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Sample records for bacterial ammonia oxidizers

  1. Inhibition of Bacterial Ammonia Oxidation by Organohydrazines in Soil Microcosms

    PubMed Central

    Wu, Yucheng; Guo, Yun; Lin, Xiangui; Zhong, Wenhui; Jia, Zhongjun

    2012-01-01

    Hydroxylamine oxidation by hydroxylamine oxidoreductase (HAO) is a key step for energy-yielding in support of the growth of ammonia-oxidizing bacteria (AOB). Organohydrazines have been shown to inactivate HAO from Nitrosomonas europaea, and may serve as selective inhibitors to differentiate bacterial from archaeal ammonia oxidation due to the absence of bacterial HAO gene homolog in known ammonia-oxidizing archaea (AOA). In this study, the effects of three organohydrazines on activity, abundance, and composition of AOB and AOA were evaluated in soil microcosms. The results indicate that phenylhydrazine and methylhydrazine at the concentration of 100 μmol g−1 dry weight soil completely suppressed the activity of soil nitrification. Denaturing gradient gel electrophoresis fingerprinting and sequencing analysis of bacterial ammonia monooxygenase subunit A gene (amoA) clearly demonstrated that nitrification activity change is well paralleled with the growth of Nitrosomonas europaea-like AOB in soil microcosms. No significant correlation between AOA community structure and nitrification activity was observed among all treatments during the incubation period, although incomplete inhibition of nitrification activity occurred in 2-hydroxyethylhydrazine-amended soil microcosms. These findings show that the HAO-targeted organohydrazines can effectively inhibit bacterial nitrification in soil, and the mechanism of organohydrazine affecting AOA remains unclear. PMID:22319517

  2. Autotrophic growth of bacterial and archaeal ammonia oxidizers in freshwater sediment microcosms incubated at different temperatures.

    PubMed

    Wu, Yucheng; Ke, Xiubin; Hernández, Marcela; Wang, Baozhan; Dumont, Marc G; Jia, Zhongjun; Conrad, Ralf

    2013-05-01

    Both bacteria and archaea potentially contribute to ammonia oxidation, but their roles in freshwater sediments are still poorly understood. Seasonal differences in the relative activities of these groups might exist, since cultivated archaeal ammonia oxidizers have higher temperature optima than their bacterial counterparts. In this study, sediment collected from eutrophic freshwater Lake Taihu (China) was incubated at different temperatures (4°C, 15°C, 25°C, and 37°C) for up to 8 weeks. We examined the active bacterial and archaeal ammonia oxidizers in these sediment microcosms by using combined stable isotope probing (SIP) and molecular community analysis. The results showed that accumulation of nitrate in microcosms correlated negatively with temperature, although ammonium depletion was the same, which might have been related to enhanced activity of other nitrogen transformation processes. Incubation at different temperatures significantly changed the microbial community composition, as revealed by 454 pyrosequencing targeting bacterial 16S rRNA genes. After 8 weeks of incubation, [(13)C]bicarbonate labeling of bacterial amoA genes, which encode the ammonia monooxygenase subunit A, and an observed increase in copy numbers indicated the activity of ammonia-oxidizing bacteria in all microcosms. Nitrosomonas sp. strain Is79A3 and Nitrosomonas communis lineages dominated the heavy fraction of CsCl gradients at low and high temperatures, respectively, indicating a niche differentiation of active bacterial ammonia oxidizers along the temperature gradient. The (13)C labeling of ammonia-oxidizing archaea in microcosms incubated at 4 to 25°C was minor. In contrast, significant (13)C labeling of Nitrososphaera-like archaea and changes in the abundance and composition of archaeal amoA genes were observed at 37°C, implicating autotrophic growth of ammonia-oxidizing archaea under warmer conditions.

  3. Autotrophic Growth of Bacterial and Archaeal Ammonia Oxidizers in Freshwater Sediment Microcosms Incubated at Different Temperatures

    PubMed Central

    Wu, Yucheng; Ke, Xiubin; Hernández, Marcela; Wang, Baozhan; Dumont, Marc G.; Jia, Zhongjun

    2013-01-01

    Both bacteria and archaea potentially contribute to ammonia oxidation, but their roles in freshwater sediments are still poorly understood. Seasonal differences in the relative activities of these groups might exist, since cultivated archaeal ammonia oxidizers have higher temperature optima than their bacterial counterparts. In this study, sediment collected from eutrophic freshwater Lake Taihu (China) was incubated at different temperatures (4°C, 15°C, 25°C, and 37°C) for up to 8 weeks. We examined the active bacterial and archaeal ammonia oxidizers in these sediment microcosms by using combined stable isotope probing (SIP) and molecular community analysis. The results showed that accumulation of nitrate in microcosms correlated negatively with temperature, although ammonium depletion was the same, which might have been related to enhanced activity of other nitrogen transformation processes. Incubation at different temperatures significantly changed the microbial community composition, as revealed by 454 pyrosequencing targeting bacterial 16S rRNA genes. After 8 weeks of incubation, [13C]bicarbonate labeling of bacterial amoA genes, which encode the ammonia monooxygenase subunit A, and an observed increase in copy numbers indicated the activity of ammonia-oxidizing bacteria in all microcosms. Nitrosomonas sp. strain Is79A3 and Nitrosomonas communis lineages dominated the heavy fraction of CsCl gradients at low and high temperatures, respectively, indicating a niche differentiation of active bacterial ammonia oxidizers along the temperature gradient. The 13C labeling of ammonia-oxidizing archaea in microcosms incubated at 4 to 25°C was minor. In contrast, significant 13C labeling of Nitrososphaera-like archaea and changes in the abundance and composition of archaeal amoA genes were observed at 37°C, implicating autotrophic growth of ammonia-oxidizing archaea under warmer conditions. PMID:23455342

  4. 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

  5. Emergence of Competitive Dominant Ammonia-Oxidizing Bacterial Populations in a Full-Scale Industrial Wastewater Treatment Plant

    PubMed Central

    Layton, Alice C.; Dionisi, Hebe; Kuo, H.-W.; Robinson, Kevin G.; Garrett, Victoria M.; Meyers, Arthur; Sayler, Gary S.

    2005-01-01

    Ammonia-oxidizing bacterial populations in an industrial wastewater treatment plant were investigated with amoA and 16S rRNA gene real-time PCR assays. Nitrosomonas nitrosa initially dominated, but over time RI-27-type ammonia oxidizers, also within the Nitrosomonas communis lineage, increased from below detection to codominance. This shift occurred even though nitrification remained constant. PMID:15691975

  6. Quantitative assessment of ammonia-oxidizing bacterial communities in the epiphyton of submerged macrophytes in shallow lakes.

    PubMed

    Coci, M; Nicol, G W; Pilloni, G N; Schmid, M; Kamst-van Agterveld, M P; Bodelier, P L E; Laanbroek, H J

    2010-03-01

    In addition to the benthic and pelagic habitats, the epiphytic compartment of submerged macrophytes in shallow freshwater lakes offers a niche to bacterial ammonia-oxidizing communities. However, the diversity, numbers, and activity of epiphytic ammonia-oxidizing bacteria have long been overlooked. In the present study, we analyzed quantitatively the epiphytic communities of three shallow lakes by a potential nitrification assay and by quantitative PCR of 16S rRNA genes. On the basis of the m(2) of the lake surface, the gene copy numbers of epiphytic ammonia oxidizers were not significantly different from those in the benthic and pelagic compartments. The potential ammonia-oxidizing activities measured in the epiphytic compartment were also not significantly different from the activities determined in the benthic compartment. No potential ammonia-oxidizing activities were observed in the pelagic compartment. No activity was detected in the epiphyton of Chara aspera, the dominant submerged macrophyte in Lake Nuldernauw in The Netherlands. The presence of ammonia-oxidizing bacterial cells in the epiphyton of Potamogeton pectinatus was also demonstrated by fluorescent in situ hybridization microscopy images. By comparing the community composition as assessed by the 16S rRNA gene PCR-denaturing gradient gel electrophoresis approach, it was concluded that the epiphytic ammonia-oxidizing communities consisted of cells that were also present in the benthic and pelagic compartments. Of the environmental parameters examined, only the water retention time, the Kjeldahl nitrogen content, and the total phosphorus content correlated with potential ammonia-oxidizing activities. None of these parameters correlated with the numbers of gene copies related to ammonia-oxidizing betaproteobacteria.

  7. The influence of synthetic sheep urine on ammonia oxidizing bacterial communities in grassland soil.

    PubMed

    Mahmood, Shahid; Prosser, James I

    2006-06-01

    In grazed, grassland soils, sheep urine generates heterogeneity in ammonia concentrations, with potential impact on ammonia oxidizer community structure and soil N cycling. The influence of different levels of synthetic sheep urine on ammonia oxidizers was studied in grassland soil microcosms. 'Total' and active ammonia oxidizers were distinguished by comparing denaturing gradient gel electrophoresis (DGGE) profiles following PCR and RT-PCR amplification of 16S rRNA gene fragments, targeting DNA and RNA, respectively. The RNA-based approach indicated earlier, more reproducible and finer scale qualitative shifts in ammonia oxidizing communities than DNA-based analysis, but led to amplification of a small number of nonammonia oxidizer sequences. Qualitative changes in RNA-derived DGGE profiles were related to changes in nitrate accumulation. Sequence analysis of excised DGGE bands revealed that ammonia oxidizing communities in synthetic sheep urine-treated soils consisted mainly of Nitrosospira clusters 2, 3 and 4. Nitrosospira cluster 2 increased in relative abundance in microcosms treated with all levels of synthetic sheep urine. Low levels additionally led to increased relative abundance of Nitrosospira cluster 4 and medium and high levels increased relative abundance of cluster 3. Synthetic sheep urine is therefore likely to influence the spatial distribution and composition of ammonia oxidizer communities, with consequent effects on nitrate accumulation.

  8. 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.

  9. 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

  10. Responses of ammonia-oxidizing bacterial and archaeal populations to organic nitrogen amendments in low-nutrient groundwater.

    PubMed

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

    2010-04-01

    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.

  11. Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure.

    PubMed

    Bouskill, Nicholas J; Eveillard, Damien; O'Mullan, Gregory; Jackson, George A; Ward, Bess B

    2011-04-01

    Microbes exhibit remarkably high genetic diversity compared with plant and animal species. Many phylogenetically diverse but apparently functionally redundant microbial taxa are detectable within a cubic centimetre of mud or a millilitre of water, and the significance of this diversity, in terms of ecosystem function, has been difficult to understand. Thus it is not known whether temporal and spatial differences in microbial community composition are linked to particular environmental factors or might modulate ecosystem response to environmental change. Fifty-three water and sediment samples from upper and lower Chesapeake Bay were analysed in triplicate arrays to determine temporal and spatial patterns and relationships between ammonia-oxidizing bacterial (AOB) communities and environmental variables. Thirty-three water samples (three depths) collected during April, August and October, 2001-2004, from the oligohaline upper region of the Bay were analysed to investigate temporal patterns in archetype distribution. Using a combination of a non-weighted discrimination analysis and principal components analysis of community composition data obtained from functional gene microarrays, it was found that co-varying AOB assemblages reoccurred seasonally in concert with specific environmental conditions, potentially revealing patterns of niche differentiation. Among the most notable patterns were correlations of AOB archetypes with temperature, DON and ammonium concentrations. Different AOB archetypes were more prevalent at certain times of the year, e.g. some were more abundant every autumn and others every spring. This data set documents the successional return to an indigenous community following massive perturbation (hurricane induced flooding) as well as the seasonal reoccurrence of specific lineages, identified by key functional genes, associated with the biogeochemically important process nitrification.

  12. 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.

  13. Simazine degradation in bioaugmented soil: urea impact and response of ammonia-oxidizing bacteria and other soil bacterial communities.

    PubMed

    Guo, Qingwei; Wan, Rui; Xie, Shuguang

    2014-01-01

    The objective of this study was to investigate the impact of exogenous urea nitrogen on ammonia-oxidizing bacteria (AOB) and other soil bacterial communities in soil bioaugmented for simazine remediation. The previously isolated simazine-degrading Arthrobacter sp. strain SD1 was used to degrade the herbicide. The effect of urea on the simazine degradation capacity of the soil bioaugmented with Arthrobacter strain SD1 was assessed using quantitative PCR targeting the s-triazine-degrading trzN and atzC genes. Structures of bacterial and AOB communities were characterized using terminal restriction fragment length polymorphism. Urea fertilizer could affect simazine biodegradation and decreased the proportion of its trzN and atzC genes in soil augmented with Arthrobacter strain SD1. Bioaugmentation process could significantly alter the structures of both bacterial and AOB communities, which were strongly affected by urea amendment, depending on the dosage. This study could provide some new insights towards s-triazine bioremediation and microbial ecology in a bioaugmented system. However, further studies are necessary in order to elucidate the impact of different types and levels of nitrogen sources on s-triazine-degraders and bacterial and AOB communities in bioaugmented soil.

  14. 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

  15. Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira.

    PubMed

    Bartelme, Ryan P; McLellan, Sandra L; Newton, Ryan J

    2017-01-01

    Recirculating aquaculture systems (RAS) are unique engineered ecosystems that minimize environmental perturbation by reducing nutrient pollution discharge. RAS typically employ a biofilter to control ammonia levels produced as a byproduct of fish protein catabolism. Nitrosomonas (ammonia-oxidizing), Nitrospira, and Nitrobacter (nitrite-oxidizing) species are thought to be the primary nitrifiers present in RAS biofilters. We explored this assertion by characterizing the biofilter bacterial and archaeal community of a commercial scale freshwater RAS that has been in operation for >15 years. We found the biofilter community harbored a diverse array of bacterial taxa (>1000 genus-level taxon assignments) dominated by Chitinophagaceae (~12%) and Acidobacteria (~9%). The bacterial community exhibited significant composition shifts with changes in biofilter depth and in conjunction with operational changes across a fish rearing cycle. Archaea also were abundant, and were comprised solely of a low diversity assemblage of Thaumarchaeota (>95%), thought to be ammonia-oxidizing archaea (AOA) from the presence of AOA ammonia monooxygenase genes. Nitrosomonas were present at all depths and time points. However, their abundance was >3 orders of magnitude less than AOA and exhibited significant depth-time variability not observed for AOA. Phylogenetic analysis of the nitrite oxidoreductase beta subunit (nxrB) gene indicated two distinct Nitrospira populations were present, while Nitrobacter were not detected. Subsequent identification of Nitrospira ammonia monooxygenase alpha subunit genes in conjunction with the phylogenetic placement and quantification of the nxrB genotypes suggests complete ammonia-oxidizing (comammox) and nitrite-oxidizing Nitrospira populations co-exist with relatively equivalent and stable abundances in this system. It appears RAS biofilters harbor complex microbial communities whose composition can be affected directly by typical system operations while

  16. Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira

    PubMed Central

    Bartelme, Ryan P.; McLellan, Sandra L.; Newton, Ryan J.

    2017-01-01

    Recirculating aquaculture systems (RAS) are unique engineered ecosystems that minimize environmental perturbation by reducing nutrient pollution discharge. RAS typically employ a biofilter to control ammonia levels produced as a byproduct of fish protein catabolism. Nitrosomonas (ammonia-oxidizing), Nitrospira, and Nitrobacter (nitrite-oxidizing) species are thought to be the primary nitrifiers present in RAS biofilters. We explored this assertion by characterizing the biofilter bacterial and archaeal community of a commercial scale freshwater RAS that has been in operation for >15 years. We found the biofilter community harbored a diverse array of bacterial taxa (>1000 genus-level taxon assignments) dominated by Chitinophagaceae (~12%) and Acidobacteria (~9%). The bacterial community exhibited significant composition shifts with changes in biofilter depth and in conjunction with operational changes across a fish rearing cycle. Archaea also were abundant, and were comprised solely of a low diversity assemblage of Thaumarchaeota (>95%), thought to be ammonia-oxidizing archaea (AOA) from the presence of AOA ammonia monooxygenase genes. Nitrosomonas were present at all depths and time points. However, their abundance was >3 orders of magnitude less than AOA and exhibited significant depth-time variability not observed for AOA. Phylogenetic analysis of the nitrite oxidoreductase beta subunit (nxrB) gene indicated two distinct Nitrospira populations were present, while Nitrobacter were not detected. Subsequent identification of Nitrospira ammonia monooxygenase alpha subunit genes in conjunction with the phylogenetic placement and quantification of the nxrB genotypes suggests complete ammonia-oxidizing (comammox) and nitrite-oxidizing Nitrospira populations co-exist with relatively equivalent and stable abundances in this system. It appears RAS biofilters harbor complex microbial communities whose composition can be affected directly by typical system operations while

  17. Investigation of total bacterial and ammonia-oxidizing bacterial community composition in a full-scale aerated submerged biofilm reactor for drinking water pretreatment in China.

    PubMed

    Qin, Ying-Ying; Li, Dao-Tang; Yang, Hong

    2007-03-01

    The community composition of total bacteria and ammonia-oxidizing bacteria in a full-scale aerated submerged biofilm reactor for drinking water pretreatment was characterized by analysis of 16S rRNA gene and the functional gene amoA, respectively. Sampling was performed in February and in July. 16S rRNA gene clone libraries revealed 13 bacterial divisions. At both sampling dates, the majority of clone sequences were related to the Alpha- and Betaproteobacteria. A minor proportion belonged to the following groups: Gammaproteobacteria, Deltaproteobacteria, Nitrospira, Firmicutes, Acidobacteria, Verrucomicrobia, Actinobacteria, Planctomycetes, Chloroflexi, Gemmatimonadetes and the Cytophaga-Flavobacterium-Bacteroides group. Some sequences related to bacteria owning high potential metabolic capacities were detected in both samples, such as Rhodobacter-like rRNA gene sequences. Surveys of cloned amoA genes from the two biofilm samples revealed ammonia-oxidizing bacterial sequences affiliated with the Nitrosomonas oligotropha lineage, Nitrosomonas communis lineage. An unknown Nitrosomonas group of amoA gene sequences was also detected.

  18. Autotrophic ammonia oxidation by soil thaumarchaea

    PubMed Central

    Zhang, Li-Mei; Offre, Pierre R.; He, Ji-Zheng; Verhamme, Daniel T.; Nicol, Graeme W.; Prosser, James I.

    2010-01-01

    Nitrification plays a central role in the global nitrogen cycle and is responsible for significant losses of nitrogen fertilizer, atmospheric pollution by the greenhouse gas nitrous oxide, and nitrate pollution of groundwaters. Ammonia oxidation, the first step in nitrification, was thought to be performed by autotrophic bacteria until the recent discovery of archaeal ammonia oxidizers. Autotrophic archaeal ammonia oxidizers have been cultivated from marine and thermal spring environments, but the relative importance of bacteria and archaea in soil nitrification is unclear and it is believed that soil archaeal ammonia oxidizers may use organic carbon, rather than growing autotrophically. In this soil microcosm study, stable isotope probing was used to demonstrate incorporation of 13C-enriched carbon dioxide into the genomes of thaumarchaea possessing two functional genes: amoA, encoding a subunit of ammonia monooxygenase that catalyses the first step in ammonia oxidation; and hcd, a key gene in the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle, which has been found so far only in archaea. Nitrification was accompanied by increases in archaeal amoA gene abundance and changes in amoA gene diversity, but no change was observed in bacterial amoA genes. Archaeal, but not bacterial, amoA genes were also detected in 13C-labeled DNA, demonstrating inorganic CO2 fixation by archaeal, but not bacterial, ammonia oxidizers. Autotrophic archaeal ammonia oxidation was further supported by coordinate increases in amoA and hcd gene abundance in 13C-labeled DNA. The results therefore provide direct evidence for a role for archaea in soil ammonia oxidation and demonstrate autotrophic growth of ammonia oxidizing archaea in soil. PMID:20855593

  19. 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.

  20. Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

    PubMed Central

    Sedlacek, Christopher J.; Nielsen, Susanne; Greis, Kenneth D.; Haffey, Wendy D.; Revsbech, Niels Peter; Ticak, Tomislav; Laanbroek, Hendrikus J.

    2016-01-01

    ABSTRACT Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism. IMPORTANCE Aerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to

  1. Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians

    PubMed Central

    Erwin, Patrick M; Pineda, Mari Carmen; Webster, Nicole; Turon, Xavier; López-Legentil, Susanna

    2014-01-01

    Ascidians are ecologically important components of marine ecosystems yet the ascidian microbiota remains largely unexplored beyond a few model species. We used 16S rRNA gene tag pyrosequencing to provide a comprehensive characterization of microbial symbionts in the tunic of 42 Great Barrier Reef ascidian samples representing 25 species. Results revealed high bacterial biodiversity (3 217 unique operational taxonomic units (OTU0.03) from 19 described and 14 candidate phyla) and the widespread occurrence of ammonia-oxidizing Thaumarchaeota in coral reef ascidians (24 of 25 host species). The ascidian microbiota was clearly differentiated from seawater microbial communities and included symbiont lineages shared with other invertebrate hosts as well as unique, ascidian-specific phylotypes. Several rare seawater microbes were markedly enriched (200–700 fold) in the ascidian tunic, suggesting that the rare biosphere of seawater may act as a conduit for horizontal symbiont transfer. However, most OTUs (71%) were rare and specific to single hosts and a significant correlation between host relatedness and symbiont community similarity was detected, indicating a high degree of host-specificity and potential role of vertical transmission in structuring these communities. We hypothesize that the complex ascidian microbiota revealed herein is maintained by the dynamic microenvironments within the ascidian tunic, offering optimal conditions for different metabolic pathways such as ample chemical substrate (ammonia-rich host waste) and physical habitat (high oxygen, low irradiance) for nitrification. Thus, ascidian hosts provide unique and fertile niches for diverse microorganisms and may represent an important and previously unrecognized habitat for nitrite/nitrate regeneration in coral reef ecosystems. PMID:24152714

  2. The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms.

    PubMed

    LaPara, Timothy M; Hope Wilkinson, Katheryn; Strait, Jacqueline M; Hozalski, Raymond M; Sadowksy, Michael J; Hamilton, Matthew J

    2015-10-01

    The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (a Variovorax sp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was a Nitrospira sp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; <0.07%) and no ammonia-oxidizing Archaea were detected in the profiles. Quantitative PCR of amoA genes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB.

  3. The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

    PubMed Central

    Hope Wilkinson, Katheryn; Strait, Jacqueline M.; Hozalski, Raymond M.; Sadowksy, Michael J.; Hamilton, Matthew J.

    2015-01-01

    The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (a Variovorax sp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was a Nitrospira sp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; <0.07%) and no ammonia-oxidizing Archaea were detected in the profiles. Quantitative PCR of amoA genes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB. PMID:26209671

  4. Resilience of the rhizosphere Pseudomonas and ammonia-oxidizing bacterial populations during phytoextraction of heavy metal polluted soil with poplar.

    PubMed

    Frey, Beat; Pesaro, Manuel; Rüdt, Andreas; Widmer, Franco

    2008-06-01

    We assessed the effects of phytoextraction on the dynamics of Pseudomonas spp. and ammonia-oxidizing bacterial populations in a heavy metal (HM) polluted soil. Hybrid poplars were grown in two-compartment root containers with a medium history (> 4 years) of HM pollution for 13 weeks. Bulk and poplar rhizosphere soils were analysed by denaturing gradient gel electrophoresis (DGGE) of Pseudomonas (sensu stricto) 16S rRNA and amoA gene fragments. DGGE patterns revealed that Pseudomonas and amoA-containing populations in the contaminated soils were markedly different from those in the uncontaminated soils. Pseudomonas and amoA profiles appeared to be stable over time in the bulk soils. In contrast, contaminated rhizosphere soils revealed a clear shift of populations with removal of HM becoming similar or at least shifted to the populations of the uncontaminated soils. The effect of phytoextraction was, however, not evident in the bulk samples, which still contained large amounts of HM. Cloning and sequencing of dominant DGGE bands revealed that Pseudomonas were phylogenetically related to the Pseudomonas fluorescens cluster and the amoA sequences to Nitrosospira spp. At the last sampling, major prominent band sequences from contaminated rhizosphere soils were identical to sequences obtained from uncontaminated rhizosphere soils, indicating that the populations were dominated by the same phylotypes. This study suggests that two taxonomically different populations are able to recover after the relief of HM stress by phytoextraction practices, whereas bulk microbial activities still remained depressed.

  5. Occurrence and elimination of antibiotics at four sewage treatment plants in Japan and their effects on bacterial ammonia oxidation.

    PubMed

    Ghosh, Gopal Chandra; Okuda, Takashi; Yamashita, Naoyuki; Tanaka, Hiroaki

    2009-01-01

    The occurrence and elimination of seventeen antibiotics (three macrolides: azithromycin, clarithromycin and roxithromycin; five quinolones: ciprofloxacin, enrofloxacin, levofloxacin, nalidixic acid and norfloxacin; five sulfonamides: sulfadimethoxine, sulfadimizine, sulfamerazine, sulfamethoxazole and sulfamonomethoxine; and others: tetracycline, lincomycin, salinomycin and trimethoprim) were investigated at four full-scale sewage treatment plants in Japan. The highest concentration was recorded for clarithromycin (1,129 to 4,820 ng/L) in influent, followed by azithromycin (160 to 1,347 ng/L), levofloxacin (255 to 587 ng/L) and norfloxacin (155 to 486 ng/L). A vary inconsistence picture was obtained with negative to over 90% removal. Nalidixic acid (53 to 100%) exhibited higher removal efficiency followed by norfloxacin (75 to 95%), levofloxacin (40 to 90%), ciprofloxacin (60 to 83%) and enrofloxacin (38 to 74%). Among macrolides, clarithromycin (50 to 88%) and azithromycin (34 to 86%) showed relatively higher removal efficiency than roxithromycin (-32 to 59%). For most of the antibiotics removal efficiency was higher in A2O and AO based secondary treatment process than CAS process. The effect of the antibiotics on bacterial ammonia oxidation determined by oxygen uptake rate presented that there was no significant effect below 0.05 mg/L of each antibiotics. Even at the same concentration, antibiotics in mixed condition had higher inhibition effects than individuals.

  6. Niche specificity of ammonia-oxidizing archaeal and bacterial communities in a freshwater wetland receiving municipal wastewater in Daqing, Northeast China.

    PubMed

    Lee, Kwok-Ho; Wang, Yong-Feng; Li, Hui; Gu, Ji-Dong

    2014-12-01

    Ecophysiological differences between ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) enable them to adapt to different niches in complex freshwater wetland ecosystems. The community characters of AOA and AOB in the different niches in a freshwater wetland receiving municipal wastewater, as well as the physicochemical parameters of sediment/soil samples, were investigated in this study. AOA community structures varied and separated from each other among four different niches. Wetland vegetation including aquatic macrophytes and terrestrial plants affected the AOA community composition but less for AOB, whereas sediment depths might contribute to the AOB community shift. The diversity of AOA communities was higher than that of AOB across all four niches. Archaeal and bacterial amoA genes (encoding for the alpha-subunit of ammonia monooxygenases) were most diverse in the dry-land niche, indicating O2 availability might favor ammonia oxidation. The majority of AOA amoA sequences belonged to the Soil/sediment Cluster B in the freshwater wetland ecosystems, while the dominant AOB amoA sequences were affiliated with Nitrosospira-like cluster. In the Nitrosospira-like cluster, AOB amoA gene sequences affiliated with the uncultured ammonia-oxidizing beta-proteobacteria constituted the largest portion (99%). Moreover, independent methods for phylogenetic tree analysis supported high parsimony bootstrap values. As a consequence, it is proposed that Nitrosospira-like amoA gene sequences recovered in this study represent a potentially novel cluster, grouping with the sequences from Gulf of Mexico deposited in the public databases.

  7. Changes in nitrogen-fixing and ammonia-oxidizing bacterial communities in soil of a mixed conifer forest after wildfire.

    PubMed

    Yeager, Chris M; Northup, Diana E; Grow, Christy C; Barns, Susan M; Kuske, Cheryl R

    2005-05-01

    This study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and amoA PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizing species was less in soil from the fire-impacted sites than from the unburned sites. The number of dominant nifH sequence types was greater in fire-impacted soils, and nifH sequences that were most closely related to those from the spore-forming taxa Clostridium and Paenibacillus were more abundant in the burned soils. In T-RFLP patterns of the ammonia-oxidizing community, terminal restriction fragments (TRFs) representing amoA cluster 1, 2, or 4 Nitrosospira spp. were dominant (80 to 90%) in unburned soils, while TRFs representing amoA cluster 3A Nitrosospira spp. dominated (65 to 95%) in fire-impacted soils. The dominance of amoA cluster 3A Nitrosospira spp. sequence types was positively correlated with soil pH (5.6 to 7.5) and NH(3)-N levels (0.002 to 0.976 ppm), both of which were higher in burned soils. The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire.

  8. 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.

  9. Ammonia- and Nitrite-Oxidizing Bacterial Communities in a Pilot-Scale Chloraminated Drinking Water Distribution System

    PubMed Central

    Regan, John M.; Harrington, Gregory W.; Noguera, Daniel R.

    2002-01-01

    Nitrification in drinking water distribution systems is a common operational problem for many utilities that use chloramines for secondary disinfection. The diversity of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in the distribution systems of a pilot-scale chloraminated drinking water treatment system was characterized using terminal restriction fragment length polymorphism (T-RFLP) analysis and 16S rRNA gene (ribosomal DNA [rDNA]) cloning and sequencing. For ammonia oxidizers, 16S rDNA-targeted T-RFLP indicated the presence of Nitrosomonas in each of the distribution systems, with a considerably smaller peak attributable to Nitrosospira-like AOB. Sequences of AOB amplification products aligned within the Nitrosomonas oligotropha cluster and were closely related to N. oligotropha and Nitrosomonas ureae. The nitrite-oxidizing communities were comprised primarily of Nitrospira, although Nitrobacter was detected in some samples. These results suggest a possible selection of AOB related to N. oligotropha and N. ureae in chloraminated systems and demonstrate the presence of NOB, indicating a biological mechanism for nitrite loss that contributes to a reduction in nitrite-associated chloramine decay. PMID:11772611

  10. Ammonia- and nitrite-oxidizing bacterial communities in a pilot-scale chloraminated drinking water distribution system.

    PubMed

    Regan, John M; Harrington, Gregory W; Noguera, Daniel R

    2002-01-01

    Nitrification in drinking water distribution systems is a common operational problem for many utilities that use chloramines for secondary disinfection. The diversity of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in the distribution systems of a pilot-scale chloraminated drinking water treatment system was characterized using terminal restriction fragment length polymorphism (T-RFLP) analysis and 16S rRNA gene (ribosomal DNA [rDNA]) cloning and sequencing. For ammonia oxidizers, 16S rDNA-targeted T-RFLP indicated the presence of Nitrosomonas in each of the distribution systems, with a considerably smaller peak attributable to Nitrosospira-like AOB. Sequences of AOB amplification products aligned within the Nitrosomonas oligotropha cluster and were closely related to N. oligotropha and Nitrosomonas ureae. The nitrite-oxidizing communities were comprised primarily of Nitrospira, although Nitrobacter was detected in some samples. These results suggest a possible selection of AOB related to N. oligotropha and N. ureae in chloraminated systems and demonstrate the presence of NOB, indicating a biological mechanism for nitrite loss that contributes to a reduction in nitrite-associated chloramine decay.

  11. Stimulation of thaumarchaeal ammonia oxidation by ammonia derived from organic nitrogen but not added inorganic nitrogen.

    PubMed

    Levičnik-Höfferle, Spela; Nicol, Graeme W; Ausec, Luka; Mandić-Mulec, Ines; Prosser, James I

    2012-04-01

    Ammonia oxidation, the first step in nitrification, is performed by autotrophic bacteria and thaumarchaea, whose relative contributions vary in different soils. Distinctive environmental niches for the two groups have not been identified, but evidence from previous studies suggests that activity of thaumarchaea, unlike that of bacterial ammonia oxidizers, is unaffected by addition of inorganic N fertilizer and that they preferentially utilize ammonia generated from the mineralization of organic N. This hypothesis was tested by determining the influence of both inorganic and organic N sources on nitrification rate and ammonia oxidizer growth and community structure in microcosms containing acidic, forest soil in which ammonia oxidation was dominated by thaumarchaea. Nitrification rate was unaffected by the incubation of soil with inorganic ammonium but was significantly stimulated by the addition of organic N. Oxidation of ammonia generated from native soil organic matter or added organic N, but not added inorganic N, was accompanied by increases in abundance of the thaumarchaeal amoA gene, a functional gene for ammonia oxidation, but changes in community structure were not observed. Bacterial amoA genes could not be detected. Ammonia oxidation was completely inhibited by 0.01% acetylene in all treatments, indicating ammonia monooxygenase-dependent activity. The findings have implications for current models of soil nitrification and for nitrification control strategies to minimize fertilizer loss and nitrous oxide production. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  12. 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.

  13. 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.

  14. 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.

  15. Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils

    PubMed Central

    Zhang, Li-Mei; Hu, Hang-Wei; Shen, Ju-Pei; He, Ji-Zheng

    2012-01-01

    Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. 13CO2-DNA-stable isotope probing results showed significant assimilation of 13C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO2 fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active 13CO2-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils. PMID:22134644

  16. Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils.

    PubMed

    Zhang, Li-Mei; Hu, Hang-Wei; Shen, Ju-Pei; He, Ji-Zheng

    2012-05-01

    Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. (13)CO(2)-DNA-stable isotope probing results showed significant assimilation of (13)C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO(2) fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active (13)CO(2)-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.

  17. Dynamics of specific ammonia-oxidizing bacterial populations and nitrification in response to controlled shifts of ammonium concentrations in wastewater.

    PubMed

    Almstrand, R; Lydmark, P; Lindgren, P-E; Sörensson, F; Hermansson, M

    2013-03-01

    Ammonia-oxidizing bacteria (AOB) are essential for the nitrification process in wastewater treatment. To retain these slow-growing bacteria in wastewater treatment plants (WWTPs), they are often grown as biofilms, e.g., on nitrifying trickling filters (NTFs) or on carriers in moving bed biofilm reactors (MBBRs). On NTFs, a decreasing ammonium gradient is formed because of the AOB activity, resulting in low ammonium concentrations at the bottom and reduced biomass with depth. To optimize the NTF process, different ammonium feed strategies may be designed. This, however, requires knowledge about AOB population dynamics. Using fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy, we followed biomass changes during 6 months, of three AOB populations on biofilm carriers. These were immersed in aerated MBBR tanks in a pilot plant receiving full-scale wastewater. Tanks were arranged in series, forming a wastewater ammonium gradient mimicking an NTF ammonium gradient. The biomass of one of the dominating Nitrosomonas oligotropha-like populations increased after an ammonium upshift, reaching levels comparable to the high ammonium control in 28 days, whereas a Nitrosomonas europaea-like population increased relatively slowly. The MBBR results, together with competition studies in NTF systems fed with wastewater under controlled ammonium regimes, suggest a differentiation between the two N. oligotropha populations, which may be important for WWTP nitrification.

  18. Bacterial and Archaea Community Present in the Pine Barrens Forest of Long Island, NY: Unusually High Percentage of Ammonia Oxidizing Bacteria

    PubMed Central

    Shah, Vishal; Shah, Shreya; Kambhampati, Murty S.; Ambrose, Jeffery; Smith, Nyesha; Dowd, Scot E.; McDonnell, Kevin T.; Panigrahi, Bishnu; Green, Timothy

    2011-01-01

    Of the few preserved areas in the northeast of United States, the soil in the Pine Barrens Forests presents a harsh environment for the microorganisms to grow and survive. In the current study we report the use of clustering methods to scientifically select the sampling locations that would represent the entire forest and also report the microbial diversity present in various horizons of the soil. Sixty six sampling locations were selected across the forest and soils were collected from three horizons (sampling depths). The three horizons were 0–10 cm (Horizon O); 11–25 cm (Horizon A) and 26–40 cm (Horizon B). Based on the total microbial substrate utilization pattern and K-means clustering analysis, the soil in the Pine Barrens Forest can be classified into four distinct clusters at each of the three horizons. One soil sample from each of the four clusters were selected and archaeal and bacterial populations within the soil studied using pyrosequencing method. The results show the microbial communities present in each of these clusters are different. Within the microbial communities present, microorganisms involved in nitrogen cycle occupy a major fraction of microbial community in the soil. High level of diversity was observed for nitrogen fixing bacteria. In contrast, Nitrosovibrio and Nitrosocaldus spp are the single bacterial and archaeal population respectively carrying out ammonia oxidation in the soil. PMID:22028845

  19. Bacterial and archaea community present in the Pine Barrens Forest of Long Island, NY: unusually high percentage of ammonia oxidizing bacteria.

    PubMed

    Shah, Vishal; Shah, Shreya; Kambhampati, Murty S; Ambrose, Jeffery; Smith, Nyesha; Dowd, Scot E; McDonnell, Kevin T; Panigrahi, Bishnu; Green, Timothy

    2011-01-01

    Of the few preserved areas in the northeast of United States, the soil in the Pine Barrens Forests presents a harsh environment for the microorganisms to grow and survive. In the current study we report the use of clustering methods to scientifically select the sampling locations that would represent the entire forest and also report the microbial diversity present in various horizons of the soil. Sixty six sampling locations were selected across the forest and soils were collected from three horizons (sampling depths). The three horizons were 0-10 cm (Horizon O); 11-25 cm (Horizon A) and 26-40 cm (Horizon B). Based on the total microbial substrate utilization pattern and K-means clustering analysis, the soil in the Pine Barrens Forest can be classified into four distinct clusters at each of the three horizons. One soil sample from each of the four clusters were selected and archaeal and bacterial populations within the soil studied using pyrosequencing method. The results show the microbial communities present in each of these clusters are different. Within the microbial communities present, microorganisms involved in nitrogen cycle occupy a major fraction of microbial community in the soil. High level of diversity was observed for nitrogen fixing bacteria. In contrast, Nitrosovibrio and Nitrosocaldus spp are the single bacterial and archaeal population respectively carrying out ammonia oxidation in the soil.

  20. Bacterial and Archaea Community Present in the Pine Barrens Forest of Long Island, NY: Unusually High Percentage of Ammonia Oxidizing Bacteria

    SciTech Connect

    Shah, V.; Green, T.; Shah, V.; Shah, S.; Kambhampati, M.; Ambrose, J.; Smith, N.; Dowd, S.; McDonnell, K.; Panigrahi, B.

    2011-10-20

    Of the few preserved areas in the northeast of United States, the soil in the Pine Barrens Forests presents a harsh environment for the microorganisms to grow and survive. In the current study we report the use of clustering methods to scientifically select the sampling locations that would represent the entire forest and also report the microbial diversity present in various horizons of the soil. Sixty six sampling locations were selected across the forest and soils were collected from three horizons (sampling depths). The three horizons were 0-10 cm (Horizon O); 11-25 cm (Horizon A) and 26-40 cm (Horizon B). Based on the total microbial substrate utilization pattern and K-means clustering analysis, the soil in the Pine Barrens Forest can be classified into four distinct clusters at each of the three horizons. One soil sample from each of the four clusters were selected and archaeal and bacterial populations within the soil studied using pyrosequencing method. The results show the microbial communities present in each of these clusters are different. Within the microbial communities present, microorganisms involved in nitrogen cycle occupy a major fraction of microbial community in the soil. High level of diversity was observed for nitrogen fixing bacteria. In contrast, Nitrosovibrio and Nitrosocaldus spp are the single bacterial and archaeal population respectively carrying out ammonia oxidation in the soil.

  1. Ammonia manipulates the ammonia-oxidizing archaea and bacteria in the coastal sediment-water microcosms.

    PubMed

    Zhang, Yan; Chen, Lujun; Dai, Tianjiao; Sun, Renhua; Wen, Donghui

    2015-08-01

    Ammonia was observed as a potential significant factor to manipulate the abundance and activity of ammonia-oxidizing microorganisms (AOMs) in water environments. For the first time, this study confirmed this phenomenon by laboratory cultivation. In a series of estuarine sediment-coastal water microcosms, we investigated the AOM's phylogenetic composition and activity change in response to ammonia concentration. Increase of ammonia concentration promoted bacterial amoA gene abundance in a linear pattern. The ratio of transcribed ammonia-oxidizing bacteria (AOB) amoA gene/ammonia-oxidizing archaea (AOA) amoA gene increased from 0.1 to 43 as NH4 (+)-N increased from less than 0.1 to 12 mg L(-1), and AOA amoA transcription was undetected under 20 mg NH4 (+)-N L(-1). The incubation of stable isotope probing (SIP) microcosms revealed a faster (13)C-NaHCO3 incorporation rate of AOA amoA gene under 0.1 mg NH4 (+)-N L(-1) and a sole (13)C-NaHCO3 utilization of the AOB amoA gene under 20 mg NH4 (+)-N L(-1). Our results indicate that ammonia concentration manipulates the structure of AOM. AOA prefers to live and perform higher amoA transcription activity than AOB in ammonia-limited water environments, and AOB tends to take the first contributor place in ammonia-rich ones.

  2. Characterizing the isotopic composition of atmospheric ammonia emission sources using passive samplers and a combined oxidation-bacterial denitrifier approach

    USDA-ARS?s Scientific Manuscript database

    Ammonia (NH3) emissions are a substantial source of nitrogen pollution to sensitive terrestrial, aquatic, and marine ecosystems. Dependable quantification of NH3 sources is of growing importance due to recently observed increases in ammonium (NH4+) deposition rates that are directly proportional to ...

  3. Effect of vortex flows on ammonia oxidation

    SciTech Connect

    Beskov, V.S.; Shpinel', E.E.

    1988-09-01

    The oxidation of ammonia over platinum sieve catalysts was investigated given the vortex flows found in industrial contact units. Mathematical and physical models were used to assess the influence of vortices on ammonia oxidation. The flow pattern of the ammonia-air mixture in the reactor was modeled as a stream with a partial recycle. It is shown that vortex flows reduce the conversion of ammonia to nitrogen monoxide and increase the passage of unconverted ammonia through the catalyst sieve. Over long contact periods, the main effect of vortices is to increase the passage of unconverted ammonia, which may lead to the formation of explosive compounds.

  4. Bacterial Ammonia Causes Significant Plant Growth Inhibition

    PubMed Central

    Weise, Teresa; Kai, Marco; Piechulla, Birgit

    2013-01-01

    Many and complex plant-bacteria inter-relationships are found in the rhizosphere, since plants release a variety of photosynthetic exudates from their roots and rhizobacteria produce multifaceted specialized compounds including rich mixtures of volatiles, e.g., the bouquet of Serratia odorifera 4Rx13 is composed of up to 100 volatile organic and inorganic compounds. Here we show that when growing on peptone-rich nutrient medium S. odorifera 4Rx13 and six other rhizobacteria emit high levels of ammonia, which during co-cultivation in compartmented Petri dishes caused alkalization of the neighboring plant medium and subsequently reduced the growth of A. thaliana. It is argued that in nature high-protein resource degradations (carcasses, whey, manure and compost) are also accompanied by bacterial ammonia emission which alters the pH of the rhizosphere and thereby influences organismal diversity and plant-microbe interactions. Consequently, bacterial ammonia emission may be more relevant for plant colonization and growth development than previously thought. PMID:23691060

  5. Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene.

    PubMed

    Offre, Pierre; Prosser, James I; Nicol, Graeme W

    2009-10-01

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

  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 representative Nitrosomonas 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.

  7. Impacts of organic and inorganic fertilizers on nitrification in a cold climate soil are linked to the bacterial ammonia oxidizer community.

    PubMed

    Fan, Fenliang; Yang, Qianbao; Li, Zhaojun; Wei, Dan; Cui, Xi'an; Liang, Yongchao

    2011-11-01

    The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38°C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification.

  8. Factors Driving Potential Ammonia Oxidation in Canadian Arctic Ecosystems: Does Spatial Scale Matter?

    PubMed Central

    Banerjee, Samiran

    2012-01-01

    Ammonia oxidation is a major process in nitrogen cycling, and it plays a key role in nitrogen limited soil ecosystems such as those in the arctic. Although mm-scale spatial dependency of ammonia oxidizers has been investigated, little is known about the field-scale spatial dependency of aerobic ammonia oxidation processes and ammonia-oxidizing archaeal and bacterial communities, particularly in arctic soils. The purpose of this study was to explore the drivers of ammonia oxidation at the field scale in cryosols (soils with permafrost within 1 m of the surface). We measured aerobic ammonia oxidation potential (both autotrophic and heterotrophic) and functional gene abundance (bacterial amoA and archaeal amoA) in 279 soil samples collected from three arctic ecosystems. The variability associated with quantifying genes was substantially less than the spatial variability observed in these soils, suggesting that molecular methods can be used reliably evaluate spatial dependency in arctic ecosystems. Ammonia-oxidizing archaeal and bacterial communities and aerobic ammonia oxidation were spatially autocorrelated. Gene abundances were spatially structured within 4 m, whereas biochemical processes were structured within 40 m. Ammonia oxidation was driven at small scales (<1m) by moisture and total organic carbon, whereas gene abundance and other edaphic factors drove ammonia oxidation at medium (1 to 10 m) and large (10 to 100 m) scales. In these arctic soils heterotrophs contributed between 29 and 47% of total ammonia oxidation potential. The spatial scale for aerobic ammonia oxidation genes differed from potential ammonia oxidation, suggesting that in arctic ecosystems edaphic, rather than genetic, factors are an important control on ammonia oxidation. PMID:22081570

  9. Diversity and dynamics of ammonia-oxidizing bacterial communities in a sponge-based trickling filter treating effluent from a UASB reactor.

    PubMed

    Mac Conell, E F A; Almeida, P G S; Zerbini, A M; Brandt, E M F; Araújo, J C; Chernicharo, C A L

    2013-01-01

    Changes in ammonia-oxidizing bacterial (AOB) population dynamics were examined in a new sponge-based trickling filter (TF) post-upflow anaerobic sludge blanket (UASB) reactor by denaturating gradient gel electrophoresis (DGGE), and these changes were linked to relevant components influencing nitrification (chemical oxygen demand (COD), nitrogen (N)). The sponge-based packing media caused strong concentration gradients along the TF, providing an ecological selection of AOB within the system. The organic loading rate (OLR) affected the population dynamics, and under higher OLR or low ammonium-nitrogen (NH4(+)-N) concentrations some AOB bands disappeared, but maintaining the overall community function for NH4(+)-N removal. The dominant bands present in the upper portions of the TF were closely related to Nitrosomonas europaea and distantly affiliated to Nitrosomonas eutropha, and thus were adapted to higher NH4(+)-N and organic matter concentrations. In the lower portions of the TF, the dominant bands were related to Nitrosomonas oligotropha, commonly found in environments with low levels of NH4(+)-N. From a technology point of view, changes in AOB structure at OLR around 0.40-0.60 kgCOD m(-3) d(-1) did not affect TF performance for NH4(+)-N removal, but AOB diversity may have been correlated with the noticeable stability of the sponge-based TF for NH4(+)-N removal at low OLR. This study is relevant because molecular biology was used to observe important features of a bioreactor, considering realistic operational conditions applied to UASB/sponge-based TF systems.

  10. Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonium amendment.

    PubMed

    Stopnisek, Nejc; Gubry-Rangin, Cécile; Höfferle, Spela; Nicol, Graeme W; Mandic-Mulec, Ines; Prosser, James I

    2010-11-01

    Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and "deep peat" lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.

  11. Mimicking the oxygen minimum zones: stimulating interaction of aerobic archaeal and anaerobic bacterial ammonia oxidizers in a laboratory-scale model system

    PubMed Central

    Yan, Jia; Haaijer, Suzanne C M; Op den Camp, Huub J M; Niftrik, Laura; Stahl, David A; Könneke, Martin; Rush, Darci; Sinninghe Damsté, Jaap S; Hu, Yong Y; Jetten, Mike S M

    2012-01-01

    In marine oxygen minimum zones (OMZs), ammonia-oxidizing archaea (AOA) rather than marine ammonia-oxidizing bacteria (AOB) may provide nitrite to anaerobic ammonium-oxidizing (anammox) bacteria. Here we demonstrate the cooperation between marine anammox bacteria and nitrifiers in a laboratory-scale model system under oxygen limitation. A bioreactor containing ‘Candidatus Scalindua profunda’ marine anammox bacteria was supplemented with AOA (Nitrosopumilus maritimus strain SCM1) cells and limited amounts of oxygen. In this way a stable mixed culture of AOA, and anammox bacteria was established within 200 days while also a substantial amount of endogenous AOB were enriched. ‘Ca. Scalindua profunda’ and putative AOB and AOA morphologies were visualized by transmission electron microscopy and a C18 anammox [3]-ladderane fatty acid was highly abundant in the oxygen-limited culture. The rapid oxygen consumption by AOA and AOB ensured that anammox activity was not affected. High expression of AOA, AOB and anammox genes encoding for ammonium transport proteins was observed, likely caused by the increased competition for ammonium. The competition between AOA and AOB was found to be strongly related to the residual ammonium concentration based on amoA gene copy numbers. The abundance of archaeal amoA copy numbers increased markedly when the ammonium concentration was below 30 μM finally resulting in almost equal abundance of AOA and AOB amoA copy numbers. Massive parallel sequencing of mRNA and activity analyses further corroborated equal abundance of AOA and AOB. PTIO addition, inhibiting AOA activity, was employed to determine the relative contribution of AOB versus AOA to ammonium oxidation. The present study provides the first direct evidence for cooperation of archaeal ammonia oxidation with anammox bacteria by provision of nitrite and consumption of oxygen. PMID:23057688

  12. Oxidative and nitrosative stress in ammonia neurotoxicity.

    PubMed

    Skowrońska, Marta; Albrecht, Jan

    2013-04-01

    Increased ammonia accumulation in the brain due to liver dysfunction is a major contributor to the pathogenesis of hepatic encephalopathy (HE). Fatal outcome of rapidly progressing (acute) HE is mainly related to cytotoxic brain edema associated with astrocytic swelling. An increase of brain ammonia in experimental animals or treatment of cultured astrocytes with ammonia generates reactive oxygen and nitrogen species in the target tissues, leading to oxidative/nitrosative stress (ONS). In cultured astrocytes, ammonia-induced ONS is invariably associated with the increase of the astrocytic cell volume. Interrelated mechanisms underlying this response include increased nitric oxide (NO) synthesis which is partly coupled to the activation of NMDA receptors and increased generation of reactive oxygen species by NADPH oxidase. ONS and astrocytic swelling are further augmented by excessive synthesis of glutamine (Gln) which impairs mitochondrial function following its accumulation in there and degradation back to ammonia ("the Trojan horse" hypothesis). Ammonia also induces ONS in other cell types of the CNS: neurons, microglia and the brain capillary endothelial cells (BCEC). ONS in microglia contributes to the central inflammatory response, while its metabolic and pathophysiological consequences in the BCEC evolve to the vasogenic brain edema associated with HE. Ammonia-induced ONS results in the oxidation of mRNA and nitration/nitrosylation of proteins which impact intracellular metabolism and potentiate the neurotoxic effects. Simultaneously, ammonia facilitates the antioxidant response of the brain, by activating astrocytic transport and export of glutathione, in this way increasing the availability of precursors of neuronal glutathione synthesis.

  13. Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream.

    PubMed

    Nishizawa, Manabu; Sakai, Sanae; Konno, Uta; Nakahara, Nozomi; Takaki, Yoshihiro; Saito, Yumi; Imachi, Hiroyuki; Tasumi, Eiji; Makabe, Akiko; Koba, Keisuke; Takai, Ken

    2016-08-01

    the rate of ammonia oxidation. The discovery of ammonia-oxidizing archaea (AOA) in marine and terrestrial environments has transformed the concept that ammonia oxidation is operated only by bacterial species, suggesting that AOA play a significant role in the global nitrogen cycle. However, the archaeal contribution to ammonia oxidation in the global biosphere is not yet completely understood. This study successfully identified key factors controlling nitrogen and oxygen isotopic ratios of nitrite produced from thermophilic Thaumarchaeota and elucidated the applicability and its limit of nitrite isotopes as a geochemical clock of ammonia oxidation rate in nature. Oxygen isotope analysis in this study also provided new biochemical information on archaeal ammonia oxidation. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  14. Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream

    PubMed Central

    Sakai, Sanae; Konno, Uta; Nakahara, Nozomi; Takaki, Yoshihiro; Saito, Yumi; Imachi, Hiroyuki; Tasumi, Eiji; Makabe, Akiko; Koba, Keisuke; Takai, Ken

    2016-01-01

    the regulation of the rate of ammonia oxidation. The discovery of ammonia-oxidizing archaea (AOA) in marine and terrestrial environments has transformed the concept that ammonia oxidation is operated only by bacterial species, suggesting that AOA play a significant role in the global nitrogen cycle. However, the archaeal contribution to ammonia oxidation in the global biosphere is not yet completely understood. This study successfully identified key factors controlling nitrogen and oxygen isotopic ratios of nitrite produced from thermophilic Thaumarchaeota and elucidated the applicability and its limit of nitrite isotopes as a geochemical clock of ammonia oxidation rate in nature. Oxygen isotope analysis in this study also provided new biochemical information on archaeal ammonia oxidation. PMID:27208107

  15. Manure fertilization alters the population of ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea in a paddy soil.

    PubMed

    Wang, Yu; Zhu, Guibing; Song, Liyan; Wang, Shanyun; Yin, Chengqing

    2014-03-01

    Manure fertilizers are widely used in agriculture and highly impacted the soil microbial communities such as ammonia oxidizers. However, the knowledge on the communities of archaeal versus bacterial ammonia oxidizers in paddy soil affected by manure fertilization remains largely unknown, especially for a long-term influence. In present work, the impact of manure fertilization on the population of ammonia oxidizers, related potential nitrification rates (PNRs) and the key factors manipulating the impact were investigated through studying two composite soil cores (long-term fed with manure fertilization versus undisturbed). Moreover, soil incubated with NH(4)(+) for 5 weeks was designed to verify the field research. The results showed that the copy numbers of bacterial amoA gene in the manure fed soil were significant higher than those in the unfed soil (p < 0.05), suggesting a clear stimulating effect of long-term manure fertilization on the population of ammonia-oxidizing bacteria (AOB). The detected PNRs in the manure fed soil core (14-218 nmol L(-1)  N g(-1)  h(-1)) were significant higher than those in the unfed soil core (5-72 nmol L(-1)  N g(-1)  h(-1) ; p < 0.05). Highly correlations between the PNRs and the bacterial amoA gene copies rather than archaeal amoA gene were observed, indicating strong nitrification capacity related to bacterial ammonia oxidizers. The NH(4)(+) -N significantly correlated to the abundance of AOB (p < 0.01) and explained 96.1% of the environmental variation, showing the NH(4)(+) -N was the main factor impacting the population of AOB. The incubation experiment demonstrated a clear increase of the bacterial amoA gene abundance (2.0 × 10(6) to 8.4 × 10(6)  g(-1) d.w.s. and 1.6 × 10(4) to 4.8 × 10(5)  g(-1) d.w.s.) in both soil but not for the archaeal amoA gene, in agreement with the field observation. Overall, our results suggested that manure fertilization promoted the

  16. Kinetics of NH3 -oxidation, NO-turnover, N2 O-production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers.

    PubMed

    Hink, Linda; Lycus, Pawel; Gubry-Rangin, Cécile; Frostegård, Åsa; Nicol, Graeme W; Prosser, James I; Bakken, Lars R

    2017-09-11

    Ammonia oxidising bacteria (AOB) are thought to emit more nitrous oxide (N2 O) than ammonia oxidising archaea (AOA), due to their higher N2 O yield under oxic conditions and denitrification in response to oxygen (O2 ) limitation. We determined the kinetics of growth and turnover of nitric oxide (NO) and N2 O at low cell densities of Nitrosomonas europaea (AOB) and Nitrosopumilus maritimus (AOA) during gradual depletion of TAN (NH3  + NH4+) and O2 . Half-saturation constants for O2 and TAN were similar to those determined by others, except for the half-saturation constant for ammonium in N. maritimus (0.2 mM), which is orders of magnitudes higher than previously reported. For both strains, cell-specific rates of NO turnover and N2 O production reached maxima near O2 half-saturation constant concentration (2-10 μM O2 ) and decreased to zero in response to complete O2 -depletion. Modelling of the electron flow in N. europaea demonstrated low electron flow to denitrification (≤1.2% of the total electron flow), even at sub-micromolar O2 concentrations. The results corroborate current understanding of the role of NO in the metabolism of AOA and suggest that denitrification is inconsequential for the energy metabolism of AOB, but possibly important as a route for dissipation of electrons at high ammonium concentration. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. Distribution and abundance of archaeal and bacterial ammonia oxidizers in the sediments of the Dongjiang River, a drinking water supply for Hong Kong.

    PubMed

    Sun, Wei; Xia, Chunyu; Xu, Meiying; Guo, Jun; Wang, Aijie; Sun, Guoping

    2013-01-01

    Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b- and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg(-1) sediment, NH4(+)-N >144 mg kg(-1) sediment), while Group 1.1a- and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC <4 g kg(-1) sediment, NH4(+)-N <93 mg kg(-1) sediment). Although Nitrosomonas- and Nitrosospira-related sequences of AOB were detected in the sediments, nearly 70% of the sequences fell into the Nitrosomonas-like B cluster, suggesting similar sediment AOB communities along the river. Higher abundance of AOB than AOA was observed in almost all of the sediments in the Dongjiang River, while significant correlations were only detected between the distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem.

  18. Distribution and Abundance of Archaeal and Bacterial Ammonia Oxidizers in the Sediments of the Dongjiang River, a Drinking Water Supply for Hong Kong

    PubMed Central

    Sun, Wei; Xia, Chunyu; Xu, Meiying; Guo, Jun; Wang, Aijie; Sun, Guoping

    2013-01-01

    Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b-and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg−1 sediment, NH4+-N >144 mg kg−1 sediment), while Group 1.1a- and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC <4 g kg−1 sediment, NH4+-N <93 mg kg−1 sediment). Although Nitrosomonas- and Nitrosospira-related sequences of AOB were detected in the sediments, nearly 70% of the sequences fell into the Nitrosomonas-like B cluster, suggesting similar sediment AOB communities along the river. Higher abundance of AOB than AOA was observed in almost all of the sediments in the Dongjiang River, while significant correlations were only detected between the distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem. PMID:24256973

  19. 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.

  20. 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.

  1. Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea.

    PubMed

    Hatzenpichler, Roland

    2012-11-01

    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.

  2. 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

  3. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil

    PubMed Central

    Tourna, Maria; Stieglmeier, Michaela; Spang, Anja; Könneke, Martin; Schintlmeister, Arno; Urich, Tim; Engel, Marion; Schloter, Michael; Wagner, Michael; Richter, Andreas; Schleper, Christa

    2011-01-01

    Genes of archaea encoding homologues of ammonia monooxygenases have been found on a widespread basis and in large amounts in almost all terrestrial and marine environments, indicating that ammonia oxidizing archaea (AOA) might play a major role in nitrification on Earth. However, only one pure isolate of this group from a marine environment has so far been obtained, demonstrating archaeal ammonia oxidation coupled with autotrophic growth similar to the bacterial counterparts. Here we describe the cultivation and isolation of an AOA from soil. It grows on ammonia or urea as an energy source and is capable of using higher ammonia concentrations than the marine isolate, Nitrosopumilus maritimus. Surprisingly, although it is able to grow chemolithoautotrophically, considerable growth rates of this strain are obtained only upon addition of low amounts of pyruvate or when grown in coculture with bacteria. Our findings expand the recognized metabolic spectrum of AOA and help explain controversial results obtained in the past on the activity and carbon assimilation of these globally distributed organisms. PMID:21525411

  4. Transcriptional response of the archaeal ammonia oxidizer Nitrosopumilus maritimus to low and environmentally relevant ammonia concentrations.

    PubMed

    Nakagawa, Tatsunori; Stahl, David A

    2013-11-01

    The ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2 fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeon Nitrosopumilus maritimus SCM1 growing at two ammonia concentrations, as measured by combined ammonia and ammonium, one well above the Km for ammonia oxidation (∼500 μM) and the other well below the Km (<10 nM). Transcript levels were generally immediately and differentially repressed when cells transitioned from ammonia-replete to ammonia-limiting conditions. Transcript levels for ammonia oxidation, CO2 fixation, and one of the ammonia transport genes were approximately the same at high and low ammonia availability. Transcripts for all analyzed genes decreased with time in the complete absence of ammonia, but with various rates of decay. The new steady-state mRNA levels established are presumably more reflective of the natural physiological state of ammonia-oxidizing archaea and offer a reference for interpreting message abundance patterns in the natural environment.

  5. Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

    PubMed Central

    Stahl, David A.

    2013-01-01

    The ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2 fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeon Nitrosopumilus maritimus SCM1 growing at two ammonia concentrations, as measured by combined ammonia and ammonium, one well above the Km for ammonia oxidation (∼500 μM) and the other well below the Km (<10 nM). Transcript levels were generally immediately and differentially repressed when cells transitioned from ammonia-replete to ammonia-limiting conditions. Transcript levels for ammonia oxidation, CO2 fixation, and one of the ammonia transport genes were approximately the same at high and low ammonia availability. Transcripts for all analyzed genes decreased with time in the complete absence of ammonia, but with various rates of decay. The new steady-state mRNA levels established are presumably more reflective of the natural physiological state of ammonia-oxidizing archaea and offer a reference for interpreting message abundance patterns in the natural environment. PMID:23995944

  6. The history of aerobic ammonia oxidizers: from the first discoveries to today.

    PubMed

    Monteiro, Maria; Séneca, Joana; Magalhães, Catarina

    2014-07-01

    Nitrification, the oxidation of ammonia to nitrite and nitrate, has long been considered a central biological process in the global nitrogen cycle, with its first description dated 133 years ago. Until 2005, bacteria were considered the only organisms capable of nitrification. However, the recent discovery of a chemoautotrophic ammonia-oxidizing archaeon, Nitrosopumilus maritimus, changed our concept of the range of organisms involved in nitrification, highlighting the importance of ammonia-oxidizing archaea (AOA) as potential players in global biogeochemical nitrogen transformations. The uniqueness of these archaea justified the creation of a novel archaeal phylum, Thaumarchaeota. These recent discoveries increased the global scientific interest within the microbial ecology society and have triggered an analysis of the importance of bacterial vs archaeal ammonia oxidation in a wide range of natural ecosystems. In this mini review we provide a chronological perspective of the current knowledge on the ammonia oxidation pathway of nitrification, based on the main physiological, ecological and genomic discoveries.

  7. Archaea produce lower yields of N2 O than bacteria during aerobic ammonia oxidation in soil.

    PubMed

    Hink, Linda; Nicol, Graeme W; Prosser, James I

    2016-03-11

    Nitrogen fertilisation of agricultural soil contributes significantly to emissions of the potent greenhouse gas nitrous oxide (N2 O), which is generated during denitrification and, in oxic soils, mainly by ammonia oxidisers. Although laboratory cultures of ammonia oxidising bacteria (AOB) and archaea (AOA) produce N2 O, their relative activities in soil are unknown. This work tested the hypothesis that AOB dominate ammonia oxidation and N2 O production under conditions of high inorganic ammonia (NH3 ) input, but result mainly from the activity of AOA when NH3 is derived from mineralisation. 1-octyne, a recently discovered inhibitor of AOB, was used to distinguish N2 O production resulting from archaeal and bacterial ammonia oxidation in soil microcosms, and specifically inhibited AOB growth, activity and N2 O production. In unamended soils, ammonia oxidation and N2 O production were lower and resulted mainly from ammonia oxidation by AOA. The AOA N2 O yield relative to nitrite produced was half that of AOB, likely due to additional enzymatic mechanisms in the latter, but ammonia oxidation and N2 O production were directly linked in all treatments. Relative contributions of AOA and AOB to N2 O production, therefore, reflect their respective contributions to ammonia oxidation. These results suggest potential mitigation strategies for N2 O emissions from fertilised agricultural soils.

  8. Metabolism of Nitrogen Oxides in Ammonia-Oxidizing Bacteria

    NASA Astrophysics Data System (ADS)

    Kozlowski, J.; Stein, L. Y.

    2014-12-01

    Ammonia-oxidizing bacteria (AOB) are key microorganisms in the transformation of nitrogen intermediates in most all environments. Until recently there was very little work done to elucidate the physiology of ammonia-oxidizing bacteria cultivated from variable trophic state environments. With a greater variety of ammonia-oxidizers now in pure culture the importance of comparative physiological and genomic analysis is crucial. Nearly all known physiology of ammonia-oxidizing bacteria lies within the Nitrosomonas genus with Nitrosomonas europaea strain ATCC 19718 as the model. To more broadly characterize and understand the nature of obligate ammonia chemolithotrophy and the contribution of AOB to production of nitrogen oxides, Nitrosomonas spp. and Nitrosospira spp. isolated from variable trophic states and with sequenced genomes, were utilized. Instantaneous ammonia- and hydroxylamine-oxidation kinetics as a function of oxygen and substrate concentration were measured using an oxygen micro-sensor. The pathway intermediates nitric oxide and nitrous oxide were measured in real time using substrate-specific micro-sensors to elucidate whether production of these molecules is stoichiometric with rates of substrate oxidation. Genomic inventory was compared among the strains to identify specific pathways and modules to explain physiological differences in kinetic rates and production of N-oxide intermediates as a condition of their adaptation to different ammonium concentrations. This work provides knowledge of how nitrogen metabolism is differentially controlled in AOB that are adapted to different concentrations of ammonium. Overall, this work will provide further insight into the control of ammonia oxidizing chemolithotrophy across representatives of the Nitrosomonas and Nitrosospira genus, which can then be applied to examine additional genome-sequenced AOB isolates.

  9. Recovery of soil ammonia oxidation after long-term zinc exposure is not related to the richness of the bacterial nitrifying community.

    PubMed

    Ruyters, Stefan; Springael, Dirk; Smolders, Erik

    2013-08-01

    A soil sterilization-reinoculation approach was used to manipulate soil microbial diversity and to assess the effect of the diversity of the ammonia-oxidizing bacteria (AOB) on the recovery of the nitrifying community to metal stress (zinc). Gamma-irradiated soil was inoculated with 13 different combinations of up to 22 different soils collected worldwide to create varying degrees of AOB diversity. Two months after inoculation, AOB amoA DGGE based diversity (weighted richness) varied more than 10-fold among the 13 treatments, the largest value observed where the number of inocula had been largest. Subsequently, the 13 treatments were either or not amended with ZnCl2. Initially, Zn amendment completely inhibited nitrification. After 6 months of Zn exposure, recovery of the potential nitrification activity in the Zn amended soils ranged from <10 % to >100 % of the potential nitrification activity in the corresponding non-amended soils. This recovery was neither related to DGGE-based indices of AOB diversity nor to the AOB abundance assessed 2 months after inoculation (p > 0.05). However, recovery was significantly related (r = 0.75) to the potential nitrification rate before Zn amendment and only weakly to the number of soil inocula used in the treatments (r = 0.46). The lack of clear effects of AOB diversity on recovery may be related to an inherently sufficient diversity and functional redundancy of AOB communities in soil. Our data indicate that potential microbial activity can be a significant factor in recovery.

  10. The ammonia oxidizing and denitrifying prokaryotes associated with sponges from different sea areas.

    PubMed

    Han, Minqi; Li, Zhiyong; Zhang, Fengli

    2013-08-01

    Marine sponges have been suggested to play an important role in the marine nitrogen cycling. However, the role of sponge microbes in the nitrogen transformation remains limited, especially on the bacterial ammonia oxidization and denitrification. Hence, in the present study, using functional genes (amoA, nirS, nirK, and nxrA) involved in ammonia oxidization and denitrification and 16S rRNA genes for specific bacterial groups as markers, phylogenetically diverse prokaryotes including bacteria and archaea, which may be involved in the ammonia oxidization and denitrification processes in sponges, were revealed in seven sponge species. Ammonia oxidizers were found in all species, whereas three sponges (Placospongia sp., Acanthella sp., and Pericharax heteroraphis) harbor only ammonia-oxidizing bacteria (AOB), two sponges (Spirastrellidae diplastrella and Mycale fibrexilis) host only ammonia-oxidizing archaea (AOA), while the remaining two sponges (Haliclona sp. and Lamellomorpha sp.) harbor both AOB and AOA. S. diplastrella and Lamellomorpha sp. also harbor denitrifying bacteria. Nitrite reductase gene nirK was detected only in Lamellomorpha sp. with higher phylogenetic diversity than nirS gene observed only in S. diplastrella. The detected functional genes related to the ammonia oxidization and nitrite reduction in deep-sea and shallow-water sponges highlighted the potential ecological roles of prokaryotes in sponge-related nitrogen transformation.

  11. 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.

  12. Ammonia sensors based on metal oxide nanostructures

    NASA Astrophysics Data System (ADS)

    Sekhar Rout, Chandra; Hegde, Manu; Govindaraj, A.; Rao, C. N. R.

    2007-05-01

    Ammonia sensing characteristics of nanoparticles as well as nanorods of ZnO, In2O3 and SnO2 have been investigated over a wide range of concentrations (1 800 ppm) and temperatures (100 300 °C). The best values of sensitivity are found with ZnO nanoparticles and SnO2 nanostructures. Considering all the characteristics, the SnO2 nanostructures appear to be good candidates for sensing ammonia, with sensitivities of 222 and 19 at 300 °C and 100 °C respectively for 800 ppm of NH3. The recovery and response times are respectively in the ranges 12 68 s and 22 120 s. The effect of humidity on the performance of the sensors is not marked up to 60% at 300 °C. With the oxide sensors reported here no interference for NH3 is found from H2, CO, nitrogen oxides, H2S and SO2.

  13. Tin oxide nanocluster hydrogen and ammonia sensors.

    PubMed

    Lassesson, A; Schulze, M; van Lith, J; Brown, S A

    2008-01-09

    We have prepared sensitive hydrogen and ammonia sensors from thin films of tin nanoclusters with diameters between 3 and 10 nm. By baking the samples at 200 °C in ambient air the clusters were oxidized, resulting in very stable films of tin oxide clusters with similar diameters to the original Sn clusters. By monitoring the electrical resistance, it is shown that the cluster films are highly responsive to hydrogen and ammonia at relatively low temperatures, thereby making them attractive for commercial applications in which low power consumption is required. Doping of the films by depositing Pd on top of the clusters resulted in much improved sensor response and response times. It is shown that optimal sensor properties are achieved for very thin cluster films (a few monolayers of clusters).

  14. Niche specialization of terrestrial archaeal ammonia oxidizers.

    PubMed

    Gubry-Rangin, Cécile; Hai, Brigitte; Quince, Christopher; Engel, Marion; Thomson, Bruce C; James, Phillip; Schloter, Michael; Griffiths, Robert I; Prosser, James I; Nicol, Graeme W

    2011-12-27

    Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH <5), acido-neutral (5 ≤ pH <7), or alkalinophilic (pH ≥ 7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5-8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5-7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.

  15. Role of nitrogen oxides in the metabolism of ammonia-oxidizing bacteria.

    PubMed

    Kampschreur, M J; Tan, N C G; Picioreanu, C; Jetten, M S M; Schmidt, I; van Loosdrecht, M C M

    2006-02-01

    Ammonia-oxidizing bacteria (AOB) can use oxygen and nitrite as electron acceptors. Nitrite reduction by Nitrosomonas is observed under three conditions: (i) hydrogen-dependent denitrification, (ii) anoxic ammonia oxidation with nitrogen dioxide (NO(2)) and (iii) NO(x)-induced aerobic ammonia oxidation. NO(x) molecules play an important role in the conversion of ammonia and nitrite by AOB. Absence of nitric oxide (NO), which is generally detectable during ammonia oxidation, severely impairs ammonia oxidation by AOB. The lag phase of recovery of aerobic ammonia oxidation was significantly reduced by NO(2) addition. Acetylene inhibition tests showed that NO(2)-dependent and oxygen-dependent ammonia oxidation can be distinguished. Addition of NO(x) increased specific activity of ammonia oxidation, growth rate and denitrification capacity. Together, these findings resulted in a hypothetical model on the role of NO(x) in ammonia oxidation: the NO(x) cycle.

  16. 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

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

    PubMed

    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.

  18. Bacterial nitric oxide synthases.

    PubMed

    Crane, Brian R; Sudhamsu, Jawahar; Patel, Bhumit A

    2010-01-01

    Nitric oxide synthases (NOSs) are multidomain metalloproteins first identified in mammals as being responsible for the synthesis of the wide-spread signaling and protective agent nitric oxide (NO). Over the past 10 years, prokaryotic proteins that are homologous to animal NOSs have been identified and characterized, both in terms of enzymology and biological function. Despite some interesting differences in cofactor utilization and redox partners, the bacterial enzymes are in many ways similar to their mammalian NOS (mNOS) counterparts and, as such, have provided insight into the structural and catalytic properties of the NOS family. In particular, spectroscopic studies of thermostable bacterial NOSs have revealed key oxyheme intermediates involved in the oxidation of substrate L-arginine (Arg) to product NO. The biological functions of some bacterial NOSs have only more recently come to light. These studies disclose new roles for NO in biology, such as taking part in toxin biosynthesis, protection against oxidative stress, and regulation of recovery from radiation damage.

  19. Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia.

    PubMed

    Caffrey, Jane M; Bano, Nasreen; Kalanetra, Karen; Hollibaugh, James T

    2007-11-01

    Nitrification, the oxidation of NH(4)(+) to NO(2)(-) and subsequently to NO(3)(-), plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. The first and rate-limiting step in nitrification is catalyzed by the enzyme ammonia monooxygenase (AmoA). We evaluate the relationships between the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes; potential nitrification rates and environmental variables to identify factors influencing AOA abundance and nitrifier activity in estuarine sediments. Our results showed that potential nitrification rates increased as abundance of AOA amoA increased. In contrast, there was no relationship between potential nitrification rates and AOB amoA abundance. This suggests that AOA are significant in estuarine nitrogen cycling. Surprisingly, more of the variability in potential nitrification rates was predicted by salinity and pore water sulfide than by dissolved oxygen history.

  20. Growth of ammonia-oxidizing archaea and bacteria in cattle manure compost under various temperatures and ammonia concentrations.

    PubMed

    Oishi, Ryu; Tada, Chika; Asano, Ryoki; Yamamoto, Nozomi; Suyama, Yoshihisa; Nakai, Yutaka

    2012-05-01

    A recent study showed that ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) coexist in the process of cattle manure composting. To investigate their physiological characteristics, liquid cultures seeded with fermenting cattle manure compost were incubated at various temperatures (37°C, 46°C, or 60°C) and ammonium concentrations (0.5, 1, 4, or 10 mM NH (4) (+) -N). The growth rates of the AOB and AOA were monitored using real-time polymerase chain reaction analysis targeting the bacterial and archaeal ammonia monooxygenase subunit A genes. AOB grew at 37°C and 4 or 10 mM NH (4) (+) -N, whereas AOA grew at 46°C and 10 mM NH (4) (+) -N. Incubation with allylthiourea indicated that the AOB and AOA grew by oxidizing ammonia. Denaturing gradient gel electrophoresis and subsequent sequencing analyses revealed that a bacterium related to Nitrosomonas halophila and an archaeon related to Candidatus Nitrososphaera gargensis were the predominant AOB and AOA, respectively, in the seed compost and in cultures after incubation. This is the first report to demonstrate that the predominant AOA in cattle manure compost can grow and can probably oxidize ammonia under moderately thermophilic conditions.

  1. 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.

  2. Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea

    PubMed Central

    Vajrala, Neeraja; Martens-Habbena, Willm; Sayavedra-Soto, Luis A.; Schauer, Andrew; Bottomley, Peter J.; Stahl, David A.; Arp, Daniel J.

    2013-01-01

    The ammonia-oxidizing archaea have recently been recognized as a significant component of many microbial communities in the biosphere. Although the overall stoichiometry of archaeal chemoautotrophic growth via ammonia (NH3) oxidation to nitrite (NO2−) is superficially similar to the ammonia-oxidizing bacteria, genome sequence analyses point to a completely unique biochemistry. The only genomic signature linking the bacterial and archaeal biochemistries of NH3 oxidation is a highly divergent homolog of the ammonia monooxygenase (AMO). Although the presumptive product of the putative AMO is hydroxylamine (NH2OH), the absence of genes encoding a recognizable ammonia-oxidizing bacteria-like hydroxylamine oxidoreductase complex necessitates either a novel enzyme for the oxidation of NH2OH or an initial oxidation product other than NH2OH. We now show through combined physiological and stable isotope tracer analyses that NH2OH is both produced and consumed during the oxidation of NH3 to NO2− by Nitrosopumilus maritimus, that consumption is coupled to energy conversion, and that NH2OH is the most probable product of the archaeal AMO homolog. Thus, despite their deep phylogenetic divergence, initial oxidation of NH3 by bacteria and archaea appears mechanistically similar. They however diverge biochemically at the point of oxidation of NH2OH, the archaea possibly catalyzing NH2OH oxidation using a novel enzyme complex. PMID:23277575

  3. 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

  4. 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

  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. Characteristics of two novel cold- and salt-tolerant ammonia-oxidizing bacteria from Liaohe Estuarine Wetland.

    PubMed

    Huang, Xiao; Bai, Jie; Li, Kui-Ran; Zhao, Yang-Guo; Tian, Wei-Jun; Dang, Jia-Jia

    2017-01-15

    To achieve a better contaminant removal efficiency in a low-temperature and high-salt environment, two novel strains of cold- and salt-tolerant ammonia-oxidizing bacteria (AOB), i.e., Ochrobactrum sp. (HXN-1) and Aquamicrobium sp. (HXN-2), were isolated from the surface sediment of Liaohe Estuarine Wetland (LEW), China. The optimization of initial ammonia nitrogen concentration, pH, carbon-nitrogen ratio, and petroleum hydrocarbons (PHCs) to improve the ammonia-oxidation capacity of the two bacterial strains was studied. Both bacterial strains showed a high ammonia nitrogen removal rate of over 80% under a high salinity of 10‰. Even at a temperature as low as 15°C, HXN-1 and HXN-2 could achieve an ammonia nitrogen removal rate of 53% and 62%, respectively. The cold- and salt-tolerant AOB in this study demonstrated a high potential for ammonia nitrogen removal from LEW. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. 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.

  8. Removal of ammonia solutions used in catalytic wet oxidation processes.

    PubMed

    Hung, Chang Mao; Lou, Jie Chung; Lin, Chia Hua

    2003-08-01

    Ammonia (NH(3)) is an important product used in the chemical industry, and is common place in industrial wastewater. Industrial wastewater containing ammonia is generally either toxic or has concentrations or temperatures such that direct biological treatment is unfeasible. This investigation used aqueous solutions containing more of ammonia for catalytic liquid-phase oxidation in a trickle-bed reactor (TBR) based on Cu/La/Ce composite catalysts, prepared by co-precipitation of Cu(NO(3))(2), La(NO(3))(2), and Ce(NO(3))(3) at 7:2:1 molar concentrations. The experimental results indicated that the ammonia conversion of the wet oxidation in the presence of the Cu/La/Ce composite catalysts was determined by the Cu/La/Ce catalyst. Minimal ammonia was removed from the solution by the wet oxidation in the absence of any catalyst, while approximately 91% ammonia removal was achieved by wet oxidation over the Cu/La/Ce catalyst at 230 degrees C with oxygen partial pressure of 2.0 MPa. Furthermore, the effluent streams were conducted at a liquid hourly space velocity of under 9 h(-1) in the wet catalytic processes, and a reaction pathway was found linking the oxidizing ammonia to nitric oxide, nitrogen and water. The solution contained by-products, including nitrates and nitrites. Nitrite selectivity was minimized and ammonia removal maximized when the feed ammonia solution had a pH of around 12.0.

  9. 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. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Novel application of nitrifying bacterial consortia to ease ammonia toxicity in ornamental fish transport units: trials with zebrafish.

    PubMed

    Dhanasiri, A K S; Kiron, V; Fernandes, J M O; Bergh, O; Powell, M D

    2011-08-01

    To evaluate whether two commercial nitrifying bacterial consortia can function as biocontrol agents in ornamental fish transporting systems. The consortia were applied in a simulated set-up using zebrafish as the model organism in three trials. The efficacy of the bacterial consortia in controlling the ammonia level was validated by measuring water quality parameters such as total ammonia, nitrate and pH of the transport water. The bacterial community structure in the transport unit was studied using denaturing gradient gel electrophoresis. The consortia tested improved the nitrifying activity that in turn facilitated the reduction of ammonia that had accumulated during the transport. Bacterial profiles revealed the presence of both ammonia-oxidizing and nitrite-oxidizing bacteria in the transport bags. The application of the consortia during the transportation of zebrafish could profoundly improve the water quality by curbing ammonia accumulation. The potential of applying nitrifying bacteria as a bioremediation practice during the transport of ornamental fish has been demonstrated and this innovative approach contributes to the amelioration of current fish welfare in ornamental fish trade. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

  11. Ammonia transformations and abundance of ammonia oxidizers in a clay soil underlying a manure pond.

    PubMed

    Sher, Yonatan; Baram, Shahar; Dahan, Ofer; Ronen, Zeev; Nejidat, Ali

    2012-07-01

    Unlined manure ponds are constructed on clay soil worldwide to manage farm waste. Seepage of ammonia-rich liquor into underlying soil layers contributes to groundwater contamination by nitrate. To identify the possible processes that lead to the production of nitrate from ammonia in this oxygen-limited environment, we studied the diversity and abundance of ammonia-transforming microorganisms under an unlined manure pond. The numbers of ammonia-oxidizing bacteria and anammox bacteria were most abundant in the top of the soil profile and decreased significantly with depth (0.5 m), correlating with soil pore-water ammonia concentrations and soil ammonia concentrations, respectively. On the other hand, the numbers of ammonia-oxidizing archaea were relatively constant throughout the soil profile (10(7) amoA copies per g(soil)). Nitrite-oxidizing bacteria were detected mainly in the top 0.2 m. The results suggest that nitrate accumulation in the vadose zone under the manure pond could be the result of complete aerobic nitrification (ammonia oxidation to nitrate) and could exist as a byproduct of anammox activity. While the majority of the nitrogen was removed within the 0.5-m soil section, possibly by combined anammox and heterotrophic denitrification, a fraction of the produced nitrate leached into the groundwater.

  12. 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.

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

    PubMed

    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.

  14. 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

  15. RESULTS OF INITIAL AMMONIA OXIDATION TESTING

    SciTech Connect

    Nash, C.; Fowley, M.

    2016-12-30

    This memo presents an experimental survey of aqueous phase chemical processes to remove aqueous ammonia from waste process streams. Ammonia is generated in both the current Hanford waste flowsheet and in future waste processing. Much ammonia will be generated in the Low Activity Waste (LAW) melters.i Testing with simulants in glass melters at Catholic University has demonstrated the significant ammonia production.ii The primary reaction there is the reducing action of sugar on nitrate in the melter cold cap. Ammonia has been found to be a problem in secondary waste stabilization. Ammonia vapors are noxious and destruction of ammonia could reduce hazards to waste treatment process personnel. It is easily evolved especially when ammonia-bearing solutions are adjusted to high pH.

  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. 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.

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

    PubMed

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

    2011-09-02

    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.

  19. Epiphyton as a niche for ammonia-oxidizing bacteria: detailed comparison with benthic and pelagic compartments in shallow freshwater lakes.

    PubMed

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

    2008-04-01

    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.

  20. Ammonia oxidizing archaea are the predominant nitrifiers in disturbed and undisturbed southern US pine forests

    NASA Astrophysics Data System (ADS)

    Mushinski, R. M.; Boutton, T. W.; Gentry, T. J.; Dorosky, R. J.

    2016-12-01

    The rate-limiting step in nitrification, ammonia oxidation, is performed by both ammonia oxidizing bacteria (AOB) and archaea (AOA); however, reports on the relative contribution of each of these groups to forest soil nitrification has varied. We coupled qPCR and next generation sequencing of the amoA gene to a whole-soil assay that stimulates nitrification and allows for the discrimination of AOA- from AOB-activity using 1-octyne, which inhibits the activity of the bacterial ammonia monooxygenase. Soils, to a depth of 1 meter, were collected from replicated (n = 3) loblolly pine (Pinus taeda L.) stands subjected to three different intensities of timber harvest (i.e., unharvested old growth stands, bole-only harvest stands, and whole-tree harvest + forest floor removal stands). The abundance of both bacterial and archaeal amoA were influenced by harvest method and soil depth; furthermore, archaeal amoA was 13x more abundant than bacterial amoA, across all soil depths. Sequencing and subsequent annotation of the ammonia oxidizing community revealed that the AOA were dominated by Crenarchaeota and AOB were dominated by Nitrosospira. Surface mineral soils (0-10 cm) amended with 1-octyne revealed that approximately 67-86% of total nitrification can be attributable to AOA activity. The highest rates of nitrification (total and 1-octyne resistant) occurred in the soils taken from the unharvested reference stands which were significantly greater than harvested stands. We can conclude that in this pine forest system, AOA dominates AOB in regards to amoA copy number and ammonia oxidizing activity. Not only is this study one of the first to investigate the ammonia-oxidizing population in southern pine forests, but also illustrates that timber harvest can lead to long-term alterations in nitrogen cycle processes.

  1. 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.

  2. 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

  3. Nitrogen metabolism and kinetics of ammonia-oxidizing archaea.

    PubMed

    Martens-Habbena, Willm; Stahl, David A

    2011-01-01

    The discovery of ammonia-oxidizing mesophilic and thermophilic Group I archaea changed the century-old paradigm that aerobic ammonia oxidation is solely mediated by two small clades of Beta- and Gammaproteobacteria. Group I archaea are extremely diverse and ubiquitous in marine and terrestrial environments, accounting for 20-30% of the microbial plankton in the global oceans. Recent studies indicated that many of these organisms carry putative ammonia monooxygenase genes and are more abundant than ammonia-oxidizing bacteria in most natural environments suggesting a potentially significant role in the nitrogen cycle. The isolation of Nitrosopumilus maritimus strain SCM1 provided the first direct evidence that Group I archaea indeed gain energy from ammonia oxidation. To characterize the physiology of this archaeal nitrifier, we developed a respirometry setup particularly suited for activity measurements in dilute microbial cultures with extremely low oxygen uptake rates. Here, we describe the setup and review the kinetic experiments conducted with N. maritimus and other nitrifying microorganisms. These experiments demonstrated that N. maritimus is adapted to grow on ammonia concentrations found in oligotrophic open ocean environments, far below the survival threshold of ammonia-oxidizing bacteria. The described setup and experimental procedures should facilitate physiological studies on other nitrifying archaea and oligotrophic microorganisms in general. Copyright © 2011 Elsevier Inc. All rights reserved.

  4. A regulating method for reducing nitrogen loss based on enriched ammonia-oxidizing bacteria during composting.

    PubMed

    Zhang, Yun; Zhao, Yue; Chen, Yanni; Lu, Qian; Li, Mingxiao; Wang, Xueqin; Wei, Yuquan; Xie, Xinyu; Wei, Zimin

    2016-12-01

    In this study, enriched ammonia-oxidizing bacteria (AOB) were acquired by domesticated cultivation, followed by inoculation into the co-composting of rice straw and chicken manure. The effect of inoculation on nitrogen loss, the succession of bacterial community and the correlation between the key bacteria and environmental factors were investigated. The results showed that inoculation could reduce ammonia emission and nitrogen loss by transforming ammonium into nitrite. Inoculation also increased the amount and abundance of bacterial community. Redundancy analysis showed that indigenous and exogenous bacteria in inoculation group, compared with those in control group, were positively correlated with nitrite but negatively correlated with ammonium, demonstrating that the former contributed to the lower ammonia emission and nitrogen loss. Based on these results, the application of enriched AOB was proposed as a new method of resource recycle and improvement of composting technology. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. 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

  6. 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

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

    PubMed

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

    2012-10-01

    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, (15)N 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.

  8. 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

  9. 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

  10. Autotrophic ammonia oxidation in a deep-sea hydrothermal plume.

    PubMed

    Lam, Phyllis; Cowen, James P; Jones, Ronald D

    2004-02-01

    Direct evidence for autotrophic ammonia oxidation is documented for the first time in a deep-sea hydrothermal plume. Elevated NH(4) (+) concentrations of up to 341+/-136 nM were recorded in the plume core at Main Endeavour Field, Juan de Fuca Ridge. This fueled autotrophic ammonia oxidation rates as high as 91 nM day(-1), or 92% of the total net NH(4) (+) removal. High abundance of ammonia-oxidizing bacteria was detected using fluorescence in situ hybridization. Ammonia-oxidizing bacteria within the plume core (1.0-1.4x10(4) cells ml(-1)) accounted for 7.0-7.5% of the total microbial community, and were at least as abundant as methanotrophs. Ammonia-oxidizing bacteria were a substantial component of the particle-associated communities (up to 51%), with a predominance of the r-strategist Nitrosomonas-like cells. In situ chemolithoautotrophic organic carbon production via ammonia oxidation may yield 3.9-18 mg C m(-2) day(-1) within the plume directly over Main Endeavour Field. This rate was comparable to that determined for methane oxidation in a previous study, or at least four-fold greater than the flux of photosynthetic carbon reaching plume depths measured in another study. Hence, autotrophic ammonia oxidation in the neutrally buoyant hydrothermal plume is significant to both carbon and nitrogen cycling in the deep-sea water column at Endeavour, and represents another important link between seafloor hydrothermal systems and deep-sea biogeochemistry.

  11. 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.

  12. 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...

  13. Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria.

    PubMed

    Park, Byoung-Joon; Park, Soo-Je; Yoon, Dae-No; Schouten, Stefan; Sinninghe Damsté, Jaap S; Rhee, Sung-Keun

    2010-11-01

    The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and "Candidatus Nitrosopumilus maritimus" (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caused by the rapid initial growth of SOB. After biweekly transfers for ca. 20 months, archaeal cells became the dominant prokaryotes (>80%), based on quantitative PCR and fluorescence in situ hybridization analysis. The increase of archaeal 16S rRNA gene copy numbers was coincident with the amount of ammonia oxidized, and expression of the archaeal amoA gene was observed during ammonia oxidation. Bacterial amoA genes were not detected in the enrichment culture. The affinities of these AOA to oxygen and ammonia were substantially higher than those of AOB. [(13)C]bicarbonate incorporation and the presence and activation of genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle indicated autotrophy during ammonia oxidation. In the enrichment culture, ammonium was oxidized to nitrite by the AOA and subsequently to nitrate by Nitrospina-like bacteria. Our experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments.

  14. Cultivation of Autotrophic Ammonia-Oxidizing Archaea from Marine Sediments in Coculture with Sulfur-Oxidizing Bacteria▿ †

    PubMed Central

    Park, Byoung-Joon; Park, Soo-Je; Yoon, Dae-No; Schouten, Stefan; Sinninghe Damsté, Jaap S.; Rhee, Sung-Keun

    2010-01-01

    The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and “Candidatus Nitrosopumilus maritimus” (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caused by the rapid initial growth of SOB. After biweekly transfers for ca. 20 months, archaeal cells became the dominant prokaryotes (>80%), based on quantitative PCR and fluorescence in situ hybridization analysis. The increase of archaeal 16S rRNA gene copy numbers was coincident with the amount of ammonia oxidized, and expression of the archaeal amoA gene was observed during ammonia oxidation. Bacterial amoA genes were not detected in the enrichment culture. The affinities of these AOA to oxygen and ammonia were substantially higher than those of AOB. [13C]bicarbonate incorporation and the presence and activation of genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle indicated autotrophy during ammonia oxidation. In the enrichment culture, ammonium was oxidized to nitrite by the AOA and subsequently to nitrate by Nitrospina-like bacteria. Our experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments. PMID:20870784

  15. Habitat-Associated Phylogenetic Community Patterns of Microbial Ammonia Oxidizers

    PubMed Central

    Fernàndez-Guerra, Antoni; Casamayor, Emilio O.

    2012-01-01

    Microorganisms mediating ammonia oxidation play a fundamental role in the connection between biological nitrogen fixation and anaerobic nitrogen losses. Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively) have colonized similar habitats worldwide. Ammonia oxidation is the rate-limiting step in nitrification, and the ammonia monooxygenase (Amo) is the key enzyme involved. The molecular ecology of this process has been extensively explored by surveying the gene of the subunit A of the Amo (amoA gene). In the present study, we explored the phylogenetic community ecology of AOB and AOA, analyzing 5776 amoA gene sequences from >300 isolation sources, and clustering habitats by environmental ontologies. As a whole, phylogenetic richness was larger in AOA than in AOB, and sediments contained the highest phylogenetic richness whereas marine plankton the lowest. We also observed that freshwater ammonia oxidizers were phylogenetically richer than their marine counterparts. AOA communities were more dissimilar to each other than those of AOB, and consistent monophyletic lineages were observed for sediments, soils, and marine plankton in AOA but not in AOB. The diversification patterns showed a more constant cladogenesis through time for AOB whereas AOA apparently experienced two fast diversification events separated by a long steady-state episode. The diversification rate (γ statistic) for most of the habitats indicated γAOA > γAOB. Soil and sediment experienced earlier bursts of diversification whereas habitats usually eutrophic and rich in ammonium such as wastewater and sludge showed accelerated diversification rates towards the present. Overall, this work shows for the first time a global picture of the phylogenetic community structure of both AOB and AOA assemblages following the strictest analytical standards, and provides an ecological view on the differential evolutionary paths experienced by widespread ammonia-oxidizing microorganisms. The emerged

  16. [Characteristics of sulfate reduction-ammonia oxidation reaction].

    PubMed

    Yuan, Yi; Huang, Yong; Li, Xiang; Zhang, Chun-Lei; Zhang, Li; Pan, Yang; Liu, Fu-Xin

    2013-11-01

    The sulfate reduction-ammonia oxidation reaction with ANAMMOX sludge at autotrophic condition was implemented. It was found that the pH level decreased during the reaction. Elemental sulfur and nitrogen gas were the final products, while NO3(-) -N was the intermediate product during the sulfate reduction-ammonia oxidation reaction. The conversion ratio of NH4(+) -N/SO4(2-) -S decreased with the decrease in n(N)/n(S) (molar ratio) of raw water. n(N)/n(S) of raw water had little effect on the ammonia conversion ratio. Lower n(N)/n(S) could improve the SO4(2-)-S conversion ratio, but with more NH4(+) -N oxidized into NO3(-) -N, resulting in decreased n(TN)/n(TS) removal ratio. This indicates that the sulfate reduction-ammonia oxidation reaction is not an elementary reaction. Ammonia can be oxidized into NO2(-) -N or NO3(-) -N by sulfate. Shortening the reaction time would be conducive to nitrogen losses, because the reaction of NO3(-) -N production is the rate-limiting step.

  17. 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).

  18. Mechanism of bacterial pyrite oxidation.

    PubMed

    Silverman, M P

    1967-10-01

    The oxidation by Ferrobacillus ferrooxidans of untreated pyrite (FeS(2)) as well as HCl-pretreated pyrite (from which most of the acid-soluble iron species were removed) was studied manometrically. Oxygen uptake was linear during bacterial oxidation of untreated pyrite, whereas with HCl-pretreated pyrite both a decrease in oxygen uptake at 2 hr and nonlinear oxygen consumption were observed. Ferric sulfate added to HCl-pretreated pyrite restored approximately two-thirds of the decrease in total bacterial oxygen uptake and caused oxygen uptake to revert to nearly linear kinetics. Ferric sulfate also oxidized pyrite in the absence of bacteria and O(2); recovery of ferric and ferrous ions was in excellent agreement with the reaction Fe(2)(SO(4))(3) + FeS(2) = 3FeSO(4) + 2S, but the elemental sulfur produced was negligible. Neither H(2)S nor S(2)O(3) (2-) was a product of the reaction. It is probable that two mechanisms of bacterial pyrite oxidation operate concurrently: the direct contact mechanism which requires physical contact between bacteria and pyrite particles for biological pyrite oxidation, and the indirect contact mechanism according to which the bacteria oxidize ferrous ions to the ferric state, thereby regenerating the ferric ions required for chemical oxidation of pyrite.

  19. Impacts of Edaphic Factors on Communities of Ammonia-Oxidizing Archaea, Ammonia-Oxidizing Bacteria and Nitrification in Tropical Soils

    PubMed Central

    de Gannes, Vidya; Eudoxie, Gaius; Hickey, William J.

    2014-01-01

    Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (ca. 105 to 106 copies archaeal amoA g−1 soil), but AOB levels were low and bacterial amoA was infrequently detected. AOA abundance showed a significant negative correlation (p<0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by amoA terminal restriction fragment (TRF) analysis, differed significantly between soils (p<0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (p<0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (p<0.01). In clone libraries, phylotypes of archaeal amoA (predominantly Nitrososphaera) and bacterial amoA (predominanatly Nitrosospira) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (p<0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity. PMID:24586878

  20. Macroecological patterns of archaeal ammonia oxidizers in the Atlantic Ocean.

    PubMed

    Sintes, Eva; De Corte, Daniele; Ouillon, Natascha; Herndl, Gerhard J

    2015-10-01

    Macroecological patterns are found in animals and plants, but also in micro-organisms. Macroecological and biogeographic distribution patterns in marine Archaea, however, have not been studied yet. Ammonia-oxidizing Archaea (AOA) show a bipolar distribution (i.e. similar communities in the northernmost and the southernmost locations, separated by distinct communities in the tropical and gyral regions) throughout the Atlantic, detectable from epipelagic to upper bathypelagic layers (<2000 m depth). This tentatively suggests an influence of the epipelagic conditions of organic matter production on bathypelagic AOA communities. The AOA communities below 2000 m depth showed a less pronounced biogeographic distribution pattern than the upper 2000 m water column. Overall, AOA in the surface and deep Atlantic waters exhibit distance-decay relationships and follow the Rapoport rule in a similar way as bacterial communities and macroorganisms. This indicates a major role of environmental conditions in shaping the community composition and assembly (species sorting) and no, or only weak limits for dispersal in the oceanic thaumarchaeal communities. However, there is indication of a different strength of these relationships between AOA and Bacteria, linked to the intrinsic differences between these two domains. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  1. Spatiotemporal relationships between the abundance, distribution, and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments.

    PubMed

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

    2015-01-01

    The primary objective of this study was to gain an understanding of how key microbial communities involved in nitrogen cycling in estuarine sediments vary over a 12-month period. Furthermore, we sought to determine whether changes in the size of these communities are related to, or indicative of, seasonal patterns in fixed nitrogen dynamics in Elkhorn Slough--a small, agriculturally impacted estuary with a direct connection to Monterey Bay. We assessed sediment and pore water characteristics, abundance of functional genes for nitrification (bacterial and archaeal amoA, encoding ammonia monooxygenase subunit A) and denitrification (nirS and nirK, encoding nitrite reductase), and measurements of potential nitrification and denitrification activities at six sites. No seasonality in the abundance of denitrifier or ammonia oxidizer genes was observed. A strong association between potential nitrification activity and the size of ammonia-oxidizing bacterial communities was observed across the estuary. In contrast, ammonia-oxidizing archaeal abundances remained relatively constant in space and time. Unlike many other estuaries, salinity does not appear to regulate the distribution of ammonia-oxidizing communities in Elkhorn Slough. Instead, their distributions appear to be governed over two different time scales. Long-term niche characteristics selected for the gross size of archaeal and bacterial ammonia-oxidizing communities, yet covariation in their abundances between monthly samples suggests that they respond in a similar manner to short-term changes in their environment. Abundances of denitrifier and ammonia oxidizer genes also covaried, but site-specific differences in this relationship suggest differing levels of interaction (or coupling) between nitrification and denitrification.

  2. Short-term effect of ammonia concentration and salinity on activity of ammonia oxidizing bacteria.

    PubMed

    Claros, J; Jiménez, E; Borrás, L; Aguado, D; Seco, A; Ferrer, J; Serralta, J

    2010-01-01

    A continuously aerated SHARON (single reactor high activity ammonia removal over nitrite) system has been operated to achieve partial nitritation. Two sets of batch experiments were carried out to study the effect of ammonia concentration and salinity on the activity of ammonia-oxidizing bacteria (AOB). Activity of AOB raised as free ammonia concentration was increased reaching its maximum value at 4.5 mg NH3-N l(-1). The half saturation constant for free ammonia was determined (K(NH3)=0.32 mg NH3-N l(-1)). Activity decreased at TAN (total ammonium-nitrogen) concentration over 2,000 mg NH4-N l(-1). No free ammonia inhibition was detected. The effect of salinity was studied by adding different concentrations of different salts to the biomass. No significant differences were observed between the experiments carried out with a salt containing or not containing NH4. These results support that AOB are inhibited by salinity, not by free ammonia. A mathematical expression to represent this inhibition is proposed. To compare substrate affinity and salinity inhibitory effect on different AOB populations, similar experiments were carried out with biomass from a biological nutrient removal pilot plant. The AOB activity reached its maximum value at 0.008 mg NH3-N l(-1) and decreased at TAN concentration over 400 mg NH4-N l(-1). These differences can be explained by the different AOB predominating species: Nitrosomonas europaea and N. eutropha in the SHARON biomass and Nitrosomonas oligotropha in the pilot plant.

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

    PubMed

    Abeliovich, A; Azov, Y

    1976-06-01

    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.

  4. Relative contribution of ammonia oxidizing bacteria and other members of nitrifying activated sludge communities to micropollutant biotransformation.

    PubMed

    Men, Yujie; Achermann, Stefan; Helbling, Damian E; Johnson, David R; Fenner, Kathrin

    2017-02-01

    Improved micropollutant (MP) biotransformation during biological wastewater treatment has been associated with high ammonia oxidation activities, suggesting co-metabolic biotransformation by ammonia oxidizing bacteria as an underlying mechanism. The goal of this study was to clarify the contribution of ammonia oxidizing bacteria to increased MP degradation in nitrifying activated sludge (NAS) communities using a series of inhibition experiments. To this end, we treated a NAS community with two different ammonia oxidation inhibitors, namely octyne (OCT), a mechanistic inhibitor that covalently binds to ammonia monooxygenases, and allylthiourea (ATU), a copper chelator that depletes copper ions from the active center of ammonia monooxygenases. We investigated the biotransformation of 79 structurally different MPs by the inhibitor-treated and untreated sludge communities. Fifty-five compounds exhibited over 20% removal in the untreated control after a 46 h-incubation. Of these, 31 compounds were significantly inhibited by either ATU and/or OCT. For 17 of the 31 MPs, the inhibition by ATU at 46 h was substantially higher than by OCT despite the full inhibition of ammonia oxidation by both inhibitors. This was particularly the case for almost all thioether and phenylurea compounds tested, suggesting that in nitrifying activated sludge communities, ATU does not exclusively act as an inhibitor of bacterial ammonia oxidation. Rather, ATU also inhibited enzymes contributing to MP biotransformation but not to bulk ammonia oxidation. Thus, inhibition studies with ATU tend to overestimate the contribution of ammonia-oxidizing bacteria to MP biotransformation in nitrifying activated sludge communities. Biolog tests revealed only minor effects of ATU on the heterotrophic respiration of common organic substrates by the sludge community, suggesting that ATU did not affect enzymes that were essential in energy conservation and central metabolism of heterotrophs. By comparing ATU

  5. 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.

  6. Chemically reduced graphene oxide for ammonia detection at room temperature.

    PubMed

    Ghosh, Ruma; Midya, Anupam; Santra, Sumita; Ray, Samit K; Guha, Prasanta K

    2013-08-14

    Chemically reduced graphene oxide (RGO) has recently attracted growing interest in the area of chemical sensors because of its high electrical conductivity and chemically active defect sites. This paper reports the synthesis of chemically reduced GO using NaBH4 and its performance for ammonia detection at room temperature. The sensing layer was synthesized on a ceramic substrate containing platinum electrodes. The effect of the reduction time of graphene oxide (GO) was explored to optimize the response, recovery, and response time. The RGO film was characterized electrically and also with atomic force microscopy and X-ray photoelectron spectroscopy. The sensor response was found to lie between 5.5% at 200 ppm (parts per million) and 23% at 2800 ppm of ammonia, and also resistance recovered quickly without any application of heat (for lower concentrations of ammonia). The sensor was exposed to different vapors and found to be selective toward ammonia. We believe such chemically reduced GO could potentially be used to manufacture a new generation of low-power portable ammonia sensors.

  7. Microbial Community Dynamics and Stability during an Ammonia-Induced Shift to Syntrophic Acetate Oxidation

    PubMed Central

    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.

    2014-01-01

    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

  8. Substrate and nutrient limitation of ammonia-oxidizing bacteria and archaea in temperate forest soil

    Treesearch

    J.S. Norman; J.E. Barrett

    2014-01-01

    Ammonia-oxidizing microbes control the rate-limiting step of nitrification, a critical ecosystem process, which affects retention and mobility of nitrogen in soil ecosystems. This study investigated substrate (NH4þ) and nutrient (K and P) limitation of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in temperate forest soils at Coweeta Hydrologic...

  9. Quantitative analyses of ammonia-oxidizing Archaea and bacteria in the sediments of four nitrogen-rich wetlands in China.

    PubMed

    Wang, Shanyun; Wang, Yu; Feng, Xiaojuan; Zhai, Liming; Zhu, Guibing

    2011-04-01

    With the rapid development of ammonia-synthesizing industry, the ammonia-nitrogen pollution in wetlands acting as the sink of point and diffuse pollution has been increased dramatically. Most of ammonia-nitrogen is oxidized at least once by ammonia-oxidizing prokaryotes to complete the nitrogen cycle. Current research findings have expanded the known ammonia-oxidizing prokaryotes from the domain Bacteria to Archaea. However, in the complex wetlands environment, it remains unclear whether ammonia oxidation is exclusively or predominantly linked to Archaea or Bacteria as implied by specific high abundance. In this research, the abundance and composition of Archaea and Bacteria in sediments of four kinds of wetlands with different nitrogen concentration were investigated by using quantitative real-time polymerase chain reaction, cloning, and sequencing approaches based on amoA genes. The results indicated that AOA distributed widely in wetland sediments, and the phylogenetic tree revealed that archaeal amoA functional gene sequences from wetlands sediments cluster as two major evolutionary branches: soil/sediment and sediment/water. The bacteria functionally dominated microbial ammonia oxidation in different wetlands sediments on the basis of molecule analysis, potential nitrification rate, and soil chemistry. Moreover, the factors influencing AOA and AOB abundances with environmental indicator were also analyzed, and the results addressed the copy numbers of archaeal and bacterial amoA functional gene having the higher correlation with pH and ammonia concentration. The pH had relatively great negative impact on the abundance of AOA and AOB, while ammonia concentration showed positive impact on AOB abundance only. These findings could be fundamental to improve understanding of the importance of AOB and AOA in nitrogen and other nutrients cycle in wetland ecosystems. © Springer-Verlag 2011

  10. Abundance and community composition of ammonia-oxidizing archaea and bacteria in two different zones of Lake Taihu.

    PubMed

    Zeng, Jin; Zhao, Da-Yong; Huang, Rui; Wu, Qinglong L

    2012-08-01

    The abundance and community composition of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the surface sediments of 2 different zones (Meiliang Bay and Eastern Lake Taihu) of Lake Taihu were investigated using real-time quantitative polymerase chain reaction and clone libraries. The amoA gene copy numbers in the surface sediment of Meiliang Bay ranged from 4.91 × 10(5) to 8.65 × 10(6) copies/g dry sediment for the archaeal amoA gene and from 3.74 × 10(4) to 3.86 × 10(5) copies/g dry sediment for the bacterial amoA gene, which were significantly higher than those of Eastern Lake Taihu (P < 0.05). Concentrations of ammonia (NH(4)(+)), total nitrogen, organic matter, and pH of the sediments exhibited significantly negative correlations with the abundance of ammonia-oxidizing archaea or ammonia-oxidizing bacteria (P < 0.05 or P < 0.01, respectively). The potential nitrification rates show remarkable correlations with the copy numbers of the archaeal amoA gene. Diversity of the archaeal amoA gene in Eastern Lake Taihu was significantly higher than that of Meiliang Bay, whereas the bacterial amoA gene diversity was comparable for the 2 lake zones. The data obtained in this study would be useful to elucidate the role of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.

  11. Fabrication of highly selective tungsten oxide ammonia sensors

    SciTech Connect

    Llobet, E.; Molas, G.; Molinas, P.; Calderer, J.; Vilanova, X.; Brezmes, J.; Sueiras, J.E.; Correig, X.

    2000-02-01

    Tungsten oxide is shown to be a very promising material for the fabrication of highly selective ammonia sensors. Films of WO{sub 3} were deposited onto a silicon substrate by means of the drop-coating method. Then, the films were annealed in dry air at two different temperatures (300 and 400 C). X-ray photoelectron spectroscopy was used to investigate the composition of the films. Tungsten appeared both in WO{sub 2} and WO{sub 3} oxidation states, but the second state was clearly dominant. Scanning electron microscopy results showed that the oxide was amorphous or nanocrystalline. The WO{sub 3}-based devices were sensitive to ammonia vapors when operated between 250 and 350 C. The optimal operating temperature for the highest sensitivity to ammonia was 300 C. Furthermore, when the devices were operated at 300 C, their sensitivity to other reducing species such as ethanol, methane, toluene, and water vapor was significantly lower, and this resulted in a high selectivity to ammonia. A model for the sensing mechanisms of the fabricated sensors is proposed.

  12. Nitrogen losses, uptake and abundance of ammonia oxidizers in soil under mineral and organo-mineral fertilization regimes.

    PubMed

    Florio, Alessandro; Felici, Barbara; Migliore, Melania; Dell'Abate, Maria Teresa; Benedetti, Anna

    2016-05-01

    A laboratory incubation experiment and greenhouse studies investigated the impact of organo-mineral (OM) fertilization as an alternative practice to conventional mineral (M) fertilization on nitrogen (N) uptake and losses in perennial ryegrass (Lolium perenne) as well as on soil microbial biomass and ammonia oxidizers. While no significant difference in plant productivity and ammonia emissions between treatments could be detected, an increase in soil total N content and an average 17.9% decrease in nitrates leached were observed in OM fertilization compared with M fertilization. The microbial community responded differentially to treatments, suggesting that the organic matter fraction of the OM fertilizer might have influenced N immobilization in the microbial biomass in the short-medium term. Furthermore, nitrate contents in fertilized soils were significantly related to bacterial but not archaeal amoA gene copies, whereas in non-fertilized soils a significant relationship between soil nitrates and archaeal but not bacterial amoA copies was found. The application of OM fertilizer to soil maintained sufficient productivity and in turn increased N use efficiency and noticeably reduced N losses. Furthermore, in this experiment, ammonia-oxidizing bacteria drove nitrification when an N source was added to the soil, whereas ammonia-oxidizing archaea were responsible for ammonia oxidation in non-fertilized soil. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  13. 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.

  14. Competition between Ammonia-Oxidizing Bacteria and Benthic Microalgae

    PubMed Central

    Risgaard-Petersen, Nils; Nicolaisen, Mette H.; Revsbech, Niels Peter; Aa Lomstein, Bente

    2004-01-01

    The abundance, activity, and diversity of ammonia-oxidizing bacteria (AOB) were studied in prepared microcosms with and without microphytobenthic activity. In the microcosm without alga activity, both AOB abundance, estimated by real-time PCR, and potential nitrification increased during the course of the experiment. AOB present in the oxic zone of these sediments were able to fully exploit their nitrification potential because NH4+ did not limit growth. In contrast, AOB in the alga-colonized sediments reached less than 20% of their potential activity, suggesting starvation of cells. Starvation resulted in a decrease with time in the abundance of AOB as well as in nitrification potential. This decrease was correlated with an increase in alga biomass, suggesting competitive exclusion of AOB by microalgae. Induction of N limitation in the oxic zone of the alga-colonized sediments and O2 limitation of the majority of AOB in darkness were major mechanisms by which microalgae suppressed the growth and survival of AOB. The competition pressure from the algae seemed to act on the entire population of AOB, as no differences were observed by denaturing gradient gel electrophoresis of amoA fragments during the course of the experiment. Enumeration of bacteria based on 16S rRNA gene copies and d-amino acids suggested that the algae also affected other bacterial groups negatively. Our data indicate that direct competitive interaction takes place between algae and AOB and that benthic algae are superior competitors because they have higher N uptake rates and grow faster than AOB. PMID:15345441

  15. Quantitative analyses of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in fields with different soil types.

    PubMed

    Morimoto, Sho; Hayatsu, Masahito; Takada Hoshino, Yuko; Nagaoka, Kazunari; Yamazaki, Masatsugu; Karasawa, Toshihiko; Takenaka, Makoto; Akiyama, Hiroko

    2011-01-01

    Soil type is one of the key factors affecting soil microbial communities. With regard to ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), however, it has not been determined how soil type affects their community size and soil nitrification activity. Here we quantitatively analyzed the ammonia monooxygenase genes (amoA) of these ammonia oxidizers in fields with three different soil types (Low-humic Andosol [LHA], Gray Lowland Soil [GLS], and Yellow Soil [YS]) under common cropping conditions, and assessed the relationships between soil nitrification activity and the abundance of each amoA. Nitrification activity of LHA was highest, followed by that of GLS and YS; this order was consistent with that for the abundance of AOB amoA. Abundance of AOB amoA showed temporal variation, which was similar to that observed in nitrification activity, and a strong relationship (adjusted R(2)=0.742) was observed between the abundance of AOB amoA and nitrification activity. Abundance of AOA amoA also exhibited a significant relationship (adjusted R(2)=0.228) with nitrification activity, although this relationship was much weaker. Our results indicate that soil type affects the community size of AOA and AOB and the resulting nitrification activity, and that AOB are major contributors to nitrification in soils, while AOA are partially responsible.

  16. Mathematical models and bacterial communities for ammonia toxicity in mesophilic anaerobes not acclimated to high concentrations of ammonia.

    PubMed

    Park, Seyong; Cui, Fenghao; Mo, Kyung; Kim, Moonil

    In this study, we evaluated ammonia toxicity in mesophilic anaerobic digestion at various pH values and total ammonia nitrogen (TAN) concentrations. We performed anaerobic toxicity assays (ATAs) to evaluate the toxicity effects of TAN and pH on mesophilic anaerobic digestion. Modeling based on the results of the ATAs indicated that the specific methanogenic activity (SMA) decreased by 30% at a TAN concentration higher than 3.0 g/L compared to a TAN concentration of 0 g/L. In addition, the highest SMA for a given TAN level (0.5-10.0 g/L) was observed at a pH of around 7.6. The results of bacterial community analyses showed that the diversity and richness of microorganisms with increasing TAN concentration were decreased. Chloroflexi and Synergistetes were the dominant phyla at TAN concentrations less than 3.0 g/L, and Firmicutes was the dominant phylum at TAN concentrations higher than 3.0 g/L, implying that the ammonia toxicity concentration may influence the kind of dominant species. In conclusion, to start a stable mesophilic anaerobic digestion concerning ammonia toxicity, a TAN concentration less than 3.0 g/L is preferable.

  17. 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.

  18. pH rather than nitrification and urease inhibitors determines the community of ammonia oxidizers in a vegetable soil.

    PubMed

    Xi, Ruijiao; Long, Xi-En; Huang, Sha; Yao, Huaiying

    2017-12-01

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

  19. 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...

  20. 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...

  1. Ammonia Oxidation Plant at Plum Brook Ordnance Works

    NASA Image and Video Library

    1943-06-21

    An ammonia oxidation plant at the Plum Brook Ordnance Works near Sandusky, Ohio, which later became the National Aeronautics and Space Administration’s (NASA) Plum Brook Station. During World War II the ordnance works produced trinitroluene (TNT), dinitrotoluene (DNT), and pentolite which were crated and shipped to an arsenal in Ravenna, Ohio. There, the explosives were packed into shells and sent to Allied forces overseas. Plum Brook was the third largest producer of TNT during World War II. Toluene, sulfuric acid, and nitric acid were used to manufacture the TNT. Nitric Acid is made by oxidizing ammonia, adding water, and concentrating it. The facility in this photograph was used for this oxidation. The structure included air compressors, filters, aftercoolers, power recovery systems, air receivers, heaters, ammonia gasifiers, gas mixers, cooler condensers, absorption columns, and bleaching columns. The Plum Brook Ordnance Works was shut down immediately after the war and remained vacant for the next ten years. NASA’s predecessor, the National Advisory Committee for Aeronautics (NACA), acquired the 500 acres of the site in 1955 to build a nuclear test reactor. By 1963, the agency had acquired the entire 9000 acres from the Army. Almost all of the military facilities were removed in the early 1960s. Plum Brook Station contained over 30 test facilities at its peak in the late 1960s. Today there are four major facilities in operation.

  2. Dissimilatory Nitrite Reductase Genes from Autotrophic Ammonia-Oxidizing Bacteria

    PubMed Central

    Casciotti, Karen L.; Ward, Bess B.

    2001-01-01

    The presence of a copper-containing dissimilatory nitrite reductase gene (nirK) was discovered in several isolates of β-subdivision ammonia-oxidizing bacteria using PCR and DNA sequencing. PCR primers Cunir3 and Cunir4 were designed based on published nirK sequences from denitrifying bacteria and used to amplify a 540-bp fragment of the nirK gene from Nitrosomonas marina and five additional isolates of ammonia-oxidizing bacteria. Amplification products of the expected size were cloned and sequenced. Alignment of the nucleic acid and deduced amino acid (AA) sequences shows significant similarity (62 to 75% DNA, 58 to 76% AA) between nitrite reductases present in these nitrifiers and the copper-containing nitrite reductase found in classic heterotrophic denitrifiers. While the presence of a nitrite reductase in Nitrosomonas europaea is known from early biochemical work, preliminary sequence data from its genome indicate a rather low similarity to the denitrifier nirKs. Phylogenetic analysis of the partial nitrifier nirK sequences indicates that the topology of the nirK tree corresponds to the 16S rRNA and amoA trees. While the role of nitrite reduction in the metabolism of nitrifying bacteria is still uncertain, these data show that the nirK gene is present in closely related nitrifying isolates from many oceanographic regions and suggest that nirK sequences retrieved from the environment may include sequences from ammonia-oxidizing bacteria. PMID:11319103

  3. Emergent Macrophytes Act Selectively on Ammonia-Oxidizing Bacteria and Archaea

    PubMed Central

    Trias, Rosalia; Ruiz-Rueda, Olaya; García-Lledó, Arantzazu; Vilar-Sanz, Ariadna; López-Flores, Rocío; Quintana, Xavier D.; Hallin, Sara

    2012-01-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were quantified in the sediments and roots of dominant macrophytes in eight neutral to alkaline coastal wetlands. The AOA dominated in most samples, but the bacterial-to-archaeal amoA gene ratios increased with increasing ammonium levels and pH in the sediments. For all plant species, the ratios increased on the root surface relative to the adjacent bulk sediment. This suggests that root surfaces in these environments provide conditions favoring enrichment of AOB. PMID:22706066

  4. Effects of ammonia on methane oxidation in landfill cover materials.

    PubMed

    Long, Yu-Yang; Liao, Yan; Miao, Jing-Yu; Shen, Dong-Sheng

    2014-01-01

    The effects of ammonia (NH3) on CH4 attenuation in landfill cover materials consisting of landfill cover soil (LCS) and aged municipal solid waste (AMSW), at different CH4 concentrations, were investigated. The CH4 oxidation capacities of LCS and AMSW were found to be significantly affected by the CH4 concentration. The maximum oxidation rates for LCS and AMSW were obtained at CH4 concentrations of 5% and 20%(v/v), respectively, within 20 days. CH4 biological oxidation in AMSW was significantly inhibited by NH3 at low CH4 concentrations (5%, v/v) but highly stimulated at high levels (20% and 50%, v/v). Oxidation in LCS was stimulated by NH3 at all CH4 concentrations due to the higher conversion of the nitrogen in NH3 in AMSW than in LCS. NH3 increases CH4 oxidation in landfill cover materials.

  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.

    2014-11-01

    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.

  6. Impact of biodegradation of organic matters on ammonia oxidation in compost.

    PubMed

    Zeng, Yang; De Guardia, Amaury; Ziebal, Christine; De Macedo, Flávia Junqueira; Dabert, Patrick

    2013-05-01

    Nitrification plays an important role in nitrogen turnover in composting process. It has been believed that nitrification occurs mainly during the maturation phase due to the elevated temperature during the active phase of composting. In this work, the intense biodegradation of organic matters is demonstrated to be another negative impact on the ammonia oxidation, the first step of nitrification. We investigated the ammonia oxidation in compost following organic matters addition at intermediate temperature. Different indicators of ammonia oxidation were studied, respectively. The accumulation of nitrite and nitrate was 10(2)-10(3) lower in composts with organic matters addition. The nitrous oxide emissions were absent or 40-fold inferior in these composts. The nitrogen mass balance indicated a less amount of oxidized ammonia after the addition. The ammonia-oxidizing bacteria declined following the organic matters addition. In contrast, the ammonia-oxidizing archaea were supported by the organic matters. Possible mechanisms of this impact were also discussed.

  7. Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea

    PubMed Central

    Horak, Rachel E A; Qin, Wei; Schauer, Andy J; Armbrust, E Virginia; Ingalls, Anitra E; Moffett, James W; Stahl, David A; Devol, Allan H

    2013-01-01

    Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes α-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis–Menten kinetics curve for ammonia oxidation by the natural community and found that the measured Km of 98±14 nmol l−1 was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 °C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a Km for the natural community to better constrain ammonia oxidation rates determined with the commonly used 15NH4+ dilution technique. PMID:23657360

  8. [Effect of pH for the electrochemical oxidation products and oxidation pathways of ammonia].

    PubMed

    Chen, Jin-luan; Shi, Han-chang; Xu, Li-li

    2008-08-01

    The electrochemical oxidation of ammonia in wastewater was investigated in a flow electrochemical cell. The effect of pH on ammonia removal efficiency, oxidation products and oxidation pathways was elucidated. The experimental results indicated that, the higher production efficiency of free chlorine and hydroxyl radical can be obtained under the moderate alkaline condition, and the electrochemical oxidation rate of ammonia was higher in this condition. In existence of chloride ions, chloramines produced during the electrolysis of ammonia. The constituent of chloramines related with the pH of reaction system. When pH was higher than 9, monochloramine was dominant; When pH was equal to 7, monochloramine and dichloramine existed at the same time and the concentration of the two chloramines was an approximation of the same; When pH was smaller than 5, most of the production was dichloramine. The production of nitrogen trichloride can be avoided when pH was higher than 5. Under the current density of 20 mA/cm2, the concentration of hydroxyl radical produced by electrolysis was smaller than 5 x 10(-15) mol/L. The indirect oxidation was the dominant reaction in the two pathways of electrochemical oxidation of ammonia.

  9. Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria.

    PubMed

    Müller, Bettina; Sun, Li; Westerholm, Maria; Schnürer, Anna

    2016-01-01

    Syntrophic acetate oxidation (SAO) is the predominant pathway for methane production in high ammonia anaerobic digestion processes. The bacteria (SAOB) occupying this niche and the metabolic pathway are poorly understood. Phylogenetic diversity and strict cultivation requirements hinder comprehensive research and discovery of novel SAOB. Most SAOB characterised to date are affiliated to the physiological group of acetogens. Formyltetrahydrofolate synthetase is a key enzyme of both acetogenic and SAO metabolism. The encoding fhs gene has therefore been identified as a suitable functional marker, using a newly designed primer pair. In this comparative study, we used a combination of terminal restriction fragment length polymorphism profiling, clone-based comparison, qPCR and Illumina amplicon sequencing to assess the bacterial community and acetogenic sub-community prevailing in high- and low-ammonia laboratory-scale digesters in order to delineate potential SAOB communities. Potential candidates identified were further tracked in a number of low-ammonia and high-ammonia laboratory-scale and large-scale digesters in order to reveal a potential function in SAO. All methodical approaches revealed significant changes in the bacterial community composition concurrently with increasing ammonia and predominance of SAO. The acetogenic community under high ammonia conditions was revealed to be generally heterogeneous, but formed distinct phylogenetic clusters. The clusters differed clearly from those found under low-ammonia conditions and represented an acetogenic assemblage unique for biogas processes and recurring in a number of high-ammonia processes, indicating potential involvement in SAO. The phylogenetic affiliation and population dynamics observed point to a key community, belonging mainly to the Clostridia class, in particular to the orders Clostridiales and Thermoanaerobacterales, which appear to specialise in SAO rather than being metabolically versatile. Overall

  10. [Effects of transgenic Bt + CpTI cotton on rhizosphere bacteria and ammonia oxidizing bacteria population].

    PubMed

    Dong, Lianhua; Meng, Ying; Wang, Jing

    2014-03-04

    The effect of transgenic cotton on the rhizosphere bacteria can be important to the risk assessment for the genetically modified crops. We studied the rhizosphere microbial community with cultivating genetically modified cotton. The effects of transgenic Bt + CpTI Cotton (SGK321) and its receptor cotton (SY321) on rhizosphere total bacteria and ammonia oxidizing bacteria population size were studied by using droplet digital PCR. We collected rhizosphere soil before cotton planting and along with the cotton growth stage (squaring stage, flowering stage, belling stage and boll opening stage). There was no significant change on the total bacterial population between the transgenic cotton and the receptor cotton along with the growth stage. However, the abundance of ammonia oxidizing bacteria (AOB) in both type of cottons showed significant difference between different growth stages, and the variation tendency was different. In squaring stage, the numbers of AOB in rhizosphere of SY321 and SGK321 increased 4 and 2 times, respectively. In flowering stage, AOB number in rhizosphere of SY321 significantly decreased to be 5.96 x 10(5) copies/g dry soil, however, that of SGK321 increased to be 1.25 x 10(6) copies/g dry soil. In belling stage, AOB number of SY321 greatly increased to be 1.49 x 10(6) copies/g dry soil, but no significant change was observed for AOB number of SGK321. In boll opening stage, both AOB number of SY321 and SGK321 clearly decreased and they were significantly different from each other. Compared to the non-genetically modified cotton, the change in abundance of ammonia oxidizing bacteria was slightly smooth in the transgenic cotton. Not only the cotton growth stage but also the cotton type caused this difference. The transgenic cotton can slow down the speed of ammonia transformation through impacting the number of AOB, which is advantageous for plant growth.

  11. 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

  12. 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.

  13. Oxidation of nitrapyrin to 6-chloropicolinic acid by the ammonia-oxidizing bacterium nitrosomonas europaea

    SciTech Connect

    Vannelli, T.; Hooper, A.B.

    1992-07-01

    Suspensions of Nitrosomonas europaea catalyzed the oxidation of the commercial nitrification inhibitor nitrapyrin (2-chloro-6-(trichloromethyl)-pyridine). Rapid oxidation of nitrapyrin (at a concentration of 10 microM) required the concomitant oxidation of ammonia, hydroxylamine, or hydrazine. The turnover rate was highest in the presence of 10 mM ammonia (0.8 nmol of nitrapyrin per min/mg of protein). The product of the reaction was 6-chloropicolinic acid. By the use of (18)O2, it was shown that one of the oxygens in 6-chloropicolinic acid came from diatomic oxygen and that the other came from water. Approximately 13% of the radioactivity of (2,6-(14)C) nitrapyrin was shown to bind to cells. Most (94%) of the latter was bound indiscriminately to membrane proteins. The nitrapyrin bound to membrane proteins may account for the observed inactivation of ammonia oxidation. (Copyright (c) 1992, American Society for Microbiology.)

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. Interactive effects of multiple climate change factors on ammonia oxidizers and denitrifiers in a temperate steppe.

    PubMed

    Zhang, Cuijing; Shen, Jupei; Sun, Yifei; Wang, Juntao; Zhang, Limei; Yang, Zhongling; Han, Hongyan; Wan, Shiqiang; He, Jizheng

    2017-03-15

    Global climate change could have profound effects on belowground microbial communities and subsequently affect soil biogeochemical processes. The interactive effects of multiple co-occurring climate change factors on microbially-mediated processes are not well understood. A four-factorial field experiment with elevated CO2, watering, nitrogen (N) addition and night warming was conducted in a temperate steppe of northern China. Real-time polymerase chain reaction and terminal-restriction fragment length polymorphism, combined with clone library techniques were applied to examine the effects of those climate change factors on N-related microbial abundance and community composition. Only the abundance of ammonia-oxidizing bacteria significantly increased by nitrogen addition and decreased by watering. The interactions of watering × warming on the bacterial amoA community and warming × nitrogen addition on the nosZ community were found. Redundancy analysis indicated that the ammonia-oxidizing archaeal community was affected by total N and total carbon, while the community of bacterial amoA and nosZ were significantly affected by soil pH. According to a structural equation modeling analysis, climate change influenced net primary production indirectly by altering microbial abundance and activities. These results indicated that microbial responses to the combination of chronic global change tend to be smaller than expected from single-factor global change manipulations.

  19. Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium sensitive to high levels of ammonia.

    PubMed

    Suwa, Yuichi; Yuichi, Suwa; Norton, Jeanette M; Bollmann, Annette; Klotz, Martin G; Stein, Lisa Y; Laanbroek, Hendrikus J; Arp, Daniel J; Goodwin, Lynne A; Chertkov, Olga; Held, Brittany; Bruce, David; Detter, J Chris; Detter, Janine C; Tapia, Roxanne; Han, Cliff S

    2011-09-01

    Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A, which is characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower K(m)), and lower maximum growth rates than strains in Nitrosomonas cluster 7, which includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are needed, as these bacteria are found in freshwater environments, drinking water supplies, wastewater treatment systems, and soils worldwide.

  20. Archaea Dominate Ammonia Oxidizers in the Permian Water Ecosystem of Midland Basin

    PubMed Central

    Hong, Yiguo; Youshao, Wang; Chen, Feng

    2013-01-01

    We investigated the existence and characteristics of ammonia oxidizers in Permian water from Midland Basin. Molecular surveys targeting the amoA gene showed that only ammonia-oxidizing archaea (AOA) exist and have potential activity in this special environment. In contrast, no ammonia-oxidizing bacteria (AOB) were detected in the water. Phylogenetic analysis indicated that 72–89% of the total screened AOA clones were affiliated with those found in underground water, and 10–24% of the AOA clones were related to those found in marine water or sediments. Our results indicate AOA might be the most abundant ammonia-oxidizing microbes in this ecological niche. PMID:24005842

  1. Quantification of Aerobic Ammonia-Oxidizing Bacteria in Soil using Activity-Based Fluorescent Labeling of Ammonia Monooxygenase

    NASA Astrophysics Data System (ADS)

    Farnan, J.; Bennett, K.; Hyman, M. R.

    2016-12-01

    Nitrification is a key step in the biological nitrogen cycle and has a large effect on the fate of nitrogen species in both wastewater treatment systems and agricultural soils. Aerobic ammonia-oxidizing bacteria (AOB) initiate nitrification by converting ammonia (NH3) to nitrite (NO2-) and are therefore pivotal to the process. AOB are ubiquitous in the environment but are difficult to quantify as they grow poorly on solid media. Other quantification methods like iquid most-probable number techniques are slow and error-prone, while modern molecular approaches involving polymerase chain reaction amplification are faster and more accurate but do not differentiate between active and inactive AOB. In this study, we explored using activity-based fluorescent mechanisms for rapidly quantifying metabolically active forms of AOB in soils. Initial experiments using Nitrosomonas europaea aimed to establish a relationship between NH3-dependent nitrite production and bacterial cell numbers. Active AMO was treated cells with 1,7-octadiyne (17OD) to inactivate the enzyme and a subsequent copper-dependent "click" reaction attached a fluor. The labeled protein was quantified by SDS-PAGE and IR scanning. In future experiments, AOB will be stimulated in soil microcosms by adding NH4Cl. AMO will again be inactivated by adding 17OD, and total bacteria will be separated from the soil samples using gradient centrifugation. After "click" conjugation with AlexaFluor 647 azide, the abundance of AMO will be determined with SDS-PAGE and IR analysis while metabolically active AOB will be measured via fluorescence-activating cell sorting.

  2. 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.

  3. 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.

  4. 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

  5. Contribution of ammonia oxidation to chemoautotrophy in Antarctic coastal waters

    PubMed Central

    Tolar, Bradley B; Ross, Meredith J; Wallsgrove, Natalie J; Liu, Qian; Aluwihare, Lihini I; Popp, Brian N; Hollibaugh, James T

    2016-01-01

    There are few measurements of nitrification in polar regions, yet geochemical evidence suggests that it is significant, and chemoautotrophy supported by nitrification has been suggested as an important contribution to prokaryotic production during the polar winter. This study reports seasonal ammonia oxidation (AO) rates, gene and transcript abundance in continental shelf waters west of the Antarctic Peninsula, where Thaumarchaeota strongly dominate populations of ammonia-oxidizing organisms. Higher AO rates were observed in the late winter surface mixed layer compared with the same water mass sampled during summer (mean±s.e.: 62±16 versus 13±2.8 nm per day, t-test P<0.0005). AO rates in the circumpolar deep water did not differ between seasons (21±5.7 versus 24±6.6 nm per day; P=0.83), despite 5- to 20-fold greater Thaumarchaeota abundance during summer. AO rates correlated with concentrations of Archaea ammonia monooxygenase (amoA) genes during summer, but not with concentrations of Archaea amoA transcripts, or with ratios of Archaea amoA transcripts per gene, or with concentrations of Betaproteobacterial amoA genes or transcripts. The AO rates we report (<0.1–220 nm per day) are ~10-fold greater than reported previously for Antarctic waters and suggest that inclusion of Antarctic coastal waters in global estimates of oceanic nitrification could increase global rate estimates by ~9%. Chemoautotrophic carbon fixation supported by AO was 3–6% of annualized phytoplankton primary production and production of Thaumarchaeota biomass supported by AO could account for ~9% of the bacterioplankton production measured in winter. Growth rates of thaumarchaeote populations inferred from AO rates averaged 0.3 per day and ranged from 0.01 to 2.1 per day. PMID:27187795

  6. 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.

  7. 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

  8. 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

  9. Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance.

    PubMed

    Thion, Cécile E; Poirel, Jessica D; Cornulier, Thomas; De Vries, Franciska T; Bardgett, Richard D; Prosser, James I

    2016-07-01

    The influence of plants on archaeal (AOA) and bacterial (AOB) ammonia oxidisers (AO) is poorly understood. Higher microbial activity in the rhizosphere, including organic nitrogen (N) mineralisation, may stimulate both groups, while ammonia uptake by plants may favour AOA, considered to prefer lower ammonia concentration. We therefore hypothesised (i) higher AOA and AOB abundances in the rhizosphere than bulk soil and (ii) that AOA are favoured over AOB in the rhizosphere of plants with an exploitative strategy and high N demand, especially (iii) during early growth, when plant N uptake is higher. These hypotheses were tested by growing 20 grassland plants, covering a spectrum of resource-use strategies, and determining AOA and AOB amoA gene abundances, rhizosphere and bulk soil characteristics and plant functional traits. Joint Bayesian mixed models indicated no increase in AO in the rhizosphere, but revealed that AOA were more abundant in the rhizosphere of exploitative plants, mostly grasses, and less abundant under conservative plants. In contrast, AOB abundance in the rhizosphere and bulk soil depended on pH, rather than plant traits. These findings provide a mechanistic basis for plant-ammonia oxidiser interactions and for links between plant functional traits and ammonia oxidiser ecology. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Bacterial Anabaena variabilis phenylalanine ammonia lyase: a biocatalyst with broad substrate specificity.

    PubMed

    Lovelock, Sarah L; Turner, Nicholas J

    2014-10-15

    Phenylalanine ammonia lyases (PALs) catalyse the regio- and stereoselective hydroamination of cinnamic acid analogues to yield optically enriched α-amino acids. Herein, we demonstrate that a bacterial PAL from Anabaena variabilis (AvPAL) displays significantly higher activity towards a series of non-natural substrates than previously described eukaryotic PALs. Biotransformations performed on a preparative scale led to the synthesis of the 2-chloro- and 4-trifluoromethyl-phenylalanine derivatives in excellent ee, highlighting the enormous potential of bacterial PALs as biocatalysts for the synthesis of high value, non-natural amino acids.

  11. Modelling temperature effects on ammonia-oxidising bacterial biostability in chloraminated systems.

    PubMed

    Sarker, Dipok Chandra; Sathasivan, Arumugam; Joll, Cynthia A; Heitz, Anna

    2013-06-01

    The biostability concept has been successfully used to predict the onset of nitrification in drinking water distribution systems, but in certain cases deficiencies have been observed in the predictions, indicating that modifications to parameters were needed. At the biostable disinfectant residual concentration (BRC), the rate of ammonia-oxidising bacterial (AOB) growth due to the substrate (free ammonia) and the rate of inactivation due to the disinfectant are balanced. Growth and inactivation rates vary greatly with temperature, but temperature is yet to be considered in the biostability equation. In this paper, two separate novel models are proposed which take into account the temperature effects on the biostability equation. First, a novel model of specific growth rate variability with temperature was shown to be valid for different bacterial species. Then, the biostability model was modified and validated for ammonia-oxidising bacterial activity using data collected from laboratory and full-scale distribution systems. The proposed model has two important uses: while the specific growth rate model and biostability model can be widely adopted for many microbes, the biostability model for AOB also has the potential to aid water utilities in disinfectant residual management throughout yearly temperature variations. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. 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

  13. 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

  14. Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils

    Treesearch

    Xinda Lu; Peter J. Bottomley; David D. Myrold

    2015-01-01

    Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA-and AOB-supported nitrifi-cation determined both in soil-water slurries and in unsaturated...

  15. Nitrous oxide production and methane oxidation by different ammonia-oxidizing bacteria

    SciTech Connect

    Jiang, Q.Q.; Bakken, L.R.

    1999-06-01

    Ammonia-oxidizing bacteria (AOB) are thought to contribute significantly to N{sub 2}O production and methane oxidation in soils. Most knowledge derives from experiments with Nitrosomonas europaea, which appears to be of minor importance in most soils compared to Nitrosospira spp. The authors have conducted a comparative study of levels of aerobic N{sub 2}O production in six phylogenetically different Nitrosospira strains newly isolated from soils and in two N. europaea and Nitrosospira multiformis type strains. The fraction of oxidized ammonium released as N{sub 2}O during aerobic growth was remarkably constant for all the Nitrosospira strains, irrespective of the substrate supply (urea versus ammonium), the pH, or substrate limitation. N. europaea and Nitrosospira multiformis released similar fractions of N{sub 2}O when they were supplied with ample amounts of substrates, but the fractions rose sharply when they were restricted by a low pH or substrate limitation. Phosphate buffer doubled the N{sub 2}O release for all types of AOB. No detectable oxidation of atmospheric methane was detected. Calculations based on detection limits as well as data in the literature on CH{sub 4} oxidation by AOB bacteria prove that none of the tested strains contribute significantly to the oxidation of atmospheric CH{sub 4} in soils.

  16. Immobilization of ammonia-oxidizing bacteria by polyvinyl alcohol and sodium alginate.

    PubMed

    Dong, Yuwei; Zhang, Yanqiu; Tu, Baojun

    Ammonia-oxidizing bacteria were immobilized by polyvinyl alcohol (PVA) and sodium alginate. The immobilization conditions and ammonia oxidation ability of the immobilized bacteria were investigated. The following immobilization conditions were observed to be optimal: PVA, 12%; sodium alginate, 1.1%; calcium chloride, 1.0%; inoculum concentration, 1.3 immobilized balls/mL of immobilized medium; pH, 10; and temperature, 30°C. The immobilized ammonia-oxidizing bacteria exhibited strong ammonia oxidation ability even after being recycled four times. The ammonia nitrogen removal rate of the immobilized ammonia-oxidizing bacteria reached 90.30% under the optimal immobilization conditions. When compared with ammonia-oxidizing bacteria immobilized by sodium alginate alone, the bacteria immobilized by PVA and sodium alginate were superior with respect to pH resistance, the number of reuses, material cost, heat resistance, and ammonia oxidation ability. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  17. [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.

  18. 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.

  19. 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

  20. Ammonia-oxidizing activity and microbial community structure in acid tea (Camellia sinensis) orchard soil

    NASA Astrophysics Data System (ADS)

    Okamura, K.; Takanashi, A.; Yamada, T.; Hiraishi, A.

    2012-03-01

    The purpose of this study was to determine the ammonia-oxidizing activity and the phylogentic composition of microorganisms involved in acid tea (Camellia sinensis) orchard soil. All soil samples were collected from three sites located in Tahara and Toyohashi, Aichi Prefecture, Japan. The potential nitrification rate (PNR) was measured by the chlorate inhibition method. The soil pH of tea orchards studied ranged from 2.78 to 4.84, differing significantly from sample to sample, whereas that of meadow and unplanted fields ranged from 5.78 to 6.35. The PNR ranged from 0.050 to 0.193 μg NO2--Ng-1 h-1 and were positively correlated with the soil pH (r2 = 0.382, p<0.001). Bulk DNA was extracted from a tea orchard soil (pH 4.8; PNR, 0.078 μg NO2--Ng-1 h-1) and subjected to PCR-aided clone library analyses targeting archaeal and bacterial amoA genes. The detected archaeal clones separated from the cluster of the 'Soil clones' and tightly clustered with the clones originating from other acidic soil environments including the Chinese tea orchard soil. These results suggest that the specific archaeal populations dominate as the ammonia oxidizers in acid tea-orchard soils and possibly other acid soils, independent of geographic locations, which results from the adaptation to specific ecological niches.

  1. 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.

  2. Analysis of nitrification in agricultural soil and improvement of nitrogen circulation with autotrophic ammonia-oxidizing bacteria.

    PubMed

    Matsuno, Toshihide; Horii, Sachie; Sato, Takanobu; Matsumiya, Yoshiki; Kubo, Motoki

    2013-02-01

    Accumulations of inorganic nitrogen (NH₄⁺, NO₂⁻, and NO₃⁻) were analyzed to evaluate the nitrogen circulation activity in 76 agricultural soils. Accumulation of NH₄⁺ was observed, and the reaction of NH₄⁺→ NO₂⁻ appeared to be slower than that of NO₂⁻ → NO₃⁻ in agricultural soil. Two autotrophic and five heterotrophic ammonia-oxidizing bacteria (AOB) were isolated and identified from the soils, and the ammonia-oxidizing activities of the autotrophic AOB were 1.0 × 10³-1.0 × 10⁶ times higher than those of heterotrophic AOB. The relationship between AOB number, soil bacterial number, and ammonia-oxidizing activity was investigated with 30 agricultural soils. The ratio of autotrophic AOB number was 0.00032-0.26% of the total soil bacterial number. The soil samples rich in autotrophic AOB (>1.0 × 10⁴ cells/g soil) had a high nitrogen circulation activity, and additionally, the nitrogen circulation in the agricultural soil was improved by controlling the autotrophic AOBs.

  3. 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

  4. 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.

  5. Formation of Hydroxylamine on Dust Grains via Ammonia Oxidation

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    The quest to detect prebiotic molecules in space, notably amino acids, requires an understanding of the chemistry involving nitrogen atoms. Hydroxylamine (NH2OH) is considered a precursor to the amino acid glycine. Although not yet detected, NH2OH 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 NH2OH in dense cloud conditions. On ices at 14 K and with a modest activation energy barrier, NH2OH is found to be formed with an abundance that never falls below a factor 10 with respect to NH3. Suggestions of conditions for future observations are provided.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. Autotrophic Ammonia Oxidation at Low pH through Urea Hydrolysis

    PubMed Central

    Burton, Simon A. Q.; Prosser, Jim I.

    2001-01-01

    Ammonia oxidation in laboratory liquid batch cultures of autotrophic ammonia oxidizers rarely occurs at pH values less than 7, due to ionization of ammonia and the requirement for ammonium transport rather than diffusion of ammonia. Nevertheless, there is strong evidence for autotrophic nitrification in acid soils, which may be carried out by ammonia oxidizers capable of using urea as a source of ammonia. To determine the mechanism of urea-linked ammonia oxidation, a ureolytic autotrophic ammonia oxidizer, Nitrosospira sp. strain NPAV, was grown in liquid batch culture at a range of pH values with either ammonium or urea as the sole nitrogen source. Growth and nitrite production from ammonium did not occur at pH values below 7. Growth on urea occurred at pH values in the range 4 to 7.5 but ceased when urea hydrolysis was complete, even though ammonia, released during urea hydrolysis, remained in the medium. The results support a mechanism whereby urea enters the cells by diffusion and intracellular urea hydrolysis and ammonia oxidation occur independently of extracellular pH in the range 4 to 7.5. A proportion of the ammonia produced during this process diffuses from the cell and is not subsequently available for growth if the extracellular pH is less than 7. Ureolysis therefore provides a mechanism for nitrification in acid soils, but a proportion of the ammonium produced is likely to be released from the cell and may be used by other soil organisms. PMID:11425707

  12. Distinctive microbial ecology and biokinetics of autotrophic ammonia and nitrite oxidation in a partial nitrification bioreactor.

    PubMed

    Ahn, Joon Ho; Yu, Ran; Chandran, Kartik

    2008-08-15

    Biological nitrogen removal (BNR) based on partial nitrification and denitrification via nitrite is a cost-effective alternate to conventional nitrification and denitrification (via nitrate). The goal of this study was to investigate the microbial ecology, biokinetics, and stability of partial nitrification. Stable long-term partial nitrification resulting in 82.1 +/- 17.2% ammonia oxidation, primarily to nitrite (77.3 +/- 19.5% of the ammonia oxidized) was achieved in a lab-scale bioreactor by operation at a pH, dissolved oxygen and solids retention time of 7.5 +/- 0.1, 1.54 +/- 0.87 mg O(2)/L, and 3.0 days, respectively. Bioreactor ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) populations were most closely related to Nitrosomonas europaea and Nitrobacter spp., respectively. The AOB population fraction varied in the range 61 +/- 45% and was much higher than the NOB fraction, 0.71 +/- 1.1%. Using direct measures of bacterial concentrations in conjunction with independent activity measures and mass balances, the maximum specific growth rate (micro(max)), specific decay (b) and observed biomass yield coefficients (Y(obs)) for AOB were 1.08 +/- 1.03 day(-1), 0.32 +/- 0.34 day(-1), and 0.15 +/- 0.06 mg biomass COD/mg N oxidized, respectively. Corresponding micro(max), b, and Y(obs) values for NOB were 2.6 +/- 2.05 day(-1), 1.7 +/- 1.9 day(-1), and 0.04 +/- 0.02 mg biomass COD/mg N oxidized, respectively. The results of this study demonstrate that the highly selective partial nitrification operating conditions enriched for a narrow diversity of rapidly growing AOB and NOB populations unlike conventional BNR reactors, which host a broader diversity of nitrifying bacteria. Further, direct measures of microbial abundance enabled not only elucidation of mixed community microbial ecology but also estimation of key engineering parameters describing bioreactor systems supporting these communities. 2008 Wiley Periodicals, Inc.

  13. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil.

    PubMed

    Lehtovirta-Morley, Laura E; Stoecker, Kilian; Vilcinskas, Andreas; Prosser, James I; Nicol, Graeme W

    2011-09-20

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

  14. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil

    PubMed Central

    Lehtovirta-Morley, Laura E.; Stoecker, Kilian; Vilcinskas, Andreas; Prosser, James I.; Nicol, Graeme W.

    2011-01-01

    Nitrification is a fundamental component of the global nitrogen cycle and leads to significant fertilizer loss and atmospheric and groundwater pollution. Nitrification rates in acidic soils (pH < 5.5), which comprise 30% of the world's soils, equal or exceed those of neutral soils. Paradoxically, autotrophic ammonia oxidizing bacteria and archaea, which perform the first stage in nitrification, demonstrate little or no growth in suspended liquid culture below pH 6.5, at which ammonia availability is reduced by ionization. Here we report the discovery and cultivation of a chemolithotrophic, obligately acidophilic thaumarchaeal ammonia oxidizer, “Candidatus Nitrosotalea devanaterra,” from an acidic agricultural soil. Phylogenetic analysis places the organism within a previously uncultivated thaumarchaeal lineage that has been observed in acidic soils. Growth of the organism is optimal in the pH range 4 to 5 and is restricted to the pH range 4 to 5.5, unlike all previously cultivated ammonia oxidizers. Growth of this organism and associated ammonia oxidation and autotrophy also occur during nitrification in soil at pH 4.5. The discovery of Nitrosotalea devanaterra provides a previously unsuspected explanation for high rates of nitrification in acidic soils, and confirms the vital role that thaumarchaea play in terrestrial nitrogen cycling. Growth at extremely low ammonia concentration (0.18 nM) also challenges accepted views on ammonia uptake and metabolism and indicates novel mechanisms for ammonia oxidation at low pH. PMID:21896746

  15. Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary, California.

    PubMed

    Wankel, Scott D; Mosier, Annika C; Hansel, Colleen M; Paytan, Adina; Francis, Christopher A

    2011-01-01

    Ammonia oxidation-the microbial oxidation of ammonia to nitrite and the first step in nitrification-plays a central role in nitrogen cycling in coastal and estuarine systems. Nevertheless, questions remain regarding the connection between this biogeochemical process and the diversity and abundance of the mediating microbial community. In this study, we measured nutrient fluxes and rates of sediment nitrification in conjunction with the diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing betaproteobacteria (β-AOB). Sediments were examined from four sites in Elkhorn Slough, a small agriculturally impacted coastal California estuary that opens into Monterey Bay. Using an intact sediment core flowthrough incubation system, we observed significant correlations among NO(3)(-), NO(2)(-), NH(4)(+), and PO(4)(3+) fluxes, indicating a tight coupling of sediment biogeochemical processes. (15)N-based measurements of nitrification rates revealed higher rates at the less impacted, lower-nutrient sites than at the more heavily impacted, nutrient-rich sites. Quantitative PCR analyses revealed that β-AOB amoA (encoding ammonia monooxygenase subunit A) gene copies outnumbered AOA amoA gene copies by factors ranging from 2- to 236-fold across the four sites. Sites with high nitrification rates primarily contained marine/estuarine Nitrosospira-like bacterial amoA sequences and phylogenetically diverse archaeal amoA sequences. Sites with low nitrification rates were dominated by estuarine Nitrosomonas-like amoA sequences and archaeal amoA sequences similar to those previously described in soils. This is the first report measuring AOA and β-AOB amoA abundance in conjunction with (15)N-based nitrification rates in estuary sediments.

  16. Habitat specialization along a wetland moisture gradient differs between ammonia-oxidizing and denitrifying microorganisms.

    PubMed

    Peralta, Ariane L; Matthews, Jeffrey W; Kent, Angela D

    2014-08-01

    Gradients in abiotic parameters, such as soil moisture,can strongly influence microbial community structure and function. Denitrifying and ammonia-oxidizing microorganisms,in particular, have contrasting physiological responses to abiotic factors such as oxygen concentration and soil moisture. Identifying abiotic factors that govern the composition and activity of denitrifying and ammonia-oxidizing communities is critical for understanding the nitrogen cycle.The objectives of this study were to (i) examine denitrifier andarchaeal ammonia oxidizer community composition and (ii) assess the taxa occurring within each functional group related to soil conditions along an environmental gradient. Soil was sampled across four transects at four locations along a dry to saturated environmental gradient at a restored wetland. Soil pH and soil organic matter content increased from dry to saturated plots. Composition of soil denitrifier and ammonia oxidizer functional groups was assessed by terminal restriction fragment length polymorphism (T-RFLP) community analysis, and local soil factors were also characterized. Microbial community composition of denitrifiers and ammonia oxidizers differed along the moisture gradient (denitrifier:ANOSIM R = 0.739, P < 0.001; ammonia oxidizers: ANOSIMR = 0.760, P < 0.001). Individual denitrifier taxa were observed over a larger range of moisture levels than individual archaeal ammonia oxidizer taxa (Wilcoxon rank sum, W = 2413, P value = 0.0002). Together, our data suggest that variation in environmental tolerance of microbial taxa have potential to influence nitrogen cycling in terrestrial ecosystems.

  17. Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges.

    PubMed

    Radax, Regina; Hoffmann, Friederike; Rapp, Hans Tore; Leininger, Sven; Schleper, Christa

    2012-04-01

    The association of archaea with marine sponges was first described 15 years ago and their role in the nitrification process in Mediterranean and tropical sponges has been suggested. Here we explore the occurrence and abundance of potential ammonia-oxidizing archaea (AOA) in four morphologically different cold-water sponges (Phakellia ventilabrum, Geodia barretti, Antho dichotoma and Tentorium semisuberites) from the sublittoral and upper bathyal zone [Correction added on 30 December 2011, after first online publication on 19 December 2011: The term 'mesopelagic zone' has been replaced.] of the Norwegian coast, and relate them to nitrification rates determined in laboratory incubations. Net nitrification rates, calculated from the sum of nitrite and nitrate release during 24 h, were up to 1880 nmol N cm(-3) day(-1); i.e. comparable with those measured in Mediterranean sponges. Furthermore, a high abundance of archaeal cells was determined by fluorescence in situ hybridizations (CARD-FISH) and quantitative PCR, targeting archaeal amoA genes (encoding the alpha subunit of ammonia monooxygenase). AmoA genes as well as amoA transcripts were either exclusively detectable from archaea or were orders of magnitudes higher in abundance than their bacterial counterparts. Phylogenetic analyses of AOA and bacterial nitrite oxidizers (genus Nitrospira) confirmed the presence of specific populations of nitrifying microorganisms in the sponge mesohyl, which either were affiliated with groups detected earlier in marine sponges or were typical inhabitants of cold- and deep-water environments. Estimated cell-specific nitrification rates for P. ventilabrum were 0.6 to 6 fmol N archaeal cell(-1) day(-1), thus comparable with planktonic organisms. Our results identify AOA as the major drivers of nitrification in four cold-water sponges, and indicate that these archaea may be considered as a relevant factor in nitrogen cycling in ocean regions with high sponge biomass.

  18. Impacts of ammonia on zinc oxide nanoparticle toxicity to Nitrosomonas europaea

    NASA Astrophysics Data System (ADS)

    Wu, Junkang; Chang, Yan; Gao, Huan; Yu, Ran

    2017-05-01

    A Although the toxicity effects of engineering nanoparticles (NPs) in biological wastewater nitrogen removal (BNR) system have been extensively attracted, the impacts of co-existing contaminants from wastewater on NP toxicity have been less addressed. In this study, the effects of ammonia on ZnO NP toxicity to typical ammonia oxidizing bacteria-Nitrosomonas europaea were investigated, as indicated by the cell density, membrane integrity, ammonia oxidation rate, and AMO activity. After 6-h’s exposure to 10 mg/L ZnO NPs, the cell density, membrane integrity, ammonia oxidation rate, and AMO activity was dramatically suppressed despite of the increasing ammonia loading. Ammonia at varying concentrations did not obviously affect ZnO NPs toxicity to cell density. The presence of ammonia at 100 or 200 mg/L significantly alleviated the antibacterial effects of ZnO NPs on cells. The reduction of the concentration of released Zn2+ might be responsible for the compromised ZnO NPs toxicity. However, the presence of extremely dosed ammonia at 200 mg/L imposed restrictions on further alleviation of ZnO NPs toxicities probably due to the production of free ammonia and acclamation of nitrite. All these findings would provide new insights for risk assessment of the combined effects of NPs with other co-existing contaminants in the BNR system.

  19. 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.

  20. 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

  1. Bacterial sulfite-oxidizing enzymes.

    PubMed

    Kappler, Ulrike

    2011-01-01

    Enzymes belonging to the Sulfite Oxidase (SO) enzyme family are found in virtually all forms of life, and are especially abundant in prokaryotes as shown by analysis of available genome data. Despite this fact, only a limited number of bacterial SO family enzymes has been characterized in detail to date, and these appear to be involved in very different metabolic processes such as energy generation from sulfur compounds, host colonization, sulfite detoxification and organosulfonate degradation. The few characterized bacterial SO family enzymes also show an intriguing range of structural conformations, including monomeric, dimeric and heterodimeric enzymes with varying numbers and types of redox centres. Some of the bacterial enzymes even catalyze novel reactions such as dimethylsulfoxide reduction that previously had been thought not to be catalyzed by SO family enzymes. Classification of the SO family enzymes based on the structure of their Mo domain clearly shows that three distinct groups of enzymes belong to this family, and that almost all SOEs characterized to date are representatives of the same group. The widespread occurrence and obvious structural and functional plasticity of the bacterial SO family enzymes make this an exciting field for further study, in particular the unraveling of the metabolic roles of the three enzyme groups, some of which appear to be associated almost exclusively with pathogenic microorganisms. Copyright © 2010 Elsevier B.V. All rights reserved.

  2. A Zinc Oxide Nanorod Ammonia Microsensor Integrated with a Readout Circuit on-a-Chip

    PubMed Central

    Yang, Ming-Zhi; Dai, Ching-Liang; Wu, Chyan-Chyi

    2011-01-01

    A zinc oxide nanorod ammonia microsensor integrated with a readout circuit on-a-chip fabricated using the commercial 0.35 μm complementary metal oxide semiconductor (CMOS) process was investigated. The structure of the ammonia sensor is composed of a sensitive film and polysilicon electrodes. The ammonia sensor requires a post-process to etch the sacrificial layer, and to coat the sensitive film on the polysilicon electrodes. The sensitive film that is prepared by a hydrothermal method is made of zinc oxide. The sensor resistance changes when the sensitive film adsorbs or desorbs ammonia gas. The readout circuit is used to convert the sensor resistance into the voltage output. Experiments show that the ammonia sensor has a sensitivity of about 1.5 mV/ppm at room temperature. PMID:22247656

  3. A zinc oxide nanorod ammonia microsensor integrated with a readout circuit on-a-chip.

    PubMed

    Yang, Ming-Zhi; Dai, Ching-Liang; Wu, Chyan-Chyi

    2011-01-01

    A zinc oxide nanorod ammonia microsensor integrated with a readout circuit on-a-chip fabricated using the commercial 0.35 μm complementary metal oxide semiconductor (CMOS) process was investigated. The structure of the ammonia sensor is composed of a sensitive film and polysilicon electrodes. The ammonia sensor requires a post-process to etch the sacrificial layer, and to coat the sensitive film on the polysilicon electrodes. The sensitive film that is prepared by a hydrothermal method is made of zinc oxide. The sensor resistance changes when the sensitive film adsorbs or desorbs ammonia gas. The readout circuit is used to convert the sensor resistance into the voltage output. Experiments show that the ammonia sensor has a sensitivity of about 1.5 mV/ppm at room temperature.

  4. Activity of Cu-activated carbon fiber catalyst in wet oxidation of ammonia solution.

    PubMed

    Hung, Chang-Mao

    2009-07-30

    Aqueous solutions of 200-1000 mg/L of ammonia were oxidized in a trickle-bed reactor using Cu-activated carbon fiber (ACF) catalysts, which were prepared by incipient wet impregnation with aqueous solutions of copper nitrate that was deposited on ACF substrates. The results reveal that the conversion of ammonia by wet oxidation in the presence of Cu-ACF catalysts was a function of the metal loading weight ratio of the catalyst. The total conversion efficiency of ammonia was 95% during wet oxidation over the catalyst at 463 K at an oxygen partial pressure of 3.0 MPa. Moreover, the effect of the initial concentration of ammonia and the reaction temperature on the removal of ammonia from the effluent streams was also studied at a liquid space velocity of less than 3.0 h(-1).

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter

    NASA Astrophysics Data System (ADS)

    Gao, Jing-Feng; Fan, Xiao-Yan; Pan, Kai-Ling; Li, Hong-Yu; Sun, Li-Xin

    2016-12-01

    Increasing ammonia emissions could exacerbate air pollution caused by fine particulate matter (PM2.5). Therefore, it is of great importance to investigate ammonia oxidation in PM2.5. This study investigated the diversity, abundance and activity of ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB) and complete ammonia oxidizers (Comammox) in PM2.5 collected in Beijing-Tianjin-Hebei megalopolis, China. Nitrosopumilus subcluster 5.2 was the most dominant AOA. Nitrosospira multiformis and Nitrosomonas aestuarii were the most dominant AOB. Comammox were present in the atmosphere, as revealed by the occurrence of Candidatus Nitrospira inopinata in PM2.5. The average cell numbers of AOA, AOB and Ca. N. inopinata were 2.82 × 104, 4.65 × 103 and 1.15 × 103 cell m‑3 air, respectively. The average maximum nitrification rate of PM2.5 was 0.14 μg (NH4+-N) [m3 air·h]‑1. AOA might account for most of the ammonia oxidation, followed by Comammox, while AOB were responsible for a small part of ammonia oxidation. Statistical analyses showed that Nitrososphaera subcluster 4.1 was positively correlated with organic carbon concentration, and Nitrosomonas eutropha showed positive correlation with ammonia concentration. Overall, this study expanded our knowledge concerning AOA, AOB and Comammox in PM2.5 and pointed towards an important role of AOA and Comammox in ammonia oxidation in PM2.5.

  12. Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter

    PubMed Central

    Gao, Jing-Feng; Fan, Xiao-Yan; Pan, Kai-Ling; Li, Hong-Yu; Sun, Li-Xin

    2016-01-01

    Increasing ammonia emissions could exacerbate air pollution caused by fine particulate matter (PM2.5). Therefore, it is of great importance to investigate ammonia oxidation in PM2.5. This study investigated the diversity, abundance and activity of ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB) and complete ammonia oxidizers (Comammox) in PM2.5 collected in Beijing-Tianjin-Hebei megalopolis, China. Nitrosopumilus subcluster 5.2 was the most dominant AOA. Nitrosospira multiformis and Nitrosomonas aestuarii were the most dominant AOB. Comammox were present in the atmosphere, as revealed by the occurrence of Candidatus Nitrospira inopinata in PM2.5. The average cell numbers of AOA, AOB and Ca. N. inopinata were 2.82 × 104, 4.65 × 103 and 1.15 × 103 cell m−3 air, respectively. The average maximum nitrification rate of PM2.5 was 0.14 μg (NH4+-N) [m3 air·h]−1. AOA might account for most of the ammonia oxidation, followed by Comammox, while AOB were responsible for a small part of ammonia oxidation. Statistical analyses showed that Nitrososphaera subcluster 4.1 was positively correlated with organic carbon concentration, and Nitrosomonas eutropha showed positive correlation with ammonia concentration. Overall, this study expanded our knowledge concerning AOA, AOB and Comammox in PM2.5 and pointed towards an important role of AOA and Comammox in ammonia oxidation in PM2.5. PMID:27941955

  13. 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

  14. 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.

  15. 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...

  16. Nitrous oxide and ammonia emissions from injected and broadcast applied dairy slurry

    USDA-ARS?s Scientific Manuscript database

    Trade-offs associated with surface application or injection of manure pose important environmental and agronomic concerns. Manure injection can conserve nitrogen (N) by decreasing ammonia volatilization. However, the injection band also creates conditions, which potentially favor nitrous oxide produ...

  17. 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...

  18. Isolation of an autotrophic ammonia-oxidizing marine archaeon.

    PubMed

    Könneke, Martin; Bernhard, Anne E; de la Torre, José R; Walker, Christopher B; Waterbury, John B; Stahl, David A

    2005-09-22

    For years, microbiologists characterized the Archaea as obligate extremophiles that thrive in environments too harsh for other organisms. The limited physiological diversity among cultivated Archaea suggested that these organisms were metabolically constrained to a few environmental niches. For instance, all Crenarchaeota that are currently cultivated are sulphur-metabolizing thermophiles. However, landmark studies using cultivation-independent methods uncovered vast numbers of Crenarchaeota in cold oxic ocean waters. Subsequent molecular surveys demonstrated the ubiquity of these low-temperature Crenarchaeota in aquatic and terrestrial environments. The numerical dominance of marine Crenarchaeota--estimated at 10(28) cells in the world's oceans--suggests that they have a major role in global biogeochemical cycles. Indeed, isotopic analyses of marine crenarchaeal lipids suggest that these planktonic Archaea fix inorganic carbon. Here we report the isolation of a marine crenarchaeote that grows chemolithoautotrophically by aerobically oxidizing ammonia to nitrite--the first observation of nitrification in the Archaea. The autotrophic metabolism of this isolate, and its close phylogenetic relationship to environmental marine crenarchaeal sequences, suggests that nitrifying marine Crenarchaeota may be important to global carbon and nitrogen cycles.

  19. Shifts between ammonia-oxidizing bacteria and archaea in relation to nitrification potential across trophic gradients in two large Chinese lakes (Lake Taihu and Lake Chaohu).

    PubMed

    Hou, Jie; Song, Chunlei; Cao, Xiuyun; Zhou, Yiyong

    2013-05-01

    Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic ecosystems. Recent findings have expanded the known ammonia-oxidizing prokaryotes from Bacteria to Archaea. However, the relative importance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in nitrification is still debated. Here we showed that, in two large eutrophic lakes in China (Lake Taihu and Lake Chaohu), the abundance of AOA and AOB varied in opposite patterns according to the trophic state, although both AOA and AOB were abundant. In detail, from mesotrophic to eutrophic sites, the AOA abundance decreased, while the AOB increased in abundance and outnumbered the AOA at hypertrophic sites. In parallel, the nitrification rate increased along these trophic gradients and was significantly correlated with both the AOB abundance and the numerical ratio of AOB to AOA. Phylogenetic analysis of bacterial amoA sequences showed that Nitrosomonas oligotropha- and Nitrosospira-affiliated AOB dominated in both lakes, while Nitrosomonas communis-related AOB were only detected at the eutrophic sites. The diversity of AOB increased from mesotrophic to eutrophic sites and was positively correlated with the nitrification rate. Overall, this study enhances our understanding of the ecology of ammonia-oxidizing prokaryotes by elucidating conditions that AOB may numerically predominated over AOA, and indicated that AOA may play a less important role than AOB in the nitrification process of eutrophic lakes.

  20. 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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  2. 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...

  3. Ammonia-Oxidizing Bacteria Rather than Ammonia-Oxidizing Archaea were Widely Distributed in Animal Manure Composts from Field-Scale Facilities

    PubMed Central

    Yamamoto, Nozomi; Oishi, Ryu; Suyama, Yoshihisa; Tada, Chika; Nakai, Yutaka

    2012-01-01

    The distribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in cattle, swine, and chicken manure compost was analyzed. PCR-denaturing gradient gel electrophoresis (DGGE) showed that a Candidatus Nitrososphaera gargensis-like sequence dominated in cattle manure compost, while few AOA were detected in other composts. In the case of AOB, Nitrosomonas-like sequences were detected with higher diversity in cattle and swine manure composts. The relative abundance of ammonia oxidizers by real-time PCR revealed that more AOB was present in compost except in one swine manure compost. Our results indicated that AOB rather than AOA are widely distributed in animal manure compost. PMID:22972386

  4. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California.

    PubMed

    Beman, J Michael; Popp, Brian N; Francis, Christopher A

    2008-04-01

    Nitrification plays an important role in marine biogeochemistry, yet efforts to link this process to the microorganisms that mediate it are surprisingly limited. In particular, ammonia oxidation is the first and rate-limiting step of nitrification, yet ammonia oxidation rates and the abundance of ammonia-oxidizing bacteria (AOB) have rarely been measured in tandem. Ammonia oxidation rates have not been directly quantified in conjunction with ammonia-oxidizing archaea (AOA), although mounting evidence indicates that marine Crenarchaeota are capable of ammonia oxidation, and they are among the most abundant microbial groups in the ocean. Here, we have directly quantified ammonia oxidation rates by 15N labeling, and AOA and AOB abundances by quantitative PCR analysis of ammonia monooxygenase subunit A (amoA) genes, in the Gulf of California. Based on markedly different archaeal amoA sequence types in the upper water column (60 m) and oxygen minimum zone (OMZ; 450 m), novel amoA PCR primers were designed to specifically target and quantify 'shallow' (group A) and 'deep' (group B) clades. These primers recovered extensive variability with depth. Within the OMZ, AOA were most abundant where nitrification may be coupled to denitrification. In the upper water column, group A tracked variations in nitrogen biogeochemistry with depth and between basins, whereas AOB were present in relatively low numbers or undetectable. Overall, 15NH4+ oxidation rates were remarkably well correlated with AOA group A amoA gene copies (r2=0.90, P<0.001), and with 16S rRNA gene copies from marine Crenarchaeota (r2=0.85, P<0.005). These findings represent compelling evidence for an archaeal role in oceanic nitrification.

  5. 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

  6. 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.

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

    PubMed

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

    2015-03-01

    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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. 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. Copyright © 2011 Elsevier GmbH. All rights reserved.

  9. 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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  11. The Distribution of Ammonia-Oxidizing Betaproteobacteria in Stands of Black Mangroves (Avicennia germinans).

    PubMed

    Laanbroek, Hendrikus J; Keijzer, Rosalinde M; Verhoeven, Jos T A; Whigham, Dennis F

    2012-01-01

    The distribution of species of aerobic chemolitho-autotrophic microorganisms such as ammonia-oxidizing bacteria are governed by pH, salinity, and temperature as well as the availability of oxygen, ammonium, carbon dioxide, and other inorganic elements required for growth. Impounded mangrove forests in the Indian River Lagoon, a coastal estuary on the east coast of Florida, are dominated by mangroves, especially stands of Black mangrove (Avicennia germinans) that differ in the size and density of individual plants. In March 2009, the management of one impoundment was changed to a regime of pumping estuarine water into the impoundment at critical times of the year to eliminate breeding sites for noxious insects. We collected soil samples in three different Black mangrove habitats before and after the change in management to determine the impacts of the altered hydrologic regimes on the distribution of 16s rRNA genes belonging to ammonia-oxidizing betaproteobacteria (β-AOB). We also sampled soils in an adjacent impoundment in which there had not been any hydrologic alteration. At the level of 97% mutual similarity in the 16s rRNA gene, 13 different operational taxonomic units were identified; the majority related to the lineages of Nitrosomonas marina (45% of the total clones), Nitrosomonas sp. Nm143 (23%), and Nitrosospira cluster 1 (19%). Long-term summer flooding of the impoundment in 2009, after initiation of the pumping regime, reduced the percentage of N. marina by half between 2008 and 2010 in favor of the two other major lineages and the potential ammonia-oxidizing activity decreased by an average of 73%. Higher interstitial salinities, probably due to a prolonged winter drought, had a significant effect on the composition of the β-AOB in March 2009 compared to March 2008: Nitrosomonas sp. Nm143 was replaced by Nitrosospira cluster 1 as the second most important lineage. There were small, but significant differences in the bacterial communities between the

  12. The Distribution of Ammonia-Oxidizing Betaproteobacteria in Stands of Black Mangroves (Avicennia germinans)

    PubMed Central

    Laanbroek, Hendrikus J.; Keijzer, Rosalinde M.; Verhoeven, Jos T. A.; Whigham, Dennis F.

    2012-01-01

    The distribution of species of aerobic chemolitho-autotrophic microorganisms such as ammonia-oxidizing bacteria are governed by pH, salinity, and temperature as well as the availability of oxygen, ammonium, carbon dioxide, and other inorganic elements required for growth. Impounded mangrove forests in the Indian River Lagoon, a coastal estuary on the east coast of Florida, are dominated by mangroves, especially stands of Black mangrove (Avicennia germinans) that differ in the size and density of individual plants. In March 2009, the management of one impoundment was changed to a regime of pumping estuarine water into the impoundment at critical times of the year to eliminate breeding sites for noxious insects. We collected soil samples in three different Black mangrove habitats before and after the change in management to determine the impacts of the altered hydrologic regimes on the distribution of 16s rRNA genes belonging to ammonia-oxidizing betaproteobacteria (β-AOB). We also sampled soils in an adjacent impoundment in which there had not been any hydrologic alteration. At the level of 97% mutual similarity in the 16s rRNA gene, 13 different operational taxonomic units were identified; the majority related to the lineages of Nitrosomonas marina (45% of the total clones), Nitrosomonas sp. Nm143 (23%), and Nitrosospira cluster 1 (19%). Long-term summer flooding of the impoundment in 2009, after initiation of the pumping regime, reduced the percentage of N. marina by half between 2008 and 2010 in favor of the two other major lineages and the potential ammonia-oxidizing activity decreased by an average of 73%. Higher interstitial salinities, probably due to a prolonged winter drought, had a significant effect on the composition of the β-AOB in March 2009 compared to March 2008: Nitrosomonas sp. Nm143 was replaced by Nitrosospira cluster 1 as the second most important lineage. There were small, but significant differences in the bacterial communities between the

  13. Quantification of Nitrosomonas oligotropha-Like Ammonia-Oxidizing Bacteria and Nitrospira spp. from Full-Scale Wastewater Treatment Plants by Competitive PCR

    PubMed Central

    Dionisi, Hebe M.; Layton, Alice C.; Harms, Gerda; Gregory, Igrid R.; Robinson, Kevin G.; Sayler, Gary S.

    2002-01-01

    Utilizing the principle of competitive PCR, we developed two assays to enumerate Nitrosomonas oligotropha-like ammonia-oxidizing bacteria and nitrite-oxidizing bacteria belonging to the genus Nitrospira. The specificities of two primer sets, which were designed for two target regions, the amoA gene and Nitrospira 16S ribosomal DNA (rDNA), were verified by DNA sequencing. Both assays were optimized and applied to full-scale, activated sludge wastewater treatment plant (WWTP) samples. If it was assumed that there was an average of 3.6 copies of 16S rDNA per cell in the total population and two copies of the amoA gene per ammonia-oxidizing bacterial cell, the ammonia oxidizers examined represented 0.0033% ± 0.0022% of the total bacterial population in a municipal WWTP. N. oligotropha-like ammonia-oxidizing bacteria were not detected in an industrial WWTP. If it was assumed that there was one copy of the 16S rDNA gene per nitrite-oxidizing bacterial cell, Nitrospira spp. represented 0.39% ± 0.28% of the biosludge population in the municipal WWTP and 0.37% ± 0.23% of the population in the industrial WWTP. The number of Nitrospira sp. cells in the municipal WWTP was more than 62 times greater than the number of N. oligotropha-like cells, based on a competitive PCR analysis. The results of this study extended our knowledge of the comparative compositions of nitrifying bacterial populations in wastewater treatment systems. Importantly, they also demonstrated that we were able to quantify these populations, which ultimately will be required for accurate prediction of process performance and stability for cost-effective design and operation of WWTPs. PMID:11772633

  14. Effects of ammonia exposure on apoptosis, oxidative stress and immune response in pufferfish (Takifugu obscurus).

    PubMed

    Cheng, Chang-Hong; Yang, Fang-Fang; Ling, Ren-Zhi; Liao, Shao-An; Miao, Yu-Tao; Ye, Chao-Xia; Wang, An-Li

    2015-07-01

    Ammonia is one of major environmental pollutants in the freshwater aquatic system that affects the survival and growth of organisms. In the present study, we investigated the effects of ammonia exposure on apoptosis, oxidative stress and immune response in pufferfish (Takifugu obscurus). Fish were exposed to various concentrations of ammonia (0, 1.43, 3.57, 7.14mM) for 72h. The date showed that ammonia exposure could induce intracellular reactive oxygen species (ROS), interrupt intracellular Ca(2+) (cf-Ca(2+)) homeostasis, and subsequently lead to DNA damage and cell apoptosis. To test the apoptotic pathway, the expression patterns of some key apoptotic related genes including P53, Bax Bcl2, Caspase 9, Caspase 8 and Caspase 3 in the liver were examined. The results showed that ammonia stress could change these genes transcription, associated with increasing of cell apoptosis, suggesting that the P53-Bax-Bcl2 pathway and caspase-dependent apoptotic pathway could be involved in cell apoptosis induced by ammonia stress. In addition, ammonia stress could induced up-regulation of inflammatory cytokines (BAFF, TNF-α, IL-6 and IL-12) transcription, indicating that innate immune system play important roles in ammonia-induced toxicity in fish. Furthermore, the gene expressions of antioxidant enzymes (Mn-SOD, CAT, GPx, and GR) and heat shock proteins (HSP90 and HSP70) in the liver were induced by ammonia stress, suggesting that antioxidant system and heat shock proteins tried to protect cells from oxidative stress and apoptosis induced by ammonia stress. Our results will be helpful to understand the mechanism of aquatic toxicology induced by ammonia in fish. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. 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.

  16. Low-Dissolved-Oxygen Nitrifying Systems Exploit Ammonia-Oxidizing Bacteria with Unusually High Yields▿

    PubMed Central

    Bellucci, Micol; Ofiţeru, Irina D.; Graham, David W.; Head, Ian M.; Curtis, Thomas P.

    2011-01-01

    In wastewater treatment plants, nitrifying systems are usually operated with elevated levels of aeration to avoid nitrification failures. This approach contributes significantly to operational costs and the carbon footprint of nitrifying wastewater treatment processes. In this study, we tested the effect of aeration rate on nitrification by correlating ammonia oxidation rates with the structure of the ammonia-oxidizing bacterial (AOB) community and AOB abundance in four parallel continuous-flow reactors operated for 43 days. Two of the reactors were supplied with a constant airflow rate of 0.1 liter/min, while in the other two units the airflow rate was fixed at 4 liters/min. Complete nitrification was achieved in all configurations, though the dissolved oxygen (DO) concentration was only 0.5 ± 0.3 mg/liter in the low-aeration units. The data suggest that efficient performance in the low-DO units resulted from elevated AOB levels in the reactors and/or putative development of a mixotrophic AOB community. Denaturing gel electrophoresis and cloning of AOB 16S rRNA gene fragments followed by sequencing revealed that the AOB community in the low-DO systems was a subset of the community in the high-DO systems. However, in both configurations the dominant species belonged to the Nitrosomonas oligotropha lineage. Overall, the results demonstrated that complete nitrification can be achieved at low aeration in lab-scale reactors. If these findings could be extended to full-scale plants, it would be possible to minimize the operational costs and greenhouse gas emissions without risk of nitrification failure. PMID:21926211

  17. Integrated structural biology and molecular ecology of N-cycling enzymes from ammonia-oxidizing archaea

    DOE PAGES

    Tolar, Bradley B.; Herrmann, Jonathan; Bargar, John R.; ...

    2017-06-01

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

  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.

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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.

  4. Evaluation of bacterial communities by bacteriome analysis targeting 16S rRNA genes and quantitative analysis of ammonia monooxygenase gene in different types of compost.

    PubMed

    Kitamura, Rika; Ishii, Kazuo; Maeda, Isamu; Kozaki, Toshinori; Iwabuchi, Kazunori; Saito, Takahiro

    2016-01-01

    Biofiltration technology based on microbial degradation and assimilation is used for the removal of malodorous compounds, such as ammonia. Microbes that degrade malodorous and/or organic substances are involved in composting and are retained after composting; therefore, mature composts can serve as an ideal candidate for a biofilter medium. In this study, we focused on different types of raw compost materials, as these are important factors determining the bacterial community profile and the chemical component of the compost. Therefore, bacterial community profiles, the abundance of the bacterial ammonia monooxygenase gene (amoA), and the quantities of chemical components were analyzed in composts produced from either food waste or cattle manure. The community profiles with the lowest beta diversity were obtained from single type of cattle manure compost. However, cattle manure composts showed greater alpha diversity, contained higher amounts of various rRNA gene fragments than those of food waste composts and contained the amoA gene by relative quantification, and Proteobacteria were abundantly found and nitrifying bacteria were detected in it. Nitrifying bacteria are responsible for ammonia oxidation and mainly belong to the Proteobacteria or Nitrospira phyla. The quantities of chemical components, such as salt, phosphorus, and nitrogen, differed between the cattle manure and food waste composts, indicating that the raw materials provided different fermentation environments that were crucial for the formation of different community profiles. The results also suggest that cattle manure might be a more suitable raw material for the production of composts to be used in the biofiltration of ammonia. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  5. 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

  6. Distinct responses in ammonia-oxidizing archaea and bacteria after addition of biosolids to an agricultural soil.

    PubMed

    Kelly, John J; Policht, Katherine; Grancharova, Tanya; Hundal, Lakhwinder S

    2011-09-01

    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.

  7. 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.

  8. Analysis of ammonia-oxidizing bacteria dominating in lab-scale bioreactors with high ammonium bicarbonate loading.

    PubMed

    Vejmelkova, Dana; Sorokin, Dimitry Y; Abbas, Ben; Kovaleva, Olga L; Kleerebezem, Robbert; Kampschreur, Marlies J; Muyzer, Gerard; van Loosdrecht, Mark C M

    2012-01-01

    The ammonia-oxidizing bacterial community (AOB) was investigated in two types of laboratory-scale bioreactors performing partial oxidation of ammonia to nitrite or nitrate at high (80 mM) to extremely high (428 mM) concentrations of ammonium bicarbonate. At all conditions, the dominant AOB was affiliated to the Nitrosomonas europaea lineage as was determined by fluorescence in situ hybridization and polymerase chain reaction in combination with denaturing gradient gel electrophoresis. Molecular analysis of the mixed populations, based on the 16S rRNA and cbbL genes, demonstrated the presence of two different phylotypes of Nitrosomonas, while microbiological analysis produced a single phylotype, represented by three different morphotypes. One of the most striking features of the AOB populations encountered in the bioreactors was the domination of highly aggregated obligate microaerophilic Nitrosomonas, with unusual cellular and colony morphology, commonly observed in nitrifying bioreactors but rarely investigated by cultural methods. The latter is probably not an adaptation to stressful conditions created by high ammonia or nitrite concentrations, but oxygen seems to be a stressful factor in these bioreactors.

  9. 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.

  10. Spatial Distribution of Total, Ammonia-Oxidizing, and Denitrifying Bacteria in Biological Wastewater Treatment Reactors for Bioregenerative Life Support

    PubMed Central

    Sakano, Yuko; Pickering, Karen D.; Strom, Peter F.; Kerkhof, Lee J.

    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. PMID:11976099

  11. Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary.

    PubMed

    Santoro, Alyson E; Francis, Christopher A; de Sieyes, Nicholas R; Boehm, Alexandria B

    2008-04-01

    Submarine groundwater discharge to coastal waters can be a significant source of both contaminants and biologically limiting nutrients. Nitrogen cycling across steep gradients in salinity, oxygen and dissolved inorganic nitrogen in sandy 'subterranean estuaries' controls both the amount and form of nitrogen discharged to the coastal ocean. We determined the effect of these gradients on betaproteobacterial ammonia-oxidizing bacteria (beta-AOB) and ammonia-oxidizing archaea (AOA) in a subterranean estuary using the functional gene encoding ammonia monooxygenase subunit A (amoA). The abundance of beta-AOB was dramatically lower in the freshwater stations compared with saline stations, while AOA abundance remained nearly constant across the study site. This differing response to salinity altered the ratio of beta-AOB to AOA such that bacterial amoA was 30 times more abundant than crenarchaeal amoA at the oxic marine station, but nearly 10 times less abundant at the low-oxygen fresh and brackish stations. As the location of the brackish mixing zone within the aquifer shifted from landward in winter to oceanward in summer, the location of the transition from a beta-AOB-dominated to an AOA-dominated community also shifted, demonstrating the intimate link between microbial communities and coastal hydrology. Analysis of ammonia-oxidizing enrichment cultures at a range of salinities revealed that AOA persisted solely in the freshwater enrichments where they actively express amoA. Diversity (as measured by total richness) of crenarchaeal amoA was high at all stations and time points, in sharp contrast to betaproteobacterial amoA for which only two sequence types were found. These results offer new insights into the ecology of AOA and beta-AOB by elucidating conditions that may favour the numerical dominance of beta-AOB over AOA in coastal sediments.

  12. 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.

  13. 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

  14. Relationship between oxidative stress and brain swelling in goldfish (Carassius auratus) exposed to high environmental ammonia.

    PubMed

    Lisser, David F J; Lister, Zachary M; Pham-Ho, Phillip Q H; Scott, Graham R; Wilkie, Michael P

    2017-01-01

    Buildups of ammonia can cause potentially fatal brain swelling in mammals, but such swelling is reversible in the anoxia- and ammonia-tolerant goldfish (Carassius auratus). We investigated brain swelling and its possible relationship to oxidative stress in the brain and liver of goldfish acutely exposed to high external ammonia (HEA; 5 mmol/l NH4Cl) at two different acclimation temperatures (14°C, 4°C). Exposure to HEA at 14°C for 72h resulted in increased internal ammonia and glutamine concentrations in the brain, and it caused cellular oxidative damage in the brain and liver. However, oxidative damage was most pronounced in brain, in which there was a twofold increase in thiobarbituric acid-reactive substances, a threefold increase in protein carbonylation, and a 20% increase in water volume (indicative of brain swelling). Increased activities of catalase, glutathione peroxidase, and glutathione reductase in the brain suggested that goldfish upregulate their antioxidant capacity to partially offset oxidative stress during hyperammonemia at 14°C. Notably, acclimation to colder (4°C) water completely attenuated the oxidative stress response to HEA in both tissues, and there was no change in brain water volume despite similar increases in internal ammonia. We suggest that ammonia-induced oxidative stress may be responsible for the swelling of goldfish brain during HEA, but further studies are needed to establish a mechanistic link between reactive oxygen species production and brain swelling. Nevertheless, a high capacity to withstand oxidative stress in response to variations in internal ammonia likely explains why goldfish are more resilient to this stressor than most other vertebrates. Copyright © 2017 the American Physiological Society.

  15. A review of ammonia-oxidizing bacteria and archaea in Chinese soils

    PubMed Central

    Shen, Ju-Pei; Zhang, Li-Mei; Di, Hong J.; He, Ji-Zheng

    2012-01-01

    Ammonia (NH3) oxidation, the first and rate-limiting step of nitrification, is a key step in the global Nitrogen (N) cycle. Major advances have been made in recent years in our knowledge and understanding of the microbial communities involved in ammonia oxidation in a wide range of habitats, including Chinese agricultural soils. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Chinese soils with variable soil properties and soil management practices. The niche differentiation of AOB and AOA in contrasting soils have been functionally demonstrated using DNA-SIP (stable isotope probing) methods, which have shown that AOA dominate nitrification processes in acidic soils, while AOB dominated in neutral, alkaline and N-rich soils. Finally, we discuss the composition and activity of ammonia oxidizers in paddy soils, as well as the mitigation of the greenhouse gas nitrous oxide (N2O) emissions and nitrate leaching via inhibition of nitrification by both AOB and AOA. PMID:22936929

  16. A review of ammonia-oxidizing bacteria and archaea in Chinese soils.

    PubMed

    Shen, Ju-Pei; Zhang, Li-Mei; Di, Hong J; He, Ji-Zheng

    2012-01-01

    Ammonia (NH(3)) oxidation, the first and rate-limiting step of nitrification, is a key step in the global Nitrogen (N) cycle. Major advances have been made in recent years in our knowledge and understanding of the microbial communities involved in ammonia oxidation in a wide range of habitats, including Chinese agricultural soils. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Chinese soils with variable soil properties and soil management practices. The niche differentiation of AOB and AOA in contrasting soils have been functionally demonstrated using DNA-SIP (stable isotope probing) methods, which have shown that AOA dominate nitrification processes in acidic soils, while AOB dominated in neutral, alkaline and N-rich soils. Finally, we discuss the composition and activity of ammonia oxidizers in paddy soils, as well as the mitigation of the greenhouse gas nitrous oxide (N(2)O) emissions and nitrate leaching via inhibition of nitrification by both AOB and AOA.

  17. Graphene oxide based recyclable dehydrogenation of ammonia borane within a hybrid nanostructure.

    PubMed

    Tang, Ziwei; Chen, Hao; Chen, Xiaowei; Wu, Limin; Yu, Xuebin

    2012-03-28

    The recyclable dehydrogenation of ammonia borane (AB) is achievable within a graphene oxide (GO)-based hybrid nanostructure, in which a combined modification strategy of acid activation and nanoconfinement by GO allows AB to release more than 2 equiv of pure H(2) at temperatures below 100 °C. This process yields polyborazylene (PB) as a single product and, thus, promotes the chemical regeneration of AB via reaction of PB with hydrazine in liquid ammonia.

  18. Effect of acetylene and ammonia as reburn fuel additions to methane in nitric oxide reburning

    SciTech Connect

    Kumpaty, S.K.; Nokku, V.P.; Subramanian, K.

    1996-12-31

    Presented in this paper are the computational results of NO reburning with (a) a combination of methane and acetylene and (b) a combination of methane and ammonia. An updated reaction mechanism that was more comprehensive in terms of predicting the ammonia and isocyanic acid oxidation chemistry was employed to run the CKINTERP program. Using the binary file created by executing the above program and the input stoichiometric ratio conditions, the CHEMKIN package predicted the exit concentrations of various species involved in NO reburning.

  19. 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

  20. 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.

  1. 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

  2. Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle.

    PubMed

    Park, Soo-Je; Kim, Jong-Geol; Jung, Man-Young; Kim, So-Jeong; Cha, In-Tae; Ghai, Rohit; Martín-Cuadrado, Ana-Belén; Rodríguez-Valera, Francisco; Rhee, Sung-Keun

    2012-12-01

    Ammonia-oxidizing archaea (AOA) typically predominate over ammonia-oxidizing bacteria in marine sediments. We herein present the draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, which was enriched in culture from a marine sediment obtained off Svalbard, within the Arctic Circle. The typical genes involved in archaeal ammonia oxidation and carbon fixation necessary for chemolithoautotrophic growth were observed. Interestingly, the AR2 genome sequence was revealed to possess, uniquely among cultivated AOA from marine environments, a capability for urea utilization.

  3. Ammonia stimulates growth and nitrite-oxidizing activity of Nitrobacter winogradskyi

    PubMed Central

    Ma, Shouguang; Zhang, Demin; Zhang, Wenjun; Wang, Yinong

    2014-01-01

    The aim of this study was to obtain a nitrite-oxidizing bacterium with high nitrite oxidation activity for controlling nitrite levels. A nitrite-oxidizing bacterium, ZS-1, was isolated from the water of a coastal Pseudosciaena crocea-rearing pond. The strain was identified as Nitrobacter winogradskyi based on the phylogenetic analyses of the 16S ribosomal ribonucleic acid gene and nxrA sequence of ZS-1. Under aerobic condition, the nitrite-oxidizing activity of ZS-1 did not change considerably in the range of pH 7–9, but was strongly inhibited by lower (pH = 6) and higher (pH = 10) pH values. The optimum temperature range is 25–32 °C. Lower temperature made the adaptive phase of ZS-1 longer but did not affect its maximum nitrite oxidization rate. The nitrite-oxidizing activity of ZS-1 started to be inhibited by ammonia and nitrate when the concentrations of ammonia and nitrate reached 25 mg L−1 and 100 mg L−1, respectively. The inhibition was stronger with higher concentration of ammonia or nitrate. The nitrite-oxidizing activity of ZS-1, however, was not inhibited by high concentration of nitrite (500 mg L−1). The nitrite-oxidizing activity of ZS-1 was increased by low ammonia concentration (1 mg L−1 to 10 mg L−1). PMID:26019486

  4. N2O production rate of an enriched ammonia-oxidising bacteria culture exponentially correlates to its ammonia oxidation rate.

    PubMed

    Law, Yingyu; Ni, Bing-Jie; Lant, Paul; Yuan, Zhiguo

    2012-06-15

    The relationship between the ammonia oxidation rate (AOR) and nitrous oxide production rate (N(2)OR) of an enriched ammonia-oxidising bacteria (AOB) culture was investigated. The AOB culture was enriched in a nitritation system fed with synthetic anaerobic digester liquor. The AOR was controlled by adjusting the dissolved oxygen (DO) and pH levels and also by varying the initial ammonium (NH(4)(+)) concentration in batch experiments. Tests were also performed directly on the parent reactor where a stepwise decrease/increase in DO was implemented to alter AOR. The experimental data indicated a clear exponential relationship between the biomass specific N(2)OR and AOR. Four metabolic models were used to analyse the experimental data. The metabolic model formulated based on aerobic N(2)O production from the decomposition of nitrosyl radical (NOH) predicted the exponential correlation observed experimentally. The experimental data could not be reproduced by models developed on the basis of N(2)O production through nitrite (NO(2)(-)) and nitric oxide (NO) reduction by AOB.

  5. Ammonia triggers the promotion of oxidative stress in the aquatic macrophyte Myriophyllum mattogrossense.

    PubMed

    Nimptsch, Jorge; Pflugmacher, Stephan

    2007-01-01

    The effect of increased ammonia content on sub-acute biochemical responses was assessed in the rooted submersed aquatic macrophyte Myriophyllum mattogrossense (common name: "Brazil Milfoil" or "Matogrosso Milfoil"), in a seven day aquarium experiment. The pH and temperature were monitored in order to determine the proportions of both ionized (NH4+) and un-ionized (NH3) forms of ammonia. Specific activities of several enzymes such as catalase (CAT), guaiacol peroxidase (POD), glutathione peroxidase (GPx) and glutathione S-transferase (GST's) were measured as well as the content of the soluble antioxidant glutathione and lipid peroxidation were determined as these parameters are considered as indicators of cell-level disorder. The results showed that ammonia is able to generate oxidative stress, expressed through an elevated GSH content and the enhancement of CAT, POD, GPx and GST's activities in treatments with elevated ammonia content. As the toxic mechanism of ammonia is a complex phenomenon, this work adds an additional point of view to explain in parts the oxidative stress generating effect of ammonia promoting oxidative stress. Additionally the different modes of action proposed by other research groups are discussed, thus trying to combine the various points of view.

  6. Effects of copper on the abundance and diversity of ammonia oxidizers during dairy cattle manure composting.

    PubMed

    Yin, Yanan; Song, Wen; Gu, Jie; Zhang, Kaiyu; Qian, Xun; Zhang, Xin; Zhang, Yajun; Li, Yang; Wang, Xiaojuan

    2016-12-01

    This study investigated the effects of adding Cu(II) at two exposure levels (50 and 500mgkg(-1), i.e., Cu50 and Cu500 treatments, respectively) on the activity of ammonia-oxidizing microorganisms during dairy cattle manure composting. The results showed that the pH, NH4(+)-N, NO3(-)-N, and potential ammonia oxidation values were inhibited significantly by the addition of Cu(II). Furthermore, the abundances of the ammonia-oxidizing archaea (AOA) amoA gene and ammonia-oxidizing bacteria (AOB) amoA gene were determined by quantitative PCR, and their compositions were evaluated by denaturing gradient gel electrophoresis (DGGE). AOA was the dominant ammonia oxidizing microorganism, of which the abundance was much higher than AOB during composting. Cu50 and Cu500 had significant inhibitory effects on the abundance of the amoA gene. The DGGE profile and statistical analysis showed that Cu(II) changed the AOA and AOB community structure and diversity, where Nitrosomonas and Crenarchaeota dominated throughout the composting process. Copyright © 2016. Published by Elsevier Ltd.

  7. Agreement between theory and measurement in quantification of ammonia-oxidizing bacteria.

    PubMed

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

    2005-10-01

    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.

  8. [Diversity and community structure of soil ammonia-oxidizing bacteria in Hulunbeier Grassland, Inner Mongolia].

    PubMed

    Wendu, Ri-le; Li, Gang; Yang, Dian-lin; Zhang, Jing-ni; Yi, Jin

    2011-04-01

    By the methods of polymerase chain reaction-denaturing gradient gel electrophoresis and sequence analysis, a comparative study was conducted on the diversity and community structure of soil ammonia-oxidizing bacteria in the Filifolium sibiricum steppe, Stipa baicalensis steppe, Leymus chinensis steppe, Stipa grandis steppe, and Stipa kryrowi steppe in Hulunbeier Grassland, Inner Mongolia. A significant difference was observed in the community structure of soil ammonia-oxidizing bacteria among the five steppes, with the similarity lower than 50%. The diversity of soil ammonia-oxidizing bacteria was the highest in F. sibiricum steppe, followed by in S. baicalensis steppe, L. chinensis steppe, S. kryrowi steppe, and S. grandis steppe. In the five steppes, Nitrosospira cluster 3 was the dominant group, and the Nitrosospira cluster 1, 2, and 4 as well as Nitrosomonas were also found. The community structure of soil ammonia oxidizing bacteria in F. sibiricum steppe was most complex, while that in L. chinensis steppe and S. grandis steppe was relatively simple. Correlation analysis indicated that there existed significant positive correlations between the diversity of soil ammonia-oxidizing bacteria and the soil moisture, total nitrogen, total organic carbon, and C/N ratio (P<0.05).

  9. 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

  10. Anaerobic ammonia oxidation in a fertilized paddy soil

    PubMed Central

    Zhu, Guibing; Wang, Shanyun; Wang, Yu; Wang, Chaoxu; Risgaard-Petersen, Nils; Jetten, Mike SM; Yin, Chengqing

    2011-01-01

    Evidence for anaerobic ammonium oxidation in a paddy field was obtained in Southern China using an isotope-pairing technique, quantitative PCR assays and 16S rRNA gene clone libraries, along with nutrient profiles of soil cores. A paddy field with a high load of slurry manure as fertilizer was selected for this study and was shown to contain a high amount of ammonium (6.2–178.8 mg kg−1). The anaerobic oxidation of ammonium (anammox) rates in this paddy soil ranged between 0.5 and 2.9 nmolN per gram of soil per hour in different depths of the soil core, and the specific cellular anammox activity observed in batch tests ranged from 2.9 to 21 fmol per cell per day. Anammox contributed 4–37% to soil N2 production, the remainder being due to denitrification. The 16S rRNA gene sequences of surface soil were closely related to the anammox bacteria ‘Kuenenia', ‘Anammoxoglobus' and ‘Jettenia'. Most of the anammox 16S rRNA genes retrieved from the deeper soil were affiliated to ‘Brocadia'. The retrieval of mainly bacterial amoA sequences in the upper part of the paddy soil indicated that nitrifying bacteria may be the major source of nitrite for anammox bacteria in the cultivated horizon. In the deeper oxygen-limited parts, only archaeal amoA sequences were found, indicating that archaea may produce nitrite in this part of the soil. It is estimated that a total loss of 76 g N m−2 per year is linked to anammox in the paddy field. PMID:21593796

  11. 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.

  12. [Quantitative and qualitative analysis of total bacteria and ammonia-oxidizing bacteria in Buji River in wet season].

    PubMed

    Sun, Hai-mei; Bai, Jiao-jiao; Sun, Wei-ling; Shao, Jun

    2012-08-01

    Microbial community structure and biomass in river water can reflect the situation of water quality in some extent. Nitrogen removal was mainly achieved by the nitrification and denitrification processes, and ammonia oxidation catalyzed by ammonia-oxidizing bacteria (AOB) is the first and rate-limiting step of nitrification. To explore the AOB community structure and biomass in nitrogen polluted river, water samples were collected from Buji River (Shenzhen) in wet season. Quantification of 16S rRNA copy numbers of total bacteria and AOB were performed by real-time PCR, and the microbial community structures were studied by denaturing gradient gel electrophoresis (DGGE). The results showed that the number of total bacterial 16S rRNA changed from 4.73 x 10(10) - 3.90 x 10(11) copies x L(-1) in the water samples. The copy numbers of AOB varied from 5.44 x 10(6) - 5.96 x 10(8)copies x L(-1). Redundancy discrimination analysis (RDA) showed that the main factors affecting the structure and the numbers of bacteria were different. For total bacteria, nitrate influenced the biomass significantly (P < 0.05) while nitrogen and heavy metals (Mn and Zn) were the main factors affecting the microbial community structures (P < 0.05). For AOB, ammonia and Zn were the main factors influencing the biomass while ammonia nitrogen and heavy metals (Mn and Zn) were the main factors affecting the microbial community structures. 16S rDNA sequences from the water samples indicated that the bacteria generally belonged to Epsilon-Proteobacteria, Gamma-Proteobacteria, Beta-Proteobacteria, and Delta-Proteobacteria. Nitrosomonas sp. and Nitrosospira sp. were the main AOB. Cluster analysis showed that water pollution in downstream resulted in evident difference in microbial community structure between upstream and downstream water samples.

  13. Diversity of Ammonia Oxidation (amoA) and Nitrogen Fixation (nifH) Genes in Lava Caves of Terceira, Azores, Portugal

    PubMed Central

    Hathaway, Jennifer J. Marshall; Sinsabaugh, Robert L.; Dapkevicius, Maria De Lurdes N. E.; Northup, Diana E.

    2015-01-01

    Lava caves are an understudied ecosystem in the subterranean world, particularly in regard to nitrogen cycling. The diversity of ammonia oxidation (amoA) and nitrogen fixation (nifH) genes in bacterial mats collected from lava cave walls on the island of Terceira (Azores, Portugal) was investigated using denaturing gradient gel electrophoresis (DGGE). A total of 55 samples were collected from 11 lava caves that were selected with regard to surface land use. Land use types above the lava caves were categorized into pasture, forested, and sea/urban, and used to determine if land use influenced the ammonia oxidizing and nitrogen fixing bacterial communities within the lava caves. The soil and water samples from each lava cave were analyzed for total organic carbon, inorganic carbon, total nitrogen, ammonium, nitrate, phosphate and sulfate, to determine if land use influences either the nutrient content entering the lava cave or the nitrogen cycling bacteria present within the cave. Nitrosospira-like sequences dominated the ammonia-oxidizing bacteria (AOB) community, and the majority of the diversity was found in lava caves under forested land. The nitrogen fixation community was dominated by Klebsiella pneumoniae-like sequences, and diversity was evenly distributed between pasture and forested land, but very little overlap in diversity was observed. The results suggest that land use is impacting both the AOB and the nitrogen fixing bacterial communities. PMID:26778867

  14. Diversity of Ammonia Oxidation (amoA) and Nitrogen Fixation (nifH) Genes in Lava Caves of Terceira, Azores, Portugal.

    PubMed

    Hathaway, Jennifer J Marshall; Sinsabaugh, Robert L; Dapkevicius, Maria De Lurdes N E; Northup, Diana E

    Lava caves are an understudied ecosystem in the subterranean world, particularly in regard to nitrogen cycling. The diversity of ammonia oxidation (amoA) and nitrogen fixation (nifH) genes in bacterial mats collected from lava cave walls on the island of Terceira (Azores, Portugal) was investigated using denaturing gradient gel electrophoresis (DGGE). A total of 55 samples were collected from 11 lava caves that were selected with regard to surface land use. Land use types above the lava caves were categorized into pasture, forested, and sea/urban, and used to determine if land use influenced the ammonia oxidizing and nitrogen fixing bacterial communities within the lava caves. The soil and water samples from each lava cave were analyzed for total organic carbon, inorganic carbon, total nitrogen, ammonium, nitrate, phosphate and sulfate, to determine if land use influences either the nutrient content entering the lava cave or the nitrogen cycling bacteria present within the cave. Nitrosospira-like sequences dominated the ammonia-oxidizing bacteria (AOB) community, and the majority of the diversity was found in lava caves under forested land. The nitrogen fixation community was dominated by Klebsiella pneumoniae-like sequences, and diversity was evenly distributed between pasture and forested land, but very little overlap in diversity was observed. The results suggest that land use is impacting both the AOB and the nitrogen fixing bacterial communities.

  15. Evidence for Different Contributions of Archaea and Bacteria to the Ammonia-Oxidizing Potential of Diverse Oregon Soils▿

    PubMed Central

    Taylor, Anne E.; Zeglin, Lydia H.; Dooley, Sandra; Myrold, David D.; Bottomley, Peter J.

    2010-01-01

    A method was developed to determine the contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to the nitrification potentials (NPs) of soils taken from forest, pasture, cropped, and fallowed (19 years) lands. Soil slurries were exposed to acetylene to irreversibly inactivate ammonia monooxygenase, and upon the removal of acetylene, the recovery of nitrification potential (RNP) was monitored in the presence and absence of bacterial or eukaryotic protein synthesis inhibitors. For unknown reasons, and despite measureable NPs, RNP did not occur consistently in forest soil samples; however, pasture, cropped, and fallowed soil RNPs commenced after lags that ranged from 12 to 30 h after acetylene removal. Cropped soil RNP was completely prevented by the bacterial protein synthesis inhibitor kanamycin (800 μg/ml), whereas a combination of kanamycin plus gentamicin (800 μg/ml each) only partially prevented the RNP (60%) of fallowed soils. Pasture soil RNP was completely insensitive to either kanamycin, gentamicin, or a combination of the two. Unlike cropped soil, pasture and fallowed soil RNPs occurred at both 30°C and 40°C and without supplemental NH4+ (≤10 μM NH4+ in solution), and pasture soil RNP demonstrated ∼50% insensitivity to 100 μM allyl thiourea (ATU). In addition, fallowed and pasture soil RNPs were insensitive to the fungal inhibitors nystatin and azoxystrobin. This combination of properties suggests that neither fungi nor AOB contributed to pasture soil RNP and that AOA were responsible for the RNP of the pasture soils. Both AOA and AOB may contribute to RNP in fallowed soil, while RNP in cropped soils was dominated by AOB. PMID:20889792

  16. 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

  17. 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.

  18. Photoelectrocatalytic oxidation of aqueous ammonia using TiO2 nanotube arrays

    NASA Astrophysics Data System (ADS)

    Wang, Hua; Zhang, Xiufang; Su, Yan; Yu, Hongtao; Chen, Shuo; Quan, Xie; Yang, Fenglin

    2014-08-01

    The photoelectrocatalytic removal of ammonia in water was investigated using highly ordered TiO2 nanotube arrays as a photoanode. The results showed that the removal efficiency of total ammonia nitrogen (TAN) was closely related to the bias potential applied on TiO2 nanotube photoanode. Even without an adjustment of pH, over 99% of TAN (initial concentration 0.145 mM) was removed in 120 min with a bias potential of 1.0 V. It is important to note that the TAN could be directly oxidized into N2 and NO3--N without accumulation of an intermediate product of NO2--N. Meanwhile, the presence of the chemical scavengers revealed that photogenerated holes were the main oxidative species for the TAN oxidation. This work highlights the potential application of photoelectrocatalysis in the field of aqueous ammonia elimination.

  19. 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.

    2016-01-01

    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.

  20. Population dynamics of ammonia-oxidizing bacteria in an aerated submerged biofilm reactor for micropolluted raw water pretreatment.

    PubMed

    Qin, Ying-Ying; Zhang, Xiao-Wen; Ren, Hong-Qiang; Li, Dao-Tang; Yang, Hong

    2008-05-01

    Population dynamics of ammonia-oxidizing bacteria (AOB) in a full-scale aerated submerged biofilm reactor for micropolluted raw water pretreatment was investigated using molecular techniques for a period of 1 year. The ammonia monooxygenase (amoA) gene fragments were amplified from DNA and RNA extracts of biofilm samples. Denaturing gradient gel electrophoresis (DGGE) profile based on the amoA messenger RNA approach exhibited a more variable pattern of temporal dynamics of AOB communities than the DNA-derived approach during the study. Phylogenetic analysis of excised DGGE bands revealed three AOB groups affiliated with the Nitrosomonas oligotropha lineage, Nitrosomonas communis lineage, and an unknown Nitrosomonas group. The population size of betaproteobacterial AOB, quantified with 16S ribosomal RNA gene real-time polymerase chain reaction assay, ranged from 6.63 x 10(5) to 2.67 x 10(9) cells per gram of dry biofilm and corresponded to 0.23-1.8% of the total bacterial fraction. Quantitative results of amoA gene of the three specific AOB groups revealed changes in competitive dominance between AOB of the N. oligotropha lineage and N. communis lineage. Water temperature is shown to have major influence on AOB population size in the reactor by the statistic analysis, and a positive correlation between AOB cell numbers and ammonia removal efficiency is suggested (r = 0.628, P < 0.05).

  1. 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.

  2. 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

  3. 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.

  4. Ammonia-Oxidizing Bacteria and Archaea in Groundwater Treatment and Drinking Water Distribution Systems▿ †

    PubMed Central

    van der Wielen, Paul W. J. J.; Voost, Stefan; van der Kooij, Dick

    2009-01-01

    The ammonia-oxidizing prokaryote (AOP) community in three groundwater treatment plants and connected distribution systems was analyzed by quantitative real-time PCR and sequence analysis targeting the amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Results demonstrated that AOB and AOA numbers increased during biological filtration of ammonia-rich anoxic groundwater, and AOP were responsible for ammonium removal during treatment. In one of the treatment trains at plant C, ammonia removal correlated significantly with AOA numbers but not with AOB numbers. Thus, AOA were responsible for ammonia removal in water treatment at one of the studied plants. Furthermore, an observed negative correlation between the dissolved organic carbon (DOC) concentration in the water and AOA numbers suggests that high DOC levels might reduce growth of AOA. AOP entered the distribution system in numbers ranging from 1.5 × 103 to 6.5 × 104 AOPs ml−1. These numbers did not change during transport in the distribution system despite the absence of a disinfectant residual. Thus, inactive AOP biomass does not seem to be degraded by heterotrophic microorganisms in the distribution system. We conclude from our results that AOA can be commonly present in distribution systems and groundwater treatment, where they can be responsible for the removal of ammonia. PMID:19465520

  5. Ammonia-oxidizing bacteria and archaea in groundwater treatment and drinking water distribution systems.

    PubMed

    van der Wielen, Paul W J J; Voost, Stefan; van der Kooij, Dick

    2009-07-01

    The ammonia-oxidizing prokaryote (AOP) community in three groundwater treatment plants and connected distribution systems was analyzed by quantitative real-time PCR and sequence analysis targeting the amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Results demonstrated that AOB and AOA numbers increased during biological filtration of ammonia-rich anoxic groundwater, and AOP were responsible for ammonium removal during treatment. In one of the treatment trains at plant C, ammonia removal correlated significantly with AOA numbers but not with AOB numbers. Thus, AOA were responsible for ammonia removal in water treatment at one of the studied plants. Furthermore, an observed negative correlation between the dissolved organic carbon (DOC) concentration in the water and AOA numbers suggests that high DOC levels might reduce growth of AOA. AOP entered the distribution system in numbers ranging from 1.5 x 10(3) to 6.5 x 10(4) AOPs ml(-1). These numbers did not change during transport in the distribution system despite the absence of a disinfectant residual. Thus, inactive AOP biomass does not seem to be degraded by heterotrophic microorganisms in the distribution system. We conclude from our results that AOA can be commonly present in distribution systems and groundwater treatment, where they can be responsible for the removal of ammonia.

  6. Ammonia Oxidation Rate is a Fundamental Control on Thaumarchaeal Lipid Composition and the TEX86 Proxy

    NASA Astrophysics Data System (ADS)

    Hurley, S.; Elling, F. J.; Könneke, M.; Buchwald, C.; Wankel, S. D.; Santoro, A. E.; Lipp, J. S.; Hinrichs, K. U.; Pearson, A.

    2016-02-01

    Planktonic Thaumarchaeota are the ocean's major aerobic oxidizers of ammonia and produce membrane lipids known as GDGTs. These lipids are the basis of the TEX86 sea surface temperature (SST) proxy - a geochemical paleothermometer used to reconstruct SST from the Jurassic to the present. However the mechanistic underpinning of the TEX86-SST proxy remains a mystery: How do GDGT lipids predict SST, when the maximum activity of Thaumarchaeota occurs below the surface mixed layer? Here we investigated the influence of ammonia oxidation rate on the distribution of GDGT lipids using isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1. The results show that TEX86 values scale inversely with the ammonia oxidation rate, indicating that this proxy depends on available reducing power. The TEX86 ratio decreases by 5.4°C of SST-calibrated temperature over a 5.5 fmol cell-1 day-1 decrease in ammonia oxidation rate. Depth profiles from the marine water column show similar patterns of minimum TEX86 values at the depth of maximum ammonia oxidation rates, consistent with the chemostat results. Our findings suggest that the integrated signal of archaeal membrane lipids reaching the sediments is a function of the dynamics of ammonia oxidation in the overlying water column. The TEX86-SST calibration is therefore likely governed by the structure of the nutricline and its relationship to ocean thermal properties. This attribute of the TEX86 ratio may make it a promising tracer for understanding the ocean's nutrient dynamics and patterns of paleoproductivity.

  7. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring.

    PubMed

    Hatzenpichler, Roland; Lebedeva, Elena V; Spieck, Eva; Stoecker, Kilian; Richter, Andreas; Daims, Holger; Wagner, Michael

    2008-02-12

    The recent discovery of ammonia-oxidizing archaea (AOA) dramatically changed our perception of the diversity and evolutionary history of microbes involved in nitrification. In this study, a moderately thermophilic (46 degrees C) ammonia-oxidizing enrichment culture, which had been seeded with biomass from a hot spring, was screened for ammonia oxidizers. Although gene sequences for crenarchaeotal 16S rRNA and two subunits of the ammonia monooxygenase (amoA and amoB) were detected via PCR, no hints for known ammonia-oxidizing bacteria were obtained. Comparative sequence analyses of these gene fragments demonstrated the presence of a single operational taxonomic unit and thus enabled the assignment of the amoA and amoB sequences to the respective 16S rRNA phylotype, which belongs to the widely distributed group I.1b (soil group) of the Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH combined with microautoradiography (MAR) demonstrated metabolic activity of this archaeon in the presence of ammonium. This finding was corroborated by the detection of amoA gene transcripts in the enrichment. CARD-FISH/MAR showed that the moderately thermophilic AOA is highly active at 0.14 and 0.79 mM ammonium and is partially inhibited by a concentration of 3.08 mM. The enriched AOA, which is provisionally classified as "Candidatus Nitrososphaera gargensis," is the first described thermophilic ammonia oxidizer and the first member of the crenarchaeotal group I.1b for which ammonium oxidation has been verified on a cellular level. Its preference for thermophilic conditions reinvigorates the debate on the thermophilic ancestry of AOA.

  8. Selective reduction of nitric oxides with ammonia using a cellular block catalyst

    SciTech Connect

    M.V. D'yakov; A.I. Kozlov; E.S. Lukin

    2004-03-15

    An aluminum-vanadium cellular block catalyst for selective reduction of nitric oxides with ammonia has been developed. With an average degree of conversion of oxides over 90%, the efficiency of the proposed catalyst is significantly higher than that of industrial catalysts currently used. Such catalyst can be recommended for use in selective plants for purification of waste gases from nitric oxides, which makes it possible to significantly decrease the cost of making a catalyst block.

  9. 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

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

    PubMed Central

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

    2014-01-01

    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 15N-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

  11. Genomes of Two New Ammonia-Oxidizing Archaea Enriched from Deep Marine Sediments

    PubMed Central

    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

  12. Responses of the terrestrial ammonia-oxidizing archaeon Ca. Nitrososphaera viennensis and the ammonia-oxidizing bacterium Nitrosospira multiformis to nitrification inhibitors.

    PubMed

    Shen, Tianlin; Stieglmeier, Michaela; Dai, Jiulan; Urich, Tim; Schleper, Christa

    2013-07-01

    Nitrification inhibitors have been used for decades to improve nitrogen fertilizer utilization in farmland. However, their effect on ammonia-oxidizing Archaea (AOA) in soil is little explored. Here, we compared the impact of diverse inhibitors on nitrification activity of the soil archaeon Ca. Nitrososphaera viennensis EN76 and compared it to that of the ammonia-oxidizing bacterium (AOB) Nitrosospira multiformis. Allylthiourea, amidinothiourea, and dicyandiamide (DCD) inhibited ammonia oxidation in cultures of both N. multiformis and N. viennensis, but the effect on N. viennensis was markedly lower. In particular, the effective concentration 50 (EC50) of allylthiourea was 1000 times higher for the AOA culture. Among the tested nitrification inhibitors, DCD was the least potent against N. viennensis. Nitrapyrin had at the maximal soluble concentration only a very weak inhibitory effect on the AOB N. multiformis, but showed a moderate effect on the AOA. The antibiotic sulfathiazole inhibited the bacterium, but barely affected the archaeon. Only the NO-scavenger carboxy-PTIO had a strong inhibitory effect on the archaeon, but had little effect on the bacterium in the concentrations tested. Our results reflect the fundamental metabolic and cellular differences of AOA and AOB and will be useful for future applications of inhibitors aimed at distinguishing activities of AOA and AOB in soil environments.

  13. Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean—from the Equator to the Bay of Bengal

    PubMed Central

    Wang, Jing; Kan, Jinjun; Zhang, Xiaodong; Xia, Zhiqiang; Zhang, Xuecheng; Qian, Gang; Miao, Yanyi; Leng, Xiaoyun; Sun, Jun

    2017-01-01

    Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) were collected during the inter-monsoon Spring 2013. One sediment sample from the South China Sea (SCS; 2,510 m) was also included for comparison. The community composition, species richness, and diversity were characterized by clone libraries (total 1,238 clones), and higher diversity of archaeal amoA genes than bacterial amoA genes was observed in all analyzed samples. Real time qPCR analysis also demonstrated higher abundances (gene copy numbers) of archaeal amoA genes than bacterial amoA genes, and the ratios of AOA/AOB ranged from 1.42 to 8.49 among sites. In addition, unique and distinct clades were found in both reconstructed AOA and AOB phylogeny, suggesting the presence of niche-specific ammonia-oxidizing microorganisms in the EIO. The distribution pattern of both archaeal and bacterial amoA genes revealed by NMDS (non-metric multidimensional scaling) showed a distinct geographic separation of the sample from the SCS and most of the samples from the EIO following nitrogen gradients. Higher abundance and diversity of archaeal amoA genes indicated that AOA may play a more important role than AOB in the deep Indian Ocean. Environmental parameters shaping the distribution pattern of AOA were different from that of AOB, indicating distinct metabolic characteristics and/or adaptation mechanisms between AOA and AOB in the EIO, especially in deep-sea environments. PMID:28360898

  14. Ammonia-oxidizing Crenarchaeota and nitrification inside the tissue of a colonial ascidian.

    PubMed

    Martínez-García, Manuel; Stief, Peter; Díaz-Valdés, Marta; Wanner, Gerhard; Ramos-Esplá, Alfonso; Dubilier, Nicole; Antón, Josefa

    2008-11-01

    Marine Crenarchaeota represent an abundant component of the oceanic microbiota that play an important role in the global nitrogen cycle. Here we report the association of the colonial ascidian Cystodytes dellechiajei with putative ammonia-oxidizing Crenarchaeota that could actively be involved in nitrification inside the animal tissue. As shown by 16S rRNA gene analysis, the ascidian-associated Crenarchaeota were phylogenetically related to Nitrosopumilus maritimus, the first marine archaeon isolated in pure culture that grows chemolithoautotrophically oxidizing ammonia to nitrite aerobically. Catalysed reporter deposition (CARD)-FISH revealed that the Crenarchaeota were specifically located inside the tunic tissue of the colony, where moreover the expression of amoA gene was detected. The amoA gene encodes the alpha-subunit of ammonia monooxygenase, which is involved in the first step of nitrification, the oxidation of ammonia to nitrite. Sequencing of amoA gene showed that they were phylogenetically related to amoA genes of N. maritimus and other putative ammonia-oxidizing marine Crenarchaeota. In order to track the suspected nitrification activity inside the ascidian colony under in vivo conditions, microsensor profiles were measured through the tunic tissue. Net NO(x) production was detected in the tunic layer 1200-1800 microm with rates of 58-90 nmol cm(-3) h(-1). Oxygen and pH microsensor profiles showed that the layer of net NO(x) production coincided with O(2) concentrations of 103-116 microM and pH value of 5.2. Together, molecular and microsensor data indicate that Crenarchaeota could oxidize ammonia to nitrite aerobically, and thus be involved in nitrification inside the ascidian tissue.

  15. [Stability of short-cut nitrification using immobilized ammonia-oxidizing bacteria].

    PubMed

    Li, Zheng-Kui; Lai, Ding-Dong; Yang, Zhu-You; Zhang, Xiao-Jiao; Li, Fang-Jie

    2008-10-01

    The ammonia-oxidizing bacteria were immobilized by copolymer with cell proliferation technology. The effects of NH(4+) -N load, HRT, free ammonia (FA) and organic matter on short-cut nitrification process were studied. The results showed that when influent NH(4+) -N load were 100 mg/L, 150 mg/L and 200 mg/L respectively, effluent NH(4+) -N concentration was less than 10 mg/L. When the system run for 3 h, 6 h and 12 h, corresponding to influent NH(4+) -N concentration of 25.8 mg/L, 51.1 mg/L and 93.3 mg/L respectively, NH(4+) -N concentration was low in effluent with high short-cut nitrification efficiency. The HRT could be adjusted to optimize the system operation with variation of influent NH(4+) -N concentration. The results also indicated that the ammonia-oxidizing bacteria were restrained while free ammonia concentration was over 9 mg/L. The activity of the ammonia-oxidizing bacteria could be enhanced under existence of low-molecular-weight organic compounds, but the short-cut nitrification efficiency was little affected. In addition, the short-cut nitrification and denitrification could be realized with existence of organic compounds during the experiment.

  16. 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

  17. 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

  18. Genome Sequence of Nitrosomonas communis Strain Nm2, a Mesophilic Ammonia-Oxidizing Bacterium Isolated from Mediterranean Soil

    PubMed Central

    Kozlowski, Jessica A.; Kits, K. Dimitri

    2016-01-01

    The complete genome sequence of Nitrosomonas communis strain Nm2, a mesophilic betaproteobacterial ammonia oxidizer isolated from Mediterranean soils in Corfu, Greece, is reported here. This is the first genome to describe a cluster 8 Nitrosomonas species and represents an ammonia-oxidizing bacterium commonly found in terrestrial ecosystems. PMID:26769932

  19. Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters

    PubMed Central

    Rice, Marlen C.; Stein, Lisa Y.; Kozlowski, Jessica; Bollmann, Annette; Sayavedra-Soto, Luis; Shapiro, Nicole; Goodwin, Lynne A.; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Varghese, Neha; Mikhailova, Natalia; Palaniappan, Krishna; Ivanova, Natalia; Mukherjee, Supratim; Reddy, T. B. K.; Yee Ngan, Chew; Daum, Chris; Kyrpides, Nikos; Woyke, Tanja

    2017-01-01

    ABSTRACT Nitrosomonas cryotolerans ATCC 49181 is a cold-tolerant marine ammonia-oxidizing bacterium isolated from seawater collected in the Gulf of Alaska. The high-quality complete genome contains a 2.87-Mbp chromosome and a 56.6-kbp plasmid. Chemolithoautotrophic modules encoding ammonia oxidation and CO2 fixation were identified. PMID:28302769

  20. Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters

    DOE PAGES

    Rice, Marlen C.; Norton, Jeanette M.; Stein, Lisa Y.; ...

    2017-03-16

    Nitrosomonas cryotoleransATCC 49181 is a cold-tolerant marine ammonia-oxidizing bacterium isolated from seawater collected in the Gulf of Alaska. The high-quality complete genome contains a 2.87-Mbp chromosome and a 56.6-kbp plasmid. Chemolithoautotrophic modules encoding ammonia oxidation and CO2 fixation were identified.

  1. Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters.

    PubMed

    Rice, Marlen C; Norton, Jeanette M; Stein, Lisa Y; Kozlowski, Jessica; Bollmann, Annette; Klotz, Martin G; Sayavedra-Soto, Luis; Shapiro, Nicole; Goodwin, Lynne A; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Varghese, Neha; Mikhailova, Natalia; Palaniappan, Krishna; Ivanova, Natalia; Mukherjee, Supratim; Reddy, T B K; Yee Ngan, Chew; Daum, Chris; Kyrpides, Nikos; Woyke, Tanja

    2017-03-16

    Nitrosomonas cryotolerans ATCC 49181 is a cold-tolerant marine ammonia-oxidizing bacterium isolated from seawater collected in the Gulf of Alaska. The high-quality complete genome contains a 2.87-Mbp chromosome and a 56.6-kbp plasmid. Chemolithoautotrophic modules encoding ammonia oxidation and CO2 fixation were identified.

  2. 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

  3. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments.

    PubMed

    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.

  4. 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. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  5. Aerobic cometabolic degradation of trichloroethene by methane and ammonia oxidizing microorganisms naturally associated with Carex comosa roots.

    PubMed

    Powell, C L; Nogaro, G; Agrawal, A

    2011-06-01

    The degradation potential of trichloroethene by the aerobic methane- and ammonia-oxidizing microorganisms naturally associated with wetland plant (Carex comosa) roots was examined in this study. In bench-scale microcosm experiments with washed (soil free) Carex comosa roots, the activity of root-associated methane- and ammonia-oxidizing microorganisms, which were naturally present on the root surface and/or embedded within the roots, was investigated. Significant methane and ammonia oxidation were observed reproducibly in batch reactors with washed roots incubated in growth media, where methane oxidation developed faster (2 weeks) compared to ammonia oxidation (4 weeks) in live microcosms. After enrichment, the methane oxidizers demonstrated their ability to degrade 150 μg l(-1) TCE effectively at 1.9 mg l(-1) of aqueous CH(4). In contrast, ammonia oxidizers showed a rapid and complete inhibition of ammonia oxidation with 150 μg l(-1) TCE at 20 mg l(-1) of NH(4)(+)-N, which may be attributed to greater sensitivity of ammonia oxidizers to TCE or its degradation product. No such inhibitory effect of TCE degradation was detected on methane oxidation at the above experimental conditions. The results presented here suggest that microorganisms associated with wetland plant roots can assist in the natural attenuation of TCE in contaminated aquatic environments.

  6. 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.

  7. A rapid collection of yet unknown ammonia oxidizers in pure culture from activated sludge.

    PubMed

    Abe, Takuma; Ushiki, Norisuke; Fujitani, Hirotsugu; Tsuneda, Satoshi

    2017-01-01

    Nitrification is an important reaction in the biological nitrogen removal process in wastewater treatment plants (WWTPs). As ammonia-oxidizing microbes are slow-growing and sensitive to environmental factors such as free ammonia, pure strains are hard to obtain, preventing our understanding of their physiological characteristics. To conquer this hurdle, we report a high-throughput isolation technique based on scattering signatures, which exploits the tendency of many ammonia-oxidizing bacteria (AOB) to form microcolonies in activated sludge. The AOB microcolonies were directly sorted from the activated sludge without long incubation and enrichment bias, and were sequentially inoculated into 96-well microtiter plates containing growth medium. Phylogenetic analysis of the pure strains isolated in this study revealed a deeply branching and unrecognized lineage and diversity within the genus Nitrosomonas, beyond our expectation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea.

    PubMed

    Dodsworth, Jeremy A; Hungate, Bruce A; Hedlund, Brian P

    2011-08-01

    Many thermophiles catalyse free energy-yielding redox reactions involving nitrogenous compounds; however, little is known about these processes in natural thermal environments. Rates of ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in source water and sediments of two ≈ 80°C springs in the US Great Basin. Ammonia oxidation and denitrification occurred mainly in sediments. Ammonia oxidation rates measured using (15)N-NO(3)(-) pool dilution ranged from 5.5 ± 0.8 to 8.6 ± 0.9 nmol N g(-1) h(-1) and were unaffected or only mildly stimulated by amendment with NH(4) Cl. Denitrification rates measured using acetylene block ranged from 15.8 ± 0.7 to 51 ± 12 nmol N g(-1) h(-1) and were stimulated by amendment with NO(3)(-) and complex organic compounds. The DNRA rate in one spring sediment measured using an (15)N-NO(3)(-) tracer was 315 ± 48 nmol N g(-1) h(-1). Both springs harboured distinct planktonic and sediment microbial communities. Close relatives of the autotrophic, ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus yellowstonii' represented the most abundant OTU in both spring sediments by 16S rRNA gene pyrotag analysis. Quantitative PCR (qPCR) indicated that 'Ca. N. yellowstonii'amoA and 16S rRNA genes were present at 3.5-3.9 × 10(8) and 6.4-9.0 × 10(8) copies g(-1) sediment. Potential denitrifiers included members of the Aquificales and Thermales. Thermus spp. comprised <1% of 16S rRNA gene pyrotags in both sediments and qPCR for T. thermophilus narG revealed sediment populations of 1.3-1.7 × 10(6) copies g(-1) sediment. These data indicate a highly active nitrogen cycle (N-cycle) in these springs and suggest that ammonia oxidation may be a major source of energy fuelling primary production.

  9. Molecular Dynamic Study to Determine the Ammonia Conduction Mechanisms in Human RhCG and Bacterial Homoloques

    NASA Astrophysics Data System (ADS)

    Akgun, Ugur

    2014-03-01

    The transport of Ammonia is provided by Amt/MEP/Rh protein superfamily. The x-ray structures of AmtB from Escherichia coli, Rh50 from Nitrosomonas europaea, and human RhCG show only few differences on periplasmic vestibules. After more than microsecond simulation on three models, we determined the striking difference on conduction mechanism between bacterial AmtB and Human RhCG proteins. In AmtB the backbone carbonyl groups at the periplasmic vestibule direct charged ammonia to the conserved aromatic cage at the bottom of the vestibule. Furthermore, two partially stacked phenyl rings of F107 and F215, separating the periplasmic vestibule from the hydrophobic lumen, flip open and closed simultaneouslywith a frequency of approximately 108 flipping events per second. During the passage from the phenyl gates charged ammonia releases its proton and becomes gas. However, the absence of an aromatic cage on Rh proteins and a strongly conserved E166 residue in the vicinity hints different conduction mechanism. Our studies confirm the conserved E166 emerges as a strong charged ammonia recruitment site for Human RhCG. The conserved phenyl gate behaves different for Rh proteins and the synchronized motion is not observed. These findings suggest a different deprotonation mechanism than bacterial AmtB.

  10. Toward understanding reactive adsorption of ammonia on Cu-MOF/graphite oxide nanocomposites.

    PubMed

    Petit, Camille; Huang, Liangliang; Jagiello, Jacek; Kenvin, Jeffrey; Gubbins, Keith E; Bandosz, Teresa J

    2011-11-01

    The adsorption of ammonia on HKUST-1 (a metal-organic framework, MOF) and HKUST-1/graphite oxide (GO) composites was investigated in two different experimental conditions. From the isotherms, the isosteric heats of adsorption were calculated from the Clausius-Clapeyron equation following the virial approach. The results on HKUST-1 were compared with those obtained using molecular simulation studies. All materials exhibit higher ammonia adsorption capacities than those reported in the literature. The ammonia adsorption on the composites is higher than that measured separately on the MOF component and on GO. The strong adsorption of ammonia caused by chemical interactions on different adsorption sites is evidenced by the trends in the isosteric heats of adsorption. The molecular simulations conducted on HKUST-1 support the trends observed experimentally. In particular, the strong chemisorption of ammonia on the metallic centers of HKUST-1 is confirmed. Nevertheless, higher adsorption capacities are predicted compared with the experimental results. This discrepancy is mainly assigned to the partial collapse of the MOF structure upon exposure to ammonia, which is not accounted for in the simulation study.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. Investigation of Pristine Graphite Oxide as Room-Temperature Chemiresistive Ammonia Gas Sensing Material.

    PubMed

    Bannov, Alexander G; Prášek, Jan; Jašek, Ondřej; Zajíčková, Lenka

    2017-02-09

    Graphite oxide has been investigated as a possible room-temperature chemiresistive sensor of ammonia in a gas phase. Graphite oxide was synthesized from high purity graphite using the modified Hummers method. The graphite oxide sample was investigated using scanning electron microscopy, energy dispersive X-ray spectroscopy, X-ray diffraction, thermogravimetry and differential scanning calorimetry. Sensing properties were tested in a wide range of ammonia concentrations in air (10-1000 ppm) and under different relative humidity levels (3%-65%). It was concluded that the graphite oxide-based sensor possessed a good response to NH₃ in dry synthetic air (ΔR/R₀ ranged from 2.5% to 7.4% for concentrations of 100-500 ppm and 3% relative humidity) with negligible cross-sensitivity towards H₂ and CH₄. It was determined that the sensor recovery rate was improved with ammonia concentration growth. Increasing the ambient relative humidity led to an increase of the sensor response. The highest response of 22.2% for 100 ppm of ammonia was achieved at a 65% relative humidity level.

  16. Abatement of ammonia and nitrous oxide emissions from dairy farms using milk urea N (MUN)

    USDA-ARS?s Scientific Manuscript database

    Urinary urea N (UUN) excreted by dairy cows is the principal nitrogen (N) source that controls emissions of ammonia (which can be hazardous to human and ecosystem health) and nitrous oxide (the most potent agricultural greenhouse gas) from dairy manure. The objectives of this study were (1) to inves...

  17. 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

    2014-06-03

    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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    PubMed Central

    Wahman, David G.; Kirisits, Mary Jo; Katz, Lynn E.; Speitel, Gerald E.

    2011-01-01

    Ammonia-oxidizing bacteria (AOB) in nitrifying biofilters degrading four regulated trihalomethanes—trichloromethane, bromodichloromethane, dibromochloromethane, and tribromomethane—were related to Nitrosomonas oligotropha. N. oligotropha is associated with chloraminated drinking water systems, and its presence in the biofilters might indicate that trihalomethane tolerance is another reason that this bacterium is dominant in chloraminated systems. PMID:21278264

  20. Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient

    Treesearch

    S. Pierre; I. Hewson; J. P. Sparks; C. M. Litton; C. Giardina; P. M. Groffman; T. J. Fahey

    2017-01-01

    Functional gene approaches have been used to better understand the roles of microbes in driving forest soil nitrogen (N) cycling rates and bioavailability. Ammonia oxidation is a rate limiting step in nitrification, and is a key area for understanding environmental constraints on N availability in forests. We studied how increasing temperature affects the role of...

  1. Ammonia and nitrous oxide model for open lot cattle production systems

    USDA-ARS?s Scientific Manuscript database

    Air emissions, such as ammonia (NH3) and nitrous oxide (N2O), vary considerably among beef and dairy open lot operations as influenced by the climate and manure pack conditions. Because of the challenges with direct measurements, process-based modeling is a recommended approach for estimating air em...

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. Chronoamperometric Study of Ammonia Oxidation in a Direct Ammonia Alkaline Fuel Cell under the Influence of Microgravity

    NASA Astrophysics Data System (ADS)

    Acevedo, Raul; Poventud-Estrada, Carlos M.; Morales-Navas, Camila; Martínez-Rodríguez, Roberto A.; Ortiz-Quiles, Edwin; Vidal-Iglesias, Francisco J.; Sollá-Gullón, José; Nicolau, Eduardo; Feliu, Juan M.; Echegoyen, Luis; Cabrera, Carlos R.

    2017-04-01

    This is a study of the chronoamperometric performance of the electrochemical oxidation of ammonia in an alkaline fuel cell for space applications. Under microgravity the performance of a fuel cell is diminished by the absence of buoyancy since nitrogen gas is produced. The following catalysts were studied: platinum nanocubes of ca. 10nm, platinum nanocubes on carbon Vulcan ™ and platinum on carbon nanoonion support of ca. 10nm. These nanomaterials were studied in order to search for catalysts that may reduce or counter the loss of ammonia oxidation current densities performance under microgravity conditions. Chronoamperometries at potential values ranging from 0.2 V to 1.2V vs. cathode potential (breathing Air/300ml/min/82737 Pa) in 1.0 M NH4OH (30ml/min in anode) were done during over 30 parabolas in NASA's C9 airplane The Weightless Wonder in January 2016 from Ellington Field Houston. The current densities at 15s in the chronoamperometry experiments showed diminishing values under microgravity and in some cases improvements of up to 92%, for Pt-carbon nanoonions, and over 70% for the three catalysts versus ground at potentials ranging from 0.2 to 0.4V after 5 minutes of chronoamperometric conditions. At higher potentials, 1.0V or higher, Pt nanocubes and Pt-carbon nanoonions showed enhancements of up to 32% and 24%, respectively. At these higher potentials we will have a contribution of oxygen evolution. The changes in current behavior are attributed to the sizes of the catalyst materials and the time needed for the N2 bubbles detachment from the Pt surface under microgravity conditions.

  7. Chronoamperometric Study of Ammonia Oxidation in a Direct Ammonia Alkaline Fuel Cell under the Influence of Microgravity

    NASA Astrophysics Data System (ADS)

    Acevedo, Raul; Poventud-Estrada, Carlos M.; Morales-Navas, Camila; Martínez-Rodríguez, Roberto A.; Ortiz-Quiles, Edwin; Vidal-Iglesias, Francisco J.; Sollá-Gullón, José; Nicolau, Eduardo; Feliu, Juan M.; Echegoyen, Luis; Cabrera, Carlos R.

    2017-08-01

    This is a study of the chronoamperometric performance of the electrochemical oxidation of ammonia in an alkaline fuel cell for space applications. Under microgravity the performance of a fuel cell is diminished by the absence of buoyancy since nitrogen gas is produced. The following catalysts were studied: platinum nanocubes of ca. 10nm, platinum nanocubes on carbon Vulcan ™ and platinum on carbon nanoonion support of ca. 10nm. These nanomaterials were studied in order to search for catalysts that may reduce or counter the loss of ammonia oxidation current densities performance under microgravity conditions. Chronoamperometries at potential values ranging from 0.2 V to 1.2V vs. cathode potential (breathing Air/300ml/min/82737 Pa) in 1.0 M NH4OH (30ml/min in anode) were done during over 30 parabolas in NASA's C9 airplane The Weightless Wonder in January 2016 from Ellington Field Houston. The current densities at 15s in the chronoamperometry experiments showed diminishing values under microgravity and in some cases improvements of up to 92%, for Pt-carbon nanoonions, and over 70% for the three catalysts versus ground at potentials ranging from 0.2 to 0.4V after 5 minutes of chronoamperometric conditions. At higher potentials, 1.0V or higher, Pt nanocubes and Pt-carbon nanoonions showed enhancements of up to 32% and 24%, respectively. At these higher potentials we will have a contribution of oxygen evolution. The changes in current behavior are attributed to the sizes of the catalyst materials and the time needed for the N2 bubbles detachment from the Pt surface under microgravity conditions.

  8. 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.

  9. Seasonal variation and ex-situ nitrification activity of ammonia oxidizing archaea in biofilm based wastewater treatment processes.

    PubMed

    Roy, Dhritikshama; McEvoy, John; Blonigen, Mark; Amundson, Maria; Khan, Eakalak

    2017-11-01

    The abundance of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) was investigated in full-scale two-stage trickling filters (TF) and moving bed bioreactor (MBBR) treating municipal wastewater. Biofilm samples were collected for 17months from nitrifying TF (NTF), biochemical oxygen demand TF (BTF), and MBBR media. The abundance of AOA and AOB was determined using a quantitative PCR approach targeting the ammonia monooxygenase subunit A gene of archaea and bacteria. AOA were dominant in the NTF and MBBR, while AOB dominated in the BTF. AOA and AOB were more abundant during warmer months, and AOA were detected in the BTF only during warmer months. In laboratory nitrification activity experiments, ammonia oxidation to nitrite decreased when AOA populations from the NTF and MBBR were inhibited, demonstrating that AOA contributed to nitrification. This study has shown that AOA outnumber AOB and contribute to ammonia oxidation in full-scale nitrifying biofilm processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Continuous measurements of ammonia, nitrous oxide and methane from air scrubbers at pig housing facilities.

    PubMed

    Van der Heyden, C; Brusselman, E; Volcke, E I P; Demeyer, P

    2016-10-01

    Ammonia, largely emitted by agriculture, involves a great risk for eutrophication and acidification leading to biodiversity loss. Air scrubbers are widely applied to reduce ammonia emission from pig and poultry housing facilities, but it is not always clear whether their performance meets the requirements. Besides, there is a growing international concern for the livestock related greenhouse gases methane and nitrous oxide but hardly any data concerning their fate in air scrubbers are available. This contribution presents the results from measurement campaigns conducted at a chemical, a biological and a two-stage biological air scrubber installed at pig housing facilities in Flanders. Ammonia, nitrous oxide and methane at the inlet and outlet of the air scrubbers were monitored on-line during one week using a photoacoustic gas monitor, which allowed to investigate diurnal fluctuations in the removal performance of air scrubbers. Additionally, the homogeneity of the air scrubbers, normally checked by gas detection tubes, was investigated in more detail using the continuous data. The biological air scrubber with extra nitrification tank performed well in terms of ammonia removal (86 ± 6%), while the two-stage air scrubber suffered from nitrifying bacteria inhibition. In the chemical air scrubber the pH was not kept constant, lowering the ammonia removal efficiency. A lower ammonia removal efficiency was found during the day, when the ventilation rate was the highest. Nitrous oxide was produced inside the biological and two-stage scrubber, resulting in an increased outlet concentration of more than 200%. Methane could not be removed in the different air scrubbers because of its low water solubility. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Urease gene-containing Archaea dominate autotrophic ammonia oxidation in two acid soils.

    PubMed

    Lu, Lu; Jia, Zhongjun

    2013-06-01

    The metabolic traits of ammonia-oxidizing archaea (AOA) and bacteria (AOB) interacting with their environment determine the nitrogen cycle at the global scale. Ureolytic metabolism has long been proposed as a mechanism for AOB to cope with substrate paucity in acid soil, but it remains unclear whether urea hydrolysis could afford AOA greater ecological advantages. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, here we show that autotrophic ammonia oxidation in two acid soils was predominately driven by AOA that contain ureC genes encoding the alpha subunit of a putative archaeal urease. In urea-amended SIP microcosms of forest soil (pH 5.40) and tea orchard soil (pH 3.75), nitrification activity was stimulated significantly by urea fertilization when compared with water-amended soils in which nitrification resulted solely from the oxidation of ammonia generated through mineralization of soil organic nitrogen. The stimulated activity was paralleled by changes in abundance and composition of archaeal amoA genes. Time-course incubations indicated that archaeal amoA genes were increasingly labelled by (13) CO2 in both microcosms amended with water and urea. Pyrosequencing revealed that archaeal populations were labelled to a much greater extent in soils amended with urea than water. Furthermore, archaeal ureC genes were successfully amplified in the (13) C-DNA, and acetylene inhibition suggests that autotrophic growth of urease-containing AOA depended on energy generation through ammonia oxidation. The sequences of AOB were not detected, and active AOA were affiliated with the marine Group 1.1a-associated lineage. The results suggest that ureolytic N metabolism could afford AOA greater advantages for autotrophic ammonia oxidation in acid soil, but the mechanism of how urea activates AOA cells remains unclear. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

  12. Adaptation of ammonia-oxidizing microorganisms to environment shift of paddy field soil.

    PubMed

    Ke, Xiubin; Lu, Yahai

    2012-04-01

    Adaptation of microorganisms to the environment is a central theme in microbial ecology. The objective of this study was to investigate the response of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) to a soil medium shift. We employed two rice field soils collected from Beijing and Hangzhou, China. These soils contained distinct AOB communities dominated by Nitrosomonas in Beijing rice soil and Nitrosospira in Hangzhou rice soil. Three mixtures were generated by mixing equal quantities of Beijing soil and Hangzhou soil (BH), Beijing soil with sterilized Hangzhou soil (BSH), and Hangzhou soil with sterilized Beijing soil (HSB). Pure and mixed soils were permanently flooded, and the surface-layer soil where ammonia oxidation occurred was collected to determine the response of AOB and AOA to the soil medium shift. AOB populations increased during the incubation, and the rates were initially faster in Beijing soil than in Hangzhou soil. Nitrosospira (cluster 3a) and Nitrosomonas (communis cluster) increased with time in correspondence with ammonia oxidation in the Hangzhou and Beijing soils, respectively. The 'BH' mixture exhibited a shift from Nitrosomonas at day 0 to Nitrosospira at days 21 and 60 when ammonia oxidation became most active. In 'HSB' and 'BSH' mixtures, Nitrosospira showed greater stimulation than Nitrosomonas, both with and without N amendment. These results suggest that Nitrosospira spp. were better adapted to soil environment shifts than Nitrosomonas. Analysis of the AOA community revealed that the composition of AOA community was not responsive to the soil environment shifts or to nitrogen amendment. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  13. Electro-thermal treatment optimization of high concentration ammonia nitrogen by gaseous oxidation in liquid phase (GOLP).

    PubMed

    Cao, Li Mei; Yang, Ji; Jia, Jin Ping

    2011-01-01

    This study is focused on optimizing the treatment parameters for high concentration ammonia using gaseous oxidation in liquid phase (GOLP). The conversion of ammonia was achieved electrothermally over mono-crystalline silicon supported CoOx catalyst. The experimental results demonstrated that factors including the co-anions, pH of the solutions, air flowrate and the current showed apparent influences on the ammonia removal. The higher the Cl(-) concentration and/or current, the better the efficiency of ammonia degradation. The increase of the air flowrate would increase the ammonia removal accordingly. And it was also observed that the pH declined during the ammonia conversion, and the neutral and alkaline pH were beneficial to the ammonia removal. The preliminary cost analysis based on lab data was also provided for future reference.

  14. Association of running manner with bacterial community dynamics in a partial short-term nitrifying bioreactor for treatment of piggery wastewater with high ammonia content.

    PubMed

    Du, Wei-Li; Huang, Qiang; Miao, Li-Li; Liu, Ying; Liu, Zhi-Pei

    2016-12-01

    Optimization of running parameters in a bioreactor requires detailed understanding of microbial community dynamics during the startup and running periods. Using a novel piggery wastewater treatment system termed "UASB + SHARON + ANAMMOX" constructed in our laboratory, we investigated microbial community dynamics using the Illumina MiSeq method, taking activated sludge samples at ~2-week intervals during a ~300-day period. Ammonia-oxidizing bacteria (AOB) were further investigated by quantification of AOB amoA genes and construction of gene clone libraries. Major changes in bacterial community composition and dynamics occurred when running manner was changed from continuous flow manner (CFM) to sequencing batch manner (SBM), and when effluent from an upflow anaerobic sludge blanket (UASB) reactor for practical treatment of real piggery wastewater was used as influent; differences among these three experimental groups were significant (R (2)  = 0.94, p < 0.01). When running manner was changed from CFM to SBM, relative abundance of the genus Nitrospira decreased sharply from 18.1 % on day 116 to 1.5 % on day 130, and to undetectable level thereafter. Relative abundance of the genus Nitrosomonas increased from ~0.67 % during the CFM period to 8.0 % by day 220, and thereafter decreased to a near-constant ~1.6 %. Environmental factors such as load ammonia, effluent ammonia, effluent nitrite, UASB effluent, pH, and DO levels collectively drove bacterial community dynamics and contributed to maintenance of effluent NH4 (+)-N/NO2 (-)-N ratio ~1. Theses results might provide useful clues for the control of the startup processes and maintaining high efficiency of such bioreactors.

  15. Nitrous oxide production by lithotrophic ammonia-oxidizing bacteria and implications for engineered nitrogen-removal systems.

    PubMed

    Chandran, Kartik; Stein, Lisa Y; Klotz, Martin G; van Loosdrecht, Mark C M

    2011-12-01

    Chemolithoautotrophic AOB (ammonia-oxidizing bacteria) form a crucial component in microbial nitrogen cycling in both natural and engineered systems. Under specific conditions, including transitions from anoxic to oxic conditions and/or excessive ammonia loading, and the presence of high nitrite (NO₂⁻) concentrations, these bacteria are also documented to produce nitric oxide (NO) and nitrous oxide (N₂O) gases. Essentially, ammonia oxidation in the presence of non-limiting substrate concentrations (ammonia and O₂) is associated with N₂O production. An exceptional scenario that leads to such conditions is the periodical switch between anoxic and oxic conditions, which is rather common in engineered nitrogen-removal systems. In particular, the recovery from, rather than imposition of, anoxic conditions has been demonstrated to result in N₂O production. However, applied engineering perspectives, so far, have largely ignored the contribution of nitrification to N₂O emissions in greenhouse gas inventories from wastewater-treatment plants. Recent field-scale measurements have revealed that nitrification-related N₂O emissions are generally far higher than emissions assigned to heterotrophic denitrification. In the present paper, the metabolic pathways, which could potentially contribute to NO and N₂O production by AOB have been conceptually reconstructed under conditions especially relevant to engineered nitrogen-removal systems. Taken together, the reconstructed pathways, field- and laboratory-scale results suggest that engineering designs that achieve low effluent aqueous nitrogen concentrations also minimize gaseous nitrogen emissions.

  16. An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil.

    PubMed

    Hayatsu, Masahito; Tago, Kanako; Uchiyama, Ikuo; Toyoda, Atsushi; Wang, Yong; Shimomura, Yumi; Okubo, Takashi; Kurisu, Futoshi; Hirono, Yuhei; Nonaka, Kunihiko; Akiyama, Hiroko; Itoh, Takehiko; Takami, Hideto

    2017-01-10

    Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates. Whereas all known gammaproteobacterial AOB (γ-AOB) species, which have been isolated from marine and saline aquatic environments, are halophiles, TAO100 is not phenotypically halophilic. Thus, TAO100 represents the first soil-originated and non-halophilic γ-AOB. The TAO100 genome is considerably smaller than those of other γ-AOB and lacks several genes associated with salt tolerance which are unnecessary for survival in soil. The ammonia monooxygenase subunit A gene of TAO100 and its transcript are higher in abundance than those of ammonia-oxidizing archaea and betaproteobacterial AOB in the strongly acidic soil. These results indicate that TAO100 plays an important role in the nitrification of acidic soils. Based on these results, we propose TAO100 as a novel species of a new genus, Candidatus Nitrosoglobus terrae.The ISME Journal advance online publication, 10 January 2017; doi:10.1038/ismej.2016.191.

  17. Investigation of Pristine Graphite Oxide as Room-Temperature Chemiresistive Ammonia Gas Sensing Material

    PubMed Central

    Bannov, Alexander G.; Prášek, Jan; Jašek, Ondřej; Zajíčková, Lenka

    2017-01-01

    Graphite oxide has been investigated as a possible room-temperature chemiresistive sensor of ammonia in a gas phase. Graphite oxide was synthesized from high purity graphite using the modified Hummers method. The graphite oxide sample was investigated using scanning electron microscopy, energy dispersive X-ray spectroscopy, X-ray diffraction, thermogravimetry and differential scanning calorimetry. Sensing properties were tested in a wide range of ammonia concentrations in air (10–1000 ppm) and under different relative humidity levels (3%–65%). It was concluded that the graphite oxide–based sensor possessed a good response to NH3 in dry synthetic air (ΔR/R0 ranged from 2.5% to 7.4% for concentrations of 100–500 ppm and 3% relative humidity) with negligible cross-sensitivity towards H2 and CH4. It was determined that the sensor recovery rate was improved with ammonia concentration growth. Increasing the ambient relative humidity led to an increase of the sensor response. The highest response of 22.2% for 100 ppm of ammonia was achieved at a 65% relative humidity level. PMID:28208762

  18. Conversion of the refractory ammonia and acetic acid in catalytic wet air oxidation of animal byproducts.

    PubMed

    Fontanier, Virginie; Zalouk, Sofiane; Barbati, Stéphane

    2011-01-01

    Wet air oxidation (WAO) and catalytic wet air oxidation (CWAO) of slaughtered animal byproducts (ABPs) were investigated. Two step experiment was carried out consisting of a non-catalysed WAO run followed by a CWAO run at 170-275 degrees C, 20 MPa, and reaction time 180 min. The WAO (1st step) of sample (5 g/L total organic carbon (TOC)) yielded (82.0 +/- 4)% TOC removal and (78.4 +/- 13.2)% conversion of the initial organic-N into NH4(+)-N. Four metal catalysts (Pd, Pt, Rh, Ru) supported over alumina have been tested in catalytic WAO (2nd step) at elevated pH to enhance ammonia conversion and organic matter removal, particularly acetic acid. It was found that the catalysts Ru, Pt, and Rh had significant effects on the TOC removal (95.1%, 99.5% and 96.7%, respectively) and on the abatement of ammonia (93.4%, 96.7% and 96.3%, respectively) with high nitrogen selectivity. The catalyst Pd was found to have the less activity while Pt had the best performance. The X-Ray diffraction analysis showed that the support of catalyst was not stable under the experimental conditions since it reacted with phosphate present in solution. Nitrite and nitrate ions were monitored during the oxidation reaction and it was concluded that CWAO of ammonia in real waste treatment framework was in good agreement with the results obtained from the literature for ideal solutions of ammonia.

  19. Method for Bacterial Growth and Ammonia Production and Effect of Inhibitory Substances in Disposable Absorbent Hygiene Products.

    PubMed

    Forsgren-Brusk, Ulla; Yhlen, Birgitta; Blomqvist, Marie; Larsson, Peter

    The purpose of this study was to evaluate a pragmatic laboratory method to provide a technique for developing incontinence products better able to reduce malodor when used in the clinical setting. Bacterial growth and bacterially formed ammonia in disposable absorbent incontinence products was measured by adding synthetic urine inoculated with bacteria to test samples cut from the crotch area of the product. The inhibitory effect's of low pH (4.5 and 4.9) and 3 antimicrobial substances-chlorhexidine, polyhexamethylene biguanide (PHMB), and thymol-at 2 concentrations each, were studied. From the initial inocula of 3.3 log colony-forming units per milliliter (cfu/mL) at baseline, the bacterial growth of the references increased to 5.0 to 6.0 log cfu/mL at 6 hours for Escherichia coli, Proteus mirabilis, and Enterococcus faecalis. At 12 hours there was a further increase to 7.0 to 8.9 log cfu/mL. Adjusting the pH of the superabsorbent in the incontinence product from 6.0 to pH 4.5 and pH 4.9 significantly (P < .05) inhibited the bacterial growth rates, in most cases, both at 6 and 12 hours. The effect was most pronounced at pH 4.5. Chlorhexidine had significant (P < .05) inhibitory effect on E. coli and E. faecalis, and at 12 hours also on P. mirabilis. For PHMB and thymol the results varied. At 6 hours, the ammonia concentration in the references (pH 6.0) was 200 to 300 ppm and it was 1500 to 1600 ppm at 8 hours. At pH 4.5, no or little ammonia production was measured at 6 and 8 hours. At pH 4.9, there was a significant reduction (P < .01). Chlorhexidine and PHMB exerted a significant (P < .01 or P < .001) inhibitory effect on ammonia production at both concentrations and at 6 and 8 hours. Thymol 0.003% and 0.03% showed inhibitory effect at both 6 hours (P < .01 or P < .001) and at 8 hours (P < .05 or P < .001). The method described in this study can be used to compare the ability of various disposable absorbent products to inhibit bacterial growth and ammonia

  20. Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil▿†

    PubMed Central

    Jung, Man-Young; Park, Soo-Je; Min, Deullae; Kim, Jin-Seog; Rijpstra, W. Irene C.; Sinninghe Damsté, Jaap S.; Kim, Geun-Joong; Madsen, Eugene L.; Rhee, Sung-Keun

    2011-01-01

    Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaeal amoA genes featured a single sequence each. No bacterial amoA genes could be detected by PCR. A [13C]bicarbonate assimilation assay showed stoichiometric incorporation of 13C into Archaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to “Candidatus Nitrosopumilus maritimus” revealed 96.9% 16S rRNA and 89.2% amoA gene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N2O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated “Candidatus Nitrosoarchaeum koreensis.” PMID:22003023

  1. 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.

  2. 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.

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

    SciTech Connect

    Kumar, Ramesh Kaur, Amarjeet

    2016-05-06

    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{sup −1} respectively. Fourier transform infra-red (FTIR) spectra consists of peak corresponds to sp{sup 2} hybridisation of carbon atoms at 1560 cm{sup −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.

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

    SciTech Connect

    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 the 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.

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

    DOE PAGES

    Katsounaros, Ioannis; Chen, Ting; Gewirth, Andrew A.; ...

    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

  6. Bioaugmentation of syntrophic acetate-oxidizing culture in biogas reactors exposed to increasing levels of ammonia.

    PubMed

    Westerholm, Maria; Levén, Lotta; Schnürer, Anna

    2012-11-01

    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 NH(4)(+)-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.

  7. 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

  8. Seasonal variation of bacterial community in biological aerated filter for ammonia removal in drinking water treatment.

    PubMed

    Liu, Hongyuan; Zhu, Liying; Tian, Xiaohe; Yin, Yeshi

    2017-10-15

    Biological aerated filter (BAF) is widely used in wastewater treatment plants (WWTPs) and shows potential application of micropolluted drinking water sources with a higher NH4(+)-N removal efficiency during short warm seasons. Here we adopted a pilot lava-based BAF setup as a pretreatment unit of drinking water treatment plant (DWTP) and achieved a great performance of ammonia removal over a two-year operation using natural river water. We respectively observed 92.62% of NH4(+)-N removal efficiency, 97.88% of NO2(-)-N removal efficiency in summer, and 77.52% NH4(+)-N removal efficiency in winter down to 5 °C. Based on DGGE analysis, AOB, NOB, as well as heterotrophic bacteria including genus Flavobacterium and Sphingomonas are responsible for the performance. Nitrosomonas and Nitrospira are found to be the dominant AOB and NOB in the BAF microbiota. The compositions of AOB including Nitrosomonas communis and Nitrosomonas oligotropha are different from the strains previously reported in BAF of WWTPs but similar to the observations in DWPTs. We observed seasonal bacterial shifts between summer and winter groups involved in AOB, NOB and heterotrophic genus Flavobacterium, which may be responsible for the seasonal performance fluctuation. The psychrophilic AOB belonging to Nitrosomonas likely contribute to the recovered NH4(+)-N removal efficiency when temperature is below 7 °C. Lack of nitrification functional psychrophilic or psychrotolerant NOB may be in charge of the severe nitrite accumulation below 7 °C. Our analysis suggests that the colonization of psychrophilic nitrifying bacteria in BAF needs at least two-year of natural acclimatization and is necessary for all-weather BAF in DWTPs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials

    PubMed Central

    Taylor, Anne E; Zeglin, Lydia H; Wanzek, Thomas A; Myrold, David D; Bottomley, Peter J

    2012-01-01

    It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a 2-year wheat/fallow cycle, and adjacent uncultivated long-term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (P⩽0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomena: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH4+-availability that exist in the field. PMID:22695861

  10. Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials.

    PubMed

    Taylor, Anne E; Zeglin, Lydia H; Wanzek, Thomas A; Myrold, David D; Bottomley, Peter J

    2012-11-01

    It is well known that the ratio of ammonia-oxidizing archaea (AOA) and bacteria (AOB) ranges widely in soils, but no data exist on what might influence this ratio, its dynamism, or how changes in relative abundance influences the potential contributions of AOA and AOB to soil nitrification. By sampling intensively from cropped-to-fallowed and fallowed-to-cropped phases of a 2-year wheat/fallow cycle, and adjacent uncultivated long-term fallowed land over a 15-month period in 2010 and 2011, evidence was obtained for seasonal and cropping phase effects on the soil nitrification potential (NP), and on the relative contributions of AOA and AOB to the NP that recovers after acetylene inactivation in the presence and absence of bacterial protein synthesis inhibitors. AOB community composition changed significantly (P0.0001) in response to cropping phase, and there were both seasonal and cropping phase effects on the amoA gene copy numbers of AOA and AOB. Our study showed that the AOA:AOB shifts were generated by a combination of different phenomena: an increase in AOA amoA abundance in unfertilized treatments, compared with their AOA counterparts in the N-fertilized treatment; a larger population of AOB under the N-fertilized treatment compared with the AOB community under unfertilized treatments; and better overall persistence of AOA than AOB in the unfertilized treatments. These data illustrate the complexity of the factors that likely influence the relative contributions of AOA and AOB to nitrification under the various combinations of soil conditions and NH(4)(+)-availability that exist in the field.

  11. 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.

  12. Nanosilver inhibits nitrification and reduces ammonia-oxidising bacterial but not archaeal amoA gene abundance in estuarine sediments.

    PubMed

    Beddow, Jessica; Stolpe, Björn; Cole, Paula A; Lead, Jamie R; Sapp, Melanie; Lyons, Brett P; Colbeck, Ian; Whitby, Corinne

    2017-02-01

    Silver nanoparticles (AgNPs) enter estuaries via wastewater treatment effluents, where they can inhibit microorganisms, because of their antimicrobial properties. Ammonia-oxidising bacteria (AOB) and archaea (AOA) are involved in the first step of nitrification and are important to ecosystem function, especially where effluent discharge results in high nitrogen inputs. Here, we investigated the effect of a pulse addition of AgNPs on AOB and AOA ammonia monooxygenase (amoA) gene abundances and benthic nitrification potential rates (NPR) in low-salinity and mesohaline estuarine sediments. Whilst exposure to 0.5 mg L(-1) AgNPs had no significant effect on amoA gene abundances or NPR, 50 mg L(-1) AgNPs significantly decreased AOB amoA gene abundance (up to 76% over 14 days), and significantly decreased NPR by 20-fold in low-salinity sediments and by twofold in mesohaline sediments, after one day. AgNP behaviour differed between sites, whereby greater aggregation occurred in mesohaline waters (possibly due to higher salinity), which may have reduced toxicity. In conclusion, AgNPs have the potential to reduce ammonia oxidation in estuarine sediments, particularly where AgNPs accumulate over time and reach high concentrations. This could lead to long-term risks to nitrification, especially in polyhaline estuaries where ammonia-oxidation is largely driven by AOB. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

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

    PubMed Central

    Bollmann, Annette; Sedlacek, Christopher J.; Norton, Jeanette; Laanbroek, Hendrikus J.; Suwa, Yuichi; Stein, Lisa Y.; Klotz, Martin G.; Arp, Daniel; Sayavedra-Soto, Luis; Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, James; Woyke, Tanja; Lucas, Susan M.; Pitluck, Sam; Pennacchio, Len; Nolan, Matt; Land, Miriam L.; Huntemann, Marcel; Deshpande, Shweta; Han, Cliff; Chen, Amy; Kyrpides, Nikos; Mavromatis, Konstantinos; Markowitz, Victor; Szeto, Ernest; Ivanova, Natalia; 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. PMID:24019993

  14. 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.

  15. Dynamics of communities of bacteria and ammonia-oxidizing microorganisms in response to simazine attenuation in agricultural soil.

    PubMed

    Wan, Rui; Wang, Zhao; Xie, Shuguang

    2014-02-15

    Autochthonous microbiota plays a crucial role in natural attenuation of s-triazine herbicides in agricultural soil. Soil microcosm study was carried out to investigate the shift in the structures of soil autochthonous microbial communities and the potential degraders associated with natural simazine attenuation. The relative abundance of soil autochthonous degraders and the structures of microbial communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. Phylogenetic composition of bacterial community was also characterized using clone library analysis. Soil autochthonous microbiota could almost completely clean up simazine (100 mg kg(-1)) in 10 days after herbicide application, indicating a strong self-remediation potential of agricultural soil. A significant increase in the proportion of s-triazine-degrading atzC gene was found in 6 days after simazine amendment. Simazine application could alter the community structures of total bacteria and ammonia-oxidizing archaea (AOA) and bacteria (AOB). AOA were more responsive to simazine application compared to AOB and bacteria. Actinobacteria, Alphaproteobacteria and Gammaproteobacteria were the dominant bacterial groups either at the initial stage after simazine amendment or at the end stage of herbicide biodegradation, but Actinobacteria predominated at the middle stage of biodegradation. Microorganisms from several bacterial genera might be involved in simazine biodegradation. This work could add some new insights on the bioremediation of herbicides contaminated agricultural soils.

  16. Ammonia produced by bacterial colonies promotes growth of ampicillin-sensitive Serratia sp. by means of antibiotic inactivation.

    PubMed

    Cepl, Jaroslav; Blahůšková, Anna; Cvrčková, Fatima; Markoš, Anton

    2014-05-01

    Volatiles produced by bacterial cultures are known to induce regulatory and metabolic alterations in nearby con-specific or heterospecific bacteria, resulting in phenotypic changes including acquisition of antibiotic resistance. We observed unhindered growth of ampicillin-sensitive Serratia rubidaea and S. marcescens on ampicillin-containing media, when exposed to volatiles produced by dense bacterial growth. However, this phenomenon appeared to result from pH increase in the medium caused by bacterial volatiles rather than alterations in the properties of the bacterial cultures, as alkalization of ampicillin-containing culture media to pH 8.5 by ammonia or Tris exhibited the same effects, while pretreatment of bacterial cultures under the same conditions prior to antibiotic exposure did not increase ampicillin resistance. Ampicillin was readily inactivated at pH 8.5, suggesting that observed bacterial growth results from metabolic alteration of the medium, rather than an active change in the target bacterial population (i.e. induction of resistance or tolerance). However, even such seemingly simple mechanism may provide a biologically meaningful basis for protection against antibiotics in microbial communities growing on semi-solid media.

  17. Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet tropical soil.

    PubMed

    Pett-Ridge, Jennifer; Petersen, Dorthe G; Nuccio, Erin; Firestone, Mary K

    2013-07-01

    Ammonia oxidation is a key process in the global nitrogen cycle. However, in tropical soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia oxidation along an elevation, moisture, and oxygen availability gradient in wet tropical soils. Soils from three forest types were incubated for up to 36 weeks in lab microcosms under three regimes: (1) static aerobic; (2) static anaerobic; and (3) fluctuating (aerobic/anaerobic). Nitrification potential was measured in field-fresh soils and incubated soils. The native ammonia-oxidizing community was also characterized, based on diversity assessments (clone libraries) and quantification of the ammonia monooxygenase α-subunit (amoA) gene. These relatively low pH soils appear to be dominated by ammonia-oxidizing archaea (AOA), and AOA communities in the three soil types differed significantly in their ability to oxidize ammonia. Soils from an intermediate elevation, and those incubated with fluctuating redox conditions, tended to have the highest nitrification potential following an influx of oxygen, although all soils retained the capacity to nitrify even after long anoxic periods. Together, these results suggest that wet tropical soil AOA are tolerant of extended periods of anoxia.

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

    PubMed

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

    1990-08-01

    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.

  19. 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

  20. Diversity and Abundance of Ammonia-Oxidizing Archaea in Hydrothermal Vent Chimneys of the Juan de Fuca Ridge▿ †

    PubMed Central

    Wang, Shufang; Xiao, Xiang; Jiang, Lijing; Peng, Xiaotong; Zhou, Huaiyang; Meng, Jun; Wang, Fengping

    2009-01-01

    The abundance and diversity of archaeal ammonia monooxygenase subunit A (amoA) genes from hydrothermal vent chimneys at the Juan de Fuca Ridge were investigated. The majority of the retrieved archaeal amoA sequences exhibited identities of less than 95% to those in the GenBank database. Novel ammonia-oxidizing archaea may exist in the hydrothermal vent environments. PMID:19395559

  1. Diversity and abundance of ammonia-oxidizing archaea in hydrothermal vent chimneys of the juan de fuca ridge.

    PubMed

    Wang, Shufang; Xiao, Xiang; Jiang, Lijing; Peng, Xiaotong; Zhou, Huaiyang; Meng, Jun; Wang, Fengping

    2009-06-01

    The abundance and diversity of archaeal ammonia monooxygenase subunit A (amoA) genes from hydrothermal vent chimneys at the Juan de Fuca Ridge were investigated. The majority of the retrieved archaeal amoA sequences exhibited identities of less than 95% to those in the GenBank database. Novel ammonia-oxidizing archaea may exist in the hydrothermal vent environments.

  2. 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.

  3. Pathways of Carbon Assimilation and Ammonia Oxidation Suggested by Environmental Genomic Analyses of Marine Crenarchaeota

    PubMed Central

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

    2006-01-01

    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

  4. 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

  5. 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.

  6. Relationship of Temporal and Spatial Variabilities of Ammonia-Oxidizing Bacteria to Nitrification Rates in Monterey Bay, California

    PubMed Central

    O'Mullan, G. D.; Ward, B. B.

    2005-01-01

    Temporal and spatial dynamics of ammonia-oxidizing bacteria (AOB) were examined using genes encoding 16S rRNA and ammonia monooxygenase subunit A (AmoA) in Monterey Bay, Calif. Samples were collected from three depths in the water column on four dates at one mid-bay station. Diversity estimators for the two genes showed a strong positive correlation, indicating that overlapping bacterial populations had been sampled by both sets of clone libraries. Some samples that were separated by only 15 m in depth had less genetic similarity than samples that were collected from the same depth months apart. Clone libraries from the Monterey Bay AOB community were dominated by Nitrosospira-like sequences and clearly differentiated from the adjacent AOB community in Elkhorn Slough. Many Monterey Bay clones clustered with previously identified 16S rRNA and amoA groups composed entirely of marine sequences, supporting the hypothesis that these groups are specific to the marine environment and are dominant marine AOB. In addition, novel, phylogenetically distinct groups of AOB sequences were identified and compared to sequences in the database. Only one cluster of gammaproteobacterial AOB was detected using 16S rRNA genes. Although significant genetic variation was detected in AOB populations from both vertical and temporal samples, no significant correlation was detected between diversity and environmental variables or the rate of nitrification. PMID:15691919

  7. 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.

  8. Metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage

    PubMed Central

    Hollibaugh, James T; Gifford, Scott; Sharma, Shalabh; Bano, Nasreen; Moran, Mary Ann

    2011-01-01

    Quantitative PCR (qPCR) analysis revealed elevated relative abundance (1.8% of prokaryotes) of marine group 1 Crenarchaeota (MG1C) in two samples of southeastern US coastal bacterioplankton, collected in August 2008, compared with samples collected from the same site at different times (mean 0.026%). We analyzed the MG1C sequences in metatranscriptomes from these samples to gain an insight into the metabolism of MG1C population growing in the environment, and for comparison with ammonia-oxidizing bacteria (AOB) in the same samples. Assemblies revealed low diversity within sequences assigned to most individual MG1C open reading frames (ORFs) and high homology with ‘Candidatus Nitrosopumilus maritimus' strain SCM1 genome sequences. Reads assigned to ORFs for ammonia uptake and oxidation accounted for 37% of all MG1C transcripts. We did not recover any reads for Nmar_1354–Nmar_1357, proposed to encode components of an alternative, nitroxyl-based ammonia oxidation pathway; however, reads from Nmar_1259 and Nmar_1667, annotated as encoding a multicopper oxidase with homology to nirK, were abundant. Reads assigned to two homologous ORFs (Nmar_1201 and Nmar_1547), annotated as hypothetical proteins were also abundant, suggesting that their unknown function is important to MG1C. Superoxide dismutase and peroxiredoxin-like transcripts were more abundant in the MG1C transcript pool than in the complete metatranscriptome, suggesting an enhanced response to oxidative stress by the MG1C population. qPCR indicated low AOB abundance (0.0010% of prokaryotes), and we found no transcripts related to ammonia oxidation and only one RuBisCO transcript among the transcripts assigned to AOB, suggesting they were not responding to the same environmental cues as the MG1C population. PMID:21085199

  9. Structural and biological studies on bacterial nitric oxide synthase inhibitors

    PubMed Central

    Holden, Jeffrey K.; Li, Huiying; Jing, Qing; Kang, Soosung; Richo, Jerry; Silverman, Richard B.; Poulos, Thomas L.

    2013-01-01

    Nitric oxide (NO) produced by bacterial NOS functions as a cytoprotective agent against oxidative stress in Staphylococcus aureus, Bacillus anthracis, and Bacillus subtilis. The screening of several NOS-selective inhibitors uncovered two inhibitors with potential antimicrobial properties. These two compounds impede the growth of B. subtilis under oxidative stress, and crystal structures show that each compound exhibits a unique binding mode. Both compounds serve as excellent leads for the future development of antimicrobials against bacterial NOS-containing bacteria. PMID:24145412

  10. 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

  11. Ammonia and nitrous oxide emissions from a commercial broiler house

    USDA-ARS?s Scientific Manuscript database

    Complex variation in gas emissions from animal facilities has been shown in recent research reports; uncertainties in these emission estimates are driving research activities concerning different animal species across the globe. Greenhouse gas (GHG, nitrous oxide (N2O) and carbon dioxide (CO2)) and ...

  12. Limitation of spatial distribution of ammonia-oxidizing microorganisms in the Haihe River, China, by heavy metals.

    PubMed

    Wang, Chao; Shan, Baoqing; Zhang, Hong; Zhao, Yu

    2014-03-01

    The Haihe River is characterized by high ammonia pollution. Therefore, it is necessary to determine how environmental factors, such as heavy metals in the river limit the spatial distribution of ammonia-oxidizing microorganisms. In this study, the relationships between five heavy metals and ammonia-oxidizing microorganisms were studied. The results showed that under high ammonia, low oxygen and high concentrations of suspended particles, ammonia-oxidizing bacteria (AOB) ranged from 10(1.3) to 10(4.8) gene copies/mL and ammonia-oxidizing archaea (AOA) ranged from 10(2.7) to 10(4.9) gene copies/mL. The average metal concentrations in water were 23.57 (Cr), 21.58 (Ni), 65.09 (Cu), 622.03 (Zn) and 10.16 (As) μg/L, with those of Zn, Cu and Cr being higher than the US EPA criteria. Scatter plots of microbial abundance and metals indicated that both AOA and AOB were limited by heavy metals, but in different ways. As had an inhibitory effect on AOB, while Ni and Zn promoted AOA, and the other metals investigated showed no significant correlation with microbial abundance. Overall, our results indicated that the effects of heavy metals on ammonia-oxidizing microorganisms in water are complex, and that the final effect is determined by the physiological role of each element in the microorganisms, as well as environmental conditions such as complexation of organic matter, not simply the total metal concentration.

  13. Active autotrophic ammonia-oxidizing bacteria in biofilm enrichments from simulated creek ecosystems at two ammonium concentrations respond to temperature manipulation.

    PubMed

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

    2011-10-01

    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 NH(4)(+), respectively) that were developed in a flow-channel experiment and incubated under three temperature regimens. By stable-isotope probing using (13)CO(2), 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 (13)C-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 (13)C-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.

  14. 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

  15. Diversity in the Ammonia-Oxidizing Nitrifier Population of a Soil †

    PubMed Central

    Belser, L. W.; Schmidt, E. L.

    1978-01-01

    Multiple genera of ammonia-oxidizing chemoautotrophic nitrifiers in a soil were detected, isolated, and studied by means of modified most-probable-number (MPN) techniques. The soil examined was a Waukegon silt loam treated with ammonium nitrate or sewage effluent. The genera Nitrosomonas and Nitrosospira were found to occur more commonly than the genus Nitrosolobus. Three different MPN media gave approximately the same overall ammonia oxidizer counts within statistical error after prolonged incubation but differed markedly in ratios of Nitrosomonas to Nitrosospira. Selectivity and counting efficiency of MPN media were studied by observing the growth response of representative pure cultures isolated from the soil. Selectivity was evident in each medium with respect to all strains tested, and the media differed greatly in incubation times required to obtain maximum counts. PMID:16345319

  16. Ammonia Oxide as a Building Block for High-Performance and Insensitive Energetic Materials.

    PubMed

    Tang, Yongxing; Mitchell, Lauren A; Imler, Gregory H; Parrish, Damon A; Shreeve, Jean'ne M

    2017-05-15

    3,5-Dinitrimino-1,2,4-triazole (2) with three protons has the potential of deprotonation to form energetic salts. Neutralization of 2 with 50 % hydroxylamine in varying molar ratios leads to the formation of the corresponding mono/dihydroxylammonium energetic salts. Additionally compound 5, an ammonia oxide adduct of dihydroxylammonium 3,5-dinitramino-1,2,4-triazolate, was prepared when excess hydroxylamine was used. The structures of 3-5 are supported by single-crystal X-ray diffraction. The energetic properties of the new materials are competitive. Utilization of ammonia oxide adducts in hydroxylammonium energetic salts could lead to future practical applications as energetic materials. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Adsorption of ammonia on graphite oxide/aluminium polycation and graphite oxide/zirconium-aluminium polyoxycation composites.

    PubMed

    Seredych, Mykola; Bandosz, Teresa J

    2008-08-01

    Graphite oxide (GO) synthesized from commercial graphite was modified with aluminium or zirconium-aluminium polyoxycations and then calcined at 350 degrees C. On the samples obtained adsorption of ammonia from moist air was investigated. The surface of materials before and after exposure to ammonia was characterized using adsorption of nitrogen, XRD, SEM, FTIR, TA, CHN analysis, and potentiometric titration. The results showed that in spite of the fact that graphite composites/pillared graphites (PG) have Keggin-like ions located between the layers, that space blocked for nitrogen molecules used to determine the specific surface area. During calcinations, the deflagration of layers occurred as a result of decomposition of epoxy groups. This results in formation of disordered graphitic carbons with some mesoporosity. Even though these materials were not porous, the significant amount of ammonia was retained on the surface. Since ammonia molecule is able to specifically interact with oxygen groups of graphite oxide and Brønsted centers of inorganic pillars, it is likely intercalated between the composite layers. While the best performance was found for GO modified with aluminium-zirconium species, after calcinations the samples containing Keggin Al(13) like cations revealed the high capacity which is linked to the high acidity of incorporated inorganic compounds.

  18. Evaluating four mathematical models for nitrous oxide production by autotrophic ammonia-oxidizing bacteria.

    PubMed

    Ni, Bing-Jie; Yuan, Zhiguo; Chandran, Kartik; Vanrolleghem, Peter A; Murthy, Sudhir

    2013-01-01

    There is increasing evidence showing that ammonia-oxidizing bacteria (AOB) are major contributors to N(2)O emissions from wastewater treatment plants (WWTPs). Although the fundamental metabolic pathways for N(2)O production by AOB are now coming to light, the mechanisms responsible for N(2)O production by AOB in WWTP are not fully understood. Mathematical modeling provides a means for testing hypotheses related to mechanisms and triggers for N(2)O emissions in WWTP, and can then also become a tool to support the development of mitigation strategies. This study examined the ability of four mathematical model structures to describe two distinct mechanisms of N(2)O production by AOB. The production mechanisms evaluated are (1) N(2)O as the final product of nitrifier denitrification with NO(2)- as the terminal electron acceptor and (2) N(2)O as a byproduct of incomplete oxidation of hydroxylamine (NH(2)OH) to NO(2)-. The four models were compared based on their ability to predict N(2)O dynamics observed in three mixed culture studies. Short-term batch experimental data were employed to examine model assumptions related to the effects of (1) NH4+ concentration variations, (2) dissolved oxygen (DO) variations, (3) NO(2)- accumulations and (4) NH(2OH as an externally provided substrate. The modeling results demonstrate that all these models can generally describe the NH4+, NO(2)-, and NO(3)- data. However, none of these models were able to reproduce all measured N(2)O data. The results suggest that both the denitrification and NH(2)OH pathways may be involved in N(2)O production and could be kinetically linked by a competition for intracellular reducing equivalents. A unified model capturing both mechanisms and their potential interactions needs to be developed with consideration of physiological complexity. Copyright © 2012 Wiley Periodicals, Inc.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

    PubMed Central

    Qin, Wei; Amin, Shady A.; Martens-Habbena, Willm; Walker, Christopher B.; Urakawa, Hidetoshi; Devol, Allan H.; Ingalls, Anitra E.; Moffett, James W.; Armbrust, E. Virginia; Stahl, David A.

    2014-01-01

    Ammonia-oxidizing archaea (AOA) are now implicated in exerting significant control over the form and availability of reactive nitrogen species in marine environments. Detailed studies of specific metabolic traits and physicochemical factors controlling their activities and distribution have not been well constrained in part due to the scarcity of isolated AOA strains. Here, we report the isolation of two new coastal marine AOA, strains PS0 and HCA1. Comparison of the new strains to Nitrosopumilus maritimus strain SCM1, the only marine AOA in pure culture thus far, demonstrated distinct adaptations to pH, salinity, organic carbon, temperature, and light. Strain PS0 sustained nearly 80% of ammonia oxidation activity at a pH as low as 5.9, indicating that coastal strains may be less sensitive to the ongoing reduction in ocean pH. Notably, the two novel isolates are obligate mixotrophs that rely on uptake and assimilation of organic carbon compounds, suggesting a direct coupling between chemolithotrophy and organic matter assimilation in marine food webs. All three isolates showed only minor photoinhibition at 15 µE⋅m−2⋅s−1 and rapid recovery of ammonia oxidation in the dark, consistent with an AOA contribution to the primary nitrite maximum and the plausibility of a diurnal cycle of archaeal ammonia oxidation activity in the euphotic zone. Together, these findings highlight an unexpected adaptive capacity within closely related marine group I Archaea and provide new understanding of the physiological basis of the remarkable ecological success reflected by their generally high abundance in marine environments. PMID:25114236

  4. 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.

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

    PubMed Central

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

    2016-01-01

    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 (R2 = 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

  6. Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation.

    PubMed

    Qin, Wei; Amin, Shady A; Martens-Habbena, Willm; Walker, Christopher B; Urakawa, Hidetoshi; Devol, Allan H; Ingalls, Anitra E; Moffett, James W; Armbrust, E Virginia; Stahl, David A

    2014-08-26

    Ammonia-oxidizing archaea (AOA) are now implicated in exerting significant control over the form and availability of reactive nitrogen species in marine environments. Detailed studies of specific metabolic traits and physicochemical factors controlling their activities and distribution have not been well constrained in part due to the scarcity of isolated AOA strains. Here, we report the isolation of two new coastal marine AOA, strains PS0 and HCA1. Comparison of the new strains to Nitrosopumilus maritimus strain SCM1, the only marine AOA in pure culture thus far, demonstrated distinct adaptations to pH, salinity, organic carbon, temperature, and light. Strain PS0 sustained nearly 80% of ammonia oxidation activity at a pH as low as 5.9, indicating that coastal strains may be less sensitive to the ongoing reduction in ocean pH. Notably, the two novel isolates are obligate mixotrophs that rely on uptake and assimilation of organic carbon compounds, suggesting a direct coupling between chemolithotrophy and organic matter assimilation in marine food webs. All three isolates showed only minor photoinhibition at 15 µE ⋅ m(-2) ⋅ s(-1) and rapid recovery of ammonia oxidation in the dark, consistent with an AOA contribution to the primary nitrite maximum and the plausibility of a diurnal cycle of archaeal ammonia oxidation activity in the euphotic zone. Together, these findings highlight an unexpected adaptive capacity within closely related marine group I Archaea and provide new understanding of the physiological basis of the remarkable ecological success reflected by their generally high abundance in marine environments.

  7. Effects of planting Phragmites australis on nitrogen removal, microbial nitrogen cycling, and abundance of ammonia-oxidizing and denitrifying microorganisms in sediments.

    PubMed

    Toyama, Tadashi; Nishimura, Yoshiko; Ogata, Yuka; Sei, Kazunari; Mori, Kazuhiro; Ike, Michihiko

    2015-10-21

    We examined the effect of planting an emergent aquatic plant (Phragmites australis) on nitrogen removal from sediments using a 42-d pot experiment. The experimental pot systems comprised two types of sediments planted with and without young P. australis. Total nitrogen (total N), total dissolved N, and NH4-N in the sediments decreased markedly after planting. In contrast, those levels decreased only slightly in the unplanted sediments. The decrease in total N in the P. australis-planted sediments was 7-20 times those in the unplanted sediments. Abundances of bacterial 16S rRNA, archaeal 16S rRNA, ammonia-oxidizing bacterial ammonia monooxygenase (amoA), ammonia-oxidizing archaeal amoA, and denitrifying bacterial nitrite reductase (nirK) genes increased significantly in sediments after planting. Phragmites australis appears to have released oxygen and created a repeating cycle of oxidizing and reducing conditions in the sediments. These conditions should promote mineralization of organic N, nitrification, and denitrification in the sediments. Phragmites australis absorbed bioavailable nitrogen generated by microbial nitrogen metabolism. During the 42-d period after planting, 31-44% of total N was removed by microbial nitrogen cycling, and 56-69% was removed via absorption by P. australis. These results suggest that planting P. australis can increase microbial populations and their activities, and that nitrogen removal can be accelerated by the combined functions of P. australis and microorganisms in the sediment. Thus, planting P. australis has considerable potential as an effective remediation technology for eutrophic sediments.

  8. Ammonia-oxidizing bacteria and archaea in wastewater treatment plant sludge and nearby coastal sediment in an industrial area in China.

    PubMed

    Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Wen, Donghui

    2015-05-01

    Under the increasing pressure of human activities, Hangzhou Bay has become one of the most seriously polluted waters along China's coast. Considering the excessive inorganic nitrogen detected in the bay, in this study, the impact of an effluent from a coastal industrial park on ammonia-oxidizing microorganisms (AOMs) of the receiving area was interpreted for the first time by molecular technologies. Revealed by real-time PCR, the ratio of archaeal amoA/bacterial amoA ranged from 5.68 × 10(-6) to 4.79 × 10(-5) in the activated sludge from two wastewater treatment plants (WWTPs) and 0.54-3.44 in the sediments from the effluent receiving coastal area. Analyzed by clone and pyrosequencing libraries, genus Nitrosomonas was the predominant ammonia-oxidizing bacteria (AOB), but no ammonia-oxidizing archaea (AOA) was abundant enough for sequencing in the activated sludge from the WWTPs; genus Nitrosomonas and Nitrosopumilus were the dominant AOB and AOA, respectively, in the coastal sediments. The different abundance of AOA but similar structure of AOB between the WWTPs and nearby coastal area probably indicated an anthropogenic impact on the microbial ecology in Hangzhou Bay.

  9. 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.

  10. 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.

  11. Responses of community structure of amoA-encoding archaea and ammonia-oxidizing bacteria in ammonia biofilter with rockwool mixtures to the gradual increases in ammonium and nitrate.

    PubMed

    Yasuda, T; Waki, M; Kuroda, K; Hanajima, D; Fukumoto, Y; Yamagishi, T; Suwa, Y; Suzuki, K

    2013-03-01

    To investigate community shifts of amoA-encoding archaea (AEA) and ammonia-oxidizing bacteria (AOB) in biofilter under nitrogen accumulation process. A laboratory-scale rockwool biofilter with an irrigated water circulation system was operated for 436 days with ammonia loading rates of 49-63 NH(3) g m(-3) day(-1). The AEA and AOB communities were investigated by denaturing gradient gel electrophoresis, sequencing and real-time PCR analysis based on amoA genes. The results indicated that changes in abundance and community compositions occurred in a different manner between archaeal and bacterial amoA during the operation. However, both microbial community structures mainly varied when free ammonia (FA) concentrations in circulation water were increasing, which caused a temporal decline in reactor performance. Dominant amoA sequences after this transition were related to Thaumarchaeotal Group I.1b, Nitrosomonas europaea lineages and one subcluster within Nitrosospira sp. cluster 3, for archaea and bacteria, respectively. The specific FA in circulation water seems to be the important factor, which relates to the AOB and AEA community shifts in the biofilter besides ammonium and pH. One of the key factors for regulating AEA and AOB communities was proposed that is useful for optimizing biofiltration technology. © 2013 The Society for Applied Microbiology.

  12. Synergistic Effect of Mixed Oxide on the Adsorption of Ammonia with Metal–Organic Frameworks

    DOE PAGES

    Mounfield, III, William P.; Taborga Claure, Micaela; Agrawal, Pradeep K.; ...

    2016-06-08

    A hydrotalcite-derived MgAl oxide (MMO) was evaluated in combination with the metal–organic frameworks (MOFs) UiO-66 and UiO-66-NH2 for the adsorption of ammonia. Analysis of the materials’ textural properties after ammonia breakthrough adsorption revealed no change in the PXRD patterns or FTIR spectra; however, a slight decrease in surface area was observed, consistent with the hypothesized presence of strongly adsorbed species after adsorption. UiO-66:MMO and UiO-66-NH2:MMO composites maintained ammonia adsorption capacity under dry conditions. An almost 2-fold increase in humid ammonia capacity was observed for the UiO-66:MMO composite, far beyond that expected through a linear combination of the two materials’ capacities.more » As a result, the synergistic effect observed in humid conditions was further investigated with water adsorption experiments, which suggested the effect is the result of the high water affinity of MMO.« less

  13. Response of Nitrosospira sp. Strain AF-Like Ammonia Oxidizers to Changes in Temperature, Soil Moisture Content, and Fertilizer Concentration▿

    PubMed Central

    Avrahami, Sharon; Bohannan, Brendan J. M.

    2007-01-01

    Very little is known regarding the ecology of Nitrosospira sp. strain AF-like bacteria, a unique group of ammonia oxidizers within the Betaproteobacteria. We studied the response of Nitrosospira sp. strain AF-like ammonia oxidizers to changing environmental conditions by applying molecular methods and physiological measurements to Californian grassland soil manipulated in the laboratory. This soil is naturally high in Nitrosospira sp. strain AF-like bacteria relative to the much-better-studied Nitrosospira multiformis-like ammonia-oxidizing bacteria. Increases in temperature, soil moisture, and fertilizer interacted to reduce the relative abundance of Nitrosospira sp. strain AF-like bacteria, although they remained numerically dominant. The overall abundance of ammonia-oxidizing bacteria increased with increasing soil moisture and decreased with increasing temperature. Potential nitrification activity was altered by interactions among temperature, soil moisture, and fertilizer, with activity tending to be higher when soil moisture and temperature were increased. The increase in potential nitrification activity with increased temperature was surprising, given that the overall abundance of ammonia-oxidizing bacteria decreased significantly under these conditions. This observation suggests that (i) Nitrosospira sp. strain AF-like bacteria may respond to increased temperature with an increase in activity, despite a decrease in abundance, or (ii) that potential nitrification activity in these soils may be due to organisms other than bacteria (e.g., archaeal ammonia oxidizers), at least under conditions of increased temperature. PMID:17158615

  14. Diversity and abundance of ammonia-oxidizing archaea and bacteria in polluted mangrove sediment.

    PubMed

    Cao, Huiluo; Li, Meng; Hong, Yiguo; Gu, Ji-Dong

    2011-11-01

    Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. Recent research results show that ammonia-oxidizing archaea (AOA) are both abundant and diverse in a range of ecosystems. In this study, we examined the abundance and diversity of AOA and ammonia-oxidizing beta-proteobacteria (AOB) in estuarine sediments in Hong Kong for two seasons using the ammonia monooxygenase A subunit gene (amoA) as molecular biomarker. Relationships between diversity and abundance of AOA and AOB and physicochemical parameters were also explored. AOB were more diverse but less abundant than AOA. A few phylogenetically distinct amoA gene clusters were evident for both AOA and AOB from the mangrove sediment. Pearson moment correlation analysis and canonical correspondence analysis (CCA) were used to explore physicochemical parameters potentially important to AOA and AOB. Metal concentrations were proposed to contribute potentially to the distributions of AOA while total phosphorus (TP) was correlated to the distributions of AOB. Quantitative PCR estimates indicated that AOA were more abundant than AOB in all samples, but the ratio of AOA/AOB (from 1.8 to 6.3) was smaller than most other studies by one to two orders. The abundance of AOA or AOB was correlated with pH and temperature while the AOA/AOB ratio was with the concentrations of ammonium. Several physicochemical factors, rather than any single one, affect the distribution patterns suggesting that a combination of factors is involved in shaping the dynamics of AOA and AOB in the mangrove ecosystem. Copyright © 2011 Elsevier GmbH. All rights reserved.

  15. 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

  16. Enrichment of Thermophilic Ammonia-Oxidizing Archaea from an Alkaline Hot Spring in the Great Basin, USA

    NASA Astrophysics Data System (ADS)

    Zhang, C.; Huang, Z.; Jiang, H.; Wiegel, J.; Li, W.; Dong, H.

    2010-12-01

    One of the major advances in the nitrogen cycle is the recent discovery of ammonia oxidation by archaea. While culture-independent studies have revealed occurrence of ammonia-oxidizing archaea (AOA) in nearly every surface niche on earth, most of these microorganisms have resisted isolation and so far only a few species have been identified. The Great Basin contains numerous hot springs, which are characterized by moderately high temperature (40-65 degree C) and circumneutral or alkaline pH. Unique thermophilic archaea have been identified based on molecular DNA and lipid biomarkers; some of which may be ammonia oxidizers. This study aims to isolate some of these archaea from a California hot spring that has pH around 9.0 and temperature around 42 degree C. Mat material was collected from the spring and transported on ice to the laboratory. A synthetic medium (SCM-5) was inoculated with the mat material and the culture was incubated under varying temperature (35-65 degree C) and pH (7.0-10.0) conditions using antibiotics to suppress bacterial growth. Growth of the culture was monitored by microscopy, decrease in ammonium and increase in nitrite, and increases in Crenarchaeota and AOA abundances over time. Clone libraries were constructed to compare archaeal community structures before and after the enrichment experiment. Temperature and pH profiles indicated that the culture grew optimally at pH 9.0 and temperature 45 degree C, which are consistent with the geochemical conditions of the natural environment. Phylogenetic analysis showed that the final OTU was distantly related to all known hyperthermophilic archaea. Analysis of the amoA genes showed two OTUs in the final culture; one of them was closely related to Candidatus Nitrososphaera gargensis. However, the enrichment culture always contained bacteria and attempts to separate them from archaea have failed. This highlights the difficulty in bringing AOA into pure culture and suggests that some of the AOA may

  17. Ammonia loading rate: an effective variable to control partial nitrification and generate the anaerobic ammonium oxidation influent.

    PubMed

    Daalkhaijav, Uranbileg; Nemati, Mehdi

    2014-01-01

    Anaerobic ammonium oxidation (ANAMMOX) is an innovative process for the treatment of ammonia-contaminated waters. ANNAMOX is usually preceded by a nitrifying step in which ammonia is partially oxidized to nitrite. The effectiveness of the overall process depends on control of the nitrification and creation of a suitable influent for ANAMMOX. In this work, impacts of ammonia concentration and loading rate on partial nitrification and composition of the resulting effluent were investigated in continuous stirred tank (CSTR) and biofilm reactors fed with various ammonia concentrations (17.6-61.5 mM; 299-1045 ppm). Regardless of ammonia concentration, loading rates from 3.1 to 5.4mM/h in the CSTR and 6.4-12.1 mM/h in the biofilm reactor generated effluents with nitrite to ammonia ratios of 1.2 +/- 0.3 (suitable ANAMMOX influent). Under these conditions, the highest ammonia loading and nitrite production rates in the CSTR and biofilm reactors were 5.4 and 2.5 mM/h (HRT: 3.7 h) and 12.1 and 6.5 mM/h (HRT: 1.6 h), respectively. Results reveal that ammonia loading rate can be used effectively to achieve suitable ANAMMOX influent without the need for precise control of dissolved oxygen (DO). Considering the difficulty in regulating DO in large-scale systems and the need for the nitrifying process to be flexible with respect to various ammonia concentrations, the loading rate appears to be a practical option to control partial nitrification. Verifying the range of ammonia loading rates that generate ANAMMOX influent allows operation of the nitrifying step with any level of ammonia in the feed, with the proper loading rate achieved through adjustment of hydraulic residence time.

  18. Inhibition of phenol on the rates of ammonia oxidation by Nitrosomonas europaea grown under batch, continuous fed, and biofilm conditions.

    PubMed

    Lauchnor, Ellen G; Semprini, Lewis

    2013-09-01

    Ammonia oxidation by Nitrosomonas europaea, an ammonia oxidizing bacterium prevalent in wastewater treatment, is inhibited in the presence of phenol, due to interaction of the phenol with the ammonia monooxygenase enzyme. Suspended cells of N. europaea were cultured in batch reactors and continuous flow reactors at dilution rates of 0.01-0.2 d(-1). The rate of ammonia oxidation in the continuous cultures correlated to the dilution rate in the reactor. The batch and continuous cultures were exposed to 20 μM phenol and ammonia oxidation activity was measured by specific oxygen uptake rates (SOURs). Inhibition of NH3 oxidation by 20 μM phenol ranged from a 77% reduction of SOUR observed with suspended cells harvested during exponential growth, to 26% in biofilms. The extent of inhibition was correlated with ammonia oxidation rates in both suspended and biofilm cells, with greater percent inhibition observed with higher initial rates of NH3 oxidation. In biofilm grown cells, an increase in activity and phenol inhibition were both observed upon dispersing the biofilm cells into fresh, liquid medium. Under higher oxygen tension, an increase in the NO2(-) production of the biofilms was observed and biofilms were more susceptible to phenol inhibition. Dissolved oxygen microsensor measurements showed oxygen limited conditions existed in the biofilms. The ammonia oxidation rate was much lower in biofilms, which were less inhibited during phenol exposure. The results clearly indicate in both suspended and attached cells of N. europaea that a higher extent of phenol inhibition is positively correlated with a higher rate of NH3 oxidation (enzyme turnover).

  19. Correlation analysis of enzyme activities and deconstruction of ammonia-pretreated switchgrass by bacterial-fungal communities.

    PubMed

    Jain, Abhiney; Bediako, Sandra H; Henson, J Michael

    2016-10-01

    The mixed microbial communities that occur naturally on lignocellulosic feedstocks can provide feedstock-specific enzyme mixtures to saccharify lignocelluloses. Bacterial-fungal communities were enriched from switchgrass bales to deconstruct ammonia-pretreated switchgrass (DSG). Correlation analysis was carried out to elucidate the relationship between microbial decomposition of DSG by these communities, enzymatic activities produced and enzymatic saccharification of DSG using these enzyme mixtures. Results of the analysis showed that β-glucosidase and xylosidase activities limited the extent of microbial deconstruction and enzymatic saccharification of DSG. The results also underlined the importance of ligninase activity for the enzymatic saccharification of pretreated lignocellulosic feedstock. The bacterial-fungal communities developed in this research can be used to produce enzyme mixtures to deconstruct DSG, and the results from the correlation analysis can be used to optimize these enzyme mixtures for efficient saccharification of DSG to produce second-generation biofuels.

  20. Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea.

    PubMed

    Chain, Patrick; Lamerdin, Jane; Larimer, Frank; Regala, Warren; Lao, Victoria; Land, Miriam; Hauser, Loren; Hooper, Alan; Klotz, Martin; Norton, Jeanette; Sayavedra-Soto, Luis; Arciero, Dave; Hommes, Norman; Whittaker, Mark; Arp, Daniel

    2003-05-01

    Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea participates in the biogeochemical N cycle in the process of nitrification. Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with approximately 47% transcribed from one strand and approximately 53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO(2) and NH(3) assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of N. europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria.

  1. Dynamics of ammonia-oxidizing Archaea and Bacteria in contrasted freshwater ecosystems.

    PubMed

    Hugoni, Mylène; Etien, Sandrine; Bourges, Antoine; Lepère, Cécile; Domaizon, Isabelle; Mallet, Clarisse; Bronner, Gisèle; Debroas, Didier; Mary, Isabelle

    2013-05-01

    Thaumarchaeota have been recognized as the main drivers of aerobic ammonia oxidation in many ecosystems. However, little is known about the role of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in lacustrine ecosystems. In this study, the photic zone of three contrasted freshwater ecosystems located in France was sampled during two periods: winter homothermy (H) and summer thermal stratification (TS), to investigate the distribution of planktonic AOA and AOB. We showed that AOB were predominant in nutrient-rich ecosystems, whereas AOA dominated when ammonia concentrations were the lowest and during winter, which could provide a favorable environment for their growth. Moreover, analyses of archaeal libraries revealed the ubiquity of the thaumarchaeal I.1a clade associated with higher diversity of AOA in the most nutrient-poor lake. More generally, this work assesses the presence of AOA in lakes, but also highlights the existence of clades typically associated with lacustrine and hot spring ecosystems and specific ecological niches occupied by these microorganisms. Copyright © 2013. Published by Elsevier Masson SAS.

  2. [Effect of ammonia-oxidizing bacteria (AOB) on chloraminated disinfection attenuation in drinking water distribution system].

    PubMed

    Bai, Xiao-Hui; Cai, Yun-Long; Zhou, Bin-Hui; Zhi, Xing-Hua

    2009-06-15

    The growth of microbe and formation of biofilm in water distribution system were important factors affecting the security of water quality. The number of ammonia-oxidizing bacteria (AOB) in biofilm of a chloraminated drinking water distribution system in Shanghai was detected by MPN-Griess method, and the relations among AOB, nitrification and chloraminated disinfection were analyzed. Meanwhile, the effects of AOB on chloraminated disinfection fastness and attenuation by simulation experiment were studied. The result indicated that the number of ammonia-oxidizing bacteria in pipe biofilm was between 1.0 x 10(2)-4.3 x 10(5) MPN/g dry biofilm. Correlation coefficients of AOB with ammonia, nitrite and nitrate were -0.563, 0.603 and -0.563. Correlation coefficients of AOB with total chlorine and mono-chloramine were -0.659 and -0.571. Fastness of AOB to chloramine was higher than heterotrophic bacteria and AOB can deplete more chloramine than HPC.

  3. Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea†

    PubMed Central

    Chain, Patrick; Lamerdin, Jane; Larimer, Frank; Regala, Warren; Lao, Victoria; Land, Miriam; Hauser, Loren; Hooper, Alan; Klotz, Martin; Norton, Jeanette; Sayavedra-Soto, Luis; Arciero, Dave; Hommes, Norman; Whittaker, Mark; Arp, Daniel

    2003-01-01

    Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea participates in the biogeochemical N cycle in the process of nitrification. Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with ∼47% transcribed from one strand and ∼53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO2 and NH3 assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of N. europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria. PMID:12700255

  4. Nitrogen and phosphorus enrichment alter the composition of ammonia-oxidizing bacteria in salt marsh sediments.

    PubMed

    Lage, Melissa D; Reed, Heather E; Weihe, Claudia; Crain, Caitlin M; Martiny, Jennifer B H

    2010-07-01

    Ammonia oxidation is a central process in the nitrogen cycle. Particularly in marine and estuarine environments, few experiments have been conducted to tease apart the factors influencing their abundance and composition. To investigate the effect of nitrogen and phosphorus availability on ammonia-oxidizing bacteria (AOB), we conducted a nutrient enrichment experiment in a Maine salt marsh and sampled sediment communities in three seasons over 2 years. We assessed community composition using terminal restriction fragment length polymorphism analysis and sequencing of cloned fragments of the ammonia monooxygenase (amoA) gene. Almost all of the amoA sequences fell within the marine and estuarine-specific Nitrosospira-like clade. Applied separately, nitrogen and phosphorus significantly altered AOB composition; however, together the nutrients had an interactive effect, and composition did not change. In contrast, nutrient enrichment did not alter AOB abundance. Furthermore, the response of AOB composition to nutrient enrichment varied over time. We conclude that closely related taxa within the marine/estuarine-specific Nitrosospira-like clade vary in their preference for nutrient concentrations, and this preference may depend on other temporally variable abiotic factors. Finally, AOB composition was highly variable within and across years even in untreated plots. Further studies are needed to test how these different aspects of compositional variability in AOB communities influence nitrogen cycling.

  5. Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions.

    PubMed

    Di, Hong J; Cameron, Keith C; Shen, Ju-Pei; Winefield, Chris S; O'Callaghan, Maureen; Bowatte, Saman; He, Ji-Zheng

    2010-06-01

    Nitrification is a key process of the nitrogen (N) cycle in soil with major environmental implications. The recent discovery of ammonia-oxidizing archaea (AOA) questions the traditional assumption of the dominant role of ammonia-oxidizing bacteria (AOB) in nitrification. We investigated AOB and AOA growth and nitrification rate in two different layers of three grassland soils treated with animal urine substrate and a nitrification inhibitor [dicyandiamide (DCD)]. We show that AOB were more abundant in the topsoils than in the subsoils, whereas AOA were more abundant in one of the subsoils. AOB grew substantially when supplied with a high dose of urine substrate, whereas AOA only grew in the Controls without the urine-N substrate. AOB growth and the amoA gene transcription activity were significantly inhibited by DCD. Nitrification rates were much higher in the topsoils than in the subsoils and were significantly related to AOB abundance, but not to AOA abundance. These results suggest that AOB and AOA prefer different soil N conditions to grow: AOB under high ammonia (NH(3)) substrate and AOA under low NH(3) substrate conditions.

  6. Molecular Analysis of Ammonia-Oxidizing Bacteria of the β Subdivision of the Class Proteobacteria in Compost and Composted Materials

    PubMed Central

    Kowalchuk, George A.; Naoumenko, Zinaida S.; Derikx, Piet J. L.; Felske, Andreas; Stephen, John R.; Arkhipchenko, Irina A.

    1999-01-01

    Although the practice of composting animal wastes for use as biofertilizers has increased in recent years, little is known about the microorganisms responsible for the nitrogen transformations which occur in compost and during the composting process. Ammonia is the principle available nitrogenous compound in composting material, and the conversion of this compound to nitrite in the environment by chemolithotrophic ammonia-oxidizing bacteria is an essential step in nitrogen cycling. Therefore, the distribution of ammonia-oxidizing members of the β subdivision of the class Proteobacteria in a variety of composting materials was assessed by amplifying 16S ribosomal DNA (rDNA) and 16S rRNA by PCR and reverse transcriptase PCR (RT-PCR), respectively. The PCR and RT-PCR products were separated by denaturing gradient gel electrophoresis (DGGE) and were identified by hybridization with a hierarchical set of oligonucleotide probes designed to detect ammonia oxidizer-like sequence clusters in the genera Nitrosospira and Nitrosomonas. Ammonia oxidizer-like 16S rDNA was detected in almost all of the materials tested, including industrial and experimental composts, manure, and commercial biofertilizers. A comparison of the DGGE and hybridization results after specific PCR and RT-PCR suggested that not all of the different ammonia oxidizer groups detected in compost are equally active. amoA, the gene encoding the active-site-containing subunit of ammonia monooxygenase, was also targeted by PCR, and template concentrations were estimated by competitive PCR. Detection of ammonia-oxidizing bacteria in the composts tested suggested that such materials may not be biologically inert with respect to nitrification and that the fate of nitrogen during composting and compost storage may be affected by the presence of these organisms. PMID:9925559

  7. 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.

  8. Distribution of sediment ammonia-oxidizing microorganisms in plateau freshwater lakes.

    PubMed

    Liu, Yong; Zhang, Jingxu; Zhao, Lei; Li, Yuzhao; Dai, Yu; Xie, Shuguang

    2015-05-01

    Both ammonia-oxidizing bacteria (AOB) and archaea (AOA) can play important roles in ammonia biotransformation in ecosystems. However, the factors regulating the distribution of these microorganisms in lacustrine ecosystems remain essentially unclear. The present study investigated the effects of geographic location on the distribution of sediment AOA and AOB in 13 freshwater lakes on the Yunnan Plateau (China). The spatial dissimilarity in the abundance and structure of sediment AOA and AOB communities was observed in these plateau lakes. AOA abundance was usually less than AOB abundance, and the AOA/AOB ratio was positively correlated with water depth. Nitrososphaera-like AOA occurred in most of the studied lakes and were dominant in two lakes. Nitrosospira was the dominant AOB species in most of the lakes, while Nitrosomonas showed high abundance only in three lakes. In addition, geographic location was found to affect lake sediment AOB community structure.

  9. Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.

    PubMed

    Sauder, Laura A; Albertsen, Mads; Engel, Katja; Schwarz, Jasmin; Nielsen, Per H; Wagner, Michael; Neufeld, Josh D

    2017-05-01

    Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1-2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown

  10. Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system

    PubMed Central

    Sauder, Laura A; Albertsen, Mads; Engel, Katja; Schwarz, Jasmin; Nielsen, Per H; Wagner, Michael; Neufeld, Josh D

    2017-01-01

    Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1–2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown

  11. 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

  12. Growth of Nitrosococcus-Related Ammonia Oxidizing Bacteria Coincides with Extremely Low pH Values in Wastewater with High Ammonia Content

    PubMed Central

    2017-01-01

    Ammonia oxidation decreases the pH in wastewaters where alkalinity is limited relative to total ammonia. The activity of ammonia oxidizing bacteria (AOB), however, typically decreases with pH and often ceases completely in slightly acidic wastewaters. Nevertheless, nitrification at low pH has been reported in reactors treating human urine, but it has been unclear which organisms are involved. In this study, we followed the population dynamics of ammonia oxidizing organisms and reactor performance in synthetic fully hydrolyzed urine as the pH decreased over time in response to a decrease in the loading rate. Populations of the β-proteobacterial Nitrosomonas europaea lineage were abundant at the initial pH close to 6, but the growth of a possibly novel Nitrosococcus-related AOB genus decreased the pH to the new level of 2.2, challenging the perception that nitrification is inhibited entirely at low pH values, or governed exclusively by β-proteobacterial AOB or archaea. With the pH shift, nitrite oxidizing bacteria were not further detected, but nitrous acid (HNO2) was still removed through chemical decomposition to nitric oxide (NO) and nitrate. The growth of acid-tolerant γ-proteobacterial AOB should be prevented, by keeping the pH above 5.4, which is a typical pH limit for the N. europaea lineage. Otherwise, the microbial community responsible for high-rate nitrification can be lost, and strong emissions of hazardous volatile nitrogen compounds such as NO are likely. PMID:28509546

  13. Formation of manganese oxides by bacterially generated superoxide

    NASA Astrophysics Data System (ADS)

    Learman, D. R.; Voelker, B. M.; Vazquez-Rodriguez, A. I.; Hansel, C. M.

    2011-02-01

    Manganese oxide minerals are among the strongest sorbents and oxidants in the environment. The formation of these minerals controls the fate of contaminants, the degradation of recalcitrant carbon, the cycling of nutrients and the activity of anaerobic-based metabolisms. Oxidation of soluble manganese(II) ions to manganese(III/IV) oxides has been primarily attributed to direct enzymatic oxidation by microorganisms. However, the physiological reason for this process remains unknown. Here we assess the ability of a common species of marine bacteria-Roseobacter sp. AzwK-3b-to oxidize manganese(II) in the presence of chemical and biological inhibitors. We show that Roseobacter AzwK-3b oxidizes manganese(II) by producing the strong and versatile redox reactant superoxide. The oxidation of manganese(II), and concomitant production of manganese oxides, was inhibited in both the light and dark in the presence of enzymes and metals that scavenge superoxide. Oxidation was also inhibited by various proteases, enzymes that break down bacterial proteins, confirming that the superoxide was bacterially generated. We conclude that bacteria can oxidize manganese(II) indirectly, through the enzymatic generation of extracellular superoxide radicals. We suggest that dark bacterial production of superoxide may be a driving force in metal cycling and mineralization in the environment.

  14. A rapid and simple respirometric biosensor with immobilized cells of Nitrosomonas europaea for detecting inhibitors of ammonia oxidation.

    PubMed

    Cui, Rong; Chung, Wook-Jin; Jahng, Deokjin

    2005-03-15

    As obligate chemolithotrophs, ammonia-oxidizing bacteria (AOB) grow very slowly and are known to be extremely sensitive to a wide variety of inhibitors. Since it is generally accepted that inhibition of ammonia oxidation by AOB results in a total failure of nitrogen removal, it is necessary to develop a method to detect inhibitors of ammonia oxidation in wastewater. Since ammonia oxidation accompanies oxygen consumption, ammonia oxidation can be easily evaluated by measuring oxygen consumption rate using a dissolved oxygen (DO) probe. In this study, a rapid and simple respirometric biosensor using the pure culture of Nitrosomonas europaea was developed. N. europaea was cultivated in a continuous fermentor operating at the dilution rate of 0.008 h(-1) to obtain physiologically constant cells and was immobilized onto the dialysis membrane through filtration. DO, determined by the biosensor, started to increase 30 s later after ammonia oxidation inhibitor was fed, and a new steady-state DO was obtained in 10-30 min. For this DO profile, steady-state kinetics was applied to evaluate ammonia oxidation efficiency. The concentration of a toxic compound causing 50% decrease of oxygen-consumption activity (EC50) was determined for different chemicals. The EC50 values obtained with the biosensor (0.018 mg l(-1) for allylthiourea, 0.027 mg l(-1) for thioacetamide, 1.10 mg l(-1) for phenol and 0.0 1mg l(-1) for thiourea) indicated that the developed biosensor was highly sensitive to a variety of the inhibitors. It was also shown that the biosensor is applicable for on-line real time monitoring.

  15. 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

  16. Acidification Enhances Hybrid N2O Production Associated with Aquatic Ammonia-Oxidizing Microorganisms

    PubMed Central

    Frame, Caitlin H.; Lau, Evan; Nolan, E. Joseph; Goepfert, Tyler J.; Lehmann, Moritz F.

    2017-01-01

    Ammonia-oxidizing microorganisms are an important source of the greenhouse gas nitrous oxide (N2O) in aquatic environments. Identifying the impact of pH on N2O production by ammonia oxidizers is key to understanding how aquatic greenhouse gas fluxes will respond to naturally occurring pH changes, as well as acidification driven by anthropogenic CO2. We assessed N2O production rates and formation mechanisms by communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in a lake and a marine environment, using incubation-based nitrogen (N) stable isotope tracer methods with 15N-labeled ammonium (15NH4+) and nitrite (15NO2−), and also measurements of the natural abundance N and O isotopic composition of dissolved N2O. N2O production during incubations of water from the shallow hypolimnion of Lake Lugano (Switzerland) was significantly higher when the pH was reduced from 7.54 (untreated pH) to 7.20 (reduced pH), while ammonia oxidation rates were similar between treatments. In all incubations, added NH4+ was the source of most of the N incorporated into N2O, suggesting that the main N2O production pathway involved hydroxylamine (NH2OH) and/or NO2− produced by ammonia oxidation during the incubation period. A small but significant amount of N derived from exogenous/added 15NO2− was also incorporated into N2O, but only during the reduced-pH incubations. Mass spectra of this N2O revealed that NH4+ and 15NO2− each contributed N equally to N2O by a “hybrid-N2O” mechanism consistent with a reaction between NH2OH and NO2−, or compounds derived from these two molecules. Nitrifier denitrification was not an important source of N2O. Isotopomeric N2O analyses in Lake Lugano were consistent with incubation results, as 15N enrichment of the internal N vs. external N atoms produced site preferences (25.0–34.4‰) consistent with NH2OH-dependent hybrid-N2O production. Hybrid-N2O formation was also observed during incubations of seawater from coastal Namibia

  17. High-rate, high-yield production of methanol by ammonia-oxidizing bacteria.

    PubMed

    Taher, Edris; Chandran, Kartik

    2013-04-02

    The overall goal of this study was to develop an appropriate biological process for achieving autotrophic conversion of methane (CH(4)) to methanol (CH3OH). In this study, we employed ammonia-oxidizing bacteria (AOB) to selectively and partially oxidize CH(4) to CH(3)OH. In fed-batch reactors using mixed nitrifying enrichment cultures from a continuous bioreactor, up to 59.89 ± 1.12 mg COD/L of CH(3)OH was produced within an incubation time of 7 h, which is approximately ten times the yield obtained previously using pure cultures of Nitrosomonas europaea. The maximum specific rate of CH(4) to CH(3)OH conversion obtained during this study was 0.82 mg CH(3)OH COD/mg AOB biomass COD-d, which is 1.5 times the highest value reported with pure cultures. Notwithstanding these positive results, CH(4) oxidation to CH(3)OH by AOB was inhibited by NH(3) (the primary substrate for the oxidative enzyme, ammonia monooxygenase, AMO) as well as the product, CH(3)OH, itself. Further, oxidation of CH(4) to CH(3)OH by AOB was also limited by reducing equivalents supply, which could be overcome by externally supplying hydroxylamine (NH(2)OH) as an electron donor. Therefore, a potential optimum design for promoting CH(4) to CH(3)OH oxidation by AOB could involve supplying NH(3) (needed to maintain AMO activity) uncoupled from the supply of NH(2)OH and CH(4). Partial oxidation of CH(4)-containing gases to CH3OH by AOB represents an attractive platform for the conversion of a gaseous mixture to an aqueous compound, which could be used as a commodity chemical. Alternately, the nitrate and CH(3) OH thus produced could be channeled to a downstream anoxic zone in a biological nitrogen removal process to effect nitrate reduction to N(2), using an internally produced organic electron donor.

  18. Archaeal amoA gene diversity points to distinct biogeography of ammonia-oxidizing Crenarchaeota in the ocean.

    PubMed

    Sintes, Eva; Bergauer, Kristin; De Corte, Daniele; Yokokawa, Taichi; Herndl, Gerhard J

    2013-05-01

    Mesophilic ammonia-oxidizing Archaea (AOA) are abundant in a diverse range of marine environments, including the deep ocean, as revealed by the quantification of the archaeal amoA gene encoding the alpha-subunit of the ammonia monooxygenase. Using two different amoA primer sets, two distinct ecotypes of marine Crenarchaeota Group I (MCGI) were detected in the waters of the tropical Atlantic and the coastal Arctic. The HAC-AOA ecotype (high ammonia concentration AOA) was ≈ 8000 times and 15 times more abundant in the coastal Arctic and the top 300 m layer of the open equatorial Atlantic, respectively, than the LAC-AOA (low ammonia concentration AOA) ecotype. In contrast, the LAC-AOA ecotype dominated the lower meso- and bathypelagic waters of the tropical Atlantic (≈ 50 times more abundant than the HAC-AOA) where ammonia concentrations are well below the detection limit using conventional spectrophotometric or fluorometric methods. Cluster analysis of the sequences from the clone libraries obtained by the two amoA primer sets revealed two phylogenetically distinct clusters. Taken together, our results suggest the presence of two ecotypes of archaeal ammonia oxidizers corresponding to the medium (1.24 µM on average in the coastal Arctic) and low ammonia concentration (< 0.01 µM) in the shallow and the deep waters respectively.

  19. Biodegradation of BOD and ammonia-free using bacterial consortium in aerated fixed film bioreactor (AF2B)

    NASA Astrophysics Data System (ADS)

    Prayitno, Rulianah, Sri; Saroso, Hadi; Meilany, Diah

    2017-06-01

    BOD and Ammonia-free (NH3-N) are pollutants of hospital wastewater which often exceed the quality standards. It is because biological processes in wastewater treatment plant (WWTP) have not been effective in degrading BOD and NH3-N. Therefore, a study on factors that influence the biodegradation of BOD and NH3-N by choosing the type of bacteria to improve the mechanisms of biodegradation processes is required. Bacterial consortium is a collection of several types of bacteria obtained from isolation process, which is known to be more effective than a single bacterial in degrading pollutants. On the other hand, AF2B is a type of reactor in wastewater treatment system. The AF2B contains a filter media that has a large surface area so that the biodegradation process of pollutants by microorganism can be improved. The objective of this research is to determine the effect of volume of starter and air supplies on decreasing BOD and NH3-N in hospital wastewater using bacterial consortium in the AF2B on batch process. The research was conducted in three stages: the making of the growth curve of the bacterial consortium, bacterial consortium acclimatization, and hospital wastewater treatment in the AF2B with batch process. The variables used are the volume of starter (65%, 75%, and 85% in volume) and air supplies (2.5, 5, and 7.5 L/min). Meanwhile, the materials used are hospital wastewater, bacterial consortium (Pseudomonas diminuta, Pseudomonas capica, Bacillius sp, and Nitrobacter sp), blower, and AF2B. AF2B is a plastic basin containing a filter media with a wasp-nest shape used as a medium for growing the bacterial consortium. In the process of making the growth curve, a solid form of bacterial consortium was dissolved in sterilized water, then grown in a nutrient broth (NB). Then, shaking and sampling were done at any time to determine the path growth of bacterial consortium. In the acclimatization process, bacterial isolates were grown using hospital wastewater as a

  20. Active ammonia oxidizers in an acidic soil are phylogenetically closely related to neutrophilic archaeon.

    PubMed

    Wang, Baozhan; Zheng, Yan; Huang, Rong; Zhou, Xue; Wang, Dongmei; He, Yuanqiu; Jia, Zhongjun

    2014-03-01

    All cultivated ammonia-oxidizing archaea (AOA) within the Nitrososphaera cluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence of Nitrososphaera-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth of Nitrososphaera-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of amoA genes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the "heavy" DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that (13)CO2 assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both (13)C-labeled amoA and 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strains Nitrososphaera viennensis EN76 and JG1 within the Nitrososphaera cluster. Our results provide strong evidence for the adaptive growth of Nitrososphaera-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated.

  1. Active Ammonia Oxidizers in an Acidic Soil Are Phylogenetically Closely Related to Neutrophilic Archaeon

    PubMed Central

    Wang, Baozhan; Zheng, Yan; Huang, Rong; Zhou, Xue; Wang, Dongmei; He, Yuanqiu

    2014-01-01

    All cultivated ammonia-oxidizing archaea (AOA) within the Nitrososphaera cluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence of Nitrososphaera-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth of Nitrososphaera-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of amoA genes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the “heavy” DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that 13CO2 assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both 13C-labeled amoA and 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strains Nitrososphaera viennensis EN76 and JG1 within the Nitrososphaera cluster. Our results provide strong evidence for the adaptive growth of Nitrososphaera-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated. PMID:24375137

  2. Ecophysiological Characterization of Ammonia-Oxidizing Archaea and Bacteria from Freshwater

    PubMed Central

    French, Elizabeth; Kozlowski, Jessica A.; Mukherjee, Maitreyee; Bullerjahn, George

    2012-01-01

    Aerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with “Candidatus Nitrosoarchaeum koreensis” and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail. PMID:22685142

  3. Ecophysiological characterization of ammonia-oxidizing archaea and bacteria from freshwater.

    PubMed

    French, Elizabeth; Kozlowski, Jessica A; Mukherjee, Maitreyee; Bullerjahn, George; Bollmann, Annette

    2012-08-01

    Aerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with "Candidatus Nitrosoarchaeum koreensis" and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from the Nitrosomonas oligotropha group (Nitrosomonas cluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.

  4. 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

  5. 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.

  6. Impact of streambed morphology on the abundance and activity of ammonia-oxidizing bacteria.

    PubMed

    Yanuka-Golub, Keren; Arnon, Shai; Nejidat, Ali

    2014-10-01

    Ammonia oxidizers catalyze the first step of nitrification. Combined microbial nitrification-denitrification activities are essential for the removal of excess nitrogen from water bodies. In sandy streambeds, bed form structures are created by water flow and lead to the creation of heterogeneous microenvironments. The objective of this study, therefore, was to investigate the effect of bed form morphology on the abundance and activity of ammonia-oxidizing bacteria (AOB) within a benthic biofilm. An 8-month-old benthic biofilm was established in a recirculating laboratory flume under controlled flow conditions and frequent amendment with ammonium. The sand bed was arranged into bed form structures. The highest concentrations of chlorophyll a (indicative of algae) were measured on the upstream side of the bed forms. The biofilm was dominated by Nitrosospira species, and amoA gene abundance was higher on the downstream sides of the bed forms with no significant difference in oxygen consumption between the upstream and downstream sections of the bed form. In contrast, potential ammonium oxidation rates were higher on the upstream sides of the bed forms. The results suggest that bed form morphology can affect the spatial distribution and activity of AOB, possibly through the creation of distinct microhabitats. These results contribute to our understanding of nitrogen transformations and removal from streams.

  7. [Ammonia-oxidizing bacteria community composition at the root zones of aquatic plants after ecological restoration].

    PubMed

    Xing, Peng; Kong, Fan-xiang; Chen, Kai-ning; Chen, Mei-jun; Wu, Xiao-dong

    2008-08-01

    To investigate the effects of aquatic plants on ammonia-oxidizing bacteria (AOB) at their root zones, four species of aquatic plants were selected, Phragmites communis, Typha angustifolia L., Potamogeton crispus L., and Limnanthemun nymphoides, which were widely used in ecological restorations. AOB in the samples were enumerated by most-probable-number (MPN) method. Nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) procedures were performed with ammonia oxidizer-selective primers. Main DGGE bands were excised from the gel and sequenced for phylogenetic affiliation. Results indicate that AOB densities are always higher at the root zones of emergent plants (Phragmites communis 2.8 x 10(5) cells/g and Typha angustifolia L.4.3 x 10(5) cells/g) than those of submerged and floating-leaved plant (Potamogeton crispus L. 9.3 x 10(4) cells/g and Limnanthemun nymphoides 7.7 x 10(4) cells/g). At the root zones, the oxidation-reduction potential is above zero and NH4+ concentration is lower than it in the bare surface sediment. Fourteen major bands were recovered from the DGGE gel, re-amplified and sequenced. Although the identified bands have their respective similar sequences in GenBank, most of them are related to Nitrosomonas-like. This type of bacteria would play an important role of nitrogen cycle in lake sediment after ecological restoration.

  8. [Community diversity of ammonia-oxidizing bacteria of three plants rhizosphere in Ebinur Lake wetland].

    PubMed

    Wang, Cuihua; Wu, Fei; Hu, Wenge; Mo, Chao; Zhang, Xiaohong

    2015-09-04

    In order to study the community diversity of rhizosphere soil ammonia-oxidizing bacteria, Halocnemum strobilaceum, Reed and Salicornia in Ebinur Lake Wetland were investigated. The clone libraries of amoA gene were constructed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and phylogenetics were analyzed. To explore the community structure of rhizosphere amomonia-oxidizing bacteria, we combined rhizosphere physicochemical factors of the three plants. Phylogenetic analysis of the amoA gene fragments showed that all of AOB sequences from shrimp of three plants rhizosphere were affiliated with Nitrosomonas or Nitrosomonas-like phyla, Nitrosospira phyla was not discovered. Three plants rhizosphere composition includes 9 OTUs,12 OTUs and 7 OTUs respectively. Coverages of all libraries of the three plants rhizosphere were over 99% and strongly representative. The richness index, chao1 index, ACE index and Shannon index of the three libraries were as follows, Reed rhizosphere AOB was much higher than Halocnemum strobilaceum rhizosphere AOB, and Salicornia rhizosphere AOB was the lowest. This study provides a basis for understanding the community diversity and structure of rhizosphere soil ammonia-oxidizing bacteria in Ebinur Lake wetland.

  9. Gas sensors based on polyaniline/zinc oxide hybrid film for ammonia detection at room temperature

    NASA Astrophysics Data System (ADS)

    Zhu, Guotao; Zhang, Qiuping; Xie, Guangzhong; Su, Yuanjie; Zhao, Kang; Du, Hongfei; Jiang, Yadong

    2016-11-01

    Polyaniline/zinc oxide (PANI/ZnO) hybrid film based sensors have been developed for ammonia (NH3) detection at room temperature (RT). Results shows that hybrid film sensor exhibits a p-type semiconductor behavior and larger response than that of pure PANI film sensor. In the system, ZnO nanorod arrays can not only create nanoscale gap for gas diffusion but also provide abundant adsorption sites, thus leading to enhancement of response. Besides, hydrothermal time is proportional to the length of nanorods, Longer nanorods will provide efficient gap for gas diffusion, which leads to better sensitivity. This work offers a promising way to optimize sensor performance.

  10. Controllable synthesis of silver nanoparticle-decorated reduced graphene oxide hybrids for ammonia detection.

    PubMed

    Cui, Shumao; Mao, Shun; Wen, Zhenhai; Chang, Jingbo; Zhang, Yang; Chen, Junhong

    2013-05-21

    We demonstrate controllable fabrication of Ag nanoparticle (NP)-decorated reduced graphene oxide (RGO/Ag) hybrids and their application for fast and selective detection of ammonia at room temperature. Ag NPs greatly improved the sensitivity of RGO. The response time (6 s) and recovery time (10 s) are comparable with our previous Ag NP-decorated multiwalled carbon nanotube (MWCNT/Ag) NH3 sensors; however, the sensitivity is about twice that of MWCNT/Ag hybrids. We found that the loading density of NPs greatly affects the sensing performance of RGO/Ag hybrids and a proper NP loading leads to maximum sensitivity.

  11. Denitrification and ammonia oxidation by Nitrosomonas europaea wild-type, and NirK- and NorB-deficient mutants.

    PubMed

    Schmidt, Ingo; van Spanning, Rob J M; Jetten, Mike S M

    2004-12-01

    The phenotypes of three different Nitrosomonas europaea strains--wild-type, nitrite reductase (NirK)-deficient and nitric oxide reductase (NorB)-deficient strains--were characterized in chemostat cell cultures, and the effect of nitric oxide (NO) on metabolic activities was evaluated. All strains revealed similar aerobic ammonia oxidation activities, but the growth rates and yields of the knock-out mutants were significantly reduced. Dinitrogen (N2) was the main gaseous product of the wild-type, produced via its denitrification activity. The mutants were unable to reduce nitrite to N2, but excreted more hydroxylamine leading to the formation of almost equal amounts of NO, nitrous oxide (N2O) and N2 by chemical auto-oxidation and chemodenitrification of hydroxylamine. Under anoxic conditions Nsm. europaea wild-type gains energy for growth via nitrogen dioxide (NO2)-dependent ammonia oxidation or hydrogen-dependent denitrification using nitrite as electron acceptor. The mutant strains were restricted to NO and/or N2O as electron acceptor and consequently their growth rates and yields were much lower compared with the wild-type. When cells were transferred from anoxic (denitrification) to oxic conditions, the wild-type strain endogenously produced NO and recovered ammonia oxidation within 8 h. In contrast, the mutant strains remained inactive. For recovery of ammonia oxidation activity the NO concentration had to be adjusted to about 10 p.p.m. in the aeration gas.

  12. 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 Tha