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Metagenomic annotation and bioinformatics analysis applied to definition of microbial bioindicators for soil agricultural management effects in sugarcane production systems

Grant number: 14/06077-8
Support Opportunities:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): July 01, 2014
Effective date (End): September 30, 2014
Field of knowledge:Agronomical Sciences - Agronomy - Soil Science
Principal Investigator:Tsai Siu Mui
Grantee:Acacio Aparecido Navarrete
Supervisor: Robert A. Edwards
Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Research place: San Diego State University, United States  
Associated to the scholarship:12/13321-7 - Taxonomic and functional microbial bio-indicators in soil under sugarcane biomass production systems, BP.PD


We present here a research internship abroad plan which main objective is to address one of two aims described in the ongoing principal research proposal (FAPESP 2012/13321-7). The main objective of this research internship abroad is to use computational method for annotation of metagenomes based on unique signature k-mers that represent members of a protein family. LEfSe algorithm will be applied to identify taxa characterizing the differences between two or more experimental treatments. This is important mainly when searching for potential taxonomic microbial bioindicators to assess agricultural soil management effects on soil. The use of bioindicators is not just restricted to a single species with a limited environmental tolerance, but biological processes or communities can also indicate the condition of the environment. Two different activities compose the work plan: (i) estimate relative abundances of bacterial community members using shotgun sequencing data obtained from soil under sugarcane production systems established at mesocosm scale in greenhouse experiment, and (ii) support the search for taxonomic microbial bioindicators using datasets obtained in the same mesocosm experiment for soil fertility and nutrients availability, soil microbial biomass, soil enzymatic activity, and CO2 and N2O emissions from soil. (AU)

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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)
MENDES, LUCAS W.; PEREZ BRAGA, LUCAS PALMA; NAVARRETE, ACACIO A.; DE SOUZA, DENNIS GOSS; SILVA, GENIVALDO G. Z.; TSAI, SIU M.. Using. Metagenomics to Connect Microbial Community Biodiversity and Functions. CURRENT ISSUES IN MOLECULAR BIOLOGY, v. 24, p. 103-118, . (15/00251-9, 13/22845-2, 12/13321-7, 10/20353-7, 11/51749-6, 14/03217-3, 14/06077-8)
NAVARRETE, ACACIO APARECIDO; DINIZ, TATIANA ROSA; PEREZ BRAGA, LUCAS PALMA; SILVA, GENIVALDO GUEIROS ZACARIAS; FRANCHINI, JULIO CEZAR; ROSSETTO, RAFFAELLA; EDWARDS, ROBERT ALAN; TSAI, SIU MUI. Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems. PLoS One, v. 10, n. 6, . (14/06077-8, 11/51749-6, 12/13321-7)
DE CHAVES, MIRIAM GONCALVES; SILVA, GENIVALDO GUEIROS Z.; ROSSETTO, RAFFAELLA; EDWARDS, ROBERT ALAN; TSAI, SIU MUI; NAVARRETE, ACACIO APARECIDO. Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers. FRONTIERS IN MICROBIOLOGY, v. 10, . (11/51749-6, 17/03575-5, 15/09436-1, 12/13321-7, 14/06077-8)

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