing factors were examined and reported for the first time from CE. The order of occurrence of these assemblages was β-proteobacteria (0.79 to 2 × 10(5) cells ml(-1)) > γ-proteobacteria (0.9 to 4.6 × 10(4) cells ml(-1)) > anammox (0.49 to 1.9 × 10(4) cells ml(-1)) > AOA (0.56 to 6.3 × 10(3) cells ml(-1)). Phylogenetic analysis of DGGE bands showed major affiliation of AOB to β-proteobacteria, while AOA was affiliated to Crenarchaeota. The abundance of AOB was mostly influenced by ammonia concentrations. The recovered ammonia oxidation rate of AOB was in the range of 45-65%, whereas for AOA, it was 15-45%, indicating that AOB were mostly responsible for the ammonia oxidation in CE during the study period. Overall, the present study provides an insight into the relevance and contribution of different groups of ammonia oxidizing bacteria in CE and emphasizes the need for further in depth studies across space and on season scale. PMID:25344857

  18. Bilogical Treatment for Ammonia Oxidation in Drinking Water Facilities

    EPA Science Inventory

    Ammonia is an unregulated compound, but is naturally occurring in many drinking water sources. It is also used by some treatment facilities to produce chloramines for disinfection purposes. Because ammonia is non-toxic, its presence in drinking water is often disregarded. Thro...

  19. Ammonia and nitrous oxide fluxes from a novel swine housing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ammonia emission and subsequent deposition can be a major source of pollution, causing nitrogen enrichment, acidification of soils and surface waters, and aerosol formation. In livestock production housing, ammonia emissions can also adversely affect the health, performance, and welfare of both ani...

  20. Ammonia-Oxidizing Bacteria in Biofilters Removing Trihalomethanes Are Related to Nitrosomonas oligotropha

    EPA Science Inventory

    Nitrifying biofilters degrading the four regulated trihalomethanes (THMs) trichloromethane (TCM), bromodichloromethane (BDCM), dibromochloromethane (DBCM), and tribromomethane (TBM) -were analyzed for the presence and activity of ammonia-oxidizing bacteria (AOB). Biofilter perfor...

  1. Ammonia-oxidizing archaea respond positively to inorganic nitrogen addition in desert soils.

    PubMed

    Marusenko, Yevgeniy; Garcia-Pichel, Ferran; Hall, Sharon J

    2015-02-01

    In soils, nitrogen (N) addition typically enhances ammonia oxidation (AO) rates and increases the population density of ammonia-oxidizing bacteria (AOB), but not that of ammonia-oxidizing archaea (AOA). We asked if long-term inorganic N addition also has similar consequences in arid land soils, an understudied yet spatially ubiquitous ecosystem type. Using Sonoran Desert top soils from between and under shrubs within a long-term N-enrichment experiment, we determined community concentration-response kinetics of AO and measured the total and relative abundance of AOA and AOB based on amoA gene abundance. As expected, N addition increased maximum AO rates and the abundance of bacterial amoA genes compared to the controls. Surprisingly, N addition also increased the abundance of archaeal amoA genes. We did not detect any major effects of N addition on ammonia-oxidizing community composition. The ammonia-oxidizing communities in these desert soils were dominated by AOA as expected (78% of amoA gene copies were related to Nitrososphaera), but contained unusually high contributions of Nitrosomonas (18%) and unusually low numbers of Nitrosospira (2%). This study highlights unique traits of ammonia oxidizers in arid lands, which should be considered globally in predictions of AO responses to changes in N availability. PMID:25764551

  2. Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China.

    PubMed

    Liang, Yueming; He, Xunyang; Liang, Shichu; Zhang, Wei; Chen, Xiangbi; Feng, Shuzheng; Su, Yirong

    2014-03-01

    Soil ammonia oxidizers play a critical role in nitrogen cycling and ecological restoration. The composition and structure of soil ammonia oxidizers and their impacting factors were studied in four typical ecosystem soils, tussock (T), shrub (S), secondary forest (SF), and primary forest (PF), during vegetation restoration in the Karst region of Southwest China. The composition and structure of the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities were characterized by sequencing the amoA and arch-amoA genes, respectively. The diversity of soil ammonia oxidizers (except in S) and plant Shannon diversity index gradually increased with vegetation restoration, and the ammonia oxidizer communities differed significantly (p < 0.001). Amplicons of AOA from the Nitrososphaera cluster dominated all four ecosystem soils. AOB Nitrosospira cluster 3b only appeared in PF and SF soils, while Nitrosospira cluster 3a species were found in all soils. Changes in AOB paralleled the changes in soil ammonium content that occurred with vegetation restoration. Redundancy analysis showed that the distribution of dominant AOB species was linked to pH, soil urease activity, and soil C/N ratio, whereas the distribution of dominant AOA species was mainly influenced by litter nitrogen content and C/N ratio. These results suggested that the composition and structure of the AOB community were more sensitive to changes in vegetation and soil ammonium content, and may be an important indicator of nitrogen availability in Karst ecosystem soils. PMID:23897748

  3. Ammonia-oxidizing microbial communities in reactors with efficient nitrification at low-dissolved oxygen

    PubMed Central

    Fitzgerald, Colin M.; Camejo, Pamela; Oshlag, J. Zachary; Noguera, Daniel R.

    2015-01-01

    Ammonia-oxidizing microbial communities involved in ammonia oxidation under low dissolved oxygen (DO) conditions (<0.3 mg/L) were investigated using chemostat reactors. One lab-scale reactor (NS_LowDO) was seeded with sludge from a full-scale wastewater treatment plant (WWTP) not adapted to low-DO nitrification, while a second reactor (JP_LowDO) was seeded with sludge from a full-scale WWTP already achieving low-DO nitrifiaction. The experimental evidence from quantitative PCR, rDNA tag pyrosequencing, and fluorescence in situ hybridization (FISH) suggested that ammonia-oxidizing bacteria (AOB) in the Nitrosomonas genus were responsible for low-DO nitrification in the NS_LowDO reactor, whereas in the JP_LowDO reactor nitrification was not associated with any known ammonia-oxidizing prokaryote. Neither reactor had a significant population of ammonia-oxidizing archaea (AOA) or anaerobic ammonium oxidation (anammox) organisms. Organisms isolated from JP_LowDO were capable of autotrophic and heterotrophic ammonia utilization, albeit without stoichiometric accumulation of nitrite or nitrate. Based on the experimental evidence we propose that Pseudomonas, Xanthomonadaceae, Rhodococcus, and Sphingomonas are involved in nitrification under low-DO conditions. PMID:25506762

  4. Nitrogen isotope fractionation during archaeal ammonia oxidation: Coupled estimates from isotopic measurements of ammonium and nitrite

    NASA Astrophysics Data System (ADS)

    Mooshammer, Maria; Stieglmeier, Michaela; Bayer, Barbara; Jochum, Lara; Melcher, Michael; Wanek, Wolfgang

    2014-05-01

    Ammonia-oxidizing archaea (AOA) are ubiquitous in marine and terrestrial environments and knowledge about the nitrogen (N) isotope effect associated with their ammonia oxidation activity will allow a better understanding of natural abundance isotope ratios, and therefore N transformation processes, in the environment. Here we examine the kinetic isotope effect for ammonia oxidation in a pure soil AOA culture (Ca. Nitrososphaera viennensis) and a marine AOA enrichment culture. We estimated the isotope effect from both isotopic signatures of ammonium and nitrite over the course of ammonia oxidation. Estimates of the isotope effect based on the change in the isotopic signature of ammonium give valuable insight, because these estimates are not subject to the same concerns (e.g., accumulation of an intermediate) as estimates based on isotopic measurements of nitrite. Our results show that both the pure soil AOA culture and a marine AOA enrichment culture have similar but substantial isotope effect during ammonia consumption (31-34 per mill; based on ammonium) and nitrite production (43-45 per mill; based on nitrite). The 15N fractionation factors of both cultures tested fell in the upper range of the reported isotope effects for archaeal and bacterial ammonia oxidation (10-41 per mill) or were even higher than those. The isotope fractionation for nitrite production was significantly larger than for ammonium consumption, indicating that (1) some intermediate (e.g., hydroxylamine) of ammonia oxidation accumulates, allowing for a second 15N fractionation step to be expressed, (2) a fraction of ammonia oxidized is lost via gaseous N forms (e.g., NO or N2O), which is 15N-enriched or (3) a fraction of ammonium is assimilated into AOA biomass, biomass becoming 15N-enriched. The significance of these mechanisms will be explored in more detail for the soil AOA culture, based on isotope modeling and isotopic measurements of biomass and N2O.

  5. Abundance of ammonia oxidizing bacteria and archaea under long-term maize cropping systems.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nitrification involves the oxidation of ammonium and is an important component of the overall N cycle. Nitrification occurs in two steps; first by oxidizing ammonium to nitrite, and then to nitrate. The first step is often the rate limiting step. Until recently ammonia-oxidizing bacteria were though...

  6. Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria.

    PubMed

    Kozlowski, Jessica A; Kits, K Dimitri; Stein, Lisa Y

    2016-01-01

    Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity. PMID:27462312

  7. Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria

    PubMed Central

    Kozlowski, Jessica A.; Kits, K. Dimitri; Stein, Lisa Y.

    2016-01-01

    Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity. PMID:27462312

  8. Ammonia effect on hydrogenotrophic methanogens and syntrophic acetate-oxidizing bacteria.

    PubMed

    Wang, Han; Fotidis, Ioannis A; Angelidaki, Irini

    2015-11-01

    Ammonia-rich substrates can cause inhibition on anaerobic digestion process. Syntrophic acetate-oxidizing bacteria (SAOB) and hydrogenotrophic methanogens are important for the ammonia inhibitory mechanism on anaerobic digestion. The roles and interactions of SAOB and hydrogenotrophic methanogens to ammonia inhibition effect are still unclear. The aim of the current study was to determine the ammonia toxicity levels of various pure strains of SAOB and hydrogenotrophic methanogens. Moreover, ammonia toxicity on the syntrophic-cultivated strains of SAOB and hydrogenotrophic methanogens was tested. Thus, four hydrogenotrophic methanogens (i.e. Methanoculleus bourgensis, Methanobacterium congolense, Methanoculleu thermophilus and Methanothermobacter thermautotrophicus), two SAOB (i.e. Tepidanaerobacter acetatoxydans and Thermacetogenium phaeum) and their syntrophic cultivation were assessed under 0.26, 3, 5 and 7 g NH4 (+)-N L(-1). The results showed that some hydrogenotrophic methanogens were equally, or in some cases, more tolerant to high ammonia levels compared to SAOB. Furthermore, a mesophilic hydrogenotrophic methanogen was more sensitive to ammonia toxicity compared to thermophilic methanogens tested in the study, which is contradicting to the general belief that thermophilic methanogens are more vulnerable to high ammonia loads compared to mesophilic. This unexpected finding underlines the fact that the complete knowledge of ammonia inhibition effect on hydrogenotrophic methanogens is still absent. PMID:26490748

  9. Ammonia Oxidizers in a Pilot-Scale Multilayer Rapid Infiltration System for Domestic Wastewater Treatment

    PubMed Central

    Lian, Yingli; Xu, Meiying; Zhong, Yuming; Yang, Yongqiang; Chen, Fanrong; Guo, Jun

    2014-01-01

    A pilot-scale multilayer rapid infiltration system (MRIS) for domestic wastewater treatment was established and efficient removal of ammonia and chemical oxygen demand (COD) was achieved in this study. The microbial community composition and abundance of ammonia oxidizers were investigated. Efficient biofilms of ammonia oxidizers in the stationary phase (packing material) was formed successfully in the MRIS without special inoculation. DGGE and phylogenetic analyses revealed that proteobacteria dominated in the MRIS. Relative abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) showed contrary tendency. In the flowing phase (water effluent), AOA diversity was significantly correlated with the concentration of dissolve oxygen (DO), NO3-N and NH3-N. AOB abundance was significantly correlated with the concentration of DO and chemical oxygen demand (COD). NH3-N and COD were identified as the key factors to shape AOB community structure, while no variable significantly correlated with that of AOA. AOA might play an important role in the MRIS. This study could reveal key environmental factors affecting the community composition and abundance of ammonia oxidizers in the MRIS. PMID:25479611

  10. Ammonia oxidizers in a pilot-scale multilayer rapid infiltration system for domestic wastewater treatment.

    PubMed

    Lian, Yingli; Xu, Meiying; Zhong, Yuming; Yang, Yongqiang; Chen, Fanrong; Guo, Jun

    2014-01-01

    A pilot-scale multilayer rapid infiltration system (MRIS) for domestic wastewater treatment was established and efficient removal of ammonia and chemical oxygen demand (COD) was achieved in this study. The microbial community composition and abundance of ammonia oxidizers were investigated. Efficient biofilms of ammonia oxidizers in the stationary phase (packing material) was formed successfully in the MRIS without special inoculation. DGGE and phylogenetic analyses revealed that proteobacteria dominated in the MRIS. Relative abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) showed contrary tendency. In the flowing phase (water effluent), AOA diversity was significantly correlated with the concentration of dissolve oxygen (DO), NO3-N and NH3-N. AOB abundance was significantly correlated with the concentration of DO and chemical oxygen demand (COD). NH3-N and COD were identified as the key factors to shape AOB community structure, while no variable significantly correlated with that of AOA. AOA might play an important role in the MRIS. This study could reveal key environmental factors affecting the community composition and abundance of ammonia oxidizers in the MRIS. PMID:25479611

  11. Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean

    PubMed Central

    Sintes, Eva; De Corte, Daniele; Haberleitner, Elisabeth; Herndl, Gerhard J.

    2016-01-01

    In marine ecosystems, Thaumarchaeota are most likely the major ammonia oxidizers. While ammonia concentrations vary by about two orders of magnitude in the oceanic water column, archaeal ammonia oxidizers (AOA) vary by only one order of magnitude from surface to bathypelagic waters. Thus, the question arises whether the key enzyme responsible for ammonia oxidation, ammonia monooxygenase (amo), exhibits different affinities to ammonia along the oceanic water column and consequently, whether there are different ecotypes of AOA present in the oceanic water column. We determined the abundance and phylogeny of AOA based on their amoA gene. Two ecotypes of AOA exhibited a distribution pattern reflecting the reported availability of ammonia and the physico-chemical conditions throughout the Atlantic, and from epi- to bathypelagic waters. The distinction between these two ecotypes was not only detectable at the nucleotide level. Consistent changes were also detected at the amino acid level. These changes include substitutions of polar to hydrophobic amino acid, and glycine substitutions that could have an effect on the configuration of the amo protein and thus, on its activity. Although we cannot identify the specific effect, the ratio of non-synonymous to synonymous substitutions (dN/dS) between the two ecotypes indicates a strong positive selection between them. Consequently, our results point to a certain degree of environmental selection on these two ecotypes that have led to their niche specialization. PMID:26903961

  12. Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean.

    PubMed

    Sintes, Eva; De Corte, Daniele; Haberleitner, Elisabeth; Herndl, Gerhard J

    2016-01-01

    In marine ecosystems, Thaumarchaeota are most likely the major ammonia oxidizers. While ammonia concentrations vary by about two orders of magnitude in the oceanic water column, archaeal ammonia oxidizers (AOA) vary by only one order of magnitude from surface to bathypelagic waters. Thus, the question arises whether the key enzyme responsible for ammonia oxidation, ammonia monooxygenase (amo), exhibits different affinities to ammonia along the oceanic water column and consequently, whether there are different ecotypes of AOA present in the oceanic water column. We determined the abundance and phylogeny of AOA based on their amoA gene. Two ecotypes of AOA exhibited a distribution pattern reflecting the reported availability of ammonia and the physico-chemical conditions throughout the Atlantic, and from epi- to bathypelagic waters. The distinction between these two ecotypes was not only detectable at the nucleotide level. Consistent changes were also detected at the amino acid level. These changes include substitutions of polar to hydrophobic amino acid, and glycine substitutions that could have an effect on the configuration of the amo protein and thus, on its activity. Although we cannot identify the specific effect, the ratio of non-synonymous to synonymous substitutions (dN/dS) between the two ecotypes indicates a strong positive selection between them. Consequently, our results point to a certain degree of environmental selection on these two ecotypes that have led to their niche specialization. PMID:26903961

  13. Ammonia-oxidizing archaea versus bacteria in two soil aquifer treatment systems.

    PubMed

    Ding, Kun; Wen, Xianghua; Li, Yuyang; Shen, Bo; Zhang, Bing

    2015-02-01

    So far, the contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation in wastewater treatment processes has not been well understood. In this study, two soil aquifer treatment (SATs) systems were built up to treat synthetic domestic wastewater (column 1) and secondary effluent (column 4), accomplishing an average of 95% ammonia removal during over 550 days of operation. Except at day 322, archaeal amoA genes always outnumbered bacterial amoA genes in both SATs as determined by using quantitative polymerase chain reaction (q-PCR). The ratios of archaeal amoA to 16S rRNA gene averaged at 0.70 ± 0.56 and 0.82 ± 0.62 in column 1 and column 4, respectively, indicating that all the archaea could be AOA carrying amoA gene in the SATs. The results of MiSeq-pyrosequencing targeting on archaeal and bacterial 16S rRNA genes with the primer pair of modified 515R/806R indicated that Nitrososphaera cluster affiliated with thaumarchaeal group I.1b was the dominant AOA species, while Nitrosospira cluster was the dominant ammonia-oxidizing bacteria (AOB). The statistical analysis showed significant relationship between AOA abundance (compared to AOB abundance) and inorganic and total nitrogen concentrations. Based on the mathematical model calculation for microbial growth, AOA had much greater capacity of ammonia oxidation as compared to the specific influent ammonia loading for AOA in the SATs, implying that a small fraction of the total AOA would actively work to oxidize ammonia chemoautotrophically whereas most of AOA would exhibit some level of functional redundancy. These results all pointed that AOA involved in microbial ammonia oxidation in the SATs. PMID:25381908

  14. Mathematical Modeling of Ammonia Electro-Oxidation on Polycrystalline Pt Deposited Electrodes

    NASA Astrophysics Data System (ADS)

    Diaz Aldana, Luis A.

    The ammonia electrolysis process has been proposed as a feasible way for electrochemical generation of fuel grade hydrogen (H2). Ammonia is identified as one of the most suitable energy carriers due to its high hydrogen density, and its safe and efficient distribution chain. Moreover, the fact that this process can be applied even at low ammonia concentration feedstock opens its application to wastewater treatment along with H 2 co-generation. In the ammonia electrolysis process, ammonia is electro-oxidized in the anode side to produce N2 while H2 is evolved from water reduction in the cathode. A thermodynamic energy requirement of just five percent of the energy used in hydrogen production from water electrolysis is expected from ammonia electrolysis. However, the absence of a complete understanding of the reaction mechanism and kinetics involved in the ammonia electro-oxidation has not yet allowed the full commercialization of this process. For that reason, a kinetic model that can be trusted in the design and scale up of the ammonia electrolyzer needs to be developed. This research focused on the elucidation of the reaction mechanism and kinetic parameters for the ammonia electro-oxidation. The definition of the most relevant elementary reactions steps was obtained through the parallel analysis of experimental data and the development of a mathematical model of the ammonia electro-oxidation in a well defined hydrodynamic system, such as the rotating disk electrode (RDE). Ammonia electro-oxidation to N 2 as final product was concluded to be a slow surface confined process where parallel reactions leading to the deactivation of the catalyst are present. Through the development of this work it was possible to define a reaction mechanism and values for the kinetic parameters for ammonia electro-oxidation that allow an accurate representation of the experimental observations on a RDE system. Additionally, the validity of the reaction mechanism and kinetic parameters

  15. Environmental Controls on Aerobic Methane Oxidation in Coastal Waters

    NASA Astrophysics Data System (ADS)

    Steinle, L.; Maltby, J.; Engbersen, N.; Zopfi, J.; Bange, H. W.; Elvert, M.; Hinrichs, K. U.; Kock, A.; Lehmann, M. F.; Treude, T.; Niemann, H.

    2015-12-01

    Large quantities of the greenhouse gas CH4 are produced in anoxic sediments of continental margins and may be liberated to the overlying water column, and later into the atmosphere. Indeed, coastal seas account for more than 75% of global oceanic CH4 emissions. Yet, aerobic CH4 oxidizing bacteria (MOB) consume an important part of CH4 in the water column, thus mitigating CH4 release to the atmosphere. Coastal oceans are highly dynamic systems, in particular with regard to the variability of temperature, salinity and oxygen concentrations, all of which are potential key environmental factors controlling MOx. To determine the most important controlling factors, we conducted a two-year time-series study with measurements of CH4, MOx, the composition of the MOB community, and physicochemical water column parameters in a coastal inlet in the Baltic Sea (Eckernförde(E-) Bay, Boknis Eck Time Series Station). In addition, we investigated the influence of temperature and oxygen on MOx during controlled laboratory experiments. In E-Bay, seasonal stratification leads to hypoxia in bottom waters towards the end of the stratification period. Methane is produced year-round in the sediments, resulting in accumulation of methane in bottom waters, and supersaturation (with respect to the atmospheric equilibrium) in surface waters. Here, we will discuss the factors impacting MOx the most, which were a) perturbations of the water column caused by storm events, currents or seasonal mixing, b) temperature and c) oxygen concentration. a) Perturbations of the water column led to a sharp decrease in MOx within hours, probably caused by replacement of 'old' water with a high standing stock of MOB by 'new' waters with a lower abundance of MOB. b) An increase in temperature generally led to higher MOx rates. c) Even though CH4 was abundant at all depths, MOx was highest in bottom waters (1-5 nM/d), which usually contain the lowest O2 concentrations. Lab-based experiments with adjusted O2

  16. Magnetron sputtered nanostructured cadmium oxide films for ammonia sensing

    SciTech Connect

    Dhivya, P.; Prasad, A.K.; Sridharan, M.

    2014-06-01

    Nanostructured cadmium oxide (CdO) films were deposited on to glass substrates by reactive dc magnetron sputtering technique. The depositions were carried out for different deposition times in order to obtain films with varying thicknesses. The CdO films were polycrystalline in nature with cubic structure showing preferred orientation in (1 1 1) direction as observed by X-ray diffraction (XRD). Field-emission scanning electron microscope (FE-SEM) micrographs showed uniform distribution of grains of 30–35 nm size and change in morphology from spherical to elliptical structures upon increasing the film thickness. The optical band gap value of the CdO films decreased from 2.67 to 2.36 eV with increase in the thickness. CdO films were deposited on to interdigitated electrodes to be employed as ammonia (NH{sub 3}) gas sensor. The fabricated CdO sensor with thickness of 294 nm has a capacity to detect NH{sub 3} as low as 50 ppm at a relatively low operating temperature of 150 °C with quick response and recovery time. - Highlights: • Nanostructured CdO films were deposited on to glass substrates using magnetron sputtering. • Deposition time was varied in order to obtain films with different thicknesses. • The CdO films were polycrystalline in nature with preferred orientation along (1 1 1) direction. • The optical bandgap values of the films decreased on increasing the thickness of the films. • CdO films with different thickness such as 122, 204, 294 nm was capable to detect NH{sub 3} down to 50 ppm at operating temperature of 150 °C.

  17. Formation of Amides from Imines via Cyanide-Mediated Metal-Free Aerobic Oxidation.

    PubMed

    Seo, Hong-Ahn; Cho, Yeon-Ho; Lee, Ye-Sol; Cheon, Cheol-Hong

    2015-12-18

    A new protocol for the direct formation of amides from imines derived from aromatic aldehydes via metal-free aerobic oxidation in the presence of cyanide is described. This protocol was applicable to various aldimines, and the desired amides were obtained in moderate to good yields. Mechanistic studies suggested that this aerobic oxidative amidation might proceed via the addition of cyanide to imines followed by proton transfer from carbon to nitrogen in the original imines, leading to carbanions of α-amino nitriles, which undergo subsequent oxidation with molecular oxygen in air to provide the desired amide compounds. PMID:26580330

  18. Response of performance and ammonia oxidizing bacteria community to high salinity stress in membrane bioreactor with elevated ammonia loading.

    PubMed

    Wang, Zhu; Luo, Gan; Li, Jun; Chen, Shi-Yu; Li, Yan; Li, Wen-Tao; Li, Ai-Min

    2016-09-01

    Effect of elevated ammonia loading rate (ALR) and increasing salinity on the operation of membrane bioreactor (MBR) and the response of microbial community were investigated. Results showed that MBR started up with 1% NaCl stress achieved amazing nitrification performance at high salinity up to 4% when treating wastewater containing 1000mg/L NH(+)4-N. Further increasing salinity to 7% led to failure of MBR unrecoverably. Steep decline of sludge activity contributed to the extremely worse performance. High-throughput sequencing analysis showed that both ALR and salinity had selective effects on the microbial community structure. In genus level, Methyloversatilis and Maribacter were enriched during the operation. Survival of salt-resistant microbes contributed to the rising of richness and diversity at 2% and 4% NaCl stress. Analysis of amoA-gene-based cloning revealed Nitrosomonas marina are chiefly responsible for catalyzing ammonia oxidation in high ALR at high salinity stress. PMID:27290667

  19. Catalytic Fehling's Reaction: An Efficient Aerobic Oxidation of Aldehyde Catalyzed by Copper in Water.

    PubMed

    Liu, Mingxin; Li, Chao-Jun

    2016-08-26

    The first example of homogeneous copper-catalyzed aerobic oxidation of aldehydes is reported. This method utilizes atmospheric oxygen as the sole oxidant, proceeds under extremely mild aqueous conditions, and covers a wide range of various functionalized aldehydes. Chromatography is generally not necessary for product purification. PMID:27505714

  20. Copper N-Heterocyclic Carbene: A Catalyst for Aerobic Oxidation or Reduction Reactions.

    PubMed

    Zhan, Le-Wu; Han, Lei; Xing, Ping; Jiang, Biao

    2015-12-18

    Copper N-heterocyclic carbene complexes can be readily used as catalysts for both aerobic oxidation of alcohols to aldehydes and reduction of imines to amines. Our methodology is universal for aromatic substrates and shows versatile tolerance to potential cascade reactions. A one-pot tandem synthetic strategy could afford useful imines and secondary amines via an oxidation-reduction strategy. PMID:26633757

  1. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta.

    PubMed

    Damashek, Julian; Smith, Jason M; Mosier, Annika C; Francis, Christopher A

    2014-01-01

    Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic

  2. Bioturbation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification

    PubMed Central

    Laverock, B.; Kitidis, V.; Tait, K.; Gilbert, J. A.; Osborn, A. M.; Widdicombe, S.

    2013-01-01

    Ocean acidification (OA), caused by the dissolution of increasing concentrations of atmospheric carbon dioxide (CO2) in seawater, is projected to cause significant changes to marine ecology and biogeochemistry. Potential impacts on the microbially driven cycling of nitrogen are of particular concern. Specifically, under seawater pH levels approximating future OA scenarios, rates of ammonia oxidation (the rate-limiting first step of the nitrification pathway) have been shown to dramatically decrease in seawater, but not in underlying sediments. However, no prior study has considered the interactive effects of microbial ammonia oxidation and macrofaunal bioturbation activity, which can enhance nitrogen transformation rates. Using experimental mesocosms, we investigated the responses to OA of ammonia oxidizing microorganisms inhabiting surface sediments and sediments within burrow walls of the mud shrimp Upogebia deltaura. Seawater was acidified to one of four target pH values (pHT 7.90, 7.70, 7.35 and 6.80) in comparison with a control (pHT 8.10). At pHT 8.10, ammonia oxidation rates in burrow wall sediments were, on average, fivefold greater than in surface sediments. However, at all acidified pH values (pH ≤ 7.90), ammonia oxidation rates in burrow sediments were significantly inhibited (by 79–97%; p < 0.01), whereas rates in surface sediments were unaffected. Both bacterial and archaeal abundances increased significantly as pHT declined; by contrast, relative abundances of bacterial and archaeal ammonia oxidation (amoA) genes did not vary. This research suggests that OA could cause substantial reductions in total benthic ammonia oxidation rates in coastal bioturbated sediments, leading to corresponding changes in coupled nitrogen cycling between the benthic and pelagic realms. PMID:23980243

  3. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta

    PubMed Central

    Damashek, Julian; Smith, Jason M.; Mosier, Annika C.; Francis, Christopher A.

    2015-01-01

    Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic

  4. Nitrification of archaeal ammonia oxidizers in a high- temperature hot spring

    NASA Astrophysics Data System (ADS)

    Chen, Shun; Peng, Xiaotong; Xu, Hengchao; Ta, Kaiwen

    2016-04-01

    The oxidation of ammonia by microbes has been shown to occur in diverse natural environments. However, the link of in situ nitrification activity to taxonomic identities of ammonia oxidizers in high-temperature environments remains poorly understood. Here, we studied in situ ammonia oxidation rates and the diversity of ammonia-oxidizing Archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3- pool dilution technique in the surface and bottom sediments were 4.80 and 5.30 nmol N g-1 h-1, respectively. Real-time quantitative polymerase chain reaction (qPCR) indicated that the archaeal 16S rRNA genes and amoA genes were present in the range of 0.128 to 1.96 × 108 and 2.75 to 9.80 × 105 gene copies g-1 sediment, respectively, while bacterial amoA was not detected. Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic Candidatus Nitrosocaldus yellowstonii, which represented the most abundant operational taxonomic units (OTU) in both surface and bottom sediments. The archaeal predominance was further supported by fluorescence in situ hybridization (FISH) visualization. The cell-specific rate of ammonia oxidation was estimated to range from 0.410 to 0.790 fmol N archaeal cell-1 h-1, higher than those in the two US Great Basin hot springs. These results suggest the importance of archaeal rather than bacterial ammonia oxidation in driving the nitrogen cycle in terrestrial geothermal environments.

  5. Respirometric characterization of aerobic sulfide, thiosulfate and elemental sulfur oxidation by S-oxidizing biomass.

    PubMed

    Mora, Mabel; López, Luis R; Lafuente, Javier; Pérez, Julio; Kleerebezem, Robbert; van Loosdrecht, Mark C M; Gamisans, Xavier; Gabriel, David

    2016-02-01

    Respirometry was used to reveal the mechanisms involved in aerobic biological sulfide oxidation and to characterize the kinetics and stoichiometry of a microbial culture obtained from a desulfurizing biotrickling filter. Physical-chemical processes such as stripping and chemical oxidation of hydrogen sulfide were characterized since they contributed significantly to the conversions observed in respirometric tests. Mass transfer coefficient for hydrogen sulfide and the kinetic parameters for chemical oxidation of sulfide with oxygen were estimated. The stoichiometry of the process was determined and the different steps in the sulfide oxidation process were identified. The conversion scheme proposed includes intermediate production of elemental sulfur and thiosulfate and the subsequent oxidation of both compounds to sulfate. A kinetic model describing each of the reactions observed during sulfide oxidation was calibrated and validated. The product selectivity was found to be independent of the dissolved oxygen to hydrogen sulfide concentration ratio in the medium at sulfide concentrations ranging from 3 to 30 mg S L(-1). Sulfide was preferentially consumed (SOURmax = 49.2 mg DO g(-1) VSS min(-1)) and oxidized to elemental sulfur at dissolved oxygen concentrations above 0.8 mg DO L(-1). Substrate inhibition of sulfide oxidation was observed (K(i,S(2-))= 42.4 mg S L(-1)). Intracellular sulfur accumulation also affected negatively the sulfide oxidation rate. The maximum fraction of elemental sulfur accumulated inside cells was estimated (25.6% w/w) and a shrinking particle equation was included in the kinetic model to describe elemental sulfur oxidation. The microbial diversity obtained through pyrosequencing analysis revealed that Thiothrix sp. was the main species present in the culture (>95%). PMID:26704759

  6. Trimetallic Au/Pt/Rh Nanoparticles as Highly Active Catalysts for Aerobic Glucose Oxidation

    NASA Astrophysics Data System (ADS)

    Zhang, Haijun; Cao, Yingnan; Lu, Lilin; Cheng, Zhong; Zhang, Shaowei

    2015-02-01

    This paper reports the findings of an investigation of the correlations between the catalytic activity for aerobic glucose oxidation and the composition of Au/Pt/Rh trimetallic nanoparticles (TNPs) with average diameters of less than 2.0 nm prepared by rapid injection of NaBH4. The prepared TNPs were characterized by UV-Vis, TEM, and HR-TEM. The catalytic activity of the alloy-structured TNPs for aerobic glucose oxidation is several times higher than that of Au monometallic nanoparticles with nearly the same particle size. The catalytic activities of the TNP catalysts were dependent not only on the composition, but also on the electronic structure. The high catalytic activities of the Au/Pt/Rh TNPs can be ascribed to the formed negative-charged Au atoms due to electron donation of Rh neighboring atoms acting as catalytically active sites for aerobic glucose oxidation.

  7. Development of Safe and Scalable Continuous-Flow Methods for Palladium-Catalyzed Aerobic Oxidation Reactions.

    PubMed

    Ye, Xuan; Johnson, Martin D; Diao, Tianning; Yates, Matthew H; Stahl, Shannon S

    2010-01-01

    The synthetic scope and utility of Pd-catalyzed aerobic oxidation reactions has advanced significantly over the past decade, and these reactions have potential to address important green-chemistry challenges in the pharmaceutical industry. This potential has been unrealized, however, because safety concerns and process constraints hinder large-scale applications of this chemistry. These limitations are addressed by the development of a continuous-flow tube reactor, which has been demonstrated on several scales in the aerobic oxidation of alcohols. Use of a dilute oxygen gas source (8% O(2) in N(2)) ensures that the oxygen/organic mixture never enters the explosive regime, and efficient gas-liquid mixing in the reactor minimizes decomposition of the homogeneous catalyst into inactive Pd metal. These results provide the basis for large-scale implementation of palladium-catalyzed (and other) aerobic oxidation reactions for pharmaceutical synthesis. PMID:20694169

  8. Bioinspired aerobic oxidation of secondary amines and nitrogen heterocycles with a bifunctional quinone catalyst.

    PubMed

    Wendlandt, Alison E; Stahl, Shannon S

    2014-01-01

    Copper amine oxidases are a family of enzymes with quinone cofactors that oxidize primary amines to aldehydes. The native mechanism proceeds via an iminoquinone intermediate that promotes high selectivity for reactions with primary amines, thereby constraining the scope of potential biomimetic synthetic applications. Here we report a novel bioinspired quinone catalyst system consisting of 1,10-phenanthroline-5,6-dione/ZnI2 that bypasses these constraints via an abiological pathway involving a hemiaminal intermediate. Efficient aerobic dehydrogenation of non-native secondary amine substrates, including pharmaceutically relevant nitrogen heterocycles, is demonstrated. The ZnI2 cocatalyst activates the quinone toward amine oxidation and provides a source of iodide, which plays an important redox-mediator role to promote aerobic catalytic turnover. These findings provide a valuable foundation for broader development of aerobic oxidation reactions employing quinone-based catalysts. PMID:24328193

  9. Bioinspired Aerobic Oxidation of Secondary Amines and Nitrogen Heterocycles with a Bifunctional Quinone Catalyst

    PubMed Central

    Wendlandt, Alison E.; Stahl, Shannon S.

    2014-01-01

    Copper amine oxidases are a family of enzymes with quinone cofactors that oxidize primary amines to aldehydes. The native mechanism proceeds via an iminoquinone intermediate that promotes high selectivity for reactions with primary amines, thereby constraining the scope of potential biomimetic synthetic applications. Here, we report a novel bioinspired quinone catalyst system, consisting of 1,10-phenanthroline-5,6-dione/ZnI2, that bypasses these constraints via an abiological pathway involving a hemiaminal intermediate. Efficient aerobic dehydrogenation of non-native secondary amine substrates, including pharmaceutically relevant nitrogen heterocycles, is demonstrated. The ZnI2 cocatalyst activates the quinone toward amine oxidation and provides a source of iodide, which plays an important redox-mediator role to promote aerobic catalytic turnover. These findings provide a valuable foundation for broader development of aerobic oxidation reactions employing quinone-based catalysts. PMID:24328193

  10. Isotopic signature of N(2)O produced by marine ammonia-oxidizing archaea.

    PubMed

    Santoro, Alyson E; Buchwald, Carolyn; McIlvin, Matthew R; Casciotti, Karen L

    2011-09-01

    The ocean is an important global source of nitrous oxide (N(2)O), a greenhouse gas that contributes to stratospheric ozone destruction. Bacterial nitrification and denitrification are thought to be the primary sources of marine N(2)O, but the isotopic signatures of N(2)O produced by these processes are not consistent with the marine contribution to the global N(2)O budget. Based on enrichment cultures, we report that archaeal ammonia oxidation also produces N(2)O. Natural-abundance stable isotope measurements indicate that the produced N(2)O had bulk δ(15)N and δ(18)O values higher than observed for ammonia-oxidizing bacteria but similar to the δ(15)N and δ(18)O values attributed to the oceanic N(2)O source to the atmosphere. Our results suggest that ammonia-oxidizing archaea may be largely responsible for the oceanic N(2)O source. PMID:21798895

  11. Kinetic analysis for ammonia decomposition in supercritical water oxidation of sewage sludge

    SciTech Connect

    Goto, Motonobu; Shiramizu, Daisuke; Kodama, Akio; Hirose, Tsutomu

    1999-11-01

    Supercritical water oxidation was applied to the destruction of municipal excess sewage sludge. The reaction was carried out in a batch reactor with hydrogen peroxide as an oxidant in the temperature range of 723--823 K. Ammonia and acetic acid are found to be refractory intermediates in supercritical water oxidation of organic wastes. Ammonia concentration produced during the reaction was measured as a function of reaction time. The dynamic data were analyzed by a first-order kinetics. The reaction rate constant coincides with those reported in the literature.

  12. Anti-Oxidative Defences Are Modulated Differentially in Three Freshwater Teleosts in Response to Ammonia-Induced Oxidative Stress

    PubMed Central

    Giblen, Terri; Zinta, Gaurav; De Rop, Michelle; Asard, Han; Blust, Ronny; De Boeck, Gudrun

    2014-01-01

    Oxidative stress and the antioxidant response induced by high environmental ammonia (HEA) were investigated in the liver and gills of three freshwater teleosts differing in their sensitivities to ammonia. The highly ammonia-sensitive salmonid Oncorhynchus mykiss (rainbow trout), the less ammonia sensitive cyprinid Cyprinus carpio (common carp) and the highly ammonia-resistant cyprinid Carassius auratus (goldfish) were exposed to 1 mM ammonia (as NH4HCO3) for 0 h (control), 3 h, 12 h, 24 h, 48 h, 84 h and 180 h. Results show that HEA exposure increased ammonia accumulation significantly in the liver of all the three fish species from 24 h–48 h onwards which was associated with an increment in oxidative stress, evidenced by elevation of xanthine oxidase activity and levels of hydrogen peroxide (H2O2) and malondialdehyde (MDA). Unlike in trout, H2O2 and MDA accumulation in carp and goldfish liver was restored to control levels (84 h–180 h); which was accompanied by a concomitant increase in superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase activity and reduced ascorbate content. Many of these defence parameters remained unaffected in trout liver, while components of the glutathione redox cycle (reduced glutathione, glutathione peroxidase and glutathione reductase) enhanced to a greater extent. The present findings suggest that trout rely mainly on glutathione dependent defensive mechanism while carp utilize SOD, CAT and ascorbate as anti-oxidative sentinels. Hepatic cells of goldfish appear to utilize each of these protective systems, and showed more effective anti-oxidative compensatory responses towards HEA than carp, while trout were least effective. The present work also indicates that HEA exposure resulted in a relatively mild oxidative stress in the gills of all three species. This probably explains the almost complete lack of anti-oxidative responses in branchial tissue. This research suggests that oxidative stress, as well as the antioxidant

  13. The abundance and diversity of ammonia-oxidizing bacteria in activated sludge under autotrophic domestication.

    PubMed

    Li, Qiang; Ma, Chao; Sun, Shifang; Xie, Hui; Zhang, Wei; Feng, Jun; Song, Cunjiang

    2013-04-01

    Ammonia-oxidizing bacteria (AOB) play a key role in nitrogen-removal wastewater treatment plants (WWTPs) as they can transform ammonia into nitrite. AOB can be enriched in activated sludge through autotrophic domestication although they are difficult to be isolated. In this study, autotrophic domestication was carried out in a lab-scale sequencing-batch-reactor (SBR) system with two activated sludge samples. The ammonia removal capacity of the sludge samples increased during the domestication, and pH exhibited a negative correlation with the ammonia removal amount, which indicated that it was one important factor of microbial ammonia oxidation. The count of AOB, measured by the most probable number (MPN) method, increased significantly during autotrophic domestication as ammonia oxidation efficiency was enhanced. We investigated the changes in the community structure of AOB before and after domestication by amoA clone library and T-RFLP profile. It showed that AOB had been successfully enriched and the community structure significantly shifted during the domestication. Two groups of AOB were found in sludge samples: Nitrosomonas-like group remained predominant all the time and Nitrosospira-like group changed obviously. Simultaneously, the total heterotrophic bacteria were investigated by MPN and Biolog assay. The metabolic diversity of heterotrophs had changed minutely, although the count of them decreased significantly and lost superiority of microbial communities in the sludge. PMID:24620598

  14. Ammonia oxidation is not required for growth of Group 1.1c soil Thaumarchaeota.

    PubMed

    Weber, Eva B; Lehtovirta-Morley, Laura E; Prosser, James I; Gubry-Rangin, Cécile

    2015-03-01

    Thaumarchaeota are among the most abundant organisms on Earth and are ubiquitous. Within this phylum, all cultivated representatives of Group 1.1a and Group 1.1b Thaumarchaeota are ammonia oxidizers, and play a key role in the nitrogen cycle. While Group 1.1c is phylogenetically closely related to the ammonia-oxidizing Thaumarchaeota and is abundant in acidic forest soils, nothing is known about its physiology or ecosystem function. The goal of this study was to perform in situ physiological characterization of Group 1.1c Thaumarchaeota by determining conditions that favour their growth in soil. Several acidic grassland, birch and pine tree forest soils were sampled and those with the highest Group 1.1c 16S rRNA gene abundance were incubated in microcosms to determine optimal growth temperature, ammonia oxidation and growth on several organic compounds. Growth of Group 1.1c Thaumarchaeota, assessed by qPCR of Group 1.1c 16S rRNA genes, occurred in soil, optimally at 30°C, but was not associated with ammonia oxidation and the functional gene amoA could not be detected. Growth was also stimulated by addition of organic nitrogen compounds (glutamate and casamino acids) but not when supplemented with organic carbon alone. This is the first evidence for non-ammonia oxidation associated growth of Thaumarchaeota in soil. PMID:25764563

  15. Agreement between Theory and Measurement in Quantification of Ammonia-Oxidizing Bacteria

    PubMed Central

    Coskuner, Gulnur; Ballinger, Stuart J.; Davenport, Russell J.; Pickering, Rheanne L.; Solera, Rosario; Head, Ian M.; Curtis, Thomas P.

    2005-01-01

    Autotrophic ammonia-oxidizing bacteria (AOB) are of vital importance to wastewater treatment plants (WWTP), as well as being an intriguing group of microorganisms in their own right. To date, corroboration of quantitative measurements of AOB by fluorescence in situ hybridization (FISH) has relied on assessment of the ammonia oxidation rate per cell, relative to published values for cultured AOB. Validation of cell counts on the basis of substrate transformation rates is problematic, however, because published cell-specific ammonia oxidation rates vary by over two orders of magnitude. We present a method that uses FISH in conjunction with confocal scanning laser microscopy to quantify AOB in WWTP, where AOB are typically observed as microcolonies. The method is comparatively simple, requiring neither detailed cell counts or image analysis, and yet it can give estimates of either cell numbers or biomass. Microcolony volume and diameter were found to have a log-normal distribution. We were able to show that virtually all (>96%) of the AOB biomass occurred as microcolonies. Counts of microcolony abundance and measurement of their diameter coupled with a calibration of microcolony dimensions against cell numbers or AOB biomass were used to determine AOB cell numbers and biomass in WWTP. Cell-specific ammonia oxidation rates varied between plants by over three orders of magnitude, suggesting that cell-specific ammonia oxidation is an important process variable. Moreover, when measured AOB biomass was compared with process-based estimates of AOB biomass, the two values were in agreement. PMID:16204554

  16. Biotransformation of Two Pharmaceuticals by the Ammonia-Oxidizing Archaeon Nitrososphaera gargensis

    PubMed Central

    2016-01-01

    The biotransformation of some micropollutants has previously been observed to be positively associated with ammonia oxidation activities and the transcript abundance of the archaeal ammonia monooxygenase gene (amoA) in nitrifying activated sludge. Given the increasing interest in and potential importance of ammonia-oxidizing archaea (AOA), we investigated the capabilities of an AOA pure culture, Nitrososphaera gargensis, to biotransform ten micropollutants belonging to three structurally similar groups (i.e., phenylureas, tertiary amides, and tertiary amines). N. gargensis was able to biotransform two of the tertiary amines, mianserin (MIA) and ranitidine (RAN), exhibiting similar compound specificity as two ammonia-oxidizing bacteria (AOB) strains that were tested for comparison. The same MIA and RAN biotransformation reactions were carried out by both the AOA and AOB strains. The major transformation product (TP) of MIA, α-oxo MIA was likely formed via a two-step oxidation reaction. The first hydroxylation step is typically catalyzed by monooxygenases. Three RAN TP candidates were identified from nontarget analysis. Their tentative structures and possible biotransformation pathways were proposed. The biotransformation of MIA and RAN only occurred when ammonia oxidation was active, suggesting cometabolic transformations. Consistently, a comparative proteomic analysis revealed no significant differential expression of any protein-encoding gene in N. gargensis grown on ammonium with MIA or RAN compared with standard cultivation on ammonium only. Taken together, this study provides first important insights regarding the roles played by AOA in micropollutant biotransformation. PMID:27046099

  17. Biotransformation of Two Pharmaceuticals by the Ammonia-Oxidizing Archaeon Nitrososphaera gargensis.

    PubMed

    Men, Yujie; Han, Ping; Helbling, Damian E; Jehmlich, Nico; Herbold, Craig; Gulde, Rebekka; Onnis-Hayden, Annalisa; Gu, April Z; Johnson, David R; Wagner, Michael; Fenner, Kathrin

    2016-05-01

    The biotransformation of some micropollutants has previously been observed to be positively associated with ammonia oxidation activities and the transcript abundance of the archaeal ammonia monooxygenase gene (amoA) in nitrifying activated sludge. Given the increasing interest in and potential importance of ammonia-oxidizing archaea (AOA), we investigated the capabilities of an AOA pure culture, Nitrososphaera gargensis, to biotransform ten micropollutants belonging to three structurally similar groups (i.e., phenylureas, tertiary amides, and tertiary amines). N. gargensis was able to biotransform two of the tertiary amines, mianserin (MIA) and ranitidine (RAN), exhibiting similar compound specificity as two ammonia-oxidizing bacteria (AOB) strains that were tested for comparison. The same MIA and RAN biotransformation reactions were carried out by both the AOA and AOB strains. The major transformation product (TP) of MIA, α-oxo MIA was likely formed via a two-step oxidation reaction. The first hydroxylation step is typically catalyzed by monooxygenases. Three RAN TP candidates were identified from nontarget analysis. Their tentative structures and possible biotransformation pathways were proposed. The biotransformation of MIA and RAN only occurred when ammonia oxidation was active, suggesting cometabolic transformations. Consistently, a comparative proteomic analysis revealed no significant differential expression of any protein-encoding gene in N. gargensis grown on ammonium with MIA or RAN compared with standard cultivation on ammonium only. Taken together, this study provides first important insights regarding the roles played by AOA in micropollutant biotransformation. PMID:27046099

  18. Copper-catalyzed aerobic oxidative coupling: From ketone and diamine to pyrazine

    PubMed Central

    Wu, Kun; Huang, Zhiliang; Qi, Xiaotian; Li, Yingzi; Zhang, Guanghui; Liu, Chao; Yi, Hong; Meng, Lingkui; Bunel, Emilio E.; Miller, Jeffrey T.; Pao, Chih-Wen; Lee, Jyh-Fu; Lan, Yu; Lei, Aiwen

    2015-01-01

    Copper-catalyzed aerobic oxidative C–H/N–H coupling between simple ketones and diamines was developed toward the synthesis of a variety of pyrazines. Various substituted ketones were compatible for this transformation. Preliminary mechanistic investigations indicated that radical species were involved. X-ray absorption fine structure experiments elucidated that the Cu(II) species 5 coordinated by two N atoms at a distance of 2.04 Å and two O atoms at a shorter distance of 1.98 Å was a reactive one for this aerobic oxidative coupling reaction. Density functional theory calculations suggested that the intramolecular coupling of cationic radicals was favorable in this transformation. PMID:26601302

  19. Cu/Nitroxyl Catalyzed Aerobic Oxidation of Primary Amines into Nitriles at Room Temperature.

    PubMed

    Kim, Jinho; Stahl, Shannon S

    2013-07-01

    An efficient catalytic method has been developed for aerobic oxidation of primary amines to the corresponding nitriles. The reactions proceed at room temperature and employ a catalyst consisting of (4,4'- (t) Bu2bpy)CuI/ABNO (ABNO = 9-azabicyclo[3.3.1]nonan-3-one N-oxyl). The reactions exhibit excellent functional group compatibility and substrate scope, and are effective with benzylic, allylic and aliphatic amines. Preliminary mechanistic studies suggest that aerobic oxidation of the Cu catalyst is the turnover-limiting step of the reaction. PMID:24015373

  20. Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California

    PubMed Central

    Beman, J. M.; Bertics, Victoria J.; Braunschweiler, Thomas; Wilson, Jesse M.

    2012-01-01

    Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation–reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation) are active and actively coupled to one another – yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O2, NH4+, and NO3−) profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock (BR) and within Catalina Harbor (CH), oxygen penetration (0.24–0.5 cm depth) and the abundance of amoA genes (up to 9.30 × 107 genes g–1) varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in BR cores, and CH cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer) demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated CH sediments, where it may be carried out by either or both ammonia-oxidizing archaea and bacteria. PMID:22837756

  1. Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters

    PubMed Central

    Sauder, Laura A.; Mosquera, Mariela; Neufeld, Josh D.; Boon, Nico

    2014-01-01

    Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4–5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81–86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium

  2. Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.

    PubMed

    Bagchi, Samik; Vlaeminck, Siegfried E; Sauder, Laura A; Mosquera, Mariela; Neufeld, Josh D; Boon, Nico

    2014-01-01

    Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4-5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥ 81-86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium

  3. Multiple factors affect diversity and abundance of ammonia-oxidizing microorganisms in iron mine soil.

    PubMed

    Xing, Yi; Si, Yan-Xiao; Hong, Chen; Li, Yang

    2015-07-01

    Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. In this study, four soil samples collected from a desert zone in an iron-exploration area and others from farmland and planted forest soil in an iron mine surrounding area. We analyzed the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in iron-mining area near the Miyun reservoir using ammonia monooxygenase. A subunit gene (amoA) as molecular biomarker. Quantitative polymerase chain reaction was applied to explore the relationships between the abundance of AOA and AOB and soil physicochemical parameters. The results showed that AOA were more abundant than AOB and may play a more dominant role in the ammonia-oxidizing process in the whole region. PCR-denaturing gradient gel electrophoresis was used to analyze the structural changes of AOA and AOB. The results showed that AOB were much more diverse than AOA. Nitrosospira cluster three constitute the majority of AOB, and AOA were dominated by group 1.1b in the soil. Redundancy analysis was performed to explore the physicochemical parameters potentially important to AOA and AOB. Soil characteristics (i.e. water, ammonia, organic carbon, total nitrogen, available phosphorus, and soil type) were proposed to potentially contribute to the distributions of AOB, whereas Cd was also closely correlated to the distributions of AOB. The community of AOA correlated with ammonium and water contents. These results highlight the importance of multiple drivers in microbial niche formation as well as their affect on ammonia oxidizer composition, both which have significant consequences for ecosystem nitrogen functioning. PMID:25860433

  4. Aerobic bacterial pyrite oxidation and acid rock drainage during the Great Oxidation Event.

    PubMed

    Konhauser, Kurt O; Lalonde, Stefan V; Planavsky, Noah J; Pecoits, Ernesto; Lyons, Timothy W; Mojzsis, Stephen J; Rouxel, Olivier J; Barley, Mark E; Rosìere, Carlos; Fralick, Phillip W; Kump, Lee R; Bekker, Andrey

    2011-10-20

    The enrichment of redox-sensitive trace metals in ancient marine sedimentary rocks has been used to determine the timing of the oxidation of the Earth's land surface. Chromium (Cr) is among the emerging proxies for tracking the effects of atmospheric oxygenation on continental weathering; this is because its supply to the oceans is dominated by terrestrial processes that can be recorded in the Cr isotope composition of Precambrian iron formations. However, the factors controlling past and present seawater Cr isotope composition are poorly understood. Here we provide an independent and complementary record of marine Cr supply, in the form of Cr concentrations and authigenic enrichment in iron-rich sedimentary rocks. Our data suggest that Cr was largely immobile on land until around 2.48 Gyr ago, but within the 160 Myr that followed--and synchronous with independent evidence for oxygenation associated with the Great Oxidation Event (see, for example, refs 4-6)--marked excursions in Cr content and Cr/Ti ratios indicate that Cr was solubilized at a scale unrivalled in history. As Cr isotope fractionations at that time were muted, Cr must have been mobilized predominantly in reduced, Cr(III), form. We demonstrate that only the oxidation of an abundant and previously stable crustal pyrite reservoir by aerobic-respiring, chemolithoautotrophic bacteria could have generated the degree of acidity required to solubilize Cr(III) from ultramafic source rocks and residual soils. This profound shift in weathering regimes beginning at 2.48 Gyr ago constitutes the earliest known geochemical evidence for acidophilic aerobes and the resulting acid rock drainage, and accounts for independent evidence of an increased supply of dissolved sulphate and sulphide-hosted trace elements to the oceans around that time. Our model adds to amassing evidence that the Archaean-Palaeoproterozoic boundary was marked by a substantial shift in terrestrial geochemistry and biology. PMID:22012395

  5. Nitrate Reduction to Nitrite, Nitric Oxide and Ammonia by Gut Bacteria under Physiological Conditions

    PubMed Central

    Tiso, Mauro; Schechter, Alan N.

    2015-01-01

    The biological nitrogen cycle involves step-wise reduction of nitrogen oxides to ammonium salts and oxidation of ammonia back to nitrites and nitrates by plants and bacteria. Neither process has been thought to have relevance to mammalian physiology; however in recent years the salivary bacterial reduction of nitrate to nitrite has been recognized as an important metabolic conversion in humans. Several enteric bacteria have also shown the ability of catalytic reduction of nitrate to ammonia via nitrite during dissimilatory respiration; however, the importance of this pathway in bacterial species colonizing the human intestine has been little studied. We measured nitrite, nitric oxide (NO) and ammonia formation in cultures of Escherichia coli, Lactobacillus and Bifidobacterium species grown at different sodium nitrate concentrations and oxygen levels. We found that the presence of 5 mM nitrate provided a growth benefit and induced both nitrite and ammonia generation in E.coli and L.plantarum bacteria grown at oxygen concentrations compatible with the content in the gastrointestinal tract. Nitrite and ammonia accumulated in the growth medium when at least 2.5 mM nitrate was present. Time-course curves suggest that nitrate is first converted to nitrite and subsequently to ammonia. Strains of L.rhamnosus, L.acidophilus and B.longum infantis grown with nitrate produced minor changes in nitrite or ammonia levels in the cultures. However, when supplied with exogenous nitrite, NO gas was readily produced independently of added nitrate. Bacterial production of lactic acid causes medium acidification that in turn generates NO by non-enzymatic nitrite reduction. In contrast, nitrite was converted to NO by E.coli cultures even at neutral pH. We suggest that the bacterial nitrate reduction to ammonia, as well as the related NO formation in the gut, could be an important aspect of the overall mammalian nitrate/nitrite/NO metabolism and is yet another way in which the microbiome

  6. Nitrate reduction to nitrite, nitric oxide and ammonia by gut bacteria under physiological conditions.

    PubMed

    Tiso, Mauro; Schechter, Alan N

    2015-01-01

    The biological nitrogen cycle involves step-wise reduction of nitrogen oxides to ammonium salts and oxidation of ammonia back to nitrites and nitrates by plants and bacteria. Neither process has been thought to have relevance to mammalian physiology; however in recent years the salivary bacterial reduction of nitrate to nitrite has been recognized as an important metabolic conversion in humans. Several enteric bacteria have also shown the ability of catalytic reduction of nitrate to ammonia via nitrite during dissimilatory respiration; however, the importance of this pathway in bacterial species colonizing the human intestine has been little studied. We measured nitrite, nitric oxide (NO) and ammonia formation in cultures of Escherichia coli, Lactobacillus and Bifidobacterium species grown at different sodium nitrate concentrations and oxygen levels. We found that the presence of 5 mM nitrate provided a growth benefit and induced both nitrite and ammonia generation in E.coli and L.plantarum bacteria grown at oxygen concentrations compatible with the content in the gastrointestinal tract. Nitrite and ammonia accumulated in the growth medium when at least 2.5 mM nitrate was present. Time-course curves suggest that nitrate is first converted to nitrite and subsequently to ammonia. Strains of L.rhamnosus, L.acidophilus and B.longum infantis grown with nitrate produced minor changes in nitrite or ammonia levels in the cultures. However, when supplied with exogenous nitrite, NO gas was readily produced independently of added nitrate. Bacterial production of lactic acid causes medium acidification that in turn generates NO by non-enzymatic nitrite reduction. In contrast, nitrite was converted to NO by E.coli cultures even at neutral pH. We suggest that the bacterial nitrate reduction to ammonia, as well as the related NO formation in the gut, could be an important aspect of the overall mammalian nitrate/nitrite/NO metabolism and is yet another way in which the microbiome

  7. Missing aerobic-phase nitrogen: The potential for heterotrophic reduction of autotrophically generated nitrous oxide in a sequencing batch reactor wastewater treatment system.

    PubMed

    Shiskowskii, D M; Mavinic, D S

    2005-08-01

    Several biochemical pathways can induce nitrogen loss from aerated, aerobic wastewater treatment bioreactors. These pathways include "traditional" simultaneous nitrification-denitrification (SND) (i.e. autotrophic nitrification - heterotrophic denitrification), autotrophic denitrification, and anaerobic ammonia oxidation. An oxygen limitation, often expressed in terms of low dissolved oxygen (DO) concentration, is a common element of these pathways. The presented research investigated the effect of mixed liquor DO concentration and biomass slowly degradable carbon (SDC) utilization rate on the heterotrophic nitrous oxide (N2O) reduction rate, for biomass cultured in an anoxic/aerobic wastewater treatment bioreactor. Biomass oxygen and SDC availability-limitation, expressed in terms of DO concentration and SDC ultilization rate, respectively, were found to significantly impact the observed heterotrophic N2O reduction rate. The findings support the hypothesis that nitrogen lost from the mixed liquor of an aerobic bioreactor could result from simultaneous autotrophic N2O generation (i.e. autotrophic denitrification) and heterotrophic N2O reduction. The results also support the idea that autotrophic N2O generation could be occurring in a bioreactor, although N2O may not be measurable in the reactor off-gas. Therefore, this autotrophic N2O generation - heterotrophic N2O reduction mechanism provides an alternative explanation to nitrogen loss, when compared to "conventional" SND, where heterotrophic organisms are assumed to reduce autotrophically generated nitrite and nitrate to dinitrogen (N2). In addition, nitrogen loss speculatively attributed to N2 formation via anaerobic ammonia oxidation in oxygen-limited environments, again because of the absence of measurable N2O, may in fact be due to the autotrophic N2O generation - heterotrophic N2O reduction mechanism. PMID:16128383

  8. Highly practical copper(I)/TEMPO catalyst system for chemoselective aerobic oxidation of primary alcohols.

    PubMed

    Hoover, Jessica M; Stahl, Shannon S

    2011-10-26

    Aerobic oxidation reactions have been the focus of considerable attention, but their use in mainstream organic chemistry has been constrained by limitations in their synthetic scope and by practical factors, such as the use of pure O(2) as the oxidant or complex catalyst synthesis. Here, we report a new (bpy)Cu(I)/TEMPO catalyst system that enables efficient and selective aerobic oxidation of a broad range of primary alcohols, including allylic, benzylic, and aliphatic derivatives, to the corresponding aldehydes using readily available reagents, at room temperature with ambient air as the oxidant. The catalyst system is compatible with a wide range of functional groups and the high selectivity for 1° alcohols enables selective oxidation of diols that lack protecting groups. PMID:21861488

  9. Catalytic wet oxidation of ammonia solution: activity of the nanoscale platinum-palladium-rhodium composite oxide catalyst.

    PubMed

    Hung, Chang-Mao

    2009-04-15

    Aqueous solutions of 400-1000 mg/L of ammonia were oxidized in a trickle-bed reactor (TBR) in this study of nanoscale platinum-palladium-rhodium composite oxide catalysts, which were prepared by the co-precipitation of H(2)PtCl(6), Pd(NO(3))(3) and Rh(NO(3))(3). Hardly any of the dissolved ammonia was removed by wet oxidation in the absence of any catalyst, whereas about 99% of the ammonia was reduced during wet oxidation over nanoscale platinum-palladium-rhodium composite oxide catalysts at 503 K in an oxygen partial pressure of 2.0 MPa. A synergistic effect exists in the nanoscale platinum-palladium-rhodium composite structure, which is the material with the highest ammonia reduction activity. The nanometer-sized particles were characterized by TEM, XRD and FTIR. The effect of the initial concentration and reaction temperature on the removal of ammonia from the effluent streams was also studied at a liquid hourly space velocity of under 9 h(-1) in the wet catalytic processes. PMID:18657902

  10. Removal of ammonia from air on molybdenum and tungsten oxide modified activated carbons.

    PubMed

    Petit, Camille; Bandosz, Teresa J

    2008-04-15

    Microporous coconut-based activated carbon was impregnated with solutions of ammonium metatungstate or ammonium molybdate and then calcined in air in order to convert the salts into their corresponding oxides. The surface of those materials was characterized using adsorption of nitrogen, potentiometric titration, Fourier-transform infrared spectroscopy, X-ray diffraction, and thermal analysis. The results indicated a significant increase in surface acidity related to the presence of tungsten or molybdenum oxides. On the materials obtained, adsorption of ammonia from either dry or moist air was carried out. The oxides distributed on the surface provided Lewis and/or Brønsted centers for interactions with ammonia molecules or ammonium ions. Water on the surface of carbon or in the gas phase increased the amount of ammonia adsorbed via involvement of Brønsted-type interactions and/or by leading to the formation of molybdate or tungstate salts on the surface. Although the amount of ammonia adsorbed is closely related to the number of moles of oxides and their acidic centers, the carbon surface also contributes to the adsorption via providing small pores where ammonia can be dissolved in the water film. PMID:18497162

  11. Abundance and diversity of ammonia-oxidizing microorganisms in the sediments of Jinshan Lake.

    PubMed

    Liu, Biao; Li, Yimin; Zhang, Jinping; Zhou, Xiaohong; Wu, Chundu

    2014-11-01

    Community structures of ammonia-oxidizing microorganisms were investigated using PCR primers designed to specifically target the ammonia monooxygenase α-subunit (amoA) gene in the sediment of Jinshan Lake. Relationships between the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), and physicochemical parameters were also explored. The AOA abundance decreased sharply from west to east; however, the AOB abundance changed slightly with AOB outnumbering AOA in two of the four sediment samples (JS), JS3 and JS4. The AOA abundance was significantly correlated with the NH4-N, NO3-N, and TP. No significant correlations were observed between the AOB abundance and environmental variables. AOB had a higher diversity and richness of amoA genes than AOA. Among the 76 archaeal amoA sequences retrieved, 57.89, 38.16, and 3.95 % fell within the Nitrosopumilus, Nitrososphaera, and Nitrososphaera sister clusters, respectively. The 130 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 72.31 % and 27.69 % of the AOB group, respectively. Compared to the other three sample sites, the AOA and AOB community compositions at JS4 showed a large difference. This work could enhance our understanding of the roles of ammonia-oxidizing microorganisms in freshwater lake environment. PMID:25008777

  12. Nitrification of archaeal ammonia oxidizers in acid soils is supported by hydrolysis of urea

    PubMed Central

    Lu, Lu; Han, Wenyan; Zhang, Jinbo; Wu, Yucheng; Wang, Baozhan; Lin, Xiangui; Zhu, Jianguo; Cai, Zucong; Jia, Zhongjun

    2012-01-01

    The hydrolysis of urea as a source of ammonia has been proposed as a mechanism for the nitrification of ammonia-oxidizing bacteria (AOB) in acidic soil. The growth of Nitrososphaera viennensis on urea suggests that the ureolysis of ammonia-oxidizing archaea (AOA) might occur in natural environments. In this study, 15N isotope tracing indicates that ammonia oxidation occurred upon the addition of urea at a concentration similar to the in situ ammonium content of tea orchard soil (pH 3.75) and forest soil (pH 5.4) and was inhibited by acetylene. Nitrification activity was significantly stimulated by urea fertilization and coupled well with abundance changes in archaeal amoA genes in acidic soils. Pyrosequencing of 16S rRNA genes at whole microbial community level demonstrates the active growth of AOA in urea-amended soils. Molecular fingerprinting further shows that changes in denaturing gradient gel electrophoresis fingerprint patterns of archaeal amoA genes are paralleled by nitrification activity changes. However, bacterial amoA and 16S rRNA genes of AOB were not detected. The results strongly suggest that archaeal ammonia oxidation is supported by hydrolysis of urea and that AOA, from the marine Group 1.1a-associated lineage, dominate nitrification in two acidic soils tested. PMID:22592820

  13. Moisture and temperature controls on nitrification differ among ammonia oxidizer communities from three alpine soil habitats

    USGS Publications Warehouse

    Osborne, Brooke B; Baron, Jill S.; Wallenstein, Matthew D.

    2015-01-01

    Climate change is altering the timing and magnitude of biogeochemical fluxes in many high elevation ecosystems. The consequent changes in alpine nitrification rates have the potential to influence ecosystem scale responses. In order to better understand how changing temperature and moisture conditions may influence ammonia oxidizers and nitrification activity, we conducted laboratory incubations on soils collected in a Colorado watershed from three alpine habitats (glacial outwash, talus, and meadow). We found that bacteria, not archaea, dominated all ammonia oxidizer communities. Nitrification increased with moisture in all soils and under all temperature treatments. However, temperature was not correlated with nitrification rates in all soils. Site-specific temperature trends suggest the development of generalist ammonia oxidizer communities in soils with greater in situ temperature fluctuations and specialists in soils with more steady temperature regimes. Rapidly increasing temperatures and changing soil moisture conditions could explain recent observations of increased nitrate production in some alpine soils.

  14. Light-Dependent Aerobic Methane Oxidation Reduces Methane Emissions from Seasonally Stratified Lakes

    PubMed Central

    Oswald, Kirsten; Milucka, Jana; Brand, Andreas; Littmann, Sten; Wehrli, Bernhard; Kuypers, Marcel M. M.; Schubert, Carsten J.

    2015-01-01

    Lakes are a natural source of methane to the atmosphere and contribute significantly to total emissions compared to the oceans. Controls on methane emissions from lake surfaces, particularly biotic processes within anoxic hypolimnia, are only partially understood. Here we investigated biological methane oxidation in the water column of the seasonally stratified Lake Rotsee. A zone of methane oxidation extending from the oxic/anoxic interface into anoxic waters was identified by chemical profiling of oxygen, methane and δ13C of methane. Incubation experiments with 13C-methane yielded highest oxidation rates within the oxycline, and comparable rates were measured in anoxic waters. Despite predominantly anoxic conditions within the zone of methane oxidation, known groups of anaerobic methanotrophic archaea were conspicuously absent. Instead, aerobic gammaproteobacterial methanotrophs were identified as the active methane oxidizers. In addition, continuous oxidation and maximum rates always occurred under light conditions. These findings, along with the detection of chlorophyll a, suggest that aerobic methane oxidation is tightly coupled to light-dependent photosynthetic oxygen production both at the oxycline and in the anoxic bottom layer. It is likely that this interaction between oxygenic phototrophs and aerobic methanotrophs represents a widespread mechanism by which methane is oxidized in lake water, thus diminishing its release into the atmosphere. PMID:26193458

  15. Active Autotrophic Ammonia-Oxidizing Bacteria in Biofilm Enrichments from Simulated Creek Ecosystems at Two Ammonium Concentrations Respond to Temperature Manipulation▿†

    PubMed Central

    Avrahami, Sharon; Jia, Zhongjun; Neufeld, Josh D.; Murrell, J. Colin; Conrad, Ralf; Küsel, Kirsten

    2011-01-01

    The first step of nitrification, the oxidation of ammonia to nitrite, is important for reducing eutrophication in freshwater environments when coupled with anammox (anaerobic ammonium oxidation) or denitrification. We analyzed active formerly biofilm-associated aerobic ammonia-oxidizing communities originating from Ammerbach (AS) and Leutra South (LS) stream water (683 ± 550 [mean ± standard deviation] and 16 ± 7 μM NH4+, respectively) that were developed in a flow-channel experiment and incubated under three temperature regimens. By stable-isotope probing using 13CO2, we found that members of the Bacteria and not Archaea were the functionally dominant autotrophic ammonia oxidizers at all temperatures under relatively high ammonium loads. The copy numbers of bacterial amoA genes in 13C-labeled DNA were lower at 30°C than at 13°C in both stream enrichment cultures. However, the community composition of the ammonia-oxidizing bacteria (AOB) in the 13C-labeled DNA responded differently to temperature manipulation at two ammonium concentrations. In LS enrichments incubated at the in situ temperature (13°C), Nitrosomonas oligotropha-like sequences were retrieved with sequences from Nitrosospira AmoA cluster 4, while the proportion of Nitrosospira sequences increased at higher temperatures. In AS enrichments incubated at 13°C and 20°C, AmoA cluster 4 sequences were dominant; Nitrosomonas nitrosa-like sequences dominated at 30°C. Biofilm-associated AOB communities were affected differentially by temperature at two relatively high ammonium concentrations, implicating them in a potential role in governing contaminated freshwater AOB distributions. PMID:21890674

  16. Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

    PubMed Central

    Santoro, Alyson E; Casciotti, Karen L

    2011-01-01

    Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98–99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH3) to nitrite (NO2−). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (15ɛNH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15ɛNH3 ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15ɛNH3 is similar. PMID:21562601

  17. Treatment of real industrial wastewater using the combined approach of advanced oxidation followed by aerobic oxidation.

    PubMed

    Ramteke, Lokeshkumar P; Gogate, Parag R

    2016-05-01

    Fenton oxidation and ultrasound-based pretreatment have been applied to improve the treatment of real industrial wastewater based on the use of biological oxidation. The effect of operating parameters such as Fe(2+) loading, contact time, initial pH, and hydrogen peroxide loading on the extent of chemical oxygen demand (COD) reduction and change in biochemical oxygen demand (BOD5)/COD ratio has been investigated. The optimum operating conditions established for the pretreatment were initial pH of 3.0, Fe(2+) loading of 2.0, and 2.5 g L(-1) for the US/Fenton/stirring and Fenton approach, respectively, and temperature of 25 °C with initial H2O2 loading of 1.5 g L(-1). The use of pretreatment resulted in a significant increase in the BOD5/COD ratio confirming the production of easily digestible intermediates. The effect of the type of sludge in the aerobic biodegradation was also investigated based on the use of primary activated sludge (PAS), modified activated sludge (MAS), and activated sludge (AS). Enhanced removal of the pollutants as well as higher biomass yield was observed for MAS as compared to PAS and AS. The use of US/Fenton/stirring pretreatment under the optimized conditions followed by biological oxidation using MAS resulted in maximum COD removal at 97.9 %. The required hydraulic retention time for the combined oxidation system was also significantly lower as compared to only biological oxidation operation. Kinetic studies revealed that the reduction in the COD followed a first-order kinetic model for advanced oxidation and pseudo first-order model for biodegradation. The study clearly established the utility of the combined technology for the effective treatment of real industrial wastewater. PMID:26846248

  18. Formation of High-Purity Indium Oxide Nanoparticles and Their Application to Sensitive Detection of Ammonia

    PubMed Central

    Bhardwaj, Sanjeev K.; Bhardwaj, Neha; Kukkar, Manil; Sharma, Amit L.; Kim, Ki-Hyun; Deep, Akash

    2015-01-01

    High-purity In2O3 nanoparticles were recovered from scrap indium tin oxide substrates in a stepwise process involving acidic leaching, liquid-liquid extraction with a phosphine oxide extractant, and combustion of the organic phase. The morphological and structural parameters of the recovered nanoparticles were investigated to support the formation of the desired products. These In2O3 nanoparticles were used for sensitive sensing of ammonia gas using a four-probe electrode device. The proposed sensor offered very quick response time (around 10 s) and highly sensitive detection of ammonia (at a detection limit of 1 ppm). PMID:26694415

  19. Conversion of upland to paddy field specifically alters the community structure of archaeal ammonia oxidizers in an acid soil

    NASA Astrophysics Data System (ADS)

    Alam, M. S.; Ren, G. D.; Lu, L.; Zheng, Y.; Peng, X. H.; Jia, Z. J.

    2013-08-01

    The function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) depends on the major energy-generating compounds (i.e., ammonia and oxygen). The diversification of AOA and AOB communities along ecological gradients of substrate availability in a complex environment have been much debated but rarely tested. In this study, two ecosystems of maize and rice crops under different fertilization regimes were selected to investigate the community diversification of soil AOA and AOB upon conversion of an upland field to a paddy field and long-term field fertilization in an acid soil. Real-time quantitative polymerase chain reaction of ammonia monooxygenase (amoA) genes demonstrated that the abundance of AOA was significantly stimulated after conversion of upland to paddy soils for more than 100 yr, whereas a slight decline in AOB numbers was observed. Denaturing gradient gel electrophoresis fingerprints of amoA genes further revealed remarkable changes in the community compositions of AOA after conversion of aerobic upland to flooded paddy field. Sequencing analysis revealed that upland soil was dominated by AOA within the soil group 1.1b lineage, whereas the marine group 1.1a-associated lineage predominated in AOA communities in paddy soils. Irrespective of whether the soil was upland or paddy soil, long-term field fertilization led to increased abundance of amoA genes in AOA and AOB compared with control treatments (no fertilization), whereas archaeal amoA gene abundances outnumbered their bacterial counterparts in all samples. Phylogenetic analyses of amoA genes showed that Nitrosospira cluster-3-like AOB dominated bacterial ammonia oxidizers in both paddy and upland soils, regardless of fertilization treatment. The results of this study suggest that the marine group 1.1a-associated AOA will be better adapted to the flooded paddy field than AOA ecotypes of the soil group 1.1b lineage, and indicate that long-term flooding is the dominant selective force driving the

  20. Cu-NHC-TEMPO catalyzed aerobic oxidation of primary alcohols to aldehydes.

    PubMed

    Liu, Xiaolong; Xia, Qinqin; Zhang, Yuejiao; Chen, Congyan; Chen, Wanzhi

    2013-09-01

    Imidazolium salts bearing TEMPO groups react with commercially available copper powder affording Cu-NHC complexes. The in situ generated Cu-NHC-TEMPO complexes are quite efficient catalysts for aerobic oxidation of primary alcohols into aldehydes. The catalyst is easily available, and various primary alcohols were selectively converted to aldehydes in excellent yields. PMID:23944937

  1. Effects of Aerobic and Microaerobic Conditions on Anaerobic Ammonium-Oxidizing (Anammox) Sludge

    PubMed Central

    Strous, M.; Van Gerven, E.; Kuenen, J. G.; Jetten, M.

    1997-01-01

    The anaerobic ammonium oxidation (Anammox) process is a promising novel option for removing nitrogen from wastewater. In this study it was shown that the Anammox process was inhibited reversibly by the presence of oxygen. Furthermore, aerobic nitrifiers were shown not to play an important role in the Anammox process. PMID:16535633

  2. Aerobic Oxidation in Nanomicelles of Aryl Alkynes, in Water at Room Temperature**

    PubMed Central

    Handa, Sachin; Fennewald, James C.; Rainey, Shane

    2014-01-01

    On the basis of the far higher solubility of oxygen gas inside the hydrocarbon core of nanomicelles, metal and peroxide free aerobic oxidation of aryl alkynes has been achieved in water at room temperature. Many examples are offered that illustrate broad functional group tolerance. The overall process is environmentally friendly, documented by the associated low E Factors. PMID:24616243

  3. High resolution and comprehensive techniques to analyze aerobic methane oxidation in mesocosm experiments

    NASA Astrophysics Data System (ADS)

    Chan, E. W.; Kessler, J. D.; Redmond, M. C.; Shiller, A. M.; Arrington, E. C.; Valentine, D. L.; Colombo, F.

    2015-12-01

    Many studies of microbially mediated aerobic methane oxidation in oceanic environments have examined the many different factors that control the rates of oxidation. However, there is debate on how quickly methane is oxidized once a microbial population is established and what factor(s) are limiting in these types of environments. These factors include the availability of CH4, O2, trace metals, nutrients, and the density of cell population. Limits to these factors can also control the temporal aspects of a methane oxidation event. In order to look at this process in its entirety and with higher temporal resolution, a mesocosm incubation system was developed with a Dissolved Gas Analyzer System (DGAS) coupled with a set of analytical tools to monitor aerobic methane oxidation in real time. With the addition of newer laser spectroscopy techniques (cavity ringdown spectroscopy), stable isotope fractionation caused by microbial processes can also be examined on a real time and automated basis. Cell counting, trace metal, nutrient, and DNA community analyses have also been carried out in conjunction with these mesocosm samples to provide a clear understanding of the biology in methane oxidation dynamics. This poster will detail the techniques involved to provide insights into the chemical and isotopic kinetics controlling aerobic methane oxidation. Proof of concept applications will be presented from seep sites in the Hudson Canyon and the Sleeping Dragon seep field, Mississippi Canyon 118 (MC 118). This system was used to conduct mesocosm experiments to examine methane consumption, O2 consumption, nutrient consumption, and biomass production.

  4. Effects of Agronomic Treatments on Structure and Function of Ammonia-Oxidizing Communities

    PubMed Central

    Phillips, Carol J.; Harris, Dave; Dollhopf, Sherry L.; Gross, Katherine L.; Prosser, James I.; Paul, Eldor A.

    2000-01-01

    The aim of this study was to determine the effects of different agricultural treatments and plant communities on the diversity of ammonia oxidizer populations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled with specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the β subgroup of the division Proteobacteria by use of DNA extracted from cultivated, successional, and native deciduous forest soils. Community profiles of the different soil types were compared with nitrification rates and most-probable-number (MPN) counts. Despite significant variation in measured nitrification rates among communities, there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incubations, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA. Nitrosomonas-like bands were seen in the MPN DNA but were not detected in the DNA extracted directly from soils. These bands were detected in some samples taken from MPN incubations carried out with medium containing 1,000 μg of NH4+-N ml−1, to the exclusion of bands detected in the native DNA. Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lower than those determined by competitive PCR (cPCR). Although no differences were seen in ammonia oxidizer MPN counts from the different soil treatments, cPCR revealed higher numbers in fertilized soils. The use of a combination of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine-scale compositions among treatments that may be associated with changes in population size and function. PMID:11097922

  5. Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada

    PubMed Central

    Sonthiphand, Puntipar; Cejudo, Eduardo; Schiff, Sherry L.

    2013-01-01

    The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH3 and NH4+) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO3− or N2), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities. PMID:24056472

  6. Phylogenetically diverse denitrifying and ammonia-oxidizing bacteria in corals Alcyonium gracillimum and Tubastraea coccinea.

    PubMed

    Yang, Shan; Sun, Wei; Zhang, Fengli; Li, Zhiyong

    2013-10-01

    To date, the association of coral-bacteria and the ecological roles of bacterial symbionts in corals remain largely unknown. In particular, little is known about the community components of bacterial symbionts of corals involved in the process of denitrification and ammonia oxidation. In this study, the nitrite reductase (nirS and nirK) and ammonia monooxygenase subunit A (amoA) genes were used as functional markers. Diverse bacteria with the potential to be active as denitrifiers and ammonia-oxidizing bacteria (AOB) were found in two East China Sea corals: stony coral Alcyonium gracillimum and soft coral Tubastraea coccinea. The 16S rRNA gene library analysis demonstrated different communities of bacterial symbionts in these two corals of the same location. Nitrite reductase nirK gene was found only in T. coccinea, while both nirK and nirS genes were detected in A. gracillimum, which might be the result of the presence of different bacterial symbionts in these two corals. AOB rather than ammonia-oxidizing archaea were detected in both corals, suggesting that AOB might play an important role in the ammonia oxidation process of the corals. This study indicates that the coral bacterial symbionts with the potential for nitrite reduction and ammonia oxidation might have multiple ecological roles in the coral holobiont, which promotes our understanding of bacteria-mediated nitrogen cycling in corals. To our knowledge, this study is the first assessment of the community structure and phylogenetic diversity of denitrifying bacteria and AOB in corals based on nirK, nirS, and amoA gene library analysis. PMID:23564007

  7. Wastewater effluent impacts ammonia-oxidizing prokaryotes of the Grand River, Canada.

    PubMed

    Sonthiphand, Puntipar; Cejudo, Eduardo; Schiff, Sherry L; Neufeld, Josh D

    2013-12-01

    The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH3 and NH4+) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO3- or N2), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities. PMID:24056472

  8. Nitrification resilience and community dynamics of ammonia-oxidizing bacteria with respect to ammonia loading shock in a nitrification reactor treating steel wastewater.

    PubMed

    Cho, Kyungjin; Shin, Seung Gu; Lee, Joonyeob; Koo, Taewoan; Kim, Woong; Hwang, Seokhwan

    2016-08-01

    The aim of this study was to investigate the nitrification resilience pattern and examine the key ammonia-oxidizing bacteria (AOB) with respect to ammonia loading shocks (ALSs) in a nitrification bioreactor treating steel wastewater. The perturbation experiments were conducted in a 4-L bioreactor operated in continuous mode with a hydraulic retention time of 10 d. Three sequential ALSs were given to the bioreactor (120, 180 and 180 mg total ammonia nitrogen (TAN)/L. When the first shock was given, the nitrification process completely recovered after 14 d of further operation. However, the resilience duration was significantly reduced to ∼1 d after the second and third ALSs. In the bioreactor, Nitrosomonas aestuarii dominated the other AOB species, Nitrosomonas europaea and N. nitrosa, throughout the process. In addition, the population of N. aestuarii increased with ammonia utilization following each ALS; i.e., this species responded to acute ammonia overloadings by contributing to ammonia oxidation. This finding suggests that N. aestuarii could be exploited to achieve stable nitrification in industrial wastewaters that contain high concentrations of ammonia. PMID:26896313

  9. Nitrous oxide production by Alcaligenes faecalis under transient and dynamic aerobic and anaerobic conditions

    SciTech Connect

    Otte, S.; Grobben, N.G.; Robertson, L.A.; Jetten, M.S.M.; Kuenen, J.G.

    1996-07-01

    Nitrous oxide production contributes to both greenhouse effect and ozone depletion in the stratosphere. A significant part of the global N2O emission can be attributed to microbial processes, especially nitrification and denitrification, used in biological wastewater treatment systems. This study looks at the efficiency of denitrification and the enzymes involved, with the emphasis on N2O production during the transient phase from aerobic to anaerobic conditions and vice versa. The effect of repetitive changing aerobic-anaerobic conditions on N2O was also studied. Alcaligenes faecalis was used as the model denitrofing organism. 35 refs., 3 figs., 1 tab.

  10. Moisture and temperature controls on nitrification differ among ammonia oxidizer communities from three alpine soil habitats

    NASA Astrophysics Data System (ADS)

    Osborne, Brooke B.; Baron, Jill S.; Wallenstein, Matthew D.

    2016-03-01

    Climate change is altering the timing and magnitude of biogeochemical fluxes in many highelevation ecosystems. The consequent changes in alpine nitrification rates have the potential to influence ecosystem scale responses. In order to better understand how changing temperature and moisture conditions may influence ammonia oxidizers and nitrification activity, we conducted laboratory incubations on soils collected in a Colorado watershed from three alpine habitats (glacial outwash, talus, and meadow). We found that bacteria, not archaea, dominated all ammonia oxidizer communities. Nitrification increased with moisture in all soils and under all temperature treatments. However, temperature was not correlated with nitrification rates in all soils. Site-specific temperature trends suggest the development of generalist ammonia oxidzer communities in soils with greater in situ temperature fluctuations and specialists in soils with more steady temperature regimes. Rapidly increasing temperatures and changing soil moisture conditions could explain recent observations of increased nitrate production in some alpine soils.

  11. Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones

    PubMed Central

    Peng, Xuefeng; Jayakumar, Amal; Ward, Bess B.

    2013-01-01

    Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments, such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature (higher in the Arabian Sea than in the ETSP) was the main factor that correlated with the differences between the AOA communities. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role, than did geography, in shaping the AOA community composition. PMID:23847601

  12. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation

    SciTech Connect

    Stein, Lisa Y; Arp, D J; Berube, PM; Chain, Patrick S. G.; Hauser, Loren John; Jetten, MSM; Klotz, Martin G; Larimer, Frank W; Norton, Jeanette M.; Op den Camp, HJM; Shin, M; Wei, Xueming

    2007-12-01

    Analysis of the structure and inventory of the genome of Nitrosomonas eutropha C91 revealed distinctive features that may explain the adaptation of N. eutropha-like bacteria to N-saturated ecosystems. Multiple gene-shuffling events are apparent, including mobilized and replicated transposition, as well as plasmid or phage integration events into the 2.66 Mbp chromosome and two plasmids (65 and 56 kbp) of N. eutropha C91. A 117 kbp genomic island encodes multiple genes for heavy metal resistance, including clusters for copper and mercury transport, which are absent from the genomes of other ammonia-oxidizing bacteria (AOB). Whereas the sequences of the two ammonia monooxygenase and three hydroxylamine oxidoreductase gene clusters in N. eutropha C91 are highly similar to those of Nitrosomonas europaea ATCC 19718, a break of synteny in the regions flanking these clusters in each genome is evident. Nitrosomonas eutropha C91 encodes four gene clusters for distinct classes of haem-copper oxidases, two of which are not found in other aerobic AOB. This diversity of terminal oxidases may explain the adaptation of N. eutropha to environments with variable O2 concentrations and/or high concentrations of nitrogen oxides. As with N. europaea, the N. eutropha genome lacks genes for urease metabolism, likely disadvantaging nitrosomonads in low-nitrogen or acidic ecosystems. Taken together, this analysis revealed significant genomic variation between N. eutropha C91 and other AOB, even the closely related N. europaea, and several distinctive properties of the N. eutropha genome that are supportive of niche specialization.

  13. Practical Aerobic Oxidations of Alcohols and Amines with Homogeneous Cu/TEMPO and Related Catalyst Systems

    PubMed Central

    Ryland, Bradford L.; Stahl, Shannon S.

    2014-01-01

    Alcohol and amine oxidations are common reactions in laboratory and industrial synthesis of organic molecules. Aerobic oxidation methods have long been sought for these transformations, but few practical methods exist that offer advantages over traditional oxidation methods. Recently developed homogeneous Cu/TEMPO (TEMPO = 2,2,6,6-tetramethylpiperidinyl-N-oxyl) and related catalyst systems appear to fill this void. The reactions exhibit high levels of chemoselectivity and broad functional-group tolerance, and they often operate efficiently at room temperature with ambient air as the oxidant. These advances, together with their historical context and recent applications, are highlighted in this minireview. PMID:25044821

  14. Mechanism of Copper/Azodicarboxylate-Catalyzed Aerobic Alcohol Oxidation: Evidence for Uncooperative Catalysis.

    PubMed

    McCann, Scott D; Stahl, Shannon S

    2016-01-13

    Cooperative catalysis between Cu(II) and redox-active organic cocatalysts is a key feature of important chemical and enzymatic aerobic oxidation reactions, such as alcohol oxidation mediated by Cu/TEMPO and galactose oxidase. Nearly 20 years ago, Markó and co-workers reported that azodicarboxylates, such as di-tert-butyl azodicarboxylate (DBAD), are effective redox-active cocatalysts in Cu-catalyzed aerobic alcohol oxidation reactions [Markó, I. E., et al. Science 1996, 274, 2044], but the nature of the cooperativity between Cu and azodicarboxylates is not well understood. Here, we report a mechanistic study of Cu/DBAD-catalyzed aerobic alcohol oxidation. In situ infrared spectroscopic studies reveal a burst of product formation prior to steady-state catalysis, and gas-uptake measurements show that no O2 is consumed during the burst. Kinetic studies reveal that the anaerobic burst and steady-state turnover have different rate laws. The steady-state rate does not depend on [O2] or [DBAD]. These results, together with other EPR and in situ IR spectroscopic and kinetic isotope effect studies, reveal that the steady-state mechanism consists of two interdependent catalytic cycles that operate in sequence: a fast Cu(II)/DBAD pathway, in which DBAD serves as the oxidant, and a slow Cu(II)-only pathway, in which Cu(II) is the oxidant. This study provides significant insight into the redox cooperativity, or lack thereof, between Cu and redox-active organic cocatalysts in aerobic oxidation reactions. PMID:26694091

  15. Copper-catalyzed aerobic oxidative C-H functionalizations: trends and mechanistic insights.

    PubMed

    Wendlandt, Alison E; Suess, Alison M; Stahl, Shannon S

    2011-11-18

    The selective oxidation of C-H bonds and the use of O(2) as a stoichiometric oxidant represent two prominent challenges in organic chemistry. Copper(II) is a versatile oxidant, capable of promoting a wide range of oxidative coupling reactions initiated by single-electron transfer (SET) from electron-rich organic molecules. Many of these reactions can be rendered catalytic in Cu by employing molecular oxygen as a stoichiometric oxidant to regenerate the active copper(II) catalyst. Meanwhile, numerous other recently reported Cu-catalyzed C-H oxidation reactions feature substrates that are electron-deficient or appear unlikely to undergo single-electron transfer to copper(II). In some of these cases, evidence has been obtained for the involvement of organocopper(III) intermediates in the reaction mechanism. Organometallic C-H oxidation reactions of this type represent important new opportunities for the field of Cu-catalyzed aerobic oxidations. PMID:22034061

  16. Estimating ammonia and nitrous oxide emissions from dairy farms using milk urea nitrogen

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dairy farms emit ammonia (NH3) from barns, manure storage, and soils, which can be hazardous to human and ecosystem health. Emissions of NH3 also contribute indirectly to emissions of nitrous oxide (N2O), a potent greenhouse gas. Direct N2O emissions occur mostly from soil after application of ferti...

  17. Abundance and Composition of Epiphytic Bacterial and Archaeal Ammonia Oxidizers of Marine Red and Brown Macroalgae

    PubMed Central

    Trias, Rosalia; García-Lledó, Arantzazu; Sánchez, Noemí; López-Jurado, José Luis; Hallin, Sara

    2012-01-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae's potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities on three species of macroalgae, Osmundaria volubilis, Phyllophora crispa, and Laminaria rodriguezii, from the Balearic Islands (western Mediterranean Sea). Quantitative PCR of bacterial and archaeal 16S rRNA and amoA genes was performed. In contrast to what has been shown for most other marine environments, the macroalgae's surfaces were dominated by bacterial amoA genes rather than those from the archaeal counterpart. On the basis of the sequences retrieved from AOB and AOA amoA gene clone libraries from each algal species, the bacterial ammonia-oxidizing communities were related to Nitrosospira spp. and to Nitrosomonas europaea and only 6 out of 15 operational taxonomic units (OTUs) were specific for the host species. Conversely, the AOA diversity was higher (43 OTUs) and algal species specific, with 17 OTUs specific for L. rodriguezii, 3 for O. volubilis, and 9 for P. crispa. Altogether, the results suggest that marine macroalgae may exert an ecological niche for AOB in marine environments, potentially through specific microbe-host interactions. PMID:22081571

  18. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    NASA Astrophysics Data System (ADS)

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-11-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g-1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments.

  19. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China

    PubMed Central

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to −25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 104 to 8.5 × 109 copies g−1), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments. PMID:26522086

  20. Species, Abundance and Function of Ammonia-oxidizing Archaea in Inland Waters across China.

    PubMed

    Zhou, Leiliu; Wang, Shanyun; Zou, Yuxuan; Xia, Chao; Zhu, Guibing

    2015-01-01

    Ammonia oxidation is the first step in nitrification and was thought to be performed solely by specialized bacteria. The discovery of ammonia-oxidizing archaea (AOA) changed this view. We examined the large scale and spatio-temporal occurrence, abundance and role of AOA throughout Chinese inland waters (n = 28). Molecular survey showed that AOA was ubiquitous in inland waters. The existence of AOA in extreme acidic, alkaline, hot, cold, eutrophic and oligotrophic environments expanded the tolerance limits of AOA, especially their known temperature tolerance to -25 °C, and substrate load to 42.04 mM. There were spatio-temporal divergences of AOA community structure in inland waters, and the diversity of AOA in inland water ecosystems was high with 34 observed species-level operational taxonomic units (OTUs; based on a 15% cutoff) distributed widely in group I.1b, I.1a, and I.1a-associated. The abundance of AOA was quite high (8.5 × 10(4) to 8.5 × 10(9) copies g(-1)), and AOA outnumbered ammonia-oxidizing bacteria (AOB) in the inland waters where little human activities were involved. On the whole AOB predominate the ammonia oxidation rate over AOA in inland water ecosystems, and AOA play an indispensable role in global nitrogen cycle considering that AOA occupy a broader habitat range than AOB, especially in extreme environments. PMID:26522086

  1. Ammonia, Dimethylamine, Trimethylamine, and Trimethylamine Oxide from Raw and Processed Fish By-Products

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Concentrations of ammonia, monomethylamine (MMA), dimethylamine (DMA), trimethylamine (TMA) and trimethylamine oxide (TMAO) in raw and processed fish by-products were determined in cold water marine fish using a capillary electrophoresis (CE) method. The CE method provides a fast and sensitive proce...

  2. AMMONIA REMOVAL AND NITROUS OXIDE PRODUCTION IN GAS-PHASE COMPOST BIOFILTERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biofiltration technology is widely utilized for treating ammonia gas (NH3), with one of its potential detrimental by-products being nitrous oxide (N2O), a greenhouse gas approximately 300 times more reactive to infrared than CO2. The present work intends to provide the relation between NH3 removal d...

  3. A Method for Cell Culture and Maintenance of Ammonia-Oxidizing Archaea in Agar Stab.

    PubMed

    Chu, Yeon-Jin; Lee, Jin-Young; Shin, So-Ra; Kim, Geun-Joong

    2015-12-01

    Ammonia oxidizing archaea (AOA) are predominantly found and closely linked with geochemical cycling of nitrogen in non-extreme habitats. However, these strains have mainly been investigated using liquid cultures of enriched cells. Here, we provide an agar stab as a simple and reliable means of cultivating and maintaining AOA. PMID:26543273

  4. CATALYTIC REDUCTION OF NITROGEN OXIDES WITH AMMONIA: UTILITY PILOT PLANT OPERATION

    EPA Science Inventory

    The report describes work to demonstrate, on a utility pilot plant scale, the performance, reliability, and practicability of reducing nitrogen oxides (NOx) emissions from steam boilers by reduction of NOx with ammonia over a platinum catalyst. A utility pilot plant treating a sl...

  5. Modeling of nitrous oxide production by autotrophic ammonia-oxidizing bacteria with multiple production pathways.

    PubMed

    Ni, Bing-Jie; Peng, Lai; Law, Yingyu; Guo, Jianhua; Yuan, Zhiguo

    2014-04-01

    Autotrophic ammonia oxidizing bacteria (AOB) have been recognized as a major contributor to N2O production in wastewater treatment systems. However, so far N2O models have been proposed based on a single N2O production pathway by AOB, and there is still a lack of effective approach for the integration of these models. In this work, an integrated mathematical model that considers multiple production pathways is developed to describe N2O production by AOB. The pathways considered include the nitrifier denitrification pathway (N2O as the final product of AOB denitrification with NO2(-) as the terminal electron acceptor) and the hydroxylamine (NH2OH) pathway (N2O as a byproduct of incomplete oxidation of NH2OH to NO2(-)). In this model, the oxidation and reduction processes are modeled separately, with intracellular electron carriers introduced to link the two types of processes. The model is calibrated and validated using experimental data obtained with two independent nitrifying cultures. The model satisfactorily describes the N2O data from both systems. The model also predicts shifts of the dominating pathway at various dissolved oxygen (DO) and nitrite levels, consistent with previous hypotheses. This unified model is expected to enhance our ability to predict N2O production by AOB in wastewater treatment systems under varying operational conditions. PMID:24571180

  6. Application of a Chemiluminescence Detector for the Measurement of Total Oxides of Nitrogen and Ammonia in the Atmosphere

    NASA Technical Reports Server (NTRS)

    Hodgeson, J. A.; Bell, J. P.; Rehme, K. A.; Krost, K. J.; Stevens, R. K.

    1971-01-01

    By means of the thermal conversion of nitrogen dioxide to the nitric oxide, the chemiluminescent nitric oxide monitor, based on the nitric oxide plus ozone reaction, may be used for monitoring nitrogen dioxide plus nitric oxide (NO(x)). Under conditions previously described, ammonia is also converted to nitric oxide and therefore interferes. A metal surface, gold wool or stainless steel, operated at two different temperatures has been used to convert only nitrogen dioxide or nitrogen dioxide plus ammonia. Quantitative conversion of nitrogen dioxide to nitric oxide has been obtained at temperatures as low as 200 C. Conversion of ammonia is effected at temperatures of 300 C or higher. By the addition of a converter the basic nitric oxide monitor may be used for measuring NO(x) or NO(x) plus ammonia. As an alternate mode, for a fixed high temperature, a specific scrubber is described for removing NH3 without affecting NO2 concentrations.

  7. Reduction of nitrogen oxides with catalytic acid resistant aluminosilicate molecular sieves and ammonia

    DOEpatents

    Pence, Dallas T.; Thomas, Thomas R.

    1980-01-01

    Noxious nitrogen oxides in a waste gas stream such as the stack gas from a fossil-fuel-fired power generation plant or other industrial plant off-gas stream is catalytically reduced to elemental nitrogen and/or innocuous nitrogen oxides employing ammonia as reductant in the presence of a zeolite catalyst in the hydrogen or sodium form having pore openings of about 3 to 10 A.

  8. Activated carbon for aerobic oxidation: Benign approach toward 2-benzoylbenzimidazoles and 2-benzoylbenzoxazoles synthesis

    PubMed Central

    Bao, Kai; Li, Fuqing; Liu, Hanjing; Wang, Zhiwei; Shen, Qirong; Wang, Jian; Zhang, Weige

    2015-01-01

    A general strategy involving a novel and highly efficient aerobic benzylic oxidation promoted by cheap, reusable activated carbon in water is developed. Application of this method has been demonstrated in the benign synthesis of bioactive 2-benzoylbenzimidazoles and 2-benzoylbenzoxazoles derivatives. Furthermore, the activated carbon catalyst could be recovered and reused at least three times without significantly losing its activity. Preliminary research suggests that the oxidation mechanism may involve intermediate hydroperoxidation and that a portion of the final carbonyl product is obtained through a secondary benzylic alcohol intermediate. Finally, theoretical calculations reveal that the oxidation yield is closely associated with the electric density at the benzylic position of the substrate. PMID:26041483

  9. Iron/ABNO-Catalyzed Aerobic Oxidation of Alcohols to Aldehydes and Ketones under Ambient Atmosphere.

    PubMed

    Wang, Lianyue; Shang, SenSen; Li, Guosong; Ren, Lanhui; Lv, Ying; Gao, Shuang

    2016-03-01

    We report a new Fe(NO3)3·9H2O/9-azabicyclo[3.3.1]nonan-N-oxyl catalyst system that enables efficient aerobic oxidation of a broad range of primary and secondary alcohols to the corresponding aldehydes and ketones at room temperature with ambient air as the oxidant. The catalyst system exhibits excellent activity and selectivity for primary aliphatic alcohol oxidation. This procedure can also be scaled up. Kinetic analysis demonstrates that C-H bond cleavage is the rate-determining step and that cationic species are involved in the reaction. PMID:26859251

  10. Copper/TEMPO-Catalyzed Aerobic Alcohol Oxidation: Mechanistic Assessment of Different Catalyst Systems.

    PubMed

    Hoover, Jessica M; Ryland, Bradford L; Stahl, Shannon S

    2013-11-01

    Combinations of homogeneous Cu salts and TEMPO have emerged as practical and efficient catalysts for the aerobic oxidation of alcohols. Several closely related catalyst systems have been reported, which differ in the identity of the solvent, the presence of 2,2'-bipyridine as a ligand, the identity of basic additives, and the oxidation state of the Cu source. These changes have a significant influence on the reaction rates, yields, and substrate scope. In this report, we probe the mechanistic basis for differences among four different Cu/TEMPO catalyst systems and elucidate the features that contribute to efficient oxidation of aliphatic alcohols. PMID:24558634

  11. Copper/TEMPO-Catalyzed Aerobic Alcohol Oxidation: Mechanistic Assessment of Different Catalyst Systems

    PubMed Central

    Hoover, Jessica M.; Ryland, Bradford L.; Stahl, Shannon S.

    2013-01-01

    Combinations of homogeneous Cu salts and TEMPO have emerged as practical and efficient catalysts for the aerobic oxidation of alcohols. Several closely related catalyst systems have been reported, which differ in the identity of the solvent, the presence of 2,2′-bipyridine as a ligand, the identity of basic additives, and the oxidation state of the Cu source. These changes have a significant influence on the reaction rates, yields, and substrate scope. In this report, we probe the mechanistic basis for differences among four different Cu/TEMPO catalyst systems and elucidate the features that contribute to efficient oxidation of aliphatic alcohols. PMID:24558634

  12. Abundance and Diversity of Archaeal Ammonia Oxidizers in a Coastal Groundwater System ▿ †

    PubMed Central

    Rogers, Daniel R.; Casciotti, Karen L.

    2010-01-01

    Nitrification, the microbially catalyzed oxidation of ammonia to nitrate, is a key process in the nitrogen cycle. Archaea have been implicated in the first part of the nitrification pathway (oxidation of ammonia to nitrite), but the ecology and physiology of these organisms remain largely unknown. This work describes two different populations of sediment-associated ammonia-oxidizing archaea (AOA) in a coastal groundwater system in Cape Cod, MA. Sequence analysis of the ammonia monooxygenase subunit A gene (amoA) shows that one population of putative AOA inhabits the upper meter of the sediment, where they may experience frequent ventilation, with tidally driven overtopping and infiltration of bay water supplying dissolved oxygen, ammonium, and perhaps organic carbon. A genetically distinct population occurs deeper in the sediment, in a mixing zone between a nitrate- and oxygen-rich freshwater zone and a reduced, ammonium-bearing saltwater wedge. Both of these AOA populations are coincident with increases in the abundance of group I crenarchaeota 16S rRNA gene copies. PMID:20971859

  13. Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest.

    PubMed

    Zhang, Li-Mei; Wang, Mu; Prosser, James I; Zheng, Yuan-Ming; He, Ji-Zheng

    2009-11-01

    To determine the abundance and distribution of bacterial and archaeal ammonia oxidizers in alpine and permafrost soils, 12 soils at altitudes of 4000-6550 m above sea level (m a.s.l.) were collected from the northern slope of the Mount Everest (Tibetan Plateau), where the permanent snow line is at 5800-6000 m a.s.l. Communities were characterized by real-time PCR and clone sequencing by targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. Archaeal amoA abundance was greater than bacterial amoA abundance in lower altitude soils (or=5700 m a.s.l.). Both archaeal and bacterial amoA abundance decreased abruptly in higher altitude soils. Communities shifted from a Nitrosospira amoA cluster 3a-dominated ammonia-oxidizing bacteria community in lower altitude soils to communities dominated by a newly designated Nitrosospira ME and cluster 2-related groups and Nitrosomonas cluster 6 in higher altitude soils. All archaeal amoA sequences fell within soil and sediment clusters, and the proportions of the major archaeal amoA clusters changed between the lower altitude and the higher altitude soils. These findings imply that the shift in the relative abundance and community structure of archaeal and bacterial ammonia oxidizers may result from selection of organisms adapted to altitude-dependent environmental factors in elevated soils. PMID:19780828

  14. Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils.

    PubMed

    Dai, Yu; Wu, Zhen; Zhou, Qiheng; Zhao, Qun; Li, Ningning; Xie, Shuguang; Liu, Yong

    2015-10-01

    Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can be involved in biotransformation of ammonia to nitrite in soil ecosystems. However, the distribution of AOA and AOB in plateau soils and influential factors remain largely unclear. In the present study, the activity, abundance and structure of ammonia oxidizers in different soils on the Yunnan Plateau were assessed using potential nitrification rates (PNRs), quantitative PCR assay and clone library analysis, respectively. Wide variation was found in both AOA and AOB communities in plateau soils. PNRs showed a significant positive correlation with AOB abundance. Both were determined by the ratio of organic carbon to nitrogen (C/N) and total phosphorous (TP). AOB could play a more important role in ammonia oxidation. AOB community diversity was likely affected by soil total nitrogen (TN) and total organic carbon (TOC) and was usually higher than AOA community diversity. Moreover, Nitrososphaera- and Nitrosospira-like organisms, respectively, were the dominant AOA and AOB in plateau soils. AOA community structure was likely shaped by TP and C/N, while AOB community structure was determined by pH. PMID:26257304

  15. Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

    NASA Astrophysics Data System (ADS)

    Frame, C. H.; Casciotti, K. L.

    2010-09-01

    Nitrous oxide (N2O) is a trace gas that contributes to the greenhouse effect and stratospheric ozone depletion. The N2O yield from nitrification (moles N2O-N produced per mole ammonium-N consumed) has been used to estimate marine N2O production rates from measured nitrification rates and global estimates of oceanic export production. However, the N2O yield from nitrification is not constant. Previous culture-based measurements indicate that N2O yield increases as oxygen (O2) concentration decreases and as nitrite (NO2-) concentration increases. Here, we have measured yields of N2O from cultures of the marine β-proteobacterium Nitrosomonas marina C-113a as they grew on low-ammonium (50 μM) media. These yields, which were typically between 4 × 10-4 and 7 × 10-4 for cultures with cell densities between 2 × 102 and 2.1 × 104 cells ml-1, were lower than previous reports for ammonia-oxidizing bacteria. The observed impact of O2 concentration on yield was also smaller than previously reported under all conditions except at high starting cell densities (1.5 × 106 cells ml-1), where 160-fold higher yields were observed at 0.5% O2 (5.1 μM dissolved O2) compared with 20% O2 (203 μM dissolved O2). At lower cell densities (2 × 102 and 2.1 × 104 cells ml-1), cultures grown under 0.5% O2 had yields that were only 1.25- to 1.73-fold higher than cultures grown under 20% O2. Thus, previously reported many-fold increases in N2O yield with dropping O2 could be reproduced only at cell densities that far exceeded those of ammonia oxidizers in the ocean. The presence of excess NO2- (up to 1 mM) in the growth medium also increased N2O yields by an average of 70% to 87% depending on O2 concentration. We made stable isotopic measurements on N2O from these cultures to identify the biochemical mechanisms behind variations in N2O yield. Based on measurements of δ15Nbulk, site preference (SP = δ15Nα-δ15Nβ), and δ18O of N2O (δ18O-N2O), we estimate that nitrifier

  16. Ammonia-induced oxidative damage in neurons is prevented by resveratrol and lipoic acid with participation of heme oxygenase 1.

    PubMed

    Bobermin, Larissa Daniele; Wartchow, Krista Minéia; Flores, Marianne Pires; Leite, Marina Concli; Quincozes-Santos, André; Gonçalves, Carlos-Alberto

    2015-07-01

    Ammonia is a metabolite that, at high concentrations, is implicated in neurological disorders, such as hepatic encephalopathy (HE), which is associated with acute or chronic liver failure. Astrocytes are considered the primary target of ammonia toxicity in the central nervous system (CNS) because glutamine synthetase (GS), responsible for ammonia metabolism in CNS, is an astrocytic enzyme. Thus, neuronal dysfunction has been associated as secondary to astrocytic impairment. However, we demonstrated that ammonia can induce direct effects on neuronal cells. The cell viability was decreased by ammonia in SH-SY5Y cells and cerebellar granule neurons. In addition, ammonia induced increased reactive oxygen species (ROS) production and decreased GSH intracellular content, the main antioxidant in CNS. As ammonia neurotoxicity is strongly associated with oxidative stress, we also investigated the potential neuroprotective roles of the antioxidants, resveratrol (RSV) and lipoic acid (LA), against ammonia toxicity in cerebellar granule neurons. RSV and LA were able to prevent the oxidative damage induced by ammonia, maintaining the levels of ROS production and GSH close to basal values. Both antioxidants also decreased ROS production and increased GSH content under basal conditions (in the absence of ammonia). Moreover, we showed that heme oxygenase 1 (HO1), a protein associated with protection against stress conditions, is involved in the beneficial effects of RSV and LA in cerebellar granule neurons. Thus, this study reinforces the neuroprotective effects of RSV and LA. Although more studies in vivo are required, RSV and LA could represent interesting therapeutic strategies for the management of HE. PMID:26003724

  17. Ammonia-oxidizer communities in an agricultural soil treated with contrasting nitrogen sources

    PubMed Central

    Habteselassie, Mussie Y.; Xu, Li; Norton, Jeanette M.

    2013-01-01

    The community of ammonia-oxidizing prokaryotes was examined in an agricultural soil treated for six seasons with contrasting nitrogen (N) sources. Molecular tools based on the genes encoding ammonia monooxygenase were used to characterize the ammonia oxidizer (AO) communities and their abundance. Soil DNA was extracted from soils sampled from silage corn plots that received no additional N (control), dairy waste compost, liquid dairy waste (LW), and ammonium sulfate (AS) treatments at approximately 100 and 200 kg available N ha-1 over 6 years. The N treatment affected the quantity of AO based on estimates of amoA by real-time PCR. Ammonia oxidizing bacteria (AOB) were higher in soils from the AS200, AS100, and LW200 treatments (2.5 × 107, 2.5 × 107, and 2.1 × 107copies g-1 soil, respectively) than in the control (8.1 × 106 copies g-1 soil) while the abundance of amoA encoding archaea [ammonia oxidizing archaea (AOA)] was not significantly affected by treatment (3.8 × 107 copies g-1 soil, average). The ratio of AOA/AOB was higher in the control and compost treated soils, both treatments have the majority of their ammonium supplied through mineralization of organic nitrogen. Clone libraries of partial amoA sequences indicated AOB related to Nitrosospira multiformis and AOA related to uncultured Nitrososphaera similar to those described by soil fosmid 54d9 were prevalent. Profiles of the amoC-amoA intergenic region indicated that both Nitrosospira- and Nitrosomonas-type AOB were present in all soils examined. In contrast to the intergenic amoC-amoA profile results, Nitrosomonas-like clones were recovered only in the LW200 treated soil-DNA. The impact of 6 years of contrasting nitrogen sources applications caused changes in AO abundance while the community composition remained relatively stable for both AOB and AOA. PMID:24223575

  18. Enhanced and selective ammonia sensing of reduced graphene oxide based chemo resistive sensor at room temperature

    NASA Astrophysics Data System (ADS)

    Kumar, Ramesh; Kaur, Amarjeet

    2016-05-01

    The reduced graphene oxide thin films were fabricated by using the spin coating method. The reduced graphene oxide samples were characterised by Raman studies to obtain corresponding D and G bands at 1360 and 1590 cm-1 respectively. Fourier transform infra-red (FTIR) spectra consists of peak corresponds to sp2 hybridisation of carbon atoms at 1560 cm-1. The reduced graphene oxide based chemoresistive sensor exhibited a p-type semiconductor behaviour in ambient conditions and showed good sensitivity to different concentration of ammonia from 25 ppm to 500 ppm and excellent selectivity at room temperature. The sensor displays selectivity to several hazardous vapours such as methanol, ethanol, acetone and hydrazine hydrate. The sensor demonstrated a sensitivity of 9.8 at 25 ppm concentration of ammonia with response time of 163 seconds.

  19. Bioaugmentation of Syntrophic Acetate-Oxidizing Culture in Biogas Reactors Exposed to Increasing Levels of Ammonia

    PubMed Central

    Westerholm, Maria; Levén, Lotta

    2012-01-01

    The importance of syntrophic acetate oxidation for process stability in methanogenic systems operating at high ammonia concentrations has previously been emphasized. In this study we investigated bioaugmentation of syntrophic acetate-oxidizing (SAO) cultures as a possible method for decreasing the adaptation period of biogas reactors operating at gradually increased ammonia concentrations (1.5 to 11 g NH4+-N/liter). Whole stillage and cattle manure were codigested semicontinuously for about 460 days in four mesophilic anaerobic laboratory-scale reactors, and a fixed volume of SAO culture was added daily to two of the reactors. Reactor performance was evaluated in terms of biogas productivity, methane content, pH, alkalinity, and volatile fatty acid (VFA) content. The decomposition pathway of acetate was analyzed by isotopic tracer experiments, and population dynamics were monitored by quantitative PCR analyses. A shift in dominance from aceticlastic methanogenesis to SAO occurred simultaneously in all reactors, indicating no influence by bioaugmentation on the prevailing pathway. Higher abundances of Clostridium ultunense and Tepidanaerobacter acetatoxydans were associated with bioaugmentation, but no influence on Syntrophaceticus schinkii or the methanogenic population was distinguished. Overloading or accumulation of VFA did not cause notable dynamic effects on the population. Instead, the ammonia concentration had a substantial impact on the abundance level of the microorganisms surveyed. The addition of SAO culture did not affect process performance or stability against ammonia inhibition, and all four reactors deteriorated at high ammonia concentrations. Consequently, these findings further demonstrate the strong influence of ammonia on the methane-producing consortia and on the representative methanization pathway in mesophilic biogas reactors. PMID:22923397

  20. Evidence for decoupled electron and proton transfer in the electrochemical oxidation of ammonia on Pt(100)

    DOE PAGESBeta

    Katsounaros, Ioannis; Chen, Ting; Gewirth, Andrew A.; Markovic, Nenad M.; Koper, Marc T. M.

    2016-01-12

    The two traditional mechanisms of the electrochemical ammonia oxidation consider only concerted proton-electron transfer elementary steps and thus they predict that the rate–potential relationship is independent of the pH on the pH-corrected RHE potential scale. In this letter we show that this is not the case: the increase of the solution pH shifts the onset of the NH3-to-N2 oxidation on Pt(100) to lower potentials and also leads to higher surface concentration of formed NOad before the latter is oxidized to nitrite. Therefore, we present a new mechanism for the ammonia oxidation which incorporates a deprotonation step occurring prior to themore » electron transfer. The deprotonation step yields a negatively charged surface-adsorbed species which is discharged in a subsequent electron transfer step before the N–N bond formation. The negatively charged species is thus a precursor for the formation of N2 and NO. The new mechanism should be a future guide for computational studies aiming at the identification of intermediates and corresponding activation barriers for the elementary steps. As a result, ammonia oxidation is a new example of a bond-forming reaction on (100) terraces which involves decoupled proton-electron transfer.« less

  1. Screening of electrocatalysts for direct ammonia fuel cell: Ammonia oxidation on PtMe (Me: Ir, Rh, Pd, Ru) and preferentially oriented Pt(1 0 0) nanoparticles

    NASA Astrophysics Data System (ADS)

    Vidal-Iglesias, F. J.; Solla-Gullón, J.; Montiel, V.; Feliu, J. M.; Aldaz, A.

    Ammonia has attracted attention as a possible fuel for direct fuel cells since it is easy to handle and to transport as liquid or as concentrated aqueous solution. However, on noble metal electrodes ammonia oxidation is a sluggish reaction and the electrocatalyst needs to be improved for developing efficient ammonia fuel cells. In this work, ammonia electrooxidation reaction on 3-4-nm bimetallic PtMe (Ir, Rh, Pd, Ru) and on preferentially oriented Pt(1 0 0) nanoparticles is reported. PtMe nanoparticles have been prepared by using water-in-oil microemulsions to obtain a narrow size distribution whereas preferentially oriented Pt nanoparticles have been prepared through colloidal routes. Among all the bimetallic samples tested, only Pt 75Ir 25 and Pt 75Rh 25 nanoparticles show, at the low potential range, an enhancement of the oxidation density current with respect to the behaviour found for pure platinum nanoparticles prepared by the same method. In addition, two Pt(1 0 0) preferentially oriented nanoparticles of different particle size (4 and 9 nm) have been also studied. These oriented nanoparticles show higher current densities than polycrystalline Pt nanoparticles due to the sensitivity of ammonia oxidation toward the presence of surface sites with square symmetry. The reactivity of the different 4-nm nanoparticles parallels well with that expected from bulk PtMe alloys and Pt single crystal electrodes.

  2. Heterogeneous Rhodium-Catalyzed Aerobic Oxidative Dehydrogenative Cross-Coupling: Nonsymmetrical Biaryl Amines.

    PubMed

    Matsumoto, Kenji; Yoshida, Masahiro; Shindo, Mitsuru

    2016-04-18

    The first heterogeneously catalyzed oxidative dehydrogenative cross-coupling of aryl amines is reported herein. 2-Naphthylamine analogues were reacted with various electron-rich arenes using a heterogeneous Rh/C catalyst under mild aerobic conditions, thus affording nonsymmetrical biaryl amines in excellent yields with high selectivities. This reaction provides a mild, operationally simple, and efficient approach for the synthesis of biaryls which are important to pharmaceutical and materials chemistry. PMID:26996772

  3. Practical Synthesis of Amides via Copper/ABNO-Catalyzed Aerobic Oxidative Coupling of Alcohols and Amines.

    PubMed

    Zultanski, Susan L; Zhao, Jingyi; Stahl, Shannon S

    2016-05-25

    A modular Cu/ABNO catalyst system has been identified that enables efficient aerobic oxidative coupling of alcohols and amines to amides. All four permutations of benzylic/aliphatic alcohols and primary/secondary amines are viable in this reaction, enabling broad access to secondary and tertiary amides. The reactions exhibit excellent functional group compatibility and are complete within 30 min-3 h at rt. All components of the catalyst system are commercially available. PMID:27171973

  4. An insight into the mechanism of the aerobic oxidation of aldehydes catalyzed by N-heterocyclic carbenes.

    PubMed

    Bortolini, O; Chiappe, C; Fogagnolo, M; Giovannini, P P; Massi, A; Pomelli, C S; Ragno, D

    2014-02-25

    N-Heterocyclic carbene catalysis for the aerobic oxidation and esterification of aromatic aldehydes was monitored by ESI-MS (MS/MS) and the key intermediates were intercepted and characterized using the charge-tag strategy. PMID:24413829

  5. Efficient cryopreservation protocol enables accessibility of a broad range of ammonia-oxidizing bacteria for the scientific community.

    PubMed

    Hoefman, Sven; Pommerening-Röser, Andreas; Samyn, Emly; De Vos, Paul; Heylen, Kim

    2013-05-01

    Long-term storage of the fastidious ammonia-oxidizing bacteria has proven difficult, which limits their public availability and results in a loss of cultured biodiversity. To enable their accessibility to the scientific community, an effective protocol for cryopreservation of ammonia-oxidizing cultures at -80 °C and in liquid nitrogen was developed. Long-term storage could be achieved using 5% DMSO as cryoprotectant, preferably in a cryoprotective preservation medium containing tenfold-diluted trypticase soy broth and 1% trehalose. As such, successful activity and growth recovery was observed for a diverse set of ammonia-oxidizing cultures. PMID:23376087

  6. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

    SciTech Connect

    Bollmann, Annette; Sedlacek, Christopher J; Laanbroek, Hendrikus J; Suwa, Yuichi; Stein, Lisa Y; Klotz, Martin G; Arp, D J; Sayavedra-Soto, LA; Lu, Megan; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, James; Woyke, Tanja; Lucas, Susan; Pitluck, Sam; Pennacchio, Len; Nolan, Matt; Land, Miriam L; Huntemann, Marcel; Deshpande, Shweta; Han, Cliff; Chen, Amy; Kyrpides, Nikos C; Mavromatis, K; Markowitz, Victor; Szeto, Ernest; Ivanova, N; Mikhailova, Natalia; Pagani, Ioanna; Pati, Amrita; Peters, Lin; Ovchinnikova, Galina; Goodwin, Lynne A.

    2013-01-01

    Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.

  7. The Aerobic Oxidation of Bromide to Dibromine Catalyzed by Homogeneous Oxidation Catalysts and Initiated by Nitrate in Acetic Acid

    SciTech Connect

    Partenheimer, Walt; Fulton, John L.; Sorensen, Christina M.; Pham, Van Thai; Chen, Yongsheng

    2014-06-01

    A small amount of nitrate, ~0.002 molal, initiates the Co/Mn catalyzed aerobic oxidation of bromide compounds (HBr,NaBr,LiBr) to dibromine in acetic acid at room temperature. At temperatures 40oC or less , the reaction is autocatalytic. Co(II) and Mn(II) themselves and mixed with ionic bromide are known homogeneous oxidation catalysts. The reaction was discovered serendipitously when a Co/Br and Co/Mn/Br catalyst solution was prepared for the aerobic oxidation of methyaromatic compounds and the Co acetate contained a small amount of impurity i.e. nitrate. The reaction was characterized by IR, UV-VIS, MALDI and EXAFS spectroscopies and the coordination chemistry is described. The reaction is inhibited by water and its rate changed by pH. The change in these variables, as well as others, are identical to those observed during homogeneous, aerobic oxidation of akylaromatics. A mechanism is proposed. Accidental addition of a small amount of nitrate compound into a Co/Mn/Br/acetic acid mixture in a large, commercial feedtank is potentially dangerous.

  8. Detection and analysis of two serotypes of ammonia-oxidizing bacteria in sewage plants by flow cytometry.

    PubMed Central

    Völsch, A; Nader, W F; Geiss, H K; Nebe, G; Birr, C

    1990-01-01

    Two different serotypes of the genus Nitrosomonas were isolated from samples of the sewage plant Heidelberg. These nitrifiers were enumerated in activated sludge of various other sewage plants after immunofluorescent labeling and staining with propidium iodide by flow cytometry. The concentrations of these serotypes of Nitrosomonas spp. were in the range of 0.1 to 2%. Also, a test for the determination of the activity of ammonia-oxidizing bacteria was developed. Nitrite-oxidizing bacteria were specifically inhibited with sodium chlorate, and the activity of ammonia-oxidizing bacteria could be calculated from the increase of nitrite. Concentrations and activities of ammonia oxidizers were measured for a period of 6 months in the sewage plant Heidelberg. With one exception, activities and concentrations of ammonia-oxidizing bacteria decreased and increased in parallel. PMID:2403253

  9. Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota.

    PubMed

    Hallam, Steven J; Mincer, Tracy J; Schleper, Christa; Preston, Christina M; Roberts, Katie; Richardson, Paul M; DeLong, Edward F

    2006-04-01

    Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems. PMID:16533068

  10. The effect of ammonia upon the electrocatalysis of hydrogen oxidation and oxygen reduction on polycrystalline platinum

    NASA Astrophysics Data System (ADS)

    Verdaguer-Casadevall, Arnau; Hernandez-Fernandez, Patricia; Stephens, Ifan E. L.; Chorkendorff, Ib; Dahl, Søren

    2012-12-01

    The influence of ammonium ions on the catalysis of hydrogen oxidation and oxygen reduction is studied by means of rotating ring-disk electrode experiments on polycrystalline platinum in perchloric acid. While ammonium does not affect the hydrogen oxidation reaction, the oxygen reduction reaction is severely poisoned. Poisoning at the cathode explains the majority of the losses observed in polymer electrolyte membrane fuel cells contaminated with ammonia. Voltammetry in deaerated solution suggest that the poisoning can be attributed to either ammonium oxidation or increased binding to OH species.

  11. The catalytic removal of ammonia and nitrogen oxides from spacecabin atmospheres

    NASA Technical Reports Server (NTRS)

    Gully, A. J.; Graham, R. R.; Halligan, J. E.; Bentsen, P. C.

    1973-01-01

    Investigations were made on methods for the removal of ammonia and to a lesser extent nitrogen oxides in low concentrations from air. The catalytic oxidation of ammonia was studied over a temperature range of 250 F to 600 F and a concentration range 20 ppm to 500 ppm. Of the catalysts studied, 0.5 percent ruthenium supported on alumina was found to be superior. This material is active at temperatures as low as 250 F and was found to produce much less nitrous oxide than the other two active catalysts, platinum on alumina and Hopcalite. A quantitative design model was developed which will permit the performance of an oxidizer to be calculated. The ruthenium was found to be relatively insensitive to low concentrations of water and to oxygen concentration between 21 percent and 100 percent. Hydrogen sulfide was found to be a poison when injected in relatively large quantities. The adsorption of ammonia by copper sulfate treated silica gel was investigated at temperatures of 72 F and 100 F. A quantitative model was developed for predicting adsorption bed behavior.

  12. Ammonia oxidizing bacteria and archaea in horizontal flow biofilm reactors treating ammonia-contaminated air at 10 °C.

    PubMed

    Gerrity, Seán; Clifford, Eoghan; Kennelly, Colm; Collins, Gavin

    2016-05-01

    The objective of this study was to demonstrate the feasibility of novel, Horizontal Flow Biofilm Reactor (HFBR) technology for the treatment of ammonia (NH3)-contaminated airstreams. Three laboratory-scale HFBRs were used for remediation of an NH3-containing airstream at 10 °C during a 90-d trial to test the efficacy of low-temperature treatment. Average ammonia removal efficiencies of 99.7 % were achieved at maximum loading rates of 4.8 g NH3 m(3) h(-1). Biological nitrification of ammonia to nitrite (NO2 (-)) and nitrate (NO3 (-)) was mediated by nitrifying bacterial and archaeal biofilm populations. Ammonia-oxidising bacteria (AOB) were significantly more abundant than ammonia-oxidising archaea (AOA) vertically at each of seven sampling zones along the vertical HFBRs. Nitrosomonas and Nitrosospira, were the two most dominant bacterial genera detected in the HFBRs, while an uncultured archaeal clone dominated the AOA community. The bacterial community composition across the three HFBRs was highly conserved, although variations occurred between HFBR zones and were driven by physicochemical variables. The study demonstrates the feasibility of HFBRs for the treatment of ammonia-contaminated airstreams at low temperatures; identifies key nitrifying microorganisms driving the removal process; and provides insights for process optimisation and control. The findings are significant for industrial applications of gas oxidation technology in temperate climates. PMID:26879980

  13. Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers.

    PubMed

    Avrahami, Sharon; Liesack, Werner; Conrad, Ralf

    2003-08-01

    We investigated the effect of temperature on the activity of soil ammonia oxidizers caused by changes in the availability of ammonium and in the microbial community structure. Both short (5 days) and long (6.5, 16 and 20 weeks) incubation of an agricultural soil resulted in a decrease in ammonium concentration that was more pronounced at temperatures between 10 and 25 degrees C than at either 4 degrees C or 30-37 degrees C. Consistently, potential nitrification was higher between 10 and 25 degrees C than at either 4 degrees C or 37 degrees C. However, as long as ammonium was not limiting, release rates of N2O increased monotonously between 4 and 37 degrees C after short-term temperature adaptation, with nitrification accounting for about 35-50% of the N2O production between 4 and 25 degrees C. In order to see whether temperature may also affect the community structure of ammonia oxidizers, we studied moist soil during long incubation at low and high concentrations of commercial fertilizer. The soil was also incubated in buffered (pH 7) slurry amended with urea. Communities of ammonia oxidizers were assayed by denaturant gradient gel electrophoresis (DGGE) of the amoA gene coding for the alpha subunit of ammonia monooxygenase. We found that a polymerase chain reaction (PCR) system using a non-degenerated reverse primer (amoAR1) gave the best results. Community shifts occurred in all soil treatments after 16 weeks of incubation. The community shifts were obviously influenced by the different fertilizer treatments, indicating that ammonium was a selective factor for different ammonia oxidizer populations. Temperature was also a selective factor, in particular as community shifts were also observed in the soil slurries, in which ammonium concentrations and pH were better controlled. Cloning and sequencing of selected DGGE bands indicated that amoA sequences belonging to Nitrosospira cluster 1 were dominant at low temperatures (4-10 degrees C), but were absent after

  14. Dissolution of Fe(III)(hydr)oxides by an Aerobic Bacterium

    SciTech Connect

    Maurice, P.

    2004-12-13

    This project investigated the effects of an aerobic Pseudomonas mendocina bacterium on the dissolution of Fe(III)(hydr)oxides. The research is important because metals and radionuclides that adsorb to Fe(III)(hydr)oxides could potentially be remobilized by dissolving bacteria. We showed that P. mendocina is capable of dissolving Fe-bearing minerals by a variety of mechanisms, including production of siderophores, pH changes, and formation of reductants. The production of siderophores by P. mendocina was quantified under a variety of growth conditions. Finally, we demonstrated that microbial siderophores may adsorb to and enhance dissolution of clay minerals.

  15. Modelling nitrous and nitric oxide emissions by autotrophic ammonia-oxidizing bacteria.

    PubMed

    Mampaey, K E; Beuckels, B; Kampschreur, M J; Kleerebezem, R; van Loosdrecht, M C M; Volcke, E I P

    2013-01-01

    The emission of greenhouse gases, such as N2O, from wastewater treatment plants is a matter of growing concern. Denitrification by ammonia-oxidizing bacteria (AOB) has been identified as the main N2O producing pathway. To estimate N2O emissions during biological nitrogen removal, reliable mathematical models are essential. In this work, a mathematical model for NO (a precursor for N2O formation) and N2O formation by AOB is presented. Based on mechanistic grounds, two possible reaction mechanisms for NO and N2O formation are distinguished, which differ in the origin of the reducing equivalents needed for denitrification by AOB. These two scenarios have been compared in a simulation study, assessing the influence of the aeration/stripping rate and the resulting dissolved oxygen (DO) concentration on the NO and N2O emission from a SHARON partial nitritation reactor. The study of the simulated model behaviour and its comparison with previously published experimental data serves in elucidating the true NO and N2O formation mechanism. PMID:24191490

  16. Spatial and temporal diversity and abundance of ammonia oxidizers in semi-arid and arid soils: indications for a differential seasonal effect on archaeal and bacterial ammonia oxidizers.

    PubMed

    Sher, Yonatan; Zaady, Eli; Nejidat, Ali

    2013-12-01

    Besides water, nitrogen is the limiting factor for biomass production in arid ecosystems. Global climatic changes are exacerbating aridity levels, and the response of nitrogen-transforming microorganisms to these changes is not clear yet. Using semi-arid and arid ecosystems as surrogates for conditions of increased aridity, we investigated the activity, abundance, and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in arid and semi-arid soils. Ammonia oxidation potentials were higher during the winter in both sites than in the summer, and higher nitrate concentrations were measured in the arid soil than in the semi-arid soil. Denaturing gradient gel electrophoresis (DGGE) patterns of AOB 16S rRNA gene fragments were similar for the arid and semi-arid soils with no seasonal variations. In contrast, the DGGE patterns of the AOA amoA gene fragments differed between the sites and a soil transfer experiment suggested that these differences are possibly associated with soil type. AOB numbers were higher during the winter than in the summer, while AOA numbers were higher during the summer. The results indicate the resistance of AOB and AOA community structure to arid conditions, albeit with seasonal variations in their abundance. Together, the results suggest the resilience of nitrification activity to increased aridity level. PMID:23855990

  17. Aerobic and anaerobic methane oxidation in terrestrial mud volcanoes in the Northern Apennines

    NASA Astrophysics Data System (ADS)

    Wrede, C.; Brady, S.; Rockstroh, S.; Dreier, A.; Kokoschka, S.; Heinzelmann, S. M.; Heller, C.; Reitner, J.; Taviani, M.; Daniel, R.; Hoppert, M.

    2012-07-01

    Methane oxidizing prokaryotes are ubiquitous in oxic and anoxic habitats wherever C1-compounds are present. Thus, methane saturated mud volcano fluids should be a preferred habitat of methane consuming prokaryotes, using the readily available electron donors. In order to understand the relevance of methane as a carbon and energy source in mud volcano communities, we investigate the diversity of prokaryotic organisms involved in oxidation of methane in fluid samples from the Salse di Nirano mud volcano field situated in the Northern Apennines. Cell counts were at approximately 0.7 × 106 microbial cells/ml. A fraction of the microbial biomass was identified as ANME (anaerobic methanotroph) archaea by fluorescence in situ hybridization (FISH) analysis. They are associated in densely colonized flakes, of some tens of μm in diameter, embedded in a hyaline matrix. Diversity analysis based on the 16S rDNA genes, retrieved from amplified and cloned environmental DNA, revealed a high proportion of archaea, involved in anaerobic oxidation of methane (AOM). Aerobic methane-oxidizing proteobacteria could be highly enriched from mud volcano fluids, indicating the presence of aerobic methanotrophic bacteria, which may contribute to methane oxidation, whenever oxygen is readily available. The results imply that biofilms, dominated by ANME archaea, colonize parts of the mud volcano venting system.

  18. Epiphyton as a Niche for Ammonia-Oxidizing Bacteria: Detailed Comparison with Benthic and Pelagic Compartments in Shallow Freshwater Lakes▿

    PubMed Central

    Coci, M.; Bodelier, P. L. E.; Laanbroek, H. J.

    2008-01-01

    Next to the benthic and pelagic compartments, the epiphyton of submerged macrophytes may offer an additional niche for ammonia-oxidizing bacteria in shallow freshwater lakes. In this study, we explored the potential activities and community compositions of ammonia-oxidizing bacteria of the epiphytic, benthic, and pelagic compartments of seven shallow freshwater lakes which differed in their trophic status, distribution of submerged macrophytes, and restoration history. PCR-denaturing gradient gel electrophoresis analyses demonstrated that the epiphytic compartment was inhabited by species belonging to cluster 3 of the Nitrosospira lineage and to the Nitrosomonas oligotropha lineage. Both the ammonia-oxidizing bacterial community compositions and the potential activities differed significantly between compartments. Interestingly, both the ammonia-oxidizing bacterial community composition and potential activity were influenced by the restoration status of the different lakes investigated. PMID:18263748

  19. Effects of drought on nitrogen turnover and abundances of ammonia-oxidizers in mountain grassland

    NASA Astrophysics Data System (ADS)

    Fuchslueger, L.; Kastl, E.-M.; Bauer, F.; Kienzl, S.; Hasibeder, R.; Ladreiter-Knauss, T.; Schmitt, M.; Bahn, M.; Schloter, M.; Richter, A.; Szukics, U.

    2014-11-01

    Future climate scenarios suggest an increased frequency of summer drought periods in the European Alpine Region. Drought can affect soil nitrogen (N) cycling, by altering N transformation rates, as well as the abundances of ammonia-oxidizing bacteria and archaea. However, the extent to which drought affects N cycling under in situ conditions is still controversial. The goal of this study was to analyse effects of drought on soil N turnover and ammonia-oxidizer abundances in soil without drought history. To this end we conducted rain-exclusion experiments at two differently managed mountain grassland sites, an annually mown and occasionally fertilized meadow and an abandoned grassland. Soils were sampled before, during and after drought and were analysed for potential gross rates of N mineralization, microbial uptake of inorganic N, nitrification, and the abundances of bacterial and archaeal ammonia-oxidizers based on gene copy numbers of the amoA gene (AOB and AOA, respectively). Drought induced different responses at the two studied sites. At the managed meadow drought increased NH4+ immobilization rates and NH4+ concentrations in the soil water solution, but led to a reduction of AOA abundance compared to controls. At the abandoned site gross nitrification and NO3- immobilization rates decreased during drought, while AOB and AOA abundances remained stable. Rewetting had only minor, short-term effects on the parameters that had been affected by drought. Seven weeks after the end of drought no differences to control plots could be detected. Thus, our findings demonstrated that in mountain grasslands drought had distinct transient effects on soil nitrogen cycling and ammonia-oxidizers, which could have been related to a niche differentiation of AOB and AOA with increasing NH4+ levels. However, the effect strength of drought was modulated by grassland management.

  20. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea

    PubMed Central

    Kim, Jong-Geol; Park, Soo-Je; Sinninghe Damsté, Jaap S.; Schouten, Stefan; Rijpstra, W. Irene C.; Jung, Man-Young; Kim, So-Jeong; Gwak, Joo-Han; Hong, Heeji; Si, Ok-Ja; Lee, SangHoon; Madsen, Eugene L.; Rhee, Sung-Keun

    2016-01-01

    Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dissolved inorganic carbon, indicating strict autotrophic growth. α-Keto acids spontaneously detoxify H2O2 via a nonenzymatic decarboxylation reaction, suggesting a role of α-keto acids as H2O2 scavengers. Indeed, agents that also scavenge H2O2, such as dimethylthiourea and catalase, replaced the α-keto acid requirement, enhancing growth of strain DDS1. In fact, in the absence of α-keto acids, strain DDS1 and other AOA isolates were shown to endogenously produce H2O2 (up to ∼4.5 μM), which was inhibitory to growth. Genomic analyses indicated catalase genes are largely absent in the AOA. Our results indicate that AOA broadly feature strict autotrophic nutrition and implicate H2O2 as an important factor determining the activity, evolution, and community ecology of AOA ecotypes. PMID:27339136

  1. Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils.

    PubMed

    Jung, Man-Young; Well, Reinhard; Min, Deullae; Giesemann, Anette; Park, Soo-Je; Kim, Jong-Geol; Kim, So-Jeong; Rhee, Sung-Keun

    2014-05-01

    N2O gas is involved in global warming and ozone depletion. The major sources of N2O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N2O produced by soil AOA and associated N2O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N2O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), δ(15)N(bulk) and δ(18)O -N2O of soil AOA strains were 13-30%, -13 to -35% and 22-36%, respectively, and strains MY1-3 and other soil AOA strains had distinct isotopic signatures. A (15)N-NH4(+)-labeling experiment indicated that N2O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N2O from AOA may be attributable to the relative contributions of these two processes. The highest N2O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N2O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N2O emissions from soil nitrification may be attributable to AOA. PMID:24225887

  2. Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX86 temperature proxy.

    PubMed

    Hurley, Sarah J; Elling, Felix J; Könneke, Martin; Buchwald, Carolyn; Wankel, Scott D; Santoro, Alyson E; Lipp, Julius Sebastian; Hinrichs, Kai-Uwe; Pearson, Ann

    2016-07-12

    Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX86 and sea surface temperature (SST) remains unresolved: How does TEX86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1 to investigate how GDGT composition changes in response to ammonia oxidation rate. We used continuous culture methods to avoid potential confounding variables that can be associated with experiments in batch cultures. The results show that the ring index scales inversely (R(2) = 0.82) with ammonia oxidation rate (ϕ), indicating that GDGT cyclization depends on available reducing power. Correspondingly, the TEX86 ratio decreases by an equivalent of 5.4 °C of calculated temperature over a 5.5 fmol·cell(-1)·d(-1) increase in ϕ. This finding reconciles other recent experiments that have identified growth stage and oxygen availability as variables affecting TEX86 Depth profiles from the marine water column show minimum TEX86 values at the depth of maximum nitrification rates, consistent with our chemostat results. Our findings suggest that the TEX86 signal exported from the water column is influenced by the dynamics of ammonia oxidation. Thus, the global TEX86-SST calibration potentially represents a composite of regional correlations based on nutrient dynamics and global correlations based on archaeal community composition and temperature. PMID:27357675

  3. Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

    PubMed Central

    Jung, Man-Young; Well, Reinhard; Min, Deullae; Giesemann, Anette; Park, Soo-Je; Kim, Jong-Geol; Kim, So-Jeong; Rhee, Sung-Keun

    2014-01-01

    N2O gas is involved in global warming and ozone depletion. The major sources of N2O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N2O produced by soil AOA and associated N2O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N2O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), δ15Nbulk and δ18O -N2O of soil AOA strains were 13–30%, −13 to −35% and 22–36%, respectively, and strains MY1–3 and other soil AOA strains had distinct isotopic signatures. A 15N-NH4+-labeling experiment indicated that N2O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N2O from AOA may be attributable to the relative contributions of these two processes. The highest N2O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N2O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N2O emissions from soil nitrification may be attributable to AOA. PMID:24225887

  4. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea.

    PubMed

    Kim, Jong-Geol; Park, Soo-Je; Sinninghe Damsté, Jaap S; Schouten, Stefan; Rijpstra, W Irene C; Jung, Man-Young; Kim, So-Jeong; Gwak, Joo-Han; Hong, Heeji; Si, Ok-Ja; Lee, SangHoon; Madsen, Eugene L; Rhee, Sung-Keun

    2016-07-12

    Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an ammonia-oxidizing archaeon (designated strain DDS1) from seawater and used this organism to study the physiology of ammonia oxidation. These findings were confirmed using four additional Thaumarchaeota strains from both marine and terrestrial habitats. Ammonia oxidation by strain DDS1 was enhanced in coculture with other bacteria, as well as in artificial seawater media supplemented with α-keto acids (e.g., pyruvate, oxaloacetate). α-Keto acid-enhanced activity of AOA has previously been interpreted as evidence of mixotrophy. However, assays for heterotrophic growth indicated that incorporation of pyruvate into archaeal membrane lipids was negligible. Lipid carbon atoms were, instead, derived from dissolved inorganic carbon, indicating strict autotrophic growth. α-Keto acids spontaneously detoxify H2O2 via a nonenzymatic decarboxylation reaction, suggesting a role of α-keto acids as H2O2 scavengers. Indeed, agents that also scavenge H2O2, such as dimethylthiourea and catalase, replaced the α-keto acid requirement, enhancing growth of strain DDS1. In fact, in the absence of α-keto acids, strain DDS1 and other AOA isolates were shown to endogenously produce H2O2 (up to ∼4.5 μM), which was inhibitory to growth. Genomic analyses indicated catalase genes are largely absent in the AOA. Our results indicate that AOA broadly feature strict autotrophic nutrition and implicate H2O2 as an important factor determining the activity, evolution, and community ecology of AOA ecotypes. PMID:27339136

  5. Effects of drought on nitrogen turnover and abundances of ammonia-oxidizers in mountain grassland

    NASA Astrophysics Data System (ADS)

    Fuchslueger, L.; Kastl, E.-M.; Bauer, F.; Kienzl, S.; Hasibeder, R.; Ladreiter-Knauss, T.; Schmitt, M.; Bahn, M.; Schloter, M.; Richter, A.; Szukics, U.

    2014-06-01

    Future climate scenarios suggest an increased frequency of summer drought periods in the European Alpine Region. Drought can affect soil nitrogen (N) cycling, by altering N transformation rates, as well as the abundances of ammonia-oxidizing bacteria and archaea. However, the extent to which drought affects N cycling under in situ conditions is still controversial. The goal of this study was to analyse effects of drought on soil N turnover and ammonia-oxidizer abundances. To this end we conducted a rain-exclusion experiment at two differently managed mountain grassland sites, an annually mown and occasionally fertilized meadow and an abandoned grassland. Soils were sampled before, during and after drought and were analysed for gross rates of N mineralization, microbial uptake of inorganic N, nitrification, and the abundances of bacterial and archaeal ammonia oxidizers based on gene copy numbers of the amoA gene (AOB and AOA, respectively). Our results showed that the response to drought differed between the two sites. Effects were stronger at the managed meadow, where NH4+ immobilization rates increased and AOA abundances decreased. At the abandoned site gross nitrification and NO3- immobilization rates decreased during drought, while neither AOB, nor AOA abundances were affected. The different responses of the two sites to drought were likely related to site specific differences, such as soil organic matter content, nitrogen pools and absolute soil water content, resulting from differences in land-management. At both sites rewetting after drought had only minor short-term effects on the parameters that had been affected by drought, and seven weeks after the drought no effects of drought were detectable anymore. Thus, our findings indicate that drought can have distinct transient effects on soil nitrogen cycling and ammonia-oxidizer abundances in mountain grasslands and that the effect strength could be modulated by grassland management.

  6. Coupling Between and Among Ammonia Oxidizers and Nitrite Oxidizers in Grassland Mesocosms Submitted to Elevated CO2 and Nitrogen Supply.

    PubMed

    Simonin, Marie; Le Roux, Xavier; Poly, Franck; Lerondelle, Catherine; Hungate, Bruce A; Nunan, Naoise; Niboyet, Audrey

    2015-10-01

    Many studies have assessed the responses of soil microbial functional groups to increases in atmospheric CO2 or N deposition alone and more rarely in combination. However, the effects of elevated CO2 and N on the (de)coupling between different microbial functional groups (e.g., different groups of nitrifiers) have been barely studied, despite potential consequences for ecosystem functioning. Here, we investigated the short-term combined effects of elevated CO2 and N supply on the abundances of the four main microbial groups involved in soil nitrification: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (belonging to the genera Nitrobacter and Nitrospira) in grassland mesocosms. AOB and AOA abundances responded differently to the treatments: N addition increased AOB abundance, but did not alter AOA abundance. Nitrobacter and Nitrospira abundances also showed contrasted responses to the treatments: N addition increased Nitrobacter abundance, but decreased Nitrospira abundance. Our results support the idea of a niche differentiation between AOB and AOA, and between Nitrobacter and Nitrospira. AOB and Nitrobacter were both promoted at high N and C conditions (and low soil water content for Nitrobacter), while AOA and Nitrospira were favored at low N and C conditions (and high soil water content for Nitrospira). In addition, Nitrobacter abundance was positively correlated to AOB abundance and Nitrospira abundance to AOA abundance. Our results suggest that the couplings between ammonia and nitrite oxidizers are influenced by soil N availability. Multiple environmental changes may thus elicit rapid and contrasted responses between and among the soil ammonia and nitrite oxidizers due to their different ecological requirements. PMID:25877793

  7. Ammonia-oxidizing archaea and nitrite-oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system.

    PubMed

    Brown, Monisha N; Briones, Aurelio; Diana, James; Raskin, Lutgarde

    2013-01-01

    This study analysed the nitrifier community in the biofilter of a zero discharge, recirculating aquaculture system (RAS) for the production of marine shrimp in a low density (low ammonium production) system. The ammonia-oxidizing populations were examined by targeting 16S rRNA and amoA genes of ammonia-oxidizing bacteria (AOB) and archaea (AOA). The nitrite-oxidizing bacteria (NOB) were investigated by targeting the 16S rRNA gene. Archaeal amoA genes were more abundant in all compartments of the RAS than bacterial amoA genes. Analysis of bacterial and archaeal amoA gene sequences revealed that most ammonia oxidizers were related to Nitrosomonas marina and Nitrosopumilus maritimus. The NOB detected were related to Nitrospira marina and Nitrospira moscoviensis, and Nitrospira marina-type NOB were more abundant than N. moscoviensis-type NOB. Water quality and biofilm attachment media played a role in the competitiveness of AOA over AOB and Nitrospira marina-over N. moscoviensis-type NOB. PMID:22775980

  8. Ultrasonic Treatment Enhanced Ammonia-Oxidizing Bacterial (AOB) Activity for Nitritation Process.

    PubMed

    Zheng, Min; Liu, Yan-Chen; Xin, Jia; Zuo, Hao; Wang, Cheng-Wen; Wu, Wei-Min

    2016-01-19

    Oxidation of ammonia to nitrite rather than nitrate is critical for nitritation process for wastewater treatment. We proposed a promising approach by using controlled ultrasonic treatment to enhance the activity of ammonia-oxidizing bacteria (AOB) and suppress that of nitrite-oxidizing bacteria (NOB). Batch activity assays indicated that when ultrasound was applied, AOB activity reached a peak level and then declined but NOB activity deteriorated continuously as the power intensity of ultrasound increased. Kinetic analysis of relative microbial activity versus ultrasonic energy density was performed to investigate the effect of operational factors (power, sludge concentration, and aeration) on AOB and NOB activities and the test parameters were selected for reactor tests. Laboratory sequential batch reactor (SBR) was further used to test the ultrasonic stimulus with 8 h per day operational cycle and synthetic waste urine as influent. With specific ultrasonic energy density of 0.09 kJ/mg VSS and continuously fed influent containing above 200 mg NH3-N/L, high AOB reproductive activity was achieved and nearly complete conversion of ammonia-N to nitrite was maintained. Microbial structure analysis confirmed that the treatment changed community of AOB, NOB, and heterotrophs. Known AOB Nitrosomonas genus remained at similar level in the biomass while typical NOB Nitrospira genus disappeared in the SBR under ultrasonic treatment and after the treatment was off for 30 days. PMID:26678011

  9. Enhanced sulfamethoxazole degradation through ammonia oxidizing bacteria co-metabolism and fate of transformation products.

    PubMed

    Kassotaki, Elissavet; Buttiglieri, Gianluigi; Ferrando-Climent, Laura; Rodriguez-Roda, Ignasi; Pijuan, Maite

    2016-05-01

    The occurrence of the widely-used antibiotic sulfamethoxazole (SFX) in wastewaters and surface waters has been reported in a large number of studies. However, the results obtained up-to-date have pointed out disparities in its removal. This manuscript explores the enhanced biodegradation potential of an enriched culture of Ammonia Oxidizing Bacteria (AOB) towards SFX. Several sets of batch tests were conducted to establish a link between SFX degradation and specific ammonia oxidation rate. The occurrence, degradation and generation of SFX and some of its transformation products (4-Nitro SFX, Desamino-SFX and N(4)-Acetyl-SFX) was also monitored. A clear link between the degradation of SFX and the nitrification rate was found, resulting in an increased SFX removal at higher specific ammonia oxidation rates. Moreover, experiments conducted under the presence of allylthiourea (ATU) did not present any removal of SFX, suggesting a connection between the AMO enzyme and SFX degradation. Long term experiments (up to 10 weeks) were also conducted adding two different concentrations (10 and 100 μg/L) of SFX in the influent of a partial nitrification sequencing batch reactor, resulting in up to 98% removal. Finally, the formation of transformation products during SFX degradation represented up to 32%, being 4-Nitro-SFX the most abundant. PMID:26938496

  10. Ammonia-oxidizing archaea in the low-oxygen water column of the Gulf of California

    NASA Astrophysics Data System (ADS)

    Beman, J.; Popp, B. N.; Francis, C. A.

    2006-12-01

    Archaea constitute a ubiquitous and exceptionally abundant component of marine microbial assemblages, yet their role in ocean biogeochemistry has remained elusive. Several recent lines of evidence suggest that many mesophilic Crenarchaeota are capable of performing ammonia oxidation, the first and rate-limiting step of chemoautotrophic nitrification. However, associations between these organisms and ammonia oxidation in the marine water column have yet to be explored--as has their means of survival under low oxygen conditions, where, paradoxically, they appear to be remarkably successful. In this study, we examined AOA diversity and abundance throughout the water column of the Gulf of California, which is characterized by highly productive near-surface waters and a pronounced oxygen minimum layer (OML) at depths below about 300 meters. We examined AOA both in the near surface and the OML of the Gulf of California, comparing across the transition to low oxygen conditions in two separate basins. Our results suggest that these organisms may play a key role in oxidizing ammonia in the Gulf of California water column, yet their presence and abundance under low oxygen conditions remains unresolved.

  11. Revealing the halide effect on the kinetics of the aerobic oxidation of Cu(I) to Cu(II)

    SciTech Connect

    Deng, Yi; Zhang, Guanghui; Qi, Xiaotian; Liu, Chao; Miller, Jeffrey T.; Kropf, A. Jeremy; Bunel, Emilio E.; Lan, Yu; Lei, Aiwen

    2015-01-01

    In situ infrared (IR) and X-ray absorption near-edge structure (XANES) spectroscopic investigations reveal that different halide ligands have distinct effects on the aerobic oxidation of Cu(I) to Cu(II) in the presence of TMEDA (tetramethylethylenediamine). The iodide ligand gives the lowest rate and thus leads to the lowest catalytic reaction rate of aerobic oxidation of hydroquinone to benzoquinone. Further DFT calculations suggest that oxidation of CuI–TMEDA involves a side-on transition state, while oxidation of CuCl–TMEDA involves an end-on transition state which has a lower activation energy.

  12. Ammonia oxidation driven by archaea rather than bacteria in the hot spring at Tengchong geothermal field, China.

    NASA Astrophysics Data System (ADS)

    Chen, Shun; Peng, Xiaotong; Xu, Hengchao; Li, Jiwei; Ta, Kaiwen

    2015-04-01

    The occurrence of microbial mediated ammonia oxidation and these organisms are present in large numbers in natural environments indicated a potential biogeochemical role for them in the global nitrogen cycle. However, very little is understood about their role and contribution to nitrification in the high temperature extreme environments. Here we explore the ammonia oxidation rates and abundance of potential ammonia-oxidizing archaea (AOA) in upper and bottom sediments from Gongxiaoshe hot spring, Tengchong, Yunnan, China. The 15N-incorporating AOA cells and cell aggregated were detected with Fluorescence in situ hybridization (FISH) and Nano secondary ion mass spectrometry (Nano-SIMS). Ammonia oxidation rates measured using 15N-NO3- pool dilution in upper and bottom sediments (without NH4+ stimulated) were 4.8 and 5.3 nmol N g-1h-1, respectively. Close relatives of the autotrophic, ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus yellowstonii' represented the most abundant OTU in both of the two spring sediments by 16S rRNA gene analysis. Furthermore, it should be noted that no ammonia-oxidizing bacterial clones detected in this study. Quantitative PCR (qPCR) indicated that AOA and 16S rRNA genes were present at 2.75-9.80×105 and 0.128-1.96×108 gene copies g-1 sediment. Based on the reaction rates and AOA abundance, we estimated the cell-specific nitrification rates were 0.41 to 0.79 fmol N archaeal cell-1 h-1, which are comparable to those observed in estuary environment. We suggest that AOA have the responsibility in nitrification in this hot spring, and these archaea rather than bacteria may be considered as a driver in nitrogen cycling in terrestrial hot ecosystems. Key words: ammonia-oxidizing archaea (AOA); nitrification; ammonia-oxidizing rate; hot spring;

  13. Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

    NASA Astrophysics Data System (ADS)

    Frame, C. H.; Casciotti, K. L.

    2010-04-01

    Nitrous oxide (N2O) is a trace gas that contributes to greenhouse warming of the atmosphere and stratospheric ozone depletion. The N2O yield from nitrification (moles N2O-N produced/mole ammonium-N consumed) has been used to estimate marine N2O production rates from measured nitrification rates and global estimates of oceanic export production. However, the N2O yield from nitrification is not constant. Previous culture-based measurements indicate that N2O yield increases as oxygen (O2) concentration decreases and as nitrite (NO2-) concentration increases. These results were obtained in substrate-rich conditions and may not reflect N2O production in the ocean. Here, we have measured yields of N2O from cultures of the marine β-proteobacterium Nitrosomonas marina C-113a as they grew on low-ammonium (50 μM) media. These yields were lower than previous reports, between 4×10-4 and 7×10-4 (moles N/mole N). The observed impact of O2 concentration on yield was also smaller than previously reported under all conditions except at high starting cell densities (1.5×10ammonia oxidizers in the ocean. The presence of excess NO2- (up to 1 mM) in the growth medium also increased N2O yields by an average of 70% to 87% depending on O2 concentration. We made stable isotopic measurements on N2O from these cultures to identify the biochemical mechanisms behind variations in N2O yield. Based on measurements of δ15N, site preference (SP=δ15Nα - δ15Nβ), and δ18O, we estimate that nitrifier-denitrification produced between 11% and 26% of N2O from cultures

  14. D1FHS, the Type Strain of the Ammonia-Oxidizing Bacterium Nitrosococcus wardiae spec. nov.: Enrichment, Isolation, Phylogenetic, and Growth Physiological Characterization

    PubMed Central

    Wang, Lin; Lim, Chee Kent; Dang, Hongyue; Hanson, Thomas E.; Klotz, Martin G.

    2016-01-01

    An ammonia-oxidizing bacterium, strain D1FHS, was enriched into pure culture from a sediment sample retrieved in Jiaozhou Bay, a hyper-eutrophic semi-closed water body hosting the metropolitan area of Qingdao, China. Based on initial 16S rRNA gene sequence analysis, strain D1FHS was classified in the genus Nitrosococcus, family Chromatiaceae, order Chromatiales, class Gammaproteobacteria; the 16S rRNA gene sequence with highest level of identity to that of D1FHS was obtained from Nitrosococcus halophilus Nc4T. The average nucleotide identity between the genomes of strain D1FHS and N. halophilus strain Nc4 is 89.5%. Known species in the genus Nitrosococcus are obligate aerobic chemolithotrophic ammonia-oxidizing bacteria adapted to and restricted to marine environments. The optimum growth (maximum nitrite production) conditions for D1FHS in a minimal salts medium are: 50 mM ammonium and 700 mM NaCl at pH of 7.5 to 8.0 and at 37°C in dark. Because pertinent conditions for other studied Nitrosococcus spp. are 100–200 mM ammonium and <700 mM NaCl at pH of 7.5 to 8.0 and at 28–32°C, D1FHS is physiologically distinct from other Nitrosococcus spp. in terms of substrate, salt, and thermal tolerance. PMID:27148201

  15. Ammonium-oxidizing bacteria facilitate aerobic degradation of sulfanilic acid in activated sludge.

    PubMed

    Chen, Gang; Ginige, Maneesha P; Kaksonen, Anna H; Cheng, Ka Yu

    2014-01-01

    Sulfanilic acid (SA) is a toxic sulfonated aromatic amine commonly found in anaerobically treated azo dye contaminated effluents. Aerobic acclimatization of SA-degrading mixed microbial culture could lead to co-enrichment of ammonium-oxidizing bacteria (AOB) because of the concomitant release of ammonium from SA oxidation. To what extent the co-enriched AOB would affect SA oxidation at various ammonium concentrations was unclear. Here, a series of batch kinetic experiments were conducted to evaluate the effect of AOB on aerobic SA degradation in an acclimatized activated sludge culture capable of oxidizing SA and ammonium simultaneously. To account for the effect of AOB on SA degradation, allylthiourea was used to inhibit AOB activity in the culture. The results indicated that specific SA degradation rate of the mixed culture was negatively correlated with the initial ammonium concentration (0-93 mM, R²= 0.99). The presence of AOB accelerated SA degradation by reducing the inhibitory effect of ammonium (≥ 10 mM). The Haldane substrate inhibition model was used to correlate substrate concentration (SA and ammonium) and oxygen uptake rate. This study revealed, for the first time, that AOB could facilitate SA degradation at high concentration of ammonium (≥ 10 mM) in an enriched activated sludge culture. PMID:25259503

  16. Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary

    PubMed Central

    Zheng, Yanling; Newell, Silvia; Liu, Min; Zhou, Junliang; Zhao, Hui; You, Lili; Cheng, Xunliang

    2014-01-01

    Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOB amoA genes was greater than that of AOA amoA genes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaeal amoA gene abundance and not with bacterial amoA gene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments. PMID:24185847

  17. Community dynamics and activity of ammonia-oxidizing prokaryotes in intertidal sediments of the Yangtze estuary.

    PubMed

    Zheng, Yanling; Hou, Lijun; Newell, Silvia; Liu, Min; Zhou, Junliang; Zhao, Hui; You, Lili; Cheng, Xunliang

    2014-01-01

    Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOB amoA genes was greater than that of AOA amoA genes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaeal amoA gene abundance and not with bacterial amoA gene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments. PMID:24185847

  18. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria.

    PubMed

    Nicol, Graeme W; Leininger, Sven; Schleper, Christa; Prosser, James I

    2008-11-01

    Autotrophic ammonia oxidation occurs in acid soils, even though laboratory cultures of isolated ammonia oxidizing bacteria fail to grow below neutral pH. To investigate whether archaea possessing ammonia monooxygenase genes were responsible for autotrophic nitrification in acid soils, the community structure and phylogeny of ammonia oxidizing bacteria and archaea were determined across a soil pH gradient (4.9-7.5) by amplifying 16S rRNA and amoA genes followed by denaturing gradient gel electrophoresis (DGGE) and sequence analysis. The structure of both communities changed with soil pH, with distinct populations in acid and neutral soils. Phylogenetic reconstructions of crenarchaeal 16S rRNA and amoA genes confirmed selection of distinct lineages within the pH gradient and high similarity in phylogenies indicated a high level of congruence between 16S rRNA and amoA genes. The abundance of archaeal and bacterial amoA gene copies and mRNA transcripts contrasted across the pH gradient. Archaeal amoA gene and transcript abundance decreased with increasing soil pH, while bacterial amoA gene abundance was generally lower and transcripts increased with increasing pH. Short-term activity was investigated by DGGE analysis of gene transcripts in microcosms containing acidic or neutral soil or mixed soil with pH readjusted to that of native soils. Although mixed soil microcosms contained identical archaeal ammonia oxidizer communities, those adapted to acidic or neutral pH ranges showed greater relative activity at their native soil pH. Findings indicate that different bacterial and archaeal ammonia oxidizer phylotypes are selected in soils of different pH and that these differences in community structure and abundances are reflected in different contributions to ammonia oxidizer activity. They also suggest that both groups of ammonia oxidizers have distinct physiological characteristics and ecological niches, with consequences for nitrification in acid soils. PMID:18707610

  19. A Mesophilic, Autotrophic, Ammonia-Oxidizing Archaeon of Thaumarchaeal Group I.1a Cultivated from a Deep Oligotrophic Soil Horizon

    PubMed Central

    Jung, Man-Young; Park, Soo-Je; Kim, So-Jeong; Kim, Jong-Geol; Sinninghe Damsté, Jaap S.

    2014-01-01

    Soil nitrification plays an important role in the reduction of soil fertility and in nitrate enrichment of groundwater. Various ammonia-oxidizing archaea (AOA) are considered to be members of the pool of ammonia-oxidizing microorganisms in soil. This study reports the discovery of a chemolithoautotrophic ammonia oxidizer that belongs to a distinct clade of nonmarine thaumarchaeal group I.1a, which is widespread in terrestrial environments. The archaeal strain MY2 was cultivated from a deep oligotrophic soil horizon. The similarity of the 16S rRNA gene sequence of strain MY2 to those of other cultivated group I.1a thaumarchaeota members, i.e., Nitrosopumilus maritimus and “Candidatus Nitrosoarchaeum koreensis,” is 92.9% for both species. Extensive growth assays showed that strain MY2 is chemolithoautotrophic, mesophilic (optimum temperature, 30°C), and neutrophilic (optimum pH, 7 to 7.5). The accumulation of nitrite above 1 mM inhibited ammonia oxidation, while ammonia oxidation itself was not inhibited in the presence of up to 5 mM ammonia. The genome size of strain MY2 was 1.76 Mb, similar to those of N. maritimus and “Ca. Nitrosoarchaeum koreensis,” and the repertoire of genes required for ammonia oxidation and carbon fixation in thaumarchaeal group I.1a was conserved. A high level of representation of conserved orthologous genes for signal transduction and motility in the noncore genome might be implicated in niche adaptation by strain MY2. On the basis of phenotypic, phylogenetic, and genomic characteristics, we propose the name “Candidatus Nitrosotenuis chungbukensis” for the ammonia-oxidizing archaeal strain MY2. PMID:24705324

  20. Ammonia-oxidizing Bacteria of the Nitrosospira cluster 1 dominate over ammonia-oxidizing Archaea in oligotrophic surface sediments near the South Atlantic Gyre.

    PubMed

    Lagostina, Lorenzo; Goldhammer, Tobias; Røy, Hans; Evans, Thomas W; Lever, Mark A; Jørgensen, Bo B; Petersen, Dorthe G; Schramm, Andreas; Schreiber, Lars

    2015-06-01

    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 Nitrososphaera and Nitrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the Nitrosospira 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. PMID:25581373

  1. Abundance and community structure of ammonia-oxidizing microorganisms in reservoir sediment and adjacent soils.

    PubMed

    Wang, Xiaoyan; Wang, Cui; Bao, Linlin; Xie, Shuguang

    2014-02-01

    Ammonia oxidation is an important process for global nitrogen cycling. Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can be the important players in nitrification process. However, their relative contribution to nitrification remains controversial. This study investigated the abundance and community structure of AOA and AOB in sediment of Miyun Reservoir and adjacent soils. Quantitative PCR assays indicated that the highest AOA abundance occurred in unplanted riparian soil, followed by reservoir sediment, reed-planted riparian soil and agricultural soil. The AOB community size in agricultural soil was much larger than that in the other habitats. Large variations in the structures of AOA and AOB were also observed among the different habitats. The abundance of Nitrosospira-like AOB species were detected in the agricultural soil and reservoir sediment. Pearson's correlation analysis showed the AOB diversity had positive significant correlations with pH and total nitrogen, while the AOA diversity might be negatively affected by nitrate nitrogen and ammonia nitrogen. This work could add new insights towards nitrification in aquatic and terrestrial ecosystems. PMID:23949998

  2. Diversity, abundance, and activity of ammonia-oxidizing bacteria and archaea in Chongming eastern intertidal sediments.

    PubMed

    Zheng, Yanling; Hou, Lijun; Liu, Min; Lu, Min; Zhao, Hui; Yin, Guoyu; Zhou, Junliang

    2013-09-01

    Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic sediments. Certain bacterial groups and a novel group of archaea, which is affiliated with the novel phylum Thaumarchaeota, can perform this initial nitrification step. We examined the diversity and abundance of ammonia-oxidizing β-Proteobacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in the sediments of Chongming eastern tidal flat using the ammonia monooxygenase-α subunit (amoA) gene as functional markers. Clone library analysis showed that AOA had a higher diversity of amoA gene than β-AOB. The β-Proteobacterial amoA community composition correlated significantly with water soluble salts in the sediments, whereas the archaeal amoA community composition was correlated more with nitrate concentrations. Quantitative PCR (qPCR) results indicated that the abundance of β-AOB amoA gene (9.11 × 10(4)-6.47 × 10(5) copies g(-1) sediment) was always greater than that of AOA amoA gene (7.98 × 10(3)-3.51 × 10(5) copies g(-1) sediment) in all the samples analyzed in this study. The β-Proteobacterial amoA gene abundance was closely related to organic carbon, while no significant correlations were observed between archaeal amoA gene abundance and the environmental factors. Potential nitrification rates were significantly greater in summer than in winter and correlated strongly with the abundance of amoA genes. Additionally, a greater contribution of single amoA gene to potential nitrification occurred in summer (1.03-5.39 pmol N copy(-1) day(-1)) compared with winter (0.16-0.38 pmol N copy(-1) day(-1)), suggesting a higher activity of ammonia-oxidizing prokaryotes in warm seasons. PMID:23108528

  3. Treatment of activated carbon to enhance catalytic activity for reduction of nitric oxide with ammonia

    SciTech Connect

    Ku, B.J.; Rhee, H.K. . Dept. of Chemical Engineering); Lee, J.K.; Park, D. )

    1994-11-01

    Catalytic activity of activated carbon treated with various techniques was examined in a fixed bed reactor for the reduction of nitric oxide with ammonia at 150 C. Activated carbon derived from coconut shell impregnated with an aqueous solution of ammonium sulfate, further treated with sulfuric acid, dried at 120 C, and then heated in an inert gas stream at 400 C, showed the highest catalytic activity within the range of experimental conditions. The enhancement of catalytic activity of modified activated carbon could be attributed to the increase in the amount of oxygen function groups which increased the adsorption site for ammonia. Catalytic activity of activated carbons depended on the surface area and the oxygen content as well.

  4. Potential of nitrous oxide recovery from an aerobic/oxic/anoxic SBR process.

    PubMed

    Zhao, Jianqiang; Huang, Nan; Hu, Bo; Jia, Luwei; Ge, Guanghuan

    2016-01-01

    A single sequencing batch reactor (SBR) with an operating mode of anaerobic/oxic/anoxic (A/O/A) was developed to determine a simpler process to recover nitrous oxide (N2O) from synthetic wastewater containing ammonia and glucose. This SBR system was initiated in A/O mode to implement nitritation (ammonia to nitrite) and then switched to A/O/A mode. Using measurements of the dissolved N2O concentration and release rate, the total production and conversion rate of N2O were calculated to reveal the potential of producing and recovering N2O in the extended anoxic phase. Results showed that the A/O/A SBR could convert the majority of the nitrite available in the system into N2O by heterotrophic denitritation over longer anoxic periods, and a conversion rate of 77% could be achieved. As a consequence, the A/O/A SBR presents potential ability to produce and recover N2O from wastewater containing ammonia and organic carbon. PMID:26942527

  5. Identification of key nitrous oxide production pathways in aerobic partial nitrifying granules.

    PubMed

    Ishii, Satoshi; Song, Yanjun; Rathnayake, Lashitha; Tumendelger, Azzaya; Satoh, Hisashi; Toyoda, Sakae; Yoshida, Naohiro; Okabe, Satoshi

    2014-10-01

    The identification of the key nitrous oxide (N2O) production pathways is important to establish a strategy to mitigate N2O emission. In this study, we combined real-time gas-monitoring analysis, (15)N stable isotope analysis, denitrification functional gene transcriptome analysis and microscale N2O concentration measurements to identify the main N2O producers in a partial nitrification (PN) aerobic granule reactor, which was fed with ammonium and acetate. Our results suggest that heterotrophic denitrification was the main contributor to N2O production in our PN aerobic granule reactor. The heterotrophic denitrifiers were probably related to Rhodocyclales bacteria, although different types of bacteria were active in the initial and latter stages of the PN reaction cycles, most likely in response to the presence of acetate. Hydroxylamine oxidation and nitrifier denitrification occurred, but their contribution to N2O emission was relatively small (20-30%) compared with heterotrophic denitrification. Our approach can be useful to quantitatively examine the relative contributions of the three pathways (hydroxylamine oxidation, nitrifier denitrification and heterotrophic denitrification) to N2O emission in mixed microbial populations. PMID:24650173

  6. Molecular Engineering of Trifunctional Supported Catalysts for the Aerobic Oxidation of Alcohols.

    PubMed

    Fernandes, Antony E; Riant, Olivier; Jensen, Klavs F; Jonas, Alain M

    2016-09-01

    We describe a simple and general method for the preparation and molecular engineering of supported trifunctional catalysts and their application in the representative Cu/TEMPO/NMI-catalyzed aerobic oxidation of benzyl alcohol. The methodology allows in one single step to immobilize, with precise control of surface composition, both pyta, Cu(I) , TEMPO, and NMI sites on azide-functionalized silica particles. To optimize the performance of the heterogeneous trifunctional catalysts, synergistic interactions are finely engineered through modulating the degree of freedom of the imidazole site as well as tuning the relative surface composition, leading to catalysts with an activity significantly superior to the corresponding homogeneous catalytic system. PMID:27430481

  7. The effect of widespread early aerobic marine ecosystems on methane cycling and the Great Oxidation

    NASA Astrophysics Data System (ADS)

    Daines, Stuart J.; Lenton, Timothy M.

    2016-01-01

    The balance of evidence suggests that oxygenic photosynthesis had evolved by 3.0-2.7 Ga, several hundred million years prior to the Great Oxidation ≈2.4 Ga. Previous work has shown that if oxygenic photosynthesis spread globally prior to the Great Oxidation, this could have supported widespread aerobic ecosystems in the surface ocean, without oxidising the atmosphere. Here we use a suite of models to explore the implications for carbon cycling and the Great Oxidation. We find that recycling of oxygen and carbon within early aerobic marine ecosystems would have restricted the balanced fluxes of methane and oxygen escaping from the ocean, lowering the atmospheric concentration of methane in the Great Oxidation transition and its aftermath. This in turn would have minimised any bi-stability of atmospheric oxygen, by weakening a stabilising feedback on oxygen from hydrogen escape to space. The result would have been a more reversible and probably episodic rise of oxygen at the Great Oxidation transition, consistent with existing geochemical evidence. The resulting drop in methane levels to ≈10 ppm is consistent with climate cooling at the time but adds to the puzzle of what kept the rest of the Proterozoic warm. A key test of the scenario of abundant methanotrophy in oxygen oases before the Great Oxidation is its predicted effects on the organic carbon isotope (δ13Corg) record. Our open ocean general circulation model predicts δC13org ≈ - 30 to -45‰ consistent with most data from 2.65 to 2.45 Ga. However, values of δC13org ≈ - 50 ‰ require an extreme scenario such as concentrated methanotroph production where shelf-slope upwelling of methane-rich water met oxic shelf water.

  8. Effect of selected monoterpenes on methane oxidation, denitrification, and aerobic metabolism by bacteria in pure culture.

    PubMed

    Amaral, J A; Ekins, A; Richards, S R; Knowles, R

    1998-02-01

    Selected monoterpenes inhibited methane oxidation by methanotrophs (Methylosinus trichosporium OB3b, Methylobacter luteus), denitrification by environmental isolates, and aerobic metabolism by several heterotrophic pure cultures. Inhibition occurred to various extents and was transient. Complete inhibition of methane oxidation by Methylosinus trichosporium OB3b with 1.1 mM (-)-alpha-pinene lasted for more than 2 days with a culture of optical density of 0.05 before activity resumed. Inhibition was greater under conditions under which particulate methane monooxygenase was expressed. No apparent consumption or conversion of monoterpenes by methanotrophs was detected by gas chromatography, and the reason that transient inhibition occurs is not clear. Aerobic metabolism by several heterotrophs was much less sensitive than methanotrophy was; Escherichia coli (optical density, 0.01), for example, was not affected by up to 7.3 mM (-)-alpha-pinene. The degree of inhibition was monoterpene and species dependent. Denitrification by isolates from a polluted sediment was not inhibited by 3.7 mM (-)-alpha-pinene, gamma-terpinene, or beta-myrcene, whereas 50 to 100% inhibition was observed for isolates from a temperate swamp soil. The inhibitory effect of monoterpenes on methane oxidation was greatest with unsaturated, cyclic hydrocarbon forms [e.g., (-)-alpha-pinene, (S)-(-)-limonene, (R)-(+)-limonene, and gamma-terpinene]. Lower levels of inhibition occurred with oxide and alcohol derivatives [(R)-(+)-limonene oxide, alpha-pinene oxide, linalool, alpha-terpineol] and a noncyclic hydrocarbon (beta-myrcene). Isomers of pinene inhibited activity to different extents. Given their natural sources, monoterpenes may be significant factors affecting bacterial activities in nature. PMID:9464387

  9. Geographic and seasonal variation of dissolved methane and aerobic methane oxidation in Alaskan lakes

    NASA Astrophysics Data System (ADS)

    Martinez-Cruz, K.; Sepulveda-Jauregui, A.; Anthony, K. Walter; Thalasso, F.

    2015-08-01

    Methanotrophic bacteria play an important role oxidizing a significant fraction of methane (CH4) produced in lakes. Aerobic CH4 oxidation depends mainly on lake CH4 and oxygen (O2) concentrations, in such a manner that higher MO rates are usually found at the oxic/anoxic interface, where both molecules are present. MO also depends on temperature, and via methanogenesis, on organic carbon input to lakes, including from thawing permafrost in thermokarst (thaw)-affected lakes. Given the large variability in these environmental factors, CH4 oxidation is expected to be subject to large seasonal and geographic variations, which have been scarcely reported in the literature. In the present study, we measured CH4 oxidation rates in 30 Alaskan lakes along a north-south latitudinal transect during winter and summer with a new field laser spectroscopy method. Additionally, we measured dissolved CH4 and O2 concentrations. We found that in the winter, aerobic CH4 oxidation was mainly controlled by the dissolved O2 concentration, while in the summer it was controlled primarily by the CH4 concentration, which was scarce compared to dissolved O2. The permafrost environment of the lakes was identified as another key factor. Thermokarst (thaw) lakes formed in yedoma-type permafrost had significantly higher CH4 oxidation rates compared to other thermokarst and non-thermokarst lakes formed in non-yedoma permafrost environments. As thermokarst lakes formed in yedoma-type permafrost have been identified to receive large quantities of terrestrial organic carbon from thaw and subsidence of the surrounding landscape into the lake, confirming the strong coupling between terrestrial and aquatic habitats and its influence on CH4 cycling.

  10. Pd/Cu-cocatalyzed aerobic oxidative carbonylative homocoupling of arylboronic acids and CO: a highly selective approach to diaryl ketones.

    PubMed

    Ren, Long; Jiao, Ning

    2014-09-01

    A highly selective Pd/Cu-cocatalyzed aerobic oxidative carbonylative homocoupling of arylboronic acids has been developed. This method employs a simple catalytic system, readily available boronic acids as the substrates, molecular oxygen as the oxidant, and 1 atm of CO/O2 , which makes this method practical for further applications. PMID:24990473

  11. Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation.

    PubMed

    Werner, Jeffrey J; Garcia, Marcelo L; Perkins, Sarah D; Yarasheski, Kevin E; Smith, Samuel R; Muegge, Brian D; Stadermann, Frank J; DeRito, Christopher M; Floss, Christine; Madsen, Eugene L; Gordon, Jeffrey I; Angenent, Largus T

    2014-06-01

    Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity. PMID:24657858

  12. Ammonia- and methane-oxidizing microorganisms in high-altitude wetland sediments and adjacent agricultural soils.

    PubMed

    Yang, Yuyin; Shan, Jingwen; Zhang, Jingxu; Zhang, Xiaoling; Xie, Shuguang; Liu, Yong

    2014-12-01

    Ammonia oxidation is known to be carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA), while methanotrophs (methane-oxidizing bacteria (MOB)) play an important role in mitigating methane emissions from the environment. However, the difference of AOA, AOB, and MOB distribution in wetland sediment and adjacent upland soil remains unclear. The present study investigated the abundances and community structures of AOA, AOB, and MOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China) and adjacent agricultural soils. Variations of AOA, AOB, and MOB community sizes and structures were found in water lily-vegetated and Acorus calamus-vegetated sediments and agricultural soils (unflooded rice soil, cabbage soil, and garlic soil and flooded rice soil). AOB community size was higher than AOA in agricultural soils and lily-vegetated sediment, but lower in A. calamus-vegetated sediment. MOB showed a much higher abundance than AOA and AOB. Flooded rice soil had the largest AOA, AOB, and MOB community sizes. Principal coordinate analyses and Jackknife Environment Clusters analyses suggested that unflooded and flooded rice soils had relatively similar AOA, AOB, and MOB structures. Cabbage soil and A. calamus-vegetated sediment had relatively similar AOA and AOB structures, but their MOB structures showed a large difference. Nitrososphaera-like microorganisms were the predominant AOA species in garlic soil but were present with a low abundance in unflooded rice soil and cabbage soil. Nitrosospira-like AOB were dominant in wetland sediments and agricultural soils. Type I MOB Methylocaldum and type II MOB Methylocystis were dominant in wetland sediments and agricultural soils. Moreover, Pearson's correlation analysis indicated that AOA Shannon diversity was positively correlated with the ratio of organic carbon to nitrogen (p < 0.05). This work could provide some new insights toward ammonia and methane oxidation in soil and wetland sediment

  13. Response of Ammonia-oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater

    SciTech Connect

    David W. Reed; Yoshiko Fujita; Jason M. Smith; Christopher A. Francis

    2010-02-01

    To better understand the fate of ammonia introduced into low-nutrient groundwater as a result of the application of a novel remediation approach for trace metal contaminants, the diversity and abundance of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) were examined in samples collected during a field trial of the approach. The ammonia is derived from microbial urea hydrolysis, which has the potential to induce the formation of calcite and remove contaminants by coprecipitation in the calcite. The in situ oxidation of the ammonia by AOB and AOA could, however, potentially destabilize the calcite and lead to elevated nitrate levels in the groundwater. To evaluate the potential for stimulating ammonia oxidation by addition of urea, samples were collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea, and subjected to PCR analysis of ammonia monooxygenase subunit A (amoA) genes. AOB and AOA were present in all of the samples tested, with the AOA amoA genes more numerous in all of the samples except those collected following urea addition, when AOB genes were slightly more abundant. Following urea addition, nitrate levels rose and ammonia-oxidizing microorganisms (AOB + AOA) increased relative to the total microbial population, evidence that nitrification was stimulated by urea hydrolysis. Bacterial amoA diversity was limited to two sequence types, whereas the archaeal amoA analyses revealed 20 unique operational taxonomic units (OTUs), including several that were significantly different from any reported previously from other environments. In view of the results from this study, the potential for stimulation of ammonia-oxidizing communities should be considered in field-scale engineering activities involving microbial urea hydrolysis in groundwater.

  14. Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond

    PubMed Central

    Lu, Shimin; Liu, Xingguo; Ma, Zhuojun; Liu, Qigen; Wu, Zongfan; Zeng, Xianlei; Shi, Xu; Gu, Zhaojun

    2016-01-01

    Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0–50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0–10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths) were grouped into the Nitrosopumilus cluster. PMID:26834709

  15. Vertical Segregation and Phylogenetic Characterization of Ammonia-Oxidizing Bacteria and Archaea in the Sediment of a Freshwater Aquaculture Pond.

    PubMed

    Lu, Shimin; Liu, Xingguo; Ma, Zhuojun; Liu, Qigen; Wu, Zongfan; Zeng, Xianlei; Shi, Xu; Gu, Zhaojun

    2015-01-01

    Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in sediment samples (0-50 cm depth) collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5- to 39.9-fold in surface sediments (0-10 cm depth), which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0-2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10-15 and 20-25 cm depths) were grouped into the Nitrosopumilus cluster. PMID:26834709

  16. Aerobic oxidation reactions catalyzed by vanadium complexes of bis(phenolate) ligands.

    PubMed

    Zhang, Guoqi; Scott, Brian L; Wu, Ruilian; Silks, L A Pete; Hanson, Susan K

    2012-07-01

    Vanadium(V) complexes of the tridentate bis(phenolate)pyridine ligand H(2)BPP (H(2)BPP = 2,6-(HOC(6)H(2)-2,4-(t)Bu(2))(2)NC(5)H(3)) and the bis(phenolate)amine ligand H(2)BPA (H(2)BPA = N,N-bis(2-hydroxy-4,5-dimethylbenzyl)propylamine) have been synthesized and characterized. The ability of the complexes to mediate the oxidative C-C bond cleavage of pinacol was tested. Reaction of the complex (BPP)V(V)(O)(O(i)Pr) (4) with pinacol afforded the monomeric vanadium(IV) product (BPP)V(IV)(O)(HO(i)Pr) (6) and acetone. Vanadium(IV) complex 6 was oxidized rapidly by air at room temperature in the presence of NEt(3), yielding the vanadium(V) cis-dioxo complex [(BPP)V(V)(O)(2)]HNEt(3). Complex (BPA)V(V)(O)(O(i)Pr) (5) reacted with pinacol at room temperature, to afford acetone and the vanadium(IV) dimer [(BPA)V(IV)(O)(HO(i)Pr)](2). Complexes 4 and 5 were evaluated as catalysts for the aerobic oxidation of 4-methoxybenzyl alcohol and arylglycerol β-aryl ether lignin model compounds. Although both 4 and 5 catalyzed the aerobic oxidation of 4-methoxybenzyl alcohol, complex 4 was found to be a more active and robust catalyst for oxidation of the lignin model compounds. The catalytic activities and selectivities of the bis(phenolate) complexes are compared to previously reported catalysts. PMID:22708725

  17. Oxidation-reduction processes in ice swimmers after ice-cold water bath and aerobic exercise.

    PubMed

    Sutkowy, Paweł; Woźniak, Alina; Boraczyński, Tomasz; Boraczyński, Michał; Mila-Kierzenkowska, Celestyna

    2015-06-01

    The effect of an ice-cold water (ICW) bath as a recovery intervention from aerobic exercise on the oxidant-antioxidant balance in healthy ice swimmers was determined. Twenty ice swimmers aged 31.2 ± 6.3 years performed a 30-min cycloergometer exercise test at room temperature (20°C, RT), followed by recovery at RT or in a pool of ice-cold water (ICW bath, 3°C, 5 min). Blood for laboratory assays was collected from the basilic vein two times: before the exercise (baseline) and 40 min after the RT or ICW recovery. The concentrations of plasma and erythrocytic thiobarbituric acid reactive substances (plTBARS and erTBARS, respectively), serum concentrations of 8-iso-prostaglandin F2α, 4-hydroxynonenal and malondialdehyde, along with the erythrocytic activities of catalase (CAT) and superoxide dismutase (SOD), as well as the serum level of total antioxidant capacity, were assessed. No statistically significant changes were observed. However, a statistically significant negative linear correlation between the erTBARS concentration and the SOD activity was found 40 min after the combination of exercise/RT recovery (r=-0.571, P<0.01). The baseline CAT and SOD activities were also linearly correlated (r=0.469, P<0.05). Both the 5-min ICW bath and the 30-min aerobic exercise have practically no impact on the oxidant-antioxidant balance in healthy ice swimmers. PMID:25910677

  18. Diversity and abundance of ammonia oxidizing archaea in tropical compost systems

    PubMed Central

    de Gannes, Vidya; Eudoxie, Gaius; Dyer, David H.; Hickey, William J.

    2012-01-01

    Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems. PMID:22787457

  19. Diversity and abundance of ammonia oxidizing archaea in tropical compost systems.

    PubMed

    de Gannes, Vidya; Eudoxie, Gaius; Dyer, David H; Hickey, William J

    2012-01-01

    Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems. PMID:22787457

  20. Ruthenium(salen)-catalyzed aerobic oxidative desymmetrization of meso-diols and its kinetics.

    PubMed

    Shimizu, Hideki; Onitsuka, Satoaki; Egami, Hiromichi; Katsuki, Tsutomu

    2005-04-20

    Chiral (nitrosyl)ruthenium(salen) complexes were found to be efficient catalysts for aerobic oxidative desymmetrization of meso-diols under photoirradiation to give optically active lactols. The scope of the applicability of this reaction ranges widely from acyclic diols to mono-cyclic diols, although fine ligand-tuning of the ruthenium(salen) complexes was required to attain high enantioselectivity (up to 93% ee). In particular, the nature of the apical ligand was found to affect not only enantioselectivity but also kinetics of the desymmetrization reaction. Spectroscopic analysis of the oxidation disclosed that irradiation of visible light is indispensable not only for dissociation of the nitrosyl ligand but also for single electron transfer from the alcohol-bound ruthenium ion to dioxygen. PMID:15826178

  1. Reduction of nitric oxide by ammonia at atmospheric pressures over platinum polycrystalline foils as model catalysts

    SciTech Connect

    Katona, T.; Guczi, L.; Somorjai, G.A.

    1991-12-01

    The reduction of nitric oxide with ammonia was studied using batch-mode and flow-mode measurements in partial pressure ranges of 70-660 Pa (0.5-5 Torr) on polycrystalline platinum foils over the temperature range of 373-633 K. The reaction products observed were nitrogen, nitrous oxide, and water. Unimolecular decompositions of NO or NH{sub 3} were not detectable under these conditions, up to 773 K. The reduction of nitric oxide with ammonia occurred in the temperature range of 548-633 K. The Arrhenius curve of the reaction showed a break in the 563-603 K range, which was slightly dependent on the reactant concentrations. In this temperature range the reaction became oscillatory. The activation energies were 102 kJ/mol in the low-temperature and 212 kJ/mol in the high-temperature ranges, respectively. The product distribution was different in the two temperature regions; in the low-temperature range the n{sub 2}/N{sub 2}O ratio was close to 1, while in the high-temperature regime N{sub 2} formation was dominant, and the previously formed N{sub 2}O was consumed as well.

  2. Biodegradation and cometabolic modeling of selected beta blockers during ammonia oxidation.

    PubMed

    Sathyamoorthy, Sandeep; Chandran, Kartik; Ramsburg, C Andrew

    2013-11-19

    Accurate prediction of pharmaceutical concentrations in wastewater effluents requires that the specific biochemical processes responsible for pharmaceutical biodegradation be elucidated and integrated within any modeling framework. The fate of three selected beta blockers-atenolol, metoprolol, and sotalol-was examined during nitrification using batch experiments to develop and evaluate a new cometabolic process-based (CPB) model. CPB model parameters describe biotransformation during and after ammonia oxidation for specific biomass populations and are designed to be integrated within the Activated Sludge Models framework. Metoprolol and sotalol were not biodegraded by the nitrification enrichment culture employed herein. Biodegradation of atenolol was observed and linked to the activity of ammonia-oxidizing bacteria (AOB) and heterotrophs but not nitrite-oxidizing bacteria. Results suggest that the role of AOB in atenolol degradation may be disproportionately more significant than is otherwise suggested by their lower relative abundance in typical biological treatment processes. Atenolol was observed to competitively inhibit AOB growth in our experiments, though model simulations suggest inhibition is most relevant at atenolol concentrations greater than approximately 200 ng·L(-1). CPB model parameters were found to be relatively insensitive to biokinetic parameter selection suggesting the model approach may hold utility for describing pharmaceutical biodegradation during biological wastewater treatment. PMID:24112027

  3. Presence of Ammonia-oxidizing Archaea and Their Influence on Nitrogen Cycling in Ilica Bay, Turkey

    NASA Astrophysics Data System (ADS)

    Gulecal, Y.; Temel, M.

    2011-12-01

    Recenlty, the processes of anaerobic ammonium oxidation (anammox), and ammonia oxidation within the domain Archaea, have been recognized as two new links in the global nitrogen cycle. The distribution and ubiquity of marine Archaea an important role in global carbon and nitrogen cycling (Ingalls et al., 2006; Leininger et al., 2006; Wuchter et al.,2006a). However, our knowledge on archaeal distribution in aquatic ecosystem was largely confined to the extreme environments for a long time until DeLong (1992, 1998) revealed the ubiquity of archaea in common marine environments. Despite the great progress, more efforts need to be given to the study of archaeal diversity in the vast oceans and of the variations in the ecological environment from coastal to oceanic waters (Massana et al.,2000). Our studying area which Ilica Bay in Izmir (Turkey) has a lot of thermal springs. The aim of study was to investigate the presence of ammonia-oxidizing Archaea and their roles of nitrogen cycling in marine enviroments.We have not only used the geochemical analyses but also genetic tools. This study will supply knowledge for marine nitrogen cycling to understanding very well, in addition how Archea genes players in the process of anammox in shallow coastal marine environments.

  4. Interaction of pyridine and ammonia with a sulfate-promoted iron oxide catalyst

    SciTech Connect

    Lee, J.S.; Park, D.S. )

    1989-11-01

    Interactions of sulfate-promoted iron oxide, SO{sup 2{minus}}{sub 4}-Fe{sub 2}O{sub 3}, with pyridine or ammonia were investigated by means of infrared spectroscopy and temperature-programmed desorption/reaction coupled with mass spectrometry. Both molecules reacted with the sulfate group upon adsorption followed by heating to change the structure of the sulfate group and the acid properties of SO{sup 2{minus}}{sub 4}-Fe{sub 2}O{sub 3}. They also promoted the decomposition of the sulfate group and its removal from the surface. These effects were more pronounced for pyridine.

  5. Antibacterial Action of Nitric Oxide-Releasing Chitosan Oligosaccharides against Pseudomonas aeruginosa under Aerobic and Anaerobic Conditions

    PubMed Central

    Reighard, Katelyn P.

    2015-01-01

    Chitosan oligosaccharides were modified with N-diazeniumdiolates to yield biocompatible nitric oxide (NO) donor scaffolds. The minimum bactericidal concentrations and MICs of the NO donors against Pseudomonas aeruginosa were compared under aerobic and anaerobic conditions. Differential antibacterial activities were primarily the result of NO scavenging by oxygen under aerobic environments and not changes in bacterial physiology. Bacterial killing was also tested against nonmucoid and mucoid biofilms and compared to that of tobramycin. Smaller NO payloads were required to eradicate P. aeruginosa biofilms under anaerobic versus aerobic conditions. Under oxygen-free environments, the NO treatment was 10-fold more effective at killing biofilms than tobramycin. These results demonstrate the potential utility of NO-releasing chitosan oligosaccharides under both aerobic and anaerobic environments. PMID:26239983

  6. Ammonia oxidation is not required for growth of Group 1.1c soil Thaumarchaeota

    PubMed Central

    Weber, Eva B.; Lehtovirta-Morley, Laura E.; Prosser, James I.; Gubry-Rangin, Cécile

    2015-01-01

    Thaumarchaeota are among the most abundant organisms on Earth and are ubiquitous. Within this phylum, all cultivated representatives of Group 1.1a and Group 1.1b Thaumarchaeota are ammonia oxidizers, and play a key role in the nitrogen cycle. While Group 1.1c is phylogenetically closely related to the ammonia-oxidizing Thaumarchaeota and is abundant in acidic forest soils, nothing is known about its physiology or ecosystem function. The goal of this study was to perform in situ physiological characterization of Group 1.1c Thaumarchaeota by determining conditions that favour their growth in soil. Several acidic grassland, birch and pine tree forest soils were sampled and those with the highest Group 1.1c 16S rRNA gene abundance were incubated in microcosms to determine optimal growth temperature, ammonia oxidation and growth on several organic compounds. Growth of Group 1.1c Thaumarchaeota, assessed by qPCR of Group 1.1c 16S rRNA genes, occurred in soil, optimally at 30°C, but was not associated with ammonia oxidation and the functional gene amoA could not be detected. Growth was also stimulated by addition of organic nitrogen compounds (glutamate and casamino acids) but not when supplemented with organic carbon alone. This is the first evidence for non-ammonia oxidation associated growth of Thaumarchaeota in soil. PMID:25764563

  7. Osmium(ii) complexes for light-driven aerobic oxidation of amines to imines.

    PubMed

    Li, Yong-Hui; Liu, Xiao-Le; Yu, Zhen-Tao; Li, Zhao-Sheng; Yan, Shi-Cheng; Chen, Guang-Hui; Zou, Zhi-Gang

    2016-08-01

    Herein, we describe the synthesis and characterization of three Os(ii) complexes (i.e., [Os(fptz)2(PPhMe2)2] (1, fptzH = 3-trifluoromethyl-5-pyridyl-1,2,4-triazole), [Os(fptz)2(CO)(L1)] (2, L1 = PPh3; 3, L1 = pyridine)) that have been successfully utilized as good photocatalysts to promote aerobic oxidative coupling of amines to imines with molecular oxygen in air as a green oxidant. Complex 1 is the most effective catalyst for the oxidative coupling of benzylamine with molecular O2 (air) as the oxidant because of the complex's strong absorption of visible light and long-lived triplet state. The application of a low catalyst loading (0.06 mol%) of complex 1 to the oxidative coupling of a wide range of amines affords the corresponding imines efficiently and selectively in most cases. The reaction mechanism was investigated via relevant control and quenching experiments. The results indicated that the reaction occurs via an active (1)O2-involved pathway. The (1)O2-generating ability of complex 1 as a photosensitizer was evaluated using 9,10-dimethylanthracene (DMA) as a chemical trap for (1)O2. PMID:27431765

  8. Responses of ammonia-oxidizing archaeal and betaproteobacterial populations to wastewater salinity in a full-scale municipal wastewater treatment plant.

    PubMed

    Wu, Yi-Ju; Whang, Liang-Ming; Fukushima, Toshikazu; Chang, Shao-Hsiung

    2013-04-01

    The diversity and abundance of ammonia-oxidizing Betaproteobacteria and archaea were investigated in a full-scale municipal wastewater treatment plant where the wastewater conductivity level varied considerably (due to seawater salinity intrusion) during this study between 2004 and 2007. Based on the quantitative polymerase chain reaction of ammonia monooxygenase subunit A (amoA) genes, an increase in the ammonia oxidizing bacteria amoA gene copies occurred with a decrease in the wastewater salinity level. A corresponding decrease in the average ammonia-oxidizing archaea to bacteria ratio, from 1.22 (2004 and 2005), 0.17 (2006), and then to 0.07 (2007), was observed. Phylogenetic analyses on amoA gene sequences indicated that Nitrosomonas marina-like ammonia oxidizing bacteria and Thaumarcheota Ⅰ.1a (marina group) ammonia-oxidizing archaea were dominant when the wastewater salinity level fluctuated at high values with an average of 4.83 practical salinity unit (psu), while Nitrosomonas urea-like ammonia oxidizing bacteria and Thaumarcheota Ⅰ.1b (soil group) ammonia-oxidizing archaea became dominant when the wastewater salinity decreased to a more stable lower level with an average of 1.93 psu. Based on the amoA gene-based terminal restriction fragment length polymorphism analyses, results from this study demonstrated that the observed shift in ammonia oxidizing bacteria and archaea populations is likely caused by a change of the wastewater salinity level. PMID:23232030

  9. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

    PubMed Central

    Alves, Ricardo J Eloy; Wanek, Wolfgang; Zappe, Anna; Richter, Andreas; Svenning, Mette M; Schleper, Christa; Urich, Tim

    2013-01-01

    The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota–AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils. PMID:23466705

  10. The reduction of nitric oxide by ammonia over polycrystalline platinum model catalysts in the presence of oxygen

    SciTech Connect

    Katona, T. Univ. of California, Berkeley Jozsef A. Univ., Szeged ); Guczi, L. Inst. of Isotopes, Budapest ); Somorjai, G.A. Univ. of California, Berkeley )

    1992-06-01

    The reaction system of nitric oxide, ammonia, and oxygen was studied using batch-mode measurements in partial pressure ranges of 65-1000 Pa (0.5-7.6 Torr) on polycrystalline Pt foils over the temperature range 423-598 K. Under these conditions the oxidation of nitric oxide was not detectable. The ammonia oxidation reaction, using dioxygen, occurred in the temperature range 423-493 K, producing nitrogen and water as the only products. The activation energy of the nitrogen formation was found to be 86 kJ/mol. Above this temperature range, flow-mode measurements showed the formation of both nitrous oxide and nitric oxide. The reaction rate between ammonia and oxygen was greatly decreased (about a factor of 10) by nitric oxide, while the reaction rate between nitric oxide and ammonia was accelerated (about 10-fold) due to the presence of oxygen. Nitric oxide reduction by ammonia in the presence of oxygen occurred in the temperature range 423-598 K. The products of the reaction were nitrogen, oxygen nitrous oxide, and water. The Arrhenius plot of the reaction showed a break near 523 K. Below this temperature the activation energy of the reaction was 13 kJ/mol, and in the higher-temperature range it was 62 kJ/mol. At 473 K, the N[sub 2]/N[sub 2]O ratio was about 0.6 and O[sub 2] formation was also monitored. At 573 K, the N[sub 2]N[sub 2]O ratio was approximately 2 and oxygen was consumed in the course of the reaction as well.

  11. Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils ▿ †

    PubMed Central

    Yao, Huaiying; Gao, Yangmei; Nicol, Graeme W.; Campbell, Colin D.; Prosser, James I.; Zhang, Limei; Han, Wenyan; Singh, Brajesh K.

    2011-01-01

    Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches. PMID:21571885

  12. The influence of land use on the abundance and diversity of ammonia oxidizers.

    PubMed

    Zhao, Dayong; Luo, Juan; Wang, Jianqun; Huang, Rui; Guo, Kun; Li, Yi; Wu, Qinglong L

    2015-02-01

    Nitrification plays a significant role in soil nitrogen cycling, a process in which the first step can be catalyzed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). In this study, six soil samples with distinct land-use regimes (forestland soil, paddy soil, wheat-planted soil, fruit-planted soil, grassland soil, and rape-planted soil) were collected from Chuzhou city in the Anhui province to elucidate the effects of land use on the abundance and diversity of AOA and AOB. The abundance of the archaeal amoA gene ranged from 2.12 × 10(4) copies per gram of dry soil to 2.57 × 10(5) copies per gram of dry soil, while the abundance of the bacterial amoA gene ranged from 5.58 × 10(4) copies per gram of dry soil to 1.59 × 10(8) copies per gram of dry soil. The grassland and the rape-planted soil samples maintained the highest abundance of the bacterial and archaeal amoA genes, respectively. The abundance of the archaeal amoA gene was positively correlated with the pH (P < 0.05). The ammonia concentrations exhibited a significantly positive relation with the abundance of the bacterial amoA gene (P < 0.01) and the number of OTUs of AOB (P < 0.05). The community composition of AOB was more sensitive to the land-use regimes than that of AOA. The data obtained in this study may be useful to better understand the nitrification process in soils with different land-use regimes. PMID:25331793

  13. Ecosystem-specific selection of microbial ammonia oxidizers in an acid soil

    NASA Astrophysics Data System (ADS)

    Saiful Alam, M.; Ren, G.; Lu, L.; Zheng, Y.; Peng, X.; Jia, Z.

    2013-01-01

    The function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) depends on the availability of ammonia substrate and the supply of oxygen. The interactions and evolutions of AOA and AOB communities along ecological gradients of substrate availability in complex environment have been much debated, but rarely tested. In this study, two ecosystems of maize and rice crops under different fertilization regimes were selected to investigate the community diversification of soil AOA and AOB in response to long-term field fertilization and flooding management in an acid soil. Real-time quantitative PCR of amoA genes demonstrated that the abundance of AOA was significantly stimulated after conversion of upland to paddy soils, while slight decline of AOB populations was observed. DGGE fingerprints of amoA genes further revealed remarkable changes in community compositions of AOA in paddy soil when compared to upland soil. Sequencing analysis revealed that upland soil was dominated by AOA within the soil group 1.1b lineage, while the marine group 1.1a lineage predominated AOA communities in paddy soils. Irrespective of upland and paddy soils, long-term field fertilizations led to higher abundance of amoA genes of AOA and AOB than control treatment that received no fertilization, whereas archaeal amoA gene abundances outnumbered their bacterial counterpart in all samples. Phylogenetic analyses of amoA genes showed that Nitrosospira cluster 3-like AOB dominated bacterial ammonia oxidizers in both paddy and upland soils, regardless of fertilization treatments. The results of this study suggest that the marine group 1.1a AOA could be better adapted to low-oxygen environment than AOA ecotypes of the soil group 1.1b lineage, and implicate that long-term flooding as the dominant selective force driving the community diversification of AOA populations in the acid soil tested.

  14. pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils.

    PubMed

    Stempfhuber, Barbara; Engel, Marion; Fischer, Doreen; Neskovic-Prit, Ganna; Wubet, Tesfaye; Schöning, Ingo; Gubry-Rangin, Cécile; Kublik, Susanne; Schloter-Hai, Brigitte; Rattei, Thomas; Welzl, Gerhard; Nicol, Graeme W; Schrumpf, Marion; Buscot, Francois; Prosser, James I; Schloter, Michael

    2015-05-01

    In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH. PMID:25501889

  15. Aquarium Nitrification Revisited: Thaumarchaeota Are the Dominant Ammonia Oxidizers in Freshwater Aquarium Biofilters

    PubMed Central

    Sauder, Laura A.; Engel, Katja; Stearns, Jennifer C.; Masella, Andre P.; Pawliszyn, Richard; Neufeld, Josh D.

    2011-01-01

    Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS) indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology. PMID:21858055

  16. Aquarium nitrification revisited: Thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters.

    PubMed

    Sauder, Laura A; Engel, Katja; Stearns, Jennifer C; Masella, Andre P; Pawliszyn, Richard; Neufeld, Josh D

    2011-01-01

    Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS) indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology. PMID:21858055

  17. Effects of allylthiourea, salinity, and pH on ammonia/ammonium-oxidizing prokaryotes in mangrove sediment incubated in laboratory microcosms.

    PubMed

    Wang, Yong-Feng; Gu, Ji-Dong

    2014-04-01

    Anaerobic ammonium-oxidizing (anammox) bacteria, aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB) are three groups of ammonia/ammonium-oxidizing prokaryotes (AOPs) involved in the biochemical nitrogen cycling. In this study, the effects of allylthiourea (ATU), pH, and salinity on these three groups from mangrove sediment were investigated through microcosm incubation in laboratory. ATU treatments (50, 100, and 500 mg L(-1)) obviously affected the community structure of anammox bacteria and AOB, but only slightly for AOA. ATU began to inhibit anammox bacteria growth slightly from day 10, but had an obvious inhibition on AOA growth from the starting of the study. At 100 mg L(-1) of ATU or higher, AOB growth was inhibited, but only lasted for 5 days. The pH treatments showed that acidic condition (pH 5) had a slight effect on the community structure of anammox bacteria and AOA, but an obvious effect on AOB. Acidic condition promoted the growth of all groups of AOPs in different extent, but alkaline condition (pH 9) had a weak effect on AOB community structure and a strong effect on both anammox bacteria and AOA. Alkaline condition obviously inhibited anammox bacteria growth, slightly promoted AOA, and slightly promoted AOB in the first 20 days, but inhibited afterward. Salinity treatment showed that higher salinity (20 and 40 ‰) resulted in higher anammox bacteria diversity, and both AOA and AOB might have species specificity to salinity. High salinity promoted the growth of both anammox bacteria and AOB, inhibited AOA between 5 and 10 days, but promoted afterward. The results help to understand the role of these microbial groups in biogeochemical nitrogen cycling and their responses to the changing environments. PMID:24270897

  18. Nitrosomonas stercoris sp. nov., a Chemoautotrophic Ammonia-Oxidizing Bacterium Tolerant of High Ammonium Isolated from Composted Cattle Manure

    PubMed Central

    Nakagawa, Tatsunori; Takahashi, Reiji

    2015-01-01

    Among ammonia-oxidizing bacteria, Nitrosomonas eutropha-like microbes are distributed in strongly eutrophic environments such as wastewater treatment plants and animal manure. In the present study, we isolated an ammonia-oxidizing bacterium tolerant of high ammonium levels, designated strain KYUHI-ST, from composted cattle manure. Unlike the other known Nitrosomonas species, this isolate grew at 1,000 mM ammonium. Phylogenetic analyses based on 16S rRNA and amoA genes indicated that the isolate belonged to the genus Nitrosomonas and formed a unique cluster with the uncultured ammonia oxidizers found in wastewater systems and animal manure composts, suggesting that these ammonia oxidizers contributed to removing higher concentrations of ammonia in strongly eutrophic environments. Based on the physiological and phylogenetic data presented here, we propose and call for the validation of the provisional taxonomic assignment Nitrosomonas stercoris, with strain KYUHI-S as the type strain (type strain KYUHI-ST = NBRC 110753T = ATCC BAA-2718T). PMID:26156554

  19. [Microbial diversity and ammonia-oxidizing microorganism of a soil sample near an acid mine drainage lake].

    PubMed

    Liu, Ying; Wang, Li-Hua; Hao, Chun-Bo; Li, Lu; Li, Si-Yuan; Feng, Chuan-Ping

    2014-06-01

    The main physicochemical parameters of the soil sample which was collected near an acid mine drainage reservoir in Anhui province was analyzed. The microbial diversity and community structure was studied through the construction of bacteria and archaea 16S rRNA gene clone libraries and ammonia monooxygenase gene clone library of archaea. The functional groups which were responsible for the process of ammonia oxidation were also discussed. The results indicated that the soil sample had extreme low pH value (pH < 3) and high ions concentration, which was influenced by the acid mine drainage (AMD). All the 16S rRNA gene sequences of bacteria clone library fell into 11 phyla, and Acidobacteria played the most significant role in the ecosystem followed by Verrucomicrobia. A great number of acidophilic bacteria existed in the soil sample, such as Candidatus Koribacter versatilis and Holophaga sp.. The archaea clone library consisted of 2 phyla (Thaumarchaeota and Euryarchaeota). The abundance of Thaumarchaeota was remarkably higher than Euryarchaeota. The ammonia oxidation in the soil environment was probably driven by ammonia-oxidizing archaea, and new species of ammonia-oxidizing archaea existed in the soil sample. PMID:25158511

  20. Comparison of the community structures of ammonia-oxidizing bacteria and archaea in rhizoplanes of floating aquatic macrophytes.

    PubMed

    Wei, Bo; Yu, Xin; Zhang, Shuting; Gu, Li

    2011-09-20

    Some common floating aquatic macrophytes could remove nutrients, such as nitrogen, from eutrophic water. However, the relationship between these macrophytes and the ammonia-oxidizing microorganisms on their rhizoplanes is still unknown. In this study, we examined communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) on the rhizoplanes of common floating aquatic macrophytes (Eichhornia crassipes, Pistia stratiotes and Ipomoea aquatic) in a eutrophic reservoir.The results show that AOB were the predominant ammonia-oxidizer on the three rhizoplanes. The principal AOB were Nitrosomonas europaea and Nitrosomonas ureae clades. The principal group of AOA was most similar to the clone from activated sludge. The ratio of AOB amoA gene copies to AOA varied from 1.36 (on E. crassipes) to 41.90 (on P. stratiotes). Diversity of AOA was much lower than that of AOB in most samples, with the exception of P. stratiotes. PMID:21239153

  1. Aerobic addition of secondary phosphine oxides to vinyl sulfides: a shortcut to 1-hydroxy-2-(organosulfanyl)ethyl(diorganyl)phosphine oxides

    PubMed Central

    Malysheva, Svetlana F; Artem’ev, Alexander V; Gusarova, Nina K; Belogorlova, Nataliya A; Albanov, Alexander I; Liu, C W

    2015-01-01

    Summary Secondary phosphine oxides react with vinyl sulfides (both alkyl- and aryl-substituted sulfides) under aerobic and solvent-free conditions (80 °C, air, 7–30 h) to afford 1-hydroxy-2-(organosulfanyl)ethyl(diorganyl)phosphine oxides in 70–93% yields. PMID:26664618

  2. Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem

    PubMed Central

    Hu, Ziye; Meng, Han; Shi, Jin-Huan; Bu, Nai-Shun; Fang, Chang-Ming; Quan, Zhe-Xue

    2014-01-01

    Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA) are much higher than that of ammonia oxidizing bacteria (AOB). The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition. PMID:25101072

  3. Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments.

    PubMed

    Bouskill, Nicholas J; Eveillard, Damien; Chien, Diana; Jayakumar, Amal; Ward, Bess B

    2012-03-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in bridging the input of fixed nitrogen, through N-fixation and remineralization, to its loss by denitrification and anammox. Yet the major environmental factors determining AOB and AOA population dynamics are little understood, despite both groups having a wide environmental distribution. This study examined the relative abundance of both groups of ammonia-oxidizing organisms (AOO) and the diversity of AOA across large-scale gradients in temperature, salinity and substrate concentration and dissolved oxygen. The relative abundance of AOB and AOA varied across environments, with AOB dominating in the freshwater region of the Chesapeake Bay and AOA more abundant in the water column of the coastal and open ocean. The highest abundance of the AOA amoA gene was recorded in the oxygen minimum zones (OMZs) of the Eastern Tropical South Pacific (ETSP) and the Arabian Sea (AS). The ratio of AOA : AOB varied from 0.7 in the Chesapeake Bay to 1600 in the Sargasso Sea. Relative abundance of both groups strongly correlated with ammonium concentrations. AOA diversity, as determined by phylogenetic analysis of clone library sequences and archetype analysis from a functional gene DNA microarray, detected broad phylogenetic differences across the study sites. However, phylogenetic diversity within physicochemically congruent stations was more similar than would be expected by chance. This suggests that the prevailing geochemistry, rather than localized dispersal, is the major driving factor determining OTU distribution. PMID:22050634

  4. Ammonia gas sensors based on chemically reduced graphene oxide sheets self-assembled on Au electrodes

    PubMed Central

    2014-01-01

    We present a useful ammonia gas sensor based on chemically reduced graphene oxide (rGO) sheets by self-assembly technique to create conductive networks between parallel Au electrodes. Negative graphene oxide (GO) sheets with large sizes (>10 μm) can be easily electrostatically attracted onto positive Au electrodes modified with cysteamine hydrochloride in aqueous solution. The assembled GO sheets on Au electrodes can be directly reduced into rGO sheets by hydrazine or pyrrole vapor and consequently provide the sensing devices based on self-assembled rGO sheets. Preliminary results, which have been presented on the detection of ammonia (NH3) gas using this facile and scalable fabrication method for practical devices, suggest that pyrrole-vapor-reduced rGO exhibits much better (more than 2.7 times with the concentration of NH3 at 50 ppm) response to NH3 than that of rGO reduced from hydrazine vapor. Furthermore, this novel gas sensor based on rGO reduced from pyrrole shows excellent responsive repeatability to NH3. Overall, the facile electrostatic self-assembly technique in aqueous solution facilitates device fabrication, the resultant self-assembled rGO-based sensing devices, with miniature, low-cost portable characteristics and outstanding sensing performances, which can ensure potential application in gas sensing fields. PMID:24917701

  5. Community structure of ammonia-oxidizing microorganisms in the Grand Canal, Zhenjiang, of Jiangsu Province, China.

    PubMed

    Liu, Biao; Wu, Chundu; Zhou, Xiaohong

    2014-01-01

    In this study, we simultaneously investigated the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the Grand Canal (the Zhenjiang section). Both clone library and qPCR (quantitative polymerase chain reaction) indicated that the abundance and diversity of AOB were higher than AOA in the Grand Canal for all four seasons. Among the 109 archaeal amoA sequences retrieved, 62.39 and 37.61% fell within the Nitrosopumilus and Nitrososphaera clusters, respectively. The 128 bacterial amoA gene sequences obtained in this study were grouped with known AOB sequences in the Nitrosomonas and Nitrosospira genera, which occupied 81.25 and 18.75% of the AOB group, respectively. The AOA abundance was significantly and positively correlated with the NH4-N. The AOB abundance did not show significant correlations with the measured parameters. Obvious differences were observed for the AOA community compositions obtained from different seasons. The community structure of AOB changed slightly. It indicated that AOB seemed to play a more important role for the nitrification process than AOA in this environment, and was more adapted to this environment. PMID:25259486

  6. [Characteristics of soil ammonia-oxidation microbial communities in different subtropical forests, China].

    PubMed

    Li, Yong-Chun; Liu, Bu-Rong; Guo, Shuai; Wu, Qi-Feng; Qin, Hua; Wu, Jia-Sen; Xu, Qiu-Fang

    2014-01-01

    To investigate the effects of different forest stands in subtropical China on the communities of soil ammonia-oxidizing microorganisms, we characterized the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and the community structure of AOA in soils under stands of broad-leaved (BF) , Chinese fir (CF) , Pinus massoniana (PF) and moso bamboo (MB) forests using real-time quantitative PCR and denaturing gradient gel electrophoresis (DGGE). The results showed that the AOA gene copy numbers (1.62 x 10(6)-1.88 x 10(7) per gram of dry soil) were significantly higher than those of AOB genes (2.41 x 10(5)-4.36 x 10(5) per gram of dry soil). Significantly higher soil AOA abundance was detected in the MB than that in the CF (P < 0.05), and the latter was significantly higher than that in the BF and PF soils (P < 0.05). There were no significant differences in the soil AOB abundance among the four forest stands. As indicated by DGGE pattern, soil AOA species varied among the four forest stands. There was a difference in the soil AOA communities between the CF and MB stands. The AOA demonstrated a competitive advantage over the AOB in the soils under these major subtropical forests. Soil pH, concentrations of soil available potassium and organic carbon as well as the forest type were the main factors that influence the variation of AOA community structure and diversity. PMID:24765851

  7. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

    NASA Astrophysics Data System (ADS)

    Alves, Ricardo J. E.; Wanek, Wolfgang; Zappe, Anna; Richter, Andreas; Svenning, Mette M.; Schleper, Christa; Urich, Tim

    2014-05-01

    The functioning of Arctic soil ecosystems is crucially important for global climate, although basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and therefore it is particularly important to gain a better understanding of the microbial populations catalyzing transformations that influence N bioavailability. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils from Svalbard were analyzed through a polyphasic approach, including determination of gross nitrification rates through a 15N pool dilution method, qualitative and quantitative analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) populations based on the functional marker gene amoA (encoding the ammonia monooxygenase subunit A), and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils, and outnumbered AOB by 1 to 3 orders of magnitude in most others. AOA showed a great overall phylogenetic diversity that was differentially distributed across soil ecosystems, and exhibited an uneven population composition that reflected the dominance of a single AOA phylotype in each population. Moreover, AOA populations showed a multifactorial association with the soil properties, which reflected an overall distribution associated with tundra type and with several physico-chemical parameters combined, namely pH and soil moisture and N contents (i.e., NO3- and dissolved organic N). Remarkably, the different gross in situ and potential nitrification rates between soils were associated with distinct AOA phylogenetic clades, suggesting differences in their nitrifying potential, both under the native NH3 conditions and as a response to higher NH3 availability. This was further supported by the selective enrichment of two AOA clades that exhibited

  8. Metabolic reprogramming during neuronal differentiation from aerobic glycolysis to neuronal oxidative phosphorylation

    PubMed Central

    Zheng, Xinde; Boyer, Leah; Jin, Mingji; Mertens, Jerome; Kim, Yongsung; Ma, Li; Ma, Li; Hamm, Michael; Gage, Fred H; Hunter, Tony

    2016-01-01

    How metabolism is reprogrammed during neuronal differentiation is unknown. We found that the loss of hexokinase (HK2) and lactate dehydrogenase (LDHA) expression, together with a switch in pyruvate kinase gene splicing from PKM2 to PKM1, marks the transition from aerobic glycolysis in neural progenitor cells (NPC) to neuronal oxidative phosphorylation. The protein levels of c-MYC and N-MYC, transcriptional activators of the HK2 and LDHA genes, decrease dramatically. Constitutive expression of HK2 and LDHA during differentiation leads to neuronal cell death, indicating that the shut-off aerobic glycolysis is essential for neuronal survival. The metabolic regulators PGC-1α and ERRγ increase significantly upon neuronal differentiation to sustain the transcription of metabolic and mitochondrial genes, whose levels are unchanged compared to NPCs, revealing distinct transcriptional regulation of metabolic genes in the proliferation and post-mitotic differentiation states. Mitochondrial mass increases proportionally with neuronal mass growth, indicating an unknown mechanism linking mitochondrial biogenesis to cell size. DOI: http://dx.doi.org/10.7554/eLife.13374.001 PMID:27282387

  9. Impact of aerobic and anaerobic exercise training on oxidative stress and antioxidant defense in athletes

    PubMed Central

    Park, Song-Young; Kwak, Yi-Sub

    2016-01-01

    Exercise mediates an excessive free radical production leading to oxidative stress (OS). The body has natural antioxidant systems that help decrease OS, and these systems may be enhanced with exercise training. However, only a few studies have investigated the differences in resting OS and antioxidant capacity (AOC) between aerobically trained athletes (ET), anaerobically trained athletes (RT), and untrained individuals (UT). Therefore, this study sought to investigate the resting and postexercise OS and AOC in ET, RT, and UT. Sixty healthy young males (26.6±0.8 yr) participated in this study. Subjects were divided into three groups, ET, RT, and UT by distinct training background. Resting plasma malondialdehyde (MDA) and protein carbonyls (PC) were not significantly different in ET, RT, and UT. However, MDA and PC were significantly increased following a graded exercise test (GXT) in UT but not in ET and RT. Resting total antioxidant capacity (TAC) levels and TAC were not different in ET, RT, and UT. Interestingly, TAC levels significantly decreased after the GXT in all groups. Additionally, UT showed lower post-exercise TAC levels compared to ET and RT. These results showed that ET, RT, and UT have similar OS and AOC at rest. However, both ET and RT have greater AOC against exercise mediated OS compared to UT. These findings may explain, at least in part, why both aerobic and anaerobic types of exercise training improve redox balance. However, it appears there is no specific exercise type effect in terms of redox balance. PMID:27162773

  10. Impact of aerobic and anaerobic exercise training on oxidative stress and antioxidant defense in athletes.

    PubMed

    Park, Song-Young; Kwak, Yi-Sub

    2016-04-01

    Exercise mediates an excessive free radical production leading to oxidative stress (OS). The body has natural antioxidant systems that help decrease OS, and these systems may be enhanced with exercise training. However, only a few studies have investigated the differences in resting OS and antioxidant capacity (AOC) between aerobically trained athletes (ET), anaerobically trained athletes (RT), and untrained individuals (UT). Therefore, this study sought to investigate the resting and postexercise OS and AOC in ET, RT, and UT. Sixty healthy young males (26.6±0.8 yr) participated in this study. Subjects were divided into three groups, ET, RT, and UT by distinct training background. Resting plasma malondialdehyde (MDA) and protein carbonyls (PC) were not significantly different in ET, RT, and UT. However, MDA and PC were significantly increased following a graded exercise test (GXT) in UT but not in ET and RT. Resting total antioxidant capacity (TAC) levels and TAC were not different in ET, RT, and UT. Interestingly, TAC levels significantly decreased after the GXT in all groups. Additionally, UT showed lower post-exercise TAC levels compared to ET and RT. These results showed that ET, RT, and UT have similar OS and AOC at rest. However, both ET and RT have greater AOC against exercise mediated OS compared to UT. These findings may explain, at least in part, why both aerobic and anaerobic types of exercise training improve redox balance. However, it appears there is no specific exercise type effect in terms of redox balance. PMID:27162773

  11. Comparative in silico analysis of PCR primers suited for diagnostics and cloning of ammonia monooxygenase genes from ammonia-oxidizing bacteria.

    PubMed

    Junier, Pilar; Kim, Ok-Sun; Molina, Verónica; Limburg, Petra; Junier, Thomas; Imhoff, Johannes F; Witzel, Karl-Paul

    2008-04-01

    Over recent years, several PCR primers have been described to amplify genes encoding the structural subunits of ammonia monooxygenase (AMO) from ammonia-oxidizing bacteria (AOB). Most of them target amoA, while amoB and amoC have been neglected so far. This study compared the nucleotide sequence of 33 primers that have been used to amplify different regions of the amoCAB operon with alignments of all available sequences in public databases. The advantages and disadvantages of these primers are discussed based on the original description and the spectrum of matching sequences obtained. Additionally, new primers to amplify the almost complete amoCAB operon of AOB belonging to Betaproteobacteria (betaproteobacterial AOB), a primer pair for DGGE analysis of amoA and specific primers for gammaproteobacterial AOB, are also described. The specificity of these new primers was also evaluated using the databases of the sequences created during this study. PMID:18248438

  12. Supercritical carbon dioxide, a new medium for aerobic alcohol oxidations catalysed by copper-TEMPO.

    PubMed

    Herbert, Matthew; Montilla, Francisco; Galindo, Agustín

    2010-01-21

    The copper catalysed aerobic oxidation of selected alcohol substrates in supercritical carbon dioxide (scCO(2)), employing a range of simple copper(II) catalyst compounds, is here described. The copper acetate complex of polydimethylsiloxane (PDMS) functionalised pyridine (1), compound 2, has previously been synthesised and characterised by us and its solubility in scCO(2) demonstrated. Due to this solubility we anticipated that the selective aerobic oxidation of alcohols to aldehydes could be homogeneously catalysed by this compound in scCO(2) in combination with the co-catalyst 2,2,6,6-tetramethylpiperidin-1-yloxy free radical (TEMPO). Our initial results showed that complete oxidation of 4-nitrobenzyl alcohol was achieved within 4 h of reaction. However, the activities of analogous copper derivatives containing simpler pyridine substituents, [Cu(AcO)(2)(py)](2) and [Cu(AcO)(2)(4VP)](2) (4VP = 4-vinylpyridine), were shown to be similar, in spite of their negligible solubility in scCO(2). When we repeated the reactions in highly non-polar hexane rather than scCO(2) similar observations were made. In both cases, as 2 is soluble and the pyridine analogues are not, a much higher reaction rate was anticipated for 2 as it is the only compound capable of homogeneous catalysis. However, in some cases slightly better activities were observed for [Cu(AcO)(2)(py)](2) rather than for the PDMS functionalised analogue, 2. Thus, despite poor catalyst solubility typically being very inhibitory in this type of catalytic process, in this system solubilisation of the catalyst is not necessary. In continuation the activity of silica supported copper complexes was therefore investigated. Employing such catalysts the 4-nitrobenzyl and benzyl alcohol substrates were completely oxidised to the corresponding aldehydes in scCO(2), this time employing lower catalyst loadings. Other types of alcohol substrate showed more limited conversions however. To conclude, alcohol oxidation in the non

  13. A Stability Study of Ni/Yttria-Stabilized Zirconia Anode for Direct Ammonia Solid Oxide Fuel Cells.

    PubMed

    Yang, Jun; Molouk, Ahmed Fathi Salem; Okanishi, Takeou; Muroyama, Hiroki; Matsui, Toshiaki; Eguchi, Koichi

    2015-12-30

    In recent years, solid oxide fuel cells fueled with ammonia have been attracting intensive attention. In this work, ammonia fuel was supplied to the Ni/yttria-stabilized zirconia (YSZ) cermet anode at 600 and 700 °C, and the change of electrochemical performance and microstructure under the open-circuit state was studied in detail. The influence of ammonia exposure on the microstructure of Ni was also investigated by using Ni/YSZ powder and Ni film deposited on a YSZ disk. The obtained results demonstrated that Ni in the cermet anode was partially nitrided under an ammonia atmosphere, which considerably roughened the Ni surface. Moreover, the destruction of the anode support layer was confirmed for the anode-supported cell upon the temperature cycling test between 600 and 700 °C because of the nitriding phenomenon of Ni, resulting in severe performance degradation. PMID:26642379

  14. Spatial Interaction of Archaeal Ammonia-Oxidizers and Nitrite-Oxidizing Bacteria in an Unfertilized Grassland Soil

    PubMed Central

    Stempfhuber, Barbara; Richter-Heitmann, Tim; Regan, Kathleen M.; Kölbl, Angelika; Wüst, Pia K.; Marhan, Sven; Sikorski, Johannes; Overmann, Jörg; Friedrich, Michael W.; Kandeler, Ellen; Schloter, Michael

    2016-01-01

    Interrelated successive transformation steps of nitrification are performed by distinct microbial groups – the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m2. Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira) selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onward, indicating its important role in nitrite oxidation. PMID:26834718

  15. A template-free solvent-mediated synthesis of high surface area boron nitride nanosheets for aerobic oxidative desulfurization.

    PubMed

    Wu, Peiwen; Zhu, Wenshuai; Chao, Yanhong; Zhang, Jinshui; Zhang, Pengfei; Zhu, Huiyuan; Li, Changfeng; Chen, Zhigang; Li, Huaming; Dai, Sheng

    2016-01-01

    Hexagonal boron nitride nanosheets (h-BNNs) with rather high specific surface area (SSA) are important two-dimensional layer-structured materials. Here, a solvent-mediated synthesis of h-BNNs revealed a template-free lattice plane control strategy that induced high SSA nanoporous structured h-BNNs with outstanding aerobic oxidative desulfurization performance. PMID:26502800

  16. Cu(II)-catalyzed esterification reaction via aerobic oxidative cleavage of C(CO)-C(alkyl) bonds.

    PubMed

    Ma, Ran; He, Liang-Nian; Liu, An-Hua; Song, Qing-Wen

    2016-02-01

    A novel Cu(II)-catalyzed aerobic oxidative esterification of simple ketones for the synthesis of esters has been developed with wide functional group tolerance. This process is assumed to go through a tandem sequence consisting of α-oxygenation/esterification/nucleophilic addition/C-C bond cleavage and carbon dioxide is released as the only byproduct. PMID:26698150

  17. Soluble porous coordination polymers by mechanochemistry: from metal-containing films/membranes to active catalysts for aerobic oxidation.

    PubMed

    Zhang, Pengfei; Li, Haiying; Veith, Gabriel M; Dai, Sheng

    2015-01-14

    Soluble porous coordination polymers from mechanochemical synthesis are presented through a coordination polymerization between highly contorted, rigid tetraphenol and a broad variety of transition metal ions. These polymers can be easily cast as metal-containing films or freestanding membranes. Importantly, as-made coordination polymers are highly active and stable in the aerobic oxidation of allylic C-H bonds. PMID:25389070

  18. The effect of aerobic exercise on hepatotoxicity induced by intratracheal instillation of iron oxide nanoparticles in Wistar rats.

    PubMed

    Vasili, Azadeh; Sharifi, Gholamreza; Faramarzi, Mohammad; Noori, Ali; Yazdanshenas, Shora

    2016-01-01

    Iron oxide nanoparticles (IONPs) can cause significant health problems due to their unique physicochemical properties and environmental characteristics. They are found as ultrafine particles in ambient air. After inhalation, these particles move from the lung to phagocytosis tissues, especially the liver. The aim of present study was to investigate the effect of concurrent aerobic exercise and IONPs on liver enzymes and histological hepatic appearance. 48 rats were divided into six groups: experimental 1 (aerobic exercise), experimental 2 (nanoparticle, anesthesia), experimental 3 (aerobic exercise, nanoparticles, anesthesia), placebo 4 (distilled water, anesthesia), placebo 5 (aerobic exercise, anesthesia), and control group. In groups 2 and 3, 40 mg/kg/b.w. of IONPs was injected via intratracheal installation every other day for 14 days. Groups 1, 3, and 5 [corrected] run on treadmill for 30 minutes with the intensity of 35-40% VO2max (maximal oxygen consumption) every day. ALT was increased in group 1 but decreased in groups 2 and 3. AST was not significant in any of the groups, while ALP was reduced significantly in groups 2 and 3 (p < 0.05). Histological examination of the liver showed that, in groups 2 and 3, hepatic cells were damaged and also the congestion, inflammation, mononuclear cell infiltration, and ballooning degeneration were occurred. Tissue injuries in group 3 were less than those of group 2. These findings indicated that hepatotoxicity was caused by iron oxide nanoparticles; however, low-intensity aerobic exercise could decrease the damage somewhat. PMID:26492071

  19. Aerobic and Anaerobic Thiosulfate Oxidation by a Cold-Adapted, Subglacial Chemoautotroph.

    PubMed

    Harrold, Zoë R; Skidmore, Mark L; Hamilton, Trinity L; Desch, Libby; Amada, Kirina; van Gelder, Will; Glover, Kevin; Roden, Eric E; Boyd, Eric S

    2016-03-01

    Geochemical data indicate that protons released during pyrite (FeS2) oxidation are important drivers of mineral weathering in oxic and anoxic zones of many aquatic environments, including those beneath glaciers. Oxidation of FeS2 under oxic, circumneutral conditions proceeds through the metastable intermediate thiosulfate (S2O3 (2-)), which represents an electron donor capable of supporting microbial metabolism. Subglacial meltwaters sampled from Robertson Glacier (RG), Canada, over a seasonal melt cycle revealed concentrations of S2O3 (2-) that were typically below the limit of detection, despite the presence of available pyrite and concentrations of the FeS2 oxidation product sulfate (SO4 (2-)) several orders of magnitude higher than those of S2O3 (2-). Here we report on the physiological and genomic characterization of the chemolithoautotrophic facultative anaerobe Thiobacillus sp. strain RG5 isolated from the subglacial environment at RG. The RG5 genome encodes genes involved with pathways for the complete oxidation of S2O3 (2-), CO2 fixation, and aerobic and anaerobic respiration with nitrite or nitrate. Growth experiments indicated that the energy required to synthesize a cell under oxygen- or nitrate-reducing conditions with S2O3 (2-) as the electron donor was lower at 5.1°C than 14.4°C, indicating that this organism is cold adapted. RG sediment-associated transcripts of soxB, which encodes a component of the S2O3 (2-)-oxidizing complex, were closely affiliated with soxB from RG5. Collectively, these results suggest an active sulfur cycle in the subglacial environment at RG mediated in part by populations closely affiliated with RG5. The consumption of S2O3 (2-) by RG5-like populations may accelerate abiotic FeS2 oxidation, thereby enhancing mineral weathering in the subglacial environment. PMID:26712544

  20. Aerobic and Anaerobic Thiosulfate Oxidation by a Cold-Adapted, Subglacial Chemoautotroph

    PubMed Central

    Harrold, Zoë R.; Skidmore, Mark L.; Hamilton, Trinity L.; Desch, Libby; Amada, Kirina; van Gelder, Will; Glover, Kevin; Roden, Eric E.

    2015-01-01

    Geochemical data indicate that protons released during pyrite (FeS2) oxidation are important drivers of mineral weathering in oxic and anoxic zones of many aquatic environments, including those beneath glaciers. Oxidation of FeS2 under oxic, circumneutral conditions proceeds through the metastable intermediate thiosulfate (S2O32−), which represents an electron donor capable of supporting microbial metabolism. Subglacial meltwaters sampled from Robertson Glacier (RG), Canada, over a seasonal melt cycle revealed concentrations of S2O32− that were typically below the limit of detection, despite the presence of available pyrite and concentrations of the FeS2 oxidation product sulfate (SO42−) several orders of magnitude higher than those of S2O32−. Here we report on the physiological and genomic characterization of the chemolithoautotrophic facultative anaerobe Thiobacillus sp. strain RG5 isolated from the subglacial environment at RG. The RG5 genome encodes genes involved with pathways for the complete oxidation of S2O32−, CO2 fixation, and aerobic and anaerobic respiration with nitrite or nitrate. Growth experiments indicated that the energy required to synthesize a cell under oxygen- or nitrate-reducing conditions with S2O32− as the electron donor was lower at 5.1°C than 14.4°C, indicating that this organism is cold adapted. RG sediment-associated transcripts of soxB, which encodes a component of the S2O32−-oxidizing complex, were closely affiliated with soxB from RG5. Collectively, these results suggest an active sulfur cycle in the subglacial environment at RG mediated in part by populations closely affiliated with RG5. The consumption of S2O32− by RG5-like populations may accelerate abiotic FeS2 oxidation, thereby enhancing mineral weathering in the subglacial environment. PMID:26712544

  1. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments

    PubMed Central

    Reis, Mariana P.; Ávila, Marcelo P.; Keijzer, Rosalinde M.; Barbosa, Francisco A. R.; Chartone-Souza, Edmar; Nascimento, Andréa M. A.; Laanbroek, Hendrikus J.

    2015-01-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms. PMID:26379659

  2. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments.

    PubMed

    Reis, Mariana P; Ávila, Marcelo P; Keijzer, Rosalinde M; Barbosa, Francisco A R; Chartone-Souza, Edmar; Nascimento, Andréa M A; Laanbroek, Hendrikus J

    2015-01-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms. PMID:26379659

  3. [Diversity of ammonia-oxidizing archaea in Tibetan Zoige plateau wetland ].

    PubMed

    Zheng, Youkun; Wang, Xianbin; Gu, Yunfu; Zhang, Xiaoping

    2014-09-01

    [ OBJECTIVE ] Investigation of ammonia-oxidizing archaea (AOA) in nature environments is important to understand the global nitrogen cycling. However, little is known about the AOA community in plateau wetland. Therefore, we studied the composition and diversity of AOA in Zoige plateau wetland swamp soil. [METHODS] Total DNA was extracted from the swamp soil of three typical wetlands including A'xi pastoral area, Maixi pastoral area and Fenqu pastoral area locate in Zoige plateau wetland, and amoA gene was amplified with universally AOA amoA gene primers and then cloned. Then 80 positive clones for each clone library were chosen for further restriction fragment length polymorphism (RFLP) analysis, and the typical RFLP types were selected for sequencing and clustered into operational taxonomic units (OTUs) at 98% cutoff using the Mothur software. The MEGA 5. 0 software was used for the amoA gene phylogeny analysis. [RESULTS] A total of 240 positive clones for all 3 libraries were used for RFLP analysis, and 15 specific amoA sequences were sequenced and clustered into 7 OTUs at 98% cutoff. Among them, OTU6 was detected in all of the 3 libraries and included 27% of the total specific clones. The phylogeny analysis showed that the 15 amoA sequences were grouped into 3 subgroups consisted of Zoige Wetland Clade 1 (4 OTUs), Zoige Wetland Clade 2 (2 OTUs) and Zoige Wetland Clade 3 (1 OTU). BLAST analysis showed that all OTUs were affiliated with the phylum Crenarchaeota. Correlation analysis showed that the Shannon diversity index (H') was significantly correlated with ammonia, nitrate/nitrite (P <0. 05). [ CONCLUSION] AOA in the Zoige plateau wetland swamp soil are all belonged to the Crenarchaeota, and their diversity is significantly correlated with soil ammonia, nitrate/nitrite content. PMID:25522598

  4. Impact of free ammonia on anammox rates (anoxic ammonium oxidation) in a moving bed biofilm reactor.

    PubMed

    Jaroszynski, L W; Cicek, N; Sparling, R; Oleszkiewicz, J A

    2012-06-01

    Using a bench scale moving bed bioreactor (MBBR), the effect of free ammonia (FA, NH(3), the un-ionized form of ammonium NH(4)(+)) concentration on anoxic ammonium oxidation (anammox) was evaluated based on the volumetric nitrogen removal rate (NRR). Although, a detailed microbial analysis was not conducted, the major NRR observed was assumed to be by anammox, based on the nitrogen conversion ratios of nitrite to ammonium and nitrate to ammonium. Since the concentration of free ammonia as a proportion of the total ammonia concentration is pH-dependent, the impact of changing the operating pH from 6.9 to 8.2, was investigated under constant nitrogen loading conditions during continuous reactor operation. Furthermore, the effect of sudden nitrogen load changes was investigated under constant pH conditions. Batch tests were conducted to determine the immediate response of the anammox consortium to shifts in pH and FA concentrations. It was found that FA was inhibiting NRR at concentrations exceeding 2 mg N L(-1). In the pH range 7-8, the decrease in anammox activity was independent of pH and related only to the concentration of FA. Nitrite concentrations of up to 120 mg N L(-1) did not negatively affect NRR for up to 3.5 h. It was concluded that a stable NRR in a moving bed biofilm reactor depended on maintaining FA concentrations below 2 mg N L(-1) when the pH was maintained between 7 and 8. PMID:22483855

  5. Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake

    PubMed Central

    Auguet, Jean-Christophe; Triadó-Margarit, Xavier; Nomokonova, Natalya; Camarero, Lluís; Casamayor, Emilio O

    2012-01-01

    Freshwater habitats have been identified as one of the largest reservoirs of archaeal genetic diversity, with specific lineages of ammonia-oxidizing archaea (AOA) populations different from soils and seas. The ecology and biology of lacustrine AOA is, however, poorly known. In the present study, vertical changes in archaeal abundance by CARD-FISH, quantitative PCR (qPCR) analyses and identity by clone libraries were correlated with environmental parameters in the deep glacial high-altitude Lake Redon. The lake is located in the central Spanish Pyrenees where atmospheric depositions are the main source of reactive nitrogen. Strong correlations were found between abundance of thaumarchaeotal 16S rRNA gene, archaeal amoA gene and nitrite concentrations, indicating an ammonium oxidation potential by these microorganisms. The bacterial amoA gene was not detected. Three depths with potential ammonia-oxidation activity were unveiled along the vertical gradient, (i) on the top of the lake in winter–spring (that is, the 0 oC slush layers above the ice-covered sheet), (ii) at the thermocline and (iii) the bottom waters in summer—autumn. Overall, up to 90% of the 16S rRNA gene sequences matched Thaumarchaeota, mostly from both the Marine Group (MG) 1.1a (Nitrosoarchaeum-like) and the sister clade SAGMGC−1 (Nitrosotalea-like). Clone-libraries analysis showed the two clades changed their relative abundances with water depth being higher in surface and lower in depth for SAGMGC−1 than for MG 1.1a, reflecting a vertical phylogenetic segregation. Overall, the relative abundance and recurrent appearance of SAGMGC−1 suggests a significant environmental role of this clade in alpine lakes. These results expand the set of ecological and thermal conditions where Thaumarchaeota are distributed, unveiling vertical positioning in the water column as a key factor to understand the ecology of different thaumarchaeotal clades in lacustrine environments. PMID:22495069

  6. Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake.

    PubMed

    Auguet, Jean-Christophe; Triadó-Margarit, Xavier; Nomokonova, Natalya; Camarero, Lluís; Casamayor, Emilio O

    2012-09-01

    Freshwater habitats have been identified as one of the largest reservoirs of archaeal genetic diversity, with specific lineages of ammonia-oxidizing archaea (AOA) populations different from soils and seas. The ecology and biology of lacustrine AOA is, however, poorly known. In the present study, vertical changes in archaeal abundance by CARD-FISH, quantitative PCR (qPCR) analyses and identity by clone libraries were correlated with environmental parameters in the deep glacial high-altitude Lake Redon. The lake is located in the central Spanish Pyrenees where atmospheric depositions are the main source of reactive nitrogen. Strong correlations were found between abundance of thaumarchaeotal 16S rRNA gene, archaeal amoA gene and nitrite concentrations, indicating an ammonium oxidation potential by these microorganisms. The bacterial amoA gene was not detected. Three depths with potential ammonia-oxidation activity were unveiled along the vertical gradient, (i) on the top of the lake in winter-spring (that is, the 0 (o)C slush layers above the ice-covered sheet), (ii) at the thermocline and (iii) the bottom waters in summer-autumn. Overall, up to 90% of the 16S rRNA gene sequences matched Thaumarchaeota, mostly from both the Marine Group (MG) 1.1a (Nitrosoarchaeum-like) and the sister clade SAGMGC-1 (Nitrosotalea-like). Clone-libraries analysis showed the two clades changed their relative abundances with water depth being higher in surface and lower in depth for SAGMGC-1 than for MG 1.1a, reflecting a vertical phylogenetic segregation. Overall, the relative abundance and recurrent appearance of SAGMGC-1 suggests a significant environmental role of this clade in alpine lakes. These results expand the set of ecological and thermal conditions where Thaumarchaeota are distributed, unveiling vertical positioning in the water column as a key factor to understand the ecology of different thaumarchaeotal clades in lacustrine environments. PMID:22495069

  7. Microsensor Measurements of Sulfate Reduction and Sulfide Oxidation in Compact Microbial Communities of Aerobic Biofilms

    PubMed Central

    Kühl, Michael; Jørgensen, Bo Barker

    1992-01-01

    The microzonation of O2 respiration, H2S oxidation, and SO42- reduction in aerobic trickling-filter biofilms was studied by measuring concentration profiles at high spatial resolution (25 to 100 μm) with microsensors for O2, S2-, and pH. Specific reaction rates were calculated from measured concentration profiles by using a simple one-dimensional diffusion reaction model. The importance of electron acceptor and electron donor availability for the microzonation of respiratory processes and their reaction rates was investigated. Oxygen respiration was found in the upper 0.2 to 0.4 mm of the biofilm, whereas sulfate reduction occurred in deeper, anoxic parts of the biofilm. Sulfate reduction accounted for up to 50% of the total mineralization of organic carbon in the biofilms. All H2S produced from sulfate reduction was reoxidized by O2 in a narrow reaction zone, and no H2S escaped to the overlying water. Turnover times of H2S and O2 in the reaction zone were only a few seconds owing to rapid bacterial H2S oxidation. Anaerobic H2S oxidation with NO3- could be induced by addition of nitrate to the medium. Total sulfate reduction rates increased when the availability of SO42- or organic substrate increased as a result of deepening of the sulfate reduction zone or an increase in the sulfate reduction intensity, respectively. PMID:16348687

  8. Oxidative stability of pork emulsion containing tomato products and pink guava pulp during refrigerated aerobic storage.

    PubMed

    Joseph, Serlene; Chatli, Manish K; Biswas, Ashim K; Sahoo, Jhari

    2014-11-01

    Lipid oxidation-induced quality problems can be minimized with the use of natural antioxidants. Antioxidant potential of tomato puree (10 %; T-1), tomato pulp (12.5 %; T-2), lyophilized tomato peel (6 %; T-3), and pink guava pulp (10 %; T-4) was evaluated in raw pork emulsion during refrigerated storage for 9 days under aerobic packaging. The lycopene and β-carotene content varied in pork emulsion as T-3 > T-1 > T-2 > T-4 and decreased (P < 0.05) during storage. The surface redness (a* value) increased (P < 0.05) with the incorporation of tomato products and pink guava pulp. Furthermore, metmyoglobin formation and lipid oxidation were lower (P < 0.05) in tomato- and guava-treated emulsions than in control. Overall, incorporation of tomato products and pink guava pulp improved the visual colour and odour scores of raw pork emulsion. These results indicated that tomato products and guava pulp can be utilized as sources of natural antioxidants in raw pork products to minimize lipid oxidation, off-odour development, and surface discolouration. PMID:26396313

  9. Copper-catalyzed domino synthesis of quinazolinones via Ullmann-type coupling and aerobic oxidative C-H amidation.

    PubMed

    Xu, Wei; Jin, Yibao; Liu, Hongxia; Jiang, Yuyang; Fu, Hua

    2011-03-18

    An efficient copper-catalyzed approach to quinazolinone derivatives has been developed, and the protocol uses cheap and readily available substituted 2-halobenzamides and (aryl)methanamines as the starting materials as well as economical and environmentally friendly air as the oxidant. This can be the first example of constructing N-heterocycles via sequential Ullmann-type coupling under air and aerobic oxidative C-H amidation. PMID:21344914

  10. Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

    NASA Astrophysics Data System (ADS)

    Zheng, Y.; Huang, R.; Wang, B. Z.; Bodelier, P. L. E.; Jia, Z. J.

    2014-06-01

    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and functional genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity 6-fold during a 19-day incubation period, while ammonia oxidation activity was significantly suppressed in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like MOB, and nitrifying communities appeared to be partially inhibited by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to an equal increase in Methylosarcina and Methylobacter-related type Ia MOB, indicating the differential growth requirements of representatives of these genera. An increase in 13C assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition partially inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, as well as growth of nitrite-oxidizing bacteria. These

  11. Atmospheric cycles of nitrogen oxides and ammonia. [source strengths and destruction rates

    NASA Technical Reports Server (NTRS)

    Bottger, A.; Ehhalt, D. H.; Gravenhorst, G.

    1981-01-01

    The atmospheric cycles of nitrogenous trace compounds for the Northern and Southern Hemispheres are discussed. Source strengths and destruction rates for the nitrogen oxides: NO, NO2 and HNO3 -(NOX) and ammonia (NH3) are given as a function of latitude over continents and oceans. The global amounts of NOX-N and NH3-N produced annually in the period 1950 to 1975 (34 + 5 x one trillion g NOx-N/yr and 29 + or - 6 x one trillion g NH3-N/yr) are much less than previously assumed. Globally, natural and anthropogenic emissions are of similar magnitude. The NOx emission from anthropogenic sources is 1.5 times that from natural processes in the Northern Hemisphere, whereas in the Southern Hemisphere, it is a factor of 3 or 4 less. More than 80% of atmospheric ammonia seems to be derived from excrements of domestic animals, mostly by bulk deposition: 24 + or - 9 x one trillion g NO3 -N/yr and 21 + or - 9 x one trillion g NH4+-N/yr. Another fraction may be removed by absorption on vegetation and soils.

  12. Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil.

    PubMed

    Sher, Yonatan; Ronen, Zeev; Nejidat, Ali

    2016-08-01

    Ammonia-oxidizing archaea and bacteria (AOA, AOB) catalyze the first and rate-limiting step of nitrification. To examine their differential responses to the wetting of dry and salty arid soil, AOA and AOB amoA genes (encoding subunit A of the ammonia monooxygenase) and transcripts were enumerated in dry (summer) and wet (after the first rainfall) soil under the canopy of halophytic shrubs and between the shrubs. AOA and AOB were more abundant under shrub canopies than between shrubs in both the dry and wetted soil. Soil wetting caused a significant decrease in AOB abundance under the canopy and an increase of AOA between the shrubs. The abundance of the archaeal amoA gene transcript was similar for both the wet and dry soil, and the transcript-to-gene ratios were < 1 independent of niche or water content. In contrast, the bacterial amoA transcript-to-gene ratios were between 78 and 514. The lowest ratio was in dry soil under the canopy and the highest in the soil between the shrubs. The results suggest that the AOA are more resilient to stress conditions and maintain a basic activity in arid ecosystems, while the AOB are more responsive to changes in the biotic and abiotic conditions. PMID:27037935

  13. Catalytic oxidation of ammonia on RuO2(110) surfaces: mechanism and selectivity.

    PubMed

    Wang, Y; Jacobi, K; Schöne, W-D; Ertl, G

    2005-04-28

    The selective oxidation of ammonia to either N2 or NO on RuO2(110) single-crystal surfaces was investigated by a combination of vibrational spectroscopy (HREELS), thermal desorption spectroscopy (TDS) and steady-state rate measurements under continuous flow conditions. The stoichiometric RuO2(110) surface exposes coordinatively unsaturated (cus) Ru atoms onto which adsorption of NH3 (NH3-cus) or dissociative adsorption of oxygen (O-cus) may occur. In the absence of O-cus, ammonia desorbs completely thermally without any reaction. However, interaction between NH3-cus and O-cus starts already at 90 K by hydrogen abstraction and hydrogenation to OH-cus, leading eventually to N-cus and H2O. The N-cus species recombine either with each other to N2 or with neighboring O-cus leading to strongly held NO-cus which desorbs around 500 K. The latter reaction is favored by higher concentrations of O-cus. Under steady-state flow condition with constant NH3 partial pressure and varying O2 pressure, the rate for N2 formation takes off first, passes through a maximum and then decreases again, whereas that for NO production exhibits an S-shape and rises continuously. In this way at 530 K almost 100% selectivity for NO formation (with fairly high reaction probability for NH3) is reached. PMID:16851919

  14. Latitudinal Distribution of Ammonia-Oxidizing Bacteria and Archaea in the Agricultural Soils of Eastern China

    PubMed Central

    Huang, Liuqin; Deng, Ye; Wang, Shang; Zhou, Yu; Liu, Li

    2014-01-01

    The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients. PMID:25002421

  15. Sediment Ammonia-Oxidizing Microorganisms in Two Plateau Freshwater Lakes at Different Trophic States.

    PubMed

    Yang, Yuyin; Zhang, Jingxu; Zhao, Qun; Zhou, Qiheng; Li, Ningning; Wang, Yilin; Xie, Shuguang; Liu, Yong

    2016-02-01

    Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can contribute to ammonia biotransformation in freshwater lake ecosystems. However, the factors shaping the distribution of sediment AOA and AOB in plateau freshwater lake remains unclear. The present study investigated sediment AOA and AOB communities in two freshwater lakes (hypertrophic Dianchi Lake and mesotrophic Erhai Lake) on the Yunnan Plateau (China). A remarkable difference in the abundance, diversity, and composition of sediment AOA and AOB communities was observed between Dianchi Lake and Erhai Lake. AOB usually outnumbered AOA in Dianchi Lake, but AOA showed the dominance in Erhai Lake. Organic matter (OM), total nitrogen (TN), and total phosphorus (TP) might be the key determinants of AOB abundance, while AOA abundance was likely influenced by the ration of OM to TN (C/N). AOA or AOB community structure was found to be relatively similar in the same lake. TN and TP might play important roles in shaping sediment AOA and AOB compositions in Dianchi Lake and Erhai Lake. Moreover, Nitrososphaera-like AOA were detected in Dianchi Lake. Nitrosospira- and Nitrosomonas-like AOB were dominant in Dianchi Lake and Erhai Lake, respectively. Sediment AOA and AOB communities in Dianchi Lake and Erhai Lake were generally regulated by trophic state. PMID:26111964

  16. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics.

    PubMed

    Li, Yuyang; Ding, Kun; Wen, Xianghua; Zhang, Bing; Shen, Bo; Yang, Yunfeng

    2016-01-01

    Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with "Ca. Nitrosotenuis chungbukensis"), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C-33 °C) and neutrophilic (pH 5.0-7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name "Candidatus Nitrosotenuis cloacae" for the strain SAT1. PMID:27030530

  17. Latitudinal distribution of ammonia-oxidizing bacteria and archaea in the agricultural soils of eastern China.

    PubMed

    Jiang, Hongchen; Huang, Liuqin; Deng, Ye; Wang, Shang; Zhou, Yu; Liu, Li; Dong, Hailiang

    2014-09-01

    The response of soil ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to individual environmental variables (e.g., pH, temperature, and carbon- and nitrogen-related soil nutrients) has been extensively studied, but how these environmental conditions collectively shape AOB and AOA distributions in unmanaged agricultural soils across a large latitudinal gradient remains poorly known. In this study, the AOB and AOA community structure and diversity in 26 agricultural soils collected from eastern China were investigated by using quantitative PCR and bar-coded 454 pyrosequencing of the amoA gene that encodes the alpha subunit of ammonia monooxygenase. The sampling locations span over a 17° latitude gradient and cover a range of climatic conditions. The Nitrosospira and Nitrososphaera were the dominant clusters of AOB and AOA, respectively; but the subcluster-level composition of Nitrosospira-related AOB and Nitrososphaera-related AOA varied across the latitudinal gradient. Variance partitioning analysis showed that geography and climatic conditions (e.g., mean annual temperature and precipitation), as well as carbon-/nitrogen-related soil nutrients, contributed more to the AOB and AOA community variations (∼50% in total) than soil pH (∼10% in total). These results are important in furthering our understanding of environmental conditions influencing AOB and AOA community structure across a range of environmental gradients. PMID:25002421

  18. Ammonia-oxidizing bacteria and archaea in sediments of the Gulf of Mexico.

    PubMed

    Flood, Matthew; Frabutt, Dylan; Floyd, Dalton; Powers, Ashley; Ezegwe, Uche; Devol, Allan; Tiquia-Arashiro, Sonia M

    2015-01-01

    The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of the Gulf of Mexico was examined. Using polymerase chain reaction primers designed to specifically target the archaeal ammonia monooxygenase-subunit (amoA) gene and bacterial amoA gene, we found AOA and AOB to be present in all three sampling sites. Archaeal amoA libraries were dominated by a few widely distributed Nitrosopumilus-like sequence types, whereas AOB diversity showed significant variation in both richness and community composition. Majority of the bacterial amoA sequences recovered belong to Betaproteobacteria and very few belong to Gammaproteobacteria. Results suggest that water depth and nutrient availability were identified as potential drivers that affected the selection of the AOA and AOB communities. Besides influencing the abundance of individual taxa, these environmental factors also had an impact on the overall richness of the overall AOA and AOB communities. The richness and diversity of AOA and AOB genes were higher at the shallowest sediments (100 m depth) and the deepest sediments (1300 m depth). The reduced diversity in the deepest sediments could be explained by much lower nutrient availability. PMID:25409591

  19. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics

    NASA Astrophysics Data System (ADS)

    Li, Yuyang; Ding, Kun; Wen, Xianghua; Zhang, Bing; Shen, Bo; Yang, Yunfeng

    2016-03-01

    Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with “Ca. Nitrosotenuis chungbukensis”), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C–33 °C) and neutrophilic (pH 5.0–7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name “Candidatus Nitrosotenuis cloacae” for the strain SAT1.

  20. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics

    PubMed Central

    Li, Yuyang; Ding, Kun; Wen, Xianghua; Zhang, Bing; Shen, Bo; Yang, Yunfeng

    2016-01-01

    Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with “Ca. Nitrosotenuis chungbukensis”), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C–33 °C) and neutrophilic (pH 5.0–7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name “Candidatus Nitrosotenuis cloacae” for the strain SAT1. PMID:27030530

  1. Self-assembled dicopper(II) diethanolaminate cores for mild aerobic and peroxidative oxidation of alcohols.

    PubMed

    Figiel, Paweł J; Kirillov, Alexander M; Guedes da Silva, M Fátima C; Lasri, Jamal; Pombeiro, Armando J L

    2010-11-01

    The new dicopper(ii) complexes [Cu(2)(μ-Hmdea)(2)(NCS)(2)] (1) and [Cu(2)(μ-Hedea)(2)(N(3))(2)]·(H(2)O)(0.25) (2) with the {Cu(2)(μ-O)(2)} diethanolaminate cores have been easily generated by aqueous medium self-assembly reactions of copper(ii) nitrate with N-methyl- or N-ethyldiethanolamine (H(2)mdea or H(2)edea, respectively), in the presence of sodium thiocyanate (for 1) or sodium azide (for 2) as ancillary ligands sources. They have been isolated as air-stable crystalline solids and fully characterized by IR and UV-vis spectroscopies, ESI-MS(+), elemental and single-crystal X-ray diffraction analyses. The latter complex also features a fourfold linkage of neighbouring dimeric units via strong intermolecular O-HO hydrogen bonds, giving rise to the formation of tetracopper aggregates. The catalytic activity of compounds 1 and 2 has been studied for the mild (50-80 °C) and selective oxidations of alcohols, namely for (i) the aerobic aqueous medium oxidation of benzyl alcohols to benzaldehydes, mediated by TEMPO radical, and for (ii) the solvent-free oxidation of secondary alcohols to ketones by t-BuOOH under microwave (MW) irradiation. Complex 2 shows the highest efficiency in both oxidation systems, resulting in up to 99% molar yields (based on the alcohol substrate) of products. In addition, remarkably high values of TON (1020) and TOF (4080 h(-1)) have been achieved in the MW-assisted peroxidative oxidation of 1-phenylethanol to acetophenone (model reaction). Attractive green features of these catalytic systems include the operation in aqueous or solvent-free reaction medium, under mild conditions and with high yields and selectivities, using Cu catalyst precursors that are readily available by self-assembly in water of simple chemicals. PMID:20844801

  2. Aerobic training prevents oxidative profile and improves nitric oxide and vascular reactivity in rats with cardiometabolic alteration.

    PubMed

    Medeiros, Renata F; Gaique, Thaiane G; Bento-Bernardes, Thais; Motta, Nádia A V; Brito, Fernanda C F; Fernandes-Santos, Caroline; Castro-Pinheiro, Camila; Oliveira, Karen J; Nóbrega, Antonio C L

    2016-07-01

    Cardiovascular disease is the major cause of death worldwide; therefore it is important to understand the natural history of the pathophysiologic process and develop strategies to halt its progression. Thus this study investigated the protective effect of aerobic training on pathophysiological mechanisms involved in subclinical cardiometabolic alterations in a model with constant exposure to a prejudicial agent. Male Wistar rats were divided into a control group (C), which received drinking water, fructose group (F), which was fed 10% fructose in drinking water for 10 wk, and control training (CT) and fructose training groups (FT), in which moderate aerobic training was added in the last 8 wk of the study. Insulin, triacylglycerol, and isoprostane were higher and superoxide dismutase (SOD) was lower in the F group. There was no difference in thoracic aorta histology, but a decreased vascularization was seen in the F group, avoided by training in left ventricle. Regarding vascular function, the F group exhibited increased vasoconstrictory reactivity to phenylephrine. The F group presented impaired vasodilation to acetylcholine. Regarding endothelial nitric oxide synthase (eNOS), the F group presented a lower expression, and phosphorylated eNOS was higher in the trained groups than in their respective control groups. This same pattern was observed for nitric oxide bioavailability, antioxidant protein expression in aorta, left ventricle, and muscle (catalase, SOD, and glutathione peroxidase), serum SOD activity, and muscle mass. These results suggest that exercise training enhanced the antioxidant pathway and, as a consequence, the eNOS pathway, preventing an impairment in vascular vasodilatory capacity. PMID:27255525

  3. Reduced graphene oxide-rose bengal hybrid film for improved ammonia detection with low humidity interference at room temperature

    NASA Astrophysics Data System (ADS)

    Midya, Anupam; Ghosh, Ruma; Santra, Sumita; Ray, Samit K.; Guha, Prasanta K.

    2016-02-01

    Development of chemoresistive ammonia sensor that does not suffer with humidity interference is highly desirable for practical environmental monitoring systems. We report enhanced ammonia sensing using chemically reduced graphene oxide (RGO) and rose bengal (RB) nanocomposite fabricated in a very simple and cost effective manner. The RGO-RB nanocomposites were synthesized using three different concentrations (2 mg mL-1, 5 mg mL-1 and 10 mg mL-1) of RB keeping the RGO concentration same. Ammonia and humidity sensing of these three different composites were explored. Interestingly, it was observed that with increasing concentration of RB, the sensitivity of the sensor towards ammonia was increased but the sensitivity towards humidity was decreased. The response of the nanocomposites varied from ˜9-45% against 400-2800 ppm of ammonia whereas intrinsic RGO showed a response of merely 17% against 2800 ppm of ammonia. On the other hand the response of the nanocomposite based sensor was reduced from 18% to 7% against 100% relative humidity. Also, the sensor was found to be selective towards ammonia when tested against other toxic volatile organic compounds. The limit of detection of the RGO-RB based sensor was calculated to be as low as 0.9 ppm. Field emission scanning electron microscopy, transmission electron microscopy, Raman spectroscopy, Fourier transform infrared spectroscopy and UV-vis spectroscopy were carried out for the detailed structural characterizations of the sensing layer. These results are believed to be very useful for the cost effective fabrication of graphene based ammonia sensors which have reduced effects of humidity.

  4. Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

    NASA Astrophysics Data System (ADS)

    Zheng, Y.; Huang, R.; Wang, B. Z.; Bodelier, P. L. E.; Jia, Z. J.

    2014-03-01

    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and pmoA genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity by 6-fold during a 19 day incubation period, while ammonia oxidation activity was significantly inhibited in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like type Ia MOB, and nitrifying communities appeared to be suppressed by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to equal increase in Methylosarcina and Methylobacter-related MOB, indicating the differential growth requirements of representatives of these genera. Strikingly, type Ib MOB did not respond to methane nor to urea. Increase in 13C-assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, in addition of nitrite-oxidizing

  5. Biological Oxidation of Ammonia and Arsenic in Pilot-scale Rapid Sand Filters

    EPA Science Inventory

    The removal of ammonia from source water entering a drinking water distribution system is desirable, as excess levels have been correlated with nitrification, chlorine demand, corrosion, and biological re-growth. Several technologies exist to remove ammonia with recent interest...

  6. Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil

    PubMed Central

    Sterngren, Anna E.; Hallin, Sara; Bengtson, Per

    2015-01-01

    Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil. PMID:26648926

  7. Emissions of Ammonia, Methane, Carbon Dioxide and Nitrous Oxide From Dairy Cattle Housing and Manure Management Systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Concentrated animal feeding operations emit trace gases such as ammonia (NH3), methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) to the atmosphere. The implementation of air quality regulations in livestock-producing states increases the need for accurate on-farm determination of emissio...

  8. Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil.

    PubMed

    Rice, Marlen C; Norton, Jeanette M; Valois, Frederica; Bollmann, Annette; Bottomley, Peter J; Klotz, Martin G; Laanbroek, Hendrikus J; Suwa, Yuichi; Stein, Lisa Y; Sayavedra-Soto, Luis; Woyke, Tanja; Shapiro, Nicole; Goodwin, Lynne A; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Kyrpides, Nikos; Varghese, Neha; Mikhailova, Natalia; Markowitz, Victor; Palaniappan, Krishna; Ivanova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Daum, Chris

    2016-01-01

    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. PMID:27471578

  9. Biotransformation of pharmaceuticals by ammonia oxidizing bacteria in wastewater treatment processes.

    PubMed

    Xu, Yifeng; Yuan, Zhiguo; Ni, Bing-Jie

    2016-10-01

    Pharmaceutical residues could potentially pose detrimental effects on aquatic ecosystems and human health, with wastewater treatment being one of the major pathways for pharmaceuticals to enter into the environment. Enhanced removal of pharmaceuticals by ammonia oxidizing bacteria (AOB) has been widely observed in wastewater treatment processes. This article reviews the current knowledge on the biotransformation of pharmaceuticals by AOB. The relationship between the pharmaceuticals removal and nitrification process was revealed. The important role of AOB-induced cometabolism on the biotransformation of pharmaceuticals as well as their transformation products and pathways was elucidated. Kinetics and mathematical models describing the biotransformation of pharmaceuticals by AOB were also reviewed. The results highlighted the high degradation capabilities of AOB toward some refractory pharmaceuticals, with their degradations being clearly related to the nitrification rate and their transformation products being identified, which may exhibit similar or higher ecotoxicological impacts compared to the parent compound. PMID:27243932

  10. Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: A review.

    PubMed

    Zhu, Jing; Wang, Qian; Yuan, Mengdong; Tan, Giin-Yu Amy; Sun, Faqian; Wang, Cheng; Wu, Weixiang; Lee, Po-Heng

    2016-03-01

    Aerobic methane oxidation coupled to denitrification (AME-D) is an important link between the global methane and nitrogen cycles. This mini-review updates discoveries regarding aerobic methanotrophs and denitrifiers, as a prelude to spotlight the microbial mechanism and the potential applications of AME-D. Until recently, AME-D was thought to be accomplished by a microbial consortium where denitrifying bacteria utilize carbon intermediates, which are excreted by aerobic methanotrophs, as energy and carbon sources. Potential carbon intermediates include methanol, citrate and acetate. This mini-review presents microbial thermodynamic estimations and postulates that methanol is the ideal electron donor for denitrification, and may serve as a trophic link between methanotrophic bacteria and denitrifiers. More excitingly, new discoveries have revealed that AME-D is not only confined to the conventional synergism between methanotrophic bacteria and denitrifiers. Specifically, an obligate aerobic methanotrophic bacterium, Methylomonas denitrificans FJG1, has been demonstrated to couple partial denitrification with methane oxidation, under hypoxia conditions, releasing nitrous oxide as a terminal product. This finding not only substantially advances the understanding of AME-D mechanism, but also implies an important but unknown role of aerobic methanotrophs in global climate change through their influence on both the methane and nitrogen cycles in ecosystems. Hence, further investigation on AME-D microbiology and mechanism is essential to better understand global climate issues and to develop niche biotechnological solutions. This mini-review also presents traditional microbial techniques, such as pure cultivation and stable isotope probing, and powerful microbial techniques, such as (meta-) genomics and (meta-) transcriptomics, for deciphering linked methane oxidation and denitrification. Although AME-D has immense potential for nitrogen removal from wastewater, drinking

  11. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment.

    PubMed

    Norton, Jeanette M; Klotz, Martin G; Stein, Lisa Y; Arp, Daniel J; Bottomley, Peter J; Chain, Patrick S G; Hauser, Loren J; Land, Miriam L; Larimer, Frank W; Shin, Maria W; Starkenburg, Shawn R

    2008-06-01

    The complete genome of the ammonia-oxidizing bacterium Nitrosospira multiformis (ATCC 25196(T)) consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2,827 putative proteins. Of the 2,827 putative proteins, 2,026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and Nitrosomonas eutropha were the best match for 42% of the predicted genes in N. multiformis. The N. multiformis genome contains three nearly identical copies of amo and hao gene clusters as large repeats. The features of N. multiformis that distinguish it from N. europaea include the presence of gene clusters encoding urease and hydrogenase, a ribulose-bisphosphate carboxylase/oxygenase-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced genomes of ammonia-oxidizing bacteria. Gene clusters encoding proteins associated with outer membrane and cell envelope functions, including transporters, porins, exopolysaccharide synthesis, capsule formation, and protein sorting/export, were abundant. Numerous sensory transduction and response regulator gene systems directed toward sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate, and cyanophycin storage and utilization were identified, providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments. PMID:18390676

  12. Copper(I)/ABNO-catalyzed aerobic alcohol oxidation: alleviating steric and electronic constraints of Cu/TEMPO catalyst systems.

    PubMed

    Steves, Janelle E; Stahl, Shannon S

    2013-10-23

    Cu/TEMPO catalyst systems promote efficient aerobic oxidation of sterically unhindered primary alcohols and electronically activated substrates, but they show reduced reactivity with aliphatic and secondary alcohols. Here, we report a catalyst system, consisting of ((MeO)bpy)Cu(I)(OTf) and ABNO ((MeO)bpy = 4,4'-dimethoxy-2,2'-bipyridine; ABNO = 9-azabicyclo[3.3.1]nonane N-oxyl), that mediates aerobic oxidation of all classes of alcohols, including primary and secondary allylic, benzylic, and aliphatic alcohols with nearly equal efficiency. The catalyst exhibits broad functional group compatibility, and most reactions are complete within 1 h at room temperature using ambient air as the source of oxidant. PMID:24128057

  13. Continuous Flow Aerobic Alcohol Oxidation Reactions Using a Heterogeneous Ru(OH)x/Al2O3 Catalyst

    PubMed Central

    2015-01-01

    Ru(OH)x/Al2O3 is among the more versatile catalysts for aerobic alcohol oxidation and dehydrogenation of nitrogen heterocycles. Here, we describe the translation of batch reactions to a continuous-flow method that enables high steady-state conversion and single-pass yields in the oxidation of benzylic alcohols and dehydrogenation of indoline. A dilute source of O2 (8% in N2) was used to ensure that the reaction mixture, which employs toluene as the solvent, is nonflammable throughout the process. A packed bed reactor was operated isothermally in an up-flow orientation, allowing good liquid–solid contact. Deactivation of the catalyst during the reaction was modeled empirically, and this model was used to achieve high conversion and yield during extended operation in the aerobic oxidation of 2-thiophene methanol (99+% continuous yield over 72 h). PMID:25620869

  14. Temperature and moisture effects on ammonia oxidizer communities in cryoturbated Arctic soils

    NASA Astrophysics Data System (ADS)

    Aiglsdorfer, Stefanie; Alves, Ricardo J. E.; Bárta, Jiří; Kohoutová, Iva; Bošková, Hana; Diáková, Katerina; Čapek, Petr; Schnecker, Jörg; Wild, Birgit; Mooshammer, Maria; Urich, Tim; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Mikutta, Robert; Lashchinskiy, Nikolay; Richter, Andreas; Šantrůčková, Hana; Shibistova, Olga; Schleper, Christa

    2014-05-01

    Arctic permafrost-affected soils contain large amounts of soil organic carbon (SOC) and are expected to experience drastic changes in environmental conditions, such as moisture and temperature, due to the high surface temperature increase predicted for these regions. Although the SOC decomposition processes driven by the microbiota are considered to be nitrogen (N) limited, little information about the microbial groups involved in N cycle is currently available, including their reactions to environmental changes. Here, we investigate the presence of ammonia oxidizing archaea (AOA) and bacteria (AOB) in distinct soil horizons from the Taymyr peninsula (Siberia, Russia), and investigate their activities under changing temperature and moisture regimes. These two groups of organisms perform the first step in nitrification, an important and rate limiting process in the global N cycle, which involves the oxidation of ammonia to nitrate via nitrite. The soil samples were separated into different horizons: organic topsoil (O) and subducted organic topsoil (Ajj). The samples were incubated for 18 weeks at 4, 12 and 20° C and 50, 80 and 100 % water holding capacity (WHC). AOA and AOB abundances were quantified by quantitative PCR targeting genes of the key metabolic enzyme, ammonia monooxygenase. AOA diversity was analyzed in-depth by high-throughput amplicon sequencing of the same gene. Additionally, gross and net nitrification and mineralization rates were determined in order to investigate potential relationships between AOA and AOB populations and these processes, in response to the incubation treatments. We found higher abundances of AOA than AOB in the organic topsoil, whereas AOB dominated in the subducted organic topsoil. Increased temperature resulted in higher numbers of both groups at low WHC %, with AOB showing a more pronounced response. However, these effects were not observed under anaerobic conditions (100 % WHC). Deep sequencing of AOA amoA genes revealed

  15. Highly Dispersed Gold Nanoparticles Supported on SBA-15 for Vapor Phase Aerobic Oxidation of Benzyl Alcohol.

    PubMed

    Kumar, Ashish; Sreedhar, Bojja; Chary, Komandur V R

    2015-02-01

    Gold nanoparticles supported on SBA-15 are prepared by homogenous deposition-precipitation method (HDP) using urea as the precipitating agent. The structural features of the synthesized catalysts were characterized by various techniques such as X-ray diffraction (XRD), transmission electron microscopy (TEM), nitrogen adsorption-desorption (BET), pore size distribution (PSD), CO chemisorption and X-ray photoelectron spectroscopy (XPS). The catalytic activity and stability of the Au/SBA-15 catalysts are investigated during the vapor phase aerobic oxidation of benzyl alcohol. The BJH pore size distribution results of SBA-15 support and Au/SBA-15 catalysts reveals that the formation of mesoporous structure in all the samples. TEM results suggest that Au nanoparticles are highly dispersed over SBA-15 and long range order of hexagonal mesopores of SBA-15 is well retained even after the deposition of Au metallic nanoparticles. XPS study reveals the formation of Au (0) after chemical reduction by NaBH4. The particle size measured from CO-chemisorption and TEM analysis are well correlated with the TOF values of the reaction. Au/SBA-1 5 catalysts are found to show higher activity compare to Au/TiO2 and Au/MgO catalysts during the vapor phase oxidation of benzyl alcohol. The catalytic functionality are well substantiated with particle size measured from TEM. The crystallite size of Au in both fresh and spent catalysts were measured from X-ray diffraction. PMID:26353720

  16. Metal-free aerobic oxidations mediated by N-hydroxyphthalimide. A concise review

    PubMed Central

    Melone, Lucio

    2013-01-01

    Summary Since the beginning of the century, N-hydroxyphthalimide and related compounds have been revealed to be efficient organocatalysts for free-radical processes and have found ample application in promoting the aerobic oxidation of a wide range of organic substrates. When combined with different co-catalysts, they are activated to the corresponding N-oxyl radical species and become able to promote radical chains, involving molecular oxygen, directly or indirectly. Most of the examples reported in the literature describe the use of these N-hydroxy derivatives in the presence of transition-metal complexes. However, eco-friendly standards, including the demand for highly selective transformations, impose the development of metal-free processes, especially for large-scale productions, as in the case of the oxygenation of hydrocarbons. For this reason, many efforts have been devoted in the past decade to the design of new protocols for the activation of N-hydroxy imides in the presence of nonmetal initiators. Herein we provide a concise overview of the most significant and successful examples in this field, with the final aim to furnish a useful instrument for all scientists actively involved in the O2-mediated selective oxidation of organic compounds and looking for environmentally safe alternatives to metal catalysis. PMID:23843925

  17. Mechanistic insight into aerobic alcohol oxidation using NOx-nitroxide catalysis based on catalyst structure-activity relationships.

    PubMed

    Shibuya, Masatoshi; Nagasawa, Shota; Osada, Yuji; Iwabuchi, Yoshiharu

    2014-11-01

    The mechanism of an NOx-assisted, nitroxide(nitroxyl radical)-catalyzed aerobic oxidation of alcohols was investigated using a set of sterically and electronically modified nitroxides (i.e., TEMPO, AZADO (1), 5-F-AZADO (2), 5,7-DiF-AZADO (3), 5-MeO-AZADO (4), 5,7-DiMeO-AZADO (5), oxa-AZADO (6), TsN-AZADO (7), and DiAZADO (8)). The motivation for the present study stemmed from our previous observation that the introduction of an F atom at a remote position from the nitroxyl radical moiety on the azaadamantane nucleus effectively enhanced the catalytic activity under typical NOx-mediated aerobic-oxidation conditions. The kinetic profiles of the azaadamantane-N-oxyl-[AZADO (1)-, 5-F-AZADO (2)-, and 5,7-DiF-AZADO (3)]-catalyzed aerobic oxidations were closely investigated, revealing that AZADO (1) showed a high initial reaction rate compared to 5-F-AZADO (2) and 5,7-DiF-AZADO (3); however, AZADO-catalyzed oxidation exhibited a marked slowdown, resulting in ∼90% conversion, whereas 5-F-AZADO-catalyzed oxidation smoothly reached completion without a marked slowdown. The reasons for the marked slowdown and the role of the fluoro group are discussed. Oxa-AZADO (6), TsN-AZADO (7), and DiAZADO (8) were designed and synthesized to confirm their comparable catalytic efficiency to that of 5-F-AZADO (2), providing supporting evidence for the electronic effect on the catalytic efficiency of the heteroatoms under NOx-assisted aerobic-oxidation conditions. PMID:25286356

  18. Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake.

    PubMed

    Yang, Yuyin; Li, Ningning; Zhao, Qun; Yang, Mengxi; Wu, Zhen; Xie, Shuguang; Liu, Yong

    2016-08-01

    Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure. PMID:27109114

  19. Composition of ammonia-oxidizing archaea and their contribution to nitrification in a high-temperature hot spring

    NASA Astrophysics Data System (ADS)

    Chen, S.; Peng, X.-T.; Xu, H.-C.; Ta, K.-W.

    2015-10-01

    The oxidation of ammonia by microbes and associated organisms has been shown to occur in diverse natural environments. However, the contribution of ammonia-oxidizing archaea to nitrification in high-temperature environments remains unclear. Here, we studied in situ ammonia oxidation rates and the abundance of ammonia-oxidizing archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3- pool dilution technique in the surface sinter and bottom sediments were 4.8 and 5.3 nmol N g-1 h-1, respectively. Relative abundances of Crenarchaea in both samples were determined by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic "Candidatus Nitrosocaldus yellowstonii", which represented the most abundant operation taxonomic units (OTU) in both sediments. Furthermore, bacterial amoA was not detected in this study. Quantitative PCR (qPCR) indicated that AOA and 16S rRNA genes were present in the range of 2.75 to 9.80 × 105 and 0.128 to 1.96 × 108 gene copies g-1 sediment. The cell-specific nitrification rates were estimated to be in the range of 0.41 to 0.79 fmol N archaeal cell-1 h-1, which is consistent with earlier estimates in estuary environments. This study demonstrated that AOA were widely involved in nitrification in this hot spring. It further indicated the importance of archaea rather than bacteria in driving the nitrogen cycle in terrestrial geothermal environments.

  20. Techno-economic evaluation of the application of ozone-oxidation in a full-scale aerobic digestion plant.

    PubMed

    Chiavola, Agostina; D'Amato, Emilio; Gori, Riccardo; Lubello, Claudio; Sirini, Piero

    2013-04-01

    This paper deals with the application of the ozone-oxidation in a full scale aerobic sludge digester. Ozonation was applied continuously to a fraction of the biological sludge extracted from the digestion unit; the ozonated sludge was then recirculated to the same digester. Three different ozone flow rates were tested (60,500 and 670g O3 h(-1)) and their effects evaluated in terms of variation of the total and soluble fractions of COD, nitrogen and phosphorous, of total and volatile suspended solids concentrations and Sludge Volume Index in the aerobic digestion unit. During the 7-month operation of the ozonation process, it was observed an appreciable improvement of the aerobic digestion efficiency (up to about 20% under the optimal conditions) and of the sludge settleability properties. These results determined an average reduction of about 60% in the biological sludge extracted from the plant and delivered to final disposal. A thorough economic analysis showed that this reduction allowed to achieve a significant cost saving for the plant with respect to the previous years operated without ozonation. Furthermore, it was determined the threshold disposal cost above which implementation of the ozone oxidation in the aerobic digestion units of similar WWTPs becomes economically convenient (about 60€t(-1) of sludge). PMID:23384542

  1. Dissimilatory perchlorate reduction linked to aerobic methane oxidation via chlorite dismutase

    NASA Astrophysics Data System (ADS)

    Oremland, R. S.; Baesman, S. M.; Miller, L. G.

    2013-12-01

    The presence of methane (CH4) in the atmosphere of Mars is controversial yet the evidence has aroused scientific interest, as CH4 could be a harbinger of extant or extinct microbial life. There are various oxidized compounds present on the surface of Mars that could serve as electron acceptors for the anaerobic oxidation of CH4, including perchlorate (ClO4-). We examined the role of perchlorate, chlorate (ClO3-) and chlorite (ClO2-) as oxidants linked to CH4 oxidation. Dissimilatory perchlorate reduction begins with reduction of ClO4- to ClO2- and ends with dismutation of chlorite to yield chloride (Cl-) and molecular oxygen (O2). We explored the potential for aerobic CH4 oxidizing bacteria to couple with oxygen derived from chlorite dismutation during dissimilatory perchlorate reduction. Methane (0.2 kPa) was completely removed within several days from the N2-flushed headspace above cell suspensions of methanotrophs (Methylobacter albus strain BG8) and perchlorate reducing bacteria (Dechloromonas agitata strain CKB) in the presence of 5 mM ClO2-. Similar rates of CH4 consumption were observed for these mixed cultures whether they were co-mingled or segregated under a common headspace, indicating that direct contact of cells was not required for methane consumption to occur. We also observed complete removal of 0.2 kPa CH4 in bottles containing dried soil (enriched in methanotrophs by CH4 additions over several weeks) and D. agitata CKB and in the presence of 10 mM ClO2-. This soil (seasonally exposed sediment) collected from the shoreline of a freshwater lake (Searsville Lake, CA) demonstrated endogenous CH4 uptake as well as perchlorate, chlorate and chlorite reduction/dismutation. However, these experiments required physical separation of soil from the aqueous bacterial culture to allow for the partitioning of O2 liberated from chlorite dismutation into the shared headspace. Although dissimilatory reduction of ClO4- and ClO3- could be inferred from the

  2. Impact of herbicides on the abundance and structure of indigenous beta-subgroup ammonia-oxidizer communities in soil microcosms.

    PubMed

    Chang, Y J; Hussain, A K; Stephen, J R; Mullen, M D; White, D C; Peacock, A

    2001-11-01

    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 beta-subclass Proteobacteria autotrophic ammonia-oxidizer (beta-AAO) community was assessed. The beta-AAO population abundances were estimated by competitive polymerase chain reaction (PCR) targeting the gene amoA, encoding the alpha-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 beta-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. PMID:11699770

  3. Responses of Ammonia-Oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater ▿

    PubMed Central

    Reed, David W.; Smith, Jason M.; Francis, Christopher A.; Fujita, Yoshiko

    2010-01-01

    To evaluate the potential for organic nitrogen addition to stimulate the in situ growth of ammonia oxidizers during a field scale bioremediation trial, samples collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea were subjected to PCR analysis of ammonia monooxygenase subunit A (amoA) genes. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were present in all of the samples tested, with AOA amoA genes outnumbering AOB amoA genes in all of the samples. Following urea addition, nitrate levels rose and bacterial amoA copy numbers increased dramatically, suggesting that urea hydrolysis stimulated nitrification. Bacterial amoA diversity was limited to two Nitrosomonas phylotypes, whereas archaeal amoA analyses revealed 20 distinct operational taxonomic units, including several that were markedly different from all previously reported sequences. Results from this study demonstrate the likelihood of stimulating ammonia-oxidizing communities during field scale manipulation of groundwater conditions to promote urea hydrolysis. PMID:20190081

  4. Plutonium Oxidation State Distribution under Aerobic and Anaerobic Subsurface Conditions for Metal-Reducing Bacteria

    NASA Astrophysics Data System (ADS)

    Reed, D. T.; Swanson, J.; Khaing, H.; Deo, R.; Rittmann, B.

    2009-12-01

    The fate and potential mobility of plutonium in the subsurface is receiving increased attention as the DOE looks to cleanup the many legacy nuclear waste sites and associated subsurface contamination. Plutonium is the near-surface contaminant of concern at several DOE sites and continues to be the contaminant of concern for the permanent disposal of nuclear waste. The mobility of plutonium is highly dependent on its redox distribution at its contamination source and along its potential migration pathways. This redox distribution is often controlled, especially in the near-surface where organic/inorganic contaminants often coexist, by the direct and indirect effects of microbial activity. The redox distribution of plutonium in the presence of facultative metal reducing bacteria (specifically Shewanella and Geobacter species) was established in a concurrent experimental and modeling study under aerobic and anaerobic conditions. Pu(VI), although relatively soluble under oxidizing conditions at near-neutral pH, does not persist under a wide range of the oxic and anoxic conditions investigated in microbiologically active systems. Pu(V) complexes, which exhibit high chemical toxicity towards microorganisms, are relatively stable under oxic conditions but are reduced by metal reducing bacteria under anaerobic conditions. These facultative metal-reducing bacteria led to the rapid reduction of higher valent plutonium to form Pu(III/IV) species depending on nature of the starting plutonium species and chelating agents present in solution. Redox cycling of these lower oxidation states is likely a critical step in the formation of pseudo colloids that may lead to long-range subsurface transport. The CCBATCH biogeochemical model is used to explain the redox mechanisms and final speciation of the plutonium oxidation state distributions observed. These results for microbiologically active systems are interpreted in the context of their importance in defining the overall migration

  5. The distribution and relative abundance of ammonia-oxidizing bacteria in lakes of the McMurdo Dry Valley, Antarctica

    USGS Publications Warehouse

    Voytek, M.A.; Priscu, J.C.; Ward, B.B.

    1999-01-01

    Marked differences in the concentrations of major ions and cations, macronutrient chemistry and general trophic status exist among the lakes of the McMurdo dry valleys in Antarctica. These differences have been attributed to both variations in stream inputs and in situ lake processes (Priscu, 1995; Lizotte et al., 1996, Spigel and Priscu, 1996). This study examines the role of nitrifying bacteria in nitrogen transformations in these lakes. Applying two polymerase chain reaction (PCR) assays targeting the 16S rRNA genes of ammonia-oxidizing bacteria and the active site of the ammonia monooxygenase gene (amoA), the distribution of ammonia-oxidizers was examined in six Antarctic lakes: Lake Bonney, Lake Hoare, Lake Fryxell and Lake Joyce in the Taylor Valley, Lake Miers in the the Miers Valley and Lake Vanda in the Wright Valley. Using a two stage amplification procedure, ammonia-oxidizers from both the beta and gamma- subclasses of the Proteobacteria were detected and their relative abundances were determined in samples collected from all sites. Ammonia-oxidizers were detected in all lakes sampled. Members of the gamma subclass were only present in the saline lakes. In general, nitrifiers were most abundant at depths above the pycnocline and were usually associated with lower concentrations of NH4 and elevated concentrations of NO3 or NO2. The distribution of nitrifiers suggests that the primary N2O peak observed in most of the lakes was produced via nitrification. Preliminary data on the rate of nitrification (Priscu et al., 1996) support the occurrence of nitrification and the presence of nitrifiers at the depth intervals where nitrifiers were detected. In all lakes, except Lake Miers, the data indicate that nitrifying bacteria have an important role in the vertical distribution of nitrogen compounds in these systems.

  6. Inhibitory Effects of C2 to C10 1-Alkynes on Ammonia Oxidation in Two Nitrososphaera Species

    PubMed Central

    Taylor, K.; Tennigkeit, B.; Palatinszky, M.; Stieglmeier, M.; Myrold, D. D.; Schleper, C.; Wagner, M.; Bottomley, P. J.

    2015-01-01

    A previous study showed that ammonia oxidation by the Thaumarchaeota Nitrosopumilus maritimus (group 1.1a) was resistant to concentrations of the C8 1-alkyne, octyne, which completely inhibits activity by ammonia-oxidizing bacteria. In this study, the inhibitory effects of octyne and other C2 to C10 1-alkynes were evaluated on the nitrite production activity of two pure culture isolates from Thaumarchaeota group 1.1b, Nitrososphaera viennensis strain EN76 and Nitrososphaera gargensis. Both N. viennensis and N. gargensis were insensitive to concentrations of octyne that cause complete and irreversible inactivation of nitrite production by ammonia-oxidizing bacteria. However, octyne concentrations (≥20 μM) that did not inhibit N. maritimus partially inhibited nitrite production in N. viennensis and N. gargensis in a manner that did not show the characteristics of irreversible inactivation. In contrast to previous studies with an ammonia-oxidizing bacterium, Nitrosomonas europaea, octyne inhibition of N. viennensis was: (i) fully and immediately reversible, (ii) not competitive with NH4+, and (iii) without effect on the competitive interaction between NH4+ and acetylene. Both N. viennensis and N. gargensis demonstrated the same overall trend in regard to 1-alkyne inhibition as previously observed for N. maritimus, being highly sensitive to ≤C5 alkynes and more resistant to longer-chain length alkynes. Reproducible differences were observed among N. maritimus, N. viennensis, and N. gargensis in regard to the extent of their resistance/sensitivity to C6 and C7 1-alkynes, which may indicate differences in the ammonia monooxygenase binding and catalytic site(s) among the Thaumarchaeota. PMID:25576608

  7. Polyclonal Antibodies Recognizing the AmoB Protein of Ammonia Oxidizers of the β-Subclass of the Class Proteobacteria

    PubMed Central

    Pinck, Claudia; Coeur, Caroline; Potier, Patrick; Bock, Eberhard

    2001-01-01

    A 41-kDa protein of Nitrosomonas eutropha was purified, and the N-terminal amino acid sequence was found to be nearly identical with the sequence of AmoB, a subunit of ammonia monooxygenase. This protein was used to develop polyclonal antibodies, which were highly specific for the detection of the four genera of ammonia oxidizers of the β-subclass of Proteobacteria (Nitrosomonas, including Nitrosococcus mobilis, which belongs phylogenetically to Nitrosomonas; Nitrosospira; Nitrosolobus; and Nitrosovibrio). In contrast, the antibodies did not react with ammonia oxidizers affiliated with the γ-subclass of Proteobacteria (Nitrosococcus oceani and Nitrosococcus halophilus). Moreover, methane oxidizers (Methylococcus capsulatus, Methylocystis parvus, and Methylomonas methanica) containing the related particulate methane monooxygenase were not detected. Quantitative immunoblot analysis revealed that total cell protein of N. eutropha consisted of approximately 6% AmoB, when cells were grown using standard conditions (mineral medium containing 10 mM ammonium). This AmoB amount was shown to depend on the ammonium concentration in the medium. About 14% AmoB of total protein was found when N. eutropha was grown with 1 mM ammonium, whereas 4% AmoB was detected when 100 mM ammonium were used. In addition, the cellular amount of AmoB was influenced by the absence of the substrate. Cells starved for more than 2 months contained nearly twice as much AmoB as actively growing cells, although these cells possessed low ammonia-oxidizing activity. AmoB was always present and could even be detected in cells of Nitrosomonas after 1 year of ammonia starvation. PMID:11133435

  8. Dynamics of ultrathin V-oxide layers on Rh(111) in catalytic oxidation of ammonia and CO.

    PubMed

    von Boehn, B; Preiss, A; Imbihl, R

    2016-07-20

    Catalytic oxidation of ammonia and CO has been studied in the 10(-4) mbar range using a catalyst prepared by depositing ultra-thin vanadium oxide layers on Rh(111) (θV ≈ 0.2 MLE). Using photoemission electron microscopy (PEEM) as a spatially resolving method, we observe that upon heating in an atmosphere of NH3 and O2 the spatial homogeneity of the VOx layer is removed at 800 K and a pattern consisting of macroscopic stripes develops; at elevated temperatures this pattern transforms into a pattern of circular VOx islands. Under reaction conditions the neighboring VOx islands become attracted by each other and coalesce. Similar processes of pattern formation and island coalescence are observed in catalytic CO oxidation. Reoxidation of the reduced VOx catalyst proceeds via surface diffusion of oxygen adsorbed onto Rh(111). A pattern consisting of macroscopic circular VOx islands can also be obtained by heating a Rh(111)/VOx catalyst in pure O2. PMID:27380822

  9. Batch culture enrichment of ANAMMOX populations from anaerobic and aerobic seed cultures.

    PubMed

    Suneethi, S; Joseph, Kurian

    2011-01-01

    Discharge of nitrate and ammonia rich wastewaters into the natural waters encourage eutrophication, and contribute to aquatic toxicity. Anaerobic ammonium oxidation process (ANAMMOX) is a novel biological nitrogen removal alternative to nitrification-denitrification, that removes ammonia using nitrite as the electron acceptor. The feasibility of enriching the ANAMMOX bacteria from the anaerobic digester sludge of a biomethanation plant treating vegetable waste and aerobic sludge from an activated sludge process treating domestic sewage is reported in this paper. ANAMMOX bacterial activity was monitored and established in terms of nitrogen transformations to ammonia, nitrite and nitrate along with formation of hydrazine and hydroxylamine. PMID:20729077

  10. Ammonia-oxidizing bacteria in a chloraminated distribution system: seasonal occurrence, distribution and disinfection resistance.

    PubMed Central

    Wolfe, R L; Lieu, N I; Izaguirre, G; Means, E G

    1990-01-01

    Nitrification in chloraminated drinking water can have a number of adverse effects on water quality, including a loss of total chlorine and ammonia-N and an increase in the concentration of heterotrophic plate count bacteria and nitrite. To understand how nitrification develops, a study was conducted to examine the factors that influence the occurrence of ammonia-oxidizing bacteria (AOB) in a chloraminated distribution system. Samples were collected over an 18-month period from a raw-water source, a conventional treatment plant effluent, and two covered, finished-water reservoirs that previously experienced nitrification episodes. Sediment and biofilm samples were collected from the interior wall surfaces of two finished-water pipelines and one of the covered reservoirs. The AOB were enumerated by a most-probable-number technique, and isolates were isolated and identified. The resistance of naturally occurring AOB to chloramines and free chlorine was also examined. The results of the monitoring program indicated that the levels of AOB, identified as members of the genus Nitrosomonas, were seasonally dependent in both source and finished waters, with the highest levels observed in the warm summer months. The concentrations of AOB in the two reservoirs, both of which have floating covers made of synthetic rubber (Hypalon; E.I. du Pont de Nemours & Co., Inc., Wilmington, Del.), had most probable numbers that ranged from less than 0.2 to greater than 300/ml and correlated significantly with temperature and levels of heterotrophic plate count bacteria. No AOB were detected in the chloraminated reservoirs when the water temperature was below 16 to 18 degrees C. The study indicated that nitrifiers occur throughout the chloraminated distribution system. Higher concentrations of AOB were found in the reservoir and pipe sediment materials than in the pipe biofilm samples. The AOB were approximately 13 times more resistant to monochloramine than to free chlorine. After 33 min

  11. Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC 19707

    SciTech Connect

    Klots, Martin G.; Arp, D J; Chain, Patrick S; El-Sheikh, Amal F.; Hauser, Loren John; Hommes, Norman G.; Larimer, Frank W; Malfatti, Stephanie; Norton, Jeanette M.; Poret-Peterson, Amisha T.; Vergez, Lisa; Ward, Bess B.

    2006-01-01

    The gammaproteobacterium Nitrosococcus oceani (ATCC 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; G+C content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. Contrary to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor, were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle, and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance, and ability to assimilate carbon via gluconeogenesis. One set of genes for type I ribulose-1,5-bisphosphate carboxylase/oxygenase was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H+-dependent F0F1 type, one Na+-dependent V type).

  12. The Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC19707

    SciTech Connect

    Klotz, M G; Arp, D J; Chain, P S; El-Sheikh, A F; Hauser, L J; Hommes, N G; Larimer, F W; Malfatti, S A; Norton, J M; Poret-Peterson, A T; Vergez, L M; Ward, B B

    2006-08-03

    The Gammaproteobacterium, Nitrosococcus oceani (ATCC 19707), is a Gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; 50.4% G+C) and a plasmid (40,420 bp) that contain 3052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. In contrast to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance and the ability to assimilate carbon via gluconeogenesis. One set of genes for type I RuBisCO was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H{sup +}-dependent F{sub 0}F{sub 1}-type, one Na{sup +}-dependent V-type).

  13. Hydrothermally synthesized Copper Oxide (CuO) superstructures for ammonia sensing.

    PubMed

    Bhuvaneshwari, S; Gopalakrishnan, N

    2016-10-15

    According to environmental protection agencies (EPA), the emission threshold of NH3 in air is 1000kg/yr which is now about 20Tg/yr. Hence, there is a rapid increase in need of NH3 sensors to timely detect and control NH3 emissions. Metal oxide nanostructures such as CuO with special features are potential candidates for NH3 sensing. In the present study, morphology controlled 3-dimensional CuO superstructures were synthesized by surfactant-free hydrothermal method for NH3 detection. In addition to conventional hydrothermal method where water as solvent, a modified approach using a mixture of water and ethylene glycol (EG) was used as solvent to control the growth process. Hierarchical superstructures namely, snowflake-like, flower-like, hollow-sphere-like and urchin-like feature with particle dimensions ranging from 0.3 to 1μm were obtained by varying water/EG ratio and reaction temperature. The synthesized nanostructures exhibited morphology dependent luminescence and gas sensing properties. The surface area and pore distribution determined by BET surface analysis also largely influenced by the presence of EG in the reaction system. The average pore diameter enhanced from 6nm to 14nm by the addition of 10ml EG as solvent. The room temperature ammonia sensing behavior of all samples was studied using an indigenous gas sensing set-up. It was found that hollow-sphere like CuO nanostructures showed a maximum sensitivity of 150% towards 600ppm ammonia with a response and recovery time of 6min. The hydrothermal synthesis strategy reported here has the advantage of producing shape controlled hierarchical materials are highly suitable for various technological applications. PMID:27416288

  14. Ammonia exposure induces oxidative stress, endoplasmic reticulum stress and apoptosis in hepatopancreas of pacific white shrimp (Litopenaeus vannamei).

    PubMed

    Liang, Zhongxiu; Liu, Rui; Zhao, Depeng; Wang, Lingling; Sun, Mingzhe; Wang, Mengqiang; Song, Linsheng

    2016-07-01

    Ammonia is one of major environmental pollutants in the aquatic system that poses a great threat to the survival of shrimp. In the present study, the mRNA expression of endoplasmic reticulum (ER) stress marker and unfolded protein response (UPR) related genes, as well as the change of redox enzyme and apoptosis were investigated in hepatopancreas of the pacific white shrimp, Litopenaeus vannamei after the exposure of 20 mg L(-1) total ammonia nitrogen (TAN). Compared with the control group, the superoxide dismutase (SOD) activity in hepatopancreas decreased significantly (p < 0.05) at 96 h, whereas the malonyldialdehyde (MDA) concentration increased significantly (p < 0.05). The mRNA expression levels of ER stress marker-immunoglobulin heavy chain binding protein (Bip) gene and key UPR related genes including activating transcription factor 4 (ATF4) and the spliced form of X box binding protein 1 (XBP1) increased significantly (p < 0.05) in hepatopancreas at 96 h after exposure to ammonia. In addition, apoptosis was observed obviously in the hepatopancreas of L. vannamei after exposure to ammonia by the terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assay. The results indicated that ammonia exposure could induce oxidative stress, which further caused ER stress and apoptosis in hepatopancreas of L. vannamei. PMID:27164997

  15. Remediation of a winery wastewater combining aerobic biological oxidation and electrochemical advanced oxidation processes.

    PubMed

    Moreira, Francisca C; Boaventura, Rui A R; Brillas, Enric; Vilar, Vítor J P

    2015-05-15

    Apart from a high biodegradable fraction consisting of organic acids, sugars and alcohols, winery wastewaters exhibit a recalcitrant fraction containing high-molecular-weight compounds as polyphenols, tannins and lignins. In this context, a winery wastewater was firstly subjected to a biological oxidation to mineralize the biodegradable fraction and afterwards an electrochemical advanced oxidation process (EAOP) was applied in order to mineralize the refractory molecules or transform them into simpler ones that can be further biodegraded. The biological oxidation led to above 97% removals of dissolved organic carbon (DOC), chemical oxygen demand (COD) and 5-day biochemical oxygen demand (BOD5), but was inefficient on the degradation of a bioresistant fraction corresponding to 130 mg L(-1) of DOC, 380 mg O2 L(-1) of COD and 8.2 mg caffeic acid equivalent L(-1) of total dissolved polyphenols. Various EAOPs such as anodic oxidation with electrogenerated H2O2 (AO-H2O2), electro-Fenton (EF), UVA photoelectro-Fenton (PEF) and solar PEF (SPEF) were then applied to the recalcitrant effluent fraction using a 2.2 L lab-scale flow plant containing an electrochemical cell equipped with a boron-doped diamond (BDD) anode and a carbon-PTFE air-diffusion cathode and coupled to a photoreactor with compound parabolic collectors (CPCs). The influence of initial Fe(2+) concentration and current density on the PEF process was evaluated. The relative oxidative ability of EAOPs increased in the order AO-H2O2 < EF < PEF ≤ SPEF. The SPEF process using an initial Fe(2+) concentration of 35 mg L(-1), current density of 25 mA cm(-2), pH of 2.8 and 25 °C reached removals of 86% on DOC and 68% on COD after 240 min, regarding the biologically treated effluent, along with energy consumptions of 45 kWh (kg DOC)(-1) and 5.1 kWh m(-3). After this coupled treatment, color, odor, COD, BOD5, NH4(+), NO3(-) and SO4(2-) parameters complied with the legislation targets and, in addition, a total

  16. Selective aerobic oxidation of HMF to 2,5-diformylfuran on covalent triazine frameworks-supported Ru catalysts.

    PubMed

    Artz, Jens; Mallmann, Sabrina; Palkovits, Regina

    2015-02-01

    The selective aerobic oxidation of 5-hydroxymethylfurfural (HMF) to 2,5-diformylfuran has been performed under mild conditions at 80 °C and 20 bar of synthetic air in methyl t-butyl ether. Ru clusters supported on covalent triazine frameworks (CTFs) allowed excellent selectivity and superior catalytic activity compared to other support materials such as activated carbon, γ-Al2 O3 , hydrotalcite, or MgO. CTFs with varying pore size, specific surface area, and N content could be prepared from different monomers. The structural properties of the CTF materials influence the catalytic activity of Ru/CTF significantly in the aerobic oxidation of HMF, which emphasizes the superior activity of mesoporous CTFs. Recycling of the catalysts is challenging, but promising methods to maintain high catalytic activity were developed that facilitate only minor deactivation in five consecutive recycling experiments. PMID:25586312

  17. [Enhanced Resistance of Pea Plants to Oxidative: Stress Caused by Paraquat during Colonization by Aerobic Methylobacteria].

    PubMed

    Agafonova, N V; Doronina, N Y; Trotsenko, Yu A

    2016-01-01

    The influence of colonization of the pea (Pisum sativum L.) by aerobic methylobacteria of five different species (Methylophilus flavus Ship, Methylobacterium extorquens G10, Methylobacillus arboreus Iva, Methylopila musalis MUSA, Methylopila turkiensis Sidel) on plant resistance to paraquat-induced stresses has been studied. The normal conditions of pea colonization by methylobacteria were characterized by a decrease in the activity of antioxidant enzymes (superoxide dismutase, catalase, and peroxidases) and in the concentrations of endogenous H2O2, proline, and malonic dialdehyde, which is a product of lipid peroxidation and indicator of damage to plant cell membranes, and an increase in the activity of the photosynthetic apparatus (the content of chlorophylls a, b and carotenoids). In the presence of paraquat, the colonized plants had higher activities of antioxidant enzymes, stable photosynthetic indices, and a less intensive accumulation of the products of lipid peroxidation as compared to noncolonized plants. Thus, colonization by methylobacteria considerably increased the adaptive protection of pea plants to the paraquat-induced oxidative stress. PMID:27266250

  18. Central release of nitric oxide mediates antinociception induced by aerobic exercise.

    PubMed

    Galdino, G S; Duarte, I D; Perez, A C

    2015-09-01

    Nitric oxide (NO) is a soluble gas that participates in important functions of the central nervous system, such as cognitive function, maintenance of synaptic plasticity for the control of sleep, appetite, body temperature, neurosecretion, and antinociception. Furthermore, during exercise large amounts of NO are released that contribute to maintaining body homeostasis. Besides NO production, physical exercise has been shown to induce antinociception. Thus, the present study aimed to investigate the central involvement of NO in exercise-induced antinociception. In both mechanical and thermal nociceptive tests, central [intrathecal (it) and intracerebroventricular (icv)] pretreatment with inhibitors of the NO/cGMP/KATP pathway (L-NOArg, ODQ, and glybenclamide) prevented the antinociceptive effect induced by aerobic exercise (AE). Furthermore, pretreatment (it, icv) with specific NO synthase inhibitors (L-NIO, aminoguanidine, and L-NPA) also prevented this effect. Supporting the hypothesis of the central involvement of NO in exercise-induced antinociception, nitrite levels in the cerebrospinal fluid increased immediately after AE. Therefore, the present study suggests that, during exercise, the NO released centrally induced antinociception. PMID:25517916

  19. Rh- and Cu-Cocatalyzed Aerobic Oxidative Approach to Quinazolines via [4 + 2] C-H Annulation with Alkyl Azides.

    PubMed

    Wang, Xiaoyang; Jiao, Ning

    2016-05-01

    A novel and efficient rhodium- and copper-co-catalyzed C-H bond activation and annulation for the construction of bioactively important quinazolines has been developed. This [4 + 2] annulation strategy utilizing alkyl azides as the carbon-heteroatom synthons shows high efficiency in the synthesis of six-membered benzoheterocycles containing two heteroatoms. This aerobic oxidative protocol provides a useful application of simple alkyl azides in N-heterocycle synthesis with N2 and H2O as byproducts. PMID:27081916

  20. TEMPO-catalyzed aerobic oxidation of alcohols to aldehydes and ketones in ionic liquid [bmim][PF6].

    PubMed

    Ansari, Imtiaz A; Gree, Rene

    2002-05-01

    [reaction: see text]. A simple and mild TEMPO-CuCl catalyzed aerobic oxidation of primary and secondary alcohols to the corresponding aldehydes and ketones in ionic liquid [bmim][PF6] with no trace of overoxidation to carboxylic acids has been developed. The product can be isolated by a simple extraction with organic solvent, and the ionic liquid can be recycled or reused. PMID:11975615

  1. Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm.

    PubMed

    Foesel, Bärbel U; Gieseke, Armin; Schwermer, Carsten; Stief, Peter; Koch, Liat; Cytryn, Eddie; de la Torré, José R; van Rijn, Jaap; Minz, Dror; Drake, Harold L; Schramm, Andreas

    2008-02-01

    Zero-discharge marine aquaculture systems are an environmentally friendly alternative to conventional aquaculture. In these systems, water is purified and recycled via microbial biofilters. Here, quantitative data on nitrifier community structure of a trickling filter biofilm associated with a recirculating marine aquaculture system are presented. Repeated rounds of the full-cycle rRNA approach were necessary to optimize DNA extraction and the probe set for FISH to obtain a reliable and comprehensive picture of the ammonia-oxidizing community. Analysis of the ammonia monooxygenase gene (amoA) confirmed the results. The most abundant ammonia-oxidizing bacteria (AOB) were members of the Nitrosomonas sp. Nm143-lineage (6.7% of the bacterial biovolume), followed by Nitrosomonas marina-like AOB (2.2% of the bacterial biovolume). Both were outnumbered by nitrite-oxidizing bacteria of the Nitrospira marina-lineage (15.7% of the bacterial biovolume). Although more than eight other nitrifying populations were detected, including Crenarchaeota closely related to the ammonia-oxidizer 'Nitrosopumilus maritimus', their collective abundance was below 1% of the total biofilm volume; their contribution to nitrification in the biofilter is therefore likely to be negligible. PMID:18093145

  2. Microstructure and electrical-optical properties of cesium tungsten oxides synthesized by solvothermal reaction followed by ammonia annealing

    SciTech Connect

    Liu Jingxiao; Ando, Yoshihiko; Dong Xiaoli; Shi Fei; Yin Shu; Adachi, Kenji; Chonan, Takeshi; Tanaka, Akikazu; Sato, Tsugio

    2010-10-15

    Cesium tungsten oxides (Cs{sub x}WO{sub 3}) were synthesized by solvothermal reactions using ethanol and 57.1 vol% ethanol aqueous solution at 200 {sup o}C for 12 h, and the effects of post annealing in ammonia atmosphere on the microstructure and electrical-optical properties were investigated. Agglomerated particles consisting of disk-like nanoparticles and nanorods of Cs{sub x}WO{sub 3} were formed in the pure ethanol and ethanol aqueous solutions, respectively. The samples retained the original morphology and crystallinity after annealing in ammonia atmosphere up to 500 {sup o}C, while a small amount of nitrogen ion were incorporated in the lattice. The as-prepared Cs{sub x}WO{sub 3} sample showed excellent near infrared (NIR) light shielding ability as well as high transparency in the visible light region. The electrical resistivity of the pressed pellets of the powders prepared in pure ethanol and 57.1 vol% ethanol aqueous solution greatly decreased after ammonia annealing at 500 {sup o}C, i.e., from 734 to 31.5 and 231 to 3.58 {Omega} cm, respectively. - Graphical abstract: Cesium tungsten oxides (Cs{sub x}WO{sub 3}) with different morphology were synthesized by solvothermal reaction, and the effects of post-ammonia annealing on the microstructure and electrical-optical properties were investigated.

  3. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations.

    PubMed

    Rotthauwe, J H; Witzel, K P; Liesack, W

    1997-12-01

    The naturally occurring genetic heterogeneity of autotrophic ammonia-oxidizing populations belonging to the beta subclass of the Proteobacteria was studied by using a newly developed PCR-based assay targeting a partial stretch of the gene which encodes the active-site polypeptide of ammonia monooxygenase (amoA). The PCR yielded a specific 491-bp fragment with all of the nitrifiers tested, but not with the homologous stretch of the particulate methane monooxygenase, a key enzyme of methane-oxidizing bacteria. The assay also specifically detected amoA in DNA extracted from various aquatic and terrestrial environments. The resulting PCR products retrieved from rice roots, activated sludge, a freshwater sample, and an enrichment culture were used for the generation of amoA gene libraries. No false positives were detected in a set of 47 randomly selected clone sequences that were analyzed further. The majority of the environmental sequences retrieved from rice roots and activated sludge grouped within the phylogenetic radiation defined by cultured strains of the genera Nitrosomonas and Nitrosospira. The comparative analysis identified members of both of these genera in activated sludge; however, only Nitrosospira-like sequences with very similar amino acid patterns were found on rice roots. Further differentiation of these molecular isolates was clearly possible on the nucleic acid level due to the accumulation of synonymous mutations, suggesting that several closely related but distinct Nitrosospira-like populations are the main colonizers of the rhizosphere of rice. Each of the amoA gene libraries obtained from the freshwater sample and the enrichment culture was dominated by a novel lineage that shared a branch with the Nitrosospira cluster but could not be assigned to any of the known pure cultures. Our data suggest that amoA represents a very powerful molecular tool for analyzing indigenous ammonia-oxidizing communities due to (i) its specificity, (ii) its fine

  4. Ammonia toxicity induces glutamine accumulation, oxidative stress and immunosuppression in juvenile yellow catfish Pelteobagrus fulvidraco.

    PubMed

    Li, Ming; Gong, Shiyan; Li, Qing; Yuan, Lixia; Meng, Fanxing; Wang, Rixin

    2016-01-01

    A study was carried to test the response of yellow catfish for 28days under two ammonia concentrations. Weight gain of fish exposure to high and low ammonia abruptly increased at day 3. There were no significant changes in fish physiological indexes and immune responses at different times during 28-day exposure to low ammonia. Fish physiological indexes and immune responses in the treatment of high ammonia were lower than those of fish in the treatment of low ammonia. When fish were exposed to high ammonia, the ammonia concentration in the brain increased by 19-fold on day 1. By comparison, liver ammonia concentration reached its highest level much earlier at hour 12. In spite of a significant increase in brain and liver glutamine concentration, there was no significant change in glutamate level throughout the 28-day period. The total superoxide dismutase (SOD), glutathione peroxidase (GPX) and glutathione reductase (GR) activities in the brain gradually decreased from hour 0 to day 28. Liver SOD, GPX and GR activities reached the highest levels at hour 12, and then gradually decreased. Thiobarbituric acid reactive substance brain and liver content gradually increased throughout the 28-day period. Lysozyme, acid phosphatase and alkaline phosphatase activities in the liver reached exceptionally low levels after day 14. This study indicated that glutamine accumulation in the brain was not the major cause of ammonia poisoning, the toxic reactive oxygen species is not fully counter acted by the antioxidant enzymes and immunosuppression is a process of gradual accumulation of immunosuppressive factors. PMID:26811908

  5. Differential responses of ammonia/ammonium-oxidizing microorganisms in mangrove sediment to amendment of acetate and leaf litter.

    PubMed

    Wang, Yong-Feng; Li, Xiao-Yan; Gu, Ji-Dong

    2014-04-01

    The effects of acetate and leaf litter powder on ammonia/ammonium-oxidizing microorganisms (AOMs) in mangrove sediment were investigated in a laboratory incubation study for a period of 60 days. The results showed that different AOMs responded differently to the addition of acetate and leaf litter. A higher diversity of anaerobic ammonium-oxidizing (anammox) bacteria was observed when acetate or leaf litter was added than the control. However, acetate and leaf litter generally inhibited the growth of anammox bacteria despite that leaf litter promoted their growth in the first 5 days. The inhibitory effects on anammox bacteria were more pronounced by acetate than by leaf litter. Neither acetate nor leaf litter affected ammonia-oxidizing archaea (AOA) community structures, but promoted their growth. For ammonia-oxidizing bacteria (AOB), the addition of acetate or leaf litter resulted in changes of community structures and promoted their growth in the early phase of the incubation. In addition, the promoting effects by leaf litter on AOB growth were more obvious than acetate. These results indicated that organic substances affect AOM community structures and abundances. The study suggests that leaf litter has an important influence on the community structures and abundances of AOMs in mangrove sediment and affects the nitrogen cycle in such ecosystem. PMID:24169949

  6. Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil

    PubMed Central

    Soares, Johnny R.; Cassman, Noriko A.; Kielak, Anna M.; Pijl, Agata; Carmo, Janaína B.; Lourenço, Kesia S.; Laanbroek, Hendrikus J.; Cantarella, Heitor; Kuramae, Eiko E.

    2016-01-01

    Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4+-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane. PMID:27460335

  7. Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil.

    PubMed

    Soares, Johnny R; Cassman, Noriko A; Kielak, Anna M; Pijl, Agata; Carmo, Janaína B; Lourenço, Kesia S; Laanbroek, Hendrikus J; Cantarella, Heitor; Kuramae, Eiko E

    2016-01-01

    Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4(+)-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane. PMID:27460335

  8. Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil

    NASA Astrophysics Data System (ADS)

    Soares, Johnny R.; Cassman, Noriko A.; Kielak, Anna M.; Pijl, Agata; Carmo, Janaína B.; Lourenço, Kesia S.; Laanbroek, Hendrikus J.; Cantarella, Heitor; Kuramae, Eiko E.

    2016-07-01

    Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4+-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane.

  9. Diversity of Ammonia-Oxidizing Archaea and Bacteria Across Physical-Chemical Gradients in San Francisco Bay Estuary Sediments

    NASA Astrophysics Data System (ADS)

    Mosier, A. C.; Francis, C. A.

    2006-12-01

    A combination of recent metagenomic analyses and the cultivation of a novel, ammonia-oxidizing, marine crenarchaeota revealed the first evidence for nitrification within the Archaeal domain. Further genetic and metagenomic studies demonstrated the presence of ammonia-oxidizing crenarchaea in diverse marine and terrestrial environments. These discoveries challenge the currently accepted view of the global nitrogen cycle and validate the need for further research on microbial diversity and function. In particular, it is imperative to reexamine the microbial communities involved in ammonia oxidation in marine and estuarine sediments, where this process plays a pivotal role in the cycling and removal of nitrogen. Using phylogenetic analyses of ammonia monooxygenase subunit A (amoA) gene sequences, we examined the distribution and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in San Francisco Bay, the largest estuary on the West coast of the United States. The highly impacted bay, encompassing nearly 178,000 km2, effectively connects two estuaries with varying physical-chemical characteristics to the Pacific Ocean. We recovered archaeal and bacterial amoA genes from 11 sites distributed throughout the bay, spanning the northern and southern estuaries and the central region where they connect to the ocean. Richness estimates varied considerably across all sites examined, with archaeal amoA estimates being generally higher than bacterial amoA. Several of the bacterial amoA libraries were represented by fewer than 3 genotypes. Archaeal amoA sequences were phylogenetically diverse and grouped within previously described sediment and soil/sediment clusters. Several sequences were closely related to the only cultivated AOA, Nitrosopumilus maritimus. Both the archaeal and bacterial amoA sequences showed significant regional specificity. Distinct populations exist in the northern and southern estuaries and sequences from the northernmost and southernmost sites

  10. Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea.

    PubMed

    Lösekann, Tina; Knittel, Katrin; Nadalig, Thierry; Fuchs, Bernhard; Niemann, Helge; Boetius, Antje; Amann, Rudolf

    2007-05-01

    Submarine mud volcanoes are formed by expulsions of mud, fluids, and gases from deeply buried subsurface sources. They are highly reduced benthic habitats and often associated with intensive methane seepage. In this study, the microbial diversity and community structure in methane-rich sediments of the Haakon Mosby Mud Volcano (HMMV) were investigated by comparative sequence analysis of 16S rRNA genes and fluorescence in situ hybridization. In the active volcano center, which has a diameter of about 500 m, the main methane-consuming process was bacterial aerobic oxidation. In this zone, aerobic methanotrophs belonging to three bacterial clades closely affiliated with Methylobacter and Methylophaga species accounted for 56%+/-8% of total cells. In sediments below Beggiatoa mats encircling the center of the HMMV, methanotrophic archaea of the ANME-3 clade dominated the zone of anaerobic methane oxidation. ANME-3 archaea form cell aggregates mostly associated with sulfate-reducing bacteria of the Desulfobulbus (DBB) branch. These ANME-3/DBB aggregates were highly abundant and accounted for up to 94%+/-2% of total microbial biomass at 2 to 3 cm below the surface. ANME-3/DBB aggregates could be further enriched by flow cytometry to identify their phylogenetic relationships. At the outer rim of the mud volcano, the seafloor was colonized by tubeworms (Siboglinidae, formerly known as Pogonophora). Here, both aerobic and anaerobic methane oxidizers were found, however, in lower abundances. The level of microbial diversity at this site was higher than that at the central and Beggiatoa species-covered part of the HMMV. Analysis of methyl-coenzyme M-reductase alpha subunit (mcrA) genes showed a strong dominance of a novel lineage, mcrA group f, which could be assigned to ANME-3 archaea. Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and

  11. Unexpected copper-catalyzed aerobic oxidative cleavage of C(sp3)-C(sp3) bond of glycol ethers.

    PubMed

    Liu, Zhong-Quan; Zhao, Lixing; Shang, Xiaojie; Cui, Zili

    2012-06-15

    An unexpected Cu-catalyzed oxidative cleavage of the C(sp(3))-C(sp(3)) bond in glycol ethers by using air or molecular oxygen as the terminal stoichiometric oxidant is demonstrated. As a result, the corresponding α-acyloxy ethers and formates of 1,2-ethanediol are formed by direct coupling of carboxylic acids and aldehydes with glycol ethers under the reaction conditions. This method represents the first example of Cu-catalyzed aerobic cleavage of saturated C-C bond in ethers. PMID:22668348

  12. Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils.

    PubMed

    Ramond, Jean-Baptiste; Lako, Joseph D W; Stafford, William H L; Tuffin, Marla I; Cowan, Don A

    2015-08-01

    Ammonia-oxidizing bacteria (AOB) are essential in the biogeochemical cycling of nitrogen as they catalyze the rate-limiting oxidation of ammonia into nitrite. Since their first isolation in the late 19th century, chemolithoautotrophic AOBs have been identified in a wide range of natural (e.g., soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g., wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs, particularly in the nutrient-starved fynbos terrestrial biome. In this study, we evaluated the diversity of AOBs in the plant canopy of three South African fynbos-specific plant species, namely Leucadendron xanthoconus, Leucospermum truncatulum and Leucadendron microcephalum, through the construction of amoA-gene clone libraries. Our results clearly demonstrate that plant-species specific and monophyletic AOB clades are present in fynbos canopy soils. PMID:25721729

  13. Acclimatization of communities of ammonia oxidizing bacteria to seasonal changes in optimal conditions in a coke wastewater treatment plant.

    PubMed

    Kim, Young Mo

    2013-11-01

    The goal of this study was to investigate the correlation between optimal conditions of ammonia oxidation rates (AORs) and communities of ammonia oxidizing bacteria (AOB) adapting to seasonal changes in a full-scale wastewater treatment plant (WWTP). The optimal temperature and pH of specific AORs reflected seasonal variation patterns, showing the lowest values during the cold season, while the highest values in the warm season. Throughout the study period, Nitrosomonas europaea/eutropha and Nitrosomonas nitrosa remained the dominant AOB, indicating resistance to the influences of a changing environment. These results show that the optimal conditions for AOR can be adjusted to accommodate changing environmental conditions, relying on the acclimatization of a stable AOB community to given conditions, without any visible shift in the AOB community. PMID:24001689

  14. OXIDES OF NITROGEN/AMMONIA CONTROL TECHNOLOGY FOR OIL SHALE RETORT EMISSIONS

    EPA Science Inventory

    The retorting of oil shale yields several undesirable pollutants. The nitrogen in the shale and the reducing conditions under which the retorting is carried out results in the formation of sizeable amounts of ammonia in the gas stream. If not removed, the ammonia will make a sign...

  15. Rapid and dissimilar response of ammonia oxidizing archaea and bacteria to nitrogen and water amendment in two temperate forest soils.

    PubMed

    Szukics, Ute; Hackl, Evelyn; Zechmeister-Boltenstern, Sophie; Sessitsch, Angela

    2012-01-20

    Biochemical processes relevant to soil nitrogen (N) cycling are performed by soil microorganisms affiliated with diverse phylogenetic groups. For example, the oxidation of ammonia, representing the first step of nitrification, can be performed by ammonia oxidizing bacteria (AOB) and, as recently reported, also by ammonia oxidizing archaea (AOA). However, the contribution to ammonia oxidation of the phylogenetically separated AOA versus AOB and their respective responsiveness to environmental factors are still poorly understood. The present study aims at comparing the capacity of AOA and AOB to momentarily respond to N input and increased soil moisture in two contrasting forest soils. Soils from the pristine Rothwald forest and the managed Schottenwald forest were amended with either NH(4)(+)-N or NO(3)(-)-N and were incubated at 40% and 70% water-filled pore space (WFPS) for four days. Nitrification rates were measured and AOA and AOB abundance and community composition were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP) analysis of bacterial and archaeal amoA genes. Our study reports rapid and distinct changes in AOA and AOB abundances in the two forest soils in response to N input and increased soil moisture but no significant effects on net nitrification rates. Functional microbial communities differed significantly in the two soils and responded specifically to the treatments during the short-term incubation. In the Rothwald soil the abundance and community composition of AOA were affected by the water content, whereas AOB communities responded to N amendment. In the Schottenwald soil, by contrast, AOA responded to N addition. These results suggest that AOA and AOB may be selectively influenced by soil and management factors. PMID:21632226

  16. Nitrous oxide (N2O) emissions from biotrickling filters used for ammonia removal at livestock facilities.

    PubMed

    Melse, Roland W; Mosquera, Julio

    2014-01-01

    Recently several manufacturers of nitrifying biotrickling filters for ammonia (NH3) removal at animal houses have started to add a denitrification step to the installation, aiming to reduce the amount of discharge water by conversion of NH3 to nitrogen gas (N2). The aim of this research was to quantify the possible formation of nitrous oxide (N2O), which is a potent greenhouse gas, in three of these farm-scale installations. Furthermore, the removal efficiency of NH3 and odor was determined. All installations were successful in reducing the amount of discharge water. The average NH3 removal efficiency for the three locations was 85, 71 and 86%, respectively. However, a significant part of the NH3 removed from the inlet air was not converted to N2 but to N2O, which is a potent greenhouse gas. The part of the inlet NH3-N that was converted to N2O-N amounted to 17, 66 and 24%, respectively. The high N2O production might have been caused by a too low scarcity of biodegradable carbon/N ratio for complete denitrification. The average odor removal efficiency was 21, 32 and 48%, respectively. Further research is necessary to explore how process conditions can be adjusted and controlled in order to reduce the production and emission of N2O from these types of systems. PMID:24622548

  17. Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments.

    PubMed

    Park, Soo-Je; Ghai, Rohit; Martín-Cuadrado, Ana-Belén; Rodríguez-Valera, Francisco; Chung, Won-Hyong; Kwon, KaeKyoung; Lee, Jung-Hyun; Madsen, Eugene L; Rhee, Sung-Keun

    2014-01-01

    Ammonia-oxidizing archaea (AOA) are ubiquitous and abundant and contribute significantly to the carbon and nitrogen cycles in the ocean. In this study, we assembled AOA draft genomes from two deep marine sediments from Donghae, South Korea, and Svalbard, Arctic region, by sequencing the enriched metagenomes. Three major microorganism clusters belonging to Thaumarchaeota, Epsilonproteobacteria, and Gammaproteobacteria were deduced from their 16S rRNA genes, GC contents, and oligonucleotide frequencies. Three archaeal genomes were identified, two of which were distinct and were designated Ca. "Nitrosopumilus koreensis" AR1 and "Nitrosopumilus sediminis" AR2. AR1 and AR2 exhibited average nucleotide identities of 85.2% and 79.5% to N. maritimus, respectively. The AR1 and AR2 genomes contained genes pertaining to energy metabolism and carbon fixation as conserved in other AOA, but, conversely, had fewer heme-containing proteins and more copper-containing proteins than other AOA. Most of the distinctive AR1 and AR2 genes were located in genomic islands (GIs) that were not present in other AOA genomes or in a reference water-column metagenome from the Sargasso Sea. A putative gene cluster involved in urea utilization was found in the AR2 genome, but not the AR1 genome, suggesting niche specialization in marine AOA. Co-cultured bacterial genome analysis suggested that bacterial sulfur and nitrogen metabolism could be involved in interactions with AOA. Our results provide fundamental information concerning the metabolic potential of deep marine sedimentary AOA. PMID:24798206

  18. Gold and silver nanoparticle effects on ammonia-oxidizing bacteria cultures under ammoxidation.

    PubMed

    Luo, Zhuanxi; Chen, Zheng; Qiu, Zhaozheng; Li, Yancai; Laing, Gijs Du; Liu, Aifen; Yan, Changzhou

    2015-02-01

    Owing to their wide application in industry and manufacturing, understanding the environmental safety of gold (Au) and silver (Ag) nanoparticles entering aquatic environment is a global issue of concern. For this study, ammonia-oxidizing bacteria (AOB) enrichment cultures reproduced from surface sediments taken from the Jiulong River estuary wetlands (Fujian Province, China) were spiked with nano-Ag and nano-Au to determine their impact on ammoxidation and the mechanisms involved in the process. Results showed that nano-Ag significantly inhibited bacterial ammoxidation in aquatic environment, with the average ammoxidation rate decreasing with increasing nano-Ag concentration. The average ammoxidation rate was significantly correlated to the Shannon index, the Simpson index, and AOB abundance. This suggested that ammoxidation inhibition resulted primarily from AOB biodiversity and abundance reduction, caused by the antibacterial property of nano-Ag. However, AOB biodiversity and abundance as well as bacterial ammoxidation were not inhibited by nano-Au (with a maximum experimental concentration of 2 mg L(-1)). Moreover, an insignificant correlation was found between AOB biodiversity and abundance and the average ammoxidation rate under the nano-Au treatment. Given that ammoxidation is regarded as a rate-limiting procedure in nitrogen (N) circulation, nano-Ag would affect N cycling but nano-Au would not after entering aquatic environments. Identified nano-Ag and nano-Au impacts on ammonium nitrogen transformation could be generalized in aquatic environment according to their extensive representation in the phylogenetic tree. PMID:24559932

  19. The role of ammonia oxide in the reaction of hydroxylamine with carboxylic esters.

    PubMed

    Silva, Carlos M; Dias, Isabela C; Pliego, Josefredo R

    2015-06-14

    Theoretical calculations indicate that hydroxylamine can exist in both neutral and zwitterionic (ammonia oxide) forms in aqueous solution, the former being 3.5 kcal mol(-1) more stable. In this report, we have studied the reaction mechanism of hydroxylamine with phenyl acetate and analyzed the role of the zwitterionic isomer. We have observed that the main reaction pathway takes place through the zwitterionic form with a concerted mechanism, not involving the classical tetrahedral intermediate. Attack by the nitrogen atom (via neutral isomer) has a minor contribution and it is also a concerted process. The activation free energy barriers in aqueous solution were calculated at the MP4/TZVPP + diff level for gas phase energies, CPCM for optimization and frequencies, and through single point calculation of the solvation free energy using the SM8 method. Our theoretically predicted barriers are 20.8 and 23.8 kcal mol(-1) for O and N attack, respectively, in very good agreement with the experimental values of 20.4 and 22.3 kcal mol(-1), respectively. Our results support the view that hydroxylamine is a very special nucleophile and the reactivity of this functional group should be further investigated. PMID:25960004

  20. Temperature Responses of Ammonia-Oxidizing Prokaryotes in Freshwater Sediment Microcosms

    PubMed Central

    Yu, Zhongbo; Huang, Rui; Wu, Qinglong L.

    2014-01-01

    In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups. PMID:24959960

  1. Temperature responses of ammonia-oxidizing prokaryotes in freshwater sediment microcosms.

    PubMed

    Zeng, Jin; Zhao, Dayong; Yu, Zhongbo; Huang, Rui; Wu, Qinglong L

    2014-01-01

    In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups. PMID:24959960

  2. High-Potential Electrocatalytic O2 Reduction with Nitroxyl / NOx Mediators: Implications for Fuel Cells and Aerobic Oxidation Catalysis

    SciTech Connect

    Gerken, James B.; Stahl, Shannon S.

    2015-07-15

    Efficient reduction of O2 to water is a central challenge in energy conversion and aerobic oxidation catalysis. In the present study, we investigate the electrochemical reduction of O2 with soluble organic nitroxyl and nitrogen oxide (NOx) mediators. When used alone, neither organic nitroxyls, such as TEMPO (2,2,6,6-tetramethyl-1-piperidinyl-N-oxyl), nor NOx species, such as sodium nitrite, are effective mediators of electrochemical O2 reduction. The combination of nitroxyl/NOx species, however, mediates sustained O2 reduction at electrochemical potentials of 0.19–0.33 V (vs. Fc/Fc+) in acetonitrile containing trifluoroacetic acid. Mechanistic analysis of the coupled redox reactions supports a process in which the nitrogen oxide catalyst drives aerobic oxidation of a nitroxyl mediator to an oxoammonium species, which then is reduced back to the nitroxyl at the cathode. The electrolysis potential is dictated by the oxoammonium/nitroxyl reduction potential. The high potentials observed with this ORR system benefit from the mechanism-based specificity for four-electron reduction of oxygen to water mediated by NOx species, together with kinetically efficient reduction of oxidized NOx species by TEMPO and other organic nitroxyls. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center, funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.

  3. High-Potential Electrocatalytic O2 Reduction with Nitroxyl/NOx Mediators: Implications for Fuel Cells and Aerobic Oxidation Catalysis

    PubMed Central

    2015-01-01

    Efficient reduction of O2 to water is a central challenge in energy conversion and many aerobic oxidation reactions. Here, we show that the electrochemical oxygen reduction reaction (ORR) can be achieved at high potentials by using soluble organic nitroxyl and nitrogen oxide (NOx) mediators. When used alone, neither organic nitroxyls, such as 2,2,6,6-tetramethyl-1-piperidinyl-N-oxyl (TEMPO), nor NOx species, such as sodium nitrite, are effective ORR mediators. The combination of nitroxyl/NOx species, however, mediates sustained O2 reduction with overpotentials as low as 300 mV in acetonitrile containing trifluoroacetic acid. Mechanistic analysis of the coupled redox reactions supports a process in which the nitrogen oxide catalyst drives aerobic oxidation of a nitroxyl mediator to an oxoammonium species, which then is reduced back to the nitroxyl at the cathode. The electrolysis potential is dictated by the oxoammonium/nitroxyl reduction potential. The overpotentials accessible with this ORR system are significantly lower than widely studied molecular metal-macrocycle ORR catalysts and benefit from the mechanism-based specificity for four-electron reduction of oxygen to water mediated by NOx species, together with kinetically efficient reduction of oxidized NOx species by TEMPO and other organic nitroxyls. PMID:27162977

  4. Revision of N2O-producing pathways in the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC 19718.

    PubMed

    Kozlowski, Jessica A; Price, Jennifer; Stein, Lisa Y

    2014-08-01

    Nitrite reductase (NirK) and nitric oxide reductase (NorB) have long been thought to play an essential role in nitrous oxide (N2O) production by ammonia-oxidizing bacteria. However, essential gaps remain in our understanding of how and when NirK and NorB are active and functional, putting into question their precise roles in N2O production by ammonia oxidizers. The growth phenotypes of the Nitrosomonas europaea ATCC 19718 wild-type and mutant strains deficient in expression of NirK, NorB, and both gene products were compared under atmospheric and reduced O2 tensions. Anoxic resting-cell assays and instantaneous nitrite (NO2 (-)) reduction experiments were done to assess the ability of the wild-type and mutant N. europaea strains to produce N2O through the nitrifier denitrification pathway. Results confirmed the role of NirK for efficient substrate oxidation of N. europaea and showed that NorB is involved in N2O production during growth at both atmospheric and reduced O2 tensions. Anoxic resting-cell assays and measurements of instantaneous NO2 (-) reduction using hydrazine as an electron donor revealed that an alternate nitrite reductase to NirK is present and active. These experiments also clearly demonstrated that NorB was the sole nitric oxide reductase for nitrifier denitrification. The results of this study expand the enzymology for nitrogen metabolism and N2O production by N. europaea and will be useful to interpret pathways in other ammonia oxidizers that lack NirK and/or NorB genes. PMID:24907318

  5. Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions

    PubMed Central

    Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

    2014-01-01

    Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. PMID:24245852

  6. Six weeks of aerobic dance exercise improves blood oxidative stress status and increases interleukin-2 in previously sedentary women.

    PubMed

    Leelarungrayub, Donrawee; Saidee, Kunteera; Pothongsunun, Prapas; Pratanaphon, Sainetee; YanKai, Araya; Bloomer, Richard J

    2011-07-01

    This study evaluated the change in blood oxidative stress, blood interleukin-2, and physical performance following 6 weeks of moderate intensity and duration aerobic dance exercise in 24 sedentary women. Blood samples were collected at rest twice before (baseline) and after the 6-week intervention for analysis of protein hydroperoxide (PrOOH), malondialdehyde (MDA), total anti-oxidant capacity (TAC), and interleukin-2 (IL-2) levels. Maximal treadmill run time (Time(max)) and maximal oxygen consumption (VO(2max)) were also measured. All variables were statistically analyzed with a repeated measurement ANOVA and Tukey post hoc. No differences were noted in any variable during the baseline period (p > 0.05). After aerobic dance exercise, VO(2max), Time(max), TAC and IL-2 were significantly increased, whereas MDA levels were decreased significantly (p < 0.05). PrOOH did not change either between baseline measures or after exercise. It can be concluded that aerobic dance exercise at a moderate intensity and duration can improve physical fitness, decrease MDA, and increase TAC and IL-2 in previously sedentary women. PMID:21665113

  7. High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations.

    PubMed

    Zhang, Yu; Tian, Zhe; Liu, Miaomiao; Shi, Zhou Jason; Hale, Lauren; Zhou, Jizhong; Yang, Min

    2015-08-01

    To evaluate the potential effects of antibiotics on ammonia-oxidizing microbes, multiple tools including quantitative PCR (qPCR), 454-pyrosequencing, and a high-throughput functional gene array (GeoChip) were used to reveal the distribution of ammonia-oxidizing archaea (AOA) and archaeal amoA (Arch-amoA) genes in three wastewater treatment systems receiving spiramycin or oxytetracycline production wastewaters. The qPCR results revealed that the copy number ratios of Arch-amoA to ammonia-oxidizing bacteria (AOB) amoA genes were the highest in the spiramycin full-scale (5.30) and pilot-scale systems (1.49 × 10(-1)), followed by the oxytetracycline system (4.90 × 10(-4)), with no Arch-amoA genes detected in the control systems treating sewage or inosine production wastewater. The pyrosequencing result showed that the relative abundance of AOA affiliated with Thaumarchaeota accounted for 78.5-99.6% of total archaea in the two spiramycin systems, which was in accordance with the qPCR results. Mantel test based on GeoChip data showed that Arch-amoA gene signal intensity correlated with the presence of spiramycin (P < 0.05). Antibiotics explained 25.8% of variations in amoA functional gene structures by variance partitioning analysis. This study revealed the selection of AOA in the presence of high concentrations of spiramycin in activated sludge systems. PMID:26125322

  8. Spatial distribution and factors shaping the niche segregation of ammonia-oxidizing microorganisms in the Qiantang River, China.

    PubMed

    Liu, Shuai; Shen, Lidong; Lou, Liping; Tian, Guangming; Zheng, Ping; Hu, Baolan

    2013-07-01

    Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, the current knowledge of the distribution, diversity, and relative abundance of these two microbial groups in freshwater sediments is insufficient. We examined the spatial distribution and analyzed the possible factors leading to the niche segregation of AOA and AOB in the sediments of the Qiantang River, using clone library construction and quantitative PCR for both archaeal and bacterial amoA genes. pH and NH4(+)-N content had a significant effect on AOA abundance and AOA operational taxonomy unit (OTU) numbers. pH and organic carbon content influenced the ratio of AOA/AOB OTU numbers significantly. The influence of these factors showed an obvious spatial trend along the Qiantang River. This result suggested that AOA may contribute more than AOB to the upstream reaches of the Qiantang River, where the pH is lower and the organic carbon and NH4(+)-N contents are higher, but AOB were the principal driver of nitrification downstream, where the opposite environmental conditions were present. PMID:23624482

  9. Effects of lignite application on ammonia and nitrous oxide emissions from cattle pens.

    PubMed

    Sun, Jianlei; Bai, Mei; Shen, Jianlin; Griffith, David W T; Denmead, Owen T; Hill, Julian; Lam, Shu Kee; Mosier, Arvin R; Chen, Deli

    2016-09-15

    Beef cattle feedlots are a major source of ammonia (NH3) emissions from livestock industries. We investigated the effects of lignite surface applications on NH3 and nitrous oxide (N2O) emissions from beef cattle feedlot pens. Two rates of lignite, 3 and 6kgm(-2), were tested in the treatment pen. No lignite was applied in the control pen. Twenty-four Black Angus steers were fed identical commercial rations in each pen. We measured NH3 and N2O concentrations continuously from 4th Sep to 13th Nov 2014 using Quantum Cascade Laser (QCL) NH3 analysers and a closed-path Fourier Transform Infrared Spectroscopy analyser (CP-FTIR) in conjunction with the integrated horizontal flux method to calculate NH3 and N2O fluxes. During the feeding period, 16 and 26% of the excreted nitrogen (N) (240gNhead(-1)day(-1)) was lost via NH3 volatilization from the control pen, while lignite application decreased NH3 volatilization to 12 and 18% of the excreted N, for Phase 1 and Phase 2, respectively. Compared to the control pen, lignite application decreased NH3 emissions by approximately 30%. Nitrous oxide emissions from the cattle pens were small, 0.10 and 0.14gN2O-Nhead(-1)day(-1) (<0.1% of excreted N) for the control pen, for Phase 1 and Phase 2, respectively. Lignite application increased direct N2O emissions by 40 and 57%, to 0.14 and 0.22gN2O-Nhead(-1)day(-1), for Phase 1 and Phase 2, respectively. The increase in N2O emissions resulting from lignite application was counteracted by the lower indirect N2O emission due to decreased NH3 volatilization. Using 1% as a default emission factor of deposited NH3 for indirect N2O emissions, the application of lignite decreased total N2O emissions. PMID:27161136

  10. Silver(I) as a widely applicable, homogeneous catalyst for aerobic oxidation of aldehydes toward carboxylic acids in water—“silver mirror”: From stoichiometric to catalytic

    PubMed Central

    Liu, Mingxin; Wang, Haining; Zeng, Huiying; Li, Chao-Jun

    2015-01-01

    The first example of a homogeneous silver(I)-catalyzed aerobic oxidation of aldehydes in water is reported. More than 50 examples of different aliphatic and aromatic aldehydes, including natural products, were tested, and all of them successfully underwent aerobic oxidation to give the corresponding carboxylic acids in extremely high yields. The reaction conditions are very mild and greener, requiring only a very low silver(I) catalyst loading, using atmospheric oxygen as the oxidant and water as the solvent, and allowing gram-scale oxidation with only 2 mg of our catalyst. Chromatography is completely unnecessary for purification in most cases. PMID:26601150

  11. Solvent-free aerobic oxidation of hydrocarbons and alcohols with Pd@N-doped carbon from glucose.

    PubMed

    Zhang, Pengfei; Gong, Yutong; Li, Haoran; Chen, Zhirong; Wang, Yong

    2013-01-01

    The development of efficient systems for selective aerobic oxidation of hydrocarbons and alcohols to produce more functional compounds (aldehydes, ketones, acids or esters) with atmospheric air or molecular oxygen is a grand challenge for the chemical industry. Here we report the synthesis of palladium nanoparticles supported on novel nanoporous nitrogen-doped carbon, and their impressive performance in the controlled oxidation of hydrocarbons and alcohols with air. In terms of catalytic activity, these catalysts afford much higher turnover frequencies (up to 863 turnovers per hour for hydrocarbon oxidation and up to ~210,000 turnovers per hour for alcohol oxidation) than most reported palladium catalysts under the same reaction conditions. This work provides great potential for the application of ambient air and recyclable palladium catalysts in fine-chemical production with high activity. PMID:23481401

  12. Diversity, Abundance, and Niche Differentiation of Ammonia-Oxidizing Prokaryotes in Mud Deposits of the Eastern China Marginal Seas.

    PubMed

    Yu, Shaolan; Yao, Peng; Liu, Jiwen; Zhao, Bin; Zhang, Guiling; Zhao, Meixun; Yu, Zhigang; Zhang, Xiao-Hua

    2016-01-01

    The eastern China marginal seas (ECMS) are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in mud deposits of the South Yellow Sea (SYS) and the East China Sea (ECS) by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia, and silicate (SiO[Formula: see text]), was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ(15)NTN and SiO[Formula: see text], and nitrate and δ(13)C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO[Formula: see text]. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits. PMID:26904010

  13. Diversity, Abundance, and Niche Differentiation of Ammonia-Oxidizing Prokaryotes in Mud Deposits of the Eastern China Marginal Seas

    PubMed Central

    Yu, Shaolan; Yao, Peng; Liu, Jiwen; Zhao, Bin; Zhang, Guiling; Zhao, Meixun; Yu, Zhigang; Zhang, Xiao-Hua

    2016-01-01

    The eastern China marginal seas (ECMS) are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in mud deposits of the South Yellow Sea (SYS) and the East China Sea (ECS) by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia, and silicate (SiO32-), was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ15NTN and SiO32-, and nitrate and δ13C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO32-. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits. PMID:26904010

  14. Spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenerative life support

    NASA Technical Reports Server (NTRS)

    Sakano, Yuko; Pickering, Karen D.; Strom, Peter F.; Kerkhof, Lee J.; Janes, H. W. (Principal Investigator)

    2002-01-01

    Bioregenerative life support systems may be necessary for long-term space missions due to the high cost of lifting supplies and equipment into orbit. In this study, we investigated two biological wastewater treatment reactors designed to recover potable water for a spacefaring crew being tested at Johnson Space Center. The experiment (Lunar-Mars Life Support Test Project-Phase III) consisted of four crew members confined in a test chamber for 91 days. In order to recycle all water during the experiment, an immobilized cell bioreactor (ICB) was employed for organic carbon removal and a trickling filter bioreactor (TFB) was utilized for ammonia removal, followed by physical-chemical treatment. In this study, the spatial distribution of various microorganisms within each bioreactor was analyzed by using biofilm samples taken from four locations in the ICB and three locations in the TFB. Three target genes were used for characterization of bacteria: the 16S rRNA gene for the total bacterial community, the ammonia monooxygenase (amoA) gene for ammonia-oxidizing bacteria, and the nitrous oxide reductase (nosZ) gene for denitrifying bacteria. A combination of terminal restriction fragment length polymorphism (T-RFLP), sequence, and phylogenetic analyses indicated that the microbial community composition in the ICB and the TFB consisted mainly of Proteobacteria, low-G+C gram-positive bacteria, and a Cytophaga-Flexibacter-Bacteroides group. Fifty-seven novel 16S rRNA genes, 8 novel amoA genes, and 12 new nosZ genes were identified in this study. Temporal shifts in the species composition of total bacteria in both the ICB and the TFB and ammonia-oxidizing and denitrifying bacteria in the TFB were also detected when the biofilms were compared with the inocula after 91 days. This result suggests that specific microbial populations were either brought in by the crew or enriched in the reactors during the course of operation.

  15. Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis.

    PubMed

    Blainey, Paul C; Mosier, Annika C; Potanina, Anastasia; Francis, Christopher A; Quake, Stephen R

    2011-01-01

    Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is ∼1.77 Mb with >2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is ∼70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these low-salinity AOA appear to be motile, based on the presence of numerous motility- and chemotaxis-associated genes in the genome. This genome data will be used to inform targeted physiological and metabolic studies of this novel group of AOA, which may ultimately advance our understanding of AOA metabolism and their impacts on the global carbon and nitrogen cycles. PMID

  16. Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

    PubMed Central

    Potanina, Anastasia; Francis, Christopher A.; Quake, Stephen R.

    2011-01-01

    Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles. We sequenced the genome of AOA in an enrichment culture from low-salinity sediments in San Francisco Bay using single-cell and metagenomic genome sequence data. Five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic DNA was amplified by multiple displacement amplification (MDA) in 50 nL volumes and then sequenced by high-throughput DNA pyrosequencing. This microscopy-based approach to single-cell genomics minimizes contamination and allows correlation of high-resolution cell images with genomic sequences. Statistical properties of coverage across the five single cells, in combination with the contrasting properties of the metagenomic dataset allowed the assembly of a high-quality draft genome. The genome of this AOA, which we designate Candidatus Nitrosoarchaeum limnia SFB1, is ∼1.77 Mb with >2100 genes and a G+C content of 32%. Across the entire genome, the average nucleotide identity to Nitrosopumilus maritimus, the only AOA in pure culture, is ∼70%, suggesting this AOA represents a new genus of Crenarchaeota. Phylogenetically, the 16S rRNA and ammonia monooxygenase subunit A (amoA) genes of this AOA are most closely related to sequences reported from a wide variety of freshwater ecosystems. Like N. maritimus, the low-salinity AOA genome appears to have an ammonia oxidation pathway distinct from ammonia oxidizing bacteria (AOB). In contrast to other described AOA, these low-salinity AOA appear to be motile, based on the presence of numerous motility- and chemotaxis-associated genes in the genome. This genome data will be used to inform targeted physiological and metabolic studies of this novel group of AOA, which may ultimately advance our understanding of AOA metabolism and their impacts on the global carbon and nitrogen cycles. PMID

  17. Communities of ammonia oxidizers at different stages of Spartina alterniflora invasion in salt marshes of Yangtze River estuary.

    PubMed

    Xia, Fei; Zeleke, Jemaneh; Sheng, Qiang; Wu, Ji-Hua; Quan, Zhe-Xue

    2015-05-01

    Spartina alterniflora, an aggressive invasive plant species at the estuarine wetlands of China's coasts, has become a major threat to the natural ecosystems. To understand its potential influence on nitrification processes, the community structures and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated using 454-pyrosequencing and quantitative real-time PCR (qPCR) in S. alterniflora invading salt marsh sediments at the Yangtze River estuary in Chongming island, Shanghai, China. Copy numbers of archaeal and bacterial ammonia monooxygenase subunit A (amoA) genes did not show accordant shifts with S. alterniflora invasion in the two sampling sites. However, the copy numbers of archaeal amoA gene were higher in summer than in spring. Phylogenetic analysis indicated that more than 90% of the archaeal and 92% of the bacterial amoA gene sequences were closely related to marine group I.1a and the clusters 13 and 15 in Nitrosospira lineage, respectively. The effect of different seasons (spring and summer) was important for the abundance variation of AOA, while different stages of S. alterniflora invasion did not show significant effect for both AOA and AOB. Variation of AOA community was significantly related to total carbon (TC) and sulfate concentration (P < 0.05), whereas the AOB community was significantly related to sulfate concentration, total nitrogen (TN), TC and pH (P < 0.05). In conclusion, the abundance and diversity of ammonia oxidizing microbial communities were not strongly affected by S. alterniflora invasion. PMID:25935302

  18. Whole-Genome Transcriptional Analysis of Chemolithoautotrophic Thiosulfate Oxidation by Thiobacillus denitrificans Under Aerobic vs. Denitrifying Conditions

    SciTech Connect

    Beller, H R; Letain, T E; Chakicherla, A; Kane, S R; Legler, T C; Coleman, M A

    2006-04-22

    Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with ke chemolithoautotrophic functions (such as sulfur-compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately ten percent of the genome) as differentially expressed using Robust Multi-array Average statistical analysis and a 2-fold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated respectively with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur-compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription, quantitative PCR analysis was used to validate these trends.

  19. Development and Comparison of the Substrate Scope of Pd-Catalysts for the Aerobic Oxidation of Alcohols

    PubMed Central

    Schultz, Mitchell J.; Hamilton, Steven S.; Jensen, David R.; Sigman, Matthew S.

    2009-01-01

    Three catalysts for aerobic oxidation of alcohols are discussed and the effectiveness of each is evaluated for allylic, benzylic, aliphatic, and functionalized alcohols. Additionally, chiral nonracemic substrates as well as chemoselective and diastereoselective oxidations are investigated. In this study, the most convenient system for the Pd-catalyzed aerobic oxidation of alcohols is Pd(OAc)2 in combination with triethylamine. This system functions effectively for the majority of alcohols tested and uses mild conditions (3 to 5 mol % of catalyst, room temperature). Pd(IiPr)(OAc)2(H2O) (1) also successfully oxidizes the majority of alcohols evaluated. This system has the advantage of significantly lowering catalyst loadings but requires higher temperatures (0.1 to 1 mol % of catalyst, 60 °C). A new catalyst is also disclosed, Pd(IiPr)(OPiv)2 (2). This catalyst operates under very mild conditions (1 mol %, room temperature, and air as the O2 source) but with a more limited substrate scope. PMID:15844968

  20. Chiral N-salicylidene vanadyl carboxylate-catalyzed enantioselective aerobic oxidation of α-hydroxy esters and amides

    PubMed Central

    Weng, Shiue-Shien; Shen, Mei-Wen; Kao, Jun-Qi; Munot, Yogesh S.; Chen, Chien-Tien

    2006-01-01

    A series of chiral vanadyl carboxylates derived from N-salicylidene-l-α-amino acids and vanadyl sulfate has been developed. These configurationally well defined complexes were examined for the kinetic resolution of double- and mono-activated 2° alcohols. The best chiral templates involve the combination of l-tert-leucine and 3,5-di-t-butyl-, 3,5-diphenyl-, or 3,4-dibromo-salicylaldehyde. The resulting vanadyl(V)-methoxide complexes after recrystallization from air-saturated methanol serve as highly enantioselective catalysts for asymmetric aerobic oxidation of α-hydroxyl-esters and amides with a diverse array of α-, O-, and N-substituents at ambient temperature in toluene. The asymmetric inductions of the oxidation process are in the range of 10 to >100 in terms of selectivity factors (krel) in most instances. The previously undescribed aerobic oxidation protocol is also applicable to the kinetic resolution of C-13 taxol side chain with high selectivity factor (krel = 35). X-ray crystallographic analysis of an adduct between a given vanadyl complex and N-benzyl-mandelamide allows for probing the stereochemical origin of the nearly exclusive asymmetric control in the oxidation process. PMID:16501046

  1. Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating

    PubMed Central

    Daebeler, Anne; Abell, Guy C. J.; Bodelier, Paul L. E.; Bodrossy, Levente; Frampton, Dion M. F.; Hefting, Mariet M.; Laanbroek, Hendrikus J.

    2012-01-01

    The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively) to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilization site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA) gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative polymerase chain reaction suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while soil physio-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization. PMID:23060870

  2. [Abundance and Community Composition of Ammonia-Oxidizing Archaea in Two Completely Autotrophic Nitrogen Removal over Nitrite Systems].

    PubMed

    Gao, Jing-feng; Li, Ting; Zhang, Shu-jun; Fan, Xiao-yan; Pan, Kai-ling; Ma, Qian; Yuan, Ya-lin

    2015-08-01

    Ammonia oxidation is the first and rate-limiting step of nitrification, which was thought to be only performed by ammonia-oxidizing bacteria (AOB). In recent years, ammonia-oxidizing archaea (AOA) was also confirmed to take part in ammonia oxidation. The diversity and abundance of AOA have been investigated in various environments, however, little is known regarding the AOA in the completely autotrophic nitrogen removal over nitrite (CANON) wastewater treatment process. In this study, the abundance and diversity of AOA were investigated in the biofilm and flocculent activated sludge collected in a lab-scale (L) CANON system and a pilot-scale (P) CANON systems, respectively. The quantitative real time PCR (qPCR) was applied to investigate the abundance of AOA and the diversity of AOA was determined by polymerase chain reaction (PCR), cloning and sequencing. The qPCR results showed that the average abundance of AOA amoA gene of L and P was 2.42 x 10(6) copies x g(-1) dry sludge and 6.51 x 10(6) copies x g(-1) dry sludge, respectively. The abundance of AOA in biofilm was 10.1-14.1 times higher than that in flocculent activated sludge. For P system, the abundance of AOA in flocculent activated sludge was 1.8 times higher than that in biofilm. The results indicated that the abundance of AOA might be affected by different sludge morphology. The diversity of AOA in P system was extremely limited, only one OTU was observed, which was classified into Nitrosopumilus subcluster 5.2. The diversity of AOA in L system was higher, eight OTUs were observed, which were classified into five genera: Nitrososphaera subcluster 9, subcluster 8.1, subcluster 4.1, subcluster 1.1 and Nitrosopumilus subcluster 5.2. The diversity and abundance of AOA were different in CANON systems with different sludge morphology. AOA may play an important role in ammonia oxidation in CANON system. PMID:26592025

  3. The structure-function relationship for alumina supported platinum during the formation of ammonia from nitrogen oxide and hydrogen in the presence of oxygen.

    PubMed

    Adams, Emma Catherine; Merte, Lindsay Richard; Hellman, Anders; Skoglundh, Magnus; Gustafson, Johan; Bendixen, Eva Charlotte; Gabrielsson, Pär; Bertram, Florian; Evertsson, Jonas; Zhang, Chu; Carlson, Stefan; Carlsson, Per-Anders

    2016-04-20

    We study the structure-function relationship of alumina supported platinum during the formation of ammonia from nitrogen oxide and dihydrogen by employing in situ X-ray absorption and Fourier transform infrared spectroscopy. Particular focus has been directed towards the effect of oxygen on the reaction as a model system for emerging technologies for passive selective catalytic reduction of nitrogen oxides. The suppressed formation of ammonia observed as the feed becomes net-oxidizing is accompanied by a considerable increase in the oxidation state of platinum as well as the formation of surface nitrates and the loss of NH-containing surface species. In the presence of (excess) oxygen, the ammonia formation is proposed to be limited by weak interaction between nitrogen oxide and the oxidized platinum surface. This leads to a slow dissociation rate of nitrogen oxide and thus low abundance of the atomic nitrogen surface species that can react with the adsorbed hydrogen species. In this case the consumption of hydrogen through the competing water formation reaction and decomposition/oxidation of ammonia are of less importance for the net ammonia formation. PMID:27039829

  4. Abundance, Activity, and Diversity of Ammonia-oxidizing Bacteria and Archaea in Oligotrophic Alpine Lakes of Yosemite National Park, California

    NASA Astrophysics Data System (ADS)

    Beman, J.; Hayden, C.

    2013-12-01

    Lakes play critical roles in biogeochemical cycles as integrators of carbon and nitrogen cycling across watersheds. They are also ';sentinels' that may be strongly affected by environmental change--yet the responses of lake biogeochemical processes are dictated by microbial communities that we still know little about. We quantified nitrification rates, carbon respiration rates, and the abundance and diversity of involved microbes, within lakes located along an elevational gradient in Yosemite National Park, USA. Temperature, atmospheric nitrogen (N) deposition, and exposure to UV all vary along this transect, allowing us to test how these variables may act together to influence microbial biogeochemical processes. We found surprisingly high abundances of ammonia-oxidizing bacteria (AOB)--despite low nutrient conditions and high light levels that may favor other organisms, and/or inhibit AOB. We also examined community composition and diversity of AOB and ammonia-oxidizjng archaea (AOA) using Illumina sequencing of 16S rRNA genes, and measured ammonia oxidation rates using 15N tracer. All of these data are indicative of active N cycling by a dynamic microbial community. In Yosemite and other wilderness areas, atmospheric N deposition supplies a critical nutrient that may alter naturally nutrient-poor ecosystems; in the Sierra Nevada, much of this deposition occurs in the form of ammonium, suggesting a key role for nitrification in converting deposited N into more mobile forms. Our data indicate that oligotrophic alpine lakes may be nitrification hotspots in Yosemite.

  5. Effects of submerged macrophytes on the abundance and community composition of ammonia-oxidizing prokaryotes in a eutrophic lake.

    PubMed

    Zhao, Da-yong; Luo, Juan; Zeng, Jin; Wang, Meng; Yan, Wen-ming; Huang, Rui; Wu, Qinglong L

    2014-01-01

    Abundances and community compositions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in unvegetated sediment and the rhizosphere sediments of three submerged macrophytes (Ceratophyllum demersum, Vallisneria spinulosa, and Potamogeton crispus) were investigated in a large, eutrophic freshwater lake, Lake Taihu. Abundances of archaeal ammonia monooxygenase alpha-subunit (amoA) gene (from 6.56 × 10(6) copies to 1.06 × 10(7) copies per gram of dry sediment) were higher than those of bacterial amoA (from 6.13 × 10(5) to 3.21 × 10(6) copies per gram of dry sediment) in all samples. Submerged macrophytes exhibited no significant effect on the abundance and diversity of archaeal amoA gene. C. demersum and V. spinulosa increased the abundance and diversity of bacterial amoA gene in their rhizosphere sediment. However, the diversity of bacterial amoA gene in the rhizosphere sediments of P. crispus was decreased. The data obtained in this study would be helpful to elucidate the roles of submerged macrophytes involved in the nitrogen cycling of eutrophic lake ecosystems. PMID:23784056

  6. Response of ammonia-oxidizing archaea and bacteria to long-term industrial effluent-polluted soils, Gujarat, Western India.

    PubMed

    Subrahmanyam, Gangavarapu; Shen, Ju-Pei; Liu, Yu-Rong; Archana, Gattupalli; He, Ji-Zheng

    2014-07-01

    Soil nitrifiers have been showing an important role in assessing environmental pollution as sensitive biomarkers. In this study, the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in long-term industrial waste effluent (IWE) polluted soils. Three different IWE polluted soils characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) were collected in triplicate along Mahi River basin, Gujarat, Western India. Quantitative numbers of ammonia monooxygenase α-subunit (amoA) genes as well as 16S rRNA genes indicated apparent deleterious effect of IWE on abundance of soil AOA, AOB, bacteria, and archaeal populations. Relatively, AOB was more abundant than AOA in the highly contaminated soil R3, while predominance of AOA was noticed in uncontaminated (R1) and moderately contaminated (R2) soils. Soil potential nitrification rate (PNR) significantly (P < 0.05) decreased in polluted soils R2 and R3. Reduced diversity accompanied by apparent community shifts of both AOB and AOA populations was detected in R2 and R3 soils. AOB were dominated with Nitrosospira-like sequences, whereas AOA were dominated by Thaumarchaeal "group 1.1b (Nitrososphaera clusters)." We suggest that the significant reduction in abundance and diversity AOA and AOB could serve as relevant bioindicators for soil quality monitoring of polluted sites. These results could be further useful for better understanding of AOB and AOA communities in polluted soils. PMID:24554021

  7. Depth-related changes of sediment ammonia-oxidizing microorganisms in a high-altitude freshwater wetland.

    PubMed

    Liu, Yong; Zhang, Jingxu; Zhang, Xiaoling; Xie, Shuguang

    2014-06-01

    Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) might be the key microorganisms in ammonia conversion in ecosystems. However, the depth-related change of AOA and AOB in sediment ecosystem is still not clear. The relative contribution of AOA and AOB to nitrification in wetland sediment remains also unclear. Moreover, information about ammonia-oxidizing microorganisms in high-altitude freshwater wetland is still lacking. The present study investigated the relative abundances and community structures of AOA and AOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China). Variations of the relative abundances and community structures of AOA and AOB were found in the wetland sediments, dependent on both sampling site and sediment depth. The relative abundances of AOA and AOB (0.04-3.84 and 0.01-0.52 %) and the AOA/AOB ratio (0.12-4.65) showed different depth-related change patterns. AOB community size was usually larger than AOA community size. AOB diversity was usually higher than AOA diversity. AOA diversity decreased with the increase of sediment depth, while AOB diversity showed no obvious link with the sediment depth. Pearson's correlation analysis showed that AOA diversity had a positive significant correlation with available phosphorus. Nitrosospira-like sequences, with different compositions, predominated in the wetland sediment AOB communities. This work could provide some new insights toward nitrification in freshwater sediment ecosystems. PMID:24619246

  8. Spatial and temporal dynamics of ammonia oxidizers in the sediments of the Gulf of Finland, Baltic Sea.

    PubMed

    Vetterli, Adrien; Hietanen, Susanna; Leskinen, Elina

    2016-02-01

    The diversity and dynamics of ammonia-oxidizing bacteria (AOB) and archaea (AOA) nitrifying communities in the sediments of the eutrophic Gulf of Finland (GoF) were investigated. Using clone libraries of ammonia monooxygenase (amoA) gene fragments and terminal restriction fragment length polymorphism (TRFLP), we found a low richness of both AOB and AOA. The AOB amoA phylogeny matched that of AOB 16S ribosomal genes from the same samples. AOA communities were characterized by strong spatial variation while AOB communities showed notable temporal patterns. At open sea sites, where transient anoxic conditions prevail, richness of both AOA and AOB was lowest and communities were dominated by organisms with gene signatures unique to the GoF. Given the importance of nitrification as a link between the fixation of nitrogen and its removal from aquatic environments, the low diversity of ammonia-oxidizing microbes across the GoF could be of relevance for ecosystem resilience in the face of rapid global environmental changes. PMID:26722795

  9. A comparative study of silver-graphene oxide nanocomposites as a recyclable catalyst for the aerobic oxidation of benzyl alcohol: Support effect

    NASA Astrophysics Data System (ADS)

    Zahed, Bahareh; Hosseini-Monfared, Hassan

    2015-02-01

    Three different nanocomposites of silver and graphene oxide, namely silver nanoparticles (AgNPs) immobilized on reduced graphene oxide (AgNPs/rGO), partially reduced graphene oxide (AgNPs/GO) and thiolated partially reduced graphene oxide (AgNPs/GOSH), were synthesized in order to compare their properties. Characterizations were carried out by infrared and UV-Vis and Raman spectroscopy, ICP, X-ray diffraction, SEM and TEM, confirming both the targeted chemical modification and the composite formation. The nanocomposites were successfully employed in the aerobic oxidation of benzyl alcohol at atmospheric pressure. AgNPs/GOSH is stable and recyclable catalyst which showed the highest activity in the aerobic oxidation of benzyl alcohol in the presence of N-hydroxyphthalimide (NHPI) to give benzaldehyde with 58% selectivity in 24 h at 61% conversion. The favorite properties of AgNPs/GOSH are reasonably attributed to the stable and well distributed AgNPs over GOSH due to strong adhesion between AgNPs and GOSH.

  10. [Electrochemical oxidation of ammonia nitrogen wastewater using Ti/RuO2-TiO2-IrO2-SnO2 electrode].

    PubMed

    Xu, Li-li; Shi, Han-chang; Chen, Jin-luan

    2007-09-01

    Electrochemical oxidation ammonia is a new method of ammonia nitrogen wastewater treatment. A study was undertaken of electrochemical oxidation ammonia wastewater in cycle mobil-electrobath. The anode was Ti/RuO2-TiO2-IrO2-SnO2 expanded metal sheet electrode. The cathode was expanded metal sheet electrode. The parameters investigated were the optimal available time for the measurement of ammonia nitrogen, flowrate and current density. The energy consumption, anode efficiency and current efficiency were analysed in different current densities. Experimental results show that when the concentration of the chlorine ion was 400 mg/L and the initial ammoniac nitrogen concentration was 40 mg/L, the flowrate had little impact on ammonia nitrogen removal, but current density had greater impact. Under the condition with flowrate 600 mL/min, current density 20 mA/cm2, electrolytic time 90 min, ammonia nitrogen removal ratio was 99.37%. The energy consumption was 500 kW x h and the anode efficiency was 2.68 h x m2 x A per kg NH4+ -N removed, and instantaneous current efficiency (ICE) was 0.28. Research has shown that electrochemical oxidation ammonia wastewater has better prospects. PMID:17990548

  11. Effects of 30 Years of Crop Rotation and Tillage on Bacterial and Archaeal Ammonia Oxidizers.

    PubMed

    Munroe, Jake W; McCormick, Ian; Deen, William; Dunfield, Kari E

    2016-05-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) both mediate soil nitrification and may have specialized niches in the soil. Little is understood of how these microorganisms are affected by long-term crop rotation and tillage practices. In this study, we assessed abundance and gene expression of AOB and AOA under two contrasting crop rotations and tillage regimes at a 30-yr-old long-term experiment on a Canadian silt loam soil. Continuous corn ( L.) (CC) was compared with a corn-corn-soybean [ (L.) Merr.]-winter wheat ( L.) rotation under-seeded with red clover ( L.) (RC), with conventional tillage (CT) and no-till (NT) as subplot treatments. Soil sampling was performed during the first corn year at four time points throughout the 2010 season and at three discrete depths (0-5, 5-15, and 15-30 cm). Overall, AOA abundance was found to be more than 10 times that of AOB, although AOA transcriptional activity was below detectable levels across all treatments. Crop rotation had a marginally significant effect on AOB abundance, with 1.3 times as many gene copies under the simpler CC rotation than under the more diverse RC rotation. More pronounced effects of depth on AOB abundance and gene expression were observed under NT versus CT management, and NT supported higher abundances of total archaea and AOA than CT across the growing season. We suggest that AOB may be more functionally important than AOA in this high-input agricultural soil but that NT management can promote enhanced soil archaeal populations. PMID:27136161

  12. Microsite Differentiation Drives the Abundance of Soil Ammonia Oxidizing Bacteria along Aridity Gradients

    PubMed Central

    Delgado-Baquerizo, Manuel; Maestre, Fernando T.; Eldridge, David J.; Singh, Brajesh K.

    2016-01-01

    Soil ammonia oxidizing bacteria (AOB) and archaea (AOA) are responsible for nitrification in terrestrial ecosystems, and play important roles in ecosystem functioning by modulating the rates of N losses to ground water and the atmosphere. Vascular plants have been shown to modulate the abundance of AOA and AOB in drylands, the largest biome on Earth. Like plants, biotic and abiotic features such as insect nests and biological soil crusts (biocrusts) have unique biogeochemical attributes (e.g., nutrient availability) that may modify the local abundance of AOA and AOB. However, little is known about how these biotic and abiotic features and their interactions modulate the abundance of AOA and AOB in drylands. Here, we evaluate the abundance of amoA genes from AOB and AOA within six microsites commonly found in drylands (open areas, biocrusts, ant nests, grasses, nitrogen-fixing shrubs, and trees) at 21 sites from eastern Australia, including arid and mesic ecosystems that are threatened by predicted increases in aridity. Our results from structural equation modeling suggest that soil microsite differentiation alters the abundance of AOB (but not AOA) in both arid and mesic ecosystems. While the abundance of AOA sharply increased with increasing aridity in all microsites, the response of AOB abundance was microsite-dependent, with increases (nitrogen-fixing shrubs, ant nests), decreases (open areas) or no changes (grasses, biocrusts, trees) in abundance with increasing aridity. Microsites supporting the highest abundance of AOB were trees, nitrogen-fixing shrubs, and ant nests. These results are linked to particular soil characteristics (e.g., total carbon and ammonium) under these microsites. Our findings advance our understanding of key drivers of functionally important microbial communities and N availability in highly heterogeneous ecosystems such as drylands, which may be obscured when different soil microsites are not explicitly considered. PMID:27148194

  13. Microsite Differentiation Drives the Abundance of Soil Ammonia Oxidizing Bacteria along Aridity Gradients.

    PubMed

    Delgado-Baquerizo, Manuel; Maestre, Fernando T; Eldridge, David J; Singh, Brajesh K

    2016-01-01

    Soil ammonia oxidizing bacteria (AOB) and archaea (AOA) are responsible for nitrification in terrestrial ecosystems, and play important roles in ecosystem functioning by modulating the rates of N losses to ground water and the atmosphere. Vascular plants have been shown to modulate the abundance of AOA and AOB in drylands, the largest biome on Earth. Like plants, biotic and abiotic features such as insect nests and biological soil crusts (biocrusts) have unique biogeochemical attributes (e.g., nutrient availability) that may modify the local abundance of AOA and AOB. However, little is known about how these biotic and abiotic features and their interactions modulate the abundance of AOA and AOB in drylands. Here, we evaluate the abundance of amoA genes from AOB and AOA within six microsites commonly found in drylands (open areas, biocrusts, ant nests, grasses, nitrogen-fixing shrubs, and trees) at 21 sites from eastern Australia, including arid and mesic ecosystems that are threatened by predicted increases in aridity. Our results from structural equation modeling suggest that soil microsite differentiation alters the abundance of AOB (but not AOA) in both arid and mesic ecosystems. While the abundance of AOA sharply increased with increasing aridity in all microsites, the response of AOB abundance was microsite-dependent, with increases (nitrogen-fixing shrubs, ant nests), decreases (open areas) or no changes (grasses, biocrusts, trees) in abundance with increasing aridity. Microsites supporting the highest abundance of AOB were trees, nitrogen-fixing shrubs, and ant nests. These results are linked to particular soil characteristics (e.g., total carbon and ammonium) under these microsites. Our findings advance our understanding of key drivers of functionally important microbial communities and N availability in highly heterogeneous ecosystems such as drylands, which may be obscured when different soil microsites are not explicitly considered. PMID:27148194

  14. Emissions of ammonia, nitrous oxide and methane from cattle manure heaps: effect of compaction and covering

    NASA Astrophysics Data System (ADS)

    Chadwick, D. R.

    The effect of compaction and covering during storage of beef cattle ( Bos taurus) farmyard manure (FYM) on ammonia (NH 3), nitrous oxide (N 2O) and methane (CH 4) emissions was determined. Gaseous emission measurements were made over three separate storage periods of between 90 and 109 days. The effect of the different storage treatments on manure chemical composition was also determined. Compaction was carried out as the manure was put into store and the compacted manures covered with plastic sheeting. Compaction and covering significantly reduced NH 3 emissions from manure by over 90% during the first summer storage period (P<0.05). Over the subsequent storage periods NH 3 emissions from the FYM were small and unaffected by storage treatment. However, during the second storage period heavy and persistent rainfall during heap establishment and the following week appeared to reduce NH 3 emissions markedly. The low ammonium-N content of the FYM in the third storage period may have reduced the risk of NH 3 emission and reduced the relative effect of the compaction/covering treatment. Compaction and covering also significantly reduced N 2O emissions from cattle FYM (P<0.05) by ca. 30% during the first storage period. Subsequent N 2O emissions were unaffected by treatment. Methane emissions from cattle FYM were unaffected by treatment over the first storage period and were decreased by compaction in the second storage period yet was increased by compaction during the third storage period. It would appear that compacting and covering manure heaps does have the potential to reduce emissions of both NH 3 and N 2O when the manure contains relatively high ammonium-N contents. Additional benefits are that N and K are retained in the manure heap for agronomic benefit.

  15. Determination of surface coverage of catalysts: Temperature programmed experiments on platinum and iridium sponge catalysts after low temperature ammonia oxidation

    SciTech Connect

    Broek, A.C.M. van den; Grondelle, J. van; Santen, R.A. van

    1999-07-25

    The activity of iridium and platinum sponge catalysts was studied in the low temperature gas phase oxidation of ammonia with oxygen. Under the reaction conditions used, iridium was found to be more active and more selective to nitrogen than platinum. Furthermore it was established from activity measurements that both catalysts lose activity as a function of time on stream due to inhibition of the surface by reaction intermediates. The used catalysts were studied by XPS and temperature programmed techniques. It was found that the surface of the catalysts had a high coverage of NH and OH and some additional NH{sub 2}. It seems most likely that the reaction mechanism proceeds through a stepwise dehydrogenation of the ammonia molecule. It appears that the last dehydrogenation step (NH by OH to N and water) is the rate determining step. The high selectivity of iridium to nitrogen can be explained by the higher activity of iridium in dissociating NO.

  16. Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

    PubMed Central

    Wu, Dongying; Raymond, Jason; Wu, Martin; Chatterji, Sourav; Ren, Qinghu; Graham, Joel E.; Bryant, Donald A.; Robb, Frank; Colman, Albert; Tallon, Luke J.; Badger, Jonathan H.; Madupu, Ramana; Ward, Naomi L.; Eisen, Jonathan A.

    2009-01-01

    In order to enrich the phylogenetic diversity represented in the available sequenced bacterial genomes and as part of an “Assembling the Tree of Life” project, we determined the genome sequence of Thermomicrobium roseum DSM 5159. T. roseum DSM 5159 is a red-pigmented, rod-shaped, Gram-negative extreme thermophile isolated from a hot spring that possesses both an atypical cell wall composition and an unusual cell membrane that is composed entirely of long-chain 1,2-diols. Its genome is composed of two circular DNA elements, one of 2,006,217 bp (referred to as the chromosome) and one of 919,596 bp (referred to as the megaplasmid). Strikingly, though few standard housekeeping genes are found on the megaplasmid, it does encode a complete system for chemotaxis including both chemosensory components and an entire flagellar apparatus. This is the first known example of a complete flagellar system being encoded on a plasmid and suggests a straightforward means for lateral transfer of flagellum-based motility. Phylogenomic analyses support the recent rRNA-based analyses that led to T. roseum being removed from the phylum Thermomicrobia and assigned to the phylum Chloroflexi. Because T. roseum is a deep-branching member of this phylum, analysis of its genome provides insights into the evolution of the Chloroflexi. In addition, even though this species is not photosynthetic, analysis of the genome provides some insight into the origins of photosynthesis in the Chloroflexi. Metabolic pathway reconstructions and experimental studies revealed new aspects of the biology of this species. For example, we present evidence that T. roseum oxidizes CO aerobically, making it the first thermophile known to do so. In addition, we propose that glycosylation of its carotenoids plays a crucial role in the adaptation of the cell membrane to this bacterium's thermophilic lifestyle. Analyses of published metagenomic sequences from two hot springs similar to the one from which this strain

  17. A nonenzymatic biosensor based on gold electrodes modified with peptide self-assemblies for detecting ammonia and urea oxidation.

    PubMed

    Bianchi, Roberta C; da Silva, Emerson Rodrigo; Dall'Antonia, Luiz H; Ferreira, Fabio Furlan; Alves, Wendel Andrade

    2014-09-30

    We have developed a nonenzymatic biosensor for the detection of ammonia and urea oxidation based on the deposition of peptide microstructures onto thiolated gold electrodes. FF-MNSs/MCP/Au assemblies were obtained by modifying gold substrates with 4-mercaptopyridine (MCP), followed by coating with l,l-diphenylalanine micro/nanostructures (FF-MNSs) grown in the solid-vapor phase. Benzene rings and amide groups with peptide micro/nanostructures interact with synthetic NH4(+) receptors through cation-π and hydrogen bonding. AuOH clusters on the Au surface provided the catalytic sites. The application of a predetermined concentration of analytes at the peptide interfaces activated the catalytic sites. We observed a relationship between the stability of films and the crystal structure of peptides, and we organized the FF-MNSs into an orthorhombic symmetry that was the most suitable assembly for creation of our biosensors. At 0.1 mol L(-1) NaOH, these FF-MNSs/MCP/Au electrodes have electrocatalytic properties regarding ammonia and urea oxidation that are comparable to those of enzyme-based architectures. Under optimal conditions, the electrocatalytic response is proportional to the ammonia and urea concentration in the range 0.1-1.0 mmol L(-1). The sensitivity was calculated as 2.83 and 81.3 μA mmol L(-1) cm(-2) for ammonia and urea, respectively, at +0.40 V (vs SCE). Our detection method is easy to follow, does not require a mediator or enzyme, and has strong potential for detecting urea via nonenzymatic routes. PMID:25188339

  18. Cu-Catalyzed Consecutive Hydroxylation and Aerobic Oxidative Cycloetherification under Microwave Conditions: Entry to 2-Arylbenzofuran-3-carboxylic Acids.

    PubMed

    Xu, Tianlong; Zhang, Ensheng; Wang, Dejian; Wang, Yan; Zou, Yong

    2015-05-01

    A convenient one-pot synthesis of 2-arylbenzofuran-3-carboxylic acids from (E)-2-(2-bromophenyl)-3-phenylacrylic acids via Cu-catalyzed consecutive hydroxylation and aerobic oxidative cycloetherification under microwave conditions has been developed. This protocol employed the reagent combination of Cu(OAc)2, 1,10-phen, and KOH in DMSO/H2O (1:1), all of which are cost-effective, readily available, and easily removable from the reaction mixture. Utilizing this synthetic protocol, various 2-arylbenzofuran-3-carboxylic acids as well as the natural product moracin M have been synthesized in satisfactory yields under mild conditions. PMID:25836742

  19. Stable TEMPO and ABNO Catalyst Solutions for User-Friendly (bpy)Cu/Nitroxyl-Catalyzed Aerobic Alcohol Oxidation.

    PubMed

    Steves, Janelle E; Stahl, Shannon S

    2015-11-01

    Two solutions, one consisting of bpy/TEMPO/NMI and the other bpy/ABNO/NMI (bpy =2,2'-bipyridyl; TEMPO = 2,2,6,6-tetramethylpiperidine N-oxyl, ABNO = 9-azabicyclo[3.3.1]nonane N-oxyl; NMI = N-methylimidazole), in acetonitrile are shown to have good long-term stability (≥1 year) under air at 5 °C. The solutions may be combined in appropriate quantities with commercially available [Cu(MeCN)4]OTf to provide a convenient catalyst system for the aerobic oxidation of primary and secondary alcohols. PMID:26457658

  20. Experimental Limiting Oxygen Concentrations for Nine Organic Solvents at Temperatures and Pressures Relevant to Aerobic Oxidations in the Pharmaceutical Industry

    PubMed Central

    2015-01-01

    Applications of aerobic oxidation methods in pharmaceutical manufacturing are limited in part because mixtures of oxygen gas and organic solvents often create the potential for a flammable atmosphere. To address this issue, limiting oxygen concentration (LOC) values, which define the minimum partial pressure of oxygen that supports a combustible mixture, have been measured for nine commonly used organic solvents at elevated temperatures and pressures. The solvents include acetic acid, N-methylpyrrolidone, dimethyl sulfoxide, tert-amyl alcohol, ethyl acetate, 2-methyltetrahydrofuran, methanol, acetonitrile, and toluene. The data obtained from these studies help define safe operating conditions for the use of oxygen with organic solvents. PMID:26622165

  1. Mechanistic study of copper-catalyzed aerobic oxidative coupling of arylboronic esters and methanol: insights into an organometallic oxidase reaction.

    PubMed

    King, Amanda E; Brunold, Thomas C; Stahl, Shannon S

    2009-04-15

    Copper-catalyzed aerobic oxidative coupling of arylboronic acid derivatives and heteroatom nucleophiles is a highly useful method for the formation of aryl-heteroatom bonds. Mechanistic studies reveal that this reaction proceeds via an "oxidase"-style mechanism. Kinetic and spectroscopic studies establish that transmetalation of the aryl group from boron to Cu(II) is the turnover-limiting step and reoxidation of the reduced catalyst by O(2) is rapid. Further mechanistic analysis implicates the involvement of an aryl-copper(III) intermediate that undergoes facile C-O bond formation. PMID:19309072

  2. Nitrogenous fertilizers: Global distribution of consumption and associated emissions of nitrous oxide and ammonia

    SciTech Connect

    Matthews, E.

    1994-12-01

    The global distribution of nitrogen input via application of chemical nitrogenous fertilizers to agricultural ecosystems is presented. The suite of 1{degrees} (latitude/longitude) resolution data bases includes primary data on fertilizer consumption, as well as supporting data sets defining the distribution and intensity of agriculture associated with fertilizer use. The data were developed from a variety of sources and reflect conditions for the mid-1980s. East Asia, where fertilizer use is increasing at {approximately}10%/year, accounted for {approximately}37% of the total, while North America and western Europe, where fertilizer use is leveling off, accounted for 40% of the world`s total in the mid-1980s. While almost every country consumes urea, {approximately}75% of the large East Asian fertilizer use is supplied by this one fertilizer. Ammonium nitrate, used primarily in the former centrally planned economies of Europe, in West Asia, and in Africa, accounted for about one quarter of global consumption. These data were used to estimate distributions of the annual emission of nitrous oxide (N{sub 2}O) and ammonia (NH{sub 3}) associated with the use of fertilizers. Applying published ranges of emission coefficients for fertilizer types in the data base yields a median emission of 0.1 Tg N{sub 2}O-N, with lower and upper values of 0.03 and 2.0 Tg N{sub 2}O-N in 1984. This equals <1% to {approximately}3% of the total nitrogen applied via commercial fertilizers and represents ,=<1% to 15% of the annual emission of N{sub 2}O from terrestrial sources. Assuming that the {approximately}4% annual increase in consumption of nitrogenous fertilizers during the 1980s corresponds to a {approximately}4% rise in the release of N{sub 2}O-N, yearly increases in emissions from fertilizer use are <0.01 to 0.08 Tg N{sub 2}O-N equal to <1% to 3% of the current growth of atmospheric nitrous oxide. 98 refs., 3 figs., 5 tabs.

  3. N2O production by ammonia oxidizing bacteria in an enriched nitrifying sludge linearly depends on inorganic carbon concentration.

    PubMed

    Peng, Lai; Ni, Bing-Jie; Ye, Liu; Yuan, Zhiguo

    2015-05-01

    The effect of inorganic carbon (IC) on nitrous oxide (N2O) production by ammonia oxidizing bacteria (AOB) was investigated over a concentration range of 0-12 mmol C/L, encompassing typical IC levels in a wastewater treatment reactors. The AOB culture was enriched along with nitrite-oxidizing bacteria (NOB) in a sequencing batch reactor (SBR) to perform complete nitrification. Batch experiments were conducted with continuous carbon dioxide (CO2) stripping or at controlled IC concentrations. The results revealed a linear relationship between N2O production rate (N2OR) and IC concentration (R(2) = 0.97) within the IC range studied, suggesting a substantial effect of IC on N2O production by AOB. Similar results were also obtained with an AOB culture treating anaerobic sludge digestion liquor. The fundamental mechanism responsible for this dependency is unclear; however, in agreement with previous studies, it was observed that the ammonia oxidation rate (AOR) was also influenced by the IC concentration, which could be well described by the Monod kinetics. These resulted in an exponential relationship between N2OR and AOR, as previously observed in experiments where AOR was altered by varying dissolved oxygen and ammonia concentrations. It is therefore possible that IC indirectly affected N2OR by causing a change in AOR. The observation in this study indicates that alkalinity (mostly contributed by IC) could be a significant factor influencing N2O production and should be taken into consideration in estimating and mitigating N2O emissions in wastewater treatment systems. PMID:25706224

  4. Density functional theory study of the oxidation of ammonia on the IrO2(110) surface.

    PubMed

    Wang, Chia-Ching; Siao, Shih Syong; Jiang, Jyh-Chiang

    2011-12-01

    In this study, we employed density functional theory (DFT) to investigate the oxidation of ammonia (NH(3)) on the IrO(2)(110) surface. We characterized the possible reaction pathways for the dehydrogenation of NH(x) species (x = 1-3) and for the formation of the oxidation products N(2), N(2)O, NO, NO(2), and H(2)O. The presence of oxygen atoms on coordinatively unsaturated sites (O(cus)) of the oxygen-rich IrO(2)(110) surface promotes the oxidation of NH(3) on the surface. In contrast, NH(3) molecules prefer undergoing desorption over oxidation on the stoichiometric IrO(2)(110) surface. Moreover, the O(cus) atoms are also the major oxidants leading to the formation of oxidation products; none of the oxidations mediated by the bridge oxygen atoms were favorable reactions. The energy barrier for formation of H(2)O as a gaseous oxidation product on the IrO(2)(110) surface is high (from 1.83 to 2.29 eV), potentially leading to the formation of nitrogen-atom-containing products at high temperature. In addition, the selectivity toward the nitrogen-atom-containing products is dominated by the coverage of O(cus) atoms on the surface; for example, a higher coverage of O(cus) atoms results in greater production of nitrogen oxides (NO, NO(2)). PMID:22047008

  5. Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil.

    PubMed

    Yao, Huaiying; Huang, Sha; Qiu, Qiongfen; Li, Yaying; Wu, Lianghuan; Mi, Wenhai; Dai, Feng

    2016-08-01

    Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community. PMID:27063014

  6. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments

    PubMed Central

    Li, Xi; Zhang, Miaomiao; Liu, Feng; Li, Yong; He, Yang; Zhang, Shunan; Wu, Jinshui

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different waters were treated by M. elatinoides in microcosms for one month. The five waters included tap water (Control), swine wastewater (SW), 50% diluted swine wastewater (50% SW), and two synthetic wastewaters: 200 mg NH4+-N L−1 (200 NH4+-N) and 400 mg NH4+-N L−1 (400 NH4+-N). The most dramatic changes were in NH4+-N and total N (TN) concentrations, with average removal rates of 84% and 90%, respectively, in the treatments containing swine wastewater. On days 7, 14, and 28, the dissolved oxygen (DO) increased by 81.8%, 210.4% and 136.5%, respectively, compared with on day 0, in the swine wastewater. The results also showed that the bacterial amoA (AOB) copy numbers in the sediments of the treatments were significantly higher than those of archaeal amoA (AOA) copy numbers (p = 0.015). In addition, the high DO concentrations in swine wastewater responded well to the high abundance of AOB. The AOA and AOB community distributions were positively related with NO3-N and were negatively related with DO in swine wastewater treatments. In summary, our experimental results suggested that the M. elatinoides purification system could improve the activity of ammonia-oxidizing microorganisms and consequently might contribute to the significant N removal from the swine wastewater. PMID:26444015

  7. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes.

    PubMed

    Zhang, Jinping; Zhou, Xiaohong; Chen, Lei; Chen, Zhigang; Chu, Jinyu; Li, Yimin

    2016-05-01

    The abundance, diversity and community structure of ammonia oxidizing archaea (AOA) and bacteria (AOB) in rice rhizosphere soils under three different irrigation cultivated modes, named continuous irrigation mode (C), intermittent irrigation mode (I) and semi-arid mode (M), respectively, were investigated using amoA gene as a molecular biomarker. Clone libraries and quantitative polymerase chain reaction results indicated the highest number of archaeal amoA gene copy was detected in M cultivation mode, then in I and C, whereas, their order of amoA gene copy numbers were I > M > C for AOB, and those were obvious higher than in the bulk soil. The ratios of AOA/AOB were greater than 1 for all samples, suggested the predominance of AOA throughout the period of rice growth in the three different irrigation cultivation modes. Diversity index (SChao1 and Shannon H) have an obvious variation in three different irrigation cultivation modes. For AOA, SChao1 was highest in M and lowest in I mode, whereas, Shannon H was highest in M cultivation mode and lowest in C mode. For AOB, mode M exhibited the highest diversity index (SChao1 and Shannon H), while C showed the lowest highest diversity, suggested long-term water input (continuous mode) may decrease diversity of ammonia oxidizers, whereas mode M may be more appropriate for them. In addition, AOA sequences fall within Nitrososphaera, Nitrosopumilus and Nitrosotalea cluster with proportion of 89.38, 8.85 and 1.77 %, respectively. AOB gene sequences belonged to the Nitrosomonas and Nitrosospira genera with proportion of 90.97 and 9.03 %, respectively. In addition, the abundances, diversity and community structure had an obvious temporal variation in three developmental stages of rice, further suggested rice growth obviously affected the ammonia oxidizing prokaryotes in their rhizosphere soil. PMID:27038955

  8. Enhanced ammonia removal at room temperature by pH controlled partial nitrification and subsequent anaerobic ammonium oxidation.

    PubMed

    Durán, U; del Val Río, A; Campos, J L; Mosquera-Corral, A; Méndez, R

    2014-01-01

    The Anammox-based processes are suitable for the treatment of wastewaters characterized by a low carbon to nitrogen (C/N) ratio. The application of the Anammox process requires the availability of an effluent with a NO2- -N/NH4+ -N ratio composition around 1 g g-1, which involves the necessity of a previous step where the partial nitrification is performed. In this step, the inhibition of the nitrite-oxidizing bacteria (NOB) is crucial. In the present work, a combined partial nitrification-ANaerobic AMmonia OXidation (Anammox) two-units system operated at room temperature (20 degreeC) has been tested for the nitrogen removal of pre-treated pig slurry. To achieve the successful partial nitrification and inhibit the NOB activity, different ammonium/inorganic carbon (NH4+/IC) ratios were assayed from 1.19 to 0.82g NH4+-Ng-1 HCO3-C. This procedure provoked a decrease of the pH value to 6.0 to regulate the inhibitory effect over ammonia-oxidizing bacteria caused by free ammonia. Simultaneously, the NOB experienced the inhibitory effect of free nitrous acid which avoided the presence of nitrate in the effluent. The NH4+/IC ratio which allowed the obtaining of the desired effluent composition (50% of both ammonium and nitrite) was 0.82 +/- 0.02 g NH4+-N g-1 HCO3- -C. The Anammox reactor was fed with the effluent of the partial nitrification unit containing a NO2 -N/NH4+ -N ratio of 1 g g-1' where a nitrogen loading rate of 0.1 g N L-1 d-1 was efficiently removed. PMID:24600878

  9. Aerobic oxidation of starch catalyzed by isopolyoxovanadate Na4Co(H2O)6V10O28.

    PubMed

    Chen, Xiaoli; Yan, Siqi; Wang, Hang; Hu, Zhiyun; Wang, Xiaohong; Huo, Mingxin

    2015-03-01

    The partial oxidation of starch was achieved in the presence of oxygen with Na4Co(H2O)6V10O28·18H2O (abbreviated as CoV10) as catalyst. The oxidation degree of starch was determined by FT-IR, XRD and SEM measurements, which indicated that the aerobic oxidation of starch was promoted by oxidative catalyst CoV10. The application of CoV10 could give a high oxidation degree (DO) of 1.35 COOH/100 GU and 2.07 CO/100 GU with 86 wt.% yield of solid starch under mild reaction conditions (pH=6; reaction time, 8 h; temperature, 50 °C; catalyst amount, 8 mg, when 1.5 g starch was used as substrate; atmospheric pressure). Among some vanadium compounds, CoV10 exhibited 4-fold activity higher than orthovanadate due to its coordination effect of cobalt and V10O28. Meanwhile, CoV10 could be recycled for six times with only a slight decrease in activity. Thus, CoV10/O2 is one of the most efficient systems for partial oxidation of starch reported so far. PMID:25498687

  10. P-Doped Porous Carbon as Metal Free Catalysts for Selective Aerobic Oxidation with an Unexpected Mechanism.

    PubMed

    Patel, Mehulkumar A; Luo, Feixiang; Khoshi, M Reza; Rabie, Emann; Zhang, Qing; Flach, Carol R; Mendelsohn, Richard; Garfunkel, Eric; Szostak, Michal; He, Huixin

    2016-02-23

    An extremely simple and rapid (seconds) approach is reported to directly synthesize gram quantities of P-doped graphitic porous carbon materials with controlled P bond configuration. For the first time, it is demonstrated that the P-doped carbon materials can be used as a selective metal free catalyst for aerobic oxidation reactions. The work function of P-doped carbon materials, its connectivity to the P bond configuration, and the correlation with its catalytic efficiency are studied and established. In direct contrast to N-doped graphene, the P-doped carbon materials with higher work function show high activity in catalytic aerobic oxidation. The selectivity trend for the electron donating and withdrawing properties of the functional groups attached to the aromatic ring of benzyl alcohols is also different from other metal free carbon based catalysts. A unique catalytic mechanism is demonstrated, which differs from both GO and N-doped graphene obtained by high temperature nitrification. The unique and unexpected catalytic pathway endows the P-doped materials with not only good catalytic efficiency but also recyclability. This, combined with a rapid, energy saving approach that permits fabrication on a large scale, suggests that the P-doped porous materials are promising materials for "green catalysis" due to their higher theoretical surface area, sustainability, environmental friendliness, and low cost. PMID:26751165

  11. Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization

    PubMed Central

    Xue, Chao; Zhang, Xu; Zhu, Chen; Zhao, Jun; Zhu, Ping; Peng, Chang; Ling, Ning; Shen, Qirong

    2016-01-01

    Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB. PMID:27356769

  12. Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization.

    PubMed

    Xue, Chao; Zhang, Xu; Zhu, Chen; Zhao, Jun; Zhu, Ping; Peng, Chang; Ling, Ning; Shen, Qirong

    2016-01-01

    Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB. PMID:27356769

  13. Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization

    NASA Astrophysics Data System (ADS)

    Xue, Chao; Zhang, Xu; Zhu, Chen; Zhao, Jun; Zhu, Ping; Peng, Chang; Ling, Ning; Shen, Qirong

    2016-06-01

    Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.

  14. The synthesis of a bifunctional copper metal organic framework and its application in the aerobic oxidation/Knoevenagel condensation sequential reaction.

    PubMed

    Miao, Zongcheng; Luan, Yi; Qi, Chao; Ramella, Daniele

    2016-09-21

    A novel one-pot aerobic oxidation/Knoevenagel condensation reaction system was developed employing a Cu(ii)/amine bifunctional, basic metal-organic framework (MOF) as the catalyst. The sequential aerobic alcohol oxidation/Knoevenagel condensation reaction was efficiently promoted by the Cu3TATAT MOF catalyst in the absence of basic additives. The benzylidenemalononitrile product was produced in high yield and selectivity from an inexpensive benzyl alcohol starting material under an oxygen atmosphere. The role of the basic functionality was studied to demonstrate its role in the aerobic oxidation and Knoevenagel condensation reactions. The reaction progress was monitored in order to identify the reaction intermediate and follow the accumulation of the desired product. Lastly, results showed that the yield was not significantly compromised by the reuse of a batch of catalyst, even after more than five cycles. PMID:27523776

  15. Diversity, Abundance, and Spatial Distribution of Sediment Ammonia-Oxidizing Betaproteobacteria in Response to Environmental Gradients and Coastal Eutrophication in Jiaozhou Bay, China▿ †

    PubMed Central

    Dang, Hongyue; Li, Jing; Chen, Ruipeng; Wang, Lin; Guo, Lizhong; Zhang, Zhinan; Klotz, Martin G.

    2010-01-01

    Ongoing anthropogenic eutrophication of Jiaozhou Bay offers an opportunity to study the influence of human activity on bacterial communities that drive biogeochemical cycling. Nitrification in coastal waters appears to be a sensitive indicator of environmental change, suggesting that function and structure of the microbial nitrifying community may be associated closely with environmental conditions. In the current study, the amoA gene was used to unravel the relationship between sediment aerobic obligate ammonia-oxidizing Betaproteobacteria (Beta-AOB) and their environment in Jiaozhou Bay. Protein sequences deduced from amoA gene sequences grouped within four distinct clusters in the Nitrosomonas lineage, including a putative new cluster. In addition, AmoA sequences belonging to three newly defined clusters in the Nitrosospira lineage were also identified. Multivariate statistical analyses indicated that the studied Beta-AOB community structures correlated with environmental parameters, of which nitrite-N and sediment sand content had significant impact on the composition, structure, and distribution of the Beta-AOB community. Both amoA clone library and quantitative PCR (qPCR) analyses indicated that continental input from the nearby wastewater treatment plants and polluted rivers may have significant impact on the composition and abundance of the sediment Beta-AOB assemblages in Jiaozhou Bay. Our work is the first report of a direct link between a sedimentological parameter and the composition and distribution of the sediment Beta-AOB and indicates the potential for using the Beta-AOB community composition in general and individual isolates or environmental clones in the Nitrosomonas oligotropha lineage in particular as bioindicators and biotracers of pollution or freshwater or wastewater input in coastal environments. PMID:20511433

  16. Nitrosomonas communis strain YNSRA, an ammonia-oxidizing bacterium, isolated from the reed rhizoplane in an aquaponics plant.

    PubMed

    Tokuyama, Tatsuaki; Mine, Atsusi; Kamiyama, Kaoru; Yabe, Ryuichi; Satoh, Kazuo; Matsumoto, Hirotoshi; Takahashi, Reiji; Itonaga, Koji

    2004-01-01

    An ammonia-oxidizing bacterium (strain YNSRA) was isolated from the rhizoplane of the reed (Phragmites communis) used in an aquaponics plant which is a wastewater treatment plant. Strain YNSRA was identified as Nitrosomonas communis by taxonomic studies. The hydroxylamine-cytochrome c reductase (HCR) of strain YNSRA was found to have a higher activity (25.60 u/mg) than that of Nitrosomonas europaea ATCC25978T (8.94 u/mg). Ribulose-1,5-bisphosphate carboxylase (RubisCO) activity was detected at very low levels in strain YNSRA, whereas strain ATCC25978T had definite activity. PMID:16233712

  17. Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management

    SciTech Connect

    Wessen, E.; Nyberg, K.; Jansson, J.K.; Hallin, S.

    2010-05-01

    Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) co-exist in soil, but their relative distribution may vary depending on the environmental conditions. Effects of changes in soil organic matter and nutrient content on the AOB and AOA are poorly understood. Our aim was to compare effects of long-term soil organic matter depletion and amendments with labile (straw) and more recalcitrant (peat) organic matter, with and without easily plant-available nitrogen, on the activities, abundances and community structures of AOB and AOA. Soil was sampled from a long-term field site in Sweden that was established in 1956. The potential ammonia oxidation rates, the AOB and AOA amoA gene abundances and the community structures of both groups based on T-RFLP of amoA genes were determined. Straw amendment during 50 years had not altered any of the measured soil parameters, while the addition of peat resulted in a significant increase of soil organic carbon as well as a decrease in pH. Nitrogen fertilization alone resulted in a small decrease in soil pH, organic carbon and total nitrogen, but an increase in primary production. Type and amount of organic matter had an impact on the AOB and AOA community structures and the AOA abundance. Our findings confirmed that AOA are abundant in soil, but showed that under certain conditions the AOB dominate, suggesting niche differentiation between the two groups at the field site. The large differences in potential rates between treatments correlated to the AOA community size, indicating that they were functionally more important in the nitrification process than the AOB. The AOA abundance was positively related to addition of labile organic carbon, which supports the idea that AOA could have alternative growth strategies using organic carbon. The AOB community size varied little in contrast to that of the AOA. This indicates that the bacterial ammonia oxidizers as a group have a greater ecophysiological diversity and

  18. Apparatus for purifying arsine, phosphine, ammonia, and inert gases to remove Lewis acid and oxidant impurities therefrom

    DOEpatents

    Tom, Glenn M.; Brown, Duncan W.

    1991-01-08

    An apparatus for purifying a gaseous mixture comprising arsine, phosphine, ammonia, and/or inert gases, to remove Lewis acid and/or oxidant impurities therefrom, comprising a vessel containing a bed of a scavenger, the scavenger including a support having associated therewith an anion which is effective to remove such impurities, such anion being selected from one or more members of the group consisting of: (i) carbanions whose corresponding protonated compounds have a pK.sub.a value of from about 22 to about 36; and (ii) anions formed by reaction of such carbanions with the primary component of the mixture.

  19. Evaluating Primers for Profiling Anaerobic Ammonia Oxidizing Bacteria within Freshwater Environments

    PubMed Central

    Sonthiphand, Puntipar; Neufeld, Josh D.

    2013-01-01

    Anaerobic ammonia oxidizing (anammox) bacteria play an important role in transforming ammonium to nitrogen gas and contribute to fixed nitrogen losses in freshwater environments. Understanding the diversity and abundance of anammox bacteria requires reliable molecular tools, and these are not yet well established for these important Planctomycetes. To help validate PCR primers for the detection of anammox bacteria within freshwater ecosystems, we analyzed representative positive controls and selected samples from Grand River and groundwater sites, both from Ontario, Canada. The objectives of this study were to identify a suitable anammox denaturing gradient gel electrophoresis (DGGE) fingerprint method by using GC-clamp modifications to existing primers, and to verify the specificity of anammox-specific primers used for DGGE, cloning and qPCR methods. Six primer combinations were tested from four published primer sets (i.e. A438f/A684r, Amx368f/Amx820r, An7f/An1388r, and Pla46/1392r) for both direct and nested PCR amplifications. All PCR products were run subsequently on DGGE gels to compare the resulting patterns. Two anammox-specific primer combinations were also used to generate clone libraries and quantify anammox bacterial 16S rRNA genes with qPCR. The primer set A438f/A684r was highly specific to anammox bacteria, provided reliable DGGE fingerprints and generated a high proportion of anammox-related clones. A second primer set (Amx368f/Amx820r) was anammox specific, based on clone library analysis, but PCR products from different candidate species of anammox bacteria resolved poorly using DGGE analysis. Both DGGE and cloning results revealed that Ca. Brocadia and an uncharacterized anammox bacterial cluster represented the majority of anammox bacteria found in Grand River sediment and groundwater samples, respectively. Together, our results demonstrate that although Amx368f/Amx820r was useful for anammox-specific qPCR and clone library analysis, A438f/A684r

  20. Design of Highly Selective Platinum Nanoparticle Catalysts for the Aerobic Oxidation of KA-Oil using Continuous-Flow Chemistry.

    PubMed

    Gill, Arran M; Hinde, Christopher S; Leary, Rowan K; Potter, Matthew E; Jouve, Andrea; Wells, Peter P; Midgley, Paul A; Thomas, John M; Raja, Robert

    2016-03-01

    Highly active and selective aerobic oxidation of KA-oil to cyclohexanone (precursor for adipic acid and ɛ-caprolactam) has been achieved in high yields using continuous-flow chemistry by utilizing uncapped noble-metal (Au, Pt & Pd) nanoparticle catalysts. These are prepared using a one-step in situ methodology, within three-dimensional porous molecular architectures, to afford robust heterogeneous catalysts. Detailed spectroscopic characterization of the nature of the active sites at the molecular level, coupled with aberration-corrected scanning transmission electron microscopy, reveals that the synthetic methodology and associated activation procedures play a vital role in regulating the morphology, shape and size of the metal nanoparticles. These active centers have a profound influence on the activation of molecular oxygen for selective catalytic oxidations. PMID:26833972

  1. Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei.

    PubMed

    Feng, Guofang; Sun, Wei; Zhang, Fengli; Karthik, Loganathan; Li, Zhiyong

    2016-01-01

    Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei. PMID:27113140

  2. Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei

    PubMed Central

    Feng, Guofang; Sun, Wei; Zhang, Fengli; Karthik, Loganathan; Li, Zhiyong

    2016-01-01

    Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei. PMID:27113140

  3. Palladium-Catalyzed Aerobic Oxidative Dehydrogenation of Cyclohexenes to Substituted Arene Derivatives

    PubMed Central

    Iosub, Andrei V.; Stahl, Shannon S.

    2015-01-01

    A palladium(II) catalyst system has been identified for aerobic dehydrogenation of substituted cyclohexenes to the corresponding arene derivatives. Use of sodium anthraquinone-2-sulfonate (AMS) as a co-catalyst enhances the product yields. A wide range of functional groups are tolerated in the reactions, and the scope and limitations of the method are described. The catalytic dehydrogenation of cyclohexenes is showcased in an efficient route to a phthalimide-based TRPA1 activity modulator. PMID:25734414

  4. Methane oxidation in a crude oil contaminated aquifer: Delineation of aerobic reactions at the plume fringes

    USGS Publications Warehouse

    Amos, R.T.; Bekins, B.A.; Delin, G.N.; Cozzarelli, I.M.; Blowes, D.W.; Kirshtein, J.D.

    2011-01-01

    High resolution direct-push profiling over short vertical distances was used to investigate CH4 attenuation in a petroleum contaminated aquifer near Bemidji, Minnesota. The contaminant plume was delineated using dissolved gases, redox sensitive components, major ions, carbon isotope ratios in CH4 and CO2, and the presence of methanotrophic bacteria. Sharp redox gradients were observed near the water table. Shifts in ??13CCH4 from an average of - 57.6??? (?? 1.7???) in the methanogenic zone to - 39.6??? (?? 8.7???) at 105 m downgradient, strongly suggest CH4 attenuation through microbially mediated degradation. In the downgradient zone the aerobic/anaerobic transition is up to 0.5 m below the water table suggesting that transport of O2 across the water table is leading to aerobic degradation of CH4 at this interface. Dissolved N2 concentrations that exceeded those expected for water in equilibrium with the atmosphere indicated bubble entrapment followed by preferential stripping of O2 through aerobic degradation of CH4 or other hydrocarbons. Multivariate and cluster analysis were used to distinguish between areas of significant bubble entrapment and areas where other processes such as the infiltration of O 2 rich recharge water were important O2 transport mechanisms. ?? 2011 Elsevier B.V. All rights reserved.

  5. Mechanistic studies on a Cu-catalyzed aerobic oxidative coupling reaction with N-phenyl tetrahydroisoquinoline: structure of intermediates and the role of methanol as a solvent.

    PubMed

    Boess, Esther; Sureshkumar, Devarajulu; Sud, Abhishek; Wirtz, Cornelia; Farès, Christophe; Klussmann, Martin

    2011-06-01

    The mechanism of an aerobic copper-catalyzed oxidative coupling reaction with N-phenyl tetrahydroisoquinoline was investigated. The oxidized species formed from the reaction of the amine with the copper catalyst were analyzed by NMR-spectroscopy. An iminium dichlorocuprate was found to be the reactive intermediate and could be structurally characterized by X-ray crystallography. The effect of methanol to effectively stabilize the iminium ion was investigated and shown to be beneficial in an oxidative allylation reaction. PMID:21561084

  6. Method for forming ammonia

    DOEpatents

    Kong, Peter C.; Pink, Robert J.; Zuck, Larry D.

    2008-08-19

    A method for forming ammonia is disclosed and which includes the steps of forming a plasma; providing a source of metal particles, and supplying the metal particles to the plasma to form metal nitride particles; and providing a substance, and reacting the metal nitride particles with the substance to produce ammonia, and an oxide byproduct.

  7. Isolated and combined exposure to ammonia and nitrite in giant freshwater pawn (Macrobrachium rosenbergii): effects on the oxidative stress, antioxidant enzymatic activities and apoptosis in haemocytes.

    PubMed

    Zhang, Yufan; Ye, Chaoxia; Wang, Anli; Zhu, Xuan; Chen, Changhong; Xian, Jianan; Sun, Zhenzhu

    2015-10-01

    The residual contaminators such as ammonia and nitrite are widely considered as relevant sources of aquatic environmental pollutants, posing a great threat to shrimp survival. To study the toxicological effects of ammonia and nitrite exposure on the innate immune response in invertebrates, we investigated the oxidative stress and apoptosis in haemocytes of freshwater prawn (Macrobrachium rosenbergii) under isolated and combined exposure to ammonia and nitrite in order to provide useful information about adult prawn immune responses. M. rosenbergii (13.44 ± 2.75 g) were exposed to 0, 5, and 25 mg/L total ammonia-N (TAN) and 0, 5, and 20 mg/L nitrite-N for 24 h. All ammonia concentrations were combined with all nitrite concentrations, making a total of nine treatments studied. Following the exposure treatment, antioxidant enzyme activity, reactive oxygen species (ROS) generation, nitric oxide (NO) generation, and apoptotic cell ratio of haemocytes were measured using flow cytometry. Results indicated that ROS generation was sensitive to the combined effect of ammonia and nitrite, which subsequently affected the Cu-Zn SOD activity. In addition, CAT showed the highest activity at 5 mg/L TAN while GPx decreased at 5 mg/L TAN and returned towards baseline at 25 mg/L. NO generation synchronized with the apoptotic cell ratio in haemocytes, indicating that NO production was closely associated with programmed cell death. Both NO production and apoptotic ratios significantly decreased following 25 mg/L TAN, which may be due to the antagonistic regulation of NO and GPx. We hypothesized that the toxicological effect of nitrite exhibited less change in physiological changes compared to that of ammonia, because of the high tolerance to nitrite exposure in mature M. rosenbergii and/or the competitive effects of chloride ions. Taken together, these results showed that ammonia and nitrite caused a series of combined oxidative stress and apoptosis in M. rosenbergi, but further

  8. Relating the Diversity, Abundance, and Activity of Ammonia-Oxidizing Archaeal Communities to Nitrification Rates in the Coastal Ocean

    NASA Astrophysics Data System (ADS)

    Tolar, B. B.; Smith, J. M.; Chavez, F.; Francis, C.

    2015-12-01

    Ammonia oxidation, the rate-limiting first step of nitrification, is an important link between reduced (ammonia) and oxidized (nitrate) nitrogen, and controls the relative distribution of these forms of inorganic nitrogen. This process is catalyzed via the ammonia monooxygenase enzyme of both ammonia-oxidizing Bacteria (AOB) and Archaea (AOA); the α subunit of this enzyme is encoded by the amoA gene and has been used as the molecular marker to detect this process. In the ocean, AOA are typically 10-1000 times more and are likely more active than AOB, and thus are key players in the marine nitrogen cycle. Monterey Bay is a dynamic site to study nitrification, as seasonal upwelling brings deep water and nutrients into surface waters, which can promote phytoplankton blooms and impact biogeochemical processes such as the nitrogen cycle. We have sampled two sites within Monterey Bay bimonthly for two years as part of the ongoing Monterey Bay Time Series (MBTS) to quantify AOA genes, transcripts, and nitrification rates. Two ecotypes of AOA are routinely found in Monterey Bay - the 'shallow' water column A (WCA) and 'deep' water column B (WCB) clades, which are thought to have distinct physiological properties and can be distinguished based on the amoA gene sequence. Previous work has shown a strong relationship between nitrification rates in Monterey Bay with the abundance of WCA amoA genes and transcripts. Additionally, we found a correlation between the relative abundance of Marine Group I (MGI) Thaumarchaeota 16S rRNA reads (as % of total) and the absolute abundance of AOA amoA genes (determined via qPCR) in Monterey Bay and the California Current System. AOA 16S rRNA gene abundances in turn correlated significantly with changes in nitrification rate with depth, while the relative abundance of genes and transcripts binned to a single AOA (Nitrosopumilus maritimus) was not significantly correlated to nitrification rate. Further analysis of the sequenced AOA

  9. Seasonal dynamics of ammonia/ammonium-oxidizing prokaryotes in oxic and anoxic wetland sediments of subtropical coastal mangrove.

    PubMed

    Wang, Yong-Feng; Feng, Yao-Yu; Ma, Xiaojun; Gu, Ji-Dong

    2013-09-01

    Mangrove wetlands are an important ecosystem in tropical and subtropical regions, and the sediments may contain both oxic and anoxic zones. In this study, ammonia/ammonium-oxidizing prokaryotes (AOPs) in yellow and black sediments with vegetation and non-vegetated sediments in a mangrove wetland of subtropical Hong Kong were investigated in winter and summer. The phylogenetic diversity of anammox bacterial 16S rRNA genes and archaeal and bacterial amoA genes (encoding ammonia monooxygenase alpha-subunit) were analyzed using PCR amplification and denaturing gradient gel electrophoresis to reveal their community structures. Quantitative PCR was also used to detect their gene abundances. The results showed that seasonality had little effect, but sediment type had a noticeable influence on the community structures and abundances of anammox bacteria. For ammonia-oxidizing archaea (AOA), seasonality had a small effect on their community structures, but a significant effect on their abundances: AOA amoA genes were significantly higher in winter than in summer. In winter, the vegetated yellow sediments had lower AOA amoA genes than the other types of sediments, but in summer, the vegetated yellow sediments had higher AOA amoA genes than the other types of sediments. Sediment type had no apparent effect on AOA community structures in winter. In summer, however, the vegetated yellow sediments showed obviously different AOA community structures from the other types of sediments. For ammonia-oxidizing bacteria (AOB), seasonality had a significant effect on their community structures and abundances: AOB amoA genes in winter were apparently higher than in summer, and AOB community structures were different between winter and summer. Sediment type had little effect on AOB community structures, but had a noticeable effect on the abundances: AOB amoA genes of the vegetated yellow sediments were obviously lower than the black ones in both seasons. This study has demonstrated that

  10. Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil▿

    PubMed Central

    Kelly, John J.; Policht, Katherine; Grancharova, Tanya; Hundal, Lakhwinder S.

    2011-01-01

    The recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare−1 year−1) and double the agronomic rate (54 Mg hectare−1 year−1), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare−1 year−1). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterial amoA genes. In addition, only archaeal amoA gene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaeal amoA genes were significantly higher than copy numbers of bacterial amoA genes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches. PMID:21803892

  11. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray.

    PubMed

    Ward, Bess B; Eveillard, Damien; Kirshtein, Julie D; Nelson, Joshua D; Voytek, Mary A; Jackson, George A

    2007-10-01

    The relationship between environmental factors and functional gene diversity of ammonia-oxidizing bacteria (AOB) was investigated across a transect from the freshwater portions of the Chesapeake Bay and Choptank River out into the Sargasso Sea. Oligonucleotide probes (70-bp) designed to represent the diversity of ammonia monooxygenase (amoA) genes from Chesapeake Bay clone libraries and cultivated AOB were used to construct a glass slide microarray. Hybridization patterns among the probes in 14 samples along the transect showed clear variations in amoA community composition. Probes representing uncultivated members of the Nitrosospira-like AOB dominated the probe signal, especially in the more marine samples. Of the cultivated species, only Nitrosospira briensis was detected at appreciable levels. Discrimination analysis of hybridization signals detected two guilds. Guild 1 was dominated by the marine Nitrosospira-like probe signal, and Guild 2's largest contribution was from upper bay (freshwater) sediment probes. Principal components analysis showed that Guild 1 was positively correlated with salinity, temperature and chlorophyll a concentration, while Guild 2 was positively correlated with concentrations of oxygen, dissolved organic carbon, and particulate nitrogen and carbon, suggesting that different amoA sequences represent organisms that occupy different ecological niches within the estuarine/marine environment. The trend from most diversity of AOB in the upper estuary towards dominance of a single type in the polyhaline region of the Bay is consistent with the declining importance of AOB with increasing salinity, and with the idea that AO-Archaea are the more important ammonia oxidizers in the ocean. PMID:17803777

  12. Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.

    PubMed

    Tago, Kanako; Okubo, Takashi; Shimomura, Yumi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Nagayama, Atsushi; Hayatsu, Masahito

    2015-01-01

    The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers' fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers' sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 10(5)-9.2 × 10(6) and 1.7 × 10(6)-5.3 × 10(7) gene copies g dry soil(-1), respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields. PMID:25736866

  13. Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray

    USGS Publications Warehouse

    Ward, B.B.; Eveillard, D.; Kirshtein, J.D.; Nelson, J.D.; Voytek, M.A.; Jackson, G.A.

    2007-01-01

    The relationship between environmental factors and functional gene diversity of ammonia-oxidizing bacteria (AOB) was investigated across a transect from the freshwater portions of the Chesapeake Bay and Choptank River out into the Sargasso Sea. Oligonucleotide probes (70-bp) designed to represent the diversity of ammonia monooxygenase (amoA) genes from Chesapeake Bay clone libraries and cultivated AOB were used to construct a glass slide microarray. Hybridization patterns among the probes in 14 samples along the transect showed clear variations in amoA community composition. Probes representing uncultivated members of the Nitrosospira-like AOB dominated the probe signal, especially in the more marine samples. Of the cultivated species, only Nitrosospira briensis was detected at appreciable levels. Discrimination analysis of hybridization signals detected two guilds. Guild 1 was dominated by the marine Nitrosospira-like probe signal, and Guild 2???s largest contribution was from upper bay (freshwater) sediment probes. Principal components analysis showed that Guild 1 was positively correlated with salinity, temperature and chlorophyll a concentration, while Guild 2 was positively correlated with concentrations of oxygen, dissolved organic carbon, and particulate nitrogen and carbon, suggesting that different amoA sequences represent organisms that occupy different ecological niches within the estuarine/marine environment. The trend from most diversity of AOB in the upper estuary towards dominance of a single type in the polyhaline region of the Bay is consistent with the declining importance of AOB with increasing salinity, and with the idea that AO-Archaea are the more important ammonia oxidizers in the ocean. ?? 2007 The Authors.

  14. Divergent role of nitric oxide in insulin-stimulated aortic vasorelaxation between low- and high-intrinsic aerobic capacity rats.

    PubMed

    Crissey, Jacqueline M; Padilla, Jaume; Vieira-Potter, Victoria J; Thorne, Pamela K; Koch, Lauren G; Britton, Steven L; Thyfault, John P; Laughlin, M Harold

    2015-07-01

    Low-intrinsic aerobic capacity is associated with increased risk for cardiovascular and metabolic diseases and is a strong predictor of early mortality. The effects of intrinsic aerobic capacity on the vascular response to insulin are largely unknown. We tested the hypothesis that rats selectively bred for a low capacity to run (LCR) exhibit vascular dysfunction and impaired vascular reactivity to insulin compared to high capacity running (HCR) rats. Mature female LCR (n = 21) and HCR (n = 17) rats were maintained under sedentary conditions, and in vitro thoracic aortic vascular function was assessed. LCR exhibited greater body mass (13%), body fat (35%), and subcutaneous, perigonadal, and retroperitoneal adipose tissue mass, than HCR. During an intraperitoneal glucose tolerance test, glucose area under the curve (AUC) was not different but insulin AUC was 2-fold greater in LCR than HCR. Acetylcholine and insulin-stimulated aortic vasorelaxation was significantly greater in LCR (65.2 ± 3.8%, and 32.7 ± 4.1%) than HCR (55.0 ± 3.3%, and 16.7 ± 2.8%). Inhibition of nitric oxide synthase (NOS) with L-NAME entirely abolished insulin-mediated vasorelaxation in the aorta of LCR, with no effect in HCR. LCR rats exhibited greater expression of Insulin Receptor protein, lower Endothelin Receptor-A protein, a down-regulation of transcripts for markers of immune cell infiltration (CD11C, CD4, and F4/80) and up-regulation of pro-atherogenic inflammatory genes (VCAM-1 and MCP-1) in the aorta wall. Contrary to our hypothesis, low-aerobic capacity was associated with enhanced aortic endothelial function and NO-mediated reactivity to insulin, despite increased adiposity and evidence of whole body insulin resistance. PMID:26197933

  15. Ultrafine MnO2 nanoparticles decorated on graphene oxide as a highly efficient and recyclable catalyst for aerobic oxidation of benzyl alcohol.

    PubMed

    Hu, Zonggao; Zhao, Yafei; Liu, Jindun; Wang, Jingtao; Zhang, Bing; Xiang, Xu

    2016-12-01

    The highly active and selective aerobic oxidation of aromatic alcohols over earth-abundant, inexpensive and recyclable catalysts is highly desirable. We fabricated herein MnO2/graphene oxide (GO) composites by a facile in-situ growth approach at room temperature and used them in selective aerobic oxidation of benzyl alcohol to benzaldehyde. TEM, XRD, FTIR, XPS and N2 adsorption/desorption analysis were employed to systematically investigate the morphology, particle size, structure and surface properties of the catalysts. The 96.8% benzyl alcohol conversion and 100% benzaldehyde selectivity over the MnO2/GO (10/100) catalyst with well dispersive ultrafine MnO2 nanoparticles (ca. 3nm) can be obtained within 3h under 383K. Simultaneously, no appreciable loss of activity and selectivity occurred after recycling use up to six times. Due to their significant low cost, excellent catalytic performance, the MnO2/GO composites have huge application prospect in organic synthesis. PMID:27544446

  16. Large-scale synthesis of ultrathin tungsten oxide nanowire networks: an efficient catalyst for aerobic oxidation of toluene to benzaldehyde under visible light.

    PubMed

    Bai, Hua; Yi, Wencai; Liu, Jingyao; Lv, Qing; Zhang, Qing; Ma, Qiang; Yang, Haifeng; Xi, Guangcheng

    2016-07-14

    As a very important chemical raw material, the selective formation of benzaldehyde from toluene at preparative or industrial levels requires the use of highly corrosive chlorine and high reaction temperatures, which severely corrodes equipment, pollutes the environment, and consumes a lot of energy. Herein, we report a robust and highly active catalyst for the benzaldehyde evolution reaction that is constructed by the surfactant-free growth of oxygen vacancy-rich W18O49 ultrathin nanowire networks. Under atmospheric pressure and visible-light irradiation, the new catalyst can selectively (92% selectivity) catalyze the aerobic oxidation of toluene to benzaldehyde with yields of above 95%. PMID:27357748

  17. Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from South of Chile.

    PubMed

    Hernández, Marcela; Dumont, Marc G; Calabi, Marcela; Basualto, Daniel; Conrad, Ralf

    2014-02-01

    Ammonia oxidation, performed by specialized microorganisms belonging to the Bacteria and Archaea, is the first and most limiting step of soil nitrification. Nitrification has not yet been examined in young volcanic soils. The aim of the present work was to evaluate the abundance and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in acidic volcanic soils (andisols) of different defined ages to determine their relative contribution to nitrification and soil colonization. Soil was collected from three vegetated sites on Llaima Volcano (Chile) recolonized after lava eruptions in 1640, 1751 and 1957. Quantitative polymerase chain reaction, terminal restriction fragment length polymorphism and clone sequence analyses of the amoA gene were performed for the AOA and AOB communities. All soils showed high nitrification potentials, but they were highest in the younger soils. Archaeal amoA genes outnumbered bacterial amoA genes at all sites, and AOA abundances were found to be proportional to the nitrification potentials. Sequencing indicated the presence of AOA related to Nitrososphaera and Nitrosotalea, and AOB related primarily to Nitrosospira and sporadically to Nitrosomonas. The study showed that both AOA and AOB are early colonizers of andisols, but that AOA outnumber AOB and play an important role in nitrification. PMID:24596264

  18. Electrodeposited platinum thin films with preferential (100) orientation: Characterization and electrocatalytic properties for ammonia and formic acid oxidation

    NASA Astrophysics Data System (ADS)

    Bertin, Erwan; Garbarino, Sébastien; Guay, Daniel; Solla-Gullón, José; Vidal-Iglesias, Francisco J.; Feliu, Juan M.

    2013-03-01

    The electrocatalytic activity of preferentially oriented {100} Pt electrodes for the electro-oxidation of ammonia (0.2 M NaOH + 0.1 M NH3) and formic acid (0.5 M HCOOH + 0.5 M H2SO4) was assessed. They were prepared without using any surfactant through potentiostatic deposition (Ed = -0.10 V vs RHE, [HCl] = 10 mM and [Na2PtCl6·6H2O] = 0.5 mM) and by varying the deposition charge. For comparison, polycrystalline Pt thin films were prepared using the same solution but with Ed = +0.10 V vs RHE. Quantification of the fraction of (111) and (100) sites was performed by bismuth irreversible adsorption and deconvolution of the hydrogen region, respectively. Samples with as much as 47% of (100) surface sites were obtained. The preferential orientation was further confirmed by CO stripping voltammetry that exhibits similar characteristic features, as well as a similar potential of zero total charge than those expected for a preferential (100) surface. As compared to polycrystalline Pt, the occurrence of Pt (100) surface sites leads to an electrocatalytic activity enhancement by a factor of 4.8 and 2.6 (expressed as μA cmPt-2) for the oxidation of ammonia and formic acid, respectively.

  19. Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay.

    PubMed

    Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Zheng, Wei; Wen, Donghui

    2016-07-01

    The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge. PMID:26960319

  20. Metallic Sn spheres and SnO2@C core-shells by anaerobic and aerobic catalytic ethanol and CO oxidation reactions over SnO2 nanoparticles

    PubMed Central

    Kim, Won Joo; Lee, Sung Woo; Sohn, Youngku

    2015-01-01

    SnO2 has been studied intensely for applications to sensors, Li-ion batteries and solar cells. Despite this, comparatively little attention has been paid to the changes in morphology and crystal phase that occur on the metal oxide surface during chemical reactions. This paper reports anaerobic and aerobic ethanol and CO oxidation reactions over SnO2 nanoparticles (NPs), as well as the subsequent changes in the nature of the NPs. Uniform SnO2@C core-shells (10 nm) were formed by an aerobic ethanol oxidation reaction over SnO2 NPs. On the other hand, metallic Sn spheres were produced by an anaerobic ethanol oxidation reaction at 450 °C, which is significantly lower than that (1200 °C) used in industrial Sn production. Anaerobic and aerobic CO oxidation reactions were also examined. The novelty of the methods for the production of metallic Sn and SnO2@C core-shells including other anaerobic and aerobic reactions will contribute significantly to Sn and SnO2-based applications. PMID:26300041

  1. The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors

    PubMed Central

    Hu, Hang-Wei; Zhang, Li-Mei; Yuan, Chao-Lei; Zheng, Yong; Wang, Jun-Tao; Chen, Deli; He, Ji-Zheng

    2015-01-01

    Paddy soils distribute widely from temperate to tropical regions, and are characterized by intensive nitrogen fertilization practices in China. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in soil nitrification, but little is known about their biogeographic distribution patterns in paddy ecosystems. Here, we used barcoded pyrosequencing to characterize the effects of climatic, geochemical and spatial factors on the distribution of ammonia oxidizers from 11 representative rice-growing regions (75–1945 km apart) of China. Potential nitrification rates varied greatly by more than three orders of magnitude, and were significantly correlated with the abundances of AOA and AOB. The community composition of ammonia oxidizer was affected by multiple factors, but changes in relative abundances of the major lineages could be best predicted by soil pH. The alpha diversity of AOA and AOB displayed contrasting trends over the gradients of latitude and atmospheric temperature, indicating a possible niche separation between AOA and AOB along the latitude. The Bray–Curtis dissimilarities in ammonia-oxidizing community structure significantly increased with increasing geographical distance, indicating that more geographically distant paddy fields tend to harbor more dissimilar ammonia oxidizers. Variation partitioning analysis revealed that spatial, geochemical and climatic factors could jointly explain majority of the data variation, and were important drivers defining the ecological niches of AOA and AOB. Our findings suggest that both AOA and AOB are of functional importance in paddy soil nitrification, and ammonia oxidizers in paddy ecosystems exhibit large-scale biogeographic patterns shaped by soil pH, geographic distance, and climatic factors. PMID:26388866

  2. The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors.

    PubMed

    Hu, Hang-Wei; Zhang, Li-Mei; Yuan, Chao-Lei; Zheng, Yong; Wang, Jun-Tao; Chen, Deli; He, Ji-Zheng

    2015-01-01

    Paddy soils distribute widely from temperate to tropical regions, and are characterized by intensive nitrogen fertilization practices in China. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in soil nitrification, but little is known about their biogeographic distribution patterns in paddy ecosystems. Here, we used barcoded pyrosequencing to characterize the effects of climatic, geochemical and spatial factors on the distribution of ammonia oxidizers from 11 representative rice-growing regions (75-1945 km apart) of China. Potential nitrification rates varied greatly by more than three orders of magnitude, and were significantly correlated with the abundances of AOA and AOB. The community composition of ammonia oxidizer was affected by multiple factors, but changes in relative abundances of the major lineages could be best predicted by soil pH. The alpha diversity of AOA and AOB displayed contrasting trends over the gradients of latitude and atmospheric temperature, indicating a possible niche separation between AOA and AOB along the latitude. The Bray-Curtis dissimilarities in ammonia-oxidizing community structure significantly increased with increasing geographical distance, indicating that more geographically distant paddy fields tend to harbor more dissimilar ammonia oxidizers. Variation partitioning analysis revealed that spatial, geochemical and climatic factors could jointly explain majority of the data variation, and were important drivers defining the ecological niches of AOA and AOB. Our findings suggest that both AOA and AOB are of functional importance in paddy soil nitrification, and ammonia oxidizers in paddy ecosystems exhibit large-scale biogeographic patterns shaped by soil pH, geographic distance, and climatic factors. PMID:26388866

  3. Organization of the Escherichia coli aerobic enzyme complexes of oxidative phosphorylation in dynamic domains within the cytoplasmic membrane

    PubMed Central

    Erhardt, Heiko; Dempwolff, Felix; Pfreundschuh, Moritz; Riehle, Marc; Schäfer, Caspar; Pohl, Thomas; Graumann, Peter; Friedrich, Thorsten

    2014-01-01

    The Escherichia coli cytoplasmic membrane contains the enzyme complexes of oxidative phosphorylation (OXPHOS). Not much is known about their supramolecular organization and their dynamics within the membrane in this model organism. In mitochondria and other bacteria, it was demonstrated by nondenaturing electrophoretic methods and electron microscopy that the OXPHOS complexes are organized in so-called supercomplexes, stable assemblies with a defined number of the individual enzyme complexes. To investigate the organization of the E. coli enzyme complexes of aerobic OXPHOS in vivo, we established fluorescent protein fusions of the NADH:ubiquinone oxidoreductase, the succinate:ubiquinone oxidoreductase, the cytochrome bd-I, and the cytochrome bo3 terminal oxidases, and the FoF1 ATP-synthase. The fusions were integrated in the chromosome to prevent artifacts caused by protein overproduction. Biochemical analysis revealed that all modified complexes were fully assembled, active, and stable. The distribution of the OXPHOS complexes in living cells was determined using total internal reflection fluorescence microscopy. The dynamics within the membrane were detected by fluorescence recovery after photobleaching. All aerobic OXPHOS complexes showed an uneven distribution in large mobile patches within the E. coli cytoplasmic membrane. It is discussed whether the individual OXPHOS complexes are organized as clustered individual complexes, here called “segrazones.” PMID:24729508

  4. Gas sensors based on carbon nanoflake/tin oxide composites for ammonia detection.

    PubMed

    Lee, Soo-Keun; Chang, Daeic; Kim, Sang Wook

    2014-03-15

    Carbon nanoflake (CNFL) was obtained from graphite pencil by using the electrochemical method and the CNFL/SnO2 composite material assessed its potential as an ammonia gas sensor. A thin film resistive gas sensor using the composite material was manufactured by the drop casting method, and the sensor was evaluated to test in various ammonia concentrations and operating temperatures. Physical and chemical characteristics of the composite material were assessed using SEM, TEM, SAED, EDS and Raman spectroscopy. The composite material having 10% of SnO2 showed 3 times higher sensor response and better repeatability than the gas sensor using pristine SnO2 nano-particle at the optimal temperature of 350°C. PMID:24473403

  5. Optimization of the tungsten oxide technique for measurement of atmospheric ammonia

    NASA Technical Reports Server (NTRS)

    Brown, Kenneth G.

    1987-01-01

    Hollow tubes coated with tungstic acid have been shown to be of value in the determination of ammonia and nitric acid in ambient air. Practical application of this technique was demonstrated utilizing an automated sampling system for in-flight collection and analysis of atmospheric samples. Due to time constraints these previous measurements were performed on tubes that had not been well characterized in the laboratory. As a result the experimental precision could not be accurately estimated. Since the technique was being compared to other techniques for measuring these compounds, it became necessary to perform laboratory tests which would establish the reliability of the technique. This report is a summary of these laboratory experiments as they are applied to the determination of ambient ammonia concentration.

  6. Aqueous aerobic oxidation of alkyl arenes and alcohols catalyzed by copper(II) phthalocyanine supported on three-dimensional nitrogen-doped graphene at room temperature.

    PubMed

    Mahyari, Mojtaba; Laeini, Mohammad Sadegh; Shaabani, Ahmad

    2014-07-25

    Copper(ii) tetrasulfophthalocyanine supported on three-dimensional nitrogen-doped graphene-based frameworks was synthesized and introduced as a bifunctional catalyst for selective aerobic oxidation of alkyl arenes and alcohols to the corresponding carbonyl compounds. The ease of catalyst separation, high turnover, low catalyst loading and recyclability could potentially render it applicable in industrial setting. PMID:24912023

  7. One-pot synthesis of amides by aerobic oxidative coupling of alcohols or aldehydes with amines using supported gold and base as catalysts.

    PubMed

    Kegnæs, Søren; Mielby, Jerrik; Mentzel, Uffe V; Jensen, Thomas; Fristrup, Peter; Riisager, Anders

    2012-02-28

    Synthesis of amides by aerobic oxidative coupling of alcohols or aldehydes with amines via intermediate formation of methyl esters is highly efficient and selective when using a catalytic system comprised of supported gold nanoparticles and added base in methanol. PMID:22274843

  8. Large-scale synthesis of ultrathin tungsten oxide nanowire networks: an efficient catalyst for aerobic oxidation of toluene to benzaldehyde under visible light

    NASA Astrophysics Data System (ADS)

    Bai, Hua; Yi, Wencai; Liu, Jingyao; Lv, Qing; Zhang, Qing; Ma, Qiang; Yang, Haifeng; Xi, Guangcheng

    2016-07-01

    As a very important chemical raw material, the selective formation of benzaldehyde from toluene at preparative or industrial levels requires the use of highly corrosive chlorine and high reaction temperatures, which severely corrodes equipment, pollutes the environment, and consumes a lot of energy. Herein, we report a robust and highly active catalyst for the benzaldehyde evolution reaction that is constructed by the surfactant-free growth of oxygen vacancy-rich W18O49 ultrathin nanowire networks. Under atmospheric pressure and visible-light irradiation, the new catalyst can selectively (92% selectivity) catalyze the aerobic oxidation of toluene to benzaldehyde with yields of above 95%.As a very important chemical raw material, the selective formation of benzaldehyde from toluene at preparative or industrial levels requires the use of highly corrosive chlorine and high reaction temperatures, which severely corrodes equipment, pollutes the environment, and consumes a lot of energy. Herein, we report a robust and highly active catalyst for the benzaldehyde evolution reaction that is constructed by the surfactant-free growth of oxygen vacancy-rich W18O49 ultrathin nanowire networks. Under atmospheric pressure and visible-light irradiation, the new catalyst can selectively (92% selectivity) catalyze the aerobic oxidation of toluene to benzaldehyde with yields of above 95%. Electronic supplementary information (ESI) available: Experimental procedure, XRD patterns, TEM and HRTEM images, energy-dispersive X-ray spectra, UV-vis spectra, X-ray photoelectron spectroscopy (XPS), and EDS. See DOI: 10.1039/c6nr02949c

  9. New evidence for Cu-decorated binary-oxides mediating bacterial inactivation/mineralization in aerobic media.

    PubMed

    Rtimi, S; Pulgarin, C; Bensimon, M; Kiwi, J

    2016-08-01

    Binary oxide semiconductors TiO2-ZrO2 and Cu-decorated TiO2-ZrO2 (TiO2-ZrO2-Cu) uniform films were sputtered on polyester (PES). These films were irradiated under low intensity solar simulated light and led to bacterial inactivation in aerobic and anaerobic media as evaluated by CFU-plate counting. But bacterial mineralization was only induced by TiO2-ZrO2-Cu in aerobic media. The highly oxidative radicals generated on the films surface under light were identified by the use of appropriate scavengers. The hole generated on the TiO2-ZrO2 films is shown to be the main specie leading to bacterial inactivation. TiO2-ZrO2 and Cu-decorated TiO2-ZrO2 films release Zr and Ti <1ppb and Cu 4.6ppb/cm(2) as determined by inductively coupled plasma mass spectrometry (ICP-MS) This level is far below the citotoxicity permitted level allowed for mammalian cells suggesting that bacterial disinfection proceeds through an oligodynamic effect. By Fourier transform attenuated infrared spectroscopy (ATR-FTIR) the systematic shift of the predominating νs(CH2) vibrational-rotational peak making up most of the bacterial cell-wall content in C was monitored. Based on this evidence a mechanism suggested leading to CH bond stretching followed by cell lysis and cell death. Bacterial inactivation cycling was observed on TiO2-ZrO2-Cu showing the stability of these films leading to bacterial inactivation. PMID:27088192

  10. Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil.

    PubMed

    Scharko, Nicole K; Schütte, Ursel M E; Berke, Andrew E; Banina, Lauren; Peel, Hannah R; Donaldson, Melissa A; Hemmerich, Chris; White, Jeffrey R; Raff, Jonathan D

    2015-12-01

    Nitrous acid (HONO) is a photochemical source of hydroxyl radical and nitric oxide in the atmosphere that stems from abiotic and biogenic processes, including the activity of ammonia-oxidizing soil microbes. HONO fluxes were measured from agricultural and urban soil in mesocosm studies aimed at characterizing biogenic sources and linking them to indigenous microbial consortia. Fluxes of HONO from agricultural and urban soil were suppressed by addition of a nitrification inhibitor and enhanced by amendment with ammonium (NH4(+)), with peaks at 19 and 8 ng m(-2) s(-1), respectively. In addition, both agricultural and urban soils were observed to convert (15)NH4(+) to HO(15)NO. Genomic surveys of soil samples revealed that 1.5-6% of total expressed 16S rRNA sequences detected belonged to known ammonia oxidizing bacteria and archaea. Peak fluxes of HONO were directly related to the abundance of ammonia-oxidizer sequences, which in turn depended on soil pH. Peak HONO fluxes under fertilized conditions are comparable in magnitude to fluxes reported during field campaigns. The results suggest that biogenic HONO emissions will be important in soil environments that exhibit high nitrification rates (e.g., agricultural soil) although the widespread occurrence of ammonia oxidizers implies that biogenic HONO emissions are also possible in the urban and remote environment. PMID:26248160

  11. Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a pelagic redox gradient in the Baltic Sea

    PubMed Central

    Berg, Carlo; Listmann, Luisa; Vandieken, Verona; Vogts, Angela; Jürgens, Klaus

    2015-01-01

    Ammonia-oxidizing archaea (AOA) are an important component of the planktonic community in aquatic habitats, linking nitrogen and carbon cycles through nitrification and carbon fixation. Therefore, measurements of these processes in culture-based experiments can provide insights into their contributions to energy conservation and biomass production by specific AOA. In this study, by enriching AOA from a brackish, oxygen-depleted water-column in the Landsort Deep, central Baltic Sea, we were able to investigate ammonium oxidation, chemoautotrophy, and growth in seawater batch experiments. The highly enriched culture consisted of up to 97% archaea, with maximal archaeal numbers of 2.9 × 107 cells mL−1. Phylogenetic analysis of the 16S rRNA and ammonia monooxygenase subunit A (amoA) gene sequences revealed an affiliation with assemblages from low-salinity and freshwater habitats, with Candidatus Nitrosoarchaeum limnia as the closest relative. Growth correlated significantly with nitrite production, ammonium consumption, and CO2 fixation, which occurred at a ratio of 10 atoms N oxidized per 1 atom C fixed. According to the carbon balance, AOA biomass production can be entirely explained by chemoautotrophy. The cellular carbon content was estimated to be 9 fg C per cell. Single-cell-based 13C and 15N labeling experiments and analysis by nano-scale secondary ion mass spectrometry provided further evidence that cellular carbon was derived from bicarbonate and that ammonium was taken up by the cells. Our study therefore revealed that growth by an AOA belonging to the genus Nitrosoarchaeum can be sustained largely by chemoautotrophy. PMID:25642221

  12. Investigation of oxidative phosphorylation in continuous cultures. A non-equilibrium thermodynamic approach to energy transduction for Escherichia coli in aerobic condition

    NASA Astrophysics Data System (ADS)

    Ghafuri, Mohazabeh; Nosrati, Mohsen; Hosseinkhani, Saman

    2015-03-01

    Adenosine triphosphate (ATP) production in living cells is very important. Different researches have shown that in terms of mathematical modeling, the domain of these investigations is essentially restricted. Recently the thermodynamic models have been suggested for calculation of the efficiency of oxidative phosphorylation process and rate of energy loss in animal cells using chemiosmotic theory and non-equilibrium thermodynamics equations. In our previous work, we developed a mathematical model for mitochondria of animal cells. In this research, according to similarities between oxidative phosphorylation process in microorganisms and animal cells, Golfar's model was developed to predict the non-equilibrium thermodynamic behavior of the oxidative phosphorylation process for bacteria in aerobic condition. With this model the rate of energy loss, P/O ratio, and efficiency of oxidative phosphorylation were calculated for Escherichia coli in aerobic condition. The results then were compared with experimental data given by other authors. The thermodynamic model had an acceptable agreement with the experimental data.

  13. Copper-catalyzed aerobic oxidation and cleavage/formation of C-S bond: a novel synthesis of aryl methyl sulfones from aryl halides and DMSO.

    PubMed

    Yuan, Gaoqing; Zheng, Junhua; Gao, Xiaofang; Li, Xianwei; Huang, Liangbin; Chen, Huoji; Jiang, Huanfeng

    2012-08-01

    With atmospheric oxygen as the oxidant, a novel copper(I)-catalyzed synthesis of aryl methyl sulfones from aryl halides and widely available DMSO is described. The procedure tolerates aryl halides with various functional groups (such as methoxy, acetyl, chloro, fluoro and nitro groups), which could afford aryl methyl sulfones in moderate to high yields. The copper-catalyzed aerobic oxidation and the cleavage/formation of C-S bond are the key steps for this transformation. PMID:22728918

  14. Composition of extracellular polymeric substances in a partial nitrification reactor treating high ammonia wastewater and nitrous oxide emission.

    PubMed

    Wei, Dong; Du, Bin; Zhang, Jian; Hu, Zhen; Liang, Shuang; Li, Yiran

    2015-08-01

    The objective of this study was to characterize the composition of extracellular polymeric substances (EPS) during the achievement of partial nitrification and subsequent nitrous oxide (N2O) emission treating high ammonia wastewater. After operation of 120days, the reactor achieved high ammonia removal efficiency and stable nitrite accumulation. The average size of sludge flocs in the reactor increased from 102.6 to 258.5μm. The main compositions of EPS, including protein (PN) and polysaccharide (PS), increased to 65.46±3.27 and 21.63±1.08mg/g VSS, respectively. Results of three-dimensional excitation-emission matrix spectroscopy implied that EPS transferred to tryptophan PN-like and humic acid-like substrates. N2O emission accounts for 11.67% of removed nitrogen during the steady state of partial nitrification reactor. The obtained results could contribute a better understanding the achievement of partial nitrification through the composition changes of EPS, and provide more information to determine nitrogen removal by considering N2O emission. PMID:25772219

  15. Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill

    PubMed Central

    Bernhard, Anne E.; Sheffer, Roberta; Giblin, Anne E.; Marton, John M.; Roberts, Brian J.

    2016-01-01

    The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain. PMID:27375576

  16. Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill.

    PubMed

    Bernhard, Anne E; Sheffer, Roberta; Giblin, Anne E; Marton, John M; Roberts, Brian J

    2016-01-01

    The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain. PMID:27375576

  17. Nitrogen cycling through swine production systems: ammonia, dinitrogen, and nitrous oxide emissions.

    PubMed

    Harper, Lowry A; Sharpe, Ron R; Parkin, Tim B; De Visscher, Alex; van Cleemput, Oswald; Byers, F Michael

    2004-01-01

    Ammonia (NH(3)) emissions from animal systems have become a primary concern for all of livestock production. The purpose of this research was to establish the relationship of nitrogen (N) emissions to specific components of swine production systems and to determine accurate NH(3) emission factors appropriate for the regional climate, geography, and production systems. Micrometeorological instrumentation and gas sensors were placed over two lagoons in North Carolina during 1997-1999 to obtain information for determining ammonia emissions over extended periods and without interfering with the surrounding climate. Ammonia emissions varied diurnally and seasonally and were related to lagoon ammonium concentration, acidity, temperature, and wind turbulence. Conversion of significant quantities of ammonium NH(4)(+) to dinitrogen gas (N(2)) were measured in all lagoons with the emission rate largely dependent on NH(4)(+) concentration. Lagoon NH(4)(+) conversion to N(2) accounted for the largest loss component of the N entering the farm (43% as N(2)); however, small amounts of N(2)O were emitted from the lagoon (0.1%) and from field applications (0.05%) when effluent was applied nearby. In disagreement with previous and current estimates of NH(3) emissions from confined animal feeding operation (CAFO) systems, and invalidating current assumptions that most or all emissions are in the form of NH(3), we found much smaller NH(3) emissions from animal housing (7%), lagoons (8%), and fields (2%) using independent measurements of N transformation and transport. Nitrogen input and output in the production system were evaluated, and 95% of input N was accounted for as output N from the system. PMID:15254100

  18. Biofilter for removal of nitrogen oxides from contaminated gases under aerobic conditions

    DOEpatents

    Apel, W.A.

    1998-08-18

    A biofilter is described for reducing concentrations of gaseous nitrogen oxides in a polluted gas comprises a porous organic filter bed medium disposed in a housing, the filter bed medium including a mixed culture of naturally occurring denitrifying bacteria for converting the nitrogen oxides to nitrogen gas, carbon dioxide, and water. A method is described of reducing concentrations of nitrogen oxides in polluted gas comprises conducting the polluted gas through the biofilter so that the denitrifying bacteria can degrade the nitrogen oxides. A preferred filter medium is wood compost, however composts of other organic materials are functional. Regulation of pH, moisture content, exogenous carbon sources, and temperature are described. 6 figs.

  19. Biofilter for removal of nitrogen oxides from contaminated gases under aerobic conditions

    DOEpatents

    Apel, William A.

    1998-01-01

    A biofilter for reducing concentrations of gaseous nitrogen oxides in a polluted gas comprises a porous organic filter bed medium disposed in a housing, the filter bed medium including a mixed culture of naturally occurring denitrifying bacteria for converting the nitrogen oxides to nitrogen gas, carbon dioxide, and water. A method of reducing concentrations of nitrogen oxides in polluted gas comprises conducting the polluted gas through the biofilter so that the denitrifying bacteria can degrade the nitrogen oxides. A preferred filter medium is wood compost, however composts of other organic materials are functional. Regulation of pH, moisture content, exogenous carbon sources, and temperature are described.

  20. Selective isolation of ammonia-oxidizing bacteria from autotrophic nitrifying granules by applying cell-sorting and sub-culturing of microcolonies

    PubMed Central

    Fujitani, Hirotsugu; Kumagai, Asami; Ushiki, Norisuke; Momiuchi, Kengo; Tsuneda, Satoshi

    2015-01-01

    Nitrification is a key process in the biogeochemical nitrogen cycle and biological wastewater treatment that consists of two stepwise reactions, ammonia oxidation by ammonia-oxidizing bacteria (AOB) or archaea followed by nitrite oxidation by nitrite-oxidizing bacteria. One of the representatives of the AOB group is Nitrosomonas mobilis species. Although a few pure strains of this species have been isolated so far, approaches to their preservation in pure culture have not been established. Here, we report isolation of novel members of the N. mobilis species from autotrophic nitrifying granules used for ammonia-rich wastewater treatment. We developed an isolation method focusing on microcolonies formation of nitrifying bacteria. Two kinds of distinctive light scattering signatures in a cell-sorting system enabled to separate microcolonies from single cells and heterogeneous aggregates within granule samples. Inoculation of a pure microcolony into 96-well microtiter plates led to successful sub-culturing and increased probability of isolation. Obtained strain Ms1 is cultivated in the liquid culture with relatively high ammonia or nitrite concentration, not extremely slow growing. Considering environmental clones that were closely related to N. mobilis and detected in various environments, the availability of this novel strain would facilitate to reveal this member’s ecophysiology in a variety of habitats. PMID:26528282

  1. Molybdenum-based additives to mixed-metal oxides for use in hot gas cleanup sorbents for the catalytic decomposition of ammonia in coal gases

    DOEpatents

    Ayala, Raul E.

    1993-01-01

    This invention relates to additives to mixed-metal oxides that act simultaneously as sorbents and catalysts in cleanup systems for hot coal gases. Such additives of this type, generally, act as a sorbent to remove sulfur from the coal gases while substantially simultaneously, catalytically decomposing appreciable amounts of ammonia from the coal gases.

  2. Analysis of ammonia-oxidizing bacteria from hypersaline Mono Lake, California, on the basis of 16S rRNA sequences.

    PubMed

    Ward, B B; Martino, D P; Diaz, M C; Joye, S B

    2000-07-01

    Ammonia-oxidizing bacteria were detected by PCR amplification of DNA extracted from filtered water samples throughout the water column of Mono Lake, California. Ammonia-oxidizing members of the beta subdivision of the division Proteobacteria (beta-subdivision Proteobacteria) were detected using previously characterized PCR primers; target sequences were detected by direct amplification in both surface water and below the chemocline. Denaturing gradient gel electrophoresis analysis indicated the presence of at least four different beta-subdivision ammonia oxidizers in some samples. Subsequent sequencing of amplified 16S rDNA fragments verified the presence of sequences very similar to those of cultured Nitrosomonas strains. Two separate analyses, carried out under different conditions (different reagents, locations, PCR machines, sequencers, etc.), 2 years apart, detected similar ranges of sequence diversity in these samples. It seems likely that the physiological diversity of nitrifiers exceeds the diversity of their ribosomal sequences and that these sequences represent members of the Nitrosomonas europaea group that are acclimated to alkaline, high-salinity environments. Primers specific for Nitrosococcus oceanus, a marine ammonia-oxidizing bacterium in the gamma subdivision of the Proteobacteria, did not amplify target from any samples. PMID:10877781

  3. Comparison of ammonia-oxidizing bacterial community structure in membrane-assisted bioreactors using PCR-DGGE and FISH.

    PubMed

    Ziembińska, A; Ciesielski, S; Gnida, A; Zabczyńki, S; Surmacz-Górska, J; Miksch, K

    2012-08-01

    The ammonia-oxidizing bacterial (AOB) communities in three membrane bioreactors (MBRs) were monitored for 2 months after an acclimation period in order to investigate the influence of sludge age and medium type on AOB changeability and its connection with nitrification effectiveness. One MBR with a sludge age of 4 days was fed with a synthetic medium, whereas the other two with sludge ages of 8 and 32 days were fed with landfill leachate. The research revealed that landfill leachate can be effectively treated in an MBR with a higher sludge age for longer periods of time and that this improvement in performance was correlated with an increase in AOB biodiversity. Interestingly, the medium type has a stronger influence on AOB biocenosis formation than the sludge age. PMID:22713978

  4. The effect of dissolved oxygen on N2O production by ammonia-oxidizing bacteria in an enriched nitrifying sludge.

    PubMed

    Peng, Lai; Ni, Bing-Jie; Erler, Dirk; Ye, Liu; Yuan, Zhiguo

    2014-12-01

    Dissolved oxygen (DO) is commonly recognized as an important factor influencing nitrous oxide (N2O) production by ammonia-oxidizing bacteria (AOB). However, it has been difficult to separate the true effect of DO from that of nitrite, as DO variation often affects nitrite accumulation. The effect of DO on N2O production by an enriched nitrifying sludge, consisting of both AOB and nitrite-oxidizing bacteria (NOB), was investigated in this study. Nitrite accumulation was minimised by augmenting nitrite oxidation through the addition of an enriched NOB sludge. It was demonstrated that the specific N2O production rate increased from 0 to 1.9 ± 0.09 (n = 3) mg N2O-N/hr/g VSS with an increase of DO concentration from 0 to 3.0 mg O2/L, whereas N2O emission factor (the ratio between N2O nitrogen emitted and the ammonium nitrogen converted) decreased from 10.6 ± 1.7% (n = 3) at DO = 0.2 mg O2/L to 2.4 ± 0.1% (n = 3) at DO = 3.0 mg O2/L. The site preference measurements indicated that both the AOB denitrification and hydroxylamine (NH2OH) oxidation pathways contributed to N2O production, and DO had an important effect on the relative contributions of the two pathways. This finding is supported by analysis of the process data using an N2O model describing both pathways. As DO increased from 0.2 to 3.0 mg O2/L, the contribution of AOB denitrification decreased from 92% - 95%-66% - 73%, accompanied by a corresponding increase in the contribution by the NH2OH oxidation pathway. PMID:25179869

  5. Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)

    PubMed Central

    Yakimov, Michail M; Cono, Violetta La; Smedile, Francesco; DeLuca, Thomas H; Juárez, Silvia; Ciordia, Sergio; Fernández, Marisol; Albar, Juan Pablo; Ferrer, Manuel; Golyshin, Peter N; Giuliano, Laura

    2011-01-01

    Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and urease were identified and their affiliation demonstrated the presence of ‘deep-sea' clades distinct from ‘shallow' representatives. Measured deep-sea dark CO2 fixation estimates were comparable to the median value of photosynthetic biomass production calculated for this area of Tyrrhenian Sea, pointing to the significance of this process in the C cycle of aphotic marine ecosystems. To elucidate the pivotal organisms in this process, we targeted known marine crenarchaeal autotrophy-related genes, coding for acetyl-CoA carboxylase (accA) and 4-hydroxybutyryl-CoA dehydratase (4-hbd). As in case of nirK and ureC, these genes are grouped with deep-sea sequences being distantly related to those retrieved from the epipelagic zone. To pair the molecular data with specific functional attributes we performed [14C]HCO3 incorporation experiments followed by analyses of radiolabeled proteins using shotgun proteomics approach. More than 100 oligopeptides were attributed to 40 marine crenarchaeal-specific proteins that are involved in 10 different metabolic processes, including autotrophy. Obtained results provided a clear proof of chemolithoautotrophic physiology of bathypelagic crenarchaeota and indicated that this numerically predominant group of microorganisms facilitate a hitherto unrecognized sink for inorganic C of a global importance. PMID:21209665

  6. Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea).

    PubMed

    Yakimov, Michail M; Cono, Violetta La; Smedile, Francesco; DeLuca, Thomas H; Juárez, Silvia; Ciordia, Sergio; Fernández, Marisol; Albar, Juan Pablo; Ferrer, Manuel; Golyshin, Peter N; Giuliano, Laura

    2011-06-01

    Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and urease were identified and their affiliation demonstrated the presence of 'deep-sea' clades distinct from 'shallow' representatives. Measured deep-sea dark CO(2) fixation estimates were comparable to the median value of photosynthetic biomass production calculated for this area of Tyrrhenian Sea, pointing to the significance of this process in the C cycle of aphotic marine ecosystems. To elucidate the pivotal organisms in this process, we targeted known marine crenarchaeal autotrophy-related genes, coding for acetyl-CoA carboxylase (accA) and 4-hydroxybutyryl-CoA dehydratase (4-hbd). As in case of nirK and ureC, these genes are grouped with deep-sea sequences being distantly related to those retrieved from the epipelagic zone. To pair the molecular data with specific functional attributes we performed [(14)C]HCO(3) incorporation experiments followed by analyses of radiolabeled proteins using shotgun proteomics approach. More than 100 oligopeptides were attributed to 40 marine crenarchaeal-specific proteins that are involved in 10 different metabolic processes, including autotrophy. Obtained results provided a clear proof of chemolithoautotrophic physiology of bathypelagic crenarchaeota and indicated that this numerically predominant group of microorganisms facilitate a hitherto unrecognized sink for inorganic C of a global importance. PMID:21209665

  7. Vertical distribution of ammonia-oxidizing archaea (AOA) in the hyporheic zone of a eutrophic river in North China.

    PubMed

    Wang, Zhixin; Wang, Ziyuan; Huang, Caihong; Pei, Yuansheng

    2014-04-01

    Nitrification plays a significant role in the global nitrogen cycle, and this concept has been challenged with the discovery of ammonia-oxidizing archaea (AOA) in the environment. In this paper, the vertical variations of the diversity and abundance of AOA in the hyporheic zone of the Fuyang River in North China were investigated by molecular techniques, including clone libraries, phylogenetic analysis and real-time polymerase chain reaction. The archaeal amoA gene was detected in all sediments along the profile, and all AOA fell within marine group 1.1a and soil group1.1b of the Thaumarchaeota phylum, with the latter being the dominant type. The diversity of AOA decreased with the sediment depth, and there was a shift in AOA community between top-sediments (0-5 cm) and sub-sediments (5-70 cm). The abundance of the archaeal amoA gene (1.48 × 10⁷ to 5.50 × 10⁷ copies g⁻¹ dry sediment) was higher than that of the bacterial amoA gene (4.01 × 10⁴ to 1.75 × 10⁵ copies g⁻¹ dry sediment) in sub-sediments, resulting in a log₁₀ ratio of AOA to ammonia-oxidizing bacteria (AOB) from 2.27 to 2.69, whereas AOB outnumbered AOA in top-sediments with a low log10 ratio of (-0.24). The variations in the AOA community were primarily attributed to the combined effect of the nutrients (ammonium-N, nitrate-N and total organic carbon) and oxygen in sediments. Ammonium-N was the major factor influencing the relative abundance of AOA and AOB, although other factors, such as total organic carbon, were involved. This study helps elucidate the roles of AOA and AOB in the nitrogen cycling of hyporheic zone. PMID:24242890

  8. Differential responses of ammonia-oxidizing archaea and bacteria to long-term fertilization in a New England salt marsh

    PubMed Central

    Peng, Xuefeng; Yando, Erik; Hildebrand, Erica; Dwyer, Courtney; Kearney, Anne; Waciega, Alex; Valiela, Ivan; Bernhard, Anne E.

    2013-01-01

    Since the discovery of ammonia-oxidizing archaea (AOA), new questions have arisen about population and community dynamics and potential interactions between AOA and ammonia-oxidizing bacteria (AOB). We investigated the effects of long-term fertilization on AOA and AOB in the Great Sippewissett Marsh, Falmouth, MA, USA to address some of these questions. Sediment samples were collected from low and high marsh habitats in July 2009 from replicate plots that received low (LF), high (HF), and extra high (XF) levels of a mixed NPK fertilizer biweekly during the growing season since 1974. Additional untreated plots were included as controls (C). Terminal restriction fragment length polymorphism analysis of the amoA genes revealed distinct shifts in AOB communities related to fertilization treatment, but the response patterns of AOA were less consistent. Four AOB operational taxonomic units (OTUs) predictably and significantly responded to fertilization, but only one AOA OTU showed a significant pattern. Betaproteobacterial amoA gene sequences within the Nitrosospira-like cluster dominated at C and LF sites, while sequences related to Nitrosomonas spp. dominated at HF and XF sites. We identified some clusters of AOA sequences recovered primarily from high fertilization regimes, but other clusters consisted of sequences recovered from all fertilization treatments, suggesting greater physiological diversity. Surprisingly, fertilization appeared to have little impact on abundance of AOA or AOB. In summary, our data reveal striking patterns for AOA and AOB in response to long-term fertilization, and also suggest a missing link between community composition and abundance and nitrogen processing in the marsh. PMID:23346081

  9. Aerobic oxidation of lignin models using a base metal vanadium catalyst.