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Doctoral Thesis
DOI
10.11606/T.64.2013.tde-22042013-163134
Document
Author
Full name
Acacio Aparecido Navarrete
E-mail
Institute/School/College
Knowledge Area
Date of Defense
Published
Piracicaba, 2012
Supervisor
Committee
Mui, Tsai Siu (President)
Mendes, Rodrigo
Zucchi, Tiago Domingues
Kuramae, Eiko Eurya
Oliveira, Valéria Maia de
Title in English
Bacterial ecology in Amazonian soils under deforestation and agricultural management
Keywords in English
Amazon tropical soils
Land-use changes
Microbial ecology
Molecular ecology
Soil microbiology
Abstract in English
This thesis assessed effects of Amazonian deforestation on artificial association networks of bacteria to bacteria and to abiotic soil factors and networks based on categories of bacterial functions and abiotic soil factors, and sought a better insight into community of Acidobacteria in Amazon soils under agricultural management of soybean based on culture-dependent and molecular approaches. Bacterial community was studied based on next-generation sequencing technologies (Roche GS FLX Titanium and Illumina HiSeq 2000 platforms), quantitative real-time PCR, fingerprinting technique and basic procedures for bacteria culture. The general objective of this thesis was achieved by development of three different studies. The Study 1 analyzed the total bacterial community based on 16S ribosomal DNA pyrotag (425 thousand sequences), shotgun metagenomics (266 million sequences) and environmental parameters from soil samples collected in three real replicate of intact Amazon rainforest and adjacent deforested site after 2-4 months of forest clearing and burning in the Brazilian Amazon. This study showed that deforestation of Amazon forest soils led to a consistent decline in the abundance of Verrucomicrobia and alterations in verrucomicrobial community structure, and simplified association networks among different bacterial taxonomic groups and abiotic soil factors. In order to adapt to this condition function-based associations network were enhanced, indicating a higher degree of risk spreading for the maintenance of soil functioning. The Study 2, in turn, correlated relative abundance of Acidobacteria subgroups - based on approximately 33 thousand sequences of acidobacterial 16S rRNA genes - and abiotic soil factors, and showed differential response of Acidobacteria subgroups to abiotic soil factors in Amazon forest soils into soybean croplands. This study opened the possibilites to explore acidobacterial subgroups as early-warning bio-indicators of agricultural soil management effects in the Amazon area. Lastly, the Study 3 reported the culturability and molecular detection of Acidobacteria subgroups 1 and 3 concomitantly to other bacterial groups from Amazon soils on enriched culture medium with carbon source and incubated for relatively long period in hypoxic atmosphere (2% O2 [vol/vol], 2% CO2 [vol/vol] and 96% N2 [vol/vol]), and validated the combination of traditional procedures for bacteria culture and molecular techniques for recover and detection of Acidobacteria from Amazon soils
Title in Portuguese
Ecologia bacteriana em solos da Amazônia sob desmatamento e manejo agrícola
Keywords in Portuguese
Ecologia microbiana
Ecologia molecular
Microbiologia do solo
Mudanças de uso da terra
Solos tropicais da Amazônia
Abstract in Portuguese
Este trabalho de tese avaliou o efeito do desmatamento sobre redes artificiais de associação entre grupos taxonômicos de Bacteria e fatores abióticos do solo e redes baseadas em funções bacterianas e fatores abióticos do solo, e utilizou técnicas moleculares e abordagem dependente de cultivo para compreender a dinâmica da comunidade de Acidobacteria em solos da floresta Amazônica convertidos em áreas agrícolas para produção de soja. Para estudo das comunidades bacterianas foram utilizadas tecnologias de sequenciamento de nova geração (plataformas 454 GS FLX Titanium da Roche e Illumina HiSeq 2000), PCR quantitativo em tempo-real, método de fingerprinting e procedimentos tradicionais para cultivo de bactérias. O objetivo geral desta tese foi alcançado com o desenvolvimento de três diferentes estudos. O Estudo 1 considerou aproximadamente 425 mil sequências do gene 16S rRNA de Bacteria e 266 milhões de sequências de DNA bacteriano obtidas por análise metagenômica a partir de solos coletados em três réplicas verdadeiras de floresta intacta na Amazônia e área desmatada adjacente após corte e queima da cobertura vegetal. Com isso, este estudo mostrou que o desmatamento declina a abundância e altera a estrutura de comunidade de Verrucomicrobia no solo e simplifica as redes artificiais de associação entre diferentes grupos bacterianos. A rede artificial de associação entre categorias funcionais e fatores de solo revelou-se mais complexa em solos desmatados, indicando um alto grau de dispersão de risco para a manutenção do funcionamento do solo. Por sua vez, o Estudo 2 correlacionou a abundância de subgrupos de Acidobacteria - com base em aproximadamente 33 mil sequências do gene 16S rRNA de Acidobacteria - com fatores abióticos do solo, e mostrou que subgrupos de Acidobacteria respondem diferentemente aos efeitos do manejo agrícola de solos da floresta Amazônica dentro de áreas de produção de soja. Este estudo abriu possibilidades de explorar subgrupos de Acidobacteria como bio-indicadores dos efeitos do manejo agrícola do solo na região da Amazônia. Por fim, o Estudo 3 reportou a culturabilidade e detecção molecular de Acidobacteria subgrupos 1 e 3 e outros grupos bacterianos presentes em solos Amazônicos em meio de cultura enriquecido com carbono e incubado sob atmosfera hipóxica (2% O2 [vol/vol], 2% CO2 [vol/vol] e 96% N2 [vol/vol]), atestando, assim, a combinação de procedimentos tradicionais de cultivo e técnicas moleculares para a recuperação e detecção de Acidobacteria de solos da Amazônia
 
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Publishing Date
2013-05-27
 
WARNING: The material described below relates to works resulting from this thesis or dissertation. The contents of these works are the author's responsibility.
  • NAVARRETE, Acácio A., et al. Acidobacterial community responses to agricultural management of soybean in Amazon forest soils [doi:10.1111/1574-6941.12018]. FEMS Microbiology Ecology [online], 2013, vol. 83, n. 3, p. 607-621.
  • NAVARRETE, Acácio Aparecido, et al. Molecular detection on culture medium of Acidobacteria from Amazon soils [doi:10.7243/2052-6180-1-1]. Microbiology Discovery [online], 2013, vol. 1, n. 1, p. 1.
All rights of the thesis/dissertation are from the authors
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