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Christopher A. Francis - One of the best experts on this subject based on the ideXlab platform.

  • ecophysiology of an Ammonia Oxidizing Archaeon adapted to low salinity habitats
    Microbial Ecology, 2012
    Co-Authors: Annika C. Mosier, Marie Lund, Christopher A. Francis
    Abstract:

    Ammonia oxidation in marine and terrestrial ecosystems plays a pivotal role in the cycling of nitrogen and carbon. Recent discoveries have shown that Ammonia-Oxidizing archaea (AOA) are both abundant and diverse in these systems, yet very little is known about their physiology. Here we report a physiological analysis of a novel low-salinity-type AOA enriched from the San Francisco Bay estuary, Candidatus Nitrosoarchaeum limnia strain SFB1. N. limnia has a slower growth rate than Nitrosopumilus maritimus and Nitrososphaera viennensis EN76, the only pure AOA isolates described to date, but the growth rate is comparable to the growth of marine AOA enrichment cultures. The growth rate only slightly decreased when N. limnia was grown under lower-oxygen conditions (5.5 % oxygen in the headspace). Although N. limnia was capable of growth at 75 % of seawater salinity, there was a longer lag time, incomplete oxidation of Ammonia to nitrite, and slower overall growth rate. Allylthiourea (ATU) only partially inhibited growth and Ammonia oxidation by N. limnia at concentrations known to completely inhibit bacterial Ammonia oxidation. Using electron microscopy, we confirmed the presence of flagella as suggested by various flagellar biosynthesis genes in the N. limnia genome. We demonstrate that N. limnia is representative of a low-salinity estuarine AOA ecotype and that more than 85 % of its proteins have highest identity to other coastal and estuarine metagenomic sequences. Our findings further highlight the physiology of N. limnia and help explain its ecological adaptation to low-salinity niches.

  • genome sequence of candidatus nitrosopumilus salaria bd31 an Ammonia Oxidizing Archaeon from the san francisco bay estuary
    Journal of Bacteriology, 2012
    Co-Authors: Annika C. Mosier, Eric E. Allen, Maria Kim, Steven Ferriera, Christopher A. Francis
    Abstract:

    Ammonia-Oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine and terrestrial ecosystems. Here, we present the draft genome sequence for the Ammonia-Oxidizing Archaeon "Candidatus Nitrosopumilus salaria" BD31, which was enriched in culture from sediments of the San Francisco Bay estuary. The genome sequences revealed many similarities to the genome of Nitrosopumilus maritimus.

  • genome sequence of candidatus nitrosoarchaeum limnia bg20 a low salinity Ammonia Oxidizing Archaeon from the san francisco bay estuary
    Journal of Bacteriology, 2012
    Co-Authors: Annika C. Mosier, Eric E. Allen, Maria Kim, Steven Ferriera, Christopher A. Francis
    Abstract:

    Here, we present the draft genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, an Ammonia-Oxidizing Archaeon enriched in culture from low-salinity sediments of the San Francisco Bay estuary. The genome sequence revealed many similarities to the previously sequenced genome of "Ca. Nitrosoarchaeum limnia" SFB1 (enriched from a nearby site in San Francisco Bay) and is representative of a clade of Ammonia-Oxidizing archaea (AOA) found in low-salinity habitats worldwide.

  • Genome Sequence of “Candidatus Nitrosopumilus salaria” BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary
    Journal of bacteriology, 2012
    Co-Authors: Annika C. Mosier, Eric E. Allen, Maria Kim, Steven Ferriera, Christopher A. Francis
    Abstract:

    Ammonia-Oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine and terrestrial ecosystems. Here, we present the draft genome sequence for the Ammonia-Oxidizing Archaeon "Candidatus Nitrosopumilus salaria" BD31, which was enriched in culture from sediments of the San Francisco Bay estuary. The genome sequences revealed many similarities to the genome of Nitrosopumilus maritimus.

  • Genome Sequence of “Candidatus Nitrosoarchaeum limnia” BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary
    Journal of bacteriology, 2012
    Co-Authors: Annika C. Mosier, Eric E. Allen, Maria Kim, Steven Ferriera, Christopher A. Francis
    Abstract:

    Here, we present the draft genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, an Ammonia-Oxidizing Archaeon enriched in culture from low-salinity sediments of the San Francisco Bay estuary. The genome sequence revealed many similarities to the previously sequenced genome of "Ca. Nitrosoarchaeum limnia" SFB1 (enriched from a nearby site in San Francisco Bay) and is representative of a clade of Ammonia-Oxidizing archaea (AOA) found in low-salinity habitats worldwide.

Sungkeun Rhee - One of the best experts on this subject based on the ideXlab platform.

  • Indications for enzymatic denitrification to N2O at low pH in an Ammonia-Oxidizing Archaeon
    The ISME journal, 2019
    Co-Authors: Manyoung Jung, Craig W. Herbold, Michael Wagner, Jonggeol Kim, Eugene L. Madsen, Joo-han Gwak, Lena Rohe, Anette Giesemann, Reinhard Well, Sungkeun Rhee
    Abstract:

    Nitrous oxide (N2O) is a key climate change gas and nitrifying microbes living in terrestrial ecosystems contribute significantly to its formation. Many soils are acidic and global change will cause acidification of aquatic and terrestrial ecosystems, but the effect of decreasing pH on N2O formation by nitrifiers is poorly understood. Here, we used isotope-ratio mass spectrometry to investigate the effect of acidification on production of N2O by pure cultures of two Ammonia-Oxidizing archaea (AOA; Nitrosocosmicus oleophilus and Nitrosotenuis chungbukensis) and an Ammonia-Oxidizing bacterium (AOB; Nitrosomonas europaea). For all three strains acidification led to increased emission of N2O. However, changes of 15N site preference (SP) values within the N2O molecule (as indicators of pathways for N2O formation), caused by decreasing pH, were highly different between the tested AOA and AOB. While acidification decreased the SP value in the AOB strain, SP values increased to a maximum value of 29‰ in N. oleophilus. In addition, 15N-nitrite tracer experiments showed that acidification boosted nitrite transformation into N2O in all strains, but the incorporation rate was different for each Ammonia oxidizer. Unexpectedly, for N. oleophilus more than 50% of the N2O produced at pH 5.5 had both nitrogen atoms from nitrite and we demonstrated that under these conditions expression of a putative cytochrome P450 NO reductase is strongly upregulated. Collectively, our results indicate that N. oleophilus might be able to enzymatically denitrify nitrite to N2O at low pH.

  • plant growth promoting archaea trigger induced systemic resistance in arabidopsis thaliana against pectobacterium carotovorum and pseudomonas syringae
    Environmental Microbiology, 2019
    Co-Authors: Geun Cheol Song, Hyunjoo Im, Jihye Jung, Manyoung Jung, Sungkeun Rhee
    Abstract:

    : Archaea have inhabited the earth for a long period of time and are ubiquitously distributed in diverse environments. However, few studies have focused on the interactions of archaea with other organisms, including eukaryotes such as plants, since it is difficult to cultivate sufficient numbers of archaeal cells for analysis. In this study, we investigated the interaction between soil archaea and Arabidopsis thaliana. We demonstrate for the first time that soil archaea promote plant growth and trigger induced systemic resistance (ISR) against the necrotrophic bacterium Pectobacterium carotovorum subsp. carotovorum SCC1 and biotrophic bacterium Pseudomonas syringae pv. tomato DC3000. Ammonia-Oxidizing Archaeon Nitrosocosmicus oleophilus MY3 cells clearly colonized the root surface of Arabidopsis plants, and increased resistance against both pathogenic species via the salicylic acid-independent signalling pathway. This mechanism of bacterial resistance resembles that underlying soil bacteria- and fungi-mediated ISR signalling. Additionally, volatile emissions from N. oleophilus MY3 were identified as major archaeal determinants that elicit ISR. Our results lay a foundation for archaea-plant interactions as a new field of research.

  • Plant growth‐promoting archaea trigger induced systemic resistance in Arabidopsis thaliana against Pectobacterium carotovorum and Pseudomonas syringae
    Environmental microbiology, 2019
    Co-Authors: Geun Cheol Song, Jihye Jung, Manyoung Jung, Sungkeun Rhee, Soohyun Lee, Choong-min Ryu
    Abstract:

    Archaea have inhabited the earth for a long period of time and are ubiquitously distributed in diverse environments. However, few studies have focused on the interactions of archaea with other organisms, including eukaryotes such as plants, since it is difficult to cultivate sufficient numbers of archaeal cells for analysis. In this study, we investigated the interaction between soil archaea and Arabidopsis thaliana. We demonstrate for the first time that soil archaea promote plant growth and trigger induced systemic resistance (ISR) against the necrotrophic bacterium Pectobacterium carotovorum subsp. carotovorum SCC1 and biotrophic bacterium Pseudomonas syringae pv. tomato DC3000. Ammonia-Oxidizing Archaeon Nitrosocosmicus oleophilus MY3 cells clearly colonized the root surface of Arabidopsis plants, and increased resistance against both pathogenic species via the salicylic acid-independent signalling pathway. This mechanism of bacterial resistance resembles that underlying soil bacteria- and fungi-mediated ISR signalling. Additionally, volatile emissions from N. oleophilus MY3 were identified as major archaeal determinants that elicit ISR. Our results lay a foundation for archaea-plant interactions as a new field of research.

  • Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, Ammonia-Oxidizing Archaeon member of the phylum Thaumarchaeota isolated from agricultural soil
    International journal of systematic and evolutionary microbiology, 2018
    Co-Authors: Manyoung Jung, Jonggeol Kim, Arafat Islam, Joo-han Gwak, Sungkeun Rhee
    Abstract:

    A mesophilic, chemolithoautotrophic, neutrophilic and aerobic Ammonia-Oxidizing Archaeon, designated strain MY1T, was isolated from agricultural soil. Microscopic observation revealed short, rod-shaped cells with a diameter of 0.3–0.5 µm and length of 0.6–1.0 µm. The isolate had no flagella and pili, and possessed no genes associated with archaeal flagella synthesis. The major membrane lipids consisted mainly of the glycerol dibiphytanyl glycerol tetraether (GDGT) lipids GDGT-0 to GDGT-4 and crenarchaeol. The major intact polar lipids (IPLs) were determined as hexose plus phosphohexose IPL and dihexose IPL. Strain MY1T obtains energy by aerobically Oxidizing Ammonia and carbon by fixing CO2. An optimal growth was observed at 25 °C, at pH 7 and with 0.2–0.4 % (w/v) salinity that corresponds with its terrestrial habitat. The addition of α-keto acids was necessary to stimulate growth. The strain tolerated ammonium and nitrite concentrations up to 10 and 5 mM, respectively. The MY1T genome has a DNA G+C content of 32.7 mol%. Phylogenetic analysis based on the 16S rRNA gene showed that strain MY1T belongs to the family Nitrosopumilaceae of the phylum Thaumarchaeota , sharing the highest 16S rRNA gene sequence similarity (96.6–97.1 %) with marine isolates of the genus Nitrosopumilus . The average nucleotide identity was 78 % between strain MY1T and Nitrosopumilus maritimus SCM1T, indicating distant relatedness. Based on the phenotypic, phylogenetic and genomic analyses, it was concluded that strain MY1T belongs to the novel genus Nitrosarchaeum, under which the name Nitrosarchaeum koreense sp. nov. is proposed as the type species. The type strain is MY1T (=JCM 31640T=KCTC 4249T).

  • a mesophilic autotrophic Ammonia Oxidizing Archaeon of thaumarchaeal group i 1a cultivated from a deep oligotrophic soil horizon
    Applied and Environmental Microbiology, 2014
    Co-Authors: Manyoung Jung, Sooje Park, Sojeong Kim, Jonggeol Kim, Jaap Sinninghe S Damste, Che Ok Jeon, Sungkeun Rhee
    Abstract:

    Soil nitrification plays an important role in the reduction of soil fertility and in nitrate enrichment of groundwater. Various Ammonia-Oxidizing archaea (AOA) are considered to be members of the pool of Ammonia-Oxidizing microorganisms in soil. This study reports the discovery of a chemolithoautotrophic Ammonia oxidizer that belongs to a distinct clade of nonmarine thaumarchaeal group I.1a, which is widespread in terrestrial environments. The archaeal strain MY2 was cultivated from a deep oligotrophic soil horizon. The similarity of the 16S rRNA gene sequence of strain MY2 to those of other cultivated group I.1a thaumarchaeota members, i.e., Nitrosopumilus maritimus and “Candidatus Nitrosoarchaeum koreensis,” is 92.9% for both species. Extensive growth assays showed that strain MY2 is chemolithoautotrophic, mesophilic (optimum temperature, 30°C), and neutrophilic (optimum pH, 7 to 7.5). The accumulation of nitrite above 1 mM inhibited Ammonia oxidation, while Ammonia oxidation itself was not inhibited in the presence of up to 5 mM Ammonia. The genome size of strain MY2 was 1.76 Mb, similar to those of N. maritimus and “Ca. Nitrosoarchaeum koreensis,” and the repertoire of genes required for Ammonia oxidation and carbon fixation in thaumarchaeal group I.1a was conserved. A high level of representation of conserved orthologous genes for signal transduction and motility in the noncore genome might be implicated in niche adaptation by strain MY2. On the basis of phenotypic, phylogenetic, and genomic characteristics, we propose the name “Candidatus Nitrosotenuis chungbukensis” for the Ammonia-Oxidizing archaeal strain MY2.

Annika C. Mosier - One of the best experts on this subject based on the ideXlab platform.

  • ecophysiology of an Ammonia Oxidizing Archaeon adapted to low salinity habitats
    Microbial Ecology, 2012
    Co-Authors: Annika C. Mosier, Marie Lund, Christopher A. Francis
    Abstract:

    Ammonia oxidation in marine and terrestrial ecosystems plays a pivotal role in the cycling of nitrogen and carbon. Recent discoveries have shown that Ammonia-Oxidizing archaea (AOA) are both abundant and diverse in these systems, yet very little is known about their physiology. Here we report a physiological analysis of a novel low-salinity-type AOA enriched from the San Francisco Bay estuary, Candidatus Nitrosoarchaeum limnia strain SFB1. N. limnia has a slower growth rate than Nitrosopumilus maritimus and Nitrososphaera viennensis EN76, the only pure AOA isolates described to date, but the growth rate is comparable to the growth of marine AOA enrichment cultures. The growth rate only slightly decreased when N. limnia was grown under lower-oxygen conditions (5.5 % oxygen in the headspace). Although N. limnia was capable of growth at 75 % of seawater salinity, there was a longer lag time, incomplete oxidation of Ammonia to nitrite, and slower overall growth rate. Allylthiourea (ATU) only partially inhibited growth and Ammonia oxidation by N. limnia at concentrations known to completely inhibit bacterial Ammonia oxidation. Using electron microscopy, we confirmed the presence of flagella as suggested by various flagellar biosynthesis genes in the N. limnia genome. We demonstrate that N. limnia is representative of a low-salinity estuarine AOA ecotype and that more than 85 % of its proteins have highest identity to other coastal and estuarine metagenomic sequences. Our findings further highlight the physiology of N. limnia and help explain its ecological adaptation to low-salinity niches.

  • genome sequence of candidatus nitrosopumilus salaria bd31 an Ammonia Oxidizing Archaeon from the san francisco bay estuary
    Journal of Bacteriology, 2012
    Co-Authors: Annika C. Mosier, Eric E. Allen, Maria Kim, Steven Ferriera, Christopher A. Francis
    Abstract:

    Ammonia-Oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine and terrestrial ecosystems. Here, we present the draft genome sequence for the Ammonia-Oxidizing Archaeon "Candidatus Nitrosopumilus salaria" BD31, which was enriched in culture from sediments of the San Francisco Bay estuary. The genome sequences revealed many similarities to the genome of Nitrosopumilus maritimus.

  • genome sequence of candidatus nitrosoarchaeum limnia bg20 a low salinity Ammonia Oxidizing Archaeon from the san francisco bay estuary
    Journal of Bacteriology, 2012
    Co-Authors: Annika C. Mosier, Eric E. Allen, Maria Kim, Steven Ferriera, Christopher A. Francis
    Abstract:

    Here, we present the draft genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, an Ammonia-Oxidizing Archaeon enriched in culture from low-salinity sediments of the San Francisco Bay estuary. The genome sequence revealed many similarities to the previously sequenced genome of "Ca. Nitrosoarchaeum limnia" SFB1 (enriched from a nearby site in San Francisco Bay) and is representative of a clade of Ammonia-Oxidizing archaea (AOA) found in low-salinity habitats worldwide.

  • Genome Sequence of “Candidatus Nitrosopumilus salaria” BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary
    Journal of bacteriology, 2012
    Co-Authors: Annika C. Mosier, Eric E. Allen, Maria Kim, Steven Ferriera, Christopher A. Francis
    Abstract:

    Ammonia-Oxidizing archaea (AOA) play important roles in nitrogen and carbon cycling in marine and terrestrial ecosystems. Here, we present the draft genome sequence for the Ammonia-Oxidizing Archaeon "Candidatus Nitrosopumilus salaria" BD31, which was enriched in culture from sediments of the San Francisco Bay estuary. The genome sequences revealed many similarities to the genome of Nitrosopumilus maritimus.

  • Genome Sequence of “Candidatus Nitrosoarchaeum limnia” BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary
    Journal of bacteriology, 2012
    Co-Authors: Annika C. Mosier, Eric E. Allen, Maria Kim, Steven Ferriera, Christopher A. Francis
    Abstract:

    Here, we present the draft genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, an Ammonia-Oxidizing Archaeon enriched in culture from low-salinity sediments of the San Francisco Bay estuary. The genome sequence revealed many similarities to the previously sequenced genome of "Ca. Nitrosoarchaeum limnia" SFB1 (enriched from a nearby site in San Francisco Bay) and is representative of a clade of Ammonia-Oxidizing archaea (AOA) found in low-salinity habitats worldwide.

Manyoung Jung - One of the best experts on this subject based on the ideXlab platform.

  • Indications for enzymatic denitrification to N2O at low pH in an Ammonia-Oxidizing Archaeon
    The ISME journal, 2019
    Co-Authors: Manyoung Jung, Craig W. Herbold, Michael Wagner, Jonggeol Kim, Eugene L. Madsen, Joo-han Gwak, Lena Rohe, Anette Giesemann, Reinhard Well, Sungkeun Rhee
    Abstract:

    Nitrous oxide (N2O) is a key climate change gas and nitrifying microbes living in terrestrial ecosystems contribute significantly to its formation. Many soils are acidic and global change will cause acidification of aquatic and terrestrial ecosystems, but the effect of decreasing pH on N2O formation by nitrifiers is poorly understood. Here, we used isotope-ratio mass spectrometry to investigate the effect of acidification on production of N2O by pure cultures of two Ammonia-Oxidizing archaea (AOA; Nitrosocosmicus oleophilus and Nitrosotenuis chungbukensis) and an Ammonia-Oxidizing bacterium (AOB; Nitrosomonas europaea). For all three strains acidification led to increased emission of N2O. However, changes of 15N site preference (SP) values within the N2O molecule (as indicators of pathways for N2O formation), caused by decreasing pH, were highly different between the tested AOA and AOB. While acidification decreased the SP value in the AOB strain, SP values increased to a maximum value of 29‰ in N. oleophilus. In addition, 15N-nitrite tracer experiments showed that acidification boosted nitrite transformation into N2O in all strains, but the incorporation rate was different for each Ammonia oxidizer. Unexpectedly, for N. oleophilus more than 50% of the N2O produced at pH 5.5 had both nitrogen atoms from nitrite and we demonstrated that under these conditions expression of a putative cytochrome P450 NO reductase is strongly upregulated. Collectively, our results indicate that N. oleophilus might be able to enzymatically denitrify nitrite to N2O at low pH.

  • plant growth promoting archaea trigger induced systemic resistance in arabidopsis thaliana against pectobacterium carotovorum and pseudomonas syringae
    Environmental Microbiology, 2019
    Co-Authors: Geun Cheol Song, Hyunjoo Im, Jihye Jung, Manyoung Jung, Sungkeun Rhee
    Abstract:

    : Archaea have inhabited the earth for a long period of time and are ubiquitously distributed in diverse environments. However, few studies have focused on the interactions of archaea with other organisms, including eukaryotes such as plants, since it is difficult to cultivate sufficient numbers of archaeal cells for analysis. In this study, we investigated the interaction between soil archaea and Arabidopsis thaliana. We demonstrate for the first time that soil archaea promote plant growth and trigger induced systemic resistance (ISR) against the necrotrophic bacterium Pectobacterium carotovorum subsp. carotovorum SCC1 and biotrophic bacterium Pseudomonas syringae pv. tomato DC3000. Ammonia-Oxidizing Archaeon Nitrosocosmicus oleophilus MY3 cells clearly colonized the root surface of Arabidopsis plants, and increased resistance against both pathogenic species via the salicylic acid-independent signalling pathway. This mechanism of bacterial resistance resembles that underlying soil bacteria- and fungi-mediated ISR signalling. Additionally, volatile emissions from N. oleophilus MY3 were identified as major archaeal determinants that elicit ISR. Our results lay a foundation for archaea-plant interactions as a new field of research.

  • Plant growth‐promoting archaea trigger induced systemic resistance in Arabidopsis thaliana against Pectobacterium carotovorum and Pseudomonas syringae
    Environmental microbiology, 2019
    Co-Authors: Geun Cheol Song, Jihye Jung, Manyoung Jung, Sungkeun Rhee, Soohyun Lee, Choong-min Ryu
    Abstract:

    Archaea have inhabited the earth for a long period of time and are ubiquitously distributed in diverse environments. However, few studies have focused on the interactions of archaea with other organisms, including eukaryotes such as plants, since it is difficult to cultivate sufficient numbers of archaeal cells for analysis. In this study, we investigated the interaction between soil archaea and Arabidopsis thaliana. We demonstrate for the first time that soil archaea promote plant growth and trigger induced systemic resistance (ISR) against the necrotrophic bacterium Pectobacterium carotovorum subsp. carotovorum SCC1 and biotrophic bacterium Pseudomonas syringae pv. tomato DC3000. Ammonia-Oxidizing Archaeon Nitrosocosmicus oleophilus MY3 cells clearly colonized the root surface of Arabidopsis plants, and increased resistance against both pathogenic species via the salicylic acid-independent signalling pathway. This mechanism of bacterial resistance resembles that underlying soil bacteria- and fungi-mediated ISR signalling. Additionally, volatile emissions from N. oleophilus MY3 were identified as major archaeal determinants that elicit ISR. Our results lay a foundation for archaea-plant interactions as a new field of research.

  • Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, Ammonia-Oxidizing Archaeon member of the phylum Thaumarchaeota isolated from agricultural soil
    International journal of systematic and evolutionary microbiology, 2018
    Co-Authors: Manyoung Jung, Jonggeol Kim, Arafat Islam, Joo-han Gwak, Sungkeun Rhee
    Abstract:

    A mesophilic, chemolithoautotrophic, neutrophilic and aerobic Ammonia-Oxidizing Archaeon, designated strain MY1T, was isolated from agricultural soil. Microscopic observation revealed short, rod-shaped cells with a diameter of 0.3–0.5 µm and length of 0.6–1.0 µm. The isolate had no flagella and pili, and possessed no genes associated with archaeal flagella synthesis. The major membrane lipids consisted mainly of the glycerol dibiphytanyl glycerol tetraether (GDGT) lipids GDGT-0 to GDGT-4 and crenarchaeol. The major intact polar lipids (IPLs) were determined as hexose plus phosphohexose IPL and dihexose IPL. Strain MY1T obtains energy by aerobically Oxidizing Ammonia and carbon by fixing CO2. An optimal growth was observed at 25 °C, at pH 7 and with 0.2–0.4 % (w/v) salinity that corresponds with its terrestrial habitat. The addition of α-keto acids was necessary to stimulate growth. The strain tolerated ammonium and nitrite concentrations up to 10 and 5 mM, respectively. The MY1T genome has a DNA G+C content of 32.7 mol%. Phylogenetic analysis based on the 16S rRNA gene showed that strain MY1T belongs to the family Nitrosopumilaceae of the phylum Thaumarchaeota , sharing the highest 16S rRNA gene sequence similarity (96.6–97.1 %) with marine isolates of the genus Nitrosopumilus . The average nucleotide identity was 78 % between strain MY1T and Nitrosopumilus maritimus SCM1T, indicating distant relatedness. Based on the phenotypic, phylogenetic and genomic analyses, it was concluded that strain MY1T belongs to the novel genus Nitrosarchaeum, under which the name Nitrosarchaeum koreense sp. nov. is proposed as the type species. The type strain is MY1T (=JCM 31640T=KCTC 4249T).

  • A hydrophobic Ammonia-Oxidizing Archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment.
    Environmental microbiology reports, 2016
    Co-Authors: Manyoung Jung, Sojeong Kim, Jonggeol Kim, W. Irene C. Rijpstra, Jaap S. Sinninghe Damsté, Eugene L. Madsen, Heeji Hong, Melina Kerou, Christa Schleper
    Abstract:

    A wide diversity of Ammonia-Oxidizing archaea (AOA) within the phylum Thaumarchaeota exists and plays a key role in the N cycle in a variety of habitats. In this study, we isolated and characterized an Ammonia-Oxidizing Archaeon, strain MY3, from a coal tar-contaminated sediment. Phylogenetically, strain MY3 falls in clade 'Nitrosocosmicus' of the thaumarchaeotal group I.1b. The cells of strain MY3 are large 'walnut-like' cocci, divide by binary fission along a central cingulum, and form aggregates. Strain MY3 is mesophilic and neutrophilic. An assay of 13 C-bicarbonate incorporation into archaeal membrane lipids indicated that strain MY3 is capable of autotrophy. In contrast to some other AOA, TCA cycle intermediates, i.e. pruvate, oxaloacetate and α-ketoglutarate, did not affect the growth rates and yields of strain MY3. The attachment of cells of strain MY3 to XAD-7 hydrophobic beads and to the adsorbent vermiculite demonstrated the potential of strain MY3 to form biofilms. The cell surface was confirmed to be hydrophobic by the extraction of strain MY3 from an aqueous medium with p-xylene. Our finding of a strong potential for surface attachment by strain MY3 may reflect an adaptation to the selective pressures in hydrophobic terrestrial environments.

Steven Ferriera - One of the best experts on this subject based on the ideXlab platform.