Metagenomic analysis of the microbiota associated with copper mine environments

Author(s)

Daniel Bedo Assumpção Castro

• Document type: Master's Dissertation
• Press: Campinas, SP.
• Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia
• Defense date: 2015-08-14

Examining board members

Laura Maria Mariscal Ottoboni; Valeria Maia de Oliveira; Edmilson Ricardo Gonçalves

• Advisor: Renato Vicentini; Laura Maria Mariscal Ottoboni

Abstract

Many investigations seek to understand the diversity and distribution of the microbial communities in the mine drainage, but few studies aim to assess the genomes present in the copper mine environments, especially in the neutral drainages and the ore pile that generates them. Thus, in this work, metagenomic evaluations, from two soil samples contaminated with neutral mine drainage and three samples from copper pile soil, were carried out to identify genes and metabolic pathways of biotechnological, industrial and environmental interest. All the samples were obtained in the Sossego mine, and their chemical analysis showed an alkaline pH and large contents of copper and nickel. The taxonomic annotation of the metagenomes showed a predominance of sequences associated with the phyla Proteobacteria and Actinobacteria. Differently from the metagenomes of other mines, the Sossego mine metagenomes revealed higher percentage of sequences related to the phylum Cyanobacteria. The statistical analyzes of the five metagenomes showed that the samples from copper pile soils are enriched with genes that encode proteins involved in the lipid metabolism, and are related to the acquisition of carbon and nitrogen. The comparative analyses of the metagenomes of this study with thirty-one metagenomes available in databases revealed higher amounts of protein-coding genes associated with tolerance to copper, active subtilisin at alkaline pH and proteins involved in the cell stability, which suggest that the microbiota is adapted to the Sossego mine. The search for metal tolerance genes showed that the microbiota has common mechanisms to deal with different metals and the reconstruction of the sulfur metabolism pathway indicated that the microorganisms are capable to oxidize and reduce sulfur compounds, which has industrial and environmental importance. The metagenomes revealed genes that encode proteins for the degradation of aromatic compounds and the reconstruction of the xenobiotic degradation pathways showed genes involved in the catabolism of phenol and benzene, and in the cathecol production. Two genomes, belonging to the Geitlerinema (Cyanobacteria) and Meiothermus (Deinococcus-Thermus) genus, were recovered from the metagenomes. They presented genes related to the hydrolysis of different sources of carbohydrate, acquisition of nitrogen and antibiotic resistance. The comparative genomics of the recovered Geitlerinema and Meiothermus revealed several genes for transposase and tolerance to copper, suggesting the adaptation of these microorganisms to the Sossego mine environment. The results obtained in this study help to understand the functional diversity in soils impacted by neutral mine drainage and copper ore pile, generating information that did not exist in databases. Furthermore, the metagenomes revealed genes and metabolic pathways of industrial and environmental interest (AU)

• FAPESP's process: 13/03382-1 - Metagenomic Analysis of the Microbiota Associated with Copper Mine Environment
• Grantee: Daniel Bedo Assumpção Castro
• Support Opportunities: Scholarships in Brazil - Master