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Diversity and evolution of functional genomic traits associated with methane and nitrogen cycles in amazonian soil metagenomes

Grant number: 17/24037-1
Support Opportunities:Scholarships abroad - Research Internship - Doctorate
Effective date (Start): April 01, 2018
Effective date (End): March 31, 2019
Field of knowledge:Biological Sciences - Microbiology - Applied Microbiology
Principal Investigator:Tsai Siu Mui
Grantee:Leandro Nascimento Lemos
Supervisor: Christa Schleper
Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Research place: University of Vienna, Austria  
Associated to the scholarship:16/18215-1 - Multi-omics integrated and in silico modelling of Archaea communities associated with methanogenis in amazon soils., BP.DR


The development of next-generation sequencing technologies and the improvement of new software used in Bioinformatics have revolutionized the studies of Archaea Biology. In the last ten years, approximately ten new Archaea phyla were proposed, including the ammonia-oxiding Thaumarchaeota and a potential methanogenic Bathyarchaeota phylum. In a previous study, using a soil microcosm experiment, we discovered that the Thaumarchaeota phylum is the most abundant Archaea phylum in forest and pasture Amazonian soils and is resistant to long and short-term perturbations. Meanwhile, the Bathyarchaeota phylum is associated with an increase in methane emission and land-use changes. These findings reinforce the need for a deeper understanding of the functions that modulate the Archaea community structure, diversity and evolution in Amazonian soils. However, the amount of biological complexity and information generated in large datasets of metagenomics and metatranscriptomics studies demands an expertise team, specialized in analyzing and interpreting multi-omics data. Here, we propose a joint project between the Laboratory of Cell and Molecular Biology at the University of Sao Paulo (Brazil) and the Archaea Biology and Ecogenomics Division at the University of Vienna (Austria). Under the joint supervision of Prof. Tsai Siu Mui and Prof. Christa Schleper, we will determine the microbial functional genomic traits associated with methane and nitrogen cycles in amazonian metagenomes (forest, pasture, agriculture, deforested and wetland soil samples). This internship proposal will be divided into two main studies. The first study (Study I) will focus on metagenomic annotation and identification of microbial traits associated with methane and nitrogen cycles using a reference gene catalogue and metagenome-assembled genomes (MAGs). With this reference genes catalogue, we will be able to test whether or not land-use changes alter the abundance of functions associated with Bathyarchaeota and Thaumarchaeota. The second (Study II) includes the evolution analyses of Archaea MAGs using phylogenomic frameworks. The Schleper lab has a database with published and unpublished Archaea genomes that will be used together to generate a reference gene catalog and to analyze the evolutionary processes of Amazon Archaea genomes. We will explore the Archaea functions using a multi-omic dataset generated from a microcosm experiment, wetland field samples and public datasets. It is important to highlight that 100% of the raw data to be explored in this model (Study II) were already generated by Prof. Tsai laboratory´s 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; 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)

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