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Sample records for nirk denitrifying genes

  1. Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers

    OpenAIRE

    2016-01-01

    Background Copper dependent nitrite reductase, NirK, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. Distinct structural NirK classes and phylogenetic clades of NirK-type denitrifiers have previously been observed based on a limited set of NirK sequences, however, their environmental distribution or ecological strategies are currently unknown. In addition, environmental nirK-type denitrifiers are currently underestimated in PCR-dependent surveys due to prime...

  2. Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples

    Energy Technology Data Exchange (ETDEWEB)

    Braker, G.; Witzel, K.P. [Max-Planck-Inst. fuer Limnologie, Ploen (Germany); Fesefeldt, A. [Univ. Kiel (Germany). Inst. fuer Allgemeine Mikrobiologie

    1998-10-01

    A system was developed for the detection of denitrifying bacteria by the application of specific nitrite reductase gene fragments with PCR. Primer sequences were found for the amplification of fragments from both nitrite reductase genes (nirK and nirS) after comparative sequence analysis. Whenever amplification was tried with these primers, the known nir type of denitrifying laboratory cultures could be confirmed. Likewise, the method allowed a determination of the nir type of five laboratory strains. The nirK gene could be amplified from Blastobacter denitrificans, Alcaligenes xylosoxidans, and Alcaligenes sp. (DSM 30128); the nirS gene was amplified from Alcaligenes eutrophus DSM 530 and from the denitrifying isolate IFAM 3698. For each of the two genes, at least one primer combination amplified successfully for all of the test strains. Specific amplification products were not obtained wit h nondenitrifying bacteria or with strains of the other nir type. The specificity of the amplified products was confirmed by subsequent sequencing. These results suggest the suitability of the method for the qualitative detection of denitrifying bacteria in environmental samples. This was shown by applying the generally amplifying primer combination for each nir gene developed in this study to total DNA preparations from aquatic habitats.

  3. The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers.

    Science.gov (United States)

    Heylen, Kim; Gevers, Dirk; Vanparys, Bram; Wittebolle, Lieven; Geets, Joke; Boon, Nico; De Vos, Paul

    2006-11-01

    Gene sequence analysis of nirS and nirK, both encoding nitrite reductases, was performed on cultivated denitrifiers to assess their incidence in different bacterial taxa and their taxonomical value. Almost half of the 227 investigated denitrifying strains did not render an nir amplicon with any of five previously described primers. NirK and nirS were found to be prevalent in Alphaproteobacteria and Betaproteobacteria, respectively, nirK was detected in the Firmicutes and Bacteroidetes and nirS and nirK with equal frequency in the Gammaproteobacteria. These observations deviated from the hitherto reported incidence of nir genes in bacterial taxa. NirS gene phylogeny was congruent with the 16S rRNA gene phylogeny on family or genus level, although some strains did group within clusters of other bacterial classes. Phylogenetic nirK gene sequence analysis was incongruent with the 16S rRNA gene phylogeny. NirK sequences were also found to be significantly more similar to nirK sequences from the same habitat than to nirK sequences retrieved from highly related taxa. This study supports the hypothesis that horizontal gene transfer events of denitrification genes have occurred and underlines that denitrification genes should not be linked with organism diversity of denitrifiers in cultivation-independent studies.

  4. Impact of Long-Term Fertilization on Community Structure of Ammonia Oxidizing and Denitrifying Bacteria Based on amoA and nirK Genes in a Rice Paddy from Tai Lake Region, China

    Institute of Scientific and Technical Information of China (English)

    JIN Zhen-jiang; LI Lian-qing; LIU Xiao-yu; PAN Gen-xing; Qaiser Hussein; LIU Yong-zhuo

    2014-01-01

    Ammonia oxidizing (AOB) and denitrifying bacteria (DNB) play an important role in soil nitrogen transformation in natural and agricultural ecosystems. Effects of long-term fertilization on abundance and community composition of AOB and DNB were studied with targeting ammonia monooxygenase (amoA) and nitrite reductase (nirK) genes using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR, respectively. A ifeld trial with different fertilization treatments in a rice paddy from Tai Lake region, centre East China was used in this study, including no fertilizer application (NF), balanced chemical fertilizers (CF), combined organic/inorganic fertilizer of balanced chemical fertilizers plus pig manure (CFM), and plus rice straw return (CFS). The abundances and richnesses of amoA and nirK were increased in CF, CFM and CFS compared to NF. Principle component analysis of DGGE proifles showed signiifcant difference in nirK and amoA genes composition between organic amended (CFS and CFM) and the non-organic amended (CF and NF) plots. Number of amoA copies was signiifcantly positively correlated with normalized soil nutrient richness (NSNR) of soil organic carbon (SOC) and total nitrogen (T-N), and that of nirK copies was with NSNR of SOC, T-N plus total phosphorus. Moreover, nitriifcation potential showed a positive correlation with SOC content, while a signiifcantly lower denitriifcation potential was found under CFM compared to under CFS. Therefore, SOC accumulation accompanied with soil nutrient richness under long-term balanced and organic/inorganic combined fertilization promoted abundance and diversity of AOB and DNB in the rice paddy.

  5. Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils

    DEFF Research Database (Denmark)

    Priemé, Anders; Braker, Gesche; Tiedje, James M.

    2002-01-01

    The genetic heterogeneity of nitrite reductase gene (nirK and nirS) fragments from denitrifying prokaryotes in forested upland and marsh soil was investigated using molecular methods. nirK gene fragments could be amplified from both soils, whereas nirS gene fragments could be amplified only from...... the marsh soil. PCR products were cloned and screened by restriction fragment length polymorphism (RFLP), and representative fragments were sequenced. The diversity of nirK clones was lower than the diversity of nirS clones. Among the 54 distinct nirK RFLP patterns identified in the two soils, only one...... marsh clones and all upland clones. Only a few of the nirK clone sequences branched with those of known denitrifying bacteria. The nirS clones formed two major clusters with several subclusters, but all nirS clones showed less than 80% identity to nirS sequences from known denitrifying bacteria. Overall...

  6. The effect of nitrate addition on abundance of nirK, nirS and gln genes in acidified Norway spruce forest soil

    Science.gov (United States)

    Bárta, Jiří; Tahovská, Karolina; Kaåa, Jiří; Antrå¯Čková, Hana Å.

    2010-05-01

    The denitrification is the main biotic process leading to loses of fixed nitrogen as well as removal of excess of nitrate (NO3-) from the soil environment. The reduction of NO2- to nitric oxide (NO) distinguishes the 'true' denitrifiers from other nitrate-respiring bacteria. This reaction is catalyzed by two different types of nitrite reductases, either a cytochrome cd1 encoded by nirS gene (nirS denitrifiers) or a Cu-containing enzyme encoded by nirK gene (nirK denitrifiers). The nirS denitrifiers are located mostly in rhizosphere, while the nirK denitrifiers are more abundant in bulk soil. These two groups can be also classified as markers of denitrification. Glutamine synthetase is one of the main bacterial NH4+ assimilating enzymes; it is coded by glnI gene. Glutamine synthetase is mostly active when N is the limiting factor for bacterial growth. There is recent evidence that the activity may be affected by the presence of alternative N source (i.e. NO3-). However, in anaerobic condition NO3- can be used also by the denitrifying bacteria so there may be strong competition for this nutrient. The laboratory experiment was performed to evaluate the effect of nitrates (NO3-) on abundance of nirK, nirS and gln gene copy numbers. The amount of NO3- corresponded to the actual atmospheric depositions on experimental sites in the Bohemian Forest. Litter organic layer (0-5cm of soil) was used for laboratory incubation experiment. Four replicates of control (no addition of NO3-), and NO3-addition were incubated anaerobically for one month. After the incubation DNA was extracted and the number of nirK, nirS and gln gene copies was determined using qPCR (SYBRGreen methodology). Results showed that the addition of NO3- significantly increased the number of nirK and nirS denitrifiers from 5.9x106 to 1.1x107 and from not detectable amount to 1.4x106, respectively. The gln gene copy number was also higher after NO3-addition. However, the difference was not statistically

  7. Tillage Management and Seasonal Effects on Denitrifier Community Abundance, Gene Expression and Structure over Winter.

    Science.gov (United States)

    Tatti, Enrico; Goyer, Claudia; Burton, David L; Wertz, Sophie; Zebarth, Bernie J; Chantigny, Martin; Filion, Martin

    2015-10-01

    Tillage effects on denitrifier communities and nitrous oxide (N2O) emissions were mainly studied during the growing season. There is limited information for the non-growing season, especially in northern countries where winter has prolonged periods with sub-zero temperatures. The abundance and structure of the denitrifier community, denitrification gene expression and N2O emissions in fields under long-term tillage regimes [no-tillage (NT) vs conventional tillage (CT)] were assessed during two consecutive winters. NT exerted a positive effect on nirK and nosZ denitrifier abundance in both winters compared to CT. Moreover, the two contrasting managements had an opposite influence on nirK and nirS RNA/DNA ratios. Tillage management resulted in different denitrifier community structures during both winters. Seasonal changes were observed in the abundance and the structure of denitrifiers. Interestingly, the RNA/DNA ratios were greater in the coldest months for nirK, nirS and nosZ. N2O emissions were not influenced by management but changed over time with two orders of magnitude increase in the coldest month of both winters. In winter of 2009-2010, emissions were mainly as N2O, whereas in 2010-2011, when soil temperatures were milder due to persistent snow cover, most emissions were as dinitrogen. Results indicated that tillage management during the growing season induced differences in denitrifier community structure that persisted during winter. However, management did not affect the active cold-adapted community structure.

  8. Does the source of carbon influence the abundance of nirK, nirS and nosZ functional genes in laboratory denitrification bioreactors?

    Science.gov (United States)

    Barrett, Maria; Fenton, Owen; Ibrahim, Tristan G.; O'Flaherty, Vincent; Healey, Mark G.

    2014-05-01

    Biological denitrification in soil is the main producer of nitrous oxide (N2O) emissions. Denitrifying soil microbes are capable of reducing nitrate (NO3-) to nitrite (NO2-) to N2O and di-nitrogen gas (N2). One third of these denitrifers possess a truncated functional gene pathway, which may lack the nosZ gene and emit N2O as a final emission product instead of the more benign N2. A carbon rich environment, specific to certain types of carbon sources, has been shown to foster an anaerobic environment, which positively impacts microbial denitrification rates. The present study examined the effect of varying carbon sources in laboratory-scale denitrification bioreactors on NO3- removal and also correlated performance with the abundance of the denitrifying microbial consortia possessing the denitrifying functional genes nirK, nirS and nosZ in each bioreactor. The bioreactors comprised either lodgepole pine woodchips (LPW), lodgepole pine needles (LPN), barley straw (BBS), or cardboard (CCB), each mixed with soil in a 1:1 ratio (by volume) and subject to sequentially increasing hydraulic loading rates of 3, 5 and 10 cm d-1 for a total operation period of up to 744 days. A reactor containing soil only (CSO) was used as the study control. The abundance of denitrifers was determined by targeting nirK, nirS, nosZ functional genes and the overall microbial population was determined by targeting bacterial and archaeal 16sRNA genes. Nitrate removal from all bioreactors was > 99.7%, but when pollution swapping was considered, this ranged from 67% for LPW to 95% for the CCB ; this was also mirrored in the average nirk/nirS/nosZ gene abundance (CCB, c. 94% (c. 108); LPN, 75% (c. 107); BBS, c. 74% (c. 106/107); LPW, 70% (c. 105). Bacterial 16sRNA gene abundance was similar in all reactors including the control (P=0.0362). The abundance of nosZ genes and the genetic potential for N2 emissions varied in all reactors in comparison to the control CSO, BBS (P=0.0051); CCB (P=0

  9. The different potential of sponge bacterial symbionts in N₂ release indicated by the phylogenetic diversity and abundance analyses of denitrification genes, nirK and nosZ.

    Directory of Open Access Journals (Sweden)

    Xia Zhang

    Full Text Available Nitrogen cycle is a critical biogeochemical process of the oceans. The nitrogen fixation by sponge cyanobacteria was early observed. Until recently, sponges were found to be able to release nitrogen gas. However the gene-level evidence for the role of bacterial symbionts from different species sponges in nitrogen gas release is limited. And meanwhile, the quanitative analysis of nitrogen cycle-related genes of sponge microbial symbionts is relatively lacking. The nirK gene encoding nitrite reductase which catalyzes soluble nitrite into gas NO and nosZ gene encoding nitrous oxide reductase which catalyzes N₂O into N₂ are two key functional genes in the complete denitrification pathway. In this study, using nirK and nosZ genes as markers, the potential of bacterial symbionts in six species of sponges in the release of N2 was investigated by phylogenetic analysis and real-time qPCR. As a result, totally, 2 OTUs of nirK and 5 OTUs of nosZ genes were detected by gene library-based saturated sequencing. Difference phylogenetic diversity of nirK and nosZ genes were observed at OTU level in sponges. Meanwhile, real-time qPCR analysis showed that Xestospongia testudinaria had the highest abundance of nosZ gene, while Cinachyrella sp. had the greatest abundance of nirK gene. Phylogenetic analysis showed that the nirK and nosZ genes were probably of Alpha-, Beta-, and Gammaproteobacteria origin. The results from this study suggest that the denitrification potential of bacteria varies among sponges because of the different phylogenetic diversity and relative abundance of nosZ and nirK genes in sponges. Totally, both the qualitative and quantitative analyses of nirK and nosZ genes indicated the different potential of sponge bacterial symbionts in the release of nitrogen gas.

  10. Denitrification and the denitrifier community in a coastal microbial mats

    NARCIS (Netherlands)

    Fan, H.; Bolhuis, H.; Stal, L.J.

    2015-01-01

    Denitrification was measured in three structurally different coastal microbial mats by using the stable isotope technique. The composition of the denitrifying community was determined by analyzing the nitrite reductase (nirS and nirK) genes using clone libraries and the GeoChip. The highest

  11. Denitrification and the denitrifier community in coastal microbial mats

    NARCIS (Netherlands)

    Fan, H.; Bolhuis, H.; Stal, L.J.

    2015-01-01

    Denitrification was measured in three structurally different coastal microbial mats by using the stable isotope technique. The composition of the denitrifying community was determined by analyzing the nitrite reductase (nirS and nirK) genes using clone libraries and the GeoChip. The highest potentia

  12. Who is actively denitrifying in activated sludge?

    DEFF Research Database (Denmark)

    Hansen, Aviaja Anna; Nielsen, Jeppe Lund

    transcripts came from Gammaproteobacteria. A clear taxonomic discrepancy was observed between the nirS and nirK expressing bacteria, which primarily belonged to Beta- and Alphaproteobacteria, respectively. The nosZ gene was expressed by both taxonomic groups and it was therefore surprising that the highest......-scale wastewater treatment plant the transcripts (mRNA) of the nirS, nirK and nosZ denitrification genes expressed under acetate or amino acid consumption were amplified, sequenced and identified. This revealed that the majority of the denitrifiers belonged to Alpha- and Betaproteobacteria, while only few...... genetic diversity was observed from the nirS transcripts and not the nosZ transcripts. Likewise, denitrifying cultures obtained from the activated sludge affiliated with the same Alpha- and Betaproteobacteria as detected with the denitrification genes, except one culture, which affiliated...

  13. IDENTIFICATION AND ECOPHYSIOLOGY OF ACTIVE DENITRIFIERS IN ACTIVATED SLUDGE

    DEFF Research Database (Denmark)

    Hansen, Aviaja Anna; Le-Quy, Vang; Nielsen, Kåre Lehmann

    reactor studies. To obtain better identification of active denitrifying communities in full-scale wastewater treatment plants (WWTPs) we applied DNA-SIP with 13C-labelled substrates, and RT-PCR of expressed denitrification genes (nirS, nirK and nosZ) upon various substrate-inductions. To come around...... the bias of horizontal gene transfer, the identities were verified by microautoradiography (MAR) combined with fluorescence in situ hybridization (FISH) with incorporation of radio-labelled substrates under denitrifying conditions. The in situ abundances of the identified denitrifiers in different WWTPs...... were determined with quantitative FISH, while their active metabolic pathways were investigated directly in activated sludge with a tag-based metatranscriptomic approach under acetate-utilizing and denitrifying conditions. The different methods revealed a majority of denitrifiers in all WWTPs belonging...

  14. IDENTIFICATION AND ECOPHYSIOLOGY OF ACTIVE DENITRIFIERS IN ACTIVATED SLUDGE

    DEFF Research Database (Denmark)

    Hansen, Aviaja Anna; Le-Quy, Vang; Nielsen, Kåre Lehmann;

    and when external carbon sources were supplemented to the activated sludge the composition of the denitrifying communities was significantly affected. Transcriptome profiling provided detailed insight in the metabolic pathways in several of the active denitrifiers in activated sludge. In conclusion...... reactor studies. To obtain better identification of active denitrifying communities in full-scale wastewater treatment plants (WWTPs) we applied DNA-SIP with 13C-labelled substrates, and RT-PCR of expressed denitrification genes (nirS, nirK and nosZ) upon various substrate-inductions. To come around...... were determined with quantitative FISH, while their active metabolic pathways were investigated directly in activated sludge with a tag-based metatranscriptomic approach under acetate-utilizing and denitrifying conditions. The different methods revealed a majority of denitrifiers in all WWTPs belonging...

  15. Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Zhu Wang

    Full Text Available Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.

  16. Diversity and activity of denitrifiers of Chilean arid soil ecosystems

    Directory of Open Access Journals (Sweden)

    Julieta eOrlando

    2012-04-01

    Full Text Available The Chilean sclerophyllous matorral is a Mediterranean semiarid ecosystem affected by erosion, with low soil fertility and limited by nitrogen. However, limitation of resources is even more severe for desert soils such as from the Atacama Desert, one of the most extreme arid deserts on Earth. Topsoil organic matter, nitrogen and moisture content were significantly higher in the semiarid soil compared to the desert soil. Although the most significant loss of biologically preferred nitrogen from terrestrial ecosystems occurs via denitrification, virtually nothing is known on the activity and composition of denitrifier communities thriving in arid soils. In this study, we explored denitrifier communities from two soils with profoundly distinct edaphic factors. While denitrification activity in the desert soil was below detection limit, the semiarid soil sustained denitrification activity. To elucidate the genetic potential of the soils to sustain denitrification processes we performed community analysis of denitrifiers based on nitrite reductase (nirK and nirS genes as functional marker genes for this physiological group. Presence of nirK-type denitrifiers in both soils was demonstrated but failure to amplify nirS from the desert soil suggests very low abundance of nirS-type denitrifiers shedding light on the lack of denitrification activity. Phylogenetic analysis showed a very low diversity of nirK with only three distinct genotypes in the desert soil which conditions presumably exert a high selection pressure. While nirK diversity was also limited to only few, albeit distinct genotypes, the semiarid matorral soil showed a surprisingly broad genetic variability of the nirS gene. The Chilean matorral is a shrub land plant community which form vegetational patches stabilizing the soil and increasing its nitrogen and carbon content. These islands of fertility may sustain the development and activity of the overall microbial community and of

  17. Does reactor staging influence microbial structure and functions in biofilm systems? The case of pre-denitrifying MBBRs

    DEFF Research Database (Denmark)

    Polesel, Fabio; Torresi, Elena; Jensen, Marlene Mark

    community based on qPCR (quantitative polymerase chain reaction) showed differences in the abundance of genes (nirS, nirK, nosZ) encoding for denitrifying enzymes in the three staged MBBRs. Further microbial characterization through 16sRNA sequencing (Illumina) is currently under investigation to determine...

  18. Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments

    DEFF Research Database (Denmark)

    Priemé, Anders; Wolsing, Martin

    2004-01-01

    Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kg N ha-1 year-1) and cattle manure (75 and 150 kg N ha-1 year-1) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified...... a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different...... nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed...

  19. Impacts of nitrogen application rates on the activity and diversity of denitrifying bacteria in the Broadbalk Wheat Experiment.

    Science.gov (United States)

    Clark, Ian M; Buchkina, Natalya; Jhurreea, Deveraj; Goulding, Keith W T; Hirsch, Penny R

    2012-05-05

    Bacterial denitrification results in the loss of fertilizer nitrogen and greenhouse gas emissions as nitrous oxides, but ecological factors in soil influencing denitrifier communities are not well understood, impeding the potential for mitigation by land management. Communities vary in the relative abundance of the alternative dissimilatory nitrite reductase genes nirK and nirS, and the nitrous oxide reductase gene nosZ; however, the significance for nitrous oxide emissions is unclear. We assessed the influence of different long-term fertilization and cultivation treatments in a 160-year-old field experiment, comparing the potential for denitrification by soil samples with the size and diversity of their denitrifier communities. Denitrification potential was much higher in soil from an area left to develop from arable into woodland than from a farmyard manure-fertilized arable treatment, which in turn was significantly higher than inorganic nitrogen-fertilized and unfertilized arable plots. This correlated with abundance of nirK but not nirS, the least abundant of the genes tested in all soils, showing an inverse relationship with nirK. Most genetic variation was seen in nirK, where sequences resolved into separate groups according to soil treatment. We conclude that bacteria containing nirK are most probably responsible for the increased denitrification potential associated with nitrogen and organic carbon in this soil.

  20. Sediment denitrifier community composition and nirS gene expression investigated with functional gene microarrays

    DEFF Research Database (Denmark)

    Francis, C.A.; Jackson, G.A.; Ward, B.B.

    2008-01-01

    total RNA extracts) targets were hybridized to the same array to compare the profiles of community composition at the DNA (relative abundance) and mRNA (gene expression) levels. Only the three dominant denitrifying groups (in terms of relative strength of DNA hybridization signal) were detected at the m......A functional gene microarray was used to investigate denitrifier community composition and nitrite reductase (nirS) gene expression in sediments along the estuarine gradient in Chesapeake Bay, USA. The nirS oligonucleotide probe set was designed to represent a sequence database containing 539...

  1. Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

    Science.gov (United States)

    Jha, Neha; Saggar, Surinder; Giltrap, Donna; Tillman, Russ; Deslippe, Julie

    2017-09-01

    Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N2O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N2O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N2O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N2O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N2O

  2. Diversity of Denitrifying Bacteria in the San Francisco Bay

    Science.gov (United States)

    Atluri, A.; Lee, J.; Francis, C. A.

    2012-12-01

    We compared the diversity of communities of denitrifying bacteria from the San Francisco Bay to investigate whether environmental factors affect diversity. To do this, we studied the sequence diversity of the marker gene nirK. nirK codes for the enzyme nitrite reductase which helps reduce nitrite to nitric oxide, an important step in denitrification. Sediment samples were collected spatially from five different locations and temporally during the four different seasons along a salinity gradient in the bay. After collecting samples and extracting DNA from them, we used PCR to amplify our gene of interest, created clone libraries for sequencing, and compared phylogenetic trees from the different communities. Based on several phylogenetic analyses on our tree and environments, we saw that denitrifying bacteria from the North and Central Bay form distinct spatial clusters; Central Bay communities are very similar to each other, while communities from the North Bay are more distinct from each other and from communities in the Central Bay. Bacteria from site 8.1M (Carquinez Strait) showed the most cm-scale spatial diversity, and there was the most species richness during the winter. All this suggests that diversity of communities of denitrifying bacteria may be affected by spatial and temporal environmental factors.

  3. The diversity of denitrifying bacteria in the alpine meadow soil of Sanjiangyuan natural reserve in Tibet Plateau

    Institute of Scientific and Technical Information of China (English)

    XU Haiping; ZHANG Yuguang; SUN Yanping; LI Diqiang; CHEN Xinmou; WANG Huimin; XIAO Qiming; LIU Xueduan

    2006-01-01

    This is the first time to describe the diversity of denitrifying bacteria in Sanjiangyuan natural reserve in Tibet Plateau by investigating the molecular diversity and phylogenetic analysis of nirK and nosZ genes using PCR-RFLP and sequencing. Four soil samples were collected from alpine meadow communities from over an altitude of 4600 m which had different physicochemical properties by principal component analysis (PCA). For the genes fragment of nirKand nosZ, the diverse PCR products were characterized by cloning, restriction fragment length polymorphism (RFLP) analysis and sequenced. A total of 253 nirK clones and 283 nosZ clones were received in four samples, and 78 operational taxonomic units (OTUs) of nirK and 120 OTUs of nosZ by the restriction enzymes Mspl and Rsal digested. The analysis of environmental factors showed that altitude and C/N ratio in soil may be the key factors to the denitrifying bacteria community. 36 nirK clones and 17 nosZ clones were sequenced, and their levels of nucleotide identity were from 69% to 98% and 57% to 97%, respectively. The phylogenetic tree was constructed using the Clustal W and Mega softwares, and all the sequenced clones could be subdivided into 4 groups. Some of clone sequences were related to the nirK and nosZ genes belonging to three phylogenetic subdivisions (α-, β- and Y subclasses of the Proteobacteria), while most of the clones were closely related to the genes of the uncultured bacteria. The sequence distributions were not clear relating to the sample sites in the tree.

  4. Nitrous oxide emission and denitrifier communities in drip-irrigated calcareous soil as affected by chemical and organic fertilizers.

    Science.gov (United States)

    Tao, Rui; Wakelin, Steven A; Liang, Yongchao; Hu, Baowei; Chu, Guixin

    2017-08-31

    The effects of consecutive application of chemical fertilizer with or without organic fertilizer on soil N2O emissions and denitrifying community structure in a drip-irrigated field were determined. The four fertilizer treatments were (i) unfertilized, (ii) chemical fertilizer, (iii) 60% chemical fertilizer plus cattle manure, and (iv) 60% chemical fertilizer plus biofertilizer. The treatments with organic amendments (i.e. cattle manure and biofertilizer) reduced cumulative N2O emissions by 4.9-9.9%, reduced the N2O emission factor by 1.3-42%, and increased denitrifying enzyme activities by 14.3-56.2%. The nirK gene copy numbers were greatest in soil which received only chemical fertilizer. In contrast, nirS- and nosZ-copy numbers were greatest in soil amended with chemical fertilizer plus biofertilizer. Chemical fertilizer application with or without organic fertilizer significantly changed the community structure of nirK-type denitrifiers relative to the unfertilized soil. In comparison, the nirS- and nosZ-type denitrifier genotypes varied in treatments receiving organic fertilizer but not chemical fertilizer alone. The changes in the denitrifier communities were closely associated with soil organic carbon (SOC), NO3(-), NH4(+), water holding capacity, and soil pH. Modeling indicated that N2O emissions in this soil were primarily associated with the abundance of nirS type denitrifying bacteria, SOC, and NO3(-). Overall, our findings indicate that (i) the organic fertilizers increased denitrifying enzyme activity, increased denitrifying-bacteria gene copy numbers, but reduced N2O emissions, and (ii) nirS- and nosZ-type denitrifiers were more sensitive than nirK-type denitrifiers to the organic fertilizers. Copyright © 2017. Published by Elsevier B.V.

  5. Characterization of the denitrifying bacterial community in a full-scale rockwool biofilter for compost waste-gas treatment.

    Science.gov (United States)

    Yasuda, Tomoko; Waki, Miyoko; Fukumoto, Yasuyuki; Hanajima, Dai; Kuroda, Kazutaka; Suzuki, Kazuyoshi

    2017-07-07

    The potential denitrification activity and the composition of the denitrifying bacterial community in a full-scale rockwool biofilter used for treating livestock manure composting emissions were analyzed. Packing material sampled from the rockwool biofilter was anoxically batch-incubated with (15)N-labeled nitrate in the presence of different electron donors (compost extract, ammonium, hydrogen sulfide, propionate, and acetate), and responses were compared with those of activated sludge from a livestock wastewater treatment facility. Overnight batch-incubation showed that potential denitrification activity for the rockwool samples was higher with added compost extract than with other potential electron donors. The number of 16S rRNA and nosZ genes in the rockwool samples were in the range of 1.64-3.27 × 10(9) and 0.28-2.27 × 10(8) copies/g dry, respectively. Denaturing gradient gel electrophoresis analysis targeting nirK, nirS, and nosZ genes indicated that the distribution of nir genes was spread in a vertical direction and the distribution of nosZ genes was spread horizontally within the biofilter. The corresponding denitrifying enzymes were mainly related to those from Phyllobacteriaceae, Bradyrhizobiaceae, and Alcaligenaceae bacteria and to environmental clones retrieved from agricultural soil, activated sludge, freshwater environments, and guts of earthworms or other invertebrates. A nosZ gene fragment having 99% nucleotide sequence identity with that of Oligotropha carboxidovorans was also detected. Some nirK fragments were related to NirK from micro-aerobic environments. Thus, denitrification in this full-scale rockwool biofilter might be achieved by a consortium of denitrifying bacteria adapted to the intensely aerated ecosystem and utilizing mainly organic matter supplied by the livestock manure composting waste-gas stream.

  6. Carbon amendment and soil depth affect the distribution and abundance of denitrifiers in agricultural soils.

    Science.gov (United States)

    Barrett, M; Khalil, M I; Jahangir, M M R; Lee, C; Cardenas, L M; Collins, G; Richards, K G; O'Flaherty, V

    2016-04-01

    The nitrite reductase (nirS and nirK) and nitrous oxide reductase-encoding (nosZ) genes of denitrifying populations present in an agricultural grassland soil were quantified using real-time polymerase chain reaction (PCR) assays. Samples from three separate pedological depths at the chosen site were investigated: horizon A (0-10 cm), horizon B (45-55 cm), and horizon C (120-130 cm). The effect of carbon addition (treatment 1, control; treatment 2, glucose-C; treatment 3, dissolved organic carbon (DOC)) on denitrifier gene abundance and N2O and N2 fluxes was determined. In general, denitrifier abundance correlated well with flux measurements; nirS was positively correlated with N2O, and nosZ was positively correlated with N2 (P soil (GCC) varied in response to carbon type amendment (P soil depth directly affected bacterial, archaeal, and denitrifier abundance, possibly due to changes in soil carbon availability with depth.

  7. Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning.

    Science.gov (United States)

    Liu, Xian; Chen, Chengrong; Wang, Weijin; Hughes, Jane M; Lewis, Tom; Hou, Enqing; Shen, Jupei

    2015-11-01

    Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH(4)(+)), and nitrate (NO(3)(-)), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime.

  8. Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates.

    Science.gov (United States)

    Henry, S; Texier, S; Hallet, S; Bru, D; Dambreville, C; Chèneby, D; Bizouard, F; Germon, J C; Philippot, L

    2008-11-01

    To determine to which extent root-derived carbon contributes to the effects of plants on nitrate reducers and denitrifiers, four solutions containing different proportions of sugar, organic acids and amino acids mimicking maize root exudates were added daily to soil microcosms at a concentration of 150 microg C g(-1) of soil. Water-amended soils were used as controls. After 1 month, the size and structure of the nitrate reducer and denitrifier communities were analysed using the narG and napA, and the nirK, nirS and nosZ genes as molecular markers respectively. Addition of artificial root exudates (ARE) did not strongly affect the structure or the density of nitrate reducer and denitrifier communities whereas potential nitrate reductase and denitrification activities were stimulated by the addition of root exudates. An effect of ARE composition was also observed on N(2)O production with an N(2)O:(N(2)O + N(2)) ratio of 0.3 in microcosms amended with ARE containing 80% of sugar and of 1 in microcosms amended with ARE containing 40% of sugar. Our study indicated that ARE stimulated nitrate reduction or denitrification activity with increases in the range of those observed with the whole plant. Furthermore, we demonstrated that the composition of the ARE affected the nature of the end-product of denitrification and could thus have a putative impact on greenhouse gas emissions.

  9. Abundance, composition and activity of ammonia oxidizer and denitrifier communities in metal polluted rice paddies from South China.

    Directory of Open Access Journals (Sweden)

    Yuan Liu

    Full Text Available While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg-1. Copy numbers of amoA (AOA and AOB genes were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils.

  10. Nitrate removal, communities of denitrifiers and adverse effects in different carbon substrates for use in denitrification beds.

    Science.gov (United States)

    Warneke, Sören; Schipper, Louis A; Matiasek, Michael G; Scow, Kate M; Cameron, Stewart; Bruesewitz, Denise A; McDonald, Ian R

    2011-11-01

    Denitrification beds are containers filled with wood by-products that serve as a carbon and energy source to denitrifiers, which reduce nitrate (NO(3)(-)) from point source discharges into non-reactive dinitrogen (N(2)) gas. This study investigates a range of alternative carbon sources and determines rates, mechanisms and factors controlling NO(3)(-) removal, denitrifying bacterial community, and the adverse effects of these substrates. Experimental barrels (0.2 m(3)) filled with either maize cobs, wheat straw, green waste, sawdust, pine woodchips or eucalyptus woodchips were incubated at 16.8 °C or 27.1 °C (outlet temperature), and received NO(3)(-) enriched water (14.38 mg N L(-1) and 17.15 mg N L(-1)). After 2.5 years of incubation measurements were made of NO(3)(-)-N removal rates, in vitro denitrification rates (DR), factors limiting denitrification (carbon and nitrate availability, dissolved oxygen, temperature, pH, and concentrations of NO(3)(-), nitrite and ammonia), copy number of nitrite reductase (nirS and nirK) and nitrous oxide reductase (nosZ) genes, and greenhouse gas production (dissolved nitrous oxide (N(2)O) and methane), and carbon (TOC) loss. Microbial denitrification was the main mechanism for NO(3)(-)-N removal. Nitrate-N removal rates ranged from 1.3 (pine woodchips) to 6.2 g N m(-3) d(-1) (maize cobs), and were predominantly limited by C availability and temperature (Q(10) = 1.2) when NO(3)(-)-N outlet concentrations remained above 1 mg L(-1). The NO(3)(-)-N removal rate did not depend directly on substrate type, but on the quantity of microbially available carbon, which differed between carbon sources. The abundance of denitrifying genes (nirS, nirK and nosZ) was similar in replicate barrels under cold incubation, but varied substantially under warm incubation, and between substrates. Warm incubation enhanced growth of nirS containing bacteria and bacteria that lacked the nosZ gene, potentially explaining the greater N(2)O emission in

  11. Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils.

    Science.gov (United States)

    Penton, Christopher R; St Louis, Derek; Pham, Amanda; Cole, James R; Wu, Liyou; Luo, Yiqi; Schuur, E A G; Zhou, Jizhong; Tiedje, James M

    2015-01-01

    Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.

  12. Denitrification potential under different fertilization regimes is closely coupled with changes in the denitrifying community in a black soil.

    Science.gov (United States)

    Yin, Chang; Fan, Fenliang; Song, Alin; Cui, Peiyuan; Li, Tingqiang; Liang, Yongchao

    2015-07-01

    Preferable inorganic fertilization over the last decades has led to fertility degradation of black soil in Northeast China. However, how fertilization regimes impact denitrification and its related bacterial community in this soil type is still unclear. Here, taking advantage of a suit of molecular ecological tools in combination of assaying the potential denitrification (DP), we explored the variation of activity, community structure, and abundance of nirS and nirK denitrifiers under four different fertilization regimes, namely no fertilization control (N0M0), organic pig manure (N0M1), inorganic fertilization (N1M0), and combination of inorganic fertilizer and pig manure (N1M1). The results indicated that organic fertilization increased DP, but inorganic fertilization had no impacts. The increase of DP was mirrored by the shift of nirS denitrifiers' community structure but not by that of nirK denitrifiers'. Furthermore, the change of DP coincided with the variation of abundances of both denitrifiers. Shifts of community structure and abundance of nirS and nirK denitrifiers were correlated with the change of soil pH, total nitrogen (TN), organic matter (OM), C:P, total phosphorus (TP), and available phosphorus (Olsen P). Our results suggest that the change of DP under these four fertilization regimes was closely related to the shift of denitrifying bacteria communities resulting from the variation of properties in the black soil tested.

  13. Nitrogen removal and spatial distribution of denitrifier and anammox communities in a bioreactor for mine drainage treatment.

    Science.gov (United States)

    Herbert, Roger B; Winbjörk, Harry; Hellman, Maria; Hallin, Sara

    2014-12-01

    Mine drainage water may contain high levels of nitrate (NO3(-)) due to undetonated nitrogen-based explosives. The removal of NO3(-) and nitrite (NO2(-)) in cold climates through the microbial process of denitrification was evaluated using a pilot-scale fixed-bed bioreactor (27 m(3)). Surface water was diverted into the above-ground bioreactor filled with sawdust, crushed rock, and sewage sludge. At hydraulic residence times of ca.15 h and with the addition of acetate, NO3(-) and NO2(-) were removed to below detection levels at a NO3(-) removal rate of 5-10 g N m(-3) (bioreactor material) d(-1). The functional groups contributing to nitrogen removal in the bioreactor were studied by quantifying nirS and nirK present in denitrifying bacteria, nosZI and nosZII genes from the nitrous oxide - reducing community, and a taxa-specific part of the16S rRNA gene for the anammox community. The abundances of nirS and nirK were almost 2 orders of magnitude greater than the anammox specific 16S rRNA gene, indicating that denitrification was the main process involved in nitrogen removal. The spatial distribution of the quantified genes was heterogeneous in the bioreactor, with trends observed in gene abundance as a function of depth, distance from the bioreactor inlet, and along specific flowpaths. There was a significant relationship between the abundance of nirS, nirK, and nosZI genes and depth in the bioreactor, such that the abundance of organisms containing these genes may be controlled by oxygen diffusion and substrate supply in the partially or completely water-saturated material. Among the investigated microbial functional groups, nirS and anammox bacterial 16S rRNA genes exhibited a systematic trend of decreasing and increasing abundance, respectively, with distance from the inlet, which suggested that the functional groups respond differently to changing environmental conditions. The greater abundance of nirK along central flowpaths may indicate that the bioreactor

  14. Insights into the effect of soil pH on N(2)O and N(2) emissions and denitrifier community size and activity.

    Science.gov (United States)

    Cuhel, Jirí; Simek, Miloslav; Laughlin, Ronnie J; Bru, David; Chèneby, Dominique; Watson, Catherine J; Philippot, Laurent

    2010-03-01

    The objective of this study was to investigate how changes in soil pH affect the N(2)O and N(2) emissions, denitrification activity, and size of a denitrifier community. We established a field experiment, situated in a grassland area, which consisted of three treatments which were repeatedly amended with a KOH solution (alkaline soil), an H(2)SO(4) solution (acidic soil), or water (natural pH soil) over 10 months. At the site, we determined field N(2)O and N(2) emissions using the (15)N gas flux method and collected soil samples for the measurement of potential denitrification activity and quantification of the size of the denitrifying community by quantitative PCR of the narG, napA, nirS, nirK, and nosZ denitrification genes. Overall, our results indicate that soil pH is of importance in determining the nature of denitrification end products. Thus, we found that the N(2)O/(N(2)O + N(2)) ratio increased with decreasing pH due to changes in the total denitrification activity, while no changes in N(2)O production were observed. Denitrification activity and N(2)O emissions measured under laboratory conditions were correlated with N fluxes in situ and therefore reflected treatment differences in the field. The size of the denitrifying community was uncoupled from in situ N fluxes, but potential denitrification was correlated with the count of NirS denitrifiers. Significant relationships were observed between nirS, napA, and narG gene copy numbers and the N(2)O/(N(2)O + N(2)) ratio, which are difficult to explain. However, this highlights the need for further studies combining analysis of denitrifier ecology and quantification of denitrification end products for a comprehensive understanding of the regulation of N fluxes by denitrification.

  15. Effects of warming and drought on potential N2O emissions and denitrifying bacteria abundance in grasslands with different land-use.

    Science.gov (United States)

    Keil, Daniel; Niklaus, Pascal A; von Riedmatten, Lars R; Boeddinghaus, Runa S; Dormann, Carsten F; Scherer-Lorenzen, Michael; Kandeler, Ellen; Marhan, Sven

    2015-07-01

    Increased warming in spring and prolonged summer drought may alter soil microbial denitrification. We measured potential denitrification activity and denitrifier marker gene abundances (nirK, nirS, nosZ) in grasslands soils in three geographic regions characterized by site-specific land-use indices (LUI) after warming in spring, at an intermediate sampling and after summer drought. Potential denitrification was significantly increased by warming, but did not persist over the intermediate sampling. At the intermediate sampling, the relevance of grassland land-use intensity was reflected by increased potential N2O production at sites with higher LUI. Abundances of total bacteria did not respond to experimental warming or drought treatments, displaying resilience to minor and short-term effects of climate change. In contrast, nirS- and nirK-type denitrifiers were more influenced by drought in combination with LUI and pH, while the nosZ abundance responded to the summer drought manipulation. Land-use was a strong driver for potential denitrification as grasslands with higher LUI also had greater potentials for N2O emissions. We conclude that both warming and drought affected the denitrifying communities and the potential denitrification in grassland soils. However, these effects are overruled by regional and site-specific differences in soil chemical and physical properties which are also related to grassland land-use intensity. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. Microbial community structure and function in response to the shift of sulfide/nitrate loading ratio during the denitrifying sulfide removal process.

    Science.gov (United States)

    Huang, Cong; Li, Zhi-Ling; Chen, Fan; Liu, Qian; Zhao, You-Kang; Zhou, Ji-Zhong; Wang, Ai-Jie

    2015-12-01

    Influence of acetate-C/NO3(-)-N/S(2-) ratio to the functional microbial community during the denitrifying sulfide removal process is poorly understood. Here, phylogenetic and functional bacterial community for elemental sulfur (S(0)) recovery and nitrate (NO3(-)) removal were investigated with the switched S(2-)/NO3(-) molar ratio ranged from 5/2 to 5/9. Optimized S(2-)/NO3(-) ratio was evaluated as 5/6, with the bacterial genera predominated with Thauera, Enterobacter, Thiobacillus and Stappia, and the sqr gene highly expressed. However, insufficient or high loading of acetate and NO3(-) resulted in the low S(0) recovery, and also significantly modified the bacterial community and genetic activity. With S(2-)/NO3(-) ratio of 5/2, autotrophic S(2-) oxidization genera were dominated and NO3(-) reduction activity was low, confirmed by the low expressed nirK gene. In contrast, S(2-)/NO3(-) ratio switched to 5/8 and 5/9 introduced diverse heterotrophic nitrate reduction and S(0) over oxidization genera in accompanied with the highly expressed nirK and sox genes.

  17. Soil environmental conditions and microbial build-up mediate the effect of plant diversity on soil nitrifying and denitrifying enzyme activities in temperate grasslands.

    Directory of Open Access Journals (Sweden)

    Xavier Le Roux

    Full Text Available Random reductions in plant diversity can affect ecosystem functioning, but it is still unclear which components of plant diversity (species number - namely richness, presence of particular plant functional groups, or particular combinations of these and associated biotic and abiotic drivers explain the observed relationships, particularly for soil processes. We assembled grassland communities including 1 to 16 plant species with a factorial separation of the effects of richness and functional group composition to analyze how plant diversity components influence soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively, the abundance of nitrifiers (bacterial and archaeal amoA gene number and denitrifiers (nirK, nirS and nosZ gene number, and key soil environmental conditions. Plant diversity effects were largely due to differences in functional group composition between communities of identical richness (number of sown species, though richness also had an effect per se. NEA was positively related to the percentage of legumes in terms of sown species number, the additional effect of richness at any given legume percentage being negative. DEA was higher in plots with legumes, decreased with increasing percentage of grasses, and increased with richness. No correlation was observed between DEA and denitrifier abundance. NEA increased with the abundance of ammonia oxidizing bacteria. The effect of richness on NEA was entirely due to the build-up of nitrifying organisms, while legume effect was partly linked to modified ammonium availability and nitrifier abundance. Richness effect on DEA was entirely due to changes in soil moisture, while the effects of legumes and grasses were partly due to modified nitrate availability, which influenced the specific activity of denitrifiers. These results suggest that plant diversity-induced changes in microbial specific activity are important for facultative activities such as denitrification

  18. Ammonia-oxidizing archaea are more resistant than denitrifiers to seasonal precipitation changes in an acidic subtropical forest soil

    Science.gov (United States)

    Chen, Jie

    2017-04-01

    More frequent droughts and storms will occur globally in the prediction of global climate change model, which will influence soil microorganisms and nutrient cycles. Understanding the resistance of soil functional microorganisms and the associated biogeochemical cycles to such climate changes is important in evaluating responses of ecosystem functioning. In order to clarify the responses of soil functional microorganisms involved in nitrogen (N) cycle to the predicted precipitation scenarios, two contrasting precipitation manipulation experiments were conducted in an acidic subtropical forest soil. One experiment manipulated drier dry-season and wetter wet-season (DD) by reducing dry-season rainfall and adding the equivalently reduced rainfall to wet-season. Another experiment manipulated extending dry-season and wetter wet-season (ED) by reducing spring-season rainfall and adding the equivalent rainfall in the late wet-season. The resistance index of ammonia-oxidizing archaea (AOA) amoA and denitrifying (nirK, nirS and nosZ) genes abundance, soil net N mineralization and nitrification rates were calculated during experiments to examine their responses to precipitation changes. As the results, the resistance index of functional microbial abundance (-0.03 ± 0.08) was much lower than that of net N transformation rates (0.55 ± 0.02), indicating more sensitive of functional microorganisms in response to precipitation changes than the related N processes. Extending dry-season showed greater effects on both AOA amoA and denitrifying genes abundance than drier dry-season, with significant increases of these microbial abundance after extending dry-season. This was mainly due to the interaction effects of soil water content (SWC), dissolve organic carbon (DOC) and NH4+ concentration during rainfall reduction in spring-season. Interestingly, the resistance index of AOA amoA abundance was significantly higher than that of denitrifying gene abundance, indicating more

  19. Diversity of nitrite reductase genes (nirS) in the denitrifying water column of the coastal Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Jayakumar, D.A.; Francis, C.A.; Naqvi, S.W.A.; Ward, B.B.

    and 1 sequence from Sample G840. Cluster VIII contained the majority (23 of 26) of the sequences from Sample V400. Many of the se- quences in Cluster VIII were virtually identical to the nirS sequence of the cultivated denitrifier Pseudo- monas... environmental clone, exhibiting close identity to a cul- tured denitrifier species, was also observed in a recent study of the River Colne estuary sediments, in which virtually identical nirS sequences were obtained from a Flavobacterium isolate and from 2 RT...

  20. Denitrifying bacterial communities affect current production and nitrous oxide accumulation in a microbial fuel cell.

    Directory of Open Access Journals (Sweden)

    Ariadna Vilar-Sanz

    Full Text Available The biocathodic reduction of nitrate in Microbial Fuel Cells (MFCs is an alternative to remove nitrogen in low carbon to nitrogen wastewater and relies entirely on microbial activity. In this paper the community composition of denitrifiers in the cathode of a MFC is analysed in relation to added electron acceptors (nitrate and nitrite and organic matter in the cathode. Nitrate reducers and nitrite reducers were highly affected by the operational conditions and displayed high diversity. The number of retrieved species-level Operational Taxonomic Units (OTUs for narG, napA, nirS and nirK genes was 11, 10, 31 and 22, respectively. In contrast, nitrous oxide reducers remained virtually unchanged at all conditions. About 90% of the retrieved nosZ sequences grouped in a single OTU with a high similarity with Oligotropha carboxidovorans nosZ gene. nirS-containing denitrifiers were dominant at all conditions and accounted for a significant amount of the total bacterial density. Current production decreased from 15.0 A · m(-3 NCC (Net Cathodic Compartment, when nitrate was used as an electron acceptor, to 14.1 A · m(-3 NCC in the case of nitrite. Contrarily, nitrous oxide (N2O accumulation in the MFC was higher when nitrite was used as the main electron acceptor and accounted for 70% of gaseous nitrogen. Relative abundance of nitrite to nitrous oxide reducers, calculated as (qnirS+qnirK/qnosZ, correlated positively with N2O emissions. Collectively, data indicate that bacteria catalysing the initial denitrification steps in a MFC are highly influenced by main electron acceptors and have a major influence on current production and N2O accumulation.

  1. Functional gene pyrosequencing and network analysis: an approach to examine the response of denitrifying bacteria to increased nitrogen supply in salt marsh sediments

    Directory of Open Access Journals (Sweden)

    Jennifer L. Bowen

    2013-11-01

    Full Text Available Functional gene pyrosequencing is emerging as a useful tool to examine the diversity and abundance of microbes that facilitate key biogeochemical processes. One such process, denitrification, is of particular importance because it converts fixed nitrate (NO3- to N2 gas, which returns to the atmosphere. In N limited salt marshes, removal of NO3- prior to entering adjacent waters helps prevent eutrophication. Understanding the dynamics of salt marsh microbial denitrification is thus imperative for the maintenance of healthy coastal ecosystems. We used pyrosequencing of the nirS gene to examine the denitrifying community response to fertilization in experimentally enriched marsh plots. A key challenge in the analysis of sequence data derived from pyrosequencing is understanding whether small differences in gene sequences are ecologically meaningful. We apply a novel approach from information theory that determined that the optimal similarity level for clustering DNA sequences into OTUs, while still capturing the ecological complexity of the system, was 88% similarity. With this clustering, phylogenetic analysis yielded 6 dominant clades of denitrifiers, the largest of which, accounting for more than half of all the sequences collected, had no close cultured representatives. Of the 638 OTUs identified, only 11 were present in all plots and no single OTU was dominant. We did, however, find a large number of specialist OTUs that were present only in a single plot. The high degree of endemic OTUs, while accounting for a large proportion of the nirS diversity in the plots, were found in lower abundance than the generalist taxa. The proportion of specialist taxa increased with increasing supply of nutrients, suggesting that addition of fertilizer may create conditions that expand the niche space for denitrifying organisms and may enhance the genetic capacity for denitrification.

  2. Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil

    Directory of Open Access Journals (Sweden)

    Jie Chen

    2017-07-01

    Full Text Available Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD and extending the dry-season duration (ED but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08 was much lower than that of the net N transformation rate (0.55 ± 0.02 throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA and denitrifying genes (nirK, nirS, and nosZ, while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4+ and dissolved organic carbon concentrations] during the experiment.

  3. Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

    Science.gov (United States)

    Palmer, Katharina; Biasi, Christina; Horn, Marcus A

    2012-01-01

    Cryoturbated peat circles (that is, bare surface soil mixed by frost action; pH 3–4) in the Russian discontinuous permafrost tundra are nitrate-rich ‘hotspots' of nitrous oxide (N2O) emissions in arctic ecosystems, whereas adjacent unturbated peat areas are not. N2O was produced and subsequently consumed at pH 4 in unsupplemented anoxic microcosms with cryoturbated but not in those with unturbated peat soil. Nitrate, nitrite and acetylene stimulated net N2O production of both soils in anoxic microcosms, indicating denitrification as the source of N2O. Up to 500 and 10 μ nitrate stimulated denitrification in cryoturbated and unturbated peat soils, respectively. Apparent maximal reaction velocities of nitrite-dependent denitrification were 28 and 18 nmol N2O gDW−1 h−1, for cryoturbated and unturbated peat soils, respectively. Barcoded amplicon pyrosequencing of narG, nirK/nirS and nosZ (encoding nitrate, nitrite and N2O reductases, respectively) yielded ≈49 000 quality-filtered sequences with an average sequence length of 444 bp. Up to 19 species-level operational taxonomic units were detected per soil and gene, many of which were distantly related to cultured denitrifiers or environmental sequences. Denitrification-associated gene diversity in cryoturbated and in unturbated peat soils differed. Quantitative PCR (inhibition-corrected per DNA extract) revealed higher copy numbers of narG in cryoturbated than in unturbated peat soil. Copy numbers of nirS were up to 1000 × higher than those of nirK in both soils, and nirS nirK−1 copy number ratios in cryoturbated and unturbated peat soils differed. The collective data indicate that the contrasting N2O emission patterns of cryoturbated and unturbated peat soils are associated with contrasting denitrifier communities. PMID:22134649

  4. Impact of Land Use Management and Soil Properties on Denitrifier Communities of Namibian Savannas.

    Science.gov (United States)

    Braker, Gesche; Matthies, Diethart; Hannig, Michael; Brandt, Franziska Barbara; Brenzinger, Kristof; Gröngröft, Alexander

    2015-11-01

    We studied potential denitrification activity and the underlying denitrifier communities in soils from a semiarid savanna ecosystem of the Kavango region in NE Namibia to help in predicting future changes in N(2)O emissions due to continuing changes of land use in this region. Soil type and land use (pristine, fallow, and cultivated soils) influenced physicochemical characteristics of the soils that are relevant to denitrification activity and N(2)O fluxes from soils and affected potential denitrification activity. Potential denitrification activity was assessed by using the denitrifier enzyme activity (DEA) assay as a proxy for denitrification activity in the soil. Soil type and land use influenced C and N contents of the soils. Pristine soils that had never been cultivated had a particularly high C content. Cultivation reduced soil C content and the abundance of denitrifiers and changed the composition of the denitrifier communities. DEA was strongly and positively correlated with soil C content and was higher in pristine than in fallow or recently cultivated soils. Soil type and the composition of both the nirK- and nirS-type denitrifier communities also influenced DEA. In contrast, other soil characteristics like N content, C:N ratio, and pH did not predict DEA. These findings suggest that due to greater availability of soil organic matter, and hence a more effective N cycling, the natural semiarid grasslands emit more N(2)O than managed lands in Namibia.

  5. Field-Scale Pattern of Denitrifying Microorganisms and N2O Emission Rates Indicate a High Potential for Complete Denitrification in an Agriculturally Used Organic Soil.

    Science.gov (United States)

    Schulz, Stefanie; Kölbl, Angelika; Ebli, Martin; Buegger, Franz; Schloter, Michael; Fiedler, Sabine

    2017-05-11

    More than 50% of all anthropogenic N2O emissions come from the soil. Drained Histosols that are used for agricultural purposes are particularly potent sources of denitrification due to higher stocks of organic matter and fertiliser application. However, conditions that favour denitrification can vary considerably across a field and change significantly throughout the year. Spatial and temporal denitrifier dynamics were assessed in a drained, intensely managed Histosol by focusing on the genetic nitrite and N2O reduction potential derived from the abundance of nirK, nirS and nosZ genes. These data were correlated with soil properties at two different points in time in 2013. N2O emissions were measured every 2 weeks over three vegetation periods (2012-2014). Very low N2O emission rates were measured throughout the entire period of investigation in accordance with the geostatistical data that revealed an abundance of microbes carrying the N2O reductase gene nosZ. This, along with neutral soil pH values, is indicative of high microbial denitrification potential. While the distribution of the microbial communities was strongly influenced by total organic carbon and nitrogen pools in March, the spatial distribution pattern was not related to the distribution of soil properties in October, when higher nutrient availability was observed. Different nitrite reducer groups prevailed in spring and autumn. While nirS, followed by nosZ and nirK, was most abundant in March, the latter was the dominant nitrite reductase in October.

  6. Linkage between N2O emission and functional gene abundance in an intensively managed calcareous fluvo-aquic soil

    Science.gov (United States)

    Yang, Liuqing; Zhang, Xiaojun; Ju, Xiaotang

    2017-02-01

    The linkage between N2O emissions and the abundance of nitrifier and denitrifier genes is unclear in the intensively managed calcareous fluvo-aquic soils of the North China Plain. We investigated the abundance of bacterial amoA for nitrification and narG, nirS, nirK, and nosZ for denitrification by in situ soil sampling to determine how the abundance of these genes changes instantly during N fertilization events and is related to high N2O emission peaks. We also investigated how long-term incorporated straw and/or manure affect(s) the abundance of these genes based on a seven-year field experiment. The overall results demonstrate that the long-term application of urea-based fertilizer and/or manure significantly enhanced the number of bacterial amoA gene copies leading to high N2O emission peaks after N fertilizer applications. These peaks contributed greatly to the annual N2O emissions in the crop rotation. A significant correlation between annual N2O emissions and narG, nirS, and nirK gene numbers indicates that the abundance of these genes is related to N2O emission under conditions for denitrification, thus partly contributing to the annual N2O emissions. These findings will help to draw up appropriate measures for mitigation of N2O emissions in this ‘hotspot’ region.

  7. Anaerobic degradation of sodium dodecyl sulfate (SDS) by denitrifying bacteria

    NARCIS (Netherlands)

    Paulo, A.; Plugge, C.M.; Garcia Encina, P.A.; Stams, A.J.M.

    2013-01-01

    Two denitrifying bacteria were isolated using sodium dodecyl sulfate (SDS) as substrate. Strains SN1 and SN2 were isolated from an activated sludge reactor of a wastewater treatment plant (WWTP) with Anaerobic–Anoxic–Oxic (A2/O) steps. Based on 16S rRNA gene analysis strain SN1 is 99% similar to Pse

  8. Anaerobic degradation of sodium dodecyl sulfate (SDS) by denitrifying bacteria

    NARCIS (Netherlands)

    Paulo, A.; Plugge, C.M.; Garcia Encina, P.A.; Stams, A.J.M.

    2013-01-01

    Two denitrifying bacteria were isolated using sodium dodecyl sulfate (SDS) as substrate. Strains SN1 and SN2 were isolated from an activated sludge reactor of a wastewater treatment plant (WWTP) with Anaerobic–Anoxic–Oxic (A2/O) steps. Based on 16S rRNA gene analysis strain SN1 is 99% similar to

  9. 氮肥对稻田土壤反硝化细菌群落结构和丰度的影响%Response of denitrifying bacteria community structure and abundance to nitrogen in paddy fields

    Institute of Scientific and Technical Information of China (English)

    宋亚娜; 林智敏; 林艳

    2012-01-01

    Denitrification is critical for nitrogen cycle in the ecosystem,where fixed nitrogen is released into the atmosphere as N2.Nitrite reductase,the product of nirS or nirK nitrite reductase genes,is the key enzyme of bacteria dissimilatory denitrification process.Denitrifying bacteria community composition varies with environmental factors such as temperature,moisture,pH,O2 and nutrient availability.There is obvious denitrification process in flooded paddy fields.Hence denitrifying bacteria community structure and abundance in paddy fields are used to investigate the response of denitrifying bacteria to nitrogen fertilizer application in paddy fields.The experiment was conducted in a second-year nitrogen fertilization field with the aid of denaturing gradient gel electropho-resis and real-time PCR assay copies of nirS gene.DGGE images of nirS gene in root-zone soil and surface soil showed rich abun-dance of denitrifying bacteria in paddy soils.DGGE band number in surface soil image was higher than that in root-zone soil.Principle components analysis (PCA) of nirS gene DGGE profile showed that denitrifying bacteria community structure in root-zone or surface soil of paddy fields with nitrogen fertilizer [N: 150 kg(N)-hm-2] was similar to that of paddy fields without fertilizer (CK) during rice growth stages of tillering,heading and maturity.Also no difference was noted in denitrifying bacteria community structure in root-zone soil or surface soil among different growth stages of rice.Denitrifying bacteria nirS gene copy abundance in root-zone or in surface soil with nitrogen fertilizer treatment was significantly (P < 0.05) higher than that of CK treatment during rice growth.In both nitrogen fertilizer and CK treatments,denitrifying bacteria nirS gene copies in root-zone soil markedly (P < 0.05) dropped at maturity stage of rice growth.There were,however,no differences in nirS gene copies in surface soil among the different rice growth stages.At maturity stage

  10. Analysis of denitrifier community in a bioaugmented sequencing batch reactor for the treatment of coking wastewater containing pyridine and quinoline

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Yaohui; Xing, Rui; Wen, Donghui; Tang, Xiaoyan [Peking Univ., Beijing (CN). Key Lab. of Water and Sediment Sciences (Ministry of Education); Sun, Qinghua [Peking Univ., Beijing (CN). Key Lab. of Water and Sediment Sciences (Ministry of Education); Chinese Center for Disease Control and Prevention, Beijing (China). Inst. of Environmental Health and Related Product Safety

    2011-05-15

    The denitrifier community and associated nitrate and nitrite reduction in the bioaugmented and general sequencing batch reactors (SBRs) during the treatment of coking wastewater containing pyridine and quinoline were investigated. The efficiency and stability of nitrate and nitrite reduction in SBR was considerably improved after inoculation with four pyridine- or quinoline-degrading bacterial strains (including three denitrifying strains). Terminal restriction fragment length polymorphism (T-RFLP) based on the nosZ gene revealed that the structures of the denitrifier communities in bioaugmented and non-bioaugmented reactors were distinct and varied during the course of the experiment. Bioaugmentation protected indigenous denitrifiers from disruptions caused by pyridine and quinoline. Clone library analysis showed that one of the added denitrifiers comprised approximately 6% of the denitrifier population in the bioaugmented sludge. (orig.)

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

    Science.gov (United States)

    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.

  12. Identification of the autotrophic denitrifying community in nitrate removal reactors by DNA-stable isotope probing.

    Science.gov (United States)

    Xing, Wei; Li, Jinlong; Cong, Yuan; Gao, Wei; Jia, Zhongjun; Li, Desheng

    2017-04-01

    Autotrophic denitrification has attracted increasing attention for wastewater with insufficient organic carbon sources. Nevertheless, in situ identification of autotrophic denitrifying communities in reactors remains challenging. Here, a process combining micro-electrolysis and autotrophic denitrification with high nitrate removal efficiency was presented. Two batch reactors were fed organic-free nitrate influent, with H(13)CO3(-) and H(12)CO3(-) as inorganic carbon sources. DNA-based stable-isotope probing (DNA-SIP) was used to obtain molecular evidence for autotrophic denitrifying communities. The results showed that the nirS gene was strongly labeled by H(13)CO3(-), demonstrating that the inorganic carbon source was assimilated by autotrophic denitrifiers. High-throughput sequencing and clone library analysis identified Thiobacillus-like bacteria as the most dominant autotrophic denitrifiers. However, 88% of nirS genes cloned from the (13)C-labeled "heavy" DNA fraction showed low similarity with all culturable denitrifiers. These findings provided functional and taxonomical identification of autotrophic denitrifying communities, facilitating application of autotrophic denitrification process for wastewater treatment.

  13. nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China.

    Science.gov (United States)

    Gao, Juan; Hou, Lijun; Zheng, Yanling; Liu, Min; Yin, Guoyu; Li, Xiaofei; Lin, Xianbiao; Yu, Chendi; Wang, Rong; Jiang, Xiaofen; Sun, Xiuru

    2016-10-01

    For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.

  14. Denitrification characteristics of a marine origin psychrophilic aerobic denitrifying bacterium

    Institute of Scientific and Technical Information of China (English)

    Haiyan Zheng; Ying Liu; Guangdong Sun; Xiyan Gao; Qingling Zhang; Zhipei Liu

    2011-01-01

    A psychrophilic aerobic denitrifying bacterium,strain S1-1,was isolated from a biological aerated filter conducted for treatment of recirculating water in a marine aquaculture system.Strain S1-1 was preliminarily identified as Psychrobacter sp.based on the analysis of its 16S rRNA gene sequence,which showed 100% sequence similarity to that of Psychrobacter sp.TSBY-70.Strain S 1-1 grew well either in high nitrate or high nitrite conditions with a removal of 100% nitrate or 63.50% nitrite,and the total nitrogen removal rates could reach to 46.48% and 31.89%,respectively.The results indicated that nitrate was mainly reduced in its logarithmic growth phase with a very low leve 1 accumulation of nitrite,suggesting that the aerobic denitrification process of strain S l-1 occurred mainly in this phase.The GC-MS results showed that N2O was formed as the major intermediate during the aerobic denitrifying process of strain S1-1.Finally,factors affecting the growth of strain Sl-1 and its aerobic denitrifying ability were also investigated.Results showed that the optimum aerobic denitrification conditions for strain S1-1 were sodium succinate as carbon source,C/N ratio15,salinity 10 g/L NaCl,incubation temperature 20℃ and initial pH 6.5.

  15. A doubling of microphytobenthos biomass coincides with a tenfold increase in denitrifier and total bacterial abundances in intertidal sediments of a temperate estuary.

    Directory of Open Access Journals (Sweden)

    Helen Decleyre

    Full Text Available Surface sediments are important systems for the removal of anthropogenically derived inorganic nitrogen in estuaries. They are often characterized by the presence of a microphytobenthos (MPB biofilm, which can impact bacterial communities in underlying sediments for example by secretion of extracellular polymeric substances (EPS and competition for nutrients (including nitrogen. Pyrosequencing and qPCR was performed on two intertidal surface sediments of the Westerschelde estuary characterized by a two-fold difference in MPB biomass but no difference in MPB composition. Doubling of MPB biomass was accompanied by a disproportionately (ten-fold increase in total bacterial abundances while, unexpectedly, no difference in general community structure was observed, despite significantly lower bacterial richness and distinct community membership, mostly for non-abundant taxa. Denitrifier abundances corresponded likewise while community structure, both for nirS and nirK denitrifiers, remained unchanged, suggesting that competition with diatoms for nitrate is negligible at concentrations in the investigated sediments (appr. 1 mg/l NO3-. This study indicates that MPB biomass increase has a general, significantly positive effect on total bacterial and denitrifier abundances, with stimulation or inhibition of specific bacterial groups that however do not result in a re-structured community.

  16. Mapping spatial patterns of denitrifiers for bridging community ecology and microbial processes along environmental gradients

    Science.gov (United States)

    Bru, D.; Cuhel, J.; Saby, N.; Cheneby, D.; Chronokova, A.; Arrouays, D.; Martin-Laurent, F.; Simek, M.

    2010-12-01

    While there is ample evidence that microbial processes can exhibit large variations at a field scale, very little is known about the spatial distribution of the communities mediating these processes. To explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes.We used geostatistical modeling to map the distribution of size and activity of the denitrifier community in the pasture. Size of the denitrifier community was estimated by PCR quantification of the denitrification gene copy numbers while its activity was estimated by measuring potential denitrification activity and potential N2O emissions. Non-random distribution patterns of the size and of the activity of the denitrifier community were observed with a field-scale spatial dependence. The soil properties, which were strongly affected by presence of cattle, imposed significant control on potential denitrification activity, potential N2O production but not on the size of the denitrifier community. The relative abundance of bacteria possessing the nosZ gene encoding the N2O reductase within the total bacterial community was a strong predictor of the N2O/N2 ratio. Our results clearly indicated that patterns of distribution of the abundance of denitrifiers can be modelled at a field scale. Characterization of such pattern at a field-scale constitutes the first step in modelling distribution of functional bacterial communities at a scale compatible with land management strategies. The absolute abundance of most denitrification genes was not correlated with potential denitrification activity or potential N2O production. However, the relative abundance of bacteria possessing the nosZ gene in the total bacterial community was a strong predictor of the N2O/(N2+N2O) ratio, suggesting a relationship between ecosystem processes and bacterial community composition.

  17. Denitrifying kinetics and nitrous oxide emission under different copper concentrations.

    Science.gov (United States)

    Wu, Guangxue; Zhai, Xiaofeng; Jiang, Chengai; Guan, Yuntao

    2014-01-01

    Denitrifying activities and nitrous oxide (N2O) emission during denitrification can be affected by copper concentrations. Different denitrifiers were acclimated in sequencing batch reactors with acetate or methanol as the electron donor and nitrate as the electron acceptor. The effect of copper concentrations on the denitrifying activity and N2O emission for the acclimated denitrifiers was examined in batch experiments. Denitrifying activities of the acclimated denitrifiers declined with increasing copper concentrations, and the copper concentration exhibited a higher effect on denitrifiers acclimated with acetate than those acclimated with methanol. Compared with the control without the addition of copper, at the copper concentration of 1 mg/L, the acetate utilization rate reduced by 89% for acetate-acclimated denitrifiers, while the methanol utilization rate only reduced by 15% for methanol-acclimated denitrifiers. Copper also had different effects on N2O emission during denitrification carried out by various types of denitrifiers. For the acetate-acclimated denitrifiers, N2O emission initially increased and then decreased with increasing copper concentrations, while for the methanol-acclimated denitrifiers, N2O emission decreased with increasing copper concentrations.

  18. Anaerobic degradation of long-chain alkylamines by a denitrifying Pseudomonas stutzeri

    NARCIS (Netherlands)

    Nguyen, P.D.; Ginkel, van C.G.; Plugge, C.M.

    2008-01-01

    The anaerobic degradation of tetradecylamine and other long-chain alkylamines by a newly isolated denitrifying bacterium was studied. Strain ZN6 was isolated from a mixture of soil and active sludge and was identified as representing Pseudomonas stutzeri, based on partial 16S rRNA gene sequence anal

  19. Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems

    DEFF Research Database (Denmark)

    McIlroy, Simon Jon; Szyszka, Anna; Starnawski, Piotr Marian;

    2016-01-01

    incubations, under nitrite reducing conditions, in order to better capture the diversity of active denitrifiers present. Members of the Rhodoferax, Dechloromonas and Sulfuritalea were well represented in the 16S rRNA gene clone libraries from DNA enriched in 13 C, with FISH probes designed here...

  20. Warming-induced changes in denitrifier community structure modulate the ability of phototrophic river biofilms to denitrify

    Energy Technology Data Exchange (ETDEWEB)

    Boulêtreau, Stéphanie, E-mail: stephanie.bouletreau@univ-tlse3.fr [Université de Toulouse, UPS, INP, EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), 118 route de Narbonne, F-31062 Toulouse (France); CNRS, EcoLab, F-31062 Toulouse (France); Lyautey, Emilie [Université de Toulouse, UPS, INP, EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), 118 route de Narbonne, F-31062 Toulouse (France); CNRS, EcoLab, F-31062 Toulouse (France); Dubois, Sophie [Université de Bordeaux, EPOC - OASU, UMR 5805, Station Marine d' Arcachon, 2 rue du Professeur Jolyet, 33120 Arcachon (France); Compin, Arthur [Université de Toulouse, UPS, INP, EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), 118 route de Narbonne, F-31062 Toulouse (France); CNRS, EcoLab, F-31062 Toulouse (France); Delattre, Cécile; Touron-Bodilis, Aurélie [EDF Recherche et Développement, LNHE (Laboratoire National d' Hydraulique et Environnement), 6 quai Watier, F-78401 Chatou (France); Mastrorillo, Sylvain [Université de Toulouse, UPS, INP, EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement), 118 route de Narbonne, F-31062 Toulouse (France); CNRS, EcoLab, F-31062 Toulouse (France); Garabetian, Frédéric [Université de Bordeaux, EPOC - OASU, UMR 5805, Station Marine d' Arcachon, 2 rue du Professeur Jolyet, 33120 Arcachon (France)

    2014-01-01

    Microbial denitrification is the main nitrogen removing process in freshwater ecosystems. The aim of this study was to show whether and how water warming (+ 2.5 °C) drives bacterial diversity and structuring and how bacterial diversity affects denitrification enzymatic activity in phototrophic river biofilms (PRB). We used water warming associated to the immediate thermal release of a nuclear power plant cooling circuit to produce natural PRB assemblages on glass slides while testing 2 temperatures (mean temperature of 17 °C versus 19.5 °C). PRB were sampled at 2 sampling times during PRB accretion (6 and 21 days) in both temperatures. Bacterial community composition was assessed using ARISA. Denitrifier community abundance and denitrification gene mRNA levels were estimated by q-PCR and qRT-PCR, respectively, of 5 genes encoding catalytic subunits of the denitrification key enzymes. Denitrification enzyme activity (DEA) was measured by the acetylene-block assay at 20 °C. A mean water warming of 2.5 °C was sufficient to produce contrasted total bacterial and denitrifier communities and, therefore, to affect DEA. Indirect temperature effect on DEA may have varied between sampling time, increasing by up to 10 the denitrification rate of 6-day-old PRB and decreasing by up to 5 the denitrification rate of 21-day-old PRB. The present results suggest that indirect effects of warming through changes in bacterial community composition, coupled to the strong direct effect of temperature on DEA already demonstrated in PRB, could modulate dissolved nitrogen removal by denitrification in rivers and streams. - Highlights: •We produced river biofilms in 2 mean temperature conditions: 17 vs 19.5 °C. •We compared their denitrifiers' structuring and functioning in 6d- and 21d-old biofilms. •A difference of 2.5 °C produced contrasted denitrifier communities. •The indirect temperature effect on denitrification activity shifted between biofilm age.

  1. Soil denitrifier community size changes with land use change to perennial bioenergy cropping systems

    Science.gov (United States)

    Thompson, Karen A.; Deen, Bill; Dunfield, Kari E.

    2016-10-01

    Dedicated biomass crops are required for future bioenergy production. However, the effects of large-scale land use change (LUC) from traditional annual crops, such as corn-soybean rotations to the perennial grasses (PGs) switchgrass and miscanthus, on soil microbial community functioning is largely unknown. Specifically, ecologically significant denitrifying communities, which regulate N2O production and consumption in soils, may respond differently to LUC due to differences in carbon (C) and nitrogen (N) inputs between crop types and management systems. Our objective was to quantify bacterial denitrifying gene abundances as influenced by corn-soybean crop production compared to PG biomass production. A field trial was established in 2008 at the Elora Research Station in Ontario, Canada (n  =  30), with miscanthus and switchgrass grown alongside corn-soybean rotations at different N rates (0 and 160 kg N ha-1) and biomass harvest dates within PG plots. Soil was collected on four dates from 2011 to 2012 and quantitative PCR was used to enumerate the total bacterial community (16S rRNA) and communities of bacterial denitrifiers by targeting nitrite reductase (nirS) and N2O reductase (nosZ) genes. Miscanthus produced significantly larger yields and supported larger nosZ denitrifying communities than corn-soybean rotations regardless of management, indicating large-scale LUC from corn-soybean to miscanthus may be suitable in variable Ontario climatic conditions and under varied management, while potentially mitigating soil N2O emissions. Harvesting switchgrass in the spring decreased yields in N-fertilized plots, but did not affect gene abundances. Standing miscanthus overwinter resulted in higher 16S rRNA and nirS gene copies than in fall-harvested crops. However, the size of the total (16S rRNA) and denitrifying bacterial communities changed differently over time and in response to LUC, indicating varying controls on these communities.

  2. Distribution Characteristics of Nitrifiers and Denitrifiers in the Rive r Sediments of Tongling City%铜陵市河流沉积物中硝化和反硝化微生物分布特征

    Institute of Scientific and Technical Information of China (English)

    程建华; 窦智勇; 孙庆业

    2016-01-01

    Rivers in mining areas were influenced by contaminants such as nitrogen, phosphorus and organic matter due to domestic and agricultural wastewater discharge in addition to pollutants caused by mining activities. In this study, surface sediment samples of rivers in Tongling city were collected to address the effect of season and pollution type on the abundance of nitrifiers and denitrifiers using quantitative polymerase chain reaction ( QPCR) technique targeting at the ammonia monooxygenase ( amoA) and nitrite reductase (nir) genes. The results showed that the average abundance of ammonia oxidizing archaea (AOA) (ranging from 1. 74 × 105 to 1. 45 × 108 copies•g-1 ) was 4. 39 times that of ammonia oxidizing bacteria ( AOB) ( ranging from 1. 39 × 105 to 3. 39 × 107 copies•g-1 );and the average abundance of nirK gene ( ranging from 4. 45 × 106 to 1. 51 × 108 copies•g-1 ) was almost a thirtieth part of nirS gene ( ranging from 1. 69 × 107 to 8. 55 × 109 copies•g-1 ) . The abundance of AOA was higher in spring and autumn, and lower in summer and winter. And sediment AOB abundance was higher in spring and winter than in summer and autumn. Meanwhile, the abundance of nir genes was in the order of spring ( nirS)/autumn ( nirK) ﹥summer ﹥ winter ﹥ autumn ( nirS)/spring ( nirK). Moreover, the abundance of bacterial and archaeal amoA and nirS genes in sediments influenced by mine pollution was generally higher than that in sediments influenced by agricultural non-point pollution, whereas the abundance of nirK gene showed an opposite trend.%矿区河流不仅受到矿业活动带来污染物的影响,还受到区域内生活污水及农田退水中氮、磷和有机物的污染.本研究以铜陵市河流表层沉积物为研究对象,采用荧光定量PCR技术分析季节和污染类型对沉积物样品中硝化( amoA )和反硝化( nirS和nirK)功能基因丰度的影响.结果表明,沉积物样品中氨氧化古菌( AOA)和细菌( AOB)基因

  3. Anaerobic degradation of long-chain alkylamines by a denitrifying Pseudomonas stutzeri.

    Science.gov (United States)

    Nguyen, Phuong D; van Ginkel, Cornelis G; Plugge, Caroline M

    2008-10-01

    The anaerobic degradation of tetradecylamine and other long-chain alkylamines by a newly isolated denitrifying bacterium was studied. Strain ZN6 was isolated from a mixture of soil and active sludge and was identified as representing Pseudomonas stutzeri, based on partial 16S rRNA gene sequence analysis. Strain ZN6 was a mesophilic, motile, Gram-negative rod-shaped bacterium and was able to grow on a variety of compounds including even-numbered primary fatty amines with alkyl chains ranging from C(4) to C(18) coupled to nitrate reduction. Alkylamines were used as sole carbon, energy and nitrogen source and were completely mineralized. Nitrate was dissimilated by ZN6 to nitrite. When strain ZN6 was grown under nitrate limitation, nitrite was slowly dissimilated further. When cocultivated with the complete denitrifier Castellaniella defragens ZN3, anaerobic degradation under denitrifying of alkylamines by strain ZN6 was slightly faster. Strain ZN3 is a complete denitrifier, unable to convert tetradecylamine, and was copurified from the same enrichment culture as strain ZN6. The proposed pathway for the degradation of alkylamines in strain ZN6 starts with C-N cleavages to alkanals and further oxidation to the corresponding fatty acids.

  4. Mapping field-scale spatial patterns of size and activity of the denitrifier community.

    Science.gov (United States)

    Philippot, Laurent; Cuhel, Jiri; Saby, Nicolas P A; Chèneby, Dominique; Chronáková, Alicia; Bru, David; Arrouays, Dominique; Martin-Laurent, Fabrice; Simek, Miloslav

    2009-06-01

    There is ample evidence that microbial processes can exhibit large variations in activity on a field scale. However, very little is known about the spatial distribution of the microbial communities mediating these processes. Here we used geostatistical modelling to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We observed a non-random distribution pattern of the size of the denitrifier community estimated by quantification of the denitrification genes copy numbers with a macro-scale spatial dependence (6-16 m) and mapped the distribution of this functional guild in the field. The spatial patterns of soil properties, which were strongly affected by presence of cattle, imposed significant control on potential denitrification activity, potential N(2)O production and relative abundance of some denitrification genes but not on the size of the denitrifier community. Absolute abundance of most denitrification genes was not correlated with the distribution patterns of potential denitrification activity or potential N(2)O production. However, the relative abundance of bacteria possessing the nosZ gene encoding the N(2)O reductase in the total bacterial community was a strong predictor of the N(2)O/(N(2) + N(2)O) ratio, which provides evidence for a relationship between bacterial community composition based on the relative abundance of denitrifiers in the total bacterial community and ecosystem processes. More generally, the presented geostatistical approach allows integrated mapping of microbial communities, and hence can facilitate our understanding of relationships between the ecology of microbial communities and microbial processes along environmental gradients.

  5. Screening and identification of aerobic denitrifiers

    Science.gov (United States)

    Shao, K.; Deng, H. M.; Chen, Y. T.; Zhou, H. J.; Yan, G. X.

    2016-08-01

    With the standards of the effluent quality more stringent, it becomes a quite serious problem for municipalities and industries to remove nitrogen from wastewater. Bioremediation is a potential method for the removal of nitrogen and other pollutants because of its high efficiency and low cost. Seven predominant aerobic denitrifiers were screened and characterized from the activated sludge in the CAST unit. Some of these strains removed 87% nitrate nitrogen at least. Based on their phenotypic and phylogenetic characteristics, the isolates were identified as the genera of Ralstonia, Achromobacter, Aeromonas and Enterobacter.

  6. [Analysis on Diversity of Denitrifying Microorganisms in Sequential Batch Bioreactor Landfill].

    Science.gov (United States)

    Li, Wei-Hua; Sun, Ying-Jie; Liu, Zi-Liang; Ma, Qiang; Yang, Qiang

    2016-01-15

    A denitrification functional microorganism gene clone library (amoA, nosZ) and the PCR-RFLP technology was constructed to investigate the microbial diversity of denitrifying microorganisms in the late period of stabilization of sequential batch bioreactor landfill. The results indicated that: the bacterial diversity of ammonia oxidizing bacteria in the aged refuse reactor was very high, and most of them were unknown groups, also, all bacteria were unculturable or had not been isolated. The phylogenetic analysis suggested that the dominant ammonia oxidizing bacteria were presumably Nitrosomonas of 6-Proteobacteria. The diversity of denitrifying bacteria in fresh refuse reactor was abundant, which mainly included Thauera and Thiobacillus of 6-Proteobacteria. As Thauera sp. has the denitrification characteristics under the condition of aerobic while Thiobacillus denitrificans has the autotrophic denitrification characteristics, it was speculated that aerobic denitrification and autotrophic denitrification might be the main pathways for nitrogen removal in the fresh refuse reactor at the late period of stabilization. Additionally, another group in the gene clone library of denitrifying bacteria may be classified as Bradyrhizobiaceae of alpha-Proteobacteria.

  7. New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

    Science.gov (United States)

    Imhoff, Johannes F.

    2016-01-01

    During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane

  8. New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

    Directory of Open Access Journals (Sweden)

    Johannes F. Imhoff

    2016-05-01

    Full Text Available During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA as target for the green sulfur bacteria and of two reaction center proteins (pufLM for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS reductase (aprA, sulfate thioesterase (soxB and dissimilatory sulfite reductase (dsrAB for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK for denitrifying bacteria and with genes

  9. New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment.

    Science.gov (United States)

    Imhoff, Johannes F

    2016-05-24

    During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane

  10. A comparative study of the bacterial community in denitrifying and traditional enhanced biological phosphorus removal processes.

    Science.gov (United States)

    Lv, Xiao-Mei; Shao, Ming-Fei; Li, Chao-Lin; Li, Ji; Gao, Xin-Lei; Sun, Fei-Yun

    2014-09-17

    Denitrifying phosphorus removal is an attractive wastewater treatment process due to its reduced carbon source demand and sludge minimization potential. Two lab-scale sequencing batch reactors (SBRs) were operated in alternating anaerobic-anoxic (A-A) or anaerobic-oxic (A-O) conditions to achieve denitrifying enhanced biological phosphate removal (EBPR) and traditional EBPR. No significant differences were observed in phosphorus removal efficiencies between A-A SBR and A-O SBR, with phosphorus removal rates being 87.9% and 89.0% respectively. The community structures in denitrifying and traditional EBPR processes were evaluated by high-throughput sequencing of the PCR-amplified partial 16S rRNA genes from each sludge. The results obtained showed that the bacterial community was more diverse in A-O sludge than in A-A sludge. Taxonomy and β-diversity analyses indicated that a significant shift occurred in the dominant microbial community in A-A sludge compared with the seed sludge during the whole acclimation phase, while a slight fluctuation was observed in the abundance of the major taxonomies in A-O sludge. One Dechloromonas-related OTU outside the 4 known Candidatus "Accumulibacter" clades was detected as the main OTU in A-A sludge at the stationary operation, while Candidatus "Accumulibacter" dominated in A-O sludge.

  11. Isolation and denitrification characteristic of an aerobic denitrifier

    Institute of Scientific and Technical Information of China (English)

    ZHOU Dan-dan; MA Fang; WANG Hong-yu; DONG Shuang-shi; WANG Ai-jie

    2006-01-01

    Aerobic denitrifiers were enriched by activated sludge cultivation method. By this way, 105 strains were isolated from the activated sludge and 25 strains were confirmed to be capable of obtaining energy by deoxidization of nitrate to nitrogen gas under aerobic condition. The characteristic of one denitrifier, Pseudomonas chloritidismutans strain, was particularly studied due to its higher nitrogen removal rate. It was found that Pseudomonas chloritidismutans can use nitrite, nitrate and oxygen for aerobic respiration in liquid medium, and the pH increased and ORP decreased by activated denitrifier. When they used nitrite or nitrate for respiration, nitrogen removal effect was high and nitrite could be reduced more efficiently than nitrate. Denitrification process was accomplished faster when both nitrite and nitrate existed in the medium compared to each of which existed alone. Particularly, at denitrifying activity, the nitrogen removal rate of strain was not affected by the DO concentration in the culture media.

  12. Nitrogen removal and nitrifying and denitrifying bacteria quantification in a stormwater bioretention system.

    Science.gov (United States)

    Chen, Xiaolu; Peltier, Edward; Sturm, Belinda S M; Young, C Bryan

    2013-03-15

    In this study, we examine the biological processes involved in ammonia and nitrate removal in a bioretention system characterized by low infiltration rates and long drainage times. The system removed 33% of influent nitrate and 56% of influent total nitrogen. While influent ammonia concentrations were low (bioretention cell also removed ammonia produced within the treatment system. Soil cores collected from the bioretention cell were analyzed for total 16S rDNA and both nitrification and denitrification genes (amoA, nirS, nirK, norB, and nosZ) using quantitative PCR. Total bacterial 16S rDNA levels in the surface layer were similar to those in very sandy soils. Gene counts for both nitrification and denitrification genes decreased as a function of depth in the media, and corresponded to similar changes in total 16S rDNA. The abundance of denitrification genes was also positively correlated with the average inundation time at each sampling location, as determined by modeling of stormwater data from a three-year period. These results suggest that both nitrification and denitrification can occur in bioretention media. Time of saturation, filter medium, and organic carbon content can all affect the extent of denitrification in bioretention systems.

  13. Investigation of denitrifying microbial communities within an agricultural drainage system fitted with low-grade weirs.

    Science.gov (United States)

    Baker, Beth H; Kröger, Robert; Brooks, John P; Smith, Renotta K; Czarnecki, Joby M Prince

    2015-12-15

    Enhancing wetland characteristics in agricultural drainage ditches with the use of low-grade weirs, has been identified as a best management practice (BMP) to mitigate nutrient runoff from agriculture landscapes. A major objective of utilizing low-grade weirs as a BMP includes fostering environments suitable for the biogeochemical removal of nitrogen via denitrification. This study examined the spatial resolution of microbial communities involved in denitrification in agricultural drainage systems fitted with low-grade weirs. Appropriate sampling scales of microbial communities were investigated using 16S rRNA and denitrification functional genes nosZ, nirS, and nirK via quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP) analysis. Genes 16S rRNA, nosZ, and nirS were all successfully detected in soil samples, while nirK was below the detection limit throughout the study. Utilizing a combination of three sampling regimes (management, reach, catchment) was found to be effective in capturing microbial community patterns, as ANOVA results revealed nosZ gene abundance was significantly greater at the management rather than reach scale (p = 0.045; F = 3.311), although, no significant differences were observed in 16S rRNA or nirS between sampling scales (p > 0.05). A Pearson correlation matrix confirmed that 16S rRNA and nosZ gene abundances were positively correlated with soil carbon (C), nitrogen (N), and moisture, while nirS abundance was only positively correlated with soil C and soil moisture. This highlights the potential for wetland-like characteristics to be recovered in agricultural drainage systems, as weir proximity is observed to enhance soil moisture and conditions for N remediation. This study provides the basis for additional investigations of these unique environments in the Mississippi Alluvial Valley and a starting point for adaptive management to enhance agricultural drainage systems for microbial

  14. Molecular identification of potential denitrifying bacteria and use of D-optimal mixture experimental design for the optimization of denitrification process.

    Science.gov (United States)

    Ben Taheur, Fadia; Fdhila, Kais; Elabed, Hamouda; Bouguerra, Amel; Kouidhi, Bochra; Bakhrouf, Amina; Chaieb, Kamel

    2016-04-01

    Three bacterial strains (TE1, TD3 and FB2) were isolated from date palm (degla), pistachio and barley. The presence of nitrate reductase (narG) and nitrite reductase (nirS and nirK) genes in the selected strains was detected by PCR technique. Molecular identification based on 16S rDNA sequencing method was applied to identify positive strains. In addition, the D-optimal mixture experimental design was used to optimize the optimal formulation of probiotic bacteria for denitrification process. Strains harboring denitrification genes were identified as: TE1, Agrococcus sp LN828197; TD3, Cronobacter sakazakii LN828198 and FB2, Pedicoccus pentosaceus LN828199. PCR results revealed that all strains carried the nirS gene. However only C. sakazakii LN828198 and Agrococcus sp LN828197 harbored the nirK and the narG genes respectively. Moreover, the studied bacteria were able to form biofilm on abiotic surfaces with different degree. Process optimization showed that the most significant reduction of nitrate was 100% with 14.98% of COD consumption and 5.57 mg/l nitrite accumulation. Meanwhile, the response values were optimized and showed that the most optimal combination was 78.79% of C. sakazakii LN828198 (curve value), 21.21% of P. pentosaceus LN828199 (curve value) and absence (0%) of Agrococcus sp LN828197 (curve value).

  15. Detection of N2O-producing fungi in environment using nitrite reductase gene (nirK)-targeting primers.

    Science.gov (United States)

    Chen, Huaihai; Yu, Fangbo; Shi, Wei

    2016-12-01

    Fungal denitrification has been increasingly investigated, but its community ecology is poorly understood due to the lack of culture-independent tools. In this work, four pairs of nirK-targeting primers were designed and evaluated for primer specificity and efficiency using thirty N2O-producing fungal cultures and an agricultural soil. All primers amplified nirK from fungi and soil, but their efficiency and specificity were different. A primer set, FnirK_F3/R2 amplified ∼80 % of tested fungi, including Aspergillus, Fusarium, Penicillium, and Trichoderma, as compared to ∼40-70 % for other three primers. The nirK fragments of fungal and soil DNA amplified by FnirK_F3/R2 were phylogenetically related to denitrifying fungi in the orders Eurotiales, Hypocreales, and Sordariales; and clone sequences were also distributed in the clusters of Chaetomium, Metarhizium, and Myceliophthora that were uncultured from soil in our previous work. This proved the wide-range capability of primers for amplifying diverse denitrifying fungi from environment. However, our primers and recently-developed other primers amplified bacterial nirK from soil and this co-amplification of fungal and bacterial nirK was theoretically discussed. The FnirK_F3/R2 was further compared with published primers; results from clone libraries demonstrated that FnirK_F3/R2 was more specifically targeted on fungi and had broader taxonomical coverage than some others. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  16. Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities.

    Science.gov (United States)

    Hanke, Anna; Berg, Jasmine; Hargesheimer, Theresa; Tegetmeyer, Halina E; Sharp, Christine E; Strous, Marc

    2015-01-01

    In coastal marine sediments, denitrification and fermentation are important processes in the anaerobic decomposition of organic matter. Microbial communities performing these two processes were enriched from tidal marine sediments in replicated, long term chemostat incubations at 10 and 25°C. Whereas denitrification rates at 25°C were more or less stable over time, at 10°C denitrification activity was unstable and could only be sustained either by repeatedly increasing the amount of carbon substrates provided or by repeatedly decreasing the dilution rate. Metagenomic and transcriptomic sequencing was performed at different time points and provisional whole genome sequences (WGS) and gene activities of abundant populations were compared across incubations. These analyses suggested that a temperature of 10°C selected for populations related to Vibrionales/Photobacterium that contributed to both fermentation (via pyruvate/formate lyase) and nitrous oxide reduction. At 25°C, denitrifying populations affiliated with Rhodobacteraceae were more abundant. The latter performed complete denitrification, and may have used carbon substrates produced by fermentative populations (cross-feeding). Overall, our results suggest that a mixture of competition-for substrates between fermentative and denitrifying populations, and for electrons between both pathways active within a single population -, and cross feeding-between fermentative and denitrifying populations-controlled the overall rate of denitrification. Temperature was shown to have a strong selective effect, not only on the populations performing either process, but also on the nature of their ecological interactions. Future research will show whether these results can be extrapolated to the natural environment.

  17. Identification and Metabolic Mechanism of Non-fermentative Short-cut Denitrifying Phosphorus-removing Bacteria

    Institute of Scientific and Technical Information of China (English)

    LIU Hui; SUN Yanfu; JIA Xiaoshan; LI Jun; ZHOU Kangqun; QU Xiangdong; TAO Xueqin

    2013-01-01

    To investigate the characteristics and metabolic mechanism of short-cut denitrifying phosphorus-removing bacteria (SDPB) that are capable of enhanced biological phosphorus removal (EBPR) using nitrite as an electron acceptor,an aerobic/anoxic sequencing batch reactor was operated under three phases.An SDPB-strain YC was screened after the sludge enrichment and was identified by morphological,physiological,biochemical properties and 16S rDNA gene sequence analysis.Denitrifying phosphorus-removing experiments were conducted to study anaerobic and anoxic metabolic mechanisms by analyzing the changes of chemical oxygen demand (COD),phosphate,nitrite,poly-fβ-hydroxybutyrate (PHB),and glycogen.The results show that strain YC is a non-fermentative SDPB similar to Paracoccus denitrificans.As a kind of non-fermentative bacteria,the energy of strain YC was mainly generated from phosphorus release (96.2%) under anaerobic conditions with 0.32 mg P per mg synthesized PHB.Under anoxic conditions,strain YC accumulated 0.45 mg P per mg degraded PHB,which produced most of energy for phosphate accumulation (91.3%) and a little for glycogen synthesis (8.7%).This metabolic mechanism of strain YC is different from that of traditional phosphorus-accumulating organisms (PAOs).It is also found that PHB,a kind of intracellular polymer,plays a very important role in denitrifying and accumulating phosphorus by supplying sufficient energy for phosphorous accumulation and carbon sources for denitrification.Therefore,monitoring △P/△PHB and △NO2--N/△PHB is more necessary than monitoring △P/△COD,△NO2--N/△COD,or △P/△NO2--N.

  18. Selective pressure of temperature on competition and cross-feeding within denitrifying and fermentative microbial communities

    Directory of Open Access Journals (Sweden)

    Anna eHanke

    2016-01-01

    Full Text Available In coastal marine sediments, denitrification and fermentation are important processes in the anaerobic decomposition of organic matter. Microbial communities performing these two processes were enriched from tidal marine sediments in replicated, long term chemostat incubations at 10ºC and 25ºC. Whereas denitrification rates at 25ºC were more or less stable over time, at 10ºC denitrification activity was unstable and could only be sustained either by repeatedly increasing the amount of carbon substrates provided or by repeatedly decreasing the dilution rate. Metagenomic and transcriptomic sequencing was performed at different time points and provisional whole genome sequences and gene activities of abundant populations were compared across incubations. These analyses suggested that a temperature of 10ºC selected for populations related to Vibrionales/Photobacterium that contributed to both fermentation (via pyruvate/formate lyase and nitrous oxide reduction. At 25ºC, denitrifying populations affiliated with Rhodobacteracaea were more abundant. The latter performed complete denitrification, and may have used carbon substrates produced by fermentative populations (cross-feeding. Overall, our results suggest that a mixture of competition – for substrates between fermentative and denitrifying populations, and for electrons between both pathways active within a single population –, and cross feeding – between fermentative and denitrifying populations – controlled the overall rate of denitrification. Temperature was shown to have a strong selective effect, not only on the populations performing either process, but also on the nature of their ecological interactions. Future research will show whether these results can be extrapolated to the natural environment.

  19. Responses of activities, abundances and community structures of soil denitrifiers to short-term mercury stress

    Institute of Scientific and Technical Information of China (English)

    Zhifeng Zhou; Yuanming Zheng; Jupei Shen; Limei Zhang; Yurong Liu; Jizheng He

    2012-01-01

    The responses of activities,abundances and community structures of soil denitrifiers to mercury(Hg)stress were investigated through a short-term incubation experiment.Four soil treatments with different concentrations of Hg(CK,Hg25,Hg50,and Hgl00,denoted as 0,25,50,and 100 mg Hg/kg dry soil,respectively)were incubated for 28 days.Soil denitrification enzyme activity(DEA)was measured at day 3,7 and 28.The abundances and community structures of two denitrification concerning genes,nirS(Cd1-nitrite reductase gene)and nosZ(nitrous oxide reductase gene),were analyzed using real-time PCR and denaturing gradient gel electrophoresis(DGGE).Results showed that soil DEA was significantly stimulated in the treatments of Hg25 and Hg50 compared with others at day 7.Meanwhile,no difference in the abundances of soil nirS and nosZ was found between Hg spiked treatments and CK,except the lower abundance of nirS(P < 0.05)in the Hg added treatments compared with that in the CK at day 28.The community structures of denitrifiers based on nirS gene presented obvious change at day 7 along with the Hg additions,however,no variation was found in all treatments based on the nosZ gene.The results indicated that Hg(Hg25 and Hg50)had a strongly short-term stimulation on soil DEA,and nirS gene is more sensitive than nosZ gene to Hg stress.

  20. Specific microbial gene abundances and soil parameters contribute to C, N, and greenhouse gas process rates after land use change in Southern Amazonian Soils

    Directory of Open Access Journals (Sweden)

    Daniel Renato Lammel

    2015-10-01

    Full Text Available Ecological processes regulating soil carbon (C and nitrogen (N cycles are still poorly understood, especially in the world’s largest agricultural frontier in Southern Amazonia. We analyzed soil parameters in samples from pristine rainforest and after land use change to pasture and crop fields, and correlated them with abundance of functional and phylogenetic marker genes (amoA, nirK, nirS, norB, nosZ, nifH, mcrA, pmoA, and 16S/18S rRNA. Additionally, we integrated these parameters using path analysis and multiple regressions. Following forest removal, concentrations of soil C and N declined, and pH and nutrient levels increased, which influenced microbial abundances and biogeochemical processes. A seasonal trend was observed, suggesting that abundances of microbial groups were restored to near native levels after the dry winter fallow. Integration of the marker gene abundances with soil parameters using path analysis and multiple regressions provided good predictions of biogeochemical processes, such as the fluxes of NO3, N2O, CO2, and CH4. In the wet season, agricultural soil showed the highest abundance of nitrifiers (amoA and Archaea, however forest soils showed the highest abundances of denitrifiers (nirK, nosZ and high N, which correlated with increased N2O emissions. Methanogens (mcrA and methanotrophs (pmoA were more abundant in forest soil, but methane flux was highest in pasture sites, which was related to soil compaction. Rather than analyzing direct correlations, the data integration using multivariate tools provided a better overview of biogeochemical processes. Overall, in the wet season, land use change from forest to agriculture reduced the abundance of different functional microbial groups related to the soil C and N cycles; integrating the gene abundance data and soil parameters provided a comprehensive overview of these interactions. Path analysis and multiple regressions addressed the need for more comprehensive approaches

  1. Study on separation and induction of high efficient denitrifier

    Institute of Scientific and Technical Information of China (English)

    HUO Ai-qun; YU Tao; TAN Xin; ZHAO Lin

    2005-01-01

    A kind of denitrifier HY - 1 initially obtained from activated sludge was domesticated and inducted with UV and illumination to a new species bacterium HY -2 that has high bioactivity at low temperature. HY 2 was most active at 13 ℃. Nitrate and CODer removal efficiency was investigated under different temperature and C/N ratio.

  2. Hydraulic flow characteristics of agricultural residues for denitrifying bioreactor media

    Science.gov (United States)

    Denitrifying bioreactors are a promising technology to mitigate agricultural subsurface drainage nitrate-nitrogen losses, a critical water quality goal for the Upper Mississippi River Basin. This study was conducted to evaluate the hydraulic properties of agricultural residues that are potential bio...

  3. Denitrifying bioreactors for nitrate removal from tile drained cropland

    Science.gov (United States)

    Denitrification bioreactors are a promising technology for mitigation of nitrate-nitrogen (NO3-N) losses in subsurface drainage water. Bioreactors are constructed with carbon substrates, typically wood chips, to provide a substrate for denitrifying microorganisms. Researchers in Iowa found that for ...

  4. Isolation and characteristic of an aerobic denitrifier with high ...

    African Journals Online (AJOL)

    Administrator

    2011-09-12

    Sep 12, 2011 ... intermittent aeration mode, and each running period lasted for 24 h, including periods of ... and suspended in 30% glycerol solution at -40 °C for long-term storage. .... energy and electron need of denitrify 420 mg/l nitrate. The.

  5. Emergent macrophytes select for nitrifying and denitrifying microorganisms in constructed wetlands

    Science.gov (United States)

    Trias, Rosalia; Ramió Pujol, Sara; Bañeras, Lluis

    2014-05-01

    The use of constructed wetlands for wastewater treatment is a reliable low-cost alternative that has been widely developed during the last years. Several processes involving plants, sediments, and microbial communities contribute to nitrogen removal in wetlands. Vegetation plays an important role in this process, not only by nutrient assimilation but also by the stimulation of the plant associated microbiota. Plants supply oxygen at the close proximity of the root surface that may favour ammonia oxidizers. At the same time, exudation of organic compounds potentially speeds-up denitrification in the anoxic environment. The aim of this work was to understand the plant-microbe interactions at the root level in the Empuriabrava free water surface constructed wetland (Spain). The roots of the macrophytes Typha latifolia, Typha angustifolia, Phragmites australis and Bolboschoenus maritimus were sampled at four dates from January to September 2012, covering all the stages of plant growth. Additionally, sediment surrounding vegetation and non-vegetated sediments were sampled. Microbial community structure was analysed by pyrosequencing of bacterial and archaeal 16S rDNA and functional genes (nirK, nirS, nosZ and amoA). Bacterial communities were significantly different in sediments of the vegetated areas compared to the root surface. Plant roots exhibited a higher proportion of proteobacteria whereas Actinobacteria were dominant in sediments. The nitrifiers Nitrosomonas sp. and Nitrosococcus sp. accounted for less than 1% of all sequences. Archaeal communities were dominated by the Miscellaneous Crenarchaeotic Groups C2 and C3 and Methanomicrobia. Higher relative abundances of MCG were found in roots of P. australis, B. maritimus and T. angustifolia. Ammonia oxidizing archaea accounted for less than 0.1% of all sequences but were consistently more abundant in sediment samples compared to roots. NirK and NirS-type bacterial communities showed clearly distinct distribution

  6. Trace Gas Emission from in-Situ Denitrifying Bioreactors

    Science.gov (United States)

    Pluer, W.; Walter, M. T.; Geohring, L.

    2014-12-01

    Despite decades of concerted effort to mitigate nonpoint source nitrate (NO3-) pollution from agricultural lands, these efforts have not been sufficient to arrest eutrophication. A primary process for removing excess NO3- from water is denitrification, where denitrifying bacteria use NO3- for respiration in the absence of oxygen. Denitrification results in reduced forms of nitrogen, often dinitrogen gas (N2) but also nitrous oxide (N2O), an aggressive greenhouse gas. A promising solution to NO3- pollution is to intercept agricultural discharges with denitrifying bioreactors (DNBRs). DNBRs provide conditions ideal for denitrifiers: an anaerobic environment, sufficient organic matter, and excess NO3-. These conditions are also ideal for methanogens, which produce methane (CH4), another harmful trace gas. While initial results from bioreactor studies show that they can cost-effectively remove NO3-, trace gas emissions are an unintended consequence. This study's goal was to determine how bioreactor design promotes denitrification while limiting trace gas production. Reactor inflow and outflow water samples were tested for nutrients, including NO3-, and dissolved inflow and outflow gas samples were tested for N2O and CH4. NO3- reduction and trace gas production were evaluated at various residence times, pHs, and inflow NO3- concentrations in field and lab-scale reactors. Low NO3- reduction indicated conditions that stressed denitrifying bacteria while high reductions indicated designs that optimized pollutant treatment for water quality. Several factors influenced high N2O, suggesting non-ideal conditions for the final step of complete denitrification. High CH4 emissions pointed to reactor media choice for discouraging methanogens, which may remove competition with denitrifiers. It is critical to understand all of potential impacts that DNBRs may have, which means identifying processes and design specifications that may affect them.

  7. Impact of varying electron donors on the molecular microbial ecology and biokinetics of methylotrophic denitrifying bacteria.

    Science.gov (United States)

    Baytshtok, Vladimir; Lu, Huijie; Park, Hongkeun; Kim, Sungpyo; Yu, Ran; Chandran, Kartik

    2009-04-15

    The goal of this study was to identify bacterial populations that assimilated methanol in a denitrifying sequencing batch reactor (SBR), using stable isotope probing (SIP) of (13)C labeled DNA and quantitatively track changes in these populations upon changing the electron donor from methanol to ethanol in the SBR feed. Based on SIP derived (13)C 16S rRNA gene clone libraries, dominant SBR methylotrophic bacteria were related to Methyloversatilis spp. and Hyphomicrobium spp. These methylotrophic populations were quantified via newly developed real-time PCR assays. Upon switching the electron donor from methanol to ethanol, Hyphomicrobium spp. concentrations decreased significantly in accordance with their obligately methylotrophic nutritional mode. In contrast, Methyloversatilis spp. concentrations were relatively unchanged, in accordance with their ability to assimilate both methanol and ethanol. Direct assimilation of ethanol by Methyloversatilis spp. but not Hyphomicrobium spp. was also confirmed via SIP. The reduction in methylotrophic bacterial concentration upon switching to ethanol was paralleled by a significant decrease in the methanol supported denitrification biokinetics of the SBR on nitrate. In sum, the results of this study demonstrate that the metabolic capabilities (methanol assimilation and metabolism) and substrate specificity (obligately or facultatively methylotrophic) of two distinct methylotrophic bacterial populations contributed to their survival or washout in denitrifying bioreactors. 2008 Wiley Periodicals, Inc.

  8. Responses of bacterial community structure and denitrifying bacteria in biofilm to submerged macrophytes and nitrate

    Science.gov (United States)

    Zhang, Songhe; Pang, Si; Wang, Peifang; Wang, Chao; Guo, Chuan; Addo, Felix Gyawu; Li, Yi

    2016-10-01

    Submerged macrophytes play important roles in constructed wetlands and natural water bodies, as these organisms remove nutrients and provide large surfaces for biofilms, which are beneficial for nitrogen removal, particularly from submerged macrophyte-dominated water columns. However, information on the responses of biofilms to submerged macrophytes and nitrogen molecules is limited. In the present study, bacterial community structure and denitrifiers were investigated in biofilms on the leaves of four submerged macrophytes and artificial plants exposed to two nitrate concentrations. The biofilm cells were evenly distributed on artificial plants but appeared in microcolonies on the surfaces of submerged macrophytes. Proteobacteria was the most abundant phylum in all samples, accounting for 27.3-64.8% of the high-quality bacterial reads, followed by Chloroflexi (3.7-25.4%), Firmicutes (3.0-20.1%), Acidobacteria (2.7-15.7%), Actinobacteria (2.2-8.7%), Bacteroidetes (0.5-9.7%), and Verrucomicrobia (2.4-5.2%). Cluster analysis showed that bacterial community structure can be significantly different on macrophytes versus from those on artificial plants. Redundancy analysis showed that electrical conductivity and nitrate concentration were positively correlated with Shannon index and operational taxonomic unit (OTU) richness (log10 transformed) but somewhat negatively correlated with microbial density. The relative abundances of five denitrifying genes were positively correlated with nitrate concentration and electrical conductivity but negatively correlated with dissolved oxygen.

  9. DRIVERS OF THE DYNAMICS OF DIAZOTROPHS AND DENITRIFIERS IN NORTH SEA BOTTOM WATERS AND SEDIMENTS

    Directory of Open Access Journals (Sweden)

    Lucas eStal

    2015-07-01

    Full Text Available The fixation of dinitrogen (N2 and denitrification are two opposite processes in the nitrogen cycle. The former transfers atmospheric dinitrogen gas into bound nitrogen in the biosphere, while the latter returns this bound nitrogen back to atmospheric dinitrogen. It is unclear whether or not these processes are intimately connected in any microbial ecosystem or that they are spatially and/or temporally separated. Here, we measured seafloor nitrogen fixation and denitrification as well as pelagic nitrogen fixation by using the stable isotope technique. Alongside, we measured the diversity, abundance, and activity of nitrogen-fixing and denitrifying microorganisms at three stations in the southern North Sea. Nitrogen fixation ranged from undetectable to 2.4 nmol N L-1 d-1 and from undetectable to 8.2 nmol N g-1 d-1 in the water column and seafloor, respectively. The highest rates were measured in August at Doggersbank, both for the water column and for the seafloor. Denitrification ranged from 1.7 to 208.8 µmol m-2 d-1 and the highest rates were measured in May at the Oyster Grounds. DNA sequence analysis showed sequences of nifH, a structural gene for nitrogenase, related to sequences from anaerobic sulfur/iron reducers and sulfate reducers. Sequences of the structural gene for nitrite reductase, nirS, were related to environmental clones from marine sediments. Quantitative polymerase chain reaction (qPCR data revealed the highest abundance of nifH and nirS genes at the Oyster Grounds. Quantitative reverse transcription polymerase chain reaction (qRT-PCR data revealed the highest nifH expression at Doggersbank and the highest nirS expression at the Oyster Grounds. The distribution of the diazotrophic and denitrifying communities seems to be subject to different selecting factors, leading to spatial and temporal separation of nitrogen fixation and denitrification. These selecting factors include temperature, organic matter availability, and

  10. [Mass spectrometry assay for denitrifying enzyme activity measurement].

    Science.gov (United States)

    Zhang, Li-li; Wu, Zhi-jie; Song, Yu-chao

    2010-07-01

    Nitrification inhibitors exert inhibition function in soil nitrification process (NH4(+)-N to NO3(-)-N) and are widely applied in order to improve N fertilizer use efficiency. Before the new nitrification inhibitor is used, its effects on denitrification process must be investigated and denitrifying enzyme activity (DEA) is an effective indicator to show this process. In the present paper, a mass spectrometery (MS) method was taken to measure the denitrifying enzyme activity in the new nitrification inhibitor 3, 4-dimethylpyrazole phosphate (DMPP) incubation system. The results showed that the method measured the concentration of N2O in the incubation system accurately and the concentration measured by MS had marked correlation with that measured by gas chromatogram (GC) (MS(N2O) = -0.45 + 1.03GC(N2O, R2 = 0.995). At the same time, enrichment of 15 N2O and 15 N2 was measured to discriminate the nitrate reductase and N2O reductase. Differed with traditional method, the enzymatic inhibitor-acetylene was not appended. The results showed that DMPP had no influence on the denitrifying enzyme activity and indicated that the denitrification process was not influenced by DMPP.

  11. Community composition of nirS-type denitrifier in a shallow eutrophic lake.

    Science.gov (United States)

    Yang, Jiang-Ke; Cheng, Zhan-Bing; Li, Jia; Miao, Li-Hong

    2013-11-01

    Denitrification is a major biological process to reduce nitrate to molecular nitrogen (N2). In shallow eutrophic lakes, this process can remove the largest portion of fixed nitrogen and plays an important role in self-purification of this ecosystem. To understand the structure of denitrifying communities in a shallow eutrophic lake, denitrifier communities in four sub-lakes of East Lake in Wuhan, China, were explored by restriction fragment length polymorphisms (RFLP) analysis and sequencing of nirS gene clone libraries. nirS is a functional marker gene for denitrification encoding cytochrome cd 1-containing nitrite reductase, which catalyzes the reduction of nitrite to nitric oxide. Both RFLP fingerprints clustering analysis and phylogeny analysis based on the amino acid sequences of NirS revealed that NirS-type communities in East Lake sediment could be roughly divided into three clusters. Cluster I accounted for 74-82 % of clones from the moderately eutrophic sub-lakes Tuan, Tang Ling, and Guo Zheng. Cluster II accounted for 76 % of the communities in hypertrophic sub-lake Miao Lake and cluster III as a minor group (7 % of the total), mainly presented in Miao Lake. Phylogenetic analysis revealed that cluster I was related to the reference clones from a broad range of ecological environments, and clusters II and III were more phylogenetically related to the reference clones from entrophic environments. Canonical correspondence analysis indicated that total nitrogen, total phosphate, total organic carbon, and NH4-N and NO2-N were important environmental factors affecting the dispersion of NirS-type denitrifier in the sediments. Cluster I showed a weak relationship with the nutrient content, while cluster II and III were positively related with the nutrient content. Principal coordinates analysis indicated that NirS-type communities from Tuan Lake, Tang Ling Lake, and Guo Zheng Lake sediments were divergent from those found in river, estuary sediment, and forest

  12. [Denitrifying and phosphorus accumulating mechanisms of denitrifying phosphorus accumulating organisms (DPAOs) for wastewater treatment--a review].

    Science.gov (United States)

    Yu, Hongting; Li, Min

    2015-03-04

    Eutrophication has raised increasing concerns due to its adverse effects on creatures. It is widely accepted that microbes are capable of removing nitrogen (N) and phosphate (P) via denitrification and P accumulation. So far, several strains can do this work. Therefore, more studies are focused on looking for micro-organisms that have both denitrification and P accumulation ability. Whether exposed to aerobic or anaerobic environment, microbial N and P removal mechanisms differ. Proton Motive Force and Electron Acceptor Theory are involved in the chemical process, whereas denitrifying enzymes polyphosphate kinases are regarded as the leading participators in the enzymatic systems. Studies have shown the influences of N on P accumulation, but further investigation should identify the influences of P on N removal. Here we reviewed the aspects of N and P removal mechanisms in denitrifying phosphorus accumulating organisms (DPAOs) and their potential to remove N and P from water system. Moreover, future works on clarifying denitrifying phosphorus accumulating mechanisms in depth and improving efficiency of removing N and P by DPAOs are provided.

  13. Whole-Genome Transcriptional Analysis of Chemolithoautotrophic Thiosulfate Oxidation by Thiobacillus denitrificans Under Aerobic vs. Denitrifying Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Beller, H R; Letain, T E; Chakicherla, A; Kane, S R; Legler, T C; Coleman, M A

    2006-04-22

    Thiobacillus denitrificans is one of the few known obligate chemolithoautotrophic bacteria capable of energetically coupling thiosulfate oxidation to denitrification as well as aerobic respiration. As very little is known about the differential expression of genes associated with ke chemolithoautotrophic functions (such as sulfur-compound oxidation and CO2 fixation) under aerobic versus denitrifying conditions, we conducted whole-genome, cDNA microarray studies to explore this topic systematically. The microarrays identified 277 genes (approximately ten percent of the genome) as differentially expressed using Robust Multi-array Average statistical analysis and a 2-fold cutoff. Genes upregulated (ca. 6- to 150-fold) under aerobic conditions included a cluster of genes associated with iron acquisition (e.g., siderophore-related genes), a cluster of cytochrome cbb3 oxidase genes, cbbL and cbbS (encoding the large and small subunits of form I ribulose 1,5-bisphosphate carboxylase/oxygenase, or RubisCO), and multiple molecular chaperone genes. Genes upregulated (ca. 4- to 95-fold) under denitrifying conditions included nar, nir, and nor genes (associated respectively with nitrate reductase, nitrite reductase, and nitric oxide reductase, which catalyze successive steps of denitrification), cbbM (encoding form II RubisCO), and genes involved with sulfur-compound oxidation (including two physically separated but highly similar copies of sulfide:quinone oxidoreductase and of dsrC, associated with dissimilatory sulfite reductase). Among genes associated with denitrification, relative expression levels (i.e., degree of upregulation with nitrate) tended to decrease in the order nar > nir > nor > nos. Reverse transcription, quantitative PCR analysis was used to validate these trends.

  14. Halobacterium denitrificans sp. nov., an extremely halophilic denitrifying bacterium

    Science.gov (United States)

    Tomlinson, G. A.; Jahnke, L. L.; Hochstein, L. I.

    1986-01-01

    Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5 percent), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005 percent yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production.

  15. Halobacterium denitrificans sp. nov. - An extremely halophilic denitrifying bacterium

    Science.gov (United States)

    Tomlinson, G. A.; Jahnke, L. L.; Hochstein, L. I.

    1986-01-01

    Halobacterium denitrificans was one of several carbohydrate-utilizing, denitrifying, extremely halophilic bacteria isolated by anaerobic enrichment in the presence of nitrate. Anaerobic growth took place only when nitrate (or nitrite) was present and was accompanied by the production of dinitrogen. In the presence of high concentrations of nitrate (i.e., 0.5 percent), nitrous oxide and nitrite were also detected. When grown aerobically in a mineral-salts medium containing 0.005 percent yeast extract, H. denitrificans utilized a variety of carbohydrates as sources of carbon and energy. In every case, carbohydrate utilization was accompanied by acid production.

  16. Can functional gene abundance predict N-fluxes? Examples from a well-studied hydrological flow path in a forested watershed in SW China

    Science.gov (United States)

    Liu, Binbin; Muzammil, Bushra; Dörsch, Peter; Zhu, Jing; Mulder, Jan; Frostegård, Åsa

    2014-05-01

    Edaphic, climatic and management factors shape soil microbial communities taxonomically and functionally, resulting in spatial separation of nitrogen (N) oxidation and reduction processes along hydrological flowpaths. In a recent study, we investigated N-cycling processes and N2O emissions along a mesic hillslope (HS) and a hydrologically connected groundwater discharge zone (GDZ) in a forested headwater catchment dominated by acid soils (pH 4.0 - 4.5) in subtropical China (Chongqing). The watershed receives 50 kg N ha-1 a-1 through atmogenic deposition (2/3 as ammonium), most of which is removed before discharge. Surprisingly, N2O emissions were found to be greatest on the well-drained HS, whereas a drop of NO3- concentrations along the flow path indicated that N removal was highest in the moist GDZ. Nitrification was assumed to be none-limiting as the total flux of NO3- leaving the hill slope soils roughly equalled the input of NH4+. To understand watershed N-cycling and removal in more detail, we studied the abundance of functional genes involved in ammonium oxidation (amoA of AOB and AOA), nitrite oxidation (nxrB) and denitrification (nirK, nirS, nosZ) in top soils from 8 locations along the flow path spanning from the hilltop to the outlet of the GDZ. 16S rRNA gene abundance was assessed as a general marker for bacterial abundance. All genes showed highest abundance per gram soil in the heavily disturbed GDZ (formerly cultivated terraces), despite lower soil organic carbon content (1-4% w/w as opposed to 10-20% w/w in HS topsoil) and periodically stagnant conditions due to high water tables after monsoonal rainfalls. Ratios of nosZ/nirS+nirK, commonly used to predict denitrification product stoichiometry (N2O/N2), yielded counterintuitive results with higher values for HS than for GDZ. However, comparing nir gene with 16S rRNA gene abundance revealed that denitrifiers accounted for up to 10% of the bacterial community in the GDZ soils whereas this value was

  17. Dynamic Metabolic Modeling of Denitrifying Bacterial Growth: The Cybernetic Approach

    Energy Technology Data Exchange (ETDEWEB)

    Song, Hyun-Seob; Liu, Chongxuan

    2015-06-29

    Denitrification is a multistage reduction process converting nitrate ultimately to nitrogen gas, carried out mostly by facultative bacteria. Modeling of the denitrification process is challenging due to the complex metabolic regulation that modulates sequential formation and consumption of a series of nitrogen oxide intermediates, which serve as the final electron acceptors for denitrifying bacteria. In this work, we examined the effectiveness and accuracy of the cybernetic modeling framework in simulating the growth dynamics of denitrifying bacteria in comparison with kinetic models. In four different case studies using the literature data, we successfully simulated diauxic and triauxic growth patterns observed in anoxic and aerobic conditions, only by tuning two or three parameters. In order to understand the regulatory structure of the cybernetic model, we systematically analyzed the effect of cybernetic control variables on simulation accuracy. The results showed that the consideration of both enzyme synthesis and activity control through u- and v-variables is necessary and relevant and that uvariables are of greater importance in comparison to v-variables. In contrast, simple kinetic models were unable to accurately capture dynamic metabolic shifts across alternative electron acceptors, unless an inhibition term was additionally incorporated. Therefore, the denitrification process represents a reasonable example highlighting the criticality of considering dynamic regulation for successful metabolic modeling.

  18. Simultaneous denitrifying phosphorus accumulation in a sequencing batch reactor

    Institute of Scientific and Technical Information of China (English)

    YUAN Linjiang; HAN Wei; WANG Lei; YANG Yongzhe; WANG Zhiying

    2007-01-01

    In order to achieve simultaneous nitrogen and phosphorus removal in the biological treatment process,denitrifying phosphorus accumulation(DNPA)and its affecting factors were studied in a sequencing batch reactor(SBR)with synthetic wastewater.The results showed that when acetate was used as the sole carbon resource in the influent.the sludge acclimatized under anaerobic/aerobic operation had good phosphorus removal ability.Denitrifying phosphorus accumulation was observed soon when fed with nitrate instead of aeration following the anaerobic stage,which is a vital premise to DNPA.If DNPA sludge is fed with nitrate prior to the anaerobic stage,the DNPA would weaken or even disappear.At the high concen tration of nitrate fed in the anoxic stage,the longer anoxic time needed,the better the DNPA was.Induced DNPA did not disappear even though an aerobic stage followed the anoxic stage,but the shorter the aerobic stage lasted,the higher the proportions of phosphorus removal via DNPA to total removal.

  19. [Influences of long-term application of organic and inorganic fertilizers on the composition and abundance of nirS-type denitrifiers in black soil].

    Science.gov (United States)

    Yin, Chang; Fan, Fen-Liang; Li, Zhao-Jun; Song, A-Lin; Zhu, Ping; Peng, Chang; Liang, Yong-Chao

    2012-11-01

    The objectives of this study were to explore the effects of long-term organic and inorganic fertilizations on the composition and abundance of nirS-type denitrifiers in black soil. Soil samples were collected from 4 treatments (i. e. no fertilizer treatment, CK; organic manure treatment, OM; chemical fertilizer treatment (NPK) and combination of organic and chemical fertilizers treatment (MNPK)) in Gongzhuling Long-term Fertilization Experiment Station. Composition and abundance of nirS-type denitrifiers were analyzed with terminal restriction fragment length polymorphism (T-RFLP) and real-time quantitative PCR (Q-PCR), respectively. Denitrification enzyme activity (DEA) and soil properties were also measured. Application of organic fertilizers (OM and MNPK) significantly increased the DEAs of black soil, with the DEAs in OM and MNPK being 5.92 and 6.03 times higher than that in CK treatment, respectively, whereas there was no significant difference between NPK and CK. OM and MNPK treatments increased the abundances of nirS-type denitrifiers by 2.73 and 3.83 times relative to that of CK treatment, respectively. The abundance of nirS-type denitrifiers in NPK treatment was not significantly different from that of CK. The T-RFLP analysis of nirS genes showed significant differences in community composition between organic and inorganic treatments, with the emergence of a 79 bp T-RF, a significant decrease in relative abundance of the 84 bp T-RF and a loss of the 99 bp T-RF in all organic treatments. Phylogenetic analysis indicated that the airS-type denitrifiers in the black soil were mainly composed of alpha, beta and gamma-Proteobacteria. The 79 bp-type denitrifiers inhabiting exclusively in organic treatments (OM and MNPK) were affiliated to Pseudomonadaceae in gamma-Proteobacteria and Burkholderiales in beta-Proteobacteria. The 84 bp-types were related to Burkholderiales and Rhodocyclales. Correlation analysis indicated that pH, concentrations of total nitrogen

  20. Coexistence of nitrifying, anammox and denitrifying bacteria in a sequencing batch reactor

    Directory of Open Access Journals (Sweden)

    Michela eLangone

    2014-02-01

    Full Text Available Elevated nitrogen removal efficiencies from ammonium-rich wastewaters have been demonstrated by several applications, that combine nitritation and anammox processes. Denitrification will occur simultaneously when organic carbon is also present. In this study, the activity of aerobic ammonia oxidizing, anammox and denitrifying bacteria in a full scale Sequencing Batch Reactor, treating digester supernatants, was studied by means of batch-assays. AOB and anammox activities were maximum at pH of 8.0 and 7.8-8.0, rispectively. Short term effect of nitrite on anammox activity was studied, showing nitrite up to 42 mg/L did not result in inhibition. Both denitrification via nitrate and nitrite were measured. To reduce nitrite-oxidizing activity, high of NH3 – N (1.9-10 mg N-NH3/L and low nitrite (3-8 mg TNN/L are required conditions during the whole SBR cycle.Molecular analysis showed the nitritation-anammox sludge harbored a high microbial diversity, where each microorganism has a specific role. Using ammonia monooxygenase α –subunit (amoA gene as a marker, our analyses suggested different macro- and micro-environments in the reactor strongly affect the AOB community, allowing the development of different AOB species, such as N. europaea/eutropha and N. oligotropha groups, which improve the stability of nitritation process. A specific PCR primer set, used to target the 16S rRNA gene of anammox bacteria, confirmed the presence of the Ca. Brocadia fulgida type, able to grow in precence of organic matter and to tolerate high nitrite concentrations. The diversity of denitrifiers was assessed by using dissimilatory nitrite reductase (nirS gene-based analyses, who showed denitifiers were related to different betaproteobacterial genera, such as Thauera, Pseudomonas, Dechloromonas and Aromatoleum, able to assist in forming microbial aggregates. Concerning possible secondary processes, no n-damo bacteria were found while NOB from the genus of Nitrobacter

  1. Greenhouse Gas Emission from In-situ Denitrifying Bioreactors

    Science.gov (United States)

    Pluer, W.; Walter, M. T.; Geohring, L.

    2013-12-01

    Despite decades of concerted effort to mitigate nonpoint source nitrate (NO3-) pollution from agricultural lands, these efforts have not been sufficient to arrest eutrophication, which continues to be a serious and chronic problem. Two primary processes for removing excess NO3- from water are biological assimilation and denitrification. Denitrifying bacteria use NO3- as the electron acceptor for respiration in the absence of oxygen. Denitrification results in reduced forms of nitrogen, often dinitrogen gas (N2) but also nitrous oxide (N2O), an aggressive greenhouse gas (GHG). A promising solution to NO3- pollution is to intercept agricultural discharges with denitrifying bioreactors (DNBRs), though research has been limited to NO3- level reduction and omitted process mechanisms. DNBRs work by providing an anaerobic environment with plenty of organic matter (commonly woodchips) for denitrifying bacteria to flourish. While, initial results from bioreactor studies show that they can cost-effectively remove NO3-, GHG emission could be an unintended consequence. The study's goal is to determine how bioreactor design promotes microbial denitrification while limiting N2O production. It specifically focuses on expanding the body of knowledge concerning DNBRs in the areas of design implications and internal processes by measuring intermediate compounds and not solely NO3-. Nutrient samples are collected at inflow and outflow structures and tested for NO3- and nitrite (NO2-). Dissolved and headspace gas samples are collected and tested for N2O. Additional gas samples will be analyzed for naturally-occurring isotopic N2 to support proposed pathways. Designs will be analyzed both through the N2O/N2 production ratio and NO2- production caused by various residence times and inflow NO3- concentrations. High GHG ratios and NO2- production suggest non-ideal conditions or flow patterns for complete denitrification. NO3- reduction is used for comparison with previous studies. Few

  2. Shifts in the microbial community, nitrifiers and denitrifiers in the biofilm in a full-scale rotating biological contactor.

    Science.gov (United States)

    Peng, Xingxing; Guo, Feng; Ju, Feng; Zhang, Tong

    2014-07-15

    The objective of this study was to investigate the microbial community shifts, especially nitrifiers and denitrifiers, in the biofilm of two rotating biological contactor (RBC) trains with different running times along the plug flowpath. The microbial consortia were profiled using multiple approaches, including 454 high-throughput sequencing of the V3-V4 region of 16S rRNA gene, clone libraries, and quantitative polymerase chain reaction (qPCR). The results demonstrated that (1) the overall microbial community at different locations had distinct patterns, that is, there were similar microbial communities at the beginnings of the two RBC trains and completely different populations at the ends of the two RBC trains; (2) nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB, Nitrosomonas) and nitrite-oxidizing bacteria (NOB, Nitrospira), increased in relative abundance in the biofilm along the flowpath, whereas denitrifiers (Rhodanobacter, Paracoccus, Thauera, and Azoarcus) markedly decreased; (3) the AOA were subdominant to the AOB in all sampled sections; and (4) strong ecological associations were shown among different bacteria. Overall, the results of this study provided more comprehensive information regarding the biofilm community composition and assemblies in full-scale RBCs.

  3. Performance of denitrifying microbial fuel cell with biocathode over nitrite

    Directory of Open Access Journals (Sweden)

    Zhao eHuimin

    2016-03-01

    Full Text Available Microbial fuel cell (MFC with nitrite as an electron acceptor in cathode provided a new technology for nitrogen removal and electricity production simultaneously. The influences of influent nitrite concentration and external resistance on the performance of denitrifying MFC were investigated. The optimal effectiveness were obtained with the maximum total nitrogen (TN removal rate of 54.80±0.01 g m-3 d-1. It would be rather desirable for the TN removal than electricity generation at lower external resistance. Denaturing gradient gel electrophoresis suggested that Proteobacteria was the predominant phylum, accounting for 35.72%. Thiobacillus and Afipia might benefit to nitrite removal. The presence of nitrifying Devosia indicated that nitrite was oxidized to nitrate via a biochemical mechanism in the cathode. Ignavibacterium and Anaerolineaceae was found in the cathode as a heterotrophic bacterium with sodium acetate as substrate, which illustrated that sodium acetate in anode was likely permeated through proton exchange membrane to the cathode .

  4. Diversity of Nitrate-Reducing and Denitrifying Bacteria in a Marine Aquaculture Biofilter and their Response to Sulfide

    DEFF Research Database (Denmark)

    Krieger, Bärbel; Schwermer, Carsten U.; Rezakhani, Nastaran

    2006-01-01

    their response to sulfide concentrations relevant for the system. Almost 500 nitrate-consuming isolates were screened by 16S rRNA gene-RFLP; for each RFLP pattern representatives were sequenced. In total, 40 different strains were identified, some of them novel species, mostly affiliating...... with Alphaproteobacteria but also including Beta- and Gammaproteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The diversity of the isolates was compared to the cultivation-independent diversity of nitrate-reducing and denitrifying bacteria based on narG and nosZ as functional marker genes. Growth experiments...... revealed great differences in sulfide-tolerance among isolates, ranging from generally resulted in increased nitrous oxide production. Batch incubations of anaerobic sludge with 15N-nitrate confirmed...

  5. Degradation pathway of 2-chloroethanol in Pseudomonas stutzeri strain JJ under denitrifying conditions

    NARCIS (Netherlands)

    Dijk, J.A.; Gerritse, J.; Schraa, G.; Stams, A.J.M.

    2004-01-01

    The pathway of 2-chloroethanol degradation in the denitrifying Pseudomonas stutzeri strain JJ was investigated. In cell-free extracts, activities of a phenazine methosulfate (PMS)-dependent chloroethanol dehydrogenase, an NAD-dependent chloroacetaldehyde dehydrogenase, and a chloroacetate dehalogena

  6. Interactions between nitrifying and denitrifying bacteria in gnotobiotic microcosms planted with the emergent macrophyte Glyceria maxima

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Duyts, H.; Blom, C.W.P.M.; Laanbroek, H.J.

    1998-01-01

    The population dynamics of the chemolithoautotrophic nitrifiers Nitrosomonas europaea and Nitrobacter winogradskyi were studied in gnotobiotic microcosms fed with ammonium in response to the presence or absence of the emergent macrophyte Glyceria maxima and the heterotrophic denitrifying bacterium P

  7. Elimination of pharmaceuticals in single- and three-stage pre-denitrifying MBBR

    DEFF Research Database (Denmark)

    Polesel, Fabio; Torresi, Elena; Loreggian, L.;

    This study investigated the elimination of pharmaceuticals in pre-denitrifying moving bed biofilm reactors (MBBRs) in single- and three-stage configurations. Under batch conditions, biotransformation and retransformation of two pharmaceuticals (trimethoprim, sulfamethoxazole) occurred at comparable...

  8. BIODEGRADATION OF AROMATIC COMPOUNDS UNDER MIXED OXYGEN/DENITRIFYING CONDITIONS: A REVIEW

    Science.gov (United States)

    Bioremediation of aromatic hydrocarbons in groundwater and sediments is often limited by dissolved oxygen. Many aromatic hydrocarbons degrade very slowly or not at all under anaerobic conditions. Nitrate is a good alternative electron acceptor to oxygen, and denitrifying bacteria...

  9. INHIBITION OF ALKYLBENZENE BIODEGRADATION UNDER DENITRIFYING CONDITIONS BY USING THE ACETYLENE BLOCK TECHNIQUE

    Science.gov (United States)

    Addition of acetylene to microcosms simultaneously amended with nitrate and alkylbenzenes resulted in inhibition of the rate of alkylbenzene biodegradation under denitrifying conditions. Toluene, xylenes, and 1,2,4-trimethylbenzene were recalcitrant, whereas ethylbenzene was degr...

  10. Microbiological Denitrification and Denitrifying Activity of Paracoccus Denitrificans

    Institute of Scientific and Technical Information of China (English)

    万曦; 万国江; 等

    2000-01-01

    With rapidly industrial and agricultural development,more and more fertilizers,chemicals and heavy ions will be discharged into lakes and rivers,which would cause lake eutrophication and quality deterioration in drinking water sources.Therefore,denitrification is essential for controlling the amounts of nitrogen,During the transformation process from nitrate to the end products-nitrogen and several intermediated[e.g.nitrite(NO2-),nitrous oxide(N2O) and nitric oxide(NO)]may be accumulated,which have more toxic influences on the environment.in This study,the denitrification effect of Paracoccus Denitrificans was examined on the changes between oxic and anoxic conditions at varying pH.At pH=7.5,denitrification proceeded well after 3 switches from oxic to anoxic conditions and vice versa,Production of N2 was constant and the amounts of NO2-,N2O and NO were extremely low.How ever,at pH=6.8,denitrification activity was inhitied and there large amounts of the intermaediates.The denitrifying bacteria decreased violently in dry weight and were washed out.

  11. Nutrient removal efficiency in a rice-straw denitrifying bioreactor.

    Science.gov (United States)

    Liang, Xinqiang; Lin, Limin; Ye, Yushi; Gu, Jiatao; Wang, Zhibo; Xu, Lixian; Jin, Yi; Ru, Qiukai; Tian, Guangming

    2015-12-01

    Rice straw was used as a carbon source in a denitrifying bioreactor, for the removal of nutrients from agricultural drainage. Nutrient removal efficiency was evaluated by: (a) nutrient loading rates (low, medium, and high); (b) hydraulic retention time, and (c) comparison with another carbon source (woodchip). The results show that concentrations of nitrate nitrogen (NO3(-)-N), ammonia nitrogen (NH4(+)-N), total nitrogen (TN), and orthophosphate phosphorus (PO4(3-)-P) in the rice-straw bioreactor effluents were reduced by 53%, 25%, 40%, and 35%, respectively, compared with influents at the medium nutrient loading rate (NO3(-)-N: 10-15 mg N L(-1), NH4(+)-N: 10-15 mg N L(-1), PO4(3-)-P: 1.0-1.5 mg P L(-1)) and long hydraulic retention time (HRT, 24h), with a corresponding denitrification rate (DR) of 0.40 mg N L(-1)h(-1). Moreover, the rice-straw bioreactor showed significantly higher (pbioreactor at the medium nutrient loading rate and 24h HRT. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Denitrifying bacteria from the genus Rhodanobacter dominate bacterial communities in the highly contaminated subsurface of a nuclear legacy waste site.

    Science.gov (United States)

    Green, Stefan J; Prakash, Om; Jasrotia, Puja; Overholt, Will A; Cardenas, Erick; Hubbard, Daniela; Tiedje, James M; Watson, David B; Schadt, Christopher W; Brooks, Scott C; Kostka, Joel E

    2012-02-01

    The effect of long-term mixed-waste contamination, particularly uranium and nitrate, on the microbial community in the terrestrial subsurface was investigated at the field scale at the Oak Ridge Integrated Field Research Challenge (ORIFRC) site in Oak Ridge, TN. The abundance, community composition, and distribution of groundwater microorganisms were examined across the site during two seasonal sampling events. At representative locations, subsurface sediment was also examined from two boreholes, one sampled from the most heavily contaminated area of the site and another from an area with low contamination. A suite of DNA- and RNA-based molecular tools were employed for community characterization, including quantitative PCR of rRNA and nitrite reductase genes, community composition fingerprinting analysis, and high-throughput pyrotag sequencing of rRNA genes. The results demonstrate that pH is a major driver of the subsurface microbial community structure and that denitrifying bacteria from the genus Rhodanobacter (class Gammaproteobacteria) dominate at low pH. The relative abundance of bacteria from this genus was positively correlated with lower-pH conditions, and these bacteria were abundant and active in the most highly contaminated areas. Other factors, such as the concentration of nitrogen species, oxygen level, and sampling season, did not appear to strongly influence the distribution of Rhodanobacter bacteria. The results indicate that these organisms are acid-tolerant denitrifiers, well suited to the acidic, nitrate-rich subsurface conditions, and pH is confirmed as a dominant driver of bacterial community structure in this contaminated subsurface environment.

  13. Positive role of nitrite as electron acceptor on anoxic denitrifying phosphorus removal process

    Institute of Scientific and Technical Information of China (English)

    HUANG RongXin; LI Dong; LI XiangKun; BAO LinLin; JIANG AnXi; ZHANG Jie

    2007-01-01

    Literatures revealed that the electron acceptor-nitrite could be inhibitory or toxic in the denitrifying phosphorus removal process.Batch test experiments were used to investigate the inhibitory effect during the anoxic condition.The inoculated activated sludge was taken from a continuous double- sludge denitrifying phosphorus and nitrogen removal system.Nitrite was added at the anoxic stage.One time injection and sequencing batch injection were carried on in the denitrifying dephosphorus procedure.The results indicated that the nitrite concentration higher than 30 mg/L would inhibit the anoxic phosphate uptake severely, and the threshold inhibitory concentration was dependent on the characteristics of the activated sludge and the operating conditions; instead, lower than the inhibitory concentration would not be detrimental to anoxic phosphorus uptake, and it could act as good electron acceptor for the anoxic phosphate accumulated.Positive effects performed during the denitrifying biological dephosphorus all the time.The utility of nitrite as good electron acceptor would provide a new feasible way in the denitrifying phosphorus process.

  14. Effect of denitrifying bacteria on the electrochemical reaction of activated carbon fiber in electrochemical biofilm system

    Institute of Scientific and Technical Information of China (English)

    YING Diwen; JIA Jinping; ZHANG Lehua

    2007-01-01

    An electrochemical-activated denitrifying biofilm system consisting of activated carbon fiber electrodes immobilized with denitrifying bacteria film as cathode was studied.A revised model for an electrochemical-activated denitrifying biofilm was developed and validated by electrochemical analysis of cathodal polarization curves and nitrate consumption rate.The cathodal polarization curve and nitrate consumption rate were introduced to verify the rate of electrochemical reaction and the activity of denitrifying bacteria,respectively.It was shown that the denitrification process effectively strengthened the electrochemical reaction while the electron also intensified denitrification activity.Electron was transferred between electrochemical process and biological process not only by hydrogen molecule but also by new produced active hydrogen atom.Additionally,a parameter of apparent exchange current density was deprived from the cathodal polarization curve with high overpotential,and a new bio-effect current density was defined through statistical analysis,which was linearly dependent to the activity of denitrification bacteria.Activated carbon fiber (ACF) electrode was also found to be more suitable to the electrochemical denitrifying system compared with graphite and platinum.

  15. Denitrifying Bacteria in Paddy Soils of Taihu Lake Basin,China

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hua-Yong; LI Zhen-Gao; PAN Ying-Hua; LI Liang-Mo

    2004-01-01

    This study attempted to determine the characteristics of the communities, the ecological factors, and the denitrifying enzyme activity for denitrifying bacteria found in the paddy soils of the Taihu Lake Basin, China. Samples of the six main soil types of the basin were taken from paddy fields with different fertilities. The total numbers of bacteria and denitrifying bacteria in the high fertility soils were much more than those in low fertility soils, and the number of denitrifying bacteria accounted for 49% to 80% of the total number of bacteria. The O2 content was an important ecological factor that affected denitrification. Of test the strains isolated from the paddy soils in the Taihu Lake Basin, some (e.g., Pseudomonas spp.)grew well under low oxygen partial pressure, while others (e.g., Bacillus spp.) had no strict predilection with O2 content.Another critical ecological factor was the nitrogen concentration. Three selected denitrifying bacteria grew better in a culture medium with 135 instead of 276 mg L-1 nitrogen. At the same time 67% of the test strains were able to reduce NO-3 to NO-2 and 56% had N2O reductase.

  16. Phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice-soybean rotation fields.

    Science.gov (United States)

    Tago, Kanako; Ishii, Satoshi; Nishizawa, Tomoyasu; Otsuka, Shigeto; Senoo, Keishi

    2011-01-01

    Denitrifiers can produce and consume nitrous oxide (N(2)O). While little N(2)O is emitted from rice paddy soil, the same soil produces N(2)O when the land is drained and used for upland crop cultivation. In this study, we collected soils from two types of fields each at three locations in Japan; one type of field had been used for continuous cultivation of rice and the other for rotational cultivation of rice and soybean. Active denitrifiers were isolated from these soils using a functional single-cell isolation method, and their taxonomy and denitrifying properties were examined. A total of 110 denitrifiers were obtained, including those previously detected by a culture-independent analysis. Strains belonging to the genus Pseudogulbenkiania were dominant at all locations, suggesting that Pseudogulbenkiania denitrifiers are ubiquitous in various rice paddy soils. Potential denitrifying activity was similar among the strains, regardless of the differences in taxonomic position and soil of origin. However, relative amounts of N(2) in denitrification end products varied among strains isolated from different locations. Our results also showed that crop rotation had minimal impact on the functional diversity of the denitrifying strains. These results indicate that soil and other environmental factors, excluding cropping systems, could select for N(2)-producing denitrifiers.

  17. Abundance and diversity of denitrifying and anammox bacteria in seasonally hypoxic and sulfidic sediments of the saline lake grevelingen

    NARCIS (Netherlands)

    Lipsewers, Yvonne A.; Hopmans, Ellen C.; Meysman, Filip J.R.; Sinninghe Damsté, Jaap S.|info:eu-repo/dai/nl/07401370X; Villanueva, Laura

    2016-01-01

    Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox,

  18. Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen

    NARCIS (Netherlands)

    Lipsewers, Y.A.; Hopmans, E.C.; Meysman, F.J.R.; Sinninghe Damsté, J.S.; Villanueva, L.

    2016-01-01

    Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox,

  19. Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen

    NARCIS (Netherlands)

    Lipsewers, Y.A.; Hopmans, E.C.; Meysman, F.J.R.; Sinninghe Damsté, J.S.; Villanueva, L.

    2016-01-01

    Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, an

  20. Differential Isotopic Fractionation during Cr(VI) Reduction by an Aquifer-Derived Bacterium under Aerobic versus Denitrifying Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Han, R.; Qin, L.; Brown, S. T.; Christensen, J. N.; Beller, H. R.

    2012-01-27

    We studied Cr isotopic fractionation during Cr(VI) reduction by Pseudomonas stutzeri strain RCH2. Finally, despite the fact that strain RCH2 reduces Cr(VI) cometabolically under both aerobic and denitrifying conditions and at similar specific rates, fractionation was markedly different under these two conditions (ε was ~2‰ aerobically and ~0.4‰ under denitrifying conditions).

  1. Environmental controls on denitrifying communities and denitrification rates: insights from molecular methods.

    Science.gov (United States)

    Wallenstein, Matthew D; Myrold, David D; Firestone, Mary; Voytek, Mary

    2006-12-01

    The advent of molecular techniques has improved our understanding of the microbial communities responsible for denitrification and is beginning to address their role in controlling denitrification processes. There is a large diversity of bacteria, archaea, and fungi capable of denitrification, and their community composition is structured by long-term environmental drivers. The range of temperature and moisture conditions, substrate availability, competition, and disturbances have long-lasting legacies on denitrifier community structure. These communities may differ in physiology, environmental tolerances to pH and O2, growth rate, and enzyme kinetics. Although factors such as O2, pH, C availability, and NO3- pools affect instantaneous rates, these drivers act through the biotic community. This review summarizes the results of molecular investigations of denitrifier communities in natural environments and provides a framework for developing future research for addressing connections between denitrifier community structure and function.

  2. Effect of electro-stimulation on activity of heterotrophic denitrifying bacteria and denitrification performance.

    Science.gov (United States)

    Liu, Hengyuan; Tong, Shuang; Chen, Nan; Liu, Ying; Feng, Chuanping; Hu, Qili

    2015-11-01

    The effects of electro-stimulation on heterotrophic denitrifying bacterial activity and nitrate removal were investigated using a bench-scale bio-electrochemical reactor in this study. Results showed that the maximum nitrate removal efficiency was 100% at the optimum current density of 200mA/m(2), at which low nitrite production and high ATP aggregate level were obtained. The activity of denitrifying bacteria was highest at the range densities of 200-250mA/m(2), although the terminative pH increased to 8.62 at 200mA/m(2) and 9.63 at 250mA/m(2). This demonstrates that suitable current densities could improve the activity of denitrifying bacteria. Therefore, this study provides a number of useful information to improve the bio-electrochemical reactor designs and promote the removal efficiency of pollutants. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Factors affecting biological denitrifying dephosphatation in anaerobic/anoxic/aerobic sequencing batch reactor

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This study was conducted to verify and discuss the denitrifying dephosphatation under different levels of nitrate concentration and retention time of anoxic/aerobic process in a Sequencing Batch Reactor ( SBR ).The results of tests demonstrated that there were two kinds of phosphorus-accumulating organisms (PAOs) in the biological excess phosphorus removal (BEPR) system. One was non-DNPAOs that could only use oxygen as terminal electron acceptors, the other was denitrifying PAOs (DNPAOs) that could use both nitrate and oxygen as terminal electron acceptors. Phosphorus uptake efficiency could be attained under anoxic period ranging from 28.7%-96.7% in an anacrobic/anoxic/aerobic system. Experimental results showed that nitrate concentration and retention time of anoxic/aerobic process were the key factors affecting the course of denitrifying dephosphatation.

  4. Identification of a denitrifying bacterium and verification of its anaerobic ammonium oxidation ability

    Institute of Scientific and Technical Information of China (English)

    HU; Baolan; ZHENG; Ping; LI; Jinye; XU; Xiangyang; JIN; Rencun

    2006-01-01

    A strain D3 of denitrifying bacterium was isolated from an anammox reactor, and identified as Pseudomonas mendocina based on the morphological and physiological assay, Vitek test,Biolog test, (G+C) mol% content, and 16S rDNA phylogenetic analysis. As a typical denitrifying bactration of 88.5 mg N/L. The optimal pH and growth temperature were 7.84 and 34.9℃, respectively.Strain D3 was able to oxidize ammonia under anaerobic condition. The maximum nitrate and ammoof ammonia to nitrate was 1:1.91. Electron microscopic observation revealed peculiar cell inclusions in strain D3. Because of its relation to anammox activity, strain D3 was presumed to be anammoxosome.The present investigation proved that denitrifying bacteria have the anammox ability, and the results have engorged the range of anammox populations.

  5. Characterization of Two Efficient Aerobic Denitrifying Strains Isolated from Shallow Aquifers in Suzhou City, China

    Science.gov (United States)

    Ruan, X.; Zhu, X.; Sun, H.; Li, M.

    2010-12-01

    Sixty two stains that can utilize nitrate as source of nitrogen under aerobic conditions were isolated from shallow aquifer samples in Suzhou city, China. Two of the strains, XK42 and PJ21, can convert nitrate into nitrogen gas efficiently without obvious accumulation of nitite. According to morphological, biochemical/biophysical and 16S rDNA gene sequence analysis, XK42 and PJ21 were identified as Pseudomonas Stutzeri and Pseudomonas Mendocica, respectively. The generation time, optimum pH value range and optimum growth temperature range were 4.64h, 6.5˜8.0, 25˜35°C for XK42 and 8.39h, 6.5˜8.5, 25˜35°C for PJ21. Under aerobic conditions (DO=6.9˜7.8 mg/L), the nitrate concentrations in the medium inoculated with XK42 and PJ21 decreased to 42.35 mg/L and 35.69 mg/L with initial nitrate concentration of 276.25 mg/L within 12 hours, respectively. The nitrite concentrations reached to 3.06 mg/L and 3.70 mg/L, and their nitrate removal rates reached 18.24 mg/L●h and 17.51 mg/L●h. The total nitrogen loss through denitrification of XK42 and PJ21 were 70.9% and 66.3%, respectively. The nitrate reduction efficiencies within 60 hours was up to 95.13% (strain XK42) and 95.55% (strain PJ21). The results indicate that the isolated strians XK42 and PJ21 are aerobic denitrifiers with high nitrogen removal efficiency, and can be used for in-situ bioremediation of nitrogen-contaminated shallow groundwater and biotreatment of wasterwater.

  6. The role of paraffin oil on the interaction between denitrifying anaerobic methane oxidation and Anammox processes.

    Science.gov (United States)

    Fu, Liang; Ding, Zhao-Wei; Ding, Jing; Zhang, Fang; Zeng, Raymond J

    2015-10-01

    Methane is sparingly soluble in water, resulting in a slow reaction rate in the denitrifying anaerobic methane oxidation (DAMO) process. The slow rate limits the feasibility of research to examine the interaction between the DAMO and the anaerobic ammonium oxidation (Anammox) process. In this study, optimized 5 % (v/v) paraffin oil was added as a second liquid phase to improve methane solubility in a reactor containing DAMO and Anammox microbes. After just addition, methane solubility was found to increase by 25 % and DAMO activity was enhanced. After a 100-day cultivation, the paraffin reactor showed almost two times higher consumption rates of NO3 (-) (0.2268 mmol/day) and NH4 (+) (0.1403 mmol/day), compared to the control reactor without paraffin oil. The microbes tended to distribute in the oil-water interface. The quantitative (q) PCR result showed the abundance of gene copies of DAMO archaea, DAMO bacteria, and Anammox bacteria in the paraffin reactor were higher than those in the control reactor after 1 month. Fluorescence in situ hybridization revealed that the percentages of the three microbes were 55.5 and 77.6 % in the control and paraffin reactors after 100 days, respectively. A simple model of mass balance was developed to describe the interactions between DAMO and Anammox microbes and validate the activity results. A mechanism was proposed to describe the possible way that paraffin oil enhanced DAMO activity. It is quite clear that paraffin oil enhances not only DAMO activity but also Anammox activity via the interaction between them; both NO3 (-) and NH4 (+) consumption rates were about two times those of the control.

  7. Denitrifying phosphorus removal in a step-feed CAST with alternating anoxic-oxic operational strategy.

    Science.gov (United States)

    Ma, Juan; Peng, Yongzhen; Wang, Shuying; Wang, Li; Liu, Yang; Ma, Ningping

    2009-01-01

    A bench-scale cyclic activated sludge technology (CAST) was operated to study the biological phosphorus removal performance and a series of batch tests was carried out to demonstrate the accumulation of denitrifying polyphosphate-accumulating organisms (DNPAOs) in CAST system. Under all operating conditions, step-feed CAST with enough carbon sources in influent had the highest nitrogen and phosphorus removal efficiency as well as good sludge settling performance. The average removal rate of COD, NH4+-N, PO4(3-)-P and total nitrogen (TN) was 88.2%, 98.7%, 97.5% and 92.1%, respectively. The average sludge volume index (SVI) was 133 mL/g. The optimum anaerobic/aerobic/anoxic (AOA) conditions for the cultivation of DNPAOs could be achieved by alternating anoxic/oxic operational strategy, thus a significant denitrifying phosphorus removal occurred in step-feed CAST. The denitrification of NOx(-)-N completed quickly due to step-feed operation and enough carbon sources, which could enhance phosphorus release and further phosphorus uptake capability of the system. Batch tests also proved that polyphosphate-accumulating organisms (PAOs) in the step-feed process had strong denitrifying phosphorus removal capacity. Both nitrate and nitrite could be used as electron acceptors in denitrifying phosphorus removal. Low COD supply with step-feed operation strategy would favor DNPAOs accumulation.

  8. On the renewal of the denitrifying layer in the Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Somasundar, K.; Naqvi, S.W.A.

    that denitrification in the Arabian Sea conforms to global trends, the Liu-Kaplan model (1984) is applied to determine the renewal time of the denitrifying layer (ca.150-600m) as 1.6.-3.4a. This is consistent with some recent results supporting the view that Arabian...

  9. Optimization of denitrifying bioreactor performance with agricultural residue-based filter media

    Science.gov (United States)

    Denitrification bioreactors are a promising technology for mitigation of nitrate-nitrogen (NO3-N) losses in subsurface drainage water. Bioreactors are constructed with carbon substrates, typically wood chips, to provide a substrate for denitrifying microorganisms. Columns were packed with wood chips...

  10. Optimizing hydraulic retention times in denitrifying woodchip bioreactors treating recirculating aquaculture system wastewater

    Science.gov (United States)

    The performance of wood-based denitrifying bioreactors to treat high-nitrate wastewaters from aquaculture systems has not previously been demonstrated. Four pilot-scale woodchip bioreactors (approximately 1:10 scale) were constructed and operated for 268 d to determine the optimal range of design hy...

  11. Effect of carbon source and nitrate concentration on denitrifying phosphorus removal by DPB sludge

    Institute of Scientific and Technical Information of China (English)

    WANG Ya-yi; PENG Yong-zhen; Wang Shu-ying; PAN Mian-li

    2004-01-01

    Effect of added carbon source and nitrate concentration on the denitrifying phosphorus removal by DPB sludge was systematically studied using batch experiments, at the same time the variation of ORP was investigated.Results showed that the denitrifying and phosphorus uptake rate in anoxic phase increased with the high initial anaerobic carbon source addition. However once the initial COD concentration reached a certain level, which was in excess to the PHB saturation of poly-P bacteria, residual COD carried over to anoxic phase inhibited the subsequent denitrifying phosphorus uptake. Simultaneously, phosphate uptake continued until all nitrate was removed, following a slow endogenous release of phosphate. High nitrate concentration in anoxic phase increased the initial denitrifying phosphorus rate. Once the nitrate was exhausted, phosphate uptake changed to release. Moreover, the time of this turning point occurred later with the higher nitrate addition. On the other hand, through on-line monitoring the variation of the ORP with different initial COD concentration , it was found ORP could be used as a control parameter for phosphorus release, but it is impossible to utilize ORP for controlling the denitrificaion and anoxic phosphorus uptake operations.

  12. Denitrifying woodchip bioreactor and phosphorus filter pairing to minimize pollution swapping

    Science.gov (United States)

    Pairing denitrifying woodchip bioreactors and phosphorus-sorbing filters provides a unique, engineered approach for dual nutrient removal from waters impaired with both nitrogen (N) and phosphorus (P). This column study aimed to test placement of two P-filter media (acid mine drainage treatment resi...

  13. Influence of carbon source and temperature on the denitrifying phosphorus removal process

    Institute of Scientific and Technical Information of China (English)

    WANG Yayi; WANG Shuying; PENG Yongzhen; Zhu Guibing; LING Yunfang

    2007-01-01

    To supply the valuable operating parameters for the popular usage of the new denitrifying phosphors removal process,it is essential to study the dominant biochemical reactions and the characteristics of denitriflying phosphorus removing bacteria(DPB).Thus,parallel batch experiments using DPB sludge were carried out to assess the effect of substrates(sewage,HAc,and endogenous carbon source)on denitriflying dephosphorus removal efficiency in this study.The results showed that the initial specific phosphorus release rate increased with the high concentration of the short-chain volatile fatty acids ratio in the influent,and sufficient phosphorus was released by DPB.This improved the subsequent denitrification and phosphorus uptake efficiency.The specific endogenous denitrification mainly relies on the internal carbon source(PHB)stored by poly-P bacteria.Denitrifying phosphorus removing bacteria were very hungry when the internal PHB was consumed.Consequently,the specific endogenous denitrification rate was low and the phosphorus uptake did not happen.On the other hand,in the experiment,the denitrifying phosphorus removal performance under two temperature conditions(8-10℃ and 25-26℃)was also investigated and analyzed.It was found that the lower temperature decreased the specific phosphorus release and uptake rate,but did not inhibit the denitrifying phosphorus removal completely.Therefore,the negative influence of the low temperature on the overall phosphorus removal was not significant.

  14. Plastic biofilm carrier after corn cobs reduces nitrate loading in laboratory denitrifying bioreactors

    Science.gov (United States)

    Nitrate-nitrogen removal rates can be increased substantially in denitrifying bioreactors with a corn cob bed medium compared to woodchips; however, additional organic carbon (C) is released into the effluent. This laboratory column experiment was conducted to test the performance of a post-bed cha...

  15. Post-cold-storage conditioning time affects soil denitrifying enzyme activity

    DEFF Research Database (Denmark)

    Chirinda, Ngonidzashe; Olesen, Jørgen Eivind; Porter, John Roy

    2011-01-01

    Soil denitrifying enzyme activity (DEA) is often assessed after cold storage. Previous studies using the short-term acetylene inhibition method have not considered conditioning time (post-cold-storage warm-up time prior to soil analysis) as a factor influencing results. We observed fluctuations...

  16. Spatiotemporal heterogeneity of core functional bacteria and their synergetic and competitive interactions in denitrifying sulfur conversion-assisted enhanced biological phosphorus removal.

    Science.gov (United States)

    Zhang, Yan; Yu, Mei; Guo, Jianhua; Wu, Di; Hua, Zheng-Shuang; Chen, Guang-Hao; Lu, Hui

    2017-09-07

    Denitrifying sulfur conversion-assisted enhanced biological phosphorus removal (DS-EBPR) has recently been developed for simultaneously removing nitrogen and phosphorus from saline sewage with minimal sludge production. This novel process could potentially enable sustainable wastewater treatment. Yet, the core functional bacteria and their roles are unknown. Here, we used high-throughput 16S rRNA gene sequencing coupled with principal coordinates analysis and ANOVA with Tukey's test to unravel the spatiotemporal heterogeneity of functional bacteria and their synergetic and competitive interactions. We did not find any obvious spatial heterogeneity within the bacterial population in different size-fractionated sludge samples, but the main functional bacteria varied significantly with operation time. Thauera was enriched (9.26~13.63%) as become the core functional genus in the DS-EBPR reactors and links denitrifying phosphorus removal to sulfide oxidation. The other two functional genera were sulfate-reducing Desulfobacter (4.31~12.85%) and nitrate-reducing and sulfide-oxidizing Thiobacillus (4.79~9.92%). These bacteria cooperated in the DS-EBPR process: Desulfobacter reduced sulfate to sulfide for utilization by Thiobacillus, while Thauera and Thiobacillus competed for nitrate and sulfide as well as Thauera and Desulfobacter competed for acetate. This study is the first to unravel the interactions among core functional bacteria in DS-EBPR, thus improving our understanding of how this removal process works.

  17. Simultaneous removal of sulfide, nitrate and acetate under denitrifying sulfide removal condition: Modeling and experimental validation

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Xijun; Chen, Chuan; Wang, Aijie; Guo, Wanqian; Zhou, Xu [State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090 (China); Lee, Duu-Jong, E-mail: djlee@ntu.edu.tw [State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090 (China); Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan (China); Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan (China); Ren, Nanqi, E-mail: rnq@hit.edu.cn [State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090 (China); Chang, Jo-Shu [Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan, Taiwan (China)

    2014-01-15

    Graphical abstract: Model evaluation applied to case study 1: (A-G) S{sup 2−}, NO{sub 3}{sup −}-N, NO{sub 2}{sup −}-N, and Ac{sup −}-C profiles under initial sulfide concentrations of 156.2 (A), 539 (B), 964 (C), 1490 (D), 342.7 (E), 718 (F), and 1140.7 (G) mg L{sup −1}. The solid line represents simulated result and scatter represents experimental result. -- Highlights: • This work developed a mathematical model for DSR process. • Kinetics of sulfur–nitrogen–carbon and interactions between denitrifiers were studied. • Kinetic parameters of the model were estimated via data fitting. • The model described kinetic behaviors of DSR processes over wide parametric range. -- Abstract: Simultaneous removal of sulfide (S{sup 2−}), nitrate (NO{sub 3}{sup −}) and acetate (Ac{sup −}) under denitrifying sulfide removal process (DSR) is a novel biological wastewater treatment process. This work developed a mathematical model to describe the kinetic behavior of sulfur–nitrogen–carbon and interactions between autotrophic denitrifiers and heterotrophic denitrifiers. The kinetic parameters of the model were estimated via data fitting considering the effects of initial S{sup 2−} concentration, S{sup 2−}/NO{sub 3}{sup −}-N ratio and Ac{sup −}-C/NO{sub 3}{sup −}-N ratio. Simulation supported that the heterotrophic denitratation step (NO{sub 3}{sup −} reduction to NO{sub 2}{sup −}) was inhibited by S{sup 2−} compared with the denitritation step (NO{sub 2}{sup −} reduction to N{sub 2}). Also, the S{sup 2−} oxidation by autotrophic denitrifiers was shown two times lower in rate with NO{sub 2}{sup −} as electron acceptor than that with NO{sub 3}{sup −} as electron acceptor. NO{sub 3}{sup −} reduction by autotrophic denitrifiers occurs 3–10 times slower when S{sup 0} participates as final electron donor compared to the S{sup 2−}-driven pathway. Model simulation on continuous-flow DSR reactor suggested that the adjustment of

  18. Comparative analysis of microbial community between different cathode systems of microbial fuel cells for denitrification.

    Science.gov (United States)

    Li, Chao; Xu, Ming; Lu, Yi; Fang, Fang; Cao, Jiashun

    2016-01-01

    Two types of cathodic biofilm in microbial fuel cells (MFC) were established for comparison on their performance and microbial communities. Complete autotrophic simultaneous nitrification and denitrification (SND) without organics addition was achieved in nitrifying-MFC (N-MFC) with a total nitrogen (TN) removal rate of 0.35 mg/(L·h), which was even higher than that in denitrifying-MFC (D-MFC) at same TN level. Integrated denaturing gradient gel electrophoresis analysis based on both 16S rRNA and nirK genes showed that Alpha-, Gammaproteobacteria were the main denitrifier communities. Some potential autotrophic denitrifying bacteria which can use electrons and reducing power from cathodes, such as Shewanella oneidensis, Shewanella loihica, Pseudomonas aeruginosa, Starkeya novella and Rhodopseudomonas palustris were identified and selectively enriched on cathode biofilms. Further, relative abundance of denitrifying bacteria characterized by nirK/16S ratios was much higher in biofilm than suspended sludge according to real-time polymerase chain reaction. The highest enrichment efficiency for denitrifiers was obtained in N-MFC cathode biofilms, which confirmed autotrophic denitrifying bacteria enrichment is the key factor for a D-MFC system.

  19. Marine Oxygen-Deficient Zones Harbor Depauperate Denitrifying Communities Compared to Novel Genetic Diversity in Coastal Sediments.

    Science.gov (United States)

    Bowen, Jennifer L; Weisman, David; Yasuda, Michie; Jayakumar, Amal; Morrison, Hilary G; Ward, Bess B

    2015-08-01

    Denitrification is a critically important biogeochemical pathway that removes fixed nitrogen from ecosystems and thus ultimately controls the rate of primary production in nitrogen-limited systems. We examined the community structure of bacteria containing the nirS gene, a signature gene in the denitrification pathway, from estuarine and salt marsh sediments and from the water column of two of the world's largest marine oxygen-deficient zones (ODZs). We generated over 125,000 nirS gene sequences, revealing a large degree of genetic diversity including 1,815 unique taxa, the vast majority of which formed clades that contain no cultured representatives. These results underscore how little we know about the genetic diversity of metabolisms underlying this critical biogeochemical pathway. Marine sediments yielded 1,776 unique taxa when clustered at 95 % sequence identity, and there was no single nirS denitrifier that was a competitive dominant; different samples had different highly abundant taxa. By contrast, there were only 39 unique taxa identified in samples from the two ODZs, and 99 % of the sequences belonged to 5 or fewer taxa. The ODZ samples were often dominated by nirS sequences that shared a 92 % sequence identity to a nirS found in the anaerobic ammonium-oxidizing (anammox) genus Scalindua. This sequence was abundant in both ODZs, accounting for 38 and 59 % of all sequences, but it was virtually absent in marine sediments. Our data indicate that ODZs are remarkably depauperate in nirS genes compared to the remarkable genetic richness found in coastal sediments.

  20. Denitrifying bacterial community composition changes associated with stages of denitrification in oxygen minimum zones

    Digital Repository Service at National Institute of Oceanography (India)

    Jayakumar, D.A.; O'Mullan, G.D.; Naqvi, S.W.A.; Ward, B.B.

    mixing two water masses with different cell number–nitrite relationships. In addition, the assignment of stages is somewhat complicated because it combines the net result of the history of the water and in situ microbial activity. Diversity... that are characteristic of OMZs in active stages of denitrification suggest that the removal of fixed nitrogen may occur via episodically enhanced growth of denitrifying organisms in the core of an OMZ. These hot spots are driven by the episodic blooms of surface...

  1. Denitrifying woodchip bioreactor and phosphorus filter pairing to minimize pollution swapping

    Science.gov (United States)

    Christianson, Laura E.; Lepine, Christine; Sibrell, Philip; Penn, Chad J.; Summerfelt, Steven T.

    2017-01-01

    Pairing denitrifying woodchip bioreactors and phosphorus-sorbing filters provides a unique, engineered approach for dual nutrient removal from waters impaired with both nitrogen (N) and phosphorus (P). This column study aimed to test placement of two P-filter media (acid mine drainage treatment residuals and steel slag) relative to a denitrifying system to maximize N and P removal and minimize pollution swapping under varying flow conditions (i.e., woodchip column hydraulic retention times (HRTs) of 7.2, 18, and 51 h; P-filter HRTs of 7.6–59 min). Woodchip denitrification columns were placed either upstream or downstream of P-filters filled with either medium. The configuration with woodchip denitrifying systems placed upstream of the P-filters generally provided optimized dissolved P removal efficiencies and removal rates. The P-filters placed upstream of the woodchip columns exhibited better P removal than downstream-placed P-filters only under overly long (i.e., N-limited) retention times when highly reduced effluent exited the woodchip bioreactors. The paired configurations using mine drainage residuals provided significantly greater P removal than the steel slag P-filters (e.g., 25–133 versus 8.8–48 g P removed m−3 filter media d−1, respectively), but there were no significant differences in N removal between treatments (removal rates: 8.0–18 g N removed m−3 woodchips d−1; N removal efficiencies: 18–95% across all HRTs). The range of HRTs tested here resulted in various undesirable pollution swapping by-products from the denitrifying bioreactors: nitrite production when nitrate removal was not complete and sulfate reduction, chemical oxygen demand production and decreased pH during overly long retention times. The downstream P-filter placement provided a polishing step for removal of chemical oxygen demand and nitrite.

  2. Kinetics of Nitrate Utilization by Mixed Populations of Denitrifying Bacteria †

    OpenAIRE

    Murray, Robert E.; Parsons, Laura L.; Smith, M. Scott

    1989-01-01

    Kinetics of nitrate utilization by mixed bacterial populations from two agricultural soils and a pond sediment in Kentucky were measured by using progress curves of nitrous oxide production. Nitrous oxide production from anaerobic soil and sediment slurries containing added nitrate and acetylene exhibited first-order kinetics. Nitrate affinity (Km) for mixed populations of denitrifying bacteria in unfertilized agricultural soils and pond sediments ranged from 1.8 to 13.7 μM. The affinity of b...

  3. Fertilization stimulates anaerobic fuel degradation of antarctic soils by denitrifying microorganisms.

    Science.gov (United States)

    Powell, Shane M; Ferguson, Susan H; Snape, Ian; Siciliano, Steven D

    2006-03-15

    Human activities in the Antarctic have resulted in hydrocarbon contamination of these fragile polar soils. Bioremediation is one of the options for remediation of these sites. However, little is known about anaerobic hydrocarbon degradation in polar soils and the influence of bioremediation practices on these processes. Using a field trial at Old Casey Station, Antarctica, we assessed the influence of fertilization on the anaerobic degradation of a 20-year old fuel spill. Fertilization increased hydrocarbon degradation in both anaerobic and aerobic soils when compared to controls, but was of most benefit for anaerobic soils where evaporation was negligible. This increased biodegradation in the anaerobic soils corresponded with a shift in the denitrifier community composition and an increased abundance of denitrifiers and benzoyl-CoA reductase. A microcosm study using toluene and hexadecane confirmed the degradative capacity within these soils under anaerobic conditions. It was observed that fertilized anaerobic soil degraded more of this hydrocarbon spike when incubated anaerobically than when incubated aerobically. We conclude that denitrifiers are actively involved in hydrocarbon degradation in Antarctic soils and that fertilization is an effective means of stimulating their activity. Further, when communities stimulated to degrade hydrocarbons under anaerobic conditions are exposed to oxygen, hydrocarbon degradation is suppressed. The commonly accepted belief that remediation of polar soils requires aeration needs to be reevaluated in light of this new data.

  4. Isolation and Physiological Characterization of Psychrophilic Denitrifying Bacteria from Permanently Cold Arctic Fjord Sediments (Svalbard, Norway)

    Science.gov (United States)

    Canion, Andy; Prakash, Om; Green, Stefan J.; Jahnke, Linda; Kuypers, Marcel M. M.; Kostka, Joel E.

    2013-01-01

    A large proportion of reactive nitrogen loss from polar sediments is mediated by denitrification, but microorganisms mediating denitrification in polar environments remain poorly characterized. A combined approach of most-probable-number (MPN) enumeration, cultivation and physiological characterization was used to describe psychrophilic denitrifying bacterial communities in sediments of three Arctic fjords in Svalbard (Norway). A MPN assay showed the presence of 10(sup 3)-10(sup 6) cells of psychrophilic nitrate-respiring bacteria g(sup -1) of sediment. Fifteen strains within the Proteobacteria were isolated using a systematic enrichment approach with organic acids as electron donors and nitrate as an electron acceptor. Isolates belonged to five genera, including Shewanella, Pseudomonas, Psychromonas (Gammaproteobacteria), Arcobacter (Epsilonproteobacteria) and Herminiimonas (Betaproteobacteria). All isolates were denitrifiers, except Shewanella, which exhibited the capacity for dissimilatory nitrate reduction to ammonium (DNRA). Growth from 0 to 40 degC demonstrated that all genera except Shewanella were psychrophiles with optimal growth below 15 degC, and adaptation to low temperature was demonstrated as a shift from primarily C16:0 saturated fatty acids to C16:1 monounsaturated fatty acids at lower temperatures. This study provides the first targeted enrichment and characterization of psychrophilic denitrifying bacteria from polar sediments, and two genera, Arcobacter and Herminiimonas, are isolated for the first time from permanently cold marine sediments.

  5. Simultaneous enrichment of denitrifying anaerobic methane-oxidizing microorganisms and anammox bacteria in a hollow-fiber membrane biofilm reactor.

    Science.gov (United States)

    Ding, Zhao-Wei; Lu, Yong-Ze; Fu, Liang; Ding, Jing; Zeng, Raymond J

    2017-01-01

    In this study, the coculture system of denitrifying anaerobic methane oxidation (DAMO) microbes and anaerobic ammonium oxidation (anammox) bacteria was successfully enriched in a hollow-fiber membrane biofilm reactor (HfMBR) using freshwater sediment as the inoculum. The maximal removal rates of nitrate and ammonium were 78 mg N/L/day (131 mg N/m(2)/day) and 26 mg N/L/day (43 mg N/m(2)/day), respectively. Due to the high rate of methane mass transfer in HfMBR, the activity of DAMO archaea continued to increase during the enrichment period, indicating that HfMBR could be a powerful tool to enrich DAMO microorganisms. Effects of partial methane pressure, temperature, and pH on the cocultures were obvious. However, the microbial activity in HfMBR could be recovered quickly after the shock change of environmental factors. Furthermore, the result also found that DAMO bacteria likely had a stronger competitive advantage than anammox bacteria under the operating conditions in this study. High-throughput sequencing 16S rRNA genes illustrated that the dominant microbes were NC10, Euryarchaeota, Proteobacteria, Planctomycetes, and Chlorobi with relative abundance of 38.8, 26.2, 13.78, 6.2, and 3.6 %, respectively.

  6. Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment.

    Science.gov (United States)

    Han, Song-Ih; Kim, Ju-Ok; Lee, Ye-Rim; Ekpeghere, Kalu I; Koh, Sung-Cheol; Whang, Kyung-Sook

    2016-06-01

    A denitrifying bacterium, designated strain E4-1(T), was isolated from a bioreactor for tannery wastewater treatment, and its taxonomic position was investigated using a polyphasic approach. Strain E4-1(T), a facultative anaerobic bacterium, was observed to grow between 0 and 12 % (w/v) NaCl, between pH 3.0 and 12.0. Cells were found to be oxidase-positive and catalase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain E4-1(T) forms a distinct lineage with respect to closely related genera in the family Xanthomonadaceae, and is closely related to Chiayiivirga, Aquimonas and Dokdonella, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93.9 %. The predominant respiratory quinone was determined to be ubiquinone-8 (Q-8) and the major cellular fatty acids were determined to be iso-C15:0, iso-C17:1 ω9c, iso-C11:0 and iso-C11:0 3OH. Based on physiological, biochemical and chemotaxonomic properties together with results of comparative 16S rRNA gene sequence analysis, strain E4-1(T) is considered to represent a novel species in a new genus, for which the name Denitratimonas tolerans gen. nov., sp. nov. is proposed. The type strain is E4-1(T) (=KACC 17565(T) = NCAIM B 025327(T)).

  7. Nitrogen assimilation in denitrifier Bacillus azotoformans LMG 9581(T).

    Science.gov (United States)

    Sun, Yihua; De Vos, Paul; Willems, Anne

    2017-07-19

    Until recently, it has not been generally known that some bacteria can contain the gene inventory for both denitrification and dissimilatory nitrate (NO3(-))/nitrite (NO2(-)) reduction to ammonium (NH4(+)) (DNRA). Detailed studies of these microorganisms could shed light on the differentiating environmental drivers of both processes without interference of organism-specific variation. Genome analysis of Bacillus azotoformans LMG 9581(T) shows a remarkable redundancy of dissimilatory nitrogen reduction, with multiple copies of each denitrification gene as well as DNRA genes nrfAH, but a reduced capacity for nitrogen assimilation, with no nas operon nor amtB gene. Here, we explored nitrogen assimilation in detail using growth experiments in media with different organic and inorganic nitrogen sources at different concentrations. Monitoring of growth, NO3(-) NO2(-), NH4(+) concentration and N2O production revealed that B. azotoformans LMG 9581(T) could not grow with NH4(+) as sole nitrogen source and confirmed the hypothesis of reduced nitrogen assimilation pathways. However, NH4(+) could be assimilated and contributed up to 50% of biomass if yeast extract was also provided. NH4(+) also had a significant but concentration-dependent influence on growth rate. The mechanisms behind these observations remain to be resolved but hypotheses for this deficiency in nitrogen assimilation are discussed. In addition, in all growth conditions tested a denitrification phenotype was observed, with all supplied NO3(-) converted to nitrous oxide (N2O).

  8. Effect of methyl parathion on nitrous oxide production: a laboratory study.

    Science.gov (United States)

    Rojas-Oropeza, Marcelo; Fernández, Francisco J; Dendooven, Luc; Cabirol, Nathalie

    2012-03-01

    We investigated the diversity of a denitrifying gene (nirK) and the emission of CO(2) and N(2)O, in a "chinampa" soil contaminated with methyl parathion. Soil at 40% of water holding capacity was spiked with methyl parathion at four concentrations (i.e. 0, 0.7, 1.47 and 4.27 g kg(-1) dry soil), while emission of N(2)O and CO(2) and nirK diversity was determined after 0, 1, 14, 30, 60 and 90 days. The emission of N(2)O on a daily base and the cumulative emission of CO(2) was not affected by the different concentrations of methyl parathion applied to soil. The diversity of the nirK gene, determined by using temperature gradient gel electrophoresis (TGGE), decreased with increased methyl parathion application. It was found that methyl parathion had effect on the emissions of N(2)O and CO(2), and reduced the diversity of the nirK gene. Consequently, the reduced diversity of the nirK gene could affect the emission of N(2)O.

  9. Habitat Distribution of Denitrifier and Denitrification Activity in the Tidal Flat of the Interior Parts of the Ariake Sea

    Science.gov (United States)

    Koga, Akane; Seguchi, Masahiro; Koriyama, Masumi

    The spatial distributions of denitrifier numbers in the tidal sediment (0∼4cm depth) in the interior parts of the Ariake Sea changed largely with the properties of tidal flat and seasons. The denitrifier numbers in summer were many in the muddy tidal flat in the interior parts of this bay and about 18,000MPNs/g-dry on the average. But, its numbers were few in the sandy and mud-sandy tidal flats in the east and west coast areas and about 1,700MPN/g-dry on the average. A close relation between the denitrifier numbers in the tidal sediment (0∼4cm depth) and its mud (clay and silt) content was found and its numbers rose with the increase of mud content. The vertical distribution of denitrifier numbers in the muddy tidal flat was high near the surface layer (0∼2cm depth) where Eh was almost zero in summer, but its distribution decreased in other season. The denitrification rate in the muddy tidal flat changed largely with time (0.35-13.86mg-N·m-2·d-1). The denitrification activity in the muddy tidal flat was assumed to be affected by the environmental factors and substrate concentration other than the denitrifier numbers.

  10. Nitrogen Removal Characteristics of a Newly Isolated Indigenous Aerobic Denitrifier from Oligotrophic Drinking Water Reservoir, Zoogloea sp. N299

    Directory of Open Access Journals (Sweden)

    Ting-Lin Huang

    2015-05-01

    Full Text Available Nitrogen is considered to be one of the most widespread pollutants leading to eutrophication of freshwater ecosystems, especially in drinking water reservoirs. In this study, an oligotrophic aerobic denitrifier was isolated from drinking water reservoir sediment. Nitrogen removal performance was explored. The strain was identified by 16S rRNA gene sequence analysis as Zoogloea sp. N299. This species exhibits a periplasmic nitrate reductase gene (napA. Its specific growth rate was 0.22 h−1. Obvious denitrification and perfect nitrogen removal performances occurred when cultured in nitrate and nitrite mediums, at rates of 75.53% ± 1.69% and 58.65% ± 0.61%, respectively. The ammonia removal rate reached 44.12% ± 1.61% in ammonia medium. Zoogloea sp. N299 was inoculated into sterilized and unsterilized reservoir source waters with a dissolved oxygen level of 5–9 mg/L, pH 8–9, and C/N 1.14:1. The total nitrogen removal rate reached 46.41% ± 3.17% (sterilized and 44.88% ± 4.31% (unsterilized. The cell optical density suggested the strain could survive in oligotrophic drinking water reservoir water conditions and perform nitrogen removal. Sodium acetate was the most favorable carbon source for nitrogen removal by strain N299 (p < 0.05. High C/N was beneficial for nitrate reduction (p < 0.05. The nitrate removal efficiencies showed no significant differences among the tested inoculums dosage (p > 0.05. Furthermore, strain N299 could efficiently remove nitrate at neutral and slightly alkaline and low temperature conditions. These results, therefore, demonstrate that Zoogloea sp. N299 has high removal characteristics, and can be used as a nitrogen removal microbial inoculum with simultaneous aerobic nitrification and denitrification in a micro-polluted reservoir water ecosystem.

  11. In situ detection of denitrifying bacteria by mRNA-targeted nucleic acid probes and catalyzed reporter deposition

    DEFF Research Database (Denmark)

    Kofoed, Michael Vedel; Stief, Peter; Poulsen, Morten

    In situ detection of denitrifying bacteria by mRNA-targeted nucleic acid probes and catalyzed reporter deposition   Michael V.W. Kofoed, Peter Stief, Morten Poulsen, and Andreas Schramm Department of Biological Sciences, Microbiology, University of Aarhus, Denmark Denitrification, the sequential...... reduction of nitrate to dinitrogen gas, is essential for the removal of fixed nitrogen from natural and engineered ecosystems. However, community structure and activity dynamics of denitrifying bacteria in most systems are poorly understood, partially due to difficulties in identifying and quantifying...... and catalyzed fluorescent reporter deposition (CARD-FISH). The general feasibility of the approach was first tested with pure cultures of Pseudomonas stutzeri and various denitrifying and nitrate-reducing isolates. Detailed studies of probe specificity and hybridization conditions using Clone-FISH of nar...

  12. In situ detection of denitrifying bacteria by mRNA-targeted nucleic acid probes and catalyzed reporter deposition

    DEFF Research Database (Denmark)

    Kofoed, Michael Vedel; Stief, Peter; Poulsen, Morten

    In situ detection of denitrifying bacteria by mRNA-targeted nucleic acid probes and catalyzed reporter deposition   Michael V.W. Kofoed, Peter Stief, Morten Poulsen, and Andreas Schramm Department of Biological Sciences, Microbiology, University of Aarhus, Denmark Denitrification, the sequential...... reductase) and nosZ (encoding nitrous oxide reductase), to detect nitrate-reducing and completely denitrifying bacteria, respectively. Enzyme-labelled oligonucleotide probes and digoxygenin-labelled polynucleotide probes were evaluated for in situ hybridization in combination with immunochemical detection...... reduction of nitrate to dinitrogen gas, is essential for the removal of fixed nitrogen from natural and engineered ecosystems. However, community structure and activity dynamics of denitrifying bacteria in most systems are poorly understood, partially due to difficulties in identifying and quantifying...

  13. Characteristics of self-alkalization in high-rate denitrifying automatic circulation (DAC) reactor fed with methanol and sodium acetate.

    Science.gov (United States)

    Li, Wei; Zheng, Ping; Guo, Jun; Ji, Junyuan; Zhang, Meng; Zhang, Zonghe; Zhan, Enchao; Abbas, Ghulam

    2014-02-01

    Denitrification is a self-alkalization process. In this experiment, the characteristics of self-alkalization in high-rate heterotrophic denitrifying automatic circulation (DAC) reactor fed with methanol and sodium acetate were investigated, respectively. The results showed that, (1) The self-alkalization of high-rate denitrifying reactors was remarkably strong both with methanol and sodium acetate as carbon sources, while the effluent pH was much lower than the stoichiometric values and the malfunction from self-alkalization of denitrification was far less serious than expected. (2) The self-adaptation of the reactors was attributed to the neutralization of carbon dioxide (oxidization product of organic matter) and the self-adaptation of denitrifying sludge. The formation and discharge of calcium carbonate precipitates gave rise to lower effluent pH and alkalinity than the stoichiometric values.

  14. Moving Denitrifying Bioreactors beyond Proof of Concept: Introduction to the Special Section.

    Science.gov (United States)

    Christianson, Laura E; Schipper, Louis A

    2016-05-01

    Denitrifying bioreactors are organic carbon-filled excavations designed to enhance the natural process of denitrification for the simple, passive treatment of nitrate-nitrogen. Research on and installation of these bioreactors has accelerated within the past 10 years, particularly in watersheds concerned about high nonpoint-source nitrate loads and also for tertiary wastewater treatment. This special section, inspired by the meeting of the Managing Denitrification in Agronomic Systems Community at the 2014 Annual Meeting of the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, aims to firmly establish that denitrifying bioreactors for treatment of nitrate in drainage waters, groundwater, and some wastewaters have moved beyond the proof of concept. This collection of 14 papers expands the peer-reviewed literature of denitrifying bioreactors into new locations, applications, and environmental conditions. There is momentum behind the pairing of wood-based bioreactors with other media (biochar, corn cobs) and in novel designs (e.g., use within treatment trains or use of baffles) to broaden applicability into new kinds of waters and pollutants and to improve performance under challenging field conditions such as cool early season agricultural drainage. Concerns about negative bioreactor by-products (nitrous oxide and hydrogen sulfide emissions, start-up nutrient flushing) are ongoing, but this translates into a significant research opportunity to develop more advanced designs and to fine tune management strategies. Future research must think more broadly to address bioreactor impacts on holistic watershed health and greenhouse gas balances and to facilitate collaborations that allow investigation of mechanisms within the bioreactor "black box."

  15. Drinking Water Denitrification using Autotrophic Denitrifying Bacteria in a Fluidized Bed Bioreactor 

    Directory of Open Access Journals (Sweden)

    Abdolmotaleb Seid-mohammadi

    2013-02-01

    Full Text Available Background and Objectives: Contamination of drinking water sources with nitrate may cause adverse effects on human health. Due to operational and maintenance problems of physicochemical nitrate removal processes, using biological denitrification processes have been performed. The aim of this study is to evaluate nitrate removal efficiency from drinking water using autotrophic denitrifying bacteria immobilized on sulfur impregnated activated carbon in a fluidized bed bioreactor. Materials and Methods: After impregnating activated carbon by sulfur as a microorganism carriers and enrichment and inoculation of denitrifying bacteria, a laboratory-scale fluidized bed bioreactor was operated. Nitrate removal efficiency, nitrite, turbidity, hardness and TOC in the effluent were examined during the whole experiment under various conditions including constant influent nitrate concentration as 90 mg NO3--N/l corresponding to different HRT ranging from 5.53 to 1.5 hr. Results: We found that  the denitrification rates was depended on the hydraulic retention time and the nitrate removal efficiency was up to 98%  and nitrite concentration was lower than 1mg/l at optimum HRT=2.4 hr respectively. Moreover, there was no difference in hardness between influent and effluent due to supplying sodium bicarbonate as carbon source for denitrifying bacteria.  However pH, TOC, hardness, and turbidity of the effluent met the W.H.O guidelines for drinking water.  Conclusion: This study demonstrated that an innovative carrier as sulfur impregnated activated carbon could be used as both the biofilm carrier and energy source for treating nitrate contaminated drinking water in the lab-scale fluidized bed bioreactor.

  16. Nitrifying and denitrifying bacteria in aerobic granules formed in sequencing batch airlift reactors

    Institute of Scientific and Technical Information of China (English)

    WANG Fang; YANG Fenglin; QI Aijiu

    2007-01-01

    The purpose of this study was to investigate nitrifying bacteria and denitrifying bacteria isolated from aerobic granules.Aerobic granules were formed in an internal-circulate sequencing batch airlift reactor(SBAR)and biodegradation of NH3 -N was analyzed in the reactor.Bacteria were isolated and determined from aerobic granules using selected media.The growth properties and morphology of bacteria colonies were observed by controlling aerobic or anaerobic conditions in the culture medium.It was found that bacteria in aerobic granules were diverse and some of them were facultative aerobes.The diversity of bacteria in aerobic granules was a premise of simultaneous nitrification and denitrification.

  17. Pseudomonads Isolated from Pristine Background Groundwater Proliferate More Effectively in Co-culture than in Monoculture Under Denitrifying Conditions

    Science.gov (United States)

    Aaring, A. B.; Lancaster, A.; Novichkov, P.; Adams, M. W. W.; Deutschbauer, A. M.; Chakraborty, R.

    2016-12-01

    As part of the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) consortium, we study the microbial community at the U.S. Department of Energy's Field Research Center (FRC) in Oak Ridge. The groundwater at this site contains plumes of nitrate with concentrations up to 14,000mg/L among other contaminants, though molybdenum concentrations are low. Because molybdenum is essential to nitrate reduction, this can be inhibitory to growth. Several strains of Pseudomonas were isolated from the same background groundwater sample. These isolates utilized diverse carbon sources ranging from acetate to glucose while growing under denitrifying conditions. The strains were also screened for nitrate tolerance and a couple of them were shown to be tolerant to 300-400 mM nitrate under anaerobic conditions. In the field site the bacteria live in consortia rather than in isolation, therefore we hypothesized that growth of these strains will be more robust in co-culture, as the denitrification pathway was segmented between the species. Three of the isolates (Pseudomonas fluorescens strains N1B4, N2E2, N2E3) were selected for in-depth analysis based on growth in pairwise co-cultures relative to monocultures, and the availability of the relevant genetic tools, such as transposon mutant libraries. Full genome sequencing showed that strain N2E3 has a truncated dentrification pathway: it lacks nitrous oxide reductase. Our results show strain N2E2 grow to maximum cell density an average of 45 hours more quickly when grown with strain N2E3 than in monoculture. Utilizing RB-TnSeq libraries of our strains, it was also found that some genes involved in nitrate reduction, sulfate permeability, molybdenum utilization, and anaerobic reduction are important for growth under these conditions. In addition, a few unexpected genes were also shown to be positively correlated to growth, such as genes homologous to genes for DNA proofreading or antibiotic production. These

  18. Inhibitory Effect of Gamma-Irradiated Chitosan on the Growth of Denitrifiers

    Directory of Open Access Journals (Sweden)

    Javier Vilcáez

    2009-01-01

    Full Text Available In order to find an environmentally benign substitute to hazardous inhibitory agents, the inhibitory effect of -irradiated chitosans against a mixed culture of denitrifying bacteria was experimentally evaluated. Unlike other studies using pure aerobic cultures, the observed effect was not a complete inhibition but a transient inhibition reflected by prolonged lag phases and reduced growth rates. Raw chitosan under acid conditions (pH 6.3 exerted the strongest inhibition followed by the 100 kGy and 500 kGy irradiated chitosans, respectively. Therefore, because the molecular weight of chitosan decreases with the degree of -irradiation, the inhibitory properties of chitosan due to its high molecular weight were more relevant than the inhibitory properties gained due to the modification of the surface charge and/or chemical structure by -irradiation. High dosage of -irradiated appeared to increase the growth of mixed denitrifying bacteria in acid pH media. However, in neutral pH media, high dosage of -irradiation appeared to enhance the inhibitory effect of chitosan.

  19. Simultaneous domestic wastewater and nitrate sewage treatment by DEnitrifying AMmonium OXidation (DEAMOX) in sequencing batch reactor.

    Science.gov (United States)

    Du, Rui; Cao, Shenbin; Li, Baikun; Wang, Shuying; Peng, Yongzhen

    2017-05-01

    A novel DEAMOX system was developed for nitrogen removal from domestic wastewater and nitrate (NO3(-)-N) sewage in sequencing batch reactor (SBR). High nitrite (NO2(-)-N) was produced from NO3(-)-N reduction in partial-denitrification process, which served as electron acceptor for anammox and was removed with ammonia (NH4(+)-N) in domestic wastewater simultaneously. A 500-days operation demonstrated that the efficient and stable nitrogen removal performance could be achieved by DEAMOX. The total nitrogen (TN) removal efficiency was as high as 95.8% with influent NH4(+)-N of 63.58 mg L(-1) and NO3(-)-N of 69.24 mg L(-1). The maximum NH4(+)-N removal efficiency reached up to 94.7%, corresponding to the NO3(-)-N removal efficiency of 97.8%. The biomass of partial-denitrification and anammox bacteria was observed to be wall-growth. The deteriorated nitrogen removal performance occurred due to excess denitrifying microbial growth in the outer layer of sludge consortium, which prevented the substrate transfer for anammox inside. However, an excellent nitrogen removal could be guaranteed by scrapping the superficial denitrifying biomass at regular intervals. Furthermore, the high-throughput sequencing analysis revealed that the Thauera genera (26.33%) was possibly responsible for the high NO2(-)-N accumulation in partial-denitrification and Candidatus Brocadia (1.7%) was the major anammox species.

  20. The start-up of denitrifying phosphorus removal system by using nitrite as electron acceptor

    Science.gov (United States)

    Li, W.; Liu, J.; Sun, H. Z.; Fu, J. X.; Gao, Y.; Sun, J.

    2017-08-01

    The inoculation of short-cut denitrifying polyphosphate-accumulating organisms (DPAOs) mainly included two-phase inoculation and three-phase inoculation. The short-cut denitrifying phosphorus removal bacteria were quickly inoculated by sequencing batch reactor (SBR) to treatment domestic wastewater. The results showed that the average effluent concentration of TP was 0.85 mg/L after 132 cycles by 44 days in two-phase inoculation. The removal rates of NO2 --N, TP and COD were 94.73%, 95.47% and 89.96% after 126 cycles by 42 days in three-phase inoculation, and the effluent concentrations were separately 1.31 mg/L, 0.45 mg/L and 17.07 mg/L, which reached the first A class requirement of Urban sewage treatment plant pollutant discharge standard. It was indicated that the efficiency of three-phase inoculation was higher. Anoxic phosphorus uptake was influenced seriously by anaerobic residual carbon, and it was the difference of the two inoculations.

  1. Experimental Study on Denitrification Using Coated Electrode of Immobilized Denitrifying Bacteria

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Objective To develop a coated electrode of immobilized denitrificants and to evaluate the performance of a bioelectrochemical reactor to enhance and control denitrification. Methods Denitrifying bacteria were developed by batch incubation and immobilized with polyvinyl alcohol (PVA) on the surface of activated carbon fiber (ACF) to make a coated electrode. Then the coated electrode (cathode) and graphite electrode (anode) were transferred to the reactor to reduce nitrate. Results After acclimated to the mixtrophic and autotrophic denitrification stages, the denitrifying bacteria could use hydrogen as an electron donor to reduce nitrate. When the initial nitrate concentration was 30.2 mg NO3--N/L, the denitrification efficiency was 57.3% at an applied electric current of 15 mA and a hydraulic retention time (HRT) of 12 hours.Correspondingly, the current density was 0.083 mA / cm2. The nitrate removal rate of the reactor was 34.4 g NO3--N / m3·d, and the surface area loading was 1.34 g NO3--N / m2·d. Conclusion The coated electrode may keep high quantity of biomass, thus achieving a high denitrification rate. Denitrification efficiencies are related to HRT, current density, oxidation reduction potential (ORP), dissolved oxygen (DO), pH value, and temperature.

  2. Full-scale post denitrifying biofilters: sinks of dissolved N2O?

    Science.gov (United States)

    Bollon, Julien; Filali, Ahlem; Fayolle, Yannick; Guerin, Sabrina; Rocher, Vincent; Gillot, Sylvie

    2016-09-01

    In this study, nitrous oxide (N2O) emissions from a full-scale denitrifying biofilter plant were continuously monitored over two periods (summer campaign in September 2014 and winter campaign in February 2015). Results of the summer campaign showed that the major part (>99%) of N2O flux was found in the liquid phase and was discharged with the effluent. N2O emissions were highly variable and represented in average 1.28±1.99% and 0.22±0.31% of the nitrate uptake rate during summer and winter campaigns, respectively. Denitrification was able to consume a large amount of dissolved N2O coming from the upstream nitrification stage. In the absence of methanol injection failure and with an influent BOD/NO3-N ratio higher than 3, average reduction of N2O was estimated to be of 93%. The control of exogenous carbon dosage is essential to minimize N2O production from denitrifying biofilters, in correlation to NO2-N concentrations in the filter.

  3. Optimizing and real-time control of biofilm formation, growth and renewal in denitrifying biofilter.

    Science.gov (United States)

    Liu, Xiuhong; Wang, Hongchen; Long, Feng; Qi, Lu; Fan, Haitao

    2016-06-01

    A pilot-scale denitrifying biofilter (DNBF) with a treatment capacity of 600m(3)/d was used to study real-time control of biofilm formation, removal and renewal. The results showed biofilm formation, growth and removal can be well controlled using on-line monitored turbidity. The status of filter layer condition can be well indicated by Turb break points on turbidity profile. There was a very good linear relationship between biofilm growth degree (Xbiof) and filter clogging degree (Cfilter) with R(2) higher than 0.99. Filter layer clogging coefficient (Yc) lower than 0.27 can be used to determine stable filter layer condition. Since variations of turbidity during backwash well fitted normal distribution with R(2) higher than 0.96, biofilm removal during backwash also can be well optimized by turbidity. Although biofilm structure and nirK-coding denitrifying communities using different carbon sources were much more different, DNBF was still successfully and stably optimized and real-time controlled via on-line turbidity. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Production of NO and N2O by Pure Cultures of Nitrifying and Denitrifying Bacteria during Changes in Aeration

    NARCIS (Netherlands)

    Kester, R.A.; Boer, W. de; Laanbroek, H.J.

    1997-01-01

    Peak emissions of NO and N2O are often observed after wetting of soil. The reactions to sudden changes in the aeration of cultures of nitrifying and denitrifying bacteria with respect to NO and N2O emissions were compared to obtain more information about the microbiological aspects of peak emissions

  5. Short exposure to acetylene to distinguish between nitrifier and denitrifier nitrous oxide production in soil and sediment samples

    NARCIS (Netherlands)

    Kester, R.A.; De Boer, W.; Laanbroek, H.J.

    1996-01-01

    The contribution of nitrifiers and denitrifiers to the nitrous oxide production in slurries of calcareous silt loam and river bank sediment at different oxygen concentrations was determined using acetylene as nitrification inhibitor. The addition of 10 Pa acetylene resulted in inhibition of nitrous

  6. Short exposure to acetylene to distinguish between nitrifier and denitrifier nitrous oxide production in soil and sediment samples

    NARCIS (Netherlands)

    Kester, R.A.; Boer, W. de; Laanbroek, H.J.

    1996-01-01

    The contribution of nitrifiers and denitrifiers to the nitrous oxide production in slurries of calcareous silt loam and river bank sediment at different oxygen concentrations was determined using acetylene as nitrification inhibitor. The addition of 10 Pa acetylene resulted in inhibition of nitrous

  7. Using T-RFLP data on denitrifier community composition to inform understanding of denitrification in stream sediments (Invited)

    Science.gov (United States)

    Wang, S.; Somers, K.; Sudduth, E.; Hassett, B.; Bernhardt, E. S.; Urban, D. L.

    2010-12-01

    We used terminal restriction fragment length polymorphism (T-RFLP), a molecular fingerprinting method, to characterize denitrifier communities in sediments taken from 48 study streams in North Carolina, USA. In addition to characterizing denitrifier communities, we also used denitrification enzyme activity (DEA) assays to measure potential denitrification rates. Due to differences in watershed land-use, study streams covered a gradient of nitrogen and carbon concentrations, as well as a gradient of contaminant loading from stormwater and sanitary sewers. Nitrogen and carbon (i.e., substrate) concentrations are commonly used to make predictions about denitrification rates in streams. Such models do not take into account denitrifier community composition, which may be an important, independent control of denitrification rates, particularly under stressful conditions (e.g., high contaminant loading) that prevent communities from capitalizing on high substrate availability. Our results indicate that substrate availability by itself was a weak predictor of denitrification rates; the same was also true for denitrifier community composition. However, when both factors were incorporated in a multiple regression model, the percent variation explained increased substantially. These findings suggest that T-RFLP, a relatively cost-effective method, can be used to improve our understanding of controls on denitrification rates in streams with varying watershed land-uses.

  8. The Control of Microcystis spp. Bloom by Combining Indigenous Denitrifying Bacteria From Sutami Reservoir with Fimbristylis globulosa and Vetiveria zizanoides

    Directory of Open Access Journals (Sweden)

    Bayu Agung Prahardika

    2013-04-01

    Full Text Available The purpose of this research is to know the ability of polyculture macrophyte (Fimbristylis globulosa and Vetiveria zizanoides and the combination of both with consortium of indigenous denitrifying bacteria from Sutami reservoir that was added by Microcystis spp. or not to reduce the concentration of nitrate, dissolved phosphate and the carrying capacity of Microcystis spp. The experiment was done in a medium filled up with Sutami reservoir water enriched with 16 ppm of nitrate and 0.4 ppm of phosphate. The denitrifying bacteria used in this research were DR-14, DU-27-1, DU-30-1, DU-30-2, TA-8 and DU-27-4 isolated from Sutami reservoir. The treatments were incubated within 15 days. Microcystis spp. abundance was calculated every day, but the measurement of the concentration of nitrate and dissolved phosphate was done every six days. The results showed that both treatment and the combination of both macrophytes with a consortium of denitrifying indigenous bacteria were added or not either Microcystis able to reduce nitrate at 99% and 93-99% orthophosphoric. The combination of macrophytes with denitrifying indigenous bacterial consortium from Sutami reservoir was able to inhibit the carrying capacity of Microcystis spp. highest up to 47.87%. They could also significantly reduce the abundance of Microcystis from 107 cells/mL in earlier days of the treatment into 0.35x104 cells/mL after fifteen days of incubation.

  9. 反硝化除磷菌筛选及其特性研究%Studies on the screening of denitrifying and phosphorus removal bacteria and its characteristics

    Institute of Scientific and Technical Information of China (English)

    安健; 伏光辉; 阮记明; 陈百尧; 龚琪本; 唐兴本; 杨先乐

    2012-01-01

    [Objective] In order to study on the characteristics of denitrifying and phosphorus removal bacteria. [Methods] Many strains with denitrification and phosphorus removal characteristics under aerobic condition were isolated by screening of microorganism and methods of biological characteristics from the water and sediment samples of shrimp culture ponds. [Results] Among them strain LY-1 could remove nitrite nitrogen from 10 mg/L to 0.04 mg/L, and the PO43- -P from 10 mg/L to 0.05 mg/L in 18 h, respectively; and approximately to 100% of denitrifying and phosphorus removal rate were reached at the DO concentration of 5.0-5.9 mg/L. Furthermore, in comparison with a denitrifying and phosphorus removal bacterium, Bacillus subtilis selected as the positive control and Escherichia coli as the negative control, strain LY-1 was tested under different pH, temperature, salty, PO43--P and nitrite concentration, its denitrifying removal rate was reached approximately 99%, and phosphorus removal rate reached 86% at the pH of 5-9; the denitrifying and phosphorus removal rate of strain YX-6 reached proximately 100% at 30 °C; The rate almost reached 99% when salty ranged between 5 and 15, phosphorus concentration was 10 mg/L and nitrite nitrogen concentration was 20 mg/L. [Conclusion] The results showed that the denitrifying and phosphorus removal of LY-1 was significantly higher than that of the two controls (P<0.05). According to the morphological, physiological and biochemical properties, and the analysis of its 16S rRNA gene sequence, strain LY-1 was identified as Bacillus cereus primarily.%[目的]研究反硝化除磷菌特性.[方法]通过微生物筛选和生物学特性研究方法,从对虾养殖池塘中筛选出多株可在有氧条件下同时具有反硝化除磷功能的菌种.[结果]菌株LY-1可在18h内将初始量为10 mg/L的亚硝酸盐氮降低至0.04 mg/L,PO43--P降低至0.05 mg/L.在DO浓度为5.0-5.9 mg/L时,该菌反硝化除磷率近100%.试验选取

  10. Optimization of hard clams, polychaetes, physical disturbance and denitrifying bacteria of removing nutrients in marine sediment.

    Science.gov (United States)

    Shen, Hui; Thrush, Simon F; Wan, Xihe; Li, Hui; Qiao, Yi; Jiang, Ge; Sun, Ruijian; Wang, LiBao; He, Peimin

    2016-09-15

    Marine organisms are known to play important roles in transforming nutrients in sediments, however, guidelines to optimize sediment restoration are not available. We conducted a laboratory mesocosm experiment to investigate the role of hard clams, polychaetes, the degree of physical disturbance and denitrifying bacterial concentrations in removing total nitrogen (TN), total phosphorus (TP), and total organic carbon (TOC) in marine sediments. Response surface methodology was employed to analyze the results of initial experiments and in a subsequent experiment identified optimal combinations of parameters. Balancing the TN, TP, TOC removal efficiency, our model predicted 39% TN removal, 33% TP removal, and 42% TOC removal for a 14-day laboratory bioremediation trial using hard clams biomass of 1.2kgm(-2), physical disturbance depth of 16.4cm, bacterial density of 0.18Lm(-2), and polychaetes biomass of 0.16kgm(-2), respectively. These results emphasize the value of combining different species in field-based bioremediation.

  11. Soil functional operating range linked to microbial biodiversity and community composition using denitrifiers as model guild.

    Directory of Open Access Journals (Sweden)

    Sara Hallin

    Full Text Available Soil microorganisms are key players in biogeochemical cycles. Yet, there is no consistent view on the significance of microbial biodiversity for soil ecosystem functioning. According to the insurance hypothesis, declines in ecosystem functioning due to reduced biodiversity are more likely to occur under fluctuating, extreme or rapidly changing environmental conditions. Here, we compare the functional operating range, a new concept defined as the complete range of environmental conditions under which soil microbial communities are able to maintain their functions, between four naturally assembled soil communities from a long-term fertilization experiment. A functional trait approach was adopted with denitrifiers involved in nitrogen cycling as our model soil community. Using short-term temperature and salt gradients, we show that the functional operating range was broader and process rates were higher when the soil community was phylogenetically more diverse. However, key bacterial genotypes played an important role for maintaining denitrification as an ecosystem functioning under certain conditions.

  12. Nitrate removal by nitrate-dependent Fe(II) oxidation in an upflow denitrifying biofilm reactor.

    Science.gov (United States)

    Zhou, Jun; Wang, Hongyu; Yang, Kai; Sun, Yuchong; Tian, Jun

    2015-01-01

    A continuous upflow biofilm reactor packed with ceramsite was constructed for nitrate removal under an anaerobic atmosphere without an organic carbon source. Denitrifying bacteria, Pseudomonas sp. W1, Pseudomonas sp. W2 and Microbacterium sp. W5, were added to the bioreactor as inocula. Nitrate concentration, nitrite accumulation and nitrogen removal efficiency in the effluent were investigated under various conditions set by several parameters including pH, hydraulic retention time (HRT), ratios of carbon to nitrogen (C/N) and temperature. The results illustrated that the maximum removal efficiency of nitrogen was 85.39%, under optimum reaction parameters, approximately pH 6.5-7, HRT = 48 hours and C/N = 13.1:1 at temperature of 30 °C, which were determined by experiment.

  13. Enhanced Performance of Denitrifying Sulifde Removal Process by 1,2-Naphthoquinone-4-Sulphonate

    Institute of Scientific and Technical Information of China (English)

    Liu Chunshuang; Han Kang; Zhao Dongfeng; Guo Yadonag; Liu Lihong; Liu Fang; Zhao Chaocheng

    2016-01-01

    The denitrifying sulifde removal (DSR) process with bio-granules comprising both heterotrophic and autotrophic denitriifers can simultaneously convert nitrate, sulifde and acetate species into di-nitrogen gas, elemental sulfur and carbon dioxide, respectively, at high loading rates. This study has determined that the reaction rate of sulifde oxidized into sulfur could be enhanced in the presence of 1,2-naphthoquinone-4-sulphonate (NQS). The presence of NQS mitigated the inhibi-tion effects of sulifde species on denitriifcation. Furthermore, the reaction rates of nitrate and acetate to nitrogen gas and CO2, respectively, were also promoted in the presence of NQS, thereby enhancing the performance of DSR granules. The advantages and disadvantages of applying the NQS-DSR process are discussed.

  14. Continuous treatment of azo acid dyes by photo-dependent denitrifying sludge

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Simultaneous removals of dye and nitrate by photo-dependent denitrifying sludge(PDDS) have been demonstrated in a continuousflow bench-scale reactor.The best C/N for the degradation of azo dyes by PDDS was 1.5.The specific removal rate of azo dye AB92 decreased with a decrease in hydraulic retention time and increased with a decrease in solids retention time.The degradation rate of TOC decreased with a decrease in hydraulic retention time.AB92,which has nitro and hydroxyl substitutions in non-para positions,was uniquely degraded.During continuous flow treatment experiments using PDDS,complete degradation of azo dyes AB92 and AO20 at influent concentrations of 40 mg/L and 30 mg/L,respectively,was achieved with an HRT of 16.

  15. Heterotrophic ammonium removal characteristics of an aerobic heterotrophic nitrifying-denitrifying bacterium, Providencia rettgeri YL

    Institute of Scientific and Technical Information of China (English)

    TAYLOR Shauna M; HE Yiliang; ZHAO Bin; HUANG Jue

    2009-01-01

    Bacterium Providencia rettgeri YL was found to exhibit an unusual ability to heterotrophically nitrify and aerobically denitrify various concentrations of ammonium (NH4+-N). In order to further analyze its removal ability, several experiments were conducted to identify the growth and ammonium removal response in different carbon to nitrogen (C/N) mass ratios, shaking speeds, temperatures, ammonium concentrations and to qualitatively verify the production of nitrogen gas using gas chromatography techniques. Results showed that under optimum conditions (C/N 10, 30℃, 120 r/min), YL can significantly remove low and high concentrations of ammonium within 12 to 48 h of growth. The nitrification products hydroxylamine (NH2OH), nitrite (NO2-) and nitrate (NO3-) as well as the denitrification product, nitrogen gas (N2), were detected under completely aerobic conditions.

  16. Maintaining granulation in a denitrifying upflow sludge-blanket reactor treating groundwater with low hardness.

    Science.gov (United States)

    Rouse, Joseph D; Nakashima, Takahiro; Furukawa, Kenji

    2003-01-01

    Maintenance of denitrifying granular sludge for treating soft groundwater (total hardness = 75 mg calcium carbonate/L) in an upflow sludge-blanket reactor was demonstrated with complete removal of applied nitrate (20 mg N/L) over extended operation and a hydraulic residence time of 34 minutes. A high pH of approximately 9.0 was shown to be important for generation of mineral precipitation needed for production of heavy granular sludge with good retention characteristics. As a method of increasing precipitation potential, pH adjustment was determined to be more economically favorable than calcium or alkalinity supplementation. In addition, temporary increases in substrate loading were shown to be effective for enhancing biomass levels in a manageable granular sludge. The significance of biomass in promoting mineral precipitation was discussed.

  17. Modeling of Cr(VI) Bioreduction Under Fermentative and Denitrifying Conditions

    Science.gov (United States)

    Molins, S.; Steefel, C.; Yang, L.; Beller, H. R.

    2011-12-01

    The mechanisms of bioreductive immobilization of Cr(VI) were investigated by reactive transport modeling of a set of flow-through column experiments performed using natural Hanford 100H aquifer sediment. The columns were continuously eluted with 5 μM Cr(VI), 5 mM lactate as the electron donor, and selected electron acceptors (tested individually). Here we focus on the two separate experimental conditions that showed the most removal of Cr(VI) from solution: fermentation and denitrification. In each case, a network of enzymatic and abiotic reaction pathways was considered to interpret the rate of chromate reduction. The model included biomass growth and decay, and thermodynamic limitations on reaction rates, and was constrained by effluent concentrations measured by IC and ICP-MS and additional information from bacterial isolates from column effluent. Under denitrifying conditions, Cr(VI) reduction was modeled as co-metabolic with nitrate reduction based on experimental observations and previous studies on a denitrifying bacterium derived from the Hanford 100H aquifer. The reactive transport model results supported this interpretation of the reaction mechanism and were used to quantify the efficiency of the process. The models results also suggest that biomass growth likely relied on a nitrogen source other than ammonium (e.g. nitrate). Under fermentative conditions and based on cell suspension studies performed on a bacterial isolate from the columns, the model assumes that Cr(VI) reduction is carried out directly by fermentative bacteria that convert lactate into acetate and propionate. The evolution to complete lactate fermentation and Cr(VI) reduction took place over a week's time and simulations were used to determine an estimate for a lower limit of the rate of chromate reduction by calibration with the flow-through column experimental results. In spite of sulfate being added to these columns, sulfate reduction proceeded at a slow rate and was not well

  18. Nitrous Oxide Emission and Denitrifier Abundance in Two Agricultural Soils Amended with Crop Residues and Urea in the North China Plain

    Science.gov (United States)

    Jin, Haiyang; Liu, Yuan; Bai, Xueying; Ma, Dongyun; Zhu, Yunji; Wang, Chenyang; Guo, Tiancai

    2016-01-01

    from the treatments of 250 kg N ha-1 were 1.1–3.3 times higher than those of treatments with 200 kg N ha-1 in both soils with adding equal amounts of the same type of crop residue. Abundance of the 16S rRNA gene did not significantly change in all treatments in two soils, but the nosZ and nirS genes were more abundant in soils amended with crop residues compared with CK or N-only treatments. N2O emission, however, were not related to the abundance of denitrifier containing nirS or nosZ. The research provided some information regarding the effect of crop residues with N fertilizer on N2O emissions and denitrifier abundances in two soils. Our results imply the property of crop residue and rate of N fertilizer are important influencing factors of N2O emission when crop residues combined with N fertilizer are applied to different agricultural soils. PMID:27152647

  19. Nitrous Oxide Emission and Denitrifier Abundance in Two Agricultural Soils Amended with Crop Residues and Urea in the North China Plain.

    Directory of Open Access Journals (Sweden)

    Jianmin Gao

    emissions from the treatments of 250 kg N ha-1 were 1.1-3.3 times higher than those of treatments with 200 kg N ha-1 in both soils with adding equal amounts of the same type of crop residue. Abundance of the 16S rRNA gene did not significantly change in all treatments in two soils, but the nosZ and nirS genes were more abundant in soils amended with crop residues compared with CK or N-only treatments. N2O emission, however, were not related to the abundance of denitrifier containing nirS or nosZ. The research provided some information regarding the effect of crop residues with N fertilizer on N2O emissions and denitrifier abundances in two soils. Our results imply the property of crop residue and rate of N fertilizer are important influencing factors of N2O emission when crop residues combined with N fertilizer are applied to different agricultural soils.

  20. Community structure and denitrification ability of aerobic and anaerobic denitrifying bacteria from mangrove wetland%红树林湿地中好氧-厌氧反硝化菌脱氮特性及其种群结构分析

    Institute of Scientific and Technical Information of China (English)

    林娜; 郭楚玲; 郭延萍; 柯林; 党志; 谭凤仪

    2012-01-01

    Mangrove wetlands dominate the coastline of tropical and subtropical regions. With the expansion of human activity along riverine and coastal shorelines, mangroves are subject to anthropogenic inputs, which introduee additional nitrogen to mangrove ecosystems. In the present study, both traditional cultivation and molecular method ( clone library and RFLP) were used to investigate the community strueture and abilities of denitrifying microorganism from Mai Po mangrove sediment. Twenty aerobic and anaerobic denitrifying bacteria strains were obtained and most of them had the abilities to remove 98% NO3- -N in 2 days. The aerobic denitrifying bacterial strains belonged to the genera of Pseudomonas, Comamonas and Acinetobacter. The anaerobie denitrifying bacterial strains were Pseudomonas, Agrobacterium, Uncultured Betaproteobacteria bacterium. To investigate the diversity of denitrifying bacteria in the mangrove sediments, nosZ gene clone library were constructed. 26 out of 50 clones belonged to 11 unknown groups, while the others were the Pennisetum (26%) , the β-proteobacterium (10%) , the Entandrophragma ( 4 % ) , the Pseudomonas ( 4 % ) and the denitrifying bacterium (4%). This indicated that Mai Po mangrove had high degree of taxonomic diversity of denitrifiers.%随着沿岸水体氮素富营养化的加剧,生物脱氮作用越来越受重视,位于海陆交界的湿地红树林生态系统作为一个自然脱氮体系备受关注.本研究以典型亚热带湿地红树林(香港Mai Po)作为对象,结合传统的富集筛选和分子生物学方法--建立nosZ基因克隆文库和RFLP分析技术对红树林沉积物中反硝化细菌脱氮能力、种群结构和丰度进行研究.从Mai Po红树林沉积物中共筛选到12株好氧反硝化菌和8株厌氧反硝化菌,其中好氧反硝化菌包括Pseudomonas(4株)、Comamonas(2株)和Acinetobacter(2株)等7个菌属,厌

  1. Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities

    OpenAIRE

    Florio, Alessandro; Pommier, Thomas; Gervaix, Jonathan; Berard, Annette; Le Roux, Xavier

    2017-01-01

    Maize inoculation by Azospirillum stimulates root growth, along with soil nitrogen (N) uptake and root carbon (C) exudation, thus increasing N use efficiency. However, inoculation effects on soil N-cycling microbial communities have been overlooked. We hypothesized that inoculation would (i) increase roots-nitrifiers competition for ammonium, and thus decrease nitrifier abundance; and (ii) increase roots-denitrifiers competition for nitrate and C supply to denitrifiers by root exudation, and ...

  2. The Denitrifying Biological Phosphorus Removal Performance in Anaerobic/Anoxic Sequencing Batch Reactor: The Effect of Carbon Source

    OpenAIRE

    Gürtekin, Engin; ŞEKERDAĞ, Nusret

    2015-01-01

    In this study, the effect of carbon source on denitrifying biological phosphorus removal performance in acetate and glucose fed two anaerobic/anoxic sequencinq batch reactor (SBR) was investigated. Glucose and acetate were used as the substrates. In acetate and glucose fed reactors, the COD (Chemical Oxygen Demand) removal efficiencies were 91,90% and PO4-P removal efficiencies were 87,51% respectively. These results shows that the phosphorus removal efficiency is lower in glucose fed reactor.

  3. The Denitrifying Biological Phosphorus Removal Performance in Anaerobic/Anoxic Sequencing Batch Reactor: The Effect of Carbon Source

    OpenAIRE

    Gürtekin, Engin; ŞEKERDAĞ, Nusret

    2015-01-01

    In this study, the effect of carbon source on denitrifying biological phosphorus removal performance in acetate and glucose fed two anaerobic/anoxic sequencinq batch reactor (SBR) was investigated. Glucose and acetate were used as the substrates. In acetate and glucose fed reactors, the COD (Chemical Oxygen Demand) removal efficiencies were 91,90% and PO4-P removal efficiencies were 87,51% respectively. These results shows that the phosphorus removal efficiency is lower in glucose fed reactor.

  4. Simultaneous pollutant removal and electricity generation in denitrifying microbial fuel cell with boric acid-borate buffer solution.

    Science.gov (United States)

    Chen, Gang; Zhang, Shaohui; Li, Meng; Wei, Yan

    2015-01-01

    A double-chamber denitrifying microbial fuel cell (MFC), using boric acid-borate buffer solution as an alternative to phosphate buffer solution, was set up to investigate the influence of buffer solution concentration, temperature and external resistance on electricity generation and pollutant removal efficiency. The result revealed that the denitrifying MFC with boric acid-borate buffer solution was successfully started up in 51 days, with a stable cell voltage of 205.1 ± 1.96 mV at an external resistance of 50 Ω. Higher concentration of buffer solution favored nitrogen removal and electricity generation. The maximum power density of 8.27 W/m(3) net cathodic chamber was obtained at a buffer solution concentration of 100 mmol/L. An increase in temperature benefitted electricity generation and nitrogen removal. A suitable temperature for this denitrifying MFC was suggested to be 25 °C. Decreasing the external resistance favored nitrogen removal and organic matter consumption by exoelectrogens.

  5. Molecular characterization of denitrifying bacteria isolated from the anoxic reactor of a modified DEPHANOX plant performing enhanced biological phosphorus removal.

    Science.gov (United States)

    Zafiriadis, Ilias; Ntougias, Spyridon; Mirelis, Paraskevi; Kapagiannidis, Anastasios G; Aivasidis, Alexander

    2012-06-01

    Enhanced Biological Phosphorus Removal (EBPR) under anoxic conditions was achieved using a Biological Nutrient Removal (BNR) system based on a modification of the DEPHANOX configuration. Double-probe Fluorescence in Situ Hybridization (FISH) revealed that Polyphosphate Accumulating Organisms (PAOs) comprised 12.3 +/- 3.2% of the total bacterial population in the modified DEPHANOX plant. The growing bacterial population on blood agar and Casitone Glycerol Yeast Autolysate agar (CGYA) medium was 16.7 +/- 0.9 x 10(5) and 3.0 +/- 0.6 x 10(5) colony forming units (cfu) mL(-1) activated sludge, respectively. A total of 121 bacterial isolates were characterized according to their denitrification ability, with 26 bacterial strains being capable of reducing nitrate to gas. All denitrifying isolates were placed within the alpha-, beta-, and gamma-subdivisions of Proteobacteria and the family Flavobacteriaceae. Furthermore, a novel denitrifying bacterium within the genus Pseudomonas was identified. This is the first report on the isolation and molecular characterization of denitrifying bacteria from EBPR sludge using a DEPHANOX-type plant.

  6. Enhanced performance of denitrifying sulfide removal process at high carbon to nitrogen ratios under micro-aerobic condition.

    Science.gov (United States)

    Chen, Chuan; Zhang, Ruo-Chen; Xu, Xi-Jun; Fang, Ning; Wang, Ai-Jie; Ren, Nan-Qi; Lee, Duu-Jong

    2017-05-01

    The success of denitrifying sulfide removal (DSR) processes, which simultaneously degrade sulfide, nitrate and organic carbon in the same reactor, counts on synergetic growths of autotrophic and heterotrophic denitrifiers. Feeding wastewaters at high C/N ratio would stimulate overgrowth of heterotrophic bacteria in the DSR reactor so deteriorating the growth of autotrophic denitrifiers. The DSR tests at C/N=1.26:1, 2:1 or 3:1 and S/N =5:6 or 5:8 under anaerobic (control) or micro-aerobic conditions were conducted. Anaerobic DSR process has removal with no elemental sulfur transformation. Under micro-aerobic condition to remove removal is achieved by the DSR consortia. Continuous-flow tests under micro-aerobic condition have 70% sulfide removal and 55% elemental sulfur recovery. Trace oxygen enhances activity of sulfide-oxidizing, nitrate-reducing bacteria to accommodate properly the wastewater with high C/N ratios. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Nitrogen-removal efficiency of a novel aerobic denitrifying bacterium, Pseudomonas stutzeri strain ZF31, isolated from a drinking-water reservoir.

    Science.gov (United States)

    Huang, Tinglin; Guo, Lin; Zhang, Haihan; Su, Junfeng; Wen, Gang; Zhang, Kai

    2015-11-01

    An aerobic denitrifier, identified as Pseudomonas stutzeri strain ZF31, was isolated from the Zhoucun drinking-water reservoir. Strain ZF31 removed 97% of nitrate nitrogen after 16h, without nitrite accumulation. Sequence amplification indicated the presence of the denitrification genes napA, nirS, norB, and nosZ. Nitrogen balance analysis revealed that approximately 75% of the initial nitrogen was removed as gas products. Response surface methodology (RSM) experiments showed that maximum removal of total nitrogen (TN) occurred at pH 8.23, a C/N ratio of 6.68, temperature of 27.72°C, and with shaking at 54.15rpm. The TN removal rate at low C/N ratio (i.e., 3) and low temperature (i.e., 10°C) was 73.30% and 60.08%, respectively. These results suggest that strain ZF31 has potential applications for the bioremediation of slightly polluted drinking-water reservoirs.

  8. Denitrification in Sinorhizobium meliloti.

    Science.gov (United States)

    Torres, María J; Rubia, María I; Bedmar, Eulogio J; Delgado, María J

    2011-12-01

    Denitrification is the complete reduction of nitrate or nitrite to N2, via the intermediates nitric oxide (NO) and nitrous oxide (N2O), and is coupled to energy conservation and growth under O2-limiting conditions. In Bradyrhizobium japonicum, this process occurs through the action of the napEDABC, nirK, norCBQD and nosRZDFYLX gene products. DNA sequences showing homology with nap, nirK, nor and nos genes have been found in the genome of the symbiotic plasmid pSymA of Sinorhizobium meliloti strain 1021. Whole-genome transcriptomic analyses have demonstrated that S. meliloti denitrification genes are induced under micro-oxic conditions. Furthermore, S. meliloti has also been shown to possess denitrifying activities in both free-living and symbiotic forms. Despite possessing and expressing the complete set of denitrification genes, S. meliloti is considered a partial denitrifier since it does not grow under anaerobic conditions with nitrate or nitrite as terminal electron acceptors. In the present paper, we show that, under micro-oxic conditions, S. meliloti is able to grow by using nitrate or nitrite as respiratory substrates, which indicates that, in contrast with anaerobic denitrifiers, O2 is necessary for denitrification by S. meliloti. Current knowledge of the regulation of S. meliloti denitrification genes is also included.

  9. Microbial community analysis of an aerobic nitrifying-denitrifying MBR treating ABS resin wastewater.

    Science.gov (United States)

    Chang, Chia-Yuan; Tanong, Kulchaya; Xu, Jia; Shon, Hokyong

    2011-05-01

    A two-stage aerobic membrane bioreactor (MBR) system for treating acrylonitrile butadiene styrene (ABS) resin wastewater was carried out in this study to evaluate the system performance on nitrification. The results showed that nitrification of the aerobic MBR system was significant and the highest TKN removal of approximately 90% was obtained at hydraulic retention time (HRT) 18 h. In addition, the result of nitrogen mass balance revealed that the percentage of TN removal due to denitrification was in the range of 8.7-19.8%. Microbial community analysis based on 16s rDNA molecular approach indicated that the dominant ammonia oxidizing bacteria (AOB) group in the system was a β-class ammonia oxidizer which was identified as uncultured sludge bacterium (AF234732). A heterotrophic aerobic denitrifier identified as Thauera mechernichensis was found in the system. The results indicated that a sole aerobic MBR system for simultaneous removals of carbon and nitrogen can be designed and operated for neglect with an anaerobic unit.

  10. The effect of urban landfill leachate characteristics on the coexistence of anammox bacteria and heterotrophic denitrifiers.

    Science.gov (United States)

    Ruscalleda, M; Puig, S; Mora, X; López, H; Ganigué, R; Balaguer, M D; Colprim, J

    2010-01-01

    Heterotrophic denitrification coexists with the anammox process contributing to N removal owing to the biodegradable organic matter supply from urban landfill leachate and the decay of microorganisms. Both biomasses consumed nitrite increasing the nitrite requirements of the system. The aim of this paper is the study of the causes which induce the system to decrease nitrogen removal efficiency. In this study, urban landfill leachate has been treated in an anammox Sequencing Batch Reactor (SBR) for 360 days. The anammox reactor treated on average 0.24 kgN m(-3) d(-1) obtaining nitrogen removal efficiencies up to 89%. The results demonstrated that i) a suitable influent nitrite to ammonium molar ratio is a crucial factor to avoid troubles in the anammox reactor performance; ii) an excess of nitrite implied nitrite accumulation in the reactor; iii) a lower nitrite supply than the necessary for the system could force a loss of specific anammox activity due to nitrite competition with denitrifiers. These results pointed out the importance of the previous partial-nitritation process control in order to obtain a correct influent nitrite to ammonium molar ratio for the anammox reactor. In addition, sudden variation of the leachate characteristics must be avoided.

  11. Microbial Characterization of Denitrifying Sulifde Removal Sludge Using High-Throughput Amplicon Sequencing Method

    Institute of Scientific and Technical Information of China (English)

    Ma Wenjuan; Liu Chunshuang; Zhao Dongfeng; Guo Yadong; Wang Aijie; Jia Kuili

    2015-01-01

    The denitrifying sulifde removal (DSR) process has recently been studied extensively from an engineering per-spective. However, the importance of microbial communities of this process was generally underestimated. In this study, the microbial community structure of a lab-scale DSR reactor was characterized in order to provide a comprehensive insight into the key microbial groups in DSR system. Results from high-throughput sequencing analysis revealed that the frac-tion of autotrophic denitriifers increased from 2.34 % to 10.93% and 44.51% in the DSR system when the inlfuent NaCl increased from 0 g/L, to 4 g/L and 30 g/L, respectively. On the contrary, the fraction of heterotrophic denitriifers decreased from 61.74% to 39.57%, and 24.12%, respectively.Azoarcus andThiobacillus were the main autotrophic denitriifers, and Thauera was the main hetetrophic denitriifer during the whole process. This study could be useful for better understanding the interaction between autotrophs and heterotrophs in DSR system.

  12. Formaldehyde and urea removal in a denitrifying granular sludge blanket reactor.

    Science.gov (United States)

    Eiroa, M; Kennes, C; Veiga, M C

    2004-09-01

    Simultaneous formaldehyde biodegradation, urea hydrolysis and denitrification in anoxic batch assays and in a continuous laboratory anoxic reactor were investigated. In batch assays, the initial formaldehyde biodegradation rate was around 0.7 g CH(2)Og VSS(-1)d(-1) and independent of the urea concentration (90- 370 mg N-NH(2)CONH(2)l(-1)). Urea was completely hydrolyzed to ammonium in the presence of 430 mg l(-1) formaldehyde and complete denitrification took place in all cases (125 mg N-NO(-)(3)l(-1)). Formaldehyde removal efficiencies above 99.5% were obtained in a lab-scale denitrifying upflow sludge blanket reactor at organic loading rates between 0.37 and 2.96 kg CODm(-3)d(-1) (625-5000 mg CH(2)Ol(-1)). The urea loading rate was increased from 0.06 to 0.44 kg Nm(-3)d(-1) (100-800 mg N-NH(2)CONH(2)l(-1)) and hydrolysis to ammonium was around 77.5% at all loading rates. The denitrification process was always almost complete (100-800 mg N-NO(3)(-)l(-1)), due to the high COD/N ratio of 6.7 in the influent. A minimum value of 3.5 was found to be required for full denitrification. The composition of the biogas indicated that denitrification and methanogenesis occurred simultaneously in the same unit. A good granulation of the sludge was observed.

  13. A biofilm model to understand the onset of sulfate reduction in denitrifying membrane biofilm reactors.

    Science.gov (United States)

    Tang, Youneng; Ontiveros-Valencia, Aura; Feng, Liang; Zhou, Chen; Krajmalnik-Brown, Rosa; Rittmann, Bruce E

    2013-03-01

    This work presents a multispecies biofilm model that describes the co-existence of nitrate- and sulfate-reducing bacteria in the H(2)-based membrane biofilm reactor (MBfR). The new model adapts the framework of a biofilm model for simultaneous nitrate and perchlorate removal by considering the unique metabolic and physiological characteristics of autotrophic sulfate-reducing bacteria that use H(2) as their electron donor. To evaluate the model, the simulated effluent H(2), UAP (substrate-utilization-associated products), and BAP (biomass-associated products) concentrations are compared to experimental results, and the simulated biomass distributions are compared to real-time quantitative polymerase chain reaction (qPCR) data in the experiments for parameter optimization. Model outputs and experimental results match for all major trends and explain when sulfate reduction does or does not occur in parallel with denitrification. The onset of sulfate reduction occurs only when the nitrate concentration at the fiber's outer surface is low enough so that the growth rate of the denitrifying bacteria is equal to that of the sulfate-reducing bacteria. An example shows how to use the model to design an MBfR that achieves satisfactory nitrate reduction, but suppresses sulfate reduction.

  14. Achieving partial denitrification through control of biofilm structure during biofilm growth in denitrifying biofilter.

    Science.gov (United States)

    Cui, Bin; Liu, Xiuhong; Yang, Qing; Li, Jianmin; Zhou, Xueyang; Peng, Yongzhen

    2017-08-01

    Partial denitrification was one of most effective ways to provide nitrite for annamox; whereas very limited research has been done to achieve nitrite accumulation in biofilm system. In this study, partial denitrification was studied in a lab-scale denitrifying biofilter (DNBF). The results showed biofilm structure variations caused the differences between nitrate specific reduction rate (NaSRR) and nitrite specific reduction rate (NiSRR), which led to nitrite accumulation in different degree at different biofilm formation phases. Hydrodynamic conditions also significantly influenced biofilm structure, nitrate and nitrite reduction activities. At the filtration velocity of 3.86mh(-1), not only biofilm structure, NaSRR and NiSRR kept relatively stable, but also 60% of nitrite accumulation and no nitrate in the effluent were achieved. Furthermore, Thauera genus bacteria, benefited for nitrite accumulation, became the dominant communities in high nitrite accumulation conditions. The partial denitrification combine with anammox in biofilter have the great potential applied in WWTPs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Characteristics of a Novel Aerobic Denitrifying Bacterium, Enterobacter cloacae Strain HNR.

    Science.gov (United States)

    Guo, Long-Jie; Zhao, Bin; An, Qiang; Tian, Meng

    2016-03-01

    A novel aerobic denitrifier strain HNR, isolated from activated sludge, was identified as Enterobacter cloacae by16S rRNA sequencing analysis. Glucose was considered as the most favorable C-source for strain HNR. The logistic equation well described the bacterial growth, yielding a maximum growth rate (μmax) of 0.283 h(-1) with an initial NO3 (-)-N concentration of 110 mg/L. Almost all NO3 (-)-N was removed aerobically within 30 h with an average removal rate of 4.58 mg N L(-1) h(-1). Nitrogen balance analysis revealed that proximately 70.8 % of NO3 (-)-N was removed as gas products and only 20.7 % was transformed into biomass. GC-MS result indicates that N2 was the end product of aerobic denitrification. The enzyme activities of nitrate reductase and nitrite reductase, which are related to the process of aerobic denitrification, were 0.0688 and 0.0054 U/mg protein, respectively. Thus, the aerobic denitrification of reducing NO3 (-) to N2 by strain HNR was demonstrated. The optimal conditions for nitrate removal were C/N ratio 13, pH value 8, shaking speed 127 rpm and temperature 30 °C. These findings show that E. cloacae strain HNR has a potential application on wastewater treatment to achieve nitrate removal under aerobic conditions.

  16. Simultaneous Nitrogen and Phosphorus Removal by Denitrifying Dephosphatation in a (AO)2 Sequencing Batch Reactor

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yan-ping; PENG Yong-zhen; WANG Shu-ying; WANG Shao-po

    2005-01-01

    A 24 L working volume reactor was used for the research on simultaneous phosphorus (P) and nitrogen (N) removal by denitrifying dephosphatation in an anaerobic-oxid-anoxic-oxid sequencing batch reactor ((AO)2SBR) system. The durations of each phase are: anaerobic 1.5 h, aerobic 2.5 h, anoxic 1.5 h, post-aerobic 0.5 h, settling 1.0 h, fill 0.5 h. The successful removal of nitrogen and phosphorus is achieved in a stable (AO)2SBR. The effluent P concentrations is below 1 mg/L, and the COD,TN and P average removal efficiency is 88.9%, 77.5% and 88.7%, respectively. The batch experiment results show that the durations of aerobic and anoxic phase influence the P removal efficiency. Some feature points are found on the DO, ORP and pH curves to demonstrate the complete of phosphate release and phosphate uptake. These feature points can be used for the control of (AO)2 SBR.

  17. Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions.

    Directory of Open Access Journals (Sweden)

    Daniel R H Graf

    Full Text Available Nitrous oxide (N2O is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N2O is the nitrous oxide reductase, encoded by the nosZ gene, which is present among bacteria and archaea capable of either complete denitrification or only N2O reduction to di-nitrogen gas. To determine whether the occurrence of nosZ, being a proxy for the trait N2O reduction, differed among taxonomic groups, preferred habitats or organisms having either NirK or NirS nitrite reductases encoded by the nirK and nirS genes, respectively, 652 microbial genomes across 18 phyla were compared. Furthermore, the association of different co-occurrence patterns with enzymes reducing nitric oxide to N2O encoded by nor genes was examined. We observed that co-occurrence patterns of denitrification genes were not randomly distributed across taxa, as specific patterns were found to be more dominant or absent than expected within different taxonomic groups. The nosZ gene had a significantly higher frequency of co-occurrence with nirS than with nirK and the presence or absence of a nor gene largely explained this pattern, as nirS almost always co-occurred with nor. This suggests that nirS type denitrifiers are more likely to be capable of complete denitrification and thus contribute less to N2O emissions than nirK type denitrifiers under favorable environmental conditions. Comparative phylogenetic analysis indicated a greater degree of shared evolutionary history between nosZ and nirS. However 30% of the organisms with nosZ did not possess either nir gene, with several of these also lacking nor, suggesting a potentially important role in N2O reduction. Co-occurrence patterns were also non-randomly distributed amongst preferred habitat categories, with several habitats showing significant differences in the frequencies of nirS and nirK type denitrifiers. These results demonstrate that the denitrification pathway is highly modular, thus

  18. Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions

    Science.gov (United States)

    Graf, Daniel R. H.; Jones, Christopher M.; Hallin, Sara

    2014-01-01

    Nitrous oxide (N2O) is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N2O is the nitrous oxide reductase, encoded by the nosZ gene, which is present among bacteria and archaea capable of either complete denitrification or only N2O reduction to di-nitrogen gas. To determine whether the occurrence of nosZ, being a proxy for the trait N2O reduction, differed among taxonomic groups, preferred habitats or organisms having either NirK or NirS nitrite reductases encoded by the nirK and nirS genes, respectively, 652 microbial genomes across 18 phyla were compared. Furthermore, the association of different co-occurrence patterns with enzymes reducing nitric oxide to N2O encoded by nor genes was examined. We observed that co-occurrence patterns of denitrification genes were not randomly distributed across taxa, as specific patterns were found to be more dominant or absent than expected within different taxonomic groups. The nosZ gene had a significantly higher frequency of co-occurrence with nirS than with nirK and the presence or absence of a nor gene largely explained this pattern, as nirS almost always co-occurred with nor. This suggests that nirS type denitrifiers are more likely to be capable of complete denitrification and thus contribute less to N2O emissions than nirK type denitrifiers under favorable environmental conditions. Comparative phylogenetic analysis indicated a greater degree of shared evolutionary history between nosZ and nirS. However 30% of the organisms with nosZ did not possess either nir gene, with several of these also lacking nor, suggesting a potentially important role in N2O reduction. Co-occurrence patterns were also non-randomly distributed amongst preferred habitat categories, with several habitats showing significant differences in the frequencies of nirS and nirK type denitrifiers. These results demonstrate that the denitrification pathway is highly modular, thus underpinning the

  19. [Localization of denitrification genes in plasmid DNA of bacteria Azospirillum brasilense].

    Science.gov (United States)

    Petrova, L P; Varshalomidze, O É; Shelud'ko, A V; Katsy, E I

    2010-07-01

    In 85-Mda plasmid (p85) of plant-associated bacteria Azospirillum brasilense Sp245 model strain, the genes encoding copper-containing nitrite reductase (nirK); heterodimeric NO-reductase (norCB); NorQ and NorD proteins affecting synthesis and (or) activation of NirK and (or) NO-reductase (norQD); catalytic subunit I ofcytochrom c oxidase (CccoN); presumable NO sensor carrying two hemeerythrine domains (orf181); and an enzyme required for synthesis of presumable NO antagonist, homocystein (metC) were identified. In the same region of p85, orf293 encoding transcriptional regulator of LysR type, orf208 whose protein product carries a formylmethanofuran dehydrogenase subunit E domain, and an orf164-encoding conservative secretory protein with unknown function were also found. Localization of a set of denitrification genes in the plasmid DNA A. brasilense Sp245 adjacent to IS elements ISAzba1 and ISAzba2 indicates potential mobility of these genes and high probability of their horizontal transfer among populations of rhizospheric bacteria. A site homologous to p85 nirK-orf208-orf181 genes was detected in the 115 kb plasmid of A. brasilense Sp7 type strain.

  20. Nitrogen Removal from Micro-Polluted Reservoir Water by Indigenous Aerobic Denitrifiers

    Directory of Open Access Journals (Sweden)

    Ting-Lin Huang

    2015-04-01

    Full Text Available Treatment of micro-polluted source water is receiving increasing attention because of environmental awareness on a global level. We isolated and identified aerobic denitrifying bacteria Zoogloea sp. N299, Acinetobacter sp. G107, and Acinetobacter sp. 81Y and used these to remediate samples of their native source water. We first domesticated the isolated strains in the source water, and the 48-h nitrate removal rates of strains N299, G107, and 81Y reached 33.69%, 28.28%, and 22.86%, respectively, with no nitrite accumulation. We then conducted a source-water remediation experiment and cultured the domesticated strains (each at a dry cell weight concentration of 0.4 ppm together in a sample of source water at 20–26 °C and a dissolved oxygen concentration of 3–7 mg/L for 60 days. The nitrate concentration of the system decreased from 1.57 ± 0.02 to 0.42 ± 0.01 mg/L and that of a control system decreased from 1.63 ± 0.02 to 1.30 ± 0.01 mg/L, each with no nitrite accumulation. Total nitrogen of the bacterial system changed from 2.31 ± 0.12 to 1.09 ± 0.01 mg/L, while that of the control system changed from 2.51 ± 0.13 to 1.72 ± 0.06 mg/L. The densities of aerobic denitrification bacteria in the experimental and control systems ranged from 2.8 × 104 to 2 × 107 cfu/mL and from 7.75 × 103 to 5.5 × 105 cfu/mL, respectively. The permanganate index in the experimental and control systems decreased from 5.94 ± 0.12 to 3.10 ± 0.08 mg/L and from 6.02 ± 0.13 to 3.61 ± 0.11 mg/L, respectively, over the course of the experiment. Next, we supplemented samples of the experimental and control systems with additional bacteria or additional source water and cultivated the systems for another 35 days. The additional bacteria did little to improve the water quality. The additional source water provided supplemental carbon and brought the nitrate removal rate in the experimental system to 16.97%, while that in the control system reached only 3

  1. Nitrogen removal from micro-polluted reservoir water by indigenous aerobic denitrifiers.

    Science.gov (United States)

    Huang, Ting-Lin; Zhou, Shi-Lei; Zhang, Hai-Han; Zhou, Na; Guo, Lin; Di, Shi-Yu; Zhou, Zi-Zhen

    2015-04-10

    Treatment of micro-polluted source water is receiving increasing attention because of environmental awareness on a global level. We isolated and identified aerobic denitrifying bacteria Zoogloea sp. N299, Acinetobacter sp. G107, and Acinetobacter sp. 81Y and used these to remediate samples of their native source water. We first domesticated the isolated strains in the source water, and the 48-h nitrate removal rates of strains N299, G107, and 81Y reached 33.69%, 28.28%, and 22.86%, respectively, with no nitrite accumulation. We then conducted a source-water remediation experiment and cultured the domesticated strains (each at a dry cell weight concentration of 0.4 ppm) together in a sample of source water at 20-26 °C and a dissolved oxygen concentration of 3-7 mg/L for 60 days. The nitrate concentration of the system decreased from 1.57 ± 0.02 to 0.42 ± 0.01 mg/L and that of a control system decreased from 1.63 ± 0.02 to 1.30 ± 0.01 mg/L, each with no nitrite accumulation. Total nitrogen of the bacterial system changed from 2.31 ± 0.12 to 1.09 ± 0.01 mg/L, while that of the control system changed from 2.51 ± 0.13 to 1.72 ± 0.06 mg/L. The densities of aerobic denitrification bacteria in the experimental and control systems ranged from 2.8 × 10(4) to 2 × 10(7) cfu/mL and from 7.75 × 10(3) to 5.5 × 10(5) cfu/mL, respectively. The permanganate index in the experimental and control systems decreased from 5.94 ± 0.12 to 3.10 ± 0.08 mg/L and from 6.02 ± 0.13 to 3.61 ± 0.11 mg/L, respectively, over the course of the experiment. Next, we supplemented samples of the experimental and control systems with additional bacteria or additional source water and cultivated the systems for another 35 days. The additional bacteria did little to improve the water quality. The additional source water provided supplemental carbon and brought the nitrate removal rate in the experimental system to 16.97%, while that in the control system reached only 3.01%, with no nitrite

  2. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils.

    Science.gov (United States)

    Pajares, Silvia; Bohannan, Brendan J M

    2016-01-01

    Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.

  3. DECREASING OF SODIUM NITRITE CONTENT IN COOKED SAUSAGES USING DENITRIFYING MICROORGANISMS

    Directory of Open Access Journals (Sweden)

    Bal-Prylypko L. V.

    2015-08-01

    Full Text Available The purpose of this work was to study reduction of sodium nitrite in cooked sausages by adding of the optimized amount of denitrifying microorganisms to the bacterial preparation maintaining quality characteristics of the product. To develop biotechnology of boiled sausages «Naturel» we selected bacterial preparation based on nitrite-reducing strains of Staphylococcus carnosus and S. carnosus ssp.utilis. It was used generally accepted and special methods. The content of total pigments and nitrozopigments was determined by a method based on the extraction of meat pigments by aqueous acetone; color stability of final products was evaluated as the difference in optical density of nitroso pigment extracts before and after exposure (40 min of the sample under the light source; analytical processing of the experimental data was carried out using modern software; quantitative evaluation of color characteristics was performed in the RGB using a multifunctional device Epson Stylus TX400. Mathematical modeling was carried out on the basis of full factorial experiment such as 22, the optimization was performed by Box–Wilson. According to the study, using of the bacterial preparation based on nitrite-reducing strains of Staphylococcus carnosus and S. carnosus ssp. utilis in biotechnology of boiled sausages «Naturel» has a positive effect on the formation of the complex of required color characteristics of final products (for prototypes of sausages the index redness was 1. 61 times higher compared to the control. Degradation of sodium nitrite and formation of nitroso pigments were intensified that improved the stability of color during the storage (the index of color fastness of experimental cooked sausages was higher by 19%. The results of performed investigations illustrate the possibility of production of cooked sausages with a minimized content of synthetic food additives and ingredients.

  4. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils

    Science.gov (United States)

    Pajares, Silvia; Bohannan, Brendan J. M.

    2016-01-01

    Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research. PMID:27468277

  5. Tertiary Denitrification of the Secondary Effluent by Denitrifying Biofilters Packed with Different Sizes of Quartz Sand

    Directory of Open Access Journals (Sweden)

    Nan Wei

    2014-05-01

    Full Text Available Tertiary denitrification of the secondary effluent in wastewater treatment plants is necessary to control the eutrophication of receiving water bodies. Two denitrifying biofilters (DNBF, one packed with quart sand with sizes of 2–4 mm (DNBFS and the other of 4–6 mm (DNBFL, were operated for tertiary denitrification under empty bed retention times (EBRTs of 30 min, 15 min and 7.5 min, respectively. Under EBRTs of 30 min, 15 min and 7.5 min, the NO3−-N removal percentages were 93%, 82% and 83% in DNBFS, and were 92%, 68% and 36% in DNBFL, respectively. The nitrogen removal loading rates increased with decreasing EBRTs, and at the EBRT of 7.5 min, the rate was 2.15 kg/(m3·d in DNBFS and 1.08 kg/(m3·d in DNBFL. The half-order denitrification coefficient of DNBFS increased from 0.42 (mg/L1/2/min at the EBRT of 30 min to 0.70 (mg/L1/2/min at the EBRT of 7.5 min, while did not vary much in DNBFL with values from 0.22 to 0.25 (mg/L1/2/min. The performance of both DNBFs was stable within each backwashing cycle, with the NO3−-N removal percentage variation within 5%. Better denitrification was achieved in DNBFS but with a slightly high decreased flow rate during the operation.

  6. Structure of a new azurin from the denitrifying bacterium Alcaligenes xylosoxidans at high resolution.

    Science.gov (United States)

    Dodd, F E; Hasnain, S S; Abraham, Z H; Eady, R R; Smith, B E

    1995-11-01

    It has been reported previously that Alcaligenes xylosoxidans (NC1MB 11015) grown under denitrifying conditions produces two azurins instead of the single previously identified azurin [Dodd, Hasnain, Hunter, Abraham, Debenham, Kanzler, Eldridge, Eady, Ambler & Smith (1995). Biochemistry. In the press]. The new azurin, called azurin II, has been crystallized as blue elongated rectangular prisms with the tetragonal space group P4(1)22 and unit-cell parameters a = b = 52.65, c = 100.63 A. X-ray crystallographic data extending to 1.9 A resolution were collected by the Weissenberg method using 200 x 400 mm image plates and synchrotron X-rays of wavelength 0.97 A. The three-dimensional structure of azurin II has been solved by the molecular-replacement method using the structure of azurin from Alcaligenes denitrificans NCTC 8582 with which this new azurin shows a close homology. The quality of the initial map was sufficient to predict a number of sequence differences. The model is currently refined to an R-factor of 18.8% with X-ray data between 8.5 and 1.9 A. The final model of 961 protein atoms, one Cu atom and 50 water molecules has r.m.s. deviations from ideality of 0.009 A for bond lengths and 1.7 degrees for bond angles. The overall structure is similar to that of the azurin from A. denitrificans NCTC 8582. It has a beta-barrel structure with the Cu atom located near the top end of the molecule. The Cu atom is coordinated to Ndelta of His46 and His117 at 2.02 A and to Sgamma of Cys112 at 2.12 A, while the carbonyl O atom of Gly45 and Sdelta atom of Met121 provide the additional interactions at 2.75 and 3.26 A, respectively.

  7. Effect on the Growth of Denitrifying Bacteria from Different Carbon Sources%不同碳源对反硝化细菌生长的影响

    Institute of Scientific and Technical Information of China (English)

    李建; 潘康成

    2012-01-01

    The growth of bacteria was relative to carbon sources intimately. The experiment was designed to find the best carbon source in enlarging denitrifying bacteria by research into effect on the growth of denitrifying bacteria from different carbon sources. The 5 carbon sources including glucose, potassium sodium tartrate, cane sugar, acetic acid and ethanol were used as the only carbon source respectively taking denitrifying bacteria into liquid culture media in the contrast test. Live bacteria number was used to denitrifying bacteria from different carbon sources. The results made it clear that of denitrifying bacteria more remarkably than the others. The results indicated others in enlarging denitrifying bacteria. estimate effect on the growth of glucose could promote the growth that glucose was better than the%细菌的生长速度和碳源有非常密切的关系,研究不同碳源对反硝化细菌生长的影响,以找到适合用于扩大培养菌种的最佳碳源。分别采用葡萄糖、酒石酸钾钠、蔗糖、乙酸和乙醇5种碳源作为唯一碳源,接种反硝化细菌进行对比实验,采用活菌数来反映不同碳源对反硝化细菌生长的影响。结果显示,葡萄糖促进反硝化细菌生长的作用明显优于其余4种碳源。对反硝化细菌进行扩大培养,葡萄糖的效果是比较好的。

  8. Responses of bacterial community and functional marker genes of nitrogen cycling to biochar, compost and combined amendments in soil.

    Science.gov (United States)

    Wu, Haipeng; Zeng, Guangming; Liang, Jie; Chen, Jin; Xu, Jijun; Dai, Juan; Li, Xiaodong; Chen, Ming; Xu, Piao; Zhou, Yaoyu; Li, Fei; Hu, Liang; Wan, Jia

    2016-10-01

    Biochar and compost are seen as two attractive waste management options and are used for soil amendment and pollution remediation. The interaction between biochar and composting may improve the potential benefits of biochar and compost. We investigated soil physicochemical properties, bacterial community, bacterial 16S rRNA, and functional marker genes of nitrogen cycling of the soil remedied with nothing (S), compost (SC), biochar (SB), a mixture of compost and biochar (SBC), composted biochar (SBced), and a composted mixture of biochar and biomass (SBCing). The results were that all amendments (1) increased the bacterial community richness (except SB) and SBCing showed the greatest efficiency; (2) increased the bacterial community diversity (SBCing > SBC > SC > SBced > SB > S); and (3) changed the gene copy numbers of 16S rRNA, nirK, nirS, and nosZ genes of bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB). All amendments (except SB) could increase the gene copy number of 16S rRNA, and SBCing had the greatest efficiency. The changes of soil bacterial community richness and diversity and the gene copy numbers of 16S rRNA, nirK, nirS, nosZ, AOA, and AOB would affect carbon and nitrogen cycling of the ecosystem and also implied that BCing had the greatest efficiency on soil amendment.

  9. Isolation of aerobic denitrifier and characteristics of enhanced nitrogen removal in concentric-circles reactor with diversion wall

    Institute of Scientific and Technical Information of China (English)

    许晓毅; 汤丽娟; 罗固源; 蒋真玉

    2009-01-01

    Three strains of aerobic denitrifiers,named as AT3,AT6 and AT7,were isolated from concentric-circles reactor with diversion wall possessing simultaneous nitrification and denitrification (SND) effect of 69%. The three strains are all gram-positive and rod-shaped,and their colonial colors are pale yellow,milk white and pink,respectively. Combined with 16SrDNA sequence homology comparison and biochemical tests,AT3 and AT7 were identified to belong to Rhodococcus,and AT6 to Gordonia. These bacterial strains could grow well in the medium with potassium nitrate as nitrogen source and sodium citrate as carbon source. Based on the enhanced nitrogen removal experiments of selected bacteria mixture for activated sludge,the inoculum amount of 5% was supposed to be proper. The mixed biomass suspension of selected strains with PVA immobilization was put into the concentric-circles reactor in order to study the characteristics of enhanced nitrogen removal after amplifying cultivation with inoculated amount of 5%. The experimental results show that the average removal efficiencies of ammonia nitrogen (NH3-N) and total nitrogen (TN) in the reactor enhanced with aerobic denitrifying bacteria using PVA are 92.18% and 79.14% respectively,increasing by 5.29% and 7.83% respectively compared with removal effects of control group without strains enhancement.

  10. Estimate of denitrifying microbiota in tertiary sewage treatment and kinetics of the denitrification process using different sources of carbon

    Directory of Open Access Journals (Sweden)

    Marchetto Margarida

    2003-01-01

    Full Text Available A study of the kinetics of denitrification was carried out in the laboratory based on the quantification of N2O, the final product of the activity of denitrifying microorganisms, when the enzymatic reduction of N2O to N2 was blocked by acetylene. Concentrated mixed liquor (sludge from a reactor with intermittent aeration used for sewage treatment was used as the inoculum, while methanol, acetic acid, glucose, effluent sewage from an anaerobic fluidized bed reactor and synthetic substrate simulating domestic sewage were used as carbon sources. The mean concentration of nitrate was 20 mg/L. Maxima of N2O production and NO3- consumption occurred between 0.5h and 2.0h of incubation using all the carbon sources, which characterized the denitrification process. Acetic acid and methanol were responsible for the highest rates of N2O production. The estimated number of denitrifying microorganisms in the reactor with intermittent aeration, using the MPN technique, varied from 10(9 to 10(10 MPN/g VSS, indicating a high potential for the occurrence of denitrification.

  11. Removal of nitrogen and phosphorus from the secondary effluent in tertiary denitrifying biofilters combined with micro-coagulation.

    Science.gov (United States)

    Wei, Nan; Shi, Yunhong; Wu, Guangxue; Hu, Hongying; Guo, Yumei; Wu, Yihui; Wen, Hui

    2016-01-01

    Effective control of nitrogen and phosphorus in secondary effluent can reduce or avoid the eutrophication of receiving water bodies. Two denitrifying biofilters (DNBFs) packed with different sizes of quartz sands combined with micro-coagulation were operated for simultaneous removal of nitrogen and phosphorus from the secondary effluent. The quartz sand size in one DNBF was 2-4 mm (DNBFS), and in the other was 4-6 mm (DNBFL). In both DNBFs, methanol was used as the electron donor and different organic carbon to nitrogen (C/N) ratios were applied. Under C/N ratios of 1.5, 1.25, and 0.75 g/g, the nitrate nitrogen (NO3(-)-N) removal percentages were 73%, 77%, and 50% in DNBFS, and 43%, 25%, and 21% in DNBFL; the effluent total phosphorus concentrations were 0.15, 0.14, and 0.18 mg/L in DNBFS, and 0.29, 0.35, and 0.24 mg/L in DNBFL. The performance of both biofilters was quite stable within a backwashing cycle. The NO3(-)-N reduction rates were 1.31, 1.10, and 0.48 mg/(L·min) in DNBFS, and 0.97, 0.27, and 0.10 mg/(L·min) in DNBFL. For biomass detached from both biofilters, their denitrifying activities were similar. Biofilm biomass in DNBFS was higher than that in DNBFL, inducing a high denitrification efficiency in DNBFS.

  12. Effects of Selected Root Exudate Components on Nitrogen Removal and Development of Denitrifying Bacteria in Constructed Wetlands

    Directory of Open Access Journals (Sweden)

    Hailu Wu

    2017-06-01

    Full Text Available Root exudates, particularly low molecular weight carbon (LMWC substrates, are major drivers of bacterial diversity and activity in the rhizosphere environment. However, it is not well understood how specific LMWC compounds—such as organic acids, soluble sugars, and amino acids—influence the community structures of denitrifying bacteria or if there are specific functions of LMWC substrates that preferentially respond to nitrogen (N removal in constructed wetlands (CWs. To address these knowledge gaps, we added mixtures of artificial exudates to CW microcosms containing N pollutant. N removal efficiency was observed over a 48-h experimental period, and at the end of the experiment, DNA was extracted from microbial samples for assessment of the bacterial community. The removal efficiencies of TN for the exudates treatments were higher than for control groups by 47.1–58.67%. Organic acid and soluble sugar treatments increased N removal, while amino acids were negative to N removal. The microbial community was changed when artificial exudates were added, but there were no significant relationships between LMWC compounds and bacterial community composition. These results indicate that although the responses of community structures of denitrifying bacteria to LMWC additions are still uncertain, there is evidence for N removal in response to exudate additions across LMWC types.

  13. Isotopologue effects during N2O reduction in soils and in pure cultures of denitrifiers

    Science.gov (United States)

    Ostrom, Nathaniel E.; Pitt, Adam; Sutka, Robin; Ostrom, Peggy H.; Grandy, A. Stuart; Huizinga, Kristin M.; Robertson, G. Philip

    2007-06-01

    Site preference (SP), the difference in δ15N between the central and outer nitrogen atoms in N2O, is a powerful approach for apportioning fluxes of N2O from soils to nitrification and denitrification (Sutka et al., 2006). A critical aspect of the use of SP data to apportion sources of N2O to nitrification and denitrification is the need to evaluate data for isotope shifts that may have occurred during N2O reduction in soils prior to its escape to the atmosphere. We present data on the isotopologue effects during reduction of N2O during anaerobic incubation of soils and pure cultures of denitrifying bacteria. Isotopic enrichment factors for N2O reduction in soil mesocosms experiments varied between -9.2 and -1.8‰ for nitrogen and between -25.1 and -5.1‰ for oxygen. In pure cultures of Psuedomonas stutzeri and Psuedomonas denitrificans we observed isotopic enrichment factors for SP of -5.0 and -6.8‰, respectively. We further find that N2O consumption produces consistent relationships between δ18O and δ15N and δ18O and the δ15N of the central N atom in N2O of 2.5 and 1.6, respectively, which are clearly diagnostic of this process. Our results indicate that SP may be altered during reduction of N2O and thus bias evaluations of its origins. To understand the impacts of N2O reduction in soil flux studies on source isotope signals we modeled the isotope effects of N2O production occurring simultaneous with reduction and find increasingly curvilinear relationships between δ18O and δ15N and δ18O and δ15Nα with increased reduction. Consequently, a deviation from the linear mixing relationship between soil-derived and atmospheric N2O is an indication of extensive reduction. On the basis of our characterization of isotopic fractionation during N2O reduction, we show that the rate of reduction would have to be substantially greater than 10% of that of production to impact SP estimates of N2O from denitrification by more than a few percent. Nonetheless, reduction

  14. Genetic basis for denitrification in Ensifer meliloti.

    Science.gov (United States)

    Torres, Maria J; Rubia, Maria I; de la Peña, Teodoro Coba; Pueyo, José J; Bedmar, Eulogio J; Delgado, María J

    2014-06-02

    Denitrification is defined as the dissimilatory reduction of nitrate or nitrite to nitric oxide (NO), nitrous oxide (N2O), or dinitrogen gas (N2). N2O is a powerful atmospheric greenhouse gas and cause of ozone layer depletion. Legume crops might contribute to N2O production by providing nitrogen-rich residues for decomposition or by associating with rhizobia that are able to denitrify under free-living and symbiotic conditions. However, there are limited direct empirical data concerning N2O production by endosymbiotic bacteria associated with legume crops. Analysis of the Ensifer meliloti 1021 genome sequence revealed the presence of the napEFDABC, nirK, norECBQD and nosRZDFYLX denitrification genes. It was recently reported that this bacterium is able to grow using nitrate respiration when cells are incubated with an initial O2 concentration of 2%; however, these cells were unable to use nitrate respiration when initially incubated anoxically. The involvement of the nap, nirK, nor and nos genes in E. meliloti denitrification has not been reported. E. meliloti nap, nirK and norC mutant strains exhibited defects in their ability to grow using nitrate as a respiratory substrate. However, E meliloti nosZ was not essential for growth under these conditions. The E. meliloti napA, nirK, norC and nosZ genes encode corresponding nitrate, nitrite, nitric oxide and nitrous oxide reductases, respectively. The NorC component of the E. meliloti nitric oxide reductase has been identified as a c-type cytochrome that is 16 kDa in size. Herein, we also show that maximal expression of the E. meliloti napA, nirK, norC and nosZ genes occurred when cells were initially incubated anoxically with nitrate. The E. meliloti napA, nirK, norC and nosZ genes are involved in nitrate respiration and in the expression of denitrification enzymes in this bacterium. Our findings expand the short list of rhizobia for which denitrification gene function has been demonstrated. The inability of E

  15. Production of NO and N(inf2)O by Pure Cultures of Nitrifying and Denitrifying Bacteria during Changes in Aeration

    NARCIS (Netherlands)

    Kester, R.A.; De Boer, W.; Laanbroek, H.J.

    1997-01-01

    Peak emissions of NO and N2O are often observed after wetting of soil, The reactions to sudden changes in the aeration of cultures of nitrifying and denitrifying bacteria with respect to NO and N2O emissions were compared to obtain more information about the microbiological aspects of peak emissions

  16. Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards.

    Science.gov (United States)

    Wang, Hua; Yang, Shao-hui; Yang, Jing-ping; Lv, Ya-min; Zhao, Xing; Pang, Ji-liang

    2014-11-01

    It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer (OF), chemical fertilizer (CF), and unfertilized control (CK) treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA (rRNA) gene using terminal restriction fragment length polymorphism (T-RFLP) profiling. The abundances of total bacteria, total archaea, and selected functional genes (bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ) were determined by quantitative polymerase chain reaction (qPCR). The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was significantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of microbial communities and the abundance of genes involved in the nitrogen cycle.

  17. Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter

    Directory of Open Access Journals (Sweden)

    Christopher Ryan Penton

    2013-09-01

    Full Text Available Targeting sequencing to genes involved in key environmental processes, i.e. ecofunctional genes, provides an opportunity to sample nature’s gene guilds to greater depth and help link community structure to process-level outcomes. Vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. The overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknown diversity. To illustrate current issues surrounding amplicon read processing we provide examples for three ecofunctional gene groups. A combination of in-silico, environmental and cultured strain sequences was used to test new primers targeting the dioxin and dibenzofuran degrading genes dxnA1, dbfA1, and carAa. The majority of obtained environmental sequences were classified into novel sequence clusters, illustrating the discovery value of the approach. For the nitrite reductase step in denitrification, the well-known nirK primers exhibited deficiencies in reference database coverage, illustrating the need to refine primer-binding sites and/or to design multiple primers, while nirS primers exhibited bias against five phyla. Amino acid-based OTU clustering of these two N-cycle genes from soil samples yielded only 114 unique nirK and 45 unique nirS genus-level groupings, likely a reflection of constricted primer coverage. Finally, supervised and non-supervised OTU analysis methods were compared using the nifH gene of nitrogen fixation, with generally similar outcomes, but the clustering (non-supervised method yielded higher diversity estimates and stronger site-based differences. High throughput amplicon sequencing can provide inexpensive and rapid access to nature’s related sequences by circumventing the culturing barrier, but each unique gene requires individual considerations in terms of primer design and sequence processing and classification.

  18. Structure and Dynamics of Microbial Community in the Denitrifying Sulfide Removal Process%反硝化脱硫工艺中微生物群落结构及动态分析

    Institute of Scientific and Technical Information of China (English)

    于皓; 王爱杰; 陈川

    2013-01-01

    In order to investigate the relationship between the structure of microbial community and the operational efficiency of the denitrifying sulfide removal ( DSR) process, whole genomic DNA was extracted from sludge samples at each operational stage. Functional gene arrays ( FGAs ) , a high throughput metagenomic technology , was employed to characterize the change of microbial community structure in DSR process. The results of diversity indices (Simpson and Shannon indices) and clustering showed that the microbial community structure changed greatly with stages according to the operational conditions. In stage Ⅰ and Ⅱ , diversity indices and richness decreased due to acclimation of the microbial community to the environment, whereas they increased notably according to the maturing of sludge which may indicate that the bioreactor entered the steady stage. Analysis of key functional genes showed that the abundance of genes did not only reflect the activities of functional bacteria but also had a close relationship with the reactor performance.%为了研究反硝化脱硫工艺(denitrifying sulfide removal,DSR)中微生物群落与工艺运行的相关性,实验提取了反应器运行不同阶段污泥样品中微生物的全基因组DNA,利用高通量宏基因组学技术——基因芯片来解析各阶段功能微生物群落的结构特征及其演替过程.通过对功能基因的Simpson、Shannon多样性指数和聚类分析表明,微生物群落结构会随着反应器运行的阶段进行相应调整,且变化较大.在运行的前两个阶段,由于不适应环境,微生物群落的多样性指数比起始时明显减少,随着反应器的运行污泥逐渐成熟,多样性指数迅速增加,也标志着反应器进入稳定运行阶段.通过对反硝化脱硫过程中关键基因相对丰度的分析发现,功能基因的丰度不仅能反映功能菌群的活性,而且与工艺处理效果密切相关.

  19. Elucidation of major contributors involved in nitrogen removal and transcription level of nitrogen-cycling genes in activated sludge from WWTPs

    Science.gov (United States)

    Che, You; Liang, Peixin; Gong, Ting; Cao, Xiangyu; Zhao, Ying; Yang, Chao; Song, Cunjiang

    2017-01-01

    We investigated nitrogen-cycle bacterial communities in activated sludge from 8 municipal wastewater treatment plants (WWTPs). Redundancy analyses (RDA) showed that temperature was the most significant driving force in shaping microbial community structure, followed by influent NH4+ and total nitrogen (TN). The diversity of ammonia oxidizing and nitrite reducing bacteria were investigated by the construction of amoA, nirS and nirK gene clone libraries. Phylogenetic analysis indicated that Thauera and Mesorhizobium were the predominant nitrite reducing bacteria, and Nitrosomonas was the only detected ammonia oxidizing bacteria in all samples. Quantification of transcription level of nirS and nirK genes indicated that nirS-type nitrite reducing bacteria played the dominant roles in nitrite reduction process. Transcription level of nirS gene positively correlated with influent NH4+ and TN significantly, whereas inversely linked with hydraulic retention time. Temperature had a strong positive correlation to transcription level of amoA gene. Overall, this study deepened our understanding of the major types of ammonia oxidizing and nitrite reducing bacteria in activated sludge of municipal WWTPs. The relationship between transcription level of nitrogen-cycle genes and operational or environmental variables of WWTPs revealed in this work could provide guidance for optimization of operating parameters and improving the performance of nitrogen removal. PMID:28294196

  20. Denitrifying Phosphorus Removal in MUCT-MBR%MUCT-MBR工艺反硝化除磷脱氮研究

    Institute of Scientific and Technical Information of China (English)

    刘鹏霄; 张捍民; 王晓琳; 肖景霓; 杨凤林

    2009-01-01

    自行设计的双反应器MUCT-MBR简化了MUCT工艺,将反应池由5个简化到2个,减小了工艺占地面积,并且采用膜过滤取代二沉池出水,操作简单,出水安全可靠.针对MUCT-MBR工艺脱氮除磷性能,尤其是反硝化除磷功能进行研究.结果表明,当进水C/N/P比在33.3/5/1~25/5.5/1范围内,整个实验过程中COD、TN和TP平均去除率分别达到89.3%、75.4%、79.2%;且膜出水不受污泥沉降性的影响.缺氧段的反硝化吸磷是MUCT-MBR工艺除磷的关键,系统运行至第58 d,系统中反硝化除磷菌(DPAOs)所占比例达84.2%,反硝化除磷占系统总磷去除的67.07%.%The self-designed MUCT-MBR simplifies the MUCT process with reducing reactors from 5 to 2, which greatly reduces land occupied by equipment. Instead of secondary sedimentation tank, the. membrane effluent quality is quite safe, and the operation is simple. In the investigation about simultaneous phosphorus and nitrogen removal of MUCT-MBR, the results showed that: when the proportions of C, N and P in the influent were 33.3/5/1-25/5.5/1, the average removal rate of COD, TN and TP in the whole experimental process were 89.3%,75.4% and 79.2 % , respectively. And the sludge settling capacity had no influence on the membrane effluent quality. The key factor of N and P removal rates is denitrifying phosphorus removal in anoxic condition. The proportion of denitrifying phosphate accumulating organisms (DPAOs) and the rate of denitrifying phosphorous removal were 84.2% and 67.07% on the 58th day, respectively.

  1. Diversity of Nitrate-Reducing and Denitrifying Bacteria in a Marine Aquaculture Biofilter and their Response to Sulfide

    DEFF Research Database (Denmark)

    Krieger, Bärbel; Schwermer, Carsten U.; Rezakhani, Nastaran

    2006-01-01

    DIVERSITY OF NITRATE-REDUCING AND DENITRIFYING BACTERIA IN A MARINE AQUACULTURE BIOFILTER AND THEIR RESPONSE TO SULFIDE B.U. Krieger 1,5, C. Schwermer 2, N. Rezakhani 5, M.A. Horn 1, A. Gieseke 2, E. Cytryn 3, D. Minz 3, J. van Rijn 4, H.L. Drake 1, A. Schramm 5 1 Dept. of Ecological Microbiology......, University of Bayreuth, Bayreuth, Germany; 2 Max Planck Institute for Marine Microbiology, Bremen, Germany; 3 Institute for Soil, Water and Environmental Sciences, ARO, The Volcani Center, Bet Dagan, Israel; 4 Faculty of Agricultural, Food And Environmental Quality Sciences, The Hebrew University...... of Jerusalem, Rehovot, Israel; 5 Dept of Biological Sciences, Microbiology, University of Aarhus, Denmark Conventional aquaculture systems release nitrogen compounds and organic matter into marine environments. As an environmentally-friendly alternative, a zero-discharge mariculture system recently...

  2. Comparison of endogenous metabolism during long-term anaerobic starvation of nitrite/nitrate cultivated denitrifying phosphorus removal sludges.

    Science.gov (United States)

    Wang, Yayi; Zhou, Shuai; Wang, Hong; Ye, Liu; Qin, Jian; Lin, Ximao

    2015-01-01

    Denitrifying phosphorus removal (DPR) by denitrifying phosphorus-accumulating organisms (DPAOs) is a promising approach for reducing energy and carbon usage. However, influent fluctuations or interruptions frequently expose the DPAOs biomass to starvation conditions, reducing biomass activity and amount, and ultimately degrading the performance of DPR. Therefore, a better understanding of the endogenous metabolism and recovery ability of DPAOs is urgently required. In the present study, anaerobic starvation (12 days) and recovery were investigated in nitrite- and nitrate-cultivated DPAOs at 20 ± 1 °C. The cell decay rates in nitrite-DPAOs sludges from the end of the anaerobic and aerobic phase were 0.008 day⁻¹ and 0.007 day⁻¹, respectively, being 64% and 68% lower than those of nitrate-DPAOs sludges. Nitrite-DPAOs sludges also recovered more rapidly than nitrate-DPAOs sludge after 12 days of starvation. The maintenance energy of nitrite-DPAOs sludges from the end of the anaerobic and aerobic phase were approximately 31% and 34% lower, respectively, than those of nitrate-DPAOs sludges. Glycogen and polyphosphate (poly-P) sequentially served as the main maintenance energy sources in both nitrite-and nitrate-DPAOs sludges. However, the transformation pathway of the intracellular polymers during starvation differed between them. Nitrate-DPAOs sludge used extracellular polymeric substances (EPS) (mainly polysaccharides) as an additional maintenance energy source during the first 3 days of starvation. During this phase, EPS appeared to contribute to 19-27% of the ATP production in nitrate-DPAOs, but considerably less to the cell maintenance of nitrite-DPAOs. The high resistance of nitrite-DPAOs to starvation might be attributable to frequent short-term starvation and exposure to toxic substances such as nitrite/free nitrous acids in the parent nitrite-fed reactor. The strong resistance of nitrite-DPAOs sludge to anaerobic starvation may be exploited in P removal

  3. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  4. Evaluation of the microbial diversity in sequencing batch reactor treating linear alkylbenzene sulfonate under denitrifying and mesophilic conditions using swine sludge as inoculum

    Directory of Open Access Journals (Sweden)

    Iolanda Cristina Silveira Duarte

    2015-06-01

    Full Text Available The objective of this study was to evaluate the degradation of Linear Alkylbenzene Sulfonate (LAS in anaerobic sequencing batch reactor (ASBR under denitrifying conditions using swine sludge as inoculum. The reactor was operated for 104 days with synthetic substrate containing nitrate, and LAS was added later (22 mg/L. Considering the added mass of the LAS, the adsorbed mass in the sludge and discarded along with the effluent, degradation of the surfactant at the end of operation was 87%, removal of chemical oxygen demand was 86% and nitrate was 98%. The bacterial community was evaluated by cutting the bands and sequencing of polymerase chain reaction (PCR fragments and denaturing gradient gel electrophoresis (DGGE. The sequences obtained were related to the phylum Proteobacteria and the alpha-and beta-proteobacteria classes, these bacteria were probably involved in the degradation of LAS. The efficiently degraded LAS in the reactor was operated in batch sequences in denitrifying conditions.

  5. Evaluation of the microbial diversity in sequencing batch reactor treating linear alkylbenzene sulfonate under denitrifying and mesophilic conditions using swine sludge as inoculum

    OpenAIRE

    2015-01-01

    The objective of this study was to evaluate the degradation of Linear Alkylbenzene Sulfonate (LAS) in anaerobic sequencing batch reactor (ASBR) under denitrifying conditions using swine sludge as inoculum. The reactor was operated for 104 days with synthetic substrate containing nitrate, and LAS was added later (22 mg/L). Considering the added mass of the LAS, the adsorbed mass in the sludge and discarded along with the effluent, degradation of the surfactant at the end of operation was 87%, ...

  6. Effects of carbon-to-sulfur (C/S) ratio and nitrate (N) dosage on Denitrifying Sulfur cycle-associated Enhanced Biological Phosphorus Removal (DS-EBPR)

    Science.gov (United States)

    Yu, Mei; Lu, Hui; Wu, Di; Zhao, Qing; Meng, Fangang; Wang, Yudan; Hao, Xiaodi; Chen, Guang-Hao

    2016-03-01

    In this study, the Denitrifying Sulfur cycle-associated Enhanced Biological Phosphorous Removal (DS-EBPR) with 20 mg P/L/d of the volumetric P removal rate was successfully achieved in a Sequencing Batch Reactor (SBR). The effects of carbon-to-sulfur (C/S) mass ratio and nitrate (N) dosage were investigated through two batch tests to reveal the role of wastewater compositions in DS-EBPR performance. The optimal specific P release and uptake rates (0.4 and 2.4 mg P/g VSS/h, respectively) were achieved at C/S/P/N mass ratio of 150/200/20/20, and poly-S is supplied as a potential electron and energy storage. The nitrate dosage in a range of 10-50 mg N/L had no significant influence on P uptake rates (2.1 ~ 2.4 mg P/g VSS/h), but significantly affected the storage of inclusion poly-S, the poly-S oxidation rate was increased about 16% while dosing nitrate from 20 to 30 mg N/L. It implies that nitrate is denitrified in the P uptake phase, and excess nitrate is further consumed by poly-S. Moreover, the microbial analysis showed that the functional bacteria should mostly belong to denitrifying bacteria or Unclassified genera.

  7. Bioremediation of chlorimuron-ethyl-contaminated soil by Hansschlegelia sp. strain CHL1 and the changes of indigenous microbial population and N-cycling function genes during the bioremediation process.

    Science.gov (United States)

    Yang, Liqiang; Li, Xinyu; Li, Xu; Su, Zhencheng; Zhang, Chenggang; Zhang, Huiwen

    2014-06-15

    Long-term and excessive application of the herbicide chlorimuron-ethyl has led to soil degradation and crop rotation barriers. In the current study, we isolated bacterial strain Hansschlegelia sp. CHL1, which can utilize chlorimuron-ethyl as its sole carbon and energy source, and investigated its application in soil bioremediation. Indigenous microbial populations and N-cycling function in the soil were also investigated during the bioremediation process by monitoring the copy numbers of bacterial and fungal marker genes, as well as N-cycling functional genes (nifH, amoA, nirS, and nirK). Results showed that >95% of chlorimuron-ethyl could be degraded within 45 days in soils inoculated with CHL1. Inoculation at two time points resulted in a higher remediation efficiency and longer survival time than a single inoculation. At the end of the 60-day incubation, the copy numbers of most indicator genes were recovered to the level of the control, even in the single-inoculation soils. A double inoculation was necessary for recovery of nifH. However, the abundance of nirK and ammonia-oxidizing bacterial genes were significantly inhibited regardless of inoculum. The results suggested that CHL1 is effective for the remediation of chlorimuron-ethyl-contaminated soil, and could partially reduce the toxic effects of chlorimuron-ethyl on soil microorganisms.

  8. Operation of three parallel AN/AO processes to enrich denitrifying phosphorus removing bacteria for low strength wastewater treatment

    Institute of Scientific and Technical Information of China (English)

    XIA Si-qing; LIU Hong-bo

    2006-01-01

    Three parallel anaerobic-anoxic/anaerobic-aerobic (AN/AO) processes were developed to enrich denitrifying phosphorus removal bacteria (DPB) for low strength wastewater treatment. The main body of the parallel AN/AO process consists of an AN(anaerobic-anoxic) process and an AO (anaerobic-aerobic) process. In the AO process, the common phosphorus accumulating organisms (PAOs) was dominate, while in the AN process, DPB was dominate. The volume of anaerobic zone(Vana):anoxic zone(Vano):aerobic zone (Vaer) for the parallel AN/AO process is 1:1:1 in contrast with a Vana:Vaer and Vano,:Vaer of 1:2 and 1:4 for a traditional biological nutrient removal process (BNR). Process 3 excels in the 3 processes on the basis of COD, TN and TP removal. For 4 month operation, the effluent COD concentration of process 3 did not exceed 60 mg/L; the effluent TN concentration of process 3 was lower than 15 mg/L; and the effluent TP concentration of process 3 was lower than 1 mg/L.

  9. Degradation of toluene and m-xylene and transformation of o-xylene by denitrifying enrichment cultures.

    Science.gov (United States)

    Evans, P J; Mang, D T; Young, L Y

    1991-01-01

    Seven different sources of inocula that included sediments, contaminated soils, groundwater, process effluent, and sludge were used to establish enrichment cultures of denitrifying bacteria on benzene, toluene, and xylenes in the absence of molecular oxygen. All of the enrichment cultures demonstrated complete depletion of toluene and partial depletion of o-xylene within 3 months of incubation. The depletion of o-xylene was correlated to and dependent on the metabolism of toluene. No losses of benzene, p-xylene, or m-xylene were observed in these initial enrichment cultures. However, m-xylene was degraded by a subculture that was incubated on m-xylene alone. Complete carbon, nitrogen, and electron balances were determined for the degradation of toluene and m-xylene. These balances showed that these compounds were mineralized with greater than 50% conversion to CO2 and significant assimilation into biomass. Additionally, the oxidation of these compounds was shown to be dependent on nitrate reduction and denitrification. These microbial degradative capabilities appear to be widespread, since the widely varied inoculum sources all yielded similar results. PMID:2014990

  10. Nitrogen source effects on the denitrifying anaerobic methane oxidation culture and anaerobic ammonium oxidation bacteria enrichment process.

    Science.gov (United States)

    Fu, Liang; Ding, Jing; Lu, Yong-Ze; Ding, Zhao-Wei; Zeng, Raymond J

    2017-05-01

    The co-culture system of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) has a potential application in wastewater treatment plant. This study explored the effects of permutation and combination of nitrate, nitrite, and ammonium on the culture enrichment from freshwater sediments. The co-existence of NO3(-), NO2(-), and NH4(+) shortened the enrichment time from 75 to 30 days and achieved a total nitrogen removal rate of 106.5 mg/L/day on day 132. Even though ammonium addition led to Anammox bacteria increase and a higher nitrogen removal rate, DAMO bacteria still dominated in different reactors with the highest proportion of 64.7% and the maximum abundance was 3.07 ± 0.25 × 10(8) copies/L (increased by five orders of magnitude) in the nitrite reactor. DAMO bacteria showed greater diversity in the nitrate reactor, and one was similar to M. oxyfera; DAMO bacteria in the nitrite reactor were relatively unified and similar to M. sinica. Interestingly, no DAMO archaea were found in the nitrate reactor. This study will improve the understanding of the impact of nitrogen source on DAMO and Anammox co-culture enrichment.

  11. Pyruvic Oxime Nitrification and Copper and Nickel Resistance by a Cupriavidus pauculus, an Active Heterotrophic Nitrifier-Denitrifier

    Directory of Open Access Journals (Sweden)

    Miguel Ramirez

    2014-01-01

    Full Text Available Heterotrophic nitrifiers synthesize nitrogenous gasses when nitrifying ammonium ion. A Cupriavidus pauculus, previously thought an Alcaligenes sp. and noted as an active heterotrophic nitrifier-denitrifier, was examined for its ability to produce nitrogen gas (N2 and nitrous oxide (N2O while heterotrophically nitrifying the organic substrate pyruvic oxime [CH3–C(NOH–COOH]. Neither N2 nor N2O were produced. Nucleotide and phylogenetic analyses indicated that the organism is a member of a genus (Cupriavidus known for its resistance to metals and its metabolism of xenobiotics. The microbe (a Cupriavidus pauculus designated as C. pauculus strain UM1 was examined for its ability to perform heterotrophic nitrification in the presence of Cu2+ and Ni2+ and to metabolize the xenobiotic phenol. The bacterium heterotrophically nitrified well when either 1 mM Cu2+ or 0.5 mM Ni2+ was present in either enriched or minimal medium. The organism also used phenol as a sole carbon source in either the presence or absence of 1 mM Cu2+ or 0.5 mM Ni2+. The ability of this isolate to perform a number of different metabolisms, its noteworthy resistance to copper and nickel, and its potential use as a bioremediation agent are discussed.

  12. Structural and functional analysis of denitrification genes in Pseudomonas stutzeri A1501

    Institute of Scientific and Technical Information of China (English)

    YAN Yongliang; LIN Min; WANG Yiping; JIN Qi; YANG Jian; CHEN Lihong; YANG Fan; DONG Jie; XUE Ying; XU Xingye; ZHU Yafang; YAO Zhijian

    2005-01-01

    Four gene clusters associated with denitrification were identified in the genome of A1501 strain, nar, nir, nor and nos, including 40 genes totally, which encode proteins for substance transportation, gene regulation and reductases. The three gene clusters, nir, nor and nos are adjacent on chromosome and are far from nar gene cluster. Compared with other denitrifying bacteria, the 40 denitrification genes in A1501 strain compose a complete denitrification catalysis system. In A1501 strain, this system has the following characteristics: (i) only one copy of narK gene is found in nar gene cluster; (ii) a narM gene is present between narK and narG; (iii) two genes, dnarE and orfl are identified at downstream of narX and narL genes, of which dnrE perhaps is a transcriptional factor belonging to FNR family; (iv) there are 16 nir genes in A1501, the most in the known denitrifying bacteria; (v) it is for the first time that norR gene has been found in A1501 and also in Pseudomonas; (vi) nos gene cluster is relatively conservative, with a completely identical composition and arrangement of genome to the reference bacteria strain.

  13. Influence of nutrient inputs, hexadecane, and temporal variations on denitrification and community composition of river biofilms.

    Science.gov (United States)

    Chénier, M R; Beaumier, D; Fortin, N; Roy, R; Driscoll, B T; Lawrence, J R; Greer, C W

    2006-01-01

    Biofilms were cultivated on polycarbonate strips in rotating annular reactors using South Saskatchewan River water during the fall of 1999 and the fall of 2001, supplemented with carbon (glucose), nitrogen (NH4Cl), phosphorus (KH2PO4), or combined nutrients (CNP), with or without hexadecane, a model compound representing aliphatic hydrocarbons used to simulate a pollutant. In fall 1999 and fall 2001, comparable denitrification activities and catabolic potentials were observed in the biofilms, implying that denitrifying populations showed similar activity patterns and catabolic potentials during the fall from year to year in this river ecosystem, when environmental conditions were similar. Both nirS and nirK denitrification genes were detected by PCR amplification, suggesting that both denitrifying bacterial subpopulations can potentially contribute to total denitrification. Between 91.7 and 99.8% of the consumed N was emitted in the form of N2, suggesting that emission of N2O, a major potent greenhouse gas, by South Saskatchewan River biofilms is low. Denitrification was markedly stimulated by the addition of CNP, and nirS and nirK genes were predominant only in the presence of CNP. In contrast, individual nutrients had no impact on denitrification and on the occurrence of nirS and nirK genes detected by PCR amplification. Similarly, only CNP resulted in significant increases in algal and bacterial biomass relative to control biofilms. Biomass measurements indicated a linkage between autotrophic and heterotrophic populations in the fall 1999 biofilms. Correlation analyses demonstrated a significant relationship (P < or = 0.05) between the denitrification rate and the biomass of algae and heterotrophic bacteria but not cyanobacteria. At the concentration assessed (1 ppb), hexadecane partially inhibited denitrification in both years, slightly more in the fall of 2001. This study suggested that the response of the anaerobic heterotrophic biofilm community may be

  14. Effect of land use on the density of nitrifying and denitrifying bacteria in the Colombian Coffee Region

    Directory of Open Access Journals (Sweden)

    Vallejo Quintero Victoria Eugenia

    2011-12-01

    Full Text Available

    Soil microbial communities involved in the cycling of nitrogen (N are essential to maintaining and improving soil fertility, productivity and functionality of natural and agricultural ecosystems. However, some compounds generated during the metabolic processes performed by nitrifying (NB and denitrifying (DB bacteria are associated with the production of greenhouse gases, groundwater pollution and acidification. Therefore, the study of these bacteria is essential for economic and environmental sustainability. This study evaluated the effect of different land uses in two river basins (La Vieja and Otun on NB and DB densities. Two sampling events (SE were conducted by selecting the most representative land uses. Physicochemical (T °, pH, moisture and nitrate and microbiological properties (NB and DB densities were evaluated. In both SEs, significantly higher densities of NB and DB were observed in the land uses: pasture, guadua (DB only and unshaded coffee (La Vieja and onion (Otun. These land uses, excluding guadua, are dependent on nitrogen fertilizers, which together with the activities of grazing livestock on pastures may lead to greater availability of substrates for the NB. The use of agricultural machinery and overgrazing in pasture and onion uses generate compacted soil and other physical disturbances, encouraging the growth of DB. Forests had the lowest densities of NB and DB possibly due to a reduced availability of N and the releasing of allelopathic compounds from certain plants. Finally, the densities of ammonium-oxidizing bacteria had the greatest differences between the land uses evaluated, demonstrating its high sensitivity to agricultural management practices and livestock. We suggest that changes in the abundance of this community could

  15. Succession of Denitrifying Community Composition in Coastal Wetland Soils Along a Salinity Gradient

    Institute of Scientific and Technical Information of China (English)

    PIAO Zhe; ZHANG Wen-Wen; MA Shuai; LI Yu-Min; YIN Shi-Xue

    2012-01-01

    To better understand the effect of salinity on denitrification communities,soils along a salinity gradient (ranging from 7.32 to 1.70 mS cm-1) in a wetland along the Yellow Sea coastline in Jiangsu Province,China,were studied using both culture-dependent and -independent methods.Culture efforts yielded 82 isolates in total,81.7% of which were close relatives of Bacillus sp.based on partial sequences of their 16S rRNA genes.Denaturing gradient gel electrophoresis (DGGE) analysis based on 16S rRNA sequences suggested possible existence of bacterial community succession along the salinity gradient.Clone library analysis based on nosZ gene sequences (coding nitrous oxide reductase) showed that operational taxonomic units (OTUs) associated with α-proteobacteria dominated in all three soils,whereas those associated with β-and γ-subdivisions showed a clear succession.In the high salinity soil,only the OTUs associated with α-subdivision were found.In the medium salinity soil,small proportions ofβ- (6.5%) and γ-associated (19.6%) OTUs were found.In the low salinity soil,the proportions were further increased to 33% and 25% for β- and γ-Proteobacteria,respectively.Statistic analysis using Unifrac P test showed that nosZ-communities in different saline soils were significantly different from each other.It could be concluded that α-subdivision of nosZ-community tended to be sustained in high salinity environments whereas β- and γ-subdivisions,especially the former,tended to be sustained in low salinity environments.Salinity was the key determinant of nosZ-community composition in the environment.

  16. Diagnosis and quantification of glycerol assimilating denitrifying bacteria in an integrated fixed-film activated sludge reactor via 13C DNA stable-isotope probing.

    Science.gov (United States)

    Lu, Huijie; Chandran, Kartik

    2010-12-01

    Glycerol, a byproduct of biodiesel and oleo-chemical manufacturing operations, represents an attractive alternate to methanol as a carbon and electron donor for enhanced denitrification. However, unlike methanol, little is known about the diversity and activity of glycerol assimilating bacteria in activated sludge. In this study, the microbial ecology of glycerol assimilating denitrifying bacteria in a sequencing batch integrated fixed film activated sludge (SB-IFAS) reactor was investigated using (13)C-DNA stable isotope probing (SIP). During steady state SB-IFAS reactor operation, near complete nitrate removal (92.7 ± 5.8%) was achieved. Based on (13)C DNA clone libraries obtained after 360 days of SB-IFAS reactor operation, bacteria related to Comamonas spp. and Diaphorobacter spp. dominated in the suspended phase communities. (13)C assimilating members in the biofilm community were phylogenetically more diverse and were related to Comamonas spp., Bradyrhizobium spp., and Tessaracoccus spp. Possibly owing to greater substrate availability in the suspended phase, the glycerol-assimilating denitrifying populations (quantified by real-time PCR) were more abundant therein than in the biofilm phase. The biomass in the suspended phase also had a higher specific denitrification rate than the biofilm phase (p = 4.33e-4), and contributed to 69.7 ± 4.5% of the overall N-removal on a mass basis. The kinetics of glycerol based denitrification by suspended phase biomass were approximately 3 times higher than with methanol. Previously identified methanol assimilating denitrifying bacteria were not associated with glycerol assimilation, thereby suggesting limited cross-utilization of these two substrates for denitrification in the system tested.

  17. Effect of dissolved oxygen on nitrate removal using polycaprolactone as an organic carbon source and biofilm carrier in fixed-film denitrifying reactors.

    Science.gov (United States)

    Luo, Guozhi; Xu, Guimei; Gao, Jinfang; Tan, Hongxin

    2016-05-01

    Nitrate-nitrogen (NO3(-)-N) always accumulates in commercial recirculating aquaculture systems (RASs) with aerobic nitrification units. The ability to reduce NO3(-)-N consistently and confidently could help RASs to become more sustainable. The rich dissolved oxygen (DO) content and sensitive organisms stocked in RASs increase the difficulty of denitrifying technology. A denitrifying process using biologically degradable polymers as an organic carbon source and biofilm carrier was proposed because of its space-efficient nature and strong ability to remove NO3(-)-N from RASs. The effect of dissolved oxygen (DO) levels on heterotrophic denitrification in fixed-film reactors filled with polycaprolactone (PCL) was explored in the current experiment. DO conditions in the influent of the denitrifying reactors were set up as follows: the anoxic treatment group (Group A, average DO concentration of 0.28±0.05mg/L), the low-oxygen treatment DO group (Group B, average DO concentration of 2.50±0.24mg/L) and the aerated treatment group (Group C, average DO concentration of 5.63±0.57mg/L). Feeding with 200mg/L of NO3(-)-N, the NO3(-)-N removal rates were 1.53, 1.60 and 1.42kg/m(3) PCL/day in Groups A, B and C, respectively. No significant difference in NO3(-)-N removal rates was observed among the three treatments. It was concluded that the inhibitory effects of DO concentrations lower than 6mg/L on heterotrophic denitrification in the fixed-film reactors filled with PCL can be mitigated.

  18. A novel denitrifying methanotroph of the NC10 phylum and its microcolony

    Science.gov (United States)

    He, Zhanfei; Cai, Chaoyang; Wang, Jiaqi; Xu, Xinhua; Zheng, Ping; Jetten, Mike S. M.; Hu, Baolan

    2016-09-01

    The NC10 phylum is a candidate phylum of prokaryotes and is considered important in biogeochemical cycles and evolutionary history. NC10 members are as-yet-uncultured and are difficult to enrich, and our knowledge regarding this phylum is largely limited to the first species ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera). Here, we enriched NC10 members from paddy soil and obtained a novel species of the NC10 phylum that mediates the anaerobic oxidation of methane (AOM) coupled to nitrite reduction. By comparing the new 16S rRNA gene sequences with those already in the database, this new species was found to be widely distributed in various habitats in China. Therefore, we tentatively named it ‘Candidatus Methylomirabilis sinica’ (M. sinica). Cells of M. sinica are roughly coccus-shaped (0.7–1.2 μm), distinct from M. oxyfera (rod-shaped; 0.25–0.5 × 0.8–1.1 μm). Notably, microscopic inspections revealed that M. sinica grew in honeycomb-shaped microcolonies, which was the first discovery of microcolony of the NC10 phylum. This finding opens the possibility to isolate NC10 members using microcolony-dependent isolation strategies.

  19. 一株高效反硝化聚磷菌的筛选及脱氮除磷效能%Isolation and identification of denitrifying polyphosphate-accumulating organisms and its efficiency of nitrogen and phosphorus removal

    Institute of Scientific and Technical Information of China (English)

    马放; 杨菲菲; 张倩; 李昂; 姜欣欣; 张晓昕

    2011-01-01

    In this paper,16 denitrifying phosphate-accumulating organisms(DNPAOs) were isolated in the special medium from the anaerobic/aerobic/anoxic SBR reactor,and the most efficient DNPAOs called Q-hrb05,was screened by a phosphate uptake experiment,where nitrates were denitrified to gas and through inspection of the poly-P.Strain Q-hrb05 was identified by 16S rDNA gene analysis,and the accession number of 16 S rDNA gene sequence of strain Q-hrb05 in GenBank was GU214826.The result showed that the strain Q-hrb05 belonged to Bacillus sp,of which the homology could reach to 99%,that also corresponded to the result of biochemical features.The average phosphorus uptake rate of strain Q-hrb05 was at 85% within 12 hours,and it had the denitrification capacity in the aerobic condition.It could be found that the phosphorus uptake rate was related to the content change of PHB.Under anaerobic condition,the maximal P-release rate was 66%,which could reach to 12% of the dry cell weight.The P-uptake rate was 92% with the decreasing of PHB content.%高效的反硝化聚磷菌的分离及脱氮除磷效能的研究对于反硝化聚磷机理及脱氮除磷工艺的创新具有重要意义.采用专性培养基,从稳定运行的A/O/A SBR反应器中分离得到16株反硝化聚磷菌.通过poly-P染色试验、吸磷试验、硝酸盐还原产气及脱氮效能试验相结合的方法,筛选得到一株高效的反硝化聚磷菌Q-hrb05.实验结果表明:经16S rDNA初步鉴定菌株Q-hrb05为芽孢杆菌,相似度为99%.菌株Q-hrb05的16S rDNA序列登录GenBank,登录号为GU214826.结合生理生化结果,确定菌株Q-hrb05为芽孢杆菌.菌株Q-hrb05属于好氧反硝化菌,且除磷效率高,在12 h内除磷率可达85%.经过厌氧/缺氧培养,发现菌株Q-hrb05的吸磷率与菌株内PHB的变化呈正相关.厌氧段,PHB在菌体内合成,约占细胞干质量的12%,释磷率为66%;缺氧段,菌体内PHB质量下降,吸磷率为92%.

  20. Two-step nitrification in a pure moving bed biofilm reactor-membrane bioreactor for wastewater treatment: nitrifying and denitrifying microbial populations and kinetic modeling.

    Science.gov (United States)

    Leyva-Díaz, J C; González-Martínez, A; Muñío, M M; Poyatos, J M

    2015-12-01

    The moving bed biofilm reactor-membrane bioreactor (MBBR-MBR) is a novel solution to conventional activated sludge processes and membrane bioreactors. In this study, a pure MBBR-MBR was studied. The pure MBBR-MBR mainly had attached biomass. The bioreactor operated with a hydraulic retention time (HRT) of 9.5 h. The kinetic parameters for heterotrophic and autotrophic biomasses, mainly nitrite-oxidizing bacteria (NOB), were evaluated. The analysis of the bacterial community structure of the ammonium-oxidizing bacteria (AOB), NOB, and denitrifying bacteria (DeNB) from the pure MBBR-MBR was carried out by means of pyrosequencing to detect and quantify the contribution of the nitrifying and denitrifying bacteria in the total bacterial community. The relative abundance of AOB, NOB, and DeNB were 5, 1, and 3%, respectively, in the mixed liquor suspended solids (MLSS), and these percentages were 18, 5, and 2%, respectively, in the biofilm density (BD) attached to carriers. The pure MBBR-MBR had a high efficiency of total nitrogen (TN) removal of 71.81±16.04%, which could reside in the different bacterial assemblages in the fixed biofilm on the carriers. In this regard, the kinetic parameters for autotrophic biomass had values of YA=2.3465 mg O2 mg N(-1), μm, A=0.7169 h(-1), and KNH=2.0748 mg NL(-1).

  1. Impact of electro-stimulation on denitrifying bacterial growth and analysis of bacterial growth kinetics using a modified Gompertz model in a bio-electrochemical denitrification reactor.

    Science.gov (United States)

    Liu, Hengyuan; Chen, Nan; Feng, Chuanping; Tong, Shuang; Li, Rui

    2017-05-01

    This study aimed to investigate the effect of electro-stimulation on denitrifying bacterial growth in a bio-electrochemical reactor, and the growth were modeled using modified Gompertz model under different current densities at three C/Ns. It was found that the similar optimum current density of 250mA/m(2) was obtained at C/N=0.75, 1.00 and 1.25, correspondingly the maximum nitrate removal efficiencies were 98.0%, 99.2% and 99.9%. Moreover, ATP content and cell membrane permeability of denitrifying bacteria were significantly increased at optimum current density. Furthermore, modified Gompertz model fitted well with the microbial growth curves, and the highest maximum growth rates (µmax) and shorter lag time were obtained at the optimum current density for all C/Ns. This study demonstrated that the modified Gompertz model could be used for describing microbial growth under different current densities and C/Ns in a bio-electrochemical denitrification reactor, and it provided an alternative for improving the performance of denitrification process.

  2. Bioaugmentation of nitrate-dependent anaerobic ferrous oxidation by heterotrophic denitrifying sludge addition: A promising way for promotion of chemoautotrophic denitrification.

    Science.gov (United States)

    Wang, Ru; Zheng, Ping; Zhang, Meng; Zhao, He-Ping; Ji, Jun-Yuan; Zhou, Xiao-Xin; Li, Wei

    2015-12-01

    Nitrate-dependent anaerobic ferrous oxidation (NAFO) is a new and valuable bio-process for the treatment of wastewaters with low C/N ratio, and the NAFO process is in state of the art. The heterotrophic denitrifying sludge (HDS), possessing NAFO activity, was used as bioaugmentation to enhance NAFO efficiency. At a dosage of 6% (V/V), the removal of nitrate and ferrous was 2.4 times and 2.3 times of as primary, and the volumetric removal rate (VRR) of nitrate and ferrous was 2.4 times and 2.2 times of as primary. Tracing experiments of HDS indicated that the bioaugmentation on NAFO reactor was resulted from the NAFO activity by HDS itself. The predominant bacteria in HDS were identified as Thauera (52.5%) and Hyphomicrobium (20.0%) which were typical denitrifying bacteria and had potential ability to oxidize ferrous. In conclusion, HDS could serve as bioaugmentation or a new seeding sludge for operating high-efficiency NAFO reactors. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. 亚硝化-反硝化除磷技术研究进展%Advance of Research on the Technology of Nitrite-denitrifying Phosphorus Removal

    Institute of Scientific and Technical Information of China (English)

    叶丽红; 李冬; 张杰; 张金库; 曾辉平

    2016-01-01

    With nitrogen and phosphorus in water body caused the environmental problem, removal of the nitrogen and phosphorus in water body with low cost has become a challenge to the biological wastewater treatment worldwide. The technology of nitrite-denitrifying phosphorus removal has advantages of reducing carbon source consumption, saving occupied area, improving water treatment equipment utilization, and decreasing sludge production. But it remains unclear about the cognition of phosphorus accumulating organisms( PAOs) , and the stable operation of the whole technology that ammonia is reduced to nitrite and denitrifying phosphorus removal is not reported at present. Simultaneously, according to different researchers, PAOs has different classification, while the main results of the mechanism with short-cut denitrifying phosphorus removal are phosphate release and storage energy in anaerobic, then the energy supply for denitrifying phosphorus uptake with nitrite as the electron acceptor in anoxic. The effect of nitrogen and phosphorus removal is influenced by temperature, pH, the kind of carbon source, the value of ρ(C)/ρ(P) and other factors, so, in order to achieve the stable and efficient treatment of sewage wastewater, the reaction conditions of short-cut denitrifying phosphorus removal is necessarily reasonable. It is necessary to summerize the relevant research reported on the nitrite-denitrification and phosphorus removal to guide and overcome the disadvantages of the biological nitrogen and phosphorus removal.%氮磷引起的环境问题已引起世界关注,低成本减少水体氮磷污染是生物处理工艺面临的挑战。亚硝化-反硝化除磷工艺具有节约碳源和能源、节省空间及占地、提高水处理设备利用率、减少污泥产量等优势,但关于聚磷菌( PAOs)的认知缺乏深入了解,且目前尚未见氨氮亚硝化-反亚硝酸除磷整体工艺的稳定运行报道。关于PAOs的分类,不同研究者有不

  4. Denitrifying sulfur conversion-associated EBPR: The effect of pH on anaerobic metabolism and performance.

    Science.gov (United States)

    Guo, Gang; Wu, Di; Hao, Tianwei; Mackey, Hamish Robert; Wei, Li; Chen, Guanghao

    2017-10-15

    The performance of the denitrifying sulfur conversion-associated enhanced biological phosphorus removal (DS-EBPR) process tends to be unstable and requires further study and development. This in turn requires extensive study of the anaerobic metabolism in terms of its stoichiometry and kinetics. This study evaluates the corresponding responses of DS-EBPR to pH, as it significantly influences both stoichiometry and biochemical kinetics. The impacts of five representative pH values ranging between 6.5 and 8.5 on the anaerobic metabolism were investigated, followed by identification of the optimal pH for performance optimization. A mature DS-EBPR sludge was used in the study, enriched with approximately 30% sulfate-reducing bacteria (SRB) and 33% sulfide-oxidizing bacteria (SOB). Through a series of batch tests, the optimal pH range was determined as 7.0-7.5. In this pH range, the anaerobic stoichiometry of phosphorus released/volatile fatty acid (VFA) uptake ratio, sulfate reduction, and internal polymer production (including poly-β-hydroxyalkanoates and polysulfide and/or elemental sulfur) all increased along with the anaerobic kinetics of the VFA uptake ratio. Consequently, phosphorus removal was maximized at this pH range (≥95% vs. 84-93% at other pH values), as was sulfur conversion (16 mg S/L vs. 10-13 mg S/L). This pH range therefore favors the activity and synergy of the key functional bacteria (i.e. SRB and SOB). Anaerobic maintenance tests showed these bacteria required 38-61% less energy for maintenance than that reported for GAOs regardless of pH changes, improving their ability to cope with anaerobic starvation. Adversely, both bacteria showed much lower VFA uptake rates than that of GAOs at all tested pH values (0.03-0.06 vs. 0.2-0.24 mol-C/C-mol biomass/h), possibly revealing the primary cause of frequent instability in the DS-EBPR process. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Detection of denitrification genes by in situ rolling circle amplification - fluorescence in situ hybridization (in situ RCA-FISH) to link metabolic potential with identity inside bacterial cells

    DEFF Research Database (Denmark)

    Hoshino, Tatsuhiko; Schramm, Andreas

    2010-01-01

    A target-primed in situ rolling circle amplification (in situ RCA) protocol was developed for detection of single-copy genes inside bacterial cells and optimized with Pseudomonas stutzeri, targeting nitrite and nitrous oxide reductase genes (nirS and nosZ). Two padlock probes were designed per gene......). Nevertheless, multiple genes (nirS and nosZ; nirS and the 16S rRNA gene) could be detected simultaneously in P. stutzeri. Environmental application of in situ RCA-FISH was demonstrated on activated sludge by the differential detection of two types of nirS-defined denitrifiers; one of them was identified...

  6. Oxygen at nanomolar levels reversibly suppresses process rates and gene expression in anammox and denitrification in the oxygen minimum zone off Northern Chil

    DEFF Research Database (Denmark)

    Dalsgaard, Tage; Stewart, Frank J.; Thamdrup, Bo

    2014-01-01

    UNLABELLED: A major percentage (20 to 40%) of global marine fixed-nitrogen loss occurs in oxygen minimum zones (OMZs). Concentrations of O2 and the sensitivity of the anaerobic N2-producing processes of anammox and denitrification determine where this loss occurs. We studied experimentally how O2...... at nanomolar levels affects anammox and denitrification rates and the transcription of nitrogen cycle genes in the anoxic OMZ off Chile. Rates of anammox and denitrification were reversibly suppressed, most likely at the enzyme level. Fiftypercent inhibition of N2 and N2O production by denitrification....... This O2 concentration did not suppress the transcription of other dissimilatory nitrogen cycle genes, including nitrate reductase (narG), hydrazine oxidoreductase (hzo), and nitrite reductase (nirK). However, taxonomic characterization of transcripts suggested inhibition of narG transcription...

  7. Cultivation of Denitrifying Polyphosphate-accumulating Organisms in Sequencing Batch Reactor%SBR反应器中反硝化除磷菌的快速富集

    Institute of Scientific and Technical Information of China (English)

    夏灵敏; 王弘宇; 田俊; 杨开; 张静

    2013-01-01

    Denitrifying polyphosphate-accumulating organisms (DPAOs),a principal part in the denitrifying phosphorus removal process,can remove nitrogen and phosphorus simultaneously under anoxic condition.The cultivation of DPAOs was achieved in a two-stage sequencing batch reactor (SBR) system,using the returned sludge from a secondary settling tank of Wuhan Shahu WWTP.The first-stage SBR operated in anaerobic/aerobic (A/O) mode to achieve the cultivation of PAOs.After 13 d,the removal rates of nitrogen and phosphorus were all above 85%.The second-stage SBR operated in anaerobic/aerobic/anoxic (A/O/A) mode to achieve the cultivation of DPAOs.After 26 d,the removal rates of ammonia nitrogen and phosphate were 92.2% and 91.2%,respectively.There was a linear relationship between phosphorus uptake and nitrate consumption,which suggested that the denitrifying phosphorus removal ability of the system was enhanced significantly.%反硝化除磷菌(DPAOs)能够在缺氧条件下同步完成脱氮除磷,是反硝化除磷工艺的主体.以武汉沙湖污水处理厂二沉池的回流污泥为种泥,采用二段式SBR工艺实现了反硝化除磷菌的快速富集.在第一阶段反应器采用厌氧/好氧(A/O)模式运行,可以实现对除磷菌(PAOs)的快速诱导和富集,运行13d后,SBR反应器对氮、磷的去除率均达到85%以上.而后进入第二阶段,采用厌氧/好氧/缺氧(A/O/A)模式运行,以快速富集培养反硝化除磷菌,经过26 d的运行,反应器对氨氮和磷酸盐的去除率分别达到92.2%和91.2%左右,且典型周期内硝酸盐的消耗量与磷的吸收量基本呈线性关系,表明系统的反硝化除磷能力得到显著增强.

  8. Nitrogen removal characteristics of enhanced in situ indigenous aerobic denitrification bacteria for micro-polluted reservoir source water.

    Science.gov (United States)

    Zhou, Shilei; Huang, Tinglin; Zhang, Haihan; Zeng, Mingzheng; Liu, Fei; Bai, Shiyuan; Shi, Jianchao; Qiu, Xiaopeng; Yang, Xiao

    2016-02-01

    Indigenous oligotrophic aerobic denitrifiers nitrogen removal characteristics, community metabolic activity and functional genes were analyzed in a micro-polluted reservoir. The results showed that the nitrate in the enhanced system decreased from 1.71±0.01 to 0.80±0.06mg/L, while the control system did little to remove and there was no nitrite accumulation. The total nitrogen (TN) removal rate of the enhanced system reached 38.33±1.50% and the TN removal rate of surface sediment in the enhanced system reached 23.85±2.52%. TN removal in the control system experienced an 85.48±2.37% increase. The densities of aerobic denitrifiers in the enhanced system ranged from 2.24×10(5) to 8.13×10(7)cfu/mL. The abundance of nirS and nirK genes in the enhanced system were higher than those of in the control system. These results suggest that the enhanced in situ indigenous aerobic denitrifiers have potential applications for the bioremediation of micro-polluted reservoir system. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Degradation of toluene by a mixed population of archetypal aerobes, microaerophiles, and denitrifiers: laboratory sand column experiment and multispecies biofilm model formulation.

    Science.gov (United States)

    Kim, Hyun-Su; Jaffé, Peter R

    2008-02-01

    An experiment was conducted in a saturated sand column with three bacterial strains that have different growth characteristics on toluene, Pseudomonas putida F1 which degrades toluene only under aerobic conditions, Thauera aromatica T1 which degrades toluene only under denitrifying conditions, and Ralstonia pickettii PKO1 has a facultative nature and can perform nitrate-enhanced biodegradation of toluene under hypoxic conditions (DO concentration profiles showed that oxygen and nitrate appeared to be utilized simultaneously, regardless of the dissolved oxygen concentration and the results from fluorescent in-situ hybridization (FISH) indicated that PKO1 maintained stable cells numbers throughout the column, even when the pore water oxygen concentration was high. Since PKO1's growth rate under aerobic condition is much lower than that of F1, except under hypoxic conditions, these observations were not anticipated. Therefore these observations require a mechanistic explanation that can account for localized low oxygen concentrations under aerobic conditions. To simulate the observed dynamics, a multispecies biofilm model was implemented. This model formulation assumes the formation of a thin biofilm that is composed of the three bacterial strains. The individual strains grow in response to the substrate and electron acceptor flux from bulk fluid into the biofilm. The model was implemented such that internal changes in bacterial composition and substrate concentration can be simulated over time and space. The model simulations from oxic to denitrifying conditions compared well to the experimental profiles of the chemical species and the bacterial strains, indicating the importance of accounting for the biological activity of individual strains in biofilms that span different redox conditions. (c) 2007 Wiley Periodicals, Inc.

  10. Detoxification of tar water by anaerobic treatment in an UASB reactor - A study of the degradation of phenolic compounds in a combined denitrifying and anaerobic UASB reactor

    Energy Technology Data Exchange (ETDEWEB)

    Skibsted Mogensen, A.; Schmidt, J.E.; Ahring, B.K. [Technical Univ., Dept. of Environmental Science and Engineering, Lyngby (Denmark)

    1998-08-01

    The digestion of pyrolysis condensate (PC) in two combined anaerobic and denitrifying upflow anaerobic sludge blanket (UASB) reactors was studied. A COD removal of 80% was achieved with an influent concentration of 1.43% PC{sub pH}. When the reactor was fed with 100% PC during a period of 10 days good reactor operation was observed. Despite less than one retention time of operation, the results indicated clearly, that PC could be used as substrate in the biogas process, even in very high concentrations. A combined anaerobic and denitrifying UASB reactor was successfully digesting 5.5% of wet oxidised PC, but further loading increments deteriorated the anaerobic digestion process. The detoxification of PC was studied by determining the degradation of phenols during reactor operation and the toxicity of PC was decreased more than 77 times witnessed through decreased inhibition of the nitrification process. Phenol, methyl and dimethyl phenols along with methoxyphenols were shown to be degraded within the reactor systems. Degradation rates for phenol and substituted phenols were determined by the reactor experiment indicating that the biomass was selective towards the substrates. Maximum growth rates and half saturation constants for phenol, 4-Methylphenol and 2-Methoxy-4-methylphenol were determined in batch experiments. The degradation rates of phenols determined in batches were significantly higher compared to degradation rates observed in the reactor systems digesting pyrolysis condensate. Determination of the population of methanogens revealed, that Methanosarcina was found only in one reactor, while Methanobacterium and Methanosaeta were found in reactors and inoculum. A UASB reactor was designed for the treatment of pyrolysis condensate at the gasification plant at Harbooere, Denmark. (au) 35 refs.

  11. Enhancing effect of induced crystallization process on denitrifying phosphorus removal%诱导结晶对反硝化除磷的强化作用

    Institute of Scientific and Technical Information of China (English)

    顾倩; 吕锡武; 史静; 李洁

    2013-01-01

    To investigate the enhancing effect of induced crystallization on the denitrifying phosphorus removal,experiments were carried out by combining the two-sludge system and the induced crystallization process.The results show that the phosphorus recovery rate of induced crystallizer is not greatly improved when the mole ratio of n(Ca2+)/n(PO43--P) reaches 5∶1.The optimum value of n (Ca2 +)/n (PO43--P) is 3∶1 which achieves a phosphorus recovery rate of 62.05 %.Appropriately increasing the amount of phosphorus recovery does not have a significant effect on the amount of anaerobic phosphorus release.When the amount of phosphorus release maintains at (13.44 ± 0.55)mg/L,the amount of phosphorus uptake decreases from 21.11 to 16.42 mg/L.The ratio of phosphorus uptake amount to release amount falls from 1.51 to 1.24 along with a high recovery rate,which means that the burden of bio-P removal is lightened.During the prior period of denitrifying phosphorus removal,the rate of phosphorus uptake goes down while the amount of phosphorus recovery increases,but the reaction of denitrifying phosphorus removal all ends after 30 min.Chemical phosphorus recovery do not cause negative effect on biological phosphorus removal.Moreover,the process which combines biological phosphorus removal with chemical phosphorus recovery can ensure that the effluent quality meets the related requirements under the condition of low influent CODto-phosphorus mass ratio.%以双污泥-诱导结晶工艺为研究对象,考察诱导结晶工艺回收磷对反硝化除磷的强化作用.结果表明,当摩尔比n(Ca2+)/n(PO43--P)提高到5∶1时,反应器内回收率没有明显的提高,最佳n(Ca2+)/n(PO43--P)为3∶1,回收率可达62.05%;提高磷回收量对厌氧释磷影响并不大,当释磷量保持在(13.44±0.55) mg/L时,聚磷量由21.11 mg/L降至16.42 mg/L,聚磷量与释磷量之比从1.51降至1.24,化学回收磷减轻了生物除磷负担;提高结晶磷回收量会降低聚磷

  12. 溶解氧浓度对连续流活性污泥工艺反硝化除磷的影响%Effects of dissolved oxygen concentration on denitrifying phosphorus removal in continuous-flow activated sludge process

    Institute of Scientific and Technical Information of China (English)

    王荣昌; 司书鹏; 郑翔; 杨殿海; 励建全; 赵建夫

    2011-01-01

    @@ 引言 随着水体富营养化问题的日渐突出,污水处理技术逐渐从单一去除有机物为目的的阶段进入既要去除有机物又要脱氮除磷的深度处理阶段[1].%Effects of dissolved oxygen (DO) concentration on removal performance of nitrogen and phosphorus were investigated in a pilot-scale anaerobic-anoxic-aerobic (A2/O) activated sludge process for treating municipal wastewater. During run operation, sludge recycling ratio and internal mixed liquid recirculation ratio were kept constant at 150% and 100%, respectively. The results showed that DO concentration played an important role in nutrient removal by A2/O process. Denitrifying phosphorus removal was observed when aerobic tank was kept at low DO (DO=1. 0-1.5 mg · L-1) conditions. The best performance of nutrient removal was achieved when DO concentration was kept at 0. 2 mg · L-1 in anoxic tank and 1.0 mg · L-1 in aerobic tank. Total nitrogen (TN) and total phosphorus (TP) removal was about 64.6% and 89.6%, respectively. TN and TP concentration in the effluent was (11.9± 5. 3)mg · L-1and (0. 17±0.09) mg· L-1 , respectively. TP removal in anoxic tank was about 48.2% of the total TP removal by the whole process. Denitrifying phosphorus removal became an important way of dephosphorization. Denitrifying phosphorus removal bacteria (DPB) accounted for 55.7% of the total phosphorus accumulating organisms (PAOs) based on the results of denitrifying phosphorus removal activity analysis. The analysis for particle diameter distributions showed that the particle diameter of activated sludge in aerobic tank was larger than those in anaerobic and anoxic tanks. Larger particle diameter resulted in the existence of anaerobic or anoxic microenvironments in the sludge particles in aerobic tank, which favored the survival and propagation of DPBs in the whole system. Therefore, the nutrient removal performance and cost-efficiency of conventional activated sludge processes can

  13. Investigation on the effect of denitrified fly ash on the properties of cement%脱硝粉煤灰对水泥性能影响的研究

    Institute of Scientific and Technical Information of China (English)

    王穆君; 徐玲玲; 刘方; 汪洋; 叶强; 杨尚富; 刘韬

    2011-01-01

    Denitrified fly ash is a solid by-product of thermal power plant denitrificat]on process used to reduce NOx emissions. With the popularizing of this technique in power plant,fly ash produced by low-NOx combustion will be the major type of fly ash. Therefore,its comprehensive utilization has practical significance. In this paper three samples of fly ash with low-NOx combustion from different power plants have been studied to replace the cement with weight percentage of 10%,20%,30% and 40%. Their effects on cement properties were tested. The results show that the effect of denitrified fly ash is nearly the same as that of ordinary fly ash. As it has certain water reducing effect.the flowability of cement is increased,setting time is prolonged and the earlier stage strength is lowered. Such effect strengthens with the increasing of denitrified fly ash content. To ensure the stability of cement with denitrified fly ash,the CaO content in denitrified fly ash should be considered when determining the percentage of fly ash adding into cement.%脱硝粉煤灰是火电厂采用脱硝工艺减少NOx气体排放时的固体副产物,随着脱硝工艺的普及,脱硝粉煤灰将成为主要的粉煤灰种类,因此其综合利用具有重大的实际意义.主要研究了3种采集自不同电厂的脱硝粉煤灰以10%、20%、30%和40%掺入水泥中对水泥性能的影响,结果表明,脱硝粉煤灰对水泥性能的作用类似于普通粉煤灰,具有一定的减水作用,提高了水泥的流动度,但延长了水泥的凝结时间,并降低了水泥的早期强度,这些作用随着粉煤灰掺量的增加而增强.在设计粉煤灰掺量时必须考虑粉煤灰中CaO的含量,以保证水泥的安定性合格.

  14. Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing.

    Science.gov (United States)

    Wang, Lei; Huang, Xu; Zheng, Tian-Ling

    2016-08-15

    This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (pmangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation.

  15. Polyphasic characterization of poly-3-hydroxybutyrate-co-3-hydroxyvalerate (p(HB-co-HV)) metabolizing and denitrifying Acidovorax sp. strains.

    Science.gov (United States)

    Schloe, K; Gillis, M; Hoste, B; Pot, B; Vancanneyt, M; Mergaert, J; Swings, J; Biedermann, J; Süssmuth, R

    2000-10-01

    For the purpose of denitrification in small drinking water plants, a bacterial mixed population was isolated from a packed bed column bioreactor with poly-3-hydroxybutyrate-co-3-hydroxyvalerate (P(HB-co-HV)) as a substrate for the denitrification of ground water (10 degrees C). Isolates 2nIII from the mixed culture, with the ability to denitrify and metabolize P(HB-co-HV), were used as starter cultures for the elimination of nitrate in ground water. The strains were characterized by diverse techniques. Classical phenotypic studies lead to rRNA group III of the genus Pseudomonas. Results obtained by molecular techniques demonstrated that the 2nIII strains are members of the Comamonadaceae and shows similarities to the genus Acidovorax. However, an integration of the 2nIII isolates within one of the known Acidovorax species is not possible for the moment. The 2nIII starter cultures clustered close to Av. temperans according to their whole cell proteins and fatty acids, whereas in DNA/DNA hybridization no significant DNA binding (< 25%) was found. In contrast a significant but low degree of DNA/DNA hybridization was found between the 2nIII strains and Av. facilis and Av. delafieldii. Our polyphasic results lead to the conclusion that the 2nIII strains may constitute a separate Acicdovorax species.

  16. Complete Nitrogen Removal from Synthetic Anaerobic Sludge Digestion Liquor through Integrating Anammox and Denitrifying Anaerobic Methane Oxidation in a Membrane Biofilm Reactor.

    Science.gov (United States)

    Xie, Guo-Jun; Cai, Chen; Hu, Shihu; Yuan, Zhiguo

    2017-01-17

    Partial nitritation and Anammox processes are increasingly used for nitrogen removal from anaerobic sludge digestion liquor. However, their nitrogen removal efficiency is often limited due to the production of nitrate by the Anammox reaction and the sensitivity to the nitrite to ammonium ratio. This work develops and demonstrates an innovative process that achieves complete nitrogen removal from partially nitrified anaerobic sludge digestion liquor through the use of a membrane biofilm reactor (MBfR), with methane supplied through hollow fiber membranes. When steady state with a hydraulic retention time (HRT) of 1 day was reached, the process achieved complete nitrite and ammonium removal at rates of 560 mg N/L/d and 470 mg N/L/d, respectively, without any nitrate accumulation. The process is relatively insensitive to the nitrite to ammonium ratio, achieving complete nitrogen removal when their ratio in influent varied in the range of 1.125-1.32. Pyrosequencing and fluorescence in situ hybridization analysis revealed that denitrifying anaerobic methane oxidation (DAMO) archaea, Anammox bacteria and DAMO bacteria jointly dominated the microbial community. Mass balance analysis showed that nitrate produced by Anammox (122.2 mg N/L/d) was entirely converted to nitrite by DAMO archaea, while nitrite in the feed and produced by DAMO archaea was jointly removed by Anammox (90%) and DAMO bacteria (10%). The nitrogen removal rate of over 1 kg N/m(3)/d is comparable to the practical rates reported for side-stream nitrogen removal processes.

  17. Nitrous oxide reductase genes (nosZ) of denitrifying populations in soil and the earthworm gut are phylogenetically similar

    DEFF Research Database (Denmark)

    Horn, Marcus A.; Drake, Harold L.; Schramm, Andreas

    2006-01-01

    -derived sequences, or were related to N2O reductases of the genera Bradyrhizobium, Brucella, Dechloromonas, Flavobacterium, Pseudomonas, Ralstonia, and Sinorhizobium. Although the numbers of estimators for genotype richness of sequence data from the gut were higher than those of soil, only one gut-derived nos...

  18. Final Technical Report: DOE-Biological Ocean Margins Program. Microbial Ecology of Denitrifying Bacteria in the Coastal Ocean.

    Energy Technology Data Exchange (ETDEWEB)

    Lee Kerkhof

    2013-01-01

    The focus of our research was to provide a comprehensive study of the bacterioplankton populations off the coast of New Jersey near the Rutgers University marine field station using terminal restriction fragment polymorphism analysis (TRFLP) coupled to 16S rRNA genes for large data set studies. Our three revised objectives to this study became: (1) to describe bacterioplankton population dynamics in the Mid Atlantic Bight using TRFLP analysis of 16S rRNA genes. (2) to determine whether spatial and temporal factors are driving bacterioplankton community dynamics in the MAB using monthly samping along our transect line over a 2-year period. (3) to identify dominant members of a coastal bacterioplankton population by clonal library analysis of 16S rDNA genes and sequencing of PCR product corresponding to specific TRFLP peaks in the data set. Although open ocean time-series sites have been areas of microbial research for years, relatively little was known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35m (n=178). The data revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth (figure 2-next page). Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally

  19. Climate change induces shifts in abundance and activity pattern of bacteria and archaea catalyzing major transformation steps in nitrogen turnover in a soil from a mid-European beech forest.

    Directory of Open Access Journals (Sweden)

    Silvia Gschwendtner

    Full Text Available Ongoing climate change will lead to more extreme weather events, including severe drought periods and intense drying rewetting cycles. This will directly influence microbial nitrogen (N turnover rates in soil by changing the water content and the oxygen partial pressure. Therefore, a space for time climate change experiment was conducted by transferring intact beech seedling-soil mesocosms from a northwest (NW exposed site, representing today's climatic conditions, to a southwest (SW exposed site, providing a model climate for future conditions with naturally occurring increased soil temperature (+0.8°C in average. In addition, severe drought and intense rainfall was simulated by a rainout shelter at SW and manual rewetting after 39 days drought, respectively. Soil samples were taken in June, at the end of the drought period (August, 24 and 72 hours after rewetting (August and after a regeneration period of four weeks (September. To follow dynamics of bacterial and archaeal communities involved in N turnover, abundance and activity of nitrifiers, denitrifiers, N2-fixing microbes and N-mineralizers was analyzed based on marker genes and the related transcripts by qPCR from DNA and RNA directly extracted from soil. Abundance of the transcripts was reduced under climate change with most pronounced effects for denitrification. Our results revealed that already a transfer from NW to SW without further treatment resulted in decreased cnor and nosZ transcripts, encoding for nitric oxide reductase and nitrous oxide reductase, respectively, while nirK transcripts, encoding for nitrite reductase, remained unaffected. Severe drought additionally led to reduced nirK and cnor transcripts at SW. After rewetting, nirK transcripts increased rapidly at both sites, while cnor and nosZ transcripts increased only at NW. Our data indicate that the climate change influences activity pattern of microbial communities involved in denitrification processes to a

  20. Climate change induces shifts in abundance and activity pattern of bacteria and archaea catalyzing major transformation steps in nitrogen turnover in a soil from a mid-European beech forest.

    Science.gov (United States)

    Gschwendtner, Silvia; Tejedor, Javier; Bimüller, Carolin; Bimueller, Carolin; Dannenmann, Michael; Kögel-Knabner, Ingrid; Knabner, Ingrid Kögel; Schloter, Michael

    2014-01-01

    Ongoing climate change will lead to more extreme weather events, including severe drought periods and intense drying rewetting cycles. This will directly influence microbial nitrogen (N) turnover rates in soil by changing the water content and the oxygen partial pressure. Therefore, a space for time climate change experiment was conducted by transferring intact beech seedling-soil mesocosms from a northwest (NW) exposed site, representing today's climatic conditions, to a southwest (SW) exposed site, providing a model climate for future conditions with naturally occurring increased soil temperature (+0.8°C in average). In addition, severe drought and intense rainfall was simulated by a rainout shelter at SW and manual rewetting after 39 days drought, respectively. Soil samples were taken in June, at the end of the drought period (August), 24 and 72 hours after rewetting (August) and after a regeneration period of four weeks (September). To follow dynamics of bacterial and archaeal communities involved in N turnover, abundance and activity of nitrifiers, denitrifiers, N2-fixing microbes and N-mineralizers was analyzed based on marker genes and the related transcripts by qPCR from DNA and RNA directly extracted from soil. Abundance of the transcripts was reduced under climate change with most pronounced effects for denitrification. Our results revealed that already a transfer from NW to SW without further treatment resulted in decreased cnor and nosZ transcripts, encoding for nitric oxide reductase and nitrous oxide reductase, respectively, while nirK transcripts, encoding for nitrite reductase, remained unaffected. Severe drought additionally led to reduced nirK and cnor transcripts at SW. After rewetting, nirK transcripts increased rapidly at both sites, while cnor and nosZ transcripts increased only at NW. Our data indicate that the climate change influences activity pattern of microbial communities involved in denitrification processes to a different extend

  1. Microbial Ecological Niche Partitioning Affects N2 gas Production in the Largest Marine Oxygen Minimum Zone

    Science.gov (United States)

    Fuchsman, C. A.; Penn, J. L.; Devol, A.; Palevsky, H. I.; Deutsch, C. A.; Keil, R.; Ward, B. B.; Rocap, G.

    2016-02-01

    Up to half of oceanic N2 production occurs in oxygen minimum zones (OMZs). In the Eastern Tropical North Pacific OMZ in April 2012, we measured a nine station coast to open ocean transect of N2 gas in the heart of the ETNP OMZ. Depth profiles of excess N2 gas had dual maxima located at the top of the OMZ and at 300m. An ecosystem biogeochemical model of the ETNP was also found to produce dual maxima at stations with a shallow OMZ. The model indicated that high N2 production rates caused the upper N2 maxima while long water residence time caused the deeper maxima. At a low productivity open ocean station where dual N2 maxima were observed, we obtained a depth profile of metagenomic sequences from both free living and >30 μm fractions to determine which N2 producing microbes were living in these three ecological niches. We use a phylogenetically-aware approach to identify metagenomic sequences by placing them on reference trees, which allows us to utilize them in a semi-quantitative manner. Overall, genes for denitrification (napA, nirS, nirK, qnor, nosZ) were enriched on particles while anammox was free-living. However, separation of genes into phylotypes indicated that the system is more complicated. For example, 4 out of 5 N2O reductase denitrifier phylotypes were actually free-living, while the fifth, most abundant phylotype was particle-attached. In the water column, denitrifier and anammox genes were spatially separated with depth with denitrifiers focused on the top section of the OMZ and with anammox becoming abundant slightly deeper and being more dominant at the deep N2 maxima. Interestingly, different phylotypes of denitrifiers have different depth profiles, implying individual adaptations and niches. The presence of measurable ammonia (>200 nM) at the top 20m of the OMZ along with the very low numbers of anammox bacteria is consistent with recent shoaling of the OMZ at the time of sampling. Thus the spatial separation of denitrifiers and anammox at the

  2. Technical considerations for the use of passive samplers to quantify the isotopic composition of NOx and NO2 using the denitrifier method

    Science.gov (United States)

    Dahal, Bigyan; Hastings, Meredith G.

    2016-10-01

    The isotopic composition of nitrogen oxides (NOx = NO + NO2) hold potential to trace emissions sources, as well as chemistry in the atmosphere. Passive samplers that collect NOx and NO2 as nitrite could provide a simple and inexpensive means by which to collect samples in a variety of environments, and we report here on several methodological considerations when using Ogawa passive collectors of NOx and NO2 for concentration analysis via colorimetric methods and isotopic analysis via the denitrifier method. Using Ogawa samplers, NOx and NO2 were collected in Providence, RI, USA (41.8°N, 71.4°W) with exposure times of seven, fourteen, twenty-one, and twenty-eight days during summer and winter in an area dominated by vehicle emissions, particularly diesel delivery trucks. Average values were -9.7 ± 0.7‰ for δ15N-NOx and -8.3 ± 0.9‰ for δ15N-NO2 based on duplicate seven, fourteen, twenty-one, and twenty-eight day exposures (n = 8) in summertime, and -11.9 ± 0.7‰ for δ15N-NOx and -6.4 ± 1.4‰ for δ15N-NO2 based on seven, fourteen, twenty-one, and twenty-eight day exposures (n = 7) in wintertime. The oxygen isotopic composition (δ18O, Δ17O) was also determined with averages of: 36.3 ± 2.4‰ for δ18O-NOx (n = 8), 50.5 ± 3.2‰ for δ18O-NO2 (n = 8), 6.2 ± 0.8‰ for Δ17O-NOx and 10.8 ± 0.6‰ for Δ17O-NO2 (n = 4) in summer; and 38.7 ± 2.9‰ for δ18O-NOx and 47.4 ± 1.2‰ for δ18O-NO2 (n = 7), 7.7 ± 1.5‰ for Δ17O-NO2 (n = 4) and 5.3 ± 1.2‰ for Δ17O-NOx (n = 5), in winter. Our isotopic results differ from previous studies that utilized passive samplers and suggest specific nitrogen and oxygen isotopic signatures associated with vehicular emissions. To collect sufficient sample for multiple isotopic analyses (e.g., 10 nmol N for δ15N and δ18O; 50 nmol N for Δ17O) the exposure time for the samplers, even in urban areas, is at least days. This necessarily results in collection of a mixture of local emissions sources, as well as

  3. 好氧反硝化菌的筛选鉴定及其脱氮特性研究%SCREENING, IDENTIFICATION AND DENITRIFICATION CHARACTERISTICS OF AEROBIC DENITRIFIERS

    Institute of Scientific and Technical Information of China (English)

    张宇燕; 贺根和; 陆丽君; 刘佳; 黄翔峰; 梁亮亮

    2014-01-01

    通过分离筛选获得3株好氧反硝化菌S1、S2和S3,初步鉴定S1为土生拉乌尔菌属(Raoultella terrigena), S2和S3均为解鸟氨酸拉乌尔菌属(Raoultella ornithinolytica)。这3株菌为好氧反硝化菌属首次报道,对其好氧反硝化脱氮特性的研究结果表明,培养液中氮含量的大幅变化均发生于菌株的对数生长期;在以硝酸盐或亚硝酸盐为唯一氮源的研究中,NO3--N和NO2--N的24 h去除率分别约为26%和67%,说明这3株菌更容易利用亚硝酸盐进行好氧反硝化;而且研究结果还表明,S3为脱氮效率最优的菌株,对低氮浓度的富营养化水质有较好的反硝化效果,4 h时S3的反硝化速率最大,达0.62 mg·L-1·h-1,对TN的反硝化脱氮贡献率可达52.5%。%Three aerobic denitrifiers(S1, S2 and S3)were abtained by isolating and screening. Strain S1 was identified as Raoultella terrigena, while strains S2 and S3 were identified as Raoultella ornithinolytica. It is first reported that the three bacteria are aerobic denitrifiers. Studies on their aerobic denitrification characteristics showed that significant changes of nitrogen level in culture media occurred in the logarithmic growth phase of strains; in the studies on using nitrate or nitrite as sole nitrogen source, respectively, the removal rates of NO3--N and NO2--N were 26%and 67%at 24 h, respectively, which proved that nitrite was used more easily for aerobic denitrification of three strains;Results also showed that S3 was optimal strain with the highest removal efficiency of nitrogen, which had better denitrification effects on eutrophic water with low concentration nitrogen, and S3 had the highest denitrification rate of 0.62 mg·L-1·h-1 and denitrification contribution rate of TN up to 52.5%at 4 h.

  4. Cr(VI) removal from aqueous solution by thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1 in the presence of single and multiple heavy metals.

    Science.gov (United States)

    Li, Han; Huang, Shaobin; Zhang, Yongqing

    2016-09-01

    Cr(VI) pollution is increasing continuously as a result of ongoing industrialization. In this study, we investigated the thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1, isolated from the biofilm of a biotrickling filter used in nitrogen oxides (NOX) removal, with respect to its ability to remove Cr(VI) from an aqueous solution. TAD1 was capable of reducing Cr(VI) from an initial concentration of 10 mg/L to non-detectable levels over a pH range of 7-9 and at a temperature range of 30-50°C. TAD1 simultaneously removed both Cr(VI) and NO3 (-)-N at 50°C, when the pH was 7 and the initial Cr(VI) concentration was 15 mg/L. The reduction of Cr(VI) to Cr(III) correlated with the growth metabolic activity of TAD1. The presence of other heavy metals (Cu, Zn, and Ni) inhibited the ability of TAD1 to remove Cr(VI). The metals each individually inhibited Cr(VI) removal, and the extent of inhibition increased in a cooperative manner in the presence of a combination of the metals. The addition of biodegradable cellulose acetate microspheres (an adsorption material) weakened the toxicity of the heavy metals; in their presence, the Cr(VI) removal efficiency returned to a high level. The feasibility and applicability of simultaneous nitrate removal and Cr(VI) reduction by strain TAD1 is promising, and may be an effective biological method for the clean-up of wastewater.

  5. Coupling simultaneous dissolved nitrate measurements with quantum cascade laser based nitrous oxide flux and isotopocule analysis to investigate the biogeochemical processes occurring in a denitrifying bioreactor.

    Science.gov (United States)

    Williams, D. J.; Maxwell, B.; Deshmukh, P.; Chen, H.

    2016-12-01

    Denitrifying bioreactors are used to treat nitrogen enriched water from agricultural operations. These systems may also be an important source of nitrous oxide emissions, a potent greenhouse gas. Bioreactors also provide researchers with an opportunity to investigate the biogeochemical processes occurring in soils under controlled conditions. A pilot-scale bioreactor with woodchip media was injected with KNO3 at a constant flow rate through the system. The water-filled-pore-space (WFPS) was varied in separate experiments to create differing aerobic conditions. A quantum cascade laser spectroscopy system was used to determine the flux and isotopic signature of N2O emissions from woodchip bioreactor media over time. Simultaneous nitrate concentration measurements were made using an optical method at multiple points in the bioreactor. Isotopic site-preference (SP) characterization of N2O emissions was used to estimate production sources from soil nitrification and denitrification. A dynamic gas sampling method was used to measure N2O mixing ratios, which required ambient air to equalize chamber atmospheric pressure during sampling. Precise instrument calibration using gas samples of known isotopic abundances, provided by the Swiss Federal Labs (EMPA), together with a Keeling plot method to account for variations in isotopocule composition in ambient air, produced reliable SP estimates. Initial experiments during 100% WFPS show that SP and δ15Nbulk values were varied from -6‰ to 3‰ and -23‰ to -12‰, respectively. The trend of these values indicated that the N2O source was slightly changed from partial nitrification to denitrification during the measuring period of time. The peak rate of nitrous oxide production occurred 7 hours after peak nitrate removal. These results and others to be presented show the utility of coupling real-time dissolved and gas phase measurements for studying nitrogen cycling in soils.

  6. Assessment of the endogenous respiration rate and the observed biomass yield for methanol-fed denitrifying bacteria under anoxic and aerobic conditions.

    Science.gov (United States)

    Alikhani, Jamal; Al-Omari, Ahmed; De Clippeleir, Haydee; Murthy, Sudhir; Takacs, Imre; Massoudieh, Arash

    2017-01-01

    In this study, the endogenous respiration rate and the observed biomass yield of denitrifying methylotrophic biomass were estimated through measuring changes in denitrification rates (DNR) as a result of maintaining the biomass under methanol deprived conditions. For this purpose, activated sludge biomass from a full-scale wastewater treatment plant was kept in 10-L batch reactors for 8 days under fully aerobic and anoxic conditions at 20 °C without methanol addition. To investigate temperature effects, another biomass sample was placed under starvation conditions over a period of 10 days under aerobic conditions at 25 °C. A series of secondary batch tests were conducted to measure DNR and observed biomass yields. The decline in DNR over the starvation period was used as a surrogate to biomass decay rate in order to infer the endogenous respiration rates of the methylotrophs. The regression analysis on the declining DNR data shows 95% confidence intervals of 0.130 ± 0.017 day(-1) for endogenous respiration rate under aerobic conditions at 20 °C, 0.102 ± 0.013 day(-1) under anoxic conditions at 20 °C, and 0.214 ± 0.044 day(-1) under aerobic conditions at 25 °C. Results indicated that the endogenous respiration rate of methylotrophs is 20% slower under anoxic conditions than under aerobic conditions, and there is a significant temperature dependency, with an Arrhenius coefficient of 1.10. The observed biomass yield value showed an increasing trend from approximately 0.2 to 0.6 when the starvation time increased from 0 to 10 days.

  7. Potential application of aerobic denitrifying bacterium Pseudomonas aeruginosa PCN-2 in nitrogen oxides (NOx) removal from flue gas.

    Science.gov (United States)

    Zheng, Maosheng; Li, Can; Liu, Shufeng; Gui, Mengyao; Ni, Jinren

    2016-11-15

    Conventional biological removal of nitrogen oxides (NOx) from flue gas has been severely restricted by the presence of oxygen. This paper presents an efficient alternative for NOx removal at varying oxygen levels using the newly isolated bacterial strain Pseudomonas aeruginosa PCN-2 which was capable of aerobic and anoxic denitrification. Interestingly, nitric oxide (NO), as the obligatory intermediate, was negligibly accumulated during nitrate and nitrite reduction. Moreover, normal nitrate reduction with decreasing NO accumulation was realized under O2 concentration ranging from 0 to 100%. Reverse transcription and real-time quantitative polymerase chain reaction (RT-qPCR) analysis revealed that high efficient NO removal was attributed to the coordinate regulation of gene expressions including napA (for periplasmic nitrate reductase), nirS (for cytochrome cd1 nitrite reductase) and cnorB (for NO reductase). Further batch experiments demonstrated the immobilized strain PCN-2 possessed high capability of removing NO and nitrogen dioxide (NO2) at O2 concentration of 0-10%. A biotrickling filter established with present strain achieved high NOx removal efficiencies of 91.94-96.74% at inlet NO concentration of 100-500ppm and O2 concentration of 0-10%, which implied promising potential applications in purifying NOx contaminated flue gas.

  8. Autotrophic carbon dioxide fixation via the Calvin-Benson-Bassham cycle by the denitrifying methanotroph "Candidatus Methylomirabilis oxyfera".

    Science.gov (United States)

    Rasigraf, Olivia; Kool, Dorien M; Jetten, Mike S M; Sinninghe Damsté, Jaap S; Ettwig, Katharina F

    2014-04-01

    Methane is an important greenhouse gas and the most abundant hydrocarbon in the Earth's atmosphere. Methanotrophic microorganisms can use methane as their sole energy source and play a crucial role in the mitigation of methane emissions in the environment. "Candidatus Methylomirabilis oxyfera" is a recently described intra-aerobic methanotroph that is assumed to use nitric oxide to generate internal oxygen to oxidize methane via the conventional aerobic pathway, including the monooxygenase reaction. Previous genome analysis has suggested that, like the verrucomicrobial methanotrophs, "Ca. Methylomirabilis oxyfera" encodes and transcribes genes for the Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. Here we provide multiple independent lines of evidence for autotrophic carbon dioxide fixation by "Ca. Methylomirabilis oxyfera" via the CBB cycle. The activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), a key enzyme of the CBB cycle, in cell extracts from an "Ca. Methylomirabilis oxyfera" enrichment culture was shown to account for up to 10% of the total methane oxidation activity. Labeling studies with whole cells in batch incubations supplied with either (13)CH4 or [(13)C]bicarbonate revealed that "Ca. Methylomirabilis oxyfera" biomass and lipids became significantly more enriched in (13)C after incubation with (13)C-labeled bicarbonate (and unlabeled methane) than after incubation with (13)C-labeled methane (and unlabeled bicarbonate), providing evidence for autotrophic carbon dioxide fixation. Besides this experimental approach, detailed genomic and transcriptomic analysis demonstrated an operational CBB cycle in "Ca. Methylomirabilis oxyfera." Altogether, these results show that the CBB cycle is active and plays a major role in carbon assimilation by "Ca. Methylomirabilis oxyfera" bacteria. Our results suggest that autotrophy might be more widespread among methanotrophs than was previously assumed and implies that a methanotrophic

  9. Activity and abundance of denitrifying bacteria in the subsurface biosphere of diffuse hydrothermal vents of the Juan de Fuca Ridge

    Science.gov (United States)

    Bourbonnais, A.; Juniper, S. K.; Butterfield, D. A.; Devol, A. H.; Kuypers, M. M. M.; Lavik, G.; Hallam, S. J.; Wenk, C. B.; Chang, B. X.; Murdock, S. A.; Lehmann, M. F.

    2012-11-01

    Little is known about fixed nitrogen (N) transformation and elimination at diffuse hydrothermal vents where anoxic fluids are mixed with oxygenated crustal seawater prior to discharge. Oceanic N sinks that remove bio-available N ultimately affect chemosynthetic primary productivity in these ecosystems. Using 15N paired isotope techniques, we determined potential rates of fixed N loss pathways (denitrification, anammox) and dissimilatory nitrate reduction to ammonium (DNRA) in sulfidic hydrothermal vent fluids discharging from the subsurface at several sites at Axial Volcano and the Endeavour Segment on the Juan de Fuca Ridge. We also measured physico-chemical parameters (i.e., temperature, pH, nutrients, H2S and N2O concentrations) as well as the biodiversity and abundance of chemolithoautotrophic nitrate-reducing, sulfur-oxidizing γ-proteobacteria (SUP05 cluster) using sequence analysis of amplified small subunit ribosomal RNA (16S rRNA) genes in combination with taxon-specific quantitative polymerase chain reaction (qPCR) assays. Denitrification was the dominant N loss pathway in the subsurface biosphere of the Juan de Fuca Ridge, with rates of up to ~1000 nmol N l-1 day-1. In comparison, anammox rates were always waters. Taxon-specific qPCR revealed that γ-proteobacteria of the SUP05 cluster sometimes dominated the microbial community (SUP05/total bacteria up to 38%). Significant correlations were found between fixed N loss (i.e., denitrification, anammox) rates and in situ nitrate and dissolved inorganic nitrogen (DIN) deficits in the fluids, indicating that DIN availability may ultimately regulate N loss in the subsurface. Based on our rate measurements, and on published data on hydrothermal fluid fluxes and residence times, we estimated that up to ~10 Tg N yr-1 could globally be removed in the subsurface biosphere of hydrothermal vents systems, thus, representing a small fraction of the total marine N loss (~275 to > 400 Tg N yr-1).

  10. Activity and abundance of denitrifying bacteria in the subsurface biosphere of diffuse hydrothermal vents of the Juan de Fuca Ridge

    Directory of Open Access Journals (Sweden)

    A. Bourbonnais

    2012-11-01

    Full Text Available Little is known about fixed nitrogen (N transformation and elimination at diffuse hydrothermal vents where anoxic fluids are mixed with oxygenated crustal seawater prior to discharge. Oceanic N sinks that remove bio-available N ultimately affect chemosynthetic primary productivity in these ecosystems. Using 15N paired isotope techniques, we determined potential rates of fixed N loss pathways (denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA in sulfidic hydrothermal vent fluids discharging from the subsurface at several sites at Axial Volcano and the Endeavour Segment on the Juan de Fuca Ridge. We also measured physico-chemical parameters (i.e., temperature, pH, nutrients, H2S and N2O concentrations as well as the biodiversity and abundance of chemolithoautotrophic nitrate-reducing, sulfur-oxidizing γ-proteobacteria (SUP05 cluster using sequence analysis of amplified small subunit ribosomal RNA (16S rRNA genes in combination with taxon-specific quantitative polymerase chain reaction (qPCR assays. Denitrification was the dominant N loss pathway in the subsurface biosphere of the Juan de Fuca Ridge, with rates of up to ~1000 nmol N l−1 day−1. In comparison, anammox rates were always < 5 nmol N l−1 day−1 and below the detection limit at most of the sites. DNRA rates were up to ~150 nmol N l−1 day−1. These results suggest that bacterial denitrification out-competes anammox in sulfidic hydrothermal vent waters. Taxon-specific qPCR revealed that γ-proteobacteria of the SUP05 cluster sometimes dominated the microbial community (SUP05/total bacteria up to 38%. Significant correlations were found between fixed N loss (i.e., denitrification, anammox rates and in situ nitrate and dissolved inorganic nitrogen (DIN deficits in the fluids, indicating that DIN availability may ultimately regulate N loss in the subsurface

  11. Microbial N Transformations and N2O Emission after Simulated Grassland Cultivation: Effects of the Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate (DMPP).

    Science.gov (United States)

    Duan, Yun-Feng; Kong, Xian-Wang; Schramm, Andreas; Labouriau, Rodrigo; Eriksen, Jørgen; Petersen, Søren O

    2017-01-01

    Grassland cultivation can mobilize large pools of N in the soil, with the potential for N leaching and N2O emissions. Spraying with the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) before cultivation was simulated by use of soil columns in which the residue distribution corresponded to plowing or rotovation to study the effects of soil-residue contact on N transformations. DMPP was sprayed on aboveground parts of ryegrass and white clover plants before incorporation. During a 42-day incubation, soil mineral N dynamics, potential ammonia oxidation (PAO), denitrifying enzyme activity (DEA), nitrifier and denitrifier populations, and N2O emissions were investigated. The soil NO3(-) pool was enriched with (15)N to trace sources of N2O. Ammonium was rapidly released from decomposing residues, and PAO was stimulated in soil near residues. DMPP effectively reduced NH4(+) transformation irrespective of residue distribution. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) were both present, but only the AOB amoA transcript abundance correlated with PAO. DMPP inhibited the transcription of AOB amoA genes. Denitrifier genes and transcripts (nirK, nirS, and clades I and II of nosZ) were recovered, and a correlation was found between nirS mRNA and DEA. DMPP showed no adverse effects on the abundance or activity of denitrifiers. The (15)N enrichment of N2O showed that denitrification was responsible for 80 to 90% of emissions. With support from a control experiment without NO3(-) amendment, it was concluded that DMPP will generally reduce the potential for leaching of residue-derived N, whereas the effect of DMPP on N2O emissions will be significant only when soil NO3(-) availability is limiting. Residue incorporation following grassland cultivation can lead to mobilization of large pools of N and potentially to significant N losses via leaching and N2O emissions. This study proposed a mitigation strategy of applying 3,4-dimethylpyrazole phosphate (DMPP

  12. Effect of inoculant on diversity of denitrifying bacteria in composting%添加外源菌剂对堆肥中反硝化菌多样性的影响

    Institute of Scientific and Technical Information of China (English)

    许修宏; 卢欣颖; 姜虎; 李洪涛; 陈会海

    2014-01-01

    一氧化二氮还原酶是堆肥发酵中反硝化菌代表性的酶,可较准确地反映出堆肥中反硝化菌的活动状态及反硝化作用状态。文章采用PCR-DGGE方法研究堆肥中反硝化菌群落的变化,结果表明,添加菌剂的堆肥(堆肥Ⅰ和Ⅱ)中反硝化菌的数量与种类都有所增加(尤其是在堆肥Ⅱ中)。通过对DGGE图谱上的条带进行克隆测序,发现测序条带多为假单胞菌。%Nitrous oxide reductase is the representative of denitrifying bacteria accurately reflecting the state of the organisms and denitrification in compost. In this study, PCR-DGGE was used to study the structure and diversity of nitrous oxide reductase bacteria community in compost. The results showed that the number and species of denitrifying bacteria increased in compost (compost Ⅰ and Ⅱ, especial y in compost Ⅱ) inoculated with exogenous organisms. The cloning and sequencing of the DGGE bands revealed that they were affiliated to Pseudomonas.

  13. Molecular Approaches to Understanding C & N Dynamics in MArine Sediments

    Energy Technology Data Exchange (ETDEWEB)

    Arturo Massol; James Tiedje; Jizhong Zhou; Allan Devol

    2007-05-16

    Continental margin sediments constitute only about 10% of the total sediment surface area in the world’s oceans, nevertheless they are the dominant sites of nitrogen (N) cycling. Recent studies suggest that the oceanic nitrogen budget is unbalanced, primarily due to a higher nitrogen removal rate in contrast to the fixation rate, and it has been suggested that denitrification activity contributes significantly to this imbalance. Although denitrification in marine environments has been studied intensively at the process level, little is known about the species abundance, composition, distribution, and functional differences of the denitrifying population. Understanding the diversity of microbial populations in marine environments, their responses to various environmental factors such as NO3-, and how this impact the rate of denitrification is critical to predict global N dynamics. Environmental Microbiology has the prompt to study the influence of each microbial population on a biogeochemical process within a given ecosystem. Culture-dependent and –independent techniques using nucleic acid probes can access the identity and activity of cultured and uncultured microorganisms. Nucleic acid probes can target distintict genes which set phylogenetic relationships, such as rDNA 16S, DNA gyrase (gyrB) and RNA polymerase sigma 70 factor (rpoD). In the other hand, the genetic capabilities and their expression could be tracked using probes that target several functional genes, such as nirS, nirK, nosZ, and nifH, which are genes involved in denitrification. Selective detection of cells actively expressing functional genes within a community using In Situ Reverse Transcription-PCR (ISRT-PCR) could become a powerful culture-independent technique in microbial ecology. Here we describe an approach to study the expression of nirS genes in denitrifying bacteria. Pure cultures of Pseudomonas stutzeri and Paracoccus denitrificans, as well as co-cultures with non-denitrifying

  14. Myriophyllum aquaticum Constructed Wetland Effectively Removes Nitrogen in Swine Wastewater

    Directory of Open Access Journals (Sweden)

    Haishu Sun

    2017-10-01

    Full Text Available Removal of nitrogen (N is a critical aspect in the functioning of constructed wetlands (CWs, and the N treatment in CWs depends largely on the presence and activity of macrophytes and microorganisms. However, the effects of plants on microorganisms responsible for N removal are poorly understood. In this study, a three-stage surface flow CW was constructed in a pilot-scale within monospecies stands of Myriophyllum aquaticum to treat swine wastewater. Steady-state conditions were achieved throughout the 600-day operating period, and a high (98.3% average ammonia removal efficiency under a N loading rate of 9 kg ha-1 d-1 was observed. To determine whether this high efficiency was associated with the performance of active microbes, the abundance, structure, and interactions of microbial community were compared in the unvegetated and vegetated samples. Real-time quantitative polymerase chain reactions showed the abundances of nitrifying genes (archaeal and bacterial amoA and denitrifying genes (nirS, nirK, and nosZ were increased significantly by M. aquaticum in the sediments, and the strongest effects were observed for the archaeal amoA (218-fold and nirS genes (4620-fold. High-throughput sequencing of microbial 16S rRNA gene amplicons showed that M. aquaticum greatly changed the microbial community, and ammonium oxidizers (Nitrosospira and Nitrososphaera, nitrite-oxidizing bacteria (Nitrospira, and abundant denitrifiers including Rhodoplanes, Bradyrhizobium, and Hyphomicrobium, were enriched significantly in the sediments. The results of a canonical correspondence analysis and Mantle tests indicated that M. aquaticum may shift the sediment microbial community by changing the sediment chemical properties. The enriched nitrifiers and denitrifiers were distributed widely in the vegetated sediments, showing positive ecological associations among themselves and other bacteria based on phylogenetic molecular ecological networks.

  15. Cyclohexane-1,2-dione hydrolase from denitrifying Azoarcus sp. strain 22Lin, a novel member of the thiamine diphosphate enzyme family.

    Science.gov (United States)

    Steinbach, Alma K; Fraas, Sonja; Harder, Jens; Tabbert, Anja; Brinkmann, Henner; Meyer, Axel; Ermler, Ulrich; Kroneck, Peter M H

    2011-12-01

    Alicyclic compounds with hydroxyl groups represent common structures in numerous natural compounds, such as terpenes and steroids. Their degradation by microorganisms in the absence of dioxygen may involve a C-C bond ring cleavage to form an aliphatic intermediate that can be further oxidized. The cyclohexane-1,2-dione hydrolase (CDH) (EC 3.7.1.11) from denitrifying Azoarcus sp. strain 22Lin, grown on cyclohexane-1,2-diol as a sole electron donor and carbon source, is the first thiamine diphosphate (ThDP)-dependent enzyme characterized to date that cleaves a cyclic aliphatic compound. The degradation of cyclohexane-1,2-dione (CDO) to 6-oxohexanoate comprises the cleavage of a C-C bond adjacent to a carbonyl group, a typical feature of reactions catalyzed by ThDP-dependent enzymes. In the subsequent NAD(+)-dependent reaction, 6-oxohexanoate is oxidized to adipate. CDH has been purified to homogeneity by the criteria of gel electrophoresis (a single band at ∼59 kDa; calculated molecular mass, 64.5 kDa); in solution, the enzyme is a homodimer (∼105 kDa; gel filtration). As isolated, CDH contains 0.8 ± 0.05 ThDP, 1.0 ± 0.02 Mg(2+), and 1.0 ± 0.015 flavin adenine dinucleotide (FAD) per monomer as a second organic cofactor, the role of which remains unclear. Strong reductants, Ti(III)-citrate, Na(+)-dithionite, and the photochemical 5-deazaflavin/oxalate system, led to a partial reduction of the FAD chromophore. The cleavage product of CDO, 6-oxohexanoate, was also a substrate; the corresponding cyclic 1,3- and 1,4-diones did not react with CDH, nor did the cis- and trans-cyclohexane diols. The enzymes acetohydroxyacid synthase (AHAS) from Saccharomyces cerevisiae, pyruvate oxidase (POX) from Lactobacillus plantarum, benzoylformate decarboxylase from Pseudomonas putida, and pyruvate decarboxylase from Zymomonas mobilis were identified as the closest relatives of CDH by comparative amino acid sequence analysis, and a ThDP binding motif and a 2-fold Rossmann fold

  16. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  17. Väike Hüüru ja suur Laagri / Liia Nirk

    Index Scriptorium Estoniae

    Nirk, Lia

    2016-01-01

    Laagri keskuses asuva Saue vallaraamatukogu ning Hüüru külaseltsi vahel sõlmiti 2014. a. raamleping, mille alusel vallaraamatukogu maksab külaseltsile raamatukoguteenuse osutamise eest ja raamatukoguhoidjaks on MTÜ palgatud kultuuritöötaja

  18. Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

    Directory of Open Access Journals (Sweden)

    Rachid Caio TCC

    2012-08-01

    Full Text Available Abstract Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane, next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA and denitrifying (nirK genes, greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil

  19. Performance of Denitrifying Bioreactors at Reducing  Agricultural Nitrogen Pollution in a Humid  Subtropical Coastal Plain Climate

    Directory of Open Access Journals (Sweden)

    Timothy Rosen

    2017-02-01

    Full Text Available Denitrifying bioreactors are an agricultural best management practice developed in the  midwestern United States to treat agricultural drainage water enriched with nitrate‐nitrogen (NO3N. The practice is spreading rapidly to agricultural regions with poor water quality due to nutrient  enrichment. This makes it imperative to track bioreactor NO3‐N reduction efficiency as this practice  gets deployed to new regions. This study evaluated the application and performance of denitrifying  bioreactors in the humid subtropical coastal plain environment of the Chesapeake Bay catchment to  provide data about regionally specific NO3‐N reduction efficiencies. NO3‐N samples were taken  before  and  after  treatment  at  three  denitrifying  bioreactors,  in  addition  to  other  nutrients  (orthophosphate‐phosphorus,  PO4‐P;  ammonium‐nitrogen,  NH4‐N;  total  nitrogen,  TN;  total  phosphorus,  TP  and  water  quality  parameters  (dissolved  oxygen,  DO;  oxidation  reduction  potential,  ORP;  pH;  specific  conductance,  SPC.  Total  removal  ranged  drastically  between  bioreactors from 10 to 133 kg N, with removal efficiencies of 9.0% to 62% and N removal rates of  0.21 to 5.36 g N removed per m3 of bioreactor per day. As the first bioreactor study in the humid  subtropical coastal plain, this data provides positive proof of concept that denitrifying bioreactor is  another tool for reducing N loads in agricultural tile drainage in this region.

  20. Performance and influencing factors of halophilic activated sludge in denitrifying of nitrite%嗜盐污泥反硝化亚硝酸盐的性能及其影响因素

    Institute of Scientific and Technical Information of China (English)

    崔有为; 丁洁然; 卢鹏飞; 彭永臻

    2012-01-01

    淡水污泥反硝化高盐废水受到盐度抑制而导致处理的失败.为了突破高盐废水脱氮的技术瓶颈,本研究通过采集人海口河底泥发展嗜盐脱氮生物系统实现了高盐废水的脱氮.本文系统地探讨了盐度、温度、pH和碳源类型等关键影响因素对嗜盐污泥反硝化亚硝酸的影响.试验结果表明:采集人海口底泥发展的嗜盐系统可以以亚硝酸盐作为电子受体进行反硝化.在38 g·L-1盐度下,嗜盐反硝化菌以甲醇作为碳源的最大反硝化速率为3.29 mg N·(g VSS)-1·h-1.系统最适宜盐度为15~51 g· L-1,最佳pH范围为8.0~9.0.反硝化碳源类型影响着反硝化速率.在测试的4种碳源类型中,嗜盐反硝化污泥利用甲醇进行反硝化较快.作为新认知的生物系统,确定高盐废水嗜盐生物处理系统的反硝化特性和影响因素对于实现高盐废水的高效处理具有重要的意义.%It is not successful to denitrify waste-water with high content of salt by freshwater activated sludge because of salinity choking. To overcome this problem, halophilic activated sludge must be developed. In this study, activated sediment at estuary of a river was collected and cultured to get halophilic activated sludge. The effect of key factors, such as salinity, temperature, pH and carbon source etc. , on denitrifying-nitrite performance of the halophilic activated sludge was studied. The results show that nitrite can be denitrified by the halophilic system via utilizing it as electron acceptor. As a result, the halophilic activated sludge is of ability to denitrify highly saline wastewater. At 38 g · L-1 salinity environment,the maximum specific denitrification rate of the biological system is 3. 29 mg N · (g VSS)-1 · h-1. These key operation parameters were optimized for further engineering design; the optimal survival salinity is 15-51 g · L-1 and pH 8. 0-9. 0. Carbon source has a great influence on denitrification rate. Among

  1. Comparison of membrane biofouling of autotrophic nitrifying and heterotrophic denitrifying sludge%自养硝化与异养反硝化污泥膜污染特性的对比

    Institute of Scientific and Technical Information of China (English)

    王朝朝; 李军

    2013-01-01

    Batch filtration tests were carried out to investigate the membrane biofouling characterizations of nitrifying and denitrifying sludge from a continuous-flow nitrogen and phosphorus removal bench-scale membrane bioreactor under the stable operation.Biofouling mechanisms of denitrifying sludge by using different electron donors were also analyzed and discussed.The test results show that the denitrifying rate by using the acetic acid as the electron donor is 13.8 mg/(g·h),higher than methanol 3.4 mg/(g·h),ethanol 10.2 mg/(g·h) at 25 C; compared with nitrifying sludge,the protein of soluble microbial products from denitrifying sludges increases in the range of < 1 kDa and > 100 kDa,being the main factor for the increased resistance of soluble substances in the mixed liquor,thereby increasing the pore blocking resistance of soluble substances,and denitrification process by using the methanol as the electron donor is the most obvious.It is also found that the decrease of extracellular polymeric substances produced through denitrification processes and relative hydrophobicity of carbohydrate and protein substances becomes the main factor for the decreased resistance of SS fraction in the mixed liquor; the relative molecular mass distributions of extracellular polymericsubstances becomes slightly different after denitrification,but Fourier transform infrared spectroscopy of the functional groups of extracellular polymeric substances shows that the chemical composition of extracellular polymeric substances produced by nitrifying sludge and denitrifying sludge by using three different electron donors have not changed.The modified fouling index of denitrifying sludge by using acetic as the electron donor becomes the lowest one.%以同步脱氮除磷连续流膜生物反应器小试稳定运行时的污泥为考查对象,采用序批式过滤试验对比考查硝化污泥与反硝化污泥的污染特性,并对不同电子供体下反硝化污泥

  2. Isolation of Denitrifying Bacteria in Sea Sediment and Simulated Experiment of Removing Nitrate-N from Seawater%海洋沉积物中反硝化细菌的分离及去除硝酸盐氮的模拟试验

    Institute of Scientific and Technical Information of China (English)

    全为民; 沈新强; 甘居利; 沈晓盛; 陈亚瞿

    2006-01-01

    从长江口沉积物中筛选分离出了海洋反硝化细菌,模拟了该细菌对不同浓度水平硝酸盐氮的去除效率.研究结果表明,分离出的海洋反硝化细菌能有效去除海水中硝酸盐氮,在硝酸盐氮的初始浓度为1 mg/L,l d内硝酸盐氮去除率就达到了70%;在100 mg/L硝酸盐氮模拟试验中,约在一周内能将90%硝酸盐氮去除.试验证明反硝化细菌的生长与水体中硝酸盐氮浓度有一定的相关关系,一旦生物修复过程完成,反硝化细菌就会大量死亡,水体重新恢复到清澈透明状况.%The objective of this research was to isolate denitrifying bacteria from sea sediment and simulate the removal efficiency of nitrate-N by denitrifying bacteria from seawater. The result showed that the isolated denitrifying bacteria could effectively remove nitrate-N from seawater. About 90 % of nitrate-N was removed by denitrifying bacteria from seawater within a week in the simulated experiment I (the initial concentration of nitrate-N was 100 mg/L). The removal efficiency of nitrate-N reached about 70 % within one day in the simulated experiment Ⅱ (initial concentration of nitrate-N was 1 mg/L). The final removal efficiency was about 98 % and 85 % in the simulated experiments Ⅰ and Ⅱ, respectively. It was found that there was positive correlation between the concentration of nitrate-N and the number of denitrifying bacteria in seawater. Lots of denitrifying bacteria would disappear and the seawater would become transparent once the process of bioremediation was completed.

  3. Biogas-based denitrification in a biotrickling filter: Influence of nitrate concentration and hydrogen sulfide.

    Science.gov (United States)

    López, Juan C; Porca, Estefanía; Collins, Gavin; Pérez, Rebeca; Rodríguez-Alija, Alberto; Muñoz, Raúl; Quijano, Guillermo

    2017-03-01

    The feasibility of NO3(-) removal by the synergistic action of a prevailing denitrifying anoxic methane oxidising (DAMO), and nitrate-reducing and sulfide-oxidising bacterial (NR-SOB) consortium, using CH4 and H2 S from biogas as electron donors in a biotrickling filter was investigated. The influence of NO3(-) concentration on N2 O production during this process was also evaluated. The results showed that NO3(-) was removed at rates up to 2.8 g mreactor(-3)  h(-1) using CH4 as electron donor. N2 O production rates correlated with NO3(-) concentration in the liquid phase, with a 10-fold increase in N2 O production as NO3(-) concentration increased from 50 to 200 g m(-3) . The use of H2 S as co-electron donor resulted in a 13-fold increase in NO3(-) removal rates (∼18 gNO3(-)  m(-3)  h(-1) ) and complete denitrification under steady-state conditions, which was supported by higher abundances of narG, nirK, and nosZ denitrifying genes. Although the relative abundance of the DAMO population in the consortium was reduced from 60% to 13% after H2 S addition, CH4 removals were not compromised and H2 S removal efficiencies of 100% were achieved. This study confirmed (i) the feasibility of co-oxidising CH4 and H2 S with denitrification, as well as (ii) the critical need to control NO3(-) concentration to minimize N2 O production by anoxic denitrifiers. Biotechnol. Bioeng. 2017;114: 665-673. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. Effects of Wheat and Faba Bean Intercropping on Microorganism Involved in Nitrogen Transformation in the Rhizosphere Soils

    Directory of Open Access Journals (Sweden)

    TANG Yan-fen

    2016-09-01

    Full Text Available Soil microorganism is one of the key factors that affects soil ecological activity. It is an important symbol of soil health, and the soil nitrogen cycle is closely related to the microorganisms. The relationship between nitrogen and microorganisms under the intercropping is im-portant for the farmland ecosystem. In this paper, phospholipid fatty acids(PLFA analysis was used to determine soil microbial communi-ties, e.g., biomasses of anaerobic bacteria, aerobic bacteria, bacteria, fungi and actinobacteria. The abundance of nitrifying genes(AOB, AOA and three denitrifying genes (nirK, norB, nosZ were measured using real-time quantitative polymerase chain reaction. The enzymes, nitrate and ammonium concentrations were measured using conventional methods. The results showed that along with the growth period, the TPLFAs(total phospholipid fatty acids increased and the bacterias, fungus, actinomyces and aerobic bacterias significantly(P<0.05 dif-fered between intercropping and monoculture. The greater abundance of AOB than AOA and the variation range of 105~106 were observed in all samples. The gene copies of norB and nosZ were pronounced by intercropping in the rhizosphere of faba bean at elongation and heading stages, respectively. The abundance of nirK remarkably(P<0.05differed between intercropping and monoculture. In intercropping rhizo-sphere, the contents of NO3--N were lower than monoculture, while the NH4+-N contents were converse (P<0.05. Conclusively, wheat and fa-ba bean intercropping system could change rhizosphere microenvironment, and then the microbial community structure in the soils, which would facilitate the conservation and supplying of soil nitrogen and reduce the nitrogen loss and pollution under the intercropping conditions to some extent. This might be the nitrogen nutrition mechanism for the overyielding of wheat and faba bean intercropping system.

  5. Ação do imazapic+imazapyr sobre a tiririca (Cyperus rotundus e os desnitrificadores em milho Action of imazapic+imazapyr on purple nutsedge (Cyperus rotundus and denitrifying bacteria in corn

    Directory of Open Access Journals (Sweden)

    A.V. Ulbrich

    2004-12-01

    Full Text Available Os objetivos do experimento foram avaliar a eficácia do imazapic+imazapyr sobre a tiririca e a influência desta planta daninha sobre a população de desnitrificadores em solo cultivado com milho. O experimento foi realizado em caixas de 0,70 x 0,30 x 0,30 m, onde foram semeados o milho tolerante às imidazolinonas (C-901CL e plantados 50 bulbos de tiririca. O delineamento experimental foi o inteiramente casualizado, com seis repetições. Os tratamentos foram constituídos por: 1. milho sem tiririca; 2. milho com tiririca; 3. milho com tiririca capinada; 4. milho com tiririca e imazapic+imazapyr (63+21g ha-1 de i.a. em pós-emergência; e 5. milho com tiririca e imazapic+imazapyr (63+21g ha-1 de i.a. em pré-emergência. O herbicida foi eficiente em pós-emergência, diminuindo as manifestações epígeas da tiririca em 41% e proporcionando controle visual de 88% aos 21 dias após a aplicação. Os desnitrificadores do solo aumentaram em seis e dez vezes aos 24 e 54 dias após a semeadura do milho, respectivamente, com a presença de tiririca. A aplicação do herbicida em pós-emergência reduziu a população de desnitrificadores para 1,91x10(5 NMP (número mais provável, 89% menor que a testemunha capinada (16,78x10(5 NMP.The objective of this work was to evaluate the efficacy of imazapic+imazapyr in controling purple nutsedge and its effect on the population of denitrifying bacteria in soil cultivated with corn. The trial was set up in 0.70 x 0.30 x 0.30 m boxes where imidazolinone tolerant corn (C901CL was seeded together with 50 purple nutsedge bulbs. The experimental design was randomized with six replications. The treatments were: 1 corn without nutsedge; 2 corn with nutsedge; 3 corn with cut nutsedge; 4 corn with nutsedge treated with imazapic+imazapyr (63+21 g ha-1 i.a applied in post-emergence and 5 corn with nutsedge treated with imazapic+imazapyr (63+21 g ha-1 i.a, applied in pre-emergence. The herbicide was efficient when

  6. Functional genes reveal the intrinsic PAH biodegradation potential in creosote-contaminated groundwater following in situ biostimulation.

    Science.gov (United States)

    Nyyssönen, Mari; Kapanen, Anu; Piskonen, Reetta; Lukkari, Tuomas; Itävaara, Merja

    2009-08-01

    A small-scale functional gene array containing 15 functional gene probes targeting aliphatic and aromatic hydrocarbon biodegradation pathways was used to investigate the effect of a pilot-scale air sparging and nutrient infiltration treatment on hydrocarbon biodegradation in creosote-contaminated groundwater. Genes involved in the different phases of polycyclic aromatic hydrocarbon (PAH) biodegradation were detected with the functional gene array in the contaminant plume, thus indicating the presence of intrinsic biodegradation potential. However, the low aerobic fluorescein diacetate hydrolysis, the polymerase chain reaction (PCR) amplification of 16S rRNA genes closely similar to sulphate-reducing and denitrifying bacteria and the negligible decrease in contaminant concentrations showed that aerobic PAH biodegradation was limited in the anoxic groundwater. Increased abundance of PAH biodegradation genes was detected by functional gene array in the monitoring well located at the rear end of the biostimulated area, which indicated that air sparging and nutrient infiltration enhanced the intrinsic, aerobic PAH biodegradation. Furthermore, ten times higher naphthalene dioxygenase gene copy numbers were detected by real-time PCR in the biostimulated area, which was in good agreement with the functional gene array data. As a result, functional gene array analysis was demonstrated to provide a potential tool for evaluating the efficiency of the bioremediation treatment for enhancing hydrocarbon biodegradation in field-scale applications.

  7. A2/O工艺强化反硝化除磷控制策略研究%STUDY ON THE STRATEGIES OF ENHANCING DENITRIFYING PHOSPHORUS REMOVAL IN THE ANAEROBIC-ANOXIC-OXIC PROCESS

    Institute of Scientific and Technical Information of China (English)

    姚晓园

    2012-01-01

    Based on the conventional anaerobic-anoxic-oxic process, the nutrient removal ability of AVO process treating low C/N domestic sewage was improved by installing the pre-anoxic zone (forming the pre-anoxic/anaerobic/anoxic/aerobic process), adding the external carbon sources. The results showed that, these strategies enhanced the AVO reactor removal efficiency of COD, TN and TP, the removal rates of COD, TN and TP reached 92% -98% and 85% respectively. The system showed an obvious denitrifying phosphorus removal phenomenon, the phosphorus removal proportion by the anoxic zone reached up to 17.18% of the total phosphorus removal. The occurrence of denitrifying phosphorus removal decreased the affect of the carbon sources to the AVO process nutrient removal ability, raising the carbon utilizing efficiency. This paper offered an experience to the waste water treatment plant treating low C/N domestic sewage with the A2/O process.%在传统A2/O工艺的基础上,通过设立预缺氧区(即建立A-A2/O工艺)、外加碳源等手段,强化A2/O工艺处理低C/N生活污水的脱氮除磷能力.试验结果表明,经过强化后的A2/O反应器对COD、TN及TP去除效果良好,COD、TN及TP的去除率分别为92%、98%、85%.系统表现出明显的反硝化除磷现象,缺氧区除磷量占总除磷量的17.18%.反硝化除磷现象的产生降低了碳源缺乏对A2/O工艺脱氮除磷性能的影响,提高碳源的利用效率.为采用A2/O工艺处理低C/N生活污水的污水处理厂提供理论依据.

  8. 反硝化芽孢杆菌的筛选鉴定及反硝化特性%Screening and identification of denitrifying bacillus strain and its denitrification characteristics

    Institute of Scientific and Technical Information of China (English)

    郑喜春; 郭晓军; 姚娜; 曹晓璐; 李潞滨; 朱宝成

    2012-01-01

    采用加热富集及硝酸盐还原产气试验和反硝化活力定量分析,从乌梁素海的底泥中筛选出了一株具有高效反硝化性能的芽孢杆菌,命名为TGR30.通过形态观察、生理生化试验及16S rDNA序列同源性分析,将其鉴定为巨大芽孢杆菌(Bacillus megaterium).通过单因素试验明确了碳源、碳氮比、盐浓度、pH以及溶解氧与反硝化特性的关系.结果表明,该菌在盐度为6%或pH 12时都具有较高的反硝化活性;以可溶性淀粉为唯一碳源、C/N为14、pH 8.0、DO为4 mg·L-1时脱氮效果最佳,脱氮率为92%.%By the methods of heating accumulation, nitrate-reduction gas production, and quantitative analysis of denitrification, a bacillus strain with high-efficient denitrifying capability named as TGR30 was isolated from the sediment of Wuliangsuhai Lake. The isolate was identified as Bacillus megaterium, based on its morphological feature, biochemical characteristics, and 16S rDNA sequence analysis. Single factor experiment was conducted to investigate the influences of medium carbon, C/N, salinity, pH, and dissolved oxygen on the denitrifying characteristics of the strain. When the medium salinity was 6% or the pH value was 12, the strain still had high nitrogen removal capability, and the optimal conditions for the nitrogen removal were the medium C/N ratio 14, pH value 8.0, and dissolved oxygen concentration 4 mg · L-1 when soluble starch was used as the sole carbon source.

  9. Culture and Phosphorus Removal Property of Granular Sludge for Denitrifying Phosphorus Removal%反硝化除磷颗粒污泥的培养与除磷性能

    Institute of Scientific and Technical Information of China (English)

    李军; 张宇坤; 韦甦; 王亚宜; 马骁; 彭永臻

    2012-01-01

    The granular sludge for denitrifying phosphorus removal is successfully formed in a sequencing batch reactor (SBR) fed with synthetic wastewater, by controlling the operational modes of anaerobic/ anoxic/aerobic, anoxie addition of the nitrate, and selection pressure. The granular sludge turns into ashape with a diameter of 0.3 to 0.5 mm, and sludge volume index (SVI) and mixed solid (MLSS) are maintained at 45 mL/g and 4 000 rag/L, respectively, during the The granular sludge for the denitrifying phosphorus removal also shows a good nutrient re steady moval suspended operation. capability,with the COD, ammonia nitrogen and phosphorus removal effieiencies of 88%, 96% and 90%, respectively. The fate of phosphorus and the X-ray diffraction test results suggest the existence of granular sludge phosphate precipitation phosphorus removal phenomena. Granular sludge for the denitrifyingphosphorus removal in the experiment uses biological phosphorus removal, and it also has phosphorus removal through phosphate precipitation in granular sludge.%摘要:以普通絮状污泥为接种污泥,人工配制生活污水,采用厌氧/缺氧/好氧的运行方式,通过在缺氧段投加硝酸盐氮和控制选择压,经98d的培养与调整在SBR中获得具有反硝化除磷功能的颗粒污泥.稳定运行的颗粒污泥粒径主要在0.3-0.5mm,SVI约为45mL/g,p(MLSS)约为4000mg/L.具有反硝化除磷功能的颗粒污泥对COD、氨氮和磷酸盐的去除率分别可达88%、96%和90%.通过分析磷的去向及X射线衍射检测结果可知存在颗粒污泥的磷酸盐沉淀除磷现象.培养的反硝化除磷颗粒污泥除生物除磷外,还具有磷酸盐固化于污泥颗粒方式除磷。

  10. ISOLATION, IDENTIFICATION OF AN AEROBIC DENITRIFIER AND ITS EFFECT OF NITROGEN REMOVAL%一株好氧反硝化细菌的筛选鉴定及其脱氮效果

    Institute of Scientific and Technical Information of China (English)

    贺根和; 梁亮亮; 尹丽; 肖小雨

    2014-01-01

    An aerobic denitrifying bacteria was isolated from the sludge of municipal waste water treatment plant by enrichment and denitrification potential test, and identified through 16S rDNA sequence analysis. Then it was inoculated into simulation of eutrophication system, aiming to enhance the denitrification capacity. The strain was identified as Klebsiella sp. and designated HLNR05. It could remove 96.6% or 92.1% of the nitrate nitrogen and the total nitrogen at 24 h, respectively. Moreover, the nitrogen which was removed from the inoculation system is higher than assimilated into the cell. In addition, it could remove 91.4% and 88.2% of the nitrate nitrogen and the total nitrogen in the simulated eutrophic wastewater system at 24 h, respectively. It can be concluded that the aerobic denitrifier has a strong ability of aerobic denitrification.%经过富集培养和反硝化能力测定,从城市污水处理厂活性污泥中筛选得到1株好氧反硝化细菌。通过16S rDNA 同源性分析对该菌进行分子鉴定,并将菌接种到模拟富营养化水体中以探究其对系统中硝态氮和总氮的去除能力。结果表明,该菌属于Klebsiella sp.,命名为 HLNR05。菌株HLNR05在24 h内NO3--N的去除率达96.6%, TN去除率达92.1%,而且其从培养体系中完全去除的氮明显多于同化到细胞的氮。利用HLNR05处理模拟富营养化废水,结果发现其在24 h内对模拟废水中的NO3--N和TN去除率达91.4%和88.2%。表明菌株HLNR05具有较强的好氧反硝化能力。

  11. Draft Genome Sequence of Pseudomonas hussainii Strain MB3, a Denitrifying Aerobic Bacterium Isolated from the Rhizospheric Region of Mangrove Trees in the Andaman Islands, India.

    Science.gov (United States)

    Jaiswal, Shubham K; Saxena, Rituja; Mittal, Parul; Gupta, Ankit; Sharma, Vineet K

    2017-02-02

    The genome sequence of Pseudomonas hussainii MB3, isolated from the rhizospheric region of mangroves in the Andaman Islands, is comprised of 3,644,788 bp and 3,159 protein coding genes. Draft genome analysis indicates that MB3 is an aerobic bacterium capable of performing assimilatory sulfate reduction, dissimilatory nitrate reduction, and denitrification.

  12. Assessment of Anaerobic Toluene Biodegradation Activity by bssA Transcript/Gene Ratios

    Science.gov (United States)

    Brow, Christina N.; O'Brien Johnson, Reid; Johnson, Richard L.

    2013-01-01

    Benzylsuccinate synthase (bssA) genes associated with toluene degradation were profiled across a groundwater contaminant plume under nitrate-reducing conditions and were detected in significant numbers throughout the plume. However, differences between groundwater and core sediment samples suggested that microbial transport, rather than local activity, was the underlying cause of the high copy numbers within the downgradient plume. Both gene transcript and reactant concentrations were consistent with this hypothesis. Expression of bssA genes from denitrifying toluene degraders was induced by toluene but only in the presence of nitrate, and transcript abundance dropped rapidly following the removal of either toluene or nitrate. The drop in bssA transcripts following the removal of toluene could be described by an exponential decay function with a half-life on the order of 1 h. Interestingly, bssA transcripts never disappeared completely but were always detected at some level if either inducer was present. Therefore, the detection of transcripts alone may not be sufficient evidence for contaminant degradation. To avoid mistakenly associating basal-level gene expression with actively degrading microbial populations, an integrated approach using the ratio of functional gene transcripts to gene copies is recommended. This approach minimizes the impact of microbial transport on activity assessment and allows reliable assessments of microbial activity to be obtained from water samples. PMID:23811506

  13. Rates of N2 production and diversity and abundance of functional genes associated with denitrification and anaerobic ammonium oxidation in the sediment of the Amundsen Sea Polynya, Antarctica

    Science.gov (United States)

    Choi, Ayeon; Cho, Hyeyoun; Kim, Sung-Han; Thamdrup, Bo; Lee, SangHoon; Hyun, Jung-Ho

    2016-01-01

    A combination of molecular microbiological analyses and metabolic rate measurements was conducted to elucidate the diversity and abundance of denitrifying and anaerobic ammonium oxidation (anammox) bacteria and the nitrogen gas (N2) production rates in sediment underlying the highly productive polynya (Stns. 10 and 17) and the sea-ice zone on the outer shelf (Stn. 83) of the Amundsen Sea, Antarctica. Despite the high water column productivity, the N2 production rates by denitrification (0.04-0.31 nmol N cm-3sed. h-1) and anammox (0.13-0.26 nmol N cm-3 sed. h-1) were lower than those measured in other polar regions. In contrast, gene copy number (106-107 copies cm-3 of nirS and nosZ genes targeting denitirifiers and 105-107 copies cm-3 of 16S rRNA genes related to anammox bacteria) of the two bacterial groups at Stn. 17 was similar compared to those of other organic-rich environments. The majority of the nirS sequences were affiliated with Gammaproteobacteria (54% and 61% of the total nirS gene at Stns. 17 and 83, respectively), which were closely related to Pseudomonas aeruginosa. Most nosZ sequences (92% and 72% of the total nosZ genes at Stns. 17 and 83, respectively) were related to the Alphaproteobacteria, which were closely related to Ruegeria pomeroyi and Roseobacter denitrificans. Most (98%) of the sequences related to anammox bacteria were affiliated with Candidatus Scalindua at Stn. 17. Consequently, despite the low metabolic activity, the abundance and composition of most denitrifying and anammox bacteria detected from the ASP were similar to those reported from a variety of marine environments. Our results further imply that increased labile organic matter production resulting from a shift of the phytoplankton community from Phaeocystis to diatoms in response to rapid melting of sea ice stimulates metabolic activities of the denitrifying and anammox bacteria, thereby enhancing the N removal process in the ASP.

  14. Studying Genes

    Science.gov (United States)

    ... NIGMS NIGMS Home > Science Education > Studying Genes Studying Genes Tagline (Optional) Middle/Main Content Area Other Fact Sheets What are genes? Genes are segments of DNA that contain instructions ...

  15. Nitrate removal in shallow, open-water treatment wetlands.

    Science.gov (United States)

    Jasper, Justin T; Jones, Zackary L; Sharp, Jonathan O; Sedlak, David L

    2014-10-07

    The diffuse biomat formed on the bottom of shallow, open-water unit process wetland cells contains suboxic zones that provide conditions conducive to NO3(-) removal via microbial denitrification, as well as anaerobic ammonium oxidation (anammox). To assess these processes, nitrogen cycling was evaluated over a 3-year period in a pilot-scale wetland cell receiving nitrified municipal wastewater effluent. NO3(-) removal varied seasonally, with approximately two-thirds of the NO3(-) entering the cell removed on an annual basis. Microcosm studies indicated that NO3(-) removal was mainly attributable to denitrification within the diffuse biomat (i.e., 80 ± 20%), with accretion of assimilated nitrogen accounting for less than 3% of the NO3(-) removed. The importance of denitrification to NO3(-) removal was supported by the presence of denitrifying genes (nirS and nirK) within the biomat. While modest when compared to the presence of denitrifying genes, a higher abundance of the anammox-specific gene hydrazine synthase (hzs) at the biomat bottom than at the biomat surface, the simultaneous presence of NH4(+) and NO3(-) within the biomat, and NH4(+) removal coupled to NO2(-) and NO3(-) removal in microcosm studies, suggested that anammox may have been responsible for some NO3(-) removal, following reduction of NO3(-) to NO2(-) within the biomat. The annual temperature-corrected areal first-order NO3(-) removal rate (k20 = 59.4 ± 6.2 m yr(-1)) was higher than values reported for more than 75% of vegetated wetlands that treated water in which NO3(-) was the primary nitrogen species (e.g., nitrified secondary wastewater effluent and agricultural runoff). The inclusion of open-water cells, originally designed for the removal of trace organic contaminants and pathogens, in unit-process wetlands may enhance NO3(-) removal as compared to existing vegetated wetland systems.

  16. Screening and Identification of an Achromobacter Strain for Both Arsenic Oxidizing and Denitrifying Abilities%一株具砷氧化和反硝化功能的无色杆菌的筛选和鉴定

    Institute of Scientific and Technical Information of China (English)

    曾琳; 朱琼芳; 卢贯能; 陈来琳; 匡庐峰; 柯林

    2011-01-01

    利用含As(3+)肉汤培养基,从广西河池砷污染地区水样和沉积物样中通过多次分离、纯化获取砷耐受菌.进一步从砷耐受菌中筛选出在好氧条件下可以同时进行砷氧化和反硝化的多功能菌株cll-35.对该菌株进行形态观察,并利用16SrDNA序列分析方法进行鉴定,发现该菌株为革兰氏阴性菌,与Achromobacter denitrificans strain 22426和Achromobacter xylosoxidans strain C8B的同源性均达99%;该菌株在NO(3)-和As(3+)同时存在的条件下好氧反硝化能力和砷氧化速率均得到提高;在只含NO(3)-的条件下,NO(3)-的去除率为53.65%,而在As(3+)和NO(3)-同时存在的条件下,NO(3)-的去除率为75.27%.在不含NO(3)-和含NO(3)-的条件下,As(3+)的转化率都在99%以上,而在含NONO(3)-的条件下,As(3+)的氧化速率更快.这种相互促进可能与反硝化过程中的电子传递和砷氧化过程中的动态平衡有关.%Water and sediment samples were taken from an arsenic-contaminated region in Hechi, Cuangxi Province. Arsenite-resisting strains were isolated and purified several times from broth medium containing As3+. Cll-35, the arsenite-oxidizer and aerobic denitrifier was further screened from arsenite-resisting strains. Morphological studies and 16S rDNA sequencing revealed that the isolate was Gram negative, and had 99% homogeneity to Achromobacter denitrificans strain 22426 and Achromobacter xylosoxidans strain C8B. The aerobic denitrifying and arsenite-oxidizing ability of this strain was enhanced when arsenite and nitrate were present together. The removal rate of nitrate was 53. 65% when only nitrate was present, while the removal rate increased to 75. 27% when both arsenite and nitrate were present. The conversion rate of As3+ was above 99% with and without nitrate, and the oxidation rate was enhanced by the presence of nitrate. This phenomenon may be related to the electron transmission process of aerobic denitrification and the dynamic balance

  17. Stress of Cl-, SO42- and PO43- on the heterotrophic denitrifying sludge%Cl-、SO42-和PO43-对异养反硝化污泥的胁迫效应

    Institute of Scientific and Technical Information of China (English)

    王茹; 郑平; 杨程; 许少怡; 戴陈琳; AbbasGhulam

    2016-01-01

    As the functional part of denitrification, denitrifier was obviously stressed by anions. To investigate the effects and the mechanism of anions on heterotrophic denitrifying sludge (HDS) are of great significance for the practical application of high-rate denitrification in saline nitrogen-rich wastewater treatments. Nitrate reductase and alkaline phosphatase were chosen as the indices to determine the effects of Cl-, SO42- and PO43- on the enzyme activities in HDS, while the ratios of live/dead cells and cellular morphology were examined and observed to characterise the effects of Cl-, SO42- and PO43- on the cell structures in HDS. Results showed that, the IC50values of Cl-, SO42- and PO43- for nitrate reductase were 0.15, 0.12 and 0.05mol/L respectively, while the IC50values of Cl-, SO42- and PO43- for alkaline phosphatase were 1.14, 0.75 and 0.49mol/L, respectively. Anions with high concentrations (1.71mol/L Cl-, 0.85mol/L SO42-, 0.57mol/L PO43-) resulted in the damage of cell membranes, and caused the leakage of cell inclusion. In conclusion, the effects of anions on HDS were attributed to the osmotic stresses which affected the enzyme activities, and the ion stresses which caused the damage of cell membranes.%反硝化菌是反硝化作用的驱动者,探明Cl-、SO42-和PO43-对异养反硝化污泥(HDS)的胁迫效应,有助于含盐废水生物脱氮技术的研发和优化.选用硝酸盐还原酶(周质酶)和碱性磷酸酯酶(胞内酶)作为指标,考察了不同Cl-、SO42-和PO43-浓度对HDS酶活的影响;通过观测HDS中的活菌水平和细胞形态,考察了不同Cl-、SO42-和PO43-浓度对HDS微生物细胞结构的影响.结果表明,Cl-、SO42-和PO43-对HDS硝酸盐还原酶的半抑制浓度分别为0.15、0.12和0.05mol/L,对碱性磷酸酯酶的半抑制浓度为1.14、0.75和0.49mol/L;高浓度Cl-、SO42-和PO43-导致HDS微生物细胞膜结构破损,通透性增加,细胞物质外泄.阴离子对HDS的胁迫可分为渗透胁迫和

  18. PARALLEL A2O/MBR OF DENITRIFYING PHOSPHORUS REMOVAL PROCESS%并联式A2O/MBR反硝化聚磷工艺试验研究

    Institute of Scientific and Technical Information of China (English)

    张明虎; 王亮; 张宏伟; 马术岭; 吴晓娜

    2012-01-01

    基于反硝化聚磷理论,结合MBR工艺的优点,在传统A2O工艺的基础上提出新型并联式同步脱氮除磷工艺.工艺解决了传统工艺中的碳源不足、硝酸盐氮供需矛盾等问题;通过省去沉淀池,节约了占地面积.针对常规城市污水,研究了不同工艺条件对处理效果的影响.结果表明,当污泥体积回流比为50%,内体积回流比为100%时具有较好的去除效果,COD、NH4+-N、TP和TN去除率分别达到了90%、99%、94.4%和67%.%This paper describes the theory of denitrifying phosphorus, combining with the advantages of MBR technology, I proposed a new parallel synchronization nitrogen and phosphorus removal process which based on the traditional A*O process. It resolved the problem of insufficient carbon source and the contradictions of nitrate supply and demand in the traditional process. By eliminating the settling tank, small footprint were needed. For conventional municipal sewage, it studied the effects of treatment efficiency in different process condition. The experimental results showed that when the sludge return ratio was 50%, the reflux ratio was 100%, this process achieved a good nitrogen and phosphorus removal efficiency: COD, ammonia nitrogen, TP and TN removal rates reached 90%, 99%, 94.4% and 67%, respectively.

  19. 同位素质谱法对土壤反硝化酶活性的测定研究%Mass Spectrometery Assay for Denitrifying Enzyme Activity Measurement

    Institute of Scientific and Technical Information of China (English)

    张丽莉; 武志杰; 宋玉超

    2010-01-01

    在评价硝化抑制剂的作用效果时,需要确认此硝化抑制剂对反硝化过程有无影响.而对此过程的确认是通过反硝化酶活性(denitrifying enzyme activity,简写为DEA)的测定来实现的.采用加入同位素标记底物结合同位素质谱仪来测定新型硝化抑制剂3,4-二甲基吡唑磷酸盐作用下的反硝化酶活性.结果表明,此新型方法能够较准确的测定培养体系中的N2O的浓度,与气相色谱法的测定结果具有良好的相关性(MSN2O=0.45+1.03GCN2O,R2=0.995).通过测定15N2O和15N2的丰度能够较好的区分2种反硝化酶活性(硝酸还原酶和N2O还原酶),且克服了传统测定中需要加入乙炔作为酶抑制剂的弊端.对DMPP作用下土壤反硝化酶的测定表明,DMPP对反硝化酶无显著影响,说明DMPP在使用中不会影响土壤中的反硝化过程.

  20. Immunoglobulin genes

    Energy Technology Data Exchange (ETDEWEB)

    Honjo, T. (Kyoto Univ. (Japan)); Alt, F.W. (Columbia Univ., Dobbs Ferry, NY (USA). Hudson Labs.); Rabbitts, T.H. (Medical Research Council, Cambridge (UK))

    1989-01-01

    This book reports on the structure, function, and expression of the genes encoding antibodies in normal and neoplastic cells. Topics covered are: B Cells; Organization and rearrangement of immunoglobin genes; Immunoglobin genes in disease; Immunoglobin gene expression; and Immunoglobin-related genes.

  1. Subsurface Nitrogen-Cycling Microbial Communities at Uranium Contaminated Sites in the Colorado River Basin

    Science.gov (United States)

    Cardarelli, E.; Bargar, J.; Williams, K. H.; Dam, W. L.; Francis, C.

    2015-12-01

    Throughout the Colorado River Basin (CRB), uranium (U) persists as a relic contaminant of former ore processing activities. Elevated solid-phase U levels exist in fine-grained, naturally-reduced zone (NRZ) sediments intermittently found within the subsurface floodplain alluvium of the following Department of Energy-Legacy Management sites: Rifle, CO; Naturita, CO; and Grand Junction, CO. Coupled with groundwater fluctuations that alter the subsurface redox conditions, previous evidence from Rifle, CO suggests this resupply of U may be controlled by microbially-produced nitrite and nitrate. Nitrification, the two-step process of archaeal and bacterial ammonia-oxidation followed by bacterial nitrite oxidation, generates nitrate under oxic conditions. Our hypothesis is that when elevated groundwater levels recede and the subsurface system becomes anoxic, the nitrate diffuses into the reduced interiors of the NRZ and stimulates denitrification, the stepwise anaerobic reduction of nitrate/nitrite to dinitrogen gas. Denitrification may then be coupled to the oxidation of sediment-bound U(IV) forming mobile U(VI), allowing it to resupply U into local groundwater supplies. A key step in substantiating this hypothesis is to demonstrate the presence of nitrogen-cycling organisms in U-contaminated, NRZ sediments from the upper CRB. Here we investigate how the diversity and abundances of nitrifying and denitrifying microbial populations change throughout the NRZs of the subsurface by using functional gene markers for ammonia-oxidation (amoA, encoding the α-subunit of ammonia monooxygenase) and denitrification (nirK, nirS, encoding nitrite reductase). Microbial diversity has been assessed via clone libraries, while abundances have been determined through quantitative polymerase chain reaction (qPCR), elucidating how relative numbers of nitrifiers (amoA) and denitrifiers (nirK, nirS) vary with depth, vary with location, and relate to uranium release within NRZs in sediment

  2. Phylogenetic and functional potential links pH and N2O emissions in pasture soils

    Science.gov (United States)

    Samad, M. D. Sainur; Biswas, Ambarish; Bakken, Lars R.; Clough, Timothy J.; de Klein, Cecile A. M.; Richards, Karl G.; Lanigan, Gary J.; Morales, Sergio E.

    2016-10-01

    Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2.

  3. 象山港海域硝化细菌与反硝化细菌的时空分布特征及其与环境因子的关系%Spatiotemporal distribution of nitrifying and denitrifying bacteria with related to environmental factors in Xiangshan Bay

    Institute of Scientific and Technical Information of China (English)

    王海丽; 杨季芳; 陈吉刚; 石刚德; 冯辉强

    2011-01-01

    分别于2007年的7月(夏季)、11月(秋季)与2008年的1月(冬季)、4月(春季)采用高保真、无扰动重力柱状取样器替代常规抓斗式采样,研究了象山港海域表层海水、上覆水及沉积物中N素转化细菌(硝化细菌与反硝化细菌)丰度的时空分布特征,并采用主成分分析及多元逐步回归分析方法研究了影响该海域N素转化细菌时空分布的主要因素.调查期间,象山港海域水样和沉积物样品中N素转化细菌数量的变化范围分别为30×104~2.4×104 cells·ml-1和30×104~2.4×104 cells·g-1.表层海水、上覆水和沉积物中的硝化细菌数量均值分别2.24×103cells·ml-1、3.61×103 cells·ml-1和6.45×103 cells·g-1,表层海水、上覆水和沉积物中的反硝化细菌数量均值分别为4.84×103 cells·ml-1、5.31×103 cells·ml-1和3.12×103 cells·g-1.表层海水和上覆水硝化细菌数量均值冬季明显高于其他季节,而沉积物中硝化细菌数量均值为秋季、冬季高于其他季节;冬季、春季的反硝化细菌数量高于秋季、夏季.调查期间,象山港海域的硝化细菌及反硝化细菌的空间分布特征明显:垂直分布特征,反硝化细菌表现为表层海水高于上覆水及沉积物,而硝化细菌则表现为沉积物及上覆水高于表层海水;平面分布特征,象山港中部及支港与主港交汇处的站点N素转化细菌数量较高,近岸工农业活动造成的陆源污染及海水增养殖活动造成的养殖污染是造成此空间分布特征的主要因为.多元统计分析表明,N、P营养盐、DO、水温、盐度、有机质污染及初级生产力等是影响象山港海域N素转化细菌分布的主要因素.%In July ( summer) and October ( autumn) 2007 and in January ( winter) and April ( spring) 2008, an investigation was made on the spatiotemporal distribution of nitrifying and denitrifying bacteria in the surface seawater, overlying water, and sediment in Xiangshan Bay

  4. 异养硝化/好氧反硝化菌的分离鉴定及其在不同培养条件下产N_2O研究%Isolation of Heterotrophic Nitrifiers/Aerobic Denitrifiers and Their Roles in N_2O Production for Different Incubations

    Institute of Scientific and Technical Information of China (English)

    蒋静艳; 胡正华; 黄耀

    2009-01-01

    Soil microorganisms are important sources of N_2O for the atmosphere. Peak emissions of N_2O are often observed after wetting of soil. The simultaneous heterotrophic: nitrifying and aerobic denitrifying hacteria with respect to N_2O emission were studied to obtain more information about the microbiological aspects of peak emissions. Using acelamide as the C and N source, two strains of nitrifying and denitrifying bacteria were isolated,coded as XM1 and HX2,respectively. XMlstrain was Gram-negative chain-like bacilli,and the HX2 was Gram-negative cocci. In enrichment culture,N_2O production of HX2 was 76 times more than XM1 . Two strains could grow with glucose,mannitol or sodium tartrate as sole carbon source,respectively. They could nitrify with sodium nitrate or denitrify with ammonium sulfate as unique nitrogen source, and produce intermediate product nitrite. XMlstrain growth velocity and nitrite formation were obviously higher than HX2. The phylogentic analysis based on partial 16S rDNA showed that two isolated strains were the closest relative of Pseudomonas sp.99% sequence similarity. Under different WFPS (water-filled-pore-space) conditions, the aerobic autoclaved soil incubation trial showed that, HX2 strain was suitable for growing in 30% WFPS,and N_2O production was (36.01 ± 2.48) ng/g which was 1.9 times than that in 60% WFPS. But XM1 was suitable for growing in 60% WFPS and almost had no N_2O production. To investigate the nitrifying and denitrifying mechanisms of heterotrophic nitrifiers/aerobic denitrifiers should be useful for mastering the mitigation way of soil N_2O emission in future.%以乙酰胺为唯一碳氮源分离纯化出2株既能异养硝化又能好氧反硝化的菌株XM1和HX2,革兰氏阴性,分别为链状杆菌和球状菌.在富集培养基中,菌株HX2产N_2O量为XM1的76倍;两菌株均能分别以葡萄糖、甘露醇、酒石酸钠为唯一碳源进行生长;也可分别以硝酸钠和硫酸铵为唯一氮源进行硝化

  5. ρ(C)/ρ(N)对3 BER-S工艺特性及反硝化细菌群落特征的影响%Influence of ρ(C)/ρ(N) Ratio on Technology Characteristics and Denitrifying Bacteria Community for 3 BER-S

    Institute of Scientific and Technical Information of China (English)

    郝瑞霞; 任晓克; 孟成成; 王建超; 王润众; 赵文莉

    2015-01-01

    In order to improve the nitrogen removal efficiency of three-dimension-electrode biofilm process, the effects of ρ( C )/ρ( N ) on operation characteristics and denitrifying bacteria population community characteristics of a coupled 3-dimensional biofilm-electrode with sulfur autotrophic denitrification technology ( 3DBER-S ) were investigated at different ρ( C )/ρ( N ) conditions. The operating result indicates that there is no significant impact ofρ( C)/ρ( N) on denitrification performance in 3BER-S. And the TN removal efficiency is more than 80% at different ρ( C)/ρ( N) conditions. Moreover, the effects ofρ(C)/ρ(N) on denitrifying bacteria population and denitrification nutrition types in 3BER-S system were found. At high ρ( C)/ρ( N) condition, there is less species of denitrifying bacteria in 3BER-S system, where the Thauera acts as the dominant bacteria and heterotrophic denitrification is the main process. When the ρ( C )/ρ( N ) is reduced, both the denitrifying bacteria species and the proportion of sulfur autotrophic denitrification bacteria increase. In a word, the 3BER-S system maintains high and stable nitrogen removal efficiency at differentρ( C)/ρ( N) conditions, because the sulfur makes up for the deficiency of the denitrifying electronic donor in 3BER-S at low ρ(C)/ρ(N)condition.%为提高三维电极生物膜工艺脱氮效率,通过运行不同TOC与TN的质量浓度比(ρ( C)/ρ( N))条件下三维电极生物膜-硫自养耦合工艺(3BER-S),并建立基于反硝化特异性基因 nirS克隆文库,研究了ρ(C)/ρ(N)对3BER-S运行特性及反硝化细菌群落的影响。结果表明:ρ( C)/ρ( N)对3BER-S工艺的脱氮效率影响较小,不同ρ(C)/ρ(N)条件下的TN去除效率基本稳定在80%以上。ρ(C)/ρ(N)对3BER-S体系内的反硝化细菌种群结构和营养类型均有一定影响。高ρ(C)/ρ(N)条件下,反硝化细菌种类较少,Thauera(陶厄氏菌属)是体系内的优势菌群,脱氮作用以异养

  6. Functional bacteria and process metabolism of the Denitrifying Sulfur conversion-associated Enhanced Biological Phosphorus Removal (DS-EBPR) system: An investigation by operating the system from deterioration to restoration.

    Science.gov (United States)

    Guo, Gang; Wu, Di; Hao, Tianwei; Mackey, Hamish Robert; Wei, Li; Wang, Haiguang; Chen, Guanghao

    2016-05-15

    A sulfur conversion-associated Enhanced Biological Phosphorus (P) Removal (EBPR) system is being developed to cater for the increasing needs to treat saline/brackish wastewater resulting from seawater intrusion into groundwater and sewers and frequent use of sulfate coagulants during drinking water treatment, as well as to meet the demand for eutrophication control in warm climate regions. However, the major functional bacteria and metabolism in this emerging biological nutrient removal system are still poorly understood. This study was thus designed to explore the functional microbes and metabolism in this new EBPR system by manipulating the deterioration, failure and restoration of a lab-scale system. This was achieved by changing the mixed liquor suspended solids (MLSS) concentration to monitor and evaluate the relationships among sulfur conversion (including sulfate reduction and sulfate production), P removal, variation in microbial community structures, and stoichiometric parameters. The results show that the stable Denitrifying Sulfur conversion-associated EBPR (DS-EBPR) system was enriched by sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB). These bacteria synergistically participated in this new EBPR process, thereby inducing an appropriate level of sulfur conversion crucial for achieving a stable DS-EBPR performance, i.e. maintaining sulfur conversion intensity at 15-40 mg S/L, corresponding to an optimal sludge concentration of 6.5 g/L. This range of sulfur conversion favors microbial community competition and various energy flows from internal polymers (i.e. polysulfide or elemental sulfur (poly-S(2-)/S(0)) and poly-β-hydroxyalkanoates (PHA)) for P removal. If this range was exceeded, the system might deteriorate or even fail due to enrichment of glycogen-accumulating organisms (GAOs). Four methods of restoring the failed system were investigated: increasing the sludge concentration, lowering the salinity or doubling the COD

  7. a Modified Denitrifying Bacteria Method for Dual Stable Isotopic Analysis of of Soil Nitrate in Kcl Extracts: Identification of Bioindicators of Nitrogen Deposition Along a Gradient in the Sonoran Desert

    Science.gov (United States)

    Bell, M. D.; Sickman, J. O.; Allen, E. B.

    2011-12-01

    Previous studies performing dual isotopic analysis of nitrate in KCl soil extracts using denitrifying bacteria have not incorporated alterations in the method to compensate for the increased N2O blank produced when the bacteria are exposed to KCl in solution. When 1M KCl is used as a blank, the amount of N2O released from the concentrated bacteria solution is more than four times as high as when using a DI water blank. The excess N2O produced is not an artifact of nitrate impurity in the KCl, although the blank increases with the molarity of KCl up to 1M. The introduction of N2O gas is significant enough to alter the values of IAEA USGS standards (3 μg in 3ml KCl) which in turn results in an inaccurate regression for unknown samples. We reduced the size of the KCl blank and its effect on the standards by adding 3ml of KCl to the bacteria solution prior to purging the sample with He gas. This removes the N2O gas which is released by the bacteria when they initially come in contact with the KCl, and allows for standards to be calibrated to a precision of ± 0.1 % δ15N and ± 0.2 % δ18O. Using this new method, we measured δ15N and δ18O of nitrate in 1M KCl soil extracts taken from surface soil (5cm cores) along a nitrogen deposition gradient spanning the Coachella Valley in the western Sonoran Desert during the summer. Early germinating winter annual plant species (Schismus barbatus, Chaenactic fremontii, and Malacothrix glabrata) were collected as seedlings early in the growing season and again in late spring before senescence. Leaves from the dominant shrub, Larrea tridentata, were also collected from each site. Soil nitrogen from sites on the eastern edge of the valley had δ18O values between +30 and +41%, indicating an influence of atmospheric nitrate in plant available nitrate. There was an inverse correlation (r2=0.907) between soil δ18O and the δ15N of the C.fremontii leaf tissue, which suggests that in areas of high N deposition, some seedlings are

  8. Different land use intensities in grassland ecosystems drive ecology of microbial communities involved in nitrogen turnover in soil.

    Science.gov (United States)

    Meyer, Annabel; Focks, Andreas; Radl, Viviane; Keil, Daniel; Welzl, Gerhard; Schöning, Ingo; Boch, Steffen; Marhan, Sven; Kandeler, Ellen; Schloter, Michael

    2013-01-01

    Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes) in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM), intensely used mown pastures (IP) and extensively used pastures (EP), respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK). The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation) might be independently regulated by different abiotic and biotic factors in response to land use intensity.

  9. Different land use intensities in grassland ecosystems drive ecology of microbial communities involved in nitrogen turnover in soil.

    Directory of Open Access Journals (Sweden)

    Annabel Meyer

    Full Text Available Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM, intensely used mown pastures (IP and extensively used pastures (EP, respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK. The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation might be independently regulated by different abiotic and biotic factors in response to land use intensity.

  10. Different Land Use Intensities in Grassland Ecosystems Drive Ecology of Microbial Communities Involved in Nitrogen Turnover in Soil

    Science.gov (United States)

    Meyer, Annabel; Focks, Andreas; Radl, Viviane; Keil, Daniel; Welzl, Gerhard; Schöning, Ingo; Boch, Steffen; Marhan, Sven; Kandeler, Ellen; Schloter, Michael

    2013-01-01

    Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes) in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM), intensely used mown pastures (IP) and extensively used pastures (EP), respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK). The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation) might be independently regulated by different abiotic and biotic factors in response to land use intensity. PMID:24039974

  11. Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

    Directory of Open Access Journals (Sweden)

    Huhe

    Full Text Available In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively. The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.

  12. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers

    Science.gov (United States)

    Simonin, Marie; Richaume, Agnès; Guyonnet, Julien P.; Dubost, Audrey; Martins, Jean M. F.; Pommier, Thomas

    2016-01-01

    Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg−1 dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function. PMID:27659196

  13. Pilot-scale study on nitrogen and aromatic compounds removal in printing and dyeing wastewater by reinforced hydrolysis-denitrification coupling process and its microbial community analysis.

    Science.gov (United States)

    Li, Chao; Ren, Hongqiang; Yin, Erqin; Tang, Siyuan; Li, Yi; Cao, Jiashun

    2015-06-01

    Aiming to efficiently dispose printing and dyeing wastewater with "high organic nitrogen and aromatic compounds, but low carbon source quality", the reinforced anaerobic hydrolysis-denitrification coupling process, based on improved UASB reactors and segregated collection-disposition strategy, was designed and applied at the pilot scale. Results showed that the coupling process displayed efficient removal for these two kinds of pollutants (nitrogen and aromatics), since the concentration of NH3-N (shortened as ρ (NH3-N)) aromatics reduced greatly by UASBs according to GC-MS. Microbial community analysis by PCR-DGGE showed that Bacteroidetes and Alphaproteobacteria were the dominant communities in the bioreactors and some kinds of VFAs-producing, denitrifying and aromatic ring opening microorganisms were discovered. Further, the nirK and bcrA genes quantification also indicated the coupling process owned outstanding denitrification and aromatic compound-degrading potential, which demonstrates that the coupling process owns admirable applicability for this kind of wastewater treatment.

  14. Titanium dioxide nanoparticles strongly impact soil microbial function by affecting archaeal nitrifiers

    Science.gov (United States)

    Simonin, Marie; Richaume, Agnès; Guyonnet, Julien P.; Dubost, Audrey; Martins, Jean M. F.; Pommier, Thomas

    2016-09-01

    Soils are facing new environmental stressors, such as titanium dioxide nanoparticles (TiO2-NPs). While these emerging pollutants are increasingly released into most ecosystems, including agricultural fields, their potential impacts on soil and its function remain to be investigated. Here we report the response of the microbial community of an agricultural soil exposed over 90 days to TiO2-NPs (1 and 500 mg kg‑1 dry soil). To assess their impact on soil function, we focused on the nitrogen cycle and measured nitrification and denitrification enzymatic activities and by quantifying specific representative genes (amoA for ammonia-oxidizers, nirK and nirS for denitrifiers). Additionally, diversity shifts were examined in bacteria, archaea, and the ammonia-oxidizing clades of each domain. With strong negative impacts on nitrification enzyme activities and the abundances of ammonia-oxidizing microorganism, TiO2-NPs triggered cascading negative effects on denitrification enzyme activity and a deep modification of the bacterial community structure after just 90 days of exposure to even the lowest, realistic concentration of NPs. These results appeal further research to assess how these emerging pollutants modify the soil health and broader ecosystem function.

  15. Characterization of cycP gene expression in Achromobacter xylosoxidans NCIMB 11015 and high-level heterologous synthesis of cytochrome c' in Escherichia coli.

    Science.gov (United States)

    Harris, Roger L; Barbieri, Sonia; Paraskevopoulos, Kostas; Murphy, Loretta M; Eady, Robert R; Hasnain, S Samar; Sawers, R Gary

    2010-01-01

    The cycP gene encoding a periplasmic cytochrome c' from the denitrifying beta-proteobacterium Achromobacter xylosoxidans was characterized. The genes flanking cycP encode components of a mobile genetic element characteristic of the beta-proteobacteria, suggesting that cycP has inserted within a transposon or insertion element. The gene therefore does not form part of a denitrification operon or gene cluster. The level of expression of the cycP gene and the level of synthesis of its corresponding gene product were found to increase by maximally 3-fold anaerobically. Expression of cycP appears to occur mainly by non-specific read-through transcription from portions of the insertion element. Conditions were developed for high-level overproduction of cytochrome c' in Escherichia coli, which resulted in signal peptide cleavage concomitant with secretion of the protein into the periplasm. Using a single-step purification, 20-30 mg of pure protein were isolated from a 1-litre culture. Based on UV-visible spectrophotometry the dimeric protein was shown to have a full complement of haem and to be indistinguishable from the native protein purified from A. xylosoxidans. This system provides an excellent platform to facilitate biochemical and structural dissection of the mechanism underlying the novel specificity of NO binding to the proximal face of the haem.

  16. Comparison between traditional biological phosphorus removal by anaerobic/aerobic and denitrifying phosphorus removal by anaerobic/aerobic%传统厌氧/好氧生物除磷与厌氧/缺氧反硝化除磷效能的比较

    Institute of Scientific and Technical Information of China (English)

    苏婉琳; 韩萍芳

    2011-01-01

    采用序批式反应器(SBR),对比厌氧/好氧(A/O)和厌氧/缺氧(A/A)2种运行模式对模拟生活和工业混合污水同时脱氮除磷的效能.结果表明:反硝化聚磷菌完全可以在厌氧/缺氧交替运行条件下得到富集,稳定运行的2种模式对有机物和P的去除率分别保持在90%和85%以上,且A/A SBR具有更强的释磷能力,其释磷量比A/O SBR高出1.2倍.进一步试验表明:磷的释放在有无硝酸盐的情况下效果是不同的.2个系统内污泥均有反硝化除磷能力,A/A SBR中所含反硝化聚磷菌(DPAO)的比例是A/O SBR的4.56倍.2种模式出水水质都能取得较好的效果,且能实现同步除磷脱氮,而反硝化除磷在生物除磷方面更具优势.%Two sequence batch reactors(SBRs) in A/O and A/A run modes were operated in parallel to compare their ability of simultaneous phosphorus and nitrogen removal. The results showed that the ability of the anaerobic/anoxic strategy enriched the growth of denitrifying phosphorus bacteria capable of taking up phosphate under anoxic condition, and the removal of COD and phosphorus were averaged over 90% and 85% in the steady-state, respectively. A/A SBR had the stronger anaerobic phosphorus release ability; its amount of anaerobic released phosphorus is higher than 1. 2 times compared with A/O SBR. It is shown that interpretation of phosphorus release tests with or without nitrate present was different. The proportion of denitrifying phosphate accumulating organism ( DPAO) was 4. 56 times compared with the one of A/O SBR. The qualities of effluent were met the criteria, and DPAO systems could obtaia get simultaneous denitrifying and phosphorus removal. Thus, DPAO had more advantages than PAO for biological phosphorus removal.

  17. Nitrogen Fixation in Denitrified Marine Waters

    OpenAIRE

    Camila Fernandez; Laura Farías; Osvaldo Ulloa

    2011-01-01

    Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria), whereas nitrogen losses occur in oxygen-depleted intermediate wat...

  18. Denitrifying bioreactor clogging potential during wastewater treatment.

    Science.gov (United States)

    Christianson, Laura E; Lepine, Christine; Sharrer, Kata L; Summerfelt, Steven T

    2016-11-15

    Chemoheterotrophic denitrification technologies using woodchips as a solid carbon source (i.e., woodchip bioreactors) have been widely trialed for treatment of diffuse-source agricultural nitrogen pollution. There is growing interest in the use of this simple, relatively low-cost biological wastewater treatment option in waters with relatively higher total suspended solids (TSS) and chemical oxygen demand (COD) such as aquaculture wastewater. This work: (1) evaluated hydraulic retention time (HRT) impacts on COD/TSS removal, and (2) assessed the potential for woodchip clogging under this wastewater chemistry. Four pilot-scale woodchip denitrification bioreactors operated for 267 d showed excellent TSS removal (>90%) which occurred primarily near the inlet, and that COD removal was maximized at lower HRTs (e.g., 56% removal efficiency and 25 g of COD removed per m(3) of bioreactor per d at a 24 h HRT). However, influent wastewater took progressively longer to move into the woodchips likely due to a combination of (1) woodchip settling, (2) clogging due to removed wastewater solids and/or accumulated bacterial growth, and (3) the pulsed flow system pushing the chips away from the inlet. The bioreactor that received the highest loading rate experienced the most altered hydraulics. Statistically significant increases in woodchip P content over time in woodchip bags placed near the bioreactor outlets (0.03 vs 0.10%P2O5) and along the bioreactor floor (0.04 vs. 0.12%P2O5) confirmed wastewater solids were being removed and may pose a concern for subsequent nutrient mineralization and release. Nevertheless, the excellent nitrate-nitrogen and TSS removal along with notable COD removal indicated woodchip bioreactors are a viable water treatment technology for these types of wastewaters given they are used downstream of a filtration device. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. Denitrifying bioreactor clogging potential during wastewater treatment

    Science.gov (United States)

    Chemoheterotrophic denitrification technologies using woodchips as a solid carbon source (i.e., woodchip bioreactors) have been widely trialed for treatment of diffuse-source agricultural nitrogen pollution. There is growing interest in the use of this simple, relatively low-cost biological wastewat...

  20. Study on the Removal of Nitrate from Groundwater Using Different Carbon Source for the Embedded Denitrifying Bacteria%利用不同碳源包埋反硝化菌去除地下水中硝酸盐

    Institute of Scientific and Technical Information of China (English)

    李军; 张淑亚; 冯雷; 姚松涛; 杨双

    2011-01-01

    目的 比较乙酸钠( NaAc)(液相)和稻秆(固相)作为碳源的包埋反硝化菌反硝化性能,确定固相碳源反硝化过程的工艺条件.方法 自配水样,采用自制厌氧反应器,利用NaAc作为碳源实现反硝化的启动并探讨其反硝化性能;通过试验研究固相碳源反硝化过程的影响因素.结果 以NaAc为碳源,停留时间为6h、进水pH在7~7.5时,NO3- -N去除率接近100%,且出水没有NO2- -N的积累,NO3- -N最大处理负荷87 mg· (L·h)-1,出水pH在8~8.5;以稻秆为碳源,温度20℃,停留时间6.3h时,NO3- -N去除率达98%,基本没有NO2- -N积累,且出水pH呈中性.结论 以NaAc作为碳源包埋菌对NO3- -N处理负荷较大;稻秆具有缓释碳源的性能,且降解出一定的有机酸,可中和反硝化生成的出水碱度.%The experiment chose the up-flow anaerobic reactor filled with the embedded denitrifying bacteri-a,self-equipped NO3- -N water as influent. The start-up of denitrification reactor using the sodium acetate as the carbon source and impact of various factors on denitrification process using rice straws as the solid carbon source were studied. The results show that when using the sodium acetate as the carbon source,6 h of hydraulic retention time(HRT) ,7-7.5 of pH,100% of nitrate could be removed,nitrite of the effluent was not detected,the influent loading of NO3--N could reach 87 mg? (L·h)-1,however,pH of the effluent increased to 8-8. 5;when using rice straws as the solid carbon source,6 h of HRT,4.5-10. 5 of pH,20 ℃of temperature,98% of nitrate could be removed,the NO2--N did not accumulated,pH of the effluent was always 7-8. The result shows the nitrate was removed when rice straw is as solid carbon, moreover the process has a great ability of acid and alkali resistance.

  1. 一株耐冷反硝化菌的分离鉴定及其反硝化特性%Identification and Denitrification Characteristics of a Strain of Psychrotrophic Denitrifying Bacteria

    Institute of Scientific and Technical Information of China (English)

    李军; 闫爽; 邓娴; 王立军; 张雅南; 杨宏宇

    2012-01-01

    A psychrotrophic denitrifying bacteria (designated Y2)with high efficiency degradation of nitrate nitrogen was isolated from the submerged mud in winter water at 151 which was used to treat high-nitrate wastewater at low temperature. According to the results of morphological observation,physiological and biochemical test .sequence analyses of the 16S rDNA, strain Y2 was identified as Brevibacterium. The NO," -N removal rate of Y2 can reach 51. 6% in denitrification medium at 151 in 3 days,and 99. 3% in 7 days. The optimum carbon source and the optimum nitrogen source of Y2 were sodium acetate and potassium nitrate. The suitable molar ratio of carbon/nitrogen for denitrification of the bacteria was 3= 1,the optimum pH value was 7.5, and the optimum temperature was 25 t. It showed Y2 was suitable for the nitrate elimination of ni-trates at low temperature.%目的 筛选分离出一株具有高效降解硝态氮的耐冷反硝化菌,以提高低温下硝酸盐废水处理的生物反硝化速率.方法 在15℃条件下从冬季淹水泥中分离纯化出一株耐冷反硝化细菌Y2,通过对该菌株的形态观察、生理生化试验以及16S rRNA序列分析,对菌株进行鉴定;通过批试验研究不同因素对菌株单位生物量脱氮率的影响.结果 初步确定Y2菌株为黄色短杆菌(Brevibacterium).该菌株能在15℃下在反硝化培养基中3d内对NO3- -N的去除率达到51.6%,7d能达到99.3%,该菌的最适碳源为乙酸钠、最适氮源为硝酸钾,最适碳氮比为3:1、最适pH值为7.5、最适温度25℃.结论 菌株Y2在低温下表现出良好的反硝化性能,NO3- -N质量浓度达300 mg/L时,去除率可达99.8%,适用于低温硝酸盐废水处理.

  2. Gene therapy

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    2005147 CNHK200-hA-a gene-viral therapeutic system and its antitumor effect on lung cancer. WANG Wei-guo(王伟国),et al. Viral & Gene Ther Center, Eastern Hepatobilli Surg Instit 2nd Milit Univ, Shanghai 200438. Chin J Oncol,2005:27(2):69-72. Objective: To develop a novel vector system, which combines the advantages of the gene therapy,

  3. Quantification of Key Genes Steering the Microbial Nitrogen Cycle in the Rhizosphere of Sorghum Cultivars in Tropical Agroecosystems ▿

    Science.gov (United States)

    Hai, Brigitte; Diallo, Ndeye Hélène; Sall, Saidou; Haesler, Felix; Schauss, Kristina; Bonzi, Moussa; Assigbetse, Komi; Chotte, Jean-Luc; Munch, Jean Charles; Schloter, Michael

    2009-01-01

    The effect of agricultural management practices on geochemical cycles in moderate ecosystems is by far better understood than in semiarid regions, where fertilizer availability and climatic conditions are less favorable. We studied the impact of different fertilizer regimens in an agricultural long-term observatory in Burkina Faso at three different plant development stages (early leaf development, flowering, and senescence) of sorghum cultivars. Using real-time PCR, we investigated functional microbial communities involved in key processes of the nitrogen cycle (nitrogen fixation, ammonia oxidation, and denitrification) in the rhizosphere. The results indicate that fertilizer treatments and plant development stages combined with environmental factors affected the abundance of the targeted functional genes in the rhizosphere. While nitrogen-fixing populations dominated the investigated communities when organic fertilizers (manure and straw) were applied, their numbers were comparatively reduced in urea-treated plots. In contrast, ammonia-oxidizing bacteria (AOB) increased not only in absolute numbers but also in relation to the other bacterial groups investigated in the urea-amended plots. Ammonia-oxidizing archaea exhibited higher numbers compared to AOB independent of fertilizer application. Similarly, denitrifiers were also more abundant in the urea-treated plots. Our data imply as well that, more than in moderate regions, water availability might shape microbial communities in the rhizosphere, since low gene abundance data were obtained for all tested genes at the flowering stage, when water availability was very limited. PMID:19502431

  4. [Dynamic changes in functional genes for nitrogen bioremediation of petroleum-contaminated soil cycle during].

    Science.gov (United States)

    Wu, Bin-Bin; Lu, Dian-Nan; Liu, Zheng

    2012-06-01

    Microorganisms in nitrogen cycle serve as an important part of the ecological function of soil. The aim of this research was to monitor the abundance of nitrogen-fixing, denitrifying and nitrifying bacteria during bioaugmentation of petroleum-contaminated soil using real-time polymerase chain reaction (real-time PCR) of nifH, narG and amoA genes which encode the key enzymes in nitrogen fixation, nitrification and ammoniation respectively. Three different kinds of soils, which are petroleum-contaminated soil, normal soil, and remediated soil, were monitored. It was shown that the amounts of functional microorganisms in petroleum-contaminated soil were far less than those in normal soil, while the amounts in remediated soil and normal soil were comparable. Results of this experiment demonstrate that nitrogen circular functional bacteria are inhibited in petroleum-contaminated soil and can be recovered through bioremediation. Furthermore, copies of the three functional genes as well as total petroleum hydrocarbons (TPH) for soils with six different treatments were monitored. Among all treatments, the one, into which both E. cloacae as an inoculant and wheat straw as an additive were added, obtained the maximum copies of 2.68 x 10(6), 1.71 x 10(6) and 8.54 x 10(4) per gram dry soil for nifH, narG and amoA genes respectively, companying with the highest degradation rate (48% in 40 days) of TPH. The recovery of functional genes and removal of TPH were better in soil inoculated with E cloacae and C echinulata collectively than soil inoculated with E cloacae only. All above results suggest that the nitrogen circular functional genes could be applied to monitor and assess the bioremediation of petroleum-contaminated soil.

  5. The bamA Gene for Anaerobic Ring Fission is Widely Distributed in the Environment

    Directory of Open Access Journals (Sweden)

    Abigail W. Porter

    2013-10-01

    Full Text Available Aromatic compounds are a major component of the global carbon pool, and include a diverse range of compounds such as humic acid, lignin, amino acids, and industrial chemicals. Due to the prevalence of aromatic compounds in the environment, microorganisms have evolved mechanisms to metabolize that available carbon. While anaerobic monoaromatic degradation can be initiated in a number of different ways, the signature central metabolite for these pathways is benzoyl-CoA. Aromatic chemicals with different upstream degradation pathways all funnel into the downstream benzoyl-CoA pathway. Different genes encoding enzymes of the benzoyl-CoA pathway could be used as biomarkers, however the ring opening hydrolase, encoded by the bamA gene, is ideal because it is detected under a range of respiratory conditions, including denitrifying, iron-reducing, sulfate-reducing, and fermentative conditions. In this work we evaluated a number of DNA samples from diverse environments for the presence of the bamA gene, and had positive results for every sample. We further explored the bamA gene diversity in six of these sites as compared to published genome sequences and found that our clones were distributed throughout the dendrogram, although there were clone sequences from two sites that formed a unique clade. When we used a functional operational taxonomic unit based clustering analysis to compare the diversity of our sites to several locations reported in the literature, we found that there were two clusters of sites, and benzene contaminated sites were present in both clusters. Given the number of potential upstream inputs from natural and manmade monoaromatic compounds, the benzoyl-CoA pathway and the bamA gene play an important role in the global carbon cycle that has thus far been understudied.

  6. Trichoderma genes

    Science.gov (United States)

    Foreman, Pamela [Los Altos, CA; Goedegebuur, Frits [Vlaardingen, NL; Van Solingen, Pieter [Naaldwijk, NL; Ward, Michael [San Francisco, CA

    2012-06-19

    Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

  7. Gene Therapy.

    Science.gov (United States)

    Thorne, Barb; Takeya, Ryan; Vitelli, Francesca; Swanson, Xin

    2017-03-14

    Gene therapy refers to a rapidly growing field of medicine in which genes are introduced into the body to treat or prevent diseases. Although a variety of methods can be used to deliver the genetic materials into the target cells and tissues, modified viral vectors represent one of the more common delivery routes because of its transduction efficiency for therapeutic genes. Since the introduction of gene therapy concept in the 1970s, the field has advanced considerably with notable clinical successes being demonstrated in many clinical indications in which no standard treatment options are currently available. It is anticipated that the clinical success the field observed in recent years can drive requirements for more scalable, robust, cost effective, and regulatory-compliant manufacturing processes. This review provides a brief overview of the current manufacturing technologies for viral vectors production, drawing attention to the common upstream and downstream production process platform that is applicable across various classes of viral vectors and their unique manufacturing challenges as compared to other biologics. In addition, a case study of an industry-scale cGMP production of an AAV-based gene therapy product performed at 2,000 L-scale is presented. The experience and lessons learned from this largest viral gene therapy vector production run conducted to date as discussed and highlighted in this review should contribute to future development of commercial viable scalable processes for vial gene therapies.

  8. Gene Therapy

    Science.gov (United States)

    ... or improve your body's ability to fight disease. Gene therapy holds promise for treating a wide range of diseases, such as cancer, cystic fibrosis, heart disease, diabetes, hemophilia and AIDS. Researchers are still studying how and ...

  9. Genes V.

    Energy Technology Data Exchange (ETDEWEB)

    Lewin, B.

    1994-12-31

    This fifth edition book encompasses a wide range of topics covering 1,272 pages. The book is arranged into nine parts with a total of 36 chapters. These nine parts include Introduction; DNA as a Store of Information; Translation; Constructing Cells; Control of Prokaryotypic Gene Expression; Perpetuation of DNA; Organization of the Eukaryotypic Genome; Eukaryotypic Transcription and RNA Processing; The Dynamic Genome; and Genes in Development.

  10. 双污泥反硝化除磷系统中氨氮容积负荷的优化%Optimization of ammonium volumetric loading in two-sludge denitrifying phosphorus removal process

    Institute of Scientific and Technical Information of China (English)

    刘青松; 彭永臻; 侯锋; 张为堂; 刘晔; 王淑莹

    2013-01-01

    The universal features of rural domestic wastewater were small quantity, scattered distribution, and great diurnal variation, etc. So it was difficult to centralize, treat, and reuse such wastewater. However, discharging such untreated rural domestic sewage with the characteristics of comparatively high nitrogen and phosphorus concentration to the environment brought about seriously eutrophication. Therefore, it was necessary to research and develop a treatment process which has the advantages of relatively high efficiency, less land occupied, investigated savings, and also easy management and maintenance for nutrient removal from the rural sewage. On the basis of these considerations above, an enhanced denitrifying phosphorus removal system, that is, a two-sludge process integrating anaerobic/anoxic/oxic (AAO) reactor with biological aerated filter (BAF)( AAO-BAF for short), was developed to treat domestic sewage, especially the decentralized sewage in rural areas. In this innovation system, the AAO unit, consisting of nine compartments in sequence, was used mainly for the removal of organic compounds and nutrients without ammonium oxidation, while the BAF unit was mainly responsible for nitrification. The BAF unit, an important component of the two-sludge system, was 1.8m in height and 10cm in diameter, with a light-weight ceramic filled in it. Nine sampling ports were placed along the BAF, marked as B1 to B9 from bottom to top in turn. In this study, a series of experiments were carried out to research the effect of the ammonium volumetric loading on nitrifying characteristics and effluent SS of the BAF. The ammonium volumetric loading, by changing the hydraulic loading (marked as mode 1) and adjusting the effective volume of the BAF unit (marked as mode 2), was varied from 0.43 kg/(m3·d) to 1.2 kg/(m3·d). Mode 1 lasted for 90 d, during which hydraulic loading soared from 1.53 m3/(m2·h) to 4.37 m3/(m2·h). Mode 2 ran for 60 d, and during that period BAF

  11. DREB genes

    African Journals Online (AJOL)

    Unipar

    2015-03-12

    Mar 12, 2015 ... to AP2/ERF family, dehydration-responsive element-binding protein (DREB) genes, (CitsERF01 to ... Protein sequences of DREB subfamilies belonging to group I, .... position 37, and it was present in consensus in all protein.

  12. Biological and chemical factors driving the temporal distribution of cyanobacteria and heterotrophic bacteria in a eutrophic lake (West Lake, China).

    Science.gov (United States)

    Song, Hao; Xu, Jiahui; Lavoie, Michel; Fan, Xiaoji; Liu, Guangfu; Sun, Liwei; Fu, Zhengwei; Qian, Haifeng

    2017-02-01

    Physico-chemical parameters, hydrological conditions, and microbial interactions can affect the growth and persistence of cyanobacteria, but the interacting effects among these bloom-forming factors are still poorly known. This hampers our capacity to predict the occurrence of cyanobacterial bloom accurately. Here, we studied the relationship between temperature, N and P cycles, and the microbial community abundance and diversity at 0.5 m under the surface of West Lake (China) from January 21 to November 20, 2015, in order to better understand the key factors regulating temporal changes in the cyanobacterial community. Using high throughput sequencing of the 16S rRNA gene V3-V4 region, we studied the diversity and abundance of bacteria. In parallel, we measured physico-chemical parameters and followed the abundance of key genes involved in N fixation, denitrification, and nutrient uptake. Multivariate analyses suggest that P concentration and water temperature are the key factors controlling the outbreak of summer cyanobacterial bloom. RT-qPCR analyses of the bacterial community and measurements of the copy number of denitrification-related gene (nirK, nosZ, nirS) show that denitrification potential and denitrifying bacteria relative abundance (Pseudomonas and Bacillus) increased in concert with diazotrophic cyanobacterial genera (Anabaena, Nostoc, Aphanizomenon flos-aquae) and the common bloom-forming non-diazotrophic cyanobacterium genus Microcystis. The present study brings new insights on the complex interplay between physico-chemical parameters, heterotrophic bacterial community composition, nitrogen cycle, and cyanobacteria dominance in a eutrophic lake.

  13. The effects of wastewater discharge on the microbiological nitrogen cycle of the lake sediments

    Science.gov (United States)

    Saarenheimo, Jatta; Aalto, Sanni L.; Tiirola, Marja

    2016-04-01

    Anthropogenic wastewater inputs alter the natural dynamics of nitrogen (N) cycle by providing high concentrations of nitrate and organic matter to the sediment microbes. It can also change the microbial community composition and N removal potential but this is currently not that well studied. To study these aspects, we conducted ecosystem-scale experiment in Lake Keurusselkä, Finland. In the experiment, the wastewater discharge to the recipient lake was optimized with sediment filtration, which increased the surface and retention time of the nitrified wastewater with the sediment. In addition to N transformation rates, which showed that optimization enhanced denitrification, we studied the microbial responses at the sediment. Genetic potential of nitrogen transformation processes, such as denitrification, dissimilatory nitrate reduction to ammonium (DNRA) and nitrification were studied by targeting the functional genes (i.e. nirS, nirK, nosZI, nosZII, nrfA, amoAarchaea and amoAbacteria) with quantitative PCR and digital droplet PCR. In addition, changes in the microbial community composition along the wastewater gradient were examined by using next generation sequencing of the 16S rRNA genes. In line with our hypothesis, the relative abundance of denitrifying genes followed the observed denitrification rates, being highest near the nitrate-rich wastewater discharge. Furthermore the microbial community composition in the discharge point differed clearly from the control and downstream sites, having also the highest numbers of rare OTUs. Abundance of nitrifying bacteria was higher than nitrifying archaea near the waste water discharge, whereas the opposite was seen at the control site. The results indicate that wastewater is not only increasing the denitrification rates, but can also alter the structure and genetic potential microbial communities.

  14. Factors denitrifying bacteria in wastewater treatment applications in aquaculture and treatment effectiveness analysis%反硝化细菌在水产养殖污水处理中的应用及影响其处理效果的因素分析

    Institute of Scientific and Technical Information of China (English)

    刘昔; 陈国梁; 李珍

    2015-01-01

    Aquatic productivity is usualy based on the quantity and quality of nitrogen,which plays an important role in aquaculture system.As a serious threat to the aquaculture organisms,accumulated ammonia and nitrite in the aquaculture water should be highly concerned.Aimed at biological nitrogen removal in aquaculture system,the article describes the application of denitrifying bacteria in sewage treatment.And combined with domestic and foreign research results,the article analyzes the various factors affecting the biological denitrification.%氮元素是水产养殖水体中较常见的一种限制初级生产力的营养元素,对水产养殖影响巨大。养殖水体中积累的氨氮和亚硝态氮对水产养殖生物可造成巨大危害,其影响不容忽视。本论文围绕水产养殖废水生物脱氮这一主题,介绍反硝化细菌在污水处理中的应用研究,并结合中外研究成果,分析影响生物反硝化作用的各种因素。

  15. Repair Effect of Thiobacillus Denitrificans and Denitrifying Bacterium on Pollution in Tianjin Waste Landfill Sites%脱氮硫杆菌和反硝化菌对天津市垃圾填埋场污染的修复研究

    Institute of Scientific and Technical Information of China (English)

    季彦; 郝金山; 薛祈

    2013-01-01

    Aiming at waste leachate samples from Tianjin waste landfill sites,the situation of waste with nitrifying bacteria and sulfate reducting bacteria in laboratory was discussed.The results showed that the metabolizable action of Thiobacillus denitrificans and denitrifying bacterium had strong function for nitrogen and organics removal.Under favorable conditions,it also could remove some metal pollutants.Through strengthening metabolizable action of some microorganism,the pollution system could be controlled and repaired.%针对天津市各大垃圾填埋场的渗沥液试样,论述试验室对垃圾掺入氮化物转化的硝化菌、硫化物转化的硫酸盐还原菌情况.结果表明:脱氮硫杆菌及反硝化菌的代谢作用具有较强的除氮及除去有机物的功能,有利条件下,还去除某些金属污染物质;通过强化某些微生物的代谢作用,可以对污染系统进行调控和修复.

  16. Endothelial Genes

    Science.gov (United States)

    2005-06-01

    8217Department of Surgery, Division of Oncology , and 2Department of BRCA-l and BRCA-2 (breast cancer susceptibility genes), Pathology, University of...Suppression subtractive hybridization re- Cancer: principles and practice of oncology . Philadelphia: Lippincott- vealed an RNA sequence (GenBank accession...Lippman ME. Cancer of the breast: molecular biology angiogenesis in sarcomas and carcinomas. Clin Cancer Res 1999;5: of breast cancer. In: DeVita VT

  17. Gene Ontology

    Directory of Open Access Journals (Sweden)

    Gaston K. Mazandu

    2012-01-01

    Full Text Available The wide coverage and biological relevance of the Gene Ontology (GO, confirmed through its successful use in protein function prediction, have led to the growth in its popularity. In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated proteins. While several GO similarity measures exist, none adequately addresses all issues surrounding the design and usage of the ontology. We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on their GO annotations. We assess the performance of this metric using a ROC analysis on human protein-protein interaction datasets and correlation coefficient analysis on the selected set of protein pairs from the CESSM online tool. This metric achieves good performance compared to the existing annotation-based GO measures. We used this new metric to assess functional similarity between orthologues, and show that it is effective at determining whether orthologues are annotated with similar functions and identifying cases where annotation is inconsistent between orthologues.

  18. Gene doping: gene delivery for olympic victory

    OpenAIRE

    2012-01-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called ‘gene doping’. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted...

  19. Design and evaluation of universal 16S rRNA gene primers for high-throughput sequencing to simultaneously detect DAMO microbes and anammox bacteria.

    Science.gov (United States)

    Lu, Yong-Ze; Ding, Zhao-Wei; Ding, Jing; Fu, Liang; Zeng, Raymond J

    2015-12-15

    To develop universal 16S rRNA gene primers for high-throughput sequencing for the simultaneous detection of denitrifying anaerobic methane oxidation (DAMO) archaea, DAMO bacteria, and anaerobic ammonium oxidation (anammox) bacteria, four published primer sets (PS2-PS5) were modified. The overall coverage of the four primer pairs was evaluated in silico with the Silva SSU r119 dataset. Based on the virtual evaluation, the two best primer pairs (PS4 and PS5) were selected for further verification. Illumina MiSeq sequencing of a freshwater sediment and a culture from a DAMO-anammox reactor using these two primer pairs revealed that PS5 (341b4F-806R) was the most promising universal primer pair. This pair of primers detected both archaea and bacteria with less bias than PS4. Furthermore, an anaerobic fermentation culture and a wastewater treatment plant culture were used to verify the accuracy of PS5. More importantly, it detected DAMO archaea, DAMO bacteria, and anammox bacteria simultaneously with no false positives appeared. This universal 16S rRNA gene primer pair extends the existing molecular tools for studying the community structures and distributions of DAMO microbes and their potential interactions with anammox bacteria in different environments. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. GeneEd -- A Genetics Educational Resource

    Science.gov (United States)

    ... Javascript on. Feature: Genetics 101 GeneEd — A Genetics Educational Resource Past Issues / Summer 2013 Table of Contents Science ... The Hereditary Material of Life / GeneEd — A Genetics Educational Resource / Using The Genetics Home Reference Website / Understanding the ...

  1. Effect of Inoculation of Acacia senegal mature trees with Mycorrhiza and Rhizobia on soil properties and microbial community structure

    Science.gov (United States)

    Assigbetsé, K.; Ciss, I.; Bakhoum, N.; Dieng, L.

    2012-04-01

    Inoculation of legume plants with symbiotic microorganisms is widely used to improve their development and productivity. The objective of this study was to investigate the effect of inoculation of Acacia senegal mature trees with rhizobium (Sinorhizobium) and arbuscular mycorrhizal fungus (G. mosseae, G. fasciculatum, G. intraradices) either singly or in combination, on soil properties, activity and the genetic structure of soil microbial communities. The experiment set up in Southern Senegal consisted of 4 randomized blocks of A. senegal mature trees with 4 treatments including inoculated trees with Rhizobium (R), mycorrhizal fungus (M) and with Rhizobium+mycorhizal fungus (RM) and non-inoculated control (CON). Soil were sampled 2 years after the inoculation. Soil pH, C and N and available P contents were measured. The microbial abundance and activity were measured in terms of microbial biomass C (MBC) and basal soil respiration. The community structure of the total bacterial, diazotrophic and denitrifying communities was assessed by denaturing gradient gel electrophoresis of 16S rDNA, nifH and nirK genes respectively. Inoculations with symbiont under field conditions have increased soil pH. The C and N contents were enhanced in the dual-inoculated treatments (RM). The mycorrhized treatment have displayed the lowest available P contents while RM and R treatments exhibited higher contents rates. The microbial biomass C rates were higher in treatments co-inoculated with AM fungi and Rhizobium than in those inoculated singly with AM fungi or Rhizobium strains. The basal soil respiration were positively correlated to MBC, and the highest rates were found in the co-inoculated treatments. Fingerprints of 16S rDNA gene exhibited similar patterns between inoculated treatments and the control showing that the inoculation of mature trees have not impacted the total bacterial community structure. In contrast, the inoculated treatments have displayed individually different

  2. Effects of dairy manure management in annual and perennial cropping systems on soil microbial communities associated with in situ N2O fluxes

    Science.gov (United States)

    Dunfield, Kari; Thompson, Karen; Bent, Elizabeth; Abalos, Diego; Wagner-Riddle, Claudia

    2016-04-01

    Liquid dairy manure (LDM) application and ploughing events may affect soil microbial community functioning differently between perennial and annual cropping systems due to plant-specific characteristics stimulating changes in microbial community structure. Understanding how these microbial communities change in response to varied management, and how these changes relate to in situ N2O fluxes may allow the creation of predictive models for use in the development of best management practices (BMPs) to decrease nitrogen (N) losses through choice of crop, plough, and LDM practices. Our objectives were to contrast changes in the population sizes and community structures of genes associated with nitrifier (amoA, crenamoA) and denitrifier (nirK, nirS, nosZ) communities in differently managed annual and perennial fields demonstrating variation in N2O flux, and to determine if differences in these microbial communities were linked to the observed variation in N2O fluxes. Soil was sampled in 2012 and in 2014 in a 4-ha spring-applied LDM grass-legume (perennial) plot and two 4-ha corn (annual) treatments under fall or spring LDM application. Soil DNA was extracted and used to target N-cycling genes via qPCR (n=6) and for next-generation sequencing (Illumina Miseq) (n=3). Significantly higher field-scale N2O fluxes were observed in the annual plots compared to the perennial system; however N2O fluxes increased after plough down of the perennial plot. Nonmetric multidimensional scaling (NMS) indicated differences in N-cycling communities between annual and perennial cropping systems, and some communities became similar between annual and perennial plots after ploughing. Shifts in these communities demonstrated relationships with agricultural management, which were associated with differences in N2O flux. Indicator species analysis was used to identify operational taxonomic units (OTUs) most responsible for community shifts related to management. Nitrifying and denitrifying soil

  3. Characteristics of phosphorus removal microorganisms in denitrifying phosphorus removal and induced crystallization phosphorus recovery process for waste water treatment%污水处理反硝化除磷-诱导结晶磷回收工艺中除磷微生物特性

    Institute of Scientific and Technical Information of China (English)

    邹海明; 吕锡武; 李婷

    2014-01-01

    为探究反硝化除磷-诱导结晶磷回收工艺中缺氧池污泥释磷、吸磷以及微生物特征,利用荧光原位杂交(fluorescence in situ hybridization,FISH)技术、电子扫描显微镜(scanning electron microscope,SEM)观察了微生物的数量、分布和形态;通过批次试验考察了污泥在厌氧/好氧和厌氧/缺氧2种模式下的释磷和吸磷特征。结果表明:该双污泥系统缺氧池中聚磷菌占总细菌比例的69.7%,明显高于单污泥系统中富集的聚磷菌比例,污泥中的微生物多呈杆状;厌氧/好氧、厌氧/缺氧模式下单位污泥浓度(mixed liquor suspended solids,MLSS)总吸磷量(以PO43--P计)分别为22.84、18.60 mg/g,反硝化聚磷菌(denitrifying polyphosphate-accumulating organisms, DPAO)占聚磷菌(polyphosphate-accumulating organisms,PAO)的比例为81.44%,表明在长期的厌氧/缺氧运行条件下可以富集到以硝酸盐为电子受体的反硝化聚磷菌,同时还存在着仅以氧气为电子受体的聚磷菌;通过 pH值和氧化还原电位(oxidation reduction potential,ORP)的实时监测可以快速地了解污水生物处理系统中各类反应的进程,对调控工艺参数有着重要的意义。综上所述,为保证污水生物处理工艺的正常稳定运行,将微生物分析与常规的化学参数分析结合起来考察将是未来发展的必然趋势。%A novel wastewater treatment process in our previous research can perform denitrifying simultaneous nitrogen and phosphorus removal and phosphorus recovery via induced crystallization (thereafter called BNR-IC process). Generally, removal efficiencies of contaminants including carbon, nitrogen and phosphorus through wastewater biological treatment process may be attributed to characteristics of predominant microorganisms in activated sludge. In this BNR-IC process, microorganism enriched in the anoxic tank is one of key factors influencing

  4. Special Issue: Gene Conversion in Duplicated Genes

    Directory of Open Access Journals (Sweden)

    Hideki Innan

    2011-06-01

    Full Text Available Gene conversion is an outcome of recombination, causing non-reciprocal transfer of a DNA fragment. Several decades later than the discovery of crossing over, gene conversion was first recognized in fungi when non-Mendelian allelic distortion was observed. Gene conversion occurs when a double-strand break is repaired by using homologous sequences in the genome. In meiosis, there is a strong preference to use the orthologous region (allelic gene conversion, which causes non-Mendelian allelic distortion, but paralogous or duplicated regions can also be used for the repair (inter-locus gene conversion, also referred to as non-allelic and ectopic gene conversion. The focus of this special issue is the latter, interlocus gene conversion; the rate is lower than allelic gene conversion but it has more impact on phenotype because more drastic changes in DNA sequence are involved.

  5. Principles of gene therapy

    OpenAIRE

    Mammen Biju; Ramakrishnan T; Sudhakar Uma; Vijayalakshmi

    2007-01-01

    Genes are specific sequences of bases that encode instructions to make proteins. When genes are altered so that encoded proteins are unable to carry out their normal functions, genetic disorders can result. Gene therapy is designed to introduce genetic material into cells to compensate for abnormal genes or to make a beneficial protein. This article reviews the fundamentals in gene therapy and its various modes of administration with an insight into the role of gene therapy in Periodontics an...

  6. Organization of immunoglobulin genes.

    Science.gov (United States)

    Tonegawa, S; Brack, C; Hozumi, N; Pirrotta, V

    1978-01-01

    The nucleotide-sequence determination of a cloned, embryonic Vlambda gene directly demonstrated that V genes are separate from a corresponding C gene in embryonic cells. Analysis by restriction enzymes of total cellular DNA from various sources strongly suggested that the two separate immunoglobulin genes become continuous during differentiation of B lymphocytes. There seems to be a strict correlation between the joining event and activation of the joined genes. Cloning of more immunoglobulin genes from embryo and plasma cells will not only provide direct demonstration of such a gene-joining event but also help in the elucidation of a possible relationship of the event to gene activation mechanisms.

  7. Transcriptional analysis of the nirS gene, encoding cytochrome cd1 nitrite reductase, of Paracoccus pantotrophus LMD 92.63.

    Science.gov (United States)

    Saunders, N F; Ferguson, S J; Baker, S C

    2000-02-01

    The gene for cytochrome cd1 nitrite reductase of Paracoccus pantotrophus, a protein of known crystal structure, is nirS. This gene is shown to be flanked by genes previously recognized in other organisms to encode proteins involved in the control of its transcription (nirI) and the biosynthesis of the d1 cofactor (nirE). Northern blot analysis has established under anaerobic conditions that a monocistronic transcript is produced from nirS, in contrast to observations with other denitrifying bacteria in which arrangement of flanking genes is different and the messages produced are polycistronic. The lack of a transcript under aerobic conditions argues against a role for cytochrome cd1 in the previously proposed aerobic denitrification pathway in Pa. pantotrophus. A putative rho-independent transcription termination sequence immediately following nirS, and preceding nirE, can be identified. The independent transcription of nirS and nirE indicates that it should be possible to produce site-directed mutants of nirS borne on a plasmid in a nirS deletion mutant. The transcript start point for nirS has been determined by two complementary techniques, 5'-RACE (Rapid amplification of cDNA 5' ends) and primer extension. It is 29 bp upstream of the AUG of nirS. An anaerobox, which presumably binds Nnr, is centred a further 41.5 bp upstream of the transcript start. No standard sigma70 DNA sequence motifs can be identified, but a conserved sequence (T-T-GIC-C-G/C-G/C) can be found in approximately the same position (-16) upstream of the transcript starts of nirS and nirI, whose products are both involved in the conversion of nitrite to nitric oxide.

  8. Gene doping: gene delivery for olympic victory.

    Science.gov (United States)

    Gould, David

    2013-08-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called 'gene doping'. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted from the engineered cells or is retained locally to, or inside engineered cells will, to some extent, determine the likelihood of detection. It is clear that effective gene delivery technologies now exist and it is important that detection and prevention plans are in place.

  9. Gene Cluster Statistics with Gene Families

    Science.gov (United States)

    Durand, Dannie

    2009-01-01

    Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such “gene clusters” is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters). Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. Surprisingly, despite the simplicity of the underlying assumption, our method accurately approximates the true cluster probabilities. It slightly overestimates these probabilities, yielding a conservative test. We present additional simulation results indicating the best choice of parameter values for data

  10. Effect of C/N ratio and pH on nitrous oxide production of themophic aerobic denitrifier%C/N和pH值对高温好氧反硝化菌产N_2O的影响研究

    Institute of Scientific and Technical Information of China (English)

    张苗; 黄少斌; 肖先念

    2012-01-01

    以50℃高温、好氧条件下能进行高效好氧反硝化的菌株TAD1为研究对象,在不同C/N和pH值培养条件下,对其24 h的反硝化效率和反硝化过程中N2O的逸出量进行了研究。结果显示,C/N和pH值对菌株TAD1的反硝化效率和N2O产生量有明显影响.菌株TAD1最适宜的C/N为9,pH值为7,此时反硝化效率达到99.12%,N2O产生量仅为3.35×10-2 mg/L,N2 O转化率为0.045%,反硝化产物以氮气为主。另外,菌株TAD1不适宜在酸性条件下生长,pH值为6时反硝化效率为83.18%,N2O产生量为13.88×10-2 mg/L,是pH值为7时的4.14倍,是pH值为8时的5.07倍。%Under different C/N ratios and pH,the experiment investigated the nitrogen removal efficiency and nitrous oxide production of thermophic aerobic denitrifier strain TAD1.The results indicated that the nitrogen removal efficiency and nitrous oxide production were influenced by C/N ratio and pH.The nitrogen removal efficiency was up to 99.12%,and nitrous oxide production was only 3.35×10-2 mg/L,N2O conversion rate was 0.045%,the major end production of denitrification was nitrogen under the optimum C/N ratio of 9 and pH 7.Additionally,acidity was not favorable for aerobic denitrification between 6 and 8 in pH,the nitrogen removal efficiency was 83.18% with pH 6,and the production of nitrous oxide was up to 13.88×10-2 mg/L,which was 4.14 times higher than that of pH 7 and 5.07 times higher than that of pH 8.

  11. Lateral gene transfer, rearrangement, reconciliation

    NARCIS (Netherlands)

    Patterson, M.D.; Szollosi, G.; Daubin, V.; Tannier, E.

    2013-01-01

    Background. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene trees. These models have so far ignored lateral gene transfer,

  12. 土壤浸提液中硝酸盐氮氧同位素组成的反硝化细菌法测定%Determination of 15N and 18O isotope abundance in the extractable soil nitrate by the denitrifier method

    Institute of Scientific and Technical Information of China (English)

    徐春英; 李玉中; 李巧珍; 毛丽丽; 林伟; 强晓晶; 郑欠

    2016-01-01

    本研究优化了采用反硝化细菌法同时测定土壤浸提液中硝酸盐氮氧同位素组成的方法。在已有研究结果的基础上,通过采用5000~8000 r·min-1的转速离心、高纯氮气吹扫1 h、减少加样量及改造仪器自动进样器等措施对已发表方法进行了优化。对国际标准样品 USGS34的分析表明,0.1~0.8μg NO-3-N 样品量即可以得到较稳定、准确的测定值和校正值;同一时间内制备的硝酸盐δ15N 的 SD 介于0.05‰~0.09‰之间,δ18O 的 SD 介于0.28‰~0.48‰之间;在三个月之内δ15N 和δ18O 的测定值基本一致,表明该方法具有较好的准确度、精密度和稳定性。通过研究浸提剂、保存条件以及加热对测定土壤浸提液中硝酸盐氮氧同位素组成的影响,结果表明:常用的去离子水、KCl、CaCl2可能都含有微量的硝酸盐,随着加样量增大,浸提剂中含有的硝酸盐可能就会影响δ15N 和δ18O的测定;对于土壤硝酸盐的浸提液,冷冻保存效果较好,保证了土壤硝酸盐氮氧同位素的准确性和稳定性;尽管加热对硝酸盐标准样品 USGS34和 IAEA-NO3的δ15N 没有显著影响,但δ18O 显著升高,说明加热易引起氧同位素分馏;而土壤硝酸盐浸提液样品加热前后的δ15N 和δ18O 的测定值没有显著变化,因此为避免产生氧同位素分馏和节省测试时间,建议同时测定土壤浸提液硝酸盐δ15N和δ18O 时直接和反硝化细菌反应。应用本方法对不同肥料处理田间土壤浸提液硝酸盐的氮氧同位素组成进行了测定。%A method has been established for determing simultaneously 15N and 18O isotope abundance in the extractable soil nitrate using denitrifier bacteria. The method was optimized by using 5000~8000 r·min-1 centrifugal rotational speed, purging 1 h with high pure N2, re-ducing the amounts of samples and improving the autosampler based on the preliminary findings

  13. Effects of carbon source on nitrogen removal of heterotrophic nitrifying and aerobic denitrifying bacteria strain qy37%包埋异养硝化好氧反硝化菌株qy37脱氮效果的碳源选择

    Institute of Scientific and Technical Information of China (English)

    张培玉; 张晨; 孙梦; 吴玉光

    2011-01-01

    This paper is concerned about the influence of the carbon source on the nitrogen removing rate in case of the heterotrophic nitrifying and aerobic denitrifying bacteria strain qy37. As is known, carbon source and its concentration may have significant effects on the bio-denitrification process. To solve the problem of low nitrogen removing rate due to the shortage of organic carbon, we have made thorough revision of the advances made in the world in recent years and explored the related mechanisms and factors affecting denitrifica-tion along with the analysis of the carbon source choice. Furthermore, we have conducted experiments in testing the potential of immobilized denitrifier of a strain coded as qy37 so as to reduce the nitrate at the presence of five different carbon sources, namely, lactose, sodium citrate, soluble starch, cane sugar and glucose. According to the features of carbon source and the potential influence on the water denitri-fication, we have chosen soluble starch as an available plant carbon source. The results of our study show the order of the nitrogen removal rate turns to be as follows: soluble starch > glucose > cane sugar > sodium citrate > lactose, of which soluble starch comes first. It has also been found that nitrogen removal rate can be made as high as above 85% . Right amount of soluble starch added helps to improve the removing rate while enhancing the mechanical strength of sodium alga acid and PVA ball, reducing the adsorption of PVA and water swelling simultaneously. Besides, the most appropriate concentration of the nitrogen removal has been found by changing different concentrations of the carbon source, for example, concentrations of 3 g/L, 5 g/L, 8 g/L, 10 g/L with soluble starch as carbon source. The results of our study indicate that the optimal concentration of carbon sources should be 8 g/L. Besides, we have also studied the method of embedding carbon source, that is, the denitrification rate by embedding carbon

  14. Gene doping in sports.

    Science.gov (United States)

    Unal, Mehmet; Ozer Unal, Durisehvar

    2004-01-01

    Gene or cell doping is defined by the World Anti-Doping Agency (WADA) as "the non-therapeutic use of genes, genetic elements and/or cells that have the capacity to enhance athletic performance". New research in genetics and genomics will be used not only to diagnose and treat disease, but also to attempt to enhance human performance. In recent years, gene therapy has shown progress and positive results that have highlighted the potential misuse of this technology and the debate of 'gene doping'. Gene therapies developed for the treatment of diseases such as anaemia (the gene for erythropoietin), muscular dystrophy (the gene for insulin-like growth factor-1) and peripheral vascular diseases (the gene for vascular endothelial growth factor) are potential doping methods. With progress in gene technology, many other genes with this potential will be discovered. For this reason, it is important to develop timely legal regulations and to research the field of gene doping in order to develop methods of detection. To protect the health of athletes and to ensure equal competitive conditions, the International Olympic Committee, WADA and International Sports Federations have accepted performance-enhancing substances and methods as being doping, and have forbidden them. Nevertheless, the desire to win causes athletes to misuse these drugs and methods. This paper reviews the current status of gene doping and candidate performance enhancement genes, and also the use of gene therapy in sports medicine and ethics of genetic enhancement.

  15. Human Gene Therapy: Genes without Frontiers?

    Science.gov (United States)

    Simon, Eric J.

    2002-01-01

    Describes the latest advancements and setbacks in human gene therapy to provide reference material for biology teachers to use in their science classes. Focuses on basic concepts such as recombinant DNA technology, and provides examples of human gene therapy such as severe combined immunodeficiency syndrome, familial hypercholesterolemia, and…

  16. Genes and Hearing Loss

    Science.gov (United States)

    ... Find an ENT Doctor Near You Genes and Hearing Loss Genes and Hearing Loss Patient Health Information News media interested in covering ... One of the most common birth defects is hearing loss or deafness (congenital), which can affect as many ...

  17. Essential Bacillus subtilis genes

    DEFF Research Database (Denmark)

    Kobayashi, K.; Ehrlich, S.D.; Albertini, A.

    2003-01-01

    To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximate to4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were...... predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related...... to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from...

  18. Cochlear Gene Therapy

    OpenAIRE

    2012-01-01

    The purpose of this review is to highlight recent advances in cochlear gene therapy over the past several years. Cochlear gene therapy has undergone tremendous advances over the past decade. Beginning with some groundbreaking work in 2005 documenting hair cell regeneration using virallymediated delivery of the mouse atonal 1 gene, gene therapy is now being explored as a possible treatment for a variety of causes of hearing loss.

  19. Discovering genes underlying QTL

    Energy Technology Data Exchange (ETDEWEB)

    Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

    2002-02-01

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  20. Reading and Generalist Genes

    Science.gov (United States)

    Haworth, Claire M. A.; Meaburn, Emma L.; Harlaar, Nicole; Plomin, Robert

    2007-01-01

    Twin-study research suggests that many (but not all) of the same genes contribute to genetic influence on diverse learning abilities and disabilities, a hypothesis called "generalist genes". This generalist genes hypothesis was tested using a set of 10 DNA markers (single nucleotide polymorphisms [SNPs]) found to be associated with early reading…

  1. Anaerobic degradation of anionic surfactants by denitrifying bacteria

    NARCIS (Netherlands)

    Paulo, A.

    2014-01-01

    De verwijdering van organische stof alsook van stikstof en fosfor wordt in RWZI vaak bewerkstelligd middels een anaëroob-anoxisch-aëroob (A2/O) proces. Met behulp van het A2/O proces kunnen oppervlakte-actieve stoffen al in het anaërobe dan wel anoxische compartiment afgebroken worden. In dit proefs

  2. Macrofaunal Impact on the Denitrifying Bacterial Community in Freshwater Sediment

    DEFF Research Database (Denmark)

    Poulsen, Morten; Stief, Peter; Schramm, Andreas

    actively expressed in the gut contents of C. plumosus. The remaining increase may be due to the creation of a (on the microscale) more structured habitat by larval activities like burrow construction, bioturbation, and water pumping, possibly combined with a general activation of microbes by enriching...

  3. Biodegradation of a surrogate naphthenic acid under denitrifying conditions.

    Science.gov (United States)

    Gunawan, Yetty; Nemati, Mehdi; Dalai, Ajay

    2014-03-15

    Extraction of bitumen from the shallow oil sands generates extremely large volumes of waters contaminated by naphthenic acid which pose severe environmental and ecological risks. Aerobic biodegradation of NA in properly designed bioreactors has been investigated in our earlier works. In the present work, anoxic biodegradation of trans-4-methyl-1-cyclohexane carboxylic acid (trans-4MCHCA) coupled to denitrification was investigated as a potential ex situ approach for the treatment of oil sand process waters in bioreactors whereby excessive aeration cost could be eliminated, or as an in situ alternative for the treatment of these waters in anoxic stabilization ponds amended with nitrate. Using batch and continuous reactors (CSTR and biofilm), effects of NA concentration (100-750mgL(-1)), NA loading rate (up to 2607.9mgL(-1)h(-1)) and temperature (10-35°C) on biodegradation and denitrification processes were evaluated. In the batch system biodegradation of trans-4MCHCA coupled to denitrification occurred even at the highest concentration of 750mgL(-1). Consistent with the patterns reported for aerobic biodegradation, increase in initial concentration of NA led to higher biodegradation and denitrification rates and the optimum temperature was determined as 23-24°C. In the CSTR, NA removal and nitrate reduction rates passed through a maximum due to increases in NA loading rate. NA loading rate of 157.8mgL(-1)h(-1) at which maximum anoxic NA and nitrate removal rates (105.3mgL(-1)h(-1) and 144.5mgL(-1)h(-1), respectively) occurred was much higher than those reported for the aerobic alternative (NA loading and removal rates: 14.2 and 9.6mgL(-1)h(-1), respectively). In the anoxic biofilm reactor removal rates of NA and nitrate were dependent on NA loading rate in a linear fashion for the entire range of applied loading rates. The highest loading and removal rates for NA were 2607.9 and 2028.1mgL(-1)h(-1), respectively which were at least twofold higher than the values reported for the aerobic biofilm reactor. The highest nitrate removal rate coincided with maximum removal rate of NA and was 3164.7mgL(-1)h(-1).

  4. Journey from Jumping Genes to Gene Therapy.

    Science.gov (United States)

    Whartenby, Katharine A

    2015-01-01

    Gene therapy for cancer is a still evolving approach that resulted from a long history of studies into genetic modification of organisms. The fascination with manipulating gene products has spanned hundreds if not thousands of years, beginning with observations of the hereditary nature of traits in plants and culminating to date in the alteration of genetic makeup in humans via modern technology. From early discoveries noting the potential for natural mobility of genetic material to the culmination of clinical trials in a variety of disease, gene transfer has had an eventful and sometimes tumultuous course. Within the present review is a brief history of the biology of gene transfer, how it came to be applied to genetic diseases, and its early applications to cancer therapies. Some of the different types of methods used to modify cells, the theories behind the approaches, and some of the limitations encountered along the way are reviewed.

  5. Effect of heavy metals on nitrification activity as measured by RNA- and DNA-based function-specific assays

    Science.gov (United States)

    Heavy metals can inhibit nitrification, a key process for nitrogen removal in wastewater treatment. The transcriptional responses of functional genes (amoA, hao, nirK and norB) were measured in conjunction with specific oxygen uptake rate (sOUR) for nitrifying enrichment cultures...

  6. Gene conversion in human rearranged immunoglobulin genes.

    Science.gov (United States)

    Darlow, John M; Stott, David I

    2006-07-01

    Over the past 20 years, many DNA sequences have been published suggesting that all or part of the V(H) segment of a rearranged immunoglobulin gene may be replaced in vivo. Two different mechanisms appear to be operating. One of these is very similar to primary V(D)J recombination, involving the RAG proteins acting upon recombination signal sequences, and this has recently been proven to occur. Other sequences, many of which show partial V(H) replacements with no addition of untemplated nucleotides at the V(H)-V(H) joint, have been proposed to occur by an unusual RAG-mediated recombination with the formation of hybrid (coding-to-signal) joints. These appear to occur in cells already undergoing somatic hypermutation in which, some authors are convinced, RAG genes are silenced. We recently proposed that the latter type of V(H) replacement might occur by homologous recombination initiated by the activity of AID (activation-induced cytidine deaminase), which is essential for somatic hypermutation and gene conversion. The latter has been observed in other species, but not in human Ig genes, so far. In this paper, we present a new analysis of sequences published as examples of the second type of rearrangement. This not only shows that AID recognition motifs occur in recombination regions but also that some sequences show replacement of central sections by a sequence from another gene, similar to gene conversion in the immunoglobulin genes of other species. These observations support the proposal that this type of rearrangement is likely to be AID-mediated rather than RAG-mediated and is consistent with gene conversion.

  7. Gene therapy in periodontics

    Directory of Open Access Journals (Sweden)

    Anirban Chatterjee

    2013-01-01

    Full Text Available GENES are made of DNA - the code of life. They are made up of two types of base pair from different number of hydrogen bonds AT, GC which can be turned into instruction. Everyone inherits genes from their parents and passes them on in turn to their children. Every person′s genes are different, and the changes in sequence determine the inherited differences between each of us. Some changes, usually in a single gene, may cause serious diseases. Gene therapy is ′the use of genes as medicine′. It involves the transfer of a therapeutic or working gene copy into specific cells of an individual in order to repair a faulty gene copy. Thus it may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. It has a promising era in the field of periodontics. Gene therapy has been used as a mode of tissue engineering in periodontics. The tissue engineering approach reconstructs the natural target tissue by combining four elements namely: Scaffold, signaling molecules, cells and blood supply and thus can help in the reconstruction of damaged periodontium including cementum, gingival, periodontal ligament and bone.

  8. Regulated Gene Therapy.

    Science.gov (United States)

    Breger, Ludivine; Wettergren, Erika Elgstrand; Quintino, Luis; Lundberg, Cecilia

    2016-01-01

    Gene therapy represents a promising approach for the treatment of monogenic and multifactorial neurological disorders. It can be used to replace a missing gene and mutated gene or downregulate a causal gene. Despite the versatility of gene therapy, one of the main limitations lies in the irreversibility of the process: once delivered to target cells, the gene of interest is constitutively expressed and cannot be removed. Therefore, efficient, safe and long-term gene modification requires a system allowing fine control of transgene expression.Different systems have been developed over the past decades to regulate transgene expression after in vivo delivery, either at transcriptional or post-translational levels. The purpose of this chapter is to give an overview on current regulatory system used in the context of gene therapy for neurological disorders. Systems using external regulation of transgenes using antibiotics are commonly used to control either gene expression using tetracycline-controlled transcription or protein levels using destabilizing domain technology. Alternatively, specific promoters of genes that are regulated by disease mechanisms, increasing expression as the disease progresses or decreasing expression as disease regresses, are also examined. Overall, this chapter discusses advantages and drawbacks of current molecular methods for regulated gene therapy in the central nervous system.

  9. Gene therapy: An overview

    Directory of Open Access Journals (Sweden)

    Sudip Indu

    2013-01-01

    Full Text Available Gene therapy "the use of genes as medicine" involves the transfer of a therapeutic or working copy of a gene into specific cells of an individual in order to repair a faulty gene copy. The technique may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. The objective of gene therapy is to introduce new genetic material into target cells while causing no damage to the surrounding healthy cells and tissues, hence the treatment related morbidity is decreased. The delivery system includes a vector that delivers a therapeutic gene into the patient′s target cell. Functional proteins are created from the therapeutic gene causing the cell to return to a normal stage. The vectors used in gene therapy can be viral and non-viral. Gene therapy, an emerging field of biomedicine, is still at infancy and much research remains to be done before this approach to the treatment of condition will realize its full potential.

  10. Gene therapy in periodontics.

    Science.gov (United States)

    Chatterjee, Anirban; Singh, Nidhi; Saluja, Mini

    2013-03-01

    GENES are made of DNA - the code of life. They are made up of two types of base pair from different number of hydrogen bonds AT, GC which can be turned into instruction. Everyone inherits genes from their parents and passes them on in turn to their children. Every person's genes are different, and the changes in sequence determine the inherited differences between each of us. Some changes, usually in a single gene, may cause serious diseases. Gene therapy is 'the use of genes as medicine'. It involves the transfer of a therapeutic or working gene copy into specific cells of an individual in order to repair a faulty gene copy. Thus it may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. It has a promising era in the field of periodontics. Gene therapy has been used as a mode of tissue engineering in periodontics. The tissue engineering approach reconstructs the natural target tissue by combining four elements namely: Scaffold, signaling molecules, cells and blood supply and thus can help in the reconstruction of damaged periodontium including cementum, gingival, periodontal ligament and bone.

  11. Cyanobacterial signature genes.

    Science.gov (United States)

    Martin, Kirt A; Siefert, Janet L; Yerrapragada, Sailaja; Lu, Yue; McNeill, Thomas Z; Moreno, Pedro A; Weinstock, George M; Widger, William R; Fox, George E

    2003-01-01

    A comparison of 8 cyanobacterial genomes reveals that there are 181 shared genes that do not have obvious orthologs in other bacteria. These signature genes define aspects of the genotype that are uniquely cyanobacterial. Approximately 25% of these genes have been associated with some function. These signature genes may or may not be involved in photosynthesis but likely they will be in many cases. In addition, several examples of widely conserved gene order involving two or more signature genes were observed. This suggests there may be regulatory processes that have been preserved throughout the long history of the cyanobacterial phenotype. The results presented here will be especially useful because they identify which of the many genes of unassigned function are likely to be of the greatest interest.

  12. 好氧反硝化菌AD-1处理大豆乳清废水厌氧出水的性能评价%Performance Assessment on An Aerobic Denitrifier AD-1 Treating Soybean Whey Wastewater Anaerobic Effluent

    Institute of Scientific and Technical Information of China (English)

    蔡广潞; 吴培; 张国宁; 吴世晗

    2011-01-01

    To increase nitrogen removal efficiency, the study screened a high-efficiency aerobic denitrifier AD-1 in the activated sludge originated from a university previous designed CAAC (Continuous Aerobic-anaerobic Coupled)reactor treating SWWAE (Soybean Whey Wastewater Anaerobic Effluent).The strain was identified as pseudomonas putida according to the 16S rDNA sequence homology comparison and phyletic evolution analysis.The denitrification efficiency of Pseudomonas putida AD-1 was analyzed in DM medium feeding nitrate as the sole nitrogen source by shake-flask batch culture.After 48h the TN and nitrate removal rate reached 63.31% and 63.35%, respectively.Nitrite concentration was always at low level but fluctuated.At the later culture stage the low COD/TN ratio was one of main rate-limiting factors.AD-1 had high-efficiency denitrification with 100% nitrate removal rate in the process of treating SWWAE.Results indicated thai AD-1 was a good bioaugmentation agent for SWWAE and other nitrogenous wastewater treatment.%为了提高污水中氮素的去除效率,本研究自某大学微生物实验室开发的处理大豆乳清废水厌氧出水的CAAC(Continuous Aerobicanaerobic Coupled)反应器污泥中筛选出l株高效好氧反硝化菌AD-1,经16S rDNA序列同源性比较和系统发育分析初步鉴定为恶臭假单胞菌(pseudomonas putida).通过摇瓶批次培养考察菌株AD-1对以硝酸盐为唯一氮源的DM反硝化培养基的脱氮性能.48h时AD-1的TN和N03-N去除率分别达到63.31%和63.35%,N02-N浓度虽始终处于较低水平却呈高低波动状态,培养后期CODcr/TN下降是限制AD-1反硝化效率的主要因素之一.AD-1处理大豆乳清废水厌氧出水时NO3-N去除率接近100%,具有较高效的反硝化特性.结果表明,该菌株可作为处理大豆乳清废水厌氧出水及其它含氮废水的生物强化剂.

  13. Primetime for Learning Genes

    Science.gov (United States)

    Keifer, Joyce

    2017-01-01

    Learning genes in mature neurons are uniquely suited to respond rapidly to specific environmental stimuli. Expression of individual learning genes, therefore, requires regulatory mechanisms that have the flexibility to respond with transcriptional activation or repression to select appropriate physiological and behavioral responses. Among the mechanisms that equip genes to respond adaptively are bivalent domains. These are specific histone modifications localized to gene promoters that are characteristic of both gene activation and repression, and have been studied primarily for developmental genes in embryonic stem cells. In this review, studies of the epigenetic regulation of learning genes in neurons, particularly the brain-derived neurotrophic factor gene (BDNF), by methylation/demethylation and chromatin modifications in the context of learning and memory will be highlighted. Because of the unique function of learning genes in the mature brain, it is proposed that bivalent domains are a characteristic feature of the chromatin landscape surrounding their promoters. This allows them to be “poised” for rapid response to activate or repress gene expression depending on environmental stimuli. PMID:28208656

  14. Primetime for Learning Genes.

    Science.gov (United States)

    Keifer, Joyce

    2017-02-11

    Learning genes in mature neurons are uniquely suited to respond rapidly to specific environmental stimuli. Expression of individual learning genes, therefore, requires regulatory mechanisms that have the flexibility to respond with transcriptional activation or repression to select appropriate physiological and behavioral responses. Among the mechanisms that equip genes to respond adaptively are bivalent domains. These are specific histone modifications localized to gene promoters that are characteristic of both gene activation and repression, and have been studied primarily for developmental genes in embryonic stem cells. In this review, studies of the epigenetic regulation of learning genes in neurons, particularly the brain-derived neurotrophic factor gene (BDNF), by methylation/demethylation and chromatin modifications in the context of learning and memory will be highlighted. Because of the unique function of learning genes in the mature brain, it is proposed that bivalent domains are a characteristic feature of the chromatin landscape surrounding their promoters. This allows them to be "poised" for rapid response to activate or repress gene expression depending on environmental stimuli.

  15. An Ontology of Gene

    OpenAIRE

    Masuya, Hiroshi; Mizoguchi, Riichiro

    2012-01-01

    The concept of a gene was established in the era of classical genetics and is now essential for life science for elucidating the molecular basis of the coding of genetic information necessary to realize the body of an organism and its biological functions. However, an ontology fully representing multiple aspects of a gene is still not available. In this study, we dissected the biological and ontological definitions of bearers of genetic information, including genes and alleles. Based on this ...

  16. Placental gene therapy

    OpenAIRE

    David, A. L.; Ashcroft, R

    2009-01-01

    Gene therapy uses genetic material as a drug delivery vehicle to express therapeutic proteins. Placental gene therapy may be useful for correction of two important obstetric conditions, foetal growth restriction and pre-eclampsia in which there is a failure of the physiological trophoblast remodelling of the uterine spiral arteries in early pregnancy. The patient in this scenario is the foetus. Placental gene therapy might be justifiable when: there is reasonable certainty that the foetus wil...

  17. Antisense gene silencing

    DEFF Research Database (Denmark)

    Nielsen, Troels T; Nielsen, Jørgen E

    2013-01-01

    Since the first reports that double-stranded RNAs can efficiently silence gene expression in C. elegans, the technology of RNA interference (RNAi) has been intensively exploited as an experimental tool to study gene function. With the subsequent discovery that RNAi could also be applied to mammal......Since the first reports that double-stranded RNAs can efficiently silence gene expression in C. elegans, the technology of RNA interference (RNAi) has been intensively exploited as an experimental tool to study gene function. With the subsequent discovery that RNAi could also be applied...

  18. History of gene therapy.

    Science.gov (United States)

    Wirth, Thomas; Parker, Nigel; Ylä-Herttuala, Seppo

    2013-08-10

    Two decades after the initial gene therapy trials and more than 1700 approved clinical trials worldwide we not only have gained much new information and knowledge regarding gene therapy in general, but also learned to understand the concern that has persisted in society. Despite the setbacks gene therapy has faced, success stories have increasingly emerged. Examples for these are the positive recommendation for a gene therapy product (Glybera) by the EMA for approval in the European Union and the positive trials for the treatment of ADA deficiency, SCID-X1 and adrenoleukodystrophy. Nevertheless, our knowledge continues to grow and during the course of time more safety data has become available that helps us to develop better gene therapy approaches. Also, with the increased understanding of molecular medicine, we have been able to develop more specific and efficient gene transfer vectors which are now producing clinical results. In this review, we will take a historical view and highlight some of the milestones that had an important impact on the development of gene therapy. We will also discuss briefly the safety and ethical aspects of gene therapy and address some concerns that have been connected with gene therapy as an important therapeutic modality.

  19. Ammonia Oxidation and Nitrite Reduction in the Verrucomicrobial Methanotroph Methylacidiphilum fumariolicum SolV

    Directory of Open Access Journals (Sweden)

    Sepehr S. Mohammadi

    2017-09-01

    Full Text Available The Solfatara volcano near Naples (Italy, the origin of the recently discovered verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV was shown to contain ammonium (NH4+ at concentrations ranging from 1 to 28 mM. Ammonia (NH3 can be converted to toxic hydroxylamine (NH2OH by the particulate methane monooxygenase (pMMO, the first enzyme of the methane (CH4 oxidation pathway. Methanotrophs rapidly detoxify the intermediate NH2OH. Here, we show that strain SolV performs ammonium oxidation to nitrite at a rate of 48.2 nmol NO2-.h−1.mg DW−1 under O2 limitation in a continuous culture grown on hydrogen (H2 as an electron donor. In addition, strain SolV carries out nitrite reduction at a rate of 74.4 nmol NO2-.h−1.mg DW−1 under anoxic condition at pH 5–6. This range of pH was selected to minimize the chemical conversion of nitrite (NO2- potentially occurring at more acidic pH values. Furthermore, at pH 6, we showed that the affinity constants (Ks of the cells for NH3 vary from 5 to 270 μM in the batch incubations with 0.5–8% (v/v CH4, respectively. Detailed kinetic analysis showed competitive substrate inhibition between CH4 and NH3. Using transcriptome analysis, we showed up-regulation of the gene encoding hydroxylamine dehydrogenase (haoA cells grown on H2/NH4+ compared to the cells grown on CH4/NO3- which do not have to cope with reactive N-compounds. The denitrifying genes nirk and norC showed high expression in H2/NH4+ and CH4/NO3- grown cells compared to cells growing at μmax (with no limitation while the norB gene showed downregulation in CH4/NO3- grown cells. These cells showed a strong upregulation of the genes in nitrate/nitrite assimilation. Our results demonstrate that strain SolV can perform ammonium oxidation producing nitrite. At high concentrations of ammonium this may results in toxic effects. However, at low oxygen concentrations strain SolV is able to reduce nitrite to N2O to cope with this toxicity.

  20. Delivery Systems in Gene Therapy

    Institute of Scientific and Technical Information of China (English)

    Liu Hu; Anas El-Aneed; Cui Guohui

    2005-01-01

    1 Gene therapy Gene therapy includes the treatment of both genetically based and infectious diseases by introducing genetic materials which have therapeutic effects[1~3]. In its simplest terms, a wild type gene (which is non-functional in the cell leading to disease development) is introduced into the somatic cell lacking this gene to restore the normal gene function in this cell. Many gene therapy strategies, however, utilize genes to destroy specific cells.

  1. Gene promoters dictate histone occupancy within genes.

    Science.gov (United States)

    Perales, Roberto; Erickson, Benjamin; Zhang, Lian; Kim, Hyunmin; Valiquett, Elan; Bentley, David

    2013-10-01

    Spt6 is a transcriptional elongation factor and histone chaperone that reassembles transcribed chromatin. Genome-wide H3 mapping showed that Spt6 preferentially maintains nucleosomes within the first 500 bases of genes and helps define nucleosome-depleted regions in 5' and 3' flanking sequences. In Spt6-depleted cells, H3 loss at 5' ends correlates with reduced pol II density suggesting enhanced transcription elongation. Consistent with its 'Suppressor of Ty' (Spt) phenotype, Spt6 inactivation caused localized H3 eviction over 1-2 nucleosomes at 5' ends of Ty elements. H3 displacement differed between genes driven by promoters with 'open'/DPN and 'closed'/OPN chromatin conformations with similar pol II densities. More eviction occurred on genes with 'closed' promoters, associated with 'noisy' transcription. Moreover, swapping of 'open' and 'closed' promoters showed that they can specify distinct downstream patterns of histone eviction/deposition. These observations suggest a novel function for promoters in dictating histone dynamics within genes possibly through effects on transcriptional bursting or elongation rate.

  2. Smart Genes, Stupid Science.

    Science.gov (United States)

    Randerson, Sherman; Mahadeva, Madhu N.

    1983-01-01

    Because many people still believe that specific, identifiable genes dictate the level of human intelligence and that the number/quality of these genes can be evaluated, presents evidence from human genetics (related to nervous system development) to counter this view. Also disputes erroneous assumptions made in "heritability studies" of human…

  3. XLMR genes: update 2000.

    NARCIS (Netherlands)

    Chiurazzi, P.; Hamel, B.C.J.; Neri, G.

    2001-01-01

    This is the sixth edition of the catalogue of XLMR genes, ie X-linked genes whose malfunctioning causes mental retardation. The cloning era is not yet concluded, actually much remains to be done to account for the 202 XLMR conditions listed in this update. Many of these may eventually prove to be du

  4. Glaucoma Genes and Mechanisms.

    Science.gov (United States)

    Wiggs, Janey L

    2015-01-01

    Genetic studies have yielded important genes contributing to both early-onset and adult-onset forms of glaucoma. The proteins encoded by the current collection of glaucoma genes participate in a broad range of cellular processes and biological systems. Approximately half the glaucoma-related genes function in the extracellular matrix, however proteins involved in cytokine signaling, lipid metabolism, membrane biology, regulation of cell division, autophagy, and ocular development also contribute to the disease pathogenesis. While the function of these proteins in health and disease are not completely understood, recent studies are providing insight into underlying disease mechanisms, a critical step toward the development of gene-based therapies. In this review, genes known to cause early-onset glaucoma or contribute to adult-onset glaucoma are organized according to the cell processes or biological systems that are impacted by the function of the disease-related protein product.

  5. Gene therapy for hemophilia.

    Science.gov (United States)

    Chuah, M K; Evens, H; VandenDriessche, T

    2013-06-01

    Hemophilia A and B are X-linked monogenic disorders resulting from deficiencies of factor VIII and FIX, respectively. Purified clotting factor concentrates are currently intravenously administered to treat hemophilia, but this treatment is non-curative. Therefore, gene-based therapies for hemophilia have been developed to achieve sustained high levels of clotting factor expression to correct the clinical phenotype. Over the past two decades, different types of viral and non-viral gene delivery systems have been explored for hemophilia gene therapy research with a variety of target cells, particularly hepatocytes, hematopoietic stem cells, skeletal muscle cells, and endothelial cells. Lentiviral and adeno-associated virus (AAV)-based vectors are among the most promising vectors for hemophilia gene therapy. In preclinical hemophilia A and B animal models, the bleeding phenotype was corrected with these vectors. Some of these promising preclinical results prompted clinical translation to patients suffering from a severe hemophilic phenotype. These patients receiving gene therapy with AAV vectors showed long-term expression of therapeutic FIX levels, which is a major step forwards in this field. Nevertheless, the levels were insufficient to prevent trauma or injury-induced bleeding episodes. Another challenge that remains is the possible immune destruction of gene-modified cells by effector T cells, which are directed against the AAV vector antigens. It is therefore important to continuously improve the current gene therapy approaches to ultimately establish a real cure for hemophilia. © 2013 International Society on Thrombosis and Haemostasis.

  6. Gene amplification in carcinogenesis

    Directory of Open Access Journals (Sweden)

    Lucimari Bizari

    2006-01-01

    Full Text Available Gene amplification increases the number of genes in a genome and can give rise to karyotype abnormalities called double minutes (DM and homogeneously staining regions (HSR, both of which have been widely observed in human tumors but are also known to play a major role during embryonic development due to the fact that they are responsible for the programmed increase of gene expression. The etiology of gene amplification during carcinogenesis is not yet completely understood but can be considered a result of genetic instability. Gene amplification leads to an increase in protein expression and provides a selective advantage during cell growth. Oncogenes such as CCND1, c-MET, c-MYC, ERBB2, EGFR and MDM2 are amplified in human tumors and can be associated with increased expression of their respective proteins or not. In general, gene amplification is associated with more aggressive tumors, metastases, resistance to chemotherapy and a decrease in the period during which the patient stays free of the disease. This review discusses the major role of gene amplification in the progression of carcinomas, formation of genetic markers and as possible therapeutic targets for the development of drugs for the treatment of some types of tumors.

  7. Antisense gene silencing

    DEFF Research Database (Denmark)

    Nielsen, Troels T; Nielsen, Jørgen E

    2013-01-01

    Since the first reports that double-stranded RNAs can efficiently silence gene expression in C. elegans, the technology of RNA interference (RNAi) has been intensively exploited as an experimental tool to study gene function. With the subsequent discovery that RNAi could also be applied...... to mammalian cells, the technology of RNAi expanded from being a valuable experimental tool to being an applicable method for gene-specific therapeutic regulation, and much effort has been put into further refinement of the technique. This review will focus on how RNAi has developed over the years and how...

  8. Gene Therapy of Cancerous Diseases

    OpenAIRE

    Valenčáková, A.; Dziaková, A.; Hatalová, E.

    2015-01-01

    Gene therapy of cancerous diseases provides new means of curing patients with oncologic illnesses. There are several approaches in treating cancer by gene therapy. Most commonly used methods are: cancer immunogene therapy, suicide gene therapy, application of tumor-suppressor genes, antiangiogenic therapy, mesenchymal stem cells used as vectors, gene directed enzyme/prodrug therapy and bacteria used as anti-cancer agents. Cancer gene immunotherapy uses several immunologic agents for the purp...

  9. "Bad genes" & criminal responsibility.

    Science.gov (United States)

    González-Tapia, María Isabel; Obsuth, Ingrid

    2015-01-01

    The genetics of the accused is trying to break into the courts. To date several candidate genes have been put forward and their links to antisocial behavior have been examined and documented with some consistency. In this paper, we focus on the so called "warrior gene", or the low-activity allele of the MAOA gene, which has been most consistently related to human behavior and specifically to violence and antisocial behavior. In preparing this paper we had two objectives. First, to summarize and analyze the current scientific evidence, in order to gain an in depth understanding of the state of the issue and determine whether a dominant line of generally accepted scientific knowledge in this field can be asserted. Second, to derive conclusions and put forward recommendations related to the use of genetic information, specifically the presence of the low-activity genotype of the MAOA gene, in modulation of criminal responsibility in European and US courts.

  10. Gene Expression Omnibus (GEO)

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene Expression Omnibus is a public functional genomics data repository supporting MIAME-compliant submissions of array- and sequence-based data. Tools are provided...

  11. Gene therapy in ophthalmology.

    Science.gov (United States)

    Uthra, Satagopan; Kumaramanickavel, Govindasamy

    2009-09-01

    It has been more than a year since ophthalmologists and scientists under Dr. Robin Ali's team at the Moorsfield Eye Hospital and the Institute of Ophthalmology, University College London, successfully treated patients with a severely blinding disease, Leber's congenital amaurosis (LCA) using gene therapy. This success does not look to be transient, and this achievement in gene replacement therapy clinical trial for LCA has instilled hope in numerous families with patients suffering from this and similar retinal degenerative diseases, for whom restoration of lost vision has remained a distant dream so far. The encouragement that this success has given is expected to also lead to start of clinical trials for other blinding ocular diseases for which gene therapy experiments at the laboratory and animal levels have been successful. This article reviews the various studies that have led to the understanding of gene therapy outcomes in human ocular diseases and attempts to provide a brief sketch of successful clinical trials.

  12. Gene therapy for hemophilia.

    Science.gov (United States)

    Hortelano, G; Chang, P L

    2000-01-01

    Hemophilia A and B are X-linked genetic disorders caused by deficiency of the coagulation factors VIII and IX, respectively. Because of the health hazards and costs of current product replacement therapy, much effort is devoted to the development of gene therapy for these disorders. Approaches to gene therapy for the hemophilias include: ex vivo gene therapy in which cells from the intended recipients are explanted, genetically modified to secrete Factor VIII or IX, and reimplanted into the donor; in vivo gene therapy in which Factor VIII or IX encoding vectors are directly injected into the recipient; and non-autologous gene therapy in which universal cell lines engineered to secrete Factor VIII or IX are enclosed in immuno-protective devices before implantation into recipients. Research into these approaches is aided by the many murine and canine models available. While problems of achieving high and sustained levels of factor delivery, and issues related to efficacy, safety and cost are still to be resolved, progress in gene therapy for the hemophilias has been encouraging and is likely to reach human clinical trial in the foreseeable future.

  13. Evidence for homosexuality gene

    Energy Technology Data Exchange (ETDEWEB)

    Pool, R.

    1993-07-16

    A genetic analysis of 40 pairs of homosexual brothers has uncovered a region on the X chromosome that appears to contain a gene or genes for homosexuality. When analyzing the pedigrees of homosexual males, the researcheres found evidence that the trait has a higher likelihood of being passed through maternal genes. This led them to search the X chromosome for genes predisposing to homosexuality. The researchers examined the X chromosomes of pairs of homosexual brothers for regions of DNA that most or all had in common. Of the 40 sets of brothers, 33 shared a set of five markers in the q28 region of the long arm of the X chromosome. The linkage has a LOD score of 4.0, which translates into a 99.5% certainty that there is a gene or genes in this area that predispose males to homosexuality. The chief researcher warns, however, that this one site cannot explain all instances of homosexuality, since there were some cases where the trait seemed to be passed paternally. And even among those brothers where there was no evidence that the trait was passed paternally, seven sets of brothers did not share the Xq28 markers. It seems likely that homosexuality arises from a variety of causes.

  14. Gene-gene, gene-environment, gene-nutrient interactionsand single nucleotide polymorphisms of inflammatorycytokines

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    Inflammation plays a significant role in the etiologyof type 2 diabetes mellitus (T2DM). The rise in thepro-inflammatory cytokines is the essential step inglucotoxicity and lipotoxicity induced mitochondrialinjury, oxidative stress and beta cell apoptosis inT2DM. Among the recognized markers are interleukin(IL)-6, IL-1, IL-10, IL-18, tissue necrosis factor-alpha(TNF-α), C-reactive protein, resistin, adiponectin, tissueplasminogen activator, fibrinogen and heptoglobins.Diabetes mellitus has firm genetic and very strongenvironmental influence; exhibiting a polygenic modeof inheritance. Many single nucleotide polymorphisms(SNPs) in various genes including those of pro and antiinflammatorycytokines have been reported as a riskfor T2DM. Not all the SNPs have been confirmed byunifying results in different studies and wide variationshave been reported in various ethnic groups. Theinter-ethnic variations can be explained by the factthat gene expression may be regulated by gene-gene,gene-environment and gene-nutrient interactions. Thisreview highlights the impact of these interactions ondetermining the role of single nucleotide polymorphismof IL-6, TNF-α, resistin and adiponectin in pathogenesisof T2DM.

  15. Identification of four soybean reference genes for gene expression normalization

    Science.gov (United States)

    Gene expression analysis requires the use of reference genes stably expressed independently of specific tissues or environmental conditions. Housekeeping genes (e.g., actin, tubulin, ribosomal, polyubiquitin and elongation factor 1-alpha) are commonly used as reference genes with the assumption tha...

  16. The Mycoplasma hominis vaa gene displays a mosaic gene structure

    DEFF Research Database (Denmark)

    Boesen, Thomas; Emmersen, Jeppe M. G.; Jensen, Lise T.;

    1998-01-01

    Mycoplasma hominis contains a variable adherence-associated (vaa) gene. To classify variants of the vaa genes, we examined 42 M. hominis isolated by PCR, DNA sequencing and immunoblotting. This uncovered the existence of five gene categories. Comparison of the gene types revealed a modular compos...

  17. Long-term nutrient addition differentially alters community composition and diversity of genes that control nitrous oxide flux from salt marsh sediments

    Science.gov (United States)

    Kearns, Patrick J.; Angell, John H.; Feinman, Sarah G.; Bowen, Jennifer L.

    2015-03-01

    Enrichment of natural waters, soils, and sediments by inorganic nutrients, including nitrogen, is occurring at an increasing rate and has fundamentally altered global biogeochemical cycles. Salt marshes are critical for the removal of land-derived nitrogen before it enters coastal waters. This is accomplished via multiple microbially mediated pathways, including denitrification. Many of these pathways, however, are also a source of the greenhouse gas nitrous oxide (N2O). We used clone libraries and quantative PCR (qPCR) to examine the effect of fertilization on the diversity and abundance of two functional genes associated with denitrification and N2O production (norB and nosZ) in experimental plots at the Great Sippewissett Salt Marsh (Falmouth, MA, USA) that have been enriched with nutrients for over 40 years. Our data showed distinct nosZ and norB community structures at different nitrogen loads, especially at the highest level of fertilization. Furthermore, calculations of the Shannon Diversity Index and Chao1 Richness Estimator indicated that nosZ gene diversity and richness increased with increased nitrogen supply, however no such relationship existed with regard to richness and diversity of the norB gene. Results from qPCR demonstrated that nosZ gene abundance was an order of magnitude lower in the extra-highly fertilized plots compared to the other plots, but the abundance of norB was not affected by fertilization. The majority of sequences obtained from the marsh plots had no close cultured relatives and they were divergent from previously sequenced norB and nosZ fragments. Despite their divergence from any cultured representatives, most of the norB and nosZ sequences appeared to be from members of the Alpha- and Betaproteobacteria, suggesting that these classes are particularly important in salt marsh nitrogen cycling. Our results suggest that both norB and nosZ containing microbes are affected by fertilization and that the Great Sippewissett Marsh may

  18. Hox genes and study of Hox genes in crustacean

    Institute of Scientific and Technical Information of China (English)

    HOU Lin; CHEN Zhijuan; XU Mingyu; LIN Shengguo; WANG Lu

    2004-01-01

    Homeobox genes have been discovered in many species. These genes are known to play a major role in specifying regional identity along the anterior-posterior axis of animals from a wide range of phyla.The products of the homeotic genes are a set of evolutionarily conserved transcription factors that control elaborate developmental processes and specify cell fates in metazoans. Crustacean, presenting a variety of body plans not encountered in any other class or phylum of the Metazoa, has been shown to possess a single set of homologous Hox genes like insect. The ancestral crustacean Hox gene complex comprised ten genes: eight homologous to the hometic Hox genes and two related to nonhomeotic genes presented within the insect Hox complexes. The crustacean in particular exhibits an abundant diversity segment specialization and tagmosis. This morphological diversity relates to the Hox genes. In crustacean body plan, different Hox genes control different segments and tagmosis.

  19. Entrez Gene: gene-centered information at NCBI

    OpenAIRE

    Maglott, Donna; Ostell, Jim; Pruitt, Kim D; Tatusova, Tatiana

    2006-01-01

    Entrez Gene () is NCBI's database for gene-specific information. Entrez Gene includes records from genomes that have been completely sequenced, that have an active research community to contribute gene-specific information or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of both curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases and from other databases wit...

  20. Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium oxysporum.

    Science.gov (United States)

    Matsuoka, Masaki; Kumar, Ashutosh; Muddassar, Muhammad; Matsuyama, Akihisa; Yoshida, Minoru; Zhang, Kam Y J

    2017-02-27

    The efficient application of nitrogenous fertilizers is urgently required, as their excessive and inefficient use is causing substantial economic loss and environmental pollution. A significant amount of applied nitrogen in agricultural soils is lost as nitrous oxide (N2O) in the environment due to the microbial denitrification process. The widely distributed fungus Fusarium oxysporum is a major denitrifier in agricultural soils and its denitrification activity could be targeted to reduce nitrogen loss in the form of N2O from agricultural soils. Here, we report the discovery of first small molecule inhibitors of copper nitrite reductase (NirK) from F. oxysporum, which is a key enzyme in the fungal denitrification process. The inhibitors were discovered by a hierarchical in silico screening approach consisting of pharmacophore modeling and molecular docking. In vitro evaluation of F. oxysporum NirK activity revealed several pyrimidone and triazinone based compounds with potency in the low micromolar range. Some of these compounds suppressed the fungal denitrification in vivo as well. The compounds reported here could be used as starting points for the development of nitrogenous fertilizer supplements and coatings as a means to prevent nitrogen loss by targeting fungal denitrification.

  1. Gene therapy for brain tumors.

    Science.gov (United States)

    Bansal, K; Engelhard, H H

    2000-09-01

    "Gene therapy" can be defined as the transfer of genetic material into a patient's cells for therapeutic purposes. To date, a diverse and creative assortment of treatment strategies utilizing gene therapy have been devised, including gene transfer for modulating the immune system, enzyme prodrug ("suicide gene") therapy, oncolytic therapy, replacement/therapeutic gene transfer, and antisense therapy. For malignant glioma, gene-directed prodrug therapy using the herpes simplex virus thymidine kinase gene was the first gene therapy attempted clinically. A variety of different strategies have now been pursued experimentally and in clinical trials. Although, to date, gene therapy for brain tumors has been found to be reasonably safe, concerns still exist regarding issues related to viral delivery, transduction efficiency, potential pathologic response of the brain, and treatment efficacy. Improved viral vectors are being sought, and potential use of gene therapy in combination with other treatments is being investigated.

  2. Introns in higher plant genes

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The intron is an important component of eukaryotic gene. Extensive studies have been conducted to get a better understanding of its structure and function. This paper presents a brief review of the structure and function of introns in higher plant genes. It is shown that higher plant introns possess structural properties shared by all eukaryotic introns, however, they also exhibit a striking degree of diversity. The process of intron splicing in higher plant genes involves interaction between multiple cis-acting elements and trans-acting factors, such as 5′ splicing site, 3′ splicing site and many protein factors. The process of intron splicing is an important level at which gene expression is regulated. Especially alternative splicing of intron can regulate time and space of gene expression. In addition, some introns in higher plant genes also regulate gene expression by affecting the pattern of gene expression, enhancing the level of gene expression and driving the gene expression.

  3. Gene therapy prospects--intranasal delivery of therapeutic genes.

    Science.gov (United States)

    Podolska, Karolina; Stachurska, Anna; Hajdukiewicz, Karolina; Małecki, Maciej

    2012-01-01

    Gene therapy is recognized to be a novel method for the treatment of various disorders. Gene therapy strategies involve gene manipulation on broad biological processes responsible for the spreading of diseases. Cancer, monogenic diseases, vascular and infectious diseases are the main targets of gene therapy. In order to obtain valuable experimental and clinical results, sufficient gene transfer methods are required. Therapeutic genes can be administered into target tissues via gene carriers commonly defined as vectors. The retroviral, adenoviral and adeno-associated virus based vectors are most frequently used in the clinic. So far, gene preparations may be administered directly into target organs or by intravenous, intramuscular, intratumor or intranasal injections. It is common knowledge that the number of gene therapy clinical trials has rapidly increased. However, some limitations such as transfection efficiency and stable and long-term gene expression are still not resolved. Consequently, great effort is focused on the evaluation of new strategies of gene delivery. There are many expectations associated with intranasal delivery of gene preparations for the treatment of diseases. Intranasal delivery of therapeutic genes is regarded as one of the most promising forms of pulmonary gene therapy research. Gene therapy based on inhalation of gene preparations offers an alternative way for the treatment of patients suffering from such lung diseases as cystic fibrosis, alpha-1-antitrypsin defect, or cancer. Experimental and first clinical trials based on plasmid vectors or recombinant viruses have revealed that gene preparations can effectively deliver therapeutic or marker genes to the cells of the respiratory tract. The noninvasive intranasal delivery of gene preparations or conventional drugs seems to be very encouraging, although basic scientific research still has to continue.

  4. FunGene: the Functional Gene Pipeline and Repository

    Directory of Open Access Journals (Sweden)

    Jordan A. Fish

    2013-10-01

    Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  5. Gene decay in archaea

    Directory of Open Access Journals (Sweden)

    M. W. J. van Passel

    2007-01-01

    Full Text Available The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.

  6. A review on microcephaly genes

    Directory of Open Access Journals (Sweden)

    Irshad S.

    2012-06-01

    Full Text Available This review aims to summarize the recent findings regarding microcephaly genes. We have discussed the molecular genetics studies of microcephaly genes including a comprehensive appraisal of the seven mapped loci (MCPH1–MCPH7, their corresponding genes and protein products of the genes, their likely role in normal brain development and the details of the mutations reported in these genes.

  7. Gene therapy for skin diseases.

    Science.gov (United States)

    Gorell, Emily; Nguyen, Ngon; Lane, Alfred; Siprashvili, Zurab

    2014-04-01

    The skin possesses qualities that make it desirable for gene therapy, and studies have focused on gene therapy for multiple cutaneous diseases. Gene therapy uses a vector to introduce genetic material into cells to alter gene expression, negating a pathological process. This can be accomplished with a variety of viral vectors or nonviral administrations. Although results are promising, there are several potential pitfalls that must be addressed to improve the safety profile to make gene therapy widely available clinically.

  8. Gene Therapy for Skin Diseases

    OpenAIRE

    2014-01-01

    The skin possesses qualities that make it desirable for gene therapy, and studies have focused on gene therapy for multiple cutaneous diseases. Gene therapy uses a vector to introduce genetic material into cells to alter gene expression, negating a pathological process. This can be accomplished with a variety of viral vectors or nonviral administrations. Although results are promising, there are several potential pitfalls that must be addressed to improve the safety profile to make gene thera...

  9. Correlating Expression Data with Gene Function Using Gene Ontology

    Institute of Scientific and Technical Information of China (English)

    LIU,Qi; DENG,Yong; WANG,Chuan; SHI,Tie-Liu; LI,Yi-Xue

    2006-01-01

    Clustering is perhaps one of the most widely used tools for microarray data analysis. Proposed roles for genes of unknown function are inferred from clusters of genes similarity expressed across many biological conditions.However, whether function annotation by similarity metrics is reliable or not and to what extent the similarity in gene expression patterns is useful for annotation of gene functions, has not been evaluated. This paper made a comprehensive research on the correlation between the similarity of expression data and of gene functions using Gene Ontology. It has been found that although the similarity in expression patterns and the similarity in gene functions are significantly dependent on each other, this association is rather weak. In addition, among the three categories of Gene Ontology, the similarity of expression data is more useful for cellular component annotation than for biological process and molecular function. The results presented are interesting for the gene functions prediction research area.

  10. The gene tree delusion.

    Science.gov (United States)

    Springer, Mark S; Gatesy, John

    2016-01-01

    Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are required to unravel deep-level phylogenetic problems that have stymied concatenation. Here, we reanalyze Song et al.'s (2012) data and leverage these re-analyses to explore key issues in systematics including the recombination ratchet, gene tree stoichiometry, the proportion of gene tree incongruence that results from deep coalescence versus other factors, and simulations that compare the performance of coalescence and concatenation methods in species tree estimation. Song et al. (2012) reported an average locus length of 3.1 kb for the 447 protein-coding genes in their phylogenomic dataset, but the true mean length of these loci (start codon to stop codon) is 139.6 kb. Empirical estimates of recombination breakpoints in primates, coupled with consideration of the recombination ratchet, suggest that individual coalescence genes (c-genes) approach ∼12 bp or less for Song et al.'s (2012) dataset, three to four orders of magnitude shorter than the c-genes reported by these authors. This result has general implications for the application of coalescence methods in species tree estimation. We contend that it is illogical to apply coalescence methods to complete protein-coding sequences. Such analyses amalgamate c-genes with different evolutionary histories (i.e., exons separated by >100,000 bp), distort true gene tree stoichiometry that is required for accurate species tree inference, and contradict the central rationale for applying coalescence methods to difficult phylogenetic problems. In addition, Song et al.'s (2012) dataset of 447 genes includes 21 loci with switched taxonomic names, eight duplicated loci, 26 loci with non-homologous sequences that are

  11. Neighboring Genes Show Correlated Evolution in Gene Expression

    Science.gov (United States)

    Ghanbarian, Avazeh T.; Hurst, Laurence D.

    2015-01-01

    When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

  12. Enhanced long-term ammonium removal and its ranked contribution of microbial genes associated with nitrogen cycling in a lab-scale multimedia biofilter.

    Science.gov (United States)

    Wang, Honglei; Ji, Guodong; Bai, Xueyuan

    2015-11-01

    The multimedia biofilter achieved high and stable removal efficiencies for chemical oxygen demand (COD, 62-98%) and NH4(+) (68-98%) without costly aeration. Results revealed that lower CL (less than 13.9gCOD/m(3)d) and ACL (less than 2.8gNH4(+)-N/m(3)d) or a C/N ratio exceeding five was required to reduce NO3(-)-N accumulation and NO/N2O emission. Integrated analyses indicated that the coupling of simultaneous nitrification, anammox and denitrification processes (SNAD) were the primary reason accounted for the enhanced NH4(+)-N treatment performance. NH4(+)-N removal pathways can be ranked as follows: nitrification (amoA, archaeal) (54.6%)>partial denitrification (nirS, nirK) and anammox (37.8%)>anammox and partial denitrification (narG, napA) (12.6%). Specifically, NH4(+)-N removal was significantly inhibited by NO2(-)-N accumulation in the system (-21.6% inhibition). Results from stepwise regression analysis suggested that the NH4(+) removal rate was collectively controlled by amoA, archaeal, anammox, nirS, nirK, narG and napA. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Searching for speciation genes

    DEFF Research Database (Denmark)

    Holt, Benjamin George; Côté, Isabelle M; Emerson, Brent C

    2011-01-01

    Closely related species that show clear phenotypic divergence, but without obvious geographic barriers, can provide opportunities to study how diversification can occur when opportunities for allopatric speciation are limited. We examined genetic divergence in the coral reef fish genus Hypoplectr...... evidence for genes that may be associated with colour morphotype in the genus Hypoplectrus....

  14. Gene therapy in ophthalmology

    Directory of Open Access Journals (Sweden)

    Satagopan Uthra

    2009-01-01

    Full Text Available It has been more than a year since ophthalmologists and scientists under Dr. Robin Ali′s team at the Moorsfield Eye Hospital and the Institute of Ophthalmology, University College London, successfully treated patients with a severely blinding disease, Leber′s congenital amaurosis (LCA using gene therapy. This success does not look to be transient, and this achievement in gene replacement therapy clinical trial for LCA has instilled hope in numerous families with patients suffering from this and similar retinal degenerative diseases, for whom restoration of lost vision has remained a distant dream so far. The encouragement that this success has given is expected to also lead to start of clinical trials for other blinding ocular diseases for which gene therapy experiments at the laboratory and animal levels have been successful. This article reviews the various studies that have led to the understanding of gene therapy outcomes in human ocular diseases and attempts to provide a brief sketch of successful clinical trials.

  15. Carbon and nitrogen limitation explain the contrasting responses of rhizospheric N-cycling microbial communities to maize inoculation by Azospirillum lipoferum CRT1

    Science.gov (United States)

    Florio, Alessandro; Pommier, Thomas; Gervaix, Jonathan; Bréfort, Caroline; Bérard, Annette; Le Roux, Xavier

    2017-04-01

    , inoculation-induced changes in denitrifier activity and abundance (nirK, nirS) were consistent across sites and ranged from -23% to +84% depending on sites. Particularly, in soils with high C limitation levels, inoculation increased nirS-denitrifier abundance and denitrification, likely by stimulating root C exudation. Conversely, in soils with lower C limitation, the stimulating effect of inoculation on root C exudation was less critical for denitrifiers whereas the increased competition between roots and denitrifiers for NO3- became prominent, thus resulting in slightly decreased nirS-denitrifier abundance and denitrification. Pot experiment results revealed that the inoculation effect on denitrification decreased with increased amount of root exudates-like amended to soil. Discussion Maize seed inoculation with the beneficial Azospirillum lipoferum CRT1 can be a sustainable, though soil-specific, agricultural practice providing both beneficial agronomic and environmental effects. Our findings may indicate that the crop seed inoculation practice would increase potential N2O losses from agricultural soils where denitrifiers are highly C-limited. However, our results also demonstrate that the responses of nitrite reducers and N2O reducers to inoculation are tightly coupled, and that inoculation thus does not necessarily represent a risk for increased N2O losses from C-limited soils. Finally, the nirS-denitrifier abundance to microbial basal respiration ratio could be successfully used as a proxy of gaseous-N losses through denitrification from the soil-plant system following inoculation.

  16. Old genes experience stronger translational selection than young genes.

    Science.gov (United States)

    Yin, Hongyan; Ma, Lina; Wang, Guangyu; Li, Mengwei; Zhang, Zhang

    2016-09-15

    Selection on synonymous codon usage for translation efficiency and/or accuracy has been identified as a widespread mechanism in many living organisms. However, it remains unknown whether translational selection associates closely with gene age and acts differentially on genes with different evolutionary ages. To address this issue, here we investigate the strength of translational selection acting on different aged genes in human. Our results show that old genes present stronger translational selection than young genes, demonstrating that translational selection correlates positively with gene age. We further explore the difference of translational selection in duplicates vs. singletons and in housekeeping vs. tissue-specific genes. We find that translational selection acts comparably in old singletons and old duplicates and stronger translational selection in old genes is contributed primarily by housekeeping genes. For young genes, contrastingly, singletons experience stronger translational selection than duplicates, presumably due to redundant function of duplicated genes during their early evolutionary stage. Taken together, our results indicate that translational selection acting on a gene would not be constant during all stages of evolution, associating closely with gene age. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Genes2FANs: connecting genes through functional association networks

    Directory of Open Access Journals (Sweden)

    Dannenfelser Ruth

    2012-07-01

    Full Text Available Abstract Background Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs, researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Results Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI network to build subnetworks that connect lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user’s PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well-studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. Conclusions Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our

  18. Industrial scale gene synthesis.

    Science.gov (United States)

    Notka, Frank; Liss, Michael; Wagner, Ralf

    2011-01-01

    The most recent developments in the area of deep DNA sequencing and downstream quantitative and functional analysis are rapidly adding a new dimension to understanding biochemical pathways and metabolic interdependencies. These increasing insights pave the way to designing new strategies that address public needs, including environmental applications and therapeutic inventions, or novel cell factories for sustainable and reconcilable energy or chemicals sources. Adding yet another level is building upon nonnaturally occurring networks and pathways. Recent developments in synthetic biology have created economic and reliable options for designing and synthesizing genes, operons, and eventually complete genomes. Meanwhile, high-throughput design and synthesis of extremely comprehensive DNA sequences have evolved into an enabling technology already indispensable in various life science sectors today. Here, we describe the industrial perspective of modern gene synthesis and its relationship with synthetic biology. Gene synthesis contributed significantly to the emergence of synthetic biology by not only providing the genetic material in high quality and quantity but also enabling its assembly, according to engineering design principles, in a standardized format. Synthetic biology on the other hand, added the need for assembling complex circuits and large complexes, thus fostering the development of appropriate methods and expanding the scope of applications. Synthetic biology has also stimulated interdisciplinary collaboration as well as integration of the broader public by addressing socioeconomic, philosophical, ethical, political, and legal opportunities and concerns. The demand-driven technological achievements of gene synthesis and the implemented processes are exemplified by an industrial setting of large-scale gene synthesis, describing production from order to delivery.

  19. Endovascular Gene Delivery from a Stent Platform: Gene- Eluting Stents.

    Science.gov (United States)

    Fishbein, Ilia; Chorny, Michael; Adamo, Richard F; Forbes, Scott P; Corrales, Ricardo A; Alferiev, Ivan S; Levy, Robert J

    A synergistic impact of research in the fields of post-angioplasty restenosis, drug-eluting stents and vascular gene therapy over the past 15 years has shaped the concept of gene-eluting stents. Gene-eluting stents hold promise of overcoming some biological and technical problems inherent to drug-eluting stent technology. As the field of gene-eluting stents matures it becomes evident that all three main design modules of a gene-eluting stent: a therapeutic transgene, a vector and a delivery system are equally important for accomplishing sustained inhibition of neointimal formation in arteries treated with gene delivery stents. This review summarizes prior work on stent-based gene delivery and discusses the main optimization strategies required to move the field of gene-eluting stents to clinical translation.

  20. Tumor-specific gene expression patterns with gene expression profiles

    Institute of Scientific and Technical Information of China (English)

    RUAN Xiaogang; LI Yingxin; LI Jiangeng; GONG Daoxiong; WANG Jinlian

    2006-01-01

    Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods to address the problem of selection of tumor-specific genes and analysis of their differential expressions in tumor tissues. First, a variation of the Relief algorithm, "RFE_Relief algorithm" was proposed to learn the relations between genes and tissue types. Then, a support vector machine was employed to find the gene subset with the best classification performance for distinguishing cancerous tissues and their counterparts. After tissue-specific genes were removed, cross validation experiments were employed to demonstrate the common deregulated expressions of the selected gene in tumor tissues. The results indicate the existence of a specific expression fingerprint of these genes that is shared in different tumor tissues, and the hallmarks of the expression patterns of these genes in cancerous tissues are summarized at the end of this paper.

  1. Entrez Gene: gene-centered information at NCBI.

    Science.gov (United States)

    Maglott, Donna; Ostell, Jim; Pruitt, Kim D; Tatusova, Tatiana

    2011-01-01

    Entrez Gene (http://www.ncbi.nlm.nih.gov/gene) is National Center for Biotechnology Information (NCBI)'s database for gene-specific information. Entrez Gene maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis. The content represents the integration of curation and automated processing from NCBI's Reference Sequence project (RefSeq), collaborating model organism databases, consortia such as Gene Ontology and other databases within NCBI. Records in Entrez Gene are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, genomic location, gene products and their attributes, markers, phenotypes and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities) and for bulk transfer by FTP.

  2. Gene set analysis for longitudinal gene expression data

    Directory of Open Access Journals (Sweden)

    Piepho Hans-Peter

    2011-07-01

    Full Text Available Abstract Background Gene set analysis (GSA has become a successful tool to interpret gene expression profiles in terms of biological functions, molecular pathways, or genomic locations. GSA performs statistical tests for independent microarray samples at the level of gene sets rather than individual genes. Nowadays, an increasing number of microarray studies are conducted to explore the dynamic changes of gene expression in a variety of species and biological scenarios. In these longitudinal studies, gene expression is repeatedly measured over time such that a GSA needs to take into account the within-gene correlations in addition to possible between-gene correlations. Results We provide a robust nonparametric approach to compare the expressions of longitudinally measured sets of genes under multiple treatments or experimental conditions. The limiting distributions of our statistics are derived when the number of genes goes to infinity while the number of replications can be small. When the number of genes in a gene set is small, we recommend permutation tests based on our nonparametric test statistics to achieve reliable type I error and better power while incorporating unknown correlations between and within-genes. Simulation results demonstrate that the proposed method has a greater power than other methods for various data distributions and heteroscedastic correlation structures. This method was used for an IL-2 stimulation study and significantly altered gene sets were identified. Conclusions The simulation study and the real data application showed that the proposed gene set analysis provides a promising tool for longitudinal microarray analysis. R scripts for simulating longitudinal data and calculating the nonparametric statistics are posted on the North Dakota INBRE website http://ndinbre.org/programs/bioinformatics.php. Raw microarray data is available in Gene Expression Omnibus (National Center for Biotechnology Information with

  3. Optimal Reference Genes for Gene Expression Normalization in Trichomonas vaginalis.

    Science.gov (United States)

    dos Santos, Odelta; de Vargas Rigo, Graziela; Frasson, Amanda Piccoli; Macedo, Alexandre José; Tasca, Tiana

    2015-01-01

    Trichomonas vaginalis is the etiologic agent of trichomonosis, the most common non-viral sexually transmitted disease worldwide. This infection is associated with several health consequences, including cervical and prostate cancers and HIV acquisition. Gene expression analysis has been facilitated because of available genome sequences and large-scale transcriptomes in T. vaginalis, particularly using quantitative real-time polymerase chain reaction (qRT-PCR), one of the most used methods for molecular studies. Reference genes for normalization are crucial to ensure the accuracy of this method. However, to the best of our knowledge, a systematic validation of reference genes has not been performed for T. vaginalis. In this study, the transcripts of nine candidate reference genes were quantified using qRT-PCR under different cultivation conditions, and the stability of these genes was compared using the geNorm and NormFinder algorithms. The most stable reference genes were α-tubulin, actin and DNATopII, and, conversely, the widely used T. vaginalis reference genes GAPDH and β-tubulin were less stable. The PFOR gene was used to validate the reliability of the use of these candidate reference genes. As expected, the PFOR gene was upregulated when the trophozoites were cultivated with ferrous ammonium sulfate when the DNATopII, α-tubulin and actin genes were used as normalizing gene. By contrast, the PFOR gene was downregulated when the GAPDH gene was used as an internal control, leading to misinterpretation of the data. These results provide an important starting point for reference gene selection and gene expression analysis with qRT-PCR studies of T. vaginalis.

  4. Dominance from the perspective of gene-gene and gene-chemical interactions.

    Science.gov (United States)

    Gladki, Arkadiusz; Zielenkiewicz, Piotr; Kaczanowski, Szymon

    2016-02-01

    In this study, we used genetic interaction (GI) and gene-chemical interaction (GCI) data to compare mutations with different dominance phenotypes. Our analysis focused primarily on Saccharomyces cerevisiae, where haploinsufficient genes (HI; genes with dominant loss-of-function mutations) were found to be participating in gene expression processes, namely, the translation and regulation of gene transcription. Non-ribosomal HI genes (mainly regulators of gene transcription) were found to have more GIs and GCIs than haplosufficient (HS) genes. Several properties seem to lead to the enrichment of interactions, most notably, the following: importance, pleiotropy, gene expression level and gene expression variation. Importantly, after these properties were appropriately considered in the analysis, the correlation between dominance and GI/GCI degrees was still observed. Strikingly, for the GCIs of heterozygous strains, haploinsufficiency was the only property significantly correlated with the number of GCIs. We found ribosomal HI genes to be depleted in GIs/GCIs. This finding can be explained by their high variation in gene expression under different genetic backgrounds and environmental conditions. We observed the same distributions of GIs among non-ribosomal HI, ribosomal HI and HS genes in three other species: Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens. One potentially interesting exception was the lack of significant differences in the degree of GIs between non-ribosomal HI and HS genes in Schizosaccharomyces pombe.

  5. Gene-gene interaction between tuberculosis candidate genes in a South African population.

    Science.gov (United States)

    de Wit, Erika; van der Merwe, Lize; van Helden, Paul D; Hoal, Eileen G

    2011-02-01

    In a complex disease such as tuberculosis (TB) it is increasingly evident that gene-gene interactions play a far more important role in an individual's susceptibility to develop the disease than single polymorphisms on their own, as one gene can enhance or hinder the expression of another gene. Gene-gene interaction analysis is a new approach to elucidate susceptibility to TB. The possibility of gene-gene interactions was assessed, focusing on 11 polymorphisms in nine genes (DC-SIGN, IFN-γ, IFNGR1, IL-8, IL-1Ra, MBL, NRAMP1, RANTES, and SP-D) that have been associated with TB, some repeatedly. An optimal model, which best describes and predicts TB case-control status, was constructed. Significant interactions were detected between eight pairs of variants. The models fitted the observed data extremely well, with p activation is greatly enhanced by IFN-γ and IFN-γ response elements that are present in the human NRAMP1 promoter region, providing further evidence for their interaction. This study enabled us to test the theory that disease outcome may be due to interaction of several gene effects. With eight instances of statistically significant gene-gene interactions, the importance of epistasis is clearly identifiable in this study. Methods for studying gene-gene interactions are based on a multilocus and multigene approach, consistent with the nature of complex-trait diseases, and may provide the paradigm for future genetic studies of TB.

  6. Gene doping in modern sport.

    Directory of Open Access Journals (Sweden)

    MAREK SAWCZUK

    2009-01-01

    Full Text Available Background: The subject of this paper is gene doping, which should be understood as "he non-therapeutic use of cells, genes, genetic elements, or of the modulation of gene expression, having the capacity to improve athletic performance". The authors of this work, based on the review of literature and previous research, make an attempt at wider characterization of gene doping and the discussion of related potential threats.Methods: This is a comprehensive survey of literature on the latest applications of molecular biology in medicine. The analysis involves a dozen scientific databases examined in order to find genes used in gene therapy and potentially useful in gene doping. Results: The obtained results enable better recognition of gene doping and indicate genes used in medicine that could be used in gene doping. This paper describes potential effects of their use and associated risk, and predicts the possible developments of gene doping in the future. Conclusion: Gene doping is undoubtedly a part of modern sport. Although WADA included gene doping on the list of banned methods as early as 2004, as previously stated above, it has not managed to develop efficient methods of detection.

  7. [Gene pool and gene geography of the USSR population].

    Science.gov (United States)

    Rychkov, Iu G; Balanovskaia, E V

    1992-01-01

    Gene pool and gene geography are discussed from the point of view of their conceptual history beginning from the original concept of A.S. Serebrovskiĭ (1928). Difference between the present-day gene geography and gene geography of gene pool is accentuated: the former only represents a portion of the latter. Historical and territorial integrity of the USSR population gene pool, in conjunction with its huge diversity, is the main problem being analysed by various means of computerized genetic cartography. Coupled with the gene frequency mapping, following methods were also used: mapping of average heterozygosity, of interpopulation differentiation, of principal component scores and mapping of geographical trend for each mapped genetic parameter. The work is based on 100 allelic genes and haplotypes from 30 independent loci studied on the average in 225 local populations. Statistical analysis of gene geographical maps is based on 3975 nodes of regular cartographic net for the USSR territory. The wind rose of systematic changes in the USSR gene pool has three main geographic orientations: W-E, SW-NE and S-N. At the same time, there are only two main systematic forces of gene pool evolution: the force of social history with predominant W-E orientation and the force of natural history with predominant S-N orientation of their actions. The heterozygosity level of gene pool declines strictly in accordance with the resultant in the SW-NE direction.

  8. Immunotherapy and gene therapy.

    Science.gov (United States)

    Simpson, Elizabeth

    2004-02-01

    The Immunotherapy and Gene Therapy meeting of the Academy of Medical Sciences reviewed the state-of-the-art and translational prospects for therapeutic interventions aimed at killing tumor cells, correcting genetic defects and developing vaccines for chronic infections. Crucial basic science concepts and information about dendritic cells, the structure and function of T-cell receptors, and manipulation of the immune response by cytokine antagonists and peptides were presented. This information underpins vaccine design and delivery, as well as attempts to immunomodulate autoimmune disease. Results from studies using anticancer DNA vaccines, which include appropriate signals for both the innate and adaptive immune response, were presented in several talks. The vaccines incorporated helper epitopes and cancer target epitopes such as immunoglobulin idiotypes (for lymphomas and myelomas), melanoma-associated antigens (for melanoma and other solid tumors) and minor histocompatibility antigens (for leukemia). The results of using vaccines employing similar principles and designed to reduce viral load in HIV/AIDS patients were also presented. The introduction of suicide genes incorporating the bacterial enzyme nitroreductase gene (ntr) targeted at tumor cells prior to administration of the prodrug CB-1954, converted by ntr into a toxic alkylating agent, was discussed against the background of clinical trials and improved suicide gene design. The introduction into hematopoietic stem cells of missing genes for the common gamma-chain, deficiency of which causes severe combined immunodeficiency (SCID), used similar retroviral transduction. The outcome of treating six SCID patients in the UK, and ten in France was successful immune reconstitution in the majority of patients, but in two of the French cases a complication of lymphoproliferative disease due to insertional mutagenesis was observed. The adoptive transfer of T-cells specific for minor histocompatibility antigens (for

  9. Phosphorus applications improved the soil microbial responses under nitrogen additions in Chinese fir plantations of subtropical China

    Science.gov (United States)

    Zhang, Xinyu; Li, Dandan; Yang, Yang; Tang, Yuqian; Wang, Huimin; Chen, Fusheng; Sun, Xiaomin

    2016-04-01

    Nitrogen (N) deposition and low soil phosphorus (P) content aggravate the P limitation in subtropical forest soils. However, the responses of soil microbial communities, enzyme kinetics, and N cycling genes to P additions in subtropical plantations are still not clear. The hypothesis that P application can alleviate the limitation and improve the soil microbial properties was tested by long term field experiment in the Chinese fir plantations in subtropical China. Thirty 20m×20m plots were established in November 2011 and six different treatments were randomly distributed with five replicates. The treatments are control (CK, no N and P application), low N addition (N1: 50 kg N ha-1 yr-1), high N addition (N2: 100 kg N ha-1 yr-1), P addition (P: 50 kg P ha-1 yr-1), low N and P addition (N1P: 50 kg N ha-1 yr-1 and 50 kg P ha-1 yr-1) and high N and P addition (N2P: 100 kg N ha-1 yr-1 and 50 kg P ha-1 yr-1). A suite of responses of soil microorganism across four years (2012-2015) during three seasons (spring, summer and autumn) were measured. Following 4 years of N amendments, fertilized soils were more acidic and had lower soil microbial biomass carbon contents than CK. However, P alleviated the soil acidification and increased the soil microbial biomass carbon contents. Increases in microbial PLFA biomarkers and exoenzyme kinetics in N fertilized plots were observed in the initial year (2013) but reduced since then (2014 and 2015). Whereas P amendments increased the soil PLFA biomarkers and exoenzyme kinetics through the four years except that the acid phosphatase activities declined after 3 years applications. P applications enhanced the soil N cycling by increases the abundances of nitrifiers (ammonia-oxidizing archea) and denitrifiers (nos Z, norG, and nirK). The bacterial and fungal residue carbons (calculated by amino sugar indicators) were higher under NP fertilizations than the other treatments. Our results suggest that P application could improve the soil

  10. Response of anaerobic carbon cycling to water table manipulation in an Alaskan rich fen

    Science.gov (United States)

    Kane, E.S.; Chivers, M.R.; Turetsky, M.R.; Treat, C.C.; Petersen, D.G.; Waldrop, M.; Harden, J.W.; McGuire, A.D.

    2013-01-01

    To test the effects of altered hydrology on organic soil decomposition, we investigated CO2 and CH4 production potential of rich-fen peat (mean surface pH = 6.3) collected from a field water table manipulation experiment including control, raised and lowered water table treatments. Mean anaerobic CO2 production potential at 10 cm depth (14.1 ± 0.9 μmol C g−1 d−1) was as high as aerobic CO2 production potential (10.6 ± 1.5 μmol C g−1 d−1), while CH4 production was low (mean of 7.8 ± 1.5 nmol C g−1 d−1). Denitrification enzyme activity indicated a very high denitrification potential (197 ± 23 μg N g−1 d−1), but net NO-3 reduction suggested this was a relatively minor pathway for anaerobic CO2 production. Abundances of denitrifier genes (nirK and nosZ) did not change across water table treatments. SO2-4 reduction also did not appear to be an important pathway for anaerobic CO2 production. The net accumulation of acetate and formate as decomposition end products in the raised water table treatment suggested that fermentation was a significant pathway for carbon mineralization, even in the presence of NO-3. Dissolved organic carbon (DOC) concentrations were the strongest predictors of potential anaerobic and aerobic CO2 production. Across all water table treatments, the CO2:CH4 ratio increased with initial DOC leachate concentrations. While the field water table treatment did not have a significant effect on mean CO2 or CH4 production potential, the CO2:CH4 ratio was highest in shallow peat incubations from the drained treatment. These data suggest that with continued drying or with a more variable water table, anaerobic CO2 production may be favored over CH4 production in this rich fen. Future research examining the potential for dissolved organic substances to facilitate anaerobic respiration, or alternative redox processes that limit the effectiveness of organic acids as substrates in anaerobic metabolism, would help explain additional

  11. SOX genes: architects of development.

    Science.gov (United States)

    Prior, H M; Walter, M A

    1996-07-01

    Development in higher organisms involves complex genetic regulation at the molecular level. The emerging picture of development control includes several families of master regulatory genes which can affect the expression of down-stream target genes in developmental cascade pathways. One new family of such development regulators is the SOX gene family. The SOX genes are named for a shared motif called the SRY box a region homologous to the DNA-binding domain of SRY, the mammalian sex determining gene. Like SRY, SOX genes play important roles in chordate development. At least a dozen human SOX genes have been identified and partially characterized (Tables 1 and 2). Mutations in SOX9 have recently been linked to campomelic dysplasia and autosomal sex reversal, and other SOX genes may also be associated with human disease.

  12. Brains, genes, and primates.

    Science.gov (United States)

    Izpisua Belmonte, Juan Carlos; Callaway, Edward M; Caddick, Sarah J; Churchland, Patricia; Feng, Guoping; Homanics, Gregg E; Lee, Kuo-Fen; Leopold, David A; Miller, Cory T; Mitchell, Jude F; Mitalipov, Shoukhrat; Moutri, Alysson R; Movshon, J Anthony; Okano, Hideyuki; Reynolds, John H; Ringach, Dario; Sejnowski, Terrence J; Silva, Afonso C; Strick, Peter L; Wu, Jun; Zhang, Feng

    2015-05-06

    One of the great strengths of the mouse model is the wide array of genetic tools that have been developed. Striking examples include methods for directed modification of the genome, and for regulated expression or inactivation of genes. Within neuroscience, it is now routine to express reporter genes, neuronal activity indicators, and opsins in specific neuronal types in the mouse. However, there are considerable anatomical, physiological, cognitive, and behavioral differences between the mouse and the human that, in some areas of inquiry, limit the degree to which insights derived from the mouse can be applied to understanding human neurobiology. Several recent advances have now brought into reach the goal of applying these tools to understanding the primate brain. Here we describe these advances, consider their potential to advance our understanding of the human brain and brain disorders, discuss bioethical considerations, and describe what will be needed to move forward.

  13. Alphaviruses in Gene Therapy

    Directory of Open Access Journals (Sweden)

    Kenneth Lundstrom

    2009-04-01

    Full Text Available Alphaviruses are enveloped single stranded RNA viruses, which as gene therapy vectors provide high-level transient gene expression. Semliki Forest virus (SFV, Sindbis virus (SIN and Venezuelan Equine Encephalitis (VEE virus have been engineered as efficient replication-deficient and -competent expression vectors. Alphavirus vectors have frequently been used as vehicles for tumor vaccine generation. Moreover, SFV and SIN vectors have been applied for intratumoral injections in animals implanted with tumor xenografts. SIN vectors have demonstrated natural tumor targeting, which might permit systemic vector administration. Another approach for systemic delivery of SFV has been to encapsulate replication-deficient viral particles in liposomes, which can provide passive targeting to tumors and allow repeated administration without host immune responses. This approach has demonstrated safe delivery of encapsulated SFV particles to melanoma and kidney carcinoma patients in a phase I trial. Finally, the prominent neurotropism of alphaviruses make them attractive for the treatment of CNS-related diseases.

  14. Gene Disease Diagnostic System

    Institute of Scientific and Technical Information of China (English)

    黄国亮; 张腾飞; 程京; 周玉祥; 刘诚迅; 金国藩; 邬敏贤; 严瑛白; 杨蓉

    2002-01-01

    Binary optics, where the optical element can be fabricated on a thin glass plate with micro-ion-etching film layer, has been widely applied in recent years. A novel optical scanning system for gene disease diagnostics described in this paper has four kinds of optical devices, including beam splitters, an array lens, an array filter and detection arrays. A software was developed to design the binary optics system using an iterative method. Two beam splitters were designed and fabricated, which can divide a beam into a 9×9 array or into a 13×13 array. The beam splitters have good diffraction efficiencies (>70%) and an even energy distribution. The gene disease diagnostic system is a portable biochip and binary optics technology. The binary optical devices in the non-confocal scanning system can raise the fluorescence detection sensitivity of the micro-array hybrid biochip.

  15. Gene therapy for mucopolysaccharidosis

    Science.gov (United States)

    Ponder, Katherine P; Haskins, Mark E

    2012-01-01

    Mucopolysaccharidoses (MPS) are due to deficiencies in activities of lysosomal enzymes that degrade glycosaminoglycans. Some attempts at gene therapy for MPS in animal models have involved intravenous injection of vectors derived from an adeno-associated virus (AAV), adenovirus, retrovirus or a plasmid, which primarily results in expression in liver and secretion of the relevant enzyme into blood. Most vectors can correct disease in liver and spleen, although correction in other organs including the brain requires high enzyme activity in the blood. Alternative approaches are to transduce hematopoietic stem cells, or to inject a vector locally into difficult-to-reach sites such as the brain. Gene therapy holds great promise for providing a long-lasting therapeutic effect for MPS if safety issues can be resolved. PMID:17727324

  16. Gene Porter Bridwell

    Science.gov (United States)

    1994-01-01

    Gene Porter Bridwell served as the director of the Marshall Space Flight Center from January 6, 1994 until February 3, 1996, when he retired from NASA after thirty-four years service. Bridwell, a Marshall employee since 1962, had been Marshall's Space Shuttle Projects Office Director and Space Station Redesign Team deputy manager. Under Bridwell, Marshall worked to develop its role as a Center of Excellence for propulsion and for providing access to space.

  17. Gene Porter Bridwell

    Science.gov (United States)

    1994-01-01

    Gene Porter Bridwell served as the director of the Marshall Space Flight Center from January 6, 1994 until February 3, 1996, when he retired from NASA after thirty-four years service. Bridwell, a Marshall employee since 1962, had been Marshall's Space Shuttle Projects Office Director and Space Station Redesign Team deputy manager. Under Bridwell, Marshall worked to develop its role as a Center of Excellence for propulsion and for providing access to space.

  18. Epigenetics: beyond genes

    CSIR Research Space (South Africa)

    Fossey, A

    2009-06-01

    Full Text Available to neighbouring euchromatic genes, known as position effect variegation and can be transmitted through mitosis, forming the basis of epigenetic inheritance from one cell generation to another; creating cellular memory (Brzeski and Jerzmanowski, 2004... life form, supports meiosis that produces haploid male and female spores and initiates the gametophytic generation. Gametogenesis and subsequent fertilisation take place when gametophytic and sporophytic structures interact. The product...

  19. PRRT2 gene mutations

    Science.gov (United States)

    Gardiner, Alice R.; Bhatia, Kailash P.; Stamelou, Maria; Dale, Russell C.; Kurian, Manju A.; Schneider, Susanne A.; Wali, G.M.; Counihan, Tim; Schapira, Anthony H.; Spacey, Sian D.; Valente, Enza-Maria; Silveira-Moriyama, Laura; Teive, Hélio A.G.; Raskin, Salmo; Sander, Josemir W.; Lees, Andrew; Warner, Tom; Kullmann, Dimitri M.; Wood, Nicholas W.; Hanna, Michael

    2012-01-01

    ABSTRACT Objective: The proline-rich transmembrane protein (PRRT2) gene was recently identified using exome sequencing as the cause of autosomal dominant paroxysmal kinesigenic dyskinesia (PKD) with or without infantile convulsions (IC) (PKD/IC syndrome). Episodic neurologic disorders, such as epilepsy, migraine, and paroxysmal movement disorders, often coexist and are thought to have a shared channel-related etiology. To investigate further the frequency, spectrum, and phenotype of PRRT2 mutations, we analyzed this gene in 3 large series of episodic neurologic disorders with PKD/IC, episodic ataxia (EA), and hemiplegic migraine (HM). Methods: The PRRT2 gene was sequenced in 58 family probands/sporadic individuals with PKD/IC, 182 with EA, 128 with HM, and 475 UK and 96 Asian controls. Results: PRRT2 genetic mutations were identified in 28 out of 58 individuals with PKD/IC (48%), 1/182 individuals with EA, and 1/128 individuals with HM. A number of loss-of-function and coding missense mutations were identified; the most common mutation found was the p.R217Pfs*8 insertion. Males were more frequently affected than females (ratio 52:32). There was a high proportion of PRRT2 mutations found in families and sporadic cases with PKD associated with migraine or HM (10 out of 28). One family had EA with HM and another large family had typical HM alone. Conclusions: This work expands the phenotype of mutations in the PRRT2 gene to include the frequent occurrence of migraine and HM with PKD/IC, and the association of mutations with EA and HM and with familial HM alone. We have also extended the PRRT2 mutation type and frequency in PKD and other episodic neurologic disorders. PMID:23077024

  20. Gene therapy in gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Xu Chang-tai; Guo Xue-gang; Pan Bo-rong

    2003-01-01

    @@ 1 Introduction We have reviewed the gene therapy in gastrointestinal diseases[1]. Gastric cancer is common in China[2~20] ,and its early diagnosis andtreatment are still difficult up to now[13~36]. The expression of anexogenous gene introduced by gene therapy into patients with gliomascan be monitored non- invasively by positron- emission tomography[4]. In recent years, gene study in cancer is a hotspot, and great progress hasbeen achieved[33~41].

  1. Gene therapy for gastric diseases.

    OpenAIRE

    Fumoto, Shintaro; Nishi, Junya; Nakamura, Junzo; Nishida, Koyo

    2008-01-01

    Gene therapy for gastric cancer and gastric ulcer is a rationalized strategy since various genes correlate with these diseases. Since gene expressions in non-target tissues/cells cause side effects, a selective gene delivery system targeted to the stomach and/or cancer must be developed. The route of vector transfer (direct injection, systemic, intraperitoneal, gastric serosal surface and oral administration) is an important issue which can determine efficacy and safety. Strategies for cancer...

  2. Genealogy and gene trees.

    Science.gov (United States)

    Rasmuson, Marianne

    2008-02-01

    Heredity can be followed in persons or in genes. Persons can be identified only a few generations back, but simplified models indicate that universal ancestors to all now living persons have occurred in the past. Genetic variability can be characterized as variants of DNA sequences. Data are available only from living persons, but from the pattern of variation gene trees can be inferred by means of coalescence models. The merging of lines backwards in time leads to a MRCA (most recent common ancestor). The time and place of living for this inferred person can give insights in human evolutionary history. Demographic processes are incorporated in the model, but since culture and customs are known to influence demography the models used ought to be tested against available genealogy. The Icelandic data base offers a possibility to do so and points to some discrepancies. Mitochondrial DNA and Y chromosome patterns give a rather consistent view of human evolutionary history during the latest 100 000 years but the earlier epochs of human evolution demand gene trees with longer branches. The results of such studies reveal as yet unsolved problems about the sources of our genome.

  3. Gene-gene and gene-environmental interactions of childhood asthma: a multifactor dimension reduction approach.

    Directory of Open Access Journals (Sweden)

    Ming-Wei Su

    Full Text Available BACKGROUND: The importance of gene-gene and gene-environment interactions on asthma is well documented in literature, but a systematic analysis on the interaction between various genetic and environmental factors is still lacking. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a population-based, case-control study comprised of seventh-grade children from 14 Taiwanese communities. A total of 235 asthmatic cases and 1,310 non-asthmatic controls were selected for DNA collection and genotyping. We examined the gene-gene and gene-environment interactions between 17 single-nucleotide polymorphisms in antioxidative, inflammatory and obesity-related genes, and childhood asthma. Environmental exposures and disease status were obtained from parental questionnaires. The model-free and non-parametrical multifactor dimensionality reduction (MDR method was used for the analysis. A three-way gene-gene interaction was elucidated between the gene coding glutathione S-transferase P (GSTP1, the gene coding interleukin-4 receptor alpha chain (IL4Ra and the gene coding insulin induced gene 2 (INSIG2 on the risk of lifetime asthma. The testing-balanced accuracy on asthma was 57.83% with a cross-validation consistency of 10 out of 10. The interaction of preterm birth and indoor dampness had the highest training-balanced accuracy at 59.09%. Indoor dampness also interacted with many genes, including IL13, beta-2 adrenergic receptor (ADRB2, signal transducer and activator of transcription 6 (STAT6. We also used likelihood ratio tests for interaction and chi-square tests to validate our results and all tests showed statistical significance. CONCLUSIONS/SIGNIFICANCE: The results of this study suggest that GSTP1, INSIG2 and IL4Ra may influence the lifetime asthma susceptibility through gene-gene interactions in schoolchildren. Home dampness combined with each one of the genes STAT6, IL13 and ADRB2 could raise the asthma risk.

  4. Gene therapy of cancer and development of therapeutic target gene

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Chang Min; Kwon, Hee Chung

    1998-04-01

    We applied HSV-tk/GCV strategy to orthotopic rat hepatoma model and showed anticancer effects of hepatoma. The increased expression of Lac Z gene after adenovirus-mediated gene delivery throughout hepatic artery was thought that is increased the possibility of gene therapy for curing hepatoma. With the construction of kGLP-laboratory, it is possible to produce a good quantity and quality of adenovirus in lage-scale production and purification of adenovirus vector. Also, the analysis of hepatoma related genes by PCR-LOH could be used for the diagnosis of patients and the development of therapeutic gene.

  5. Independent Gene Discovery and Testing

    Science.gov (United States)

    Palsule, Vrushalee; Coric, Dijana; Delancy, Russell; Dunham, Heather; Melancon, Caleb; Thompson, Dennis; Toms, Jamie; White, Ashley; Shultz, Jeffry

    2010-01-01

    A clear understanding of basic gene structure is critical when teaching molecular genetics, the central dogma and the biological sciences. We sought to create a gene-based teaching project to improve students' understanding of gene structure and to integrate this into a research project that can be implemented by instructors at the secondary level…

  6. Compositional gradients in Gramineae genes

    DEFF Research Database (Denmark)

    Wong, Gane Ka-Shu; Wang, Jun; Tao, Lin

    2002-01-01

    In this study, we describe a property of Gramineae genes, and perhaps all monocot genes, that is not observed in eudicot genes. Along the direction of transcription, beginning at the junction of the 5'-UTR and the coding region, there are gradients in GC content, codon usage, and amino-acid usage...

  7. Decationized polyplexes for gene delivery

    NARCIS (Netherlands)

    Novo, L.; Mastrobattista, E.; Nostrum, van C.F.; Lammers, T.G.G.M.; Hennink, W.E.

    2015-01-01

    Gene therapy has received much attention in the field of drug delivery. Synthetic, nonviral gene delivery systems have gained increasing attention as vectors for gene therapy mainly due to a favorable immunogenicity profile and ease of manufacturing as compared to viral vectors. The great majority o

  8. Ascidian gene-expression profiles

    OpenAIRE

    Jeffery, William R.

    2002-01-01

    With the advent of gene-expression profiling, a large number of genes can now be investigated simultaneously during critical stages of development. This approach will be particularly informative in studies of ascidians, basal chordates whose genomes and embryology are uniquely suited for mapping developmental gene networks.

  9. Gene electrotransfer in clinical trials

    DEFF Research Database (Denmark)

    Gehl, Julie

    2014-01-01

    Electroporation is increasingly being used for delivery of chemotherapy to tumors. Likewise, gene delivery by electroporation is rapidly gaining momentum for both vaccination purposes and for delivery of genes coding for other therapeutic molecules, such as chronic diseases or cancer. This chapte...... describes how gene therapy may be performed using electric pulses to enhance uptake and expression.......Electroporation is increasingly being used for delivery of chemotherapy to tumors. Likewise, gene delivery by electroporation is rapidly gaining momentum for both vaccination purposes and for delivery of genes coding for other therapeutic molecules, such as chronic diseases or cancer. This chapter...

  10. Gene therapy of liver cancer

    Institute of Scientific and Technical Information of China (English)

    Ruben Hernandez-Alcoceba; Bruno Sangro; Jesus Prieto

    2006-01-01

    The application of gene transfer technologies to the treatment of cancer has led to the development of new experimental approaches like gene directed enzyme/prodrug therapy (GDEPT), inhibition of oncogenes and restoration of tumor-suppressor genes. In addition,gene therapy has a big impact on other fields like cancer immunotherapy, anti-angiogenic therapy and virotherapy.These strategies are being evaluated for the treatment of primary and metastatic liver cancer and some of them have reached clinical phases. We present a review on the basis and the actual status of gene therapy approaches applied to liver cancer.

  11. Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning

    OpenAIRE

    Tsatsoulis Costas; Amthauer Heather A

    2010-01-01

    Abstract Background There is increasing evidence that gene location and surrounding genes influence the functionality of genes in the eukaryotic genome. Knowing the Gene Ontology Slim terms associated with a gene gives us insight into a gene's functionality by informing us how its gene product behaves in a cellular context using three different ontologies: molecular function, biological process, and cellular component. In this study, we analyzed if we could classify a gene in Saccharomyces ce...

  12. Gene finding in novel genomes

    Directory of Open Access Journals (Sweden)

    Korf Ian

    2004-05-01

    Full Text Available Abstract Background Computational gene prediction continues to be an important problem, especially for genomes with little experimental data. Results I introduce the SNAP gene finder which has been designed to be easily adaptable to a variety of genomes. In novel genomes without an appropriate gene finder, I demonstrate that employing a foreign gene finder can produce highly inaccurate results, and that the most compatible parameters may not come from the nearest phylogenetic neighbor. I find that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate. Conclusion Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.

  13. GeneDistiller--distilling candidate genes from linkage intervals.

    Directory of Open Access Journals (Sweden)

    Dominik Seelow

    Full Text Available BACKGROUND: Linkage studies often yield intervals containing several hundred positional candidate genes. Different manual or automatic approaches exist for the determination of the gene most likely to cause the disease. While the manual search is very flexible and takes advantage of the researchers' background knowledge and intuition, it may be very cumbersome to collect and study the relevant data. Automatic solutions on the other hand usually focus on certain models, remain "black boxes" and do not offer the same degree of flexibility. METHODOLOGY: We have developed a web-based application that combines the advantages of both approaches. Information from various data sources such as gene-phenotype associations, gene expression patterns and protein-protein interactions was integrated into a central database. Researchers can select which information for the genes within a candidate interval or for single genes shall be displayed. Genes can also interactively be filtered, sorted and prioritised according to criteria derived from the background knowledge and preconception of the disease under scrutiny. CONCLUSIONS: GeneDistiller provides knowledge-driven, fully interactive and intuitive access to multiple data sources. It displays maximum relevant information, while saving the user from drowning in the flood of data. A typical query takes less than two seconds, thus allowing an interactive and explorative approach to the hunt for the candidate gene. ACCESS: GeneDistiller can be freely accessed at http://www.genedistiller.org.

  14. RANGE: Gene Transfer of Reversibly Controlled Polycistronic Genes

    Directory of Open Access Journals (Sweden)

    Yiwei Chen

    2013-01-01

    Full Text Available We developed a single vector recombinant adeno-associated viral (rAAV expression system for spatial and reversible control of polycistronic gene expression. Our approach (i integrates the advantages of the tetracycline (Tet-controlled transcriptional silencer tTSKid and the self-cleaving 2A peptide bridge, (ii combines essential regulatory components as an autoregulatory loop, (iii simplifies the gene delivery scheme, and (iv regulates multiple genes in a synchronized manner. Controlled by an upstream Tet-responsive element (TRE, both the ubiquitous chicken β-actin promoter (CAG and the neuron-specific synapsin-1 promoter (Syn could regulate expression of tTSKid together with two 2A-linked reporter genes. Transduction in vitro exhibited maximally 50-fold regulation by doxycycline (Dox. Determined by gene delivery method as well as promoter, highly specific tissues were transduced in vivo. Bioluminescence imaging (BLI visualized reversible “ON/OFF” gene switches over repeated “Doxy-Cycling” in living mice. Thus, the reversible rAAV-mediated N-cistronic gene expression system, termed RANGE, may serve as a versatile tool to achieve reversible polycistronic gene regulation for the study of gene function as well as gene therapy.

  15. RANGE: Gene Transfer of Reversibly Controlled Polycistronic Genes.

    Science.gov (United States)

    Chen, Yiwei; Cao, Liji; Luo, Chonglin; Ditzel, Désirée Aw; Peter, Jörg; Sprengel, Rolf

    2013-04-09

    We developed a single vector recombinant adeno-associated viral (rAAV) expression system for spatial and reversible control of polycistronic gene expression. Our approach (i) integrates the advantages of the tetracycline (Tet)-controlled transcriptional silencer tTS(Kid) and the self-cleaving 2A peptide bridge, (ii) combines essential regulatory components as an autoregulatory loop, (iii) simplifies the gene delivery scheme, and (iv) regulates multiple genes in a synchronized manner. Controlled by an upstream Tet-responsive element (TRE), both the ubiquitous chicken β-actin promoter (CAG) and the neuron-specific synapsin-1 promoter (Syn) could regulate expression of tTS(Kid) together with two 2A-linked reporter genes. Transduction in vitro exhibited maximally 50-fold regulation by doxycycline (Dox). Determined by gene delivery method as well as promoter, highly specific tissues were transduced in vivo. Bioluminescence imaging (BLI) visualized reversible "ON/OFF" gene switches over repeated "Doxy-Cycling" in living mice. Thus, the reversible rAAV-mediated N-cistronic gene expression system, termed RANGE, may serve as a versatile tool to achieve reversible polycistronic gene regulation for the study of gene function as well as gene therapy.Molecular Therapy - Nucleic Acids (2013) 2, e85; doi:10.1038/mtna.2013.15; published online 9 April 2013.

  16. Genes, Children and Pediatricians

    Directory of Open Access Journals (Sweden)

    Joana Correia

    2017-01-01

    Full Text Available A male newborn, presenting hipotonia and posterior parietal bossing, developed, in the first 12 hours of life, refusal to feed and hypoglycaemia. A cranial ultrasound, skull X-ray and CT scan revealed an occipital and parietal fracture with an underlying haematoma and extensive extracranial soft-tissue swelling. He was submitted to surgical drainage. After 24 hours: new intracerebral bleeding. At the age of two-months he presented abnormal skin and sparse kinky hair. Serum copper and caeruloplasmin levels were below the normal range. Molecular diagnosis of Menkes disease was made by the identification of a new mutation in ATP7A gene.

  17. MUTATIONS IN CALMODULIN GENES

    DEFF Research Database (Denmark)

    2013-01-01

    The present invention relates to an isolated polynucleotide encoding at least a part of calmodulin and an isolated polypeptide comprising at least a part of a calmodulin protein, wherein the polynucleotide and the polypeptide comprise at least one mutation associated with a cardiac disorder. The ...... the binding of calmodulin to ryanodine receptor 2 and use of such compound in a treatment of an individual having a cardiac disorder. The invention further provides a kit that can be used to detect specific mutations in calmodulin encoding genes....

  18. MUTATIONS IN CALMODULIN GENES

    DEFF Research Database (Denmark)

    2013-01-01

    The present invention relates to an isolated polynucleotide encoding at least a part of calmodulin and an isolated polypeptide comprising at least a part of a calmodulin protein, wherein the polynucleotide and the polypeptide comprise at least one mutation associated with a cardiac disorder...... the binding of calmodulin to ryanodine receptor 2 and use of such compound in a treatment of an individual having a cardiac disorder. The invention further provides a kit that can be used to detect specific mutations in calmodulin encoding genes....

  19. Genes and Disease: Prader-Willi Syndrome

    Science.gov (United States)

    ... MD): National Center for Biotechnology Information (US); 1998-. Genes and Disease [Internet]. Show details National Center for ... 45K) PDF version of this title (3.8M) Gene sequence Genome view see gene locations Entrez Gene ...

  20. Alcoholism: genes and mechanisms.

    Science.gov (United States)

    Oroszi, Gabor; Goldman, David

    2004-12-01

    Alcoholism is a chronic relapsing/remitting disease that is frequently unrecognized and untreated, in part because of the partial efficacy of treatment. Only approximately one-third of patients remain abstinent and one-third have fully relapsed 1 year after withdrawal from alcohol, with treated patients doing substantially better than untreated [1]. The partial effectiveness of strategies for prevention and treatment, and variation in clinical course and side effects, represent a challenge and an opportunity to better understand the neurobiology of addiction. The strong heritability of alcoholism suggests the existence of inherited functional variants of genes that alter the metabolism of alcohol and variants of other genes that alter the neurobiologies of reward, executive cognitive function, anxiety/dysphoria, and neuronal plasticity. Each of these neurobiologies has been identified as a critical domain in the addictions. Functional alleles that alter alcoholism-related intermediate phenotypes include common alcohol dehydrogenase 1B and aldehyde dehydrogenase 2 variants that cause the aversive flushing reaction; catechol-O-methyltransferase (COMT) Val158Met leading to differences in three aspects of neurobiology: executive cognitive function, stress/anxiety response, and opioid function; opioid receptor micro1 (OPRM1) Asn40Asp, which may serve as a gatekeeper molecule in the action of naltrexone, a drug used in alcoholism treatment; and HTTLPR, which alters serotonin transporter function and appears to affect stress response and anxiety/dysphoria, which are factors relevant to initial vulnerability, the process of addiction, and relapse.

  1. Tetraspanin genes in plants.

    Science.gov (United States)

    Wang, Feng; Vandepoele, Klaas; Van Lijsebettens, Mieke

    2012-07-01

    Tetraspanins represent a four-transmembrane protein superfamily with a conserved structure and amino acid residues that are present in mammals, insects, fungi and plants. Tetraspanins interact with each other or with other membrane proteins to form tetraspanin-enriched microdomains that play important roles in development, pathogenesis and immune responses via facilitating cell-cell adhesion and fusion, ligand binding and intracellular trafficking. Here, we emphasize evolutionary aspects within the plant kingdom based on genomic sequence information. A phylogenetic tree based on 155 tetraspanin genes of 11 plant species revealed ancient and fast evolving clades. Tetraspanins were only present in multicellular plants, were often duplicated in the plant genomes and predicted by the electronic Fluorescent Pictograph for gene expression analysis to be either functionally redundant or divergent. Tetraspanins contain a large extracellular loop with conserved cysteines that provide the binding sites for the interactions. The Arabidopsis thaliana TETRASPANIN1/TORNADO2/EKEKO has a function in leaf and root patterning and TETRASPANIN3 was identified in the plasmodesmatal proteome, suggesting a role in cell-cell communication during plant development.

  2. Improvements to cardiovascular gene ontology.

    Science.gov (United States)

    Lovering, Ruth C; Dimmer, Emily C; Talmud, Philippa J

    2009-07-01

    Gene Ontology (GO) provides a controlled vocabulary to describe the attributes of genes and gene products in any organism. Although one might initially wonder what relevance a 'controlled vocabulary' might have for cardiovascular science, such a resource is proving highly useful for researchers investigating complex cardiovascular disease phenotypes as well as those interpreting results from high-throughput methodologies. GO enables the current functional knowledge of individual genes to be used to annotate genomic or proteomic datasets. In this way, the GO data provides a very effective way of linking biological knowledge with the analysis of the large datasets of post-genomics research. Consequently, users of high-throughput methodologies such as expression arrays or proteomics will be the main beneficiaries of such annotation sets. However, as GO annotations increase in quality and quantity, groups using small-scale approaches will gradually begin to benefit too. For example, genome wide association scans for coronary heart disease are identifying novel genes, with previously unknown connections to cardiovascular processes, and the comprehensive annotation of these novel genes might provide clues to their cardiovascular link. At least 4000 genes, to date, have been implicated in cardiovascular processes and an initiative is underway to focus on annotating these genes for the benefit of the cardiovascular community. In this article we review the current uses of Gene Ontology annotation to highlight why Gene Ontology should be of interest to all those involved in cardiovascular research.

  3. Chromatin analysis of occluded genes

    Science.gov (United States)

    Lee, Jae Hyun; Gaetz, Jedidiah; Bugarija, Branimir; Fernandes, Croydon J.; Snyder, Gregory E.; Bush, Eliot C.; Lahn, Bruce T.

    2009-01-01

    We recently described two opposing states of transcriptional competency. One is termed ‘competent’ whereby a gene is capable of responding to trans-acting transcription factors of the cell, such that it is active if appropriate transcriptional activators are present, though it can also be silent if activators are absent or repressors are present. The other is termed ‘occluded’ whereby a gene is silenced by cis-acting, chromatin-based mechanisms in a manner that blocks it from responding to trans-acting factors, such that it is silent even when activators are present in the cellular milieu. We proposed that gene occlusion is a mechanism by which differentiated cells stably maintain their phenotypic identities. Here, we describe chromatin analysis of occluded genes. We found that DNA methylation plays a causal role in maintaining occlusion for a subset of occluded genes. We further examined a variety of other chromatin marks typically associated with transcriptional silencing, including histone variants, covalent histone modifications and chromatin-associated proteins. Surprisingly, we found that although many of these marks are robustly linked to silent genes (which include both occluded genes and genes that are competent but silent), none is linked specifically to occluded genes. Although the observation does not rule out a possible causal role of these chromatin marks in occlusion, it does suggest that these marks might be secondary effect rather than primary cause of the silent state in many genes. PMID:19380460

  4. Identification of genes and gene products necessary for bacterial bioluminescence.

    OpenAIRE

    Engebrecht, J; Silverman, M.

    1984-01-01

    Expression of luminescence in Escherichia coli was recently achieved by cloning genes from the marine bacterium Vibrio fischeri. One DNA fragment on a hybrid plasmid encoded regulatory functions and enzymatic activities necessary for light production. We report the results of a genetic analysis to identify the luminescence genes (lux) that reside on this recombinant plasmid. lux gene mutations were generated by hydroxylamine treatment, and these mutations were ordered on a linear map by compl...

  5. GENE MUTATIONS, GENETIC DISEASE AND PHARMACOGENETIC GENES DISORDER

    OpenAIRE

    Ishak

    2010-01-01

    Somatic cell mutation is able to create genetic variance in a cell population and can induce cancer and tumor when gene mutations took place at repressor gene in controlling cell cycles such as p53 gene. Whereas germline cell mutation can cause genetic disease such as sickle cell anemia, breast cancer, thalassemia, parkinson’s as well as defect of biochemical pathway that influence drug-receptor interaction, which has negative effect and lead to hospitalized of patient. Most of reports mentio...

  6. PROAPOPTOTIC FUNCTION OF FHIT GENE

    Institute of Scientific and Technical Information of China (English)

    QIU Zhe-fu; HAN De-min; ZHANG Luo; ZHANG Wei

    2006-01-01

    Tumor suppressor gene plays an important role in maintaining the homeostasis between cell loss and growth. Fragile in maintaining the homeostasis between cell loss and growth. Fragile histidine triad (FHIT) gene found recently was studied in a deep going way; it becomes the focus as a result of its roleof ep going way; it becomes the focus as a result of its roleof anti-tumor in human various type of tissue. Due to the high efficiency of FHIT gene benefiting the anti-tumor, it is proposed gh efficiency of FHIT gene benefiting the anti-tumor, it is proposed as a candidate of tumor suppressor gene though there are several opposite opinions.several opposite opinions. We stress the summary of some properties of FHIT gene on proapoptosis according to the published data which showed gene on proapoptosis according to the published data which showed the stronger proapoptotic function of FHIT gene; the apoptosis induced by FHIT depends on the expression level and status of ene; the apoptosis induced by FHIT depends on the expression level and status of FHIT; and FHIT gene can alternate the cell cycling properties and reduce the tumorigenic potential; the apoptotic process e can alternate the cell cycling properties and reduce the tumorigenic potential; the apoptotic process induced by FHIT has no relation to p53 gene. In a ward, in consideration of its multiple functions against malignancies, FHIT in consideration of its multiple functions against malignancies, FHIT gene deserves attention and exploration as a selective target for searching the mechanism of tumorigenesis and clinical et for searching the mechanism of tumorigenesis and clinical therapeutic applications in further.le histidine triad (FHIT) gene; Apoptosis; Tumorigenesis; Tumor suppressor gene deserves attention and exploration as a selective target for searching the mechanism of tumorigenesis and clinical therapeutic applications in further.

  7. Regulation of gene expression by Goodwin's loop with many genes

    Science.gov (United States)

    Sielewiesiuk, Jan; Łopaciuk, Agata

    2012-01-01

    The paper presents a simple analysis of a long Goodwin's loop containing many genes. The genes form a closed series. The rate of transcription of any gene is up or down regulated by theprotein product of the preceding gene. We describe the loop with a system of ordinary differential equations of order s. Oscillatory solutions of the system are possible at the odd number of repressions and any number of inductions if the product of all Hill's coefficients, related to both repressions and inductions, is larger than:

  8. Gene: a gene-centered information resource at NCBI.

    Science.gov (United States)

    Brown, Garth R; Hem, Vichet; Katz, Kenneth S; Ovetsky, Michael; Wallin, Craig; Ermolaeva, Olga; Tolstoy, Igor; Tatusova, Tatiana; Pruitt, Kim D; Maglott, Donna R; Murphy, Terence D

    2015-01-01

    The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that they form the critical association between sequence and a tracked gene upon which additional functional and descriptive content is anchored. Additional content is integrated based on the genomic location and RefSeq transcript and protein sequence data. The content of a Gene record represents the integration of curation and automated processing from RefSeq, collaborating model organism databases, consortia such as Gene Ontology, and other databases within NCBI. Records in Gene are assigned unique, tracked integers as identifiers. The content (citations, nomenclature, genomic location, gene products and their attributes, phenotypes, sequences, interactions, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities and Entrez Direct) and for bulk transfer by FTP.

  9. Gene expression analysis identifies global gene dosage sensitivity in cancer

    DEFF Research Database (Denmark)

    Fehrmann, Rudolf S. N.; Karjalainen, Juha M.; Krajewska, Malgorzata;

    2015-01-01

    expression. We reanalyzed 77,840 expression profiles and observed a limited set of 'transcriptional components' that describe well-known biology, explain the vast majority of variation in gene expression and enable us to predict the biological function of genes. On correcting expression profiles...... for these components, we observed that the residual expression levels (in 'functional genomic mRNA' profiling) correlated strongly with copy number. DNA copy number correlated positively with expression levels for 99% of all abundantly expressed human genes, indicating global gene dosage sensitivity. By applying...

  10. PDMAEMA based gene delivery materials

    Directory of Open Access Journals (Sweden)

    Seema Agarwal

    2012-09-01

    Full Text Available Gene transfection is the transfer of genetic material like DNA into cells. Cationic polymers which form nanocomplexes with DNA, so-called non-viral gene vectors, are a highly promising platform for efficient gene transfection. Despite intensive research efforts and some of the on-going clinical trials on gene transfection, none of the existing cationic polymer systems are generally acceptable for human gene therapy. Since the process of gene transfection is complex and puts different challenges and demands on the delivery system, there is a strong requirement for the design and development of a multifunctional system in a simple way. This review will discuss recent efforts in design, synthesis, and performance of poly(2-dimethylaminoethyl methacrylate (PDMAEMA nanocomplexes with DNA.

  11. Gene targeting with retroviral vectors

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, J.; Bernstein, A. (Toronto Univ., ON (Canada))

    1989-04-01

    The authors have designed and constructed integration-defective retroviral vectors to explore their potential for gene targeting in mammalian cells. Two nonoverlapping deletion mutants of the bacterial neomycin resistance (neo) gene were used to detect homologous recombination events between viral and chromosomal sequences. Stable neo gene correction events were selected at a frequency of approximately 1 G418/sup r/ cell per 3 x 10/sup 6/ infected cells. Analysis of the functional neo gene in independent targeted cell clones indicated that unintegrated retroviral linear DNA recombined with the target by gene conversion for variable distances into regions of nonhomology. In addition, transient neo gene correction events which were associated with the complete loss of the chromosomal target sequences were observed. These results demonstrated that retroviral vectors can recombine with homologous chromosomal sequences in rodent and human cells.

  12. Denitrification in a large river: consideration of geomorphic controls on microbial activity and community structure.

    Science.gov (United States)

    Tatariw, Corianne; Chapman, Elise L; Sponseller, Ryan A; Mortazavi, Behzad; Edmonds, Jennifer W

    2013-10-01

    Ecological theory argues that the controls over ecosystem processes are structured hierarchically, with broader-scale drivers acting as constraints over the interactions and dynamics at nested levels of organization. In river ecosystems, these interactions may arise from broadscale variation in channel form that directly shapes benthic habitat structure and indirectly constrains resource supply and biological activity within individual reaches. To evaluate these interactions, we identified sediment characteristics, water chemistry, and denitrifier community structure as factors influencing benthic denitrification rates in a sixth-order river that flows through two physiographic provinces and the transitional zone between them, each with distinct geomorphological properties. We found that denitrification rates tracked spatial changes in sediment characteristics and varied seasonally with expected trends in stream primary production. Highest rates were observed during the spring and summer seasons in the physiographic province dominated by fine-grained sediments, illustrating how large-scale changes in river structure can constrain the location of denitrification hotspots. In addition, nirS and nirK community structure each responded differently to variation in channel form, possibly due to changes in dissolved oxygen and organic matter supply. This shift in denitrifier community structure coincident with higher rates of N removal via denitrification suggests that microbial community structure may influence biogeochemical processes.

  13. Brief isoflurane anaesthesia affects differential gene expression, gene ontology and gene networks in rat brain.

    Science.gov (United States)

    Lowes, Damon A; Galley, Helen F; Moura, Alessandro P S; Webster, Nigel R

    2017-01-15

    Much is still unknown about the mechanisms of effects of even brief anaesthesia on the brain and previous studies have simply compared differential expression profiles with and without anaesthesia. We hypothesised that network analysis, in addition to the traditional differential gene expression and ontology analysis, would enable identification of the effects of anaesthesia on interactions between genes. Rats (n=10 per group) were randomised to anaesthesia with isoflurane in oxygen or oxygen only for 15min, and 6h later brains were removed. Differential gene expression and gene ontology analysis of microarray data was performed. Standard clustering techniques and principal component analysis with Bayesian rules were used along with social network analysis methods, to quantitatively model and describe the gene networks. Anaesthesia had marked effects on genes in the brain with differential regulation of 416 probe sets by at least 2 fold. Gene ontology analysis showed 23 genes were functionally related to the anaesthesia and of these, 12 were involved with neurotransmitter release, transport and secretion. Gene network analysis revealed much greater connectivity in genes from brains from anaesthetised rats compared to controls. Other importance measures were also altered after anaesthesia; median [range] closeness centrality (shortest path) was lower in anaesthetized animals (0.07 [0-0.30]) than controls (0.39 [0.30-0.53], pgenes after anaesthesia and suggests future targets for investigation. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. How eukaryotic genes are transcribed

    OpenAIRE

    Venters, Bryan J; Pugh, B. Franklin

    2009-01-01

    Regulation of eukaryotic gene expression is far more complex than one might have imagined thirty years ago. However, progress towards understanding gene regulatory mechanisms has been rapid and comprehensive, which has made the integration of detailed observations into broadly connected concepts a challenge. This review attempts to integrate the following concepts: 1) a well-defined organization of nucleosomes and modification states at most genes, 2) regulatory networks of sequence-specific ...

  15. Gene set analysis for GWAS

    DEFF Research Database (Denmark)

    Debrabant, Birgit; Soerensen, Mette

    2014-01-01

    Abstract We discuss the use of modified Kolmogorov-Smirnov (KS) statistics in the context of gene set analysis and review corresponding null and alternative hypotheses. Especially, we show that, when enhancing the impact of highly significant genes in the calculation of the test statistic...... parameter and the genesis and distribution of the gene-level statistics, and illustrate the effects of differential weighting in a real-life example....

  16. Gene and genome parameters of mammalian liver circadian genes (LCGs.

    Directory of Open Access Journals (Sweden)

    Gang Wu

    Full Text Available The mammalian circadian system controls various physiology processes and behavior responses by regulating thousands of circadian genes with rhythmic expressions. In this study, we redefined circadian-regulated genes based on published results in the mouse liver and compared them with other gene groups defined relative to circadian regulations, especially the non-circadian-regulated genes expressed in liver at multiple molecular levels from gene position to protein expression based on integrative analyses of different datasets from the literature. Based on the intra-tissue analysis, the liver circadian genes or LCGs show unique features when compared to other gene groups. First, LCGs in general have less neighboring genes and larger in both genomic and 3'-UTR lengths but shorter in CDS (coding sequence lengths. Second, LCGs have higher mRNA and protein abundance, higher temporal expression variations, and shorter mRNA half-life. Third, more than 60% of LCGs form major co-expression clusters centered in four temporal windows: dawn, day, dusk, and night. In addition, larger and smaller LCGs are found mainly expressed in the day and night temporal windows, respectively, and we believe that LCGs are well-partitioned into the gene expression regulatory network that takes advantage of gene size, expression constraint, and chromosomal architecture. Based on inter-tissue analysis, more than half of LCGs are ubiquitously expressed in multiple tissues but only show rhythmical expression in one or limited number of tissues. LCGs show at least three-fold lower expression variations across the temporal windows than those among different tissues, and this observation suggests that temporal expression variations regulated by the circadian system is relatively subtle as compared with the tissue expression variations formed during development. Taken together, we suggest that the circadian system selects gene parameters in a cost effective way to improve tissue

  17. Testing for gene-gene interaction with AMMI models.

    Science.gov (United States)

    Barhdadi, Amina; Dubé, Marie-Pierre

    2010-01-01

    Studies have shown that many common diseases are influenced by multiple genes and their interactions. There is currently a strong interest in testing for association between combinations of these genes and disease, in particular because genes that affect the risk of disease only in the presence of another genetic variant may not be detected in marginal analysis. In this paper we propose the use of additive main effect and multiplicative interaction (AMMI) models to detect and to quantify gene-gene interaction effects for a quantitative trait. The objective of the present research is to demonstrate the practical advantages of these models to describe complex interaction between two unlinked loci. Although gene-gene interactions have often been defined as a deviance from additive genetic effects, the residual term has generally not been appropriately treated. The AMMI models allow for the analysis of a two way factorial data structure and combine the analysis of variance of the two main genotype effects with a principal component analysis of the residual multiplicative interaction. The AMMI models for gene-gene interaction presented here allow for the testing of non additivity between the two loci, and also describe how their interaction structure fits the existing non-additivity. Moreover, these models can be used to identify the specific two genotypes combinations that contribute to the significant gene-gene interaction. We describe the use of the biplot to display the structure of the interaction and evaluate the performance of the AMMI and the special cases of the AMMI previously described by Tukey and Mandel with simulated data sets. Our simulated study showed that the AMMI model is as powerful as general linear models when the interaction is not modeled in the presence of marginal effects. However, in the presence of pure epitasis, i.e. in the absence of marginal effects, the AMMI method was not found to be superior to other tested regression methods.

  18. Introduction: Cancer Gene Networks.

    Science.gov (United States)

    Clarke, Robert

    2017-01-01

    Constructing, evaluating, and interpreting gene networks generally sits within the broader field of systems biology, which continues to emerge rapidly, particular with respect to its application to understanding the complexity of signaling in the context of cancer biology. For the purposes of this volume, we take a broad definition of systems biology. Considering an organism or disease within an organism as a system, systems biology is the study of the integrated and coordinated interactions of the network(s) of genes, their variants both natural and mutated (e.g., polymorphisms, rearrangements, alternate splicing, mutations), their proteins and isoforms, and the organic and inorganic molecules with which they interact, to execute the biochemical reactions (e.g., as enzymes, substrates, products) that reflect the function of that system. Central to systems biology, and perhaps the only approach that can effectively manage the complexity of such systems, is the building of quantitative multiscale predictive models. The predictions of the models can vary substantially depending on the nature of the model and its inputoutput relationships. For example, a model may predict the outcome of a specific molecular reaction(s), a cellular phenotype (e.g., alive, dead, growth arrest, proliferation, and motility), a change in the respective prevalence of cell or subpopulations, a patient or patient subgroup outcome(s). Such models necessarily require computers. Computational modeling can be thought of as using machine learning and related tools to integrate the very high dimensional data generated from modern, high throughput omics technologies including genomics (next generation sequencing), transcriptomics (gene expression microarrays; RNAseq), metabolomics and proteomics (ultra high performance liquid chromatography, mass spectrometry), and "subomic" technologies to study the kinome, methylome, and others. Mathematical modeling can be thought of as the use of ordinary

  19. Genes, evolution and intelligence.

    Science.gov (United States)

    Bouchard, Thomas J

    2014-11-01

    I argue that the g factor meets the fundamental criteria of a scientific construct more fully than any other conception of intelligence. I briefly discuss the evidence regarding the relationship of brain size to intelligence. A review of a large body of evidence demonstrates that there is a g factor in a wide range of species and that, in the species studied, it relates to brain size and is heritable. These findings suggest that many species have evolved a general-purpose mechanism (a general biological intelligence) for dealing with the environments in which they evolved. In spite of numerous studies with considerable statistical power, we know of very few genes that influence g and the effects are very small. Nevertheless, g appears to be highly polygenic. Given the complexity of the human brain, it is not surprising that that one of its primary faculties-intelligence-is best explained by the near infinitesimal model of quantitative genetics.

  20. Gene-environment interaction.

    Science.gov (United States)

    Manuck, Stephen B; McCaffery, Jeanne M

    2014-01-01

    With the advent of increasingly accessible technologies for typing genetic variation, studies of gene-environment (G×E) interactions have proliferated in psychological research. Among the aims of such studies are testing developmental hypotheses and models of the etiology of behavioral disorders, defining boundaries of genetic and environmental influences, and identifying individuals most susceptible to risk exposures or most amenable to preventive and therapeutic interventions. This research also coincides with the emergence of unanticipated difficulties in detecting genetic variants of direct association with behavioral traits and disorders, which may be obscured if genetic effects are expressed only in predisposing environments. In this essay we consider these and other rationales for positing G×E interactions, review conceptual models meant to inform G×E interpretations from a psychological perspective, discuss points of common critique to which G×E research is vulnerable, and address the role of the environment in G×E interactions.

  1. Angiogenin gene polymorphism

    Institute of Scientific and Technical Information of China (English)

    Hongli Wang; Dongsheng Fan; Yingshuang Zhang

    2013-01-01

    Angiogenin is associated with the pathogenesis of diabetic peripheral neuropathy. Here, we se-quenced the coding region of the angiogenin gene in genomic DNA from 207 patients with type 2 diabetes mel itus (129 diabetic peripheral neuropathy patients and 78 diabetic non-neuropathy pa-tients) and 268 healthy controls. Al subjects were from the Han population of northern China. No mutations were found. We then compared the genotype and allele frequencies of the angiogenin synonymous single nucleotide polymorphism rs11701 between the diabetic peripheral neuropathy patients and controls, and between the diabetic neuropathy and non-neuropathy patients, using a case-control design. We detected no statistical y significant genetic associations. Angiogenin may not be associated with genetic susceptibility to diabetic peripheral neuropathy in the Han population of northern C