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Registros recuperados: 26
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An optmized protocol for simultaneous extraction of DNA and RNA from soils BJM
Costa,Rodrigo; Gomes,Newton C.M.; Milling,Annett; Smalla,Kornelia.
In this work we report an optimized protocol for simultaneous extraction of DNA and RNA from soil matrices. Treatment of soil matrices with ethanol followed by bead-beating worked as a successful strategy to lyse the cells without considerable degradation of nucleic acids, resulting in DNA and RNA of good yield and integrity. The reverse transcribed RNA could be amplified with primers targeting a glutamine synthetase (glnA) gene fragment. From both DNA and cDNA, 16S rDNA fragments were amplified and analyzed by Denaturing Gradient Gel Electrophoresis (DGGE). The method was applied to soil and rhizosphere (strawberry and oilseed rape) samples. Two other protocols for the extraction of nucleic acids from soil were applied to the same set of samples in order...
Tipo: Info:eu-repo/semantics/article Palavras-chave: RNA extraction; Nucleic acids; Rhizosphere; Microbial communities.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822004000200011
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Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin ArchiMer
Roussel, Erwan; Sauvadet, Anne-laure; Chaduteau, Carine; Fouquet, Yves; Charlou, Jean-luc; Prieur, Daniel; Cambon, Marie-anne.
P>The distribution of the archaeal communities in deep subseafloor sediments [0-36 m below the seafloor (mbsf)] from the New Caledonia and Fairway Basins was investigated using DNA- and RNA-derived 16S rRNA clone libraries, functional genes and denaturing gradient gel electrophoresis (DGGE). A new method, Co-Migration DGGE (CM-DGGE), was developed to access selectively the active archaeal diversity. Prokaryotic cell abundances at the open-ocean sites were on average similar to 3.5 times lower than at a site under terrestrial influence. The sediment surface archaeal community (0-1.5 mbsf) was characterized by active Marine Group 1 (MG-1) Archaea that co-occurred with ammonia monooxygenase gene (amoA) sequences affiliated to a group of uncultured...
Tipo: Text Palavras-chave: Marine subsurface sediments; Sea floor biosphere; Gradient gel electrophoresis; Microbial communities; Molecular diversity; Anaerobic oxidation; Sequence alignment; Phylogenetic trees; Extracellular DNA; Methane hydrate.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6801.pdf
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Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis. Repositório Alice
SILVEIRA, E.L. da; PEREIRA, R.M.; SCAQUITTO, D.C.; PEDRINHO, E.A.N.; VAL-MORAES, S.P.; WICKERT, E.; CARARETO-ALVES, L.M.; LEMOS, E.G. de M..
Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA) and an eucalyptus arboretum (EAA). PCR primers, whose target soil metagenomic 16S rDNA were used to amplify soil DNA, were cloned using pGEM-T and sequenced to determine bacterial diversity....
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Genetic diversity; Metagenomic; Microbial communities; Diversidade genética; Metagenômica; Comunidades microbianas.
Ano: 2006 URL: http://www.alice.cnptia.embrapa.br/handle/doc/121634
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Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis PAB
Silveira,Érico Leandro da; Pereira,Rodrigo Matheus; Scaquitto,Denilson César; Pedrinho,Eliamar Aparecida Nascimbém; Val-Moraes,Silvana Pómpeia; Wickert,Ester; Carareto-Alves,Lúcia Maria; Lemos,Eliana Gertrudes de Macedo.
Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversity of sympatric communities within soils from two areas, a native forest (NFA) and an eucalyptus arboretum (EAA). PCR primers, whose target soil metagenomic 16S rDNA were used to amplify soil DNA, were cloned using pGEM-T and sequenced to determine bacterial diversity....
Tipo: Info:eu-repo/semantics/article Palavras-chave: Genetic diversity; Metagenomic; Microbial communities.
Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2006001000008
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Biodiversity of Cold Seep Ecosystems Along the European Margins ArchiMer
Vanreusel, Ann; Andersen, Ann C.; Boetius, Antje; Connelly, Douglas; Cunha, Marina R.; Decker, Carole; Hilario, Ana; Kormas, Konstantinos Ar.; Maignien, Lois; Olu, Karine; Pachiadaki, Maria; Ritt, Benedicte; Rodrigues, Clara; Sarrazin, Jozee; Tyler, Paul; Van Gaever, Saskia; Vanneste, Heleen.
During the European Commission's Framework Six Programme, HERMES, we investigated three main areas along the European margin, each characterized by the presence of seep-related structures exhibiting different intensity of activity and biological diversity. These areas are: (1) the Nordic margin with the Hakon Mosby mud volcano and many pockmarks, (2) the Gulf of Cadiz, and (3) the eastern Mediterranean with its hundreds of mud volcanoes and brine pool structures. One of the main goals of the HERMES project was to unravel the biodiversity associated with these seep-associated ecosystems, and to understand their driving forces and functions, using an integrated approach. Several multidisciplinary research cruises to these three areas provided evidence of...
Tipo: Text Palavras-chave: Mosby mud volcano; Gulf of mexico; Cadiz ne atlantic; Deep sea fan; Community structure; Microbial communities; Fluid flow; Mediterranean sea; Carbonate crusts; Norwegian sea.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6375.pdf
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Brazilian microbial diversity as a source of new strains for deconstruction of lignocellulosic biomass. Repositório Alice
FAVARO, L. C. de L.; MELO, I. S. de; QUIRINO, B. F.; OLIVEIRA, A. C. B.; MENDES, T. D.; SALUM, T. F. C.; RODRIGUES, D. S.; SOUZA, G. P.; FRANCO, P. F.; QUECINE, M. C..
2014
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Bactéria; Microbial communities; Lignocellulose.
Ano: 2014 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1010904
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Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments ArchiMer
Jeanbille, Mathilde; Gury, Jérôme; Duran, Robert; Tronczynski, Jacek; Ghiglione, Jean-françois; Agogué, Hélène; Saïd, Olfa Ben; Taïb, Najwa; Debroas, Didier; Garnier, Cédric; Auguet, Jean-christophe.
Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of...
Tipo: Text Palavras-chave: Microbial communities; PAH; Chronic contamination; Coastal sediment; Functional diversity.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00347/45854/45522.pdf
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Comparing how land use change impacts soil microbial catabolic respiration in Southwestern Amazon BJM
Mazzetto,Andre Mancebo; Feigl,Brigitte Josefine; Cerri,Carlos Eduardo Pellegrino; Cerri,Carlos Clemente.
Abstract Land use changes strongly impact soil functions, particularly microbial biomass diversity and activity. We hypothesized that the catabolic respiration response of the microbial biomass would differ depending on land use and that these differences would be consistent at the landscape scale. In the present study, we analyzed the catabolic response profile of the soil microbial biomass through substrate-induced respiration in different land uses over a wide geographical range in Mato Grosso and Rondônia state (Southwest Amazon region). We analyzed the differences among native areas, pastures and crop areas and within each land use and examined only native areas (Forest, Dense Cerrado and Cerrado), pastures (Nominal, Degraded and Improved) and crop...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Amazon region; Land use change; Catabolic profile; Microbial communities.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822016000100063
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Comparison of DNA extraction protocols for microbial communities from soil treated with biochar BJM
Leite,D.C.A.; Balieiro,F.C.; Pires,C.A.; Madari,B.E.; Rosado,A.S.; Coutinho,H.L.C.; Peixoto,R.S..
Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction...
Tipo: Info:eu-repo/semantics/other Palavras-chave: Biochar; DNA extraction; PCR-DGGE; Microbial communities; DNA purity indices.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822014000100023
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Composition and functionality of the wild and cultivated common bean rhizosphere microbiome. Repositório Alice
FLORES, S. W. S.; CHIARAMONTE, J. B.; ROSSMANN, M.; MENDES, R..
Abstract: Plants rely on their rhizosphere microbiome for specific functions, such as, nutrient acquisition and protection against diseases. The domestication and subsequent plant breeding neglected the important role of the rhizosphere microbiome on plant performance. Here, we tested the hypothesis that ancestor materials have higher ability to host beneficial microorganisms in the rhizosphere when compared to modern cultivars. For this, we assessed the composition and functionality of the rhizosphere microbiome associated with a wild (Wild Mex) and with a cultivated (IAC Alvorada) common bean grown in highly biodiverse soil (Amazonian Dark Earth). Antagonistic bacteria were isolated from common bean rhizosphere and total rhizosphere DNA was extracted for...
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Wild common bean; Metagenome; Rhizobacteria; Metagenomics; Microbial communities.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1036667
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Comunidade bacteriana e fúngica da rizosfera de milho cultivado sob diferentes fontes de fosfato utilizando sequenciamento de nova geração. Repositório Alice
SILVA, U. C.; LANA, U. G. de P.; GOMES, E. A.; CUADROS, S.; MEDEIROS, J. D.; PAIVA, C. A. O.; SANTOS, V. L. dos.
2016
Tipo: Artigo em anais de congresso (ALICE) Palavras-chave: Comunidade microbiana; Fosfato de rocha; Fungo; Bactéria; Microbial communities; Fungi.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1054424
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Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil BJM
Lima,Felipe Rezende; Ferreira,Almir José; Menezes,Cristine Gobbo; Miranda,Vitor Fernandes Oliveira; Dourado,Manuella Nóbrega; Araújo,Welington Luiz.
ABSTRACT Carnivorous plant species, such as Utricularia spp., capture and digest prey. This digestion can occur through the secretion of plant digestive enzymes and/or by bacterial digestive enzymes. To comprehend the physiological mechanisms of carnivorous plants, it is essential to understand the microbial diversity related to these plants. Therefore, in the present study, we isolated and classified bacteria from different organs of Utricularia breviscapa (stolons and utricles) and from different geographic locations (São Paulo and Mato Grosso). We were able to build the first bacterium collection for U. breviscapa and study the diversity of cultivable bacteria. The results show that U. breviscapa bacterial diversity varied according to the geographic...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Utricularia breviscapa; Microbial ecology; Aquatic microbiota; Microbial communities.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000400714
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Diversité phylogénétique et fonctionnelle des communautés microbiennes incultivées des sédiments marins de la marge de Sonora, Bassin de Guaymas (Golfe de Californie) ArchiMer
Vigneron, Adrien.
At continental margins, and more particularly in cold seep areas, microbial and animal communities were locally detected at the surface of the sediments. These communities grow using reduced chemical compounds (H2S, Methane, COZ ...) contained in the percolated cold fluids and produced by both geological and microbial processes. ln order to study microbial community diversity in these ecosystems and their role in the environment as well as to understand the environmental factors influencing the distribution and ecophysiology of these communities, surface (0-20 cmbsf) but also deeper (<9 mbsf) sediments were collected at the Sonora Margin. Microbial communities have been studied using various molecular, cultural and microscopy approaches. This research...
Tipo: Text Palavras-chave: Fluides froids; Marge de Sonora; Bassin de Guaymas; Diversité moléculaire; Communautés microbiennes; Archaea; Bacteria; Méthanogènes; Methanogens; Microbial communities; Molecular diversity; Guaymas Basin; Sonora Margin; ANME; SRb; Methane; Sediments; Cold seeps.
Ano: 2012 URL: https://archimer.ifremer.fr/doc/00498/60956/64359.pdf
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Diversity of bacterial communities in acid mine drainage from the Shen-bu copper mine, Gansu province, China Electron. J. Biotechnol.
Yang,Yu; Shi,Wuyang; Wan,Minxi; Zhang,Yanfei; Zou,Lihong; Huang,Jufang; Qiu,Guanzhou; Liu,Xueduan.
This study presents bacterial population analyses of microbial communities inhabiting three sites of acid mine drainage (AMD) in the Shen-bu copper mine, Gansu Province, China. These sites were located next to acid-leached chalcopyrite slagheaps that had been abandoned since 1995. The pH values of these samples with high concentrations of metals ranged from 2.0 to 3.5. Amplified ribosomal DNA restriction analysis (ARDRA) was used to characterize the bacterial population by amplifying the 16S rRNA gene of microorganisms. A total of 39 operational taxonomic units (OTUs) were obtained from the three samples and sequenced from 384 clones. Sequence data and phylogenetic analyses showed that two dominant clones (JYC-1B, JYC-1D) in sample JYC-1 represented 69.5%...
Tipo: Journal article Palavras-chave: Acid mine drainage; Amplified ribosomal DNA restriction analysis; Microbial communities.
Ano: 2008 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582008000100001
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Etude bactériologique des sédiments abyssaux. Etude de la dynamique des communautés microbiennes et de leurs activités hétérotrophes dans les parcs conchylicoles ArchiMer
Bianchi, A..
Bacteriological study of abyssal sediments: During the Demeraby mission of the N/O Jean Charcot in the western Atlantic Ocean, a study of the microflora of the digestive tracts of echinoderms (Holothuroidea of various genera, Asteroidea, Echinoidea) was compared with that of the surrounding sediment. The bacterial concentration observed in the digestive tracts of all the animals studied is higher than that in the surrounding sediments. The largest numbers were always found in the most anterior part of the digestive tracts of the holothurians. In some cases, the increase is considerable (7.10 versus 5.2. 10 cells per millilitre): It indicates a proliferation of bacterial cells in the anterior part of the digestive tract. As the sediment moves through the...
Tipo: Text Palavras-chave: Conchylaceous parks; Microbial communities; Abyssal sediments; Bacteriological study.
Ano: 1981 URL: http://archimer.ifremer.fr/doc/1981/rapport-1926.pdf
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Exploring interactions of plant microbiomes Scientia Agricola
Andreote,Fernando Dini; Gumiere,Thiago; Durrer,Ademir.
A plethora of microbial cells is present in every gram of soil, and microbes are found extensively in plant and animal tissues. The mechanisms governed by microorganisms in the regulation of physiological processes of their hosts have been extensively studied in the light of recent findings on microbiomes. In plants, the components of these microbiomes may form distinct communities, such as those inhabiting the plant rhizosphere, the endosphere and the phyllosphere. In each of these niches, the "microbial tissue" is established by, and responds to, specific selective pressures. Although there is no clear picture of the overall role of the plant microbiome, there is substantial evidence that these communities are involved in disease control, enhance...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Microbial communities; Rhizosphere; Endophytes; Phyllosphere.
Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162014000600013
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Identification des communautés microbiennes des lobes terminaux du système turbiditique du Congo ArchiMer
Bessette, Sandrine.
The Congo deep sea fan, located in the Congo-Angola continental margin (West African coast, Equatorial South Atlantic Ocean) represents a unique deep-sea sedimentary ecosystem. It is characterized by high organic matter inputs from the Congo River, that flow along a canyon and through presently active channel system-lifted into the deeper areas (5 000 m) where the lobes system develops.The aim of this thesis is to study the spatial distribution as well as the phylogenetic and functional diversity of archaeal and bacterial communities in relation with environmental characteristics and constraints of the terminal lobes of the Congo deep see fan, one of the largest submarine fan systems in the world.This study highlights geographical distribution of microbial...
Tipo: Text Palavras-chave: Système turbiditique du Congo; Sédiment riche en matière organique; Communautés microbiennes; Bactéries méthanotrophes aérobies; Suintements de méthane; Methane seeps; Congo turbiditic system; Organic-rich sediment; Microbial communities; Aerobic methane oxidizing bacteria.
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00498/60929/64323.pdf
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Iron oxide deposits associated with the ectosymbiotic bacteria in the hydrothermal vent shrimp Rimicaris exoculata ArchiMer
Corbari, L; Cambon-bonavita, Marie-anne; Long, G; Grandjean, F; Zbinden, M; Gaill, F; Compere, P.
The Rimicaris exoculata shrimp is considered as a primary consumer that dominates the fauna of most Mid-Atlantic Ridge ( MAR) hydrothermal ecosystems. These shrimps harbour in their gill chambers an important ectosymbiotic community of chemoautotrophic bacteria associated with iron oxide deposits. The structure and elemental composition of the mineral concretions associated with these bacteria have been investigated by using LM, ESEM, TEM STEM and EDX microanalyses. The nature of the iron oxides in shrimps obtained from the Rainbow vent field has also been determined by Mossbauer spectroscopy. This multidisciplinary approach has revealed that the three layers of mineral crust in the Rimicaris exoculata shrimps consist of large concretions formed by...
Tipo: Text Palavras-chave: Mid atlantic ridge; Deep sea; Microbial communities; Oxidizing bacteria; Trophic ecology; Ferrous ions; Fe oxides; Ferrihydrite; Biomineralization; Minerals.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4702.pdf
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Microbial communities associated with benthic faunal assemblages at cold seep sediments of the Sonora Margin, Guaymas Basin ArchiMer
Cruaud, Perrine; Vigneron, Adrien; Pignet, Patricia; Caprais, Jean-claude; Lesongeur, Francoise; Toffin, Laurent; Godfroy, Anne; Cambon-bonavita, Marie-anne.
The Sonora Margin cold seeps present a seafloor mosaic pattern consisting of different faunal assemblages and microbial mats. To better understand if sedimentary microbial communities reflect this patchy distribution, all major habitats were investigated using four complementary approaches: 16S rRNA gene sequence 454 pyrosequencing, quantitative polymerase chain reaction, fluorescence in situ hybridization and geochemistry analyses. This study reveals that sediments populated by different surface assemblages show distinct porewater geochemistry features and are associated with distinct microbial communities. In the sediments underlying the microbial mat and the surrounding macrofauna, microbial communities were dominated by anaerobic methane oxidizers...
Tipo: Text Palavras-chave: Microbial communities; Pyrosequencing; MBG-D; ANME; Faunal assemblages; Vesicomyidae; Siboglinidae; Microbial mat.
Ano: 2015 URL: https://archimer.ifremer.fr/doc/00288/39889/38434.pdf
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Microbial community modulates growth of symbiotic fungus required for stingless bee metamorphosis. Repositório Alice
PALUDO, C. R.; PISHCHANY, G.; DOMINGUEZ, A.-A.; SILVA JÚNIOR, E. A.; MENEZES, C.; NASCIMENTO, F. S.; CURRIE, C. R.; KOLTER, R.; CLARDY, J.; PUPO, M. T..
Abstract: The Brazilian stingless bee Scaptotrigona depilis requires the brood cells-associated fungus Zygosaccharomyces sp. as steroid source for metamorphosis. Besides the presence of Zygosaccharomyces sp., other fungi inhabit S. depilis brood cells, but their biological functions are unknown. Here we show that Candida sp. and Monascus ruber, isolated from cerumen of S. depilis brood provisions, interact with Zygosaccharomyces sp. and modulate its growth. Candida sp. produces volatile organic compounds (VOCs) that stimulate Zygosacchromyces sp. development. Monascus ruber inhibits Zygosacchromyces sp. growth by producing lovastatin, which blocks steroid biosynthesis. We also observed that in co-cultures M. ruber inhibits Candida sp. through the...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Abelha; Abelha Brasileira; Fungo; Metamorfose; Stingless bees; Fungi; Metamorphosis; Microbial communities.
Ano: 2019 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1115223
Registros recuperados: 26
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