B Classification of T. pantotropha
Throughout the present work the principal organism under study has been referred to by the name Thiosphaera pantotropha. However, during the course of the project the taxonomic position of this organism has come under scrutiny by a number of workers. In particular, it has been suggested that the organism should be re-classified as Paracoccus denitrificans [367]. This argument was based on two observations: first, the 16S rRNA sequence of T. pantotropha is identical to that of P. denitrificans strain LMG 4218 and second, 100% DNA homology is observed between these two organisms in hybridisation experiments. Additionally, some of the metabolic differences that originally distinguished T. pantotropha from P. denitrificans [225], particularly aerobic denitrification, appear to have become attenuated since the original isolation of T. pantotropha.
The taxonomic status of T. pantotropha therefore remains undecided, although some workers have recently adopted its transfer to P. denitrificans, based on the work of Ludwig et al. (1993) [367]. However, in the present work the name T. pantotropha has been retained, to avoid confusion between previous work in which this name was used and the much larger body of literature that refers specifically to P. denitrificans. However, recent work has shown that there is some confusion as to the history of various strains of P. denitrificans which are deposited in several culture collections around the world. The relationship between strains of P. denitrificans has been re-investigated by examining the c-type cytochrome profiles using SDS-PAGE and by analysis of the protein sequences of cytochrome c\(_{550}\) from each strain [238]. The analysis indicates that P. denitrificans LMG 4218 is closely related to T. pantotropha, but also that P. denitrificans LMG 4218 is not derived from the original type strain of P. denitrificans [368], as was thought previously. Instead, P. denitrificans LMG 4218 is placed in a group that includes a later strain of P. denitrificans, P. denitrificans LMD 52.44. The revised grouping of the strains would affect the way in which they were sub-divided, were consideration to be given to the creation of separate species within the genus Paracoccus.
To address the latter question, fatty acid methyl ester analysis (FAMES) has been used [224]. This technique uses gas chromatography to analyse the relative amounts of different fatty acids in the cell membranes of bacteria. Taxonomic classification based on these measurements has been used successfully [369] and the method is particularly well-suited to the grouping of strains at the sub-species level [370]. The results are so far unpublished, but they broadly support the assertion that P. denitrificans LMD 52.44, P. denitrificans LMG 4218 and T. pantotropha form a separate group within the genus Paracoccus, and also correlate well with a recent analysis of 16S rRNA sequences which suggested that the organism Thiobacillus versutus should be transferred to Paracoccus versutus [371]). Although all of the P. denitrificans strains studied were very similar in many respects, Thompson et al. (1997) [224] assert that there is sufficient variation within the genus to propose the creation of separate species names, and it is suggested that T. pantotropha be renamed P. pantotrophus, to reflect the findings and to promote continuity of the pantotrophus species name.