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Avaliação Da Diversidade Genética Da Comunidade Planctônica De Reservatórios De Água Doce Tropicais, Através De Análise Metagenômica

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Avaliação Da Diversidade Genética Da Comunidade Planctônica De Reservatórios De Água Doce Tropicais, Através De Análise Metagenômica MARCELE LAUX AVALIAÇÃO DA DIVERSIDADE GENÉTICA DA COMUNIDADE PLANCTÔNICA DE RESERVATÓRIOS DE ÁGUA DOCE TROPICAIS, ATRAVÉS DE ANÁLISE METAGENÔMICA Tese apresentada ao Programa de Pós-Graduação em Biologia Vegetal do Departamento de Botânica do Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, como requisito parcial à obtenção do título de Doutor em Biologia Vegetal. Área de Concentração Ecofisiologia BELO HORIZONTE – MG 2016 MARCELE LAUX AVALIAÇÃO DA DIVERSIDADE GENÉTICA DA COMUNIDADE PLANCTÔNICA DE RESERVATÓRIOS DE ÁGUA DOCE TROPICAIS, ATRAVÉS DE ANÁLISE METAGENÔMICA Tese apresentada ao Programa de Pós-Graduação em Biologia Vegetal do Departamento de Botânica do Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, como requisito parcial à obtenção do título de Doutor em Biologia Vegetal. Área de Concentração Ecofisiologia Orientador: Prof. Dr. Alessandra Giani Universidade Federal de Minas Gerais Coorientador: Prof. Dr. José Miguel Ortega Universidade Federal de Minas Gerais BELO HORIZONTE – MG 2016 2 Laux, Marcele. Avaliação da diversidade genética da comunidade planctônica de reservatórios de água doce tropicais, através de análise metagenômica. [manuscrito] / Marcele Laux. – 2016. 198 f. : il. ; 29,5 cm. Orientadora: Profa. Dra. Alessandra Giani. Coorientador: Prof. Dr. José Miguel Ortega. Tese (doutorado) – Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas. 1. Bioma tropical. 2. Reservatórios - Teses. 3. Cianobactéria - Teses. 4. Metagenômica - Teses. 5. Botânica - Teses. I. Giani, Alessandra. II. Ortega, José Miguel . III. Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas . IV. Título. CDU: 581.6 3 4 Agradecimentos Agradeço à professora Alessandra Giani pela orientação e o apoio que demonstrou mesmo antes de eu iniciar o doutorado, acreditando no nosso projeto e acreditando na minha capacidade de realizá-lo. Agradeço ao Departamento de Botânica, em especial à professora Denise Maria Trombert de Oliveira, ao professor Cleber Cunha Figueredo, ao professor João Renato Stehmann e à professora Rosy Mary dos Santos Isaias. Agradeço à equipe do Laboratório Biodados, em especial professor Miguel José Ortega, que disponibilizou seus servidores para que eu pudesse realizar meu trabalho, e ao colega Ricardo Vialle, por me ajudar nos primeiros passos da bioinformática. Agradeço aos colegas do Laboratório de Ficologia, em especial Valquíria e Elenice pelo apoio técnico. Agradeço à Selminha pelos cafés. Agradeço às escolas públicas pelas quais passei, agradeço à UFRGS e à UFMG, agradeço ao CNPq, Faufrgs, Fundep e CAPES, cujas bolsas foram essenciais para eu seguir esse caminho. Agradeço a minha família pelo apoio e estímulo. Agradeço a meus amigos pela paciência, especialmente à Dávia Talgatti. Agradeço à Cláudia, que me deu um lar e a segurança que eu precisava para ter coragem de continuar. Por fim, meu agradecimento especial é para meu país, que me disponibilizou educação plena desde a pré-escola e um contexto social e cultural que permitiu que eu escolhesse e seguisse meu objetivo. 5 Concerto para Violino em D maior, Op. 35, I. Allegro moderato Compasso 119-141, solo e tema Tchaikovsky P. I., (1881) 6 LISTA DE ABREVIATURAS WGS - “whole-genome shotgun”, estratégia de fragmentação randômica do DNA. BLAST - “Basic Local Alignment Search Tool”, ferramenta de alinhamento local. NCBI - “National Center for Biotechnology Information”, Centro Nacional para Informação de Biotecnologia. LCA - “Lowest Common Ancestor”, Menor Ancestral Comum. MEGAN - “Metagenome Analyzer” MG-RAST - “Metagenomics RAST Server” Read - fragmento de DNA da amostra ambiental. SNVs - “single nucleotide variants”, detecção de variantes de nucleotídeos. NGS - “Next Generation Sequencing”, sequenciamento de última geração. NCD - “Neighbor Cell Distance”, distância da célula vizinha. GLM - “linear generalized model”, modelo linear generalizado. OTU - “operational taxonomic unit”, unidade taxonômica operacional. SNV - “single nucleotide variants”, variantes (polimorfismos) de base única. CMI - “Candidate Metagenomic Islands”, ilhas metagenômicas candidatas. KEGG - “Kyoto Encyclopedia of Genes and Genomes” COG - “Phylogenetic classification of proteins encoded in complete genomes” 7 RESUMO GERAL No primeiro capítulo é apresentada a diversidade de picocianobactérias do reservatório de Volta Grande, através de taxonomia clássica, análises estatísticas complementares e abordagem metagenômica. A riqueza de espécies descritas morfologicamente apresentou concordância com a microdiversidade observada para os gêneros dominantes anotados de acordo com os bancos de referências NCBI (nt) e SILVA (ssu rRNA). No segundo capítulo apresentamos o perfil metagenômico do reservatório de Marimbondo em escala temporal e espacial. As variáveis ambientais apresentaram um gradiente de acordo com o aumento da biomassa da população de Microcystis. O perfil taxonômico da comunidade foi distinto entre as amostras com baixa e alta biomassa de Microcystis, inclusive correlacionado ao gradiente ambiental, porém o perfil funcional foi estável entre as amostras, indicando uma redundância funcional. Dessa forma, as distintas anotações taxonômicas podem refletir, na verdade, a dinâmica de diversificação/adaptação do conjunto gênico de uma população. O terceiro capítulo aborda a microdiversidade da população de M. aeruginosa do reservatório de Marimbondo, uma vez que um grande número de cepas foi previamente observado. As análises de recrutamento e detecção de variantes de base única (SNVs) foram empregadas para explorar os padrões de alinhamento e diferenciação entre os membros da população. A microdiversidade observada pode ser relacionada à estrutura genômica em mosaico, na qual o conjunto gênico alterna em função das necessidades funcionais da população. O capítulo quatro explora a variabilidade genética das populações de dois gêneros da família Aphanizomenonaceae da lagoa da Pampulha, um reservatório artificial urbano hipereutrófico impactado por constantes florações de cianobactérias. Através de diversas abordagens, a complexidade de gêneros e cepas estreitamente relacionadas foi explorada. O alinhamento múltiplo, incluindo gêneros e cepas da América do Sul, indicou maior similaridade da população local aos genomas de Raphidiopsis brookii D9 e Cylindrospermopsis raciborskii T3. Diversos fatores indicam que estejamos lidando com uma população ainda desconhecida, entre eles a falta de alinhamento completo com R. brookii D9, a similaridade a diversas sequências sul-americanas e a alta diversidade intraespecífica observada pela ampla distribuição de SNVs, em especial àqueles detectados nos operons de assimilação e conversão de nitrito/nitrato. Palavras-chave: Cianobactérias, Metagenômica, Reservatórios, Bioma tropical 8 ABSTRACT On the first chapter we present the diversity of picocyanobacteria in the Volta Grande reservoir, through classic taxonomy, complemmentary statistical analyses and metagenomics approach. The richness in morphologically described species was in line with the microdiversity observed in the dominant genera annotated, according to reference databases: NCBI (nt) e SILVA (ssu rRNA). On the second chapter se see the metagenomic profile of the Marimbondo reservoir, both in spacial and temporal scale. The environmental variables showed a gradient consistent with the increase of biomass in the Microcystis population. The taxonomic profile of the community was different between samples with low or high Microcystis biomass, as well as correlated with the environmental gradient. Meanwhile, the functional profile was stable among samples, indicating functional redundancy. Therefore, the distinct taxonomic annotations could actually reflect the diversification/adaptation dynamics of the gene pool in a given population. The third chapter is concerned with the microdiversity of the M. aeruginosa population in the the Marimbondo reservoir, due to number of strains previously observed. The recruitment analyses and variant calling (SNV) were used with the intent of exploring alignment patterns and differentiation among population members. The microdiversity we observed could be related to the mosaic-like genomic structure in which the gene pool alternates according to the functional needs of the population. The fourth chapter explores the genetic variability of the two genera of the Aphanizomenonaceae Family in Pampulha lake, an urban artificial hypereutrophic reservoir suffering the impact of constant cyanobacteria blooms. Through different approaches, we explored the complexity in closely related strains and genera. The alignment of south american strains and genera indicated greater similarity of the local population with the genomes of Raphidiopsis brookii D9 and Cylindrospermopsis raciborskii T3. Many factors might indicate that we are dealing with a still unknown population, among which is the lack of full alignment with R. brookii D9, the similarity with several south american sequences and the high intraspecific diversity. Said diversity was observed through the wide distribution in SNVs, especially those detected in assimilation and conversion of nitrite/nitrate operons. Key Words: Cyanobacteria, Metagenomics, Freshwater Reservoir, Tropical Biome 9 Sumário LISTA DE ABREVIATURAS .......................................................................................... 7 RESUMO GERAL ............................................................................................................ 8 ABSTRACT
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