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Sample records for ammonia-oxidizing bacterium nitrosococcus

  1. The Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC19707

    Energy Technology Data Exchange (ETDEWEB)

    Klotz, M G; Arp, D J; Chain, P S; El-Sheikh, A F; Hauser, L J; Hommes, N G; Larimer, F W; Malfatti, S A; Norton, J M; Poret-Peterson, A T; Vergez, L M; Ward, B B

    2006-08-03

    The Gammaproteobacterium, Nitrosococcus oceani (ATCC 19707), is a Gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; 50.4% G+C) and a plasmid (40,420 bp) that contain 3052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. In contrast to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance and the ability to assimilate carbon via gluconeogenesis. One set of genes for type I RuBisCO was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H{sup +}-dependent F{sub 0}F{sub 1}-type, one Na{sup +}-dependent V-type).

  2. Combined Molecular and Conventional Analyses of Nitrifying Bacterium Diversity in Activated Sludge: Nitrosococcus mobilis and Nitrospira-Like Bacteria as Dominant Populations

    OpenAIRE

    Juretschko, Stefan; Timmermann, Gabriele; Schmid, Markus; Schleifer, Karl-Heinz; Pommerening-Röser, Andreas; Koops, Hans-Peter; WAGNER, Michael

    1998-01-01

    The ammonia-oxidizing and nitrite-oxidizing bacterial populations occurring in the nitrifying activated sludge of an industrial wastewater treatment plant receiving sewage with high ammonia concentrations were studied by use of a polyphasic approach. In situ hybridization with a set of hierarchical 16S rRNA-targeted probes for ammonia-oxidizing bacteria revealed the dominance of Nitrosococcus mobilis-like bacteria. The phylogenetic affiliation suggested by fluorescent in situ hybridization (F...

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

    Energy Technology Data Exchange (ETDEWEB)

    Bollmann, Annette [Miami University, Oxford, OH; Sedlacek, Christopher J [Miami University, Oxford, OH; Laanbroek, Hendrikus J [Netherlands Institute of Ecology (NIOO-KNAW); Suwa, Yuichi [Chuo University, Tokyo, Japan; Stein, Lisa Y [University of California, Riverside; Klotz, Martin G [University of Louisville, Louisville; Arp, D J [Oregon State University; Sayavedra-Soto, LA [Oregon State University; Lu, Megan [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL)

    2013-01-01

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

  4. Draft Genome Sequence of Nitrosospira sp. Strain APG3, a Psychrotolerant Ammonia-Oxidizing Bacterium Isolated from Sandy Lake Sediment

    OpenAIRE

    Garcia, Juan C.; Urakawa, Hidetoshi; Le, Vang Q.; Stein, Lisa Y.; Klotz, Martin G; Nielsen, Jeppe L.

    2013-01-01

    Bacteria in the genus Nitrosospira play vital roles in the nitrogen cycle. Nitrosospira sp. strain APG3 is a psychrotolerant betaproteobacterial ammonia-oxidizing bacterium isolated from freshwater lake sediment. The draft genome revealed that it represents a new species of cluster 0 Nitrosospira, which is presently not represented by described species.

  5. Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment

    Energy Technology Data Exchange (ETDEWEB)

    Norton, Jeanette M. [Utah State University (USU); Klotz, Martin G [University of Louisville, Louisville; Stein, Lisa Y [University of California, Riverside; Arp, D J [Oregon State University; Bottomley, Peter J [Oregon State University; Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Larimer, Frank W [ORNL; Shin, M [U.S. Department of Energy, Joint Genome Institute; Starkenburg, Shawn R [Oregon State University

    2008-01-01

    The complete genome of the ammonia-oxidizing bacterium, Nitrosospira multiformis (ATCC 25196T), consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2827 putative proteins. Of these, 2026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and N. eutropha were the best match for 42% of the predicted genes in N. multiformis. The genome contains three nearly identical copies of amo and hao gene clusters as large repeats. Distinguishing features compared to N. europaea include: the presence of gene clusters encoding urease and hydrogenase, a RuBisCO-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced AOB genomes. Gene clusters encoding proteins associated with outer membrane and cell envelope functions including transporters, porins, exopolysaccharide synthesis, capsule formation and protein sorting/export were abundant. Numerous sensory transduction and response regulator gene systems directed towards sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate and cyanophycin storage and utilization were identified providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.

  6. Nitrosomonas communis strain YNSRA, an ammonia-oxidizing bacterium, isolated from the reed rhizoplane in an aquaponics plant.

    Science.gov (United States)

    Tokuyama, Tatsuaki; Mine, Atsusi; Kamiyama, Kaoru; Yabe, Ryuichi; Satoh, Kazuo; Matsumoto, Hirotoshi; Takahashi, Reiji; Itonaga, Koji

    2004-01-01

    An ammonia-oxidizing bacterium (strain YNSRA) was isolated from the rhizoplane of the reed (Phragmites communis) used in an aquaponics plant which is a wastewater treatment plant. Strain YNSRA was identified as Nitrosomonas communis by taxonomic studies. The hydroxylamine-cytochrome c reductase (HCR) of strain YNSRA was found to have a higher activity (25.60 u/mg) than that of Nitrosomonas europaea ATCC25978T (8.94 u/mg). Ribulose-1,5-bisphosphate carboxylase (RubisCO) activity was detected at very low levels in strain YNSRA, whereas strain ATCC25978T had definite activity. PMID:16233712

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

    Science.gov (United States)

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

    2010-09-01

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

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

    Directory of Open Access Journals (Sweden)

    C. H. Frame

    2010-09-01

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

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

    Directory of Open Access Journals (Sweden)

    C. H. Frame

    2010-04-01

    Full Text Available Nitrous oxide (N2O is a trace gas that contributes to greenhouse warming of the atmosphere and stratospheric ozone depletion. The N2O yield from nitrification (moles N2O-N produced/mole ammonium-N consumed has been used to estimate marine N2O production rates from measured nitrification rates and global estimates of oceanic export production. However, the N2O yield from nitrification is not constant. Previous culture-based measurements indicate that N2O yield increases as oxygen (O2 concentration decreases and as nitrite (NO2 concentration increases. These results were obtained in substrate-rich conditions and may not reflect N2O production in the ocean. Here, we have measured yields of N2O from cultures of the marine β-proteobacterium Nitrosomonas marina C-113a as they grew on low-ammonium (50 μM media. These yields were lower than previous reports, between 4×10−4 and 7×10−4 (moles N/mole N. The observed impact of O2 concentration on yield was also smaller than previously reported under all conditions except at high starting cell densities (1.5×10 cells ml−1, where 160-fold higher yields were observed at 0.5% O2 compared with 20% O2. At environmentally relevant cell densities (2×102 to 2.1×104 cells ml−1, cultures grown under 0.5% O2 had yields that were only 1.25- to 1.73-fold higher than cultures grown under 20% O2. Thus, previously reported many-fold increases in N2O yield with dropping O2 could be reproduced only at cell densities that far exceeded those of ammonia oxidizers in the ocean. The presence of excess NO2 (up to 1 mM in the growth medium also increased N2O yields by an average of 70% to 87% depending

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

    Energy Technology Data Exchange (ETDEWEB)

    Stein, Lisa Y [University of California, Riverside; Arp, D J [Oregon State University; Berube, PM [University of Washington, Seattle; Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Hauser, Loren John [ORNL; Jetten, MSM [Radboud University Nijmegen; Klotz, Martin G [University of Louisville, Louisville; Larimer, Frank W [ORNL; Norton, Jeanette M. [Utah State University (USU); Op den Camp, HJM [Radboud University Nijmegen; Shin, M [U.S. Department of Energy, Joint Genome Institute; Wei, Xueming [Oregon State University

    2007-12-01

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

  11. Effects of Soil and Water Content on Methyl Bromide Oxidation by the Ammonia-Oxidizing Bacterium Nitrosomonas europaea†

    OpenAIRE

    Duddleston, Khrystyne N.; Bottomley, Peter J; Porter, Angela; Arp, Daniel J.

    2000-01-01

    Little information exists on the potential of NH3-oxidizing bacteria to cooxidize halogenated hydrocarbons in soil. A study was conducted to examine the cooxidation of methyl bromide (MeBr) by an NH3-oxidizing bacterium, Nitrosomonas europaea, under soil conditions. Soil and its water content modified the availability of NH4+ and MeBr and influenced the relative rates of substrate (NH3) and cosubstrate (MeBr) oxidations. These observations highlight the complexity associated with characterizi...

  12. Catalyst for Ammonia Oxidation

    DEFF Research Database (Denmark)

    2015-01-01

    The present invention relates to a bimetallic catalyst for ammonia oxidation, a method for producing a bimetallic catalyst for ammonia oxidation and a method for tuning the catalytic activity of a transition metal. By depositing an overlayer of less catalytic active metal onto a more catalytic...

  13. Niche specialization of terrestrial archaeal ammonia oxidizers

    OpenAIRE

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

    2011-01-01

    Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were...

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

    OpenAIRE

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

    2011-01-01

    Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA...

  15. Autotrophic ammonia oxidation by soil thaumarchaea

    OpenAIRE

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

    2010-01-01

    Nitrification plays a central role in the global nitrogen cycle and is responsible for significant losses of nitrogen fertilizer, atmospheric pollution by the greenhouse gas nitrous oxide, and nitrate pollution of groundwaters. Ammonia oxidation, the first step in nitrification, was thought to be performed by autotrophic bacteria until the recent discovery of archaeal ammonia oxidizers. Autotrophic archaeal ammonia oxidizers have been cultivated from marine and thermal spring environments, bu...

  16. The effect of outside conditions on anaerobic ammonia oxidation reaction

    Institute of Scientific and Technical Information of China (English)

    YANG Min; WANG Shu-bo

    2016-01-01

    Organic carbon, inorganic carbon, temperature, pH and ORP are all to have a certain influence on the anaerobic ammonia oxidation reaction. We can draw some conclusions on the optimum conditions of anaerobic ammonia oxidation reaction. The optimum temperature of the anaerobic ammonia oxidation reaction is 30-35℃. And the optimum pH of the anaerobic ammonia reaction is 7.5-8.3. The presence of organic matters can affect the anaerobic ammonia reaction, and different organic matters have different influence on it. The concentration of the inorganic carbon also exist great influence on the reaction. High inorganic carbon concentration also can inhibit anaerobic ammonia oxidation reaction.

  17. Molecular analysis of enrichment cultures of ammonia oxidizers from the Salar de Huasco, a high altitude saline wetland in northern Chile.

    Science.gov (United States)

    Dorador, Cristina; Busekow, Annika; Vila, Irma; Imhoff, Johannes F; Witzel, Karl-Paul

    2008-05-01

    We analyzed enrichment cultures of ammonia-oxidizing bacteria (AOB) collected from different areas of Salar de Huasco, a high altitude, saline, pH-neutral water body in the Chilean Altiplano. Samples were inoculated into mineral media with 10 mM NH4+ at five different salt concentrations (10, 200, 400, 800 and 1,400 mM NaCl). Low diversity (up to three phylotypes per enrichment) of beta-AOB was detected using 16S rDNA and amoA clone libraries. Growth of beta-AOB was only recorded in a few enrichment cultures and varied according to site or media salinity. In total, five 16S rDNA and amoA phylotypes were found which were related to Nitrosomonas europaea/Nitrosococcus mobilis, N. marina and N. communis clusters. Phylotype 1-16S was 97% similar with N. halophila, previously isolated from Mongolian soda lakes, and phylotypes from amoA sequences were similar with yet uncultured beta-AOB from different biofilms. Sequences related to N. halophila were frequently found at all salinities. Neither gamma-AOB nor ammonia-oxidizing Archaea were recorded in these enrichment cultures. PMID:18305895

  18. Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers.

    Directory of Open Access Journals (Sweden)

    Antoni Fernàndez-Guerra

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

  19. Ammonia oxidation rates and nitrification in the Arabian Sea

    Science.gov (United States)

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

    2011-12-01

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

  20. Ammonia-oxidizing Bacteria and Archaea in the Rhizosphere of Freshwater Macrophytes

    DEFF Research Database (Denmark)

    Herrmann, Martina; Schramm, Andreas

    2007-01-01

    rate measurements revealed clear differences in ammonia oxidation rates. The diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was assessed using the ammonia monooxygenase (amoA) gene as functional marker. Both AOA and AOB could be detected in the rhizosphere of all...

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

    Science.gov (United States)

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

    2015-10-01

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

  2. Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

    OpenAIRE

    Vidya eDe Gannes; Gaius eEudoxie; Dyer, David H.; William James Hickey

    2012-01-01

    Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the p...

  3. Production of oceanic nitrous oxide by ammonia-oxidizing archaea

    Science.gov (United States)

    Löscher, C. R.; Kock, A.; Könneke, M.; LaRoche, J.; Bange, H. W.; Schmitz, R. A.

    2012-07-01

    The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA) over their bacterial counterparts (AOB) in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O) that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been reported to produce N2O. Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA) were detectable throughout the water column of the eastern tropical North Atlantic (ETNA) and eastern tropical South Pacific (ETSP) Oceans. Particularly in the ETNA, comparable patterns of abundance and expression of archaeal amoA genes and N2O co-occurred in the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved oxygen in the ocean.

  4. Global Ecological Pattern of Ammonia-Oxidizing Archaea

    OpenAIRE

    Huiluo Cao; Jean-Christophe Auguet; Ji-Dong Gu

    2013-01-01

    BACKGROUND: The global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent. METHODOLOGY AND RESULTS: We condu...

  5. Inhibition of bacterial ammonia oxidation by organohydrazines in soil microcosms

    Directory of Open Access Journals (Sweden)

    Yucheng eWu

    2012-01-01

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

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

    OpenAIRE

    Trias, R. (Rosalía); García-Lledó A. (Arantzazu); Sánchez, N.; López-Jurado, J. L.; Hallin, S. (Sara); Bañeras, Ll. (Lluís)

    2012-01-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae’s potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities o...

  7. Detection of Ammonia-Oxidizing Archaea in Fish Processing Effluent Treatment Plants

    OpenAIRE

    Devivaraprasad Reddy, A.; Subrahmanyam, Gangavarapu; Shivani Kallappa, Girisha; Karunasagar, Iddya; Karunasagar, Indrani

    2014-01-01

    Ammonia oxidation is the rate limiting step in nitrification and thus have an important role in removal of ammonia in natural and engineered systems with participation of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, their relative distribution and activity in fish processing effluent treatment plants (FPETPs) though significant, is hitherto unreported. Presence of AOA in sludge samples obtained from FPETPs was studied by amplification and sequencing of t...

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

    OpenAIRE

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

    2013-01-01

    Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes α-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcr...

  9. Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment▿ †

    OpenAIRE

    Stopnišek, Nejc; Gubry-Rangin, Cécile; Höfferle, Špela; Nicol, Graeme W.; Mandič-Mulec, Ines; Prosser, James I.

    2010-01-01

    Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils...

  10. Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

    Directory of Open Access Journals (Sweden)

    Vidya eDe Gannes

    2012-07-01

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

  11. Production of oceanic nitrous oxide by ammonia-oxidizing archaea

    Directory of Open Access Journals (Sweden)

    C. R. Löscher

    2012-07-01

    Full Text Available The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA over their bacterial counterparts (AOB in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been reported to produce N2O.

    Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA were detectable throughout the water column of the eastern tropical North Atlantic (ETNA and eastern tropical South Pacific (ETSP Oceans. Particularly in the ETNA, comparable patterns of abundance and expression of archaeal amoA genes and N2O co-occurred in the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved

  12. Production of oceanic nitrous oxide by ammonia-oxidizing archaea

    Directory of Open Access Journals (Sweden)

    C. R. Loescher

    2012-02-01

    Full Text Available The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA over their bacterial counterparts (AOB in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O which occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been described to produce N2O. Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA were detectable throughout the water column of the Eastern Tropical North Atlantic (ETNA and Eastern Tropical South Pacific Oceans (ETSP. Particularly in the ETNA, maxima in abundance and expression of archaeal amoA genes correlated with the N2O maximum and the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved oxygen

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

    Directory of Open Access Journals (Sweden)

    Mariusz Cycoń

    2015-01-01

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

  14. A Potentiometric Flow Biosensor Based on Ammonia-Oxidizing Bacteria for the Detection of Toxicity in Water

    Directory of Open Access Journals (Sweden)

    Qianyu Zhang

    2013-05-01

    Full Text Available A flow biosensor for the detection of toxicity in water using the ammonia-oxidizing bacterium (AOB Nitrosomonas europaea as a bioreceptor and a polymeric membrane ammonium-selective electrode as a transducer is described. The system is based on the inhibition effects of toxicants on the activity of AOB, which can be evaluated by measuring the ammonium consumption rates with the ammonium-selective membrane electrode. The AOB cells are immobilized on polyethersulfone membranes packed in a holder, while the membrane electrode is placed downstream in the flow cell. Two specific inhibitors of the ammonia oxidation‒allylthiourea and thioacetamide‒have been tested. The IC50 values defined as the concentration of an inhibitor causing a 50% reduction in the ammonia oxidation activity have been measured as 0.17 μM and 0.46 μM for allylthiourea and thioacetamide, respectively. The proposed sensor offers advantages of simplicity, speed and high sensitivity for measuring toxicity in water.

  15. Drivers of archaeal ammonia-oxidizing communities in soil

    Directory of Open Access Journals (Sweden)

    KaterynaZhalnina

    2012-06-01

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

  16. Vertical segregation and phylogenetic characterization of ammonia-oxidizing bacteria and archaea in the sediment of a freshwater aquaculture pond

    OpenAIRE

    Shimin eLu; Xingguo eLiu; Qigen eLiu; Zhuojun eMa; Zongfan eWu; Xianlei eZeng; Xu eShi; Zhaojun eGu

    2016-01-01

    Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) a...

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

    OpenAIRE

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

    2016-01-01

    Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB) a...

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

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

    OpenAIRE

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

    2012-01-01

    The hydrolysis of urea as a source of ammonia has been proposed as a mechanism for the nitrification of ammonia-oxidizing bacteria (AOB) in acidic soil. The growth of Nitrososphaera viennensis on urea suggests that the ureolysis of ammonia-oxidizing archaea (AOA) might occur in natural environments. In this study, 15N isotope tracing indicates that ammonia oxidation occurred upon the addition of urea at a concentration similar to the in situ ammonium content of tea orchard soil (pH 3.75) and ...

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

    OpenAIRE

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

    2008-01-01

    The recent discovery of ammonia-oxidizing archaea (AOA) dramatically changed our perception of the diversity and evolutionary history of microbes involved in nitrification. In this study, a moderately thermophilic (46°C) ammonia-oxidizing enrichment culture, which had been seeded with biomass from a hot spring, was screened for ammonia oxidizers. Although gene sequences for crenarchaeotal 16S rRNA and two subunits of the ammonia monooxygenase (amoA and amoB) were detected via PCR, no hints fo...

  2. Ammonia oxidation at high pressure and intermediate temperatures

    DEFF Research Database (Denmark)

    Song, Yu; Hashemi, Hamid; Christensen, Jakob Munkholt;

    2016-01-01

    Ammonia oxidation experiments were conducted at high pressure (30 bar and 100 bar) under oxidizing and stoichiometric conditions, respectively, and temperatures ranging from 450 to 925 K. The oxidation of ammonia was slow under stoichiometric conditions in the temperature range investigated. Under...... oxidizing conditions the onset temperature for reaction was 850–875 K at 30 bar, while at 100 bar it was about 800 K, with complete consumption of NH3 at 875 K. The products of reaction were N2 and N2O, while NO and NO2 concentrations were below the detection limit even under oxidizing conditions. The data...... satisfactory. The main oxidation path for NH3 at high pressure under oxidizing conditions is NH3⟶+OH NH2⟶+HO2,NO2 H2NO⟶+O2 HNO⟶+O2 NO ⟶+NH2 N2. The modeling predictions are most sensitive to the reactions NH2 + NO = NNH + OH and NH2 + HO2 = H2NO + OH, which promote the ammonia consumption by forming OH...

  3. Inhibition of Direct Electrolytic Ammonia Oxidation Due to a Change in Local pH

    International Nuclear Information System (INIS)

    Electrochemical ammonia oxidation has gained a lot of attention recently as an efficient method for ammonia removal from wastewater, for the use in ammonia-based fuel cells and the production of high purity hydrogen. Thermally decomposed iridium oxide films (TDIROF) have been shown to be catalytically active for direct ammonia oxidation in aqueous solutions if NH3 is present. However, the process was reported to be rapidly inhibited on TDIROF. Herein, we show that this fast inhibition of direct ammonia oxidation does not result from surface poisoning by adsorbed elemental nitrogen (Nads). Instead, we propose that direct ammonia oxidation and oxygen evolution can lead to a drop of the local pH at the electrode resulting in a low availability of the actual reactant, NH3. The hypothesis was tested with cyclic voltammetry (CV) experiments on stagnant and rotating disk electrodes (RDE). The CV experiments on the stagnant electrode revealed that the decrease of the ammonia oxidation peaks was considerably reduced by introducing an idle phase at open circuit potential between subsequent scans. Furthermore, the polarization of the TDIROF electrode into the hydrogen evolution region (HER) resulted in increased ammonia oxidation peaks in the following anodic scans which can be explained with an increased local pH after the consumption of protons in the HER. On the RDE, the ammonia oxidation peaks did not decrease in immediately consecutive scans. These findings would not be expected if surface poisoning was responsible for the fast inhibition but they are in good agreement with the proposed mechanism of pH induced limitation by the reactant, NH3. The plausibility of the mechanism was also supported by our numerical simulations of the processes in the Nernstian diffusion layer. The knowledge about this inhibition mechanism of direct ammonia oxidation is especially important for the design of electrochemical cells for wastewater treatment. The mechanism is not only valid for

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

    OpenAIRE

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

    2014-01-01

    A pilot-scale multilayer rapid infiltration system (MRIS) for domestic wastewater treatment was established and efficient removal of ammonia and chemical oxygen demand (COD) was achieved in this study. The microbial community composition and abundance of ammonia oxidizers were investigated. Efficient biofilms of ammonia oxidizers in the stationary phase (packing material) was formed successfully in the MRIS without special inoculation. DGGE and phylogenetic analyses revealed that proteobacter...

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

    OpenAIRE

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

    2011-01-01

    Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen f...

  6. Ammonia-Oxidizer Communities in an Agricultural Soil treated with Contrasting Nitrogen Sources.

    OpenAIRE

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

    2013-01-01

    The community of ammonia-oxidizing prokaryotes was examined in an agricultural soil treated for 6 seasons with contrasting nitrogen (N) sources. Molecular tools based on the gene encoding ammonia monooxygenase were used to characterize the ammonia oxidizer communities and their abundance. Soil DNA was extracted from soils sampled from silage corn plots that received no additional N (control), dairy waste compost (DC), liquid dairy waste (LW), and ammonium sulfate (AS) treatments at approxima...

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

    Science.gov (United States)

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

    2014-04-01

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

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

    OpenAIRE

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

    2011-01-01

    Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the d...

  9. Linking Diversity and Stable Isotope Fractionation in Ammonia-Oxidizing Bacteria

    Science.gov (United States)

    Casciotti, K. L.; Sigman, D. M.; Ward, B. B.

    2002-12-01

    Ammonia-oxidizing bacteria play a key role in the regeneration of nitrate (NO3) and the production of nitrous oxide (N2O) in many marine, estuarine, and terrestrial ecosystems. While isotopic ratios (15N/14N) of dissolved inorganic nitrogen pools (NH4+ and NO3) can serve as in situ tracers for overall nitrification activity, genetic characterization of bacterial communities can provide information about the diversity and relative abundance of specific groups of ammonia-oxidizers. An important question facing microbial ecologists is how diversity in gene or protein sequences is reflected in diversity in biogeochemical activity. Here we investigate the link between similarity in amino acid sequence for ammonia monooxygenase (AmoA) and its isotopic discrimination (ɛAMO) for B-subdivision ammonia-oxidizing bacteria. Isotope effects for ammonia-oxidation were measured for 5 cultured nitrifier strains. A 20 permil range in isotope effects was observed among these nitrifiers, which could not be explained by differential rates of ammonia oxidation, transport of NH4+, accumulation of NH2OH, or N2O production among the strains. The major similarities and differences observed in ɛAMO are, however, paralleled by similarities and differences in AmoA amino sequences from these organisms. These results suggest that combining genetic and stable isotopic tools may provide complementary information regarding the activity of particular groups of ammonia-oxidizers in the environment.

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

    Science.gov (United States)

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

    2015-02-01

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

  11. Global ecological pattern of ammonia-oxidizing archaea.

    Directory of Open Access Journals (Sweden)

    Huiluo Cao

    Full Text Available BACKGROUND: The global distribution of ammonia-oxidizing archaea (AOA, which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent. METHODOLOGY AND RESULTS: We conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal amoA gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal amoA gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive amoA phylogeny was composed of three major monophyletic clusters (i.e. Nitrosopumilus, Nitrosotalea, Nitrosocaldus and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named Nitrososphaera. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats. CONCLUSION AND SIGNIFICANCE: Based on an up-to-date amoA phylogeny, this

  12. Distribution of Ammonia-Oxidizing Archaea and Bacteria in the Surface Sediments of Matsushima Bay in Relation to Environmental Variables

    OpenAIRE

    Sakami, Tomoko

    2011-01-01

    Ammonia oxidization is the first and a rate-limiting step of nitrification, which is often a critical process in nitrogen removal from estuarine and coastal environments. To clarify the correlation of environmental conditions with the distribution of ammonia oxidizers in organic matter-rich coastal sediments, ammonia-oxidizing archaea (AOA) and bacteria (AOB) ammonia monooxygenase alpha subunit gene (amoA) abundance was determined in sediments of Matsushima Bay located in northeast Japan. The...

  13. Grassland Management Regimens Reduce Small-Scale Heterogeneity and Species Diversity of β-Proteobacterial Ammonia Oxidizer Populations

    OpenAIRE

    Webster, Gordon; Embley, T Martin; Prosser, James I.

    2002-01-01

    The impact of soil management practices on ammonia oxidizer diversity and spatial heterogeneity was determined in improved (addition of N fertilizer), unimproved (no additions), and semi-improved (intermediate management) grassland pastures at the Sourhope Research Station in Scotland. Ammonia oxidizer diversity within each grassland soil was assessed by PCR amplification of microbial community DNA with both ammonia oxidizer-specific, 16S rRNA gene (rDNA) and functional, amoA, gene primers. P...

  14. Spatial Distribution and Factors Shaping the Niche Segregation of Ammonia-Oxidizing Microorganisms in the Qiantang River, China

    OpenAIRE

    Liu, Shuai; Shen, Lidong; Lou, Liping; Guangming TIAN; Zheng, Ping; Hu, Baolan

    2013-01-01

    Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, the current knowledge of the distribution, diversity, and relative abundance of these two microbial groups in freshwater sediments is insufficient. We examined the spatial distribution and analyzed the possible factors leading to the niche segregation of AOA and AOB in the sediments of the Qiantang River, using clone library construction and quantitative PCR for both archaeal ...

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

    Science.gov (United States)

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

    2015-03-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

  17. Benthic Ammonia Oxidizers Differ in Community Structure and Biogeochemical Potential Across a Riverine Delta

    Directory of Open Access Journals (Sweden)

    Julian eDamashek

    2015-01-01

    Full Text Available Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California’s Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the massive discharge of ammonium into the Sacramento River has altered this ecosystem by increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (encoding the α-subunit of ammonia monooxygenase. There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB outnumbering ammonia-oxidizing archaea (AOA only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The community structure and biogeochemical function of benthic ammonia oxidizers appears related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.

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

    Science.gov (United States)

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

    2016-04-01

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

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

    OpenAIRE

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

    2014-01-01

    Diversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity of amoA genes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA c...

  20. Monnte Carlo Simulation of Kinetics of Ammonia Oxidative Decomposition over the Commercial Propylene Ammoxidation Catalyst(Mo-Bi)

    Institute of Scientific and Technical Information of China (English)

    罗正鸿; 詹晓力; 等

    2003-01-01

    Monte Carlo method is applied to investigate the kinetics of ammonia oxidative decomposition over the commercial propylene ammoxidation catalyst(Mo-Bi).The simulation is quite in agreement with experimetal results.Monte Carlo simulation proves that the process of ammonia oxidation decomposition is a two-step reaction.

  1. Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone

    NARCIS (Netherlands)

    Pitcher, A.; Villanueva, L.; Hopmans, E.C.; Schouten, S.; Reichart, G.J.; Sinninghe Damsté, J.S.

    2011-01-01

    Ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria have emerged as significant factors in the marine nitrogen cycle and are responsible for the oxidation of ammonium to nitrite and dinitrogen gas, respectively. Potential for an interaction between these groups exists;

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

    OpenAIRE

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

    2005-01-01

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

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

    NARCIS (Netherlands)

    Jung, M.Y.; Park, S.J.; Min, D.; Kim, J.S.; Rijpstra, W.I.C.; Sinninghe Damsté, J.S.; Kim, G.J.; Madsen, E.L.; Rhee, S.K.

    2011-01-01

    Soil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizing Archaea from soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain

  4. Co-Mn-Al Mixed Oxides as Catalysts for Ammonia Oxidation to N2O.

    Czech Academy of Sciences Publication Activity Database

    Ludvíková, Jana; Jablońska, M.; Jirátová, Květa; Chmielarz, L.; Balabánová, Jana; Kovanda, F.; Obalová, L.

    2016-01-01

    Roč. 42, č. 3 (2016), s. 2669-2690. ISSN 0922-6168 R&D Projects: GA ČR GA14-13750S Institutional support: RVO:67985858 Keywords : Co-Mn-Al mixed oxides * catalytic ammonia oxidation * N2O production * mechanochemical production Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 1.221, year: 2014

  5. Geographic distribution of archaeal ammonia oxidizing ecotypes in the Atlantic Ocean

    Directory of Open Access Journals (Sweden)

    Eva eSintes

    2016-02-01

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

  6. Archaea Dominate the Ammonia-Oxidizing Community in the Rhizosphere of the Freshwater Macrophyte Littorella uniflora▿

    OpenAIRE

    Herrmann, Martina; Saunders, Aaron M.; Schramm, Andreas

    2008-01-01

    Archaeal and bacterial ammonia monooxygenase genes (amoA) had similar low relative abundances in freshwater sediment. In the rhizosphere of the submersed macrophyte Littorella uniflora, archaeal amoA was 500- to >8,000-fold enriched compared to bacterial amoA, suggesting that the enhanced nitrification activity observed in the rhizosphere was due to ammonia-oxidizing Archaea.

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

    Science.gov (United States)

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

    2015-11-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

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

    KAUST Repository

    Bagchi, Samik

    2014-12-05

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

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

    Directory of Open Access Journals (Sweden)

    Samik Bagchi

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

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

    Science.gov (United States)

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

    2015-07-01

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

  12. Ammonia-Oxidizer Communities in an Agricultural Soil treated with Contrasting Nitrogen Sources.

    Directory of Open Access Journals (Sweden)

    Mussie Y. Habteselassie

    2013-11-01

    Full Text Available The community of ammonia-oxidizing prokaryotes was examined in an agricultural soil treated for 6 seasons with contrasting nitrogen (N sources. Molecular tools based on the gene encoding ammonia monooxygenase were used to characterize the ammonia oxidizer communities and their abundance. Soil DNA was extracted from soils sampled from silage corn plots that received no additional N (control, dairy waste compost (DC, liquid dairy waste (LW, and ammonium sulfate (AS treatments at approximately 100 and 200 kg available N ha-1 over 6 years. The N treatment affected the quantity of ammonia oxidizers based on estimates of amoA by real-time PCR. Ammonia oxidizing bacteria (AOB were higher in soils from the AS200, AS100, and LW200 treatments (2.5 x107, 2.5x107, and 2.1 x107 copies g-1 soil, respectively than in the control (8.1x106copies/g while the abundance of amoA encoding archaea (AOA was not significantly affected by treatment (3.8x107copies g-1 soil, average. The ratio of AOA/AOB was higher in the control and compost treated soils, both treatments have the majority of their ammonium supplied through mineralization of organic nitrogen. Clone libraries of partial amoA sequences indicated AOB related to Nitrosospira multiformis and AOA related to uncultured Nitrososphaera similar to those described by soil fosmid 54d9 were prevalent. Profiles of the amoC-amoA intergenic region indicated that both Nitrosospira- and Nitrosomonas-type AOB were present in all soils examined. In contrast to the intergenic amoC-amoA profile results, Nitrosomonas-like clones were recovered only in the LW200 treated soil-DNA. The impact of six years of contrasting nitrogen sources applications caused changes in ammonia oxidizer abundance while the community composition remained relatively stable for both AOB and AOA.

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

    Science.gov (United States)

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

    2015-05-01

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

  14. Abundance and Community Composition of Ammonia-Oxidizers in Paddy Soil at Different Nitrogen Fertilizer Rates

    Institute of Scientific and Technical Information of China (English)

    SONG Ya-na; LIN Zhi-min

    2014-01-01

    Ammonia oxidation, the ifrst and rate-limiting step of nitriifcation, is carried out by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). However, the relative importance of AOB and AOA to nitriifcation in terrestrial ecosystems is not well understood. The aim of this study was to investigate the effect of the nitrogen input amount on abundance and community composition of AOB and AOA in red paddy soil. Soil samples of 10-20 cm (root layer soil) and 0-5 cm (surface soil) depths were taken from a red paddy. Rice in the paddy was fertilized with different rates of N as urea of N1 (75 kg N ha-1 yr-1), N2 (150 kg N ha-1 yr-1), N3 (225 kg N ha-1 yr-1) and CK (without fertilizers) in 2009, 2010 and 2011. Abundance and community composition of ammonia oxidizers was analyzed by real-time PCR and denaturing gradient gel electrophoresis (DGGE) based on amoA (the unit A of ammonia monooxygenase) gene. Archaeal amoA copies in N3 and N2 were signiifcantly (P<0.05) higher than those in CK and N1 in root layer soil or in surface soil under tillering and heading stages of rice, while the enhancement in bacterial amoA gene copies with increasing of N fertilizer rates only took on in root layer soil. N availability and soil NO3--N content increased but soil NH4+-N content didn’t change with increasing of N fertilizer rates. Otherwise, the copy numbers of archaeal amoA gene were higher (P<0.05) than those of bacterial amoA gene in root lary soil or in surface soil. Redundancy discriminate analysis based on DGGE bands showed that there were no obvious differs in composition of AOA or AOB communities in the ifeld among different N fertilizer rates. Results of this study suggested that the abundance of ammonia-oxidizers had active response to N fertilizer rates and the response of AOA was more obvious than that of AOB. Similarity in the community composition of AOA or AOB among different N fertilizer rates indicate that the community composition of ammonia-oxidizers

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

    Science.gov (United States)

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

    2016-03-01

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

  16. Bacterial domination over Archaea in ammonia oxidation in a monsoon-driven tropical estuary

    Digital Repository Service at National Institute of Oceanography (India)

    Vipindas, P.V.; Anas, A.; Jasmin, C.; Lallu, K.R.; Fausia, K.H.; Balachandran, K.K.; Muraleedharan, K.R.; Nair, S.

    rivers, seawater influx from two bar mouths [Major opening at Fort Cochin (450 m wide) and minor opening at Munambam (250 m wide)] and the prolonged southwest monsoon. Ammonia in CE accounts for 50 – 65% of the dissolved inorganic nitrogen [11... concentrations [36], while that of bacterial gets triggered at higher concentration of ammonia. CE contains high concentrations of ammonia, i.e. 50 -65 % of the dissolved inorganic nitrogen [11], and therefore the AOB’s contribution in ammonia oxidation could...

  17. Trichloroethylene biodegradation by mesophilic and psychrophilic ammonia oxidizers and methanotrophs in groundwater microcosms.

    OpenAIRE

    Moran, B N; Hickey, W J

    1997-01-01

    This study investigated the efficiency of methane and ammonium for stimulating trichloroethylene (TCE) biodegradation in groundwater microcosms (flasks and batch exchange columns) at a psychrophilic temperature (12 degrees C) typical of shallow aquifers in the northern United States or a mesophilic temperature (24 degrees C) representative of most laboratory experiments. After 140 days, TCE biodegradation rates by ammonia oxidizers and methanotrophs in mesophilic flask microcosms were similar...

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

    Science.gov (United States)

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

    2016-01-01

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

  19. Fabrication of platinum submonolayer electrodes and their high electrocatalytic activities for ammonia oxidation

    International Nuclear Information System (INIS)

    Highlights: • Pt submonolayer on the Au electrode for ammonia oxidation. • The surface coverage of the Pt submonolayer can be effectively controlled by the Cu UPD potential. • Pt submonolayer on the Au electrode has both high mass activity and specific activity. - Abstract: Pt submonolayer with different coverage on the Au electrode for ammonia oxidation was prepared by Cu underpotential deposition (UPD) followed by redox replacement of UPD Cu by Pt. The effects of the Cu UPD potential and time on the deposited Cu and the redox replaced Pt layer on the electrode were investigated. The amount of the deposited Cu and Pt was determined by the anodic stripping method. The electrocatalytic activity of the Pt decorated electrodes for ammonia oxidation was characterized by cyclic voltammetry. The results showed that the Cu UPD potential has a significant influence on the formed Cu layer and the subsequent Pt submonolayer. The Cu deposition behaviour changes from UPD process to overpotential deposition (OPD) process with the decrease of deposition potential. Besides, the amount of the deposited Cu increases as the Cu deposition potential decreases. Consequently, Pt layer with different coverage on the electrode can be effectively controlled by adjusting the Cu UPD potential. The Pt submonolayer electrodes prepared by the redox replacement of Cu UPD layer have a high mass activity for ammonia oxidation, and their mass activities are more than two times higher than that of the Pt decorated electrodes obtained by redox replacement of Cu OPD layer. Besides, the Pt submonolayer electrodes also have a higher specific activity possibly due to the modification in structural and electronic properties of the Pt submonolayer induced by the Au substrate

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

    Science.gov (United States)

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

    2014-05-01

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

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

    OpenAIRE

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

    2012-01-01

    Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the p...

  2. Bacteria dominate ammonia oxidation in soils used for outdoor cattle overwintering

    Czech Academy of Sciences Publication Activity Database

    Radl, V.; Chroňáková, Alica; Čuhel, Jiří; Šimek, Miloslav; Elhottová, Dana; Welzl, G.; Schloter, M.

    2014-01-01

    Roč. 77, May (2014), s. 68-71. ISSN 0929-1393 R&D Projects: GA MŠk LC06066 Grant ostatní: Akademie věd ČR(CZ) D-CZ 45:05/06 Institutional support: RVO:60077344 Keywords : ammonia oxidation * bacteria * archaea * amoA diversity * urea * pasture Subject RIV: EH - Ecology, Behaviour Impact factor: 2.644, year: 2014

  3. Autotrophic Ammonia-Oxidizing Bacteria Contribute Minimally to Nitrification in a Nitrogen-Impacted Forested Ecosystem

    OpenAIRE

    Jordan, F L; Cantera, JJL; Fenn, M E; Stein, L.Y.

    2005-01-01

    Deposition rates of atmospheric nitrogenous pollutants to forests in the San Bernardino Mountains range east of Los Angeles, California, are the highest reported in North America. Acidic soils from the west end of the range are N-saturated and have elevated rates of N-mineralization, nitrification, and nitrate leaching. We assessed the impact of this heavy nitrogen load on autotrophic ammonia-oxidizing communities by investigating their composition, abundance, and activity. Analysis of 177 cl...

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

    Directory of Open Access Journals (Sweden)

    L. Fuchslueger

    2014-06-01

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

  5. Molecular Characterization of Soil Ammonia-Oxidizing Bacteria Based on the Genes Encoding Ammonia Monooxygenase

    OpenAIRE

    Alzerreca, Jose Javier

    1999-01-01

    Ammonia-oxidizing bacteria (AOB) are chemolithotrophs that oxidize ammonia/ammonium to nitrite in a two-step process to obtain energy for survival. AOB are difficult to isolate from the environment and iso lated strains may not represent the diversity in soil. A genetic database and molecular tools were developed based on the ammonia monooxygenase (AMO) encoding genes that can be used to assess the diversity of AOB that exist in soil and aquatic environments without the isolation of pure cult...

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

    OpenAIRE

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

    2013-01-01

    The function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) depends on the availability of ammonia substrate and the supply of oxygen. The interactions and evolutions of AOA and AOB communities along ecological gradients of substrate availability in complex environment have been much debated, but rarely tested. In this study, two ecosystems of maize and rice crops under different fertilization regimes were selected to investigate the community diversification of soil AOA and AOB i...

  7. QPCR quantification of ammonia oxidizing bacteria: What should the target be?

    OpenAIRE

    Musovic, Sanin; Palomo, Alejandro; Diwan, Vaibhav; Dechesne, Arnaud; Smets, Barth F.

    2014-01-01

    Ammonia oxidizing bacteria (AOB) perform the first step of nitrification, a key step in the Nitrogen cycle in both natural and engineered systems. In addition to their well-known role in wastewater treatment, they are also essential in rapid sand filter at waterworks treating anaerobic groundwater for drinking water production. Being able to quantify precisely the abundance of this functional group is thus important to be able monitor these processes.AOB are moderately diverse Beta-Proteobact...

  8. Seasonal and vertical distribution of putative ammonia-oxidizing thaumarchaeotal communities in an oligotrophic lake

    OpenAIRE

    Vissers, E.W.; Blaga, C. I.; Bodelier, P.L.E.; Muyzer, G; Schleper, C.; Sinninghe Damsté, J.S.; Tourna, M.; Laanbroek, H. J.

    2013-01-01

    The discovery of Archaea carrying an amoA gene coding for the A-subunit of ammonia monooxygenase gave a boost to studies aimed at detecting this gene under diverse conditions. Despite numerous studies describing the archaeal amoA gene abundance and richness in different habitats, the understanding of the freshwater ecology of potentially archaeal ammonia oxidizers, recently positioned in the phylum Thaumarchaeota, is still lacking. In a seasonal and vertical study of deep oligotrophic Lake Lu...

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

    Science.gov (United States)

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

    2014-11-01

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

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

    Science.gov (United States)

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

    2016-07-12

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2013-04-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2015-08-01

    Ammonia was observed as a potential significant factor to manipulate the abundance and activity of ammonia-oxidizing microorganisms (AOMs) in water environments. For the first time, this study confirmed this phenomenon by laboratory cultivation. In a series of estuarine sediment-coastal water microcosms, we investigated the AOM's phylogenetic composition and activity change in response to ammonia concentration. Increase of ammonia concentration promoted bacterial amoA gene abundance in a linear pattern. The ratio of transcribed ammonia-oxidizing bacteria (AOB) amoA gene/ammonia-oxidizing archaea (AOA) amoA gene increased from 0.1 to 43 as NH4 (+)-N increased from less than 0.1 to 12 mg L(-1), and AOA amoA transcription was undetected under 20 mg NH4 (+)-N L(-1). The incubation of stable isotope probing (SIP) microcosms revealed a faster (13)C-NaHCO3 incorporation rate of AOA amoA gene under 0.1 mg NH4 (+)-N L(-1) and a sole (13)C-NaHCO3 utilization of the AOB amoA gene under 20 mg NH4 (+)-N L(-1). Our results indicate that ammonia concentration manipulates the structure of AOM. AOA prefers to live and perform higher amoA transcription activity than AOB in ammonia-limited water environments, and AOB tends to take the first contributor place in ammonia-rich ones. PMID:25797330

  15. CFD modelling of flow mal-distribution in an industrial ammonia oxidation reactor: A case study

    International Nuclear Information System (INIS)

    Ammonia oxidation reactor is widely used in nitric acid plant to cause the catalytic reaction between air and ammonia to produce nitrous gases. In this work, the flow distribution inside the ammonia oxidation reactor at Shiraz Petrochemical Complex (SPC) has been simulated using Computational Fluid Dynamics (CFD) code. The CFD results showed that the flow is non-uniformly distributed inside the reactor due to improper header design of the reactor. Measuring of the temperature distribution around the skin of the reactor has been carried out using thermograph. The thermograph experiment showed a considerable temperature difference between the left and right side of the reactor. It was found that the mal-distribution of the gas flow inside the reactor can directly affect the performance of the reactor. - Highlights: •A failure has been observed in an industrial ammonia oxidation reactor. •CFD code helps to simulate the flow inside the reactor. •The flow becomes non-uniformly distributed due to the reactor header mal-design. •The flow mal-distribution results in some drawbacks

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

    Science.gov (United States)

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

    2016-05-01

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

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

    OpenAIRE

    Xi Li; Miaomiao Zhang; Feng Liu(Central China Normal University); Yong Li; Yang He; Shunan Zhang; Jinshui Wu

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different...

  18. Nitrogen Cycling and Community Structure of Proteobacterial β-Subgroup Ammonia-Oxidizing Bacteria within Polluted Marine Fish Farm Sediments

    OpenAIRE

    McCaig, Allison E.; Phillips, Carol J.; Stephen, John R.; Kowalchuk, George A.; Harvey, S. Martyn; Herbert, Rodney A.; Embley, T. Martin; Prosser, James I

    1999-01-01

    A multidisciplinary approach was used to study the effects of pollution from a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer most-probable-number counts were determined in samples of sediment collected from beneath a fish cage and on a transect at 20 and 40 m from the cage. The data suggest that nitrogen cycling was significantl...

  19. Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil

    OpenAIRE

    Sterngren, Anna E.; Hallin, Sara; Bengtson, Per

    2015-01-01

    Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the a...

  20. Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers

    OpenAIRE

    Mußmann, M; Brito, I.; A. Pitcher; Hatzenpichler, R.; Richter, A; Nielsen, J. L.; Nielsen, P. H.; Daims, H.; MÜller, A.; Wagner, M.; Head, I.M.

    2011-01-01

    Nitrification is a core process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in particular since their numerical dominance over ammonia-oxidizing bacteria (AOB) in many environments has been revealed. These and other data have led to a widely held assumption that all amoA-encoding members of the...

  1. Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers

    OpenAIRE

    Mußmann, Marc; Brito, Ivana; Pitcher, Angela; Sinninghe Damsté, Jaap S.; Hatzenpichler, Roland; Richter, Andreas; Nielsen, Jeppe L.; Nielsen, Per Halkjær; Müller, Anneliese; Daims, Holger; WAGNER, MICHAEL; Head, Ian M.

    2011-01-01

    Nitrification is a core process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in particular since their numerical dominance over ammonia-oxidizing bacteria (AOB) in many environments has been revealed. These and other data have led to a widely held assumption that all amoA-encoding members of the...

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

    OpenAIRE

    Sauder, L.A.; Peterse, F.; Schouten, S; Neufeld, J. D.

    2012-01-01

    The first step of nitrification is catalysed by both ammonia-oxidizing bacteria (AOB) and archaea (AOA), but physicochemical controls on the relative abundance and function of these two groups are not yet fully understood, especially in freshwater environments. This study investigated ammonia-oxidizing populations in nitrifying rotating biological contactors (RBCs) from a municipal wastewater treatment plant. Individual RBC stages are arranged in series, with nitrification at each stage creat...

  3. Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil▿

    OpenAIRE

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

    2011-01-01

    The recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically dige...

  4. Abundance, Diversity, and Activity of Ammonia-Oxidizing Prokaryotes in the Coastal Arctic Ocean in Summer and Winter ▿ †

    OpenAIRE

    Christman, Glenn D.; Cottrell, Matthew T.; Brian N Popp; Gier, Elizabeth; Kirchman, David L.

    2011-01-01

    Ammonia oxidation, the first step in nitrification, is performed by certain Beta- and Gammaproteobacteria and Crenarchaea to generate metabolic energy. Ammonia monooxygenase (amoA) genes from both Bacteria and Crenarchaea have been found in a variety of marine ecosystems, but the relative importance of Bacteria versus Crenarchaea in ammonia oxidation is unresolved, and seasonal comparisons are rare. In this study, we compared the abundance of betaproteobacterial and crenarchaeal amoA genes in...

  5. Niche segregation of ammonia-oxidizing archaea and anammox bacteria in the Arabian Sea oxygen minimum zone

    OpenAIRE

    Pitcher, A.; Villanueva, L; Hopmans, E.C.; Schouten, S.; G. J. Reichart; Sinninghe Damsté, J.S.

    2011-01-01

    Ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria have emerged as significant factors in the marine nitrogen cycle and are responsible for the oxidation of ammonium to nitrite and dinitrogen gas, respectively. Potential for an interaction between these groups exists; however, their distributions are rarely determined in tandem. Here we have examined the vertical distribution of AOA and anammox bacteria through the Arabian Sea oxygen minimum zone (OMZ), one of ...

  6. Protective effect of immobilized ammonia oxidizers and phenol-degrading bacteria on nitrification in ammonia- and phenol-containing wastewater

    Energy Technology Data Exchange (ETDEWEB)

    Morita, M.; Watanabe, A. [Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), Chiba (Japan); Kudo, N.; Shinozaki, H. [Materials Science Engineering, Tokyo Denki University, Tokyo (Japan); Uemoto, H.

    2007-12-15

    Phenol present in wastewaters from various industries has an inhibitory effect on nitrification even at low concentrations. Hence, the biological treatment of wastewater containing both phenol and ammonia involves a series of treatment steps. It is difficult to achieve nitrification capability in an activated sludge system that contains phenol at concentrations above the inhibitory level. Batch treatment of wastewater containing various concentrations of phenol showed that the ammonia oxidation capability of suspended Nitrosomonas europaea cells, an ammonia oxidizer, was completely inhibited in the presence of more than 5.0 mg/L phenol. To protect the ammonia oxidizer from the inhibitory effect of phenol and to achieve ammonia oxidation capability in the wastewater containing phenol at concentrations above the inhibitory level, a simple bacterial consortium composed of an ammonia oxidizer (N. europaea) and a phenol-degrading bacterial strain (Acinetobacter sp.) was used. Ammonia oxidation did not occur in the presence of phenol at concentrations above the inhibitory level when suspended or immobilized N. europaea and Acinetobacter sp. cells were used in batch treatment. Following the acclimatization of the immobilized cells, accumulation of nitrite was observed, even when the wastewater contained phenol at concentrations above the inhibitory level. These results showed that immobilization was effective in protecting N. europaea cells from the inhibitory effect of phenol present in the wastewater. (Abstract Copyright [2007], Wiley Periodicals, Inc.)

  7. amoA Gene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary, United Kingdom

    OpenAIRE

    Li, Jialin; Nedwell, David B.; Beddow, Jessica; Alex J Dumbrell; McKew, Boyd A; Thorpe, Emma L.; Whitby, Corinne

    2014-01-01

    Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA comm...

  8. Distribution and Diversity of Archaeal and Bacterial Ammonia Oxidizers in Salt Marsh Sediments▿

    OpenAIRE

    Moin, Nicole S.; Nelson, Katelyn A.; Bush, Alexander; Bernhard, Anne E.

    2009-01-01

    Diversity and abundance of ammonia-oxidizing Betaproteobacteria (β-AOB) and archaea (AOA) were investigated in a New England salt marsh at sites dominated by short or tall Spartina alterniflora (SAS and SAT sites, respectively) or Spartina patens (SP site). AOA amoA gene richness was higher than β-AOB amoA richness at SAT and SP, but AOA and β-AOB richness were similar at SAS. β-AOB amoA clone libraries were composed exclusively of Nitrosospira-like amoA genes. AOA amoA genes at SAT and SP we...

  9. Ammonia-Oxidizing β-Proteobacteria from the Oxygen Minimum Zone off Northern Chile▿

    OpenAIRE

    Molina, Verónica; Ulloa, Osvaldo; Farías, Laura; Urrutia, Homero; Ramírez, Salvador; Junier, Pilar; Witzel, Karl-Paul

    2007-01-01

    The composition of ammonia-oxidizing bacteria from the β-Proteobacteria subclass (βAOB) was studied in the surface and upper-oxycline oxic waters (2- to 50-m depth, ∼200 to 44 μM O2) and within the oxygen minimum zone (OMZ) suboxic waters (50- to 400-m depth, ≤10 μM O2) of the eastern South Pacific off northern Chile. This study was carried out through cloning and sequencing of genes coding for 16S rRNA and the ammonia monooxygenase enzyme active subunit (amoA). Sequences affiliated with Nitr...

  10. Temperature Responses of Ammonia-Oxidizing Prokaryotes in Freshwater Sediment Microcosms

    OpenAIRE

    Jin Zeng; Dayong Zhao; Zhongbo Yu; Rui Huang; Wu, Qinglong L.

    2014-01-01

    In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB), lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest d...

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

    Science.gov (United States)

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

    2013-05-01

    Thaumarchaeota have been recognized as the main drivers of aerobic ammonia oxidation in many ecosystems. However, little is known about the role of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in lacustrine ecosystems. In this study, the photic zone of three contrasted freshwater ecosystems located in France was sampled during two periods: winter homothermy (H) and summer thermal stratification (TS), to investigate the distribution of planktonic AOA and AOB. We showed that AOB were predominant in nutrient-rich ecosystems, whereas AOA dominated when ammonia concentrations were the lowest and during winter, which could provide a favorable environment for their growth. Moreover, analyses of archaeal libraries revealed the ubiquity of the thaumarchaeal I.1a clade associated with higher diversity of AOA in the most nutrient-poor lake. More generally, this work assesses the presence of AOA in lakes, but also highlights the existence of clades typically associated with lacustrine and hot spring ecosystems and specific ecological niches occupied by these microorganisms. PMID:23395876

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

    Institute of Scientific and Technical Information of China (English)

    Brooke B.OSBORNE; Jill S.BARON; Matthew D.WALLENSTEIN

    2016-01-01

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

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

    Science.gov (United States)

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

    2012-03-01

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

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

    Science.gov (United States)

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

    2015-05-01

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

  15. Isolation and characterization of facultative mixotrophic ammonia-oxidizing bacteria from constructed wetlands

    Institute of Scientific and Technical Information of China (English)

    Soulwène Kouki; Neila Saidi; Fadhel M'hiri; Houda Nasr; Hanène Cherif; Hadda Ouzari; Abdermaceur Hassen

    2011-01-01

    Autotrophic ammonia-oxidizing bacteria (AOB) have been widely studied in constructed wetlands systems,while mixotrophic AOB have been less thoroughly examined.Heterotrophic bacteria were isolated from wastewater and rhizospheres of macrophytes of constructed wetlands,and then cultivated in a mixotrophic medium containing ammonium and acetic acid.A molecular characterization was accomplished using ITS-PCR amplification,and phylogenetic analysis based on 16S rRNA gene sequences.Results showed the presence of 35 bacteria,among 400 initially heterotrophic isolates,that were able to remove ammonia.These 35 isolates were classified into 10 genetically different groups based on ITS pattern.Then,a collection of 10 isolates were selected because of their relatively high ammonia removal efficiencies (ARE ≥ 80%) and their phylogenetic diversity.In conditions of mixotrophy,these strains were shown to be able to grow (increase of optical density OD660 during incubation with assimilation of nitrogen into cellular biomass) and to oxidize ammonia (important ammonia oxidation efficiencies,AOE between 79% and 87%).Among these facultative mixotrophic AOB,four isolates were genetically related to Firmicutes (Bacillus and Exiguobacterium),three isolates were affiliated to Actinobacteria (Arthrobacter) and three other isolates were associated with Proteobacteria (Pseudomonas,Ochrobactrum and Bordetella).

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

    Science.gov (United States)

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

    2013-11-19

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

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

    Science.gov (United States)

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

    2011-09-20

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

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

    Science.gov (United States)

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

    2016-01-01

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

  19. Vertical segregation and phylogenetic characterization of ammonia-oxidizing bacteria and archaea in the sediment of a freshwater aquaculture pond

    Directory of Open Access Journals (Sweden)

    Shimin eLu

    2016-01-01

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

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

    Science.gov (United States)

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

    2015-06-01

    Sediments across the Namibian continental margin feature a strong microbial activity gradient at their surface. This is reflected in ammonium concentrations of  700 μM in upwelling areas near the coast. Here we address changes in apparent abundance and structure of ammonia-oxidizing archaeal and bacterial communities (AOA and AOB) along a transect of seven sediment stations across the Namibian shelf by analysing their respective ammonia monooxygenase genes (amoA). The relative abundance of archaeal and bacterial amoA (g(-1) DNA) decreased with increasing ammonium concentrations, and bacterial amoA frequently outnumbered archaeal amoA at the sediment-water interface [0-1 cm below seafloor (cmbsf)]. In contrast, AOA were apparently as abundant as AOB or dominated in several deeper (> 10 cmbsf), anoxic sediment layers. Phylogenetic analyses showed a change within the AOA community along the transect, from two clusters without cultured representatives at the gyre to Nitrososphaera and Nitrosopumilus clusters in the upwelling region. AOB almost exclusively belonged to the Nitrosospira cluster 1. Our results suggest that this predominantly marine AOB lineage without cultured representatives can thrive at low ammonium concentrations and is active in the marine nitrogen cycle. PMID:25581373

  1. Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China

    OpenAIRE

    Jin, Tao; ZHANG, Tong; Lin YE; Lee, On On; Wong, Yue Him; Qian, Pei Yuan

    2011-01-01

    The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. Among the 36 OTUs, six were shared by all three clone libraries, two appeared in two clone libraries, and the other 28...

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

    OpenAIRE

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

    2015-01-01

    Thaumarchaeota are among the most abundant organisms on Earth and are ubiquitous. Within this phylum, all cultivated representatives of Group 1.1a and Group 1.1b Thaumarchaeota are ammonia oxidizers, and play a key role in the nitrogen cycle. While Group 1.1c is phylogenetically closely related to the ammonia-oxidizing Thaumarchaeota and is abundant in acidic forest soils, nothing is known about its physiology or ecosystem function. The goal of this study was to perform in situ physiological ...

  3. Community analysis of ammonia oxidizer in the oxygen-limited nitritation stage of OLAND system by DGGE of PCR amplified 16S rDNA Fragments and FISH

    Institute of Scientific and Technical Information of China (English)

    ZHANG Dan; ZHANG De-min; LIU Yao-ping; CAO Wen-wei; CHEN Guan-xiong

    2004-01-01

    OLAND(oxygen limited autotrophic nitrification and denitrification) nitrogen removal system was constructed by coupling with oxygen limited nitritation stage and anaerobic ammonium oxidation stage. Ammonia oxidizer, as a kind of key bacteria in N cycle, plays an important role at the oxygen limited nitritation stage of OLAND nitrogen removal system. In this study, specific amplification of 16S rDNA fragment of ammonia oxidizer by nested PCR, separation of mixed PCR samples by denaturing gradient gel electrophoresis(DGGE), and the quantification of ammonia oxidizer by Fluorescence in situ hybridization(FISH) were combined to investigate the shifts of community composition and quantity of ammonia oxidizer of the oxygen limited nitritation stage in OLAND system. It showed that the community composition of ammonia oxidizer changed drastically when dissolved oxygen was decreased gradually, and the dominant ammonia oxidizer of the steady nitrite accumulation stage were completely different from that of the early stage of oxygen limited nitritation identified by DGGE . It was concluded that the Nitrosomonas may be the dominant genus of ammonia oxidizer at the oxygen limited nitritation stage of OLAND system characterized by nested PCR-DGGE and FISH, and the percentage of Nitrosomonas was 72.5% ( 0.8% of ammonia oxidizer at the steady nitrite accumulation stage detected by FISH.

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

    Science.gov (United States)

    Francis, Somilez Asya

    2014-01-01

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

  5. Biotransformation of pharmaceuticals by ammonia oxidizing bacteria in wastewater treatment processes.

    Science.gov (United States)

    Xu, Yifeng; Yuan, Zhiguo; Ni, Bing-Jie

    2016-10-01

    Pharmaceutical residues could potentially pose detrimental effects on aquatic ecosystems and human health, with wastewater treatment being one of the major pathways for pharmaceuticals to enter into the environment. Enhanced removal of pharmaceuticals by ammonia oxidizing bacteria (AOB) has been widely observed in wastewater treatment processes. This article reviews the current knowledge on the biotransformation of pharmaceuticals by AOB. The relationship between the pharmaceuticals removal and nitrification process was revealed. The important role of AOB-induced cometabolism on the biotransformation of pharmaceuticals as well as their transformation products and pathways was elucidated. Kinetics and mathematical models describing the biotransformation of pharmaceuticals by AOB were also reviewed. The results highlighted the high degradation capabilities of AOB toward some refractory pharmaceuticals, with their degradations being clearly related to the nitrification rate and their transformation products being identified, which may exhibit similar or higher ecotoxicological impacts compared to the parent compound. PMID:27243932

  6. Nitrogen removal from sludge dewatering effluent through anaerobic ammonia oxidation process

    Institute of Scientific and Technical Information of China (English)

    ZHANG Shao-hui; ZHENG Ping; HUA Yu-mei

    2005-01-01

    Anaerobic ammonia oxidation(Anammox) process is a novel and promising wastewater nitrogen removal process. The feasibility of transition of Anammox from denitrification and the performance of lab-scale Anammox biofilm reactor were investigated with sludge dewatering effluent. The results showed that Anammox process could be successfully started up after cultivation of denitrification biofilm and using it as inoculum. The transition of Anammox from denitrification was accomplished within 85 d. Anammox process was found suitable to remove ammonia from sludge dewatering effluent. The effluent ammonia concentration was detected to be 23.11 mgN/L at HRT of 28 h when influent ammonia concentration was fed 245 mgN/L, which was less than that for the national discharge standard Ⅱ (25 mgN/L) of 243.25 mg NH4+ -N/L and 288.31 mg NO2- -N/L.

  7. Shifts in the dominant populations of ammonia-oxidizing beta-subclass Proteobacteria along the eutrophic Schelde estuary

    NARCIS (Netherlands)

    de Bie, MJM; Speksnijder, AGCL; Kowalchuk, GA; Schuurman, T; Zwart, G; Stephen, [No Value; Diekmann, OE; Laanbroek, HJ

    2001-01-01

    The community structure of ammonia-oxidizing bacteria of the beta -subclass Proteobacteria was investigated with respect to environmental gradients along the Schelde, a eutrophic estuary system. A dominance of Nitrosomonas-Like sequences was detected using molecular techniques targeting the 16S rRNA

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

    NARCIS (Netherlands)

    Sauder, L.A.; Peterse, F.; Schouten, S.; Neufeld, J.D.

    2012-01-01

    The first step of nitrification is catalysed by both ammonia-oxidizing bacteria (AOB) and archaea (AOA), but physicochemical controls on the relative abundance and function of these two groups are not yet fully understood, especially in freshwater environments. This study investigated ammonia-oxidiz

  9. Effect of different ammonia concentrations on community succession of ammonia-oxidizing microorganisms in a simulated paddy soil column.

    Directory of Open Access Journals (Sweden)

    Hu Baolan

    Full Text Available Ammonia oxidation is performed by both ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA. To explore the effect of ammonia concentration on the population dynamic changes of ammonia-oxidizing microorganisms, we examined changes in the abundance and community composition of AOA and AOB in different layers. Most of the archaeal amoA sequences were Nitrosotalea-related and the proportion that Nitrosotalea cluster occupied decreased in the surface layer and increased in the deep layer during the cultivation process. Nitrosopumilus-related sequences were only detected in the deep layer in the first stage and disappeared later. Both phylogenetic and quantitative analysis showed that there were increased Nitrosomonas-related sequences appeared in the surface layer where the ammonia concentration was the highest. Both AOA and AOB OTU numbers in different layers decreased under selective pressure and then recovered. The potential nitrification rates were 25.06 µg · N · L(-1 · g(-1 dry soil · h(-1 in the mid layer which was higher than the other two layers. In general, obvious population dynamic changes were found for both AOA and AOB under the selective pressure of exogenous ammonia and the changes were different in three layers of the soil column.

  10. Do freshwater macrophytes influence the community structure of ammonia-oxidizing and denitrifying bacteria in the rhizospere?

    DEFF Research Database (Denmark)

    Herrmann, Martina; Schramm, Andreas

    2006-01-01

    nitrification-denitrification using the 15N isotope pairing technique. Ammonia-oxidizing and nitrate-reducing populations are analyzed based on the ammonia monooxygenase gene (amoA) and the nitrate reductase gene (narG) as functional markers. Preliminary data indicate that there in fact exist differences in the...

  11. RNA-Based Investigation of Ammonia-Oxidizing Archaea in Hot Springs of Yunnan Province, China ▿ †

    OpenAIRE

    Jiang, Hongchen; Huang, Qiuyuan; DONG, HAILIANG; WANG, Peng; Wang, Fengping; Li, Wenjun; Zhang, Chuanlun

    2010-01-01

    Using RNA-based techniques and hot spring samples collected from Yunnan Province, China, we show that the amoA gene of aerobic ammonia-oxidizing archaea can be transcribed at temperatures higher than 74°C and up to 94°C, suggesting that archaeal nitrification can potentially occur at near boiling temperatures.

  12. Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil

    Science.gov (United States)

    Sterngren, Anna E.; Hallin, Sara; Bengtson, Per

    2015-01-01

    Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil. PMID:26648926

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

    NARCIS (Netherlands)

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

    2013-01-01

    Mesophilic ammonia-oxidizing Archaea (AOA) are abundant in a diverse range of marine environments, including the deep ocean, as revealed by the quantification of the archaeal amoA gene encoding the alpha-subunit of the ammonia monooxygenase. Using two different amoA primer sets, two distinct ecotype

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

    NARCIS (Netherlands)

    Zheng, Yan; Huang, Rong; Wang, B.; Bodelier, P.L.E.; Jia, Z.

    2014-01-01

    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable iso

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Laura A Sauder

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    M. Saiful Alam

    2013-01-01

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

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

    Science.gov (United States)

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

    2015-07-01

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

  20. Influence of tropical leaf litter on nitrogen mineralization and community structure of ammonia-oxidizing bacteria

    Directory of Open Access Journals (Sweden)

    Diallo, MD.

    2015-01-01

    Full Text Available Description of the subject. The present study concerns the relationships among leaf litter decomposition, substrate quality, ammonia-oxidizing bacteria (AOB community composition and nitrogen (N availability. Decomposition of organic matter affects the biogeochemical cycling of carbon (C and N. Since the composition of the soil microbial community can alter the physiological capacity of the community, it is timely to study the litter quality effect on N dynamic in ecosystems. Objectives. The aim of this study was to determine the influence of leaf litter decomposition on N mineralization. The specific objectives of this study were to evaluate the influence of the litter biochemistry of five plants species (Faidherbia albida A.Chev., Azadirachta indica A.Juss., Casuarina equisetifolia L., Andropogon gayanus Kunth and Eragrostis tremula Hochst. ex Steud. on N mineralization in a tropical ferrous soil (Lixisol, nitrification, and genetic diversity of ammonia-oxidizing bacteria. Denaturing gradient gel electrophoresis (DGGE of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of leaf litter in soils. Method. Community structure of AOB was determined at two time periods: day 0 and day 140. Ten strains were tested and each of these strains produced a single band. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. Plant secondary compounds such as polyphenols are purported to influence nutrient cycling by affecting organic matter degradation, mineralization rates, N availability and humus formation. In a laboratory study, we investigated the influence of six phenolic acids (ferulic, gallic, vanillic, syringic, p-coumaric and p-HBA acids commonly found in the plant residues on N mineralization and NH4+ and NO3- production in soils. Results. The results showed that litter type did affect soil nitrification. Faidherbia albida litter was associated with

  1. Acclimatization of communities of ammonia oxidizing bacteria to seasonal changes in optimal conditions in a coke wastewater treatment plant.

    Science.gov (United States)

    Kim, Young Mo

    2013-11-01

    The goal of this study was to investigate the correlation between optimal conditions of ammonia oxidation rates (AORs) and communities of ammonia oxidizing bacteria (AOB) adapting to seasonal changes in a full-scale wastewater treatment plant (WWTP). The optimal temperature and pH of specific AORs reflected seasonal variation patterns, showing the lowest values during the cold season, while the highest values in the warm season. Throughout the study period, Nitrosomonas europaea/eutropha and Nitrosomonas nitrosa remained the dominant AOB, indicating resistance to the influences of a changing environment. These results show that the optimal conditions for AOR can be adjusted to accommodate changing environmental conditions, relying on the acclimatization of a stable AOB community to given conditions, without any visible shift in the AOB community. PMID:24001689

  2. Community structure of β-Proteobacterial ammonia-oxidizing bacteria in prawn farm sediment

    Institute of Scientific and Technical Information of China (English)

    Ying Ma; Lin Wang; Lumin Qian

    2008-01-01

    To examine the community structure of β-Proteobacterial ammonia-oxidizing bacteria (AOB) in prawn farm sediment, the 16S rRNA gene library was constructed with β-Proteobacterial AOB-specific primers. The library was screened by PCR-restriction fragment length polymorphism (RFLP) analysis and clones with unique RFLP patterns were sequenced. Two groups of β-Proteobacterial AOB, the Nitrosomonas and the Nitrosospira, were detected. The Nitrosomonas occupied an absolute dominant position, accounting for more than 90% of total clones in the clone library, while the Nitrosospira accounting for 5.48%. Nitrosomonas-affiliated clones were grouped into the Nitrosomonas marina and the Nitrosomonas sp. Nm 143 clusters, and Nitrosospira-affiliated clones were grouped into the Nitrosospira cluster 1. No other clusters of β-Proteobacterial AOB were found. The results enriched our knowledge of AOB diversity in the prawn farm sediment and provided important foundational data for further functional studies of these microbes in mariculture environments.

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

    Science.gov (United States)

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

    2014-12-01

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

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

    Science.gov (United States)

    Sher, Yonatan; Ronen, Zeev; Nejidat, Ali

    2016-08-01

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

  5. Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat

    Directory of Open Access Journals (Sweden)

    Steven J Biller

    2012-07-01

    Full Text Available Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. Since the initial discovery of an ammonia monooxygenase α-subunit (amoA gene associated with an archaeal metagenomic fragment, archaeal amoA sequences have been detected in a wide variety of nitrifying environments. Recent sequencing efforts have revealed extensive diversity of archaeal amoA sequences within different habitats. In this study, we have examined over 8000 amoA sequences from the literature and public databases in an effort to understand the ecological factors influencing the distribution and diversity of ammonia-oxidizing archaea (AOA, with a particular focus on sequences from aquatic habitats. This broad survey provides strong statistical support for the hypothesis that different environments contain distinct clusters of AOA amoA sequences, as surprisingly few sequences are found in more than one habitat type. Within aquatic environments, salinity, depth in the water column, and temperature were significantly correlated with the distribution of sequence types. These findings support the existence of multiple distinct aquatic AOA populations in the environment and suggest some possible selective pressures driving the partitioning of AOA amoA diversity.

  6. Temperature responses of ammonia-oxidizing prokaryotes in freshwater sediment microcosms.

    Directory of Open Access Journals (Sweden)

    Jin Zeng

    Full Text Available In order to investigate the effects of temperature on the abundances and community compositions of ammonia-oxidizing archaea (AOA and bacteria (AOB, lake microcosms were constructed and incubated at 15°C, 25°C and 35°C for 40 days, respectively. Temperature exhibited different effects on the abundance and diversity of archaeal and bacterial amoA gene. The elevated temperature increased the abundance of archaeal amoA gene, whereas the abundance of bacterial amoA gene decreased. The highest diversity of bacterial amoA gene was found in the 25°C treatment sample. However, the 25°C treatment sample maintained the lowest diversity of archaeal amoA gene. Most of the archaeal amoA sequences obtained in this study affiliated with the Nitrosopumilus cluster. Two sequences obtained from the 15°C treatment samples were affiliated with the Nitrosotalea cluster. N. oligotropha lineage was the most dominant bacterial amoA gene group. Several sequences affiliated to Nitrosospira and undefined N. europaea/NC. mobilis like lineage were found in the pre-incubation and 25°C treatment groups.

  7. A novel ammonia-oxidizing archaeon from wastewater treatment plant: Its enrichment, physiological and genomic characteristics

    Science.gov (United States)

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

    2016-03-01

    Ammonia-oxidizing archaea (AOA) are recently found to participate in the ammonia removal processes in wastewater treatment plants (WWTPs), similar to their bacterial counterparts. However, due to lack of cultivated AOA strains from WWTPs, their functions and contributions in these systems remain unclear. Here we report a novel AOA strain SAT1 enriched from activated sludge, with its physiological and genomic characteristics investigated. The maximal 16S rRNA gene similarity between SAT1 and other reported AOA strain is 96% (with “Ca. Nitrosotenuis chungbukensis”), and it is affiliated with Wastewater Cluster B (WWC-B) based on amoA gene phylogeny, a cluster within group I.1a and specific for activated sludge. Our strain is autotrophic, mesophilic (25 °C–33 °C) and neutrophilic (pH 5.0–7.0). Its genome size is 1.62 Mb, with a large fragment inversion (accounted for 68% genomic size) inside. The strain could not utilize urea due to truncation of the urea transporter gene. The lack of the pathways to synthesize usual compatible solutes makes it intolerant to high salinity (>0.03%), but could adapt to low salinity (0.005%) environments. This adaptation, together with possibly enhanced cell-biofilm attachment ability, makes it suitable for WWTPs environment. We propose the name “Candidatus Nitrosotenuis cloacae” for the strain SAT1.

  8. The inoculum effect on the ammonia-oxidizing bacterial communities in parallel sequential batch reactors.

    Science.gov (United States)

    Wittebolle, Lieven; Verstraete, Willy; Boon, Nico

    2009-09-01

    Three identical sequential batch reactors (SBRs) were each inoculated with sludge from a full-scale wastewater treatment plant (WWTP) treating a waste stream of different origin, i.e. a hospital, a meat processing company, and a municipal WWTP. The SBRs were run in parallel for 84 consecutive days to investigate whether the reactors would become more phylogenetically similar or stay separated concerning their functionality and microbial communities. Overall, the nitrification functionality was high throughout the experiment, and the size and structure of the sludge flocs were very similar. The total bacterial and ammonia-oxidizing bacterial (AOB) communities were analyzed by PCR-DGGE. Cluster analysis demonstrated very distinct bacterial communities in the three SBRs, not showing any trend becoming more similar. The carrying capacity, dynamics and functional organization of the communities were assessed by DGGE analysis and based on these patterns the range-weighted richness, moving window analysis, and constructing Pareto-Lorenz evenness distribution curves were calculated. Between the SBRs, highly comparable internal structure and dynamics of the AOB communities were observed, although they had only one AOB DGGE band in common. These observations indicate that community characteristics such as the extent of biodiversity and dynamics are more important indicators of good microbial functionality than the presence of certain specific species. PMID:19596129

  9. Environmental controls on the abundance, diversity, growth, and activity of  ammonia-oxidizing microorganisms in temperate forest soils

    OpenAIRE

    Norman, Jeffrey Stancill

    2014-01-01

    The goal of my dissertation research was to investigate the structure and function of ammonia-oxidizing microbial communities in temperate forest soils. Accomplishing this goal required a hybrid approach: I used modern molecular biology techniques alongside soil biogeochemical measurements and framed my research using ecological theory largely developed in plant systems. All of my field work was done at Coweeta Hydrologic Laboratory, a Forest Service Station and Long Term Ecological Researc...

  10. Comparison of water availability effect on ammonia-oxidizing bacteria and archaea in microcosms of a Chilean semiarid soil

    OpenAIRE

    JulietaOrlando

    2012-01-01

    Water availability is the main limiting factor in arid soils; however few studies have examined the effects of drying and rewetting on nitrifiers from these environments. The effect of water availability on the diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) from a semiarid soil of the Chilean sclerophyllous matorral was determined by microcosm assays. The addition of water every 14 days to reach 60% of the WHC significantly increased nitrate content in rewetted soil microcosm...

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

    OpenAIRE

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

    2013-01-01

    The function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) depends on the major energy-generating compounds (i.e., ammonia and oxygen). The diversification of AOA and AOB communities along ecological gradients of substrate availability in a complex environment have been much debated but rarely tested. In this study, two ecosystems of maize and rice crops under different fertilization regimes were selected to investigate the community diversification of soil AOA and AOB upon conversion...

  12. Composition of ammonia-oxidizing archaea and their contribution to nitrification in a high-temperature hot spring

    Science.gov (United States)

    Chen, S.; Peng, X.-T.; Xu, H.-C.; Ta, K.-W.

    2015-10-01

    The oxidation of ammonia by microbes and associated organisms has been shown to occur in diverse natural environments. However, the contribution of ammonia-oxidizing archaea to nitrification in high-temperature environments remains unclear. Here, we studied in situ ammonia oxidation rates and the abundance of ammonia-oxidizing archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3- pool dilution technique in the surface sinter and bottom sediments were 4.8 and 5.3 nmol N g-1 h-1, respectively. Relative abundances of Crenarchaea in both samples were determined by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic "Candidatus Nitrosocaldus yellowstonii", which represented the most abundant operation taxonomic units (OTU) in both sediments. Furthermore, bacterial amoA was not detected in this study. Quantitative PCR (qPCR) indicated that AOA and 16S rRNA genes were present in the range of 2.75 to 9.80 × 105 and 0.128 to 1.96 × 108 gene copies g-1 sediment. The cell-specific nitrification rates were estimated to be in the range of 0.41 to 0.79 fmol N archaeal cell-1 h-1, which is consistent with earlier estimates in estuary environments. This study demonstrated that AOA were widely involved in nitrification in this hot spring. It further indicated the importance of archaea rather than bacteria in driving the nitrogen cycle in terrestrial geothermal environments.

  13. Influence of Different Cultivars on Populations of Ammonia-Oxidizing Bacteria in the Root Environment of Rice

    OpenAIRE

    Briones, Aurelio M.; Okabe, Satoshi; Umemiya, Yoshiaki; Ramsing, Niels-Birger; Reichardt, Wolfgang; Okuyama, Hidetoshi

    2002-01-01

    Comparisons of the activities and diversities of ammonia-oxidizing bacteria (AOB) in the root environment of different cultivars of rice (Oryza sativa L.) indicated marked differences despite identical environmental conditions during growth. Gross nitrification rates obtained by the 15N dilution technique were significantly higher in a modern variety, IR63087-1-17, than in two traditional varieties. Phylogenetic analysis based on the ammonium monooxygenase gene (amoA) identified strains relat...

  14. Spatial distribution of ammonia-oxidizing archaea and bacteria across eight freshwater lakes in sediments from Jiangsu of China

    OpenAIRE

    Xu Sun; Aili Wang; Liuyan Yang; Liyun Guo; Qiankun Chen; Zhinxin Hu; Lijuan Jiang; Lin Xiao

    2014-01-01

    Ammonia-oxidizingarchaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role innitrogen transformation in freshwater sediments. However, it is still unclear towhat extent the distribution patterns of these microorganisms are affected bythe freshwater sediment across a large geographical scale. This study wasdesigned to gain insight into the heterogeneity distribution of AOA and AOB in32 freshwater sediments from a wide range of ecologic types. Real-time quantitative polymerasech...

  15. Composition of ammonia-oxidizing archaea and their contribution to nitrification in a high-temperature hot spring

    Directory of Open Access Journals (Sweden)

    S. Chen

    2015-10-01

    Full Text Available The oxidation of ammonia by microbes and associated organisms has been shown to occur in diverse natural environments. However, the contribution of ammonia-oxidizing archaea to nitrification in high-temperature environments remains unclear. Here, we studied in situ ammonia oxidation rates and the abundance of ammonia-oxidizing archaea (AOA in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N–NO3- pool dilution technique in the surface sinter and bottom sediments were 4.8 and 5.3 nmol N g−1 h−1, respectively. Relative abundances of Crenarchaea in both samples were determined by fluorescence in situ hybridization (FISH. Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic "Candidatus Nitrosocaldus yellowstonii", which represented the most abundant operation taxonomic units (OTU in both sediments. Furthermore, bacterial amoA was not detected in this study. Quantitative PCR (qPCR indicated that AOA and 16S rRNA genes were present in the range of 2.75 to 9.80 × 105 and 0.128 to 1.96 × 108 gene copies g−1 sediment. The cell-specific nitrification rates were estimated to be in the range of 0.41 to 0.79 fmol N archaeal cell−1 h−1, which is consistent with earlier estimates in estuary environments. This study demonstrated that AOA were widely involved in nitrification in this hot spring. It further indicated the importance of archaea rather than bacteria in driving the nitrogen cycle in terrestrial geothermal environments.

  16. Comparison of water availability effect on ammonia-oxidizing bacteria and archaea in microcosms of a Chilean semiarid soil

    OpenAIRE

    Bustamante, Mauricio; Verdejo, Valentina; Zúñiga, Catalina; Espinosa, Fernanda; Orlando, Julieta; Carú, Margarita

    2012-01-01

    Water availability is the main limiting factor in arid soils; however, few studies have examined the effects of drying and rewetting on nitrifiers from these environments. The effect of water availability on the diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) from a semiarid soil of the Chilean sclerophyllous matorral was determined by microcosm assays. The addition of water every 14 days to reach 60% of the WHC significantly increased nitrate content in rewetted soil microcos...

  17. Seasonal Changes of Freshwater Ammonia-Oxidizing Archaeal Assemblages and Nitrogen Species in Oligotrophic Alpine Lakes▿ †

    OpenAIRE

    Auguet, Jean-Christophe; Nomokonova, Natalya; Camarero, Lluis; Casamayor, Emilio O.

    2011-01-01

    The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal ...

  18. The effect of hydrology on the distribution of ammonia-oxidizing betaproteobacteria in impounded black mangroves (Avicennia germinans

    Directory of Open Access Journals (Sweden)

    Hendrikus J. eLaanbroek

    2012-04-01

    Full Text Available The distribution of species of aerobic chemolitho-autotrophic microorganisms such as the ammonia-oxidizing bacteria will be governed by pH, salinity and temperature as well as by the availability of oxygen, ammonia, carbon dioxide and other inorganic elements required for growth. Impounded mangrove forests in the Indian River Lagoon, a coastal estuary on the east coast of Florida, are dominated by mangroves, especially black mangrove (Avicennia germinans, that differ in size and density. In March 2009 the management in one of the impoundments was changed for purpose of insect control, by pumping water from the adjacent estuary. We collected soil samples in three different black mangrove habitats in this and an adjacent impoundment in 2008, 2009 and 2010, always in March, to determine the pre- and post-management effects of summer flooding on the distribution of 16s rRNA genes belonging to ammonia-oxidizing betaproteobacteria (β-AOB.At the level of 95% mutual similarity in the 16s rRNA gene, 11 different Operational Taxonomic Units were identified; the majority related to the lineages Nitrosomonas marina (57% of the total, Nitrosomonas sp. Nm143 (23% and Nitrosospira cluster 1 (18%. Higher salinities of interstitial water, probably due to severe winter drought, had a significant effect on the composition of the β-AOB in March 2009 compared to March 2008. Nitrosomonas sp. Nm143 was replaced as second important lineage by Nitrosospira cluster 1. Simultaneously with the community change, the level of potential ammonia-oxidizing activities decreased by an average of 67%. Long-term summer flooding in 2009 reduced the percentage of N. marina by half in favor of the two other major lineages, but decreased again the potential ammonia-oxidizing activities by 41% on average. No significant differences were observed between the flooded and non-flooded impoundment. There were differences in the community composition of the bacteria in the three black

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

    OpenAIRE

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

    2014-01-01

    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and pmoA genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communitie...

  20. High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations.

    Science.gov (United States)

    Zhang, Yu; Tian, Zhe; Liu, Miaomiao; Shi, Zhou Jason; Hale, Lauren; Zhou, Jizhong; Yang, Min

    2015-08-01

    To evaluate the potential effects of antibiotics on ammonia-oxidizing microbes, multiple tools including quantitative PCR (qPCR), 454-pyrosequencing, and a high-throughput functional gene array (GeoChip) were used to reveal the distribution of ammonia-oxidizing archaea (AOA) and archaeal amoA (Arch-amoA) genes in three wastewater treatment systems receiving spiramycin or oxytetracycline production wastewaters. The qPCR results revealed that the copy number ratios of Arch-amoA to ammonia-oxidizing bacteria (AOB) amoA genes were the highest in the spiramycin full-scale (5.30) and pilot-scale systems (1.49 × 10(-1)), followed by the oxytetracycline system (4.90 × 10(-4)), with no Arch-amoA genes detected in the control systems treating sewage or inosine production wastewater. The pyrosequencing result showed that the relative abundance of AOA affiliated with Thaumarchaeota accounted for 78.5-99.6% of total archaea in the two spiramycin systems, which was in accordance with the qPCR results. Mantel test based on GeoChip data showed that Arch-amoA gene signal intensity correlated with the presence of spiramycin (P amoA functional gene structures by variance partitioning analysis. This study revealed the selection of AOA in the presence of high concentrations of spiramycin in activated sludge systems. PMID:26125322

  1. Abundance and diversity of ammonia-oxidizing bacteria in relation to ammonium in a Chinese shallow eutrophic urban lake

    Directory of Open Access Journals (Sweden)

    Shanlian Qiu

    2010-03-01

    Full Text Available The measures of most-probable-number and restriction fragment length polymorphism analysis were used to analyze the abundance and diversity of ammonia-oxidizing bacteria in sediment of a Chinese shallow eutrophic urban lake (Lake Yuehu. Among the 5 sampling sites, ammonia concentration in interstitial water was positively proportional not only to the content of organic matter, but also to ammonia-oxidizing bacteria numbers (at a magnitude of 10(5 cells g-1 dry weight in sediment significantly. Furthermore, the diversity of ammonia-oxidizing bacteria were determined by means of PCR primers targeting the amoA gene with five gene libraries created and restriction pattern analysis. The 13 restriction patterns were recorded with 4 ones being common among all sampling sites. The 8 restriction patterns including 4 unique ones were found at the site with the highest NH4+ concentrations in interstitial water, while, there were only common patterns without unique ones at the site with the lowest NH4+ concentrations in interstitial water. Phylogenetic analysis showed that the amoA fragments retrieved belong to Nitrosomonas oligotropha & ureae lineage, N. europaea lineage, N. communis lineage and Nitrosospira lineage, most of which were affiliated with the genus Nitrosomonas. The N. oligotropha & ureae-like bacteria were the dominant species. Thus, the abundance and diversity of sediment AOB is closely linked to ammonium status in eutrophic lakes.

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

    Science.gov (United States)

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

    2015-01-01

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

  3. Spatial distribution and factors shaping the niche segregation of ammonia-oxidizing microorganisms in the Qiantang River, China.

    Science.gov (United States)

    Liu, Shuai; Shen, Lidong; Lou, Liping; Tian, Guangming; Zheng, Ping; Hu, Baolan

    2013-07-01

    Ammonia oxidation is performed by both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, the current knowledge of the distribution, diversity, and relative abundance of these two microbial groups in freshwater sediments is insufficient. We examined the spatial distribution and analyzed the possible factors leading to the niche segregation of AOA and AOB in the sediments of the Qiantang River, using clone library construction and quantitative PCR for both archaeal and bacterial amoA genes. pH and NH4(+)-N content had a significant effect on AOA abundance and AOA operational taxonomy unit (OTU) numbers. pH and organic carbon content influenced the ratio of AOA/AOB OTU numbers significantly. The influence of these factors showed an obvious spatial trend along the Qiantang River. This result suggested that AOA may contribute more than AOB to the upstream reaches of the Qiantang River, where the pH is lower and the organic carbon and NH4(+)-N contents are higher, but AOB were the principal driver of nitrification downstream, where the opposite environmental conditions were present. PMID:23624482

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

    Science.gov (United States)

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

    2013-01-01

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

  5. Diversity of Ammonia-Oxidizing Archaea and Bacteria in the Sediments of a Hypernutrified Subtropical Estuary: Bahía del Tóbari, Mexico▿

    OpenAIRE

    Beman, J. Michael; Francis, Christopher A.

    2006-01-01

    Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilic Crenarchaeota are capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (...

  6. Abundance and Diversity of Ammonia-Oxidizing Archaea and Bacteria in Sediments of Trophic End Members of the Laurentian Great Lakes, Erie and Superior

    OpenAIRE

    Annette Bollmann; Bullerjahn, George S.; Robert Michael McKay

    2014-01-01

    Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA) and Bacteria (AOB). Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA) gene. Diversity was accessed by a pyro-sequencing approach and th...

  7. [Abundance and Community Composition of Ammonia-Oxidizing Archaea in Two Completely Autotrophic Nitrogen Removal over Nitrite Systems].

    Science.gov (United States)

    Gao, Jing-feng; Li, Ting; Zhang, Shu-jun; Fan, Xiao-yan; Pan, Kai-ling; Ma, Qian; Yuan, Ya-lin

    2015-08-01

    Ammonia oxidation is the first and rate-limiting step of nitrification, which was thought to be only performed by ammonia-oxidizing bacteria (AOB). In recent years, ammonia-oxidizing archaea (AOA) was also confirmed to take part in ammonia oxidation. The diversity and abundance of AOA have been investigated in various environments, however, little is known regarding the AOA in the completely autotrophic nitrogen removal over nitrite (CANON) wastewater treatment process. In this study, the abundance and diversity of AOA were investigated in the biofilm and flocculent activated sludge collected in a lab-scale (L) CANON system and a pilot-scale (P) CANON systems, respectively. The quantitative real time PCR (qPCR) was applied to investigate the abundance of AOA and the diversity of AOA was determined by polymerase chain reaction (PCR), cloning and sequencing. The qPCR results showed that the average abundance of AOA amoA gene of L and P was 2.42 x 10(6) copies x g(-1) dry sludge and 6.51 x 10(6) copies x g(-1) dry sludge, respectively. The abundance of AOA in biofilm was 10.1-14.1 times higher than that in flocculent activated sludge. For P system, the abundance of AOA in flocculent activated sludge was 1.8 times higher than that in biofilm. The results indicated that the abundance of AOA might be affected by different sludge morphology. The diversity of AOA in P system was extremely limited, only one OTU was observed, which was classified into Nitrosopumilus subcluster 5.2. The diversity of AOA in L system was higher, eight OTUs were observed, which were classified into five genera: Nitrososphaera subcluster 9, subcluster 8.1, subcluster 4.1, subcluster 1.1 and Nitrosopumilus subcluster 5.2. The diversity and abundance of AOA were different in CANON systems with different sludge morphology. AOA may play an important role in ammonia oxidation in CANON system. PMID:26592025

  8. Diversity of Ammonia-Oxidizing Archaea and Bacteria Across Physical-Chemical Gradients in San Francisco Bay Estuary Sediments

    Science.gov (United States)

    Mosier, A. C.; Francis, C. A.

    2006-12-01

    A combination of recent metagenomic analyses and the cultivation of a novel, ammonia-oxidizing, marine crenarchaeota revealed the first evidence for nitrification within the Archaeal domain. Further genetic and metagenomic studies demonstrated the presence of ammonia-oxidizing crenarchaea in diverse marine and terrestrial environments. These discoveries challenge the currently accepted view of the global nitrogen cycle and validate the need for further research on microbial diversity and function. In particular, it is imperative to reexamine the microbial communities involved in ammonia oxidation in marine and estuarine sediments, where this process plays a pivotal role in the cycling and removal of nitrogen. Using phylogenetic analyses of ammonia monooxygenase subunit A (amoA) gene sequences, we examined the distribution and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in San Francisco Bay, the largest estuary on the West coast of the United States. The highly impacted bay, encompassing nearly 178,000 km2, effectively connects two estuaries with varying physical-chemical characteristics to the Pacific Ocean. We recovered archaeal and bacterial amoA genes from 11 sites distributed throughout the bay, spanning the northern and southern estuaries and the central region where they connect to the ocean. Richness estimates varied considerably across all sites examined, with archaeal amoA estimates being generally higher than bacterial amoA. Several of the bacterial amoA libraries were represented by fewer than 3 genotypes. Archaeal amoA sequences were phylogenetically diverse and grouped within previously described sediment and soil/sediment clusters. Several sequences were closely related to the only cultivated AOA, Nitrosopumilus maritimus. Both the archaeal and bacterial amoA sequences showed significant regional specificity. Distinct populations exist in the northern and southern estuaries and sequences from the northernmost and southernmost sites

  9. Microsite Differentiation Drives the Abundance of Soil Ammonia Oxidizing Bacteria along Aridity Gradients.

    Science.gov (United States)

    Delgado-Baquerizo, Manuel; Maestre, Fernando T; Eldridge, David J; Singh, Brajesh K

    2016-01-01

    Soil ammonia oxidizing bacteria (AOB) and archaea (AOA) are responsible for nitrification in terrestrial ecosystems, and play important roles in ecosystem functioning by modulating the rates of N losses to ground water and the atmosphere. Vascular plants have been shown to modulate the abundance of AOA and AOB in drylands, the largest biome on Earth. Like plants, biotic and abiotic features such as insect nests and biological soil crusts (biocrusts) have unique biogeochemical attributes (e.g., nutrient availability) that may modify the local abundance of AOA and AOB. However, little is known about how these biotic and abiotic features and their interactions modulate the abundance of AOA and AOB in drylands. Here, we evaluate the abundance of amoA genes from AOB and AOA within six microsites commonly found in drylands (open areas, biocrusts, ant nests, grasses, nitrogen-fixing shrubs, and trees) at 21 sites from eastern Australia, including arid and mesic ecosystems that are threatened by predicted increases in aridity. Our results from structural equation modeling suggest that soil microsite differentiation alters the abundance of AOB (but not AOA) in both arid and mesic ecosystems. While the abundance of AOA sharply increased with increasing aridity in all microsites, the response of AOB abundance was microsite-dependent, with increases (nitrogen-fixing shrubs, ant nests), decreases (open areas) or no changes (grasses, biocrusts, trees) in abundance with increasing aridity. Microsites supporting the highest abundance of AOB were trees, nitrogen-fixing shrubs, and ant nests. These results are linked to particular soil characteristics (e.g., total carbon and ammonium) under these microsites. Our findings advance our understanding of key drivers of functionally important microbial communities and N availability in highly heterogeneous ecosystems such as drylands, which may be obscured when different soil microsites are not explicitly considered. PMID:27148194

  10. Impact of acetochlor on ammonia-oxidizing bacteria in microcosm soils

    Institute of Scientific and Technical Information of China (English)

    LI Xinyu; ZHANG Huiwen; WU Minna; SU Zhencheng; ZHANG Chenggang

    2008-01-01

    Acetochlor is an increasingly used herbicide on corn in North China. Currently, the effect of acetochlor on soil ammonia-oxidizing bacteria (AOB) communities is not well documented. Here, we studied the diversity and community composition of AOB in soil amended with three concentrations of acetochlor (50, 150, 250 mg/kg) and the control (0 mg acetochlor/kg soil) in a microcosm experiment by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and the phylogenetic analysis of excised DGGE bands. DGGE profiles showed that acetochlor had a stimulating effect on AOB at the early stage after acetochlor amended, and the order of intensity and duration is medium-acetochlor amended samples (AM) > low-acetochlor amended samples (AL) > high-acetochlor amended samples (AH). At the end of 60 d microcosm, acetochlor had a negative effect on the diversity of AOB. Cluster analysis of DGGE profiles showed that acetochlor had a greater effect on the community structure of AOB on day 60 than on day 1. The phylogenetic analysis revealed that all the sequences of excised DGGE bands were closely related to members of the genus Nitrosospira and formed two separate subclusters designated as subcluster 1 and subcluster 2 affiliated respectively with clusters 3 and 4 in Nitrosospira as defined by Stephen. Some dominant AOB had a change from subcluster 2 to subcluster 1 with the incubation. The results showed that acetochlor had an effect on the AOB on a long-term basis and the chronic effect of acetochlor should be paid more attention in future.

  11. Microsite Differentiation Drives the Abundance of Soil Ammonia Oxidizing Bacteria along Aridity Gradients

    Science.gov (United States)

    Delgado-Baquerizo, Manuel; Maestre, Fernando T.; Eldridge, David J.; Singh, Brajesh K.

    2016-01-01

    Soil ammonia oxidizing bacteria (AOB) and archaea (AOA) are responsible for nitrification in terrestrial ecosystems, and play important roles in ecosystem functioning by modulating the rates of N losses to ground water and the atmosphere. Vascular plants have been shown to modulate the abundance of AOA and AOB in drylands, the largest biome on Earth. Like plants, biotic and abiotic features such as insect nests and biological soil crusts (biocrusts) have unique biogeochemical attributes (e.g., nutrient availability) that may modify the local abundance of AOA and AOB. However, little is known about how these biotic and abiotic features and their interactions modulate the abundance of AOA and AOB in drylands. Here, we evaluate the abundance of amoA genes from AOB and AOA within six microsites commonly found in drylands (open areas, biocrusts, ant nests, grasses, nitrogen-fixing shrubs, and trees) at 21 sites from eastern Australia, including arid and mesic ecosystems that are threatened by predicted increases in aridity. Our results from structural equation modeling suggest that soil microsite differentiation alters the abundance of AOB (but not AOA) in both arid and mesic ecosystems. While the abundance of AOA sharply increased with increasing aridity in all microsites, the response of AOB abundance was microsite-dependent, with increases (nitrogen-fixing shrubs, ant nests), decreases (open areas) or no changes (grasses, biocrusts, trees) in abundance with increasing aridity. Microsites supporting the highest abundance of AOB were trees, nitrogen-fixing shrubs, and ant nests. These results are linked to particular soil characteristics (e.g., total carbon and ammonium) under these microsites. Our findings advance our understanding of key drivers of functionally important microbial communities and N availability in highly heterogeneous ecosystems such as drylands, which may be obscured when different soil microsites are not explicitly considered. PMID:27148194

  12. Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil.

    Science.gov (United States)

    Yao, Huaiying; Huang, Sha; Qiu, Qiongfen; Li, Yaying; Wu, Lianghuan; Mi, Wenhai; Dai, Feng

    2016-08-01

    Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community. PMID:27063014

  13. Communities of ammonia oxidizers at different stages of Spartina alterniflora invasion in salt marshes of Yangtze River estuary.

    Science.gov (United States)

    Xia, Fei; Zeleke, Jemaneh; Sheng, Qiang; Wu, Ji-Hua; Quan, Zhe-Xue

    2015-05-01

    Spartina alterniflora, an aggressive invasive plant species at the estuarine wetlands of China's coasts, has become a major threat to the natural ecosystems. To understand its potential influence on nitrification processes, the community structures and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated using 454-pyrosequencing and quantitative real-time PCR (qPCR) in S. alterniflora invading salt marsh sediments at the Yangtze River estuary in Chongming island, Shanghai, China. Copy numbers of archaeal and bacterial ammonia monooxygenase subunit A (amoA) genes did not show accordant shifts with S. alterniflora invasion in the two sampling sites. However, the copy numbers of archaeal amoA gene were higher in summer than in spring. Phylogenetic analysis indicated that more than 90% of the archaeal and 92% of the bacterial amoA gene sequences were closely related to marine group I.1a and the clusters 13 and 15 in Nitrosospira lineage, respectively. The effect of different seasons (spring and summer) was important for the abundance variation of AOA, while different stages of S. alterniflora invasion did not show significant effect for both AOA and AOB. Variation of AOA community was significantly related to total carbon (TC) and sulfate concentration (P < 0.05), whereas the AOB community was significantly related to sulfate concentration, total nitrogen (TN), TC and pH (P < 0.05). In conclusion, the abundance and diversity of ammonia oxidizing microbial communities were not strongly affected by S. alterniflora invasion. PMID:25935302

  14. Archaeal Ammonia Oxidizers and Total Production of N2O and CH4 in Arctic Polar Desert Soils

    Science.gov (United States)

    Brummell, Martin; Robert, Stan; Bodrossy, Levente; Abell, Guy; Siciliano, Steven

    2014-05-01

    Ammonia-oxidizing Archaea are abundant in Arctic desert soils and appear to be responsible for the majority of ammonia oxidation activity in these cold and dry ecosystems. We used DNA microarrays to characterize the microbial community consisting of ammonia-oxidizing Archaea and methane-oxidizing Bacteria in three polar deserts from Ellesmere Island, Canada. Patterns of net greenhouse gas production, including production and consumption of CO2, CH4, and N2O were compared with community relative richness and abundance in a structural equation model that tested causal hypotheses relating edaphic factors to the biological community and net gas production. We extracted and amplified DNA sequences from soils collected at three polar deserts on Ellesmere Island in the Canadian high Arctic, and characterized the community structure using DNA microarrays. The functional genes Archaeal AmoA and pMMO were used to compare patterns of biological community structure to the observed patterns of net greenhouse gas production from those soils, as measured in situ. Edaphic factors including water content, bulk density, pH, and nutrient levels such as nitrate, ammonia, and extractable organic carbon were also measured for each soil sample, resulting in a highly multivariate dataset. Both concentration and net production of the three greenhouse gases were correlated, suggesting underlying causal factors. Edaphic factors such as soil moisture and pH had important, direct effects on the community composition of both functional groups of microorganisms, and pH further had a direct effect on N2O production. The structural relationship between the examined microbial communities and net production of both N2O and CH4 was strong and consistent between varying model structures and matrices, providing high confidence that this model relationship accurately reflects processes occurring in Arctic desert soils.

  15. Effect of chemical fertilization and green manure on the abundance and community structure of ammonia oxidizers in a paddy soil

    Directory of Open Access Journals (Sweden)

    Yu Fang

    2015-12-01

    Full Text Available Ammonia oxidization is a critical step in the soil N cycle and can be affected by the fertilization regimes. Chinese milk-vetch (Astragalus sinicus L., MV is a major green manure of rice (Oryza sativa L. fields in southern China, which is recommended as an important agronomic practice to improve soil fertility. Soil chemical properties, abundance and community structures of ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA in a MV-rice rotation field under different fertilization regimes were investigated. The field experiment included six treatments: control, without MV and chemical fertilizer (CK; 100% chemical fertilizer (NPK; 18 000 kg MV ha-1 plus 100% chemical fertilizer (NPKM1; 18 000 kg MV ha-1 plus 40% chemical fertilizer (NPKM2; 18 000 kg MV ha-1 alone (MV; and 18 000 kg MV ha-1 plus 40% chemical fertilizer plus straw (NPKMS. Results showed that NPKMS treatment could improve the soil fertility greatly although the application of 60% chemical fertilizer. The abundance of AOB only in the MV treatment had significant difference with the control; AOA were more abundant than AOB in all corresponding treatments. The NPKMS treatment had the highest AOA abundance (1.19 x 10(8 amoA gene copies g-1 and the lowest abundance was recorded in the CK treatment (3.21 x 10(7 amoA gene copies g-1. The abundance of AOA was significantly positively related to total N, available N, NH4+-N, and NO3--N. The community structure of AOA exhibited little variation among different fertilization regimes, whereas the community structure of AOB was highly responsive. Phylogenetic analysis showed that all AOB sequences were affiliated with Nitrosospira or Nitrosomonas and all AOA denaturing gradient gel electrophoresis (DGGE bands belonged to the soil and sediment lineage. These findings could be fundamental to improve our understanding of AOB and AOA in the N cycle in the paddy soil.

  16. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes.

    Science.gov (United States)

    Zhang, Jinping; Zhou, Xiaohong; Chen, Lei; Chen, Zhigang; Chu, Jinyu; Li, Yimin

    2016-05-01

    The abundance, diversity and community structure of ammonia oxidizing archaea (AOA) and bacteria (AOB) in rice rhizosphere soils under three different irrigation cultivated modes, named continuous irrigation mode (C), intermittent irrigation mode (I) and semi-arid mode (M), respectively, were investigated using amoA gene as a molecular biomarker. Clone libraries and quantitative polymerase chain reaction results indicated the highest number of archaeal amoA gene copy was detected in M cultivation mode, then in I and C, whereas, their order of amoA gene copy numbers were I > M > C for AOB, and those were obvious higher than in the bulk soil. The ratios of AOA/AOB were greater than 1 for all samples, suggested the predominance of AOA throughout the period of rice growth in the three different irrigation cultivation modes. Diversity index (SChao1 and Shannon H) have an obvious variation in three different irrigation cultivation modes. For AOA, SChao1 was highest in M and lowest in I mode, whereas, Shannon H was highest in M cultivation mode and lowest in C mode. For AOB, mode M exhibited the highest diversity index (SChao1 and Shannon H), while C showed the lowest highest diversity, suggested long-term water input (continuous mode) may decrease diversity of ammonia oxidizers, whereas mode M may be more appropriate for them. In addition, AOA sequences fall within Nitrososphaera, Nitrosopumilus and Nitrosotalea cluster with proportion of 89.38, 8.85 and 1.77 %, respectively. AOB gene sequences belonged to the Nitrosomonas and Nitrosospira genera with proportion of 90.97 and 9.03 %, respectively. In addition, the abundances, diversity and community structure had an obvious temporal variation in three developmental stages of rice, further suggested rice growth obviously affected the ammonia oxidizing prokaryotes in their rhizosphere soil. PMID:27038955

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

    Directory of Open Access Journals (Sweden)

    Y. Zheng

    2014-03-01

    Full Text Available Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable isotope probing and pyrosequencing of 16S rRNA and pmoA genes, we report on biogeochemical and molecular evidence for growth stimulation of methanotrophic communities by ammonium fertilization, and that methane modulates nitrogen cycling by competitive inhibition of nitrifying communities in a rice paddy soil. Pairwise comparison between microcosms amended with CH4, CH4+Urea, and Urea indicated that urea fertilization stimulated methane oxidation activity by 6-fold during a 19 day incubation period, while ammonia oxidation activity was significantly inhibited in the presence of CH4. Pyrosequencing of the total 16S rRNA genes revealed that urea amendment resulted in rapid growth of Methylosarcina-like type Ia MOB, and nitrifying communities appeared to be suppressed by methane. High-throughput sequencing of the 13C-labeled DNA further revealed that methane amendment resulted in clear growth of Methylosarcina-related MOB while methane plus urea led to equal increase in Methylosarcina and Methylobacter-related MOB, indicating the differential growth requirements of representatives of these genera. Strikingly, type Ib MOB did not respond to methane nor to urea. Increase in 13C-assimilation by microorganisms related to methanol oxidizers clearly indicated carbon transfer from methane oxidation to other soil microbes, which was enhanced by urea addition. The active growth of type Ia methanotrops was significantly stimulated by urea amendment, and the pronounced growth of methanol-oxidizing bacteria occurred in CH4-treated microcosms only upon urea amendment. Methane addition inhibited the growth of Nitrosospira and Nitrosomonas in urea-amended microcosms, in

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

    Science.gov (United States)

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

    2014-06-01

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

  19. Temperature and moisture effects on ammonia oxidizer communities in cryoturbated Arctic soils

    Science.gov (United States)

    Aiglsdorfer, Stefanie; Alves, Ricardo J. E.; Bárta, Jiří; Kohoutová, Iva; Bošková, Hana; Diáková, Katerina; Čapek, Petr; Schnecker, Jörg; Wild, Birgit; Mooshammer, Maria; Urich, Tim; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Mikutta, Robert; Lashchinskiy, Nikolay; Richter, Andreas; Šantrůčková, Hana; Shibistova, Olga; Schleper, Christa

    2014-05-01

    Arctic permafrost-affected soils contain large amounts of soil organic carbon (SOC) and are expected to experience drastic changes in environmental conditions, such as moisture and temperature, due to the high surface temperature increase predicted for these regions. Although the SOC decomposition processes driven by the microbiota are considered to be nitrogen (N) limited, little information about the microbial groups involved in N cycle is currently available, including their reactions to environmental changes. Here, we investigate the presence of ammonia oxidizing archaea (AOA) and bacteria (AOB) in distinct soil horizons from the Taymyr peninsula (Siberia, Russia), and investigate their activities under changing temperature and moisture regimes. These two groups of organisms perform the first step in nitrification, an important and rate limiting process in the global N cycle, which involves the oxidation of ammonia to nitrate via nitrite. The soil samples were separated into different horizons: organic topsoil (O) and subducted organic topsoil (Ajj). The samples were incubated for 18 weeks at 4, 12 and 20° C and 50, 80 and 100 % water holding capacity (WHC). AOA and AOB abundances were quantified by quantitative PCR targeting genes of the key metabolic enzyme, ammonia monooxygenase. AOA diversity was analyzed in-depth by high-throughput amplicon sequencing of the same gene. Additionally, gross and net nitrification and mineralization rates were determined in order to investigate potential relationships between AOA and AOB populations and these processes, in response to the incubation treatments. We found higher abundances of AOA than AOB in the organic topsoil, whereas AOB dominated in the subducted organic topsoil. Increased temperature resulted in higher numbers of both groups at low WHC %, with AOB showing a more pronounced response. However, these effects were not observed under anaerobic conditions (100 % WHC). Deep sequencing of AOA amoA genes revealed

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

    Science.gov (United States)

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

    2014-05-01

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

  1. Evaluating primers for profiling anaerobic ammonia oxidizing bacteria within freshwater environments.

    Directory of Open Access Journals (Sweden)

    Puntipar Sonthiphand

    Full Text Available Anaerobic ammonia oxidizing (anammox bacteria play an important role in transforming ammonium to nitrogen gas and contribute to fixed nitrogen losses in freshwater environments. Understanding the diversity and abundance of anammox bacteria requires reliable molecular tools, and these are not yet well established for these important Planctomycetes. To help validate PCR primers for the detection of anammox bacteria within freshwater ecosystems, we analyzed representative positive controls and selected samples from Grand River and groundwater sites, both from Ontario, Canada. The objectives of this study were to identify a suitable anammox denaturing gradient gel electrophoresis (DGGE fingerprint method by using GC-clamp modifications to existing primers, and to verify the specificity of anammox-specific primers used for DGGE, cloning and qPCR methods. Six primer combinations were tested from four published primer sets (i.e. A438f/A684r, Amx368f/Amx820r, An7f/An1388r, and Pla46/1392r for both direct and nested PCR amplifications. All PCR products were run subsequently on DGGE gels to compare the resulting patterns. Two anammox-specific primer combinations were also used to generate clone libraries and quantify anammox bacterial 16S rRNA genes with qPCR. The primer set A438f/A684r was highly specific to anammox bacteria, provided reliable DGGE fingerprints and generated a high proportion of anammox-related clones. A second primer set (Amx368f/Amx820r was anammox specific, based on clone library analysis, but PCR products from different candidate species of anammox bacteria resolved poorly using DGGE analysis. Both DGGE and cloning results revealed that Ca. Brocadia and an uncharacterized anammox bacterial cluster represented the majority of anammox bacteria found in Grand River sediment and groundwater samples, respectively. Together, our results demonstrate that although Amx368f/Amx820r was useful for anammox-specific qPCR and clone library

  2. Changes in Nitrogen-Fixing and Ammonia-Oxidizing Bacterial Communities in Soil of a Mixed Conifer Forest after Wildfire

    OpenAIRE

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

    2005-01-01

    This study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and amoA PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizin...

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

    OpenAIRE

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

    2013-01-01

    Mesophilic ammonia-oxidizing Archaea (AOA) are abundant in a diverse range of marine environments, including the deep ocean, as revealed by the quantification of the archaeal amoA gene encoding the alpha-subunit of the ammonia monooxygenase. Using two different amoA primer sets, two distinct ecotypes of marine Crenarchaeota Group I (MCGI) were detected in the waters of the tropical Atlantic and the coastal Arctic. The HAC-AOA ecotype (high ammonia concentration AOA) was ≍ 8000 times and 15 ti...

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

    OpenAIRE

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

    2010-01-01

    The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and “Candidatus Nitrosopumilus maritimus” (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichmen...

  5. Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management

    Energy Technology Data Exchange (ETDEWEB)

    Wessen, E.; Nyberg, K.; Jansson, J.K.; Hallin, S.

    2010-05-01

    Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) co-exist in soil, but their relative distribution may vary depending on the environmental conditions. Effects of changes in soil organic matter and nutrient content on the AOB and AOA are poorly understood. Our aim was to compare effects of long-term soil organic matter depletion and amendments with labile (straw) and more recalcitrant (peat) organic matter, with and without easily plant-available nitrogen, on the activities, abundances and community structures of AOB and AOA. Soil was sampled from a long-term field site in Sweden that was established in 1956. The potential ammonia oxidation rates, the AOB and AOA amoA gene abundances and the community structures of both groups based on T-RFLP of amoA genes were determined. Straw amendment during 50 years had not altered any of the measured soil parameters, while the addition of peat resulted in a significant increase of soil organic carbon as well as a decrease in pH. Nitrogen fertilization alone resulted in a small decrease in soil pH, organic carbon and total nitrogen, but an increase in primary production. Type and amount of organic matter had an impact on the AOB and AOA community structures and the AOA abundance. Our findings confirmed that AOA are abundant in soil, but showed that under certain conditions the AOB dominate, suggesting niche differentiation between the two groups at the field site. The large differences in potential rates between treatments correlated to the AOA community size, indicating that they were functionally more important in the nitrification process than the AOB. The AOA abundance was positively related to addition of labile organic carbon, which supports the idea that AOA could have alternative growth strategies using organic carbon. The AOB community size varied little in contrast to that of the AOA. This indicates that the bacterial ammonia oxidizers as a group have a greater ecophysiological diversity and

  6. Comparison among amoA Primers Suited for Quantification and Diversity Analyses of Ammonia-Oxidizing Bacteria in Soil

    OpenAIRE

    Shimomura, Yumi; Morimoto, Sho; Hoshino, Yuko Takada; Uchida, Yoshitaka; akiyama, Hiroko; Hayatsu, Masahito

    2011-01-01

    Ammonia monooxygenase subunit A gene (amoA) is frequently used as a functional gene marker for diversity analysis of ammonia-oxidizing bacteria (AOB). To select a suitable amoA primer for real-time PCR and PCR-denaturing gradient gel electrophoresis (DGGE), three reverse primers (degenerate primer amoA-2R; non-degenerate primers amoA-2R-GG and amoA-2IR) were examined. No significant differences were observed among the three primers in terms of quantitative values of amoA from environmental sa...

  7. Effect of Soil Ammonium Concentration on N2O Release and on the Community Structure of Ammonia Oxidizers and Denitrifiers

    OpenAIRE

    Avrahami, Sharon; Conrad, Ralf; Braker, Gesche

    2002-01-01

    The effect of ammonium addition (6.5, 58, and 395 μg of NH4+-N g [dry weight] of soil−1) on soil microbial communities was explored. For medium and high ammonium concentrations, increased N2O release rates and a shift toward a higher contribution of nitrification to N2O release occurred after incubation for 5 days at 4°C. Communities of ammonia oxidizers were assayed after 4 weeks of incubation by denaturant gradient gel electrophoresis (DGGE) of the amoA gene coding for the small subunit of ...

  8. Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR

    DEFF Research Database (Denmark)

    Dechesne, Arnaud; Musovic, Sanin; Palomo, Alejandro;

    2016-01-01

    quantitative PCR methods to enumerate ammonia-oxidizing bacteria (AOB): one targeting the phylogenetic gene 16S rRNA and the other, the functional gene amoA. Cloning-sequencing with both primer sets on DNA from two waterworks revealed contrasting images of AOB diversity. The amoA-based approach preferentially...... analysis against sequences of AOB (both isolates and high-quality environmental sequences). The difference in primer coverage significantly impacted the estimation of AOB abundance at the waterworks with high Cluster 6A prevalence, with estimates up to 50-fold smaller for amoA than for 16S r...

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

    Directory of Open Access Journals (Sweden)

    Yvonne Antonia Lipsewers

    2014-09-01

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

  10. Seasonal and spatial distribution of ammonia-oxidizing microorganism communities in surface sediments from the East China Sea

    Institute of Scientific and Technical Information of China (English)

    HE Hui; ZHEN Yu; MI Tiezhu; LU Xinglan; YU Zhigang

    2015-01-01

    Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Seasonal and spatial distribution of ammonia-oxidizing archaea (AOA) and betaproteobacteria (β-AOB) in surface sediments from the East China Sea (ECS) were investigated using ammonia monooxygenaseα subunit (amoA) gene. In order to characterize the community of AOA andβ-AOB, real-time quantitative polymerase chain reaction (qPCR) was carried out in this study, along with environmental parameters. The abundance ofβ-AOBamoA gene (2.17×106–4.54×107 copy numbers per gram wet weight sediment) was always greater than that of AOAamoA gene (2.18×105–9.89×106 copy numbers per gram wet weight sediment) in all sampling stations. The qPCR results were correlated with environmental parameters. AOAamoA gene copy numbers in April were positively related to temperature and nitrite concentration (p<0.05).β-AOBamoA gene copy numbers in August correlated negatively with salinity (p<0.01), and correlated positively with ammonium concentration (p<0.05). With the increase of salinity, theamoA gene copy ratio of AOB to AOA had a tendency to decrease, which suggestedβ-AOB dominated in the area of high level ammonium and AOA preferred high salinity area.

  11. Population and diversity of ammonia-oxidizing archaea and bacteria in a pollutants' receiving area in Hangzhou Bay.

    Science.gov (United States)

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

    2016-07-01

    The community structure of ammonia-oxidizing microorganisms is sensitive to various environmental factors, including pollutions. In this study, real-time PCR and 454 pyrosequencing were adopted to investigate the population and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) temporally and spatially in the sediments of an industrial effluent receiving area in the Qiantang River's estuary, Hangzhou Bay. The abundances of AOA and AOB amoA genes fluctuated in 10(5)-10(7) gene copies per gram of sediment; the ratio of AOA amoA/AOB amoA ranged in 0.39-5.52. The AOA amoA/archaeal 16S rRNA, AOB amoA/bacterial 16S rRNA, and AOA amoA/AOB amoA were found to positively correlate with NH4 (+)-N concentration of the seawater. Nitrosopumilus cluster and Nitrosomonas-like cluster were the dominant AOA and AOB, respectively. The community structures of both AOA and AOB in the sediments exhibited significant seasonal differences rather than spatial changes in the effluent receiving area. The phylogenetic distribution of AOB in this area was consistent with the wastewater treatment plants (WWTPs) discharging the effluent but differed from the Qiantang River and other estuaries, which might be an outcome of long-term effluent discharge. PMID:26960319

  12. Human settlement as driver of bacterial, but not of archaeal, ammonia oxidizers abundance and community structure in tropical stream sediments

    Directory of Open Access Journals (Sweden)

    Mariana De Paula Reis

    2015-08-01

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

  13. Spatial and temporal dynamics of ammonia oxidizers in the sediments of the Gulf of Finland, Baltic Sea.

    Science.gov (United States)

    Vetterli, Adrien; Hietanen, Susanna; Leskinen, Elina

    2016-02-01

    The diversity and dynamics of ammonia-oxidizing bacteria (AOB) and archaea (AOA) nitrifying communities in the sediments of the eutrophic Gulf of Finland (GoF) were investigated. Using clone libraries of ammonia monooxygenase (amoA) gene fragments and terminal restriction fragment length polymorphism (TRFLP), we found a low richness of both AOB and AOA. The AOB amoA phylogeny matched that of AOB 16S ribosomal genes from the same samples. AOA communities were characterized by strong spatial variation while AOB communities showed notable temporal patterns. At open sea sites, where transient anoxic conditions prevail, richness of both AOA and AOB was lowest and communities were dominated by organisms with gene signatures unique to the GoF. Given the importance of nitrification as a link between the fixation of nitrogen and its removal from aquatic environments, the low diversity of ammonia-oxidizing microbes across the GoF could be of relevance for ecosystem resilience in the face of rapid global environmental changes. PMID:26722795

  14. Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary

    Institute of Scientific and Technical Information of China (English)

    Xiao-ran LI; Yi-ping XIAO; Wen-wei REN; Zeng-fu LIU; Jin-huan SHI; Zhe-xue QUAN

    2012-01-01

    Tidal fiats are soil resources of great significance.Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments.We determined the abundance as well as composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in different soils during land reclamation process.The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction (PCR).The different abundances of AOB and AOA were negatively correlated with the salinity.The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene.Among AOB,nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process,i.e.,tidal flats,while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process,farm land and wild land.The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate.As for AOA,there was no obvious correlation with the changes in the physicochemical properties of the soil.This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages.

  15. Quantitative and compositional responses of ammonia-oxidizing archaea and bacteria to long-term field fertilization

    Science.gov (United States)

    Xue, Chao; Zhang, Xu; Zhu, Chen; Zhao, Jun; Zhu, Ping; Peng, Chang; Ling, Ning; Shen, Qirong

    2016-06-01

    Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM), and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.

  16. Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from South of Chile.

    Science.gov (United States)

    Hernández, Marcela; Dumont, Marc G; Calabi, Marcela; Basualto, Daniel; Conrad, Ralf

    2014-02-01

    Ammonia oxidation, performed by specialized microorganisms belonging to the Bacteria and Archaea, is the first and most limiting step of soil nitrification. Nitrification has not yet been examined in young volcanic soils. The aim of the present work was to evaluate the abundance and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in acidic volcanic soils (andisols) of different defined ages to determine their relative contribution to nitrification and soil colonization. Soil was collected from three vegetated sites on Llaima Volcano (Chile) recolonized after lava eruptions in 1640, 1751 and 1957. Quantitative polymerase chain reaction, terminal restriction fragment length polymorphism and clone sequence analyses of the amoA gene were performed for the AOA and AOB communities. All soils showed high nitrification potentials, but they were highest in the younger soils. Archaeal amoA genes outnumbered bacterial amoA genes at all sites, and AOA abundances were found to be proportional to the nitrification potentials. Sequencing indicated the presence of AOA related to Nitrososphaera and Nitrosotalea, and AOB related primarily to Nitrosospira and sporadically to Nitrosomonas. The study showed that both AOA and AOB are early colonizers of andisols, but that AOA outnumber AOB and play an important role in nitrification. PMID:24596264

  17. Spatial distribution of ammonia-oxidizing archaea and bacteria across eight freshwater lakes in sediments from Jiangsu of China

    Directory of Open Access Journals (Sweden)

    Xu Sun

    2014-03-01

    Full Text Available Ammonia-oxidizingarchaea (AOA and ammonia-oxidizing bacteria (AOB play an important role innitrogen transformation in freshwater sediments. However, it is still unclear towhat extent the distribution patterns of these microorganisms are affected bythe freshwater sediment across a large geographical scale. This study wasdesigned to gain insight into the heterogeneity distribution of AOA and AOB in32 freshwater sediments from a wide range of ecologic types. Real-time quantitative polymerasechain reaction PCR(qPCR combined with the terminal restrictionfragment length polymorphism(T-RFLP were employed to characterize the abundance, diversity, and communitystructure of the AOA and AOB in 32 freshwater sediments. AOA and AOB wereubiquitous in all sediments, and archaeal amoA far outnumbered bacterial amoA inmost sediments with lower organic matters. The abundance of AOA and AOB did notvary with the freshwater ecological type (macrophyte dominated region and algaedominated region. Based on  the T-RFLP of an amoA gene, this research found that organicmatters in pore water rather than other factors affect the AOA communitystructure in sediments, while the AOB were not significantly different in thefreshwater sediments. Phylogenetic analysis showed that all archaeal amoAsequences fell within either the Crenarchaeotal Group (CG I.1b or the CGI.1asubgroup, and all AOB clustered with genus Nitrosomonas or Nitrosospira. The data obtained inthis study elucidates the role of ammonia-oxidizing archaea andammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.

  18. Distribution and Abundance of Archaea in South China Sea Sponge Holoxea sp. and the Presence of Ammonia-Oxidizing Archaea in Sponge Cells

    Directory of Open Access Journals (Sweden)

    Fang Liu

    2011-01-01

    Full Text Available Compared with bacterial symbionts, little is known about archaea in sponges especially about their spatial distribution and abundance. Understanding the distribution and abundance of ammonia-oxidizing archaea will help greatly in elucidating the potential function of symbionts in nitrogen cycling in sponges. In this study, gene libraries of 16S rRNA gene and ammonia monooxygenase subunit A (amoA genes and quantitative real-time PCR were used to study the spatial distribution and abundance of archaea in the South China Sea sponge Holoxea sp. As a result, Holoxea sp. specific AOA, mainly group C1a (marine group I: Crenarchaeota were identified. The presence of ammonia-oxidizing crenarchaea was observed for the first time within sponge cells. This study suggested a close relationship between sponge host and its archaeal symbionts as well as the archaeal potential contribution to sponge host in the ammonia-oxidizing process of nitrification.

  19. Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating

    Directory of Open Access Journals (Sweden)

    Anne eDaebeler

    2012-10-01

    Full Text Available The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of the associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilisation site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative PCR suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while the measured soil physico-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization.

  20. The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance and climatic factors

    Directory of Open Access Journals (Sweden)

    Hangwei eHu

    2015-09-01

    Full Text Available Paddy soils distribute widely from temperate to tropical regions, and are characterized by intensive nitrogen fertilization practices in China. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA and bacteria (AOB in soil nitrification, but little is known about their biogeographic distribution patterns in paddy ecosystems. Here, we used barcoded pyrosequencing to characterize the effects of climatic, geochemical and spatial factors on the distribution of ammonia oxidizers from 11 representative rice-growing regions (75-1945 km apart of China. Potential nitrification rates varied greatly by more than three orders of magnitude, and were significantly correlated with the abundances of AOA and AOB. The community composition of ammonia oxidizer was affected by multiple factors, but changes in relative abundances of the major lineages could be best predicted by soil pH. The alpha diversity of AOA and AOB displayed contrasting trends over the gradients of latitude and atmospheric temperature, indicating a possible niche separation between AOA and AOB along the latitude. The Bray-Curtis dissimilarities in ammonia-oxidizing community structure significantly increased with increasing geographical distance, indicating that more geographically distant paddy fields tend to harbor more dissimilar ammonia oxidizers. Variation partitioning analysis revealed that spatial, geochemical and climatic factors could jointly explain majority of the data variation, and were important drivers defining the ecological niches of AOA and AOB. Our findings suggest that both AOA and AOB are of functional importance in paddy soil nitrification, and ammonia oxidizers in paddy ecosystems exhibit large-scale biogeographic patterns shaped by soil pH, geographic distance, and climatic factors.

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

    Science.gov (United States)

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

    2010-12-01

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

  2. Comparison of ammonia-oxidizing bacterial community structure in membrane-assisted bioreactors using PCR-DGGE and FISH.

    Science.gov (United States)

    Ziembińska, A; Ciesielski, S; Gnida, A; Zabczyńki, S; Surmacz-Górska, J; Miksch, K

    2012-08-01

    The ammonia-oxidizing bacterial (AOB) communities in three membrane bioreactors (MBRs) were monitored for 2 months after an acclimation period in order to investigate the influence of sludge age and medium type on AOB changeability and its connection with nitrification effectiveness. One MBR with a sludge age of 4 days was fed with a synthetic medium, whereas the other two with sludge ages of 8 and 32 days were fed with landfill leachate. The research revealed that landfill leachate can be effectively treated in an MBR with a higher sludge age for longer periods of time and that this improvement in performance was correlated with an increase in AOB biodiversity. Interestingly, the medium type has a stronger influence on AOB biocenosis formation than the sludge age. PMID:22713978

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

    Science.gov (United States)

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

    2016-09-01

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

  4. Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils.

    Science.gov (United States)

    Ramond, Jean-Baptiste; Lako, Joseph D W; Stafford, William H L; Tuffin, Marla I; Cowan, Don A

    2015-08-01

    Ammonia-oxidizing bacteria (AOB) are essential in the biogeochemical cycling of nitrogen as they catalyze the rate-limiting oxidation of ammonia into nitrite. Since their first isolation in the late 19th century, chemolithoautotrophic AOBs have been identified in a wide range of natural (e.g., soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g., wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs, particularly in the nutrient-starved fynbos terrestrial biome. In this study, we evaluated the diversity of AOBs in the plant canopy of three South African fynbos-specific plant species, namely Leucadendron xanthoconus, Leucospermum truncatulum and Leucadendron microcephalum, through the construction of amoA-gene clone libraries. Our results clearly demonstrate that plant-species specific and monophyletic AOB clades are present in fynbos canopy soils. PMID:25721729

  5. Spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenerative life support

    Science.gov (United States)

    Sakano, Yuko; Pickering, Karen D.; Strom, Peter F.; Kerkhof, Lee J.; Janes, H. W. (Principal Investigator)

    2002-01-01

    Bioregenerative life support systems may be necessary for long-term space missions due to the high cost of lifting supplies and equipment into orbit. In this study, we investigated two biological wastewater treatment reactors designed to recover potable water for a spacefaring crew being tested at Johnson Space Center. The experiment (Lunar-Mars Life Support Test Project-Phase III) consisted of four crew members confined in a test chamber for 91 days. In order to recycle all water during the experiment, an immobilized cell bioreactor (ICB) was employed for organic carbon removal and a trickling filter bioreactor (TFB) was utilized for ammonia removal, followed by physical-chemical treatment. In this study, the spatial distribution of various microorganisms within each bioreactor was analyzed by using biofilm samples taken from four locations in the ICB and three locations in the TFB. Three target genes were used for characterization of bacteria: the 16S rRNA gene for the total bacterial community, the ammonia monooxygenase (amoA) gene for ammonia-oxidizing bacteria, and the nitrous oxide reductase (nosZ) gene for denitrifying bacteria. A combination of terminal restriction fragment length polymorphism (T-RFLP), sequence, and phylogenetic analyses indicated that the microbial community composition in the ICB and the TFB consisted mainly of Proteobacteria, low-G+C gram-positive bacteria, and a Cytophaga-Flexibacter-Bacteroides group. Fifty-seven novel 16S rRNA genes, 8 novel amoA genes, and 12 new nosZ genes were identified in this study. Temporal shifts in the species composition of total bacteria in both the ICB and the TFB and ammonia-oxidizing and denitrifying bacteria in the TFB were also detected when the biofilms were compared with the inocula after 91 days. This result suggests that specific microbial populations were either brought in by the crew or enriched in the reactors during the course of operation.

  6. Differential responses of ammonia-oxidizing archaea and bacteria to long-term fertilization in a New England salt marsh

    Directory of Open Access Journals (Sweden)

    Xuefeng ePeng

    2013-01-01

    Full Text Available Since the discovery of ammonia-oxidizing archaea (AOA, new questions have arisen about population and community dynamics and potential interactions between AOA and ammonia-oxidizing Bacteria (AOB. We investigated the effects of long-term fertilization on AOA and AOB in the Great Sippewissett Marsh, Falmouth, MA, USA to address some of these questions. Sediment samples were collected from low and high marsh habitats in July 2009 from replicate plots that received low (LF, high (HF, and extra high (XF levels of a mixed NPK fertilizer biweekly during the growing season since 1974. Additional untreated plots were included as controls (C. Terminal restriction fragment length polymorphism analysis of the amoA genes revealed distinct shifts in AOB communities related to fertilization treatment, but the response patterns of AOA were less consistent. Four AOB operational taxonomic units (OTUs predictably and significantly responded to fertilization, but only one AOA OTU showed a significant pattern. Betaproteobacterial amoA gene sequences within the Nitrosospira-like cluster dominated at C and LF sites, while sequences related to Nitrosomonas spp. dominated at HF and XF sites. We identified some clusters of AOA sequences recovered primarily from high fertilization regimes, but other clusters consisted of sequences recovered from all fertilization treatments, suggesting greater physiological diversity. Surprisingly, fertilization appeared to have little impact on abundance of AOA or AOB. In summary, our data reveal striking patterns for AOA and AOB in response to long-term fertilization, and also suggest a missing link between community composition and abundance and nitrogen processing in the marsh.

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

    Science.gov (United States)

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

    2016-01-01

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

  8. Spatial interaction of archaeal ammonia-oxidizers and nitrite-oxidizing bacteria in an unfertilized grassland soil

    Directory of Open Access Journals (Sweden)

    Barbara eStempfhuber

    2016-01-01

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

  9. Ammonia-oxidizing archaea and bacteria in water columns and sediments of a highly eutrophic plateau freshwater lake.

    Science.gov (United States)

    Yang, Yuyin; Li, Ningning; Zhao, Qun; Yang, Mengxi; Wu, Zhen; Xie, Shuguang; Liu, Yong

    2016-08-01

    Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can play important roles in the microbial oxidation of ammonia nitrogen in freshwater lake, but information on spatiotemporal variation in water column and sediment community structure is still limited. Additionally, the drivers of the differences between sediment and water assemblages are still unclear. The present study investigated the variation of AOA and AOB communities in both water columns and sediments of eutrophic freshwater Dianchi Lake. The abundance, diversity, and structure of both planktonic and sediment ammonia-oxidizing microorganisms in Dianchi Lake showed the evident changes with sampling site and time. In both water columns and sediments, AOB amoA gene generally outnumbered AOA, and the AOB/AOA ratio was much higher in summer than in autumn. The total AOA amoA abundance was relatively great in autumn, while sediment AOB was relatively abundant in summer. Sediment AOA amoA abundance was likely correlated with ammonia nitrogen (rs = 0.963). The AOB/AOA ratio in lake sediment was positively correlated with total phosphorus (rs = 0.835), while pH, dissolved organic carbon, and ammonia nitrogen might be the key driving forces for the AOB/AOA ratio in lake water. Sediment AOA and AOB diversity was correlated with nitrate nitrogen (rs = -0.786) and total organic carbon (rs = 0.769), respectively, while planktonic AOB diversity was correlated with ammonia nitrogen (rs = 0.854). Surface water and sediment in the same location had a distinctively different microbial community structure. In addition, sediment AOB community structure was influenced by total phosphorus, while total phosphorus might be a key determinant of planktonic AOB community structure. PMID:27109114

  10. Spatial distribution of archaeal and bacterial ammonia oxidizers in the littoral buffer zone of a nitrogen-rich lake

    Institute of Scientific and Technical Information of China (English)

    Yu Wang; Guibing Zhu; Lei Ye; Xiaojuan Feng; Huub J. M. Op den Camp; Chengqing Yin

    2012-01-01

    The spatial distribution and diversity of archaeal and bacterial ammonia oxidizers (AOA and AOB) were evaluated targeting amoA genes in the gradient of a littoral buffer zone which has been identified as a hot spot for N cycling.Here we found high spatial heterogeneity in the nitrification rate and abundance of ammonia oxidizers in the five sampling sites.The bacterial amoA gene was numerically dominant in most of the surface soil but decreased dramatically in deep layers.Higher nitrification potentials were detected in two sites near the land/water interface at 4.4-6.1 μg NO2--N/(g dry weight soil.hr),while only 1.0-1.7 μg NO2- -N/(gdry weight soil·hr) was measured at other sites.The potential nitrification rates were proportional to the amoA gene abundance for AOB,hut with no significant correlation with AOA.The NH4+ concentration was the most determinative parameter for the abundance of AOB and potential nitrification rates in this study.Higher richness in the surface layer was found in the analysis of biodiversity.Phylogenetic analysis revealed that most of the bacterial amoA sequences in surface soil were affiliated with the genus of Nitrosopira while the archaeal sequences were almost equally affiliated with Candidatus ‘Nitrososphaera gargensis' and Candidatus ‘Nitrosoealdus yellowstonii'.The spatial distribution of AOA and AOB indicated that bacteria may play a more important role in nitrification in the littoral buffer zone of a N-rich lake.

  11. N2O production by ammonia oxidizing bacteria in an enriched nitrifying sludge linearly depends on inorganic carbon concentration.

    Science.gov (United States)

    Peng, Lai; Ni, Bing-Jie; Ye, Liu; Yuan, Zhiguo

    2015-05-01

    The effect of inorganic carbon (IC) on nitrous oxide (N2O) production by ammonia oxidizing bacteria (AOB) was investigated over a concentration range of 0-12 mmol C/L, encompassing typical IC levels in a wastewater treatment reactors. The AOB culture was enriched along with nitrite-oxidizing bacteria (NOB) in a sequencing batch reactor (SBR) to perform complete nitrification. Batch experiments were conducted with continuous carbon dioxide (CO2) stripping or at controlled IC concentrations. The results revealed a linear relationship between N2O production rate (N2OR) and IC concentration (R(2) = 0.97) within the IC range studied, suggesting a substantial effect of IC on N2O production by AOB. Similar results were also obtained with an AOB culture treating anaerobic sludge digestion liquor. The fundamental mechanism responsible for this dependency is unclear; however, in agreement with previous studies, it was observed that the ammonia oxidation rate (AOR) was also influenced by the IC concentration, which could be well described by the Monod kinetics. These resulted in an exponential relationship between N2OR and AOR, as previously observed in experiments where AOR was altered by varying dissolved oxygen and ammonia concentrations. It is therefore possible that IC indirectly affected N2OR by causing a change in AOR. The observation in this study indicates that alkalinity (mostly contributed by IC) could be a significant factor influencing N2O production and should be taken into consideration in estimating and mitigating N2O emissions in wastewater treatment systems. PMID:25706224

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

    Science.gov (United States)

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

    2015-10-01

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

  13. Effect of toxic metals on indigenous soil {beta}-subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Stephen, J.R.; Chang, Y.J.; MacNaughton, S.J.; Leung, K.T.; Flemming, C.A. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; Kowalchuk, G.A. [Netherlands Inst. of Ecology, Heteren (Netherlands); White, D.C. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology]|[Oak Ridge National Lab., TN (United States). Biological Sciences Div.

    1999-01-01

    Contamination of soils with toxic metals is a major problem on military, industrial, and mining sites worldwide. Of particular interest to the field of bioremediation is the selection of biological markers for the end point of remediation. In this microcosm study, the authors focus on the effect of addition of a mixture of toxic metals (cadmium, cobalt, cesium, and strontium as chlorides) to soil on the population structure and size of the ammonia, oxidizers that are members of the beta subgroup of the Proteobacteria. In a parallel experiment, the soils were also treated by the addition of five strains of metal-resistant heterotrophic bacteria. Effects on nitrogen cycling were measured by monitoring the NH{sub 3} and NH{sub 4}{sup +} levels in soil samples. The gene encoding the {alpha}-subunit of ammonia monooxygenase (amoA) was selected as a functional molecular marker for the {beta}-subgroup ammonia oxidizing bacteria. Community structure comparisons were performed with clone libraries of PCR-amplified fragments of amoA recovered from contaminated and control microcosms for 8 weeks. Analysis was performed by restriction digestion and sequence comparison. The abundance of ammonia oxidizers in these microcosms was also monitored by competitive PCR. All amoA gene fragments recovered grouped with sequences derived from cultured Nitrosospira. These comprised four novel sequence clusters and a single unique clone. Specific changes in the community structure of {beta}-subgroup ammonia oxidizers were associated with the addition of metals. These changes were not seen in the presence of the inoculated metal-resistant bacteria. Neither treatment significantly altered the total number of {beta}-subgroup ammonia-oxidizing cells per gram of soil compared to untreated controls. Following an initial decrease in concentration, ammonia began to accumulate in metal-treated soils toward the end of the experiment.

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

    Science.gov (United States)

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

    2013-12-01

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

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

    Directory of Open Access Journals (Sweden)

    M. S. Alam

    2013-08-01

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

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

    Science.gov (United States)

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

    2013-08-01

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

  17. Relating the Diversity, Abundance, and Activity of Ammonia-Oxidizing Archaeal Communities to Nitrification Rates in the Coastal Ocean

    Science.gov (United States)

    Tolar, B. B.; Smith, J. M.; Chavez, F.; Francis, C.

    2015-12-01

    Ammonia oxidation, the rate-limiting first step of nitrification, is an important link between reduced (ammonia) and oxidized (nitrate) nitrogen, and controls the relative distribution of these forms of inorganic nitrogen. This process is catalyzed via the ammonia monooxygenase enzyme of both ammonia-oxidizing Bacteria (AOB) and Archaea (AOA); the α subunit of this enzyme is encoded by the amoA gene and has been used as the molecular marker to detect this process. In the ocean, AOA are typically 10-1000 times more and are likely more active than AOB, and thus are key players in the marine nitrogen cycle. Monterey Bay is a dynamic site to study nitrification, as seasonal upwelling brings deep water and nutrients into surface waters, which can promote phytoplankton blooms and impact biogeochemical processes such as the nitrogen cycle. We have sampled two sites within Monterey Bay bimonthly for two years as part of the ongoing Monterey Bay Time Series (MBTS) to quantify AOA genes, transcripts, and nitrification rates. Two ecotypes of AOA are routinely found in Monterey Bay - the 'shallow' water column A (WCA) and 'deep' water column B (WCB) clades, which are thought to have distinct physiological properties and can be distinguished based on the amoA gene sequence. Previous work has shown a strong relationship between nitrification rates in Monterey Bay with the abundance of WCA amoA genes and transcripts. Additionally, we found a correlation between the relative abundance of Marine Group I (MGI) Thaumarchaeota 16S rRNA reads (as % of total) and the absolute abundance of AOA amoA genes (determined via qPCR) in Monterey Bay and the California Current System. AOA 16S rRNA gene abundances in turn correlated significantly with changes in nitrification rate with depth, while the relative abundance of genes and transcripts binned to a single AOA (Nitrosopumilus maritimus) was not significantly correlated to nitrification rate. Further analysis of the sequenced AOA

  18. Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill

    Science.gov (United States)

    Bernhard, Anne E.; Sheffer, Roberta; Giblin, Anne E.; Marton, John M.; Roberts, Brian J.

    2016-01-01

    The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain. PMID:27375576

  19. Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil

    Science.gov (United States)

    Soares, Johnny R.; Cassman, Noriko A.; Kielak, Anna M.; Pijl, Agata; Carmo, Janaína B.; Lourenço, Kesia S.; Laanbroek, Hendrikus J.; Cantarella, Heitor; Kuramae, Eiko E.

    2016-07-01

    Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4+-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane.

  20. Large cryoconite aggregates on a Svalbard glacier support a diverse microbial community including ammonia-oxidizing archaea

    Science.gov (United States)

    Zarsky, Jakub D.; Stibal, Marek; Hodson, Andy; Sattler, Birgit; Schostag, Morten; Hansen, Lars H.; Jacobsen, Carsten S.; Psenner, Roland

    2013-09-01

    The aggregation of surface debris particles on melting glaciers into larger units (cryoconite) provides microenvironments for various microorganisms and metabolic processes. Here we investigate the microbial community on the surface of Aldegondabreen, a valley glacier in Svalbard which is supplied with carbon and nutrients from different sources across its surface, including colonies of seabirds. We used a combination of geochemical analysis (of surface debris, ice and meltwater), quantitative polymerase chain reactions (targeting the 16S ribosomal ribonucleic acid and amoA genes), pyrosequencing and multivariate statistical analysis to suggest possible factors driving the ecology of prokaryotic microbes on the surface of Aldegondabreen and their potential role in nitrogen cycling. The combination of high nutrient input with subsidy from the bird colonies, supraglacial meltwater flow and the presence of fine, clay-like particles supports the formation of centimetre-scale cryoconite aggregates in some areas of the glacier surface. We show that a diverse microbial community is present, dominated by the cyanobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria, that are well-known in supraglacial environments. Importantly, ammonia-oxidizing archaea were detected in the aggregates for the first time on an Arctic glacier.

  1. Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR.

    Science.gov (United States)

    Dechesne, Arnaud; Musovic, Sanin; Palomo, Alejandro; Diwan, Vaibhav; Smets, Barth F

    2016-07-01

    Molecular methods to investigate functional groups in microbial communities rely on the specificity and selectivity of the primer set towards the target. Here, using rapid sand filters for drinking water production as model environment, we investigated the consistency of two commonly used quantitative PCR methods to enumerate ammonia-oxidizing bacteria (AOB): one targeting the phylogenetic gene 16S rRNA and the other, the functional gene amoA. Cloning-sequencing with both primer sets on DNA from two waterworks revealed contrasting images of AOB diversity. The amoA-based approach preferentially recovered sequences belonging to Nitrosomonas Cluster 7 over Cluster 6A ones, while the 16S rRNA one yielded more diverse sequences belonging to three AOB clusters, but also a few non-AOB sequences, suggesting broader, but partly unspecific, primer coverage. This was confirmed by an in silico coverage analysis against sequences of AOB (both isolates and high-quality environmental sequences). The difference in primer coverage significantly impacted the estimation of AOB abundance at the waterworks with high Cluster 6A prevalence, with estimates up to 50-fold smaller for amoA than for 16S rRNA. In contrast, both approaches performed very similarly at waterworks with high Cluster 7 prevalence. Our results highlight that caution is warranted when comparing AOB abundances obtained using different qPCR primer sets. PMID:27166579

  2. Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill.

    Science.gov (United States)

    Bernhard, Anne E; Sheffer, Roberta; Giblin, Anne E; Marton, John M; Roberts, Brian J

    2016-01-01

    The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain. PMID:27375576

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

    Science.gov (United States)

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

    2015-08-01

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

  4. Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil.

    Science.gov (United States)

    Soares, Johnny R; Cassman, Noriko A; Kielak, Anna M; Pijl, Agata; Carmo, Janaína B; Lourenço, Kesia S; Laanbroek, Hendrikus J; Cantarella, Heitor; Kuramae, Eiko E

    2016-01-01

    Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O emissions, and to determine the impacts of the N sources on the soil microbiome. In a field experiment, nitrogen was applied as calcium nitrate, urea, urea with dicyandiamide or 3,4 dimethylpyrazone phosphate nitrification inhibitors (NIs), and urea coated with polymer and sulfur (PSCU). Urea caused the highest N2O emissions (1.7% of N applied) and PSCU did not reduce cumulative N2O emissions compared to urea. NIs reduced N2O emissions (95%) compared to urea and had emissions comparable to those of the control (no N). Similarly, calcium nitrate resulted in very low N2O emissions. Interestingly, N2O emissions were significantly correlated only with bacterial amoA, but not with denitrification gene (nirK, nirS, nosZ) abundances, suggesting that ammonia-oxidizing bacteria, via the nitrification pathway, were the main contributors to N2O emissions. Moreover, the treatments had little effect on microbial composition or diversity. We suggest nitrate-based fertilizers or the addition of NIs in NH4(+)-N based fertilizers as viable options for reducing N2O emissions in tropical soils and lessening the environmental impact of biofuel produced from sugarcane. PMID:27460335

  5. Spatial Variability in Nitrification Rates and Ammonia-Oxidizing Microbial Communities in the Agriculturally Impacted Elkhorn Slough Estuary, California ▿ †

    OpenAIRE

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

    2010-01-01

    Ammonia oxidation—the microbial oxidation of ammonia to nitrite and the first step in nitrification—plays a central role in nitrogen cycling in coastal and estuarine systems. Nevertheless, questions remain regarding the connection between this biogeochemical process and the diversity and abundance of the mediating microbial community. In this study, we measured nutrient fluxes and rates of sediment nitrification in conjunction with the diversity and abundance of ammonia-oxidizing archaea (AOA...

  6. 古菌氨氧化与amoA基因的扩增%Archaeal Ammonia Oxidation and Amplification of amoA Gene

    Institute of Scientific and Technical Information of China (English)

    蒋敏芝; 黄秋雨

    2012-01-01

    Ammonia oxidation is a obligate aerobic: chemoautotrophic process taken by a small part bacterial community of Hymenomycetes. Ammonia-oxidizing bacteria (AOB) is a inorganic: autntrophic micro-organism, responsible for converting NH4+ to NO2- in the nitrification reaction, ammonia oxidizing archaea (AOA) is independent of the AOB clade. The paper introduced discovery and ammonia oxidation of AOA, extracted, purified and amplified amoA genes according to its features. The results confirmed exist of AOA, and provided basis for follow-up study.%氨氧化过程是由变形菌纲中的一小部分细菌类群所进行的专性好氧的化能自养过程,氨氧化细菌(AOB)是硝化反应中负责将NH4+转化为NO2-的一类无机自养微生物,氨氧化古菌(AOA)是独立于AOB进化枝之外的能进行氨氧化作用的古菌。介绍了AOA古菌的发现过程及其氨氧化作用,提取、纯化了amoA基因并利用amoA基因的特征,对它进行扩增,证实了AOA古菌的存在,并为后续研究提供了依据。

  7. The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys

    OpenAIRE

    Magalhães, Catarina M.; Machado, Ana; Frank-Fahle, Béatrice; Lee, Charles K; Cary, S. Craig

    2014-01-01

    The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Va...

  8. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations.

    OpenAIRE

    Rotthauwe, J H; K. P. WITZEL; Liesack, W.

    1997-01-01

    The naturally occurring genetic heterogeneity of autotrophic ammonia-oxidizing populations belonging to the beta subclass of the Proteobacteria was studied by using a newly developed PCR-based assay targeting a partial stretch of the gene which encodes the active-site polypeptide of ammonia monooxygenase (amoA). The PCR yielded a specific 491-bp fragment with all of the nitrifiers tested, but not with the homologous stretch of the particulate methane monooxygenase, a key enzyme of methane-oxi...

  9. Community shift of ammonia-oxidizing bacteria along an anthropogenic pollution gradient from the Pearl River Delta to the South China Sea

    OpenAIRE

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

    2012-01-01

    The phylogenetic diversity and abundance of ammonia-oxidizing beta-proteobacteria (beta-AOB) was analyzed along an anthropogenic pollution gradient from the coastal Pearl River Delta to the South China Sea using the ammonia monooxygenase subunit A (amoA) gene. Along the gradient from coastal to the open ocean, the phylogenetic diversity of the dominant genus changed from Nitrosomonas to Nitrosospira, indicating the niche specificity by these two genera as both salinity and anthropogenic influ...

  10. 3,4-Dimethylpyrazole phosphate (DMPP) reduces activity of ammonia oxidizers without adverse effects on non-target soil microorganisms and functions

    DEFF Research Database (Denmark)

    Kong, Xianwang; Duan, Yun-Feng (Kevin); Schramm, Andreas;

    2016-01-01

    The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is widely used within agriculture to reduce nitrate leaching and improve nitrogen use efficiency of fertilizers, but few studies examined effects on non-target soil functions and microorganisms, i.e. other than the intended delay of......, this study indicated that DMPP effectively inhibited nitrification activity without effects on ammonia oxidizer populations, as well as non-target soil microorganisms or functions....

  11. Responses of soil hydrolytic enzymes, ammonia-oxidizing bacteria and archaea to nitrogen applications in a temperate grassland in Inner Mongolia.

    Science.gov (United States)

    Zhang, Xinyu; Tang, Yuqian; Shi, Yao; He, Nianpeng; Wen, Xuefa; Yu, Qiang; Zheng, Chunyu; Sun, Xiaomin; Qiu, Weiwen

    2016-01-01

    We used a seven-year urea gradient applied field experiment to investigate the effects of nitrogen (N) applications on soil N hydrolytic enzyme activity and ammonia-oxidizing microbial abundance in a typical steppe ecosystem in Inner Mongolia. The results showed that N additions inhibited the soil N-related hydrolytic enzyme activities, especially in 392 kg N ha(-1 )yr(-1) treatment. As N additions increased, the amoA gene copy ratios of ammonia-oxidizing archaea (AOA) to ammonia-oxidizing bacteria (AOB) decreased from 1.13 to 0.65. Pearson correlation analysis showed that the AOA gene copies were negatively related with NH4(+)-N content. However, the AOB gene copies were positively correlated with NO3(-)-N content. Moderate N application rates (56-224 kg N ha(-1 )yr(-1)) accompanied by P additions are beneficial to maintaining the abundance of AOB, as opposed to the inhibition of highest N application rate (392 kg N ha(-1 )yr(-1)) on the abundance of AOB. This study suggests that the abundance of AOB and AOA would not decrease unless N applications exceed 224 kg N ha(-1 )yr(-1) in temperate grasslands in Inner Mongolia. PMID:27596731

  12. Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm.

    Science.gov (United States)

    Foesel, Bärbel U; Gieseke, Armin; Schwermer, Carsten; Stief, Peter; Koch, Liat; Cytryn, Eddie; de la Torré, José R; van Rijn, Jaap; Minz, Dror; Drake, Harold L; Schramm, Andreas

    2008-02-01

    Zero-discharge marine aquaculture systems are an environmentally friendly alternative to conventional aquaculture. In these systems, water is purified and recycled via microbial biofilters. Here, quantitative data on nitrifier community structure of a trickling filter biofilm associated with a recirculating marine aquaculture system are presented. Repeated rounds of the full-cycle rRNA approach were necessary to optimize DNA extraction and the probe set for FISH to obtain a reliable and comprehensive picture of the ammonia-oxidizing community. Analysis of the ammonia monooxygenase gene (amoA) confirmed the results. The most abundant ammonia-oxidizing bacteria (AOB) were members of the Nitrosomonas sp. Nm143-lineage (6.7% of the bacterial biovolume), followed by Nitrosomonas marina-like AOB (2.2% of the bacterial biovolume). Both were outnumbered by nitrite-oxidizing bacteria of the Nitrospira marina-lineage (15.7% of the bacterial biovolume). Although more than eight other nitrifying populations were detected, including Crenarchaeota closely related to the ammonia-oxidizer 'Nitrosopumilus maritimus', their collective abundance was below 1% of the total biofilm volume; their contribution to nitrification in the biofilter is therefore likely to be negligible. PMID:18093145

  13. A survey of 16S rRNA and amoA genes related to autotrophic ammonia-oxidizing bacteria of the beta-subdivision of the class proteobacteria in contaminated groundwater

    Energy Technology Data Exchange (ETDEWEB)

    Ivanova, I. A.; Stephen, J. R.; Chang, Y-J.; Bruggemann, J.; Macnaughton, S. J.; White, D. C. [Tennessee Univ., Center for Environmental Biotechnology, Knoxville, TN (United States); Long, P. E.; McKinley, J. P. [Pacific Northwest National Laboratory, Richland, WA (United States); Kowalchuk, G. A. [Netherlands Inst. of Ecology, Centre for Terrestrial Ecology, Heteren (Netherlands)

    2000-11-01

    Various genetic study methods were combined to profile beta-proteobacterial ammonia-oxidizing populations in ground water extracted from the subsurface of a contamination plume resulting from the disposal of tailings from a uranium mill at Shiprock, New Mexico. The objectives of this study were to characterize the ammonia-oxidizing populations at this site in terms of the diversity of dominant ammonia-oxidizing bacteria 16S and amoA genes, and to determine whether the ground water ammonia-oxidizing populations were linked to the dissolved nitrate concentration. Several studies have suggested that the genus Nitrosospira dominates over Nitrosomonas in bulk soil environments. Ammonia-oxidizing bacterial population sizes were estimated by competitive polymerase chain reaction targeting the gene amoA; it correlated significantly with nitrate concentration. Both 16S rDNA and amoA analyses suggested that all samples were dominated by Nitrosomonas over Nitrosospira in ground water, suggesting that ground water ammonia oxidizers are more like those dominating freshwater sediments than those dominant in bulk soil. It was concluded that the failure of the Shiprock site to remediate anthropogenic nitrogen is not likely to be related to the toxic effects of uranium on autotrophic nitrification. Indeed, it is more likely to be the result of factors such as the availability of organic carbon or other electron donors. 45 refs., 1 tab., 3 figs.

  14. Abundance and diversity of ammonia-oxidizing archaea in response to various habitats in Pearl River Delta of China, a subtropical maritime zone

    Institute of Scientific and Technical Information of China (English)

    Zhixin Li; Wenbiao Jin; Zhaoyun Liang; Yangyang Yue; Junhong Lv

    2013-01-01

    Ammonia-oxidizing archaea (AOA) are widely considered key to ammonia oxidation in various environments.However,little work has been conducted to simultaneously investigate the abundance and diversity of AOA as well as correlations between archaeal amoA genotypes and environmental parameters of different ecosystems at one district.To understand the abundance,diversity,and distribution of AOA in Pearl River Delta of China in response to various habitats,the archaeal amoA genes in soil,marine,river,lake,hot spring and wastewater treatment plant (WWTP) samples were investigated using real-time fluorescent quantitative PCR and clone libraries.Our analyses indicated that the diversity of AOA in various habitats was different and could be clustered into five major clades,i.e.,estuary sediment,marine water/sediment,soil,hot spring and Cluster 1.Phylogenetic analyses revealed that the structure of AOA communities in similar ecological habitats exhibited strong relation.The canonical correspondence method indicated that the AOA community structure was strongly correlated to temperature,pH,total organic carbon,total nitrogen and dissolved oxygen variables.Assessing AOA amoA gene copy numbers,ranging from 6.84 × 106 to 9.45 × 107 copies/g in dry soil/sediment,and 6.06 × 106 to 2.41 × 107 copies/L in water samples,were higher than ammonia-oxidizing bacteria (AOB) by 1-2 orders of magnitude.However,AOA amoA copy numbers were much lower than AOB in WWTP activated sludge samples.Overall,these studies suggested that AOA may be a major contributor to ammonia oxidation in natural habitats but play a minor role in highly aerated activated sludge.The result also showed the ratio of AOA to AOB amoA gene abundance was positively correlated with temperature and less correlated with other environmental parameters.New data from our study provide increasing evidence for the relative abundance and diversity of ammonia-oxidizing archaea in the global nitrogen cycle.

  15. Comparison of PCR-DGGE and Nested-PCR-DGGE Approach for Ammonia Oxidizers Monitoring in Membrane Bioreactors’ Activated Sludge

    Directory of Open Access Journals (Sweden)

    Ziembińska-Buczyńska Aleksandra

    2014-12-01

    Full Text Available Nitritation, the first stage of ammonia removal process is known to be limiting for total process performance. Ammonia oxidizing bacteria (AOB which perform this process are obligatory activated sludge habitants, a mixture consisting of Bacteria, Protozoa and Metazoa used for biological wastewater treatment. Due to this fact they are an interesting bacterial group, from both the technological and ecological point of view. AOB changeability and biodiversity analyses both in wastewater treatment plants and lab-scale reactors are performed on the basis of 16S rRNA gene sequences using PCR-DGGE (Polymerase Chain Reaction – Denaturing Gradient Gel Electrophoresis as a molecular biology tool. AOB researches are usually led with nested PCR. Because the application of nested PCR is laborious and time consuming, we have attempted to check the possibility of using only first PCR round to obtain DGGE fingerprinting of microbial communities. In this work we are comparing the nested and non-nested PCR-DGGE monitoring of an AOB community and presenting advantages and disadvantages of both methods used. The experiment revealed that PCR technique is a very sensitive tool for the amplification of even a minute amount of DNA sample. But in the case of nested-PCR, the sensitivity is higher and the template amount could be even smaller. The nested PCR-DGGE seems to be a better tool for AOB community monitoring and complexity research in activated sludge, despite shorter fragments of DNA amplification which seems to be a disadvantage in the case of bacteria identification. It is recommended that the sort of analysis approach should be chosen according to the aim of the study: nested-PCR-DGGE for community complexity analysis, while PCR-DGGE for identification of the dominant bacteria.

  16. Empowering a mesophilic inoculum for thermophilic nitrification: Growth mode and temperature pattern as critical proliferation factors for archaeal ammonia oxidizers.

    Science.gov (United States)

    Courtens, Emilie N P; Vandekerckhove, Tom; Prat, Delphine; Vilchez-Vargas, Ramiro; Vital, Marius; Pieper, Dietmar H; Meerbergen, Ken; Lievens, Bart; Boon, Nico; Vlaeminck, Siegfried E

    2016-04-01

    Cost-efficient biological treatment of warm nitrogenous wastewaters requires the development of thermophilic nitrogen removal processes. Only one thermophilic nitrifying bioreactor was described so far, achieving 200 mg N L(-1) d(-1) after more than 300 days of enrichment from compost samples. From the practical point of view in which existing plants would be upgraded, however, a more time-efficient development strategy based on mesophilic nitrifying sludge is preferred. This study evaluated the adaptive capacities of mesophilic nitrifying sludge for two linear temperature increase patterns (non-oscillating vs. oscillating), two different slopes (0.25 vs. 0.08 °C d(-1)) and two different reactor types (floc vs. biofilm growth). The oscillating temperature pattern (0.25 °C d(-1)) and the moving bed biofilm reactor (0.08 °C d(-1)) could not reach nitrification at temperatures higher than 46 °C. However, nitrification rates up to 800 mg N L(-1) d(-1) and 150 mg N g(-1) volatile suspended solids d(-1) were achieved at a temperature as high as 49 °C by imposing the slowest linear temperature increase to floccular sludge. Microbial community analysis revealed that this successful transition was related with a shift in ammonium oxidizing archaea dominating ammonia oxidizing bacteria, while for nitrite oxidation Nitrospira spp. was constantly more abundant than Nitrobacter spp.. This observation was accompanied with an increase in observed sludge yield and a shift in maximal optimum temperature, determined with ex-situ temperature sensitivity measurements, predicting an upcoming reactor failure at higher temperature. Overall, this study achieved nitrification at 49 °C within 150 days by gradual adaptation of mesophilic sludge, and showed that ex-situ temperature sensitivity screening can be used to monitor and steer the transition process. PMID:26841233

  17. Activity and Composition of Ammonia-Oxidizing Bacteria in an Aquic Brown Soil as Influenced by Land Use and Fertilization

    Institute of Scientific and Technical Information of China (English)

    YU Wan-Tai; XU Yong-Gang; BI Ming-Li; MA Qiang; ZHOU Hua

    2010-01-01

    The effects of long-term(19 years)different land use and fertilization on activity and composition of ammonia-oxidizing bacteria(AOB)in an aquic brown soil were investigated in a field experiment in Liaoning Province,China.The 19-year experiment conducted from 1990 to 2008 involved seven treatments designed: cropping rotation of soybean-corn-corn with no fertilizer(control,CK),recycled manure(RM),fertilizer nitrogen(N),phosphorous(P)and potassium(K)(NPK),NPK+RM,and no-crop bare land,mowed fallow,and non-mowed fallow.The results showed that the potential nitrification rates of the RM,NPK+RM,mowed fallow,and non-mowed fallow treatments were significantly higher(P < 0.05)than those of the CK and NPK treatments,indicating that the long-term applications of recycled manure and return of plant residues both significantly increased the activity of AOB.Although the application of NPK did not enhance soil potential nitrification because of decreased pH,available K had an important effect on potential nitrification.Denaturing gradient gel electrophoresis(DGGE)fingerprint profiles showed that no-crop treatments had an increase in the diversity of the AOB community compared to the CK,RM,and NPK treatments,implying that agricultural practices,especially tillage,had an adverse effect on the soil AOB community.The NPK+RM treatment had the most diverse DGGE patterns possibly because of the increased available P in this treatment.A phylogenetic analysis showed that most of the DGGE bands derived belonged to Nitrosoxpira cluster 3,not Nitrosospira cluster 2.These demonstrated that different land use and fertilization significantly influenced the activity and composition of the AOB community by altering the soil properties,mainly including pH,total C,available K,and available P.

  18. The effect of dissolved oxygen on N2O production by ammonia-oxidizing bacteria in an enriched nitrifying sludge.

    Science.gov (United States)

    Peng, Lai; Ni, Bing-Jie; Erler, Dirk; Ye, Liu; Yuan, Zhiguo

    2014-12-01

    Dissolved oxygen (DO) is commonly recognized as an important factor influencing nitrous oxide (N2O) production by ammonia-oxidizing bacteria (AOB). However, it has been difficult to separate the true effect of DO from that of nitrite, as DO variation often affects nitrite accumulation. The effect of DO on N2O production by an enriched nitrifying sludge, consisting of both AOB and nitrite-oxidizing bacteria (NOB), was investigated in this study. Nitrite accumulation was minimised by augmenting nitrite oxidation through the addition of an enriched NOB sludge. It was demonstrated that the specific N2O production rate increased from 0 to 1.9 ± 0.09 (n = 3) mg N2O-N/hr/g VSS with an increase of DO concentration from 0 to 3.0 mg O2/L, whereas N2O emission factor (the ratio between N2O nitrogen emitted and the ammonium nitrogen converted) decreased from 10.6 ± 1.7% (n = 3) at DO = 0.2 mg O2/L to 2.4 ± 0.1% (n = 3) at DO = 3.0 mg O2/L. The site preference measurements indicated that both the AOB denitrification and hydroxylamine (NH2OH) oxidation pathways contributed to N2O production, and DO had an important effect on the relative contributions of the two pathways. This finding is supported by analysis of the process data using an N2O model describing both pathways. As DO increased from 0.2 to 3.0 mg O2/L, the contribution of AOB denitrification decreased from 92% - 95%-66% - 73%, accompanied by a corresponding increase in the contribution by the NH2OH oxidation pathway. PMID:25179869

  19. Comparison of water availability effect on ammonia-oxidizing bacteria and archaea in microcosms of a Chilean semiarid soil

    Directory of Open Access Journals (Sweden)

    Mauricio eBustamante

    2012-08-01

    Full Text Available Water availability is the main limiting factor in arid soils; however few studies have examined the effects of drying and rewetting on nitrifiers from these environments. The effect of water availability on the diversity of ammonia-oxidizing bacteria (AOB and archaea (AOA from a semiarid soil of the Chilean sclerophyllous matorral was determined by microcosm assays. The addition of water every 14 days to reach 60% of the WHC significantly increased nitrate content in rewetted soil microcosms (p<0.001. This stimulation of net nitrification by water addition was inhibited by acetylene addition at 100 Pa. The composition of AOA and AOB assemblages from the soils microcosms was determined by clone sequencing of amoA genes (A-amoA and B-amoA, respectively, and the 16S rRNA genes specific for β-proteobacteria (beta-amo. Sequencing of beta-amo genes has revealed representatives of Nitrosomonas and Nitrosospira while B-amoA clones consisted only of Nitrosospira sequences. Furthermore, all clones from the archaeal amoA gene library (A-amoA were related to ‘mesophilic Crenarchaeota’ sequences (actually, reclassified as the phylum Thaumarchaeota. The effect of water availability on both microbial assemblages structure was determined by T-RFLP profiles using the genetic markers amoA for archaea, and beta-amo for bacteria. While AOA showed fluctuations in some T-RFs, AOB structure remained unchanged by water pulses. The relative abundance of AOA and AOB was estimated by the Most Probable Number coupled to Polymerase Chain Reaction (MPN-PCR assay. AOB was the predominant guild in this soil and higher soil water content did not affect their abundance, in contrast to AOA, which slightly increased under these conditions. Therefore, these results suggest that water addition to these semiarid soil microcosms could favor archaeal contribution to ammonium oxidation.

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

    Directory of Open Access Journals (Sweden)

    Xuefeng ePeng

    2013-07-01

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

  1. Chemoautotrophic growth of ammonia-oxidizing Thaumarchaeota enriched from a pelagic redox gradient in the Baltic Sea

    Directory of Open Access Journals (Sweden)

    Carlo eBerg

    2015-01-01

    Full Text Available Ammonia-oxidizing archaea (AOA are an important component of the planktonic community in aquatic habitats, linking nitrogen and carbon cycles through nitrification and carbon fixation. Therefore, measurements of these processes in culture-based experiments can provide insights into their contributions to energy conservation and biomass production by specific AOA. In this study, by enriching AOA from a brackish, oxygen-depleted water-column in the Landsort Deep, central Baltic Sea, we were able to investigate ammonium oxidation, chemoautotrophy, and growth in seawater batch experiments. The highly enriched culture consisted of up to 97% archaea, with maximal archaeal numbers of 2.9 × 107 cells mL-1. Phylogenetic analysis of the 16S rRNA and ammonia monooxygenase subunit A (amoA gene sequences revealed an affiliation with assemblages from low-salinity and freshwater habitats, with Candidatus Nitrosoarchaeum limnia as the closest relative. Growth correlated significantly with nitrite production, ammonium consumption, and CO2 fixation, which occurred at a ratio of 10 atoms N oxidized per 1 atom C fixed. According to the carbon balance, AOA biomass production can be entirely explained by chemoautotrophy. The cellular carbon content was estimated to be 9 fg C per cell. Single-cell-based 13C and 15N labeling experiments and analysis by nano-scale secondary ion mass spectrometry provided further evidence that cellular carbon was derived from bicarbonate and that ammonium was taken up by the cells. Our study therefore revealed that growth by an AOA belonging to the genus Nitrosoarchaeum can be sustained largely by chemoautotrophy.

  2. 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.

  3. Shifts in Abundance and Diversity of Soil Ammonia-Oxidizing Bacteria and Archaea Associated with Land Restoration in a Semi-Arid Ecosystem.

    Science.gov (United States)

    Chen, Zhu; Wu, Wenliang; Shao, Xiaoming; Li, Li; Guo, Yanbin; Ding, Guochun

    2015-01-01

    The Grain to Green Project (GGP) is an unprecedented land restoration action in China. The project converted large areas (ca 10 million ha) of steep-sloped/degraded farmland and barren land into forest and grassland resulting in ecological benefits such as a reduction in severe soil erosion. It may also affect soil microorganisms involved in ammonia oxidization, which is a key step in the global nitrogen cycle. The methods for restoration that are typically adopted in semi-arid regions include abandoning farmland and growing drought tolerant grass (Lolium perenne L.) or shrubs (Caragana korshinskii Kom.). In the present study, the effects of these methods on the abundance and diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were evaluated via quantitative real-time PCR, terminal restriction fragment length polymorphism and clone library analysis of amoA genes. Comparisons were made between soil samples from three restored lands and the adjacent farmland in Inner Mongolia. Both the abundance and community composition of AOB were significantly different between the restored lands and the adjacent control. Significantly lower nitrification activity was observed for the restored land. Clone library analysis revealed that all AOB amoA gene sequences were affiliated with Nitrosospira. Abundance of the populations that were associated with Nitrosospira sp. Nv6 which had possibly adapted to high concentrations of inorganic nitrogen, decreased on the restored land. Only a slight difference in the AOB communities was observed between the restored land with and without the shrub (Caragana korshinskii Kom.). A minor effect of land restoration on AOA was observed. In summary, land restoration negatively affected the abundance of AOB and soil nitrification activities, suggesting the potential role of GGP in the leaching of nitrates, and in the emission of N2O in related terrestrial ecosystems. PMID:26172994

  4. Shifts in Abundance and Diversity of Soil Ammonia-Oxidizing Bacteria and Archaea Associated with Land Restoration in a Semi-Arid Ecosystem.

    Directory of Open Access Journals (Sweden)

    Zhu Chen

    Full Text Available The Grain to Green Project (GGP is an unprecedented land restoration action in China. The project converted large areas (ca 10 million ha of steep-sloped/degraded farmland and barren land into forest and grassland resulting in ecological benefits such as a reduction in severe soil erosion. It may also affect soil microorganisms involved in ammonia oxidization, which is a key step in the global nitrogen cycle. The methods for restoration that are typically adopted in semi-arid regions include abandoning farmland and growing drought tolerant grass (Lolium perenne L. or shrubs (Caragana korshinskii Kom.. In the present study, the effects of these methods on the abundance and diversity of ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA were evaluated via quantitative real-time PCR, terminal restriction fragment length polymorphism and clone library analysis of amoA genes. Comparisons were made between soil samples from three restored lands and the adjacent farmland in Inner Mongolia. Both the abundance and community composition of AOB were significantly different between the restored lands and the adjacent control. Significantly lower nitrification activity was observed for the restored land. Clone library analysis revealed that all AOB amoA gene sequences were affiliated with Nitrosospira. Abundance of the populations that were associated with Nitrosospira sp. Nv6 which had possibly adapted to high concentrations of inorganic nitrogen, decreased on the restored land. Only a slight difference in the AOB communities was observed between the restored land with and without the shrub (Caragana korshinskii Kom.. A minor effect of land restoration on AOA was observed. In summary, land restoration negatively affected the abundance of AOB and soil nitrification activities, suggesting the potential role of GGP in the leaching of nitrates, and in the emission of N2O in related terrestrial ecosystems.

  5. Fluctuations in ammonia oxidizing communities across agricultural soils are driven by soil structure and pH

    Directory of Open Access Journals (Sweden)

    Michele C ePereira e Silva

    2012-03-01

    Full Text Available The milieu in soil in which microorganisms dwell is never constant. Conditions such as temperature, water availability, pH and nutrients frequently change, impacting the overall functioning of the soil system. To understand the effects of such factors on soil functioning, proxies (indicators of soil function are needed that, in a sensitive manner, reveal normal amplitude of variation. Thus, the so-called normal operating range (NOR of soil can be defined. In this study we determined different components of nitrification by analyzing, in eight agricultural soils, how the community structures and sizes of ammonia oxidizing bacteria and archaea (AOB and AOA, respectively, and their activity, fluctuate over spatial and temporal scales. The results indicated that soil pH and soil type are the main factors that influence the size and structure of the AOA and AOB, as well as their function. The nitrification rates varied between 0.11 ± 0.03 µgN.h-1.gdw-1 and 1.68 ± 0.11 µgN.h-1.gdw-1, being higher in soils with higher clay content (1.09 ± 0.12 µgN.h-1.gdw-1 and lower in soils with lower clay percentages (0.27 ± 0.04 µgN.h-1.gdw-1. Nitrifying activity was driven by soil pH, mostly related to its effect on AOA but not on AOB abundance. Regarding the influence of soil parameters, clay content was the main soil factor shaping the structure of both the AOA and AOB communities. Overall, the potential nitrifying activities were higher and more variable over time in the clayey than in the sandy soils. Whereas the structure of AOB fluctuated more (62.7 ± 2.10% the structure of AOA communities showed lower amplitude of variation (53.65 ± 3.37%. Similar trends were observed for the sizes of these communities. The present work represents a first step towards defining a NOR for soil nitrification. Moreover, the clear effect of soil texture established here suggests that the NOR should be defined in a soil-type-specific manner.

  6. Ammonia Oxidizing, Nitrite Reducing Bacteria and the Cycling of Nitrous Oxide in the Oxygen Minimum Zone (OMZ) of the Eastern South Pacific

    Science.gov (United States)

    Molina, V.; Castro-González, M.; Farías, L.; Farías, L.; Ulloa, O.; Braker, G.; Witzel, K.

    2004-12-01

    The distribution of nitrous oxide, oxygen, nitrite and nitrate, and 16S rDNA and functional genes (amoA,nirS) richness of ammonia oxidizing (AOB) and nitrite reducing bacteria (NRB) were studied in the water column of one of the shallowest (8 μ M) is also present at the OMZ core. The relationship among apparent oxygen utilization (AOU), apparent nitrous oxide production, and nitrate distribution allowed the differentiation among nitrification, denitrification, and the coupling between both, at AOU values of 230 and 200-230 μ mol kg-1, respectively. The richness of the AOB ribotypes (DGGE) and the NRB {it\

  7. Polygenic analysis of ammonia-oxidizing bacteria using 16S rDNA, amoA, and amoB genes

    OpenAIRE

    Calvó Perxas, Laia; Cortey Marqués, Martí; García Marín, José Luis; Garcia-Gil, L. J.

    2005-01-01

    Finding a unique molecular marker capable of quickly providing rigorous and useful phylogenetic information would facilitate assessing the diversity of ammonia-oxidizing bacteria in environmental samples. Since only one of several available markers can be used at a time in these kinds of studies, the 16S rDNA, amoA and amoB genes were evaluated individually and then compared in order to identify the one that best fits the information provided by the composite dataset. Distance-based neighbor-...

  8. Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen.

    Science.gov (United States)

    Song, He; Che, Zhao; Cao, Wenchao; Huang, Ting; Wang, Jingguo; Dong, Zhaorong

    2016-06-01

    Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation. PMID:26961528

  9. Characteristics of ammonia-oxidizing bacteria and ammonia-oxidizing archaea abundance in soil organic layer under the subalpine/alpine forest%亚高山/高山森林土壤有机层氨氧化细菌和氨氧化古菌丰度特征

    Institute of Scientific and Technical Information of China (English)

    王奥; 吴福忠; 何振华; 徐振锋; 刘洋; 谭波; 杨万勤

    2012-01-01

    Soil ammonia oxidizers play essential roles in nitrogen cycling in many forest ecosystems. Since the compositions and functions of soil ammonia oxidizer could be suffered from obviously seasonal snow cover and freeze-thaw cycles in high latitude/altitude region, there might be significant differences of soil ammonia oxidizer in different periods caused by seasonal freeze-thaw cycles. However, little attention has been paid to the variations of soil ammonia oxidizer in different key periods in subalpine/alpine regions. To determine the abundance and distribution of bacterial and archaeal ammonia oxidizers in subalpine and alpine forest, three representative forests ( primitive Abies faxoniana forest, PF; mixed A. faxoniana and Betula albosinensis forest, MF, and secondary A. faxoniana forest, SF) were selected in the alipine/ subalpine region of Western China. Soils were sampled in soil organic layer (OL) due to the sensitive responses to seasonal climate changes. Richness of ammonia oxidizers (ammonia-oxidizing bacteria, AOB; and ammonia-oxidizing archaea, AOA) in soil organic layer were characterized by a real-time quantitative PCR method from targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. Based on previous investigations, we focused on nine key stages go through three periods as soil temperature varied ( 1 ) Growing period: including early growing stage, growing stage, and later growing stage. (2 ) Freeze period; including early freezing stage, freezing stage, and later frozen stage. ( 3 ) Thawing period: including early thawing stage, thawing stage and later thawing stage. Amounts of bacterial and archaeal amok gene were detected in soil organic layer under three subalpine and alpine forests. The abundance of both bacterial and archaeal amoA showed similar tendency in different key stages, which significantly decreased from growing period to freeze period and then significantly increased, suggesting the strongly effects of

  10. 牛粪堆肥高温期氨氧化古菌与氨氧化细菌的多样性分析%Diversity of Ammonia-Oxidizing Bacteria and Ammonia-Oxidizing Archaea at High Temperature Phase during the Livestock Manure Composting Process

    Institute of Scientific and Technical Information of China (English)

    孙志远; 晏磊; 王彦杰; 林匡飞; 李辉; 王伟东

    2013-01-01

    The transmutation and loss of nitrogen materials were effected significantly by ammonia-oxidizing microorganisms during the composting process. In order to detect the diversity of Ammonia-Oxidizing Archaea (AOA)and Ammonia-Oxidizing Bacteria (AOB),the monooxygenase gene (amoA)was used to analyze as the tag at high-temperature phase during the livestock manure composting process. The results showed that Nitrosomonas genus and Nitrosospira genus were the dominant genus of AOB,and the amount of clones accounted for 59.3% and 40.7% among the clone library at the high-temperature period,respectively,and the amount of Nitrosomonas was more dominant than that of the Nitrosospira. For communities of AOA,the amount of AOA resulting from soil were greatly more than that of AOA resulting from sea. The ratio of clones of soil AOA was 94.2%,but the ratio of sea AOA accounted for only 5.8%among all of AOA clones.%堆肥化过程中,氨氧化微生物对堆肥原料的氮素转化和氮损失影响重大。为了分析牛粪堆肥高温期微生物的多样性,研究以氨单加氧酶基因(amoA)为标记,分析了牛粪堆肥高温阶段氨氧化古菌(Ammonia-Oxidizing Archaea,AOA)和氨氧化细菌(Ammonia-Oxidizing Bacteria,AOB)菌群多样性。结果表明,在AOB类群中,亚硝化单胞菌属(Nitrosomonas)和亚硝化螺菌属(Nitrosospira)克隆子数量分别占整个克隆文库的59.3%和40.7%,它们是堆肥高温期的优势氨氧化细菌,但是Nitrosomonas的数量比Nitrosospira更占优势。在AOA群落中,soil/sediment菌群占据绝对数量优势,其克隆子数量占AOA文库的94.2%,sea/sediment菌群仅占5.8%。

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Science.gov (United States)

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

    2015-10-01

    The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (a Variovorax sp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was a Nitrospira sp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; amoA genes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB. PMID:26209671

  13. A novel control method for nitritation: The domination of ammonia-oxidizing bacteria by high concentrations of inorganic carbon in an airlift-fluidized bed reactor.

    Science.gov (United States)

    Tokutomi, Takaaki; Shibayama, Chizu; Soda, Satoshi; Ike, Michihiko

    2010-07-01

    A novel nitritation method based on the addition of inorganic carbon (IC) was verified using an airlift-fluidized bed reactor packed with sponge cubes. A continuous-treatment experiment demonstrated that the type of nitrification-nitrite or nitrate accumulation-could be controlled by the addition of different alkalinity sources (NaHCO(3) or NaOH, respectively). The maximum rate of ammonia oxidation at 30 degrees C was 2.47kg-N/(m(3) d), with nitrate formation of less than 0.5% of the converted ammonia. Nitrite accumulation of over 90% was maintained stably over 250 days at 30 degrees C and was achieved even at 19 degrees C. Qualitative and quantitative shifts of nitrifying bacteria in the biofilm were monitored by real-time PCR and T-RFLP analysis. Ammonia-oxidizing bacteria (AOB) were dominant but nitrite-oxidizing bacteria (NOB) were eliminated in the reactor when NaHCO(3) was used as the alkalinity source. From the kinetic data, we inferred that high IC concentrations drive stable nitritation by promoting a higher growth rate for AOB than for NOB. PMID:20554306

  14. High abundances of potentially active ammonia-oxidizing bacteria and archaea in oligotrophic, high-altitude lakes of the Sierra Nevada, California, USA.

    Directory of Open Access Journals (Sweden)

    Curtis J Hayden

    Full Text Available Nitrification plays a central role in the nitrogen cycle by determining the oxidation state of nitrogen and its subsequent bioavailability and cycling. However, relatively little is known about the underlying ecology of the microbial communities that carry out nitrification in freshwater ecosystems--and particularly within high-altitude oligotrophic lakes, where nitrogen is frequently a limiting nutrient. We quantified ammonia-oxidizing archaea (AOA and bacteria (AOB in 9 high-altitude lakes (2289-3160 m in the Sierra Nevada, California, USA, in relation to spatial and biogeochemical data. Based on their ammonia monooxygenase (amoA genes, AOB and AOA were frequently detected. AOB were present in 88% of samples and were more abundant than AOA in all samples. Both groups showed >100 fold variation in abundance between different lakes, and were also variable through time within individual lakes. Nutrient concentrations (ammonium, nitrite, nitrate, and phosphate were generally low but also varied across and within lakes, suggestive of active internal nutrient cycling; AOB abundance was significantly correlated with phosphate (r(2 = 0.32, p<0.1, whereas AOA abundance was inversely correlated with lake elevation (r(2 = 0.43, p<0.05. We also measured low rates of ammonia oxidation--indicating that AOB, AOA, or both, may be biogeochemically active in these oligotrophic ecosystems. Our data indicate that dynamic populations of AOB and AOA are found in oligotrophic, high-altitude, freshwater lakes.

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

    Science.gov (United States)

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

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

  16. Mo-Bi系丙烯氨氧化催化剂上氨分解反应动力学的Monte Carlo模拟%Monte Carlo Simulation of Kinetics of Ammonia Oxidative Decomposition over the Commercial Propylene Ammoxidation Catalyst (Mo-Bi)

    Institute of Scientific and Technical Information of China (English)

    罗正鸿; 詹晓力; 陈丰秋; 阳永荣

    2003-01-01

    Monte Carlo method is applied to investigate the kinetics of ammonia oxidative decomposition overthe commercial propylene ammoxidation catalyst(Mo-Bi). The simulation is quite in agreement with experimentalresults. Monte Carlo simulation proves that the process of ammonia oxidation decomposition is a two-step reaction.

  17. Archaeal ammonia oxidizers respond to soil factors at smaller spatial scales than the overall archaeal community does in a high Arctic polar oasis.

    Science.gov (United States)

    Banerjee, Samiran; Kennedy, Nabla; Richardson, Alan E; Egger, Keith N; Siciliano, Steven D

    2016-06-01

    Archaea are ubiquitous and highly abundant in Arctic soils. Because of their oligotrophic nature, archaea play an important role in biogeochemical processes in nutrient-limited Arctic soils. With the existing knowledge of high archaeal abundance and functional potential in Arctic soils, this study employed terminal restriction fragment length polymorphism (t-RFLP) profiling and geostatistical analysis to explore spatial dependency and edaphic determinants of the overall archaeal (ARC) and ammonia-oxidizing archaeal (AOA) communities in a high Arctic polar oasis soil. ARC communities were spatially dependent at the 2-5 m scale (P diversity indices of both ARC and AOA communities showed high spatial dependency along the landscape and resembled scaling of edaphic factors. The spatial link between archaeal community structure and soil resources found in this study has implications for predictive understanding of archaea-driven processes in polar oases. PMID:27045904

  18. Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina -like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm

    DEFF Research Database (Denmark)

    Foesel, Bärbel U.; Gieseke, Armin; Schwermer, Carsten;

    2008-01-01

    recirculating marine aquaculture system are presented. Repeated rounds of the full-cycle rRNA approach were necessary to optimize DNA extraction and the probe set for FISH to obtain a reliable and comprehensive picture of the ammonia-oxidizing community. Analysis of the ammonia monooxygenase gene (amoA...

  19. A survey of 16S rRNA and amoA genes related to autotrophic ammonia-oxidizing bacteria of the ß-subdivision of the class proteobacteria in contaminated groundwater

    NARCIS (Netherlands)

    Ivanova, I.A.; Stephen, J.R.; Chang, Y.J.; Bruggemann, J.; Long, P.E.; McKinley, J.P.; Kowalchuk, G.A.; White, D.C.; MacNaughton, S.J.

    2000-01-01

    In this study, we investigated the size and structure of autotrophic ammonia oxidizer (AAO) communities in the groundwater of a contamination plume originating from a mill- tailings disposal site. The site has high levels of dissolved N from anthropogenic sources, and exhibited wide variations in th

  20. Irrigation water salinity and N fertilization:Effects on ammonia oxidizer abundance, enzyme activity and cotton growth in a drip irrigated cotton ifeld

    Institute of Scientific and Technical Information of China (English)

    MIN Wei; GUO Hui-juan; ZHANG Wen; ZHOU Guang-wei; MA Li-juan; YE Jun; HOU Zhen-an

    2016-01-01

    Use of saline water in irrigated agriculture has become an important means for aleviating water scarcity in arid and semi-arid regions. The objective of this ifeld experiment was to evaluate the effects of irrigation water salinity and N fertilization on soil physicochemical and biological properties related to nitriifcation and denitriifcation. A 3×2 factorial design was used with three levels of irrigation water salinity (0.35, 4.61 and 8.04 dS m–1) and two N rates (0 and 360 kg N ha–1). The results indicated that irrigation water salinity and N fertilization had signiifcant effects on many soil physicochemical properties including water content, salinity, pH, NH4-N concentration, and NO3-N concentration. The abundance (i.e., gene copy number) of ammo-nia-oxidizing archaea (AOA) was greater than that of ammonia-oxidizing bacteria (AOB) in al treatments. Irrigation water salinity had no signiifcant effect on the abundance of AOA or AOB in unfertilized plots. However, saline irrigation water (i.e., the 4.61 and 8.04 dS m–1 treatments) reduced AOA abundance, AOB abundance and potential nitriifcation rate in N fertilized plots. Regardless of N application rate, saline irrigation water increased urease activity but reduced the activities of both nitrate reductase and nitrite reductase. Irrigation with saline irrigation water signiifcantly reduced cotton biomass, N uptake and yield. Nitrogen application exacerbated the negative effect of saline water. These results suggest that brackish water and saline water irrigation could signiifcantly reduce both the abundance of ammonia oxidizers and potential nitriifcation rates. The AOA may play a more important role than AOB in nitriifcation in desert soil.

  1. Microbial ecology of á-Proteobacteria ammonia-oxidizers along a concentration gradient of dry atmospheric nitrogen deposition in the San Bernadino Mountain Range.

    Science.gov (United States)

    Jordan, F. L.; Fenn, M. E.; Stein, L. Y.

    2002-12-01

    The fate of atmospherically-deposited nitrogen from industrial pollution is of major concern in the montane ecosystems bordering the South Coast California Air Basin. Nitrogen deposition rates in the more exposed regions of the San Bernardino Mountains (SBM) are among the highest in North America often exceeding 40 kg ha-1 year-1 in throughfall deposition of nitrate and ammonium (Fenn and Poth, 1999). Forest ecosystems with elevated N deposition generally exhibit elevated accumulation of soil nitrate, leaching and runoff, elevated emissions of nitrogenous gases, increased nitrification, and decreased litter decomposition rates. The role of nitrifying microbial populations, especially those taxonomically associated with the beta-Proteobacteria ammonia-oxidizers (AOB), will provide insight into nitrogen-cycling in these extremely N-saturated environments. Using 16S ribosomal DNA-based molecular techniques (16S rDNA clone library construction and Restriction Fragment Length Polymorphism), we are comparing AOB community diversity at 3 different locations along a natural atmospheric N-deposition concentration gradient in the SBM: from high at Camp Paviaka (CP), medium at Strawberry Peak (SP) to low at Dogwood (DW). As observed for wet N-deposition systems on the east coast, we hypothesized a negative correlation between AOB community diversity, abundance and function with nitrogen loading in the dry N deposition system of SBM. Nitrification potentials determined for the 3 sites along the N-deposition gradient were in the order of CP less than SP less than DW. Preliminary results indicate no correlation between diversity of AOB and increased nitrogen loading. Shannon-Weiner diversity indices calculated for ammonia-oxidizer RFLP group units were 2.22, 2.66 and 1.80 for CP, SP and DW, respectively.

  2. Differential distribution patterns of ammonia-oxidizing archaea and bacteria in acidic soils of Nanling National Nature Reserve forests in subtropical China.

    Science.gov (United States)

    Gan, Xian-Hua; Zhang, Fang-Qiu; Gu, Ji-Dong; Guo, Yue-Dong; Li, Zhao-Qing; Zhang, Wei-Qiang; Xu, Xiu-Yu; Zhou, Yi; Wen, Xiao-Ying; Xie, Guo-Guang; Wang, Yong-Feng

    2016-02-01

    In addition to ammonia-oxidizing bacteria (AOB) the more recently discovered ammonia-oxidizing archaea (AOA) can also oxidize ammonia, but little is known about AOA community structure and abundance in subtropical forest soils. In this study, both AOA and AOB were investigated with molecular techniques in eight types of forests at surface soils (0-2 cm) and deep layers (18-20 cm) in Nanling National Nature Reserve in subtropical China. The results showed that the forest soils, all acidic (pH 4.24-5.10), harbored a wide range of AOA phylotypes, including the genera Nitrosotalea, Nitrososphaera, and another 6 clusters, one of which was reported for the first time. For AOB, only members of Nitrosospira were retrieved. Moreover, the abundance of the ammonia monooxygenase gene (amoA) from AOA dominated over AOB in most soil samples (13/16). Soil depth, rather than forest type, was an important factor shaping the community structure of AOA and AOB. The distribution patterns of AOA and AOB in soil layers were reversed: AOA diversity and abundances in the deep layers were higher than those in the surface layers; on the contrary, AOB diversity and abundances in the deep layers were lower than those in the surface layers. Interestingly, the diversity of AOA was positively correlated with pH, but negatively correlated with organic carbon, total nitrogen and total phosphorus, and the abundance of AOA was negatively correlated with available phosphorus. Our results demonstrated that AOA and AOB were differentially distributed in acidic soils in subtropical forests and affected differently by soil characteristics. PMID:26626057

  3. The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys

    Directory of Open Access Journals (Sweden)

    Catarina Maria Magalhães

    2014-09-01

    Full Text Available The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA and bacteria (AOB in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four Dry Valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity. Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA, revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints.

  4. Abundance and diversity of ammonia-oxidizing archaea and bacteria in sediments of trophic end members of the Laurentian Great Lakes, Erie and Superior.

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    Annette Bollmann

    Full Text Available Ammonia oxidation is the first step of nitrification carried out by ammonia-oxidizing Archaea (AOA and Bacteria (AOB. Lake Superior and Erie are part of the Great Lakes system differing in trophic status with Lake Superior being oligotrophic and Lake Erie meso- to eutrophic. Sediment samples were collected from both lakes and used to characterize abundance and diversity of AOA and AOB based on the ammonia monooxygenase (amoA gene. Diversity was accessed by a pyro-sequencing approach and the obtained sequences were used to determine the phylogeny and alpha and beta diversity of the AOA and AOB populations. In Lake Erie copy numbers of bacterial amoA genes were in the same order of magnitude or even higher than the copy numbers of the archaeal amoA genes, while in Lake Superior up to 4 orders of magnitude more archaeal than bacterial amoA copies were detected. The AOB detected in the samples from Lake Erie belonged to AOB that are frequently detected in freshwater. Differences were detected between the phylogenetic affiliations of the AOA from the two lakes. Most sequences detected in Lake Erie clustered in the Nitrososphaera cluster (Thaumarchaeal soil group I.1b where as most of the sequences in Lake Superior were found in the Nitrosopumilus cluster (Thaumarchaeal marine group I.1a and the Nitrosotalea cluster. Pearson correlations and canonical correspondence analysis (CCA showed that the differences in abundance and diversity of AOA are very likely related to the sampling location and thereby to the different trophic states of the lakes.

  5. Land Spreading of Wastewaters from the Fruit-Packaging Industry and Potential Effects on Soil Microbes: Effects of the Antioxidant Ethoxyquin and Its Metabolites on Ammonia Oxidizers.

    Science.gov (United States)

    Papadopoulou, Evangelia S; Tsachidou, Bella; Sułowicz, Sławomir; Menkissoglu-Spiroudi, Urania; Karpouzas, Dimitrios G

    2016-01-01

    Thiabendazole (TBZ), imazalil (IMZ), ortho-phenylphenol (OPP), diphenylamine (DPA), and ethoxyquin (EQ) are used in fruit-packaging plants (FPP) with the stipulation that wastewaters produced by their application would be depurated on site. However, no such treatment systems are currently in place, leading FPP to dispose of their effluents in agricultural land. We investigated the dissipation of those pesticides and their impact on soil microbes known to have a key role on ecosystem functioning. OPP and DPA showed limited persistence (50% dissipation time [DT50], 0.6 and 1.3 days) compared to TBZ and IMZ (DT50, 47.0 and 150.8 days). EQ was rapidly transformed to the short-lived quinone imine (QI) (major metabolite) and the more persistent 2,4-dimethyl-6-ethoxyquinoline (EQNL) (minor metabolite). EQ and OPP exerted significant inhibition of potential nitrification, with the effect of the former being more persistent. This was not reflected in the abundance (determined by quantitative PCR [qPCR]) of the amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Considering the above discrepancy and the metabolic pattern of EQ, we further investigated the hypothesis that its metabolites and not only EQ were toxic to ammonia oxidizers. Potential nitrification, amoA gene abundance, and amoA gene transcripts of AOB and AOA showed that QI was probably responsible for the inhibition of nitrification. Our findings have serious ecological and practical implications for soil productivity and N conservation in agriculturally impacted ecosystems and stress the need to include metabolites and RNA-based methods when the soil microbial toxicity of pesticides is assessed. PMID:26590271

  6. Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans in response to ammonia enrichment and more oxic conditions

    Directory of Open Access Journals (Sweden)

    Hendrikus J. Laanbroek

    2013-11-01

    Full Text Available In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans, the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e. Cluster 1 and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA. Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests.

  7. High cell density cultivation of the chemolithoautotrophic bacterium Nitrosomonas europaea.

    Science.gov (United States)

    Papp, Benedek; Török, Tibor; Sándor, Erzsébet; Fekete, Erzsébet; Flipphi, Michel; Karaffa, Levente

    2016-05-01

    Nitrosomonas europaea is a chemolithoautotrophic nitrifier, a gram-negative bacterium that can obtain all energy required for growth from the oxidation of ammonia to nitrite, and this may be beneficial for various biotechnological and environmental applications. However, compared to other bacteria, growth of ammonia oxidizing bacteria is very slow. A prerequisite to produce high cell density N. europaea cultures is to minimize the concentrations of inhibitory metabolic by-products. During growth on ammonia nitrite accumulates, as a consequence, N. europaea cannot grow to high cell concentrations under conventional batch conditions. Here, we show that single-vessel dialysis membrane bioreactors can be used to obtain substantially increased N. europaea biomasses and substantially reduced nitrite levels in media initially containing high amounts of the substrate. Dialysis membrane bioreactor fermentations were run in batch as well as in continuous mode. Growth was monitored with cell concentration determinations, by assessing dry cell mass and by monitoring ammonium consumption as well as nitrite formation. In addition, metabolic activity was probed with in vivo acridine orange staining. Under continuous substrate feed, the maximal cell concentration (2.79 × 10(12)/L) and maximal dry cell mass (0.895 g/L) achieved more than doubled the highest values reported for N. europaea cultivations to date. PMID:26358065

  8. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations.

    Science.gov (United States)

    Rotthauwe, J H; Witzel, K P; Liesack, W

    1997-12-01

    The naturally occurring genetic heterogeneity of autotrophic ammonia-oxidizing populations belonging to the beta subclass of the Proteobacteria was studied by using a newly developed PCR-based assay targeting a partial stretch of the gene which encodes the active-site polypeptide of ammonia monooxygenase (amoA). The PCR yielded a specific 491-bp fragment with all of the nitrifiers tested, but not with the homologous stretch of the particulate methane monooxygenase, a key enzyme of methane-oxidizing bacteria. The assay also specifically detected amoA in DNA extracted from various aquatic and terrestrial environments. The resulting PCR products retrieved from rice roots, activated sludge, a freshwater sample, and an enrichment culture were used for the generation of amoA gene libraries. No false positives were detected in a set of 47 randomly selected clone sequences that were analyzed further. The majority of the environmental sequences retrieved from rice roots and activated sludge grouped within the phylogenetic radiation defined by cultured strains of the genera Nitrosomonas and Nitrosospira. The comparative analysis identified members of both of these genera in activated sludge; however, only Nitrosospira-like sequences with very similar amino acid patterns were found on rice roots. Further differentiation of these molecular isolates was clearly possible on the nucleic acid level due to the accumulation of synonymous mutations, suggesting that several closely related but distinct Nitrosospira-like populations are the main colonizers of the rhizosphere of rice. Each of the amoA gene libraries obtained from the freshwater sample and the enrichment culture was dominated by a novel lineage that shared a branch with the Nitrosospira cluster but could not be assigned to any of the known pure cultures. Our data suggest that amoA represents a very powerful molecular tool for analyzing indigenous ammonia-oxidizing communities due to (i) its specificity, (ii) its fine

  9. 石墨烯载Ir催化剂对氨氧化的电催化性能%Electrocatalytic Performance of Graphene Supported Ir Catalyst for Ammonia Oxidation

    Institute of Scientific and Technical Information of China (English)

    李林儒; 付宏刚; 陆天虹

    2012-01-01

    用石墨烯(G)代替Vulcan XC-72炭(XC)作Ir的载体制备石墨烯载Ir(Ir/G)催化剂.电化学的测量结果表明,Ir/G催化剂对氨氧化的电催化性能优于XC炭载Ir( Ir/XC)催化剂.X射线衍射(XRD)谱测量结果表明,Ir/G和Ir/XC催化剂的Ir粒子平均粒径相似.拉曼光谱的测量结果表明,G的石墨化程度和电导率高于XC.因此,Ir/G催化剂对氨氧化的电催化性能优于Ir/XC催化剂.氨在Ir/G催化剂电极上氧化的电流密度与氨浓度呈很好的线性关系曲线,相关系数R为0.99557.因此,Ir/G催化剂电极可作为电流型电化学氨传感器的工作电极.%Instead Vulcan XC-72 carbon(XC) , grapheme(G) was used as the support to prepare the Ir/G catalyst. The electrochemical measurement indicted that the electrocatalytic performance of the Ir/G catalyst for the ammonia oxidation was better than that of the Ir/XC catalyst. XRD and TEM measurements indicated that the average sizes of Ir particles in Ir/G and Ir/XC catalysts were similar. The measurement of the Raman spectroscopy illustrates the graphitization extent of G is higher than that of XC. Thus, the conductivity of G is higher than that of XC. Therefore, the electrocatalytic performance of the Ir/G catalyst is better than that of the Ir/XC catalyst can be attributed to the high conductivity due to the high graphitization extent of G. The results show that there is the good linear relationship between the current density of the ammonia oxidation at the Ir/G catalyst electrode and the concentration of ammonia. The related coefficient (R) is 0. 99557. Thus, Ir/G catalyst electrode can be used as the working electrode in the current type of electrochemical ammonia sensor.

  10. N2O emission in short-cut simultaneous nitrification and denitrification process: dynamic emission characteristics and succession of ammonia-oxidizing bacteria.

    Science.gov (United States)

    Yan, Yingyan; Li, Ping; Wu, Jinhua; Zhu, Nengwu; Wu, Pingxiao; Wang, Xiangde

    2014-01-01

    A sequencing batch airlift reactor was used to investigate the characteristics of nitrous oxide (N2O) emission and the succession of an ammonia-oxidizing bacteria (AOB) community. The bioreactor could successfully switch from the complete simultaneous nitrification and denitrification (SND) process to the short-cut SND process by increasing the influent pH from 7.0-7.3 to 8.0-8.3. The results obtained showed that, compared with the complete SND process, the TN removal rate and SND efficiency were improved in the short-cut SND process by approximately 13 and 11%, respectively, while the amount of N2O emission was nearly three times larger than that in the complete SND process. The N2O emission was closely associated to nitrite accumulation. Analysis of the AOB microbial community showed that nitrifier denitrification by Nitrosomonas-like AOB could be an important pathway for the enhancement of N2O emission in the short-cut SND process. PMID:24960019

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

    Directory of Open Access Journals (Sweden)

    Vishal Shah

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

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

    Science.gov (United States)

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

    2011-11-01

    The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38°C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification. PMID:21713434

  13. Inhabitancy of active Nitrosopumilus-like ammonia-oxidizing archaea and Nitrospira nitrite-oxidizing bacteria in the sponge Theonella swinhoei.

    Science.gov (United States)

    Feng, Guofang; Sun, Wei; Zhang, Fengli; Karthik, Loganathan; Li, Zhiyong

    2016-01-01

    Nitrification directly contributes to the ammonia removal in sponges, and it plays an indispensable role in sponge-mediated nitrogen cycle. Previous studies have demonstrated genomic evidences of nitrifying lineages in the sponge Theonella swinhoei. However, little is known about the transcriptional activity of nitrifying community in this sponge. In this study, combined DNA- and transcript-based analyses were performed to reveal the composition and transcriptional activity of the nitrifiers in T. swinhoei from the South China Sea. Transcriptional activity of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in this sponge were confirmed by targeting their nitrifying genes,16S rRNA genes and their transcripts. Phylogenetic analysis coupled with RDP rRNA classification indicated that archaeal 16S rRNA genes, amoA (the subunit of ammonia monooxygenase) genes and their transcripts were closely related to Nitrosopumilus-like AOA; whereas nitrifying bacterial 16S rRNA genes, nxrB (the subunit of nitrite oxidoreductase) genes and their transcripts were closely related to Nitrospira NOB. Quantitative assessment demonstrated relative higher abundances of nitrifying genes and transcripts of Nitrosopumilus-like AOA than those of Nitrospira NOB in this sponge. This study illustrated the transcriptional potentials of Nitrosopumilus-like archaea and Nitrospira bacteria that would predominantly contribute to the nitrification functionality in the South China Sea T. swinhoei. PMID:27113140

  14. Dominance of ammonia-oxidizing archaea community induced by land use change from Masson pine to eucalypt plantation in subtropical China.

    Science.gov (United States)

    Zhang, Fang-Qiu; Pan, Wen; Gu, Ji-Dong; Xu, Bin; Zhang, Wei-Hua; Zhu, Bao-Zhu; Wang, Yu-Xia; Wang, Yong-Feng

    2016-08-01

    A considerable proportion of Masson pine forests have been converted into eucalypt plantations in the last 30 years in Guangdong Province, subtropical China, for economic reasons, which may affect the ammonia-oxidizing archaea (AOA) community and the process of ammonia transformation. In order to determine the effects of forest conversion on AOA community, AOA communities in a Masson pine (Pinus massoniana) plantation and a eucalypt (Eucalyptus urophylla) plantation, which was converted from the Masson pine, were compared. Results showed that the land use change from the Masson pine to the eucalypt plantation decreased soil nutrient levels. A significant decrease of the potential nitrification rates (PNR) was also observed after the forest conversion (p amoA gene diversity was negatively correlated with organic C and total N, respectively (p amoA gene abundance was negatively correlated with NH4 (+) and available P, respectively (p < 0.05, n = 12). However, AOA abundance was positively correlated with PNR, but not significantly (p < 0.05, n = 6), indicating AOA community change was only a partial reason for the decrease of PNR. PMID:27094186

  15. Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of nitrosospiras in the environment.

    Science.gov (United States)

    Hiorns, W D; Hastings, R C; Head, I M; McCarthy, A J; Saunders, J R; Pickup, R W; Hall, G H

    1995-11-01

    Oligonucleotide sequences selected from the 16S rRNA genes of various species of ammonia-oxidizing bacteria were evaluated as specific PCR amplification primers and probes. The specificities of primer pairs for eubacterial, Nitrosospira and Nitrosomonas rRNA genes were established with sequence databases, and the primer pairs were used to amplify DNA from laboratory cultures and environmental samples. Eubacterial rRNA genes amplified from samples of soil and activated sludge hybridized with an oligonucleotide probe specific for Nitrosospira spp., but not with a Nitrosomonas-specific probe. Lakewater and sediment samples were analysed using a nested PCR technique in which eubacterial rRNA genes were subjected to a secondary amplification with Nitrosomonas or Nitrosospira specific primers. Again, the presence of Nitrosospira DNA, but not Nitrosomonas DNA, was detected and this was confirmed by hybridization of the amplified DNA with an internal oligonucleotide probe. Enrichments of lakewater and sediment samples, incubated for two weeks in the presence of ammonium, produced nitrite and were found to contain DNA from both Nitrosospira and Nitrosomonas as determined by nested PCR amplification and probing of 16S rRNA genes. This demonstrates that Nitrosospira spp. are widespread in the environment. The implications of the detection of Nitrosomonas DNA only after enrichment culture are discussed. PMID:8535507

  16. Isotope signatures of N2O emitted from vegetable soil: Ammonia oxidation drives N2O production in NH4(+)-fertilized soil of North China.

    Science.gov (United States)

    Zhang, Wei; Li, Yuzhong; Xu, Chunying; Li, Qiaozhen; Lin, Wei

    2016-01-01

    Nitrous oxide (N2O) is a potent greenhouse gas. In North China, vegetable fields are amended with high levels of N fertilizer and irrigation water, which causes massive N2O flux. The aim of this study was to determine the contribution of microbial processes to N2O production and characterize isotopic signature effects on N2O source partitioning. We conducted a microcosm study that combined naturally abundant isotopologues and gas inhibitor techniques to analyze N2O flux and its isotopomer signatures [δ(15)N(bulk), δ(18)O, and SP (intramolecular (15)N site preference)] that emitted from vegetable soil after the addition of NH4(+) fertilizers. The results show that ammonia oxidation is the predominant process under high water content (70% water-filled pore space), and nitrifier denitrification contribution increases with increasing N content. δ(15)N(bulk) and δ(18)O of N2O may not provide information about microbial processes due to great shifts in precursor signatures and atom exchange, especially for soil treated with NH4(+) fertilizer. SP and associated two end-member mixing model are useful to distinguish N2O source and contribution. Further work is needed to explore isotopomer signature stability to improve N2O microbial process identification. PMID:27387280

  17. Isotope signatures of N2O emitted from vegetable soil: Ammonia oxidation drives N2O production in NH4+-fertilized soil of North China

    Science.gov (United States)

    Zhang, Wei; Li, Yuzhong; Xu, Chunying; Li, Qiaozhen; Lin, Wei

    2016-01-01

    Nitrous oxide (N2O) is a potent greenhouse gas. In North China, vegetable fields are amended with high levels of N fertilizer and irrigation water, which causes massive N2O flux. The aim of this study was to determine the contribution of microbial processes to N2O production and characterize isotopic signature effects on N2O source partitioning. We conducted a microcosm study that combined naturally abundant isotopologues and gas inhibitor techniques to analyze N2O flux and its isotopomer signatures [δ15Nbulk, δ18O, and SP (intramolecular 15N site preference)] that emitted from vegetable soil after the addition of NH4+ fertilizers. The results show that ammonia oxidation is the predominant process under high water content (70% water-filled pore space), and nitrifier denitrification contribution increases with increasing N content. δ15Nbulk and δ18O of N2O may not provide information about microbial processes due to great shifts in precursor signatures and atom exchange, especially for soil treated with NH4+ fertilizer. SP and associated two end-member mixing model are useful to distinguish N2O source and contribution. Further work is needed to explore isotopomer signature stability to improve N2O microbial process identification. PMID:27387280

  18. 氨氧化细菌和氨氧化古菌在百花湖沉积物中的垂直分布%Vertical Distribution of Ammonia Oxidizing Bacteria (AOB)and Ammonia Oxidizing Archaea (AOA)in the Sediments of Lake Baihua

    Institute of Scientific and Technical Information of China (English)

    梁龙; 梁小兵

    2014-01-01

    采用定量氨单加氧酶基因(amoA)的荧光定量 PCR(qPCR)方法,分析了氨氧化细菌(AOB)和氨氧化古菌(AOA)在百花湖沉积物中的垂直分布。以氨单加氧酶基因(amoA)数量来衡量氨氧化细菌(AOB)和氨氧化古菌(AOA),结果表明:百花湖沉积物中 AOA 的 amoA 基因数量在1.74×105~2.00×106拷贝/克沉积物(湿重)之间,且22~30 cm 的各层沉积物中, AOA 的数量是1~21 cm 各层沉积物的2倍左右;AOB 的 amoA 基因在百花湖沉积物中的数量随深度的增加变化不大,其拷贝数在6.10×106~3.88×107拷贝/g 沉积物(湿重)之间;AOB 与 AOA 的 amoA 基因的比例在浅层沉积物和深层沉积物中存在一定的差异。这些结果表明 AOB 和 AOA 都参与百花湖沉积物中的氨氧化作用,从两类微生物的数量来看,AOB 是参与百花湖沉积物中氨氧化作用的主要微生物,而 AOA 对氨氧化作用的贡献则随着沉积物深度的增加而提高。%The vertical distributions of ammonia-oxidizing bacteria (AOB)and ammonia-oxidizing archaea (AOA)in the sediments of Lake Baihua were analyzed using the qPCR method.Abundances of AOA and AOB were analyzed in terms of the amoA gene copy number.The results showed that the numbers of AOA amoA gene were between 1 .74×10 5 ~2.00×10 6 copies/gram sediment (wet),with significant differences between in shallow and deep sedi-ments.In contrast,the quantities of AOB amoA gene were 6.10 × 10 6 ~3.88 × 10 7 copies/gram sediment (wet) with no obvious variation in sediment layers of different depths.The ratios of AOB and AOA such changed within different sediment layers.These results indicated that both AOB and AOA participated in the ammonia oxidizing processes in sediments of the Lake Baihua.We concluded that AOB is the primary ammonia oxidizing microorgan-ism because of its high abundance,while AOA plays a more important role in deep than in shallow sediments of the Lake Baihua.

  19. PCR-DGGE研究臭氧耦合ASBR/SBR控氮磷污泥减量化工艺中的细菌多样性%Bacterial Diversity of the Combined Ozonation-ASBR/SBR Sludge Reduction with Simultaneous Nitrogen and Phosphorus Removal Process Using PCR-DGGE

    Institute of Scientific and Technical Information of China (English)

    赵林林; 王海燕; 杨慧芬; 何赞; 周岳溪; 张乐; 庞朝辉

    2011-01-01

    采用分子生物学手段PCR-DGGE技术对臭氧耦合ASBR/SBR控氮磷污泥减量化工艺中的ASBR和污泥减量化前后的SBR中的细菌多样性进行了研究.结果表明,ASBR中的主要细菌类群为Firmicutes类群,β-proteobacterium类群,γ-proteobacterium类群和Bacteroidetes类群;污泥减量化后SBR中细菌丰富度与减量前相比有所增加,但是相似性指数极高,为85%;臭氧施加进行污泥减量对SBR中的优势菌群多样性影响不大,污泥减量化前后SBR反应器内均存在Firmicutes bacterium,Candidate division TM7,ammonia-oxidizing bacterium,Bacteroidetes bacterium,β-proteobacterium,Denitrifying bacterium,Pseudomonas sp和Nitrosococcus halophilus Nc4,其中减量化后Bacteroidetes bacterium,β-proteobacterium,Denitrifying bacterium和Nitrosococcus halophilus Nc4的数量略高于污泥减量化之前.

  20. Dynamics of ammonia-oxidizing archaea and ammonia-oxidizing bacteria during composting of chicken manure and mushroom cultural waste%鸡粪菌渣好氧堆肥过程中氨氧化古菌及氨氧化细菌群落的动态变化

    Institute of Scientific and Technical Information of China (English)

    邱珊莲; 张少平; 翁伯琦; 罗涛; 林霜霜; 何炎森

    2016-01-01

    以amoA 基因为标记,通过Real-Time PCR和限制性片段长度多态性(Restriction fragment length polymorphism,RFLP)法对鸡粪菌渣好氧堆肥过程中的氨氧化古菌(Ammonia-oxidizing archaea, AOA)和氨氧化细菌(Ammonia-oxidizing bacteria, AOB)进行了丰度及群落结构的分析。结果表明,在堆制初期、好氧发酵高温期及后熟期,AOB的amoA 基因丰度均占主导优势,是AOA的38~992倍。进入好氧发酵高温期,AOA amoA 基因丰度下降至发酵前的0.9%,AOB下降至17.6%,后熟期AOA与AOB的amoA基因丰度与好氧发酵高温期相当。在上述3个阶段AOA与AOB各自存在一个绝对优势菌群,分别为Cluster 3和Nitrosomonas europaea,其中Cluster 3克隆子数目分别占整个克隆文库的70.73%、54.28%、72.45%,Nitrosomonas europaea克隆子数目分别占整个克隆文库的78.44%、93.20%、94.27%。堆肥3个阶段AOA的多样性指数变化不大,Shannon-Wiener值维持在1.53~1.60,但群落结构发生明显演替,随着堆肥温度升高,堆肥前期的一些菌群(Cluster 4、Cluster 5、Cluster 6)逐渐消失,新的菌群Cluster 1出现并成为堆肥中后期的第二大优势菌群。AOB无论是多样性指数还是群落组成,都发生剧烈的变化。AOB在堆肥前期Shannon-Wiener指数值最大(1.47),种群数最多(6个基因簇,分别为 Nitrosomonas europaea Cluster,Nitrosomonas halophila Cluster,Nitrosomonas communis Cluster,Nitrosomonas nitrosa Cluster,Nitrosospira briensis Cluster,Nitrosospira multiformis Cluster);进入高温发酵期,Shannon-Wiener下降至0.45,群落结构单一,只有Nitrosomonas europaea Cluster和Nitrosomonas halophila Cluster;进入后熟期,AOB多样性及种群数得到一定程度的回升。%The transformation and loss of nitrogen in composting materials were affected profoundly by ammonia oxidizers during the com-posting process. The abundance and composition of

  1. The Communities of Ammonia-oxidizing Organisms in Pearl River Estuary Sediments%珠江口海岸带沉积物氨氧化细菌和古菌组成及定量研究

    Institute of Scientific and Technical Information of China (English)

    陈金全; 郑燕平; 姜丽晶; 王风平

    2012-01-01

    [Objective] This study aimed to investigate the abundance and composition of ammonia-oxidizing organism in Pearl River Estuary sediment. [ Method] Based on amoA genes, we detected the abundance and composition of ammonia-oxidizing organism in Pearl River Estuary sediment by using quantitative real-time polymerase chain reaction (Q-PCR) , cloning and sequencing approaches. [ Result] The results of Q-PCR presented that ammonia-oxidizing archaea were more abundant than ammonia-oxidizing bacteria in the top of sediment cores, with AOA to AOB ratios 8.96 (site Q5) and 3. 69 (site Q7). It suggested that ammonia-oxidizing archaea maybe play more important roles than ammonia-oxidizing bacteria in the process of ammonia oxidation in the Pearl River Estuary sediment. In the top sediment layer of Q7, bacterial amoA-like gene sequences were dominated by Nitrosomonas-like sequence types, which could be classified into five groups (clusters A, B, C, D, and E). Interestingly, archeal amoA-like gene was successfully amplified while bacterial amoA-like gene failed to be detected. These archeal amoA-like genes fell into two groups "water column/sediment" cluster and "soil/sediment" cluster. Most of the sequences (93. 3% ) in the bottom sediment layer of Q7 fell into " soil/sediment" cluster. [ Conclusion] This study helps to realize the cycle of nitrogen in Pearl River Estuary region, and thus to provide theoretical support fur the treatment of nitrogen eutrophication.%[目的]对珠江口海岸带沉积物中的氨氧化细菌和古菌的组成进行分析,并进行定量研究.[方法]用构建克隆文库和Q - PCR定量的方法对珠江口沉积物中氨氧化细菌和古菌amoA基因的含量和多样性特征进行研究.[结果]在2个沉积物表层,氨氧化古菌的含量是细菌的9和22倍,揭示氨氧化古菌在珠江口的氨氧化过程中起主导作用;系统发育分析表明大多数古菌和细菌的amoA基因序列与不可培养的源于河口区和污染

  2. The combined effect of dissolved oxygen and nitrite on N2O production by ammonia oxidizing bacteria in an enriched nitrifying sludge.

    Science.gov (United States)

    Peng, Lai; Ni, Bing-Jie; Ye, Liu; Yuan, Zhiguo

    2015-04-15

    Both nitrite [Formula: see text] and dissolved oxygen (DO) play important roles in nitrous oxide (N2O) production by ammonia oxidizing bacteria (AOB). However, few studies focused on the combined effect of them on N2O production by AOB as well as the corresponding mechanisms. In this study, N2O production by an enriched nitrifying sludge, consisting of both AOB and nitrite-oxidizing bacteria (NOB), was investigated under various [Formula: see text] and DO concentrations. At each investigated DO level, both the biomass specific N2O production rate and the N2O emission factor (the ratio between N2O nitrogen emitted and the ammonium nitrogen converted) increased as [Formula: see text] concentration increased from 3 mg N/L to 50 mg N/L. However, at each investigated [Formula: see text] level, the maximum biomass specific N2O production rate occurred at DO of 0.85 mg O2/L, while the N2O emission factor decreased as DO increased from 0.35 to 3.5 mg O2/L. The analysis of the process data using a mathematical N2O model incorporating both the AOB denitrification and hydroxylamine (NH2OH) oxidation pathways indicated that the contribution of AOB denitrification pathway increased as [Formula: see text] concentration increased, but decreased as DO concentration increased, accompanied by a corresponding change in the contribution of NH2OH oxidation pathway to N2O production. The AOB denitrification pathway was predominant in most cases, with the NH2OH oxidation pathway making a comparable contribution only at high DO level (e.g. 3.5 mg O2/L). PMID:25644626

  3. Abundance and diversity of ammonia-oxidizing archaea and bacteria on granular activated carbon and their fates during drinking water purification process.

    Science.gov (United States)

    Niu, Jia; Kasuga, Ikuro; Kurisu, Futoshi; Furumai, Hiroaki; Shigeeda, Takaaki; Takahashi, Kazuhiko

    2016-01-01

    Ammonia is a precursor to trichloramine, which causes an undesirable chlorinous odor. Granular activated carbon (GAC) filtration is used to biologically oxidize ammonia during drinking water purification; however, little information is available regarding the abundance and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) associated with GAC. In addition, their sources and fates in water purification process remain unknown. In this study, six GAC samples were collected from five full-scale drinking water purification plants in Tokyo during summer and winter, and the abundance and community structure of AOA and AOB associated with GAC were studied in these two seasons. In summer, archaeal and bacterial amoA genes on GACs were present at 3.7 × 10(5)-3.9 × 10(8) gene copies/g-dry and 4.5 × 10(6)-4.2 × 10(8) gene copies/g-dry, respectively. In winter, archaeal amoA genes remained at the same level, while bacterial amoA genes decreased significantly for all GACs. No differences were observed in the community diversity of AOA and AOB from summer to winter. Phylogenetic analysis revealed high AOA diversity in group I.1a and group I.1b in raw water. Terminal-restriction fragment length polymorphism analysis of processed water samples revealed that AOA diversity decreased dramatically to only two OTUs in group I.1a after ozonation, which were identical to those detected on GAC. It suggests that ozonation plays an important role in determining AOA diversity on GAC. Further study on the cell-specific activity of AOA and AOB is necessary to understand their contributions to in situ nitrification performance. PMID:26463999

  4. Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea.

    Directory of Open Access Journals (Sweden)

    Kateryna V Zhalnina

    Full Text Available The activity of ammonia-oxidizing archaea (AOA leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.

  5. 南美白对虾养殖底泥中氨氧化细菌与氨氧化古菌多态性分析%Diversity of β-Proteobacterial ammonia-oxidizing bacteria and ammonia-oxidizing archaea in shrimp farm sediment

    Institute of Scientific and Technical Information of China (English)

    高利海; 林炜铁

    2011-01-01

    [目的]本研究皆在了解虾养殖底泥中氨氧化细菌与氨氧化古菌群落多态性.[方法]以功能基因为基础,构建氨氧化细菌(AOB)与氨氧化古菌(AOA)的氨单加氧酶α亚基基因(amoA)克隆文库.利用限制性片段长度多态性(Restriction Fragment Length Polymorphism,RFLP)技术将克隆文库阳性克隆子进行归类分析分成若干个可操作分类单元(Operational Taxa Units,OTUs).[结果]通过序列多态性分析,表明AOB amoA基因克隆文库中所有序列都属于变形杆菌门β亚纲(β-Proteobacteria)中的亚硝化单细胞菌属(Nitrosomonas)及Nitrosomonas-like,未发现亚硝化螺旋菌属(Nitrosospira).AOA amoA基因克隆文库中只有一个OTU序列属于未分类的古菌(Unclassified-Archaea),其余序列都属于泉古菌门(Crenarchaeote).AOA群落结构单一且存在一个绝对优势类群OTU3,其克隆子数日占克隆文库的57.45%.AOB和AOA amoA基因克隆文库分别包括13个OTUs和9个OTUs,其文库覆盖率分别为73.47%和90.43%.AOB amoA基因克隆文库的Shannon-Wiener指数、Evenness指数、Simpson指数、Richness指数均高于AOA.[结论]虾养殖塘底泥中存在氨氧化古菌的amoA基因,且多态性低于氨氧化细菌,表明氨氧化古菌在虾养殖塘底泥的氮循环中可能具有重要的作用.%[Objective]In order to study the diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in shrimp farm sediment.[Methods]Total microbial DNA was directly extracted from the shrimp farm sediment.The clone library of amoA genes were constructed with β-Proteobacterial-AOB and AOA specific primers.The library was screened by PCR-restriction fragment length polymorphism (RFLP) analysis and clones with unique RFLP patterns were sequenced.[Results]Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from shrimp farm sediment were affiliated with Nitrosomonas (61.54% ) or Nitrosomonas-like ( 38.46% ) species and

  6. Molecular evidence for ammonia oxidation bacteria in the sediments of shallow lake: A case study in Yangcheng Lake%浅水湖泊(阳澄湖)沉积物氨氧化菌的分子证据

    Institute of Scientific and Technical Information of China (English)

    张亚平; 阮晓红

    2012-01-01

    选择长江三角洲中型浅水湖泊--阳澄湖,应用分子生物学方法鉴定淡水系统底质中的厌氧氨氧化细菌和好氧氨氧化细菌.试验设计三组厌氧氨氧化特异性巢式引物,对沉积物细菌的16S rRNA进行特异性扩增.其中,引物对AMX368f-AMX820r从底质中扩增出了anammox特异性序列,系统发育分析表明样品序列分别与Candidatus brocadia fulgida、Candidatus brocadia anammoxidans和Candidatus scalindua属近似.应用amoA基因特异性探针在底质中扩增出的好氧氨氧化菌序列,均属于Betaproteobacteria.本研究提供了阳澄湖中好氧氨氧化菌与厌氧氨氧化菌共存的分子证据.%Sediment samples were collected from Yangcheng Lake, a middle size shallow lake in Yangtze River Delta. Molecular biology methods were adopted to detect the anaerobic ammonia oxidation (anammox) and aerobic ammonia oxidation bacteria in the samples. Three pairs of nest PCR primers were designed to amplify the 16S rRNA from the sediment samples. The specified sequences of anammox were amplified by the primer pairs AMX368f- AMX820r, and analyses of phylogenetics showed that these sequences were similar to Candidatus brocadia fulgida, Candidatus brocadia anammoxidans and Candidatus scalindua. The sequences amplified by the amoA gene specified primer from the sediment samples belonged to the Betaproteobacteria class. This study provided the molecular evidence for coexistence of anammox and aerobic-ammonia-oxidation in Yangcheng Lake.

  7. Communities and Quantitative Analysis of Ammonia-oxidizing Organisms in Pearl River Estuary Sediments%珠江口海岸带沉积物氨氧化细菌和古菌组成及定量研究

    Institute of Scientific and Technical Information of China (English)

    陈金全; 郑燕平; 姜丽晶; 王风平

    2012-01-01

    [Objective] This study aimed to investigate the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea in Pearl River Estuary sediment.[Method] Firstly,the amoA gene library was constructed;then based on that,the content and diversity of amoA genes of ammonia-oxidizing bacteria and ammonia-oxidizing archaea in Pearl River Estuary sediment were detected by using quantitative real-time polymerase chain reaction(Q-PCR).[Result] The results of Q-PCR presented that ammonia-oxidizing archaea(AOA) were more abundant than ammonia-oxidizing bacteria(AOB) in the top of sediment cores,with ratios of AOA to AOB of 22 and 9 at the two sites.It suggested that ammonia-oxidizing archaea may play more important roles than ammonia-oxidizing bacteria in the process of ammonia oxidation in the Pearl River Estuary sediment.The phylogenetic tree based on amoA gene sequences revealed that the amoA sequences of both AOA and AOB shared high similarity with the clones from uncultured environment.In the top sediment layer at site Q7,AOB amoA-like gene sequences were dominated by Nitrosomonas-like sequence types,which could be classified into five groups(clusters A,B,C,D and E).Cluster A accounted for 72.1% of the library.In the top sediment layer,the AOA amoA gene fell into two groups "water column/sediment" cluster(52.2%) and "soil/sediment" cluster(47.8%).But in the bottom sediment layer of Q7,most of the AOA amoA sequences(93.3%) fell into "soil/sediment" cluster,and a little part(6.7%) fell into the "water/sediment" cluster.In addition,the total amount of amoA genes in the bottom sediment was higher than that in top sediment.[Conclusion] This study helps to realize the cycle of nitrogen in Pearl River Estuary Region,and thus to provide theoretical support for the treatment of nitrogen eutrophication.%[目的]对珠江口海岸带沉积物中的氨氧化细菌和古菌的组成进行分析,并进行定量研究。[方法]用构建克隆文库和Q-PCR定量

  8. Community structure of ammonia-oxidizing prokaryotes at the dry-up lake in Huitengxile grassland%辉腾锡勒草原干涸湖泊中氨氧化微生物群落结构分析

    Institute of Scientific and Technical Information of China (English)

    惠丽华; 赵吉; 武琳慧; 邵玉琴; 李靖宇; 朱兵

    2012-01-01

    [目的]以内蒙古辉腾锡勒草原九十九泉湿地为对象,研究湖泊干涸过程中氨氧化微生物的群落结构及其变化.[方法]通过MPN-PCR定量测定氨氧化古菌(AOA)和氨氧化细菌(AOB)的数量;构建amoA基因克隆文库,进行系统发育分析;结合土壤环境因子,探讨湿地退化过程中影响氨氧化微生物的潜在因素.[结果]依湖泊湿地退水梯度的不同样点中,有75%的样点AOB的数量高于AOA,AOB与AOA的数量比率为0.3 -18.1.从湖心到湖岸草原带,AOA和AOB的数量有明显增加,但生物多样性呈降低趋势,二者没有呈现正相关.研究发现,AOB的数量与土壤中NH4+-N的变化存在良好响应.系统发育分析显示,退化湖泊湿地AOA克隆序列均来自于泉古菌门(Crenarchaeota);AOB的amoA基因的克隆序列大部分与亚硝化单胞菌属(Nitrosomonas)有一定同源性,较少部分与亚硝化螺菌属(Nitrosospira)有一定同源性.[结论]湖泊退水过程增加了湿地土壤氨氧化微生物的数量,而氨氧化微生物的种群丰度有所降低.AOA和AOB群落对湖泊湿地的退化过程做出了响应,其中AOB的响应较为明显,氧化条件和土壤铵浓度的改变可能是促成这种响应的重要原因.%[Objective] To investigate the structure of ammonia-oxidation microbial communities in the wetlands to dry-up process at 99 degraded lakes of the Huitengxile grassland in the Inner Mongolia Plateau. [ Methods] The microbial quantity of ammonia-oxidizing archaea ( AOA ) and ammonia oxidizing bacteria ( AOB ) were examined by most probable number-polymerase chain reaction (MPN-PCR). The clone libraries of amoA were constructed and phylogenetics were analyzed. With analysis of the soil properties, we evaluated the effects of wetlands degradation on ammonia-oxidation microbes communities. [Results] In 75% of the samples, the quantity of AOB communities was higher than that of AOA; moreover, quantity of bacterial were up to 18. 1

  9. Effect of Transgenic Soybean on Amount and Diversity of Ammonia-oxidizing Bacteria in Rhizospheric Soil%转基因大豆对土壤氨氧化细菌的影响

    Institute of Scientific and Technical Information of China (English)

    赖欣; 张永生; 赵帅; 杨殿林

    2011-01-01

    The genetically modified (GM)crops are more and more concerned by public;meanwhile more and more GM crops are planted in fields globally. Besides the food safety, the ecological risks are also gained focus. In order to deeply understand the effect of transgenic soybean on diversity of rhizoperic ammonia-oxidizing bacteria in soil,DGGE-cloning and quantitative PCR were used. Both the DGGE-cloning and qPCR results showed that seasonal changes were observed throughout the soybean growth stages, indicating the impact of crop growth stage overweigh that of exogenous gene insertion and transgenic soybean has not diversely affect on rhizosphere ammonia-oxidizing bacteria abundance and community composition in soil.%采用DGGE-cloning测序技术与定量PCR技术相结合的方法,研究了转基因大豆对土壤中氨氧化细菌群落多样性的影响.定量PCR试验结果表明,相同的生长时期转基因大豆对氨氧化细菌数量没有显著的影响,而与此同时,土壤中的氨氧化细菌的数量呈现出随生长期先增加后减少的趋势;DGGE图谱分析表明,同一生长时期不同大豆土壤中的氨氧化细菌主要条带一致,这表明生长时期的影响明显大于转基因大豆对土壤氨氧化细菌的影响.

  10. 不同施肥方式对红壤蔬菜田氨氧化细菌和氨氧化古菌群落的影响%Effect of Different Fertilization on Ammonia-oxidizing bacteria and Ammonia-oxidizing archaea in Red Soil Vegetable Field

    Institute of Scientific and Technical Information of China (English)

    周志成; 罗葵; 唐前君; 荣湘民; 刘强; 何飞飞

    2015-01-01

    通过构建氨单加氧酶基因(amoA)克隆文库,研究在红壤蔬菜田上只施用磷钾化肥(PK)、只施氮磷钾化肥(NPK)、施用腐熟有机肥(DNPK)和施用新鲜有机肥(FNPK)等4种不同施肥处理的土壤氨氧化细菌(AOB)和氨氧化古菌(AOA)群落多样性及与土壤脲酶活性的相关性。结果表明:施加有机肥处理(DNPK和FNPK)的蔬菜田土壤的AOB文库和AOA文库OTU数量和Shannon指数高于只施用无机肥(NPK和PK)处理的蔬菜田土壤;DNPK和FNPK处理的土壤优势AOB菌群为多形亚硝化叶菌(Nitrosolobus multiformis),比例分别为88.5%和68.5%,NPK和PK处理的土壤优势AOB菌群为亚硝化单胞菌属(Nitrosospira sp.),比例分别为54.8%和65.5%;DNPK、FNPK、NPK和PK处理土壤优势AOA菌群均为阿伯丁土壤亚硝化细杆菌侯选种(CandidatusNitrosotalea devanaterra),比例分别为90.9%、84.4%、77.8%和45.2%;施加有机肥处理(DNPK和FNPK)的土壤脲酶活性和氨氧化微生物的多样性指数都高于只施用无机肥处理(NPK和PK);AOA群落多样性指数与土壤脲酶活性呈显著正相关,而AOB群落多样性与土壤脲酶活性相关性不显著。总体来看,有机肥比无机肥处理提高了AOA和AOB群落多样性,且AOA在红壤蔬菜田土壤氨氧化过程中起着更为重要的作用。%AdoptingamoA gene clone library construction method,this paper studied the diversity of ammonia-oxidizing bacteria(AOB) and ammonia-oxidizing archaea (AOA)and correlations between diversity index and urease activity in red soil vegetable field by different fertilization including decomposed organic fertilizer (DNPK),fresh organic fertilizer(FNPK),Nitrogen,Phosphorus and Potassium chemical fertilizer(NPK), Phosphorus and Potassium chemical fertilizer(PK).The results showed that OTU quantity,Shannon index of AOB library and AOA library represented organic fertilizer (DNPK and FNPK

  11. Lactococcus lactis - a diploid bacterium

    DEFF Research Database (Denmark)

    Michelsen, Ole; Hansen, Flemming G.; Jensen, Peter Ruhdal

    In contrast to higher eukaryotes, bacteria are haploid, i.e. they store their genetic information in a single chromosome, which is then duplicated during the cell cycle. If the growth rate is sufficiently low, the bacterium is born with only a single copy of the chromosome, which gets duplicated...... before the bacterium divides. Fast-growing bacteria have overlapping rounds of replication, and can contain DNA corresponding to more than four genome equivalents. However, the terminus region of the chromosome is still present in just one copy after division, and is not duplicated until right before...... the next division. Thus, the regions of the chromosome that are the last to be replicated are haploid even in fast-growing bacteria. In contrast to this general rule for bacteria, we found that Lactococcus lactis, a bacterium which has been exploited for thousands of years for the production of fermented...

  12. Single Bacterium Detection Using Sers

    Science.gov (United States)

    Gonchukov, S. A.; Baikova, T. V.; Alushin, M. V.; Svistunova, T. S.; Minaeva, S. A.; Ionin, A. A.; Kudryashov, S. I.; Saraeva, I. N.; Zayarny, D. A.

    2016-02-01

    This work is devoted to the study of a single Staphylococcus aureus bacterium detection using surface-enhanced Raman spectroscopy (SERS) and resonant Raman spectroscopy (RS). It was shown that SERS allows increasing sensitivity of predominantly low frequency lines connected with the vibrations of Amide, Proteins and DNA. At the same time the lines of carotenoids inherent to this kind of bacterium are well-detected due to the resonance Raman scattering mechanism. The reproducibility and stability of Raman spectra strongly depend on the characteristics of nanostructured substrate, and molecular structure and size of the tested biological object.

  13. 子牙河水系水和沉积物好氧氨氧化微生物分布特征%The distribution of aerobic ammonia oxidizing microorganisms in Ziya River,Haihe Basin

    Institute of Scientific and Technical Information of China (English)

    王超; 单保庆

    2012-01-01

    Surface sediment and water column samples of Ziya River in Haihe Basin was collected to analyze the effect of environmental parameters such as ammonium,dissolved oxygen,and pH to the distribution of aerobic ammonia oxidizing microorganisms.The results showed that the average abundance of ammonia oxidizing bacteria (AOB) (ranging from 1.04 × 10 5 to 2.46 × 10 9 gene copies·g-1) in sediment was 8.51 times that of ammonia oxidizing archaea (AOA) (ranging from 1.05 × 10 5 to 1.18 × 10 9 gene copies·g-1).While in river water column,the average abundance of AOB (ranging from 1.75 × 10 2 to 1.56 × 10 10 gene copies·mL-1) was nearly a twentieth part of AOA (ranging from 5.21 ×10 2 to 2.44 × 10 9 gene copies·mL-1).Partial correlation analysis indicated that ammonia concentration was positively correlated with the AOB-to-AOA ratio (r=0.477,p 0.05) and pH was positively correlated with AOB abundance (r=0.466,p 0.05) in river water column.Moreover,dissolved oxygen showed positive relationship with both the AOB-to-AOA ratio and AOB abundance,with the correlation coefficients of 0.722 and 0.745,respectively (p 0.01).%采集海河流域子牙河水系河流沉积物和河流水样,分析了其好氧氨氧化微生物的分布特征,并探讨了氨氮、溶解氧和pH对其分布的影响.结果表明,沉积物中氨氧化古菌(AOA)和氨氧化细菌(AOB)丰度范围分别为1.05×105~1.18×109genecopies·g-1和1.04×105~2.46×109genecopies·g-1,水体AOA和AOB丰度范围分别为5.21×102~2.44×109genecopies·mL-1和1.75×102~1.56×1010genecopies·mL-1;沉积物中AOB占优势,平均丰度为AOA的8.51倍,水中AOA占优势,平均丰度为AOB的18.99倍.偏相关分析表明,氨氮浓度同水中AOB与AOA丰度比值显著正相关(r=0.477,p〈0.05),pH同水体AOB丰度显著正相关(r=0.466,p〈0.05),而溶解氧同水体AOB丰度及AOB、AOA丰度比值都显著正相关(r分别为0.722和0.745,p〈0.01).

  14. Succession of Abundance and Community Structure of Ammonia-Oxidizing Archaea in Paddy Soil During Flooding%淹水水稻土中氨氧化古菌丰度和群落结构演替特征

    Institute of Scientific and Technical Information of China (English)

    宋亚珩; 王媛媛; 李占明; 王保莉; 曲东

    2014-01-01

    Ammonia-oxidizing archaea(AOA)play an important role in ammonium oxidation in soil ecosystem, and predominate among am-monia-oxidizing prokaryotes in paddy soils. In this study, dynamic changes of abundance and community structures of ammonia-oxidizing archaea were investigated in paddy soils that were flooded for 1 h, 1 d, 5 d, 10 d, 20 d, 30 d, 40 d and 60 d, using sequential analysis and real-time PCR. The abundance of bacteria was 29 times that of crenarchaeota, while AOA was 4 times ammonia-oxidizing bacteria(AOB). Based-on arch-amoA gene, OTU analysis showed that the AOA community structures shifted at different flooding times:T12, a type of AOA and r-strategist organism, was present only at the early flooding time. T4, T5 and T9, k-strategist organisms, existed at the late flooding time. T1, T8 and T16, r-k-strategist symbiotic organisms, appeared during whole flooding period. AOA predominated at the late flooding time. The diversity index of dominant groups was larger at the early flooding than at the middle and late flooding times. Sequencing results showed that all 16 dominant OTU types belonged to crenarchaeota, and had a close relationship with AOA from paddy soil, dry highland soil, red soil and sediments in different regions.%采用淹水非种植水稻土微环境模式系统,对水稻土进行1 h和1、5、10、20、30、40、60 d淹水培养,利用序列分析和Real-time PCR技术分析淹水培养过程中氨氧化古菌(AOA)的丰度和群落结构变化规律。结果表明,淹水水稻土中细菌(Bac)的丰度是泉古菌(Cre)的29倍以上,而氨氧化古菌(AOA)是氨氧化细菌(AOB)的4倍之多,淹水过程改变了细菌、泉古菌、氨氧化细菌和氨氧化古菌的丰度。基于Arch-amoA基因的OTU分析显示淹水过程中AOA的群落结构发生了演替性变化:T12是r策略生存的AOA,仅存在于淹水初期;T4、T5和T9是k策略生存的AOA,存在于淹水后期;T1、T8和T16

  15. 多年蔬菜连作对土壤氨氧化微生物群落组成的影响%Effects of Continuous Cropping of Vegetables on Ammonia Oxidizers Community Structure

    Institute of Scientific and Technical Information of China (English)

    孟德龙; 杨扬; 伍延正; 吴敏娜; 秦红灵; 朱亦君; 魏文学

    2012-01-01

    Investigations were conducted on the effects of intensive application of chemical fertilizers in crop production on soil nitrifier communities and the relationship between nitrifier communities and soil nitrification ability.Two series of vegetable soils were selected from Huangxing,Changsha,reflecting continuous vegetable cropping with about 20 years and new vegetable field with only about 2 years vegetable growing history.In each series five independent topsoils(0-20 cm) were sampled and each soil was a mixture of 10 cores randomly taken in the same field.Terminal restriction fragment length polymorphism(T-RFLP) and quantity PCR(Q-PCR) were used to determine the composition and abundance of ammonia-oxidizing bacteria(AOB) and ammonia-oxidizing archaea(AOA) communities.Results indicated that long-term and continuous vegetable cropping obviously changed the compositions of both AOB and AOA amoA gene,soil pH and Olsen-P content were the dominant factors affecting the composition of AOB amoA.In the vegetable soils,although the copy number of AOA amoA gene was about 5 times higher than AOB amoA gene,no significant correlation was detected between AOA amoA gene abundance and soil nitrification rate.It was not sure whether long-term and continuous vegetable cropping could shift the abundance of AOB and AOA,but it resulted in the enrichment of some dominant AOB species and increase of soil nitrification potential(PNF).%为揭示农业生产中长期大量施用化学肥料对土壤硝化过程微生物种群的影响及其与土壤硝化能力的偶联关系,本研究通过在长沙黄兴蔬菜基地采集长期连作蔬菜(20 a以上,VL)和短期蔬菜种植地(2 a左右,VS)表层土壤(0~20 cm),利用末端限制性片段多态性(T-RFLP)和实时定量PCR(Q-PCR)等手段系统研究了蔬菜连作对氨氧化细菌(ammonia-oxidizingbacteria,AOB)和氨氧化古菌(ammonia-oxidizing archaea,AOA)的组成和丰度的

  16. Ammonia-oxidizing bacterial community composition in the nitrifying biofilter of Recirculating Aquaculture System%循环海水养殖系统硝化滤器中氨氧化微生物分析

    Institute of Scientific and Technical Information of China (English)

    刘长发; 姚敬元; 袁瑗; 刘卫东

    2012-01-01

    研究循环水养殖硝化滤器裁体上附着生物膜的微生物群落结构可以为提高其处理速率和数率,并为特异性工程菌构建提供依据.采用改良的AFLP方法分析了循环水养殖硝化滤器载体上附着的氨氧化细菌16S rRNA基因和氨单加氧酶amoA基因片段及其系统发育情况.结果表明:分析16S rRNA基因得到的序列片段比分析amoA基因片段得到了更多信息,准确度较高,可作为分析循环水养殖硝化滤器氨氧化茵群组成的有效方法.克隆测序所得序列与网上公布数据比对,可见存在于循环水养殖硝化滤器载体上的氨氧化细菌与Nitrosomonas cryotolerans、Nitrosomonas oligotropha、Nitrosospira tenuis、Nitrosomonasmarina相似度达100%,与Nitrosomornas aestuarii相似度为87%.大部分属于亚硝化单胞茵属(Nitrosomonns),仅少数序列属于亚硝化螺茵属(Nitrosospira).采用16S rRNA基因和amoA片段分析方法得到的附着于封闭循环海水养殖硝化滤器载体上的氨氧化细菌主要为变形茵(Proteobacteria)的β-亚类的亚硝化单胞茵属(Nitrosomonas)和少量的亚硝化螺茵属(Nitrosospira)氨氧化细菌,以及一定数量的y-亚类氨氧化细菌.%Ammonia-oxidizing bacteria (AOB) play an important role in transformation from ammonia nitrogen to nitrite nitrogen in the nitrifying biofilter.Studying community structure of nitrifying organisms adhered on the media of nitrification biofilter in the recirculating aquaculture system (RAS) could provide a basis of improving removal rate and performance of biofilter,and construction of nitrifying engineering bacteria for removal of ammonia from RAS.The PCR-based gene cloning and mapping of 16S rRNA gene and betaproteobacteria ammonia monooxygenase subunit A (amoA) gene of ammonia-oxidizing bacteria isolated from nitrification biofilter were surveyed by using the method of improved amplified fragment length polymorphism (AFLP) analysis.The results showed that

  17. 氨氧化工艺(AMOXP)处理高氨氮有机废水%Ammonia oxidation process for the treatment of organic wastewater containing high-cncentration ammonia nitrogen

    Institute of Scientific and Technical Information of China (English)

    刘卫霞; 张科; 刘天宇; 李丽; 高照吉

    2015-01-01

    介绍了某生物工程厂采用厌氧工艺(循环式颗粒污泥反应器,即MQIC反应器)、氨氧化工艺和絮凝沉淀池处理厂区生产废水,处理量为10000 m3/d,该工艺系统对原水中COD、NH4+-N、TN的去除率分别可达97%、98%、90%,运行稳定,整个工艺处理出水水质可达到园区接管要求。同时,对厂区MQIC反应器和氨氧化工艺的启动调试进行了阐述,实践证明该工艺系统对处理高氨氮有机废水效果显著。%The plant-produced wastewater of a bioengineering plant has been treated by anaerobic process (circula-ting granula sludge reactor,i.e. MQIC reactor),ammonia oxidation process and flocculation-sedimentation tank, whose treatment capacity is 10 000 m3/d. The removing rates of COD,NH4+-N and TN are 97%,98% and 90%, respectively. The operation is stable and the effluent water quality could meet the acceptable requirements specified by the industrial park. In addition,the statement on the start-up and debugging for MQIC reactor and AMOXP are made. The practice proves that this process has remarkable effect on the treatment of organic wastewater containing highly concentrated ammonia nitrogen.

  18. 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.

  19. 给水厂废弃铁铝泥对湖泊沉积物好氧氨氧化作用的影响%Influence of ferric and aluminum residuals on ammonia oxidation in lake sediment

    Institute of Scientific and Technical Information of China (English)

    刘娟凤; 王昌辉; 王志新; 裴元生

    2015-01-01

    给水厂废弃铁铝泥(Ferric and aluminum residuals,FARs)可用于控制湖泊沉积物磷释放.因此,在实际应用之前对FARs的风险进行评估非常重要.本研究通过室内富集实验,考察FARs对沉积物中氨氧化菌(ammonia-oxidizing bacteria,AOB)活性、丰度和多样性的影响.结果表明:投加FARs后,沉积物对氨氮的去除能力微弱提高.富集后沉积物中AOB丰度增加,投加FARs的沉积物中AOB丰度达到1.32×108 copies· g-1,而未投加FARs的沉积物中AOB丰度为1.14× 108 copies·g-1.此外,amoA基因的系统发育分析表明富集前后沉积物中的AOB均附属于Nitrosospira和Nitrosomonas两个种属,并且投加FARs沉积物中AOB的多样性略高于未投加的.综上结果表明,FARs回用于湖泊富营养化控制的同时,将有益于沉积物中好氧氨氧化作用的进行.

  20. Catalytic ammonia oxidation to nitrogen (I) oxide

    OpenAIRE

    MASALITINA NATALIYA YUREVNA; SAVENKOV ANATOLIY SERGEEVICH

    2015-01-01

    The process of synthesis of nitrous oxide by low-temperature catalytical oxidation of NH has been investigated for organic synthesis. The investigation has been carried out by the stage separation approach with NH oxidation occurring in several reaction zones, which characterized by different catalytic conditions. The selectivity for N₂O was 92–92,5 % at the ammonia conversion of 98–99.5 % in the optimal temperature range.

  1. Cloning and Sequencing of Ammonia-Oxidizing Bacteria amoA Gene from Environmental Samples%环境样品中亚硝酸细菌amoA基因的克隆与测序

    Institute of Scientific and Technical Information of China (English)

    周娟; 李君文; 郑金来; 王新为; 宋农; 古长庆

    2004-01-01

    对从环境样品中分离的亚硝酸细菌(Ammonia-oxidizing bacteria)amoA基因进行克隆与测序,为构建基因工程菌打下基础.采用亚硝酸细菌选择性培养基,从4个不同的畜牧养殖污水处理厂采集的样品(分别编号为1,2,3,4)在室温下富集培养2个月后,采取酚氯仿抽提的方法提取DNA.根据已报道的亚硝化单胞菌(Nitrosomonas sp.)amoA基因序列,设计引物AMOB/AMOE,并在AMOB,AMOE的5′-端分别加上了BamHⅠ和HindⅢ的限制性酶切位点,以利于进一步酶切和克隆.用AMOB/AMOE对4种样品的DNA进行PCR扩增,PCR产物进行琼脂糖凝胶电泳分析.结果表明,4种样品中1号和3号样品扩增得到预期长度的DNA片段,2号和4号样品扩增没有得到预期片段.回收纯化PCR产物与pGEM-T载体连接,构建amoA基因测序载体,并转化E.coli M15.测序结果提交GenBank进行Blast分析.结果显示,扩增得到的DNA片段均与Nitrosomonas sp.GH22的amoA基因有99.7%的同源性,可从环境中分离的亚硝酸细菌中克隆出amoA基因.

  2. 利用RFLP分析DO对附积床系统中AOB群落结构的影响%Analysis of ammonia-oxidizing bacteria in catching bed reactor at different DO concentrations by RFLP

    Institute of Scientific and Technical Information of China (English)

    张岩; 朱敏; 刘焕光; 孙凤侠; 甘志明; 陈敬; 史杨; 谢杭冀

    2014-01-01

    To investigate the influence of DO concentration on the characteristics of catching bed reactor, the removal efficiency of COD, NH4+-N and TN were analyzed under the DO concentrations at 1.0~2.0mg/L, 2.0~3.0mg/L and 3.0~4.0mg/L, respectively. Meanwhile, ammonia-oxidizing bacteria (AOB) community and diversity in each reactor were examined using restricted fragment length polymorphism (RFLP), and sequencing of amoA genes. The results showed that higher COD and NH4+-N removal efficiency were received under different DO concentrations, NH4+-N removal efficiency increased with the DO concentration increase. The diversity of AOB was abundant in different DO concentrations, but the communities and species of AOB were effect greatly by DO concentration.%为了解析DO浓度对附积床反应器脱氮系统中COD、NH4+-N、TN去除效率的影响,以及对氨氧化菌群(AOB)结构及多样性的影响,分析了DO分别为1.0~2.0,2.0~3.0,3.0~4.0mg/L时COD、NH4+-N、TN去除效率,并采用针对AOB功能基因氨单加氧酶(amoA)的限制性内切酶片段长度多态性技术(RFLP)分析了三组DO浓度下反应器中AOB的群落结构及多样性.结果表明,不同DO条件下,系统均取得较高的COD和NH4+-N的去除效果, NH4+-N的去除效率随着DO的增加而提高.不同DO浓度下反应器生物膜上AOB菌群多样性丰富,且与DO对AOB菌群的多样性影响较小相比,DO对AOB的菌群结构及种类的影响较大.

  3. Comparison and Analysis of Diversity of Ammonia-Oxidizing Bacteria amoA Gene in Jujube-Cotton Intercropping and Monoculture under Different Planting Patterns%枣树棉花间作与单作土壤氨氧化细菌amoA 基因多样性的比较与分析

    Institute of Scientific and Technical Information of China (English)

    何贵伦; 罗明; 韩剑; 徐金虹; 王纯利; 朱建雯

    2015-01-01

    以编码氨单加氧酶基因 amoA 作为氨氧化细菌的功能基因标志物,采用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)和扩增产物序列分析方法,研究南疆枣树与棉花间作和单作不同栽培模式下土壤氨氧化细菌群落结构和多样性差异以及与土壤理化因子的相关性.结果表明,枣树与棉花间作改变了土壤氨氧化细菌群落结构组成,与纯枣林、单作棉田差异显著,相似性低于60%.间作复合系统内冠下区、近冠区及不同层次的土壤中氨氧化细菌群落结构具有水平和垂直方向的空间变异性.系统发育分析表明,枣树与棉花间作、纯枣林和单作棉田土壤中氨氧化细菌均隶属于β-变形菌纲(β-Proteobacteria)的亚硝化螺菌属(Nitrosospira )和不可培养的氨氧化细菌,以 Nitrosospira cluster 3a 为优势菌.间作土壤中还有 cluster 3b、cluster 1和 cluster 4,群落组成较单作丰富.典范对应分析结果显示,有机碳(TOC)、全磷(TP)、速效磷(RP)和硝态氮(NO 3-N)含量对不同种植模式下氨氧化细菌的种群结构影响显著(P <0.05).枣树与棉花间作显著提高了土壤氨氧化细菌的多样性,Shannon 指数、均匀度指数和丰富度均高于纯枣林和单作棉田.土壤全磷、铵态氮、硝态氮、pH 值和土壤含水量是显著影响多样性指数的关键理化因子(P <0.05).%Using amoA gene encoding ammonia monooxygenase as functional gene marker of ammonia-oxidizing bacteria,polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE)tech-nique and sequence analysis method of amplified products were used to analyze the difference from commu-nity structure and diversity of soil ammonia-oxidizing bacteria in the Southern Xinjiang under different cul-tivation modes of jujube and cotton intercropping and monoculture,which correlated with soil physical and chemical factors.The results revealed that jujube and cotton intercropping

  4. 牛场肥水灌溉对土壤氨氧化微生物的影响%Effects of Cattle Farm Effluent Irrigation on Community Structure and Abundance of Ammonia-Oxidizing Bacteria in Soil

    Institute of Scientific and Technical Information of China (English)

    王婷; 刘丽丽; 张克强; 沈仕洲; 冯洁; 王风; 杜会英; 高文萱

    2015-01-01

    Ammonia-oxidizing bacteria(AOB)and ammonia-oxidizing archaea(AOA)play important roles in the biogeochemical cycle of N element, which is closely related to soil quality, greenhouse gas emissions and NO-3 leaching. Therefore, diversity and composition of soil AOB and AOA are valuable indicators for soil quality monitoring. In this study, the effects of five fertilization treatments, including control without fertilizers(CK), conventional fertilization(CF 300 kg N·hm-2)and three irrigation treatments with cattle farm effluent(T4 105 kg N· hm-2, T5 210 kg N·hm-2 and T11 317 kg N·hm-2), on the diversity and composition of AOA and AOB were determined through terminal re-striction fragment length polymorphism(T-RFLP)of aomA gene(encoding ammonia monooxygenase). Results showed that the diversity in-dices, Shannon-Wiener(H′)and Pielou(E), of AOB were the highest in the T5 treatment, while they were the lowest in the T11 treatment. Phylogenetic tree analysis indicated that the AOB in the soil mainly belonged to Nitrosospira and Nitrosomanas. However, the indices of Shannon-Wiener(H′),Simpson(Ds)and Pielou(E)of AOA were the highest in the T11 treatment, but the lowest in the CF treatment. AOA aomA gene sequences showed that most sequences of AOA were clustered with Cluster S. The dominant AOB was similar to one species from the rumen of China Holstein cow, which was a clue of community evolution in cattle effluent irrigated farmland. The present re-sults indicate that cattle effluent irrigation could affect the diversity and abundance of soil AOA.%以不同牛场肥水灌溉制度下河北省徐水县梁家营长期定位施肥试验田为研究对象,通过构建氨氧化细菌和氨氧化古菌的amoA 基因克隆文库,利用T-RFLP方法研究了5种施肥处理(CK:不施肥;CF:300 kg N·hm-2,120 kg P2O·hm-2,75 kg K2O·hm-2;T4:105 kg N·hm-2,39 kg P2O5·hm-2;T5:210 kg N·hm-2,78 kg P2O5·hm-2;T11:317 kg N·hm-2,117 kg P2O5·hm-2

  5. Metagenome analysis of a complex community reveals the metabolic blueprint of anammox bacterium ‘Candidatus Jettenia asiatica’

    Directory of Open Access Journals (Sweden)

    ZiyeHu

    2012-10-01

    Full Text Available Anammox bacteria are key players in the global nitrogen cycle and responsible for up to 50% of global nitrogen loss. Because of their cost effective application in anaerobic nitrogen removal, the anammox bacteria are widely implemented in wastewater treatment. Currently, five genera of anammox bacteria have been identified, together forming a deep branching order in the Planctomycetes-Verrucomicrobium- Chlamydiae (PVC superphylum. Members of all genera have been detected in wastewater treatment plants, but metagenomic information is not yet available for all genera. Here we report the metagenomic analysis of an enrichment dominated by ‘Candidatus Jettenia asiatica’. The whole microbial community o\tf a granular sludge anammox reactor was sequenced using both illumina and 454 pyrosequencing. The sludge was previously shown to have a ~50% enrichment of the anammox bacterium ‘Candidatus Jettenia asiatica’ by 16S rRNA gene analysis. After de novo assembly 37,432 contigs with an average length of 571 nt were obtained. The contigs were then analyzed by BLASTx searches against the protein sequences of ‘Candidatus Kuenenia stuttgartiensis’ and a set of 25 genes essential in anammox metabolism were detected. Additionally all reads were mapped to the genome of an anammox strain KSU-1 and de novo assembly was performed again using the reads that could be mapped on KSU-1. Using this approach, a gene encoding copper-containing nitrite reductase NirK was identified in the genome, instead of cytochrome cd1-type nitrite reductase NirS that is responsible for the nitrite reduction of ‘Ca. Kuenenia stuttgartiensis’ and ‘Ca. Scalindua profunda’. Finally, the community composition was investigated through MetaCluster analysis, 16S rRNA gene analysis and read mapping, which showed the presence of other important community members such as aerobic ammonia-oxidizing bacteria, methane producing microorganisms and denitrifying methanotroph 'Ca

  6. A first insight into the occurrence and expression of functional amoA and accA genes of autotrophic and ammonia-oxidizing bathypelagic Crenarchaeota of Tyrrhenian Sea

    Science.gov (United States)

    Yakimov, Michail M.; Cono, Violetta La; Denaro, Renata

    2009-05-01

    The autotrophic and ammonia-oxidizing crenarchaeal assemblage at offshore site located in the deep Mediterranean (Tyrrhenian Sea, depth 3000 m) water was studied by PCR amplification of the key functional genes involved in energy (ammonia mono-oxygenase alpha subunit, amoA) and central metabolism (acetyl-CoA carboxylase alpha subunit, accA). Using two recently annotated genomes of marine crenarchaeons, an initial set of primers targeting archaeal accA-like genes was designed. Approximately 300 clones were analyzed, of which 100% of amoA library and almost 70% of accA library were unambiguously related to the corresponding genes from marine Crenarchaeota. Even though the acetyl-CoA carboxylase is phylogenetically not well conserved and the remaining clones were affiliated to various bacterial acetyl-CoA/propionyl-CoA carboxylase genes, the pool of archaeal sequences was applied for development of quantitative PCR analysis of accA-like distribution using TaqMan ® methodolgy. The archaeal accA gene fragments, together with alignable gene fragments from the Sargasso Sea and North Pacific Subtropical Gyre (ALOHA Station) metagenome databases, were analyzed by multiple sequence alignment. Two accA-like sequences, found in ALOHA Station at the depth of 4000 m, formed a deeply branched clade with 64% of all archaeal Tyrrhenian clones. No close relatives for residual 36% of clones, except of those recovered from Eastern Mediterranean, was found, suggesting the existence of a specific lineage of the crenarchaeal accA genes in deep Mediterranean water. Alignment of Mediterranean amoA sequences defined four cosmopolitan phylotypes of Crenarchaeota putative ammonia mono-oxygenase subunit A gene occurring in the water sample from the 3000 m depth. Without exception all phylotypes fell into Deep Marine Group I cluster that contain the vast majority of known sequences recovered from global deep-sea environment. Remarkably, three phylotypes accounted for 91% of all Mediterranean

  7. 施肥对设施菜地氨氧化细菌群落和丰度的影响%Effects of Fertilization Treatments on Community Structure and Abundance of Ammonia-oxidizing Bacteria in Greenhouse Soil

    Institute of Scientific and Technical Information of China (English)

    王亚男; 曾希柏; 俄胜哲; 白玲玉; 李莲芳; 苏世鸣; 沈灵凤

    2012-01-01

    The effects of five fertilization treatments on the community structure and abundance of ammonia-oxidizing bacteria(AOB ) were determined by the combination of terminal restriction fragment length polymorphism(T-RFLP) and real-time quantitative PCR in the greenhouse soils in Wuwei City of Gansu Province. The results by cloning and sequencing of amoA gene fragments showed that the AOB community in soils for all treatments consisted of two major groups, i.e. Nitrosospira cluster 3 and Nitrosomanas cluster 7. The sequences related to Ni-trosospira cluster 3 were predominant. The highest abundance of the AOB both in 0~20 cm and 20~40 cm soil layers were detected in the fertilization treatment which is the half of the farmer's conventional amount( 1/2MNPK), while the amoA gene copy number was with 9.95×107 and 6.65×107 copies·g-1 soil respectively, which was 105.0% and 315.3% higher respectively in 0-20 cm and 20-40 cm soil layers for 1/2MNPK treatment than that in the unfertilized treatment. Both fertilizer types and soil layers were the important factors that deduced the changes of AOB community and abundance. The results had significant references to the further exploring characteristic and adaptation mechanism of AOB in the soil nitrogen cycle under facility cultivation conditions.%以甘肃武威设施菜地为对象,采用amoA基因末端限制性片段多态性分析(PCR-TRFLP)技术与实时荧光定量PCR(Realtime PCR)相结合的方法,研究了不同施肥处理下土壤中氨氧化细菌群落组成和丰度的变化.结果表明:设施菜地中氨氧化细菌的优势种群均为Nitrosospira cluster 3属,亦含有少量Nitrosomanas cluster 7属.定量PCR分析发现在当地农民习惯施肥用量一半的处理下(1/2 MNPK),0~20 cm和20~40 cm土层中氨氧化细菌的丰度最大值分别为每克干土9.95×107、6.65×107拷贝数,比不施肥处理增加了105.0%和315.3%.施肥类型、土壤层次均是导致氨氧化细菌群落结

  8. Dynamic changes of ammonia-oxidizing archaea community structure during aerobic composting of chicken manure%鸡粪好氧堆肥过程中氨氧化古菌群落结构的动态变化

    Institute of Scientific and Technical Information of China (English)

    解开治; 徐培智; 张发宝; 唐拴虎; 顾文杰; 黄旭; 蒋瑞萍; 卢钰升

    2012-01-01

    The polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was used to investigate the community structure and species diversity of ammonia-oxidizing archaea (AOA) during poultry species composting. The results show that the AOA community structure and species diversity at different stages of chicken manure composting are markedly changed, and the band b, which shows 96% similarity to the AOA HH - 2 (GU225872. 1 ) and band m, which shows 99% similarity to the uncultured Crenarchaeote NM-152 ( HQ875225.1 ) , represent the major AOA bacterial species during the composting. The bands c, b, f and i, and the bands m, k, ] and n represent the species of the two populations of bacteria, respectively. Shannon-Weiner index (H) and evenness index (EH) of the AOA colonies are different at different stages of the eomposting, and the following order is : day 30 〉 day 5 〉 day 25 ≈ day 45 〉 day 3 ≈ day 12 〉 day 1 ≈ day 15. The redundancy analysis of the AOA colonies at different stages of the composting shows that the AOA colony evolution is all significantly affected by the composting temperature, whole nitrogen, ammonia nitrogen and nitrate nitrogen (P 〈0. 05 ), while pH is not affected. The AOA community structure is changed markedly on days 1,5, 15, 30 and 45 of the composting. These results indicate that several parameters could control AOA community structure during composting of chicken manure.%应用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)技术,研究了好氧堆肥过程氨氧化古菌(ammonia-oxidizingarchaea,AOA)的群落结构和多样性变化。结果表明,不同堆肥时期鸡粪好氧堆肥AOA菌群的群落结构发生了明显的变化。与AOAHH-2(GU225872.1)亲缘关系较近的b条带(相似性96%)和未培养泉古菌属[uncuhured crenarchaeoteNM-152(HQ875225.1)]的m条带(相似性99%)是堆肥过程一直存在的AOA菌属。条带C、b、f、i和条带m、k、1

  9. IDENTIFICATION OF THE BACTERIUM TOMATO STEM CANKER

    Directory of Open Access Journals (Sweden)

    Goner A. Shaker

    2014-01-01

    Full Text Available Diseased tomato samples were collected from green house was evaluated for isolation, pathogenicity and biochemical tests. The symptoms of the infected tomato plants were as sudden wilting after curled on leaves and necrotic streak regions developed at the crown and base of the stem and the cavities deepen and expand up and down, brown discoloration and necrosis occurring on xylem and phloem vasculer. All of ages of tomato plant were susceptible to bacteria when the weather condition favorable and immediately, seen collapse symptom on tomato plant at once fail and die. The bacterium was isolated from diseased plant in all regions on nutrient Agar; a yellow bacterium was isolated from infected tomato plant in green houses and fields in Abu-Ghraib, Rashiedia and Qanat Al-Geiaysh nurseries in Baghdad provinces of Iraq. The bacterium was found gram positive, rod-shaped, non-motile and capable an aerobic growth and based on the morphological and biochemical characteristics revealed that this bacterium belongs to: Clavibacter michiganensis subsp. michiganensis. (smith pathogenicity and hypersensitivity of the bacterium Cmm showed the disease index were 18.33, 6.66, 16.66, 5, 0% for tomato seedlings were inoculated treatments as the wounding roots, without wounding roots, crown of the stem, petiole and control respectively.

  10. 两个 CANON 污水处理系统中氨氧化古菌的丰度和多样性研究%Abundance and Community Composition of Ammonia-Oxidizing Archaea in Two Completely Autotrophic Nitrogen Removal over Nitrite Systems

    Institute of Scientific and Technical Information of China (English)

    高景峰; 李婷; 张树军; 樊晓燕; 潘凯玲; 马谦; 袁亚林

    2015-01-01

    Ammonia oxidation is the first and rate-limiting step of nitrification, which was thought to be only performed by ammonia-oxidizing bacteria (AOB). In recent years, ammonia-oxidizing archaea (AOA) was also confirmed to take part in ammonia oxidation. The diversity and abundance of AOA have been investigated in various environments, however, little is known regarding the AOA in the completely autotrophic nitrogen removal over nitrite ( CANON) wastewater treatment process. In this study, the abundance and diversity of AOA were investigated in the biofilm and flocculent activated sludge collected in a lab-scale (L) CANON system and a pilot-scale (P) CANON systems, respectively. The quantitative real time PCR (qPCR) was applied to investigate the abundance of AOA and the diversity of AOA was determined by polymerase chain reaction ( PCR), cloning and sequencing. The qPCR results showed that the average abundance of AOA amoA gene of L and P was 2. 42 × 106 copies·g - 1 dry sludge and 6. 51 × 106 copies·g - 1 dry sludge, respectively. The abundance of AOA in biofilm was 10. 1-14. 1 times higher than that in flocculent activated sludge. For P system, the abundance of AOA in flocculent activated sludge was 1. 8 times higher than that in biofilm. The results indicated that the abundance of AOA might be affected by different sludge morphology. The diversity of AOA in P system was extremely limited, only one OTU was observed, which was classified into Nitrosopumilus subcluster 5. 2. The diversity of AOA in L system was higher, eight OTUs were observed, which were classified into five genera: Nitrososphaera subcluster 9, subcluster 8. 1, subcluster 4. 1, subcluster 1. 1 and Nitrosopumilus subcluster 5. 2. The diversity and abundance of AOA were different in CANON systems with different sludge morphology. AOA may play an important role in ammonia oxidation in CANON system.%近期,氨氧化古菌(ammonia-oxidizing archaea,AOA)在各类环境中的发现,打破了人们原

  11. Microflora of urogenital tract in pregnancy with asymptomatic bacterium

    International Nuclear Information System (INIS)

    The article contains results of research interrelationship from colonization of vagina and urinary tract diseases. E.coli one of the main factors in development asymptomatic bacterium. Presented high effects of penicillin medicaments and nitrofurans in treatment of asymptomatic bacterium

  12. Long-term Fertilization Determining Ammonia-oxidizing Organism Abundance and Distribution in Dry Highland Soil of Loess Plateau%长期施肥对旱地土壤中氨氧化微生物丰度和分布的影响

    Institute of Scientific and Technical Information of China (English)

    辛亮; 武传东; 曲东

    2012-01-01

    采用基于氨单加氧酶基因(amoA)的荧光定量PCR技术,以黄土高原旱地土为材料,研究长期施肥对土壤氨氧化细菌和氨氧化古菌丰度的影响,并分析环境因素与氨氧化菌丰度的关系.以不施肥土壤为对照(CK),设置3个施肥处理,分别为单施磷肥(P),氮、磷共施(NP)和氮、磷、有机肥共施(NPM)3个处理.结果表明,不同处理氨氧化菌amoA基因拷贝数为1.326×106~1.886×106 g1,各处理间氨氧化细菌丰度差异不显著;氨氧化古菌的arch-amoA基因拷贝数为1.329×106~4.510×106 g-1,表现为处理NPM> NP>CK>P,NPM处理为对照的3.314倍,二者呈现显著性差异.采用DCCA法对4个处理进行环境相似度分类,结果显示,P和NPM处理、CK和NP处理分别构成了2个相似类群;4个处理和12个环境因子的关联(CCA)分析表明,不同处理中的氨氧化微生物活跃度以及氨氧化过程强度表现为处理NMP>NP>CK>P;不同环境因子和不同施肥处理生境相似度分布存在不同的关系,其中反映氨氧化过程的硝态氮含量、氨氧化细菌和氨氧化古菌丰度,以及代表微生物生长主要环境因素的pH值、含水量、全氮和有机碳含量与不同施肥处理导致的生境相似度的分布关系最为紧密.%Real-time PCR with primers targeting Ammonia monooxygenase subunit A gene iamoA) was performed to quantify abundance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing ar-chaea (AOA) in dry highland soilt long-term fertilized, from Loess Plateau. We also investigated the relationship between environmental factors and abundance of ammonia-oxidizing organism. The treatments were no fertilizer (CK), phosphate (P), nitrogen/phosphate fertilizers (NP), and NP combined with organic fertilizer (NPM). We found that fertilization caused no significant difference on the amoA gene copy numbers of AOB arranging from 1, 326× 106 to 1. 886 × 106 copies · g-1 dry soil. In contrast, abundance of

  13. 长期施用氮肥和磷肥对渭北旱塬土壤中氨氧化古菌多样性的影响%Effects of Long-term Nitrogen and Phosphate Fertilization on Diversity of Ammonia-Oxidizing Archaea in Dry Highland Soil of Loess Plateau, China

    Institute of Scientific and Technical Information of China (English)

    武传东; 闫倩; 辛亮; 王保莉; 曲东

    2012-01-01

    Ammonia-oxidizing archaea are likely the most abundant ammonia-oxidizing microbes in natural environment and they also play an important role in nitrification. In order to improve nitrogen use efficiency and explicate the indicating function of ammonia-oxidizing ar-chaea( AOA) on changes of soil quality in the Loess Plateau, AOA community structure diversity was studied. The soil samples used in this research derived from Changwu Agro-ecological Experimental Station on the Loess Plateau, Chinese Academy of Sciences, which had received 23 years continuous fertilization treatments, include CK (control, without fertilizers), LD (unplanted, without fertilizers), N(nitrogen input), P(phosphorus input) and NP(combination of nitrogen and phosphorus fertilizers). The soil AOA community structure diversity was analyzed by restriction fragment length polymorphism(PCR-RFLP) and DNA sequence. Positive clones collected randomly from clone libraries were digested by Rsa I and Msp I, respectively. According to the statistics of diversity index, there were 25, 18, 29, 20 and 30 restriction endonuclease types(OTUs), respectively. The a diversity indices indicated that there was a pronounced difference among five fertilizer treatments. The OTUs were the highest in both P treatment and CK treatment, while the lowest in NP treatment. The rescaled distance matrix tree indicated that the different fertilization had weak convergence of AOA community types with the CK treatment soil. Phylogenetic tree of amoA gene amino acid sequences analysis showed all AOA sequences fell within cluster S and cluster M, but the proportions were different. These results indicated that long-term fertilization resulted in change of AOA community diversity; however, different fertilizer alkaline soil had no significant impact on the species composition of dominant AOA.%采用基于氨单加氧酶基因的PCR-RFLP和DNA测序技术,以黄土高原旱地黑垆土为材料,研究长期施用氮肥和磷肥对

  14. Isolation of a Bacterium Strain Degraded Agar

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    One in 58 strains of bacteria isolated from the compost showed clear colonies after a few days of growth on the plates containing medium made of only agar and water.Water suspension contained only agar (2 and 8g·L -1 ) with two controls (normal saline,LB medium) was inoculated with the bacterium BR5-1 to see whether there was an increasement of the alive bacteria concentration after 48 h of the growth.The results showed that there was a significant rising of the alive bacteria concentration in the agar susp...

  15. Biodegradation of heavy oils by halophilic bacterium

    Institute of Scientific and Technical Information of China (English)

    Ruixia Hao; Anhuai Lu

    2009-01-01

    A halophilic bacterial strain TM-1 was isolated from the reservoir of the Shengli oil field in East China. Strain TM-1, which was found to be able to degrade crude oils, is a gram-positive non-motile bacterium with a coccus shape that can grow at temperatures of up to 58 ℃ and in 18% NaCl solution. Depending on the culture conditions, the organism may occur in tetrads. In addition, strain TM-1 pro-duced acid from glucose without gas formation and was catalase-negative. Furthermore, strain TM-I was found to be a facultative aer-obe capable of growth under anaerobic conditions. Moreover, it produced butylated hydroxytoluene, 1,2-benzenedicarboxylic acid-bis ester and dibutyl phthalate and could use different organic substrates. Laboratory studies indicated that strain TM-1 affected different heavy oils by degrading various components and by changing the chemical properties of the oils. In addition, growth of the bacterium in heavy oils resulted in the loss of aromatic hydrocarbons, resins and asphaltenes, and enrichment with light hydrocarbons and an overall redistribution of these hydrocarbons.

  16. 氮素和水分添加对贝加尔针茅草原土壤氨氧化微生物群落结构的影响%Differential Responses of Ammonia-oxidizers Communities to Nitrogen and Water Addition inStipa baicalensis Steppe, Inner Mongolia, Northern China

    Institute of Scientific and Technical Information of China (English)

    王杰; 李刚; 赖欣; 宋晓龙; 赵建宁; 杨殿林

    2015-01-01

    Atmospheric nitrogen deposition and precipitation as an important phenomenon of global climate change have a great impact on grassland ecosystems. However, little is known about how the soil ammonia-oxidizing microorganisms respond to the both changes. Ammonia oxidization is a crucial step in the soil nitrification and greatly inlfuenced by soil nitrogen availability. We used PCR and DGGE (denaturing gradient gel electrophoresis) approaches to investigate the responses of AOB (ammonia-oxidizing bacteria) 16S rRNA and AOA (ammonia-oxidizing archaea)amoA genes to nitrogen and water input inStipa baicalensis steppe, Inner Mongolia, northern China. After two years of nitrogen and water addition treatment, it was found that PNA (potential nitriifcation activity) was greatly enhanced by lower N fertilization treatment under water addition and higher N fertilization under no-water addition, while it decreased markedly in higher N fertilization under water addition. The community structure of AOB responded more sensitively to N fertilization and water input than AOA, resulting in the significantly decreased diversity in the AOB community along with a higher N fertilizer rate, but an obvious increase in the AOA community, demonstrating the active growth of AOA in higher N fertilization soils. Phylogenetic analysis showed that AOB communities were dominated byNitrosospira clusters3, 4 andNitrososmonas clusters 6 under water addition andNitrosospira culsters 1, 3 and 4 and under no-water addition, while AOA communities were grouped intoCrenarchaeote clusters 1, 2 and 5 under no-water addition and Crenarchaeote clusters 1, 2 and water lineage under water addition. The differences between the two water addition regimes strongly suggest that water input acts as an important role in shifting AOA and AOB communities. Moreover, in contrast to the AOA, the diversity of AOB was negatively correlated with total N, NH4+, NO3-andpH under water addition, implying a signiifcant N

  17. Effects of long-term N fertilizer application and liming on nitrification and ammonia oxidizers in acidic soils%长期施加氮肥及氧化钙调节对酸性土壤硝化作用及氨氧化微生物的影响

    Institute of Scientific and Technical Information of China (English)

    张苗苗; 王伯仁; 李冬初; 贺纪正; 张丽梅

    2015-01-01

    High levels of N fertilization and acid deposition could cause soil acidification directly and indirectly. The nitrogen cycle, especially nitrification, makes a great contribution to the acidification of agricultural soils across China, which further leads to the mobilization of potentially toxic metals such as aluminum ( Al ) and manganese ( Mn ) and decerases crop yields. Chemicals ( e. g., CaO) are amended as soil conditioners to relieve soil acidification. Ammonia oxidation, the rate-limiting step in the nitrification process, is driven by ammonia-oxidizing bacteria ( AOB) and ammonia-oxidizing archaea ( AOA) . Increasing evidence demonstrates that pH is one of the most important factors determining the niche separation of AOA and AOB, and AOA play the more important role in nitrification of acidic soils. However, abundant AOB have been detected in acidic soils but little is known about their ecological function. In this study, the effects of long-term N fertilization practices and liming on nitrification and ammonia oxidizers in acidic soils were investigated using quantitative PCR and DGGE methods combined with soil physiochemical analysis. Compared with a previous study conducted 6 years ago at the same site, N fertilizer application without liming further decreased soil pH (3.35—3.47) and potential nitrification rate (PNR) (0.02—0.14 μg NO-2-N g-1 soil h-1), while 2 years liming alleviated soil acidification (pH 4.10—4.46) and increased PNR (0.22—0.34μg NO-2-N g-1 soil h-1) significantly. There was a significantly positive correlation between soil pH and PNR, indicating the increase in soil pH via liming had positive effects on nitrification in acidic soils. AOA amoA gene copy numbers ( 7. 40 × 107—4. 08 × 108 copies/g ) were significantly higher than their counterpart AOB (1.67 × 106—2.57 × 107 copies/g) in soils that received different chemical N fertilizers. Ratios of AOA and AOB amoA gene abundance ranged between 10. 9 and 44. 3

  18. Ratoon stunting disease of sugarcane: isolation of the causal bacterium.

    Science.gov (United States)

    Davis, M J; Gillaspie, A G; Harris, R W; Lawson, R H

    1980-12-19

    A small coryneform bacterium was consistently isolated from sugarcane with ratoon stunting disease and shown to be the causal agent. A similar bacterium was isolated from Bermuda grass. Both strains multiplied in sugarcane and Bermuda grass, but the Bermuda grass strain did not incite the symptoms of ratoon stunting disease in sugarcane. Shoot growth in Bermuda grass was retarded by both strains. PMID:17817853

  19. Fluctuation-Enhanced Sensing of Bacterium Odors

    CERN Document Server

    Chang, Hung-Chih; King, Maria D; Kwan, Chiman

    2009-01-01

    The goal of this paper is to explore the possibility to detect and identify bacteria by sensing their odor via fluctuation-enhanced sensing with commercial Taguchi sensors. The fluctuations of the electrical resistance during exposure to different bacterial odors, Escherichia coli and anthrax-surrogate Bacillus subtilis, have been measured and analyzed. In the present study, the simplest method, the measurement and analysis of power density spectra was used. The sensors were run in the normal heated and the sampling-and-hold working modes, respectively. The results indicate that Taguchi sensors used in these fluctuation-enhanced modes are effective tools of bacterium detection and identification even when they are utilizing only the power density spectrum of the stochastic sensor signal.

  20. Abundances of Ammonia-oxidizing Prokaryotes and Gross Nitrification Activities in Forest Soils Under Different Vegetations in a Natural Reserve%土地利用方式对万木林土壤氨氧化微生物丰度的影响

    Institute of Scientific and Technical Information of China (English)

    黄蓉; 张金波; 钟文辉; 贾仲君; 蔡祖聪

    2012-01-01

    In this study, the relative contribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) to nitrification were investigated in acidic forested soils derived from granite in Wanmulin nature reserve, Jianou, Fujian Province of southern China. The abundances of AOA and AOB communities were determined by real-time quantitative polymerase chain reaction (qPCR), while gross nitrification activity was measured using "N-pool enrichment technique in soils under five different vegetations over 600 years plantation one orange cultivation system. The results showed that soil pH, the abundance of AOB and gross nitrification rate were significantly lower in natural vegetation soil than those soil cultivated with orange plant. Furthermore, a significant correlation between the population size of soil AOB and soil gross nitrification activity suggested that AOB might dominate autotrophic nitrification in forested soil typical of the low-pH ecosystems, particularly in orange soil. The copy number ratio of archaeal amoA to crcnarchaeota-specific 16S rRNA genes varied from 0.01% - 0.64% in all five natural vegetation soils while up to 5.32% in orange soil. The results indicated that not all archaea possessed ammonia-oxidizing functional gene of amoA and fertilization may facilitate AOA growth in soils cultivated with orange as well.%以我国亚热带地区典型花岗岩发育酸性红壤为研究对象,选取福建建瓯万木林自然保护区封禁保护下5种自然植被和1种人工种植植被土壤,采用荧光实时定量PCR (Real-time PCR)技术测定了土壤氨氧化细菌(AOB)和氨氧化古菌(AOA)的群落丰度,采用m5N稳定同位素成对标记和数值模型相结合的方法测定了土壤初级硝化速率.结果显示,长期封禁保护下的自然植被土壤 pH低,土壤AOB数量偏低.人为种植和管理显著提高了土壤pH,促进了AOB的生长,其丰度比自然条件下提高了2个数量级,土壤初级硝化速率也显著提高,并与AOB

  1. Analysis of the Diversity of Ammonia Oxidizing Bacteria with amoA Gene in Deep Returning Maize Straw Soils%玉米秸秆深翻还田土壤氨氧化细菌amoA基因多样性分析

    Institute of Scientific and Technical Information of China (English)

    萨如拉; 高聚林; 于晓芳; 闹干朝鲁; 青格尔; 赵吉睿

    2015-01-01

    以常规旋耕无秸秆还田(对照)、1年秸秆深翻还田、2年秸秆深翻还田土壤总DNA为模板,采用氨氧化细菌(Ammonia-oxidizing bacteria,AOB)的氨单加氧酶α亚基(amoA)基因特异性引物扩增AOB amoA基因,构建amoA基因文库.运用BLAST程序进行序列比较发现,玉米秸秆深翻还田土壤中分布有亚硝化弧菌属(Nitrosovibrio)、亚硝化螺菌属(Nitrosospira)和亚硝化单胞菌属(Nitrosomonas)微生物菌群,秸秆深翻还田土壤AOB amoA基因序列主要与保护性耕作、长期施肥、间作、温室和植被恢复土壤中的amoA基因序列相似;常规旋耕无秸秆还田土壤AOB amoA基因序列主要与秸秆焚烧大田土壤和内蒙古草原土的amoA基因序列相似.玉米秸秆深翻还田2年处理(SF-Ⅱ)AOB amoA基因多样性指数最高,其次是玉米秸秆深翻还田1年处理(SF-Ⅰ),常规旋耕无秸秆还田(CK)最低.

  2. Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711

    OpenAIRE

    Shoemaker, William R.; Muscarella, Mario E.; Lennon, Jay T

    2015-01-01

    We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural soil. The genome provides insight into the ecological strategies of this bacterium in free-living and host-associated environments.

  3. Trichloroethylene Biodegradation by a Methane-Oxidizing Bacterium

    OpenAIRE

    Little, C. Deane; Palumbo, Anthony V; Herbes, Stephen E.; Lidstrom, Mary E.; Tyndall, Richard L.; Gilmer, Penny J.

    1988-01-01

    Trichloroethylene (TCE), a common groundwater contaminant, is a suspected carcinogen that is highly resistant to aerobic biodegradation. An aerobic, methane-oxidizing bacterium was isolated that degrades TCE in pure culture at concentrations commonly observed in contaminated groundwater. Strain 46-1, a type I methanotrophic bacterium, degraded TCE if grown on methane or methanol, producing CO2 and water-soluble products. Gas chromatography and 14C radiotracer techniques were used to determine...

  4. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    Energy Technology Data Exchange (ETDEWEB)

    Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

    1994-06-01

    The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

  5. Formation of hydroxylamine on dust grains via ammonia oxidation

    CERN Document Server

    He, Jiao; Lemaire, Jean-Louis; Garrod, Robin T

    2015-01-01

    The quest to detect prebiotic molecules in space, notably amino acids, requires an understanding of the chemistry involving nitrogen atoms. Hydroxylamine (NH$_2$OH) is considered a precursor to the amino acid glycine. Although not yet detected, NH$_2$OH is considered a likely target of detection with ALMA. We report on an experimental investigation of the formation of hydroxylamine on an amorphous silicate surface via the oxidation of ammonia. The experimental data are then fed into a simulation of the formation of NH$_2$OH in dense cloud conditions. On ices at 14 K and with a modest activation energy barrier, NH$_2$OH is found to be formed with an abundance that never falls below a factor 10 with respect to NH$_3$. Suggestions of conditions for future observations are provided.

  6. Hotspots of anaerobic ammonia oxidation in land - freshwater interfaces

    DEFF Research Database (Denmark)

    Zhu, Guibing; Wang, Shanyun; Wang, Weidong;

    2013-01-01

    sampled fromlake riparian zones in North China. Laboratory incubations in the presence of ammonium or nitrate—at concentrations equivalent to no more than 10% of those detected in situ—yielded some of the highest potential anammox activities reported for natural environments to date. Potential rates of......For decades, the conversion of organic nitrogen to dinitrogen gas by heterotrophic bacteria, termed heterotrophic denitrification, was assumed to be the main pathway of nitrogen loss in natural ecosystems. Recently, however, autotrophic bacteria have been shown to oxidize ammonium in the absence of...... anammox peaked in sediments sampled from the interface between the land and the water, as did the abundance of annamox bacteria. Scaling our findings up to the entire lake system, we estimate that interfacial anammox hotspots account for the loss of 103 gNm-2 yr-1 from this lake region, and around one...

  7. Anaerobic ammonia oxidation in a fertilized paddy soil

    DEFF Research Database (Denmark)

    Zhu, Guibing; Wang, Shanyun; Wang, Yu;

    2011-01-01

    anammox 16S rRNA genes retrieved from the deeper soil were affiliated to ‘Brocadia’. The retrieval of mainly bacterial amoA sequences in the upper part of the paddy soil indicated that nitrifying bacteria may be the major source of nitrite for anammox bacteria in the cultivated horizon. In the deeper...... oxygen-limited parts, only archaeal amoA sequences were found, indicating that archaea may produce nitrite in this part of the soil. It is estimated that a total loss of 76 g N m−2 per year is linked to anammox in the paddy field.......Evidence for anaerobic ammonium oxidation in a paddy field was obtained in Southern China using an isotope-pairing technique, quantitative PCR assays and 16S rRNA gene clone libraries, along with nutrient profiles of soil cores. A paddy field with a high load of slurry manure as fertilizer was...

  8. FORMATION OF HYDROXYLAMINE ON DUST GRAINS VIA AMMONIA OXIDATION

    International Nuclear Information System (INIS)

    The quest to detect prebiotic molecules in space, notably amino acids, requires an understanding of the chemistry involving nitrogen atoms. Hydroxylamine (NH2OH) is considered a precursor to the amino acid glycine. Although not yet detected, NH2OH is considered a likely target of detection with ALMA. We report on an experimental investigation of the formation of hydroxylamine on an amorphous silicate surface via the oxidation of ammonia. The experimental data are then fed into a simulation of the formation of NH2OH in dense cloud conditions. On ices at 14 K and with a modest activation energy barrier, NH2OH is found to be formed with an abundance that never falls below a factor 10 with respect to NH3. Suggestions of conditions for future observations are provided

  9. FORMATION OF HYDROXYLAMINE ON DUST GRAINS VIA AMMONIA OXIDATION

    Energy Technology Data Exchange (ETDEWEB)

    He, Jiao; Vidali, Gianfranco [Physics Department, Syracuse University, Syracuse, NY 13244 (United States); Lemaire, Jean-Louis [Paris Observatory, F-75014 Paris (France); Garrod, Robin T., E-mail: gvidali@syr.edu [Center for Radiophysics and Space Research, Cornell University, Ithaca, NY 14853 (United States)

    2015-01-20

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

  10. 封闭循环养殖系统中β变形菌亚纲氨氧化细菌的引物特异性%Comparing the primer specificity for betaproteobacterial ammonia-oxidizing bacteria in recirculation aquaculture systems

    Institute of Scientific and Technical Information of China (English)

    裴芳芳; 朱鹏; 闵航; 陆开宏; 叶央芳

    2011-01-01

    [目的]为探讨4对不同的引物对封闭循环养殖系统生物膜中β变形菌亚纲氨氧化细菌(β-AOB)的特异性差异.[方法]采用16S rDNA文库克隆技术对β-AOB的多样性进行了分析.[结果]以引物CTO 189f/CTO654r扩增构建的文库中所含β-AOB比例最高,可达67.3%.不同封闭循环养殖系统的生物膜对引物的扩增效率有明显的影响,其中以养殖尼罗罗非鱼的封闭循环养殖系统生物膜为DNA来源的,引物均有较高的扩增效率.[结论]针对封闭循环养殖系统生物膜中的β-AOB,特异性最高的是CTO189f/CTO654r引物.%[ Objective ] To analyze the difference of specificity of four primers for betaproteobacterial ammonia-oxidizing bacteria ( (β-AOB) 16S rDNA gene from the biofilm of closed recirculation aquaculture systems. [ Methods] We used 16S rDNA clone libraries to describe the β-AOB diversity. [Results] CTO189f/CTO654r produced the highest frequency of β-AOB-like sequences (67.3%). The amplification performance of primer was noticeably influenced by the biofilm samples. Hereinto, the biofilm of closed recirculation aquaculture systems of Tilapia nilotica resulted in the higher amplification performance of primers. [Conclusion] CTO189f/CTO654r exhibited the highest specific for β-AOB 16S rDNA gene from the biofilm of closed recirculation aquaculture systems.

  11. Extreme Ionizing-Radiation-Resistant Bacterium

    Science.gov (United States)

    Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

    2013-01-01

    potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

  12. Molybdate Reduction to Molybdenum Blue by an Antarctic Bacterium

    OpenAIRE

    S. A. Ahmad; Shukor, M. Y.; Shamaan, N. A.; W. P. Mac Cormack; Syed, M. A.

    2013-01-01

    A molybdenum-reducing bacterium from Antarctica has been isolated. The bacterium converts sodium molybdate or Mo6+ to molybdenum blue (Mo-blue). Electron donors such as glucose, sucrose, fructose, and lactose supported molybdate reduction. Ammonium sulphate was the best nitrogen source for molybdate reduction. Optimal conditions for molybdate reduction were between 30 and 50 mM molybdate, between 15 and 20°C, and initial pH between 6.5 and 7.5. The Mo-blue produced had a unique absorption spe...

  13. Draft Genome Sequence of Oral Bacterium Streptococcus mutans JH1140

    OpenAIRE

    Escano, Jerome; Deng, Peng; Lu, Shi-En; Smith, Lief

    2016-01-01

    Streptococcus mutans JH1140 is an oral bacterium known to produce the bacteriocin mutacin 1140, and the strain has been genetically engineered to combat dental caries. Here, we report the 2.0-Mb draft genome of S. mutans JH1140. This genome provides new insights into the strain’s superior colonization properties and its utility in replacement therapy.

  14. Genome of a mosquito-killing bacterium decoded

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ Researchers with the CAS Wuhan Institute of Virology (WHIOV) recently completed the genome sequencing of a mosquitocidal bacterium Bacillus shaericus C3-41. The feat, first of its kind in China, is expected to further promote the bio-control studies of mosquitoes.

  15. Rnf Genes in Purple Sulfur Bacterium Allochromatium vinosum

    OpenAIRE

    DİNÇTÜRK, H. Benan; DEMİR, Volkan

    2006-01-01

    Allochromatium vinosum is a photosynthetic, diazotrophic purple sulfur bacterium that oxidizes reduced sulfur compounds hydrogen sulfide, elemental sulfur and thiosulfide. In this article, we report the presence of rnf genes in Allochromatium vinosum, some of which have been reported to take part in nitrogen fixation in some species.

  16. Draft Genome Sequence of Oral Bacterium Streptococcus mutans JH1140

    Science.gov (United States)

    Escano, Jerome; Deng, Peng; Lu, Shi-En

    2016-01-01

    Streptococcus mutans JH1140 is an oral bacterium known to produce the bacteriocin mutacin 1140, and the strain has been genetically engineered to combat dental caries. Here, we report the 2.0-Mb draft genome of S. mutans JH1140. This genome provides new insights into the strain’s superior colonization properties and its utility in replacement therapy. PMID:27257196

  17. Shotgun Genome Sequence of the Large Purple Photosynthetic Bacterium Rhodospirillum photometricum DSM122

    OpenAIRE

    Duquesne, K.; Sturgis, James N.

    2012-01-01

    Here, we present the shotgun genome sequence of the purple photosynthetic bacterium Rhodospirillum photometricum DSM122. The photosynthetic apparatus of this bacterium has been particularly well studied by microscopy. The knowledge of the genome of this oversize bacterium will allow us to compare it with the other purple bacterial organisms to follow the evolution of the photosynthetic apparatus.

  18. 南海北部陆坡表层沉积物氨氧化古菌多样性初探%Diversity of Ammonia-Oxidizing Archaea in the Surface Sediments of the Northern Continental Slope of the South China Sea

    Institute of Scientific and Technical Information of China (English)

    刘国辉; 吴后波

    2016-01-01

    基于南海北部陆坡不同深度梯度3个站位表层沉积物古菌氨单加氧酶基因(amoA)文库,对3个站位氨氧化古菌进行多样性和系统发育学分析。多种方法构建的系统发育树表明:3个站位所有的amoA基因序列都隶属于奇古菌门中Group I分枝内的Group I.1a系群,且各站位之间氨氧化古菌多样性没有明显的差异。501站位黑色砂质沉积物中古菌amoA基因与该站位的16S rRNA基因的系统发育比对显示:这2种基因标记的系统发育树整体上具有潜在的对应关系,说明对样品的氨氧化古菌多样性分析比较全面且可靠;并进一步暗示该样品中氨的硝化作用主要由奇古菌门下的Group I.1a系群来执行。由此可以推测:Group I.1a系群可能在南海北部表层沉积物中氮素的生物地球化学循环过程中扮演重要的角色。%Surface sediment samples were taken from three sites of different water depths at the northern continental slope of the South China Sea to investigate the community structure of ammonia-oxidizing archaea (AOA). Polymerase chain reaction (PCR) was employedto amplify the archaealammonia monooxygenase αsubunit(amoA) gene of AOA. Amplicons of theamoAgene sequences were used to understand the diversity and phylogenetic relationship of AOA. The main results were as follows: 1) All of thearchaealamoAgenesequences from the three locations were affiliated toGroup I.1aThaumarchaeota; 2)all ofthe archaealamoAgene sequences from the three locations were phylogenetically closely related; and 3) the16S rRNA gene andamoAgene phylogenetic trees were ofcongruent topology.Thaumarchaeota accounted for 40% of the total archaea, indicating that AOA might play an important role in the nitrogen biogeochemical cycling in the surface sediments of the northern continental slope of the South China Sea.

  19. Effects of Long Term Application of Urea on Ammonia Oxidizing Archaea Community in Black Soil in Northeast China%长期施用尿素对东北黑土中氨氧化古菌群落的影响

    Institute of Scientific and Technical Information of China (English)

    周晶; 姜昕; 周宝库; 马鸣超; 关大伟; 赵百锁; 陈三凤; 李俊

    2016-01-01

    Objective] This paper aimed to investigate the characteristics of ammonia oxidizing archaeal (AOA) communities in black soil under long-term fertilization in Northeast China to identify the effects of different doses of urea on the abundance and structure of the AOA community. Combined with the soil physiochemical characteristics, the main driving factors would be revealed. This study provides evidence for further understanding of the nitrification process and mechanism in black soil and enhanced fertilization method.[Method]Based on a 34 year fertilization experiment in Heilongjiang Academy of Agricultural Sciences, three groups of samples were selected with different fertilization including samples without urea (without fertilizer CK and phosphorus-potassium PK), samples with one-time urea (one time nitrogen N1, nitrogen-phosphorus NP, nitrogen-phosphorus- potassium NPK and nitrogen-potassium NK) and samples with two-time urea (two time nitrogen N2). We applied 454 pyrosequencing and quantitative PCR of theArch-amoA gene to analyze the effects of urea on the AOA communities in black soil. A correlation analysis was carried out to reveal the main important factors for determining the AOA community composition.[Result]It was found that AOAArch-amoA copy numbers in black soil were obviously reduced from 2.64×107 to 8.34×105 /g soil along with the increase of the urea amount, and pH in black soil was the direct reason for the decrease of the Arch-amoA gene. Both clustering and Nonmetric Multidimensional Scaling (NMDS) analyzed result proved that the AOA community structure in each fertilizer treatment with the same urea inputs was similar with each other, while the AOA community structure in fertilizer treatments with different urea addition was significantly different with each other. And a redundancy analysis indicated that soil pH, concentration of water soluble organic carbon and nitrate were the main environmental factors (P< 0.05) affecting the AOA community

  20. A Streamlined Strategy for Biohydrogen Production with an Alkaliphilic Bacterium

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Dwayne A [ORNL; Wall, Judy D. [University of Missouri; Mormile, Dr. Melanie R. [Missouri University of Science and Technology; Begemann, Matthew B [University of Wisconsin, Madison

    2012-01-01

    Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, biohydrogen production remains inefficient and heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium strain sapolanicus, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. sapolanicus ferments a variety of 5- and 6- carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen and acetate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources.

  1. Rock Phosphate Solubilization Mechanisms of One Fungus and One Bacterium

    Institute of Scientific and Technical Information of China (English)

    LIN Qi-mei; ZHAO Xiao-rong; ZHAO Zi-juan; LI Bao-guo

    2002-01-01

    Many microorganisms can dissolve the insoluble phosphates like apatite. However, the mechanisms are still not clear. This study was an attempt to investigate the mechanisms of rock phosphate solubilization by an Aspergillus 2TCiF2 and an Arthrobacter1TCRi7. The results indicated that the fungus produced a large amount of organic acids, mainly oxalic acid. The total quantity of the organic acids produced by the fungus was 550 times higher than that by the bacterium. Different organic acids had completely different capacities to solubilize the rock. Oxalic acid and citric acid had stronger capacity to dissolve the rock than malic acid, tartaric acid, lactic acid, acetic acid, malonic acid and succinic acid. The fungus solubilized the rock through excreting both proton and organic acids. The rock solubilization of the bacterium depended on only proton.

  2. A physical map of the hyperthermophilic bacterium Aquifex pyrophilus chromosome.

    OpenAIRE

    Shao, Z; Mages, W; Schmitt, R.

    1994-01-01

    A genomic map of the hyperthermophilic hydrogen-oxidizing bacterium Aquifex pyrophilus was established with NotI (GC/GGCCGC), SpeI (A/CTAGT), and XbaI (T/CTAGA). Linking clones and cross-hybridization of restriction fragments revealed a single circular chromosome of 1.6 Mbp. A single flagellin gene and six rRNA gene units were located on this map by Southern hybridization.

  3. Isolation of a Bacterium Capable of Degrading Peanut Hull Lignin

    OpenAIRE

    Kerr, Thomas J.; Kerr, Robert D.; Benner, Ronald

    1983-01-01

    Thirty-seven bacterial strains capable of degrading peanut hull lignin were isolated by using four types of lignin preparations and hot-water-extracted peanut hulls. One of the isolates, tentatively identified as Arthrobacter sp., was capable of utilizing all four lignin preparations as well as extracted peanut hulls as a sole source of carbon. The bacterium was also capable of degrading specifically labeled [14C]lignin-labeled lignocellulose and [14C]cellulose-labeled lignocellulose from the...

  4. The effects of salinity on nitrification using halophilic nitrifiers in a Sequencing Batch Reactor treating hypersaline wastewater.

    Science.gov (United States)

    Cui, You-Wei; Zhang, Hong-Yu; Ding, Jie-Ran; Peng, Yong-Zhen

    2016-01-01

    With annual increases in the generation and use of saline wastewater, the need to avoid environmental problems such as eutrophication is critical. A previous study identified ways to start up a halophilic sludge domesticated from estuarine sediments to remove nitrogen from wastewater with a salinity of 30 g/L. This investigation expands that work to explore the impact of salinity on nitrogen removal. This study demonstrated that the mixed halophilic consortia removed nitrogen from wastewater with a salinity of 30-85 g/L. A kinetic analysis showed that halophilic nitrifiers selected based on hypersalinity were characterized by low Ks, μmax and specific ammonium oxidization rates. This explains the decrease in ammonium removal efficiency in the high salinity operational phases. Salinity inhibited ammonia oxidizing bacteria (AOB) activity, as well as the number of dominant AOB, but did not significantly affect the AOB dominant species. Three most dominant AOB lineages in the halophilic sludge were Nitrosomonas marina, Nitrosomonas europaea, and Nitrosococcus mobilis. Nitrosomonas europaea and Nitrosococcus mobilis were mainly affected by salinity, while nitrite accumulation and ammonia loading played the key role in determining the abundance of Nitrosococcus mobilis and Nitrosococcus europaea. The study contributes insights about shifts in halophilic nitrifying bacterial populations. PMID:27109617

  5. Salt-inducible promoter derivable from a lactic acid bacterium, and its use in a lactic acid bacterium for production of a desired protein

    NARCIS (Netherlands)

    Sanders, Jan Willem; Kok, Jan; Venema, Gerard; Ledeboer, Adrianus Marinus

    1998-01-01

    The invention provides a salt-inducible promoter present in SEQ ID NO: 10 and derivable from a lactic acid bacterium in isolation from the coding sequence normally controlled by said promoter in a wild-type lactic acid bacterium, with modifications and important parts thereof. Also provided are a re

  6. Effects of Long-term Fertilization on Diversity of AmmoniaOxidizing Archaea Communities and Abundance in Dry Highland Soil of Loess Plateau%长期施肥对黄土旱塬黑垆土氨氧化古菌群落多样性和丰度的影响

    Institute of Scientific and Technical Information of China (English)

    武传东; 辛亮; 李秀颖; 王保莉; 曲东

    2011-01-01

    [Objective] In order to improve the efficiency of nitrogen utilization and explicate the function of ammonia-oxidizing archaea (AOA) under the changes of soil quality in the Loess Plateau, the community structure diversity and abundance of AOA were studied. [Method] The influence of long-term fertilization treatments including CK, M, NM, PM and NPM on soil AOA community structure diversity and amoA gene copy numbers were analyzed by restriction fragment length polymorphism (PCR-RFLP) and real-time PCR. [Result] From the clone libraries of the different fertilization treatments, there were 25,18,29,20 and 30 restriction endonuclease types, respectively. The a diversity indices indicated that there was a pronounced difference among five fertilizer treatments. The OTUs was the highest in NPM treatment and the lowest diversity in M treatment. The rescaled distance matrix tree indicated that the different fertilization had the largest convergence coefficient of AOA community types with the CK treatment soil, so the different fertilization led to significant changes of AOA communities. The amoA gene copy numbers of AOA changes were different among the treatments, whereas the highest copy numbers were detected in the NPM treatment, and had a pronounced difference with other fertilizer treatments. All preponderant sequences of AOA fell within soils/fresh water sediments based on phylogenetic tree of amoA gene amino acid sequences analysis. [Conclusion] Long-term fertilization resulted in changes of AOA community diversity and abundance.%[目的]研究长期不同施肥制度下黄土旱塬黑垆土氨氧化古菌群落多样性和丰度的变化,为提高黄土高原地区氮素利用效率、检测土壤质量变化提供重要依据.[方法]利用PCR-RFLP技术和Real-time PCR技术分析无肥(cK)、有机肥(M)、氮肥+有机肥(NM)、磷肥+有机肥(PM)、氮磷肥+有机肥(NPM)等5种长期施肥处理对土壤氨氧化古菌群落结

  7. 抗草甘膦转基因大豆对根际土壤氨氧化古菌群落多样性的影响%Effects of roundup ready transgenic soybean on ammonia-oxidizing archaeal diversity in rhizospheric soil

    Institute of Scientific and Technical Information of China (English)

    刘志华; 徐广惠; 王宏燕; 刘佳

    2012-01-01

    Roundup ready transgenic soybean [ Glycine max (L. ) Merr. ] (RRS) is one of the genetically modified crops and firstly commercialized by the Monsanto Company. In recent years, more attention has been paid on the risk assessment of RRS, including the potential effects on soil biota diversity. Ammonia-oxidizing archaea (AOA) are a group of the key microbes in nitrification, playing an important role in N cycle. By using PCR-DGGE cloning, this paper studied the diversity of AOA communities in the rhizosphere soils of RRS, its non-transgenic parental iso-line (RRS-S) , wild soybean (W-S) , and cultivated soybean (D-46) , aimed to provide theoretical basis for the ecological safety assessment on the transgenic soybean. The RRS had no remarkable effects on the AOA diversity, based on the Shannon diversity index and evenness index. The principal components analysis and DGGE analysis showed that the AOA community structure in the rhizosphere of RRS was significantly different with that in the rhizosphere of WS and D-46, but had no significant difference with that in the rhizosphere of RRS-S. Moreover, the AOA amok gene sequencing of DGGE bands and the phylogenetic analysis revealed that parts of the AOA in the rhizosphere of test soybean cultivars belonged to the clusters already reported in soil/ sediment, others belonged to the unknown clusters or groups in soil, but none of them belonged to the clusters in water or sediment. There was little change in the DGGE bands, among which,bands 1, 20, and 25 were missing, and band 3 was specific for RRS. In conclusion, RRS had no apparent effect on the diversity of AOA in rhizosphere soils, but could alter the composition of AOA community.%抗草甘膦转基因大豆是孟山都公司首次进行商业化生产的转基因作物.近年来其风险评价,包括土壤生物多样性风险评价受到越来越多的重视.氨氧化古菌是硝化过程的关键微生物,在氮素循环中起重要作用.本文

  8. Research Progress and Perspectives of Nitrogen Fixing Bacterium, Gluconacetobacter diazotrophicus, in Monocot Plants

    Directory of Open Access Journals (Sweden)

    N. Eskin

    2014-01-01

    Full Text Available Gluconacetobacter diazotrophicus is a nitrogen fixing bacterium originally found in monocotyledon sugarcane plants in which the bacterium actively fixes atmosphere nitrogen and provides significant amounts of nitrogen to plants. This bacterium mainly colonizes intercellular spaces within the roots and stems of plants and does not require the formation of the complex root organ like nodule. The bacterium is less plant/crop specific and indeed G. diazotrophicus has been found in a number of unrelated plant species. Importantly, as the bacterium was of monocot plant origin, there exists a possibility that the nitrogen fixation feature of the bacterium may be used in many other monocot crops. This paper reviews and updates the research progress of G. diazotrophicus for the past 25 years but focuses on the recent research development.

  9. Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5

    OpenAIRE

    Idogawa, Nao; Amamoto, Ryuta; Murata, Kousaku; Kawai, Shigeyuki

    2014-01-01

    Gluconacetobacter diazotrophicus is a gram-negative and endophytic nitrogen-fixing bacterium that has several beneficial effects in host plants; thus, utilization of this bacterium as a biofertilizer in agriculture may be possible. G. diazotrophicus synthesizes levan, a D-fructofuranosyl polymer with β-(2→6) linkages, as an exopolysaccharide and the synthesized levan improves the stress tolerance of the bacterium. In this study, we found that phosphate enhances levan production by G. diazotro...

  10. A Plant Growth-Promoting Bacterium That Decreases Nickel Toxicity in Seedlings

    OpenAIRE

    Burd, Genrich I.; Dixon, D. George; Glick, Bernard R.

    1998-01-01

    A plant growth-promoting bacterium, Kluyvera ascorbata SUD165, that contained high levels of heavy metals was isolated from soil collected near Sudbury, Ontario, Canada. The bacterium was resistant to the toxic effects of Ni2+, Pb2+, Zn2+, and CrO4−, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. Canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride w...

  11. Magnetic guidance of the magnetotactic bacterium Magnetospirillum gryphiswaldense.

    Science.gov (United States)

    Loehr, Johannes; Pfeiffer, Daniel; Schüler, Dirk; Fischer, Thomas M

    2016-04-21

    Magnetospirillum gryphiswaldense is a magnetotactic bacterium with a permanent magnetic moment capable of swimming using two bipolarly located flagella. In their natural environment these bacteria swim along the field lines of the homogeneous geomagnetic field in a typical run and reversal pattern and thereby create non-differentiable trajectories with sharp edges. In the current work we nevertheless achieve stable guidance along curved lines of mechanical instability by using a heterogeneous magnetic field of a garnet film. The successful guidance of the bacteria depends on the right balance between motility and the magnetic moment of the magnetosome chain. PMID:26972517

  12. Intracellular iron minerals in a dissimilatory iron-reducing bacterium.

    Science.gov (United States)

    Glasauer, Susan; Langley, Sean; Beveridge, Terry J

    2002-01-01

    Among prokaryotes, there are few examples of controlled mineral formation; the formation of crystalline iron oxides and sulfides [magnetite (Fe3O4) or greigite (Fe3S4)] by magnetotactic bacteria is an exception. Shewanella putrefaciens CN32, a Gram-negative, facultative anaerobic bacterium that is capable of dissimilatory iron reduction, produced microscopic intracellular grains of iron oxide minerals during growth on two-line ferrihydrite in a hydrogen-argon atmosphere. The minerals, formed at iron concentrations found in the soil and sedimentary environments where these bacteria are active, could represent an unexplored pathway for the cycling of iron by bacteria. PMID:11778045

  13. Factors Affecting Zebra Mussel Kill by the Bacterium Pseudomonas fluorescens

    Energy Technology Data Exchange (ETDEWEB)

    Daniel P. Molloy

    2004-02-24

    The specific purpose of this research project was to identify factors that affect zebra mussel kill by the bacterium Pseudomonas fluorescens. Test results obtained during this three-year project identified the following key variables as affecting mussel kill: treatment concentration, treatment duration, mussel siphoning activity, dissolved oxygen concentration, water temperature, and naturally suspended particle load. Using this latter information, the project culminated in a series of pipe tests which achieved high mussel kill inside power plants under once-through conditions using service water in artificial pipes.

  14. Screening, identification and desilication of a silicate bacterium

    Institute of Scientific and Technical Information of China (English)

    ZHOU Hong-bo; ZENG Xiao-xi; LIU Fei-fei; QIU Guan-zhou; HU Yue-hua

    2006-01-01

    The strain Lv1-2 isolated from the Henan bauxite was characterized by morphological observation, biochemical and physiological identification, and 16S rDNA sequence analysis. The influences of temperature, initial pH value, the volume of medium, shaking speed and illite concentration on the desilicating ability of the strain Lv1-2 were investigated. The results show that the bacterium is a Gram-negative rod-shaped bacterium with oval endspores and thick capsule, but without flagellum. The biochemical and physiological tests indicate that the strain Lv1-2 is similar to Bacillus mucilaginosus. In GenBank the 16S rDNA sequence similarity of the strain Lv1-2 and the B. mucilaginosus YNUCC0001 (AY571332) is more than 99 %. Based on the above results, the strain Lv1-2 is identified as B. mucilaginosus. The optimum conditions for the strain Lv1-2 to remove silicon from illite are as follows: temperature is 30℃ ;initial pH value is 7.5; medium volume in 200 mL bottle is 60 mL; shaking speed of rotary shaker is 220 r/m; illite concentration is 1%.

  15. Biological Control of Meloidogyne hapla Using an Antagonistic Bacterium

    Directory of Open Access Journals (Sweden)

    Jiyeong Park

    2014-09-01

    Full Text Available We examined the efficacy of a bacterium for biocontrol of the root-knot nematode (RKN Meloidogyne hapla in carrot (Daucus carota subsp. sativus and tomato (Solanum lycopersicum. Among 542 bacterial isolates from various soils and plants, the highest nematode mortality was observed for treatments with isolate C1-7, which was identified as Bacillus cereus based on cultural and morphological characteristics, the Biolog program, and 16S rRNA sequencing analyses. The population density and the nematicidal activity of B. cereus C1-7 remained high until the end of culture in brain heart infusion broth, suggesting that it may have sustainable biocontrol potential. In pot experiments, the biocontrol efficacy of B. cereus C1-7 was high, showing complete inhibition of root gall or egg mass formation by RKN in carrot and tomato plants, and subsequently reducing RKN damage and suppressing nematode population growth, respectively. Light microscopy of RKN-infected carrot root tissues treated with C1-7 showed reduced formation of gall cells and fully developed giant cells, while extensive gall cells and fully mature giant cells with prominent cell wall ingrowths formed in the untreated control plants infected with RKNs. These histopathological characteristics may be the result of residual or systemic biocontrol activity of the bacterium, which may coincide with the biocontrol efficacies of nematodes in pots. These results suggest that B. cereus C1-7 can be used as a biocontrol agent for M. hapla.

  16. Isolation and characterization of luminescent bacterium for sludge biodegradation.

    Science.gov (United States)

    Zahaba, Maryam; Halmi, Mohd Izuan Effendi; Ahmad, Siti Aqlima; Shukor, Mohd Yunus; Syed, Mohd Arif

    2015-11-01

    Microtox is based on the inhibition of luminescence of the bacterium Vibrio fischeri by the toxicants. This technique has been accepted by the USEPA (United States Environmental Protection Agency) as a biomonitoring tool for remediation of toxicants such as hydrocarbon sludge. In the present study, a luminescent bacterium was isolated from yellow striped scad (Selaroides leptolepis) and was tentatively identified as Vibrio sp. isolate MZ. This aerobic isolate showed high luminescence activity in a broad range of temperature from 25 to 35 °C. In addition, optimal conditions for high bioluminescence activity in range of pH 7.5 to 8.5 and 10 gl(-1) of sodium chloride, 10 gl(-1) of peptone and 10 gl(-1) of sucrose as carbon source. Bench scale biodegradation 1% sludge (w/v) was set up and degradation was determined using gas chromatography with flame ionised detector (GC-FID). In this study, Rhodococcus sp. strain AQ5NOL2 was used to degrade the sludge. Based on the preliminary results obtained, Vibrio sp. isolate MZwas able to monitor the biodegradation of sludge. Therefore, Vibrio sp. isolate MZ has the potential to be used as a biomonitoring agent for biomonitoring of sludge biodegradation particularly in the tropical ranged environment. PMID:26688958

  17. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus.

    Science.gov (United States)

    Gardner, Jeffrey G

    2016-07-01

    Study of recalcitrant polysaccharide degradation by bacterial systems is critical for understanding biological processes such as global carbon cycling, nutritional contributions of the human gut microbiome, and the production of renewable fuels and chemicals. One bacterium that has a robust ability to degrade polysaccharides is the Gram-negative saprophyte Cellvibrio japonicus. A bacterium with a circuitous history, C. japonicus underwent several taxonomy changes from an initially described Pseudomonas sp. Most of the enzymes described in the pre-genomics era have also been renamed. This review aims to consolidate the biochemical, structural, and genetic data published on C. japonicus and its remarkable ability to degrade cellulose, xylan, and pectin substrates. Initially, C. japonicus carbohydrate-active enzymes were studied biochemically and structurally for their novel polysaccharide binding and degradation characteristics, while more recent systems biology approaches have begun to unravel the complex regulation required for lignocellulose degradation in an environmental context. Also included is a discussion for the future of C. japonicus as a model system, with emphasis on current areas unexplored in terms of polysaccharide degradation and emerging directions for C. japonicus in both environmental and biotechnological applications. PMID:27263016

  18. Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

    Science.gov (United States)

    Sparks, N.H.C.; Mann, S.; Bazylinski, D.A.; Lovley, D.R.; Jannasch, H.W.; Frankel, R.B.

    1990-01-01

    Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57Fe Mo??ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 ?? 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of {110} faces which are capped and truncated by {111} end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization. ?? 1990.

  19. Treatment of common warts with the immune stimulant Propionium bacterium parvum Tratamento das verrugas vulgares com o imunoestimulante Propionium bacterium parvum

    OpenAIRE

    Nilton Nasser

    2012-01-01

    BACKGROUND: Warts are epithelial proliferations in the skin and mucous membrane caused by various types of HPV. They can decrease spontaneously or increase in size and number according to the patient's immune status. The Propionium bacterium parvum is a strong immune stimulant and immune modulator and has important effects in the immune system and it is able to produce antibodies in the skin. OBJECTIVE: To show the efficacy of the Propionium bacterium parvum in saline solution in the treatmen...

  20. Dense populations of a giant sulfur bacterium in Namibian shelf sediments

    DEFF Research Database (Denmark)

    Schulz, HN; Brinkhoff, T.; Ferdelman, TG;

    1999-01-01

    A previously unknown giant sulfur bacterium is abundant in sediments underlying the oxygen minimum zone of the Benguela Current upwelling system. The bacterium has a spherical cell that exceeds by up to 100-fold the biovolume of the largest known prokaryotes. On the basis of 16S ribosomal DNA...

  1. Draft Genome Sequence of Ensifer adhaerens M78, a Mineral-Weathering Bacterium Isolated from Soil.

    Science.gov (United States)

    Wang, Yuanli; Chen, Wei; He, Linyan; Wang, Qi; Sheng, Xia-Fang

    2016-01-01

    Ensifer adhaerens M78, a bacterium isolated from soil, can weather potash feldspar and release Fe, Si, and Al from rock under nutrient-poor conditions. Here, we report the draft genome sequence of strain M78, which may facilitate a better understanding of the molecular mechanism involved in mineral weathering by the bacterium. PMID:27609930

  2. Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties

    NARCIS (Netherlands)

    Sessitsch, A; Coenye, T; Sturz, AV; Vandamme, P; Barka, EA; Salles, JF; Van Elsas, JD; Faure, D; Reiter, B; Glick, BR; Wang-Pruski, G; Nowak, J

    2005-01-01

    A Gram-negative, non-sporulating, rod-shaped, motile bacterium, with a single polar flagellum, designated strain PsJNT, was isolated from surface-sterilized onion roots. This isolate proved to be a highly effective plant-beneficial bacterium, and was able to establish rhizosphere and endophytic popu

  3. Effects of high LET radiation on radioresistant bacterium Deinococcus radiodurans

    International Nuclear Information System (INIS)

    It is known that Deinococcus radiodurans is extremely resistant to ionizing and ultraviolet (UV) radiations, as well as chemical agents and hyperthermia (heat treatment) which cause DNA damage. It was reported in this paper that studies on the synergistic killing effect of high LET (linear energy transfer) radiation and hyperthermia in D. radiodurans were performed in Research Reactor Institute, Kyoto University as the Visiting Researcher's Program. The difference of cellular response in this bacterium against low LET (i.e. gamma) and high LET (i.e. BNC beam and heavy ion beam) radiations was analyzed by using Kyoto University Reactor (KUR) operated at 5 MW and AVF cyclotron in Takasaki Ion Accelerator for Radiation Application (TIARA). Also, The DNA sequence specificity (hot spot) for mutation on supF gene of a shuttle vector plasmid pZ189 induced by BNC beam is being researched using Escherichia coli DNA repair capability. (author)

  4. Genome analysis of the Anerobic Thermohalophilic bacterium Halothermothrix orenii

    Energy Technology Data Exchange (ETDEWEB)

    Mavromatis, Konstantinos; Ivanova, Natalia; Anderson, Iain; Lykidis, Athanasios; Hooper, Sean D.; Sun, Hui; Kunin, Victor; Lapidus, Alla; Hugenholtz, Philip; Patel, Bharat; Kyrpides, Nikos C.

    2008-11-03

    Halothermothirx orenii is a strictly anaerobic thermohalophilic bacterium isolated from sediment of a Tunisian salt lake. It belongs to the order Halanaerobiales in the phylum Firmicutes. The complete sequence revealed that the genome consists of one circular chromosome of 2578146 bps encoding 2451 predicted genes. This is the first genome sequence of an organism belonging to the Haloanaerobiales. Features of both Gram positive and Gram negative bacteria were identified with the presence of both a sporulating mechanism typical of Firmicutes and a characteristic Gram negative lipopolysaccharide being the most prominent. Protein sequence analyses and metabolic reconstruction reveal a unique combination of strategies for thermophilic and halophilic adaptation. H. orenii can serve as a model organism for the study of the evolution of the Gram negative phenotype as well as the adaptation under thermohalophilic conditions and the development of biotechnological applications under conditions that require high temperatures and high salt concentrations.

  5. A bacterium that degrades and assimilates poly(ethylene terephthalate).

    Science.gov (United States)

    Yoshida, Shosuke; Hiraga, Kazumi; Takehana, Toshihiko; Taniguchi, Ikuo; Yamaji, Hironao; Maeda, Yasuhito; Toyohara, Kiyotsuna; Miyamoto, Kenji; Kimura, Yoshiharu; Oda, Kohei

    2016-03-11

    Poly(ethylene terephthalate) (PET) is used extensively worldwide in plastic products, and its accumulation in the environment has become a global concern. Because the ability to enzymatically degrade PET has been thought to be limited to a few fungal species, biodegradation is not yet a viable remediation or recycling strategy. By screening natural microbial communities exposed to PET in the environment, we isolated a novel bacterium, Ideonella sakaiensis 201-F6, that is able to use PET as its major energy and carbon source. When grown on PET, this strain produces two enzymes capable of hydrolyzing PET and the reaction intermediate, mono(2-hydroxyethyl) terephthalic acid. Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. PMID:26965627

  6. Algicidal lactones from the marine Roseobacter clade bacterium Ruegeria pomeroyi

    Directory of Open Access Journals (Sweden)

    Ramona Riclea

    2012-06-01

    Full Text Available Volatiles released by the marine Roseobacter clade bacterium Rugeria pomeroyi were collected by use of a closed-loop stripping headspace apparatus (CLSA and analysed by GC–MS. Several lactones were found for which structural proposals were derived from their mass spectra and unambiguously verified by the synthesis of reference compounds. An enantioselective synthesis of two exemplary lactones was performed to establish the enantiomeric compositions of the natural products by enantioselective GC–MS analyses. The lactones were subjected to biotests to investigate their activity against several bacteria, fungi, and algae. A specific algicidal activity was observed that may be important in the interaction between the bacteria and their algal hosts in fading algal blooms.

  7. The capacity of phototrophic sulfur bacterium Thiocapsa roseopersicina for chemosynthesis.

    Science.gov (United States)

    Kondratieva, E N; Zhukov, V G; Ivanovsky, R N; Petushkova, U P; Monosov, E Z

    1976-07-01

    Purple sulfur bacterium Thiocapsa roseopersicina strain BBS requiring vitamin B12 may grow in the dark in media containing no other organic compounds. Under such conditions the cells oxidize sulfide and thiosulfate with the use of O2 and assimilate carbon dioxide. After 10--30s assimilation of NaH14CO3 about 60% of radioactivity is found in phosphorylated compounds characteristic for the reductive pentose phosphate cycle. The possibility of the function of this cycle in the dark in the presence of O2 is confirmed by the capacity of cells grown under such conditions to synthesize ribulose-1,5-diphosphate carboxylase. All this evidence suggests the ability of T. roseopersicina to change from phototrophy to aerobic chemolithoautotrophy. PMID:942280

  8. Moritella viscosa, a pathogenic bacterium affecting the fillet quality in fish

    DEFF Research Database (Denmark)

    Ingerslev, Hans-Christian; Nielsen, Michael Engelbrecht

    2011-01-01

    Moritella viscosa is a bacterium belonging to the family Moritellaceae and was formerly known as Vibrio viscosus. The name ‘viscosa’ originates from the slimy nature of the bacterium. M. viscosa is considered to be the main causative agent of the phenomenon ‘winter ulcer’ or ‘cold-water ulcer......’ which affects various fish species in seawater during cold periods (Lunder et al. 1995). The bacterium is mainly a problem for farmed salmonid species, such as Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), but has also been isolated from other fish species, including Atlantic...

  9. Treatment of common warts with the immune stimulant Propionium bacterium parvum Tratamento das verrugas vulgares com o imunoestimulante Propionium bacterium parvum

    Directory of Open Access Journals (Sweden)

    Nilton Nasser

    2012-08-01

    Full Text Available BACKGROUND: Warts are epithelial proliferations in the skin and mucous membrane caused by various types of HPV. They can decrease spontaneously or increase in size and number according to the patient's immune status. The Propionium bacterium parvum is a strong immune stimulant and immune modulator and has important effects in the immune system and it is able to produce antibodies in the skin. OBJECTIVE: To show the efficacy of the Propionium bacterium parvum in saline solution in the treatment of skin warts. METHODS: A randomized double-blind study. Twenty patients with multiple warts were divided into two groups: one received 0,1ml intradermal injection of placebo solution in just one of the warts and the other received 0,1 ml of saline solution of Propionium bacterium parvum, one dose a month, for 3 to 5 months. RESULTS: Among the 20 patients who participated in the study, ten received the placebo and ten received the saline solution with Propionium bacterium parvum. In 9 patients treated with the Propionium bacterium parvum solution the warts disappeared without scars and in 1 patient it decreased in size. In 9 patients who received the placebo no change to the warts was observed and in 1 it decreased in size. CONCLUSIONS: The immune modulator and immune stimulant Propionium bacterium parvum produced antibodies in the skin which destroyed the warts without scars, with statistically significant results (PFUNDAMENTOS: Verrugas são proliferações epiteliais na pele e mucosas causadas por diversos tipos de HPV. Elas podem involuir espontaneameme ou aumentar em número e tamanho de acordo com estado imunitário do paciente. O Propionium bacterium parvum é urn potente imunoestimulador e imunomodulador e tem efeitos importantes no sistema imune e é capaz de produzir anticorpos na pele. OBJETIVO: Mostrar a eficácia do Propionium bacterium parvum diluído em solução salina no tratamento de verrugas cutâneas. MÊTODOS: Estudo duplo

  10. Bioconversion of methane to lactate by an obligate methanotrophic bacterium

    Science.gov (United States)

    Henard, Calvin A.; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G.; Pienkos, Philip T.; Guarnieri, Michael T.

    2016-01-01

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to “green” chemicals and fuels. PMID:26902345

  11. Presence of an unusual methanogenic bacterium in coal gasification waste

    Energy Technology Data Exchange (ETDEWEB)

    Tomei, F.A.; Rouse, D.; Maki, J.S.; Mitchell, R.

    1988-12-01

    Methanogenic bacteria growing on a pilot-scale, anaerobic filter processing coal gasification waste were enriched in a mineral salts medium containing hydrogen and acetate as potential energy sources. Transfer of the enrichments to methanol medium resulted in the initial growth of a strain of Methanosarcina barkeri, but eventually small cocci became dominant. The cocci growing on methanol produced methane and exhibited the typical fluorescence of methanogenic bacteria. They grew in the presence of the cell wall synthesis-inhibiting antibiotics D-cycloserine, fosfomycin, penicillin G, and vancomycin as well as in the presence of kanamycin, an inhibitor of protein synthesis in eubacteria. The optimal growth temperature was 37 degrees C, and the doubling time was 7.5 h. The strain lysed after reaching stationary phase. The bacterium grew poorly with hydrogen as the energy source and failed to grow on acetate. Morphologically, the coccus shared similarities with Methanosarcina sp. Cells were 1 ..mu..m wide, exhibited the typical thick cell wall and cross-wall formation, and formed tetrads. Packets and cysts were not formed. 62 refs., 4 figs.

  12. Bioconversion of methane to lactate by an obligate methanotrophic bacterium.

    Science.gov (United States)

    Henard, Calvin A; Smith, Holly; Dowe, Nancy; Kalyuzhnaya, Marina G; Pienkos, Philip T; Guarnieri, Michael T

    2016-01-01

    Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to "green" chemicals and fuels. PMID:26902345

  13. Electromicrobiology of Dissimilatory Sulfur Reducing Bacterium Desulfuromonas acetexigens

    KAUST Repository

    Bin Bandar, Khaled

    2014-12-01

    Bioelectrochmical systems (BES) are engineered electrochemical devices that harness hidden chemical energy of the wastewater in to the form of electricity or hydrogen. Unique microbial communities enrich in these systems for oxidation of organic matter as well as transfer of resulted electron to anode, known them as “electricigens” communities. Exploring novel electricigenesis microbial communities in the nature and understanding their electromicrobiology is one the important aspect for BES systems scale up. Herein, we report first time the electricigenesis property of an anaerobic, fresh water sediment, sulfur reducing bacterium Desulfuromona acetexigens. The electrochemical behavior of D. acetexigens biofilms grown on graphite-rod electrodes in batch-fed mode under an applied potential was investigated with traditional electroanalytical tools, and correlate the electron transfer from biofilms to electrode with a model electricigen Geobacter sulfurreducens electrochemical behavior. Research findings suggest that D. acetexigens has the ability to use electrode as electron acceptor in BES systems through establishing the direct contact with anode by expressing the membrane bound redox proteins, but not due to the secretion of soluble redox mediators. Preliminary results revealed that D. acetexigens express three distinct redox proteins in their membranes for turnover of the electrons from biofilm to electrode, and the 4 whole electricigenesis process observed to be unique in the D. acetexigens compared to that of well-studied model organism G. sulfurreducens.

  14. Molecular study on cloned endoglucanase gene from rumen bacterium.

    Science.gov (United States)

    Ozkose, Emin; Akyol, Ismail; Ekinci, Mehmet Sait

    2004-01-01

    An endoglucanase gene was subcloned from anaerobic rumen bacterium Ruminococcus flavefaciens strain 17. To express endoglucanase gene in Escherichia coli and Streptococcus bovis JB1, an endoglucanase gene fragment was inserted into pVA838-based shuttle vectors. Removal of endoglucanase gene promoter and expression of endoglucanase by promoter of S. bovis JB1 alpha-amylase gene (pACMCS) was also achieved. Survival of constructs pVACMCI, pTACMC and pACMCS, which carry endoglucanase gene, and stability of endoglucanase gene in S. bovis JB1, were observed. Maximal endoglucanase activities from S. bovis JB1/pVACMCI were 2- to 3-fold higher than from E. coli/pVACMCI. Specific cell activity of E. coli/pACMCS was found to be approximately 2- to -3 fold higher than the both E. coli/pVACMCI and E. coli/pTACMC. Specific cell activity of S. bovis JB1/pACMCS was also found to be approximately 2-fold higher than the both S. bovis/pVACMCI and S. bovis JB1/pTACMC. PMID:15925902

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

    Science.gov (United States)

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

    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 S1-1 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 level accumulation of nitrite, suggesting that the aerobic denitrification process of strain S1-1 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 S1-1 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 degrees C and initial pH 6.5. PMID:22432315

  16. 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.

  17. Isolation and characterization of Caldicellulosiruptor lactoaceticus sp. nov., an extremely thermophilic, cellulolytic, anaerobic bacterium

    DEFF Research Database (Denmark)

    Mladenovska, Zuzana; Mathrani, Indra M.; Ahring, Birgitte Kiær

    1995-01-01

    An anaerobic, extremely thermophilic, cellulolytic, non-spore-forming bacterium, strain 6A, was isolated from an alkaline hot spring in Hverageroi, Iceland. The bacterium was non-motile, rod-shaped (1.5-3.5 x 0.7 mu m) and occurred singly, in pairs or in chains and stained gram-negative. The growth...... temperature was between 50 and 78 degrees C with a temperature optimum near 68 degrees C. Growth occurred between pH 5.8 and 8.2 with an optimum mum near 7.0. The bacterium fermented microcrystalline cellulose (Avicel) and produced lactate, acetate and H-2 as the major fermentation products, and CO2...... and ethanol occurred as minor fermentation products. Only a restricted number of carbon sources (cellulose, xylan, starch, pectin, cellobiose, xylose, maltose and lactose) were used as substrates. During growth on Avicel, the bacterium produced free cellulases with carboxymethylcellulase and avicelase...

  18. Dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates

    Czech Academy of Sciences Publication Activity Database

    Biebl, H.; Allgaier, M.; Tindall, B. J.; Koblížek, Michal; Lünsdorf, H.; Pukall, R.; Wagner-Döbler, I.

    2005-01-01

    Roč. 55, - (2005), s. 1089-1096. ISSN 1466-5026 Institutional research plan: CEZ:AV0Z50200510 Keywords : Dinoroseobacter shibae * phototrophic bacterium Subject RIV: EE - Microbiology, Virology Impact factor: 2.744, year: 2005

  19. Carbohydrate utilization patterns for the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus reveal broad growth substrate preferences

    NARCIS (Netherlands)

    Vanfossen, A.L.; Verhaart, M.R.A.; Kengen, S.W.M.; Kelly, R.M.

    2009-01-01

    Co-utilization of hexoses and pentoses derived from lignocellulose is an attractive trait in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on indiv

  20. Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z

    OpenAIRE

    Vuilleumier, Stéphane; Khmelenina, Valentina N; Bringel, Françoise; Reshetnikov, Alexandr S.; Lajus, Aurélie; Mangenot, Sophie; Rouy, Zoé; Op Den Camp, Huub J M; Jetten, Mike S. M.; DiSpirito, Alan A.; Dunfield, Peter; Klotz, Martin G.; Semrau, Jeremy D.; Stein, Lisa Y.; Barbe, Valérie

    2012-01-01

    Methylomicrobium strains are widespread in saline environments. Here, we report the complete genome sequence of Methylomicrobium alcaliphilum 20Z, a haloalkaliphilic methanotrophic bacterium, which will provide the basis for detailed characterization of the core pathways of both single-carbon metabolism and responses to osmotic and high-pH stresses. Final assembly of the genome sequence revealed that this bacterium contains a 128-kb plasmid, making M. alcaliphilum 20Z the first methanotrophic...

  1. Effect of alginic acid decomposing bacterium on the growth of Laminaria japonica (Phaeophyceae)

    Institute of Scientific and Technical Information of China (English)

    WANG You; TANG Xue-xi; YANG Zhen; YU Zhi-ming

    2006-01-01

    We collected the diseased blades of Laminaria japonica from Yantai Sea Farm from October to December 2002, and the alginic acid decomposing bacterium on the diseased blade was isolated and purified, and was identified as Alteromonas espejiana. This bacterium was applied as the causative pathogen to infect the blades of L. japonica under laboratory conditions. The aim of the present study was to identify the effects of the bacterium on the growth of L. japonica, and to find the possibly effective mechanism. Results showed that: (1)The blades of L.japonica exhibited symptoms of lesion,bleaching and deterioration when infected by the bacterium,and their growth and photosynthesis were dramatically suppressed. At the same time, the reactive oxygen species (ROS) generation enhanced obviously, and the relative membrane permeability increased significantly. The contents of malonaldehyde (MDA) and free fatty acid in the microsomol membrane greatly elevated, but the phospholipid content decreased. Result suggested an obvious peroxidation and deesterrification in the blades of L. japonica when infected by the bacterium. (2) The simultaneous assay on the antioxidant enzyme activities demonstrated that superoxide dismutase (SOD) and catalase (CAT) increased greatly when infected by the bacterium, but glutathione peroxidase (Gpx) and ascorbate peroxidase (APX) did not exhibit active responses to the bacterium throughout the experiment. (3) The histomorphological observations gave a distinctive evidence of the severity of the lesions as well as the relative abundance in the bacterial population on the blades after infection. The bacterium firstly invaded into the endodermis of L. japonica and gathered around there, and then resulted in the membrane damage, cells corruption and ultimately, the death of L.japonica.

  2. High Prevalence of Antibodies against the Bacterium Treponema pallidum in Senegalese Guinea Baboons (Papio papio)

    OpenAIRE

    Knauf, Sascha; Barnett, Ulrike; Maciej, Peter; Klapproth, Matthias; Ndao, Ibrahima; Frischmann, Sieghard; Fischer, Julia; Zinner, Dietmar; Liu, Hsi

    2015-01-01

    The bacterium Treponema pallidum is known to cause syphilis (ssp. pallidum), yaws (ssp. pertenue), and endemic syphilis (ssp. endemicum) in humans. Nonhuman primates have also been reported to be infected with the bacterium with equally versatile clinical manifestations, from severe skin ulcerations to asymptomatic. At present all simian strains are closely related to human yaws-causing strains, an important consideration for yaws eradication. We tested clinically healthy Guinea baboons (Papi...

  3. Draft Genome Sequence of DLB, a Dyella-Like Bacterium from the Planthopper Hyalesthes obsoletus

    Science.gov (United States)

    Lahav, Tamar; Zchori-Fein, Einat; Naor, Vered; Freilich, Shiri

    2016-01-01

    We report here the draft genome sequence of a Dyella-like bacterium (DLB) isolated from Hyalesthes obsoletus, the insect vector of the uncultivable mollicute bacterium “Candidatus Phytoplasma.” This isolate inhibits Spiroplasma melliferum, a cultivable mollicute. The draft genome of DLB consists of 4,196,214 bp, with a 68.6% G+C content, and 3,757 genes were predicted. PMID:27445378

  4. Biosynthesis Of Gold Nanoparticles By Marine Purple Non Sulphur Bacterium, Rhodopseudomonas Sp.

    OpenAIRE

    Abirami. G; Asmathunisha. N; Kathiresan. K

    2013-01-01

    This paper describes for the first time that an anaerobic marine bacterium is capable of producing gold nanoparticles. A marine purple non-sulphur bacterium was isolated from mangrove sediment and identified as Rhodopseudomonas sp. . The bacterial culture was tested for the synthesis of gold nanoparticles by using aqueous HAuCl4 solution as substrate in darkness. The gold nanoparticles synthesized were found to be of cubical structure in the size range of 10–20 nm.

  5. Abundances of ammonia-oxidizing archaeal accA and amoA genes in response to NO2-and NO3-of hot springs in Yunnan province%云南热泉中氨氧化古菌的accA基因与amoA基因丰度与环境因子NO2-和NO3-的相关性

    Institute of Scientific and Technical Information of China (English)

    宋兆齐; 王莉; 周恩民; 王风平; 肖湘; 张传伦; 李文均

    2014-01-01

    [目的]氨氧化古菌(ammonia-oxidizing archaea,AOA)可能通过近期刚发现的3-羟基丙酸盐/4-羟基丁酸盐途径(3-hydroxypropionate/4-hydroxybutyrate cycle,HP/HB)来固定CO2,在海洋和土壤环境下进行化能自养型生长.云南热泉系统已被证明具有丰富的AOA多样性.本论文旨在调查云南不同热泉中,这种CO2固定途径的关健酶——乙酰辅酶A羧化酶基因accA和古菌氨单加氧酶基因amoA,及原核微生物16S rRNA基因的丰度变化,以及它们与环境因子的相关性.[方法]选择20处代表性热泉沉积物样品,通过荧光定量PCR技术,获得各目的基因丰度;利用R软件包对各样点地化参数进行主成分分析(Principal ComponentAnalysis,PCA),并通过Mantel test检验各目的基因和地化参数间的相关性.[结果]细菌和古菌16S rRNA基因的丰度范围分别在6.6×107至4.19×1011和1.27×106至1.51 ×1011拷贝/g沉积物;古菌accA和amoA基因的丰度范围为8.89×103至6.49×105和7.64×103至4.36×105拷贝/g沉积物,Mantel test结果显示accA和amoA基因丰度间具有极显著的相关性(R =0.98,P<0.001),两者又分别都与热泉内的NO2-和NO3-浓度存在显著相关,与pH值等其它环境因子没有明显统计学意义上的相关性.[结论]云南地区热泉间的细菌和古菌丰度,以及两者比例关系都存在较大差异;相关性的统计结果进一步证明了热泉环境下的氨氧化古菌是通过HP/HB途径进行CO2固定;本次研究并未发现氨氧化古菌的丰度与环境pH存在明显统计学意义上的相关性,这与常温土壤环境的相关研究结果存在不同.

  6. Carbonate biomineralization induced by soil bacterium Bacillus megaterium

    Science.gov (United States)

    Lian, Bin; Hu, Qiaona; Chen, Jun; Ji, Junfeng; Teng, H. Henry

    2006-11-01

    Biogenic carbonates spawned from microbial activities are common occurrences in soils. Here, we investigate the carbonate biomineralization mediated by the bacterium Bacillus megaterium, a dominant strain separated from a loess profile in China. Upon completing bacterial cultivation, the ensuring products are centrifuged, and the resultant supernatant and the concentrated bacterial sludge as well as the un-separated culture are added separately into a Ca-CO 3 containing solution for crystallization experiments. Results of XRD and SEM analysis indicate that calcite is the dominant mineral phase formed when the bacteria are present. When the supernatant alone is used, however, a significant portion of vaterite is also precipitated. Experimental results further reveal that the bacteria have a strong tendency to colonize the center area of the calcite {1 0 1¯ 4} faces. Observed crystal morphology suggests that the bacterial colony may promote the growth normal to each individual {1 0 1¯ 4} face of calcite when the cell concentration is high, but may retard it or even cause dissolution of the immediate substrate surfaces when the concentration is low. SEM images taken at earlier stages of the crystallization experiments demonstrate the nucleation of calcite on the bacterial cell walls but do not show obvious morphological changes on the nanometer- to submicron-sized nuclei. δ 13C measurements unveil that the crystals grown in the presence of bacteria are further enriched in the heavy carbon isotope, implying that the bacterial metabolism may not be the carbon sources for the mineralization. Based upon these findings, we propose a mechanism for the B. megaterium mediated calcite mineralization and conclude that the whole process involves epi- and inter-cellular growth in the local microenvironments whose conditions may be controlled by cell sequestration and proton pumping during bacterial respiration.

  7. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium.

    Science.gov (United States)

    Braakman, Rogier; Smith, Eric

    2014-01-01

    Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA) cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere. PMID:24516572

  8. Interaction of Cadmium With the Aerobic Bacterium Pseudomonas Mendocina

    Science.gov (United States)

    Schramm, P. J.; Haack, E. A.; Maurice, P. A.

    2006-05-01

    The fate of toxic metals in the environment can be heavily influenced by interaction with bacteria in the vadose zone. This research focuses on the interactions of cadmium with the strict aerobe Pseudomonas mendocina. P. mendocina is a gram-negative bacterium that has shown potential in the bioremediation of recalcitrant organic compounds. Cadmium is a common environmental contaminant of wide-spread ecological consequence. In batch experiments P. mendocina shows typical bacterial growth curves, with an initial lag phase followed by an exponential phase and a stationary to death phase; concomitant with growth was an increase in pH from initial values of 7 to final values at 96 hours of 8.8. Cd both delays the onset of the exponential phase and decreases the maximum population size, as quantified by optical density and microscopic cell counts (DAPI). The total amount of Cd removed from solution increases over time, as does the amount of Cd removed from solution normalized per bacterial cell. Images obtained with transmission electron microscopy (TEM) showed the production of a cadmium, phosphorus, and iron containing precipitate that was similar in form and composition to precipitates formed abiotically at elevated pH. However, by late stationary phase, the precipitate had been re-dissolved, perhaps by biotic processes in order to obtain Fe. Stressed conditions are suggested by TEM images showing the formation of pili, or nanowires, when 20ppm Cd was present and a marked decrease in exopolysaccharide and biofilm material in comparison to control cells (no cadmium added).

  9. Metabolic evolution of a deep-branching hyperthermophilic chemoautotrophic bacterium.

    Directory of Open Access Journals (Sweden)

    Rogier Braakman

    Full Text Available Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism and examine in detail the driving forces that have shaped it. We make extensive use of phylometabolic analysis, a method we recently introduced that generates trees of metabolic phenotypes by integrating phylogenetic and metabolic constraints. We reconstruct the evolution of a range of metabolic sub-systems, including the reductive citric acid (rTCA cycle, as well as the biosynthesis and functional roles of several amino acids and cofactors. We show that A. aeolicus uses the reconstructed ancestral pathways within many of these sub-systems, and highlight how the evolutionary interconnections between sub-systems facilitated several key innovations. Our analyses further highlight three general classes of driving forces in metabolic evolution. One is the duplication and divergence of genes for enzymes as these progress from lower to higher substrate specificity, improving the kinetics of certain sub-systems. A second is the kinetic optimization of established pathways through fusion of enzymes, or their organization into larger complexes. The third is the minimization of the ATP unit cost to synthesize biomass, improving thermodynamic efficiency. Quantifying the distribution of these classes of innovations across metabolic sub-systems and across the tree of life will allow us to assess how a tradeoff between maximizing growth rate and growth efficiency has shaped the long-term metabolic evolution of the biosphere.

  10. Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium.

    Science.gov (United States)

    Rivas, Raúl; Mateos, Pedro F; Martínez-Molina, Eustoquio; Velázquez, Encarna

    2005-01-01

    During a search for xylan-degrading micro-organisms, a sporulating bacterium was recovered from xylan-containing agar plates exposed to air in a research laboratory (Salamanca University, Spain). The airborne isolate (designated strain XIL14T) was identified by 16S rRNA gene sequencing as representing a Paenibacillus species most closely related to Paenibacillus illinoisensis JCM 9907T (99.3 % sequence similarity) and Paenibacillus pabuli DSM 3036T (98 % sequence similarity). Phenotypic, chemotaxonomic and DNA-DNA hybridization data indicated that the isolate belongs to a novel species of the genus Paenibacillus. Cells of strain XIL14T were motile, sporulating, rod-shaped, Gram-positive and facultatively anaerobic. The predominant cellular fatty acids were anteiso-C(15 : 0) and C(16 : 0). The DNA G+C content of strain XIL14T was 50.5 mol%. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. Catalase was positive and oxidase was negative. The airborne isolate produced a variety of hydrolytic enzymes, including xylanases, amylases, gelatinase and beta-galactosidase. DNA-DNA hybridization levels between strain XIL14T and P. illinoisensis DSM 11733T and P. pabuli DSM 3036T were 43.3 and 36.3 %, respectively. According to the data obtained, strain XIL14T is considered to represent a novel species for which the name Paenibacillus xylanilyticus sp. nov. is proposed (=LMG 21957T=CECT 5839T). PMID:15653909

  11. Regulation of Polyhydroxybutyrate Synthesis in the Soil Bacterium Bradyrhizobium diazoefficiens.

    Science.gov (United States)

    Quelas, J I; Mesa, S; Mongiardini, E J; Jendrossek, D; Lodeiro, A R

    2016-07-15

    Polyhydroxybutyrate (PHB) is a carbon and energy reserve polymer in various prokaryotic species. We determined that, when grown with mannitol as the sole carbon source, Bradyrhizobium diazoefficiens produces a homopolymer composed only of 3-hydroxybutyrate units (PHB). Conditions of oxygen limitation (such as microoxia, oxic stationary phase, and bacteroids inside legume nodules) were permissive for the synthesis of PHB, which was observed as cytoplasmic granules. To study the regulation of PHB synthesis, we generated mutations in the regulator gene phaR and the phasin genes phaP1 and phaP4 Under permissive conditions, mutation of phaR impaired PHB accumulation, and a phaP1 phaP4 double mutant produced more PHB than the wild type, which was accumulated in a single, large cytoplasmic granule. Moreover, PhaR negatively regulated the expression of phaP1 and phaP4 as well as the expression of phaA1 and phaA2 (encoding a 3-ketoacyl coenzyme A [CoA] thiolases), phaC1 and phaC2 (encoding PHB synthases), and fixK2 (encoding a cyclic AMP receptor protein [CRP]/fumarate and nitrate reductase regulator [FNR]-type transcription factor of genes for microoxic lifestyle). In addition to the depressed PHB cycling, phaR mutants accumulated more extracellular polysaccharides and promoted higher plant shoot dry weight and competitiveness for nodulation than the wild type, in contrast to the phaC1 mutant strain, which is defective in PHB synthesis. These results suggest that phaR not only regulates PHB granule formation by controlling the expression of phasins and biosynthetic enzymes but also acts as a global regulator of excess carbon allocation and symbiosis by controlling fixK2 IMPORTANCE: In this work, we investigated the regulation of polyhydroxybutyrate synthesis in the soybean-nodulating bacterium Bradyrhizobium diazoefficiens and its influence in bacterial free-living and symbiotic lifestyles. We uncovered a new interplay between the synthesis of this carbon reserve polymer

  12. Photoactive yellow protein from the halophilic bacterium Salinibacter ruber.

    Science.gov (United States)

    Memmi, Samy; Kyndt, John; Meyer, Terry; Devreese, Bart; Cusanovich, Michael; Van Beeumen, Jozef

    2008-02-19

    A gene for photoactive yellow protein (PYP) was identified from the genome sequence of the extremely halophilic aerobic bacterium Salinibacter ruber (Sr). The sequence is distantly related to the prototypic PYP from Halorhodospira halophila (Hh) (37% identity) and contains most of the amino acid residues identified as necessary for function. However, the Sr pyp gene is not flanked by its two biosynthetic genes as in other species. To determine as to whether the Sr pyp gene encodes a functional protein, we cloned and expressed it in Escherichia coli, along with the genes for chromophore biosynthesis from Rhodobacter capsulatus. The Sr PYP has a 31-residue N-terminal extension as compared to other PYPs that appears to be important for dimerization; however, truncation of these extra residues did not change the spectral and photokinetic properties. Sr PYP has an absorption maximum at 431 nm, which is at shorter wavelengths than the prototypical Hh PYP (at 446 nm). It is also photoactive, being reversibly bleached by either blue or white light. The kinetics of dark recovery is slower than any of the PYPs reported to date (4.27 x 10(-4) s(-1) at pH 7.5). Sr PYP appears to have a normal photocycle with the I1 and I2 intermediates. The presence of the I2' intermediate is also inferred on the basis of the effects of temperature and alchohol on recovery. Sr PYP has an intermediate spectral form in equilibrium with the 431 nm form, similar to R. capsulatus PYP and the Y42F mutant of Hh PYP. Increasing ionic strength stabilizes the 431 nm form at the expense of the intermediate spectral form, and the kinetics of recovery is accelerated 6.4-fold between 0 and 3.5 M salt. This is observed with ions from both the chaotropic and the kosmotropic series. Ionic strength also stabilizes PYP against thermal denaturation, as the melting temperature is increased from 74 degrees C in buffer alone to 92 degrees C in 2 M KCl. Sr accumulates KCl in the cytoplasm, like Halobacterium, to

  13. A plant growth-promoting bacterium that decreases nickel toxicity in seedlings

    Energy Technology Data Exchange (ETDEWEB)

    Burd, G.I.; Dixon, D.G.; Glick, B.R. [Univ. of Waterloo, Ontario (Canada). Dept. of Biology

    1998-10-01

    A plant growth-promoting bacterium, Kluyvera ascorbata SUD165, that contained high levels of heavy metals was isolated from soil collected near Sudbury, Ontario, Canada. The bacterium was resistant to the toxic effects of Ni{sup 2+}, Pb{sup 2+}, Zn{sup 2+}, and CrO{sub 4}{sup {minus}}, produced a siderophore(s), and displayed 1-aminocyclopropane-1-carboxylic acid deaminase activity. Canola seeds inoculated with this bacterium and then grown under gnotobiotic conditions in the presence of high concentrations of nickel chloride were partially protected against nickel toxicity. In addition, protection by the bacterium against nickel toxicity was evident in pot experiments with canola and tomato seeds. The presence of K. ascorbata SUD165 had no measurable influence on the amount of nickel accumulated per milligram (dry weight) of either roots or shoots of canola plants. Therefore, the bacterial plant growth-promoting effect in the presence of nickel was probably not attributable to the reduction of nickel uptake by seedlings. Rather, it may reflect the ability of the bacterium to lower the level of stress ethylene induced by the nickel.

  14. Action of the Selenomorpholine Compounds on the Bacterium Growth by Microcalorimetry

    Institute of Scientific and Technical Information of China (English)

    LI,Xi(李曦); LIU,Yi(刘义); WU,Jun(吴军); QU,Song-Sheng(屈松生)

    2002-01-01

    The action of β-(N-selenomorpholine) ethyl phenyl ketone hy drochloride and 4-(N-selenomorpholine)-2-butanone hydrochloride on Escherichia coli and Staphylococcus aureus was studied by microcalorimetry. Differences in their capacities to affect the metabolism of this bacterium were observed. The kinetics shows that the selenomorphline compounds had action on the metabolism process of Escherichia coli and Staphylococcus aureus. The rate constant (k) of the studied bacterium in the presence of the drugs are concentration-dependant. The growth rate constants decrease with an increase in the mass of the selenomorpholine compounds, but their relationship is different. As deduced from the rate constant (k) of the studied bacterium (in log phase) and the half inhibitory concentration (IC50), the experimental results reveal that the studied selenomorphline compounds all have good antibiotic activity and better antibacterial activity on Staphylococcus aureus than on Escherichia coli.

  15. Studies on the pathogenic bacterium of ulcer disease in Epinephelus awoara

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Studies were conducted to determine the cause of the acute mortality of cage-cultured Epinephelus awoara in the Tong'an Bay of Xiamen, China during the summer of 2002. Predominant bacteria strain TS-628 was isolated from the diseased grouper. The virulence test confirmed that TS-628 was the pathogenic bacterium. Biochemical characteristics of the isolates were determined using the automatic bacterial identification system and standard tube tests. To further confirm the identification, a 1 121 bp 16S rRNA gene sequence of the isolate was amplified by PCR, which had been deposited into Genbank (accession number: AY747308). According to the biochemical characteristics and by comparing the 16S rRNA gene homology of the isolate, the pathogenic bacterium was identified as Vibrio harveyi. Drug sensitivity tests showed that this pathogenic bacterium was sensitive to 16 antibacterials, especially to chloramphenicol and actinospectacin, but completely resistant to antibacterials likes vancomycin, penicillin, lincomycin, and so on.

  16. Action of the Selenomorpholine Compounds on the Bacterium Growth by Microcalorimetry

    Institute of Scientific and Technical Information of China (English)

    李曦; 刘义; 等

    2002-01-01

    The action of β-(N-selenomorpholine) ethyl phenyl ketone hydrochloride and 4-(N-selenomorpholine)-2-butanone hydro-chloride on Escherichia coli and Staphylococcus aureus was studied by microcalorimetry,Differences in their capacities to affect the metabolism of this bacterium were observed.The kinetics shows that the selenomorpholine compounds had action on the metabolism process of Escherichia coli and Staphylococcus aureus.The rate constant (k) of the studied bacterium in the presence of the drugs are concentration-dependant.The growth rate constants decrease with an increase in the mass of the selenomorpholine compounds ,but their relationship is different.As deduced from the rate constant(k) of the studied bacterium(in log phase )and the half inhibitory concentration (IC50),the experimental results reveal that the studied selenomorpholine compounds all have good antibiotic activity and better antibacterial activity on Staphylcoccus aureus than on Escherichia coli.

  17. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Gary [Los Alamos National Laboratory (LANL); Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Chertkov, Olga [Los Alamos National Laboratory (LANL); Land, Miriam L [ORNL

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  18. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    Energy Technology Data Exchange (ETDEWEB)

    Rhee, Mun Su [University of Florida, Gainesville; Moritz, Brelan E. [University of Florida, Gainesville; Xie, Gary [Los Alamos National Laboratory (LANL); Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Chertkov, Olga [Los Alamos National Laboratory (LANL); Brettin, Thomas S [ORNL; Han, Cliff [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Patel, Milind [University of Florida, Gainesville; Ou, Mark [University of Florida, Gainesville; Harbrucker, Roberta [University of Florida, Gainesville; Ingram, Lonnie O. [University of Florida; Shanmugam, Keelnathan T. [University of Florida

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  19. Removal of corper(II) Ions from aqueous solution by a lactic acid bacterium

    OpenAIRE

    M. Yilmaz(Department of Physics, Gazi University, Ankara); T. Tay; M. Kivanc; H. Turk

    2010-01-01

    Enterococcus faecium, a lactic acid bacterium (LAB), was evaluated for its ability to remove copper(II) ions from water. The effects of the pH, contact time, initial concentration of copper(II) ions, and temperature on the biosorption rate and capacity were studied. The initial concentrations of copper(II) ions used to determine the maximum amount of biosorbed copper(II) ions onto lyophilised lactic acid bacterium varied from 25 mg L-1 to 500 mg L-1. Maximum biosorption capacities were attain...

  20. Sensitivity of the bacterium Bacillus Thuringiensis as an insect disease agent to gamma-rays

    International Nuclear Information System (INIS)

    The effect of gamma radiation on the viability of the entomopathogenic spore-forming bacterium, Bacillus thuringiensis, was tested. The different gamma doses varied much in their effect on such bacterium. All irradiated Bacillus suspensions with doses below 85 krad showed different degrees of inhibitory activity. However, bacterial suspensions irradiated at a dose of 90 krad. proved to promote spore germination. Changes in the physiological, and morphological characters of the irradiated Bacillus at these levels were detected. The new observed characters were induced at a particular dose level of 90 krad. These new characters are assumed to be due to genetic changes induced at this particular gamma dose

  1. Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002

    OpenAIRE

    Weber, Karrie A; Hedrick, David B.; Peacock, Aaron D.; Thrash, J. Cameron; White, David C.; Achenbach, Laurie A.; Coates, John D.

    2009-01-01

    A lithoautotrophic, Fe(II) oxidizing, nitrate-reducing bacterium, strain 2002 (ATCC BAA-1479; =DSM 18807), was isolated as part of a study on nitrate-dependent Fe(II) oxidation in freshwater lake sediments. Here we provide an in-depth phenotypic and phylogenetic description of the isolate. Strain 2002 is a gram-negative, non-spore forming, motile, rod-shaped bacterium which tested positive for oxidase, catalase, and urease. Analysis of the complete 16S rRNA gene sequence placed strain 2002 in...

  2. Aminomonas paucivorans gen. nov., sp. nov., a mesophilic, anaerobic, amino-acid-utilizing bacterium

    OpenAIRE

    Baena, S.; Fardeau, Marie-Laure; Ollivier, Bernard; Labat, Marc; Thomas, P; Garcia, Jean-Louis; Patel, B.K.C.

    1999-01-01

    A novel, asaccharolytic, amino-acid-degrading bacterium, designated strain GLU-3T, was isolated from an anaerobic lagoon of a dairy wastewater treatment plant. Strain GLU-3T stained Gram-negative and was an obligately anaerobic, non-spore-forming, slightly curved, rod-shaped bacterium (0.3 x 4.0-6.0 micrometers) which existed singly or in pairs. The DNA G+C content was 43 mol%. Optimum growth occurred at 35°C and pH 7.5 on arginine, histidine, threonine and glycine. Acetate was the end-produc...

  3. Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism

    OpenAIRE

    Ueda, Kenji; YAMASHITA Atsushi; Ishikawa, Jun; Shimada, Masafumi; Watsuji, Tomo-o; Morimura, Kohji; Ikeda, Haruo; Hattori, Masahira; Beppu, Teruhiko

    2004-01-01

    Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium belongs to an unknown taxon in the Gram-positive bacterial cluster. Here, we describe the 3.57 Mb genome sequence of S.thermophilum. The genome consists of 3338 protein-coding sequences, out of which 2082 have functional assignments. Despite the high G + C content (68.7%), the genome is closest to that of Fir...

  4. Marinobacter hydrocarbonoclasticus NY-4, a novel denitrifying, moderately halophilic marine bacterium

    OpenAIRE

    Li, Rongpeng; Zi, Xiaoli; Wang, Xinfeng; Zhang, Xia; Gao, Haofeng; Hu, Nan

    2013-01-01

    The isolation and characterization of a novel halophilic denitrifying marine bacterium is described. The halophilic bacterium, designated as NY-4, was isolated from soil in Yancheng City, China, and identified as Marinobacter hydrocarbonoclasticus by 16S rRNA gene sequence phylogenetic analysis. This organism can grow in NaCl concentrations ranging from 20 to 120 g/L. Optimum growth occurs at 80 g/L NaCl and pH 8.0. The organism can grow on a broad range of carbon sources and demonstrated eff...

  5. Purification and Characterization of Haloalkaline, Organic Solvent Stable Xylanase from Newly Isolated Halophilic Bacterium-OKH

    OpenAIRE

    Sanghvi, Gaurav; Jivrajani, Mehul; Patel, Nirav; Jivrajani, Heta; Bhaskara, Govinal Badiger; Patel, Shivani

    2014-01-01

    A novel, alkali-tolerant halophilic bacterium-OKH with an ability to produce extracellular halophilic, alkali-tolerant, organic solvent stable, and moderately thermostable xylanase was isolated from salt salterns of Mithapur region, Gujarat, India. Identification of the bacterium was done based upon biochemical tests and 16S rRNA sequence. Maximum xylanase production was achieved at pH 9.0 and 37°C temperature in the medium containing 15% NaCl and 1% (w/v) corn cobs. Sugarcane bagasse and whe...

  6. Enhanced Cadmium (Cd) Phytoextraction from Contaminated Soil using Cd-Resistant Bacterium

    OpenAIRE

    Kunchaya Setkit; Acharaporn Kumsopa; Jaruwan Wongthanate; Benjaphorn Prapagdee

    2014-01-01

    A cadmium (Cd)-resistant bacterium, Micrococcus sp. MU1, is able to produce indole-3-acetic acid and promotes root elongation and plant growth. The potential of this bacterium on enhancement of Cd uptake and bioaccumulation of Cd in Helianthus annuus L. planted in Cd-contaminated soil was evaluated in greenhouse condition. The results showed that Micrococcus sp. MU1promoted the growth of H. annuus L. by increasing the root length, stem height, dry biomass, root to shoot ratio and also signifi...

  7. Isolation from swine feces of a bacterium which decarboxylates p-hydroxyphenylacetic acid to 4-methylphenol (p-cresol).

    OpenAIRE

    L. A. Ward; Johnson, K A; Robinson, I.M.; Yokoyama, M T

    1987-01-01

    An obligate anaerobe has been isolated from swine feces which decarboxylates p-hydroxyphenylacetic acid to 4-methylphenol (p-cresol). The bacterium was an ovoid rod, gram positive, nonsporeforming, and nonmotile. Lactate and acetate were major end products of glucose fermentation. Based on its characteristics, the bacterium is tentatively assigned to the genus Lactobacillus.

  8. New recombinant bacterium comprises a heterologous gene encoding glycerol dehydrogenase and/or an up-regulated native gene encoding glycerol dehydrogenase, useful for producing ethanol

    DEFF Research Database (Denmark)

    2010-01-01

    TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preparation (claimed): Producing recombinant bacterium having enhanced ethanol production characteristics when cultivated in growth medium comprising glycerol comprises: (a) transforming a parental bacterium by (i) the insertion of a heterologous gene encoding...... glycerol dehydrogenase; and/or (ii) up-regulating a native gene encoding glycerol dehydrogenase; and (b) obtaining the recombinant bacterium. Preferred Bacterium: In the recombinant bacterium above, the inserted heterologous gene and/or the up-regulated native gene is encoding a glycerol dehydrogenase...... dehydrogenase encoding region of the bacterium, or is inserted into a phosphotransacetylase encoding region of the bacterium, or is inserted into an acetate kinase encoding region of the bacterium. It is operably linked to an inducible, a regulated or a constitutive promoter. The up-regulated glycerol...

  9. Isolation and Structure Elucidation of a Novel Yellow Pigment from the Marine Bacterium Pseudoalteromonas tunicata

    Directory of Open Access Journals (Sweden)

    N. Kumar

    2005-10-01

    Full Text Available The marine environment is a major source for many novel natural compounds. A new yellow pigment has been isolated from the marine bacterium P. tunicata and identified as a new member of the tambjamine class of compounds. The structural identification was achieved by a combination of 1D and 2D-NMR spectroscopy and high resolution mass spectrometry data.

  10. Complete Genome Sequence of Enterobacter cloacae B2-DHA, a Chromium-Resistant Bacterium.

    Science.gov (United States)

    Rahman, Aminur; Nahar, Noor; Olsson, Björn; Mandal, Abul

    2016-01-01

    Previously, we reported a chromium-resistant bacterium, Enterobacter cloacae B2-DHA, isolated from the landfills of tannery industries in Bangladesh. Here, we investigated its genetic composition using massively parallel sequencing and comparative analysis with other known Enterobacter genomes. Assembly of the sequencing reads revealed a genome of ~4.21 Mb in size. PMID:27257201

  11. Identification and Characterization of Clostridium paraputrificum, a Chitinolytic Bacterium of Human Digestive Tract

    Czech Academy of Sciences Publication Activity Database

    Šimůnek, Jiří; Kopečný, Jan; Hodrová, Blanka; Bartoňová, Hana

    2002-01-01

    Roč. 47, č. 5 (2002), s. 559-564. ISSN 0015-5632 R&D Projects: GA AV ČR KSK5020115; GA ČR GA525/00/0984; GA AV ČR KSK5052113 Keywords : Clostridium paraputrificum * Chitinolytic bacterium * digestive tract Subject RIV: EE - Microbiology, Virology Impact factor: 0.979, year: 2002

  12. Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

    Science.gov (United States)

    Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

    2016-03-20

    We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments. PMID:26853478

  13. Draft Genome Sequence of the Moderately Thermophilic Bacterium Schleiferia thermophila Strain Yellowstone (Bacteroidetes)

    OpenAIRE

    Thiel, Vera; Hamilton, Trinity L.; Tomsho, Lynn P.; Burhans, Richard; Gay, Scott E.; Ramaley, Robert F.; Stephan C Schuster; Steinke, Laurey; Bryant, Donald A.

    2014-01-01

    The draft genome sequence of the moderately thermophilic bacterium Schleiferia thermophila strain Yellowstone (Bacteroidetes), isolated from Octopus Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 2,617,694 bp in 35 contigs. The draft genome is predicted to encode 2,457 protein coding genes and 37 tRNA encoding genes and two rRNA operons.

  14. Genome Sequence of the Acetogenic Bacterium Moorella mulderi DSM 14980T

    Science.gov (United States)

    Castillo Villamizar, Genis Andrés

    2016-01-01

    Here, we report the draft genome sequence of Moorella mulderi DSM 14980T, a thermophilic acetogenic bacterium, which is able to grow autotrophically on H2 plus CO2 using the Wood-Ljungdahl pathway. The genome consists of a circular chromosome (2.99 Mb). PMID:27231372

  15. Removal of zinc from aqueous solution by metal resistant symbiotic bacterium Mesorhizobium amorphae

    DEFF Research Database (Denmark)

    Hao, Xiuli; Mohamad, Osama Abdalla; Xie, Pin;

    2014-01-01

    Biosorption of zinc by living biomasses of metal resistant symbiotic bacterium Mesorhizobium amorphae CCNWGS0123 was investigated under optimal conditions at pH 5.0, initial metal concentrations of 100 mg L-1, and a dose of 1.0 g L-1. M. amorphae exhibited an efficient removal of Zn2+ from aqueous...

  16. Cloning, sequencing, and sequence analysis of two novel plasmids from the thermophilic anaerobic bacterium Anaerocellum thermophilum

    DEFF Research Database (Denmark)

    Clausen, Anders; Mikkelsen, Marie Just; Schrøder, I.;

    2004-01-01

    The nucleotide sequence of two novel plasmids isolated from the extreme thermophilic anaerobic bacterium Anaerocellum thermophilum DSM6725 (A. thermophilum), growing optimally at 70degreesC, has been determined. pBAS2 was found to be a 3653 bp plasmid with a GC content of 43%, and the sequence...

  17. Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field

    DEFF Research Database (Denmark)

    Tanaka, Reiji; Kawaichi, Satoshi; Nishimura, Hiroshi;

    2006-01-01

    A novel thermophilic bacterium, strain KW1T, was isolated from a coastal hydrothermal field on the Satsuma Peninsula, Kagoshima Prefecture, Japan. The variably Gram-stained cells were motile rods with flagella, did not form spores and proliferated at 52-78°C (optimum, 70°C), pH 5-8 (optimum, pH 7...

  18. The atherogenic bacterium Porphyromonas gingivalis evades circulating phagocytes by adhering to erythrocytes

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Holmstrup, Palle; Damgaard, Christian;

    2011-01-01

    A relationship between periodontitis and coronary heart disease has been investigated intensively. A pathogenic role for the oral bacterium Porphyromonas gingivalis has been suggested for both diseases. We examined whether complement activation by P. gingivalis strain ATCC 33277 allows the bacter......A relationship between periodontitis and coronary heart disease has been investigated intensively. A pathogenic role for the oral bacterium Porphyromonas gingivalis has been suggested for both diseases. We examined whether complement activation by P. gingivalis strain ATCC 33277 allows...... the bacterium to adhere to human red blood cells (RBCs) and thereby evade attack by circulating phagocytes. On incubation with normal human serum, the P. gingivalis strain efficiently fixed complement component 3 (C3). Incubation of bacteria with washed whole blood cells suspended in autologous serum resulted......) and that by monocytes after between 15 min and 30 min of incubation (by 66% and 53%, respectively). The attachment of C3b/iC3b to bacterium-bearing RBCs decreased progressively after 15 min, indicating that conversion of C3 fragments into C3dg occurred, decreasing the affinity for CR1 on RBCs. We propose that P...

  19. Isolation and algae-lysing characteristics of the algicidal bacterium B5

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Water blooms have become a worldwide environmental problem. Recently, algicidal bacteria have attracted wide attention as possible agents for inhibiting algal water blooms. In this study, one strain of algicidal bacterium B5 was isolated from activated sludge. On the basis of analysis of its physiological characteristics and 16S rDNA gene sequence, it was identified as Bacillus fusiformis. Its algae-lysing characteristics on Microcystis aeruginosa, Chlorella and Scenedesmus were tested. The results showed that: (1) the algicidal bacterium B5 is a Gram-negative bacterium. The 16S rDNA nucleotide sequence homology of strain B5 with 2 strains of B. fusiformis reached 99.86%, so B5 was identified as B. fusiformis; (2) the algal-lysing effects of the algicidal bacterium B5 on M. aeruginosa, Chlorella and Scenedesmus were pronounced. The initial bacterial and algal cell densities strongly influence the removal rates of chlorophyll-a. The greater the initial bacterial cell density, the faster the degradation of chlorophyll-a. The greater the initial algal cell density, the slower the degradation of chlorophyll-a. When the bacterial cell density was 3.6 × 107 cells/ml, nearly 90% of chlorophyll-a was removed. When the chlorophyll-a concentration was less than 550 μg/L, about 70 % was removed; (3) the strain B5 lysed algae not directly but by secreting metabolites and these metabolites could bear heat treatment.

  20. Engineering a predatory bacterium as a proficient killer agent for intracellular bio-products recovery

    DEFF Research Database (Denmark)

    Martinez, Virginia; Herencias, Cristina; Jurkevitch, Edouard;

    2016-01-01

    This work examines the potential of the predatory bacterium Bdellovibrio bacteriovorus HD100, an obligate predator of other Gram-negative bacteria, as an external cell-lytic agent for recovering valuable intracellular bio-products produced by prey cultures. The bio-product targets to be recovered...

  1. The Mechanism and Usage for Enhanced Oil Recovery by Chemotaxis of Bacterium BS2

    Institute of Scientific and Technical Information of China (English)

    LiYiqian; JingGuicheng; GaoShusheng; XungWei

    2005-01-01

    Due to its chemotaxis, the motion ability of bacterium BS2 is very strong, and under the microscope, the distribution grads of bacterium concentration can be seen at the oil-water interface. During the experiments in glass box, it can be observed, with eyes, because of the chemotaxis, that muddy gets thicker and thicker at the interface gradually, and it is measured there, from sampling, that the bacterium concentration is 109 cells/mL, pH value 4.4 and the concentration of bio-surfactant 2.87%; The microbial oil-displacement experiments are carried out in emulational network models, and the oil-displacement mechanism by the bacterium and its metabolizing production is studied. And, during oil-displacement experiments in the gravel-input glass models, because of the profile control of thalli and the production, the sweep area of subsequent waterflood becomes wider, which can be seen with eyes and the recovery is enhanced by 13.6%. Finally, the successful field test is introduced in brief: the ratio of response producers is 85.7%, and the water-cut degrades by 6.4%, while 20038t oil has increased in accumulative total in 2 years.

  2. Two-dimensional gel-based alkaline proteome of the probiotic bacterium Lactobacillus acidophilus NCFM

    DEFF Research Database (Denmark)

    Majumder, Avishek; Cai, Liyang; Ejby, Morten;

    2012-01-01

    Lactobacillus acidophilus NCFM (NCFM) is a well‐documented probiotic bacterium isolated from human gut. Detailed 2D gel‐based NCFM proteomics addressed the so‐called alkaline range, i.e., pH 6–11. Proteins were identified in 150 of the 202 spots picked from the Coomassie Brilliant Blue stained 2D...

  3. Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea

    DEFF Research Database (Denmark)

    Machado, Henrique; Giubergia, Sonia; Mateiu, Ramona Valentina;

    2015-01-01

    A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, Solomon Islands. Analysis of the 16S rRNA gene sequence and whole genome sequence data placed strain S2753T in the genus Photobacterium with the closest relative being Photobacterium halotolerans...

  4. Design of semi industrial radium separator by a new bacterium MGF-48

    International Nuclear Information System (INIS)

    Following of a research work which has been recently published in AEOI scientific Bulletin no. 14, a semi industrial bioreactor has been designed for separation of radium using a new bacterium MGF-48. This bioreactor could be utilized for a high rate separation of radium in semi industrial scale. (author)

  5. Complete Genome Sequence of Sphingomonas sp. Strain NIC1, an Efficient Nicotine-Degrading Bacterium

    Science.gov (United States)

    Zhu, Xiongyu; Wang, Weiwei; Xu, Ping

    2016-01-01

    Sphingomonas sp. strain NIC1, an efficient nicotine-degrading bacterium, was isolated from tobacco leaves. Here, we present the complete genome sequence of strain NIC1, which contains one circular chromosome and two circular plasmids. The genomic information will provide insights into its molecular mechanism for nicotine degradation. PMID:27417841

  6. First Insights into the Genome of the Moderately Thermophilic Bacterium Clostridium tepidiprofundi SG 508T.

    Science.gov (United States)

    Poehlein, Anja; Friedrich, Ines; Krüger, Larissa; Daniel, Rolf

    2016-01-01

    The moderately thermophilic bacterium Clostridium tepidiprofundi is Gram-positive and belongs to clostridial cluster I. It was isolated from a hydrothermal vent chimney. Substrates utilized by C. tepidiprofundi include casein, peptone, tryptone, yeast extract, beef extract, starch, maltose, and glucose. The genome consists of one replicon (3.06 Mb). PMID:27174286

  7. First Insights into the Genome of the Moderately Thermophilic Bacterium Clostridium tepidiprofundi SG 508T

    OpenAIRE

    Poehlein, Anja; Friedrich, Ines; Krüger, Larissa; Daniel, Rolf

    2016-01-01

    The moderately thermophilic bacterium Clostridium tepidiprofundi is Gram-positive and belongs to clostridial cluster I. It was isolated from a hydrothermal vent chimney. Substrates utilized by C. tepidiprofundi include casein, peptone, tryptone, yeast extract, beef extract, starch, maltose, and glucose. The genome consists of one replicon (3.06 Mb).

  8. Draft Genome Sequence of Photorhabdus luminescens subsp. laumondii HP88, an Entomopathogenic Bacterium Isolated from Nematodes.

    Science.gov (United States)

    Ghazal, Shimaa; Oshone, Rediet; Simpson, Stephen; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Khalil, Kamal M; Tisa, Louis S

    2016-01-01

    Photorhabdus luminescens subsp. laumondii HP88 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 5.27-Mbp draft genome sequence for P. luminescens subsp. laumondii HP88, with a G+C content of 42.4% and containing 4,243 candidate protein-coding genes. PMID:26988056

  9. Draft Genome Sequence of Photorhabdus luminescens subsp. laumondii HP88, an Entomopathogenic Bacterium Isolated from Nematodes

    OpenAIRE

    Ghazal, Shimaa; Oshone, Rediet; Simpson, Stephen; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Khalil, Kamal M.; Tisa, Louis S.

    2016-01-01

    Photorhabdus luminescens subsp. laumondii HP88 is an entomopathogenic bacterium that forms a symbiotic association with Heterorhabditis nematodes. We report here a 5.27-Mbp draft genome sequence for P. luminescens subsp. laumondii HP88, with a G+C content of 42.4% and containing 4,243 candidate protein-coding genes.

  10. Draft Genome Sequence of the Ionic Liquid-Tolerant Bacterium Bacillus amyloliquefaciens CMW1

    OpenAIRE

    Kurata, Atsushi; Hirose, Yuu; Misawa, Naomi; Hurunaka, Kohei; Kishimoto, Noriaki

    2014-01-01

    Here, we report the draft genome sequence of an ionic liquid-tolerant bacterium, Bacillus amyloliquefaciens CMW1, which is newly isolated from a Japanese fermented soybean paste. The genome sequence will allow for a characterization of the molecular mechanism of its ionic liquid tolerance.

  11. Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome

    OpenAIRE

    Vilo, Claudia; Galetovic, Alexandra; Araya, Jorge E.; Gómez-Silva, Benito; Dong, Qunfeng

    2015-01-01

    We report here the draft genome sequence of a Bacillus bacterium isolated from the microflora of Nostoc colonies grown at the Andean wetlands in northern Chile. We consider this genome sequence to be a molecular tool for exploring microbial relationships and adaptation strategies to the prevailing extreme conditions at the Atacama Desert.

  12. Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome.

    Science.gov (United States)

    Vilo, Claudia; Galetovic, Alexandra; Araya, Jorge E; Gómez-Silva, Benito; Dong, Qunfeng

    2015-01-01

    We report here the draft genome sequence of a Bacillus bacterium isolated from the microflora of Nostoc colonies grown at the Andean wetlands in northern Chile. We consider this genome sequence to be a molecular tool for exploring microbial relationships and adaptation strategies to the prevailing extreme conditions at the Atacama Desert. PMID:26294639

  13. Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower.

    Science.gov (United States)

    Ambrosini, Adriana; Sant'Anna, Fernando Hayashi; de Souza, Rocheli; Tadra-Sfeir, Michele; Faoro, Helisson; Alvarenga, Samuel M; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi; Passaglia, Luciane M P

    2015-01-01

    Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to promote plant growth and N uptake. The genome of the isolate has approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting characteristics, such as nitrate reduction and ammonification and iron-siderophore uptake. PMID:25838494

  14. Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower

    OpenAIRE

    Ambrosini, Adriana; Sant’Anna, Fernando Hayashi; de Souza, Rocheli; Tadra-Sfeir, Michele; Faoro, Helisson; Alvarenga, Samuel M.; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi; Passaglia, Luciane M. P.

    2015-01-01

    Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to promote plant growth and N uptake. The genome of the isolate has approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting characteristics, such as nitrate reduction and ammonification and iron-siderophore uptake.

  15. Draft Genome Sequence of Perfluorooctane Acid-Degrading Bacterium Pseudomonas parafulva YAB-1

    OpenAIRE

    Yi, Langbo; Tang, Chongjian; Peng, Qingjing; Peng, Qingzhong; Chai, Liyuan

    2015-01-01

    Pseudomonas parafulva YAB-1, isolated from perfluorinated compound-contaminated soil, has the ability to degrade perfluorooctane acid (PFOA) compound. Here, we report the draft genome sequence and annotation of the PFOA-degrading bacterium P. parafulva YAB-1. The data provide the basis to investigate the molecular mechanism of PFOA metabolism.

  16. Draft Genome Sequence of Perfluorooctane Acid-Degrading Bacterium Pseudomonas parafulva YAB-1

    Science.gov (United States)

    Tang, Chongjian; Peng, Qingjing; Peng, Qingzhong

    2015-01-01

    Pseudomonas parafulva YAB-1, isolated from perfluorinated compound-contaminated soil, has the ability to degrade perfluorooctane acid (PFOA) compound. Here, we report the draft genome sequence and annotation of the PFOA-degrading bacterium P. parafulva YAB-1. The data provide the basis to investigate the molecular mechanism of PFOA metabolism. PMID:26337877

  17. Comment on "A bacterium that degrades and assimilates poly(ethylene terephthalate)".

    Science.gov (United States)

    Yang, Yu; Yang, Jun; Jiang, Lei

    2016-08-19

    Yoshida et al (Report, 11 March 2016, p. 1196) reported that the bacterium Ideonella sakaiensis 201-F6 can degrade and assimilate poly(ethylene terephthalate) (PET). However, the authors exaggerated degradation efficiency using a low-crystallinity PET and presented no straightforward experiments to verify depolymerization and assimilation of PET. Thus, the authors' conclusions are rather misleading. PMID:27540159

  18. Draft Genome Sequence of Burkholderia cenocepacia Strain 869T2, a Plant-Beneficial Endophytic Bacterium.

    Science.gov (United States)

    Ho, Ying-Ning; Huang, Chieh-Chen

    2015-01-01

    An endophytic bacterium, Burkholderia cenocepacia 869T2, isolated from vetiver grass, has shown its abilities for both in planta biocontrol and plant growth promotion. Its draft genome sequence was determined to provide insights into those metabolic pathways involved in plant-beneficial activity. This is the first genome report for endophytic B. cenocepacia. PMID:26564046

  19. Expression of Heterogenous Arsenic Resistance Genes in the Obligately Autotrophic Biomining Bacterium Thiobacillus ferrooxidans

    OpenAIRE

    Peng, Ji-Bin; Yan, Wang-Ming; Bao, Xue-Zhen

    1994-01-01

    Two arsenic-resistant plasmids were constructed and introduced into Thiobacillus ferrooxidans strains by conjugation. The plasmids with the replicon of wide-host-range plasmid RSF1010 were stable in T. ferrooxidans. The arsenic resistance genes originating from the heterotroph were expressed in this obligately autotrophic bacterium, but the promoter derived from T. ferrooxidans showed no special function in its original host.

  20. Draft Genome Sequence of Sphingobium yanoikuyae TJ, a Halotolerant Di-n-Butyl-Phthalate-Degrading Bacterium

    Science.gov (United States)

    Jin, Decai; Zhu, Ying; Wang, Xinxin; Kong, Xiao; Liu, Huijun; Wang, Yafeng

    2016-01-01

    Sphingobium yanoikuyae TJ is a halotolerant di-n-butyl-phthalate-degrading bacterium, isolated from the Haihe estuary in Bohai Bay, Tianjin, China. Here, we report the 5.1-Mb draft genome sequence of this strain, which will provide insights into the diversity of Sphingobium spp. and the mechanism of phthalate ester degradation in the estuary. PMID:27313307

  1. Whole-Genome Shotgun Sequence of Pseudomonas viridiflava, a Bacterium Species Pathogenic to Arabidopsis thaliana

    OpenAIRE

    Lefort, Francois; Calmin, Gautier; Crovadore, Julien; Osteras, Magne; Farinelli, Laurent

    2013-01-01

    We report here the first whole-genome shotgun sequence of Pseudomonas viridiflava strain UASWS38, a bacterium species pathogenic to the biological model plant Arabidopsis thaliana but also usable as a biological control agent and thus of great scientific interest for understanding the genetics of plant-microbe interactions.

  2. Biohydrogen Production by the Thermophilic Bacterium Caldicellulosiruptor saccharolyticus: Current Status and Perspectives

    NARCIS (Netherlands)

    Bielen, A.A.M.; Verhaart, M.R.A.; Oost, van der J.; Kengen, S.W.M.

    2013-01-01

    Caldicellulosiruptor saccharolyticus is one of the most thermophilic cellulolytic organisms known to date. This Gram-positive anaerobic bacterium ferments a broad spectrum of mono-, di- and polysaccharides to mainly acetate, CO2 and hydrogen. With hydrogen yields approaching the theoretical limit fo

  3. Genome sequence of the mycorrhizal helper bacterium Pseudomonas fluorescens BBc6R8

    Energy Technology Data Exchange (ETDEWEB)

    Deveau, Aurelie [French National Insitute for Agricultural Research (INRA); Grob, Harald [University of Bonn, Germany; Morin, Emmanuelle [INRA, Nancy, France; Karpinets, Tatiana V [ORNL; Utturkar, Sagar M [ORNL; Mehnaz, Samina [University of the Punjab, Pakistan; Kurz, Sven [University of Bonn, Germany; Martin, Francis [INRA, Nancy, France; Frey-Klett, Pascale [INRA, Nancy, France; Labbe, Jessy L [ORNL

    2014-01-01

    We report the draft genome sequence of the mycorrhiza helper bacterium Pseudomonas fluorescens strain BBc6R8 . Several traits which could be involved in the mycorrhiza helper ability of the bacterial strain such as multiple secretion systems, auxin metabolism and phosphate mobilization were evidenced in the genome.

  4. Complete genome sequence of a novel chlorpyrifos degrading bacterium, Cupriavidus nantongensis X1.

    Science.gov (United States)

    Fang, Lian-Cheng; Chen, Yi-Fei; Zhou, Yan-Long; Wang, Dao-Sheng; Sun, Le-Ni; Tang, Xin-Yun; Hua, Ri-Mao

    2016-06-10

    Cupriavidus nantongensis X1 is a chlorpyrifos degrading bacterium, which was isolated from sludge collected at the drain outlet of a chlorpyrifos manufacture plant. It is the first time to report the complete genome sequence of C. nantongensis species, which has been reported as a novel species of Cupriavidus genus. It could provide further pathway information in chlorpyrifos degradation. PMID:27063140

  5. Toxicity of herbicides used in the sugarcane crop to diazotrophic bacterium Herbaspirillum seropedicae

    OpenAIRE

    Sergio de Oliveira Procópio; Marcelo Ferreira Fernandes; Daniele Araújo Teles; José Guedes Sena Filho; Alberto Cargnelutti Filho; Marcelo Araújo Resende; Leandro Vargas

    2014-01-01

    The objective of this work was to identify herbicides used in the sugarcane crop that affects neither the growth, the development, of nor the process of biological nitrogen fixation (BNF) by the diazotrophic bacterium Herbaspirillum seropedicae. Eighteen herbicides (paraquat, ametryne, tebuthiuron, amicarbazone, diuron, metribuzin, [hexazinone + diuron], [hexazinone + clomazone], clomazone, isoxaflutole, sulfentrazone, oxyfluorfen, imazapic, imazapyr, [trifloxysulfuron sodium + ametryne], gly...

  6. An ATP transport system in the intracellular bacterium, Bdellovibrio bacteriovorus 109J.

    OpenAIRE

    Ruby, E G; McCabe, J B

    1986-01-01

    The intracellularly growing bacterium Bdellovibrio bacteriovorus 109J transports intact ATP by a specific, energy-requiring process. ATP transport does not involve either an ADP-ATP or an AMP-ATP exchange mechanism but, instead, has characteristics of an active transport permease. Kinetically distinct systems for ATP transport are expressed by the two developmental stages of the bdellovibrio life cycle.

  7. Complete Genome Sequence of Enterobacter cloacae B2-DHA, a Chromium-Resistant Bacterium

    Science.gov (United States)

    Rahman, Aminur; Nahar, Noor; Olsson, Björn

    2016-01-01

    Previously, we reported a chromium-resistant bacterium, Enterobacter cloacae B2-DHA, isolated from the landfills of tannery industries in Bangladesh. Here, we investigated its genetic composition using massively parallel sequencing and comparative analysis with other known Enterobacter genomes. Assembly of the sequencing reads revealed a genome of ~4.21 Mb in size. PMID:27257201

  8. Draft Genome Sequence of the Radioresistant Bacterium Deinococcus grandis, Isolated from Freshwater Fish in Japan

    Science.gov (United States)

    Onodera, Takefumi; Omoso, Kota; Takeda-Yano, Kiyoko; Katayama, Takeshi; Oono, Yutaka; Narumi, Issay

    2016-01-01

    Deinococcus grandis is a radioresistant bacterium isolated from freshwater fish in Japan. Here we reported the draft genome sequence of D. grandis (4.1 Mb), which will be useful for elucidating the common principles of radioresistance in Deinococcus species through the comparative analysis of genomic sequences. PMID:26868384

  9. Genome Sequence of the Spinosyns-Producing Bacterium Saccharopolyspora spinosa NRRL 18395 ▿

    Science.gov (United States)

    Pan, Yuanlong; Yang, Xi; Li, Jing; Zhang, Ruifen; Hu, Yongfei; Zhou, Yuguang; Wang, Jun; Zhu, Baoli

    2011-01-01

    Saccharopolyspora spinosa is a Gram-positive bacterium that produces spinosad, a well-known biodegradable insecticide that is used for agricultural pest control and has an excellent environmental and mammalian toxicological profile. Here, we present the first draft genome sequence of the type strain Saccharopolyspora spinosa NRRL 18395, which consists of 22 scaffolds. PMID:21478350

  10. Genome Sequence of Marichromatium gracile YL-28, a Purple Sulfur Bacterium with Bioremediation Potential

    Science.gov (United States)

    Zhang, Xiaobo; Zhao, Chungui; Hong, Xuan

    2016-01-01

    The draft genome sequence of Marichromatium gracile YL-28 contains 3,840,251 bp, with a G+C content of 68.84%. The annotated genome sequence provides the genetic basis for revealing its role as a purple sulfur bacterium in the harvesting of energy and the development of bioremediation applications. PMID:27151789

  11. Draft Genome Sequence of the Oyster Larval Probiotic Bacterium Vibrio sp. Strain OY15

    OpenAIRE

    Harold J. Schreier; Schott, Eric J.

    2014-01-01

    We report the draft genome sequence of Vibrio sp. strain OY15, a Gram-negative marine bacterium isolated from an oyster (Crassostrea virginica) digestive tract and shown to possess probiotic activity. The availability of this genome sequence will facilitate the study of the mechanisms of probiotic activity as well as virulence capacity.

  12. Genome Sequence of the Highly Efficient Arsenite-Oxidizing Bacterium Achromobacter arsenitoxydans SY8

    OpenAIRE

    Li, Xiangyang; Hu, Yao; Gong, Jing; Lin, Yanbing; Johnstone, Laurel; Rensing, Christopher; Wang, Gejiao

    2012-01-01

    We report the draft genome sequence of Achromobacter arsenitoxydans SY8, the first reported arsenite-oxidizing bacterium belonging to the genus Achromobacter and containing a genomic arsenic island, an intact type III secretion system, and multiple metal(loid) transporters. The genome may be helpful to explore the mechanisms intertwining metal(loid) resistance and pathogenicity.

  13. A commensal symbiotic interrelationship for the growth of Symbiobacterium toebii with its partner bacterium, Geobacillus toebii

    Directory of Open Access Journals (Sweden)

    Masui Ryoji

    2011-10-01

    Full Text Available Abstract Background Symbiobacterium toebii is a commensal symbiotic thermophile that absolutely requires its partner bacterium Geobacillus toebii for growth. Despite development of an independent cultivation method using cell-free extracts, the growth of Symbiobacterium remains unknown due to our poor understanding of the symbiotic relationship with its partner bacterium. Here, we investigated the interrelationship between these two bacteria for growth of S. toebii using different cell-free extracts of G. toebii. Results Symbiobacterium toebii growth-supporting factors were constitutively produced through almost all growth phases and under different oxygen tensions in G. toebii, indicating that the factor may be essential components for growth of G. toebii as well as S. toebii. The growing conditions of G. toebii under different oxygen tension dramatically affected to the initial growth of S. toebii and the retarded lag phase was completely shortened by reducing agent, L-cysteine indicating an evidence of commensal interaction of microaerobic and anaerobic bacterium S. toebii with a facultative aerobic bacterium G. toebii. In addition, the growth curve of S. toebii showed a dependency on the protein concentration of cell-free extracts of G. toebii, demonstrating that the G. toebii-derived factors have nutrient-like characters but not quorum-sensing characters. Conclusions Not only the consistent existence of the factor in G. toebii during all growth stages and under different oxygen tensions but also the concentration dependency of the factor for proliferation and optimal growth of S. toebii, suggests that an important biosynthetic machinery lacks in S. toebii during evolution. The commensal symbiotic bacterium, S. toebii uptakes certain ubiquitous and essential compound for its growth from environment or neighboring bacteria that shares the equivalent compounds. Moreover, G. toebii grown under aerobic condition shortened the lag phase of S

  14. Organic nitrogen-driven stimulation of arbuscular mycorrhizal fungal hyphae correlates with abundance of ammonia oxidizers

    Directory of Open Access Journals (Sweden)

    Petra eBukovská

    2016-05-01

    Full Text Available Large fraction of mineral nutrients in natural soil environments is recycled from complex and heterogeneously distributed organic sources. These sources are explored by both roots and associated mycorrhizal fungi. However, the mechanisms behind the responses of arbuscular mycorrhizal (AM hyphal networks to soil organic patches of different qualities remain little understood. Therefore, we conducted a multiple-choice experiment examining hyphal responses to different soil patches within the root-free zone by two AM fungal species (Rhizophagus irregularis and Claroideoglomus claroideum associated with Medicago truncatula, a legume forming nitrogen-fixing root nodules. Hyphal colonization of the patches was assessed microscopically and by quantitative real-time PCR (qPCR using AM taxon-specific markers, and the prokaryotic and fungal communities in the patches (pooled per organic amendment treatment were profiled by 454-amplicon sequencing. Specific qPCR markers were then designed and used to quantify the abundance of prokaryotic taxa showing the strongest correlation with the pattern of AM hyphal proliferation in the organic patches as per the 454-sequencing. The hyphal density of both AM fungi increased due to nitrogen (N-containing organic amendments (i.e., chitin, DNA, albumin, and clover biomass, while no responses as compared to the non-amended soil patch were recorded for cellulose, phytate, or inorganic phosphate amendments. Abundances of several prokaryotes, including Nitrosospira sp. (an ammonium oxidizer and an unknown prokaryote with affiliation to Acanthamoeba endosymbiont, which were frequently recorded in the 454-sequencing profiles, correlated positively with the hyphal responses of R. irregularis to the soil amendments. Strong correlation between abundance of these two prokaryotes and the hyphal responses to organic soil amendments by both AM fungi was then confirmed by qPCR analyses using all individual replicate patch samples. Further research is warranted to ascertain the causality of these correlations and particularly which direct roles (if any do these prokaryotes play in the observed AM hyphal responses to organic N amendment, organic N utilization by the AM fungus and its (N-unlimited host plant. Further, possible trophic dependencies between the different players in the AM hyphosphere needs to be elucidated upon decomposing the organic N sources.

  15. Organic Nitrogen-Driven Stimulation of Arbuscular Mycorrhizal Fungal Hyphae Correlates with Abundance of Ammonia Oxidizers.

    Science.gov (United States)

    Bukovská, Petra; Gryndler, Milan; Gryndlerová, Hana; Püschel, David; Jansa, Jan

    2016-01-01

    Large fraction of mineral nutrients in natural soil environments is recycled from complex and heterogeneously distributed organic sources. These sources are explored by both roots and associated mycorrhizal fungi. However, the mechanisms behind the responses of arbuscular mycorrhizal (AM) hyphal networks to soil organic patches of different qualities remain little understood. Therefore, we conducted a multiple-choice experiment examining hyphal responses to different soil patches within the root-free zone by two AM fungal species (Rhizophagus irregularis and Claroideoglomus claroideum) associated with Medicago truncatula, a legume forming nitrogen-fixing root nodules. Hyphal colonization of the patches was assessed microscopically and by quantitative real-time PCR (qPCR) using AM taxon-specific markers, and the prokaryotic and fungal communities in the patches (pooled per organic amendment treatment) were profiled by 454-amplicon sequencing. Specific qPCR markers were then designed and used to quantify the abundance of prokaryotic taxa showing the strongest correlation with the pattern of AM hyphal proliferation in the organic patches as per the 454-sequencing. The hyphal density of both AM fungi increased due to nitrogen (N)-containing organic amendments (i.e., chitin, DNA, albumin, and clover biomass), while no responses as compared to the non-amended soil patch were recorded for cellulose, phytate, or inorganic phosphate amendments. Abundances of several prokaryotes, including Nitrosospira sp. (an ammonium oxidizer) and an unknown prokaryote with affiliation to Acanthamoeba endosymbiont, which were frequently recorded in the 454-sequencing profiles, correlated positively with the hyphal responses of R. irregularis to the soil amendments. Strong correlation between abundance of these two prokaryotes and the hyphal responses to organic soil amendments by both AM fungi was then confirmed by qPCR analyses using all individual replicate patch samples. Further research is warranted to ascertain the causality of these correlations and particularly which direct roles (if any) do these prokaryotes play in the observed AM hyphal responses to organic N amendment, organic N utilization by the AM fungus and its (N-unlimited) host plant. Further, possible trophic dependencies between the different players in the AM hyphosphere needs to be elucidated upon decomposing the organic N sources. PMID:27242732

  16. Traveling interface modulations and anisotropic front propagation in ammonia oxidation over Rh(110)

    International Nuclear Information System (INIS)

    The bistable NH3 + O2 reaction over a Rh(110) surface was explored in the pressure range 10−6–10−3 mbar and in the temperature range 300–900 K using photoemission electron microscopy and low energy electron microscopy as spatially resolving methods. We observed a history dependent anisotropy in front propagation, traveling interface modulations, transitions with secondary reaction fronts, and stationary island structures

  17. Traveling interface modulations and anisotropic front propagation in ammonia oxidation over Rh(110)

    Energy Technology Data Exchange (ETDEWEB)

    Rafti, Matías [Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Fac. Cs. Exactas, Universidad Nacional de La Plata, 64 y Diag. 113 (1900), La Plata (Argentina); Institut für Physikalische Chemie und Elektrochemie, Leibniz-Universität Hannover, Callinstr. 3-3a, D-30167 Hannover (Germany); Borkenhagen, Benjamin; Lilienkamp, Gerhard [Institut für Energieforschung und Physikalische Technologien, Technische Universität Clausthal, Leibnizstr. 4, 38678 Clausthal-Zellerfeld (Germany); Lovis, Florian; Smolinsky, Tim; Imbihl, Ronald, E-mail: imbihl@pci.uni-hannvover.de [Institut für Physikalische Chemie und Elektrochemie, Leibniz-Universität Hannover, Callinstr. 3-3a, D-30167 Hannover (Germany)

    2015-11-14

    The bistable NH{sub 3} + O{sub 2} reaction over a Rh(110) surface was explored in the pressure range 10{sup −6}–10{sup −3} mbar and in the temperature range 300–900 K using photoemission electron microscopy and low energy electron microscopy as spatially resolving methods. We observed a history dependent anisotropy in front propagation, traveling interface modulations, transitions with secondary reaction fronts, and stationary island structures.

  18. Quantification of Ammonia-Oxidizing Bacteria and Factors Controlling Nitrification in Salt Marsh Sediments

    OpenAIRE

    Dollhopf, Sherry L.; Hyun, Jung-Ho; Smith, April C.; Adams, Harold J.; O'Brien, Sean; Kostka, Joel E.

    2005-01-01

    To elucidate the geomicrobiological factors controlling nitrification in salt marsh sediments, a comprehensive approach involving sediment geochemistry, process rate measurements, and quantification of the genetic potential for nitrification was applied to three contrasting salt marsh habitats: areas colonized by the tall (TS) or short (SS) form of Spartina alterniflora and unvegetated creek banks (CBs). Nitrification and denitrification potential rates were strongly correlated with one anoth...

  19. Metagenomic analysis of ammonia oxidizing archaea affiliated with the soil group

    Directory of Open Access Journals (Sweden)

    Christa eSchleper

    2012-06-01

    Full Text Available Ammonia-oxidising archaea (AOA have recently been recognized as a significant component of many microbial communities and represent one of the most abundant prokaryotic groups in the biosphere. However, only few AOA have been successfully cultivated so far and information on the physiology and genomic content remains scarce. We have performed a metagenomic analysis to extend the knowledge of the AOA affiliated with groupI.1b that is widespread in terrestrial habitats and of which no genome sequences has been described yet. A fosmid library was generated from samples of a radioactive thermal cave (46°C in the Austrian Central Alps in which AOA had been found as a major part of the microbial community. Out of sixteen fosmids that possessed either an amoA or 16S rRNA gene affiliating with AOA, five were fully sequenced, four of which grouped with the soil/I.1b (Nitrososphaera- lineage and one with marine/I.1a (Nitrosopumilus- lineage. Phylogenetic analyses of amoBC and an associated conserved gene were congruent with earlier analyses based on amoA and 16S rRNA genes and supported the separation of the soil and marine group. Several putative genes that did not have homologues in currently available marine thaumarchaeota genomes indicated that AOA of the soil group contain specific genes that are distinct from their marine relatives. Potential cis-regulatory elements around conserved promoter motifs found upstream of the amo genes in sequenced (meta- genomes differed in marine and soil group AOA. On one fosmid, a group of genes including amoA and amoB were flanked by identical transposable insertion sequences, indicating that amoAB could potentially be co-mobilized in the form of a composite transposon. This might be one of the mechanisms that caused the greater variation in gene order compared to genomes in the marine counterparts. Our findings highlight the genetic diversity within the two major and widespread lineages of thaumarchaeota.

  20. Seasonal and vertical distribution of putative ammonia-oxidizing thaumarchaeotal communities in an oligotrophic lake

    NARCIS (Netherlands)

    Vissers, E.W.; Blaga, C.I.; Bodelier, P.L.E.; Muyzer, G.; Schleper, C.; Sinninghe Damsté, J.S.; Tourna, M.; Laanbroek, H.J.

    2013-01-01

    The discovery of Archaea carrying an amoA gene coding for the A-subunit of ammonia monooxygenase gave a boost to studies aimed at detecting this gene under diverse conditions. Despite numerous studies describing the archaeal amoA gene abundance and richness in different habitats, the understanding o

  1. Global biodiversity of aquatic ammonia-oxidizing archaea is partitioned by habitat

    OpenAIRE

    Biller, Steven J.; Mosier, Annika C.; Wells, George F.; Francis, Christopher A.

    2012-01-01

    Archaea play an important role in nitrification and are, thus, inextricably linked to the global carbon and nitrogen cycles. Since the initial discovery of an ammonia monooxygenase α-subunit (amoA) gene associated with an archaeal metagenomic fragment, archaeal amoA sequences have been detected in a wide variety of nitrifying environments. Recent sequencing efforts have revealed extensive diversity of archaeal amoA sequences within different habitats. In this study, we have examined over 800...

  2. Ammonia-Oxidizing Bacteria along Meadow-to-Forest Transects in the Oregon Cascade Mountains†

    OpenAIRE

    Mintie, A. T.; Heichen, R. S.; Cromack, Jr., K.; Myrold, D. D.; Bottomley, P. J.

    2003-01-01

    Although nitrification has been well studied in coniferous forests of Western North America, communities of NH3-oxidizing bacteria in these forests have not been characterized. Studies were conducted along meadow-to-forest transects at two sites (Lookout and Carpenter) in the H. J. Andrews Experimental Forest, located in the Cascade Mountains of Oregon. Soil samples taken at 10- or 20-m intervals along the transects showed that several soil properties, including net nitrogen mineralization an...

  3. QPCR quantification of ammonia oxidizing bacteria: What should the target be?

    DEFF Research Database (Denmark)

    Musovic, Sanin; Palomo, Alejandro; Diwan, Vaibhav;

    for drinking water production. Being able to quantify precisely the abundance of this functional group is thus important to be able monitor these processes. AOB are moderately diverse Beta-Proteobacteria that all carry the amoA gene coding for the ammonia monooxigenase. Therefore, molecular...... quantification can be carried out by targeting either the 16S rRNA gene or amoA, for which standard primer sets are widely used. Using these two approaches to quantify AOB abundance across three Danish rapid sand filters (RSFs) revealed a significant discrepancy: in two RSFs, the amoA-based qPCR consistently...... amoA primer set has a narrower coverage than the 16S rRNA one and thus led to an underestimation of AOB in RSFs hosting broad AOB diversity. This highlights the importance of the choice of primer set to quantify functional groups in environmental samples....

  4. Traveling interface modulations and anisotropic front propagation in ammonia oxidation over Rh(110)

    Science.gov (United States)

    Rafti, Matías; Borkenhagen, Benjamin; Lilienkamp, Gerhard; Lovis, Florian; Smolinsky, Tim; Imbihl, Ronald

    2015-11-01

    The bistable NH3 + O2 reaction over a Rh(110) surface was explored in the pressure range 10-6-10-3 mbar and in the temperature range 300-900 K using photoemission electron microscopy and low energy electron microscopy as spatially resolving methods. We observed a history dependent anisotropy in front propagation, traveling interface modulations, transitions with secondary reaction fronts, and stationary island structures.

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

    Science.gov (United States)

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

    2016-02-01

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

  6. Evaluation of Biosynthetic Pathways of 2Н- and 13С-Labeled Amino Acids by an Obligate Methylotrophic Bacterium Methylobacillus Flagellatum and a Facultative Methylotrophic Bacterium Brevibacterium Methylicum

    Directory of Open Access Journals (Sweden)

    Oleg Mosin

    2016-06-01

    Full Text Available By the method of electron impact mass-spectrometry was studied the pathways of biosynthesis of 2H, 13C-labeled amino acids of a facultative methylotrophic bacterium Brevibacterium methylicum and an obligate methylotrophic bacterium Methylobacillus flagellatum obtained on growth media containing as a source of stable isotopes [2H]methanol, [13C]methanol and 2H2O. For mass-spectrometric analysis the multicomponential mixtures of 2H- and 13C-labeled amino acids, derived from cultural media and protein hydrolysates after hydrolysis in 6 M 2HСl (3 % phenol and 2 M Ва(OH2 were modified into N-benzyloxycarbonyl-derivatives of amino acids as well as into methyl esters of N-5-(dimethylaminonaphthalene-1-sulfonyl chloride (dansyl derivatives of [2H, 13С]amino acids, which were preparative separated using a method of reverse-phase HCLP. Biosynthetically obtained 2H- and 13C-labeled amino acids represented the mixtures differing in quantities of isotopes incorporated into molecule. The levels of 2H and 13С enrichment of secreted amino acids and amino acid resigues of protein were found to vary from 20,0 atom % to L-leucine/isoleucine up to 97,5 atom % for L-alanine depending on concentration of 2H- and 13C-labelled substrates.

  7. Influence of pH and Oxidant Ozone to Amount of Bacterium Coliform at Hospital Waste

    International Nuclear Information System (INIS)

    Influence of pH and oxidant ozone to amount of bacterium coliform at hospital waste have been done. As sample is liquid waste Public Hospital of town (RSUD) Yogyakarta. Sample waste processed by 3 kinds of treatment, that is first certain ozone waste during, that is waste given by the third and just chalk of waste given by the certain and ozonization chalk during. From third the treatment, in the reality third treatment which can give the maximal result, that is waste given the chalk until pH waste 8.5 and ozonization during 40 minute give the following result : bacterium coliform from 810.000 MPN become 0 MPN ( cell / 100 mL). This result have fulfilled the conditions as according to decision of Governor of DIY no. 65 year 1999 for the waste of faction II, that is waste used for the irrigation of fishery and agriculture. (author)

  8. Crystal structure of ribosomal protein L1 from the bacterium Aquifex aeolicus

    Science.gov (United States)

    Nikonova, E. Yu.; Tishchenko, S. V.; Gabdulkhakov, A. G.; Shklyaeva, A. A.; Garber, M. B.; Nikonov, S. V.; Nevskaya, N. A.

    2011-07-01

    The crystal structure of ribosomal protein L1 from the bacterium Aquifex aeolicus was solved by the molecular-replacement method and refined to R cryst = 19.4% and R free = 25.1% at 2.1 Å protein consists of two domains linked together by a flexible hinge region. In the structure under consideration, the domains are in close proximity and adopt a closed conformation. Earlier, this conformation has been found in the structure of protein L1 from the bacterium Thermus thermophilus, whereas the structures of archaeal L1 proteins and the structures of all L1 proteins in the RNA-bound form have an open conformation. The fact that a closed conformation was found in the structures of two L1 proteins which crystallize in different space groups and belong to different bacteria suggests that this conformation is a characteristic feature of L1 bacterial proteins in the free form.

  9. Isolation and characterization of a new arsenic methylating bacterium from soil

    Energy Technology Data Exchange (ETDEWEB)

    Honschopp, S. [Bremen Univ. (Germany). Abt. Mikrobiologie; Brunken, N. [Bremen Univ. (Germany). Inst. fuer Anorganische und Physikalische Chemie; Nehrkorn, A. [Bremen Univ. (Germany). Abt. Mikrobiologie; Breunig, H.J. [Bremen Univ. (Germany). Inst. fuer Anorganische und Physikalische Chemie

    1996-12-31

    An arsenic resistant and arsenic methylating bacterium belonging to the Flavobacterium-Cytophaga group was isolated from soil with an arsenic content of 1.5 ppm. The growth of the bacterium is enhanced in the presence of As compounds in concentrations up to 200 ppm in the cultural media with a stronger effect of As(V) than of As(III) compounds. As a volatile product of the methylation of both NaH{sub 2}AsO{sub 3} and NaH{sub 2}AsO{sub 4} exclusively, Me{sub 3}As was formed and detected by mass spectrometry. Quantitative aspects of the methylation were studied with GC/MS. The intracellular accumulation of arsenic in the methylating strain was compared with two non methylating strains from the same soil. (orig.)

  10. Effect of Sulfate Reduced Bacterium on Corrosion Behavior of 10CrMoAl Steel

    Institute of Scientific and Technical Information of China (English)

    WANG Hua; LIANG Cheng-hao

    2007-01-01

    The effects of sulfate reduced bacterium (SRB) on the corrosion behavior of 10CrMoAl steel in seawater were studied by chemical immersion, potentiodynamic polarization, electrochemical impedance spectroscopy measurement, and scanning electron microscope techniques. The results show that the content of element sulfur in the corrosion product of 10CrMoAl steel in seawater with SRB is up to 9.23%, which is higher than that of the same in sterile seawater. X-ray diffraction demonstrates that the main corrosion product is FeS. SRB increases the corrosion rate by anodic depolarization of the metabolized sulfide product. SEM observation indicates that the corrosion product is not distributed continuously; in addition, bacilliform sulfate-reduced bacterium accumulates on the local surface of 10CrMoAl steel. Hence, SRB enhances sensitivity to the localized corrosion of 10CrMoAl steel in seawater.

  11. Isolation and biological characteristics of aerobic marine magnetotactic bacterium YSC-1

    Institute of Scientific and Technical Information of China (English)

    GAO Jun; PAN Hongmiao; YUE Haidong; SONG Tao; ZHAO Yong; CHEN Guanjun; Wu Longfei; XIAO Tian

    2006-01-01

    Magnetotactic bacteria have become a hot spot of research in microbiology attracting intensive interest of researchers in multiple disciplinary fields. However, the studies were limited in few fastidious bacteria. The objective of this study aims at isolating new marine magnetic bacteria and better comprehension of magnetotactic bacteria. In this study, an aerobic magnetotactic bacterium YSC-1 was isolated from sediments in the Yellow Sea Cold Water Mass (YSCWM). In TEM, magnetic cells have one or several circular magnetosomes in dimeter of 100nm, and consist of Fe and Co shown on energy dispersive X-ray spectrum. The biological and physiological characteristics of this bacterium were also described. The colour of YSC-1 colony is white in small rod. The gran stain is negative. Results showed that Strain YSC-1 differs from microaerophile magnetotactic bacteria MS-1 and WD-1 in biology.

  12. Microbiologically influenced corrosion of NiZn alloy coatings by Delftia acidovorans bacterium

    International Nuclear Information System (INIS)

    Highlights: ► Delftia acidovorans isolated from water treatment pipe system. ► Bacterium attached to the alloy coatings. ► Ecorr exhibited cathodic shift. ► Mass loss reached highest value after inoculation. ► Crevice corrosion was observed on the surface due to bacterium. - Abstract: In this study, Delftia acidovorans was isolated from water treatment pipe system and used to demonstrate microbiologically influenced corrosion of NiZn alloy coatings using electrochemical techniques. The surface morphologies and the corrosion products were determined using scanning electron microscopy (SEM) and energy dispersive X-ray spectra (EDS) analysis. Results showed that when the metabolic activity reached maximum level, corrosion activity of NiZn alloy coatings significantly increased in correlation with Ecorr, Icorr, QCM and Rct. Furthermore, crevice corrosion which has been seen due to bacterial adhesion confirms that D. acidovorans plays an important role in corrosion of NiZn alloy coating.

  13. N-Acyl Dehydrotyrosines, Tyrosinase Inhibitors from the Marine Bacterium Thalassotalea sp. PP2-459.

    Science.gov (United States)

    Deering, Robert W; Chen, Jianwei; Sun, Jiadong; Ma, Hang; Dubert, Javier; Barja, Juan L; Seeram, Navindra P; Wang, Hong; Rowley, David C

    2016-02-26

    Thalassotalic acids A-C and thalassotalamides A and B are new N-acyl dehydrotyrosine derivatives produced by Thalassotalea sp. PP2-459, a Gram-negative bacterium isolated from a marine bivalve aquaculture facility. The structures were elucidated via a combination of spectroscopic analyses emphasizing two-dimensional NMR and high-resolution mass spectrometric data. Thalassotalic acid A (1) displays in vitro inhibition of the enzyme tyrosinase with an IC50 value (130 μM) that compares favorably to the commercially used control compounds kojic acid (46 μM) and arbutin (100 μM). These are the first natural products reported from a bacterium belonging to the genus Thalassotalea. PMID:26824128

  14. Economic Game Theory to Model the Attenuation of Virulence of an Obligate Intracellular Bacterium.

    Science.gov (United States)

    Tago, Damian; Meyer, Damien F

    2016-01-01

    Diseases induced by obligate intracellular pathogens have a large burden on global human and animal health. Understanding the factors involved in the virulence and fitness of these pathogens contributes to the development of control strategies against these diseases. Based on biological observations, a theoretical model using game theory is proposed to explain how obligate intracellular bacteria interact with their host. The equilibrium in such a game shows that the virulence and fitness of the bacterium is host-triggered and by changing the host's defense system to which the bacterium is confronted, an evolutionary process leads to an attenuated strain. Although, the attenuation procedure has already been conducted in practice in order to develop an attenuated vaccine (e.g., with Ehrlichia ruminantium), there was a lack of understanding of the theoretical basis behind this process. Our work provides a model to better comprehend the existence of different phenotypes and some underlying evolutionary mechanisms for the virulence of obligate intracellular bacteria. PMID:27610355

  15. The bacterium Xenorhabdus nematophila inhibits phospholipases A2 from insect, prokaryote, and vertebrate sources

    Science.gov (United States)

    Park, Youngjin; Kim, Yonggyun; Stanley, David

    The bacterium, Xenorhabdus nematophila, is a virulent insect pathogen. Part of its pathogenicity is due to impairing cellular immunity by blocking biosynthesis of eicosanoids, the major recognized signal transduction system in insect cellular immunity. X. nematophila inhibits the first step in eicosanoid biosynthesis, phospholipase A2 (PLA2). Here we report that the bacterium inhibits PLA2 from two insect immune tissues, hemocytes and fat body, as well as PLA2s selected to represent a wide range of organisms, including prokaryotes, insects, reptiles, and mammals. Our finding on a bacterial inhibitor of PLA2 activity contributes new insight into the chemical ecology of microbe-host interactions, which usually involve actions rather than inhibitors of PLA2s.

  16. A Streamlined Strategy for Biohydrogen Production with Halanaerobium hydrogeniformans, an Alkaliphilic Bacterium

    Directory of Open Access Journals (Sweden)

    Matthew eBegemann

    2012-03-01

    Full Text Available Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, lignocellulosic biohydrogen production remains inefficient with pretreatments that are heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium hydrogeniformans, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. hydrogeniformans ferments a variety of 5- and 6- carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen, acetate and formate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources.

  17. Chlorhexidine resistance in a Gram-negative bacterium isolated from an aquatic source

    OpenAIRE

    Sekavec, Jeffrey G.; Moore, William T.; Gillock, Eric T.

    2013-01-01

    Aeromonas hydrophila is a Gram-negative bacterium of considerable importance in both clinical, especially nosocomial infections, and zoonotic respects, both aquatic and terrestrial infections. In addition to the ability to thrive in a wide range of conditions, A. hydrophila is resistant to numerous antibiotics and antimicrobials. In conjunction with Kansas State University and the Kansas Water Office, water samples from various locations within Kansas were screened for organisms resistant to ...

  18. Sensitivity of ribosomes of the hyperthermophilic bacterium Aquifex pyrophilus to aminoglycoside antibiotics.

    OpenAIRE

    Bocchetta, M; Huber, R.; Cammarano, P

    1996-01-01

    A poly(U)-programmed cell-free system from the hyperthermophilic bacterium Aquifex pyrophilus has been developed, and the susceptibility of Aquifex ribosomes to the miscoding-inducing and inhibitory actions of all known classes of aminoglycoside antibiotics has been assayed at temperatures (75 to 80 degrees C) close to the physiological optimum for cell growth. Unlike Thermotoga maritima ribosomes, which are systematically refractory to all known classes of aminoglycoside compounds (P. Londei...

  19. Calcium-ion mediated assembly and function of glycosylated flagellar sheath of marine magnetotactic bacterium

    OpenAIRE

    Lefèvre, Christopher T; Santini, Claire-Lise; Bernadac, Alain; Zhang, Wei-Jia; Ying LI; Wu, Long-Fei

    2010-01-01

    Abstract Flagella of some pathogens or marine microbes are sheathed by an apparent extension of the outer cell membrane. Although flagellar sheath has been reported for almost 60 years, little is known about its function and the mechanism of its assembly. Recently, we have observed a novel type of sheath that encloses a flagellar bundle, instead of a single flagellum, in a marine magnetotactic bacterium MO-1. Here, we reported isolation and characterization of the sheath which can ...

  20. Campylobacter pylori, the spiral bacterium associated with human gastritis, is not a true Campylobacter sp.

    OpenAIRE

    Romaniuk, P J; Zoltowska, B; Trust, T J; Lane, D J; Olsen, G.J.; Pace, N R; Stahl, D A

    1987-01-01

    Comparison of partial 16S rRNA sequences from representative Campylobacter species indicates that the Campylobacter species form a previously undescribed basic eubacterial group, which is related to the other major groups only by very deep branching. This analysis was extended to include the spiral bacterium associated with human gastritis, Campylobacter pylori (formerly Campylobacter pyloridis). The distance between C. pylori and the other Campylobacter species is sufficient to exclude the p...

  1. The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

    OpenAIRE

    Duan, Jin; Jiang, Wei; Cheng, Zhenyu; Heikkila, John J.; Bernard R. Glick

    2013-01-01

    The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 gen...

  2. Physiological Adaptation of the Bacterium Lactococcus lactis in Response to the Production of Human CFTR*

    OpenAIRE

    A. Steen; Wiederhold, E.; T Gandhi; Breitling, R.; D. J. Slotboom

    2010-01-01

    Biochemical and biophysical characterization of CFTR (the cystic fibrosis transmembrane conductance regulator) is thwarted by difficulties to obtain sufficient quantities of correctly folded and functional protein. Here we have produced human CFTR in the prokaryotic expression host Lactococcus lactis. The full-length protein was detected in the membrane of the bacterium, but the yields were too low (< 0.1% of membrane proteins) for in vitro functional and structural characterization, and indu...

  3. Bioinformatic Prediction of Gene Functions Regulated by Quorum Sensing in the Bioleaching Bacterium Acidithiobacillus ferrooxidans

    OpenAIRE

    Alvaro Banderas; Nicolas Guiliani

    2013-01-01

    The biomining bacterium Acidithiobacillus ferrooxidans oxidizes sulfide ores and promotes metal solubilization. The efficiency of this process depends on the attachment of cells to surfaces, a process regulated by quorum sensing (QS) cell-to-cell signalling in many Gram-negative bacteria. At. ferrooxidans has a functional QS system and the presence of AHLs enhances its attachment to pyrite. However, direct targets of the QS transcription factor AfeR remain unknown. In this study, a bioinforma...

  4. Functional Genomic Analysis of Three Nitrogenase Isozymes in the Photosynthetic Bacterium Rhodopseudomonas palustris‡

    OpenAIRE

    Oda, Yasuhiro; Samanta, Sudip K.; Rey, Federico E.; Wu, Liyou; Liu, Xiudan; Yan, Tingfen; Zhou, Jizhong; Harwood, Caroline S.

    2005-01-01

    The photosynthetic bacterium Rhodopseudomonas palustris is one of just a few prokaryotes described so far that has vnf and anf genes for alternative vanadium cofactor (V) and iron cofactor (Fe) nitrogenases in addition to nif genes for a molybdenum cofactor (Mo) nitrogenase. Transcriptome data indicated that the 32 genes in the nif gene cluster, but not the anf or vnf genes, were induced in wild-type and Mo nitrogenase-expressing strains grown under nitrogen-fixing conditions in Mo-containing...

  5. Identifying the assembly pathway of cyanophage inside the marine bacterium using electron cryo-tomography

    Directory of Open Access Journals (Sweden)

    Wei Dai

    2014-01-01

    Full Text Available Advances in electron cryo-tomography open up a new avenue to visualize the 3-D internal structure of a single bacterium before and after its infection by bacteriophages in its native environment, without using chemical fixatives, fluorescent dyes or negative stains. Such direct observation reveals the presence of assembly intermediates of the bacteriophage and thus allows us to map out the maturation pathway of the bacteriophage inside its host.

  6. Two New Cholic Acid Derivatives from the Marine Ascidian-Associated Bacterium Hasllibacter halocynthiae

    Directory of Open Access Journals (Sweden)

    Sung Hun Kim

    2012-10-01

    Full Text Available The investigation of secondary metabolites in liquid cultures of a recently discovered marine bacterium, Hasllibacter halocynthiae strain KME 002T, led to the isolation of two new cholic acid derivatives. The structures of these compounds were determined to be 3,3,12-trihydroxy-7-ketocholanic acid (1 and 3,3,12-trihydroxy-7-deoxycholanic acid (2 through HRFABMS and NMR data analyses.

  7. Draft Genome Sequence of Uncultured SAR324 Bacterium lautmerah10, Binned from a Red Sea Metagenome

    KAUST Repository

    Haroon, Mohamed F.

    2016-02-11

    A draft genome of SAR324 bacterium lautmerah10 was assembled from a metagenome of a surface water sample from the Red Sea, Saudi Arabia. The genome is more complete and has a higher G+C content than that of previously sequenced SAR324 representatives. Its genomic information shows a versatile metabolism that confers an advantage to SAR324, which is reflected in its distribution throughout different depths of the marine water column.

  8. Draft Genome Sequence of the Antitrypanosomally Active Sponge-Associated Bacterium Actinokineospora sp. Strain EG49

    KAUST Repository

    Harjes, Janno

    2014-03-06

    The marine sponge-associated bacterium Actinokineospora sp. strain EG49 produces the antitrypanosomal angucycline-like compound actinosporin A. The draft genome of Actinokineospora sp. EG49 has a size of 7.5 megabases and a GC content of 72.8% and contains 6,629 protein-coding sequences (CDS). antiSMASH predicted 996 genes residing in 36 secondary metabolite gene clusters.

  9. Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

    OpenAIRE

    Saw, Jimmy H; Mountain, Bruce W; Feng, Lu; Omelchenko, Marina V; Hou, Shaobin; Saito, Jennifer A.; Stott, Matthew B.; Li, Dan; Zhao, Guang; Wu, Junli; Galperin, Michael Y.; Koonin, Eugene V.; Makarova, Kira S.; Wolf, Yuri I; Rigden, Daniel J.

    2008-01-01

    Background Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, whic...

  10. The Genome Sequence of the Obligately Chemolithoautotrophic, Facultatively Anaerobic Bacterium Thiobacillus denitrificans

    OpenAIRE

    Beller, Harry R.; Chain, Patrick S. G.; Letain, Tracy E.; Chakicherla, Anu; Larimer, Frank W.; Richardson, Paul M.; Coleman, Matthew A.; Wood, Ann P.; Kelly, Donovan P.

    2006-01-01

    The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, β-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to...

  11. Photobacterium damselae subsp. damselae, a bacterium pathogenic for marine animals and humans

    OpenAIRE

    Amable J. Rivas; Lemos, Manuel L.; Osorio, Carlos R.

    2013-01-01

    Photobacterium damselae subsp. damselae (formerly Vibrio damsela) is a pathogen of a variety of marine animals including fish, crustaceans, molluscs, and cetaceans. In humans, it can cause opportunistic infections that may evolve into necrotizing fasciitis with fatal outcome. Although the genetic basis of virulence in this bacterium is not completely elucidated, recent findings demonstrate that the phospholipase-D Dly (damselysin) and the pore-forming toxins HlyApl and HlyAch play a main role...

  12. A Highly Stable d-Amino Acid Oxidase of the Thermophilic Bacterium Rubrobacter xylanophilus

    OpenAIRE

    Takahashi, Shouji; Furukawara, Makoto; Omae, Keishi; Tadokoro, Namiho; Saito, Yayoi; Abe, Katsumasa; Kera, Yoshio

    2014-01-01

    d-Amino acid oxidase (DAO) is a biotechnologically attractive enzyme that can be used in a variety of applications, but its utility is limited by its relatively poor stability. A search of a bacterial genome database revealed a gene encoding a protein homologous to DAO in the thermophilic bacterium Rubrobacter xylanophilus (RxDAO). The recombinant protein expressed in Escherichia coli was a monomeric protein containing noncovalently bound flavin adenine dinucleotide as a cofactor. This protei...

  13. Sexual transmission of a plant pathogenic bacterium, Candidatus Liberibacter asiaticus, between conspecific insect vectors during mating.

    Directory of Open Access Journals (Sweden)

    Rajinder S Mann

    Full Text Available Candidatus Liberibacter asiaticus is a fastidious, phloem-inhabiting, gram-negative bacterium transmitted by Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae. The bacterium is the presumed causal agent of huanglongbing (HLB, one of the most destructive and economically important diseases of citrus. We investigated whether Las is transmitted between infected and uninfected D. citri adults during courtship. Our results indicate that Las was sexually transmitted from Las-infected male D. citri to uninfected females at a low rate (<4% during mating. Sexual transmission was not observed following mating of infected females and uninfected males or among adult pairs of the same sex. Las was detected in genitalia of both sexes and also in eggs of infected females. A latent period of 7 days or more was required to detect the bacterium in recipient females. Rod shaped as well as spherical structures resembling Las were observed in ovaries of Las-infected females with transmission electron microscopy, but were absent in ovaries from uninfected D. citri females. The size of the rod shaped structures varied from 0.39 to 0.67 µm in length and 0.19 to 0.39 µm in width. The spherical structures measured from 0.61 to 0.80 µm in diameter. This investigation provides convincing evidence that a plant pathogenic bacterium is sexually transmitted from male to female insects during courtship and established evidence that bacteria persist in reproductive organs. Moreover, these findings provide an alternative sexually horizontal mechanism for the spread of Las within populations of D. citri, even in the absence of infected host trees.

  14. Expression of Heterogenous Arsenic Resistance Genes in the Obligately Autotrophic Biomining Bacterium Thiobacillus ferrooxidans.

    Science.gov (United States)

    Peng, J B; Yan, W M; Bao, X Z

    1994-07-01

    Two arsenic-resistant plasmids were constructed and introduced into Thiobacillus ferrooxidans strains by conjugation. The plasmids with the replicon of wide-host-range plasmid RSF1010 were stable in T. ferrooxidans. The arsenic resistance genes originating from the heterotroph were expressed in this obligately autotrophic bacterium, but the promoter derived from T. ferrooxidans showed no special function in its original host. PMID:16349341

  15. Physiological features of Halomonas lionensis sp. nov., a novel bacterium isolated from a Mediterranean Sea sediment

    OpenAIRE

    Gaboyer, Frederic; Vandenabeele-Trambouze, Odile; Cao, Junwei; Ciobanu, Maria-Cristina; Jebbar, Mohamed; Le Romancer, Marc; Alain, Karine

    2014-01-01

    A novel halophilic bacterium, strain RHS90T, was isolated from marine sediments from the Gulf of Lions, in the Mediterranean Sea. Its metabolic and physiological characteristics were examined under various cultural conditions, including exposure to stressful ones (oligotrophy, high pressure and high concentrations of metals). Based on phylogenetic analysis of the 16S rRNA gene, the strain was found to belong to the genus Halomonas in the class Gammaproteobacteria. Its closest relatives are H....

  16. The Potential Biotechnological Applications of the Exopolysaccharide Produced by the Halophilic Bacterium Halomonas almeriensis

    OpenAIRE

    Victoria Béjar; Emilia Quesada; Juan Antonio Mata; Inmaculada Llamas; Hakima Amjres

    2012-01-01

    We have studied the extracellular polysaccharide (EPS) produced by the type strain, M8T, of the halophilic bacterium Halomonas almeriensis, to ascertain whether it might have any biotechnological applications. All the cultural parameters tested influenced both bacterial growth and polysaccharide production. EPS production was mainly growth-associated and under optimum environmental and nutritional conditions M8T excreted about...

  17. Biohydrogen Production by the Thermophilic Bacterium Caldicellulosiruptor saccharolyticus: Current Status and Perspectives

    OpenAIRE

    Kengen, Servé W. M.; Verhaart, Marcel R. A.; John van der Oost; Abraham A. M. Bielen

    2013-01-01

    Caldicellulosiruptor saccharolyticus is one of the most thermophilic cellulolytic organisms known to date. This Gram-positive anaerobic bacterium ferments a broad spectrum of mono-, di- and polysaccharides to mainly acetate, CO2 and hydrogen. With hydrogen yields approaching the theoretical limit for dark fermentation of 4 mol hydrogen per mol hexose, this organism has proven itself to be an excellent candidate for biological hydrogen production. This review provides an overview of the resear...

  18. Copper-induced production of copper-binding supernatant proteins by the marine bacterium Vibrio alginolyticus.

    OpenAIRE

    Harwood-Sears, V; Gordon, A S

    1990-01-01

    Growth of the marine bacterium Vibrio alginolyticus is temporarily inhibited by micromolar levels of copper. During the copper-induced lag phase, supernatant compounds which complex and detoxify copper are produced. In this study two copper-inducible supernatant proteins having molecular masses of ca. 21 and 19 kilodaltons (CuBP1 and CuBP2) were identified; these proteins were, respectively, 25 and 46 times amplified in supernatants of copper-challenged cultures compared with controls. Experi...

  19. Dynamic detection of a single bacterium: nonlinear rotation rate shifts of driven magnetic microsphere stages

    OpenAIRE

    McNaughton, Brandon H.; Agayan, Rodney R.; Kopelman, Raoul

    2006-01-01

    We report on a new technique which was used to detect single Escherichia coli that is based on the changes in the nonlinear rotation of a magnetic microsphere driven by an external magnetic field. The presence of one Escherichia Coli bacterium on the surface of a 2.0 micron magnetic microsphere caused an easily measurable change in the drag of the system and, therefore, in the nonlinear rotation rate. The straight-forward measurement uses standard microscopy techniques and the observed averag...

  20. Five new amicoumacins isolated from a marine-derived Bacterium bacillus subtilis

    KAUST Repository

    Li, Yongxin

    2012-02-03

    Four novel amicoumacins, namely lipoamicoumacins A-D (1-4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. 2012 by the authors; licensee MDPI.