Genomic and genetic sequence information of strains assigned to the genus Rhodopseudomonas reveal the great heterogeneity of the group and identify strain Rhodopseudomonas palustris DSM 123T as the authentic type strain of this species

Abstract

The genus Rhodopseudomonas, containing purple nonsulfur photosynthetic Proteobacteria, has a number of strains that belong to different species, although many of them are collectively called Rhodopseudomonas palustris. The type species R. palustris and closely related species are the focus of this paper. The comparison of available genome sequences indicate that the following Rhodopseudomonas species are well recognized: R. palustris (strains ATH 2.1.6T=DSM 123T=NBRC 100419T and BisB5), Rhodopseudomonas rutila (strains R1T, DSM 126, CGA009, ATH 2.1.37, Eli 1980, ATCC 17001 and TIE1), Rhodopseudomonas pentothenatexigens JA575T and Rhodopseudomonas faecalis JCM 11668T. Other strains for which genome sequences are available are distinct from these four species. Evidence is presented that R. palustris strain ATH 2.1.6T-KCM as obtained directly from the van Niel collection by one of us (T.E.M.) is identical to the DSMZ deposit DSM 123T of ATH 2.1.6T, but not to the deposit at ATCC 17001. The amino acid sequences of the cytochromes C2 and C556 from R. palustris strain ATH 2.1.6T-KCM are in complete agreement with the translated genome sequences of R. palustris DSM 123T. In addition, the 16S rRNA gene sequence of R. palustris NBRC 100419T completely matches that of strain DSM 123T. In conclusion, the type strain of R. palustris ATH 2.1.6T is correctly represented by DSM 123T and NBRC 100419T. However, the deposit at ATCC 17001 has properties that do not conform with properties of authentic R. palustris, but rather indicate that this is a strain of R. rutila. The previously suggested assignment of the type strain of R. palustris DSM 123T to the new species R. pseudopalustris was incorrect because strain DSM 123T is the authentic type strain of R. palustris.