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Mining activities pose severe environmental risks worldwide, generating extreme pH conditions and high concentrations of heavy metals, which can have major impacts on the survival of organisms. In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. For the analysis, soil samples were collected from the slopes (geotechnical structures) and the surrounding drainage of the Sossego mine (comprising the Sossego and Sequeirinho deposits). The results revealed complex bacterial diversity, and there was no influence of deposit geographic location on the composition of the communities. However, the environment type played an important role in bacterial community divergence; the composition and frequency of OTUs in the slope samples were different from those of the surrounding drainage samples, and Acidobacteria, Chloroflexi, Firmicutes, and Gammaproteobacteria were responsible for the observed difference. Chemical analysis indicated that both types of sample presented a high metal content, while the amounts of organic matter and water were higher in the surrounding drainage samples. Non-metric multidimensional scaling (N-MDS) analysis identified organic matter and water as important distinguishing factors between the bacterial communities from the two types of mine environment. Although habitat-specific OTUs were found in both environments, they were more abundant in the surrounding drainage samples (around 50 %), and contributed to the higher bacterial diversity found in this habitat. The slope samples were dominated by a smaller number of phyla, especially Firmicutes. The bacterial communities from the slope and surrounding drainage samples were different in structure and composition, and the organic matter and water present in these environments contributed to the observed differences.

The total protein content and activity of the enzymes glutathione reductase (GR), superoxide dismutase (SOD) and thioredoxin reductase (TrxR) were evaluated in Acidithiobacillus ferrooxidans LR cells maintained in contact with the metal sulfide chalcopyrite for 1 and 10 days. A significant decrease in total protein content was observed in cells maintained for 10 days in the presence of chalcopyrite, suggesting proteolytic breakdown due to exposure to the metal sulfide. Following 10 days of contact with chalcopyrite, increases in GR, SOD and TrxR activities were detected, suggesting the formation of reactive oxygen species. After ten days, there was a fivefold increase in GR activity, of which, isoenzyme IV represented approximately 82% of the total. An increase in Fe-SOD activity following ten days exposure to chalcopyrite was also determined, as measured on non-denaturing polyacrylamide gels. Also, after 10 days, an approximately 31-fold increase was observed for TrxR activity. The presence of oxidative stress when A. ferrooxidans is in the presence of chalcopyrite could have a negative impact on bioleaching.

An actinobacterial strain, designated SO9-6, was isolated from a copper iron sulfide mineral. The organism is Gram-positive, facultatively anaerobic, and coccoid. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Kocuria. Here, we report the first draft genome sequence of Kocuria marina SO9-6 under accession JROM00000000 (http://www.ncbi.nlm.nih.gov/nuccore/725823918), which provides insights for heavy metal bioremediation and production of compounds of biotechnological interest.

Acidithiobacillus ferrooxidans is commonly used in bioleaching operations to recover copper from sulfide ores. It is commonly accepted that A. ferrooxidans attaches to mineral surfaces by means of extracellular polymeric substances (EPS), however the role of type IV pili and tight adherence genes in this process is poorly understood. Genes related to the formation of type IV pili and tight adherence were identified in the genome of the bacterium, and in this work, we show that A. ferrooxidans actively expresses these genes, as demonstrated by quantitative real-time PCR analysis using cells incubated with chalcopyrite for 2 h. Significant differences in gene expression were observed between planktonic and adhered cells, with the level of expression being much greater in planktonic cells. These results might indicate that planktonic cells can actively adhere to the substrate. A bioinformatics analysis of interaction networks of the tight adherence and type IV pilus assembly genes revealed a strong relationship between conjugation systems (tra operon) and regulatory systems (PilR, PilS).

Orientador: Laura Maria Mariscal Ottoboni Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: Acidithiobacillus ferrooxidans é uma bactéria Gram negativa, anaeróbica facultativa, acidofílica, quimiolitotrófica e mesofílica. A. ferrooxidans é capaz de utilizar ferro e enxofre como fonte de energia e é um dos microrganismos mais utilizados no processo de biolixiviação. Durante este processo a bactéria pode estar sujeita a diversos tipos de estresse, entre eles, o estresse oxidativo. Entre os principais sensores relacionados à resposta antioxidante estão: a enzima SOD e as proteínas dos sistemas tiorredoxina e glutarredoxina. A SOD atua como defesa primária na remoção de espécies reativas do oxigênio. O sistema tiorredoxina é composto por NADPH, TrxR e Trx. O sistema glutarredoxina é formado por NADPH, GR, GSH e Grx. Os sistemas tiorredoxina e glutarredoxina desempenham um papel fundamental contra espécies reativas do oxigênio e na manutenção do ambiente redutor da célula. No primeiro capítulo, a linhagem brasileiraA. ferrooxidans LR foi utilizada para o estudo da expressão de genes dos sistemas tiorredoxina e glutarredoxina, por PCR em tempo real, em diferentes condições: (a) nas taxas de 50, 75 e 100% de oxidação de Fe2+, (b) em um e dois dias após a taxa de 100% de oxidação de Fe2+, (c) na presença de calcopirita e (d) após diferentes tempos de heat shock. Em geral, nas diferentes taxas de oxidação de Fe2+, os genes do sistema tiorredoxina foram mais expressos que os do sistema glutarredoxina. Em um dia após 100% de oxidação de Fe2+, a maioria dos genes teve expressão induzida. Em dois dias a partir desta taxa de oxidação de Fe2+, apenas os genes trxB e gor foram induzidos em relação ao controle, sugerindo que os produtos desses genes podem exercer a função de chaperona durante o estresse oxidativo. Na presença de calcopirita, apenas o gene gor foi induzido, indicando que GR pode estar envolvida no controle da homeostase celular. Esta enzima também pode ser necessária para a atividade de GSH, proteína envolvida no metabolismo de enxofre. Após o heat shock, os níveis de expressão do gene que codifica a proteína Grx3 aumentaram significativamente, possivelmente devido à propriedade de co-chaperona da proteína. No segundo capítulo foram feitas análises in silico das sequências de aminoácidos das proteínas GR, TrxR e SOD de A. ferrooxidans. A análise de in silico mostrou que existem muitas semelhanças entre as proteínas TrxR e GR, como por exemplo, estrutura secundária, peso molecular, sítio ativo, motivos funcionais e domínios. Foi realizada a quantificação de proteínas totais, a determinação da atividade em espectrofotômetro das enzimas GR e TrxR, a atividade em PAGE não desnaturante das proteínas GR e SOD e a caracterização de SOD durante o crescimento de A. ferrooxidans LR em ferro e em células mantidas em contato com a calcopirita por 1 e 10 dias. A concentração de proteínas totais foi menor em células mantidas por 10 dias em contato com a calcopirita, e uma das razões pode ser o maior estresse oxidativo. A atividade das enzimas GR, TrxR e SOD aumentou neste mesmo período de tempo, sugerindo a presença de estresse. A caracterização com KCN e H2O2 mostrou que a enzima SOD de A. ferrooxidans era do tipo FeSOD. Abstract: Acidithiobacillus ferrooxidans is a Gram-negative, anaerobic facultative, acidophilic, chemolithoautotrophic and mesophilic bacterium. A. ferrooxidans is able to use iron and sulfur as energy source and is one of the microorganisms used in the bioleaching process. During this process, the bacterium may be subjected to several stressful situations including the oxidative stress. Among the proteins involved in the antioxidant response are the enzyme SOD and the proteins from the thioredoxin and the glutaredoxin systems. SOD removes the reactive oxygen species. The thioredoxin system is composed by NADPH, TrxR and Trx. The glutaredoxin system consists of NADPH, GR, GSH and Grx. The thioredoxin and the glutaredoxin systems play a key role against the reactive oxygen species and maintain the reducing environment of the cell. In the first chapter, the Brazilian strain A. ferrooxidans LR was used to study the expression of genes from the thioredoxin and the glutaredoxin systems, by real-time PCR, in different conditions: (a) at 50, 75 and 100% of Fe2+ oxidation, (b) in one a and in two days after 100% of Fe2+ oxidation, (c) in the presence of chalcopyrite and (d) after different periods of time of heat shock. In general, on the different rates of Fe2+ oxidation, the genes of the thioredoxin system showed a higher expression than the genes from the glutaredoxin system. In one day after 100% of oxidation of Fe2+, the majority of the genes had their expression induced. In two days after 100% of oxidation of Fe2+, only the genes trxB and gor were induced suggesting that the product of these genes may act as chaperones during the oxidative stress. In the presence of chalcopyrite, only the gene gor was induced, indicating that GR may be involved in the control of the cell homeostasis since it is necessary for GSH activity, a protein that participates in sulfur metabolism. After the heat shock, the expression of the gene that encodes the protein Grx3 increased, probably because this protein can act as a cochaperone. In the second chapter, an in silico analysis of the proteins GR, TrxR and SOD amino acids sequences from A. ferrooxidans was performed. This analysis showed that there are several similarities between TrxR and GR including, secondary structure, molecular weight, active site, functional motives and domains. Total protein content in cells grown until 80% of oxidation of Fe2+ and in cells kept for 1 and 10 days in the presence of chalcopyrite was determined. Also, in these conditions, the activities of GR and TrxR were determined in a spectrophotometer and the activities of GR and SOD were determined in gel. The total protein content was higher in control cells and in the contrary, enzyme activities were higher at 10 days of bacteria contact with chalcopyrite indicating the presence of oxidative stress. Assays with KCN and H2O2 showed that the A. ferrooxidans LR SOD was in fact a FeSOD. Mestrado Genética de Microorganismos Mestre em Genética e Biologia Molecular

Copper mine drainages are restricted environments that have been overlooked as sources of new biocatalysts for bioremediation and organic syntheses. Therefore, this study aimed to determine the enzymatic activities (esterase, epoxide hydrolase and monooxygenase) of 56 heterotrophic bacteria isolated from a neutral copper mine drainage (Sossego Mine, Canaã dos Carajás, Brazil). Hydrolase and monooxygenase activities were detected in 75% and 20% of the evaluated bacteria, respectively. Bacterial strains with good oxidative performance were also evaluated for biotransformation of organic sulfides. Fourteen strains with good enzymatic activity were identified by 16S rRNA gene sequencing, revealing the presence of three genera: Bacillus, Pseudomonas and Stenotrophomonas. The bacterial strains B. megaterium (SO5-4 and SO6-2) and Pseudomonas sp. (SO5-9) efficiently oxidized three different organic sulfides to their corresponding sulfoxides. In conclusion, this study revealed that neutral copper mine drainages are a promising source of biocatalysts for ester hydrolysis and sulfide oxidation/bioremediation. Furthermore, this is a novel biotechnological overview of the heterotrophic bacteria from a copper mine drainage, and this report may support further microbiological monitoring of this type of mine environment.