Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand

Kang, Minchung; Chhetri, Geeta; Kim, Jiyoun; Kim, Inhyup; Seo, Taegun

doi:10.1099/ijsem.0.004896

Cited by 17 publications

(12 citation statements)

References 57 publications

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“…Additional biochemical tests for strain Y3S6 T and its reference strains were performed using API ZYM, API E and API 20 NE kits according to the methods described by the manufacturer (bioMérieux) with the modification of adjusting the NaCl concentration to 4.0% (w/v) in all tests. Antibiotic sensitivity tests were performed using the following antibiotic discs (mg disc −1 ): cefazolin (30), ceftazidime (30), cephalexin (30), kanamycin (30), neomycin (30), novobiocin (30), tetracycline (30), ampicillin (10), erythromycin (15) and rifampicin (5). The reference strains were obtained from KCTC (H. pellis KCTC 72573 T and H. saliphila KCTC 52618 T ).…”

Section: Physiology and Chemotaxonomymentioning

confidence: 99%

“…The 16S rRNA gene of strain Y3S6 T was amplified from chromosomal DNA by Solgent Co., Ltd. (Daejeon, Republic of Korea) using the universal bacterial primer set 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′-GGTTACCTTGTTACGACTT-3′). The nearly complete 16S rRNA sequence (1465 bp) of strain Y3S6 T was assembled using SeqMan software ( dnastar ), as described previously [10]. The 16S rRNA gene sequence similarities to the closely related type strains were calculated from NCBI blast [11] searches and the EzBioCloud server (www.ezbiocloud.net) [12].…”

Section: S Rrna Gene Phylogenymentioning

confidence: 99%

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Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater

Chhetri

Kim

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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A Gram-negative, moderately halophilic bacterium, designated as strain Y3S6T, was isolated from a surface seawater sample collected from Dongangyoeng cave, Udo-myeon, Jeju-si, Jeju-do, Repulic of Korea. Cells of strain Y3S6T were aerobic, rod-shaped, non-sporulated, yellow, catalase- negative, oxidase-negative and motile with one polar flagellum. Growth of strain Y3S6T occurred at 15–40 °C (optimum: 25–30 °C), at pH 6.0–9.0 (optimum: pH 7.0) and in the presence of 0–13% NaCl (optimum: 1–6 %, w/v). The novel strain was able to produce carotenoids. Its chemotaxonomic and morphological characteristics were consistent with those of members of the genus Halomonas . Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Y3S6T formed a clade with Halomonas pellis L5T (98.97 %) and Halomonas saliphila LCB169T(98.90%). The average nucleotide identity and digital DNA–DNA hybridization values of strain Y3S6T with the most closely related strains for which whole genomes are publicly available were 82.3–85.2% and 62.8–66.1 %, respectively. The major fatty acids in strain Y3S6T were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (composed of C18 : 1 ω7c and/or C18 : 1 ω6c), and the predominant quinone was Q-9. Its polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phosphoglycolipid, one unidentified phosphoaminoglycolipid and one unidentified phospholipid. The genomic DNA G+C content based on the draft genome sequence was 64.2 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that strain Y3S6T represents a novel species in the genus Halomonas , for which the name Halomonas antri sp. nov. has been proposed. The type strain is Y3S6T (=KACC 21536T=NBRC 114315=TBRC 15164T).

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Section: Physiology and Chemotaxonomymentioning

confidence: 99%

Section: S Rrna Gene Phylogenymentioning

confidence: 99%

Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater

Chhetri

Kim

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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“…S5. In terms of antibiotic sensitivity, strain ITR2 T was susceptible to the following antibiotics (μg per disc): tetracycline (30), ampicillin (10), kanamycin (30), cefazolin (30), ceftazidime (30), novobiocin (30), cephalexin (30), erythromycin (15), neomycin (30) and rifampicin (5). Table 1 provides the detailed biochemical and physiological comparisons between strain ITR2 T and its closely related species.…”

Section: Physiology and Chemotaxonomymentioning

confidence: 99%

Tumebacillus amylolyticus sp. nov., isolated from garden soil in Korea

Kang

Chhetri

Kim

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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A starch-degrading novel strain, designated as strain ITR2T, was isolated from a soil sample collected from a garden near Dongguk University located in Goyang, Republic of Korea. The strain was identified as Gram-stain-positive, rod-shaped, and motile by means of peritrichous flagella. Moreover, 16S rRNA gene analysis revealed the novel strain to form a separate clade with Tumebacillus permanentifrigoris Eur1 9.5T (98.3 %) while also clustering with Tumebacillus flagellatus GST4T (97.9 %). Strain ITR2T grew optimally at temperatures of 20–30 °C, at pH 6.0–7.0 and at NaCl concentrations of 0–1 %. The sole quinone was menaquinone-7 and the cell-wall peptidoglycan comprised alanine, aspartic acid, glutamic acid, lysine and meso-diaminopimelic acid (type-A1γ peptidoglycan). The major fatty acids (>10%) of the novel strain were C16 : 0, iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0, while the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and one unidentified phospholipid. Other polar lipids of the novel strain included, two unidentified glycolipids, three unidentified phospholipids and one unidentified lipid. The in silico DNA–DNA hybridization values between strain ITR2T and its reference strains ( T. permanentifrigoris DSM 18773T and T. flagellatus GST4T) were 21.3 and 23.9 %, respectively, while the average nucleotide identity values were 78.5 and 81.2 %, respectively. The genomic DNA G+C content was 54.9 mol%. Based on the phylogenetic, chemotaxonomic and genomic data obtained in the present study, we propose Tumebacillus amylolyticus sp. nov. to be a novel species within the genus Tumebacillus . The type strain is ITR2T (=KCTC 43280T=NBRC 114753T).

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“…At the time of writing, the genus Sphingomonas comprises 139 species with validly published names (https://lpsn.dsmz.de/genus/sphingomonas). They were isolated from various habitats, such as soil [9], beach [10], phyllosphere [11], rhizosphere [12], human body [13] and food [14]. The present study reports on the taxonomic characterization of strains SYSU D00720 T and SYSU D00722, which were isolated from a desert soil sample by using a polyphasic approach.…”

Section: Introductionmentioning

confidence: 99%

Sphingomonas arenae sp. nov., isolated from desert soil

Dong

Lian

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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Two bacterial strains, designated as SYSU D00720T and SYSU D00722, were isolated from a desert sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped, oxidase-positive and catalase-negative. Colonies were circular, opaque, convex, smooth, orange on Reasoner’s 2A (R2A) agar. The isolates were found to grow at 4–45 °C (optimum, 28–30 °C), at pH 6.0–7.0 (optimum, 7.0) and with 0–1.5 % (w/v) NaCl (optimum, 0%). Growth was observed on R2A agar, Luria–Bertani agar and nutrient agar, but not on trypticase soy agar. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified aminolipids, one unidentified glycolipid, one unidentified aminoglycolipid, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified lipids. The main fatty acids (>10%) were C17 : 1 ω6c, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The major respiratory quinone was ubiquinone-10 and the major polyamine was sym-homospermidine. The genomic DNA G+C content was 66.0 mol%. Strains SYSU D00720T and SYSU D00722 were nearly identical with a 16S rRNA gene sequence similarity of 99.6 %, and 100.0 % average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values. Phylogenetic analyses clearly demonstrated that these two strains belonged to the same species of the genus Sphingomonas , and had highest sequence similarity to Sphingomonas lutea KCTC 23642T (97.3 %). The ANI, AAI and dDDH values of strains SYSU D00720T and SYSU D00722 to S. lutea KCTC 23642T were both 73.2, 69.9 and 19.2 %, respectively. Based on phylogenetic, phenotypic and chemotaxonomic distinctiveness, strains SYSU D00720T and SYSU D00722 represent a novel species of the genus Sphingomonas , for which the name Sphingomonas arenae sp. nov. is proposed. The type strain is SYSU D00720T (=MCCC 1K05154T=NBRC 115061T).

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Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand

Cited by 17 publications

References 57 publications

Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater

Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater

Tumebacillus amylolyticus sp. nov., isolated from garden soil in Korea

Sphingomonas arenae sp. nov., isolated from desert soil

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