Whole genome analysis of non-phototrophic, thallium-tolerant Rhodopseudomonas sp. SK50-23
1College of Environment and Resources, Inner Mongolia University, 2Ibaraki University College of Agriculture
Thallium (Tl) is a toxic heavy metal found in trace amounts in the earth’s crust, but found as a pollutant near non-ferrous metal mines, smelters, and factories using Tl. Previously, soil bacteria tolerant to 0.49 mM Tl (100 mg Tl l−1) were isolated from a non-polluted garden soil in Japan through a selective cultivation. From phylogenetic analysis, the Tl-tolerant bacteria were classified into nine groups of Alphaptoteobacteria. Strain SK50-23 represented one of the major Tl-tolerant groups and was characterized as a novel species unable to grow phototrophically in the genus Rhodopsuedomonas. Here we describe the genome analysis of strain SK50-23 in comparison with photosynthetic Rhodopsuedomonas strains. Whole genome analysis was performed with Pacific Biosciences (Pacbio) RS II system and de nove assembly.
To explore the metabolic character of strain SK50-23, the genome comparison to Rhodopsuedomonas palustris strains was carried out using the GenomeMatcher software. The genome analysis supported that strain SK50-23 was not able to grow as a phototroph, due to lack of genes encoding bacteriochlorophyll (bchC, X, Y, Z), carotenoid biosynthesis (crtI, B, C, E, F), and the reaction center complex (pufL and pufM). In addtion, the RubisCO genes responsible for CO2 fixation are missing in the strain. These results suggests that strain SK50-23 is not a facultative autotroph and phototroph and distinct from the members of the genus Rhodopsuedomonas. As for the heavy metal tolerance, genes related to the tolerance to Ni, Co, Pb and Cu were found. Further analyses are now in progress to identify the genes responsible for Tl tolerance and to know the acquisition of heavy metal tolerance in non-polluted soil environments.
keywords:genome analysis,Rhodopsuedomonas,photosynthesis genome,heavy metal resistant