title: The phylogenetic position and ultrastructure of the uncultured bacterium Achromatium oxaliferum.
abstract: Achromatium oxaliferum is a large, morphologically conspicuous, sediment-dwelling bacterium. Nothing is known concerning its phylogeny and it has eluded all attempts at laboratory cultivation. The limited physiological description of A. oxaliferum has been based on morphological features of the bacterium such as the presence of intracellular sulphur inclusions. A. oxaliferum cells were purified from a wetland region close to Rydal Water (Cumbria, UK). Scanning and transmission electron microscopy revealed that a number of morphologically distinct A. oxaliferum cell-types, based on cell surface features and the size and abundance of calcite and sulphur inclusions within the cells, were present in a single sample of purified cells. PCR was used to amplify almost full-length 16S rRNA gene sequences from DNA extracted from A. oxaliferum cells directly purified from sediments. The PCR products were cloned and partial sequences (approx. 400 bp) were determined for seven of the clones. Three different sequence clusters were recovered from the clone libraries. A near full-length (1489 bp) 16S rRNA gene sequence was determined for a representative clone of the most dominant sequence-type (52% of the sequences). Comparative sequence analysis showed A. oxaliferum to form a deep branching lineage within the gamma-subdivision of the Proteobacteria. A. oxaliferum was related most closely to the Chromatium assemblage that includes sulphur-oxidizing symbiotic bacteria, purple sulphur bacteria, and sulphur- and iron-oxidizing thiobacilli. Phylogenetic inferences made using distance, parsimony and maximum likelihood methods all placed A. oxaliferum with this group of bacteria. Bootstrap support for a relationship with any particular lineage within the assemblage was weak. The seven clone sequences recovered from the A. oxaliferum cells however formed a monophyletic group well supported by bootstrap analysis (85-100% support depending on the analysis done). It was concluded that A. oxaliferum was related to organisms of the Chromatium assemblage but constituted a novel lineage within this group of bacteria. A. oxaliferum cells were confirmed as the source of the 16S rRNA sequence obtained, by the use of a fluorescently-labelled 16S rRNA-targeted oligonucleotide specific for the A. oxaliferum rRNA sequence.
authors.affiliation: Newcastle Research Group in Fossil Fuels and Environmental Geochemistry University of Newcastle upon Tyne, UK. i.m.head@newcastle.ac.uk
authors.forename: I M
authors.initials: IM
authors.lastname: Head
authors.forename: N D
authors.initials: ND
authors.lastname: Gray
authors.forename: K J
authors.initials: KJ
authors.lastname: Clarke
authors.forename: R W
authors.initials: RW
authors.lastname: Pickup
authors.forename: J G
authors.initials: JG
authors.lastname: Jones
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D006088:Gram-Negative Aerobic Bacteria / Q000145:classification* / Q000235:genetics / Q000648:ultrastructure; D017403:In Situ Hybridization; D013058:Mass Spectrometry; D008855:Microscopy, Electron, Scanning; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000737:chemistry* / Q000648:ultrastructure; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012336:RNA, Ribosomal, 16S