Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov.

Bala, Shashi; Khanna, Richie; Dadhwal, Mandeep; Prabagaran, Solai Ramatchandirane; Shivaji, Sisinthy; Cullum, John; Lal, Rup

doi:10.1099/ijs.0.02901-0

Cited by 67 publications

(44 citation statements)

References 24 publications

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“…DNA-DNA hybridization was carried out between strain P25 T and five closely related type strains that showed more than 97 % 16S rRNA gene sequence similarity. Total genomic DNA of the six strains was extracted and purified and hybridization was done by following the protocols described by Bala et al (2004) and Tourova & Antonov (1987). The amount of bound probe DNA was calculated by using a scintillation counter (Wallac Microbeta Trilux 1450; Perkin Elmer).…”

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Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil

Bala

Sharma

Lal

2010

International Journal of Systematic and Evolutionary Microbiology

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A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterial strain, P25T , was isolated from an HCH dump site located in the northern part of India. Phylogenetic analysis based on the 16S rRNA gene sequence showed that the strain belongs to the genus Sphingobium, as it showed highest sequence similarity to Sphingobium amiense IAM 15006 T (97.7 %). The 16S rRNA gene sequence similarity between strain P25 T and members of other species of the genus Sphingobium with validly published names ranged from 94.0 to 97.7 %. The DNA-DNA relatedness between strain P25 T and Sphingobium amiense IAM 15006 T and other related strains was found be less than 30 %, confirming it to represent a novel species. The DNA G+C content of strain P25 T was 65 mol%. The polyamine profile showed the presence of spermidine.The predominant cellular fatty acids were summed feature 8 (18 : 1v7c and/or 18 : 1v6c; 48.3 %), 16 : 0 (13.7 %) and 14 : 0 2-OH (8.8 %). The polar lipid profile of strain P25 T also corresponded to those reported for sphingomonads (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid), supporting its identification as a member of the family Sphingomonadaceae. The results obtained from DNA-DNA hybridization and biochemical and physiological tests clearly distinguished strain P25 T from closely related members of the genus Sphingobium. Thus, a novel species of the genus Sphingobium is proposed, Sphingobium quisquiliarum sp. nov. The type strain is P25 T (5MTCC 9472 T 5CCM 7543 T ).Sphingomonads belong to the class Alphaproteobacteria, order Sphingomonadales. The order Sphingomonadales contains the genera Sphingomonas, Sphingobium, Novosphingobium, Sphingopyxis (Takeuchi et al., 2001) and Sphingosinicella (Maruyama et al., 2006). Previous studies of a hexachlorocyclohexane (HCH)-contaminated dump site revealed that sphingomonads were the predominant group of micro-organisms at such sites (Dadhwal et al., 2009; Böltner et al., 2005). These sphingomonads tolerate very high levels of HCH residues, and many could degrade HCH isomers (Dadhwal et al., 2009).A soil sample was collected from the HCH dump site, serially diluted and plated on nystatin/streptomycinamended Luria-Bertani (LB) agar plates (Vanbroekhoven et al., 2004;Dadhwal et al., 2009). A yellow colony that appeared within 36 h of incubation at 28 u C was picked and purified by repeated streaking on LB agar. The ability of the strain, designated P25 T , to degrade a-, b-, c-and d-HCH was determined by a resting cell assay as described previously (Sharma et al., 2006). Sphingobium indicum B90A T , which can degrade all HCH isomers, was used as a reference (Kumari et al., 2002;Raina et al., 2008) in the degradation assay ( Supplementary Fig. S1, available in IJSEM Online). Strain P25T was found to degrade all four HCH isomers, with activity decreasing in the order a.c.b.d. Moreover, strain P25T degraded the a-and c-HCH isomers faster than Sphingobium indicum B90A T ( Supple...

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Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil

Bala

Sharma

Lal

2010

International Journal of Systematic and Evolutionary Microbiology

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“…The type strains of A. lexingtonensis and A. pretoriensis, for example, share a 16S rRNA gene similarity of 99?9 % and a DNA-DNA relatedness value of 54?1 % (Labeda et al, 2003). Similarly, the type strain of A. rifamycinica has only six mismatches (99?6 % similarity) with respect to its closest neighbour, A. kentuckyensis, but shows a DNA-DNA hybridization value of only 67 % with the latter (Bala et al, 2004).…”

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Amycolatopsis australiensis sp. nov., an actinomycete isolated from arid soils

Tan

Robinson²,

Lacey³

et al. 2006

International Journal of Systematic and Evolutionary Microbiology

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The taxonomic position of a group of mesophilic actinomycetes isolated from arid Australian soils was determined using a polyphasic approach. The organisms shared chemical and morphological markers typical of members of the genus Amycolatopsis. They had identical 16S rRNA gene sequences and formed a distinct phyletic line in the Amycolatopsis mediterranei clade, being most closely related to A. mediterranei. In addition, they shared a range of phenotypic properties that distinguished them from representatives of all of the species classified in this clade. The combined genotypic and phenotypic data indicate that the strains merit species status within the genus Amycolatopsis. The name proposed for the novel species is Amycolatopsis australiensis sp. nov.; the type strain is GY048 T (=DSM 44671 T =NCIMB 14142 T ).

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“…DNA-DNA hybridization was carried out by the membrane filter method (Tourova & Antonov, 1987). DNA-DNA relatedness between the strains was determined according to Bala et al (2004). DNA (10 mg) of each strain was transferred onto a positively charged nylon membrane (Hybond-N; Amersham) using a dot blot apparatus (Bio-Rad).…”

Section: Dna-dna Hybridizationmentioning

confidence: 99%