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Pedobacter rhodius sp. nov. and Pedobacter punctiformis sp. nov., isolated from soil. Antonie Van Leeuwenhoek 2024; 117:72. [PMID: 38671237 DOI: 10.1007/s10482-024-01963-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/01/2024] [Indexed: 04/28/2024]
Abstract
Two Gram-staining negative, catalase- and oxidase-positive, pinkish-colored and rod-shaped strains, designated SJ11T and HCMS5-2 T, were isolated from soil in South Korea. The growth of strain SJ11T was observed from 15℃ to 35℃ (optimum, 30℃), from pH 6.0 to 11.0 (optimum, pH 6.0-7.0) and with NaCl 0-1% (w/v) (optimum, 0%) and that of strain HCMS5-2 T was observed from 4℃ to 40℃ (optimum, 25℃), from pH 6.0 to pH 8.0 (optimum, pH 7.0) and with NaCl 0-5% (w/v) (optimum, 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Pedobacter. Strain SJ11T had the highest 16S rRNA similarities with Pedobacter jejuensis THG-DR3T (98.5%) and strain HCMS5-2 T had the highest similarities with Pedobacter nototheniae 36B243T (98.7%). The digital DNA-DNA hybridization value of strain SJ11T with Pedobacter jejuensis THG-DR3T was 23.6%, with an average nucleotide identity value of 79.6%, and that of strain HCMS5-2 T with Pedobacter nototheniae 36B243T was 26.4%, with an average nucleotide identity value of 83.1%. The predominant cellular fatty acids (> 10%) of SJ11T and HCMS5-2 T were iso-C15:0, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) and iso-C17:0 3-OH. The genome size of strain SJ11T was approximately 4.7 Mb with a G + C content of 37.7% and that of strain HCMS5-2 T was approximately 4.1 Mb with a G + C content of 36.4%. The major polar lipid and respiratory quinone of SJ11T and HCMS5-2 T were phosphatidylethanolamine and menaquinone NK-7, respectively. Results of this study showed that strains SJ11T and HCMS5-2 T belonged to the genus Pedobacter as novel species, of which the name Pedobacter rhodius sp. nov., with the type strain SJ11T (= KACC 22884 T = TBRC 16597 T) and Pedobacter punctiformis sp. nov., with the type strain HCMS5-2 T (= KACC 22863 T = TBRC 16598 T) were respectively proposed.
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Streptomyces tagetis sp. nov., a chromomycin producing bacteria isolated from the roots of Tagetes patula. Front Microbiol 2024; 15:1361583. [PMID: 38495511 PMCID: PMC10940327 DOI: 10.3389/fmicb.2024.1361583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024] Open
Abstract
A novel halotolerant actinobacterium, designated as RG38T, capable of producing black extracellular melanin pigment on SP2 agar, was isolated from the roots of Tagetes patula. Comparative analysis of the 16S rRNA gene sequence revealed the highest similarity to Streptomyces collinus NBRC 12759T (99.3%). Phylogenetic analysis showed that strain RG38T clustered within the genus Streptomyces forming a monophyletic cluster with its close relatives. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and amino-acid identity (AAI) values between strain RG38T and related species within the genus Streptomyces were below the standard threshold for prokaryotic species delineation. The DNA G + C content of the strain RG38T was determined to be 73.3%. The genome size measured 7,150,598 bp comprising 17 contigs and encompassed 6,053 protein coding genes. AntiSMASH analysis of the whole genome revealed 35 putative biosynthetic gene clusters (BGCs) responsible for various secondary metabolites. Among these clusters, two gene clusters exhibited 100% similarity to the chromomycin A3, albaflavenone, and anthracimycin, respectively. These compounds were reported to possess significant anticancer and antibacterial activities. LC-MS-based analysis, coupled with further isolation studies, confirmed the production of chromomycins A2 (1), A3 (2), and their derivatives, along with their antibiotic activities. These findings underscore the potential of this novel strain as a novel resource for the discovery of diverse antimicrobial compounds. This study is the first to report an antimicrobial compound producing Streptomyces species isolated from medicinal plant T. patula. Based on a polyphasic study, the strain RG38T isolated from an unexplored habitat with a high potential for new natural products represents a novel species within the genus Streptomyces. Accordingly, we propose the name Streptomyces tagetis sp. nov. for this novel species, with the type strain is RG38T (=KCTC 49624T = TBRC 15113T).
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Cellulomonas alba sp. nov. and Cellulomonas edaphi sp. nov., isolated from wetland soils. Int J Syst Evol Microbiol 2024; 74. [PMID: 38214698 DOI: 10.1099/ijsem.0.006235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
Two novel strains were isolated from wetland soils in Goyang, Republic of Korea. The two Gram-stain-positive, facultatively anaerobic, rod-shaped bacterial-type strains were designated MW4T and MW9T. Phylogenomic analysis based on whole-genome sequences suggested that both strains belonged to the genus Cellulomonas. The cells of strain MW4T were non-motile and grew at 20-40 °C (optimum, 35 °C), at pH 6.0-10.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0 %). The cells of strain MW9T were non-motile and grew at 20-40 °C (optimum, 35 °C), at pH 5.0-9.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0 %). The average nucleotide identity (77.1-88.1 %) and digital DNA-DNA hybridization values (21.0-34.8 %) between the two novel strains and with their closely related strains fell within the range for the genus Cellulomonas. The novel strains MW4T and MW9T and reference strains possessed alkane synthesis gene clusters (oleA, oleB, oleC and oleD). Phylogenomic, phylogenetic, average nucleotide identity, digital DNA-DNA hybridization, physiological and biochemical data indicated that the novel strains were distinct from other members of the family Cellulomonadaceae. We propose the names Cellulomonas alba sp. nov. (type strain MW4T=KACC 23260T=TBRC 17645T) and Cellulomons edaphi sp. nov. (type strain MW9T=KACC 23261T=TBRC 17646T) for the two strains.
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Neoroseomonas alba sp. nov., Neoroseomonas nitratireducens sp. nov., Paraoseomonas indoligenes sp. nov and Paraoseomonas baculiformis sp. nov., isolated from the rhizosphere of paddy soil. Antonie Van Leeuwenhoek 2023; 116:1009-1022. [PMID: 37587352 DOI: 10.1007/s10482-023-01863-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/27/2023] [Indexed: 08/18/2023]
Abstract
Four novel Gram-stain negative bacteria, designated as HAJ6T, PWR1T, SG15T and SSH11T, were isolated from the soil sample of paddy fields from Goyang in the Republic of Korea. The isolated strains were aerobic, short-rod or rod shaped, non-sporulating. They grew optimally at 30 °C, pH 7 and without additional NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that they belong to the genus of Neoroseomonas and Pararoseomonas and closely relate to Neoroseomonas terrae DS-48T (97.5%; HJA6T), Neoroseomonas rubea MO17T (99.4%; PWR1T), Pararoseomonas pecuniae N75T (97.3%; SG15T) and Pararoseomonas rosea 173-96T (97.8%; SSH11T). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of the isolates with the most closely related strains were 72.9-90.9% and 19.1-42.5%, respectively. The major fatty acids in the isolates were C16:0, C19:0 cyclo ω8c, C18:1 2-OH and summed feature 8 (composed of C18:1 ω7c and/or C18:1 ω6c), and the predominant quinone was ubiquinone 10. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and other unidentified polar lipids. Based on the draft genome sequences, the genomic DNA G + C content of HAJ6T, PWR1T, SG15T and SSH11T were 69.5%, 72.0%, 70.8% and 69.7%, respectively. All isolates produced indole-3-acetic acid (IAA), a type of plant growth hormone in the presence of L-tryptophan. Physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that the isolates were novel species belonging to the genus Neoroseomonas and Pararoseomonas. Their proposed names were as follows: Neoroseomonas alba sp. nov. for strain HJA6T (= KACC 21545T = NBRC 114316T), Neoroseomonas nitratireducens sp. nov. for strain PWR1T (= KCTC 82687T = NBRC 114490T), Pararoseomonas indoligenes sp. nov. for strain SG15T (= KCTC 82686T = NBRC 114481T) and Paraoseomonas baculiformis sp. nov. for strain SSH11T (= KCTC 82685T = NBRC 11482T).
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Mesorhizobium liriopis sp. nov., isolated from the fermented fruit of Liriope platyphylla a medicinal plant. Int J Syst Evol Microbiol 2023; 73. [PMID: 37801075 DOI: 10.1099/ijsem.0.006086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Abstract
A facultative anaerobic and Gram-negative strain, designated RP14T, was isolated from the fruit of Liriope platyphylla fermented for 60 days at 25°C. Strain RP14T showed 98.0 % 16S rRNA similarity to Mesorhizobium huakuii IFO 15243T, but in the phylogenetic tree, Mesorhizobium terrae NIBRBAC000500504T was its closest neighbour. The average nucleotide identity and digital DNA-DNA hybridization values between strain RP14T and 15 genomes of type strains of Mesorhizobium, were 73.8-74.4% and 16.4-20.2 %, respectively, which were lower than the recommended thresholds for species delineation. The strain grew at 25-32°C (optimum, 28°C), at pH 7.0-12.0 (optimum, pH 9.0) and with 0-2% NaCl (optimum, 0 %; w/v). Cells of strain RP14T were catalase-positive, oxidase-negative, rod-shaped and formed yellow-coloured colonies. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major fatty acid were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The DNA G+C content was 62.8 mol%. Based on polyphasic evidence, we propose Mesorhizobium liriopis sp. nov as a novel species within the genus Mesorhizobium. The type strain is RP14T (=KACC 22720T=TBRC 16341T).
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Roseateles albus sp. nov., Roseateles koreensis sp. nov. and Janthinobacterium fluminis sp. nov., isolated from freshwater at Jucheon River, and emended description of Roseateles aquaticus comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37750754 DOI: 10.1099/ijsem.0.006043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023] Open
Abstract
Three Gram-stain-negative, facultatively anaerobic, rod-shaped, catalase-positive, oxidase-negative bacterial strains were designated as hw1T, hw8T and hw3T. Strains hw1T, hw8T and hw3T grew at 15-28 °C (optimum, 25 °C), 15-35 °C (optimum, 30 °C) and 4-28 °C (optimum, 20 °C), respectively, and at pH 7.0-12.0 (optimum, pH 9.0), pH 6.0-11.0 (optimum, pH 9.0) and 5.0-12.0 (optimum, pH 7.0), respectively. Additionally, strains hw1T and hw8T only grew when the NaCl concentration was 0 %, while strain hw3T grew at between 0 and 0.5 % (w/v; optimum, 0 %). The average nucleotide identity (ANI) values between strains hw1T, hw8T and the Roseateles type strains ranged from 73.8 to 84.2 %, while the digital DNA-DNA hybridization (dDDH) values ranged from 19.7 to 27.5 %. The ANI values between strain hw3T and the Janthinobacterium type strains ranged from 78.7 to 80.7 %, while dDDH values ranged from 22.3 to 23.0 %. The draft genomes of strains hw1T, hw8T and hw3T consisted of 5.5, 4.4 and 5.9 Mbp, with DNA G+C contents of 61.7, 61.8 and 66.0 mol%, respectively. The results of the dDDH, ANI, phylogenetic, biochemical and physiological analyses indicated that the novel strains were distinct from other members of their genera. Thus, we proposed the names Roseateles albus sp. nov. (type strain hw1T= KACC 22887T= TBRC 16613T), Roseateles koreensis sp. nov. (type strain hw8T= KACC 22885T= TBRC 16614T) and Janthinobacterium fluminis sp. nov. (type strain hw3T= KACC 22886T= TBRC 16615T).
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Planobacterium oryzisoli sp. nov., a novel bacterium isolated from roots of rice plant. Arch Microbiol 2023; 205:324. [PMID: 37656250 DOI: 10.1007/s00203-023-03657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023]
Abstract
A Gram-negative, aerobic, short rod-shaped, non-motile, non-spore forming bacterium, designated strain GCR5T, was isolated from soil of paddy field. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GCR5T belongs to the genus Planobacterium and is related to Planobacterium taklimakanense NCTC 13490 T (96.1%, 16S rRNA gene sequence similarity). Colonies on R2A were white but they turn into bright yellow after exponential growth. They produce carotenoid pigment after 5-6 days of incubation, before that carotenoid pigment was not found. The major isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C17:0 3OH. Polar lipids include phosphatidylethanolamine, three unidentified phosphoglycolipids, three unidentified glycolipids, one unidentified aminophosphoglycolipid and five unidentified polar lipids. The strain GCR5T was found to have a 2,106,200 bp linear genome with G + C content of 43.7%. The ANI, dDDH and AAI values between the strain GCR5T and the type strains of phylogenetically related species were 60.2-71.1%, 19-24.3%, and 60.2-69.6%, respectively. The strain designated GCR5T produced indole acetic acid (IAA) in the presence of tryptophan only, and auxin responsive genes and tryptophan biosynthesis genes were found in its genome. Based on its polyphasic characteristics, strain GCR5T represents a novel species within the genus Planobacterium, for which the name Planobacterium oryzisoli sp. nov. was proposed. The type strain is GCR5T (= KCTC 82713 T = TISTR 2996 T = TBRC 15746 T).Repositories: The draft genome and 16S rRNA gene sequences of strain GCR5T have been deposited at GenBank/EMBL/DDBJ under accession numbers JADKYY000000000 and MN955408, respectively.
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Alteromonas gilva sp. nov. and Erythrobacter fulvus sp. nov., isolated from a tidal mudflat. Int J Syst Evol Microbiol 2023; 73. [PMID: 37676705 DOI: 10.1099/ijsem.0.006032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
Strains chi3T and sf7T were collected from a tidal mudflat around Dongmak beach in Ganghwa, Republic of Korea. Both strains were Gram-stain-negative, aerobic or facultatively anaerobic, and rod-shaped. Results of phylogenetic tree analysis based on 16S rRNA and whole-genome sequences suggested that strains chi3T and sf7T belong to the genera Alteromonas and Erythrobacter, respectively. The cells of strain chi3T were non-motile and grew at 15-45 °C (optimum, 38 °C), at pH 6.0-10.0 (optimum, pH 8.0) and in the presence of 0-9.0 % (w/v) NaCl (optimum, 2.0 %). The cells of strain sf7T were motile as they had flagella and grew at 20-48 °C (optimum, 38 °C), at pH 6.0-10.0 (optimum, pH 9.0) and in the presence of 0-5.0 % (w/v) NaCl (optimum, 1.0 %). Strains chi3T and sf7T have average nucleotide identity values (70.0-70.4% and 78.9-81.7 %) and digital DNA-DNA hybridization values (21.8-22.3% and 21.0-25.6 %) with reference strains in the genera Alteromonas and Erythrobacter, respectively. Data from digital DNA-DNA hybridization, as well as phylogenetic, biochemical and physiological analyses, indicated the distinction of the two strains from the genera Alteromonas and Erythrobacter, respectively, and we thus propose the names Alteromonas gilva sp. nov. (type strain chi3T=KACC 22866T=TBRC 16612T) and Erythrobacter fulvus sp. nov. (type strain sf7T=KACC 22865T=TBRC 16611T).
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Nocardioides pini sp. nov. and Nocardioides pinisoli sp. nov., two novel actinomycetes isolated from Pinus densiflora. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755157 DOI: 10.1099/ijsem.0.006062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Two novel Gram-positive bacteria designated as strains STR2T and STR3T were isolated from the rhizosphere of a Pinus densiflora sample collected from Goyang-si, Republic of Korea. Strains STR2T and STR3T were aerobic, rod shaped, non-sporulated, catalase negative, oxidase negative and non-motile bacteria. They grew at 15-37 °C (optimum, 25-30 °C), at pH 6.0-11.0 (optimum, pH 7.0) and in the presence of 0-2% NaCl (optimum, 0 %, w/v). The chemotaxonomic and morphological characteristics of the novel strains were consistent with those of the members of Nocardioides. The phylogenetic analysis of the 16S rRNA gene sequences revealed that STR2T was closely related to N. cavernae YIM A1136T (99.3 %) and N. flavus Y4T (99.1 %), and STR3T was closely related to N. exalbidus DSM 22017T (99.0 %), N. baculatus G10T (98.8 %) and N. hwasunensis HFW-21T (98.7 %). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values of STR2T and STR3T with the most closely related strains that have publicly available whole genomes were 83.1-89.8 %, 80.9-89.6% and 26.2-39.1 %, respectively. The cell-wall peptidoglycan of strain STR2T and STR3T contained ll-diaminopimelic acid as the diagnostic amino acid. The major fatty acids in STR2T and STR3T were iso-C16 : 0 and C17 : 1 ω8c, and the predominant quinone was MK-8(H4). Their polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and other polar lipids. The draft genome sequences showed that the genomic DNA G+C content of STR2T and STR3T were both 72.2 mol%. Physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that STR2T and STR3T could represent novel Nocardioides species. Their proposed names were as follows: Nocardioides pini sp. nov. for strain STR2T (=KACC 22784T=TBRC 16336T) and Nocardioides pinisoli sp. nov. for strain STR3T (= KACC 22785T=TBRC 16337T).
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Characterization and Antioxidant Activity of Exopolysaccharides Produced by Lysobacter soyae sp. nov Isolated from the Root of Glycine max L. Microorganisms 2023; 11:1900. [PMID: 37630460 PMCID: PMC10456730 DOI: 10.3390/microorganisms11081900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Microbial exopolysaccharides (EPSs) have attracted attention from several fields due to their high industrial applicability. In the present study, rhizosphere strain CJ11T was isolated from the root of Glycine max L. in Goyang-si, Republic of Korea, and a novel exopolysaccharide was purified from the Lysobacter sp. CJ11T fermentation broth. The exopolysaccharide's average molecular weight was 0.93 × 105 Da. Its monosaccharide composition included 72.2% mannose, 17.2% glucose, 7.8% galactose, and 2.8% arabinose. Fourier-transform infrared spectroscopy identified the exopolysaccharide carbohydrate polymer functional groups, and the structural properties were investigated using nuclear magnetic resonance. In addition, a microstructure of lyophilized EPS was determined by scanning electron microscopy. Using thermogravimetric analysis, the degradation of the exopolysaccharide produced by strain CJ11T was determined to be 210 °C. The exopolysaccharide at a concentration of 4 mg/mL exhibited 2,2-diphenyl-1-picrylhydrazyl free-radical-scavenging activity of 73.47%. Phylogenetic analysis based on the 16S rRNA gene sequencing results revealed that strain CJ11T was a novel isolate for which the name Lysobacter soyae sp. nov is proposed.
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Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37490399 DOI: 10.1099/ijsem.0.005989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Two Gram-stain-negative, aerobic, yellow and rod-shaped bacteria, designated as strains PBS4-4T and GMJ5T, were isolated from soil samples collected in Goyang-si and Paju-si, Gyeonggi-do, Republic of Korea. Strains PBS4-4T and GMJ5T were both positive for catalase and oxidase. Strain PBS4-4T grew at 15-37 °C and pH 5.0-12.0. Strain GMJ5T grew at 15-37 °C and pH 5.0-11.0. Neither strain required NaCl for growth. 16S rRNA sequence analysis revealed that strains PBS4-4T and GMJ5T form a closely related cluster with the genus Chryseobacterium. The average nucleotide identity and digital DNA-DNA hybridization values between strain PBS4-4T and its closely related strains were 79.4-84.5% and 23.2-28.7 %, respectively. For GMJ5T, the values were 78.3-79.3% and 22.0-22.6 %, respectively. The major fatty acids shared by both novel strains were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Strain GMJ5T had one other major fatty acid: iso-C17 : 0 3OH. Based on phenotypic, genomic and phylogenetic results, strains PBS4-4T and GMJ5T represent novel species within the genus Chryseobacterium, and the names Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov. are proposed, respectively. The type strain of C. edaphi is PBS4-4T (=KACC 22882T=TBRC 17052T) and the type strain of C. gilvum is GMJ5T (=KACC 22883T=TBRC 17053T).
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Ideonella oryzae sp. nov., isolated from soil, and Spirosoma liriopis sp. nov., isolated from fruits of Liriope platyphylla. Int J Syst Evol Microbiol 2023; 73. [PMID: 37409567 DOI: 10.1099/ijsem.0.005943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
Gram-negative, aerobic, motile by means of two or more polar or subpolar flagella, rod-shaped strain NS12-5T and Gram-negative, facultatively anaerobic, yellow-coloured, rod-shaped strain RP8T were isolated from rice rhizosphere soil and fermented fruits of Liriope platyphylla in the Republic of Korea, respectively. The result of phylogenetic analyses based on 16S rRNA gene sequences showed that strain NS12-5T was most closely related to Ideonella aquatica 4Y11T with 99.79 % sequence similarity. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain NS12-5T and species of the genus Ideonella were 75.6-91.7 % and 20.3-43.9 %, respectively. Growth occurred at 15-40 °C and pH 5-11, and NaCl was not needed for growth. The major fatty acids of strain NS12-5T were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0, and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain NS12-5T was 69.03 mol%. The result of phylogenetic analyses based on 16S rRNA gene sequences revealed that strain RP8T was most closely related to Spirosoma aureum BT328T with 96.01 % sequence similarity. The ANI and dDDH values between strain RP8T and reference strains of the genus Spirosoma were 72.9-76.4 % and 18.6-20.0 %, respectively. Growth occurred at 15-37 °C and pH 5-11, and NaCl was not needed for growth. The major fatty acids of strain RP8T were summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 1 ω5c and iso-C15 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C contents of strain RP8T were 54.9 mol%. Based on phenotypic, genomic and phylogenetic results, strains NS12-5T and RP8T represent novel species in the genus Ideonella and Spirosoma, respectively, and the names Ideonella oryzae sp. nov. and Spirosoma liriopis sp. nov. are proposed. The type strain of I. oryzae sp. nov. is NS12-5T (=KACC 22691T=TBRC 16346T) and the type strain of S. liriopis is RP8T (=KACC 22688T=TBRC 16345T).
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Runella salmonicolor sp. nov. and Dyella lutea sp. nov., isolated from paddy field soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37358382 DOI: 10.1099/ijsem.0.005938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023] Open
Abstract
Bacterial strains were collected from the soil of a paddy field around Dongguk University in Goyang, Republic of Korea. Two Gram-stain-negative, rod-shaped, aerobic or facultatively anaerobic bacterial strains were designated S5T and SaT. The results of analysis of phylogenetic trees based on 16S rRNA and whole-genome sequences indicated that these two strains represented a member of the genus Runella and a member of the genus Dyella, respectively. S5T exhibited 99.22, 98.10 and 97.68 % similarity to Runella rosea HYN0085T, Runella aurantiaca YX9T and Runella slithyformis DSM 19594T, respectively. S5T grew at 15-40 °C (optimum, 25 °C), at pH 6.5-12.0 (optimum, pH 9.5) and in the presence of 0-0.5 % (w/v) NaCl (optimum, 0 %). SaT exhibited 99.18 %, 98.36 %, 97.82 % and 97.68 % similarity to Dyella thiooxydans ATSB10T, Frateruia defendens DHoT, Fulvimonas yonginensis 5HGs31-2T and Dyella ginsengisoli Gsoil 3046T, respectively, and grew at 20-40 °C (optimum, 30 °C), at pH 5.5-11.0 (optimum, pH 8) and in the presence of 0-4.5 % (w/v) NaCl (optimum, 2.5 %). The average nucleotide identity difference values of S5T, SaT and the species reference strains were 92.16-93.62 % and 92.71-93.43%, which confirms that the S5T and SaT represent two novel species of the genera Runella and Dyella, respectively. The draft genome of S5T consisted of 7 048 502 bp, with a DNA G+C content of 44.9 % and that of SaT of 4 398 720 bp with a DNA G+C content of 67.9 %. The phylogenetic, phenotypic and physiological characteristics permitted the distinction of the two strains from their families, and we thus propose the names Runella salmonicolor sp. nov. (type strain S5T = KACC 22689T = TBRC 16343T) and Dyella lutea sp. nov. (type strain SaT=KACC 22690T = TBRC 16344T).
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Field epidemiology, clinical findings and outcome of Scrub typhus patients admitted at Gedu District Hospital, Chhukha, Bhutan. SAGE Open Med 2023; 11:20503121231175303. [PMID: 37223671 PMCID: PMC10201154 DOI: 10.1177/20503121231175303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Objectives This study aimed to understand the field epidemiology, clinical findings, diagnostic reports and outcome of Scrub typhus patients admitted at Gedu District Hospital, Bhutan. Methods The researcher extracted data from the records of patients admitted at the hospital from 1 January 2017 to 31 December 2020, with diagnosis of Scrub typhus. A total of 185 records were used to study the demographic distribution, results of rapid diagnostic test for Scrub typhus, presence of eschar, treatment outcome and duration of admission in the hospital. Results The months of May to October had increased admissions of 137 (74%) patients with a peak in September. Three gewogs (sub-districts) had 173 (93.5%) patients; age range was 6 months to 84 years and a greater proportion of patients were females. Conclusion Scrub typhus is endemic in the district. The absence of recorded fever or a negative rapid diagnostic test report may not exclude the diagnosis of Scrub typhus.
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Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter. Antonie Van Leeuwenhoek 2023; 116:231-242. [PMID: 36525157 DOI: 10.1007/s10482-022-01800-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
A Gram-stain-negative, halotolerant bacterium designated as PTR5T was isolated from the roots of rice plants, collected in Ilsan, South Korea. Cells were, aerobic, asporogenous, motile, rod-shaped, white in color, and grew at 5-38 °C (optimum 30 °C), at pH 5.0-0-8.0 (optimum, 7.0) and tolerates up to 10% (w/v) NaCl (optimum, 0% NaCl). According to the EZbioCloud server the most closely related Devosia species to strain PTR5T based on 16 S rRNA gene sequence comparison are Devosia crocina (97.4%), followed by D. soli (97.2%), D. lucknowensis (96.9%) and D. marina (96.5%). The respiratory quinone was identified as Q-10. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. C16:0, C18:1 ω7c 11-methyl and summed feature 8 (comprising C18:1 ω7c/C18:1 ω6c) constituted the main cellular fatty acids. The draft genome sequence of strain PTR5T was 3,689,283 bp in size. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and amino acid identity (AAI) values between strain PTR5T and its close relative were 72.8-76.8%, 19-20.7% and 70.3-75%, respectively. The G + C content was 63.7%. Strain PTR5T was able to produce siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Genes for siderophore production, auxin responsive and tryptophan biosynthesis were present in the genome of novel strain. Also, gene clusters involved in detoxification of various metal pollutants and antibiotics were also revealed in the genome of novel strain PTR5T, this suggest that novel strain can facilitate bioremediation of heavy metals and antibiotics in contaminated areas. This study aimed to determine the detailed taxonomic position of the strain PTR5T using the modern polyphasic approach. On the basis of evidence presented in this study, strain PTR5T is considered to represent a novel species of the genus Devosia, for which the name Devosia oryzisoli sp. nov. (type strain PTR5T (KCTC 82691T = TBRC 15163T) is proposed.
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Paraburkholderia tagetis sp. nov., a novel species isolated from roots of Tagetes patula enhances the growth and yield of Solanum lycopersicum L. (tomato). Front Microbiol 2023; 14:1140484. [PMID: 37082173 PMCID: PMC10110911 DOI: 10.3389/fmicb.2023.1140484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023] Open
Abstract
A multifunctional, Gram-stain-negative, aerobic, motile by flagella, short-rod shaped bacteria, designated strain RG36T was isolated from roots of marigold plant (Tagetes patula) sampled at Dongguk University, Republic of Korea. A 16S rRNA sequences indicated that the closest phylogenetic neighbors were Paraburkholderia acidiphila 7Q-K02T (99.0%) and Paraburkholderia sacchari IPT101T (98.9%) of the family Burkholderiaceae. The draft genome size was 8.52 Mb (63.7% GC). The genome contained 7,381 coding sequences. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strain RG36T with its most closely related species were only 83.1-88.7 and 27.6-36.7%, respectively. Strain RG36T contained Q-8 as the major respiratory quinone and its main fatty acids (>10%) were C16:0, C17:0 cyclo, C19:0 cyclo ω8c, and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). Strain RG36T accumulates polyhydroxybutyrates (PHB) and exhibits multiple plant growth-promoting properties including production of indole-3-acetic acid (IAA), siderophores, protease, phosphate solubilization, and harboring gene clusters for its multifunctional properties. A pot experiment was conducted to evaluate the effect of PGPR on the growth of Solanum lycopersicum L. (Tomato). Result also confirmed the ability of strain RG36T to promote tomato plant growth, especially it increases the yield of tomatoes. Structural assessment of the bioplastic by Fourier transform infrared (FTIR), nuclear magnetic resonance (NMR), and GC-MS spectroscopy, which confirmed the structure of the polymer as PHB. Our study revealed the potential of strain RG36T to promote the growth of tomato plant and fruit yield by stimulating the various phytohormones, which could be use as bio-fertilizers to reduce the use of chemical fertilizers and promotes sustainable agricultural production. The phenotypic, chemotaxonomic and phylogenetic data, and genome analysis showed that strain RG36T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia tagetis sp. nov. is proposed. The type strain is RG36T (=KACC 22685T = TBRC 15696T).
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Comparative genomic analyses of four novel Ramlibacter species and the cellulose-degrading properties of Ramlibacter cellulosilyticus sp. nov. Sci Rep 2022; 12:21233. [PMID: 36482214 PMCID: PMC9731981 DOI: 10.1038/s41598-022-25718-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
In this study, four novel bacterial strains, USB13T, AW1T, GTP1T, and HM2T, were isolated from various environments in Busan and Jeju Island, Republic of Korea. The 16S rRNA sequencing results indicated that the four novel strains belong to the genus Ramlibacter. All four strains were tested for their potential cellulolytic properties, where strain USB13T was identified as the only novel bacterium and the first within its genus to show cellulolytic activity. When tested, the highest activities of endoglucanase, exoglucanase, β-glucosidase, and filter paper cellulase (FPCase) were 1.91 IU/mL, 1.77 IU/mL, 0.76 IU/mL, and 1.12 IU/mL, respectively at pH 6.0. Comparisons of draft whole genome sequences (WGS) were also made using average nucleotide identity, digital DNA-DNA hybridization values, and average amino acid identity values, while whole genome comparison was visualized using the BLAST Ring Image Generator. The G + C contents of the strains ranged from 67.9 to 69.9%, while genome sizes ranged from 4.31 to 6.15 Mbp. Based on polyphasic evidence, the novel strains represent four new species within the genus Ramlibacter, for which the names Ramlibacter cellulosilyticus sp. nov. (type strain, USB13T = KACC 21656T = NBRC 114839T) Ramlibacter aurantiacus sp. nov. (type strain, AW1T = KACC 21544T = NBRC 114862T), Ramlibacter albus sp. nov. (type strain, GTP1T = KACC 21702T = NBRC 114488T), and Ramlibacter pallidus sp. nov. (type strain, HM2T = KCTC 82557T = NBRC 114489T) are proposed.
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Sphingomonas liriopis sp. nov., Sphingomonas donggukensis sp. nov., and Sphingomonas tagetis sp. nov., isolated from Liriope platyphylla fruit, soil, and Tagetes patula roots. Arch Microbiol 2022; 205:16. [PMID: 36477930 DOI: 10.1007/s00203-022-03360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Three bacterial strains, designated RP10T, RMG20T, and MG17T, were isolated from Liriope platyphylla fruit (strain RP10T), soil (RMG20T), and Tagetes patula roots (MG17T) collected in Goyang, Republic of Korea. The 16S rRNA gene sequences revealed that strains RP10T, RMG20T, and MG17T were closely related to Sphingomonas melonis DSM 14444 T (highest similarity of the strain RP10T), Sphingomonas asaccharolytica DSM 10564 T (strain RMG20T), and Sphingomonas suaedae JCM 33850 T (strain MG17T) with 98.0-99.0% highest sequence similarity. The 16S rRNA gene sequences similarity between strains RP10T, RMG20T, and MG17T was 96.6-97.4%. Strains RP10T, RMG20T, MG17T, and the closely related type strains have digital DNA-DNA hybridization and average nucleotide identity values of 19.4-65.3% and 74.0-95.7%, respectively. Based on phylogenetic, biochemical, chemotaxonomic, and phenotypic data, strains RP10T, RMG20T, and MG17T are considered to represent novel species of the genus Sphingomonas, for which the name Sphingomonas liriopis sp. nov. (type strain RP10T = KACC 22357 T = TBRC 15161 T), Sphingomonas donggukensis sp. nov. (type strain RMG20T = KACC 22358 T = TBRC 15162 T), and Sphingomonas tagetis sp. nov. (type strain MG17T = KACC 22355 T = TBRC 15160 T), are proposed.
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Chryseolinea lacunae sp. nov. and Piscinibacter lacus sp. nov. Isolated from Artificial Pond Water. Curr Microbiol 2022; 80:25. [PMID: 36473949 DOI: 10.1007/s00284-022-03133-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Two Gram stain-negative bacterial strains designated Jin1T and Jin2T were isolated from artificial pond water in the Republic of Korea and investigated in the present study using a polyphasic taxonomic approach. Phylogenetic analysis of the 16S rRNA gene sequences indicated that these two strains belonged to the genera Chryseolinea and Piscinibacter due to their highest similarities with the 16S rRNA gene sequences of Chryseolinea serpens RYGT (98.7%) and Piscinibacter aquaticus IMCC1728T (97.1%), respectively. The dDDH and ANI values were 18.1-20.5% and 68.9-76.8% between whole-genome sequences of strain Jin1T and type trains of the selected taxa, Chryseolinea species, and 20.1-20.2% and 75.5-76.1% between those of strain Jin2T and the type strains of the selected taxa, Piscinibacter species, respectively. A threshold AAI value of 44.7-64.8% for the species boundary (95-96%) was established for strains Jin1T, Jin2T, and type strains of other species involved in the system incidence, which confirms that strains Jin1T and Jin2T represent two new species of the genera Chryseolinea and Piscinibacter, respectively. Based on the phylogenetic, chemotaxonomic, and phenotypic analyses, strains Jin1T and Jin2T represent novel species of the genera Chryseolinea and Piscinibacter, respectively, for which the names Chryseolinea lacunae sp. nov. (type strain Jin1T = KCTC 82562T = NBRC 114837T) and Piscinibacter lacus sp. nov. (type strain Jin2T = KCTC 82556T = NBRC 114838T) have been proposed.
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Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748605 DOI: 10.1099/ijsem.0.005640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Members of the genus Paenibacillus are well known for their metabolic versatility and great application potential in plant growth promotion. Three novel bacterial strains, designated N4T, JC52T and PR3T, were isolated from rhizosphere soils and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that the three strains belonged to the genus Paenibacillus and formed three independent branches distinct from all reference strains. The results of DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) analyses between the three strains and their relatives further demonstrated that the three strains represented different novel genospecies. Strain N4T exhibited the highest similarity, ANI and digital DDH values with Paenibacillus assamensis DSM 18201T (99.0/87.5/33.9 %) and Paenibacillus insulae DS80T (97.2/-/18.2±1.2 %). Values for JC52T with Paenibacillus validus NBRC 15382T were 96.9, 73.3 and 19.6 %, and with Paenibacillus rigui JCM 16352T were 96.1, 72.1 and 19.3 %. Values for PR3T with Paenibacillus ginsengiterrae DCY89T were 98.2, - and 31.8±1.5 %, with Paenibacillus cellulosilyticus ASM318225v1T were 97.8, 83.3 and 26.7 %, and with Paenibacillus kobensis NBRC 15729T were 97.6, 75.7 and 20.4 %. Cells of the three novel bacterial strains were Gram-positive, spore-forming, motile and rod-shaped. The novel species contained anteiso-C15 : 0 and MK-7 as the predominant fatty acid and menaquinone, respectively. The novel strains have numerous similar known clusters of non-ribosomal peptide synthetases, siderophores, lanthipeptide, lassopeptide-like bacillibactin, paeninodin and polyketide-like chejuenolide A/B lankacidin C. Based on the distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains N4T, JC52T and PR3T represent novel species of the genus Paenibacillus, with the names Paenibacillus agilis sp. nov. (=KACC 19717T=JCM 32775T), Paenibacillus cremeus sp. nov. (=KACC 21221T=NBRC 113867T) and Paenibacillus terricola sp. nov. (=KACC 21455T=NBRC 114385T), respectively.
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Quadrisphaera setariae sp. nov., polyphosphate-accumulating bacterium occurring as tetrad or aggregate cocci and isolated from Setaria viridis. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, orange-pigmented, aerobic, cocci (occurring in tetrads), non-spore-forming, non-motile bacterium, designated as DD2AT, was isolated from Setaria viridis collected at Dongguk University, Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene revealed that strain DD2AT was most closely related to type strains of the genus
Quadrisphaera
. Strain DD2AT showed the highest 16S rRNA gene sequence similarities to
Quadrisphaera oryzae
TBRC 8486T (99.4 %) and
Quadrisphaera granulorum
JCM 16010T (98.8 %). Strain DD2AT also showed auto-aggregation ability. The digital DNA–DNA hybridization values between strain DD2AT and the reference strains,
Q. oryzae
TBRC 8486T and
Q. granulorum
JCM 16010T were 31.1 and 27.4 %, respectively. The average nucleotide identity values between strain DD2AT and
Q. oryzae
TBRC 8486T and
Q. granulorum
JCM 16010T were 86.3 and 84.1 %, respectively. The major polar lipids of strain DD2AT were diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acid of strain DD2AT was anteiso-C15 : 0. The cell-wall peptidoglycan contained meso-diaminopimelic acid (which is a diagnostic cell-wall diamino acid), alanine and glutamic acid. The respiratory quinones was found to be menaquinone-8. The DNA G+C content of strain DD2AT was 74.8 mol%. On the basis of the findings of genotypic, phenotypic, chemotaxonomic and phylogenetic analyses, strain DD2AT was considered to represent a novel member in the genus
Quadrisphaera
, for which the name Quadrisphaera setariae sp. nov. is proposed. The type strain of Quadrisphaera setariae is DD2AT (=KACC 21165T=NBRC 113770T).
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Identification of Mucilaginibacter conchicola sp. nov., Mucilaginibacter achroorhodeus sp. nov. and Mucilaginibacter pallidiroseus sp. nov. and emended description of the genus Mucilaginibacter. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005431] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three chitinolytic, Gram-negative, light pink, capsule-forming, rod-shaped bacterial strains with gliding motion (MYSH2T, MJ1aT and dk17T) were isolated from seashells, soil and foxtail, respectively. Phylogenetic analysis of the 16S rRNA gene sequences and concatenated alignment of 92 core genes indicated that strains MYSH2T, MJ1aT and dk17T were novel species of the genus
Mucilaginibacter
and exhibited a high 16S rRNA sequence similarity (i.e. more than 97.2 %) among each other. These novel strains contained summed feature 3 (C16:1 ω7c and/or C16:1 ω6), iso-C15:0 and MK-7 as the predominant fatty acids and menaquinone. According to the CAZys coding gene of KAAS, MYSH2T and MJ1aT were interpreted as strains containing both GH18 and 19 family coding genes, except for dk17T, which shows only GH19 family genes. These strains likely degrade chitin to chitobiose or directly to N-acetyl-d-glucosamine, which may enhance their chitinolytic capacity, thus making these stains potentially useful for industrial chitin degradation. Based on distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains MYSH2T, MJ1aT and dk17T represent three novel species in the genus
Mucilaginibacter
, for which the names Mucilaginibacter conchicola sp. nov. (=KACC 19716T=JCM 32787T), Mucilaginibacter achroorhodeus sp. nov. (=KACC 19906T=NBRC 113667T) and Mucilaginibacter pallidiroseus sp. nov. (=KACC 19907T=NBRC 113666T) are proposed. An emended description of the genus
Mucilaginibacter
is proposed.
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Abstract
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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Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005272] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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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Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island. Int J Syst Evol Microbiol 2021; 71. [PMID: 34928203 DOI: 10.1099/ijsem.0.005176] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, designated MJB4T and SJ7T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella, owing to their high similarities to Nocardioides jensenii DSM 29641T (97.5 %) and Hyunsoonleella rubra FA042 T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4T, SJ7T and the reference strains, Nocardioides jensenii DSM 29641T, Nocardioides daejeonensis MJ31T and Hyunsoonleella flava T58T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4T and SJ7T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1-82.6 % for the species boundary (95-96 %), which confirms that strains MJB4T and SJ7T represent two new species of genus Nocardioides and Hyunsoonleella, respectively. Based on phylogenetic and phenotypic data, strains MJB4T and SJ7T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella, respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4T=KACC 21724T=NBRC 114402T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7T=KACC 21715T=NBRC 114486T) have been proposed.
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Pontibacter aquaedesilientis sp. nov., isolated from Jeongbang Waterfall, Jeju Island. Int J Syst Evol Microbiol 2021; 71. [PMID: 34910615 DOI: 10.1099/ijsem.0.005155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A red-pigmented, aerobic, motile by gliding, pleomorphic to long-rods and divided by budding bacterium, Gram-stain negative bacterium, designated JH31T, was isolated from stream water of Jeongbang Waterfall, famous feature of Jeju Island, Republic of Korea. The cells grew at 9-40 °C (optimum, 28-30 °C), at pH 5.0-10.0 (pH 6.5-7.5) and with 0-6% NaCl (0% NaCl). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JH31T forms a lineage within the family Hymenobacteriaceae and clusters with its closest related species Pontibacter virorsus KCTC 42941T (98.1%), Pontibacter salisaro KACC 16885T (98.0%), Pontibacter amylolyticus JCM 19653T (97.2%), Pontibacter ramchanderi KACC 17384T (97.2%) and Pontibacter lucknowensis DM9T (96.4%). Strain JH31T produced carotenoid-type pigments but no flexirubin-type pigments. The genome was 4117105 bp long with 18 contigs and 3509 protein-coding genes. The DNA G+C content was 49.7 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain JH31T and its closely related reference strains were less than 19 and 72%, respectively. The draft genome of strain JH31T contained vital gene clusters involved in resistance against various metals, antibiotics, toxic compounds and radiation. The respiratory quinone of strain JH31T was menaquinone 7 and the predominant cellular fatty acids were iso-C15:0, and summed feature 4 (comprising iso-C17:1 I and/or anteiso B). The major polar lipids were phosphatidylethanolamine, three unidentified glycolipids, one unidentified phospholipid, one unidentified phosphoglycolipid and one unidentified aminoglycolipid. The phylogenetic, physiochemical and biochemical data showed that strain JH31T should represent a novel species in the genus Pontibacter, for which the name Pontibacter aquaedesilientis sp. nov. is proposed. The type strain for this novel species is JH31T (KACC 21705T=NBRC 114480T).
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Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants. J Microbiol 2021; 60:1-10. [PMID: 34826099 DOI: 10.1007/s12275-022-1474-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/26/2022]
Abstract
Two novel Gram-negative, aerobic, asporogenous, motile, rod-shaped, orange and white pigmented, designated as LEGU1T and G19T, were isolated from the roots of rice plants, collected from Goyang, South Korea. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that they belonged to the genus Devosia and formed a different lineage and clusters with different members of the genus Devosia. These strains shared common chemotaxonomic features. In particular, they had Q-10 as the sole quinone, phosphatidylglycerol, diphosphatidylglycerol as the principal polar lipids and C16:0, C18:1ω7c 11-methyl and summed feature 8 (comprising C18:1ω7c/C18:1ω6c) as the main fatty acids. The draft genome sequences of strains LEGU1T and G19T were 3,524,978 and 3,495,520 bp in size, respectively. Their average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 72.8-81.9% and 18.7-25.1%, respectively, with each other and type strains of related species belonging to the genus Devosia, suggesting that these two strains represent novel species. The G + C content of strains LEGU1T and G19T were 62.1 and 63.8%, respectively. Of the two strains, only LEGU1T produced carotenoid and flexirubin-type pigment. Both strains produced siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Siderophore biosynthesis genes, auxin responsive genes and tryptophan biosynthesis genes were present in their genomes. The present study aimed to determine the detailed taxonomic positions of the strains using the modern polyphasic approach. Based on the results of polyphasic analysis, these strains are suggested to be two novel bacterial species within the genus Devosia. The proposed names are D. rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., respectively. The plant growth promoting effects of these strains suggest that they can be exploited to improve rice crop productivity. The type strain of D. rhizoryzae is LEGU1T (KCTC 82712T = NBRC 114485T) and D. oryziradicis is G19T (KCTC 82688T = NBRC 114842T).
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Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water. Int J Syst Evol Microbiol 2021; 71. [PMID: 34694986 DOI: 10.1099/ijsem.0.005058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, non-motile, red-pink bacterium designated SD6T was isolated from coastal marine water at Sadong Beach, Ulleung Island, South Korea. Cells of SD6T grew at 10-42 °C (optimum, 30 °C), pH 5.0-9.0 (optimum, pH 6.0-7.0) and at 0-8.0 % (w/v) NaCl (optimum, 0-3 %). Moreover, 16S rRNA gene sequence analysis indicated that strain SD6T was a member of the genus Pontibacter, sharing similarities to Pontibacter aydingkolensis XAAS-1T (98.0 %), Pontibacter amylolyticus 9-2T (97.3 %), Pontibacter korlensis X14-1T (97.2 %) and Pontibacter soli HYL7-26T (96.8 %). The predominant fatty acids of strain SD6T were identified as iso-C15 : 0 and summed feature 4 (comprising anteiso-C17 : 1 B and/or iso-C17 : 1 I) and the sole respiratory quinone was identified as MK-7 (menaquinone 7). Major polar lipids included phosphatidylethanolamine, one unidentified phosphoglycolipid, two unidentified glycolipids and one unidentified lipid. The average nucleotide identity and in silico DNA-DNA hybridization values of strain SD6T with its closely related strains were 72.8-79.8 % and 19.2-22.6 %, respectively. The genomic DNA G+C content was 45.4 mol%. In accordance with the results of phenotypic, chemotaxonomic and phylogenetic data, strain SD6T represents a novel species of the genus Pontibacter, for which the name Pontibacter cellulosilyticus sp. nov. is proposed. The type strain is SD6T (=KACC 21543T=NBRC 114313T=JCM 31022T).
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Sphingosinicella flava sp. nov., indole acetic acid producing bacteria isolated from maize field soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34605389 DOI: 10.1099/ijsem.0.005038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel isolated yellow-pigmented bacterial designated strain UDD2T was isolated from a maize field soil sample collected in Ilsan, Republic of Korea. Cells of strain UDD2T were Gram-stain-negative, non-sporulating, long rod-shaped and exhibited flagellar motility. Cells could grow at 15-42 °C and pH 5.5-11.0. Strain UDD2T was sensitive to NaCl and barely tolerated up to 1 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain UDD2T formed a separate clade with the members of genus Sphingosinicella within the family Sphingomonadaceae. Strain UDD2T showed the highest 16S rRNA gene sequence similarity to Sphingosinicella vermicomposti KCTC 224446T (98.5 %) and Sphingosinicella humi KCTC 62519T (96.7 %), followed by members of the genus Sphingomonas (96.4-94.5 %) and Sphingobium (96.1-94.9 %), but they were located in other phylogenetic clusters. Average nucleotide identity and digital DNA-DNA hybridization values between strain UDD2T and S. vermicomposti KCTC 224446T and S. humi KCTC 62519T were 80.2/24.2 and 75.6/20.4 %, respectively. The total size of the genome was 2 421 697 bp and composed of one circular chromosome, with a G+C content of 63.7 mol%. Strain UDD2T produced indole acetic acid (IAA) in the presence of l-tryptophan. Bacterial IAA is a crucial phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphate synthase and tryptophan synthase were found in the genome of strain UDD2T. To the best of our knowledge, no member of the genus Sphingosinicella has been reported to produce IAA to date. The major cellular fatty acids (>10 %) were found to be C16 : 0, C14 : 0 2OH and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH). Strain UDD2T had ubiquinone Q-10 as the major respiratory quinone and homospermidine as the major polyamine. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, three unidentified phosphoglycolipids, one unidentified phospholipid, one unidentified aminoglycophospholipid, one unidentified glycolipid and one unidentified polar lipid. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic data, strain UDD2T represents a novel species of the genus Sphingosinicella, for which the name Sphingosinicella flava is proposed. The type strain is UDD2T (=KCTC 82357T=NBRC 114507T).
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Flavobacterium tagetis sp. nov., a novel urea-hydrolysing bacterium isolated from the roots of Tagetes patula. Int J Syst Evol Microbiol 2021; 71. [PMID: 34542390 DOI: 10.1099/ijsem.0.004984] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, motile by gliding, non-sporulating and strictly aerobic bacterium, designated strain GN10T, was isolated from the roots of Tagetes patula, collected from the garden of Dongguk University, Goyang, Republic of Korea. The cells could grow at 10-42 °C and at pH 5.5-9.0. Strain GN10T was sensitive to NaCl and tolerated up to 4 % NaCl (w/v). Comparative analysis of 16S rRNA gene sequences revealed the highest similarities to Flavobacterium tistrianum GB 56.1T (98.9 %), Flavobacterium sharifuzzamanii A7.6T (98.6 %), Flavobacterium zhairuonense A5.7T (98.3 %) and Flavobacterium anhuiense D3T (98 %). Phylogenetic analysis showed that strain GN10T clustered within the genus Flavobacterium and formed a monophyletic cluster with its close relative members. The average nucleotide identity and digital DNA-DNA hybridization values between strain GN10T and related species belonging to the genus Flavobacterium were well below the standard threshold for prokaryotic species delineation. The DNA G+C content of strain GN10T was 33.6 mol%. The predominant cellular fatty acids (>10 %) were identified as iso-C15 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). Strain GN10T contained menaquinone 6 as the major respiratory quinone. The major polar lipids were phosphatidylethanolamine, three unidentified aminoglycolipids, two unidentified glycolipids, one unidentified phosphoglycolipid and five unidentified lipids. Urease is a nickel-containing enzyme found in archaea, bacteria, plants and unicellular eukaryotes. It serves as a virulence factor and is responsible for pathogenesis in humans and animals. Here, we describe a novel urease-hydrolysing bacterium, strain GN10T. The urease activity of this strain may serve as an indicator of pathogenic potential and drug resistance, which may facilitate the development of many diseases. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain GN10T from its closely related members and considered to represent novel species in the genus Flavobacterium, for which the name Flavobacterium tagetis (GN10T=KCTC 82695T=NBRC 114841T) is proposed.
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Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula. Int J Syst Evol Microbiol 2021; 71. [PMID: 34542392 DOI: 10.1099/ijsem.0.005012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Gram-stain-positive, non-motile, dull-yellow, short rod-shaped actinomycete strain, designated G10T, was isolated from Tagetes patula (marigold) roots collected from Goyang in the Republic of Korea. The isolate showed best growth on Reasoner's 2A agar at 25 °C, pH 6.5.0 and with 0% NaCl (w/v). The strain was negative for oxidase activity and positive for catalase activity. On the basis of 16S RNA gene sequence similarity, strain G10T was affiliated to the genus Nocardioides and the closest species were Nocardioides glacieisoli HLT3-15T (98.8 %), Nocardioides zhouii HLT2-9T (98.8 %), Nocardioides ganghwensis JC2055T (98.7 %), Nocardioides cavernae YIM A1136T (98.6 %), Nocardioides flavus Y4T (98.5 %), Nocardioides oleivorans DSM 16090T (98.3 %), Nocardioides alpinus Cr7-14T (98.2 %), Nocardioides exalbidus DSM 22017T (98.1 %) and Nocardioides hwasunensis KCTC 19197T (98.1 %). Strain G10T formed a monophyletic cluster with N. glacieisoli HLT3-15T, N. zhouii HLT2-9T and N. hwasunensis KCTC 19197T in all phylogenetic trees. The cell-wall peptidoglycan of strain G10T contained ll-diaminopimelic acid as the diagnostic amino acid. The predominant fatty acids were iso-C16 : 0 and C17 : 1 ω8c. MK-8(H4) was the major isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Average nucleotide identity and digital DNA-DNA hybridization values were 78.6-88.7 % and 21.5-36.2 %, respectively, with the type strains of related species of the genus Nocardioides, suggesting that strain G10T represents a novel species. The genome of strain G10T is 4 231 000 bp long with a DNA G+C content of 71.5 mol% and encodes 4071 predicted proteins, six rRNAs and 46 tRNAs. The genome of strain G10T comprises the biosynthetic gene cluster for T3PKS, terpene, NRPS-like fragment and RRE-containing element as secondary metabolites. The results of taxonomic, phylogenetic, biochemical, chemotaxonomic and genomic analysis clearly supported that strain G10T represent a novel species within the genus Nocardioides, for which the name Nocardioides baculatus sp. nov is proposed and the type strain is G10T (=KCTC 49626T=NBRC 114801T).
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Oryzicola mucosus gen. nov., sp. nov., a novel slime producing bacterium belonging to the family Phyllobacteriaceae isolated from the rhizosphere of rice plants. Antonie van Leeuwenhoek 2021; 114:1925-1934. [PMID: 34491486 DOI: 10.1007/s10482-021-01651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
A novel Gram-stain negative, asporogenous, slimy, rod-shaped, non-motile bacterium ROOL2T was isolated from the root samples collected from a rice field located in Ilsan, South Korea. Phylogenetic analysis of the 16S rRNA sequence showed 96.5% similarity to Tianweitania sediminis Z8T followed by species of genera Mesorhizobium (96.4-95.6%), Aquabacterium (95.9-95.7%), Rhizobium (95.8%) and Ochrobactrum (95.6%). Strain ROOL2T grew optimally at 30 °C in the presence of 1-6% (w/v) NaCl and at pH 7.5. The major respiratory quinone was ubiquinone-10 and the major cellular fatty acids were C18:1ω7c, summed feature 4 (comprising iso-C17:1 I and/or anteiso-C17:1 B) and summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylglycerol, one unidentified aminolipid and two unidentified lipids. The assembled draft genome of strain ROOL2T had 28 contigs with N50 value of 656,326 nt, total length of 4,894,583 bp and a DNA G + C content of 61.5%. The average amino acid identity (AAI) values of strain ROOL2T against the genomes of related members belonging to the same family were below 68% and the ANI and dDDH values between the strain ROOL2T and the type strains of phylogenetically related species were 61.8-76.3% and 19.4-21.1%, respectively. Strain ROOL2T only produces carotenoid-type pigment when grown on LB agar and slime on R2A agar. In the presence of tryptophan, strain ROOL2T produced indole acetic acid (IAA), a phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphatase and tryptophan synthase were found in the genome of strain ROOL2T. The genotypic and phenotypic characteristics indicated that strain ROOL2T represents a novel genus belonging the family Phyllobacteriaceae, for which the name Oryzicola mucosus gen. nov., sp. nov. is proposed. The type strain is ROOL2T (KCTC 82711 T = NBRC 114717 T).
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Limnohabitans radicicola sp. nov., a slow-growing bacterium isolated from rhizosphere of rice plant and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 2021; 71. [PMID: 34402776 DOI: 10.1099/ijsem.0.004957] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the present study, in an attempt to explore the diversity of bacteria in the roots of rice plants, a Gram-stain-negative, motile, facultatively anaerobic, non-pigmented, catalase-positive, oxidase-negative and rod-shaped bacterium with polar flagella was isolated. Phylogenetic analysis based on 16S rRNA gene sequences revealed highest sequence similarity to Limnohabitans parvus KCTC 42859T (98.2%) followed by Limnohabitans curvus KCTC 42562T (98%), Limnohabitans planktonicicus II-D5T (97.9%) and Limnohabitans australis MWH-BRAZ-DAM2DT (97.4%). Growth of strain JUR4T occurred at 10-37 °C (optimum, 30 °C), at pH 5.5-8.0 (optimum, 6.5-7) and in the presence of 0-0.2% NaCl (optimum, 0%, w/v). The genome size of strain JUR4T was found to be 3.34 Mb containing 3139 predicted protein-coding genes with a DNA G+C content of 61.5 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain JUR4T and closely related reference strains were 21.0-24.8% and 74.7-81.4%, respectively. Strain JUR4T contained diphosphatidylglycerol, phoshatidylethanolamine, one unidentified phosphoglycolipid, one unidentified aminophosphoglycolipid, one unidentified phospholipid and seven unidentified glycolipids. The major fatty acids were C16:0 and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c), and ubiquinone Q-8 was the sole isoprenoid quinone. So far, all species belonging to the genus Limnohabitans have been described as non-motile and devoid of flagella. All species were isolated from freshwater and are therefore denoted as planktonic bacteria. This present study introduces a novel motile member of Limnohabitans isolated from the root of rice plant, and introduces the genes associated with motility and methyl-accepting chemotaxis proteins. Phylogenetic, phenotypic, chemotaxonomic and genotypic data clearly indicates that strain JUR4T represents a novel species of the genus Limnohabitans for which the name Limnohabitans radicicola sp. nov. is proposed. The type strain is JUR4T (=KACC 21745T=NBRC 114484T).
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Abstract
A Gram-stain-negative, aerobic and non-motile bacterium, strain sand1-3T, was isolated from beach sand collected from Haeundae Beach located in Busan, Republic of Korea. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, Sphingomonas daechungensis CH15-11T (97.0 %), Sphingomonas edaphi DAC4T (96.8 %), Sphingomonas xanthus AE3T (96.5 %) and Sphingomonas oryziterrae YC6722T (96.0 %) were selected for comparing phenotypic and chemotaxonomic characteristics. Cells of strain sand1-3T grew at 7-50 °C (optimum, 30-35 °C), pH 5.0-8.0 (optimum, pH 7.0-8.0) and in the presence of 0-0.5 % (w/v) NaCl (optimum, 0 %). Major polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, one unidentified glycolipid and one unidentified phosphoglycolipid. The major fatty acids were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) and C18 : 1 2-OH. Moreover, the sole respiratory quinone and major polyamine were identified as ubiquinone-10 and homospermidine, respectively. The genomic DNA G+C content was 65.9 mol%. The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values of strain sand1-3T and its reference strains with publicly available genomes were 17.9-18.9 %, 72.0-75.3 % and 63.3-76.5 % respectively. Based on polyphasic evidence, we propose Sphingomonas sabuli sp. nov. as a novel species within the genus Sphingomonas. The type strain is sand1-3T (=KCTC 82358T=NBRC 114538T).
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Chryseobacterium caseinilyticum sp. nov., a casein hydrolyzing bacterium isolated from rice plant and emended description of Chryseobacterium piscicola. Int J Syst Evol Microbiol 2021; 71. [PMID: 34232119 DOI: 10.1099/ijsem.0.004854] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, asporogenous, catalase-positive and oxidase-negative, non-motile, golden-yellow pigmented, rod-shaped bacterium with casein-degrading ability, designated strain GCR10T, was isolated from roots of rice plants collected from a paddy field near Dongguk University, Republic of Korea. The results of subsequent 16S rRNA gene sequence analysis indicated that GCR10T shares the highest sequence identity with Chryseobacterium piscicola VQ-6316sT (98.3%). Strain GCR10T grew at 2-32 °C (optimum, 25 °C), at pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0-2.0% (w/v) NaCl (optimum in the absence of NaCl). The novel strain was able to produce carotenoid and flexirubin-type pigments. The predominant menaquinone was MK-6 and the major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. The polar lipids were phosphatidylethanolamine, four unidentified aminoglycolipids, two unidentified aminolipids and two unidentified glycolipids. The genome of GCR10T is 4.3 Mb in length with a DNA G+C content of 36.5 mol%. Average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between GCR10T and Chryseobacterium piscicola VQ-6316sT were 82.1, 25.2 and 84.3 %, respectively, which clearly indicates that the novel strain is distinct from its closest relative. The demand for natural biodegradable pigments isolated frominsects, plants or microorganisms is increasing day by day because of their beneficial pharmacological properties. Here, we describe a novel strain that produces two types of pigment, carotenoid and flexirubin. On the basis of the results from phenotypic, genotypic and chemotaxonomic analyses, strain GCR10T represents a novel species of the genus Chryseobacterium, and the name Chryseobacterium caseinilyticum sp. nov. is proposed. The type strain is GCR10T (=KACC 21707T=NBRC 114715T).
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Abstract
A Gram-positive, aerobic, flagellated, endospore-forming, rod-shaped strain, designated as G13T, was isolated from soil. The results of 16S rRNA gene sequence analysis led to the conclusion that strain G13T was phylogenetically related to Cohnella boryungensis BR29T (97.5 %) and Cohnella phaseoli CECT 7287T (96.9 %) with digital DNA-DNA hybridization values of 21.0 and 21.4 %, and distantly related to Cohnella thermotolerans CCUG 47242T (94.8 %), type species of the genus Cohnella, at 19.0 %. The genome size of strain G13T was 5 387 258 bp, with 51.3 mol% G+C content. The predominant fatty acids were summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl), anteiso-C17 : 0, iso-C17 : 0 and iso-C15 : 0. The predominant quinone was menaquinone-7 and the major polar lipids were diphosphatidyglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysylphosphatidylglycerol, three aminophospholipids, two phosphoglycolipids, three aminolipids and two unidentified lipids. Based on the data from phenotypic tests and the genotypic differences between strain G13T and its close phylogenetic relatives, strain G13T represents a new species belonging to the genus Cohnella, for which the name Cohnella terricola sp. nov. (=KACC 19905T=NBRC 113748T) is proposed.
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Flavobacterium baculatum sp. nov., a carotenoid and flexirubin-type pigment producing species isolated from flooded paddy field. Int J Syst Evol Microbiol 2021; 71. [PMID: 33709901 DOI: 10.1099/ijsem.0.004736] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, asporogenous, motile by gliding, dull-yellow, long rod-shaped bacterial strain, designated SNL9T, was isolated from a flooded paddy field near Dongguk University, Republic of Korea. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that SNL9T represents a member of the genus Flavobacterium and is most closely related to Flavobacterium ummariense DS-12T (96.2%) and Flavobacterium viscosum YIM 102796T (96.3%). The average nucleotide identity and in silico DNA-DNA hybridization (DDH) values with F. ummariense DS-12T and F. viscosum YIM 102796T were 89.3/39.1 and 87.1/33 %, respectively. The major fatty acids of SNL9T were identified as iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 9 (comprising iso-C17 : 1ω9c and/or 10 methyl C16 : 0). SNL9T contained MK-6 as the major respiratory quinone. The polar lipids were phoshatidylethanolamine, one unidentified aminophosphoglycolipid, three unidentified aminoglycolipids, two unidentified glycolipids and one unidentified phosphoglycolipid. The DNA G+C content was 34.2 mol%. SNL9T produces carotenoid and flexirubin-type pigments. Among them, carotenoids are particularly valuable for the biotechnological and pharmaceutical industries due to their antioxidant activity. Aryl polyenes (APE) pigments were also found in SNL9T which are responsible for yellow pigment in bacteria. They are stored in the bacterial membrane and protect the bacteria from oxidative stress, particularly from reactive oxygen species. In this paper, we describe a novel isolate, SNL9T, which protect itself from the attack of free radicals using specific natural products in the membrane. Because of their anti-oxidation properties, aryl polyenes may also be of interest to the cosmetic industry. On the basis of the results of phenotypic, genotypic and chemotaxonomic analyses, SNL9T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium baculatum sp. nov. is proposed. The type is SNL9T (=KACC 21170T=NBRC 113746T).
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Lewinella aurantiaca sp. nov., a carotenoid pigment-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:6180-6187. [DOI: 10.1099/ijsem.0.004515] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped, carotenoid-pigmented, motile-by-gliding bacterium, which was designated as SSH13T, was isolated from a surface seawater sample collected from Sehwa Beach in the Republic of Korea. Strain SSH13T was oxidase-negative, catalase-positive and grew at 2–37 °C (optimum, 30 °C), in the presence of 0.5–6% NaCl and within a pH range of pH 6–10 (optimum, pH 8). The novel isolate required NaCl for growth and grew optimally with approximately 2 % NaCl. Chemotaxonomic and morphological characteristics were consistent with members of the genus
Lewinella
. Furthermore, phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain SSH13T was most closely related to the type strains of the genus
Lewinella
. Strain SSH13T had highest 16S rRNA gene sequence similarities to
Lewinella persica
DSM 23188T (95.3 %) and
Lewinella agarilytica
KCTC 12774T (95.0 %). The major fatty acids of SSH13T were summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and iso-C15 : 0. Strain SSH13T contained phosphatidylethanolamine as a major polar lipid. Menaquinone-7 was the predominant respiratory quinone. The average nucleotide identity values between strain SSH13T and
L. persica
T-3T and
L. agarilytica
SST-19T were 72.9 and 72.6 %, respectively. The DNA G+C content of the genomic DNA was 52.8 mol%. The present study aimed to determine the multiple-antibiotic resistance of the novel bacterium. Based on phylogenetic and phenotypic analyses, strain SSH13T is considered to represent a novel species of the genus
Lewinella
, for which the name Lewinella aurantiaca sp. nov. (type strain SSH13T=KACC 21167T=NBRC 113866T) is proposed.
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Reinekea thalattae sp. nov., a New Species of the Genus Reinekea Isolated from Surface Seawater in Sehwa Beach. Curr Microbiol 2020; 77:4174-4179. [PMID: 33025185 DOI: 10.1007/s00284-020-02224-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/22/2020] [Indexed: 10/23/2022]
Abstract
A Gram-stain-negative, non-pigmented, curved rod-shaped, single polarly flagellated, facultatively anaerobic bacterium, designated as SSH23T, was isolated from surface seawater sample collected at the Sehwa Beach in South Korea. The novel isolate required NaCl for growth and grew optimally between 2 and 3% NaCl. Strain SSH23T showed high 16S rRNA gene sequence similarities with Reinekea marinisedimentorum DSM 15388T (96.4%), Reinekea marina KACC 17315T (96.2%), Reinekea blandensis KACC 17315T (95.9%) and Reinekea aestuarii KCTC 22813T (95.6%). The major polar lipids of strain SSH23T were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids of strain SSH23T were C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The predominant respiratory quinone was found to be ubiquinone-8. The average nucleotide identity values of strain SSH23T with R. marinisedimentorum DSM 15388T and R. blandensis MED297T were determined to be 72.2% and 69.8%, respectively. The G+C content of the genomic DNA was 45.5 mol%. Based on genotypic, phenotypic, chemotaxonomic, and phylogenetic analyses, strain SSH23T was considered to represent a novel member of the genus Reinekea, for which the name Reinekea thalattae sp. nov. is proposed. The type strain of Reinekea thalattae is SSH23T (= KACC 21168T = NBRC 113795T).
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Adhaeribacter rhizoryzae sp. nov., a fibrillar matrix-producing bacterium isolated from the rhizosphere of rice plant. Int J Syst Evol Microbiol 2020; 70:5382-5388. [DOI: 10.1099/ijsem.0.004422] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel fibrillar matrix-producing, rod-shaped, red–orange, asporogenous, aerobic bacterium, designated DK36T, was isolated from roots of a rice plant in the Ilsan region near Dongguk University, South Korea. Cells of strain DK36T were Gram-stain-negative and motile by means of gliding. The temperature and pH ranges for growth were 7–35 °C (optimum: 30 °C) and pH 5–10 (optimum: pH 7.0). The strain did not require NaCl for growth but tolerated up to 8 % (w/v) NaCl. Phylogenetic anlaysis of the 16S rRNA gene sequence revealed that DK36T formed a monophyletic clade with
Adhaeribacter aerophilus
6425 S-25T,
Adhaeribacter aerolatus
6515 J-31T and
Adhaeribacter swui
17mud1-7T with sequence similarities of 96.3, 95.5 and 95.2%, respectively. The average nucleotide identity and in silico DNA–DNA hybridization values of strain DK36T with the most closely related strains whose whole genomes are publicly available were 72.5–83.6% and 19–28 %, respectively. The strain showed the typical chemotaxonomic characteristics of the genus
Adhaeribacter
, with the presence of menaquinone MK-7 as the respiratory quinone, and C16 : 1ω5c, iso-C15 : 0 and summed feature 4 (composed of iso-C17 : 1 I/anteiso-C17 : 1 B) as the major fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, one unidentified aminophosphoglycolipid, one unidentified phospholipid, two unidentified aminolipids and five unidentified polar lipids. The genomic DNA G+C content based on the draft genome sequence was 43.4 mol%. The results of physiological and biochemical tests and 16S rRNA gene sequence analysis clearly revealed that strain DK36T represents a novel species of the genus
Adhaeribacter
, for which the name Adhaeribacter rhizoryzae sp. nov. is proposed. The type strain is DK36T (=KACC 19902T=NBRC 113689T).
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Hymenobacter setariae sp. nov., isolated from the ubiquitous weedy grass Setaria viridis. Int J Syst Evol Microbiol 2020; 70:3724-3730. [DOI: 10.1099/ijsem.0.004226] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, short-rod, aerobic, non-motile, red to pink-pigmented bacterium, designated Fur1T, was isolated from the dry spikelet clusters of a plant called Setaria viridis near Dongguk University. Phylogenetic analysis conducted based on 16S rRNA gene sequences indicated that strain Fur1T belonged to the genus
Hymenobacter
of the family
Hymenobacteraceae
. The 16S rRNA gene of Fur1T showed highest sequence similarity to those of
Hymenobacter metalli
KACC 17381T (97.5 %) and
Hymenobacter marinus
KACC 19042T (97.1 %). Growth occurred at 4–37 °C (optimum, 25–28 °C), up to 1.0 % NaCl (optimum, 0 %) and pH 5.5–9.0 (optimum, pH 6.0–7.5). The major fatty acids of strain Fur1T were identified as iso-C15 : 0, C16 : 1
ω5c, anteiso-C15 : 0, summed feature 3 (comprising C16 : 1
ω7c and/or C16 : 1
ω6c) and summed feature 4 (comprising anteiso-C17 : 1B and/or iso-C17 : 1I) as the major cellular fatty acids. The predominant respiratory quinone was identified as MK-7. The polar lipids were phosphatidylethanolamine, five unidentified aminophospholipids, two unidentified phospholipids, one unidentified glycolipid and one unidentified polar lipid. The genomic DNA G+C content based on the draft genome sequence was 58.7 mol%. DNA–DNA relatedness between strain Fur1T and its closest relative was below 70 %. Characterization based on phylogenetic, chemotaxonomic and phenotypic analyses clearly indicated that strain Fur1T represents a novel species of the genus
Hymenobacter
, for which the name Hymenobacter setariae sp. nov. is proposed. The type strain is Fur1T (=KACC 19903T=NBRC=113691T).
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Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil. Int J Syst Evol Microbiol 2020; 70:2449-2456. [DOI: 10.1099/ijsem.0.004054] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A gamma radiation-resistant and pink-pigmented bacterial strain, designated as 17Sr1-39T, was isolated from a gamma ray-irradiated soil sample collected in the Republic of Korea. Cells were Gram-stain-negative, strictly aerobic, flagellated, asporogenous, rod-shaped and methylotrophic. Results of 16S rRNA gene sequence analysis showed that strain 17Sr1-39T was phylogenetically related to
Methylobacterium currus
PR1016AT (97.3 %),
Methylobacterium aquaticum
DSM 16371T (97.2 %),
Methylobacterium platani
PMB02T (97.0 %),
Methylobacterium frigidaeris
IER25-16T (96.6 %), Methylobacterium terrae 17Sr1-28T (96.6 %) and
Methylobacterium organophilum
JCM 2833T (93.4 %). The G+C content calculated based on the genome sequence was 70.4 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain 17Sr1-39T and
M. currus
,
M. aquaticum
,
M. platani
,
M. frigidaeris
, M. terrae and
M. organophilum
were 77.3–89.9 and 22–38.2 %, respectively. The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on the data from phenotypic tests and genotypic differences between strain 17Sr1-39T and its close phylogenetic relatives, strain 17Sr1-39T represented a new species belonging to the genus
Methylobacterium
, for which the name Methylobacterium terricola sp. nov. (=KACC 52905T=NBRC 112874T) is proposed.
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Sphingomonas edaphi sp. nov., a novel species isolated from beach soil in the Republic of Korea. Int J Syst Evol Microbiol 2020; 70:522-529. [DOI: 10.1099/ijsem.0.003780] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil. J Microbiol 2019; 57:1079-1085. [DOI: 10.1007/s12275-019-9350-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/10/2019] [Accepted: 10/28/2019] [Indexed: 01/02/2023]
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Methylobacterium durans sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. Antonie van Leeuwenhoek 2019; 113:211-220. [DOI: 10.1007/s10482-019-01331-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/12/2019] [Indexed: 01/28/2023]
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Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. J Microbiol 2019; 57:959-966. [PMID: 31463788 DOI: 10.1007/s12275-019-9007-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 01/05/2023]
Abstract
A Gram-stain-negative, asporogenous, aerobic rods, motile by means of a single polar flagellum, catalase- and oxidase-positive, methylotrophic bacterium, designated 17Sr1-28T, was isolated from gamma ray-irradiated soil. The 16S rRNA gene sequence analysis showed that strain 17Sr1-28T was phylogenetically related to Methylobacterium currus PR1016AT (96.8%), Methylobacterium platani PMB02T (96.2%), Methylobacterium aquaticum DSM 16371T (96.3%), Methylobacterium tarhaniae N4211T (96.4%), Methylobacterium frigidaeris IER25-16T (95.8%), and Methylobacterium organophilum JCM 2833T (92.7%). The G+C content calculated based on genome sequence was 71.6%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain 17Sr1- 28T and M. currus, M. platani, M. aquaticum, M. tarhaniae, M. frigidaeris, and M. organophilum were 77.7-90.4% and 22-39.6%, respectively. The major fatty acids of strain 17Sr1-28T were summed feature 8 (C18:1ω7c and/or C18:1ω6c), and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. On the basis of the data from phenotypic tests and genotypic differences between strain 17Sr1-28T and its close phylogenetic relatives, strain 17Sr1-28T represents a new species belonging to the genus Methylobacterium, for which the name Methylobacterium terrae sp. nov. (= KCTC 52904T = NBRC 112873T) is proposed.
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Amnibacterium setariae sp. nov., an endophytic actinobacterium isolated from dried foxtail. Antonie van Leeuwenhoek 2019; 112:1731-1738. [PMID: 31332634 DOI: 10.1007/s10482-019-01302-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/16/2019] [Indexed: 11/30/2022]
Abstract
A Gram-stain positive, short rod-shaped, aerobic, motile by means of gliding, yellow-pigmented actinobacterium, designated strain DD4aT, was isolated from dry yellow foxtail. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DD4aT is closely related to Amnibacterium soli MB78T (98.4% similarity), Amnibacterium kyonggiense KSL51201-037T (98.2%) and Amnibacterium endophyticum 1T4Z-3T (97.43%). Strain DD4aT forms yellow colonies on R2A agar medium. The peptidoglycan was found to contains diaminopimelic acid (which is a diagnostic cell wall diamino acid), alanine, glutamic acid and lysine. The polar lipids diphosphatidylglycerol, phosphatidylglycerol, six unidentified glycolipids and an unidentified polar lipid were found to be present in strain DD4aT. The major cellular fatty acids anteiso-C15:0 (42.9%) and iso-C16:0 (34.6%) were found in strain DD4aT. The predominant respiratory quinones were found to be MK-11 and MK-12. The DNA G+C content of strain DD4aT is 73.9 mol%. DNA-DNA relatedness of strain DD4aT with A. soli MB78T, A. kyonggiense KSL51201-037T, and A. endophyticum 1T4Z-3T were 53.3% (± 1.1%), 47.0% (± 0.5%), and 47.9% (± 0.9%), respectively. The digital DNA-DNA hybridisation and average nucleotide identity values between strain DD4aT and A. kyonggiense KSL51201-037T were determined to be 26.1% and 82.7%. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, DD4aT represents a novel member of the genus Amnibacterium, for which the name Amnibacterium setariae sp. nov., is proposed. The type strain of Amnibacterium setariae is DD4aT (= KACC 19817T = JCM 32878T).
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Ilyomonas limi gen. nov., sp. nov., a new member of the family Chitinophagaceae isolated from mud. Antonie van Leeuwenhoek 2019; 112:1715-1723. [PMID: 31289977 DOI: 10.1007/s10482-019-01300-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/03/2019] [Indexed: 11/26/2022]
Abstract
A Gram-strain negative, aerobic, catalase and oxidase positive, non-motile, short rod-shaped bacterium, designated 17mud1-8T, was isolated from mud collected from Nowon-gu, Seoul, South Korea. The strain was found to be able to grow at 10-40 °C (optimum 28-30 °C), pH 5.0-8.0 (optimum 7.0), and in the absence of NaCl. The nearly full-length 16S rRNA gene of strain 17mud1-8T exhibits sequence similarity of 94.1% with that of Panacibacter ginsenosidivorans Gsoil 1550T, followed by 93.6% sequence similarity with Parafilimonas terrae DSM 28286T. Phylogenetic analysis indicated that strain 17mud1-8T belongs to the family Chitinophagaceae, sharing approximately 94.1-91.9% sequence similarity with members of closely related genera. The respiratory quinone was identified as MK-7. The predominant fatty acids were found to consist of iso-C15:0, iso-C17:1ω5c and iso-C15:1 G. The polar lipids were identified as phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid, ten unidentified aminolipids and seven unidentified lipids. The draft genome of 17mud1-8T has G+C content of 40.9 mol% and a 5.8 Mb chromosome. On the basis of the phenotypic and genotypic properties, and phylogenetic inference, strain 17mud1-8T was found to represent a novel genus in the family Chitinophagaceae, for which the name Ilyomonas limi gen. nov., sp. nov. is proposed, with the type strain 17mud1-8T(=KCTC 52874T = NBRC 112826T).
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Pontibacter oryzae sp. nov., a carotenoid-producing species isolated from a rice paddy field. Antonie van Leeuwenhoek 2019; 112:1705-1713. [DOI: 10.1007/s10482-019-01298-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/27/2019] [Indexed: 01/02/2023]
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Lysobacter caseinilyticus, sp. nov., a casein hydrolyzing bacterium isolated from sea water. Antonie van Leeuwenhoek 2019; 112:1349-1356. [DOI: 10.1007/s10482-019-01267-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/12/2019] [Indexed: 10/27/2022]
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