Abstract
Arthrobacter sp. strain SRS-W-1-2016 was isolated on high concentrations of uranium (U) from the Savannah River Site (SRS) that remains co-contaminated by radionuclides, heavy metals, and organics. SRS is located on the northeast bank of the Savannah River (South Carolina, USA), which is a U.S. Department of Energy (DOE) managed ecosystem left historically contaminated from decades of nuclear weapons production activities. Predominant contaminants within the impacted SRS environment include U and Nickel (Ni), both of which can be transformed microbially into less toxic forms via metal complexation mechanisms. Strain SRS-W-1-2016 was isolated from the uraniferous SRS soils on high concentrations of U (4200 μM) and Ni (8500 μM), but rapid growth was observed at much lower concentrations of 500 μM U and 1000 μM Ni, respectively. Microcosm studies established with strain SRS-W-1-2016 revealed a rapid decline in the concentration of spiked U such that it was almost undetectable in the supernatant by 72 h of incubation. Conversely, Ni concentrations remained unchanged, suggesting that the strain removed U but not Ni under the tested conditions. To obtain a deeper understanding of the metabolic potential, a draft genome sequence of strain SRS-W-1-2016 was obtained at a coverage of 90×, assembling into 93 contigs with an N50 contig length of 92,788 bases. The genomic size of strain SRS-W-1-2016 was found to be 4,564,701 bases with a total number of 4327 putative genes. An in-depth, genome-wide comparison between strain SRS-W-1-2016 and its four closest taxonomic relatives revealed 1159 distinct genes, representing 26.7% of its total genome; many associating with metal resistance proteins (e.g., for cadmium, cobalt, and zinc), transporter proteins, stress proteins, cytochromes, and drug resistance functions. Additionally, several gene homologues coding for resistance to metals were identified in the strain, such as outer membrane efflux pump proteins, peptide/nickel transport substrate and ATP-binding proteins, a high-affinity nickel-transport protein, and the spoT gene, which was recently implicated in bacterial resistance towards U. Detailed genome mining analysis of strain SRS-W-1-2016 also revealed the presence of a plethora of secondary metabolite biosynthetic gene clusters likely facilitating resistance to antibiotics, biocides, and metals. Additionally, several gene homologous for the well-known oxygenase enzyme system were also identified, potentially functioning to generate energy via the breakdown of organic compounds and thus enabling the successful colonization and natural attenuation of contaminants by Arthrobacter sp. SRS-W-1-2016 at the SRS site.
Highlights
Savannah River Site (SRS) located in Aiken, South Carolina, functioned as a nuclear materials production facility for the U.S Department of Energy (DOE), where metal-clad uranium (U) targets were used in the production of plutonium [1]
This study advances our understanding on the genome-wide mechanisms potentially employed by the soil-borne Arthrobacter strain SRS-W-1-2016 to resist and survive in a highly contaminated habitat
Environmental microorganisms underpin metal biotransformations, including radionuclide precipitation, sorption, intracellular accumulation, and biomineralization, and such studies enable a better understanding of genes that facilitate bacteria to successfully colonize such harsh environments, and provides a sustainable approach to remediate toxic habitats
Summary
To further understand environmentally-relevant genomic mechanisms that underpin microbial survival in radionuclide and heavy metal-rich ecosystems, we recently isolated several bacterial strains in the presence of high concentrations of both U and Ni [13]. SRS-W-1-2016, including a suite of substrate binding proteins, permeases, transport regulators, and efflux pumps- likely working in concert to potentially detoxify toxic metals and facilitating the natural attenuation of contaminants within the SRS impacted ecosystem Such genome-enabled studies will facilitate a deeper understanding of heavy metal and antibiotic resistance and hydrocarbon degradative mechanisms in complex, mixed contaminant habitats and provide recommendations for the environmental stewardship of anthropogenically-impacted environments
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