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Consulta: subjectFacets:"16S rRNA" Registros recuperados: 43 Data/hora: 08/06/2017 18:09:20 Genetic diversity of Rhizobia isolates from Amazon soils using cowpea (Vigna unguiculata) as trap plant. Provedor de dados: 119 Autores: 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 Variabilidade genética de fitoplasma e de espiroplasma isolados de milho. Provedor de dados: 119 Autores: GOMES, E. A.; JARDIM, S.N.; BRITTO, W.M.A.; OLIVEIRA, E.; SILVA, R.E.; GUIMARAES, C. T. 2002 Tipo: Artigo em anais de congresso (ALICE) Palavras-chave: Fitoplasma; Spiroplasma kunkelii; 16S rRNA; Espiralina; Sequenciamento de DNA. Ano: 2002 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. Provedor de dados: 119 Autores: 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 Diversity and capacity to promote maize growth of bacteria isolated from the Amazon Region Provedor de dados: 119 Autores: 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://dx.doi.org/10.1590/1809-4392201502502 Genetic characterization of poultry gut microbiota by 16S-rRNA gene sequencing. Provedor de dados: 119 Autores: 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 Variabilidade genética de fitoplasma e de espiroplasma isolados de milho. Provedor de dados: 119 Autores: GOMES, E.A.; JARDIM, S.N.; BRITTO, W.M.A.; OLIVEIRA, E.; SILVA, R.E.; GUIMARAES, C.T. 2002 Tipo: Artigo em anais de congresso (ALICE) Palavras-chave: Fitoplasma; Spiroplasma kunkelii; 16S rRNA; Espiralina; Sequenciamento de DNA. Ano: 2002 URL: http://www.alice.cnptia.embrapa.br/handle/doc/485703 Diversity and capacity to promote maize growth of bacteria isolated from the Amazon region Provedor de dados: 36 Autores: SILVA,Krisle da; PERIN,Liamara; GOMES,Maria de Lourdes; BARAÚNA,Alexandre Cardoso; PEREIRA,Gilmara Maria Duarte; MOSQUEIRA,Cátia Aparecida; COSTA,Ismaele Breckenfeld da; O'HARA,Graham; ZILLI,Jerri Édson. ABSTRACT Maize plants can establish beneficial associations with plant growth-promoting bacteria. However, few studies have been conducted on the characterization and inoculation of these bacteria in the Amazon region. This study aimed to characterize endophytic bacteria isolated from maize in the Amazon region and to assess their capacity to promote plant growth. Fifty-five bacterial isolates were obtained from maize grown in two types of ecosystems, i.e., a cerrado (savanna) and a forest area. The isolates were characterized by the presence of the nifH gene, their ability to synthesize indole-3-acetic acid (IAA) and solubilize calcium phosphate (CaHPO4), and 16S rRNA partial gene sequencing. Twenty-four bacteria contained the nifH gene, of which seven... Tipo: Journal article Palavras-chave: Biological nitrogen fixation; Zea mays L.; 16S rRNA. Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0044-59672016000200111 Detection of Borrelia-specific 16S rRNA sequence in total RNA extracted from Ixodes ricinus ticks Provedor de dados: 45 Autores: Radulović,Ž .; Milutinović,M.; Tomanović,S.; Mulenga,A. A reverse transcriptase - polymerase chain reaction based assay for Borrelia species detection in ticks was developed. The method was based on amplification of 552 nucleotide bases long sequence of 16S rRNA, targeted by Borrelia specific primers. In the present study, total RNA extracted from Ixodes ricinus ticks was used as template. The results showed higher sensitivity for Borrelia detection as compared to standard dark-field microscopy. Method specificity was confirmed by cloning and sequencing of obtained 552 base pairs long amplicons. Phylogenetic analysis of obtained sequences showed that they belong to B. lusitaniae and B. afzelii genospecies. RT-PCR based method presented in this paper could be very useful as a screening test for detecting... Tipo: Journal article Palavras-chave: Borrelia; RT-PCR; 16S rRNA; Ixodes ricinus. Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-09352010000400015 The complete sequence of the mitochondrial genome of the Chinook salmon, Oncorhynchus tshawytscha Provedor de dados: 48 Autores: WILHELM,VIVIAN; VILLEGAS,JAIME; MIQUEL,ÁLVARO; ENGEL,ESTEBAN; BERNALES,SEBASTIÁN; VALENZUELA,PABLO D.T.; BURZIO,LUIS O. The complete sequence of the mitochondrial genome of Chinook salmon, Oncorhynchus tshawytscha, has been determined. The circular genome consisting of 16,644 base pairs encodes thirteen proteins, the 12S and 16S ribosomal RNAs, and 22 transfer RNAs. These genes are ordered in the same way as most other vertebrates. The nucleotide and amino acid sequences of the ribosomal RNAs and the thirteen protein-coding genes were compared with those of other salmonids such as Oncorhynchus mykiss, Salmo salar, Salvelinus fontinalis, Salvelinus alpinus and Coregonus lavaretus. The sequence features of the control region (D-loop), the origin of L-strand replication and a putative peptide codified by the 16S mitochondrial RNA are described and discussed. Tipo: Journal article Palavras-chave: Salmonids; Mitochondria; Genome; Peptides; 16S rRNA. Ano: 2003 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602003000200012 Ardra profiles of bacteria and archaea in mangrove sediments with different levels of contamination in the estuarine complex of Paranaguá, Brazil Provedor de dados: 52 Autores: Ribeiro,Catherine Gérikas; Steffens,Maria Berenice Reynaud; Etto,Rafael Mazer; Galvão,Carolina Weigert; Martins,César de Castro; Pedrosa,Fábio de Oliveira; Kolm,Hedda Elisabeth. The mangrove's sediments from the coastal areas under human activities may contain significant contaminations by hydrocarbons, even when there are no visual evidences of it. The microorganisms are essential to these ecosystems, especially in the control of their chemical environment. Sediment samples were collected in two regions under different environment conditions (pristine and contaminated) of the Paranaguá Estuarine Complex (Paranaguá Bay and Laranjeiras Bay), Brazil. Aliphatic hydrocarbons were determined by the GC-FID to assess the status of contamination of the studied areas. The total DNA was extracted from these samples. The 16S rRNA gene was amplified by the PCR reactions with the pair of primers 21F and 958R for the archaeal domain, and 27F... Tipo: Journal article Palavras-chave: Diversity; Mangroves; Archaea; Bacteria; 16S rRNA; ARDRA; Aliphatic hydrocarbons. Ano: 2013 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132013000200013 Diversity of 16S rRNA genes from bacteria of sugarcane rhizosphere soil Provedor de dados: 56 Autores: Pisa,G.; Magnani,G.S.; Weber,H.; Souza,E.M.; Faoro,H.; Monteiro,R.A.; Daros,E.; Baura,V.; Bespalhok,J.P.; Pedrosa,F.O.; Cruz,L.M. Sugarcane is an important agricultural product of Brazil, with a total production of more than 500 million tons. Knowledge of the bacterial community associated with agricultural crops and the soil status is a decisive step towards understanding how microorganisms influence crop productivity. However, most studies aim to isolate endophytic or rhizosphere bacteria associated with the plant by culture-dependent approaches. Culture-independent approaches allow a more comprehensive view of entire bacterial communities in the environment. In the present study, we have used this approach to assess the bacterial community in the rhizosphere soil of sugarcane at different times and under different nitrogen fertilization conditions. At the high taxonomic level, few... Tipo: Journal article Palavras-chave: 16S rRNA; Biodiversity; Nitrogen fixation; Bacteria; Sugarcane; Soil. Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2011001200004 Genetic diversity of Rhizobia isolates from Amazon soils using cowpea (Vigna unguiculata) as trap plant Provedor de dados: 58 Autores: Silva,F.V.; Simões-Araújo,J.L.; Silva Júnior,J.P.; Xavier,G.R.; Rumjanek,N.G. The aim of this work was to characterize rhizobia isolated from the root nodules of cowpea (Vigna unguiculata) plants cultivated in Amazon soils samples by means of ARDRA (Amplified rDNA Restriction Analysis) and sequencing analysis, to know their phylogenetic relationships. The 16S rRNA gene of rhizobia was amplified by PCR (polymerase chain reaction) using universal primers Y1 and Y3. The amplification products were analyzed by the restriction enzymes HinfI, MspI and DdeI and also sequenced with Y1, Y3 and six intermediate primers. The clustering analysis based on ARDRA profiles separated the Amazon isolates in three subgroups, which formed a group apart from the reference isolates of Bradyrhizobium japonicum and Bradyrhizobium elkanii. The clustering... Tipo: Journal article Palavras-chave: BNF; Bacteria; 16S rRNA; ARDRA; Sequencing. Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822012000200033 16S rRNA region based PCR protocol for identification and subtyping of Parvimonas micra Provedor de dados: 58 Autores: Ota-Tsuzuki,C.; Brunheira,A.T.P.; Mayer,M.P.A. The present study established a PCR protocol in order to identify Parvimonas micra and to evaluate the intra-species diversity by PCR-RFLP of 16S rRNA partial sequence. The data indicated that the protocol was able to identify this species which could be clustered in five genotypes. Tipo: Journal article Palavras-chave: PCR-RFLP; 16S rRNA; Anaerobic cocci. Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822008000400001 Molecular characterization of bacterial populations of different soils Provedor de dados: 58 Autores: Pereira,Rodrigo Matheus; Silveira,Érico Leandro da; Scaquitto,Denilson César; Pedrinho,Eliamar Aparecida Nascimbém; Val-Moraes,Silvana Pompéia; Wickert,Ester; Carareto-Alves,Lúcia Maria; Lemos,Eliana Gertrudes de Macedo. Until recently, few studies were carried out in Brazil about diversity of bacterial soil communities. Aiming to characterize the bacterial population in the soil through 16S rRNA analysis, two types of soil have been analyzed: one of them characterized by intensive use where tomato, beans and corn were cultivated (CS); the other analyzed soil was under forest (FS), unchanged by man; both located in Guaíra, São Paulo State, Brazil. Using specific primers, 16S rRNA genes from metagenomic DNA in both soils were amplified by PCR, amplicons were cloned and 139 clones from two libraries were partially sequenced. The use of 16S rRNA analysis allowed identification of several bacterial populations in the soil belonging to the following phyla: Acidobacteria,... Tipo: Journal article Palavras-chave: Metagenome; Microbial diversity; 16S rRNA. Ano: 2006 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822006000400007 Bioprocessing of some agro-industrial residues for endoglucanase production by the new subsp.; Streptomyces albogriseolus subsp. cellulolyticus strain NEAE-J Provedor de dados: 58 Autores: El-Naggar,Noura El-Ahmady; Abdelwahed,Nayera A.M.; Saber,Wesam I.A.; Mohamed,Asem A. The use of low cost agro-industrial residues for the production of industrial enzymes is one of the ways to reduce significantly production costs. Cellulase producing actinomycetes were isolated from soil and decayed agricultural wastes. Among them, a potential culture, strain NEAE-J, was selected and identified on the basis of morphological, cultural, physiological and chemotaxonomic properties, together with 16S rDNA sequence. It is proposed that strain NEAE-J should be included in the species Streptomyces albogriseolus as a representative of a novel sub-species, Streptomyces albogriseolus subsp. cellulolyticus strain NEAE-J and sequencing product was deposited in the GenBank database under accession number JN229412. This organism was tested for its... Tipo: Journal article Palavras-chave: Agro-industrial residues; Endoglucanase production; Streptomyces albogriseolus; 16S rRNA; Scanning electron microscope. Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822014000200050 Role of wild birds as carriers of multi-drug resistant Escherichia coli and Escherichia vulneris Provedor de dados: 58 Autores: Shobrak,Mohammed Y.; Abo-Amer,Aly E. Emergence and distribution of multi-drug resistant (MDR) bacteria in environments pose a risk to human and animal health. A total of 82 isolates of Escherichia spp. were recovered from cloacal swabs of migrating and non-migrating wild birds. All bacterial isolates were identified and characterized morphologically and biochemically. 72% and 50% of isolates recovered from non-migrating and migrating birds, respectively, showed positive congo red dye binding (a virulence factor). Also, hemolysin production (a virulence factor) was showed in 8% of isolates recovered from non-migrating birds and 75% of isolates recovered from migrating birds. All isolates recovered from non-migrating birds were found resistant to Oxacillin while... Tipo: Journal article Palavras-chave: E. coli; E. vulneris; Multi-drug resistance (MDR); Migrating and non-migrating birds; Congo red binding; Hemolysin; API 20E; 16S rRNA; Plasmid profile. Ano: 2014 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822014000400010 Effect of plant growth-promoting bacteria on the growth and fructan production of Agave americana L. Provedor de dados: 58 Autores: De La Torre-Ruiz,Neyser; Ruiz-Valdiviezo,Víctor Manuel; Rincón-Molina,Clara Ivette; Rodríguez-Mendiola,Martha; Arias-Castro,Carlos; Gutiérrez-Miceli,Federico Antonio; Palomeque-Dominguez,Héctor; Rincón-Rosales,Reiner. ABSTRACT The effect of plant growth-promoting bacteria inoculation on plant growth and the sugar content in Agave americana was assessed. The bacterial strains ACO-34A, ACO-40, and ACO-140, isolated from the A. americana rhizosphere, were selected for this study to evaluate their phenotypic and genotypic characteristics. The three bacterial strains were evaluated via plant inoculation assays, and Azospirillum brasilense Cd served as a control strain. Phylogenetic analysis based on the 16S rRNA gene showed that strains ACO-34A, ACO-40 and ACO-140 were Rhizobium daejeonense, Acinetobacter calcoaceticus and Pseudomonas mosselii, respectively. All of the strains were able to synthesize indole-3-acetic acid (IAA), solubilize phosphate, and had nitrogenase... Tipo: Journal article Palavras-chave: Agave; Inoculation; Bacteria; Inulin; 16S rRNA. Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822016000300587 Prevalence and molecular analysis of Anaplasma platys in dogs in Lara, Venezuela Provedor de dados: 58 Autores: Huang,Haibin; Unver,Ahmet; Perez,Miriam J.; Orellana,Nelson G.; Rikihisa,Yasuko. Blood specimens from clinically normal military dogs and their trainers, in Lara, Venezuela were screened for Anaplasma platys, A. phagocytophilum, or Ehrlichia ewingii using 16S rRNA PCR tests. Sixteen percent (7/43) of dog specimens were positive by A. platys PCR test followed by sequencing of the PCR products, and all human blood specimens [25] were negative. All specimens from these dogs and humans were PCR negative for E. ewingii or A. phagocytophilum. Twelve Rhipicephalus sanguineus ticks removed from these dogs were negative for A. platys by reverse transcription PCR test. Almost the entire 16S rRNA gene (1,364 bp) and groESL operon (1,646 bp) sequences of A. platys isolated from a dog were determined, revealing that both sequences were closely... Tipo: Journal article Palavras-chave: 16S rRNA; GroESL operon; Anaplasma platys; Dogs; Venezuela. Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822005000300002 Detection of carboxylesterase and esterase activity in culturable gut bacterial flora isolated from diamondback moth, Plutella xylostella (Linnaeus), from India and its possible role in indoxacarb degradation Provedor de dados: 58 Autores: Ramya,Shanivarsanthe Leelesh; Venkatesan,Thiruvengadam; Srinivasa Murthy,Kottilingam; Jalali,Sushil Kumar; Verghese,Abraham. Abstract Diamondback moth (DBM), Plutella xylostella (Linnaeus), is a notorious pest of brassica crops worldwide and is resistant to all groups of insecticides. The insect system harbors diverse groups of microbiota, which in turn helps in enzymatic degradation of xenobiotic-like insecticides. The present study aimed to determine the diversity of gut microflora in DBM, quantify esterase activity and elucidate their possible role in degradation of indoxacarb. We screened 11 geographic populations of DBM in India and analyzed them for bacterial diversity. The culturable gut bacterial flora underwent molecular characterization with 16S rRNA. We obtained 25 bacterial isolates from larvae (n = 13) and adults (n = 12) of DBM. In larval gut isolates,... Tipo: Journal article Palavras-chave: Plutella xylostella; Bacteria; 16S rRNA; Phylogeny; Carboxylesterase; Indoxacarb. Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822016000200327 Evaluation of bacterial diversity recovered from petroleum samples using different physical matrices Provedor de dados: 58 Autores: Dellagnezze,Bruna Martins; Vasconcellos,Suzan Pantaroto de; Melo,Itamar Soares de; Santos Neto,Eugênio Vaz dos; Oliveira,Valéria Maia 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 methodologies involving DNA extraction from crude oil, microbial enrichments using different culture conditions can be applied as a way to increase the recovery of DNA from environments with 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... Tipo: Journal article Palavras-chave: Bacterial diversity; Microbial enrichment; Petroleum reservoir; Physical support; 16S rRNA. Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822016000300712 Characterization of Leptospira borgpetersenii isolates from field rats (Rattus norvegicus) by 16S rRNA and lipL32 gene sequencing Provedor de dados: 58 Autores: Vedhagiri,Kumaresan; Natarajaseenivasan,Kalimuthusamy; Prabhakaran,Shanmugarajan G.; Selvin,Joseph; Narayanan,Ramasamy; Shouche,Yogesh S.; Vijayachari,Paluru; Ratnam,Sivalingam. The main goal of this study was to evaluate the prevalence of leptospirosis among field rodents of Tiruchirappalli district, Tamil Nadu, India. In total 35 field rats were trapped and tested for seroprevalence by the microscopic agglutination test (MAT). Isolation of leptospires was performed from blood and kidney tissues and characterized to serovar level. Genomospecies identification was carried out using 16S rRNA and lipL32 gene sequencing. The molecular phylogeny was constructed to find out species segregation. Seroprevalence was about 51.4 %, and the predominant serovars were Autumnalis, Javanica, Icterohaemorrhagiae and Pomona. Two isolates from the kidneys were identified as serovar Javanica of Serogroup Javanica, and sequence based molecular... Tipo: Journal article Palavras-chave: Leptospirosis; Leptospira borgpetersenii; LipL32; 16S rRNA. Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822010000100022 Antibacterial activities of multi drug resistant Myroides odoratimimus bacteria isolated from adult flesh flies (Diptera: Sarcophagidae) are independent of metallo beta-lactamase gene Provedor de dados: 58 Autores: Dharne,M.S.; Gupta,A.K.; Rangrez,A.Y.; Ghate,H.V.; Patole,M.S.; Shouche,Y.S. Flesh flies (Diptera: Sarcophagidae) are well known cause of myiasis and their gut bacteria have never been studied for antimicrobial activity against bacteria. Antimicrobial studies of Myroides spp. are restricted to nosocomial strains. A Gram-negative bacterium, Myroides sp., was isolated from the gut of adult flesh flies (Sarcophaga sp.) and submitted to evaluation of nutritional parameters using Biolog GN, 16S rRNA gene sequencing, susceptibility to various antimicrobials by disc diffusion method and detection of metallo β-lactamase genes (TUS/MUS). The antagonistic effects were tested on Gram-negative and Gram-positive bacteria isolated from human clinical specimens, environmental samples and insect mid gut. Bacterial species included were... Tipo: Journal article Palavras-chave: Flesh fly; Myroides sp.; 16S rRNA; Antibacterial activity; Metallo beta-lactamase. Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822008000200035 ANALISIS MOLECULAR EN GASTROPODOS CHILENOS COMERCIALES BASADOS EN LAS SECUENCIAS 16S rRNA,. COI Y ITS1-5.8S rDNA-ITS2 Provedor de dados: 72 Autores: 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 Genetic differentiation of Macrodon ancylodon (Sciaenidae, Perciformes) populations in Atlantic coastal waters of South America as revealed by mtDNA analysis Provedor de dados: 74 Autores: Santos,Simôni; Schneider,Horacio; Sampaio,Iracilda. The king weakfish (pescada-gó in Portuguese - Macrodon ancylodon (Sciaenidae), a demersal (bottom-feeding) species found in South America Atlantic coastal waters from the Gulf of Paria in Venezuela to Baia Blanca in Argentina, is an economically important species because of its abundance and wide acceptance by consumers. Because of its wide distribution this fish may be subject to geographic isolation and this may have resulted in distinct populations along its coastal range. Considering that this species represents an important economic resource, confirmation of whether M. ancylodon is a single species or there are different genetic stocks spread over its wide distribution would be an important contribution to conservation policies and population... Tipo: Journal article Palavras-chave: Macrodon ancylodon; Sciaenidae; Perciformes; 16S rRNA; Cytochrome b; Genetic differentiation. Ano: 2003 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572003000200008 The history of the introduction of the giant river prawn, Macrobrachium cf. rosenbergii (Decapoda, Palaemonidae), in Brazil: new insights from molecular data Provedor de dados: 74 Autores: Iketani,Gabriel; Pimentel,Luciana; Silva-Oliveira,Glaúcia; Maciel,Cristiana; Valenti,Wagner; Schneider,Horacio; Sampaio,Iracilda. The giant river prawn, Macrobrachium cf. rosenbergii, is one of the most cultivated freshwater prawns in the world and has been introduced into more than 40 countries. In some countries, this prawn is considered an invasive species that requires close monitoring. Recent changes in the taxonomy of this species (separation of M. rosenbergii and M. dacqueti) require a re-evaluation of introduced taxa. In this work, molecular analyses were used to determine which of these two species was introduced into Brazil and to establish the geographic origin of the introduced populations that have invaded Amazonian coastal waters. The species introduced into Brazil was M. dacqueti through two introduction events involving prawns originating from Vietnam and either... Tipo: Journal article Palavras-chave: Bioinvasion; Exotic species; Giant river prawn; Macrobrachium dacqueti; COI; 16S rRNA; Amazonia. Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000100025 Development of in situ hybridisation using 16S rRNA gene to monitor black-lip pearl oyster, Pinctada margaritifera, larvae in plankton samples Provedor de dados: 5 Autores: 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 The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories Provedor de dados: 5 Autores: Gatesoupe, François-joël; Huelvan, Christine; Le Bayon, Nicolas; Le Delliou, Herve; Madec, Lauriane; Mouchel, Olivier; Quazuguel, Patrick; Mazurais, David; Zambonino, Jose-luis. Background The better understanding of how intestinal microbiota interacts with fish health is one of the key to sustainable aquaculture development. The present experiment aimed at correlating active microbiota associated to intestinal mucosa with Specific Growth Rate (SGR) and Hypoxia Resistance Time (HRT) in European sea bass individuals submitted to different nutritional histories: the fish were fed either standard or unbalanced diets at first feeding, and then mixed before repeating the dietary challenge in a common garden approach at the juvenile stage. Results A diet deficient in essential fatty acids (LH) lowered both SGR and HRT in sea bass, especially when the deficiency was already applied at first feeding. A protein-deficient diet with high... Tipo: Text Palavras-chave: Host-microbe interaction; 16S rRNA; Pyrosequencing; Autochthonous bacteria; Alternative feed ingredients; Physiological status. Ano: 2016 URL: http://archimer.ifremer.fr/doc/00356/46719/46590.pdf Archaeal Methane Cycling Communities Associated with Gassy Subsurface Sediments of Marennes-Oleron Bay (France) Provedor de dados: 5 Autores: 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 Genetic characterisation of oyster populations along the north-eastern coast of Tunisia Provedor de dados: 5 Autores: 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 Phylogenetic characterization of the bacterial assemblage associated with mucous. secretions of the hydrothermal vent polychaete Paralvinella palmiformis Provedor de dados: 5 Autores: 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: http://archimer.ifremer.fr/doc/2002/publication-661.pdf A dual symbiosis shared by two mussel species, Bathymodiolus azoricus and Bathymodiolus puteoserpentis (Bivalvia : Mytilidae), from hydrothermal vents along the northern Mid-Atlantic Ridge Provedor de dados: 5 Autores: 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 Presence and activity of anaerobic ammonium-oxidizing bacteria at deep-sea hydrothermal vents Provedor de dados: 5 Autores: Byrne, Nathalie; Strous, Marc; Crepeau, Valentin; Kartal, Boran; Birrien, Jean-louis; Schmid, Markus; Lesongeur, Francoise; Schouten, Stefan; Jaeschke, Andrea; Jetten, Mike; Prieur, Daniel; Godfroy, Anne. Recent studies indicate that ammonia is an important electron donor for the oxidation of fixed nitrogen, both in the marine water column and sediments. This process, known as anammox, has so far only been observed in a large range of temperature habitats. The present study investigated the role of anammox in hydrothermal settings. During three oceanographic expeditions to the Mid-Atlantic Ridge, hydrothermal samples were collected from five vent sites, at depths ranging from 750 to 3650m from cold to hot habitats. Evidence for the occurrence of anammox in these particular habitats was demonstrated by concurrent surveys, including the amplification of 16S rRNA gene sequences related to known anammox bacteria, ladderanes lipids analysis and measurement of a... Tipo: Text Palavras-chave: Hydrothermal vent; Ladderanes; 16S rRNA; Activity; Micro organisms; Anammox. Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6921.pdf Integrating molecular identification of pelagic eggs with geostatistical mapping to improve the delineation of North Sea fish spawning grounds Provedor de dados: 5 Autores: 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 Approches culturales et moléculaires des assemblages microbiens associés aux polychètes hydrothermaux de la famille Alvinellidae Provedor de dados: 5 Autores: 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 Cyanobacterial populations that build 'kopara' microbial mats in Rangiroa, Tuamotu Archipelago, French Polynesia Provedor de dados: 5 Autores: 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 Symbioses bactériennes de bivalves mytilidés associés aux sources de fluides en domaine océanique profond : diversité, rôle nutritionnel et influence de l'environnement Provedor de dados: 5 Autores: Duperron, Sebastien. Symbiotic associations between chemosynthetic bacteria and invertebrates are one of the major sources of primary production in deep-sea chemosynthesis-based ecosystems. Mussels of the genus Bathymodiolus (Bivalvia: Mytilidae) occur worldwide and can dominate the animal community at methane-rich cold seeps and sulfide-rich hydrothermal vents. Some species are associated with both sulfide-oxidizing and methanotrophic bacteria. These mussels are thus a good model for studying the diversity, role and ecology of multiple symbiotic associations, which are still poorly understood. For the present study, several species of mytilids were collected from seep and vent sites situated at depths from 850 to 3300 meters using submersibles. Symbiotic bacteria associated... Tipo: Text Palavras-chave: Mid Atlantic Ridge Eastern Mediterranean Gulf of Guinea Gulf of Mexico Chemosynthesis Hydrothermal vents Cold seeps Lipid analysis Stable isotopes CFB; 16S rRNA; APS; RubisCO; PmoA Methylotrophic bacteria Methanotrophic bacteria Sulfide oxidizing bacteria Idas Bathymodiolus Symbiosis Chimiosynthèse Sources hydrothermales Sources de fluides froids Analyse lipidique Isotopes stables Ride Médio Atlantique Méditerranée orientale Golfe de Guinée Golfe du Mexique CFB; ARNr 16S; APS; RubisCO; PmoA Bactéries méthylotrophes Bactéries méthanotrophes Bactéries sulfoxydantes Idas Bathymodiolus Symbiose. Ano: 2005 URL: http://archimer.ifremer.fr/doc/2005/these-2082.pdf Search for localized dysbiosis in Crohn's disease ulcerations by temporal temperature gradient gel electrophoresis of 16S rRNA Provedor de dados: 189 Autores: Seksik, P.; Lepage, P.; de la Cochetière, M.F.; Bourreille, A.; Sutren, M.; Galmiche, J.P.; Dore, J.; Marteau, P. The mucosa-associated microbiota lining the gut epithelium might play a central role in the activation and/or perpetuation of mucosal inflammation in Crohn's disease (CD). We sought for localized dysbiosis by comparing the biodiversity and composition of the microbiotas in ulcerated and nonulcerated mucosal samples from patients with CD. Biopsy samples (n = 75) of ulcerated and adjacent nonulcerated mucosa were collected during colonoscopy from 15 patients, from the ileum, right colon, left colon, and rectum. Temporal temperature gradient gel electrophoresis (TTGE) of bacterial 16S rRNAs was used to evaluate the dominant bacterial species. TTGE profiles were compared using software that calculates similarity percentages. For a given patient, average... Tipo: Journal Article Palavras-chave: CROHN'S DISEASE; INTESTINAL MUCOSA; INTESTINAL MICROBIOTA; TTGE; 16S rRNA. Ano: 2005 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD200880737e8&uri=/notices/prodinra1/2008/06/ Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study Provedor de dados: 189 Autores: 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/ Temperature gradient gel electrophoresis of fecal 16S rRNA reveals active Escherichia coli in the microbiota of patients with ulcerative colitis Provedor de dados: 189 Autores: Sokol, H.; Lepage, P.; Seksik, P.; Dore, J.; Marteau, P. Previous studies of the endogenous microbiota in patients with ulcerative colitis (UC) have not taken bacterial activity into account, yet bacteria with high transcriptional activity might have a more important pathophysiological role than inactive bacteria. We therefore analyzed the biodiversity of active bacteria in the fecal microbiota of UC patients, in comparison with that of healthy subjects. Feces were collected from nine patients with active UC and from nine healthy controls. Total DNA and RNA were extracted, and 16S ribosomal DNA and RNA were amplified by PCR and reverse transcription-PCR, respectively. Amplification products were compared by means of temporal temperature gradient gel electrophoresis (TTGE). Bands of interest were excised,... Tipo: Journal Article Palavras-chave: TTGE; ULCERATIVE COLITIS; FAECAL MICROBIOTA; 16S rRNA; PCR; BIODIVERSITY MODULATION. Ano: 2006 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2008e5b8f7c7&uri=/notices/prodinra1/2008/06/ Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach Provedor de dados: 189 Autores: Manichanh, C.; Rigottier-Gois, L.; Bonnaud, E.; Gloux, K.; Pelletier, E.; Frangeul, F.; Nalin, R.; Jarrin, C.; Chardon, P.; Marteau, P.; Roca, J.; Dore, J. Tipo: Journal Article Palavras-chave: CROHN'S DISEASE; METAGENOME; FAECAL MICROBIOTA; PHYLOGENY; FIRMICUTES; 16S rRNA; FLUORESCENT IN SITU HIBRIDIZATION. Ano: 2006 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD200817f5550b&uri=/notices/prodinra1/2009/11/ Hierarchical analysis of mtDNA variation and the use of mtDNA for isopod (Crustacea: Peracarida: Isopoda) systematics Provedor de dados: 16 Autores: 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 Dual Presence of Anaplasma phagocytophilum and Its Closely Related Anaplasma sp. in Ixodid Ticks in Hokkaido, Japan, and Their Specific Molecular Detection Provedor de dados: 19 Autores: 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 Molecular analysis of the bacterial diversity in a specialized consortium for diesel oil degradation Provedor de dados: 90 Autores: Paixão,Douglas Antonio Alvaredo; Dimitrov,Mauricio Rocha; Pereira,Rodrigo Matheus; Accorsini,Fábio Raphael; Vidotti,Maria Benincasa; Lemos,Eliana Gertrudes de Macedo. Diesel oil is a compound derived from petroleum, consisting primarily of hydrocarbons. Poor conditions in transportation and storage of this product can contribute significantly to accidental spills causing serious ecological problems in soil and water and affecting the diversity of the microbial environment. The cloning and sequencing of the 16S rRNA gene is one of the molecular techniques that allows estimation and comparison of the microbial diversity in different environmental samples. The aim of this work was to estimate the diversity of microorganisms from the Bacteria domain in a consortium specialized in diesel oil degradation through partial sequencing of the 16S rRNA gene. After the extraction of DNA metagenomics, the material was amplified by... Tipo: Journal article Palavras-chave: PCR; Cloning; 16S rRNA; Metagenomics; Soil; Biosurfactants. Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-06832010000300019