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Martin G Klotz - One of the best experts on this subject based on the ideXlab platform.
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Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters.
Genome announcements, 2017Co-Authors: Marlen C. Rice, Lisa Y Stein, Jeanette M Norton, Martin G Klotz, Jessica A Kozlowski, Annette Bollmann, Luis A. Sayavedra-soto, Nicole Shapiro, Lynne Goodwin, Marcel HuntemannAbstract: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.
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Standards in Genomic Sciences (2013) 7:469-482 DOI:10.4056/sigs.3517166 The Genomic Standards Consortium
2016Co-Authors: Annette Bollmann, Lisa Y Stein, Martin G Klotz, Hendrikus J. Laanbroek, Yuichi Suwa, Christopher J. Sedlacek, Daniel J. Arp, Jeanette Norton, Luis Sayavedra-soto, David BruceAbstract:Complete genome sequence of Nitrosomonas sp. Is79, an Ammonia Oxidizing Bacterium adapted to low ammonium concentration
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Complete genome of Nitrosospira briensis C-128, an Ammonia-Oxidizing Bacterium from agricultural soil.
Standards in genomic sciences, 2016Co-Authors: Marlen C. Rice, Lisa Y Stein, Jeanette M Norton, Martin G Klotz, Annette Bollmann, Frederica W. Valois, Peter J. Bottomley, Hendrikus J. Laanbroek, Yuichi Suwa, Luis A. Sayavedra-sotoAbstract: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.
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d1fhs the type strain of the Ammonia Oxidizing Bacterium nitrosococcus wardiae spec nov enrichment isolation phylogenetic and growth physiological characterization
Frontiers in Microbiology, 2016Co-Authors: Thomas E Hanson, Hongyue Dang, Martin G KlotzAbstract:An Ammonia-Oxidizing Bacterium, strain D1FHS, was enriched into pure culture from a sediment sample retrieved in Jiaozhou Bay, a hyper-eutrophic semi-closed water body hosting the metropolitan area of Qingdao, China. Based on initial 16S rRNA gene sequence analysis, strain D1FHS was classified in the genus Nitrosococcus, family Chromatiaceae, order Chromatiales, class Gammaproteobacteria; the 16S rRNA gene sequence with highest level of identity to that of D1FHS was obtained from Nitrosococcus halophilus Nc4T. The average nucleotide identity between the genomes of strain D1FHS and Nitrosococcus halophilus strain Nc4 is 89.5%. Known species in the genus Nitrosococcus are obligate aerobic chemolithotrophic Ammonia-Oxidizing bacteria adapted to and restricted to marine environments. The optimum growth (maximum nitrite production) conditions for D1FHS in a minimal salts medium are: 50 mM ammonium and 700 mM NaCl at pH of 7.5 to 8.0 and at 37°C in dark. Because pertinent conditions for other studied Nitrosococcus spp. are 100-200 mM ammonium and <700 mM NaCl at pH of 7.5 to 8.0 and at 28-32°C, D1FHS is physiologically distinct from other Nitrosococcus spp. in terms of substrate, salt and thermal tolerance.
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D1FHS, the Type Strain of the Ammonia-Oxidizing Bacterium Nitrosococcus wardiae spec. nov.: Enrichment, Isolation, Phylogenetic, and Growth Physiological Characterization
Frontiers in Microbiology, 2016Co-Authors: Hongyue Dang, Thomas E Hanson, Martin G KlotzAbstract:An Ammonia-Oxidizing Bacterium, strain D1FHS, was enriched into pure culture from a sediment sample retrieved in Jiaozhou Bay, a hyper-eutrophic semi-closed water body hosting the metropolitan area of Qingdao, China. Based on initial 16S rRNA gene sequence analysis, strain D1FHS was classified in the genus Nitrosococcus, family Chromatiaceae, order Chromatiales, class Gammaproteobacteria; the 16S rRNA gene sequence with highest level of identity to that of D1FHS was obtained from Nitrosococcus halophilus Nc4T. The average nucleotide identity between the genomes of strain D1FHS and Nitrosococcus halophilus strain Nc4 is 89.5%. Known species in the genus Nitrosococcus are obligate aerobic chemolithotrophic Ammonia-Oxidizing bacteria adapted to and restricted to marine environments. The optimum growth (maximum nitrite production) conditions for D1FHS in a minimal salts medium are: 50 mM ammonium and 700 mM NaCl at pH of 7.5 to 8.0 and at 37°C in dark. Because pertinent conditions for other studied Nitrosococcus spp. are 100-200 mM ammonium and
Tatsuaki Tokuyama - One of the best experts on this subject based on the ideXlab platform.
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Nitrosomonas communis strain YNSRA, an Ammonia-Oxidizing Bacterium, isolated from the reed rhizoplane in an aquaponics plant
Journal of bioscience and bioengineering, 2004Co-Authors: Tatsuaki Tokuyama, Reiji Takahashi, Atsushi Mine, Kaoru Kamiyama, Ryuichi Yabe, Kazuo Satoh, Hirotoshi Matsumoto, Koji ItonagaAbstract: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.
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Effect of root exudates on growth of newly isolated nitrifying bacteria from barley rhizoplane
Soil Science and Plant Nutrition, 2003Co-Authors: Kazuo Satoh, Reiji Takahashi, Toshikazu Yanagida, Katsunori Isobe, Hirofumi Tomiyama, Hidetoshi Iwano, Tatsuaki TokuyamaAbstract: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.
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Characteristics of an Ammonia-Oxidizing Bacterium with a plasmid isolated from alkaline soils and its phylogenetic relationship
Journal of bioscience and bioengineering, 2001Co-Authors: Reiji Takahashi, Motoki Ohishi, Mifuyu Ohshima, Masami Saitoh, Kana Omata, Tatsuaki TokuyamaAbstract: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.
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Ribulose-1,5-bisphosphate carboxylase/oxygenase from an Ammonia-Oxidizing Bacterium, Nitrosomonas sp. K1: purification and properties.
Journal of bioscience and bioengineering, 2000Co-Authors: Ryota Hatayama, Reiji Takahashi, Mifuyu Ohshima, R. I. E. Shibasaki, Tatsuaki TokuyamaAbstract:Abstract The Ammonia-Oxidizing chemoautotrophic Nitrosomonas sp. strain K1 exhibited marked ribulose-1,5-bisphosphate carboxylase (RubisCO) activity. The RubisCO [EC 4.1.1.39] was purified as an electrophoretically homogeneous protein. The molecular mass of the enzyme was estimated to be about 460 kDa by gel filtration, and it consists of two subunits [large (L): 52.2 kDa; small (S): 13.3 kDa] as demonstrated by SDS-PAGE. This confirmed that the enzyme has an L 8 S 8 structure. The K m values of the enzyme for RuBP, NaHCO 3 , and Mg 2+ were estimated to be 0.112, 0.415, and 1.063 mM, respectively. The optimum pH and temperature for its activity were approximately 7.0 and 45°C. The enzyme was stable up to 45°C and in a pH range from 7.0–9.0 (4°C, 48 h). The enzyme activity was inhibited by Cu 2+ , Hg 2+ , N -ethylmaleimide, p -chloromercuribenzoate, and SDS (0.1 mM). The activity was also inhibited by ammonium sulfate at high concentrations (38–303 mM) but the stability of the enzyme showed no inhibition at the same ammonium sulfate concentrations. The N -terminal amino acid sequences of the large and small subunits are AIKTYQAGVKEYRQTYW QPDYVPL and AIQAYHLTKKYETFSYLPQM, respectively.
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ribulose 1 5 bisphosphate carboxylase oxygenase from an Ammonia Oxidizing Bacterium nitrosomonas sp k1 purification and properties
Journal of Bioscience and Bioengineering, 2000Co-Authors: Ryota Hatayama, Reiji Takahashi, Mifuyu Ohshima, R. I. E. Shibasaki, Tatsuaki TokuyamaAbstract:Abstract The Ammonia-Oxidizing chemoautotrophic Nitrosomonas sp. strain K1 exhibited marked ribulose-1,5-bisphosphate carboxylase (RubisCO) activity. The RubisCO [EC 4.1.1.39] was purified as an electrophoretically homogeneous protein. The molecular mass of the enzyme was estimated to be about 460 kDa by gel filtration, and it consists of two subunits [large (L): 52.2 kDa; small (S): 13.3 kDa] as demonstrated by SDS-PAGE. This confirmed that the enzyme has an L 8 S 8 structure. The K m values of the enzyme for RuBP, NaHCO 3 , and Mg 2+ were estimated to be 0.112, 0.415, and 1.063 mM, respectively. The optimum pH and temperature for its activity were approximately 7.0 and 45°C. The enzyme was stable up to 45°C and in a pH range from 7.0–9.0 (4°C, 48 h). The enzyme activity was inhibited by Cu 2+ , Hg 2+ , N -ethylmaleimide, p -chloromercuribenzoate, and SDS (0.1 mM). The activity was also inhibited by ammonium sulfate at high concentrations (38–303 mM) but the stability of the enzyme showed no inhibition at the same ammonium sulfate concentrations. The N -terminal amino acid sequences of the large and small subunits are AIKTYQAGVKEYRQTYW QPDYVPL and AIQAYHLTKKYETFSYLPQM, respectively.
Lisa Y Stein - One of the best experts on this subject based on the ideXlab platform.
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Complete Genome Sequence of Nitrosomonas cryotolerans ATCC 49181, a Phylogenetically Distinct Ammonia-Oxidizing Bacterium Isolated from Arctic Waters.
Genome announcements, 2017Co-Authors: Marlen C. Rice, Lisa Y Stein, Jeanette M Norton, Martin G Klotz, Jessica A Kozlowski, Annette Bollmann, Luis A. Sayavedra-soto, Nicole Shapiro, Lynne Goodwin, Marcel HuntemannAbstract: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.
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Standards in Genomic Sciences (2013) 7:469-482 DOI:10.4056/sigs.3517166 The Genomic Standards Consortium
2016Co-Authors: Annette Bollmann, Lisa Y Stein, Martin G Klotz, Hendrikus J. Laanbroek, Yuichi Suwa, Christopher J. Sedlacek, Daniel J. Arp, Jeanette Norton, Luis Sayavedra-soto, David BruceAbstract:Complete genome sequence of Nitrosomonas sp. Is79, an Ammonia Oxidizing Bacterium adapted to low ammonium concentration
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Complete genome of Nitrosospira briensis C-128, an Ammonia-Oxidizing Bacterium from agricultural soil.
Standards in genomic sciences, 2016Co-Authors: Marlen C. Rice, Lisa Y Stein, Jeanette M Norton, Martin G Klotz, Annette Bollmann, Frederica W. Valois, Peter J. Bottomley, Hendrikus J. Laanbroek, Yuichi Suwa, Luis A. Sayavedra-sotoAbstract: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.
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genome sequence of nitrosomonas communis strain nm2 a mesophilic Ammonia Oxidizing Bacterium isolated from mediterranean soil
Genome Announcements, 2016Co-Authors: Jessica A Kozlowski, Dimitri K Kits, Lisa Y SteinAbstract:ABSTRACT The complete genome sequence of Nitrosomonas communis strain Nm2, a mesophilic betaproteobacterial Ammonia oxidizer isolated from Mediterranean soils in Corfu, Greece, is reported here. This is the first genome to describe a cluster 8 Nitrosomonas species and represents an Ammonia-Oxidizing Bacterium commonly found in terrestrial ecosystems.
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Nitrosospira lacus sp. nov., a psychrotolerant, Ammonia-Oxidizing Bacterium from sandy lake sediment.
International journal of systematic and evolutionary microbiology, 2014Co-Authors: Hidetoshi Urakawa, Lisa Y Stein, Jessica A Kozlowski, Juan C. Garcia, Jeppe Lund Nielsen, Chee Kent Lim, Andreas Pommerening-röser, Willm Martens-habbena, David A StahlAbstract:A Gram-negative, spiral-shaped, chemolithotrophic, Ammonia-Oxidizing Bacterium, designated APG3(T), was isolated into pure culture from sandy lake sediment collected from Green Lake, Seattle, WA, USA. Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain APG3(T) belongs to cluster 0 of the genus Nitrosospira, which is presently not represented by described species, with Nitrosospira multiformis (cluster 3) as the closest species with a validly published name (identity of 98.6 % to the type strain). Strain APG3(T) grew at 4 °C but could not grow at 35 °C, indicating that this Bacterium is psychrotolerant. Remarkably, the strain was able to grow over a wide range of pH (pH 5-9), which was greater than the pH range of any studied Ammonia-Oxidizing bacteria in pure culture. The DNA G+C content of the APG3(T) genome is 53.5 %, which is similar to that of Nitrosospira multiformis ATCC 25196(T) (53.9 %) but higher than that of Nitrosomonas europaea ATCC 19718 (50.7 %) and Nitrosomonas eutropha C71 (48.5 %). The average nucleotide identity (ANI) calculated for the genomes of strain APG3(T) and Nitrosospira multiformis ATCC 25196(T) was 75.45 %, significantly lower than the value of 95 % ANI that corresponds to the 70 % species-level cut-off based on DNA-DNA hybridization. Overall polyphasic taxonomy study indicated that strain APG3(T) represents a novel species in the genus Nitrosospira, for which the name Nitrosospira lacus sp. nov. is proposed (type strain APG3(T) = NCIMB 14869(T) = LMG 27536(T) = ATCC BAA-2542(T)).
Reiji Takahashi - One of the best experts on this subject based on the ideXlab platform.
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Whole-Genome Sequence of the Ammonia-Oxidizing Bacterium Nitrosomonas stercoris Type Strain KYUHI-S, Isolated from Composted Cattle Manure
Microbiology resource announcements, 2019Co-Authors: Tatsunori Nakagawa, Yuki Tsuchiya, Reiji TakahashiAbstract:ABSTRACT This work reports the complete genome sequence of a chemoautotrophic Ammonia-Oxidizing Bacterium, Nitrosomonas stercoris strain KYUHI-ST (= ATCC BAA-2718T and NBRC 110753T). The assembled genome is composed of a circular chromosome and a large plasmid.
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nitrosomonas stercoris sp nov a chemoautotrophic Ammonia Oxidizing Bacterium tolerant of high ammonium isolated from composted cattle manure
Microbes and Environments, 2015Co-Authors: Tatsunori Nakagawa, Reiji TakahashiAbstract:Among Ammonia-Oxidizing bacteria, Nitrosomonas eutropha-like microbes are distributed in strongly eutrophic environments such as wastewater treatment plants and animal manure. In the present study, we isolated an Ammonia-Oxidizing Bacterium tolerant of high ammonium levels, designated strain KYUHI-ST, from composted cattle manure. Unlike the other known Nitrosomonas species, this isolate grew at 1,000 mM ammonium. Phylogenetic analyses based on 16S rRNA and amoA genes indicated that the isolate belonged to the genus Nitrosomonas and formed a unique cluster with the uncultured Ammonia oxidizers found in wastewater systems and animal manure composts, suggesting that these Ammonia oxidizers contributed to removing higher concentrations of Ammonia in strongly eutrophic environments. Based on the physiological and phylogenetic data presented here, we propose and call for the validation of the provisional taxonomic assignment Nitrosomonas stercoris, with strain KYUHI-S as the type strain (type strain KYUHI-ST = NBRC 110753T = ATCC BAA-2718T).
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Nitrosomonas communis strain YNSRA, an Ammonia-Oxidizing Bacterium, isolated from the reed rhizoplane in an aquaponics plant
Journal of bioscience and bioengineering, 2004Co-Authors: Tatsuaki Tokuyama, Reiji Takahashi, Atsushi Mine, Kaoru Kamiyama, Ryuichi Yabe, Kazuo Satoh, Hirotoshi Matsumoto, Koji ItonagaAbstract: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.
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Effect of root exudates on growth of newly isolated nitrifying bacteria from barley rhizoplane
Soil Science and Plant Nutrition, 2003Co-Authors: Kazuo Satoh, Reiji Takahashi, Toshikazu Yanagida, Katsunori Isobe, Hirofumi Tomiyama, Hidetoshi Iwano, Tatsuaki TokuyamaAbstract: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.
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Characteristics of an Ammonia-Oxidizing Bacterium with a plasmid isolated from alkaline soils and its phylogenetic relationship
Journal of bioscience and bioengineering, 2001Co-Authors: Reiji Takahashi, Motoki Ohishi, Mifuyu Ohshima, Masami Saitoh, Kana Omata, Tatsuaki TokuyamaAbstract: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.
Daniel J. Arp - One of the best experts on this subject based on the ideXlab platform.
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Standards in Genomic Sciences (2013) 7:469-482 DOI:10.4056/sigs.3517166 The Genomic Standards Consortium
2016Co-Authors: Annette Bollmann, Lisa Y Stein, Martin G Klotz, Hendrikus J. Laanbroek, Yuichi Suwa, Christopher J. Sedlacek, Daniel J. Arp, Jeanette Norton, Luis Sayavedra-soto, David BruceAbstract:Complete genome sequence of Nitrosomonas sp. Is79, an Ammonia Oxidizing Bacterium adapted to low ammonium concentration
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Complete genome sequence of Nitrosomonas sp. Is79, an Ammonia Oxidizing Bacterium adapted to low ammonium concentrations
Standards in genomic sciences, 2013Co-Authors: Annette Bollmann, Lisa Y Stein, Jeanette M Norton, Martin G Klotz, Hendrikus J. Laanbroek, Yuichi Suwa, Christopher J. Sedlacek, Daniel J. Arp, Luis A. Sayavedra-sotoAbstract: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.
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Genome Sequence of Nitrosomonas sp. Strain AL212, an Ammonia-Oxidizing Bacterium Sensitive to High Levels of Ammonia
Journal of bacteriology, 2011Co-Authors: Suwa Yuichi, Lisa Y Stein, Jeanette M Norton, Martin G Klotz, Annette Bollmann, Lynne Goodwin, Hendrikus J. Laanbroek, Daniel J. Arp, Olga Chertkov, Brittany HeldAbstract:Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic Ammonia-Oxidizing Bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A, which is characterized by sensitivity to high Ammonia concentrations, higher substrate affinity (lower Km), and lower maximum growth rates than strains in Nitrosomonas cluster 7, which includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this Ammonia-sensitive cohort of AOB are needed, as these bacteria are found in freshwater environments, drinking water supplies, wastewater treatment systems, and soils worldwide.
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Role of a Fur homolog in iron metabolism in Nitrosomonas europaea
BMC microbiology, 2011Co-Authors: Neeraja Vajrala, Luis A. Sayavedra-soto, Peter J. Bottomley, Daniel J. ArpAbstract:Background In response to environmental iron concentrations, many bacteria coordinately regulate transcription of genes involved in iron acquisition via the ferric uptake regulation (Fur) system. The genome of Nitrosomonas europaea, an Ammonia-Oxidizing Bacterium, carries three genes (NE0616, NE0730 and NE1722) encoding proteins belonging to Fur family.
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Computational prediction and transcriptional analysis of sRNAs in Nitrosomonas europaea.
FEMS microbiology letters, 2010Co-Authors: Barbara O. Gvakharia, Luis A. Sayavedra-soto, Neeraja Vajrala, Brian Tjaden, Daniel J. ArpAbstract:Bacterial small noncoding RNAs (sRNAs) have been discovered in many genetically well-studied microorganisms and have been shown to regulate critical cellular processes at the post-transcriptional level. In this study, we used comparative genomics and microarray data to analyze the genome of the Ammonia-Oxidizing Bacterium Nitrosomonas europaea for the presence and expression of sRNAs. Fifteen genes encoding putative sRNAs (psRNAs) were identified. Most of these genes showed altered expression in a variety of experimental conditions. The transcripts of two psRNAs were further characterized by mapping their 5'- and 3'-ends and by real-time PCR. The results of these analyses suggested that one of them, psRNA11, is involved in iron homeostasis in N. europaea.