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So Y, Chhetri G, Kim I, Park S, Jung Y, Woo H, Seo T. 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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Affiliation(s)
- Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea
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Chen MS, Chen F, Chen XH, Zheng ZQ, Ma X, Tuo L. Nocardioides mangrovi sp. nov., a novel endophytic actinobacterium isolated from root of Kandelia candel. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005295] [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 novel species of endophytic actinobacterium, designated strain GBK3QG-3T, was isolated from surface-sterilized root of Kandelia candel collected from Beilun Estuary, Guangxi Zhuang Autonomous Region, PR China. Cells of strain GBK3QG-3T were Gram-stain-positive, aerobic, non-spore-forming and rod-shaped. Growth of GBK3QG-3T was observed at 10–40 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 7.0) and in the presence of 0–3 % (w/v) NaCl (optimum, 0 %). The G+C content of genomic DNA was determined to be 72.2 mol%. On the basis of 16S rRNA gene sequence analysis, strain GBK3QG-3T was most related to the type strain of
Nocardioides agrisoli
CCTCC AB 2017058T (97.7 % 16S rRNA gene sequence similarity), followed by
Nocardioides ginkgobilobae
SYP-A7303T (97.0 %) and
Nocardioides aquiterrae
GW-9T (96.9 %). Average nucleotide identity and digital DNA–DNA hybridization values between strain GBK3QG-3T and some strains of the genus
Nocardioides
with publicly available genomes were below 84.3 and 30.0 %, respectively. The cell-wall peptidoglycan contained ll-diaminopimelic acid. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and an unknown lipid. The major menaquinone was identified as MK-8(H4), and the major fatty acids were identified as iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, we propose a novel species named Nocardioides mangrovi sp. nov. The type strain is GBK3QG-3T (=CGMCC 4.7708T=JCM 34553T).
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Affiliation(s)
- Ming-Sheng Chen
- School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563006, PR China
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Feng Chen
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China
| | - Xiao-Hui Chen
- School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563006, PR China
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Zhou-Qing Zheng
- School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563006, PR China
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Xiao Ma
- School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563006, PR China
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Li Tuo
- School of Basic Medical Sciences, Zunyi Medical University, Zunyi 563006, PR China
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
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