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Open AccessArticle

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

1
School of the Environment, 1515 S. MLK Blvd., Suite 305B, Building FSHSRC, Florida A&M University, Tallahassee, FL 32307, USA
2
Savannah River Ecology Laboratory, The University of Georgia. PO Drawer E, Aiken, SC 29802, USA
3
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G2P5, Canada
4
Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2019, 10(5), 325; https://doi.org/10.3390/genes10050325
Received: 13 March 2019 / Revised: 19 April 2019 / Accepted: 24 April 2019 / Published: 28 April 2019
(This article belongs to the Section Microbial Genetics and Genomics)
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. View Full-Text
Keywords: uranium resistance; metagenomics; whole genome sequence; comparative genomics; Burkholderia; Penicillium; diffusion chamber; microbial trap uranium resistance; metagenomics; whole genome sequence; comparative genomics; Burkholderia; Penicillium; diffusion chamber; microbial trap
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Jaswal, R.; Pathak, A.; Edwards III, B.; Lewis III, R.; Seaman, J.C.; Stothard, P.; Krivushin, K.; Blom, J.; Rupp, O.; Chauhan, A. Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA. Genes 2019, 10, 325.

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