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Registros recuperados: 28
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A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and Bathymodiolus puteoserpentis (Bivalvia : Mytilidae), from hydrothermal vents along the northern Mid-Atlantic Ridge ArchiMer
Duperron, Sebastien; Bergin, C; Zielinski, F; Blazejak, A; Pernthaler, A; Mckiness, Z; Dechaine, E; Cavanaugh, C; Dubilier, Nicole.
Bathymodiolus azoricus and Bathymodiolus puteoserpentis are symbiont-bearing mussels that dominate hydrothermal vent sites along the northern Mid-Atlantic Ridge (MAR). Both species live in symbiosis with two physiologically and phylogenetically distinct Gammaproteobacteria: a sulfur-oxidizing chemoautotroph and a methane-oxidizer. A detailed analysis of mussels collected from four MAR vent sites (Menez Gwen, Lucky Strike, Rainbow, and Logatchev) using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization (FISH) showed that the two mussel species share highly similar to identical symbiont phylotypes. FISH observations of symbiont distribution and relative abundances showed no obvious differences between the two host species. In...
Tipo: Text Palavras-chave: Bacteria; Phylogeny; Fluorescence in situ hybridization (FISH); Methane oxidizer; Sulfur oxidizer; 16S rRNA; Endosymbiosis.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/publication-1864.pdf
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Análise via PCR-DGGE da microbiota associada à rizosfera de feijoeiro Olathe Pinto e Olathe Pinto 5.1 modificado geneticamente para resistência ao vírus do mosaico dourado. Repositório Alice
CUNHA, B. C. A.; PASSOS, S. R.; RUMJANEK, N. G.; XAVIER, G. R..
2011
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: PCR; 16S rRNA; DGGE; Phaseolus vulgaris; Alfaproteobactérias.
Ano: 2011 URL: http://www.alice.cnptia.embrapa.br/handle/doc/905240
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ANALISIS MOLECULAR EN GASTROPODOS CHILENOS COMERCIALES BASADOS EN LAS SECUENCIAS 16S rRNA,. COI Y ITS1-5.8S rDNA-ITS2 Gayana
Aguilera-Muñoz,Felipe; Lafarga-Cruz,Fabiola; Gallardo-Escárate,Cristian.
Gastropod mollusks are part of the principal marine resources cultivated and commercialized in Chile. There are native Chilean species such as loco (Concholepas concholepas), locate (Thais chocolata), trumulco snail (Chorus giganteus), keyhole limpets (Fissurella spp.), tegula snail (Tegula atra) as well as exotic species such as red abalone (Haliotis rufescens) and Japanese abalone (Haliotis discus hannai). Despite their importance as marine resources, molecular genetic studies establishing phylogenetic relationships and estimating population genetic parameters are scarce. The aim of this study is to establish a molecular approach among the main commercial gastropod species in Chile. The mitochondrial genes 16S rRNA and COI, and the nuclear ribosomal...
Tipo: Journal article Palavras-chave: 16S rRNA; COI; ITSl-5.8SrDNA-ITS2; Gastropod mollusks; Phylogenetic relationships.
Ano: 2009 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-65382009000100003
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Approches culturales et moléculaires des assemblages microbiens associés aux polychètes hydrothermaux de la famille Alvinellidae ArchiMer
Alain, Karine.
Cultural and molecular approaches were used to analyse the microbial assemblages associated to the deep-sea hydrothermal vent polychaete worms of the family Alvinellidae. In a first part of the work, the populations associated to three alvinellid species from the Juan de Fuca Ridge (Paralvinella palmiformis, Paralvinella pandorae and Paralvinella sulfincola) were identified by phylogenetic analyses. A wide microbial diversity was detected, like a great number of new sequences or of sequences belonging to species previously unidentified at deep-sea hydrothermal vents. All the libraries were found to be dominated by sequences affiliated to the epsilon-Proteobacteria. In other respects, fermentative micro-organisms belonging to the Thermococcales, the...
Tipo: Text Palavras-chave: Paralvinella; Alvinella; 16S rRNA; Thermophile; Hydrothermal vent; Paralvinella; Alvinella; ARNr 16S; Thermophile; Source hydrothermale.
Ano: 2003 URL: http://archimer.ifremer.fr/doc/2005/these-332.pdf
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Archaeal Methane Cycling Communities Associated with Gassy Subsurface Sediments of Marennes-Oleron Bay (France) ArchiMer
Roussel, Erwan; Sauvadet, Anne Laure; Allard, Jonathan; Chaduteau, Carine; Richard, Pierre; Cambon Bonavita, Marie-anne; Chaumillon, Eric.
In Marennes-Oleron Bay, a macro-tidal bay located on the French Atlantic coast, kilometer-scale acoustic turbidity reveals an accumulation of free gas in the sediment. Large concentrations of organic matter and rapid sedimentation rates provide ideal settings for biogenic methane cycling. We integrate seismic, sedimentologic, biogeochemical and molecular genetic approaches to determine whether microbial methane cycling is involved in this process. Here we show that the acoustic turbidity upper boundary matched with X-ray facies displaying fissures with the highest methane concentrations, demonstrating the existence of methane bubbles in the sediment. 16S rRNA and mcrA gene clone libraries were dominated by sequences affiliated to the three known ANME...
Tipo: Text Palavras-chave: Sediment; Methane; McrA; 16S rRNA; Archaea.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6165.pdf
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Bacillus megaterium: an endophytic bacteria from callus of Ilex paraguariensis with growth promotion activities. Repositório Alice
GRUNENNVALDT, R. L.; DEGENHARDT-GOLDBACH, J.; TOMASI, J. de C.; SANTOS, G. D. dos; VICENTE, V. A.; DESCHAMPS, C..
Endophytic microorganisms live inside healthy plants and their isolation and identification may favor biotechnological applications. We isolated endophytic bacteria from Ilex paraguariensis callus cultivated in vitro for five months. Sequencing of 16S rRNA region to identify two isolates as Bacillus megaterium was used. The presence of bacterial cells in the intercellular spaces of callus cultures was detected by ultra structural analyses. The isolates were also evaluated for indole acetic acid (IAA) production and their potential in plant growth promotion of Phaseolus vulgaris L. The synthesis of IAA in the presence and absence of L-tryptophan was detected by colorimetric analyze for both isolates. In the presence of extracts from strains IPC06 and IPC07...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Erva mate; 16S rRNA; Sequencing; Ilex Paraguariensis; Espécie Nativa; Cultura de Tecido; Biotecnologia; Tissue culture.
Ano: 2018 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1102141
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Caracterização metagenômica do microbioma intestinal de aves de corte através do sequenciamento parcial do gene 16S-rRNA. Repositório Alice
SAVOLDI, I. R; DAL PIZZOL, M. S.; CARMO, K. B. do; IBELLI, A. M. G.; KRAMER, B.; MORES, M. A. Z.; PEIXOTO, J. de O.; CANTAO, M. E.; JAENISCH, F. R. F.; AVILA, V. S. de; KRABBE, E. L.; LEDUR, M. C.; PANDOLFI, J. R. C..
2016
Tipo: Artigo em anais de congresso (ALICE) Palavras-chave: 16S rRNA; Frangos de corte; Microbioma intestinal; Alistipes; Ruminococcaceae; Lachnospiraceae.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1059132
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Cyanobacterial populations that build 'kopara' microbial mats in Rangiroa, Tuamotu Archipelago, French Polynesia ArchiMer
Richert, Laurent; Golubic, Stjepko; Le Guedes, Roland; Herve, Annie; Payr, Claude.
Cyanobacterial populations, the primary producers and builders of 'kopara' microbial mats were studied in four selected ponds along the rim of the Rangiroa Atoll, French Polynesia using a polyphasic approach. Seven isolates were maintained in uni-cyanobacterial cultures, characterized morphotypically and phylogenetically by evaluating sequences of the 16S rRNA gene of about 620 base pairs in length. Cyanobacteria in natural populations were analyzed microscopically, characterized morphotypically, and compared with cultured strains. Three of the isolates were identified in the field samples: Lyngbya aestuarii, Johannesbaptistia pellucida and Chroococcus submarinus were present in the mats only as minor components, whereas the species of Schizothrix that...
Tipo: Text Palavras-chave: 16S rRNA; Polyphasic approach; Phylogeny; Microbial mats; Microbial ecology; Kopara; Diversity; Cyanobacteria; Culture.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/publication-2050.PDF
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Development of in situ hybridisation using 16S rRNA gene to monitor black-lip pearl oyster, Pinctada margaritifera, larvae in plankton samples ArchiMer
Thomas, Yoann; Belliard, Corinne; Garen, Pierre; Gueguen, Yannick; Montagnani, Caroline.
In French Polynesia, the black-lip pearl oyster Pinctada margaritifera has been farmed to produce pearls since the 1980s, forming the basis of a major industry. The sustainability of this activity relies on spat collection in the lagoons. However, pearl oyster spat can be difficult to identify for the evaluation of stock variations. It is especially hard to distinguish Pinctada spp. larvae at a very early stage of development. In the present study, a whole- mount in situ hybridisation (ISH) technique was developed to allow the discrimination of larvae of closely-related pearl oyster species found in the French Polynesian atolls. Using specific ribosomal 16S-DNA sequence data, we were able to successfully differentiate between Pinctada margaritifera and...
Tipo: Text Palavras-chave: Whole larvae in situ hybridisation; 16S rRNA; Plankton; Species identification; Pearl oyster; Pinctada margaritifera.
Ano: 2011 URL: http://archimer.ifremer.fr/doc/00035/14603/11923.pdf
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Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study Inra
Mueller, S.; Saunier, K.; Hanisch, C.; Norin, E.; Alm, L.; Midvedt, T.; Cresci, A.; Silvi, S; Orpianesi, C.; Verdenelli, M.C.; Clavel, T.; Koebnick, C.; Zunft, H.J.F.; Dore, J.; Blaut, M..
A cross-sectional study on intestinal microbiota composition was performed on 230 healthy subjects at four European locations in France, Germany, Italy, and Sweden. The study participants were assigned to two age groups: 20 to 50 years (mean age, 35 years; n = 85) and >60 years (mean age, 75 years; n = 145). A set of 14 group- and species-specific 16S rRNA-targeted oligonucleotide probes was applied to the analysis of fecal samples by fluorescence in situ hybridization coupled with flow cytometry. Marked country-age interactions were observed for the German and Italian study groups. These interactions were inverse for the predominant bacterial groups Eubacterium rectale-Clostridium coccoides and Bacteroides-Prevotella. Differences between European...
Tipo: Journal Article Palavras-chave: FAECAL MICROBIOTA; 16S rRNA; AGE GROUP; GENDER; FLUORESCENT IN SITU HYBRIDIZATION; FLOW CYTOMETRY; CROSS-SECTIONAL STUDY.
Ano: 2006 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2008b1ca1f40&uri=/notices/prodinra1/2008/06/
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Diversity and capacity to promote maize growth of bacteria isolated from the Amazon Region Repositório Alice
SILVA, K. da; PERIN, L.; GOMES, M. de L.; BARAÚNA, A. C.; PEREIRA, G. M. D.; MOSQUEIRA, C. A.; COSTA, I. B. da; O'HARA, G.; ZILLI, J. E..
2016
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Biological nitrogen fixation; Zea mays L; 16S rRNA.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1044452
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Dual Presence of Anaplasma phagocytophilum and Its Closely Related Anaplasma sp. in Ixodid Ticks in Hokkaido, Japan, and Their Specific Molecular Detection OAK
YBAÑEZ, Adrian Patalinghug; MATSUMOTO, Kotaro; KISHIMOTO, Toshio; YOKOYAMA, Naoaki; INOKUMA, Hisashi; 松本, 高太郎; 横山, 直明; 猪熊, 壽.
Anaplasma phagocytophilum causes human granulocytic anaplasmosis (HGA) and tick-borne fever in ruminants. A closely related and potentially novel Anaplasma sp. in Japan was recently characterized. The aims of the study were to provide molecular evidence for the presence of these 2 species in Japan, and to develop a reliable PCR method based on the nucleotide differences within the citrate synthase (gltA) gene. DNA samples from 182 ixodid ticks (134 Ixodes persulcatus, 35 Haemaphysalis douglasii and 13 I. ovatus) collected from 2 sites in Hokkaido, Japan, were screened for A. phagocytophilum and its closely related Anaplasma sp. (herein designated as Anaplasma sp. Japan) using 16S rRNA PCR, revealing a combined prevalence rate of 27.5% (50 samples). The...
Palavras-chave: 16S rRNA; Anaplasma phagocytophilum; Anaplasma sp.; GltA; GroEL.
Ano: 2012 URL: http://ir.obihiro.ac.jp/dspace/handle/10322/3839
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Evaluation of bacterial diversity recovered from petroleum samples using different physical matrices. Repositório Alice
DELLAGNEZZE, B. M.; VASCONCELLOS, S. P. de; MELO, I. S. de; SANTOS NETO, E. V. dos; OLIVEIRA, V. M. de.
Abstract: Unraveling the microbial diversity and its complexity in petroleum reservoir environments has been a challenge throughout the years. Despite the techniques developed in order to improve crude oil, microbial enrichments using different culture conditions can be applied as a way to increase the recovery of DNA from environmentswith low cellular density for further microbiological analyses. This work aimed at the evaluation of different matrices(arenite, shale and polyurethane foam) as support materials for microbial growth and biofilm formation in enrichments using a biodegraded petroleum sample as inoculum in sulfate reducing condition. Subsequent microbial diversity characterization was carried out using Scanning Electronic Microscopy (SEM),...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Bacterial diversity; Microbial enrichment; Petroleum reservoir; Physical support; 16S rRNA; Bactéria; Biodiversidade; Petróleo; Biodegradação; Bacteria; Biodiversity.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1062180
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Genetic characterisation of oyster populations along the north-eastern coast of Tunisia ArchiMer
Dridi, S.; Romdhane, M. S.; Heurtebise, Serge; El Cafsi, M.; Boudry, Pierre; Lapegue, Sylvie.
The taxonomy of oysters has been traditionally based on characteristics of the shell. More recently, the analysis of protein and DNA polymorphism has provided a means to overcome difficulties in distinguishing the different species of oysters based solely on shell morphology. In order to identify oysters of the Tunisian north-east coast, we sequenced a 16S rRNA mitochondrial fragment from 68 oysters sampled from the Bizert Lagoon and the Gulf of Hammamet in northern Tunisia. Comparison of oyster 16S rRNA sequences available in GenBank showed the presence of both Ostreola stentina and Crassostrea gigas in our samples, which could not be detected on the basis of shell morphology only. These data confirmed that C. gigas, a non-native species, is now...
Tipo: Text Palavras-chave: 16S rRNA; Crassostrea gigas; Genetics; Mediterranean Sea; Ostreola stentina; Polymorphism.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/00000/11063/7820.pdf
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Genetic characterization of poultry gut microbiota by 16S-rRNA gene sequencing. Repositório Alice
PANDOLFI, J. R. C.; IBELLI, A. M. G.; CANTAO, M. E.; PEIXOTO, J. de O.; KRABBE, E. L.; AVILA, V. S. de; KRAMER, B.; ZANELLA, R.; JAENISCH, F. R. F.; MORES, M. A. Z.; COUTINHO, L. L.; LEDUR, M. C..
2015
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: 16S rRNA; Poultry production; Gut microbiome; Alistipes; Ruminococcaceae; Lachnospiraceae.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1033823
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Genetic diversity of Rhizobia isolates from Amazon soils using cowpea (Vigna unguiculata) as trap plant. Repositório Alice
SILVA, F. V.; ARAUJO, J. L. S. de; SILVA JUNIOR, J. P. da; XAVIER, G. R.; RUMJANEK, N. G..
2012
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: BNF; Bactéria; 16S rRNA; ARDRA; Sequencing.
Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/handle/doc/949709
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Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean ArchiMer
Pereira, Olivier; Hochart, Corentin; Auguet, Jean-christophe; Debroas, Didier; Galand, Pierre E..
Planktonic Archaea have been detected in all the world's oceans and are found from surface waters to the deep sea. The two most common Archaea phyla are Thaumarchaeota and Euryarchaeota. Euryarchaeota are generally more common in surface waters, but very little is known about their ecology and their potential metabolisms. In this study, we explore the genomic ecology of the Marine Group II (MGII), the main marine planktonic Euryarchaeota, and test if it is composed of different ecologically relevant units. We re‐analyzed Tara Oceans metagenomes from the photic layer and the deep ocean by annotating sequences against a custom MGII database and by mapping gene co‐occurrences. Our data provide a global view of the distribution of Euryarchaeota, and more...
Tipo: Text Palavras-chave: 16S rRNA; Euryarchaeota; Global ocean; Metagenomics; Poseidoniales; Proteorhodopsin.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00505/61676/65607.pdf
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Hierarchical analysis of mtDNA variation and the use of mtDNA for isopod (Crustacea: Peracarida: Isopoda) systematics Naturalis
Wetzer, R..
Carefully collected molecular data and rigorous analyses are revolutionizing today’s phylogenetic studies. Although molecular data have been used to estimate various invertebrate phylogenies lor more than a decade, this study is the first survey of different regions of mitochondrial DNA in isopod crustaceans assessing sequence divergence and hence the usefulness of these regions to infer phylogeny at different hierarchical levels. 1 evaluate three loci from the mitochondrial genome (two ribosomal RNAs (12S, 16S) and one protein-coding (COI)) for their appropriateness in inferring isopod phylogeny at the suborder level and below. The patterns are similar for all three loci with the most speciose suborders of isopods also having the most divergent...
Tipo: Article / Letter to the editor Palavras-chave: Mitochondrial DNA; Isopod; Crustacea; Molecular; 12S rRNA; 16S rRNA; COI.
Ano: 2001 URL: http://www.repository.naturalis.nl/record/534397
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Integrating molecular identification of pelagic eggs with geostatistical mapping to improve the delineation of North Sea fish spawning grounds ArchiMer
Lelievre, Stephanie; Jerome, Marc; Maes, Gregory E.; Vaz, Sandrine; Calaivany, Sachidhanandam; Verrez-bagnis, Veronique.
Maps of the spawning grounds of commercially important fishes are necessary when assessing the level of connectivity between life stages of fishes and for identifying ecologically valuable marine areas. A first step toward mapping the spawning grounds is a reliable and rapid species identification of pelagic fish eggs to assess the spatio-temporal distribution of spawning aggregations. As many species have similar egg sizes and morphology, the molecular validation of visually identified eggs is often essential for the use of such data in fisheries management. In the present study, we developed a rapid 16S rRNA PCR-restriction fragment length polymorphism (RFLP) assay to distinguish between formalin-fixed fish eggs of dab Limanda limanda, flounder...
Tipo: Text Palavras-chave: Fish eggs; PCR-RFLP; 16S rRNA; Geostatistical analyses; Distribution; Spawning grounds.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00059/16999/14536.pdf
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Phylogenetic characterization of the bacterial assemblage associated with mucous. secretions of the hydrothermal vent polychaete Paralvinella palmiformis ArchiMer
Alain, Karine; Olagnon, Michel; Desbruyeres, Daniel; Page, Antoine; Barbier, Georges; Juniper, Kim; Querellou, Joel; Cambon-bonavita, Marie-anne.
As part of an ongoing examination of microbial diversity associated with hydrothermal vent polychaetes of the family Alvinellidae, we undertook a culture-independent molecular analysis of the bacterial assemblage associated with mucous secretions of the Northeastern Pacific vent polychaete Paralvinella palmiformis. Using a molecular 16S rDNA-based phylogenetic approach, clone libraries were constructed from two samples collected from active sulfide edifices in two hydrothermal vent fields. In both cases, clone libraries were largely dominated by epsilon-Proteobacteria. Phylotypes belonging to the Cytophaga-Flavobacteria and to the Verrucomicrobia were also largely represented within the libraries. The remaining sequences were related to the taxonomic...
Tipo: Text Palavras-chave: Proteobacteria; 16S rRNA; Microbial diversity; Phylogeny; Hydrothermal vent; Paralvinella palmiformis.
Ano: 2002 URL: https://archimer.ifremer.fr/doc/2002/publication-661.pdf
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