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GeoChip-based prospection for functional microbial genes as potential bioindicators of disturbance in sugarcane soils under zinc applications

Grant number: 15/09436-1
Support Opportunities:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): August 01, 2015
Effective date (End): October 31, 2015
Field of knowledge:Agronomical Sciences - Agronomy - Soil Science
Principal Investigator:Tsai Siu Mui
Grantee:Acacio Aparecido Navarrete
Supervisor: Jizhong Zhou
Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Research place: University of Oklahoma (OU), 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 apply GeoChip 5.0, a functional gene-array-based high-throughput environmental technology for microbial community analysis, in order to identify genes that hold potential for use as bioindicators of disturbance in sugarcane soils under zinc applications in sandy-textured soil with natural low fertility. Our proposal is based on recent results from FAPESP-sponsored studies, such as: (1) correlations between zinc content and numerous carbon- and nitrogen-cycle genes in sugarcane-cultivated soils (FAPESP 2012/13321-7*), and (2) results from a broad experiment network with micronutrients conducted by the Agronomic Institute of Campinas (IAC), which have shown significant gains in sugarcane productivity with zinc application (FAPESP 2011/07459-3**). Based on these results, it became necessary to study soil microbiome responses to zinc application in sugarcane soils in order to understand better its effects on key microbially mediated processes at the soil-plant interface in order to define microbial functional genes that hold potential for use as bioindicators of disturbance in sugarcane soils under zinc applications. For this purpose, DNA was isolated from soil samples collected in two sugarcane field experiments established under the FAPESP project 2011/07459-3, in which were applied different doses of zinc to the soil. Experimental sites are located at the two major producing regions of sugarcane in the State of São Paulo: Serra Azul and Assis municipalities. Three different activities compose the work plan: (i) detect and quantify genes associated with carbon-, nitrogen-, phosphorus-, sulfur-cycle, secondary metabolism, stress response and virulence and analyze their microbial taxonomic derivation based on soil DNA from the sugarcane-cultivated soils under zinc applications by using GeoChip 5.0 platform, (ii) correlate the abundance of functional microbial genes revealed based on these soils with CO2 assimilation rate, stomatal conductance, and transpiration rate in sugarcane plants, and (iii) apply computational and statistical methods on GeoChip and physiological data in order to identify major microbial functional genes that hold potential for use as bioindicators of disturbance in sugarcane soils under zinc applications. (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)
NAVARRETE, ACACIO A.; MELLIS, ESTEVAO V.; ESCALAS, ARTHUR; LEMOS, LEANDRO N.; LAVRES JUNIOR, JOSE; QUAGGIO, JOSE ANTONIO; ZHOU, JIZHONG; TSAI, SIU M.. Zinc concentration affects the functional groups of microbial communities in sugarcane-cultivated soil. AGRICULTURE ECOSYSTEMS & ENVIRONMENT, v. 236, p. 187-197, . (12/13321-7, 11/51749-6, 15/09436-1)
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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