akamurella panacisegetis sp . nov . and proposal for reclassification of Humicoccus avidus

A novel actinobacterial strain, designated P4-7T, was isolated from soil of a ginseng field located in Geumsan County, Korea. Cells of the strain were aerobic, Gram-stain-positive, non-motile, short rods. The isolate contained MK-8(H4) as the predominant menaquinone, iso-C16:0, anteiso-C15:0 and anteiso-C17:0 as the major fatty acids, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the major polar lipids, glucose, mannose, xylose, ribose and rhamnose as whole-cell sugars, and mesodiaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P4-7T belongs to the family Nakamurellaceae and poB gene is most closely related to Nakamurella multipartita, Humicoccus flavidus and Saxeibacter lacteus (96.3, 97.0 and 96.4% similarity to the respective type strains). Based on comparative analyses of the 16S rRNA and rpoB gene sequences and chemotaxonomic data, it is proposed that H. flavidus and S. lacteus be transferred to the genus Nakamurella. Combined genotypic and phenotypic data also suggested that strain P4-7T be placed in a novel species of the genus Nakamurella, for which the name Nakamurella panacisegetis sp. nov. is proposed; the type strain is P4-7T (=KCTC 19426T = CECT 7604T). The genus Nakamurella is a strictly aerobic, Gram-positive, nonotile, non-spore-forming, coccus-shaped actinobacterium with ingle species Nakamurella multipartita, originally described as icrosphaera multipartita and transferred to the genus Nakamurella ecause of the illegitimate genus name [15,20]. The chemotaxnomic markers chracteristic of the genus Nakamurella were K-8(H4) as the predominant menaquinone, iso-C15:0, iso-C16:0 nd C18:1 as the major fatty acids and the presence of mesoiaminopimelic acid in the cell-wall peptidoglycan [20]. The family akamurellaceae was also given for a substitute of the family icrosphaeraceae [13,15]. Later, the genus Humicoccus [19] was escribed in Nakamurellaceae being distinguished from the genus akamurella by the differences in predominant menaquinones, ajor fatty acids and whole-cell sugars, and more recently, the enus Saxeibacter [9] was reported to be another deep-rooted memer of this group and characterized by some unique features with The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences f strain P4-7T and Saxeibacter lacteus KCTC 19285T are HE599560 and HE599561. hose for the rpoB gene sequences of strain P4-7T, Humicoccus flavidus KCTC 19127T nd Saxeibacter lacteus KCTC 19285T are HE613441–HE613443. ∗ Corresponding author. Tel. : +82 42 860 4618; fax: +82 42 860 4677. E-mail address: jslee@kribb.re. kr (J.-S. Lee). 723-2020/$ – see front matter © 2012 Elsevier GmbH. All rights reserved. ttp://dx.doi. org/10.1016/j.syapm. 2012.05. 002 © 2012 Elsevier GmbH. All rights reserved. respect to cell morphology, colony pigmentation and fatty acid and polar lipid profiles. At the time of writing, the family Nakamurellaceae belongs to the suborder Frankineae and contains the three aforementioned genera, each comprising only a single species described on the basis of a single strain. Strain P4-7T was recovered during the course of an investigation of the culturable aerobic bacterial community in soil from a ginseng field. On the basis of preliminary 16S rRNA gene sequence comparison, the strain was found to belong to the family Nakamurellaceae. However, the strain occupied an intermediate position between the three genera, showing a relatively high similarity (>96%) to representative members of them, which led to a polyphasic investigation designed to elucidate its taxonomic position and to re-evaluate the status of the three genera in the family Nakamurellaceae. A soil sample was collected from a ginseng field located in Geumsan County, Korea. The sample was diluted serially in sterile distilled water, and samples of each serial dilution were spread on one-tenth-strength nutrient agar and incubated at 25 ◦C for 4 weeks. A pinpoint colony, designated P4-7T, was isolated, purified by subculturing on the same medium and maintained as glycerol/water suspensions (20%, v/v) at −70 ◦C. Subsequently, it was routinely grown on nutrients agar or broth (NA or NB; Difco) at 25 ◦C for 4 days. N. multipartita KCTC 19567T, Humicoccus flavidus KCTC 19127T and Saxeibacter lacteus KCTC 19285T were used as 292 K.K. Kim et al. / Systematic and Applied Microbiology 35 (2012) 291– 296 Cryptospo rang ium arvum IFO 1596 5T (D85465 ) Cryptospo rang ium japon icum IFO 1596 6T (D85466 ) Cryptospo rang ium minu tispo rang ium IFO 1596 2T (AB037007 ) Cryptospo rang ium au ran tiacum IMSNU 2212 0T (AJ293746 ) Fodinicola feeng rotten sis HKI 050 1T (EF490376 ) Spo richthya po lymorpha IFO 1270 2T (AB025317 ) Spo richthya brevicatena YU 72 0-21T (AB006164 ) Fran kia alni ACN 14A (CT5732 13) Acido the rmus cell ulolyticus ATCC 4306 8T (CP000481 ) Nakamurell a multipa rtita DSM 4423 3T (CP001737 ) Naka mur ell a panacise getis P4-7T (HE599560 ) Nakamurell a flavida [Humicocc us flavidu s] DS-52T (DQ321750 ) Nakamurell a lactea [Saxeiba cter lacteu s] KCTC 1928 5T (HE599561 ) Geode rmatophil us rube r CPCC 20135 6T (EU438905 ) Geode rmatophil us obsc urus DSM 4316 0T (CP001867 ) Blastococcus saxob siden s DSM 4450 9T (FN600641 ) Blastococc us agg rega tus ATCC 2590 2T (L40614 ) Blastococcus jejuen sis KS T3-10T (DQ200983 ) Mode stoba cter multisep tatus AA-82 6T (Y18646 ) Mode stoba cter versicolor CP15 3-2T (AJ871304 ) Mode stoba cter marinu s 42 H12-1T (EU181225 ) 83