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Friend or Foe: Draft Genome Sequence of Bradyrhizobium sp. Strain SRS-191. Microbiol Resour Announc 2022; 11:e0075322. [PMID: 36214692 PMCID: PMC9670997 DOI: 10.1128/mra.00753-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report the genomic features of Bradyrhizobium sp. strain SRS-191, which was isolated from a former nuclear legacy site in Aiken, South Carolina, USA. With a genome size of 7,621,400 bp, the strain harbored genes not only for environmentally beneficial traits (e.g., heavy metal resistance, nitrogen fixation, and aromatic biodegradation) but also for antimicrobial resistance.
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Rogiers T, Van Houdt R, Williamson A, Leys N, Boon N, Mijnendonckx K. Molecular Mechanisms Underlying Bacterial Uranium Resistance. Front Microbiol 2022; 13:822197. [PMID: 35359714 PMCID: PMC8963506 DOI: 10.3389/fmicb.2022.822197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental uranium pollution due to industries producing naturally occurring radioactive material or nuclear accidents and releases is a global concern. Uranium is hazardous for ecosystems as well as for humans when accumulated through the food chain, through contaminated groundwater and potable water sources, or through inhalation. In particular, uranium pollution pressures microbial communities, which are essential for healthy ecosystems. In turn, microorganisms can influence the mobility and toxicity of uranium through processes like biosorption, bioreduction, biomineralization, and bioaccumulation. These processes were characterized by studying the interaction of different bacteria with uranium. However, most studies unraveling the underlying molecular mechanisms originate from the last decade. Molecular mechanisms help to understand how bacteria interact with radionuclides in the environment. Furthermore, knowledge on these underlying mechanisms could be exploited to improve bioremediation technologies. Here, we review the current knowledge on bacterial uranium resistance and how this could be used for bioremediation applications.
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Affiliation(s)
- Tom Rogiers
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Rob Van Houdt
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Adam Williamson
- Centre Etudes Nucléaires de Bordeaux Gradignan (CENBG), Bordeaux, France
| | - Natalie Leys
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
| | - Kristel Mijnendonckx
- Microbiology Unit, Interdisciplinary Biosciences, Belgian Nuclear Research Centre, SCK CEN, Mol, Belgium
- *Correspondence: Kristel Mijnendonckx,
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Gendy S, Chauhan A, Agarwal M, Pathak A, Rathore RS, Jaswal R. 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. Front Microbiol 2020; 11:1923. [PMID: 32973703 PMCID: PMC7468404 DOI: 10.3389/fmicb.2020.01923] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/21/2020] [Indexed: 12/04/2022] Open
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. Comparisons drawn between the environmentally isolated Serratia SRS-8-S-2018 with 31 other strains revealed a closer functional association with medically relevant isolates suggesting that propensity of environmental Serratia isolates in acquiring virulence traits, as a function of long-term exposure to heavy metals, which is facilitating development, recruitment and proliferation of not only metal resistant genes (MRGs) but antibiotic resistant genes (ARGs), which can potentially trigger future bacterial pathogen outbreaks emanating from contaminated environmental habitats.
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Affiliation(s)
- Sherif Gendy
- School of Allied Health Sciences, Florida A&M University, Tallahassee, FL, United States
| | - Ashvini Chauhan
- Environmental Biotechnology Laboratory, School of the Environment, FSH Science Research Center, Florida A&M University, Tallahassee, FL, United States
| | - Meenakshi Agarwal
- Environmental Biotechnology Laboratory, School of the Environment, FSH Science Research Center, Florida A&M University, Tallahassee, FL, United States
| | - Ashish Pathak
- Environmental Biotechnology Laboratory, School of the Environment, FSH Science Research Center, Florida A&M University, Tallahassee, FL, United States
| | - Rajesh Singh Rathore
- Environmental Biotechnology Laboratory, School of the Environment, FSH Science Research Center, Florida A&M University, Tallahassee, FL, United States
| | - Rajneesh Jaswal
- Environmental Biotechnology Laboratory, School of the Environment, FSH Science Research Center, Florida A&M University, Tallahassee, FL, United States
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