Metagenome of a microbial community inhabiting a metal-rich tropical stream sediment

• Published in: PloS one Vol. 10; no. 3; p. e0119465
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 05-03-2015; Public Library of Science (PLoS)
• Subjects: Ammonification; Ammonium; Annotations; Archaea - classification; Archaea - genetics; Archaea - isolation & purification; Arsenic; Bacteria; Biogeochemistry; Brazil; Candidatus Nitrospira defluvii; Candidatus Parvarchaeota; Communities; Contamination; Deoxyribonucleic acid; DNA; Ecosystems; Environmental DNA; Environmental Microbiology; Field study; Fresh Water - chemistry; Fresh Water - microbiology; Freshwater pollution; Genes; Genetic aspects; Genomes; Genotypes; Geologic Sediments - chemistry; Geologic Sediments - microbiology; Gram-positive bacteria; Historical account; Identification and classification; Iron; Metabolism; Metagenome; Metals; Metals - metabolism; Microbial colonies; Microbiomes; Microorganisms; Mining; Nitrosopumilus maritimus; Nucleotide sequence; Observations; Physiology; Proteobacteria; Proteobacteria - classification; Proteobacteria - genetics; Proteobacteria - isolation & purification; Rivers; Sediment pollution; Sediments; Sediments (Geology); Sequence Analysis, RNA; Soil contamination; Taxonomy; Tropical Climate; Brazil
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0119465

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.