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Ammonia Oxidizing Bacterium

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Martin G Klotz – One of the best experts on this subject based on the ideXlab platform.

  • Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia–Oxidizing Bacterium Isolated from Arctic Waters.
    Genome announcements, 2017
    Co-Authors: Marlen C. Rice, Martin G Klotz, Jeanette M Norton, Lisa Y Stein, Jessica A Kozlowski, Annette Bollmann, Luis A. Sayavedra-soto, Nicole Shapiro, Lynne Goodwin, Marcel Huntemann

    Abstract:

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

  • Standards in Genomic Sciences (2013) 7:469-482 DOI:10.4056/sigs.3517166 The Genomic Standards Consortium
    , 2016
    Co-Authors: Annette Bollmann, Martin G Klotz, Lisa Y Stein, Hendrikus J. Laanbroek, Yuichi Suwa, Christopher J. Sedlacek, Daniel J. Arp, Jeanette Norton, Luis Sayavedra-soto, David Bruce

    Abstract:

    Complete genome sequence of Nitrosomonas sp. Is79, an Ammonia Oxidizing Bacterium adapted to low ammonium concentration

  • Complete genome of Nitrosospira briensis C-128, an Ammonia–Oxidizing Bacterium from agricultural soil.
    Standards in genomic sciences, 2016
    Co-Authors: Marlen C. Rice, Martin G Klotz, Jeanette M Norton, Lisa Y Stein, Annette Bollmann, Frederica W. Valois, Peter J. Bottomley, Hendrikus J. Laanbroek, Yuichi Suwa, Luis A. Sayavedra-soto

    Abstract:

    Nitrosospira briensis C-128 is an Ammonia–Oxidizing Bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.

Tatsuaki Tokuyama – One of the best experts on this subject based on the ideXlab platform.

  • Nitrosomonas communis strain YNSRA, an Ammonia–Oxidizing Bacterium, isolated from the reed rhizoplane in an aquaponics plant
    Journal of bioscience and bioengineering, 2004
    Co-Authors: Tatsuaki Tokuyama, Reiji Takahashi, Atsushi Mine, Kaoru Kamiyama, Ryuichi Yabe, Kazuo Satoh, Hirotoshi Matsumoto, Koji Itonaga

    Abstract:

    Abstract 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.

  • Effect of root exudates on growth of newly isolated nitrifying bacteria from barley rhizoplane
    Soil Science and Plant Nutrition, 2003
    Co-Authors: Kazuo Satoh, Reiji Takahashi, Toshikazu Yanagida, Katsunori Isobe, Hirofumi Tomiyama, Hidetoshi Iwano, Tatsuaki Tokuyama

    Abstract:

    An Ammonia–Oxidizing Bacterium, strain PJA1, and nitrite-Oxidizing Bacterium, strain PJN1, were newly isolated from the rhizoplane of barley. The cells of strain PJA1 were lobate, compartmentalized, and showed characteristics of the genus Nitrosolobus. The similarity of the 16S rRNA gene to Nitrosolobus multiformis ATCC25196 was 99.04%. The cells of strain PJN1 were rod-shaped. The similarity of the 16S rRNA gene to Nitrobacter agilis ATCC-14123 was 98.57%. These newly isolated bacteria were identified as Nitrosolobus sp. PJA1 and Nitrobacter sp. PJN1, respectively. The exudates prepared from barley roots of both the pre-heading and post-heading stages promoted the growth of strain PJA1 (15-20% increase). The growth of the non-rhizoplane strains like Nitrosomonas europaea ATCC25978 was remarkably inhibited by the exudates. The growth of strain PJN1 was also remarkably promoted by the root exudates at the pre-heading stage (6 time increase), and by the root exudates at the post-heading stage (2.5 time increase). The root exudates did not effect the growth of Nitrobacter winogradskyi IFO14297, isolated from the non-rhizoplane.

  • Characteristics of an Ammonia–Oxidizing Bacterium with a plasmid isolated from alkaline soils and its phylogenetic relationship
    Journal of bioscience and bioengineering, 2001
    Co-Authors: Reiji Takahashi, Motoki Ohishi, Mifuyu Ohshima, Masami Saitoh, Kana Omata, Tatsuaki Tokuyama

    Abstract:

    Abstract An Ammonia–Oxidizing Bacterium, strain TCH716, was isolated from alkaline soil at Harbin city, China. The cells of strain TCH716 are lobate (0.8–1.5×1.0–2.0 μm), gram-negative, obligately aerobic, and nonmotile. Colonies (1–2 mm in diameter) on gellan gum plate culture are reddish, circular, and smooth. The G+C content of DNA is 54.78 mol%. Its percentage of 16S rRNA gene sequence similarity (%) to Nitrosolobus multiformis ATCC 25196 T (type strain) is 98.56%. This Bacterium has an optimal growth temperature and pH at 30°C and 8.0–8.5, respectively. The concentration of ammonium sulfate in the HEPES medium for optimum growth of this Bacterium is 38 mM. Strain TCH716 was found to have a plasmid (approximately 6.5 kbp) that possessed a plasmid-linked gene for sulfonamide resistance. Phosphoglycerate kinase, RubisCO and PEPC were found to possess high specific activities compared to the activities of these enzymes in strain ATCC 25978 T . In identification of strain TCH716, both morphological characteristics (compartmentalized cells) and the phylogenetic relationship based on 16S rRNA gene sequence are important. Based on results obtained, strain TCH716 belongs to the genus Nitrosolobus , and designated as Nitrosolobus sp. TCH716.

Lisa Y Stein – One of the best experts on this subject based on the ideXlab platform.

  • Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia–Oxidizing Bacterium Isolated from Arctic Waters.
    Genome announcements, 2017
    Co-Authors: Marlen C. Rice, Martin G Klotz, Jeanette M Norton, Lisa Y Stein, Jessica A Kozlowski, Annette Bollmann, Luis A. Sayavedra-soto, Nicole Shapiro, Lynne Goodwin, Marcel Huntemann

    Abstract:

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

  • Standards in Genomic Sciences (2013) 7:469-482 DOI:10.4056/sigs.3517166 The Genomic Standards Consortium
    , 2016
    Co-Authors: Annette Bollmann, Martin G Klotz, Lisa Y Stein, Hendrikus J. Laanbroek, Yuichi Suwa, Christopher J. Sedlacek, Daniel J. Arp, Jeanette Norton, Luis Sayavedra-soto, David Bruce

    Abstract:

    Complete genome sequence of Nitrosomonas sp. Is79, an Ammonia Oxidizing Bacterium adapted to low ammonium concentration

  • Complete genome of Nitrosospira briensis C-128, an Ammonia–Oxidizing Bacterium from agricultural soil.
    Standards in genomic sciences, 2016
    Co-Authors: Marlen C. Rice, Martin G Klotz, Jeanette M Norton, Lisa Y Stein, Annette Bollmann, Frederica W. Valois, Peter J. Bottomley, Hendrikus J. Laanbroek, Yuichi Suwa, Luis A. Sayavedra-soto

    Abstract:

    Nitrosospira briensis C-128 is an Ammonia–Oxidizing Bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.