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Dimensions US-BIOTA - São Paulo: collaborative research: integrating dimensions of microbial biodiversity across land use change in tropical forests

Grant number: 14/50320-4
Support type:BIOTA-FAPESP Program - Thematic Grants
Duration: October 01, 2014 - September 30, 2020
Field of knowledge:Biological Sciences - Microbiology
Cooperation agreement: NSF - Dimensions of Biodiversity and BIOTA
Principal Investigator:Tsai Siu Mui
Grantee:Tsai Siu Mui
Principal investigator abroad: Jorge Mazza Rodrigues
Institution abroad: University of Texas at Arlington (UT Arlington), United States
Home Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Co-Principal Investigators:Fernando Dini Andreote ; Plínio Barbosa de Camargo
Associated scholarship(s):19/11806-2 - Integrating the dimensions of microbial biodiversity along areas of land use change in tropical forests, BP.TT
18/09117-1 - Active microbiota in methane SEQUESTRY in forest and pasture soils revealed by Stable Isotope Probing and metagenomics, BP.DR
18/14974-0 - Dynamics of methane and sulfur microbial communities in Amazonian soils, BP.DR
+ associated scholarships 18/15882-2 - Integrating the dimensions of microbial biodiversity across land use change in tropical forest, BP.TT
18/15881-6 - Integrating the dimensions of microbial biodiversity across land use change in tropical forest, BP.TT
18/08193-6 - Abundance of communities methanotrophic bacteria in corn (Zea mays) and cowpea (Vigna unguiculata) rizosphere cultivated on Amazon Dark Earth, BP.IC
17/26138-0 - Taxonomic and functional evaluations of microbial community involved in methane cycling of Brazilian Amazon soils, BP.PD
18/02177-9 - Discrimination of methane-consuming bacteria in land use change between forestry-pasture at Amazon rainforest region, BP.IC
17/18327-7 - CH4 production and consumption in the tropical ecosystem through flows, CH4 vertical profiles and 13C and D isotopic compositions , BP.PD
17/02635-4 - Microcosms and microbiota activity of the methane and n (N2O) cycle under the influence of moisture in soils from Eastern Amazon, BP.MS
16/18745-0 - Changes in communities of methanogenic archaea communities due to changes in the land use in Amazonia, BP.MS
16/24695-6 - Spatio-temporal dynamics of the active microbiota on the methane cycling in an Amazonian soil after forest-to-pasture conversion, BP.DD
16/18215-1 - Multi-omics integrated and in silico modelling of archaea communities associated with methanogenis in Amazon soils, BP.DR
16/18141-8 - Diversity of methanotrophic organisms evaluation on soils of the Brazilian Amazonian community, BP.IC
16/02219-8 - A meta-omics approach to examine disturbances in soils of the Brazilian Amazonia, BP.PD
15/23758-1 - Functional genes of the methane biogeochemical cycle in forest and pastures areas in Amazon, BP.IC
15/13546-7 - Microbial community resilience capacity assessed by metagenomics and metatranscriptomics in Amazon Forest and pasture soils, BP.DR
15/12282-6 - Microcosms and the role of active microbiota on methane cycle in soils under forests and pasture of Eastern Amazon, BP.DR - associated scholarships

Abstract

Microorganisms drive the ecosystem processes on which all of life depends, yet we know much less about their biodiversity than we do for plants and animals. Microbial ecology is increasingly sophisticated in estimating the phylogenetic, genetic, and functional dimensions of microbial biodiversity, but integration of these dimensions has proven elusive. This project will combine recent advances in nucleic acid sequencing and ecosystem biogeochemistry to address an outstanding question of modern biogeochemistry: what controls methane cycling along gradients of land use in tropical forests? Answering this question will require that we address the fundamental biological challenge of understanding interactions and feedbacks among the three dimensions of microbial biodiversity. To address this challenge, we will assess genetic, phylogenetic, and functional dimensions of bacterial and archaeal biodiversity in two Brazilian tropical forests under threat from development: a western Amazon rainforest in Rondonia and an eastern Amazon National Forest near Santarem. These forests span a range of ecosystem types, soil characteristics and land use histories. We will assess three dimensions of soil microbial biodiversity: (1) microbial community composition and phylogenetic diversity via high throughput sequencing of methane cycling (pmoA and mcrA) genes; (2) whole-community genetic diversity (with a focus on metabolic potential) via targeted gene regions and metagenomic sequencing of functionally relevant genome fragments; and (3) whole-ecosystem functional diversity via observations of production/consumption of methane and its isotopes, which will then be compared to transcript: gene abundance ratios for methane cycling genes. To fully integrate all three dimensions of microbial biodiversity, we will use a two-tiered approach: (1) pairwise statistical integration between datasets of adjacent dimensions; and (2) simultaneous integration of all three dimensions via development of a trait-based computational model (MicroTrait-ME) that combines taxonomic identities, abundances, and trait values (inferred from gene content and expression data) to predict the response of methane cycling to land use change. This model will be useful to a wide community of researchers. (AU)

Scientific publications (12)
(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)
SOLTANGHEISI, AMIN; DE MORAES, MOACIR TUZZIN; CHERUBIN, MAURICIO ROBERTO; ALVAREZ, DASIEL OBREGON; DE SOUZA, LEANDRO FONSECA; BIELUCZYK, WANDERLEI; NAVROSKI, DEISI; BETTONI TELES, ANA PAULA; PAVINATO, PAULO SERGIO; MARTINELLI, LUIZ ANTONIO; TSAI, SIU MUI; DE CAMARGO, PLINIO BARBOSA. Forest conversion to pasture affects soil phosphorus dynamics and nutritional status in Brazilian Amazon. SOIL & TILLAGE RESEARCH, v. 194, NOV 2019. Web of Science Citations: 0.
GOSS-SOUZA, DENNIS; MENDES, LUCAS WILLIAM; BORGES, CLOVIS DANIEL; RODRIGUES, JORGE L. M.; TSAI, SIU MUI. Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept. FEMS MICROBIOLOGY ECOLOGY, v. 95, n. 3 MAR 2019. Web of Science Citations: 0.
PEDRINHO, ALEXANDRE; MENDES, LUCAS WILLIAM; MERLOTI, LUIS FERNANDO; DA FONSECA, MARILEY DE CASSIA; CANNAVAN, FABIANA DE SOUZA; TSAI, SIU MUI. Forest-to-pasture conversion and recovery based on assessment of microbial communities in Eastern Amazon rainforest. FEMS MICROBIOLOGY ECOLOGY, v. 95, n. 3 MAR 2019. Web of Science Citations: 0.
ROSA PORTILHO, IRZO ISAAC; SAVIN, MARY CATHLEEN; BORGES, CLOVIS DANIEL; TSAI, SIU MUI; MERCANTE, FABIO MARTINS; ROSCOE, RENATO; DE CARVALHO, LAERCIO ALVES. Maintenance of N cycling gene communities with crop-livestock integration management in tropical agriculture systems. AGRICULTURE ECOSYSTEMS & ENVIRONMENT, v. 267, p. 52-62, NOV 15 2018. Web of Science Citations: 0.
MORAIS, DANIEL K.; ROESCH, LUIZ F. W.; REDMILE-GORDON, MARC; SANTOS, FAUSTO G.; BALDRIAN, PETR; ANDREOTE, FERNANDO D.; PYLRO, VICTOR S. BTW-Bioinformatics Through Windows: an easy-to-install package to analyze marker gene data. PeerJ, v. 6, JUL 30 2018. Web of Science Citations: 0.
KROEGER, MARIE E.; DELMONT, TOM O.; EREN, A. M.; MEYER, KYLE M.; GUO, JIARONG; KHAN, KIRAN; RODRIGUES, JORGE L. M.; BOHANNAN, BRENDAN J. M.; TRINGE, SUSANNAH G.; BORGES, CLOVIS D.; TIEDJE, JAMES M.; TSAI, SIU M.; NUSSLEIN, KLAUS. New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes. FRONTIERS IN MICROBIOLOGY, v. 9, JUL 23 2018. Web of Science Citations: 3.
PYLRO, VICTOR SATLER; FRANCO DIAS, ARMANDO CAVALCANTE; ANDREOTE, FERNANDO DINI; MORAIS, DANIEL KUMAZAWA; VARANI, ALESSANDRO DE MELLO; FASANELLA ANDREOTE, CRISTIANE CIPOLLA; DE ALMEIDA BERNARDO, EDUARDO ROBERTO; ZUCCHI, TIAGO. Closed Genome Sequence of Phytopathogen Biocontrol Agent Bacillus velezensis Strain AGVL-005, Isolated from Soybean. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, v. 6, n. 7 FEB 2018. Web of Science Citations: 0.
GOSS-SOUZA, DENNIS; MENDES, LUCAS WILLIAM; BORGES, CLOVIS DANIEL; BARETTA, DILMAR; TSAI, SIU MUI; RODRIGUES, JORGE L. M. Soil microbial community dynamics and assembly under long-term land use change. FEMS MICROBIOLOGY ECOLOGY, v. 93, n. 10 OCT 2017. Web of Science Citations: 8.
ANDREOTE, FERNANDO DINI; PEREIRA E SILVA, MICHELE DE CASSIA. Microbial communities associated with plants: learning from nature to apply it in agriculture. Current Opinion in Microbiology, v. 37, p. 29-34, JUN 2017. Web of Science Citations: 23.
MEYER, KYLE M.; KLEIN, ANN M.; RODRIGUES, JORGE L. M.; NUESSLEIN, KLAUS; TRINGE, SUSANNAH G.; MIRZA, BABUR S.; TIEDJE, JAMES M.; BOHANNAN, BRENDAN J. M. Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms. Molecular Ecology, v. 26, n. 6, p. 1547-1556, MAR 2017. Web of Science Citations: 14.
LEMOS, LEANDRO NASCIMENTO; DE SOUZA, ROSINEIDE CARDOSO; CANNAVAN, FABIANA DE SOUZA; PATRICIO, ANDRE; PYLRO, VICTOR SATLER; HANADA, ROGERIO EIJI; MUI, TSAI SIU. Metagenome sequencing of the microbial community of two Brazilian anthropogenic Amazon dark earth sites, Brazil. GENOMICS DATA, v. 10, p. 167-168, DEC 2016. Web of Science Citations: 0.
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.

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