GENOMIC, METABOLIC, AND PHYSIOLOGICAL CHARACTERIZATION OF SERRATIA SP. SRS‐8‐S‐2018 ISOLATED FROM HEAVY METAL CONTAMINANT SOILS OF THE SAVANNAH RIVER SITE, USA

Abstract

Serratia sp. SRS‐8‐S‐2018 was isolated from mercury (Hg) contaminated soil samples collected from the Savannah River Site (SRS). SRS is located on the northeast bank of the Savannah River (South Carolina, USA). Strain SRS‐8‐S‐2018 grew in various levels of Hg ranging from 5–30 μg/ml. To understand metabolic and physiological features of strain SRS‐8‐S‐2018, Biolog Ecoplate assays were performed under different Hg concentrations, which demonstrated that strain SRS‐8‐S‐2018 actively metabolized carbohydrates, amino acids, carboxy acids, polymers, and esters; however, the physiological response was significantly hampered at increasing concentrations of Hg from 1–5 μg/ml. a draft genome sequence of strain SRS‐8‐S‐2018 was conducted, which revealed a genomic size of 5,323 630 bp and an average G+C content of 59.48 %. The genome consisted of 159 contigs, N50 of 101301 bases and L50 of 17, a coding sequence of 5,261 proteins (CDS), 55 genes for tRNA, and three genes for rRNA, An in‐depth, genome‐wide comparison between strain SRS‐8‐S‐2018 and its four closest taxonomic relatives revealed 1159 distinct genes, with multiple functions including antibiotic resistance and heavy metal resistance respectively. Further annotations revealed that strain SRS‐8‐S‐2018 consisted of 585 subsystems with the following top six categories belonging to amino acid metabolism 428 genes; carbohydrate metabolism 391 genes; vitamin and cofactor metabolism 197 genes; protein metabolism 116 genes; membrane transport 136 genes and fatty acids and lipids 136 genes respectively. Several gene homologs previously shown to be involved in the resistance against heavy metals/radionuclides, including the cobalt‐zinc‐cadmium efflux system, membrane transporters, and antimicrobial extrusion proteins, were also identified, which likely facilitates the survival of strain SRS‐8‐S‐2018 in an Hg‐contaminated soil habitat. Additionally, several genes homologous for antibiotic resistance were also identified in strain SRS‐8‐S‐2018. The relationship between heavy metal contamination and antibiotic resistance was performed using the Biolog phenotype microarray assay which confirmed the widespread resistance of strain SRS‐8‐S‐2018 to a variety of different antibiotics. Specifically, 48 different types of antibiotics were screened which unequivocally showed resistance of strain SRS‐8‐S‐2018 to 81.25% of the tested antibiotics. Overall, this study indicates that heavy metal contaminants not only pose ecological and public health toxicity risks but also stress the environmental microbiomes, which respond by acquiring metal resistant genes (MRGs) via horizontal gene transfer (HGT) or genomic mutations for survival. The metal resistant genes can possess antimicrobial activities or facilitate the recruitment of additional antimicrobial‐resistant genes (ARGs), thus exacerbating the environmental toxicity issuesSupport or Funding InformationThis work was supported by the Department of Energy (DOE) Minority Serving Institution Partnership Program (MSIPP) managed by the Savannah River National Laboratory under SRNS contract #DE‐AC09‐08SR22470 [Task Order Agreements (TOAs) 0000403081 and 0000403082].Conflict 0