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Taxonomic and functional microbial bio-indicators in soil under sugarcane biomass production systems

Grant number: 12/13321-7
Support type:Scholarships in Brazil - Post-Doctorate
Effective date (Start): February 01, 2013
Effective date (End): June 30, 2016
Field of knowledge:Agronomical Sciences - Agronomy
Principal Investigator:Tsai Siu Mui
Grantee:Acacio Aparecido Navarrete
Home Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Associated scholarship(s):15/09436-1 - GeoChip-based prospection for functional microbial genes as potential bioindicators of disturbance in sugarcane soils under zinc applications, BE.EP.PD   14/06077-8 - Metagenomic annotation and bioinformatics analysis applied to definition of microbial bioindicators for soil agricultural management effects in sugarcane production systems, BE.EP.PD

Abstract

Defining and monitoring soil quality parameters is key to sustainable primary of raw materials for bio-based industrial processes. In this sense, new methods based on DNA sequencing in association to traditional methods can cooperate to define biologically relevant assay to judge the potential impacts from the production processes on soil health. Recent results generated by Capes/Wageningen program (Navarrete et al., 2012) showed members of soil bacterial community belonging to the phyla Acidobacteria and Verrucomicrobia (at class taxonomic level) and genes encompassing the biogeochemical cycle of carbon as potential bio-indicators for deforestation effects on soil and agriculture management into soybean production fields in the State of Mato Grosso, Brazil. In this sense, this proposal aims to validate these results in a broder Brazilian agricultural context, by attesting the microbial bio-indicators for assessment of soil quality in sugarcane biomass production systems in the State of São Paulo. To this end, the objective of this project is to validate bacterial taxa (Acidobacteria and Verrucomicrobia) and identify bacterial groups and functional genes with potential use as taxonomical and functional bio-indicators and associate them to soil characteristics and processes occurring in soil, such as, fertility, nutrients availability, microbial biomass, enzyme activity and N2O, CO2 and CH4 emissions from soil in sugarcane biomass production systems in the State of São Paulo. Three different modules compose the activities plan: (i) "taxonomic bio-indicators", including abundance determination of Acidobacteria and Verrucomicrobia and also other bacterial groups in soil by sequencing partial of the 16S rRNA gene using next-generation technologies (pyrosequencing) and statistical correlation with soil physico-chemical attributes; (ii) "functional bio-indicators", including quantitative and comparative analysis of metagenomic data (shotgun MiSeq) in association to soil physical, chemical, biological and biochemical attributes and N2O, CO2 and CH4 emissions from soil; and (iii) "bioinformatic ans statistic", including computational and statistical approach to integrate results from modules "i" and "ii", aiming ensure the indication of taxonomical and functional bio-indicators for soil quality assessment in sugarcane biomass production systems.

Scientific publications (9)
(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)
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, JUL 30 2019. Web of Science Citations: 0.
BRAGA, LUCAS P. P.; ALVES, RAFAEL F.; DELLIAS, MARINA T. F.; NAVARRETE, ACACIO A.; BASSO, THIAGO O.; TSAI, SIU M. Vinasse fertirrigation alters soil resistome dynamics: an analysis based on metagenomic profiles. BIODATA MINING, v. 10, MAY 23 2017. Web of Science Citations: 4.
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, JAN 2 2017. Web of Science Citations: 4.
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, 2017. Web of Science Citations: 0.
VALADARES-PEREIRA, ALANA DE ALMEIDA; ALVES MARTINS OLIVEIRA, ELAINY CRISTINA; NAVARRETE, ACACIO APARECIDO; DE OLIVEIRA, JR., WALDESSE PIRAGE; TSAI, SIU MUI; PELUZIO, JOENES MUCCI; DE MORAIS, PAULA BENEVIDES. Fungal Community Structure as an Indicator of Soil Agricultural Management Effects in the Cerrado. Revista Brasileira de Ciência do Solo, v. 41, p. -, 2017. Web of Science Citations: 0.
VAL-MORAES, SILVANA POMPEIA; DE MACEDO, HELENA SULEIMAN; KISHI, LUCIANO TAKESHI; PEREIRA, RODRIGO MATHEUS; NAVARRETE, ACACIO APARECIDO; MENDES, LUCAS WILLIAM; DE FIGUEIREDO, EDUARDO BARRETTO; LA SCALA, JR., NEWTON; TSAI, SIU MUI; DE MACEDO LEMOS, ELIANA GERTRUDES; CARARETO ALVES, LUCIA MARIA. Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern So Paulo, Brazil. ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY, v. 109, n. 12, p. 1643-1654, DEC 2016. Web of Science Citations: 3.
NAVARRETE, ACACIO A.; VENTURINI, ANDRESSA M.; MEYER, KYLE M.; KLEIN, ANN M.; TIEDJE, JAMES M.; BOHANNAN, BRENDAN J. M.; NUESSLEIN, KLAUS; TSAI, SIU M.; RODRIGUES, JORGE L. M. Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon. FRONTIERS IN MICROBIOLOGY, v. 6, DEC 22 2015. Web of Science Citations: 18.
NAVARRETE, ACACIO APARECIDO; SOARES, TIELLE; ROSSETTO, RAFFAELLA; VAN VEEN, JOHANNES ANTONIE; TSAI, SIU MUI; KURAMAE, EIKO EURYA. Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility. ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY, v. 108, n. 3, p. 741-752, SEP 2015. Web of Science Citations: 13.
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 JUN 9 2015. Web of Science Citations: 21.

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