Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil

Singh, Hina; Du, Juan; Trinh, Huan; Won, KyungHwa; Yang, Jung Eun; Yin, Chang-Shik; Kook, MooChang; Yi, Tae–Hoo

doi:10.1099/ijsem.0.000730

Cited by 25 publications

(7 citation statements)

References 61 publications

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“…albidus and N. sambongensis [3, 5, 6]. The strains had MK-8(H 4 ) as their major quinone and ll -diaminopimelic acid as the diagnostic diamino acid of their cell-wall peptidoglycan, which is the major respiratory quinone found in other members of the genus Nocardiodes [3–8].…”

Section: Full-textmentioning

confidence: 99%

“…The DNA G+C content of members of the genus Nocardioides is around 68-74 mol% [2]. Species in the genus Nocardioides have been isolated from various sources, such as soil, sludge of domestic wastewater and plants [3][4][5][6][7][8]. Many strains of the genus Nocardioides play an important role in bioremediation and they decompose various pollutants such as alkanes, pyridine, phenols, phenanthrene, etc.…”

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confidence: 99%

“…The strains differed from Nocardioides species by the absence of a phosphatidylinositol. However, it is worth noting that the absences of phosphatidylinositol also occurs in N. dilutes, N. albidus and N. sambongensis [3,5,6]. The strains had MK-8(H 4 ) as their major quinone and ll-diaminopimelic acid as the diagnostic diamino acid of their cell-wall peptidoglycan, which is the major respiratory quinone found in other members of the genus Nocardiodes [3][4][5][6][7][8].…”

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confidence: 99%

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Nocardioides convexus sp. nov. and Nocardioides anomalus sp. nov., isolated from soil and mineral water

Park

Liu

Maeng

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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Two bacterial strains designated as W3-2-3T and HKS04T were isolated from mineral water and a soil sample, respectively, in the Republic of Korea. The 16S rRNA genes of the two strains shared a sequence similarity of 93.5 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains W3-2-3T and HKS04T formed a distinct lineage within the genus Nocardioides of the family Nocardioidaceae (order Propionibacteriales ). The closely related species of strain W3-2-3T were Nocardioides albidus (98.9 %), Nocardioides caeni (98.8 %), Nocardioides kongjuensis (98.6 %), Nocardioides aromaticivorans (98.5 %), Nocardioides nitrophenolicus (98.4 %), Nocardioides flava (98.2 %) and Nocardioides ginsengisoli (98.1 %). The closest species of strain HKS04T was Nocardioides halotolerans (98.7 %). The genome sizes of strains W3-2-3T and HKS04T were 4741198 and 5 120341 bp, respectively. The genomic DNA G+C contents of strains W3-2-3T and HKS04T were 73.3 and 72.1 mol%, respectively. The main fatty acids of strain W3-2-3T were C17:1 ω6c and iso-C16:0 and those of strain HKS04T were iso-C16:0 and iso-C16:0 H. The main polar lipids of both strains were diphosphatidylglycerol and phosphatidylglycerol and the predominant respiratory quinone was MK-8(H4), supporting the affiliation of these strains with the genus Nocardioides . Based on the results of biochemical, chemotaxonomic and phylogenetic analyses, two novel species, Nocardioides convexus W3-2-3T (KACC 21211T=LMG 31251T) and Nocardioides anomalus HKS04T (KACC 18879T=LMG 31249T), are proposed.

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Nocardioides convexus sp. nov. and Nocardioides anomalus sp. nov., isolated from soil and mineral water

Park

Liu

Maeng

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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“…Members of the genus Nocardioides are characterized as being Gram-positive and aerobic with a high DNA G+C content (68.7–74.9 mol%). Menaquinone MK-8(H 4 ) is the major respiratory quinone and ll -diaminopimelic acid is the diagnostic diamino acid of the peptidoglycan [8]. Previously, a potential novel endophytic actinobacterium, strain GBK3QG-3 T , was isolated from root of Kandelia candel .…”

Section: Full-textmentioning

confidence: 99%

Nocardioides mangrovi sp. nov., a novel endophytic actinobacterium isolated from root of Kandelia candel

Chen

et al. 2022

International Journal of Systematic and Evolutionary Microbiology

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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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“…de/ genus/ nocardioides). These species have been isolated from a wide variety of sources like soils, sediments, seawater, plants, hyper saline lake, black sand, rhizosphere, sea urchins, volcanic ash and even from glacier [3][4][5][6][7][8][9][10][11][12]. The characteristic features of these members include the presence of ll-2,6-diaminopimelic acid as the major diamino acid of the peptidoglycan in their cell wall [13].…”

Section: Introductionmentioning

confidence: 99%

Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula

Chhetri

Kim

Kang

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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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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Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil

Cited by 25 publications

References 61 publications

Nocardioides convexus sp. nov. and Nocardioides anomalus sp. nov., isolated from soil and mineral water

Nocardioides convexus sp. nov. and Nocardioides anomalus sp. nov., isolated from soil and mineral water

Nocardioides mangrovi sp. nov., a novel endophytic actinobacterium isolated from root of Kandelia candel

Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula

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