Horizontal Gene Transfer of P _IB -Type ATPases among Bacteria Isolated from Radionuclide- and Metal-Contaminated Subsurface Soils

Abstract

Aerobic heterotrophs were isolated from subsurface soil samples obtained from the U.S. Department of Energy's (DOE) Field Research Center (FRC) located at Oak Ridge, Tenn. The FRC represents a unique, extreme environment consisting of highly acidic soils with cooccurring heavy metals, radionuclides, and high nitrate concentrations. Four hundred isolates obtained from contaminated soil were assayed for heavy metal resistance, and a smaller subset was assayed for tolerance to uranium. The vast majority of the isolates were gram-positive bacteria and belonged to the high-G؉C-and low-G؉C-content genera Arthrobacter and Bacillus, respectively. Genomic DNA from a randomly chosen subset of 50 Pb-resistant (Pb r ) isolates was amplified with PCR primers specific for P IB -type ATPases (i.e., pbrA/cadA/zntA). A total of 10 pbrA/cadA/zntA loci exhibited evidence of acquisition by horizontal gene transfer. A remarkable dissemination of the horizontally acquired P IB -type ATPases was supported by unusual DNA base compositions and phylogenetic incongruence. Numerous Pb r P IB -type ATPase-positive FRC isolates belonging to the genus Arthrobacter tolerated toxic concentrations of soluble U(VI) (UO 2 2؉ ) at pH 4. These unrelated, yet synergistic, physiological traits observed in Arthrobacter isolates residing in the contaminated FRC subsurface may contribute to the survival of the organisms in such an extreme environment. This study is, to the best of our knowledge, the first study to report broad horizontal transfer of P IB -type ATPases in contaminated subsurface soils and is among the first studies to report uranium tolerance of aerobic heterotrophs obtained from the acidic subsurface at the DOE FRC.The remediation of hazardous mixed-waste sites, particularly those cocontaminated with heavy metals and radionuclides, is one of the most costly environmental challenges currently faced by the United States and other countries. Interactions between microorganisms, radionuclides, and metals that promote their precipitation and immobilization in situ are promising strategies for treatment and cleanup of the contaminated subsurface (1, 15). At mixed-waste sites where the concentrations of metal contaminants can reach toxic levels, the metal resistance of indigenous microbial populations could be critical for the success of in situ biostimulation efforts. For example, while a number of microbes can carry out reductive precipitation of radionuclides (e.g., Desulfovibrio sp., Geobacter sp., and Shewanella sp.) (28,44,63), the sensitivity of these organisms to heavy metals could possibly limit their in situ activities. Thus, the metal sensitivity of some radionuclide-reducing microbes suggests that the acquisition of metal resistance traits (e.g., P IB -type ATPases that regulate the transport of heavy metals) might be conducive to facilitating and/or enhancing microbial metabolism during subsequent biostimulation activities in metal-and radionuclide-contaminated subsurface environments.The P-type ATPases represent a chromosomally en...

Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site

“…Decades of disposal of waste derived from uranium processing has led to acidic subsurface conditions that favor bacteria from the genus Rhodanobacter. Additionally, these conditions may have resulted in a dramatic die-off of other native soil bacteria, leading to conditions favoring lateral gene transfer (27,38). In the subsurface sediment from Area 3, the shallowest depth has a level of bacterial SSU rRNA gene sequence diversity consistent with that found in pristine soils (45; data not shown).…”

“…These periods of anoxia in the nitrate-rich subsurface, however, favor bacteria capable of denitrification. Martinez et al (38) suggested that metal sensitivity of native bacteria in the ORIFRC site subsurface likely facilitated the lateral gene transfer of metal resistance genes. Similarly, Rhodanobacter spp.…”

Initial Copper Stress Strengthens the Resistance of Soil Microorganisms to a Subsequent Copper Stress

“…This phenomenon might be explained that microbial communities in the long-term field contaminated soil have already adapted to the toxic environment; therefore, microbial communities were more resistant to subsequent stress [38,39]. The adaption process of microorganisms to heavy metals might be emphasized by genetic or physiological changes of microorganisms (mutations or horizontal gene transfer) [40,41]. Moreover, at a community level, metal-sensitive species were substituted by metal-tolerant or metal-adapted species [42,43].…”

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

“…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.…”

“…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.…”