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Int J Syst Evol Microbiol 53 (2003), 1005-1007; DOI  10.1099/ijs.0.02449-0
© 2003 International Union of Microbiological Societies

Transfer of Hongia koreensis Lee et al. 2000 to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov.

Kyounghee Sohn1, Soon Gyu Hong2, Kyung Sook Bae2 and Jongsik Chun1

1 School of Biological Sciences, Seoul National University, 56-1 Shillim-dong, Kwanak-gu, Seoul 151-742, Republic of Korea
2 Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, PO Box 115, Yusong, Taejon 305-600, Republic of Korea

Correspondence
Jongsik Chun
jchun{at}snu.ac.kr


   ABSTRACT
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The taxonomic status of Hongia koreensis was investigated by molecular systematic methods. On the basis of 16S rDNA phylogeny, H. koreensis was closely associated with Kribbella flavida and Kribbella sandramycini and formed a monophyletic clade with these species. These three taxa shared over 98 % 16S rDNA sequence similarity and many chemotaxonomic properties, which strongly indicates that they belong to the same genus. DNA–DNA pairing was employed to elucidate the genomic relatedness among these taxa. H. koreensis represented a distinct genomic species that can be differentiated from members of the genus Kribbella. Physiological characteristics and phospholipid and cellular fatty acid compositions can be also used to separate H. koreensis from species of the genus Kribbella. On the basis of data presented in this and earlier studies, it is proposed that H. koreensis Lee et al. 2000Go should be transferred to the genus Kribbella Park et al. 1999Go as Kribbella koreensis comb. nov.

Published online ahead of print on 29 November 2002 as DOI 10.1099/ijs.0.02449-0.


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The genus Hongia was proposed to accommodate a nocardioform actinomycete strain isolated from gold-mine soil in Korea (Lee et al., 2000Go). Similarly, Park et al. (1999)Go independently described the genus Kribbella to encompass strains previously known as ‘Nocardioides fulvus’ IFO 14399 (now NBRC 14399) and Nocardioides sp. ATCC 39419. The proposals of these two novel genera were based on unique chemotaxonomic markers, i.e. tetrahydrogenated menaquinone with nine isoprene units, L-alanine at the first position of peptide subunits, phospholipid composition and phylogenetic analysis based on 16S rDNA. Although these genera were proposed separately, we have found that they have many common morphological and chemotaxonomic properties. Therefore, we re-examined the taxonomic status of these two genera.

16S rDNA sequences of Hongia koreensis (the only species in this genus) and two Kribbella species (namely, Kribbella flavida and Kribbella sandramycini) were determined in previous studies (Lee et al., 2000Go; Park et al., 1999Go). Corresponding 16S rRNA gene sequences of related actinomycetes were obtained from GenBank. Alignment, pairwise comparison and phylogenetic analysis were done using the PHYDIT program (available at http://plaza.snu.ac.kr/~jchun/phydit/) as described previously (Chun et al., 2000Go). It is clear from phylogenetic trees based on the Jukes & Cantor (1969)Go model, using the neighbour-joining (Saitou & Nei, 1987Go; Fig. 1Go) and Fitch & Margoliash (1967Go; not shown) methods, that H. koreensis, K. flavida and K. sandramycini formed a significant monophyletic clade. This grouping was supported by a bootstrap value of 100 %, based on the neighbour-joining algorithm. The position of H. koreensis was encompassed by the Kribbella species in the neighbour-joining tree, although H. koreensis was the sister group to the Kribbella sequences in the Fitch–Margoliash tree (data not shown). Pairwise 16S rDNA sequence similarity values of H. koreensis to K. flavida and K. sandramycini were 98·37 and 98·57 %, respectively, whereas the corresponding value between the two Kribbella species was 99·12 %. It is evident from 16S rDNA analysis that H. koreensis cannot be separated from the Kribbella species and belongs to the same genus. As the three species showed a high level of 16S rDNA sequence similarity, we employed a DNA–DNA pairing method (Chun et al., 1998Go) to check whether H. koreensis belongs to either of the described Kribbella species. DNA relatedness values between H. koreensis IMSNU 50530T and Kribbella strains were respectively 20 and 0 % for K. flavida KCTC 9580T and K. sandramycini KCTC 9609T when DNA from H. koreensis was used as the probe. These values support the description of a novel species to accommodate H. koreensis in the genus Kribbella.



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  		Fig. 1. Rooted neighbour-joining tree based on nearly complete 16S rDNA sequences, showing relationships between Hongia koreensis and related genera. Numbers at nodes indicate levels of bootstrap support based on neighbour-joining analyses of 1000 resampled datasets. Rubrobacter radiotolerans DSM 46359T (X87134) was used as the outgroup. Bar, 0·1 nucleotide substitution per nucleotide position.

 
H. koreensis shares many properties with species of the genus Kribbella. They contain aerial and vegetative hyphae which often fragment. Shared chemical properties include MK-9(H4), L-alanine at position 1 of the peptide subunit, LL-diaminopimelic acids and DNA G+C contents (71 and 68–70 mol% for H. koreensis and Kribbella, respectively). However, several properties can be weighted to separate H. koreensis from Kribbella species, including phospholipid composition and utilization of several compounds as sole carbon and energy sources (Table 1Go). We determined the cellular fatty acid profiles of the test strains using the Sherlock system (Microbial ID), according to the manufacturer's instructions, and found that they can be readily differentiated from each other (Table 2Go).


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  		Table 1. Utilization of carbon compounds as sole carbon and energy sources by Hongia koreensis and Kribbella species

H. koreensis IMSNU 50530T was positive, and K. flavida KCTC 9580T was negative, for all reactions listed. +, Positive; -, negative; W, weakly positive reaction. Data from Park et al. (1999)Go and Lee et al. (2000)Go.

 

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  		Table 2. Cellular fatty acid composition (%) of Hongia koreensis and Kribbella species

Taxa: 1, H. koreensis IMSNU 50530T; 2, K. flavida KCTC 9580T; 3, K. sandramycini KCTC 9609T.

 
From the polyphasic evidence given in this study, we propose that H. koreensis should be transferred to the genus Kribbella as Kribbella koreensis comb. nov. The description of K. koreensis and emended description of the genus Kribbella are presented below.

Emended description of Kribbella Park et al. 1999Go
The description is the same as that given by Park et al. (1999)Go except for polar lipid composition. In addition to phosphatidylcholine, K. koreensis contains diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. DNA G+C content is 68–71 mol%.

Description of Kribbella koreensis (Lee et al. 2000Go) comb. nov.
Kribbella koreensis (ko.re.en'sis. N.L. fem. adj. koreensis pertaining to Korea, the location of the soil sample from which the type strain was isolated).

The description is identical to that of Lee et al. (2000)Go.


   ACKNOWLEDGEMENTS
 
We acknowledge the support of the BK21 Research Fellowship from the Ministry of Education and Human Resources Development, Korea, and the Seoul National University Foundation.


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 REFERENCES
 
Chun, J., Bae, K. S., Moon, E. Y., Jung, S.-O., Lee, H. K. & Kim, S.-J. (2000). Nocardiopsis kunsanensis sp. nov., a moderately halophilic actinomycete isolated from a saltern. Int J Syst Evol Microbiol 50, 1909–1913.

Chun, J., Seong, C.-N., Bae, K. S., Lee, K.-J., Kang, S.-O., Goodfellow, M. & Hah, Y. C. (1998). Nocardia flavorosea sp. nov. Int J Syst Bacteriol 48, 901–905.[Abstract/Free Full Text]

Fitch, W. M. & Margoliash, E. (1967). Construction of phylogenetic trees. Science 155, 279–284.[Free Full Text]

Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.

Lee, S. D., Kang, S.-O. & Hah, Y. C. (2000). Hongia gen. nov., a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 50, 191–199.[Abstract]

Park, Y.-H., Yoon, J.-H., Shin, Y. K., Suzuki, K., Kudo, T., Seino, A., Kim, H.-J., Lee, J.-S. & Lee, S. T. (1999). Classification of ‘Nocardioides fulvus’ IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov. Int J Syst Bacteriol 49, 743–752.[Abstract/Free Full Text]

Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.[Abstract]




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