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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 11

The corresponding relationship between genetic distance and the digital DNA-DNA hybridization (dDDH), between genetic distance and dDDH and between genetic distance and dDDH in the genus and sp. nov., a novel actinobacterium from the rhizosphere soil of No Access

Abstract

Earlier studies on the genus showed that pairs of strains having over 0.02 or 0.04 genetic distance are likely to be different species. However, in this work, it was found that a genetic distance of 0.012 or a genetic distance of 0.019 or a genetic distance of 0.013 can be acted as a threshold for describing species. In light of this relationship, a novel actinobacterial strain cg13 from the rhizosphere soil of was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis revealed that strain cg13 exhibited the highest similarities to IMSNU 22139 and JCM 13279. Phylogenetic analysis of 16S rRNA gene and whole-genome sequences indicated that strain cg13 was closely related to them. But the average nucleotide identity based on MUMmer (ANIm) and digital DNA–DNA hybridization (dDDH) values between genomes of strain cg13 and these two strains were below the thresholds for delineating species, suggesting that strain cg13 may be a new species. Significant differences in phenotypic and chemotaxonomic characteristics between strain cg13 and them further provided some useful information for strain cg13 as an independent species. Furthermore, ANIm and dDDH between genomes of strain cg13 and those strains (except SE(8)3), which had more than 98.65% 16S rRNA gene sequence similarities to strain cg13, were far below the thresholds for delineating species. Although the genomic correlation between strain cg13 and SE(8)3 cannot be evaluated due to unavailable genomic data of SE(8)3, the genetic distances between them were much above the maximum range of 0.012, 0.019 and 0.013 recommended above for delineating an species. Based on all these results, strain cg13 represents a novel species, for which the name sp. nov. is proposed. The type strain is cg13=MCCC 1K09229=KCTC 59393.

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Keyword(s): Amycolatopsis rhizosphaerihabitans sp. nov. , gyrB genetic distance , gyrB+recN genetic distance , polyphasic approach and recN genetic distance
Funding
This study was supported by the:
  • Natural Science Foundation of Hunan Province (Award 2022JJ50125)
    • Principal Award Recipient: JianGao
© 2025 The Authors
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/content/journal/ijsem/10.1099/ijsem.0.006974
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The corresponding relationship between gyrB genetic distance and the digital DNA-DNA hybridization (dDDH), between recN genetic distance and dDDH and between gyrB+recN genetic distance and dDDH in the genus Amycolatopsis and Amycolatopsis rhizosphaerihabitans sp. nov., a novel actinobacterium from the rhizosphere soil of Cyclosorus parasiticus
Int J Syst Evol Microbiol 75, 006974 (2025); https://doi.org/10.1099/ijsem.0.006974
/content/journal/ijsem/10.1099/ijsem.0.006974
/content/journal/ijsem/10.1099/ijsem.0.006974
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