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Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment

Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world’s largest mining regions. Environme...

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Autores principales: Costa, Patrícia S., Reis, Mariana P., Ávila, Marcelo P., Leite, Laura R., de Araújo, Flávio M. G., Salim, Anna C. M., Oliveira, Guilherme, Barbosa, Francisco, Chartone-Souza, Edmar, Nascimento, Andréa M. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351183/
https://www.ncbi.nlm.nih.gov/pubmed/25742617
http://dx.doi.org/10.1371/journal.pone.0119465
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author Costa, Patrícia S.
Reis, Mariana P.
Ávila, Marcelo P.
Leite, Laura R.
de Araújo, Flávio M. G.
Salim, Anna C. M.
Oliveira, Guilherme
Barbosa, Francisco
Chartone-Souza, Edmar
Nascimento, Andréa M. A.
author_facet Costa, Patrícia S.
Reis, Mariana P.
Ávila, Marcelo P.
Leite, Laura R.
de Araújo, Flávio M. G.
Salim, Anna C. M.
Oliveira, Guilherme
Barbosa, Francisco
Chartone-Souza, Edmar
Nascimento, Andréa M. A.
author_sort Costa, Patrícia S.
collection PubMed
description Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world’s largest mining regions. Environmental DNA was extracted and was sequenced using SOLiD technology, and a total of 7.9 Gbp was produced. A taxonomic profile that was obtained by comparison to the Greengenes database revealed a complex microbial community with a dominance of Proteobacteria and Parvarcheota. Contigs were recruited by bacterial and archaeal genomes, especially Candidatus Nitrospira defluvii and Nitrosopumilus maritimus, and their presence implicated them in the process of N cycling in the Mina Stream sediment (MSS). Functional reconstruction revealed a large, diverse set of genes for ammonium assimilation and ammonification. These processes have been implicated in the maintenance of the N cycle and the health of the sediment. SEED subsystems functional annotation unveiled a high degree of diversity of metal resistance genes, suggesting that the prokaryotic community is adapted to metal contamination. Furthermore, a high metabolic diversity was detected in the MSS, suggesting that the historical arsenic contamination is no longer affecting the prokaryotic community. These results expand the current knowledge of the microbial taxonomic and functional composition of tropical metal-contaminated freshwater sediments.
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spelling pubmed-43511832015-03-17 Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment Costa, Patrícia S. Reis, Mariana P. Ávila, Marcelo P. Leite, Laura R. de Araújo, Flávio M. G. Salim, Anna C. M. Oliveira, Guilherme Barbosa, Francisco Chartone-Souza, Edmar Nascimento, Andréa M. A. PLoS One Research Article Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world’s largest mining regions. Environmental DNA was extracted and was sequenced using SOLiD technology, and a total of 7.9 Gbp was produced. A taxonomic profile that was obtained by comparison to the Greengenes database revealed a complex microbial community with a dominance of Proteobacteria and Parvarcheota. Contigs were recruited by bacterial and archaeal genomes, especially Candidatus Nitrospira defluvii and Nitrosopumilus maritimus, and their presence implicated them in the process of N cycling in the Mina Stream sediment (MSS). Functional reconstruction revealed a large, diverse set of genes for ammonium assimilation and ammonification. These processes have been implicated in the maintenance of the N cycle and the health of the sediment. SEED subsystems functional annotation unveiled a high degree of diversity of metal resistance genes, suggesting that the prokaryotic community is adapted to metal contamination. Furthermore, a high metabolic diversity was detected in the MSS, suggesting that the historical arsenic contamination is no longer affecting the prokaryotic community. These results expand the current knowledge of the microbial taxonomic and functional composition of tropical metal-contaminated freshwater sediments. Public Library of Science 2015-03-05 /pmc/articles/PMC4351183/ /pubmed/25742617 http://dx.doi.org/10.1371/journal.pone.0119465 Text en © 2015 Costa et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Costa, Patrícia S.
Reis, Mariana P.
Ávila, Marcelo P.
Leite, Laura R.
de Araújo, Flávio M. G.
Salim, Anna C. M.
Oliveira, Guilherme
Barbosa, Francisco
Chartone-Souza, Edmar
Nascimento, Andréa M. A.
Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment
title Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment
title_full Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment
title_fullStr Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment
title_full_unstemmed Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment
title_short Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment
title_sort metagenome of a microbial community inhabiting a metal-rich tropical stream sediment
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351183/
https://www.ncbi.nlm.nih.gov/pubmed/25742617
http://dx.doi.org/10.1371/journal.pone.0119465
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