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Multi-omics integrated and in silico modelling of Archaea communities associated with methanogenis in amazon soils.

Grant number: 16/18215-1
Support Opportunities:Scholarships in Brazil - Doctorate
Effective date (Start): December 01, 2016
Effective date (End): September 30, 2019
Field of knowledge:Biological Sciences - Microbiology - Applied Microbiology
Principal Investigator:Tsai Siu Mui
Grantee:Leandro Nascimento Lemos
Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Associated research grant:14/50320-4 - Dimensions US-BIOTA - São Paulo: collaborative research: integrating dimensions of microbial biodiversity across land use change in tropical forests, AP.BTA.TEM
Associated scholarship(s):17/24037-1 - Diversity and evolution of functional genomic traits associated with methane and nitrogen cycles in amazonian soil metagenomes, BE.EP.DR


The multi-omics data being generated in the thematic projet "Integrating Dimensions of Microbial Biodiversity across Land Use Change in Tropical Forests" (Process: 2014 / 50320-4) require a quantitative interpretation of the interactions among the three dimensions (phylogenetic, genetic and funcional) of microbial diversity. The aim of this project is to develop a data integration model, based on the relationship between phenotypic characteristics and gene functions of methanogenic Archaea from metagenomic, metatranscriptomics and target sequencing data (multi-omics approaches). The data integration will be performed by in silico modeling, based on the trait values that determine the relative fitness of methanogenic archaea in soils under different land use, environment factors (different levels of moisture and emissions of greenhouse gases) and temporal scales. These values will be extracted from the identification of methane producing Archaea: (i) 16S rRNA gene phylogenic analysis of Archaea communities and (ii) pairwise statistics integration between datasets of adjacent dimensions, based on microbial genome assembly, methanogenesis gene expression quantification and metadata measurements. Finally, the third step (iii) includes evaluating the traits using MicroTrait-ME model. Integrative modeling will rely on an massive use of bioinformatics tools, being applied to a multi-omic dataset generated from a microcosm experiment. This in situ experiment simulates a field condiction, with different moisture levels in a forest-pasture conversion system as variables. It is important to highlight that 90% of the raw data to be explored in this model was already generated by the Prof. Tsai laboratory staff.

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Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
LEMOS, LEANDRO NASCIMENTO; DE SOUZA, ROSINEIDE CARDOSO; CANNAVAN, FABIANA DE SOUZA; PATRICIO, ANDRE; PYLRO, VICTOR SATLER; HANADA, ROGERIO EIJI; MUI, TSAI SIU. Metagenome sequencing of the microbial community of two Brazilian anthropogenic Amazon dark earth sites, Brazil. GENOMICS DATA, v. 10, p. 167-168, . (13/02760-2, 14/50320-4, 16/18215-1, 11/50914-3, 16/02219-8)
LEMOS, LEANDRO NASCIMENTO; MANOHARAN, LOKESHWARAN; MENDES, LUCAS WILLIAM; VENTURINI, ANDRESSA MONTEIRO; PYLRO, VICTOR SATLER; TSAI, SIU MUI. Metagenome assembled-genomes reveal similar functional profiles ofCPR/Patescibacteria phyla in soils. ENVIRONMENTAL MICROBIOLOGY REPORTS, v. 12, n. 6, p. 651-655, . (17/24037-1, 17/09643-2, 14/50320-4, 16/18215-1, 15/13546-7)
Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
LEMOS, Leandro Nascimento. Integrative and in silico modeling of multi-omics data of Archaea and Bacteria phyla in Amazon soils. 2019. Doctoral Thesis - Universidade de São Paulo (USP). Centro de Energia Nuclear na Agricultura (CENA/STB) Piracicaba.

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