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

Abstract

The carriage of both, heavy metal and antibiotic resistance appears to be a common trait in bacterial communities native to long-term contaminated habitats, including the Savannah River Site (SRS). There is widespread soil contamination at the SRS; a United States Department of Energy (DOE) facility with long-term contamination from past industrial and nuclear weapons production activities. To further evaluate the genomic and metabolic traits that underpin metal and antibiotic resistance, a robust mercury (Hg) and uranium (U)-resistant strain-SRS-8-S-2018, was isolated. Minimum inhibitory concentration of this strain revealed resistance to Hg (10 µg/ml) and U (5 mM), the two main heavy metal contaminants at the SRS. Metabolic assessment of strain SRS-8-S-2018 using Biolog metabolic fingerprinting analysis revealed preference for carbohydrate utilization followed by polymers, amino acids, carboxy acids, and esters; this physiological activity diminished when Hg stress was provided at 1 and 3 µg/ml and completely ceased at 5 µg/ml Hg, indicating that continued release of Hg will have negative metabolic impacts to even those microorganisms that possess high resistance ability. Development of antibiotic resistance in strain SRS-8-S-2018 was evaluated at a functional level using phenomics, which confirmed broad resistance against 70.8% of the 48 antibiotics tested. Evolutionary and adaptive traits of strain SRS-8-S-2018 were further assessed using genomics, which revealed the strain to taxonomically affiliate with Serratia marcescens species, possessing a genome size of 5,323,630 bp, 5,261 proteins (CDS), 55 genes for transfer RNA (tRNA), and an average G + C content of 59.48. Comparative genomics with closest taxonomic relatives revealed 360 distinct genes in SRS-8-S-2018, with multiple functions related to both, antibiotic and heavy metal resistance, which likely facilitates the strain's survival in a metalliferous soil habitat.

Friend or Foe: Draft Genome Sequence of Bradyrhizobium sp. Strain SRS-191

“…Interestingly, the strain harbored MRGs (e.g., genes for the cobalt-zinc-cadmium resistance proteins CzcR and CzcD), as well as other environmentally beneficial genes, including genes for nitrogen fixation and biodegradation. However, it was concerning to find 56 MDR genes in SRS-191, a trait identified in several other microbes isolated from SRS soils ( 2 – 4 , 14 ). It remains to be determined whether strains such as SRS-191 are among our beneficial microbial friends or our pathogenic foes, given their possession of both MRGs and MDR traits.…”

Assessing the Ecotoxicity of Eight Widely Used Antibiotics on River Microbial Communities

“…Biolog EcoPlates™ were selected for their ability to measure the capacity of a microbial community to metabolize a set of representative organic substrates [43][44][45][46][47], which indirectly provides relevant information about changes in their functional diversity [44]. Despite its great versatility, the main limitation of this approach is that it must be complemented with a taxonomic analysis of the variety of microorganisms present in the water sample.…”

Genome sequencing of biocontrol strain Bacillus amyloliquefaciens Bam1 and further analysis of its heavy metal resistance mechanism

“…Genomic comparison is a very useful method for understanding the mechanism of microbes on biocontrol and growth-promoting (Chen et al 2007 ; Luo et al 2018 ; Yi et al 2019 ), heavy metal and antibiotic resistance (Gendy et al 2020 ), as well as metabolism or other functions (Li et al 2019 ). The whole genomes, including the complete and draft genomes, of about 102 B. amyloliquefaciens strains have been sequenced and published in NCBI.…”