Complete Genome Sequence of Rahnella sp. Strain Y9602, a Gammaproteobacterium Isolate from Metal- and Radionuclide-Contaminated Soil

Abstract

dRahnella sp. strain Y9602 is a gammaproteobacterium isolated from contaminated subsurface soils that is capable of promoting uranium phosphate mineralization as a result of constitutive phosphatase activity. Here we report the first complete genome sequence of an isolate belonging to the genus Rahnella. R ahnella sp. strain Y9602 is a gammaproteobacterium isolated from a mixed-waste-contaminated subsurface (i.e., low pH and high concentrations of nitrate, heavy metals, and radionuclides) at the U.S. Department of Energy (DOE) Oak Ridge Reservation in Oak Ridge, TN (13). Phenotypic characterization of Y9602 indicated resistance to heavy metals, uranium tolerance, and constitutive phosphatase activity. Subsequent studies indicated that the strain precipitated 95% of soluble uranium [U(VI)] as an insoluble autunite mineral during oxic and anoxic growth conditions when supplied with glycerol-3-phosphate as the sole carbon and phosphorus source (1, 2, 12). Additionally, recent microbial ecology studies of metal-, metalloid-, organic-, and radionuclide-contaminated soils have identified enrichments of Rahnella species that show promise for remediation strategies (6,10,13,15). Whole-genome sequencing was thus conducted on Rahnella sp. Y9602 to provide insights into its physiology, which promotes metal and radionuclide sequestration.

Rahnella perminowiae sp. nov., Rahnella bonaserana sp. nov., Rahnella rivi sp. nov. and Rahnella ecdela sp. nov., isolated from diverse environmental sources, and emended description of the genus Rahnella

“…These eight species contributed to the existing diversity of Rahnella with isolations of Rahnella victoriana, Rahnella variigena and Rahnella inusitata from bleeding cankers of oak; R. victoriana, R. variigena and R. woolbedingensis from asymptomatic alder and walnut; Rahnella bruchi from the gut of the Agrilus biguttatus beetle; Rahnella aceris and Rahnella laticis from sap of Acer pictum and Rahnella contaminans as a contaminant from MRSA agar plates [5][6][7]. In addition to their isolation from the natural environment, Rahnella species have been linked to nitrogen-fixation [8], metal and radionuclide sequestration [9] and biological control [10]; and more recently as possible pathogens of oak [11], poplar [12] and onion [13].…”

Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium

“…The results also indicated that the ANI and DDH values between ATCC 33071 T and other R. aquatilis strains (including HX2, ZF7, Y9602) were below 95 and 70%, respectively, and this was consistent with the previous report showing that the ANI value between R. aquatilis strains ZF7 and ATCC 33071 T was only 92.9% ( Yuan et al, 2020 ). Previous studies indicated that strain ZF7, HX2 and Y9602 were both isolated from soil ( Guo et al, 2012 ; Martinez et al, 2012a ), while ATCC 33071 T was isolated from drinking water ( Martinez et al, 2012b ), so, it may suggest that the genetic evolutionary distance could be associated with the habitat and adaptation. All five Rahnella strains harbored one or more plasmids, which could be related to genetic evolution, based on the previous report that 19% of strains in the genus Rahnella were plasmid-containing and had highly homologous regions for the same species ( Rozhon et al, 2010 ).…”

Rahnella spp. are commonly isolated from onion ( Allium cepa ) bulbs and are weakly pathogenic

“…Genes present in the three Rahnella genomes available at the time, R. aquatilis ATCC 33071, Rahnella sp. Y960 (Martinez et al, ), and R. aquatilis HX2 (Guo et al , ), but not in other available genomes, were used to search the NCBI Whole Genome Shotgun database and filtered based on length (at least 300 bp). Putative genes that appeared to be unique to the three sequenced Rahnella strains were considered good target regions for designing specific primers.…”