Kribbella hippodromi sp. nov., isolated from soil from a racecourse in South Africa

Abstract

A novel actinomycete, designated strain S1.4 T , was isolated from a soil sample collected from Kenilworth Racecourse in the Western Cape, South Africa. The strain was able to grow in the presence of 5 % NaCl. It contained LL-diaminopimelic acid and glycine in the cell-wall peptidoglycan with glucose present in the whole-cell sugar profile. Strain S1.4 T was shown to be a member of either the genus Kribbella or the genus Nocardioides based on a rapid molecular identification method by using single-enzyme restriction endonuclease digestion of the PCR-amplified 16S rRNA gene with MboI, VspI, SphI, SnaBI, SalI and AgeI. Analysis of the 16S rRNA gene sequence indicated that strain S1.4 T belonged to the genus Kribbella. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain S1.4 T was related most closely to Kribbella solani DSA1 T . Strain S1.4 T was phenotypically distinct from K. solani DSA1 T and was shown to be a separate genomic species based on DNA-DNA hybridization experiments (40.4±3.8 % DNA-DNA relatedness between the two). Strain S1.4 T (5DSM 19227 T 5NRRL B-24553 T ) is thus presented as the type strain of a novel species, for which the name Kribbella hippodromi sp. nov. is proposed.The genus Kribbella was proposed by Park et al. (1999) and contains nocardioform actinomycetes with LL-diaminopimelic acid in the cell wall. With the transfer of Hongia koreensis to the genus (Sohn et al., 2003) and more recently the descriptions of Kribbella karoonensis and Kribbella swartbergensis (Kirby et al., 2006) and Kribbella aluminosa (Carlsohn et al., 2007) there are, at the time of writing, 12 recognized Kribbella species (Euzéby, 2007). Here we describe the characterization of a novel member of the genus, isolated from a soil sample collected from a racecourse in the Western Cape, South Africa. Strain S1.4 T was isolated from soil collected in the fynbosrich area surrounded by the horse racing track at Kenilworth Racecourse, Cape Town, South Africa. The soil was ground in a pestle and mortar before being heated at 60 u C for 1 h, after which 0.1 g was added to 1 ml of sterile distilled water and agitated by vortexing for 1 min. The sample was serially diluted in sterile distilled water and spread-plated on SM1 agar (Tan et al., 2006) containing cycloheximide (50 mg ml 21 ) and nalidixic acid (10 mg ml 21 ). Strain S1.4 T was isolated after incubation at 30 u C for 21 days and was subsequently maintained on yeast extract-malt extract agar (ISP 2 medium) (Shirling & Gottlieb, 1966).Genomic DNA was extracted as described by Wang et al. (1996), with modifications to the lysis buffer to increase the lysozyme concentration to 20 mg ml 21 and to include proteinase K (0.2 mg ml 21 ); digestion was performed overnight. Treatment with RNase A was performed overnight. To allow rapid identification of the isolate to the genus level, 16S rRNA gene sequence amplification and restriction endonuclease digestion were performed as described by Cook & Meyers (2003), by using single digestions with the ...

Phylogenetic analysis of the genus Kribbella based on the gyrB gene: proposal of a gyrB-sequence threshold for species delineation in the genus Kribbella

“…Based on the gyrB-based genetic distances reported in the genus Micromonospora, the DNA relatedness between K. hippodromi DSM 19227 T and K. solani CIP 108508 T would be expected to be less than 70%. This was confirmed by DDH which showed that the DNA relatedness between K. hippodromi and K. solani CIP 108508 T is 40.4 ± 3.8% (Everest and Meyers 2008). Although the 16S rRNA gene sequence similarity between these two strains is 99.64%, based on phenotypic characterisation, gyrB gene sequence analysis and DNA relatedness, K. hippodromi should be recognised as a distinct species (Everest and Meyers 2008).…”

“…Kribbella hippodromi S1-4 T , Kribbella karoonensis Q41 T , Kribbella swartbergensis HMC25 T and Kribbella solani strain YB2 were isolated by us (Everest and Meyers 2008;Kirby et al 2006). The two K. aluminosa non-type strains (HKI-479 and HKI-480;Carlsohn et al 2007) were obtained from Drs Ingrid Groth and Karin Martin.…”

Kribbella catacumbae sp. nov. and Kribbella sancticallisti sp. nov., isolated from whitish-grey patinas in the catacombs of St Callistus in Rome, Italy

“…The geographical distribution of the strains is wide as they have been isolated in Korea, China, South Africa and Spain, mostly from soil, but also associated with plants (K. solani and K. lupini). Recently, two further species of the genus Kribbella were isolated from soil, Kribbella aluminosa from a medieval mine in Germany (Carlsohn et al, 2007) and Kribbella hippodromi (Everest & Meyers, 2008) from a racecourse soil in South Africa.…”

Kribbella albertanoniae sp. nov., isolated from a Roman catacomb, and emended description of the genus Kribbella

“…per cm 2 of adhesive tape) was carried out on R2A medium (Reasoner & Geldreich, 1985) at 28 u C for 15 days. Ten to 20 colonies were selected randomly, preliminarily characterized after transferring to tryptic soy agar (TSA; BBL) and subsequently maintained on yeast extract-malt extract agar [International Streptomyces Project (ISP) medium 2] (Shirling & Gottlieb, 1966).Genomic DNA was extracted as described by Everest & Meyers (2008). The 16S rRNA gene was amplified as described by Cook & Meyers (2003), the gyrB gene as described by Kirby et al (2010) and the atpD, recA, relA and rpoB genes as described by Curtis & Meyers (2012).…”