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Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA

Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversi...

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Autores principales: Jaswal, Rajneesh, Pathak, Ashish, Edwards III, Bobby, Lewis III, Robert, Seaman, John C., Stothard, Paul, Krivushin, Kirill, Blom, Jochen, Rupp, Oliver, Chauhan, Ashvini
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562407/
https://www.ncbi.nlm.nih.gov/pubmed/31035394
http://dx.doi.org/10.3390/genes10050325
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author Jaswal, Rajneesh
Pathak, Ashish
Edwards III, Bobby
Lewis III, Robert
Seaman, John C.
Stothard, Paul
Krivushin, Kirill
Blom, Jochen
Rupp, Oliver
Chauhan, Ashvini
author_facet Jaswal, Rajneesh
Pathak, Ashish
Edwards III, Bobby
Lewis III, Robert
Seaman, John C.
Stothard, Paul
Krivushin, Kirill
Blom, Jochen
Rupp, Oliver
Chauhan, Ashvini
author_sort Jaswal, Rajneesh
collection PubMed
description Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils.
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spelling pubmed-65624072019-06-17 Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA Jaswal, Rajneesh Pathak, Ashish Edwards III, Bobby Lewis III, Robert Seaman, John C. Stothard, Paul Krivushin, Kirill Blom, Jochen Rupp, Oliver Chauhan, Ashvini Genes (Basel) Article Despite the recent advancements in culturomics, isolation of the majority of environmental microbiota performing critical ecosystem services, such as bioremediation of contaminants, remains elusive. Towards this end, we conducted a metagenomics-guided comparative assessment of soil microbial diversity and functions present in uraniferous soils relative to those that grew in diffusion chambers (DC) or microbial traps (MT), followed by isolation of uranium (U) resistant microbiota. Shotgun metagenomic analysis performed on the soils used to establish the DC/MT chambers revealed Proteobacterial phyla and Burkholderia genus to be the most abundant among bacteria. The chamber-associated growth conditions further increased their abundances relative to the soils. Ascomycota was the most abundant fungal phylum in the chambers relative to the soils, with Penicillium as the most dominant genus. Metagenomics-based taxonomic findings completely mirrored the taxonomic composition of the retrieved isolates such that the U-resistant bacteria and fungi mainly belonged to Burkholderia and Penicillium species, thus confirming that the chambers facilitated proliferation and subsequent isolation of specific microbiota with environmentally relevant functions. Furthermore, shotgun metagenomic analysis also revealed that the gene classes for carbohydrate metabolism, virulence, and respiration predominated with functions related to stress response, membrane transport, and metabolism of aromatic compounds were also identified, albeit at lower levels. Of major note was the successful isolation of a potentially novel Penicillium species using the MT approach, as evidenced by whole genome sequence analysis and comparative genomic analysis, thus enhancing our overall understanding on the uranium cycling microbiota within the tested uraniferous soils. MDPI 2019-04-28 /pmc/articles/PMC6562407/ /pubmed/31035394 http://dx.doi.org/10.3390/genes10050325 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Jaswal, Rajneesh
Pathak, Ashish
Edwards III, Bobby
Lewis III, Robert
Seaman, John C.
Stothard, Paul
Krivushin, Kirill
Blom, Jochen
Rupp, Oliver
Chauhan, Ashvini
Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA
title Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA
title_full Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA
title_fullStr Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA
title_full_unstemmed Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA
title_short Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA
title_sort metagenomics-guided survey, isolation, and characterization of uranium resistant microbiota from the savannah river site, usa
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562407/
https://www.ncbi.nlm.nih.gov/pubmed/31035394
http://dx.doi.org/10.3390/genes10050325
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