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Development of a Kribbella-specific isolation medium and description of Kribbella capetownensis sp. nov. and Kribbella speibonae sp. nov., isolated from soil

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Abstract

Two actinobacterial strains were isolated from samples collected from the University of Cape Town, South Africa. A third actinobacterial strain was isolated from soil collected in the town of Stellenbosch, South Africa, using a newly-developed Kribbella-selective medium. Analysis of the 16S rRNA genes showed that the three strains belonged to the genus Kribbella. A multilocus sequence analysis using the concatenated gene sequences of the gyrB, rpoB, relA, recA and atpD genes showed that strains YM55T and SK5 were most closely related to the type strains of Kribbella sindirgiensis and Kribbella soli, while strain YM53T was most closely related to the type strain of Kribbella pittospori. Digital DNA–DNA hybridisation and Average Nucleotide Identity (ANI) analyses showed that strains YM55T and SK5 belong to the same genomic species (OrthoANI value = 98.4%), but are distinct from the genomic species represented by the type strains of K. sindirgiensis (OrthoANI values < 95.6%) and K. soli (OrthoANI values < 91.4%). Strain YM53T is distinct from the genomic species represented by the type strain of K. pittospori (OrthoANI value = 94.0%). Phenotypic comparisons showed that strains YM55T and SK5 are distinct from the type strains of K. sindirgiensis and K. soli and that strain YM53T is distinct from the type strain of K. pittospori. Strains YM53T and YM55T are thus presented as the type strains of novel species, for which the names Kribbella capetownensis sp. nov. (= DSM 29426T = NRRL B-65062T) and Kribbella speibonae sp. nov. (= DSM 29425T = NRRL B-59161T), respectively, are proposed.

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Acknowledgements

SMC held a National Research Foundation (NRF) Innovation Doctoral Scholarship. GJE held a Claude Leon Foundation Postdoctoral Fellowship. This work was supported by research grants to P.R.M. from the National Research Foundation (Grant Nos. 81014 and 85476) and the University Research Committee (University of Cape Town). Opinions expressed and conclusions arrived at are those of the authors and are not necessarily to be attributed to the NRF.

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Authors and Affiliations

  1. Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa

    Sarah M. Curtis, Iulia Norton, Gareth J. Everest, James G. Pelser, Marli C. de Kock & Paul R. Meyers

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  1. Sarah M. Curtis
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  2. Iulia Norton
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  3. Gareth J. Everest
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  4. James G. Pelser
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  5. Marli C. de Kock
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  6. Paul R. Meyers
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Contributions

SMC Developed the Kribbella selective medium, wrote the original manuscript (ANTO-D-14-00425), did all the multilocus-sequence analyses (MLSA) and genetic-distance calculations and constructed the concatenated-gene phylogenetic tree. Proof-read the manuscript. IN Isolated strains YM53T and YM55T and carried out the initial characterisation of these strains. GJE Carried out the polar-lipid analyses of strains YM53T and YM55T. Proof-read the manuscript. JGP Carried out a full polyphasic characterisation of strain SK5 (as a possible new species) as part of his M.Sc. studies. Proof-read the manuscript. MCdK Isolated strain SK5, carried out the initial characterisation of the strain and determined the sequences of the gyrB, rpoB, relA, recA and atpD genes. Proof-read the manuscript. PRM Carried out the comparative phenotypic testing on strains YM53T, YM55T and SK5 and their revised closest phylogenetic relatives. Constructed the 16S rRNA gene phylogenetic tree and did the genomic and phylogenomic analyses. Re-wrote the 2014 manuscript to include the updated information. Supervised the research and provided the research funding.

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Correspondence to Paul R. Meyers.

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Curtis, S.M., Norton, I., Everest, G.J. et al. Development of a Kribbella-specific isolation medium and description of Kribbella capetownensis sp. nov. and Kribbella speibonae sp. nov., isolated from soil. Antonie van Leeuwenhoek 113, 617–628 (2020). https://doi.org/10.1007/s10482-019-01365-6

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