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Yuichi Nogi - One of the best experts on this subject based on the ideXlab platform.

  • Psychromonas hadalis sp. nov., a novel piezophilic bacterium isolated from the bottom of the Japan Trench.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Yuichi Nogi, Chiaki Kato, Shoichi Hosoya, Koki Horikoshi
    Abstract:

    An obligately piezophilic bacterium was isolated from sediment collected from the bottom of the Japan Trench at a depth of 7542 m. The isolated strain, designated K41G(T), was closely affiliated with members of the genus Psychromonas on the basis of 16S rRNA gene sequence analysis. Levels of DNA-DNA relatedness between strain K41G(T) and Psychromonas reference strains were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of strain K41G(T) were 6 degrees C and 60 MPa, respectively. The DNA G+C content was 39.1 mol%. Whole-cell fatty acids consisted of significant amounts of unsaturated fatty acids C(16 : 1) (37 %) and C(14 : 1) (17 %), saturated fatty acid C(16 : 0) (31 %) and polyunsaturated fatty acid C(22 : 6) (8 %). Based on the taxonomic differences observed, strain K41G(T) is considered to represent a novel obligately piezophilic Psychromonas species. The name Psychromonas hadalis (type strain, K41G(T)=JCM 11830(T)=ATCC BAA-638(T)) is proposed. This is the second species of obligately piezophilic bacteria to be proposed in the genus Psychromonas.

  • Psychromonas profunda sp. nov., a psychropiezophilic bacterium from deep Atlantic sediments.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Ying Xu, Yuichi Nogi, Chiaki Kato, Ziyuan Liang, Hansjurgen Ruger, Daniel De Kegel, Nicolas Glansdorff
    Abstract:

    A psychropiezophilic bacterium, strain 2825T (=LMG 21260T =JCM 11437T), isolated from deep Atlantic sediments at a depth of 2770 m and a temperature of 2 degrees C, was found by polyphasic analysis to represent a novel species of the genus Psychromonas, Psychromonas profunda sp. nov. It is a strict psychrophile and a moderate piezophile, whose degree of piezophily is increased markedly when the temperature is raised to 10 degrees C. The piezophily of P. profunda is intermediate between that of the type species, Psychromonas antarctica, which is not piezophilic, and that of Psychromonas kaikoae, which is an obligate piezophile.

  • Microbial Life in the Deep Sea: Psychropiezophiles
    Psychrophiles: From Biodiversity to Biotechnology, 2017
    Co-Authors: Yuichi Nogi
    Abstract:

    Psychropiezophiles are microorganisms specialized for living in the deep-sea environment. Piezophiles display maximum growth at high pressure. Some can also grow at atmospheric pressure; those that cannot are referred to as obligatory piezophiles. A temperature change affects deep-sea psychropiezophiles more than a pressure change. Therefore, sample collection and cultivation temperature should be kept low. The preferred method for the long-term preservation and storage of psychropiezophiles is freezing in the vapor phase of liquid nitrogen. Initially, cultures of deep-sea psychropiezophilic bacteria were only species affiliated with one of five genera within the Gammaproteobacteria subgroup: Shewanella, Photobacterium, Colwellia, Moritella, and Psychromonas. However, more recently, species classified as Alphaproteobacteria and Firmicutes have also been found. The genome of several of these bacteria has been analyzed, which revealed characteristic features of these microorganisms. Psychropiezophiles contain unsaturated fatty acids in their cell membrane layers, but the presence of polyunsaturated fatty acids, like eicosapentaenoic acid and docosahexaenoic acid, is not obligatory for growth under high pressure. In the future, along with the development of culture methods and isolation techniques, a variety of other psychropiezophilic species will be discovered and the relationship between pressure and growth of psychropiezophiles will be clarified.

  • Psychromonas japonica sp nov Psychromonas aquimarina sp nov Psychromonas macrocephali sp nov and Psychromonas ossibalaenae sp nov psychrotrophic bacteria isolated from sediment adjacent to sperm whale carcasses off kagoshima japan
    International Journal of Systematic and Evolutionary Microbiology, 2008
    Co-Authors: Masayuki Miyazaki, Yuichi Nogi, Yoshihiro Fujiwara, Koki Horikoshi
    Abstract:

    Four novel species of psychrotrophic bacteria were isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan, at a depth of 228–250 m. Cells of the five isolated strains, JAMM 0394T, JAMM 0404T, JAMM 0415T, JAMM 0700 and JAMM 0738T, were Gram-negative, rod-shaped, non-sporulating and motile by means of a single polar flagellum. The novel strains were able to produce isoprenoid quinone Q-8 as the major component. The predominant fatty acids were C16 : 0 and C16 : 1. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strains represent a separate lineage within the genus Psychromonas. The G+C contents of the novel strains were 38.8–42.8 mol%. DNA–DNA hybridization values between these strains and reference strains of the genus Psychromonas were significantly lower than that generally accepted as the threshold for the phylogenetic definition of species. The names Psychromonas japonica sp. nov. (type strain JAMM 0394T=JCM 14783T=ATCC BAA-1525T), Psychromonas aquimarina sp. nov. (type strain JAMM 0404T=JCM 14784T=ATCC BAA-1526T), Psychromonas macrocephali sp. nov. (two strains, type strain JAMM 0415T=JCM 14785T=ATCC BAA-1527T) and Psychromonas ossibalaenae sp. nov. (type strain JAMM 0738T=JCM 14786T=ATCC BAA-1528T) are proposed.

  • Isolation, Cultivation, and Diversity of Deep-Sea Piezophiles
    High-Pressure Microbiology, 2008
    Co-Authors: Chiaki Kato, Yuichi Nogi, Shizuka Arakawa
    Abstract:

    This chapter focuses on the isolation, taxonomy, and diversity of piezophilic microorganisms and their habitats. Based upon several studies the authors have indicated that cultivated psychrophilic and piezophilic deep-sea bacteria could be affiliated with one of five genera within the Gammaproteobacteria subgroup: Shewanella, Photobacterium, Colwellia, Moritella, and Psychromonas, which was formally classified as ‘’an unidentified genus’’. The chapter describes taxonomic features of the piezophilic genera. For handling piezophiles for further study, JAMSTEC developed a deep-sea baropiezophile and thermophile isolation and cultivation system, referred to as the DEEPBATH system. The DEEPBATH system consists of four separate devices: (1) a pressure-retaining sampling device, (2) a dilution device under pressure conditions, (3) an isolation device, and (4) a cultivation device. From the analyses of 16S rRNA gene sequences after cultivation at 65 MPa, two groups of the bacterial genera Shewanella and Moritella were identified. The authors have analyzed the microbial community structures by the terminal restriction fragment length polymorphism for the bacterial 16S rRNA gene and determined that the community is drastically changed at different pressure conditions of cultivation using the DEEPBATH system. Piezophiles are characterized by high levels of unsaturated fatty acids in their cell membrane layers, but long-chain polyunsaturated fatty acid (PUFA) like EPA and DHA are not necessarily required for high-pressure growth. The diversity of piezophilic bacteria is closely linked with the global deep-sea ocean circulation, but some of the closed oceans, like the Japan Sea, also contain piezophilic bacteria taxonomically similar to deep-sea microbes in the open oceans.

Koki Horikoshi - One of the best experts on this subject based on the ideXlab platform.

  • Psychromonas hadalis sp. nov., a novel piezophilic bacterium isolated from the bottom of the Japan Trench.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Yuichi Nogi, Chiaki Kato, Shoichi Hosoya, Koki Horikoshi
    Abstract:

    An obligately piezophilic bacterium was isolated from sediment collected from the bottom of the Japan Trench at a depth of 7542 m. The isolated strain, designated K41G(T), was closely affiliated with members of the genus Psychromonas on the basis of 16S rRNA gene sequence analysis. Levels of DNA-DNA relatedness between strain K41G(T) and Psychromonas reference strains were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of strain K41G(T) were 6 degrees C and 60 MPa, respectively. The DNA G+C content was 39.1 mol%. Whole-cell fatty acids consisted of significant amounts of unsaturated fatty acids C(16 : 1) (37 %) and C(14 : 1) (17 %), saturated fatty acid C(16 : 0) (31 %) and polyunsaturated fatty acid C(22 : 6) (8 %). Based on the taxonomic differences observed, strain K41G(T) is considered to represent a novel obligately piezophilic Psychromonas species. The name Psychromonas hadalis (type strain, K41G(T)=JCM 11830(T)=ATCC BAA-638(T)) is proposed. This is the second species of obligately piezophilic bacteria to be proposed in the genus Psychromonas.

  • Psychromonas japonica sp nov Psychromonas aquimarina sp nov Psychromonas macrocephali sp nov and Psychromonas ossibalaenae sp nov psychrotrophic bacteria isolated from sediment adjacent to sperm whale carcasses off kagoshima japan
    International Journal of Systematic and Evolutionary Microbiology, 2008
    Co-Authors: Masayuki Miyazaki, Yuichi Nogi, Yoshihiro Fujiwara, Koki Horikoshi
    Abstract:

    Four novel species of psychrotrophic bacteria were isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan, at a depth of 228–250 m. Cells of the five isolated strains, JAMM 0394T, JAMM 0404T, JAMM 0415T, JAMM 0700 and JAMM 0738T, were Gram-negative, rod-shaped, non-sporulating and motile by means of a single polar flagellum. The novel strains were able to produce isoprenoid quinone Q-8 as the major component. The predominant fatty acids were C16 : 0 and C16 : 1. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strains represent a separate lineage within the genus Psychromonas. The G+C contents of the novel strains were 38.8–42.8 mol%. DNA–DNA hybridization values between these strains and reference strains of the genus Psychromonas were significantly lower than that generally accepted as the threshold for the phylogenetic definition of species. The names Psychromonas japonica sp. nov. (type strain JAMM 0394T=JCM 14783T=ATCC BAA-1525T), Psychromonas aquimarina sp. nov. (type strain JAMM 0404T=JCM 14784T=ATCC BAA-1526T), Psychromonas macrocephali sp. nov. (two strains, type strain JAMM 0415T=JCM 14785T=ATCC BAA-1527T) and Psychromonas ossibalaenae sp. nov. (type strain JAMM 0738T=JCM 14786T=ATCC BAA-1528T) are proposed.

  • Psychromonas hadalis sp nov a novel piezophilic bacterium isolated from the bottom of the japan trench
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Yuichi Nogi, Chiaki Kato, Shoichi Hosoya, Koki Horikoshi
    Abstract:

    An obligately piezophilic bacterium was isolated from sediment collected from the bottom of the Japan Trench at a depth of 7542 m. The isolated strain, designated K41GT, was closely affiliated with members of the genus Psychromonas on the basis of 16S rRNA gene sequence analysis. Levels of DNA–DNA relatedness between strain K41GT and Psychromonas reference strains were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of strain K41GT were 6 °C and 60 MPa, respectively. The DNA G+C content was 39.1 mol%. Whole-cell fatty acids consisted of significant amounts of unsaturated fatty acids C16 : 1 (37 %) and C14 : 1 (17 %), saturated fatty acid C16 : 0 (31 %) and polyunsaturated fatty acid C22 : 6 (8 %). Based on the taxonomic differences observed, strain K41GT is considered to represent a novel obligately piezophilic Psychromonas species. The name Psychromonas hadalis (type strain, K41GT=JCM 11830T=ATCC BAA-638T) is proposed. This is the second species of obligately piezophilic bacteria to be proposed in the genus Psychromonas.

  • Psychromonas kaikoae sp nov a novel piezophilic bacterium from the deepest cold seep sediments in the japan trench
    International Journal of Systematic and Evolutionary Microbiology, 2002
    Co-Authors: Yuichi Nogi, Chiaki Kato, Koki Horikoshi
    Abstract:

    Two strains of obligately piezophilic bacteria were isolated from sediment collected from the deepest cold-seep environment with chemosynthesis-based animal communities within the Japan Trench, at a depth of 7434 m. The isolated strains, JT7301 and JT7304 T , were closely affiliated with members of the genus Psychromonas on the basis of 16S rDNA sequence analysis. Hybridization values for DNA-DNA relatedness between these strains and the Psychromonas antarctica reference strain were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of the isolates were 10 °C and 50 MPa and they produced both eicosapentaenoic acid (C20:5ω3) and docosahexaenoic acid (C22:6) in the membrane layer. Based on the taxonomic differences observed, the isolated strains appear to represent a novel obligately piezophilic Psychromonas species. The name Psychromonas kaikoae sp. nov. (type strain JT7304 T = JCM 11054 T = ATCC BAA-363 T ) is proposed. This is the first proposed obligately piezophilic species of the genus Psychromonas.

  • Psychromonas kaikoae sp nov a novel from the deepest piezophilic bacterium cold seep sediments in the japan trench
    International Journal of Systematic and Evolutionary Microbiology, 2002
    Co-Authors: Yuichi Nogi, Chiaki Kato, Koki Horikoshi
    Abstract:

    Two strains of obligately piezophilic bacteria were isolated from sediment collected from the deepest cold-seep environment with chemosynthesis-based animal communities within the Japan Trench, at a depth of 7434 m. The isolated strains, JT7301 and JT7304T, were closely affiliated with members of the genus Psychromonas on the basis of 16S rDNA sequence analysis. Hybridization values for DNA-DNA relatedness between these strains and the Psychromonas antarctica reference strain were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of the isolates were 10 degrees C and 50 MPa and they produced both eicosapentaenoic acid (C20:5omega3) and docosahexaenoic acid (C22:6) in the membrane layer. Based on the taxonomic differences observed, the isolated strains appear to represent a novel obligately piezophilic Psychromonas species. The name Psychromonas kaikoae sp. nov. (type strain JT7304T = JCM 11054T = ATCC BAA-363T) is proposed. This is the first proposed obligately piezophilic species of the genus Psychromonas.

Chiaki Kato - One of the best experts on this subject based on the ideXlab platform.

  • Psychromonas profunda sp. nov., a psychropiezophilic bacterium from deep Atlantic sediments.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Ying Xu, Yuichi Nogi, Chiaki Kato, Ziyuan Liang, Hansjurgen Ruger, Daniel De Kegel, Nicolas Glansdorff
    Abstract:

    A psychropiezophilic bacterium, strain 2825T (=LMG 21260T =JCM 11437T), isolated from deep Atlantic sediments at a depth of 2770 m and a temperature of 2 degrees C, was found by polyphasic analysis to represent a novel species of the genus Psychromonas, Psychromonas profunda sp. nov. It is a strict psychrophile and a moderate piezophile, whose degree of piezophily is increased markedly when the temperature is raised to 10 degrees C. The piezophily of P. profunda is intermediate between that of the type species, Psychromonas antarctica, which is not piezophilic, and that of Psychromonas kaikoae, which is an obligate piezophile.

  • Psychromonas hadalis sp. nov., a novel piezophilic bacterium isolated from the bottom of the Japan Trench.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Yuichi Nogi, Chiaki Kato, Shoichi Hosoya, Koki Horikoshi
    Abstract:

    An obligately piezophilic bacterium was isolated from sediment collected from the bottom of the Japan Trench at a depth of 7542 m. The isolated strain, designated K41G(T), was closely affiliated with members of the genus Psychromonas on the basis of 16S rRNA gene sequence analysis. Levels of DNA-DNA relatedness between strain K41G(T) and Psychromonas reference strains were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of strain K41G(T) were 6 degrees C and 60 MPa, respectively. The DNA G+C content was 39.1 mol%. Whole-cell fatty acids consisted of significant amounts of unsaturated fatty acids C(16 : 1) (37 %) and C(14 : 1) (17 %), saturated fatty acid C(16 : 0) (31 %) and polyunsaturated fatty acid C(22 : 6) (8 %). Based on the taxonomic differences observed, strain K41G(T) is considered to represent a novel obligately piezophilic Psychromonas species. The name Psychromonas hadalis (type strain, K41G(T)=JCM 11830(T)=ATCC BAA-638(T)) is proposed. This is the second species of obligately piezophilic bacteria to be proposed in the genus Psychromonas.

  • Isolation, Cultivation, and Diversity of Deep-Sea Piezophiles
    High-Pressure Microbiology, 2008
    Co-Authors: Chiaki Kato, Yuichi Nogi, Shizuka Arakawa
    Abstract:

    This chapter focuses on the isolation, taxonomy, and diversity of piezophilic microorganisms and their habitats. Based upon several studies the authors have indicated that cultivated psychrophilic and piezophilic deep-sea bacteria could be affiliated with one of five genera within the Gammaproteobacteria subgroup: Shewanella, Photobacterium, Colwellia, Moritella, and Psychromonas, which was formally classified as ‘’an unidentified genus’’. The chapter describes taxonomic features of the piezophilic genera. For handling piezophiles for further study, JAMSTEC developed a deep-sea baropiezophile and thermophile isolation and cultivation system, referred to as the DEEPBATH system. The DEEPBATH system consists of four separate devices: (1) a pressure-retaining sampling device, (2) a dilution device under pressure conditions, (3) an isolation device, and (4) a cultivation device. From the analyses of 16S rRNA gene sequences after cultivation at 65 MPa, two groups of the bacterial genera Shewanella and Moritella were identified. The authors have analyzed the microbial community structures by the terminal restriction fragment length polymorphism for the bacterial 16S rRNA gene and determined that the community is drastically changed at different pressure conditions of cultivation using the DEEPBATH system. Piezophiles are characterized by high levels of unsaturated fatty acids in their cell membrane layers, but long-chain polyunsaturated fatty acid (PUFA) like EPA and DHA are not necessarily required for high-pressure growth. The diversity of piezophilic bacteria is closely linked with the global deep-sea ocean circulation, but some of the closed oceans, like the Japan Sea, also contain piezophilic bacteria taxonomically similar to deep-sea microbes in the open oceans.

  • Psychromonas hadalis sp nov a novel piezophilic bacterium isolated from the bottom of the japan trench
    International Journal of Systematic and Evolutionary Microbiology, 2007
    Co-Authors: Yuichi Nogi, Chiaki Kato, Shoichi Hosoya, Koki Horikoshi
    Abstract:

    An obligately piezophilic bacterium was isolated from sediment collected from the bottom of the Japan Trench at a depth of 7542 m. The isolated strain, designated K41GT, was closely affiliated with members of the genus Psychromonas on the basis of 16S rRNA gene sequence analysis. Levels of DNA–DNA relatedness between strain K41GT and Psychromonas reference strains were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of strain K41GT were 6 °C and 60 MPa, respectively. The DNA G+C content was 39.1 mol%. Whole-cell fatty acids consisted of significant amounts of unsaturated fatty acids C16 : 1 (37 %) and C14 : 1 (17 %), saturated fatty acid C16 : 0 (31 %) and polyunsaturated fatty acid C22 : 6 (8 %). Based on the taxonomic differences observed, strain K41GT is considered to represent a novel obligately piezophilic Psychromonas species. The name Psychromonas hadalis (type strain, K41GT=JCM 11830T=ATCC BAA-638T) is proposed. This is the second species of obligately piezophilic bacteria to be proposed in the genus Psychromonas.

  • Psychromonas profunda sp nov a psychropiezophilic bacterium from deep atlantic sediments
    International Journal of Systematic and Evolutionary Microbiology, 2003
    Co-Authors: Ying Xu, Yuichi Nogi, Chiaki Kato, Ziyuan Liang, Hansjurgen Ruger, Daniel De Kegel, Nicolas Glansdorff
    Abstract:

    A psychropiezophilic bacterium, strain 2825T (=LMG 21260T =JCM 11437T), isolated from deep Atlantic sediments at a depth of 2770 m and a temperature of 2 °C, was found by polyphasic analysis to represent a novel species of the genus Psychromonas, Psychromonas profunda sp. nov. It is a strict psychrophile and a moderate piezophile, whose degree of piezophily is increased markedly when the temperature is raised to 10 °C. The piezophily of P. profunda is intermediate between that of the type species, Psychromonas antarctica, which is not piezophilic, and that of Psychromonas kaikoae, which is an obligate piezophile.

Hiroaki Kasai - One of the best experts on this subject based on the ideXlab platform.

  • Psychromonas agarivorans sp. nov., a novel agarolytic bacterium.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Shoichi Hosoya, Jaehyuk Jang, Satoru Matsuda, Mina Yasumoto-hirose, Hiroaki Kasai
    Abstract:

    Two heterotrophic, agarolytic bacteria were isolated from marine environments. A 16S rRNA gene sequence analysis showed the isolates (designated strains J42-3A(T) and 04OZ-AS15-7A) to be positioned in a separate lineage within the genus Psychromonas. Members of the genus Psychromonas are recognized as being psychrophilic or psychrotolerant, whereas none of the currently established Psychromonas species is known to be agarolytic. The DNA G+C contents of the isolates were about 42 mol% and the predominant cellular fatty acids were 16 : 1omega7c and 16 : 0. Based on the results of the phylogenetic and phenotypic analyses and DNA-DNA hybridization data, the isolates represent a novel species, for which the name Psychromonas agarivorans sp. nov. is proposed. The type strain is J42-3A(T) (=NBRC 104585(T)=KCTC 22285(T)).

  • Psychromonas heitensis sp. nov., a psychrotolerant bacterium isolated from seawater in Japan.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Shoichi Hosoya, Mina Yasumoto-hirose, Kyoko Adachi, Atsuko Katsuta, Hiroaki Kasai
    Abstract:

    Four bacterial strains, 04HE-4-40, A4I-9, A4I-21 and AK15-027(T), were isolated from Heita Bay off Kamaishi in Japan. Based on 16S rRNA gene sequence analysis, the isolates were placed as a new lineage within the genus Psychromonas. The 16S rRNA gene sequence similarity values between the isolates and type strains of recognized Psychromonas species were less than 97 %. The DNA G+C contents of the isolates were about 38 mol%. The major respiratory quinone was Q-8, and the predominant cellular fatty acids were 16 : 1omega7c and 16 : 0. The isolates were able to grow at 30 degrees C, unlike other Psychromonas species. Based on the results of the phylogenetic analysis and phenotypic characteristics and DNA-DNA hybridization data, the isolates represent a novel species, for which the name Psychromonas heitensis sp. nov. is proposed. The type strain is AK15-027(T) (=MBIC 06898(T)=NCIMB 14416(T)).

  • Psychromonas agarivorans sp nov a novel agarolytic bacterium
    International Journal of Systematic and Evolutionary Microbiology, 2009
    Co-Authors: Shoichi Hosoya, Jaehyuk Jang, Mina Yasumotohirose, Satoru Matsuda, Hiroaki Kasai
    Abstract:

    Two heterotrophic, agarolytic bacteria were isolated from marine environments. A 16S rRNA gene sequence analysis showed the isolates (designated strains J42-3AT and 04OZ-AS15-7A) to be positioned in a separate lineage within the genus Psychromonas. Members of the genus Psychromonas are recognized as being psychrophilic or psychrotolerant, whereas none of the currently established Psychromonas species is known to be agarolytic. The DNA G+C contents of the isolates were about 42 mol% and the predominant cellular fatty acids were 16 : 1ω7c and 16 : 0. Based on the results of the phylogenetic and phenotypic analyses and DNA–DNA hybridization data, the isolates represent a novel species, for which the name Psychromonas agarivorans sp. nov. is proposed. The type strain is J42-3AT (=NBRC 104585T=KCTC 22285T).

  • Psychromonas heitensis sp nov a psychrotolerant bacterium isolated from seawater in japan
    International Journal of Systematic and Evolutionary Microbiology, 2008
    Co-Authors: Shoichi Hosoya, Mina Yasumotohirose, Kyoko Adachi, Atsuko Katsuta, Hiroaki Kasai
    Abstract:

    Four bacterial strains, 04HE-4-40, A4I-9, A4I-21 and AK15-027T, were isolated from Heita Bay off Kamaishi in Japan. Based on 16S rRNA gene sequence analysis, the isolates were placed as a new lineage within the genus Psychromonas. The 16S rRNA gene sequence similarity values between the isolates and type strains of recognized Psychromonas species were less than 97 %. The DNA G+C contents of the isolates were about 38 mol%. The major respiratory quinone was Q-8, and the predominant cellular fatty acids were 16 : 1ω7c and 16 : 0. The isolates were able to grow at 30 °C, unlike other Psychromonas species. Based on the results of the phylogenetic analysis and phenotypic characteristics and DNA–DNA hybridization data, the isolates represent a novel species, for which the name Psychromonas heitensis sp. nov. is proposed. The type strain is AK15-027T (=MBIC 06898T=NCIMB 14416T).

James T. Staley - One of the best experts on this subject based on the ideXlab platform.

  • Psychromonas ingrahamii sp. nov., a novel gas vacuolate, psychrophilic bacterium isolated from Arctic polar sea ice.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Ann J Auman, Peter Kampfer, Jennifer L Breezee, John J Gosink, James T. Staley
    Abstract:

    A gas vacuolate bacterium, designated strain 37T, was isolated from a sea ice core collected from Point Barrow, Alaska, USA. Cells of strain 37T were large (6-14 microm in length), rod-shaped, contained gas vacuoles of two distinct morphologies, and grew well at NaCl concentrations of 1-10 % and at temperatures of -12 to 10 degrees C. The DNA G+C content was 40 mol%. Whole-cell fatty acid analysis showed that 16 : 1omega7c comprised 67 % of the total fatty acid content. Phylogenetic analysis of 16S rRNA gene sequences indicated that this bacterium was closely related to members of the genus Psychromonas, with highest sequence similarity (96.8 %) to Psychromonas antarctica. Phenotypic analysis differentiated strain 37T from P. antarctica on the basis of several characteristics, including cell morphology, growth temperature range and the ability to hydrolyse polymers. DNA-DNA hybridization experiments revealed a level of relatedness of 37 % between strain 37T and P. antarctica, providing further support that it represents a distinct species. The name Psychromonas ingrahamii sp. nov. is proposed for this novel species. The type strain is 37T (=CCUG 51855T=CIP 108865T).

  • Psychromonas boydii sp nov a gas vacuolate psychrophilic bacterium isolated from an arctic sea ice core
    International Journal of Systematic and Evolutionary Microbiology, 2010
    Co-Authors: Ann J Auman, Peter Kampfer, Jennifer L Breezee, John J Gosink, Peter Schumann, Carmen R Barnes, James T. Staley
    Abstract:

    A gas-vacuolate bacterium, strain 174T, was isolated from a sea-ice core collected from Point Barrow, Alaska, USA. Comparative analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to Psychromonas ingrahamii 37T, with a similarity of >99 %. However, strain 174T could be clearly distinguished from closely related species by DNA–DNA hybridization; relatedness values determined by two different methods between strain 174T and P. ingrahamii 37T were 58.4 and 55.7 % and those between strain 174T and Psychromonas antarctica DSM 10704T were 46.1 and 33.1 %, which are well below the 70 % level used to define a distinct species. Phenotypic analysis, including cell size (strain 174T is the largest member of the genus Psychromonas, with rod-shaped cells, 8–18 μm long), further differentiated strain 174T from other members of the genus Psychromonas. Strain 174T could be distinguished from its closest relative, P. ingrahamii, by its utilization of d-mannose and d-xylose as sole carbon sources, its ability to ferment myo-inositol and its inability to use fumarate and glycerol as sole carbon sources. In addition, strain 174T contained gas vacuoles of two distinct morphologies and grew at temperatures ranging from below 0 to 10 °C and its optimal NaCl concentration for growth was 3.5 %. The DNA G+C content was 40 mol%. Whole-cell fatty acid analysis showed that 16 : 1ω7c and 16 : 0 comprised 44.9 and 26.4 % of the total fatty acid content, respectively. The name Psychromonas boydii sp. nov. is proposed for this novel species, with strain 174T (=DSM 17665T =CCM 7498T) as the type strain.

  • Psychromonas boydii sp. nov., a gas-vacuolate, psychrophilic bacterium isolated from an Arctic sea-ice core.
    International journal of systematic and evolutionary microbiology, 2009
    Co-Authors: Ann J Auman, Peter Kampfer, Jennifer L Breezee, John J Gosink, Peter Schumann, Carmen R Barnes, James T. Staley
    Abstract:

    A gas-vacuolate bacterium, strain 174(T), was isolated from a sea-ice core collected from Point Barrow, Alaska, USA. Comparative analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to Psychromonas ingrahamii 37(T), with a similarity of >99 %. However, strain 174(T) could be clearly distinguished from closely related species by DNA-DNA hybridization; relatedness values determined by two different methods between strain 174(T) and P. ingrahamii 37(T) were 58.4 and 55.7 % and those between strain 174(T) and Psychromonas antarctica DSM 10704(T) were 46.1 and 33.1 %, which are well below the 70 % level used to define a distinct species. Phenotypic analysis, including cell size (strain 174(T) is the largest member of the genus Psychromonas, with rod-shaped cells, 8-18 microm long), further differentiated strain 174(T) from other members of the genus Psychromonas. Strain 174(T) could be distinguished from its closest relative, P. ingrahamii, by its utilization of D-mannose and D-xylose as sole carbon sources, its ability to ferment myo-inositol and its inability to use fumarate and glycerol as sole carbon sources. In addition, strain 174(T) contained gas vacuoles of two distinct morphologies and grew at temperatures ranging from below 0 to 10 degrees C and its optimal NaCl concentration for growth was 3.5 %. The DNA G+C content was 40 mol%. Whole-cell fatty acid analysis showed that 16 : 1omega7c and 16 : 0 comprised 44.9 and 26.4 % of the total fatty acid content, respectively. The name Psychromonas boydii sp. nov. is proposed for this novel species, with strain 174(T) (=DSM 17665(T) =CCM 7498(T)) as the type strain.

  • Genomics of an extreme psychrophile, Psychromonas ingrahamii
    BMC Genomics, 2008
    Co-Authors: Monica Riley, James T. Staley, Antoine Danchin, Ting Zhang Wang, Thomas Brettin, Loren Hauser, Miriam Land, Linda S. Thompson
    Abstract:

    Background The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles.

  • Genomics of an extreme psychrophile, Psychromonas ingrahamii
    BMC Genomics, 2008
    Co-Authors: Monica Riley, James T. Staley, Antoine Danchin, Ting Zhang Wang, Thomas Brettin, Loren J Hauser, Miriam L Land, Linda S. Thompson
    Abstract:

    Background The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Results Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. Conclusion The results of this genomic analysis provide a springboard for further investigations into mechanisms of psychrophily. Focus on the role of asparagine excess in proteins, targeted phenotypic characterizations and gene expression investigations are needed to ascertain if and how the organism regulates various proteins in response to growth at lower temperatures.