title: Cultivated Beggiatoa spp. define the phylogenetic root of morphologically diverse, noncultured, vacuolate sulfur bacteria.
abstract: Within the last 10 years, numerous SSU rRNA sequences have been collected from natural populations of conspicuous, vacuolate, colorless sulfur bacteria, which form a phylogenetically cohesive cluster (large-vacuolate sulfur bacteria clade) in the gamma-Proteobacteria. Currently, this clade is composed of four named or de facto genera: all known Thioploca and Thiomargarita strains, all vacuolate Beggiatoa strains, and several strains of vacuolate, attached filaments, which bear a superficial similarity to Thiothrix. Some of these vacuolate bacteria accumulate nitrate for respiratory purposes. This clade encompasses the largest known prokaryotic cells (Thiomargarita namibiensis) and several strains that are important in the global marine sulfur cycle. Here, we report additional sequences from five pure culture strains of Beggiatoa spp., including the only two cultured marine strains (nonvacuolate), which firmly establish the root of this vacuolate clade. Each of several diverse metabolic motifs, including obligate and facultative chemolithoautotrophy, probable mixotrophy, and seemingly strict organoheterotrophy, is represented in at least one of the nonvacuolate strains that root the vacuolate clade. Because the genus designation Beggiatoa is interspersed throughout the vacuolate clade along with other recognized or de facto genera, the need for taxonomic revision is clear.
authors.affiliation: Section of Microbiology, University of California, Davis, 95616, USA.
authors.forename: Azeem
authors.initials: A
authors.lastname: Ahmad
authors.forename: Karen M
authors.initials: KM
authors.lastname: Kalanetra
authors.forename: Douglas C
authors.initials: DC
authors.lastname: Nelson
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D016999:Sulfur-Reducing Bacteria / Q000145:classification / Q000235:genetics*; D041962:Thiotrichaceae / Q000145:classification / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S