Redefining Paracoccus denitrificans and Paracoccus pantotrophus and the case for a reassessment of the strains held by international culture collections

This taxonomic study clarifies the identity of strains within two key Paracoccus species that have been widely used in microbiology research. Paracoccus denitrificans, established in 1969, historically encompassed diverse biotypes that were later recognized as separate species. A critical reassessment reveals that many culture collection strains labeled as P. denitrificans are actually P. pantotrophus, a species formally created in 1999 from the former Thiosphaera pantotropha. The authors document that several strains held by major international culture collections—including well-known reference strains like LMG 4218 and DSM 65—have been misidentified. Based on 16S rRNA gene sequencing, DNA-DNA hybridization, and physiological properties, the authors provide corrected assignments for numerous culture collection strains and identify cases where additional study is needed. The study emphasizes that some strains cannot be unequivocally assigned to recognized species and may represent novel lineages. The authors call for systematic re-evaluation of culture collection holdings and provide specific amendments to recent taxonomic treatments to ensure accurate species assignments in future research.

Key findings

• Many culture collection strains labeled P. denitrificans are actually P. pantotrophus, including type strain representatives like DSM 65 and LMG 4218
• 16S rRNA gene sequencing and DNA-DNA hybridization analysis confirmed misidentifications in major international culture collections, requiring strain reassignments
• Some strains (DSM 1407, DSM 1408) cannot be assigned to either P. denitrificans or P. pantotrophus and may represent novel Paracoccus species
• P. pantotrophus cannot grow on methanol as sole energy source (unlike P. denitrificans), while both species can grow chemolithoautotrophically on thiosulfate
• Systematic re-evaluation of culture collection strains through 16S rRNA sequencing is recommended to correct taxonomic assignments and ensure research integrity