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Analysis of the microbiome associated to the common bean root system

Grant number: 15/00251-9
Support Opportunities:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): August 01, 2015
Effective date (End): July 31, 2016
Field of knowledge:Agronomical Sciences - Agronomy - Soil Science
Principal Investigator:Tsai Siu Mui
Grantee:Lucas William Mendes
Supervisor: Jos M. Raaijmakers
Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Research place: Royal Netherlands Academy of Arts and Sciences, Netherlands  
Associated to the scholarship:14/03217-3 - Rhizosphere microbiome of common bean resistant to the soil pathogen Fusarium oxysporum, BP.PD


Here, we present a plan for an abroad research internship, which is complementary to the ongoing postdoctoral project (FAPESP 2014/03217-3). For this internship we propose two main activities, first, use the bioinformatics platform and know-how from the Netherlands Institute of Ecology (NIOO) to analyze the data generated in our experiments conducted in Brazil, and second, we propose an additional experiment for the analysis of the endophytic microbial community of the common bean resistant to the soil borne pathogen Fusarium oxysporum. Therefore, the first objective is the analysis of the sequencing data, i.e. 16S rRNA amplicons, shotgun metagenome and metatranscriptome, from the common bean rhizosphere microbial communities. The sequences are being obtained from mesocosms experiments using four common bean varieties, with different levels of resistance to the soil borne pathogen Fusarium oxysporum. Bioinformatics tools will be used to process and annotate the sequences, and statistical software for comparison and interpretation of the data. The second objective is to perform a new experiment to be run at NIOO, in order to assess the effect of F. oxysporum inoculation in the rhizospheric and endophytic microbial community of the resistant common bean variety IAC Milênio. This second objective will add a new dimension to the original ongoing project including the analysis of the endophytes, which was not initially planned, but represents an important contribution to achieve the overall objective of the project. In conclusion, the approval of this proposal will significantly foster the identification of potential microbial groups in the root system of common bean that is related to the suppression of the soil pathogen F. oxysporum. (AU)

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Scientific publications (5)
(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 WILLIAM; DE CHAVES, MIRIAM GONCALVES; FONSECA, MARILEY DE CASSIA; MENDES, RODRIGO; RAAIJMAKERS, JOS M.; TSAI, SIU MUI. Resistance Breeding of Common Bean Shapes the Physiology of the Rhizosphere Microbiome. FRONTIERS IN MICROBIOLOGY, v. 10, . (14/03217-3, 15/00251-9)
MENDES, LUCAS WILLIAM; MENDES, RODRIGO; RAAIJMAKERS, JOS M.; TSAI, SIU MUI. Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean. ISME Journal, v. 12, n. 12, p. 3038-3042, . (15/00251-9, 14/03217-3)
BRAGA, LUCAS P. P.; TANENTZAP, ANDREW J.; LEE, BENJAMIN; TSAI, SIU MUI; RAAIJMAKERS, JOS M.; MENDES, RODRIGO; MENDES, LUCAS W.. Diversity of viruses and viroids in the rhizosphere of common bean cultivars differing in resistance to the fungal root pathogen Fusarium oxysporum. APPLIED SOIL ECOLOGY, v. 190, p. 7-pg., . (19/16043-7, 18/19247-0, 14/03217-3, 15/00251-9)
MENDES, LUCAS WILLIAM; RAAIJMAKERS, JOS M.; DE HOLLANDER, MATTIAS; MENDES, RODRIGO; TSAI, SIU MUI. Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. ISME Journal, v. 12, n. 1, p. 212-224, . (15/00251-9, 14/03217-3)
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)

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