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| Author(s): |
Deyvid Emanuel Amgarten
Total Authors: 1
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| Document type: | Master's Dissertation |
| Press: | São Paulo. |
| Institution: | Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) |
| Defense date: | 2016-11-18 |
| Examining board members: |
João Carlos Setubal;
Armando Morais Ventura;
Paolo Marinho de Andrade Zanotto
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| Advisor: | João Carlos Setubal; Aline Maria da Silva |
| Abstract | |
The study of the viral diversity in environmental samples has become increasingly important due to key-roles that are performed by these organisms in our ecosystems. Recent publications provide evidence that viruses of bacteria (bacteriophages) may be key-players in biogeochemical cycles of large ecosystems, as oceans and forests. Besides, they may also be determinant in the genes flux among populations and in the plasticity of the communities face to environmental stresses. In this work, we propose the investigation and characterization of the viral diversity in composting samples through non-culturable and culturable-dependent approaches. In the first approach, we sampled a composting unit from the Sao Paulo Zoo Park in different time points and proceeded with metagenomic sequencing. The dataset generated was extensively mined to provide results of diversity and abundance of viral taxa through the composting process. Additionally, we proceeded with the assembly and retrieval of candidate sequences to partial or/and complete viral genomes. The two computational protocols were automatized as pipelines and can be applied to any metagenomic dataset of illumina reads. The second approach refers to the isolation and characterization of new Pseudomonas phages obtained from composting samples. Three new phages were identified and their genomes were sequenced. A detailed characterization of these genomes revealed high degree of novelty, insights about evolution of tailed-phages and the presence of tRNA genes, which may be related to a mechanism to bypass host translational bias. The experimental characterization of the new phages demonstrated great potential to lyse bacterial cells and to degrade Pseudomonas aeruginosa PA14 biofilms. In short, the data presented in this dissertation shed light to the composting virome diversity, as well as to the functional and ecological profiles of viruses in the composting environment. (AU) | |
| FAPESP's process: | 14/16450-8 - Diversity analysis of bacteriophages associated to microbial community during the composting process |
| Grantee: | Deyvid Emanuel Amgarten |
| Support Opportunities: | Scholarships in Brazil - Master |