Shotgun metagenomics analysis indicates Bradyrhizobium spp. as the predominant genera for heavy metal resistance and bioremediation in a long-term heavy metal-contaminated ecosystem

Agashe, Rohan; George, Jonathan; Pathak, Ashish; Fasakin, Olasunkanmi; Seaman, John; Chauhan, Ashvini; Stedman, ed., Kenneth M.

doi:10.1128/mra.00245-24

Title: Shotgun metagenomics analysis indicates Bradyrhizobium spp. as the predominant genera for heavy metal resistance and bioremediation in a long-term heavy metal-contaminated ecosystem

Journal Article · 11 December 2024 · Microbiology Resource Announcements

DOI: https://doi.org/10.1128/mra.00245-24 · OSTI ID:2481024

Agashe, Rohan; George, Jonathan; Pathak, Ashish; Fasakin, Olasunkanmi; Seaman, John;

; Stedman, ed., Kenneth M.

ABSTRACT Ten soil cores were collected from the long-term heavy metal-contaminated Savannah River Site (SRS) and studied using shotgun metagenomics. In-line with our previous reports, Bradyrhizobium spp. dominated the SRS soils, and thus we recommend that SRS bioremediation studies target the Bradyrhizobium genus.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: FE0032198

OSTI ID:: 2481024

Journal Information:: Microbiology Resource Announcements, Journal Name: Microbiology Resource Announcements Journal Issue: 12 Vol. 13; ISSN 2576-098X

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (14)

Heavy metals multi-tolerant Bradyrhizobium isolated from mercury mining region in Algeria Salmi, Adouda; Boulila, Farida Journal of Environmental Management, Vol. 289 https://doi.org/10.1016/j.jenvman.2021.112547	journal	July 2021
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site Thomas, Jesse C.; Oladeinde, Adelumola; Kieran, Troy J. Microbial Biotechnology, Vol. 13, Issue 4 https://doi.org/10.1111/1751-7915.13578	journal	May 2020
Announcing the Availability of a Culture Collection of Uranium-Resistant Microbial Assemblages (CURMA) Obtained from Metalliferous Soils of the Savannah River Site, USA Agarwal, Meenakshi; Rathore, Rajesh Singh; Black, Allen Microbiology Resource Announcements, Vol. 9, Issue 30 https://doi.org/10.1128/MRA.00551-20	journal	July 2020
Draft Genome Sequence of Serratia sp. Strain S1B, Isolated from Mercury-Contaminated Soil Pathak, Ashish; Jaswal, Rajneesh; Xu, Xiaoyu Genome Announcements, Vol. 6, Issue 25 https://doi.org/10.1128/genomeA.00534-18	journal	June 2018
Friend or Foe: Draft Genome Sequence of Bradyrhizobium sp. Strain SRS-191 Chauhan, Ashvini; Rathore, Rajesh Singh; Agarwal, Meenakshi Microbiology Resource Announcements, Vol. 11, Issue 11 https://doi.org/10.1128/mra.00753-22	journal	November 2022
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers Ounit, Rachid; Wanamaker, Steve; Close, Timothy J. BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1419-2	journal	March 2015
STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions Katz, Kenneth S.; Shutov, Oleg; Lapoint, Richard Genome Biology, Vol. 22, Issue 1 https://doi.org/10.1186/s13059-021-02490-0	journal	September 2021
Cutadapt removes adapter sequences from high-throughput sequencing reads Martin, Marcel EMBnet.journal, Vol. 17, Issue 1 https://doi.org/10.14806/ej.17.1.200	journal	May 2011
Chemical contaminants on DOE lands and selection of contaminant mixtures for subsurface science research Riley, R. G.; Zachara, J. M. https://doi.org/10.2172/5202264	report	April 1992
Characterization of Bacterial and Fungal Assemblages From Historically Contaminated Metalliferous Soils Using Metagenomics Coupled With Diffusion Chambers and Microbial Traps Pathak, Ashish; Jaswal, Rajneesh; Xu, Xiaoyu Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.01024	journal	June 2020
Utilizing a Metagenome Assembled Genome Approach Revealed Further Insights into Microbially Mediated Heavy-Metal Resistance in Soils from a Former Nuclear Materials Production Facility Kommu, Navya; Stothard, Paul; Chukwujindu, Christian Applied Microbiology, Vol. 4, Issue 1 https://doi.org/10.3390/applmicrobiol4010026	journal	February 2024
Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS-W-1-2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils Chauhan, Ashvini; Pathak, Ashish; Jaswal, Rajneesh Genes, Vol. 9, Issue 1 https://doi.org/10.3390/genes9010031	journal	January 2018
Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils Jaswal, Rajneesh; Pathak, Ashish; Chauhan, Ashvini Microorganisms, Vol. 7, Issue 9 https://doi.org/10.3390/microorganisms7090324	journal	September 2019

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