Comparative Genome Analysis of the Photosynthetic Betaproteobacteria of the Genus Rhodocyclus: Heterogeneity within Strains Assigned to Rhodocyclus tenuis and Description of Rhodocyclus gracilis sp. nov. as a New Species

Abstract

The genome sequences for Rhodocyclus purpureus DSM 168T and four strains assigned to Rhodocyclus tenuis (DSM 110, DSM 111, DSM 112, and IM 230) have been determined. One of the strains studied (IM 230) has an average nucleotide identity (ANI) of 97% to the recently reported genome of the type strain DSM 109 of Rcy. tenuis and is regarded as virtually identical at the species level. The ANI of 80% for three other strains (DSM 110, DSM 111, DSM 112) to the type strain of Rcy. tenuis points to a differentiation of these at the species level. Rcy. purpureus is equidistant from Rcy. tenuis and the new species, based on both ANI (78–80%) and complete proteome comparisons (70% AAI). Strains DSM 110, DSM 111, and DSM 112 are very closely related to each other based on ANI, whole genome, and proteome comparisons but clearly distinct from the Rcy. tenuis type strain DSM 109. In addition to the whole genome differentiation, these three strains also contain unique genetic differences in cytochrome genes and contain genes for an anaerobic cobalamin synthesis pathway that is lacking from both Rcy. tenuis and Rcy. purpureus. Based on genomic and genetic differences, these three strains should be considered to represent a new species, which is distinctly different from both Rcy. purpureus and Rcy. tenuis, for which the new name Rhodocyclus gracilis sp. nov. is proposed.

Genomic and Phylogenetic Characterization of Rhodopseudomonas infernalis sp. nov., Isolated from the Hell Creek Watershed (Nebraska)

“…Strain HC1 contains both forms of ribulose-1,5-bisphosphate carboxylases (RubisCO) for carbon fixation: both genes encoding Form I Cbb large and small subunits, and Form II CbbM larger single RubisCO proteins are present in the genome. The presence of two forms of RubisCO is similar to other Rhodopseudomonas strains, and a few other purple nonsulfur bacteria such as Rhodocyclus [ 51 , 52 ]. Five carbonic anhydrases (2 alpha, 2 beta and one gamma class) and genes for carbon monoxide utilization were also found.…”

Genome Sequence and Characterization of a Xanthorhodopsin-Containing, Aerobic Anoxygenic Phototrophic Rhodobacter Species, Isolated from Mesophilic Conditions at Yellowstone National Park

“…RuBisCo is an essential protein in the Calvin-Benson-Bassham cycle that catalyzes the addition of carbon dioxide to ribulose-1,5-bisphosphate. The presence of multiple RuBisCo genes is not uncommon in Proteobacteria [55][56][57][58]. In the same species, a single RuBisCo gene can be present (Form II), or alternatively, a two-subunit form of RuBisCo (Form I) consisting of large (rbcL) and small (rbcS) subunits, or both forms can be found as well [57].…”