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  • 1
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    Complete nitrification by a single microorganism (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-11-27
    Description: Nitrification is a two-step process where ammonia is first oxidized to nitrite by ammonia-oxidizing bacteria and/or archaea, and subsequently to nitrate by nitrite-oxidizing bacteria. Already described by Winogradsky in 1890, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible, and it was postulated that this process could occur under conditions selecting for species with lower growth rates but higher growth yields than canonical ammonia-oxidizing microorganisms. Still, organisms catalysing this process have not yet been discovered. Here we report the enrichment and initial characterization of two Nitrospira species that encode all the enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding of the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van Kessel, Maartje A H J -- Speth, Daan R -- Albertsen, Mads -- Nielsen, Per H -- Op den Camp, Huub J M -- Kartal, Boran -- Jetten, Mike S M -- Lucker, Sebastian -- England -- Nature. 2015 Dec 24;528(7583):555-9. doi: 10.1038/nature16459. Epub 2015 Nov 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, IWWR, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands. ; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark. ; Laboratory for Microbiology, University of Gent, K. L. Ledeganckstraat 35, 9000 Gent, Belgium. ; Department of Biotechnology, TU Delft, Julianalaan 67, 2628 BC Delft, the Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26610025" target="_blank"〉PubMed〈/a〉
    Keywords: Ammonia/*metabolism ; Bacteria/enzymology/genetics/*metabolism ; Evolution, Molecular ; Genome, Bacterial/genetics ; Nitrates/*metabolism ; *Nitrification/genetics ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Complete nitrification by Nitrospira bacteria (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-11-27
    Description: Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira-contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Daims, Holger -- Lebedeva, Elena V -- Pjevac, Petra -- Han, Ping -- Herbold, Craig -- Albertsen, Mads -- Jehmlich, Nico -- Palatinszky, Marton -- Vierheilig, Julia -- Bulaev, Alexandr -- Kirkegaard, Rasmus H -- von Bergen, Martin -- Rattei, Thomas -- Bendinger, Bernd -- Nielsen, Per H -- Wagner, Michael -- England -- Nature. 2015 Dec 24;528(7583):504-9. doi: 10.1038/nature16461. Epub 2015 Nov 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. ; Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, 119071 Moscow, Russia. ; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark. ; Helmholtz-Centre for Environmental Research - UFZ, Department of Proteomics, Permoserstrasse 15, 04318 Leipzig, Germany. ; Helmholtz-Centre for Environmental Research - UFZ, Department of Metabolomics, Permoserstrasse 15, 04318 Leipzig, Germany. ; Department of Microbiology and Ecosystem Science, Division of Computational Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria. ; DVGW-Forschungsstelle TUHH, Hamburg University of Technology, 21073 Hamburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26610024" target="_blank"〉PubMed〈/a〉
    Keywords: Ammonia/*metabolism ; Bacteria/enzymology/genetics/growth & development/*metabolism ; Evolution, Molecular ; Genome, Bacterial/genetics ; Molecular Sequence Data ; Nitrates/*metabolism ; *Nitrification/genetics ; Nitrites/*metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Growth of nitrite-oxidizing bacteria by aerobic hydrogen oxidation (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-08-30
    Description: The bacterial oxidation of nitrite to nitrate is a key process of the biogeochemical nitrogen cycle. Nitrite-oxidizing bacteria are considered a highly specialized functional group, which depends on the supply of nitrite from other microorganisms and whose distribution strictly correlates with nitrification in the environment and in wastewater treatment plants. On the basis of genomics, physiological experiments, and single-cell analyses, we show that Nitrospira moscoviensis, which represents a widely distributed lineage of nitrite-oxidizing bacteria, has the genetic inventory to utilize hydrogen (H2) as an alternative energy source for aerobic respiration and grows on H2 without nitrite. CO2 fixation occurred with H2 as the sole electron donor. Our results demonstrate a chemolithoautotrophic lifestyle of nitrite-oxidizing bacteria outside the nitrogen cycle, suggesting greater ecological flexibility than previously assumed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koch, Hanna -- Galushko, Alexander -- Albertsen, Mads -- Schintlmeister, Arno -- Gruber-Dorninger, Christiane -- Lucker, Sebastian -- Pelletier, Eric -- Le Paslier, Denis -- Spieck, Eva -- Richter, Andreas -- Nielsen, Per H -- Wagner, Michael -- Daims, Holger -- New York, N.Y. -- Science. 2014 Aug 29;345(6200):1052-4. doi: 10.1126/science.1256985.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria. ; Center for Microbial Communities, Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, 9000 Aalborg, Denmark. ; Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria. Large Instrument Facility for Advanced Isotope Research, University of Vienna, 1090 Vienna, Austria. ; Commissariat a l'Energie Atomique, Direction des Sciences du Vivant, Institut de genomique, Genoscope, 91057 Evry, France. Centre National de la Recherche Scientifique, UMR8030, 91057 Evry, France. Universite d'Evry Val d'Essonne, 91057 Evry, France. ; Biozentrum Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, 22609 Hamburg, Germany. ; Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1090 Vienna, Austria. ; Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, 1090 Vienna, Austria. daims@microbial-ecology.net.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25170152" target="_blank"〉PubMed〈/a〉
    Keywords: Aerobiosis ; Bacteria, Aerobic/genetics/*growth & development/*metabolism ; Chemoautotrophic Growth/genetics/*physiology ; Energy Metabolism ; Genetic Loci ; Hydrogen/*metabolism ; Hydrogenase/genetics ; Molecular Sequence Data ; Nitrates/metabolism ; Nitrification/genetics/physiology ; Nitrites/*metabolism ; *Nitrogen Cycle ; Oxidation-Reduction ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    A hidden Markov movement model for rapidly identifying behavioral states from animal tracks (2017)
    Wiley
    Details
    Publication Date: 2017-03-02
    Description: Electronic telemetry is frequently used to document animal movement through time. Methods that can identify underlying behaviors driving specific movement patterns can help us understand how and why animals use available space, thereby aiding conservation and management efforts. For aquatic animal tracking data with significant measurement error, a Bayesian state-space model called the first-Difference Correlated Random Walk with Switching (DCRWS) has often been used for this purpose. However, for aquatic animals, highly accurate tracking data are now becoming more common. We developed a new hidden Markov model (HMM) for identifying behavioral states from animal tracks with negligible error, called the hidden Markov movement model (HMMM). We implemented as the basis for the HMMM the process equation of the DCRWS, but we used the method of maximum likelihood and the R package TMB for rapid model fitting. The HMMM was compared to a modified version of the DCRWS for highly accurate tracks, the DCRWS , and to a common HMM for animal tracks fitted with the R package moveHMM . We show that the HMMM is both accurate and suitable for multiple species by fitting it to real tracks from a grey seal, lake trout, and blue shark, as well as to simulated data. The HMMM is a fast and reliable tool for making meaningful inference from animal movement data that is ideally suited for ecologists who want to use the popular DCRWS implementation and have highly accurate tracking data. It additionally provides a groundwork for development of more complex modeling of animal movement with TMB . To facilitate its uptake, we make it available through the R package swim . We used the R package TMB to develop a new hidden Markov model (HMM) for identifying behavioral states from animal tracks with negligible error, which we call the hidden Markov movement model (HMMM). We show that the HMMM can make meaningful inference from animal movement data collected on multiple species. It additionally provides a groundwork for development of more complex movement modelling with TMB. To facilitate its uptake, we make the HMMM available through the R package swim.
    Electronic ISSN: 2045-7758
    Topics: Biology
    Published by Wiley
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  • 5
    Electronic Resource
    Electronic Resource
    Study of two different recombination events in maize cmsT-regenerated plants during reversion to fertility (1990)
    Springer
    Theoretical and applied genetics 79 (1990), S. 593-599 
    Details
    ISSN: 1432-2242
    Keywords: Maize ; mtDNA ; Male sterility ; Recombination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The change of phenotype from sterility to fertility for some cmsT callus tissue culture regenerated plants and their progenies has been correlated with changes in their mitochondrial genome. Those changes that have been analyzed here are the result of recombination events. Two different sets of repeated sequences have been found to be involved in those recombination events. The most common one is a recombination through a 127-bp repeat between various independently isolated revertants. The second one is a recombination through a 58-bp repeat. In every case the products of recombination containing the urf13 gene have been deleted.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00226870
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  • 6
    Electronic Resource
    Electronic Resource
    Quantitative trait loci for plant height in four maize populations and their associations with qualitative genetic loci (1991)
    Springer
    Theoretical and applied genetics 83 (1991), S. 141-145 
    Details
    ISSN: 1432-2242
    Keywords: Zea mays L. ; Molecular markers ; Restriction fragment length polymorphisms (RFLPs) ; Quantitative trait loci (QTLs)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We report that plant height quantitative trait loci (QTLs) identified in a given small population are not consistent with QTLs identified in other small populations, and that most QTLs are in close proximity to mapped qualitative genetic loci. These observations provide evidence to support the hypothesis that qualitative genetic loci are the same loci that affect quantitative traits, and affirm that these modest experiments probably identify real QTLs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00226242
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  • 7
    Electronic Resource
    Electronic Resource
    Pollen and coenocytic microspore germination in male-fertile and malesterilemsl soybean (1987)
    Springer
    Euphytica 36 (1987), S. 333-343 
    Details
    ISSN: 1573-5060
    Keywords: Glycine max ; soybean ; male-sterile ; pollen germination ; fluorescence microscopy ; apomixis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary Light and fluorescence microscopy were used to study coenocytic microspore germination from male-sterile (ms1 ms1) soybean plants. Anther squashes from male-sterile plants revealed that a low frequency of natural coenocytic microspore germination occurred in male-sterile anthers of four independent lines; [ms1-North carolina (T260H),ms1-Urbana (T266H),ms1-Tonica (T267H), andms1-Ames (T268H)]. Abnormalities such as giant tubes, branched tubes, tubes with swollen areas, and multiple tubes were observed from coenocytic microspores from all four lines. The Urbana line, however, demonstrated a higher percentage of coenocytic microspore germination than did the other three lines. Flowers of the Urbana line from both malefertile and male-sterile plants, as well as gynoecia pollinated with coenocytic microspores from sterile plants, were used for in vivo studies. Pollen-tube growth appeared normal in male-fertile plants. In contrast, coenocytic microspore tubes rarely were observed in gynoecia from male-sterile plants or in gynoecia from malefertile plants that had been artificially cross-pollinated withms1 ms1 plants. Few tubes from coenocytic microspores were observed in the vicinity of the micropylar region. A low frequency of seed set was achieved in the greenhouse on Urbana male-sterile plants grown in the absence of male-fertile plants. Thus, we believe either that some gametes from coenocytic microspores are able to participate in fertilization at low frequency or that apomixis occurs inms1 ms1 plants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00730680
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  • 8
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    Phylogenetic diversity and ecophysiology of Candidate phylum Saccharibacteria in activated sludge (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-11
    Description: Candidate phylum Saccharibacteria (former TM7) are abundant and widespread in nature, but little is known about their ecophysiology and detailed phylogeny. In this study phylogeny, morphology and ecophysiology of Saccharibacteria were investigated in activated sludge from nine wastewater treatment plants (WWTPs) from Japan and Denmark using the full-cycle 16S rRNA approach in combination with microautoradiography (MAR) and fluorescence in situ hybridization (FISH). Phylogenetic analysis showed that Saccharibacteria from all WWTPs were evenly distributed within subdivision 1 and 3 and in a distinct phylogenetic clade. Three probes were designed for the distinct saccharibacterial groups, and revealed morphotypes representing thin filaments, thick filaments and rods/cocci. MAR-FISH results showed that most probe-defined Saccharibacteria utilized glucose under aerobic-, nitrate reducing- and anaerobic conditions. Some Saccharibacteria also utilized N -acetylglucosamine, oleic acid, amino acids and butyrate, which are not predicted from available genomes so far. In addition, some filamentous Saccharibacteria exhibited β-galactosidase and lipase activities determined using a combination of enzyme-labeled fluorescence and FISH (ELF-FISH). No uptake of acetate, propionate, pyruvate, glycerol and ethanol was observed. These results indicate that Saccharibacteria is a phylogenetically diverse group and play a role in the degradation of various organic compounds as well as sugar compounds under aerobic-, nitrate reducing- and anaerobic conditions.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Expanded metabolic versatility of Nitrospira [Microbiology] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-09-09
    Description: Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. However, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data from Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II, we identified ecophysiological traits that contribute to the ecological success of Nitrospira....
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    “Candidatus Accumulibacter delftensis”: A clade IC novel polyphosphate-accumulating organism without denitrifying activity on nitrate (2019)
    Elsevier
    Details
    Publication Date: 2019-09-01
    Print ISSN: 0043-1354
    Electronic ISSN: 1879-2448
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by Elsevier
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