Integrative and in silico modeling of multi-omics data of Archaea and Bacteria phyla in Amazon soils

Author(s)

Leandro Nascimento Lemos

• Document type: Doctoral Thesis
• Press: Piracicaba.
• Institution: Universidade de São Paulo (USP). Centro de Energia Nuclear na Agricultura (CENA/STB)
• Defense date: 2019-10-15

Examining board members

Tsai Siu Mui; Fernando Dini Andreote; Alessandro de Mello Varani

• Advisor: Tsai Siu Mui

Abstract

A large scale of multi-omics datasets, that have been generated in various microbiome projects, such as the \"Dimensions US-BIOTA-Sao Paulo: Collaborative Research: Integrating Dimensions of Microbial Biodiversity across Land Use Change in Tropical Forests (FAPESP 2014/50320-4)\", require a quantitative interpretation of the interactions among the three dimensions (phylogenetic, genetic and functional) of microbial diversity. This thesis was based on the need to use an integrated computational approach to investigate the role of Bacteria and Archaea in Amazon soils, using massive sequencing technologies, bioinformatics and reconstruction of genomes from metagenomes (MAGs) to understand not only the diversity, but also the evolution, metabolism and biogeography distribution. Firstly, in the Chapter 1 we introduced an overview of the main topics covered in this thesis. Then, we outlined the main approaches applied for microbiome studies based on high-throughput sequencing technologies and we introduced the most commonly used strategies for bioinformatics analyses and data integration. In the third chapter, the application of an integrative approach allowed us to discover that the nitrogen-related traits associated with nitrification in Archaea (e.g. ammonia oxidation) metabolism seems to be a derived character and emerged late in the diversification of the Thaumarchaeota (Archaea) group. Furthermore, after analyzing more than 27,000 public environmental samples, we discovered that the non-ammonia oxidizing clade has habitat-specific subgroups (e.g. Group 1.1c is more specific for soils and non-saline sediments). We also described the first Thaumarchaeota genome from tropical soils. Additionally, in the fourth chapter we discovered that the small-sized genome was a trait of the new CPR/Patescibacteria (Bacteria) phyla in cattle-pasture of Amazon soils. We also expanded the range of environments within the radiation of this new bacterial group appears and highlight the importance of MAGs methods for the expansion of reference databases. Lastly, chapter five explored the effects of forest-to-pasture conversion and an increase in soil moisture levels on Archaea composition in Amazon soils. Our results indicated that the community alterations caused by the higher soil moisture levels are most pronounced in the pasture, where communities were more sensitive, enhancing the potential of methanogenesis, while forest may act as buffers during the rainy season and harbors more stable communities. This thesis highlights the importance of the use of advanced bioinformatics tools and integrated computational approaches for a better understanding of the evolutionary processes, metabolic pathways and environmental distribution of complex soil microbiome members (AU)

• FAPESP's process: 16/18215-1 - Multi-omics integrated and in silico modelling of Archaea communities associated with methanogenis in amazon soils.
• Grantee: Leandro Nascimento Lemos
• Support Opportunities: Scholarships in Brazil - Doctorate