Microbacterium awajiense sp. nov., Microbacterium fluvii sp. nov. and Microbacterium pygmaeum sp. nov.

Kageyama, Akiko; Matsuo, Yoshihide; Kasai, Hiroaki; Shizuri, Yoshikazu; Ōmura, Satoshi; Takahashi, Yōko

doi:10.3209/saj.saj220101

Cited by 18 publications

(4 citation statements)

References 19 publications

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“…Most species in the family Microbacteriaceae have been isolated from various non-marine environments: soil, freshwater, groundwater, the rhizosphere and phyllosphere of plants, plant pathogens, air and ice samples, ponds in Antarctica and sludge (Dias & Bhat, 1962; Dias et al , 1962; Männistö et al , 2000; Zhang et al , 2008b; Kim & Lee, 2011; Reddy et al , 2003; Sheridan et al , 2003; Schumann et al , 2012). Some members of the family Microbacteriaceae have been isolated from marine environments, such as seawater, sediment, microbial mats, seaweed and seafood: Agrococcus jejuensis (Lee, 2008), Agromyces atrinae (Park et al , 2010), Gulosibacter chungangensis (Park et al , 2012), Labedella gwakjiensis (Lee, 2007), Leifsonia antarctica (Pindi et al , 2009), two species of the genus Leucobacter (Shin et al , 2011; Yun et al , 2011), Marisediminicola antarctica (Li et al , 2010), Phycicola gilvus (Lee et al , 2008), Salinibacterium amurskyense (Han et al , 2003) and 12 species of the genus Microbacterium (Kim et al , 2008, 2011; Kageyama et al , 2007a, b, 2008; Li et al , 2005; Shivaji et al , 2007; Lee et al , 2006; Takeuchi & Hatano 1998; Wu et al , 2008). Here, we describe a bacterial strain CL-TW6 T , isolated from a seawater reservoir of a solar saltern, on the basis of a polyphasic taxonomic approach.…”

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confidence: 99%

Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern

Jang

Cho

2013

International Journal of Systematic and Evolutionary Microbiology

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Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern A Gram-staining-positive, non-motile, strictly aerobic, non-spore-forming, vibrio-shaped bacterial strain, CL-TW6 T , was isolated from a reservoir seawater sample from a solar saltern in Korea. Analysis of the 16S rRNA gene sequence of strain CL-TW6 T revealed a clear affiliation with the family Microbacteriaceae. Strain CL-TW6 T showed the closest phylogenetic relationships with the genera Yonghaparkia and Microcella, with 16S rRNA gene sequence similarity of 94.8-95.3 %. The strain grew in the presence of 1-9 % sea salts, at 15-35 6C and at pH 7.0-9.0. The major cellular fatty acids of strain CL-TW6 T were anteiso-C 15 : 0 (32.6 %), iso-C 16 : 0 (20.4 %), iso-C 15 : 0 (13.2 %) and iso-C 14 : 0 (11.8 %) and the major menaquinones were MK-9 and MK-10. Cell-wall analysis showed that the peptidoglycan of strain CL-TW6 T contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G+C content of strain CL-TW6 T was 60.0 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed clearly that strain CL-TW6 T could be distinguished from members of the family Microbacteriaceae with validly published names. Thus, strain CL-TW6 T should be classified as representing a novel genus and species in the family Microbacteriaceae, for which the name Pontimonas salivibrio gen. nov., sp. nov. is proposed. The type strain of Pontimonas salivibrio is CL-TW6 T (5KCCM 90105 T 5JCM 18206 T ).

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confidence: 99%

Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern

Jang

Cho

2013

International Journal of Systematic and Evolutionary Microbiology

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“…Among the eight minor clusters (X–XVII) shown in Figure 2 , Microbacterium aquimaris Kim et al 2008– Microbacterium luteum Xie et al 2021 (Cluster XII; 81.83% OrthoANIu), Microbacterium endophyticum Alves et al 2014 – Microbacterium halimionae Alves et al 2014 (Cluster XV; 84.85% OrthoANIu), Microbacterium protaetiae Heo et al 2020– Microbacterium luticocti (Vaz-Moreira et al, 2008 ) (Cluster XIV; 80.14% OrthoANIu), Microbacterium halotolerans (Li et al, 2005 )– Microbacterium halophytorum (Li et al, 2018 ) (Cluster XVI; 80.05% OrthoANIu), and Microbacterium barkeri Takeuchi and Hatano 1998b– Microbacterium oryzae (Kumari et al, 2013 ) (Cluster XVII; 83.37% OrthoANIu) pairs ( Table 2 ) are also well supported by the 16S rRNA gene trees (Dong et al, 2020 ; Lee and Kim, 2023 ; Figure 1 ) and the previous analyses of core genomes (Dong et al, 2020 ; Bellassi et al, 2021 ; Tian et al, 2021 ; Xie et al, 2021 ; Lee and Kim, 2023 ). On the other hand, the remaining three minor clusters, namely, Microbacterium marinum Zhang et al 2012– M. oleivorans Schippers et al 2005 (Cluster X; 80.27% OrthoANIu), Microbacterium fluvii (Kageyama et al, 2007c )– Microbacterium terricola (Kageyama et al, 2007b ) (Cluster XI; 80.53% OrthoANIu), and Microbacterium wangchenii Dong et al 2020 – Microbacterium lushaniae Tian et al 2021 pairs (Cluster XIII; 90.60% OrthoANIu), formed tight clades in the core genome-based phylogenetic tree ( Figure 2 , Table 2 ), but each type strain occupied independent positions in the 16S rRNA gene trees ( Figure 1 ; Dong et al, 2020 ; Lee and Kim, 2023 ).…”

Section: Resultsmentioning

confidence: 99%

Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium

Lee,

Yang,

Kim

2023

Front. Microbiol.

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The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the Microbacterium type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus Microbacterium was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a Microbacterium liquefaciens clade and distributed further into four subclusters in the core genome-based phylogenetic tree. In vitro phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA–DNA hybridization supported that the study strains constituted four new species of the genus Microbacterium. In addition, some Microbacterium type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family Microbacteriaceae based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, Microbacterium aurugineum sp. nov., Microbacterium croceum sp. nov., Microbacterium galbinum sp. nov., and Microbacterium sufflavum sp. nov., are described, along with the proposal of Paramicrobacterium gen. nov. containing five reclassified Microbacterium species from the “Microbacterium agarici clade”, with Paramicrobacterium agarici gen. nov., comb. nov. as the type species.

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“…Members of the genus Microbacterium are characterized as having high G+C content, Gram-stain-positive, rod-shaped, non-spore-producing cells. The optimum growth temperature is 20–30 °C [6]. The cell-wall sugars mainly contain galactose and rhamnose [7], and polar lipids usually consist of diphosphatidylglycerol, phosphatidylglycerol and one or more unidentified glycolipids, and glutamic acid as cell-wall amino acids with lysine, ornithine or 2,4-diaminobutyric acid as cell-wall diamino acids [8].…”

Section: Introductionmentioning

confidence: 99%

Microbacterium nymphoidis sp. nov. and Microbacterium festucae sp. nov., two novel species with high plant-promoting potential isolated from wetland plants in China

Li,

Jin,

Yang

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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Two novel plant growth-promoting, rod-shaped, Gram-positive and non-motile rhizobacteria, W1NT and W2RT, were isolated from wetland plants Festuca elata and Nymphoides peltatum, respectively, in China. The results of the 16S rRNA sequence alignment analysis showed that they were related to Microbacterium , with the highest similarity to Microbacterium ketosireducens (98.7 %) and Microbacterium laevaniformans (98.5 %) for strain W1NT, and to Microbacterium terricola (98.1 %) and Microbacterium marinum (98.0 %) for strain W2RT. Phylogenetic analyses based on 16S rRNA gene sequences and 92 conserved concatenated proteins suggested that the two strains belong to the genus Microbacterium and were placed in two separate novel phylogenetic clades. The genome sizes of the two strains were 3.2 and 3.7 Mb, and the G+C contents were 71.7 and 68.5 mol%, respectively. The comparative genome results showed that the average nucleotide identity values between W1NT and W2RT and other species ranged from 73.5 to 83.6 %, and the digital DNA–DNA hybridization values ranged from 19.7 to 26.8 %. These two strains show physiological and biochemical features that differ from those of closely related species. Rhamnose, galactose and glucose were present in the characteristic sugar fractions of strains W1NT and W2RT. The peptidoglycan of strains W1NT and W2RT contained the amino acids ornithine, alanine and aspartic acid. C15 : 0 anteiso, C17 : 0 anteiso and C16 : 0 iso were the predominant cellular fatty acids in W1NT and W2RT. Phosphatidylglycerol and diphosphatidylglycerol are major polar lipid components. Strain W1NT not only formed bacterial biofilms but also had the ability to solubilize phosphorus and produce indole-3-acetic acid. Strain W2RT had siderophore-producing and lignin-degrading properties. Based on their genetic and phenotypic characteristics, strains W1NT and W2RT were classified as novel bacteria in the genus Microbacterium and designated as Microbacterium festucae sp. nov. (type strain W1NT=ACCC 61807T=GDMCC 1.2966T=JCM 35339T) and Microbacterium nymphoidis sp. nov. (type strain W2RT=ACCC 61808T=GDMCC 1.2967T=JCM 35340T).

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Microbacterium awajiense sp. nov., Microbacterium fluvii sp. nov. and Microbacterium pygmaeum sp. nov.

Cited by 18 publications

References 19 publications

Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern

Pontimonas salivibrio gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from a seawater reservoir of a solar saltern

Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium

Microbacterium nymphoidis sp. nov. and Microbacterium festucae sp. nov., two novel species with high plant-promoting potential isolated from wetland plants in China

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