Genomic Characterization of a Mercury Resistant Arthrobacter sp. H-02-3 Reveals the Presence of Heavy Metal and Antibiotic Resistance Determinants

Abstract

Nuclear production and industrial activities led to widespread contamination of the Department of Energy (DOE) managed Savannah River Site (SRS), located in South Carolina, United States. The H-02 wetland system was constructed in 2007 for the treatment of industrial and storm water runoff from the SRS Tritium Facility. Albeit at low levels, mercury (Hg) has been detected in the soils of the H-02 wetland ecosystem. In anoxic sediments, Hg is typically methylated by anaerobic microbiota, forming the highly neurotoxic methylmercury (MeHg), which biomagnifies across food webs. However, in surficial oxic wetland soils, microbially mediated demethylation and/or volatilization processes can transform Hg 2+ into the less toxic Hg 0 form which is released into the atmosphere, thus circumventing MeHg formation. To obtain a deeper understanding on bacterial Hg volatilization, a robust Hg-resistant (HgR) bacteria, called as strain H-02-3 was isolated from the H-02 soils. A draft genome sequence of this strain was obtained at a coverage of 700×, which assembled in 44 contigs with an N50 of 171,569 bp. The genomic size of the strain H-02-3 was 4,708,612 bp with a total number of 4,240 genes; phylogenomic analysis revealed the strain as an Arthrobacter species. Comparative genomics revealed the presence of 1100 unique genes in strain H-02-3, representing 26.7% of the total genome; many identified previously as metal resistance genes (MRGs). Specific to Hg-cycling, the presence of mercuric ion reductase (merA), the organomercurial lyase (merB), and the mercuric resistance operon regulatory protein, were identified. By inference, it can be proposed that the organomercurial lyase facilitates the demethylation of MeHg into Hg 2+ which is then reduced to Hg 0 by MerA in strain H-02-3. Furthermore, gene prediction using resistome analysis of strain H-02-3 revealed the presence of several antibiotic resistance genes (ARGs), that statistically correlated with the presence of metal resistant genes (MRGs), suggesting co-occurrence patterns of MRGs and ARGs in the strain. Overall, this study delineates

Is Long-Term Heavy Metal Exposure Driving Carriage of Antibiotic Resistance in Environmental Opportunistic Pathogens: A Comprehensive Phenomic and Genomic Assessment Using Serratia sp. SRS-8-S-2018

“…Our recent studies suggest that the metalliferous SRS soils may be serving as a reservoir for the recruitment and proliferation of metal and antimicrobial resistances in the native microbial communities ( Agarwal et al, 2019 , 2020a , 2020b ; Gendy et al, 2020a , b ; Pathak et al, 2020 ), thus presenting risks to the ecological processes and public health. Overall, this study further builds upon evidence to show that the SRS contaminated soils inherently harbor higher antibiotic resistance, relative to the reference soils, and thus driving antimicrobial resistance to the native microbiota, including several known pathogens (e.g., Burkholderia , Ralstonia , Massilia , Acinetobacter , and Pseudomonas ( Stepanauskas et al, 2006 ; Wright et al, 2006 ; Thomas et al, 2020 ).…”

“…Despite this advantage of microbially based heavy metal bioremediation, studies have also unequivocally shown that bacteria can acquire antibiotic resistance when exposed to long-term contamination, especially with Hg and U ( Benyehuda et al, 2003 ), including our previous work ( Agarwal et al, 2019 , 2020a , b ; Gendy et al, 2020a , b ; Pathak et al, 2020 ). This builds upon significant evidence that exists on the SRS soils which unequivocally shows higher levels of antibiotic resistance in contaminated SRS soils relative to reference soils ( Stepanauskas et al, 2006 ; Wright et al, 2006 ; Thomas et al, 2020 ).…”

“…Heavy metal contamination is a global environmental problem shown to cause both ecological and public health problems ( Tchounwou et al, 2012 ). However, ecosystems with pervasive and long-term heavy metal contamination, such as the Savannah River Site (SRS), located in Aiken, SC, United States, are known to harbor metal-resistant microorganisms, which have acquired genomic features to resist and circumvent metal toxicity ( Ye, 2014 ; Agarwal et al, 2018 ; Pathak et al, 2019 , 2020 ; Gendy et al, 2020a , b ). The two main heavy metal contaminants within the impacted SRS soils include mercury (Hg) and uranium (U) ( Sowder et al, 2003 ).…”

“…( Agarwal et al, 2020a , b ; Gendy et al, 2020b ). Many of these groups have been demonstrated to cycle Hg by activity of their mer operon, which consists of regulatory proteins- MerR and MerD, transport proteins- MerP, T and E, as well as protein(s) with reductase activity- MerA ( Agarwal et al, 2019 ; Pathak et al, 2020 ). In reference to U cycling processes, several different genes have been shown to render U resistance and biomineralization, such as the gene encoding uranium binding complex (UBC), uranium response in Caulobacter ( urcA ), phosphatase genes ( phoY; phoK ; and phoN ) and PIB-type ATPAse ( Martinez et al, 2006 ; Hillson et al, 2007 ; Nilgiriwala et al, 2008 ; Nongkhlaw et al, 2012 ; Yung and Jiao, 2014 ; Kulkarni et al, 2016 ; Thorgersen et al, 2017 ).…”

Prevalence of antibiotic-resistant, toxic metal-tolerant and biofilm-forming bacteria in hospital surroundings

“…Hospital effluents containing various chemical agents, such as antibiotics, toxic heavy metals etc., interact with diverse microbial agents including pathogenic bacteria and lead to an acquisition of selective pressure [20]. The relationship between microbial acquisition of antibiotic resistance and metal tolerance has been extensively studied by many researchers, and both of these resistance genes are found to be located on the same mobile genetic elements [21,22]. It is evident that the resistant bacterial strains gain entrance to the environment via the indiscriminate discharge of untreated or partially treated wastewater from domestic, clinical and industrial sources [14].…”