Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium

Yoon, Jung Hoon; Cho, Yong Gyun; Lee, Sung Taik; Suzuki, Ken‐ichiro; Nakase, Takashi; Park, Yong Ha

doi:10.1099/00207713-49-2-675

Cited by 94 publications

(72 citation statements)

References 21 publications

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“…Tweens 20, 40 and 60 are hydrolysed. Acetate, L-malate, pyruvate and L-glutamate are utilized as sole carbon and energy sources and salicin is weakly utilized, but citrate, succinate, dData from Prauser (1976Prauser ( , 1984, Collins et al (1994), Yoon et al (1997Yoon et al ( , 1999Yoon et al ( , 2004 and Lawson et al (2000); a different result was reported by Yi & Chun (2004a). Table 1. cont.…”

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confidence: 41%

“…fatty acids representing >1 % of the total) comprised the following: branched fatty acids iso-C 16 : 0 (49.7 %), anteiso-C 17 : 0 (4.9 %), iso-C 17 : 0 (2.6 %), iso-C 18 : 0 (2.3 %), iso-C 15 : 0 (1.6 %) and iso-C 16 : 1 (2.3 %); unsaturated fatty acids C 18 : 1 v9c (7.4 %), C 17 : 1 v6c (5.4 %) and C 17 : 1 v8c (1.1 %); straight-chain fatty acids C 18 : 0 (2.3 %), C 17 : 0 (1.9 %) and C 16 : 0 (1.7 %); 10-methyl fatty acids C 18 : 0 (8.3 %), C 17 : 0 (2.9 %) and C 16 : 0 (1.8 %), and summed feature 3 (C 16 : 1 v7c and/or iso-C 15 : 0 2-OH) (1.6 %). This fatty acid profile is similar to those of Nocardioides species, although there are differences in the proportions of some fatty acids, perhaps because of differences in the extraction and cultivation conditions (Yoon et al, 1997(Yoon et al, , 1999(Yoon et al, , 2004(Yoon et al, , 2005aLawson et al, 2000;Yi & Chun, 2004a, b;Kubota et al, 2005). The DNA G+C content of strain DS-51 T was 71.1 mol%.…”

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confidence: 81%

“…albus; 3, N. luteus; 4, N. simplex; 5, N. plantarum; 6, N. pyridinolyticus; 7, N. nitrophenolicus; 8, N. aquaticus; 9, N. aquiterrae; 10, N. ganghwensis; 11, N. aestuarii; 12, N. alkalitolerans; 13, N. kribbensis; 14, N. oleivorans; 15, N. aromaticivorans; 16, N. lentus; 17, N. kongjuensis. Data are from Collins et al (1989Collins et al ( , 1994, Lawson et al (2000), Prauser (1976Prauser ( , 1984Prauser ( , 1989, Suzuki & Komagata (1983), Yoon et al (1997Yoon et al ( , 1999Yoon et al ( , 2004Yoon et al ( , 2005aYoon et al ( , b, 2006a, Yi & Chun, (2004a, b), Schippers et al (2005) and Kubota et al (2005). +, Positive reaction; 2, negative reaction; ND, not determined; W, weakly positive reaction; V, variable reaction.…”

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Nocardioides insulae sp. nov., isolated from soil

Yoon

Kang

Lee

et al. 2007

International Journal of Systematic and Evolutionary Microbiology

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A Gram-positive, rod-shaped or coccoid bacterial strain, DS-51 T , was isolated from a soil in Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain DS-51 T grew optimally at pH 8.0 and 30 6C without NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-51 T forms a distinct line of descent within the radiation enclosed by the genus Nocardioides. The chemotaxonomic properties of strain DS-51 T were consistent with those of the genus Nocardioides: the cell-wall peptidoglycan type was based on LL-2,6-diaminopimelic acid, MK-8(H 4 ) was the predominant menaquinone and iso-C 16 : 0 was the major fatty acid. The DNA G+C content was 71.1 mol%. The 16S rRNA gene sequence of strain DS-51 T had similarity levels of 92.5-95.1 % with the sequences of the type strains of Nocardioides species. Strain DS-51 T could be distinguished from other Nocardioides species by differences in some phenotypic characteristics. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain DS-51 T represents a novel species of the genus Nocardioides, for which the name Nocardioides insulae sp. nov. is proposed. The type strain is DS-51 T (=KCTC 19180 T =DSM 17944 T ).

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Nocardioides insulae sp. nov., isolated from soil

Yoon

Kang

Lee

et al. 2007

International Journal of Systematic and Evolutionary Microbiology

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“…Cell-wall diamino acid was determined as described by Staneck & Roberts (1974). Most chemotaxonomical characters of strain JC2056 T were typical of the genus Nocardioides (Collins et al, 1994;Lawson et al, 2000;O'Donnell et al, 1982;Prauser, 1976Prauser, , 1986Suzuki & Komagata, 1983;Yoon et al, 1997Yoon et al, , 1999Yoon et al, , 2003); MK-8(H 4 ) as a major menaquinone, LL-DAP as a cell-wall diaminopimelic acid, 70 mol% as the DNA G+C content. The cellular fatty acid composition of our isolate also resembled that of other Nocardioides species, but was differentiated by high proportions of iso-16 : 0 (52?0 %) and iso-16 : 1 H (14?5 %).…”

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Nocardioides aestuarii sp. nov., isolated from tidal flat sediment

Chun

2004

International Journal of Systematic and Evolutionary Microbiology

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A strictly aerobic, non-motile, rod-shaped actinomycete, designated strain JC2056 T , was isolated from a sediment sample of getbol, the tidal flat of Korea. Results of 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Nocardioides, with the highest similarity being to Nocardioides luteus KCTC 9575 T (95?7 %). The major menaquinone was MK-8(H 4 ), and predominant cellular fatty acids were iso-16 : 0 and iso-16 : 1 H. The DNA G+C content was 70 mol%. Based on the morphological, physiological, biochemical and chemotaxonomical data presented in this study, strain JC2056 T should be classified as a novel species, for which the name Nocardioides aestuarii sp. nov. is proposed; the type strain is JC2056 T (=IMSNU 14029 T =KCTC 9921 T =JCM 12125 T ).Recently, a novel Nocardioides species was isolated from getbol (Korean tidal flat) of Ganghwa Island in Korea, and described as Nocardioides ganghwensis (Yi & Chun, 2004). An additional Nocardioides strain, JC2056 T , was also isolated from getbol sediment near the site (37 u 369 22?30 N, 126 u 229 59?40 E). In this study, the newly isolated strain was the subject of a taxonomic investigation to elucidate the identity; the name Nocardioides aestuarii sp. nov. is proposed for this isolate.Strain JC2056 T was isolated using MR2A [R2A (Difco) supplemented with artificial sea salts (Sigma)] and was routinely cultured on marine agar 2216 (MA; Difco) at 30 u C and maintained as a glycerol suspension (20 %, w/v) at 280 uC.Primers, PCR condition and sequencing method for the 16S rRNA gene were as described previously (Chun & Goodfellow, 1995). Phylogenetic analyses were performed following the same methods and procedure described previously (Yi & Chun, 2004) using the jPHYDIT (available at http://chunlab.snu.ac.kr/jphydit) and PAUP 4.0 (Swofford, 1998). Initial BLAST searching against GenBank using the 16S rRNA gene sequence of strain JC2056 T (1380 bp) indicated that the test strain belonged to the genus Nocardioides. The newly determined sequence was then aligned manually against representatives of the family Nocardioidaceae using secondary-structure information of bacterial 16S rRNA. Domains used to construct the phylogenetic trees were the regions available for all sequences (positions 38-1431; Escherichia coli numbering system), excluding positions showing ambiguous alignment (positions 76-95, 199-219, 455-478, 1025-1037 and 1135-1140). On the basis of 16S rRNA gene sequence similarity, the closest cultured bacterial relatives were Nocardioides species (93?6-95?7 %), Marmoricola aurantiacus DSM 12652 T (93?1 %) and Aeromicrobium species (92?7-93?0 %). The highest sequence similarity was observed with Nocardioides luteus KCTC 9575 T (95?7 %), which is below the recommended cut-off value of 97 % for bacterial species definition (Stackebrandt & Goebel, 1994). This relationship between our isolate and other members of the family Nocardioidaceae was also evident in the phylogenetic tree (Fig. 1). Although the branching position varied depending on th...

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“…each constituted >10 % of total fatty acids) are iso-C 16 : 0 , 10-methyl C 18 : 0 and C 17 : 1 v6c, although there are differences in the proportions of some fatty acids, perhaps because of differences in extraction and cultivation conditions (Yoon et al, 1997(Yoon et al, , 1999(Yoon et al, , 2004(Yoon et al, , 2005aLawson et al, 2000;Yi & Chun, 2004a, b;Kubota et al, 2005). The DNA G+C content of strain A2-4 T was 72?1 mol%.…”

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Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium

Yoon

Lee

Jung

et al. 2006

International Journal of Systematic and Evolutionary Microbiology

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A Gram-positive, rod-or coccoid-shaped and N-hexanoyl-L-homoserine lactone-degrading bacterial strain, A2-4 T , was isolated from a soil in Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain A2-4 T grew optimally at pH 7?0-8?0 and 30 6C without NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain A2-4 T is most closely related to members of the genus Nocardioides. Strain A2-4 T possessed chemotaxonomic properties indicative of members of the genus Nocardioides; the cell-wall peptidoglycan type was based on LL-diaminopimelic acid, MK-8(H 4 ) was the predominant menaquinone and iso-C 16 : 0 was the predominant fatty acid. The DNA G+C content was 72?1 mol%. The 16S rRNA gene sequence of strain A2-4 T was 98?3-99?1 % similar to those of the type strains of Nocardioides simplex, Nocardioides aromaticivorans and Nocardioides nitrophenolicus and 93?8-96?3 % similar to those of the type strains of other Nocardioides species. Strain A2-4 T could be distinguished from the three phylogenetic relatives, N. nitrophenolicus, N. aromaticivorans and N. simplex, by DNA-DNA relatedness (25-42 %) and by differences in some phenotypic characteristics. On the basis of the phenotypic, phylogenetic and genetic data, the strain represents a novel species of the genus Nocardioides, for which the name Nocardioides kongjuensis sp. nov. is proposed. The type strain is A2-4 T (=KCTC 19054 T =JCM 12609 T ).Many bacteria, particularly Gram-negative bacteria, are known to control the expression of specific genes in response to cell density by means of a signalling mechanism referred to as quorum-sensing (Salmond et al., 1995;Swift et al., 1996; Fuqua & Greenberg, 1998). This type of signalling mechanism depends on small, diffusible signal molecules, N-acylhomoserine lactones (AHLs), all of which have an identical homoserine lactone ring, although the acyl side-chain length and substitutions in the side-chain differ. The quorum-sensing system plays an important role in the control of virulence-gene expression in pathogenic bacteria, including Erwinia carotovora (Jones et al., 1993) and Pseudomonas aeruginosa (Pearson et al., 1994(Pearson et al., , 1997. Enzymic degradation of AHL molecules was reported as a useful strategy for disrupting the quorum-sensing signal system, thereby interfering with infection in the case of many pathogenic bacteria. Some AHL-degrading microorganisms and enzymes have been reported recently (Dong et al., 2000;Leadbetter & Greenberg, 2000;Lee et al., 2002; Flagan et al., 2003; Park et al., 2003;Uroz et al., 2003). In this study, an AHL-degrading Nocardioides-like bacterial strain, A2-4 T , which was isolated from a soil sample, is described. To date, bacteria that are able to degrade AHLs have not been reported for the genus Nocardioides. Accordingly, the aim of the present study was to determine the exact taxonomic position of strain A2-4 T by using a polyphasic taxonomic approach.Soil samples collected from Kongju, Korea, were used as the source ...

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Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium

Cited by 94 publications

References 21 publications

Nocardioides insulae sp. nov., isolated from soil

Nocardioides insulae sp. nov., isolated from soil

Nocardioides aestuarii sp. nov., isolated from tidal flat sediment

Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium

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