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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 Opportunities:BIOTA-FAPESP Program - Thematic Grants
Duration: October 01, 2014 - May 31, 2021
Field of knowledge:Biological Sciences - Microbiology - Applied Microbiology
Convênio/Acordo: NSF - Dimensions of Biodiversity and BIOTA
Principal Investigator:Tsai Siu Mui
Grantee:Tsai Siu Mui
Principal researcher abroad: Jorge Mazza Rodrigues
Institution abroad: University of Texas at Arlington (UT Arlington), United States
Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Pesquisadores principais:
Fernando Dini Andreote ; Plínio Barbosa de Camargo
Associated scholarship(s):20/11765-1 - Discrimination of methane-consuming bacteria in the forest-to-pasture land-use change in the Amazon region, BP.IC
20/10326-4 - Assessing the functional microbes for methane transformation in Amazonian soils, BP.IC
19/26029-1 - Analysis of the methane cycle-associated microbiota in areas of primary forest, pasture and secondary forest in the Amazon, BP.MS
+ associated scholarships 19/25931-3 - Taxonomic and functional depiction of the microbial community involved in methane transformations in soils of the Brazilian Amazonia, BP.PD
19/26400-1 - CH4 production and consumption in the tropical ecosystem through flows, vertical profiles of CH4 and its isotopic compositions 13C and D, BP.PD
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
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)

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Scientific publications (34)
(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)
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, . (14/50320-4, 16/02219-8)
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, . (14/50320-4, 12/13321-7, 08/58114-3)
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, . (13/02760-2, 14/50320-4, 16/18215-1, 11/50914-3, 16/02219-8)
KROEGER, MARIE E.; MEREDITH, LAURA K.; MEYER, KYLE M.; WEBSTER, KEVIN D.; DE CAMARGO, PLINIO BARBOSA; DE SOUZA, LEANDRO FONSECA; TSAI, SIU MUI; VAN HAREN, JOOST; SALESKA, SCOTT; BOHANNAN, BRENDAN J. M.; et al. Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon. ISME Journal, v. 15, n. 3, p. 658-672, . (14/50320-4)
OBREGON, DASIEL; MAFA-ATTOYE, TOLULOPE G.; BASKERVILLE, MEGAN; MITTER, EDUARDO K.; DE SOUZA, LEANDRO FONSECA; OELBERMANN, MAREN; THEVATHASAN, NARESH V.; TSAI, SIU MUI; DUNFIELD, KARI E.. Functionality of methane cycling microbiome during methane flux hot moments from riparian buffer systems. Science of The Total Environment, v. 870, p. 12-pg., . (18/09117-1, 14/50320-4, 18/05223-1, 16/24695-6)
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, . (14/50320-4, 08/58114-3)
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, . (14/50320-4, 13/50353-7, 13/50228-8)
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; et al. Forest conversion to pasture affects soil phosphorus dynamics and nutritional status in Brazilian Amazon. SOIL & TILLAGE RESEARCH, v. 194, . (17/18327-7, 16/24695-6, 17/11332-5, 14/50320-4)
PEDRINHO, ALEXANDRE; MENDES, LUCAS WILLIAM; MERLOTI, LUIS FERNANDO; ANDREOTE, FERNANDO DINI; TSAI, SIU MUI. The natural recovery of soil microbial community and nitrogen functions after pasture abandonment in the Amazon region. FEMS MICROBIOLOGY ECOLOGY, v. 96, n. 9, . (17/02635-4, 14/50320-4, 17/16757-4)
GONTIJO, JULIA B.; PAULA, FABIANA S.; VENTURINI, ANDRESSA M.; YOSHIURA, CAIO A.; BORGES, CLOVIS D.; MOURA, JOSE MAURO S.; BOHANNAN, BRENDAN J. M.; NUSSLEIN, KLAUS; MAZZA RODRIGUES, JORGE L.; TSAI, SIU M.. Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities. Molecular Ecology, v. 30, n. 11, p. 2560-2572, . (14/50320-4, 17/26138-0, 18/14974-0, 17/09643-2, 15/13546-7, 19/25931-3)
ALVAREZ, DASIEL OBREGON; DE SOUZA, LEANDRO FONSECA; MENDES, LUCAS WILLIAM; DE MORAES, MOACIR TUZZIN; TOSI, MICAELA; VENTURINI, ANDRESSA MONTEIRO; MEYER, KYLE M.; DE CAMARGO, PLINIO BARBOSA; BOHANNAN, BRENDAN J. M.; MAZZA RODRIGUES, JORGE L.; et al. Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin. Molecular Ecology, v. 32, n. 12, p. 19-pg., . (15/13546-7, 14/50320-4, 16/24695-6)
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, . (15/21893-9, 14/50320-4)
VENTURINI, ANDRESSA M.; GONTIJO, JULIA B.; DA FRANCA, ALINE G.; MOURA, JOSE M. S.; NUSSLEIN, KLAUS; BOHANNAN, BRENDAN J. M.; RODRIGUES, JORGE L. M.; TSAI, SIU M.. Metagenomes from Eastern Brazilian Amazonian Floodplains in the Wet and Dry Seasons. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, v. 11, n. 8, p. 4-pg., . (18/14974-0, 14/50320-4, 19/25924-7, 19/25931-3)
GONTIJO, JULIA B.; PAULA, FABIANA S.; VENTURINI, ANDRESSA M.; MANDRO, JESSICA A.; BODELIER, PAUL L. E.; TSAI, SIU M.. Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments. MICROORGANISMS, v. 10, n. 9, p. 11-pg., . (18/14974-0, 14/50320-4, 17/26138-0, 19/25924-7, 19/25931-3)
PEDRINHO, ALEXANDRE; MENDES, LUCAS WILLIAM; DO REGO BARROS, FELIPE MARTINS; MERLOTI, LUIS FERNANDO; MARTINS, MAYARA MARTINS E.; COTTA, SIMONE RAPOSO; ANDREOTE, FERNANDO DINI; TSAI, SIU MUI. Impacts of deforestation and forest regeneration on soil bacterial communities associated with phosphorus transformation processes in the Brazilian Amazon region. ECOLOGICAL INDICATORS, v. 146, p. 11-pg., . (17/02635-4, 14/50320-4)
MANDRO, JESSICA A.; NAKAMURA, FERNANDA M.; GONTIJO, JULIA B.; TSAI, SIU M.; VENTURINI, ANDRESSA M.. Metagenome-Assembled Genomes from Amazonian Soil Microbial Consortia. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, v. 11, n. 11, p. 5-pg., . (14/50320-4, 15/12282-6, 15/23758-1, 15/13546-7, 19/26029-1, 18/14974-0, 19/25931-3)
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.; et al. New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes. FRONTIERS IN MICROBIOLOGY, v. 9, . (14/50320-4)
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, . (14/50320-4, 16/02219-8)
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, . (14/50320-4, 08/58114-3)
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, . (17/16757-4, 14/50320-4)
LEMOS, LEANDRO NASCIMENTO; MANOHARAN, LOKESHWARAN; MENDES, LUCAS WILLIAM; VENTURINI, ANDRESSA MONTEIRO; PYLRO, VICTOR SATLER; TSAI, SIU MUI. Metagenome assembled-genomes reveal similar functional profiles ofCPR/Patescibacteria phyla in soils. ENVIRONMENTAL MICROBIOLOGY REPORTS, v. 12, n. 6, p. 651-655, . (17/24037-1, 17/09643-2, 14/50320-4, 16/18215-1, 15/13546-7)
MERLOTI, LUIS FERNANDO; MENDES, LUCAS WILLIAM; PEDRINHO, ALEXANDRE; DE SOUZA, LEANDRO FONSECA; FERRARI, BEATRIZ MARIA; TSAI, SIU MUI. Forest-to-agriculture conversion in Amazon drives soil microbial communities and N-cycle. SOIL BIOLOGY & BIOCHEMISTRY, v. 137, . (14/50320-4)
YOSHIURA, CAIO AUGUSTO; VENTURINI, ANDRESSA MONTEIRO; PEREZ BRAGA, LUCAS PALMA; DA FRANCA, ALINE GIOVANA; CATANHO PEREIRA DE LYRA, MARIA DO CARMO; TSAI, SIU MUI; RODRIGUES, JORGE LUIZ MAZZA. Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production. FRONTIERS IN PLANT SCIENCE, v. 12, . (13/22845-2, 15/13546-7, 15/08564-6, 16/11268-2, 14/50320-4, 19/25931-3)
MEYER, KYLE M.; MORRIS, ANDREW H.; WEBSTER, KEVIN; KLEIN, ANN M.; KROEGER, MARIE E.; MEREDITH, LAURA K.; BRAEDHOLT, ANDREAS; NAKAMURA, FERNANDA; VENTURINI, ANDRESSA; DE SOUZA, LEANDRO FONSECA; et al. Belowground changes to community structure alter methane-cycling dynamics in Amazonia. Environment International, v. 145, . (14/50320-4)
GOSS-SOUZA, DENNIS; MENDES, LUCAS WILLIAM; RODRIGUES, JORGE LUIZ MAZZA; TSAI, SIU MUI. Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion. MICROBIAL ECOLOGY, v. 79, n. 1, p. 110-122, . (14/50320-4, 08/58114-3)
DURRER, ADEMIR; MARGENOT, ANDREW J.; SILVA, LUCAS C. R.; BOHANNAN, BRENDAN J. M.; NUSSLEIN, KLAUS; VAN HAREN, JOOST; ANDREOTE, FERNANDO D.; PARIKH, SANJAI J.; RODRIGUES, JORGE L. MAZZA. Beyond total carbon: conversion of amazon forest to pasture alters indicators of soil C cycling. BIOGEOCHEMISTRY, v. 152, n. 2-3, . (14/50320-4)
MERLOTI, LUIS FERNANDO; PEDRINHO, ALEXANDRE; MENDES, LUCAS WILLIAM; GONTIJO, JULIA BRANDAO; DA FONSECA, MARILEY DE CASSIA; CHAVES, MIRIAM GONCALVES; CHAVES, SIGLEA SANNA DE FREITAS; DE CAMARGO, PLINIO BARBOSA; TSAI, SIU MUI. Long-term land use in Amazon influence the dynamic of microbial communities in soil and rhizosphere. RHIZOSPHERE, v. 21, p. 14-pg., . (20/12890-4, 14/50320-4, 19/19145-5)
VENTURINI, ANDRESSA M.; DIAS, NAISSA M. S.; GONTIJO, JULIA B.; YOSHIURA, CAIO A.; PAULA, FABIANA S.; MEYER, KYLE M.; NAKAMURA, FERNANDA M.; DA FRANCA, ALINE G.; BORGES, CLOVIS D.; BARLOW, JOS; et al. Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon. Environmental Research, v. 212, p. 13-pg., . (14/50320-4, 15/13546-7, 15/08564-6, 19/25931-3, 17/09616-5, 17/26138-0, 16/11268-2, 17/09643-2, 17/09952-5, 15/12282-6, 18/14974-0)
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. GENOME ANNOUNCEMENTS, v. 6, n. 7, p. 2-pg., . (14/50320-4, 16/02219-8)
DE SOUZA, LEANDRO FONSECA; ALVAREZ, DASIEL OBREGON; DOMEIGNOZ-HORTA, LUIZ A.; GOMES, FABIO VITORINO; ALMEIDA, CASSIO DE SOUZA; MERLOTI, LUIS FERNANDO; MENDES, LUCAS WILLIAM; ANDREOTE, FERNANDO DINI; BOHANNAN, BRENDAN J. M.; RODRIGUES, JORGE L. MAZZA; et al. Maintaining grass coverage increases methane uptake in Amazonian pastures, with a reduction of methanogenic archaea in the rhizosphere. Science of The Total Environment, v. 838, p. 11-pg., . (14/50320-4, 18/09117-1)
GOSS-SOUZA, DENNIS; TSAI, SIU MUI; RODRIGUES, JORGE LUIZ MAZZA; KLAUBERG-FILHO, OSMAR; SOUSA, JOSE PAULO; BARETTA, DILMAR; MENDES, LUCAS WILLIAM. Biogeographic responses and niche occupancy of microbial communities following long-term land-use change. ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY, v. 115, n. 9, p. 22-pg., . (20/12890-4, 14/50320-4, 08/58114-3, 19/16043-7)
VENTURINI, ANDRESSA MONTEIRO; NAKAMURA, FERNANDA MANCINI; GONTIJO, JULIA BRANDAO; DA FRANCA, ALINE GIOVANA; YOSHIURA, CAIO AUGUSTO; MANDRO, JESSICA ADRIELE; TSAI, SIU MUI. Robust DNA protocols for tropical soils. HELIYON, v. 6, n. 5, . (15/12282-6, 15/08564-6, 15/13546-7, 18/14974-0, 14/50320-4, 15/23758-1)
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, . (14/50320-4)
ALVES, KELLY JAQUELINE; PYLRO, VICTOR SATLER; NAKAYAMA, CRISTINA ROSSI; VITAL, VITOR GONCALVES; TAKETANI, RODRIGO GOUVEA; SANTOS, DANIELLE GONCALVES; RODRIGUES, JORGE L. MAZZA; TSAI, SIU MUI; ANDREOTE, FERNANDO DINI. Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change. MICROBIOLOGICAL RESEARCH, v. 265, p. 9-pg., . (14/50320-4, 16/18745-0, 16/02219-8)

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