{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,6]],"date-time":"2026-01-06T13:09:00Z","timestamp":1767704940573,"version":"3.48.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,12,4]],"date-time":"2025-12-04T00:00:00Z","timestamp":1764806400000},"content-version":"vor","delay-in-days":337,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000015","name":"Department of Energy","doi-asserted-by":"publisher","award":["DE-FE0032198"],"award-info":[{"award-number":["DE-FE0032198"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Minority Serving Institution Partnership Program","award":["800002172"],"award-info":[{"award-number":["800002172"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2200615"],"award-info":[{"award-number":["2200615"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000005","name":"Department of Defense","doi-asserted-by":"publisher","award":["#W911NF2210145"],"award-info":[{"award-number":["#W911NF2210145"]}],"id":[{"id":"10.13039\/100000005","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Remediation of mixed heavy metal contamination in U.S. nuclear legacy sites remains a persistent challenge. This study examines the genomic and functional traits of two newly isolated bacterial strains\u2014Stenotrophomonas strain 3 and Pseudomonas strain 8\u2014from the metal-contaminated D-Area Ash Plume at the Savannah River Site (SRS). Growth assays showed strain 8 tolerated cobalt (Co) (400\u00a0ppm) and copper (Cu) (1000\u00a0ppm), while strain 3 thrived in zinc (Zn) (20 000\u00a0ppm). Both exhibited limited growth under high nickel exposure, indicating distinct metal-specific resistance profiles. Whole-genome sequencing revealed distinct genomic adaptations: strain 8 carried copA, cnrA, NiCoT, and zitB, supporting its Co and Cu tolerance, while strain 3 harbored czcA and zitB, consistent with Zn resistance. Strain 3\u2032s genome comprised 61 contigs (4.41 Mb, 66.6% GC), and strain 8\u2032s included 62 contigs (6.93 Mb, 63.48% GC). Comparative genomic analysis of strains 3 and 8 with several previously reported SRS isolates revealed that Burkholderia spp. (SRS-25, SRS-46, SRS-W-2-2016) possessed the most extensive resistance gene repertoire, followed by Stenotrophomonas and Pseudomonas. Co-localized metal resistance genes and antibiotic resistance genes suggest shared stress response pathways and horizontal gene transfer potential, underscoring the bioremediation promise of native SRS bacteria for both metal and antibiotic contaminants.<\/jats:p>","DOI":"10.1093\/sumbio\/qvaf031","type":"journal-article","created":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T13:09:30Z","timestamp":1764767370000},"source":"Crossref","is-referenced-by-count":0,"title":["Genomic and physiological characterization of two heavy metal resistant bacteria isolated from a long-term metalliferous ecosystem"],"prefix":"10.1093","volume":"2","author":[{"given":"Bryan","family":"Alex","sequence":"first","affiliation":[{"name":"School of the Environment, Florida A&M University , 1515 S. Martin Luther King Blvd., Tallahassee, FL 32307 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyu","family":"Xu","sequence":"additional","affiliation":[{"name":"Savannah River Ecology Laboratory, University of Georgia , Aiken, SC 29802 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashish","family":"Pathak","sequence":"additional","affiliation":[{"name":"School of the Environment, Florida A&M University , 1515 S. Martin Luther King Blvd., Tallahassee, FL 32307 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashvini","family":"Chauhan","sequence":"additional","affiliation":[{"name":"School of the Environment, Florida A&M University , 1515 S. Martin Luther King Blvd., Tallahassee, FL 32307 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,12,4]]},"reference":[{"key":"2026010607320119500_bib1","doi-asserted-by":"publisher","first-page":"11756","DOI":"10.1007\/s11356-018-1402-3","article-title":"Genomic insights into metal resistance in Burkholderia species isolated from contaminated sites","volume":"25","author":"Agarwal","year":"2018","journal-title":"Environ Sci Pollut Res"},{"key":"2026010607320119500_bib2","doi-asserted-by":"publisher","first-page":"26181","DOI":"10.31083\/FBE26181","article-title":"Bioremediation of soil contaminated with heavy metals by using the Pseudomonas genus","volume":"17","author":"Alaleh","year":"2025","journal-title":"Front Biosci (Elite Ed)"},{"key":"2026010607320119500_bib3","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1016\/j.tim.2006.02.006","article-title":"Co-selection of antibiotic and metal resistance","volume":"14","author":"Baker-Austin","year":"2006","journal-title":"Trends Microbiol"},{"key":"2026010607320119500_bib4","doi-asserted-by":"publisher","first-page":"1550587","DOI":"10.3389\/fmicb.2025.1550587","article-title":"Microplastics and heavy metals synergistically enhance horizontal gene transfer in biofilm-associated bacteria","volume":"16","author":"Balta","year":"2025","journal-title":"Front Microbiol"},{"key":"2026010607320119500_bib5","doi-asserted-by":"publisher","first-page":"8365","DOI":"10.1038\/srep08365","article-title":"RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"Brettin","year":"2015","journal-title":"Sci Rep"},{"key":"2026010607320119500_bib6","doi-asserted-by":"publisher","first-page":"112012","DOI":"10.1016\/j.envres.2021.112012","article-title":"Bradyrhizobium species from contaminated soils: genomic adaptations to heavy metal stress","volume":"204","author":"Chauhan","year":"2022","journal-title":"Environ Res"},{"key":"2026010607320119500_bib7","doi-asserted-by":"publisher","first-page":"2595","DOI":"10.1007\/s00044-018-2222-9","article-title":"Synthesis and biological evaluation of coumarin clubbed oxazines","volume":"9","author":"Chauhan","year":"2018","journal-title":"Int J Pharm Sci Res"},{"volume-title":"Savannah River Site History 1950\u20131989","year":"2024","author":"DOE: U.S. Department of Energy","key":"2026010607320119500_bib8"},{"key":"2026010607320119500_bib9","doi-asserted-by":"publisher","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2026010607320119500_bib10","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1007\/s00248-019-01444-2","article-title":"Serratia species from polluted environments: resistance genes and bioremediation potential","volume":"80","author":"Gendy","year":"2020","journal-title":"Microb Ecol"},{"key":"2026010607320119500_bib11","doi-asserted-by":"publisher","first-page":"1389","DOI":"10.1016\/S0038-0717(97)00270-8","article-title":"Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: a review","volume":"30","author":"Giller","year":"1998","journal-title":"Soil Biol Biochem"},{"key":"2026010607320119500_bib12","doi-asserted-by":"publisher","first-page":"fuae017","DOI":"10.1093\/femsre\/fuae017","article-title":"Efflux-mediated co-selection of metal and antibiotic resistance in soil microbiomes","volume":"48","author":"Gillieatt","year":"2024","journal-title":"FEMS Microbiol Rev"},{"key":"2026010607320119500_bib13","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1093\/etojnl\/vgaf020","article-title":"Accumulation of trace elements in soil and fauna within a site historically contaminated with coal combustion residues","volume":"44","author":"Holland","year":"2025","journal-title":"Environ Toxicol Chem"},{"key":"2026010607320119500_bib14","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1002\/etc.5620190412","article-title":"Incidence and impact of axial malformations in larval bullfrogs (Ranacatesbeiana) developing in sites polluted by a coal-burning power plant","volume":"19","author":"Hopkins","year":"2000","journal-title":"Environ Toxicol Chem"},{"key":"2026010607320119500_bib15","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1289\/ehp.8457","article-title":"Reproduction, embryonic development, and maternal transfer of contaminants in the amphibian gastrophryne carolinensis","volume":"114","author":"Hopkins","year":"2006","journal-title":"Environ Health Persp"},{"key":"2026010607320119500_bib16","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1006\/gcen.1997.6969","article-title":"Increased circulating levels of testosterone and corticosterone in southern toads, bufo terrestris, exposed to coal combustion waste","volume":"108","author":"Hopkins","year":"1997","journal-title":"Gen Comp Endocrinol"},{"key":"2026010607320119500_bib17","doi-asserted-by":"publisher","first-page":"1511507","DOI":"10.3389\/fcimb.2025.1511507","article-title":"In-depth genome and comparative genome analysis of a metal-resistant environmental isolate Pseudomonas aeruginosa S-8","volume":"15","author":"Kumari","year":"2025","journal-title":"Front Cell Infect Microbiol"},{"key":"2026010607320119500_bib18","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/s44259-024-00026-7","article-title":"Co-selection for antibiotic resistance by environmental contaminants","volume":"2","author":"Murray","year":"2024","journal-title":"Npj Antimicrob Resist"},{"key":"2026010607320119500_bib19","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol"},{"key":"2026010607320119500_bib20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jhazmat.2017.08.056","article-title":"Genomic and functional characterization of Pseudomonas strains isolated from heavy metal contaminated sites","volume":"342","author":"Pathak","year":"2018","journal-title":"J Hazard Mater"},{"key":"2026010607320119500_bib21","doi-asserted-by":"publisher","first-page":"113712","DOI":"10.1016\/j.envpol.2019.113712","article-title":"Arthrobacter species from metal-contaminated sites: genomic features and resistance mechanisms","volume":"258","author":"Pathak","year":"2020","journal-title":"Environ Pollut"},{"key":"2026010607320119500_bib22","doi-asserted-by":"publisher","first-page":"e167","DOI":"10.1093\/nar\/gkx310","article-title":"Bidirectional approaches for optogenetic regulation of gene expression in mammalian cells using Arabidopsis cryptochrome 2","volume":"45","author":"Pathak","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2026010607320119500_bib23","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1089\/cmb.2009.0179","article-title":"How many bootstrap replicates are necessary?","volume":"17","author":"Pattengale","year":"2010","journal-title":"J Comput Biol"},{"key":"2026010607320119500_bib24","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1046\/j.1365-2427.1996.00123.x","article-title":"Oral deformities in tadpoles (Ranacatesbeiana) associated with coal ash deposition: effects on grazing ability and growth","volume":"36","author":"Rowe","year":"1996","journal-title":"Freshwater Biol"},{"key":"2026010607320119500_bib25","doi-asserted-by":"publisher","first-page":"625","DOI":"10.3390\/genes16060625","article-title":"Mobile genetic elements and resistance traits in urban and agricultural soils: a comparative metagenomic study","volume":"16","author":"S\u00e1nchez-Corona","year":"2025","journal-title":"Genes"},{"key":"2026010607320119500_bib26","doi-asserted-by":"publisher","first-page":"1508","DOI":"10.1897\/04-339R1.1","article-title":"Influence of larval period on responses of overwintering green frog (Rana clamitans) larvae exposed to contaminated sediments","volume":"24","author":"Snodgrass","year":"2005","journal-title":"Environ Toxicol Chem"},{"key":"2026010607320119500_bib27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.47068\/ctns.2020.v9i18.001","article-title":"Centrifugal partition chromatography (CPC)\u2013a novel method of separation and purification of natural products","volume":"1","author":"Sp\u00eenu","year":"2017","journal-title":"Nat Sci"},{"key":"2026010607320119500_bib28","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"2026010607320119500_bib29","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1007\/978-3-7643-8340-4_6","article-title":"Heavy metal toxicity and the environment","volume-title":"Molecular, Clinical and Environmental Toxicology","author":"Tchounwou","year":"2012"},{"key":"2026010607320119500_bib30","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1111\/1751-7915.13578","article-title":"Co-occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site","volume":"13","author":"Thomas","year":"2020","journal-title":"Microb Biotechnol"},{"key":"2026010607320119500_bib31","doi-asserted-by":"publisher","first-page":"D535","DOI":"10.1093\/nar\/gkw1017","article-title":"Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center","volume":"45","author":"Wattam","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2026010607320119500_bib32","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1007\/s42832-024-0244-4","article-title":"Metal-induced co-selection expands resistomes in agricultural soils","volume":"6","author":"Zhao","year":"2024","journal-title":"Soil Ecol Lett"}],"container-title":["Sustainable Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/sumbio\/advance-article-pdf\/doi\/10.1093\/sumbio\/qvaf031\/65742291\/qvaf031.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/sumbio\/article-pdf\/2\/4\/qvaf031\/65742291\/qvaf031.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/sumbio\/article-pdf\/2\/4\/qvaf031\/65742291\/qvaf031.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,6]],"date-time":"2026-01-06T12:32:08Z","timestamp":1767702728000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/sumbio\/article\/doi\/10.1093\/sumbio\/qvaf031\/8365524"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":32,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,10,7]]}},"URL":"https:\/\/doi.org\/10.1093\/sumbio\/qvaf031","relation":{},"ISSN":["2755-1970"],"issn-type":[{"type":"electronic","value":"2755-1970"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"qvaf031"}}