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Elena P Ivanova - One of the best experts on this subject based on the ideXlab platform.

  • A new family of Alteromonadaceae fam. nov., including the marine proteobacteria species Alteromonas, PseudoAlteromonas, Idiomarina i Colwellia
    Microbiology, 2020
    Co-Authors: Elena P Ivanova, Mikhaĭlov Vv
    Abstract:

    : The taxonomic position of the marine genera Alteromonas, PseudoAlteromonas, Idiomarina, and Colwellia within the gamma subclass of the class Proteobacteria were specified on the basis of their phenotypic, genotypic, and phylogenetic characteristics. Gram-negative aerobic bacteria of the genera Alteromonas, PseudoAlteromonas, and Idiomarina and facultatively anaerobic bacteria of the genus Colwellia were found to form a phylogenetic cluster with a 16S rRNA sequence homology of 90% or higher. The characteristics of these genera presented in this paper allow their reliable taxonomic identification. Based on the analysis of our experimental data and analyses available in the literature, we propose to combine the genera Alteromonas, PseudoAlteromonas, Idiomarina, and Colwellia into a new family, Alteromonadaceae fam. nov., with the type genus Alteromonas.

  • ecophysiological diversity of a novel member of the genus Alteromonas and description of Alteromonas mediterranea sp nov
    Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2015
    Co-Authors: Elena P Ivanova, Hayden K. Webb, Russell J. Crawford, Mario Lopezperez, Mila Zabalos, Song Ha Nguyen, Jason Ryan, Kiril Lagutin, Mikhail Vyssotski, Francisco Rodriguezvalera
    Abstract:

    Nine non-pigmented, motile, Gram-negative bacteria originally designated as Alteromonas macleodii deep-sea ecotypes, were isolated from seawater samples collected from four separate locations; two deep-sea sites in the Mediterranean Sea and surface water of the Aegean Sea and English Channel. The six strains studied in vitro were found to tolerate up to 20 % NaCl. The DNA–DNA relatedness between the deep-sea ecotype strains was found to be between 75 and 89 %, whilst relatedness with the validly named Alteromonas species was found to be between 31 and 69 %. The average nucleotide identity (ANI) amongst the deep-sea ecotype strains was found to be 98–100 %; the in silico genome-to-genome distance (GGD), 85–100 %; the average amino acid identity (AAI) of all conserved protein-coding genes, 95–100 %; and the strains possessed 30–32 of the Karlin’s genomic signature dissimilarity. The ANI between the deep-sea ecotype strains and A. macleodii ATCC 27126T and Alteromonas australica H 17T was found to be 80.6 and 74.6 %, respectively. A significant correlation was observed between the phenotypic data obtained in vitro and data retrieved in silico from whole genome sequences. The results of a phylogenetic study that incorporated a 16S rRNA gene sequence analysis, multilocus phylogenetic analysis (MLPA) and genomic analysis, together with the physiological, biochemical and chemotaxonomic data, clearly indicated that the group of deep-sea ecotype strains represents a distinct species within the genus Alteromonas. Based on these data, a new species, Alteromonas mediterranea, is proposed. The type strain is DET ( = CIP 110805T = LMG 28347T = DSM 17117T).

  • genomes of Alteromonas australica a world apart
    BMC Genomics, 2014
    Co-Authors: Mario Lopezperez, Elena P Ivanova, Aitor Gonzaga, Francisco Rodriguezvalera
    Abstract:

    Alteromonas is a genus of marine bacteria that is very easy to isolate and grow in the laboratory. There are genomes available of the species Alteromonas macleodii from different locations around the world and an Alteromonas sp. isolated from a sediment in Korea. We have analyzed the genomes of two strains classified by 16S rRNA (>99% similarity) as the recently described species Alteromonas australica, and isolated from opposite ends of the world; A. australica DE170 was isolated in the South Adriatic (Mediterranean) at 1000 m depth while A. australica H17T was isolated from a sea water sample collected in St Kilda Beach, Tasman Sea. Although these two strains belong to a clearly different species from A. macleodii, the overall synteny is well preserved and the flexible genomic islands seem to code for equivalent functions and be located at similar positions. Actually the genomes of all the Alteromonas species known to date seem to preserve synteny quite well with the only exception of the sediment isolate SN2. Among the specific metabolic features found for the A. australica isolates there is the degradation of xylan and production of cellulose as extracellular polymeric substance by DE170 or the potential ethanol/methanol degradation by H17T. The genomes of the two A. australica isolates are not more different than those of strains of A. macleodii isolated from the same sample. Actually the recruitment from metagenomes indicates that all the available genomes are found in most tropical-temperate marine samples analyzed and that they live in consortia of several species and multiple clones within each. Overall the hydrolytic activities of the Alteromonas genus as a whole are impressive and fit with its known capabilities to exploit sudden inputs of organic matter in their environment.

  • Updating the taxonomic toolbox: classification of Alteromonas spp. using multilocus phylogenetic analysis and MALDI-TOF mass spectrometry
    Antonie van Leeuwenhoek, 2013
    Co-Authors: Hooi Jun Ng, Valery V Mikhailov, Hayden K. Webb, Russell J. Crawford, François Malherbe, Henry Butt, Rachel Knight, Elena P Ivanova
    Abstract:

    Bacteria of the genus Alteromonas are Gram-negative, strictly aerobic, motile, heterotrophic marine bacteria known for their versatile metabolic activities. Identification and classification of novel species belonging to the genus Alteromonas generally involves DNA–DNA hybridization (DDH) as distinct species often fail to be resolved at the 97 % threshold value of the 16S rRNA gene sequence similarity. In this study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for the differentiation of Alteromonas species has been evaluated. Phylogenetic analysis incorporating five house-keeping genes ( dnaK , sucC , rpoB , gyrB , and rpoD ) revealed a threshold value of 98.9 % that could be considered as the species cut-off value for the delineation of Alteromonas spp. MALDI-TOF MS data analysis reconfirmed the Alteromonas species clustering. MLPA and MALDI-TOF MS both generated data that were comparable to that of the 16S rRNA gene sequence analysis and may be considered as useful complementary techniques for the description of new Alteromonas species.

  • Alteromonas australica sp nov isolated from the tasman sea
    Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2013
    Co-Authors: Elena P Ivanova, Natalia V Zhukova, Valery V Mikhailov, Hooi Jun Ng, Hayden K. Webb, Valeriya V Kurilenko, O N Ponamoreva, Russell J. Crawford
    Abstract:

    A non-pigmented, motile, Gram-negative bacterium designated H 17T was isolated from a seawater sample collected in Port Phillip Bay (the Tasman Sea, Pacific Ocean). The new organism displayed optimal growth between 4 and 37 °C, was found to be neutrophilic and slightly halophilic, tolerating salt water environments up to 10 % NaCl. Strain H 17T was found to be able to degrade starch and Tween 80 but unable to degrade gelatin or agar. Phosphatidylglycerol (27.7 %) and phosphatidylethanolamine (72.3 %) were found to be the only associated phospholipids. The major fatty acids identified are typical for the genus Alteromonas and include C16:0, C16:1ω7, C17:1ω8 and C18:1ω7. The G+C content of the DNA was found to be 43.4 mol%. A phylogenetic study, based on the 16S rRNA gene sequence analysis and Multilocus Phylogenetic Analysis, clearly indicated that strain H 17T belongs to the genus Alteromonas. The DNA−DNA relatedness between strain H 17T and the validly named Alteromonas species was between 30.7 and 46.4 mol%. Based on these results, a new species, Alteromonas australica, is proposed. The type strain is H 17T (= KMM 6016T = CIP 109921T).

Junghoon Yoon - One of the best experts on this subject based on the ideXlab platform.

  • Alteromonas litorea sp. nov., a slightly halophilic bacterium isolated from an intertidal sediment of the Yellow Sea in Korea.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Junghoon Yoon, Taekwang Oh, Yongha Park
    Abstract:

    A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30-37 degrees C and in the presence of 2-5% (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14% (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C(16 : 0), C(16 : 1) omega7c and/or iso-C(15 : 0) 2-OH and C(18 : 1) omega7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46.0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the gamma-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98.1-98.6%. The level of DNA-DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15.7-18.5%. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22TT (=KCCM 41775T=JCM 12188T).

  • Alteromonas marina sp. nov., isolated from sea water of the East Sea in Korea.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Junghoon Yoon, Taekwang Oh, Kook Hee Kang, Yongha Park
    Abstract:

    Two Gram-negative, motile, non-spore-forming and moderately halophilic rods (strains SW-47(T) and SW-49) were isolated from sea water of the East Sea in Korea and subjected to a polyphasic taxonomic study. The two strains grew optimally between 30 and 37 degrees C, and grew at 4 and 44 degrees C but not at temperatures above 45 degrees C. They grew optimally in the presence of 2-5 % (w/v) NaCl, but did not grow in the absence of NaCl. Strains SW-47(T) and SW-49 had ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and C(16 : 1) omega7c and/or iso-C(15 : 0) 2OH, C(16 : 0) and C(18 : 1) omega7c as the major fatty acids, which are consistent with the corresponding data for Alteromonas macleodii. The DNA G+C contents of strains SW-47(T) and SW-49 were 45 and 44 mol%, respectively. Strains SW-47(T) and SW-49 showed a high level of 16S rDNA sequence similarity (99.9 %) and a mean level of DNA-DNA relatedness of 96.5 %. Phylogenetic analyses based on 16S rDNA sequences showed that the two strains form a coherent cluster with A. macleodii. Strains SW-47(T) and SW-49 exhibited levels of 16S rDNA sequence similarity of 99.3 and 99.1 %, respectively, with A. macleodii DSM 6062(T) and of less than 89.4 % with other species used in the phylogenetic analyses. Alteromonas fuliginea CIP 105339(T) was found to be more closely related to the genus PseudoAlteromonas than to the genus Alteromonas: On the basis of phenotypic properties and phylogenetic and genomic data, strains SW-47(T) and SW-49 represent a new species of the genus Alteromonas, for which the name Alteromonas marina (type strain SW-47(T)=KCCM 41638(T)=JCM 11804(T)) is proposed.

  • Alteromonas aestuariivivens sp nov isolated from a tidal flat
    International Journal of Systematic and Evolutionary Microbiology, 2017
    Co-Authors: Sooyeon Park, Su Jung Choi, Jimin Park, Junghoon Yoon
    Abstract:

    A Gram-stain-negative, aerobic, non-spore-forming, motile and ovoid or rod-shaped bacterial strain, JDTF-113T, was isolated from a tidal flat in Jindo, an island of South Korea. Strain JDTF-113T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, revealed that strain JDTF-113T fell within the clade enclosing the type strains of species of the genus Alteromonas . Strain JDTF-113T exhibited 16S rRNA gene sequence similarity values of 97.1–98.1 % to the type strains of Alteromonas lipolytica , Alteromonas litorea , Alteromonas mediterranea , Alteromonas confluentis , Alteromonas hispanica , Alteromonas genovensis and Alteromonas marina , and of 94.8–96.9 % to those of the other species of the genus Alteromonas . Strain JDTF-113T contained Q-8 as the predominant ubiquinone and C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C18 : 1ω7c as the major fatty acids. The major polar lipids of strain JDTF-113T were phosphatidylethanolamine, phosphatidylglycerol and one unidentified glycolipid. The DNA G+C content of strain JDTF-113T was 51.1 mol% and its mean DNA–DNA relatedness values with the type strains of seven closely phylogenetically related species of the genus Alteromonas were was 10–23 %. The differential phenotypic properties and phylogenetic and genetic distinctiveness support strain JDTF-113T being separated from species of the genus Alteromonas with validly published names . On the basis of the data presented, strain JDTF-113T is considered to represent a novel species of the genus Alteromonas , for which the name Alteromonas aestuariivivens sp. nov. is proposed. The type strain is JDTF-113T (=KCTC 52655T=NBRC 112708T).

  • Alteromonas confluentis sp nov isolated from the junction between the ocean and a freshwater spring
    International Journal of Systematic and Evolutionary Microbiology, 2015
    Co-Authors: Sooyeon Park, Jimin Park, Chulhyung Kang, Junghoon Yoon
    Abstract:

    A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, DSSK2-12T, was isolated from the place where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain DSSK2-12T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain DSSK2-12T fell within the clade comprising the type strains of species of the genus Alteromonas. Strain DSSK2-12T exhibited 16S rRNA gene sequence similarity values of 97.2–98.1 % to the type strains of Alteromonas litorea, Alteromonas marina, Alteromonas hispanica and Alteromonas genovensis and of 95.39–96.98 % to those of other species of the genus Alteromonas. Strain DSSK2-12T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the major fatty acids. The major polar lipids of strain DSSK2-12T were phosphatidylethanolamine, phosphatidylglycerol and one unidentified aminolipid. The DNA G+C content of strain DSSK2-12T was 48.6 mol% and its mean DNA–DNA relatedness values with the type strains of A. litorea, A. marina, A. hispanica and A. genovensis were 9–21 %. The differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain DSSK2-12T is separated from other species of the genus Alteromonas. On the basis of the data presented, strain DSSK2-12T is considered to represent a novel species of the genus Alteromonas, for which the name Alteromonas confluentis sp. nov. is proposed. The type strain is DSSK2-12T ( = KCTC 42603T = CECT 8870T).

  • Alteromonas litorea sp nov a slightly halophilic bacterium isolated from an intertidal sediment of the yellow sea in korea
    International Journal of Systematic and Evolutionary Microbiology, 2004
    Co-Authors: Junghoon Yoon, Taekwang Oh, Yongha Park
    Abstract:

    A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30–37 °C and in the presence of 2–5 % (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14 % (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46·0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the γ-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98·1–98·6 %. The level of DNA–DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15·7–18·5 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22T (=KCCM 41775T=JCM 12188T).

Yongha Park - One of the best experts on this subject based on the ideXlab platform.

  • Alteromonas litorea sp. nov., a slightly halophilic bacterium isolated from an intertidal sediment of the Yellow Sea in Korea.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Junghoon Yoon, Taekwang Oh, Yongha Park
    Abstract:

    A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30-37 degrees C and in the presence of 2-5% (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14% (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C(16 : 0), C(16 : 1) omega7c and/or iso-C(15 : 0) 2-OH and C(18 : 1) omega7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46.0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the gamma-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98.1-98.6%. The level of DNA-DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15.7-18.5%. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22TT (=KCCM 41775T=JCM 12188T).

  • Alteromonas marina sp. nov., isolated from sea water of the East Sea in Korea.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Junghoon Yoon, Taekwang Oh, Kook Hee Kang, Yongha Park
    Abstract:

    Two Gram-negative, motile, non-spore-forming and moderately halophilic rods (strains SW-47(T) and SW-49) were isolated from sea water of the East Sea in Korea and subjected to a polyphasic taxonomic study. The two strains grew optimally between 30 and 37 degrees C, and grew at 4 and 44 degrees C but not at temperatures above 45 degrees C. They grew optimally in the presence of 2-5 % (w/v) NaCl, but did not grow in the absence of NaCl. Strains SW-47(T) and SW-49 had ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and C(16 : 1) omega7c and/or iso-C(15 : 0) 2OH, C(16 : 0) and C(18 : 1) omega7c as the major fatty acids, which are consistent with the corresponding data for Alteromonas macleodii. The DNA G+C contents of strains SW-47(T) and SW-49 were 45 and 44 mol%, respectively. Strains SW-47(T) and SW-49 showed a high level of 16S rDNA sequence similarity (99.9 %) and a mean level of DNA-DNA relatedness of 96.5 %. Phylogenetic analyses based on 16S rDNA sequences showed that the two strains form a coherent cluster with A. macleodii. Strains SW-47(T) and SW-49 exhibited levels of 16S rDNA sequence similarity of 99.3 and 99.1 %, respectively, with A. macleodii DSM 6062(T) and of less than 89.4 % with other species used in the phylogenetic analyses. Alteromonas fuliginea CIP 105339(T) was found to be more closely related to the genus PseudoAlteromonas than to the genus Alteromonas: On the basis of phenotypic properties and phylogenetic and genomic data, strains SW-47(T) and SW-49 represent a new species of the genus Alteromonas, for which the name Alteromonas marina (type strain SW-47(T)=KCCM 41638(T)=JCM 11804(T)) is proposed.

  • Alteromonas litorea sp nov a slightly halophilic bacterium isolated from an intertidal sediment of the yellow sea in korea
    International Journal of Systematic and Evolutionary Microbiology, 2004
    Co-Authors: Junghoon Yoon, Taekwang Oh, Yongha Park
    Abstract:

    A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30–37 °C and in the presence of 2–5 % (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14 % (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46·0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the γ-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98·1–98·6 %. The level of DNA–DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15·7–18·5 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22T (=KCCM 41775T=JCM 12188T).

  • Alteromonas marina sp nov isolated from sea water of the east sea in korea
    International Journal of Systematic and Evolutionary Microbiology, 2003
    Co-Authors: Junghoon Yoon, Taekwang Oh, Kook Hee Kang, Yongha Park
    Abstract:

    Two Gram-negative, motile, non-spore-forming and moderately halophilic rods (strains SW-47T and SW-49) were isolated from sea water of the East Sea in Korea and subjected to a polyphasic taxonomic study. The two strains grew optimally between 30 and 37 °C, and grew at 4 and 44 °C but not at temperatures above 45 °C. They grew optimally in the presence of 2–5 % (w/v) NaCl, but did not grow in the absence of NaCl. Strains SW-47T and SW-49 had ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and C16 : 1 ω7c and/or iso-C15 : 0 2OH, C16 : 0 and C18 : 1 ω7c as the major fatty acids, which are consistent with the corresponding data for Alteromonas macleodii. The DNA G+C contents of strains SW-47T and SW-49 were 45 and 44 mol%, respectively. Strains SW-47T and SW-49 showed a high level of 16S rDNA sequence similarity (99·9 %) and a mean level of DNA–DNA relatedness of 96·5 %. Phylogenetic analyses based on 16S rDNA sequences showed that the two strains form a coherent cluster with A. macleodii. Strains SW-47T and SW-49 exhibited levels of 16S rDNA sequence similarity of 99·3 and 99·1 %, respectively, with A. macleodii DSM 6062T and of less than 89·4 % with other species used in the phylogenetic analyses. Alteromonas fuliginea CIP 105339T was found to be more closely related to the genus PseudoAlteromonas than to the genus Alteromonas. On the basis of phenotypic properties and phylogenetic and genomic data, strains SW-47T and SW-49 represent a new species of the genus Alteromonas, for which the name Alteromonas marina (type strain SW-47T=KCCM 41638T=JCM 11804T) is proposed.

Taekwang Oh - One of the best experts on this subject based on the ideXlab platform.

  • Alteromonas litorea sp. nov., a slightly halophilic bacterium isolated from an intertidal sediment of the Yellow Sea in Korea.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Junghoon Yoon, Taekwang Oh, Yongha Park
    Abstract:

    A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30-37 degrees C and in the presence of 2-5% (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14% (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C(16 : 0), C(16 : 1) omega7c and/or iso-C(15 : 0) 2-OH and C(18 : 1) omega7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46.0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the gamma-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98.1-98.6%. The level of DNA-DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15.7-18.5%. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22TT (=KCCM 41775T=JCM 12188T).

  • Alteromonas marina sp. nov., isolated from sea water of the East Sea in Korea.
    International journal of systematic and evolutionary microbiology, 2020
    Co-Authors: Junghoon Yoon, Taekwang Oh, Kook Hee Kang, Yongha Park
    Abstract:

    Two Gram-negative, motile, non-spore-forming and moderately halophilic rods (strains SW-47(T) and SW-49) were isolated from sea water of the East Sea in Korea and subjected to a polyphasic taxonomic study. The two strains grew optimally between 30 and 37 degrees C, and grew at 4 and 44 degrees C but not at temperatures above 45 degrees C. They grew optimally in the presence of 2-5 % (w/v) NaCl, but did not grow in the absence of NaCl. Strains SW-47(T) and SW-49 had ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and C(16 : 1) omega7c and/or iso-C(15 : 0) 2OH, C(16 : 0) and C(18 : 1) omega7c as the major fatty acids, which are consistent with the corresponding data for Alteromonas macleodii. The DNA G+C contents of strains SW-47(T) and SW-49 were 45 and 44 mol%, respectively. Strains SW-47(T) and SW-49 showed a high level of 16S rDNA sequence similarity (99.9 %) and a mean level of DNA-DNA relatedness of 96.5 %. Phylogenetic analyses based on 16S rDNA sequences showed that the two strains form a coherent cluster with A. macleodii. Strains SW-47(T) and SW-49 exhibited levels of 16S rDNA sequence similarity of 99.3 and 99.1 %, respectively, with A. macleodii DSM 6062(T) and of less than 89.4 % with other species used in the phylogenetic analyses. Alteromonas fuliginea CIP 105339(T) was found to be more closely related to the genus PseudoAlteromonas than to the genus Alteromonas: On the basis of phenotypic properties and phylogenetic and genomic data, strains SW-47(T) and SW-49 represent a new species of the genus Alteromonas, for which the name Alteromonas marina (type strain SW-47(T)=KCCM 41638(T)=JCM 11804(T)) is proposed.

  • complete genome sequence of the polycyclic aromatic hydrocarbon degrading bacterium Alteromonas sp strain sn2
    Journal of Bacteriology, 2011
    Co-Authors: Haeyoung Jeong, Renukaradhya K Math, Che Ok Jeon, Eun Joung Moon, Taekwang Oh
    Abstract:

    Alteromonas sp. strain SN2, able to metabolize polycyclic aromatic hydrocarbons, was isolated from a crude oil-contaminated sea-tidal flat. Here we report the complete 4.97-Mb genome sequence and annotation of strain SN2. These will advance the understanding of strain SN2's adaptation to the sea-tidal flat ecosystem and its pollutant metabolic versatility.

  • Alteromonas litorea sp nov a slightly halophilic bacterium isolated from an intertidal sediment of the yellow sea in korea
    International Journal of Systematic and Evolutionary Microbiology, 2004
    Co-Authors: Junghoon Yoon, Taekwang Oh, Yongha Park
    Abstract:

    A Gram-negative, motile, non-spore-forming, rod-shaped bacterium, designated strain TF-22T, was isolated from an intertidal sediment in Korea. This organism grew optimally at 30–37 °C and in the presence of 2–5 % (w/v) NaCl. It did not grow without NaCl or in the presence of more than 14 % (w/v) NaCl. Strain TF-22T was characterized chemotaxonomically as having ubiquinone-8 as the predominant respiratory lipoquinone and C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and C18 : 1 ω7c as the major fatty acids. The DNA G+C content of strain TF-22T was 46·0 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-22T falls within the γ-subclass of the Proteobacteria and forms a coherent cluster with Alteromonas macleodii and Alteromonas marina. Levels of 16S rDNA similarity between strain TF-22T and the type strains of two Alteromonas species were in the range 98·1–98·6 %. The level of DNA–DNA relatedness between strain TF-22T and the type strains of two Alteromonas species was 15·7–18·5 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain TF-22T should be placed in the genus Alteromonas as a novel species, for which the name Alteromonas litorea sp. nov. is proposed. The type strain is TF-22T (=KCCM 41775T=JCM 12188T).

  • Alteromonas marina sp nov isolated from sea water of the east sea in korea
    International Journal of Systematic and Evolutionary Microbiology, 2003
    Co-Authors: Junghoon Yoon, Taekwang Oh, Kook Hee Kang, Yongha Park
    Abstract:

    Two Gram-negative, motile, non-spore-forming and moderately halophilic rods (strains SW-47T and SW-49) were isolated from sea water of the East Sea in Korea and subjected to a polyphasic taxonomic study. The two strains grew optimally between 30 and 37 °C, and grew at 4 and 44 °C but not at temperatures above 45 °C. They grew optimally in the presence of 2–5 % (w/v) NaCl, but did not grow in the absence of NaCl. Strains SW-47T and SW-49 had ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and C16 : 1 ω7c and/or iso-C15 : 0 2OH, C16 : 0 and C18 : 1 ω7c as the major fatty acids, which are consistent with the corresponding data for Alteromonas macleodii. The DNA G+C contents of strains SW-47T and SW-49 were 45 and 44 mol%, respectively. Strains SW-47T and SW-49 showed a high level of 16S rDNA sequence similarity (99·9 %) and a mean level of DNA–DNA relatedness of 96·5 %. Phylogenetic analyses based on 16S rDNA sequences showed that the two strains form a coherent cluster with A. macleodii. Strains SW-47T and SW-49 exhibited levels of 16S rDNA sequence similarity of 99·3 and 99·1 %, respectively, with A. macleodii DSM 6062T and of less than 89·4 % with other species used in the phylogenetic analyses. Alteromonas fuliginea CIP 105339T was found to be more closely related to the genus PseudoAlteromonas than to the genus Alteromonas. On the basis of phenotypic properties and phylogenetic and genomic data, strains SW-47T and SW-49 represent a new species of the genus Alteromonas, for which the name Alteromonas marina (type strain SW-47T=KCCM 41638T=JCM 11804T) is proposed.

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  • Alteromonas naphthalenivorans sp nov a polycyclic aromatic hydrocarbon degrading bacterium isolated from tidal flat sediment
    International Journal of Systematic and Evolutionary Microbiology, 2015
    Co-Authors: Che Ok Jeon
    Abstract:

    A Gram-staining-negative and halotolerant bacterium, designated SN2T, capable of biodegrading polycyclic aromatic hydrocarbons, was isolated from a tidal flat contaminated with crude oil in Korea. Cells were strictly aerobic, catalase- and oxidase-positive, motile rods, with a single polar flagellum. Growth was observed at 4–37 °C (optimum, 25–30 °C) at pH 6.0–9.0 (optimum, pH 7.0–7.5) and in the presence of 0.5–9.0 % (w/v) NaCl (optimum, 2.0 %). Only ubiquinone 8 was detected as the isoprenoid quinone, and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c and C12 : 0 were observed as the major cellular fatty acids. The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, a glycolipid, an aminolipid and three unidentified lipids. The DNA G+C content was 43.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SN2T formed a phylogenetic lineage with Alteromonas stellipolaris and Alteromonas addita within the genus Alteromonas, which was consistent with multilocus phylogenetic and MALDI-TOF MS analyses. Strain SN2T was most closely related to the type strains of A. stellipolaris, A. addita and Alteromonas macleodii, with 16S rRNA gene sequence similarities of 99.5, 99.3 and 98.4 % and DNA–DNA relatedness of 48.7 ± 6.6, 24.9 ± 7.5 and 27.9 ± 8.4 %, respectively. In conclusion, strain SN2T represents a novel species of the genus Alteromonas, for which the name Alteromonas naphthalenivorans sp. nov. is proposed. The type strain is SN2T ( = KCTC 11700BPT = JCM 17741T = KACC 18427T).

  • Alteromonas as a key agent of polycyclic aromatic hydrocarbon biodegradation in crude oil contaminated coastal sediment
    Environmental Science & Technology, 2012
    Co-Authors: Eugene L Madsen, Che Ok Jeon
    Abstract:

    Following the 2007 oil spill in South Korean tidal flats, we sought to identify microbial players influencing the environmental fate of released polycyclic aromatic hydrocarbons (PAHs). Two years of monitoring showed that PAH concentrations in sediments declined substantially. Enrichment cultures were established using seawater and modified minimal media containing naphthalene as sole carbon source. The enriched microbial community was characterized by 16S rRNA-based DGGE profiling; sequencing selected bands indicated Alteromonas (among others) were active. Alteromonas sp. SN2 was isolated and was able to degrade naphthalene, phenanthrene, anthracene, and pyrene in laboratory-incubated microcosm assays. PCR-based analysis of DNA extracted from the sediments revealed naphthalene dioxygenase (NDO) genes of only two bacterial groups: Alteromonas and Cycloclasticus, having gentisate and catechol metabolic pathways, respectively. However, reverse transcriptase PCR-based analysis of field-fixed mRNA revealed in...

  • comparative genomics reveals adaptation by Alteromonas sp sn2 to marine tidal flat conditions cold tolerance and aromatic hydrocarbon metabolism
    PLOS ONE, 2012
    Co-Authors: Renukaradhya K Math, Eugene L Madsen, Yoonsoo Hahn, Woojun Park, Che Ok Jeon
    Abstract:

    Alteromonas species are globally distributed copiotrophic bacteria in marine habitats. Among these, sea-tidal flats are distinctive: undergoing seasonal temperature and oxygen-tension changes, plus periodic exposure to petroleum hydrocarbons. Strain SN2 of the genus Alteromonas was isolated from hydrocarbon-contaminated sea-tidal flat sediment and has been shown to metabolize aromatic hydrocarbons there. Strain SN2's genomic features were analyzed bioinformatically and compared to those of Alteromonas macleodii ecotypes: AltDE and ATCC 27126. Strain SN2's genome differs from that of the other two strains in: size, average nucleotide identity value, tRNA genes, noncoding RNAs, dioxygenase gene content, signal transduction genes, and the degree to which genes collected during the Global Ocean Sampling project are represented. Patterns in genetic characteristics (e.g., GC content, GC skew, Karlin signature, CRISPR gene homology) indicate that strain SN2's genome architecture has been altered via horizontal gene transfer (HGT). Experiments proved that strain SN2 was far more cold tolerant, especially at 5°C, than the other two strains. Consistent with the HGT hypothesis, a total of 15 genomic islands in strain SN2 likely confer ecological fitness traits (especially membrane transport, aromatic hydrocarbon metabolism, and fatty acid biosynthesis) specific to the adaptation of strain SN2 to its seasonally cold sea-tidal flat habitat.

  • complete genome sequence of the polycyclic aromatic hydrocarbon degrading bacterium Alteromonas sp strain sn2
    Journal of Bacteriology, 2011
    Co-Authors: Haeyoung Jeong, Renukaradhya K Math, Che Ok Jeon, Eun Joung Moon, Taekwang Oh
    Abstract:

    Alteromonas sp. strain SN2, able to metabolize polycyclic aromatic hydrocarbons, was isolated from a crude oil-contaminated sea-tidal flat. Here we report the complete 4.97-Mb genome sequence and annotation of strain SN2. These will advance the understanding of strain SN2's adaptation to the sea-tidal flat ecosystem and its pollutant metabolic versatility.