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Search Results: 1 - 10 of 41107 matches for " 16S rDNA "
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Phylogeny of the Order Bacillales inferred from 3’ 16S rDNA and 5’ 16S-23S ITS nucleotide sequences  [PDF]
Sabarimatou Yakoubou, Dong Xu, Jean-Charles C?té
Natural Science (NS) , 2010, DOI: 10.4236/ns.2010.29121
Abstract: A short 220 bp sequence was used to study the taxonomic organization of the bacterial Order Bacillales. The nucleotide sequences of the 3’ end of the 16S rDNA and the 16S-23S Internal transcribed spacer (ITS) were determined for 32 Bacillales species and strains. The data for 40 additional Bacillales species and strains were retrieved directly from Genbank. Together, these 72 Bacillales species and strains encompassed eight families and 21 genera. The 220 bp se- quence used here covers a conserved 150 bp sequence located at the 3’ end of the 16S rDNA and a conserved 70 bp sequence located at the 5’ end of the 16S-23S ITS. A neighbor-joining phylogenetic tree was inferred from comparative analyses of all 72 nucleotide sequences. Eight major Groups were revealed. Each Group was sub-divided into sub-groups and branches. In general, the neighbor-joining tree presented here is in agreement with the currently accepted phylogeny of the Order Bacillales based on phenotypic and genotypic data. The use of this 220 bp sequence for phylogenetic analyses presents several advantages over the use of the entire 16S rRNA genes or the generation of extensive phenotypic and genotypic data. This 220 bp sequence contains 150 bp at the 3’ end of the 16S rDNA which allows discrimination among distantly related species and 70 bp at the 5’ end of the 16S-23S ITS which, owing to its higher percentage of nucleotide sequence divergence, adds discriminating power among closely related species from same genus and closely related genera from same family. The method is simple, rapid, suited to large screening programs and easily accessible to most laboratories.
Assessment of a short phylogenetic marker based on comparisons of 3’ end 16S rDNA and 5’ end 16S-23S ITS nucleotide sequences of the Bacillus cereus group  [PDF]
Sabarimatou Yakoubou, Jean-Charles C?té
Natural Science (NS) , 2010, DOI: 10.4236/ns.2010.210138
Abstract: A short phylogenetic marker previously used in the reconstruction of the Order Bacillales and the genus Bacillus was assessed here at a lower taxa level: species in the Bacillus cereus group: B. anthracis, B. cereus, B. thuringiensis and B. weihenstephanensis. This maker is 220 bp in length. It is a combination of 150 bp at the 3’ end of the 16S rDNA and 70 bp at the 5’ end of the 16S-23S ITS sequence. Three additional Bacillus species, B. halodurans, B. licheniformis and B. subtilis, and Clostridium tetani were included for comparison purposes. A total of eight bacterial species and 12 strains were analyzed. A boot- strapped neighbor-joining tree was inferred from comparative analyses of all allelic sequences of the bacterial species and strains under study. Based on its topology, four major Groups were revealed at the 90% nucleotide sequence identities, Group I to IV. Group I contains all al-leles of the Bacillus cereus group. Group II con-tains all alleles of B. halodurans. Group III con-tains all alleles of B. licheniformis and B. subtilis. Group IV contains all alleles of Clostridium tetani. The 220 bp phylogenetic marker used here could resolve different species from different genera. At the genus level, distant species could be dis-tinguished. Very closely-related species, however, were undistinguishable. Species in the B. cereus group, most notably B. cereus, B. anth- racis and B. thuringiensis, could not be distin- guished. After successfully inferring the phylo- genies of the Order Bacillales and the genus Bacillus, we have met the resolving limit of this short phy-logenetic marker: B. cereus, B. anthracis and B. thuringiensis.
Phylogeny of the Order Bacillales inferred from 3’ 16S rDNA and 5’ 16S-23S ITS nucleotide sequences  [PDF]
Sabarimatou Yakoubou,Dong Xu,Jean-Charles C?té
Natural Science (NS) , 2010, DOI: 10.4236/ns.2009.29121
Abstract: A short 220 bp sequence was used to study the taxonomic organization of the bacterial Order Bacillales. The nucleotide sequences of the 3’ end of the 16S rDNA and the 16S-23S Internal transcribed spacer (ITS) were determined for 32 Bacillales species and strains. The data for 40 additional Bacillales species and strains were retrieved directly from Genbank. Together, these 72 Bacillales species and strains encompassed eight families and 21 genera. The 220 bp se- quence used here covers a conserved 150 bp sequence located at the 3’ end of the 16S rDNA and a conserved 70 bp sequence located at the 5’ end of the 16S-23S ITS. A neighbor-joining phylogenetic tree was inferred from comparative analyses of all 72 nucleotide sequences. Eight major Groups were revealed. Each Group was sub-divided into sub-groups and branches. In general, the neighbor-joining tree presented here is in agreement with the currently accepted phylogeny of the Order Bacillales based on phenotypic and genotypic data. The use of this 220 bp sequence for phylogenetic analyses presents several advantages over the use of the entire 16S rRNA genes or the generation of extensive phenotypic and genotypic data. This 220 bp sequence contains 150 bp at the 3’ end of the 16S rDNA which allows discrimination among distantly related species and 70 bp at the 5’ end of the 16S-23S ITS which, owing to its higher percentage of nucleotide sequence divergence, adds discriminating power among closely related species from same genus and closely related genera from same family. The method is simple, rapid, suited to large screening programs and easily accessible to most laboratories.
Molecular Characterization of Pseudomonas spp. Isolated from Root Nodules of Various Leguminous Plants of Shekhawati Region, Rajasthan, India  [PDF]
Sakshi Issar, Saroj Sharma, Devendra Kumar Choudhary, Hemant Kumar Gautam, R. K. Gaur
American Journal of Plant Sciences (AJPS) , 2012, DOI: 10.4236/ajps.2012.31005
Abstract: Plant growth promontory Pseudomonas strains were isolated from root nodules of five plant species, viz., Trifolium pretense, Cicer arietinum, Amaranthus polygamus, Vigna mungo, and Trigonella foenum; that plants were denizen of Shekhawati region of Rajasthan. A total of 8 bacterial isolates were evaluated for growth promotion using PGP properties. Partial 16S rDNA sequencing data showed that these 8 bacterial isolates belonged to genus Pseudomonas. MEGA 4.0.2, software was used to construct a neighbor joining tree by employing boot strap method. Result exhibited significant diversity among recovered Pseudomonas strains.
Genetic Diversity of Marine and Fresh Water Cyanobacteria from the Gujarat State of India  [PDF]
Nilkanth Faldu, Shivani Patel, Nutan Prakash Vishwakarma, Anil Kumar Singh, Khushbu Patel, Neepa Pandhi
Advances in Bioscience and Biotechnology (ABB) , 2014, DOI: 10.4236/abb.2014.514121
Abstract: Cyanobacteria from habitats within Gujarat have been poorly studied with regard to their diversity. In the present investigation eight morphologically distinct cyanobacterial isolates were obtained and characterized from the fresh water and marine habitats. Identification was performed based on morphological features and on 16S rDNA sequences analysis. A phylogenetic tree based on 16S rDNA sequence of cyanobacterial isolates was prepared. Phylogenetic analysis clustered the eight morphologically distinct isolates into two distinct groups thus highlighting the importance of both morphological and genetic methods in studying cyanobacterial diversity.
一株产纤维素酶甲醇耐受细菌的分离与鉴定
Separation and Identification of a Bacterum Which Can Produce Cellulase and Tolerate Methanol
 [PDF]

嵇朝球, 祁鹏飞, 裴坤, 马中良
Hans Journal of Chemical Engineering and Technology (HJCET) , 2016, DOI: 10.12677/HJCET.2016.66023
Abstract:
当今时代,生物能源已经成为一种绿色经济的能源。为了更有效地利用纤维素,在这项研究中,自江苏盐城工业园区采集的土样中分离到一株既可耐受甲醇,又可产生高活性纤维素酶的细菌。通过16S rDNA序列分析,构建系统发育树,该菌株与巨大芽孢杆菌(B. megaterium)相似性为99.7%。甲醇耐受实验表明,菌株具有较高的甲醇耐受,甚至能在11.85%甲醇的M9培养基中生长。
Bioenergy is a green and economic energy in modern times. To have Celluose used more efficiently, in this study, from soil samples in Yancheng Industrial Park of Jiangsu, we isolated a bacterium that cannot only grow in the presence of methanol, but also produce higher activity cellulase Provice. By sequencing analysis of 16S rDNA, the phylogenetic tree was constructed, and the similarity between the strain and B. megaterium was 99.7%. The testing of tolerance in methanol showed that the strains had higher tolerance of methanol and could even grow in the M9 medium with 11.85% methanol.
Applicability of PCR-DGGE and 16S rDNA Sequencing for Microbiological Analysis of Otitis Media with Effusion  [PDF]
Priit Kasen?mm, Jelena ?t?epetova
International Journal of Otolaryngology and Head & Neck Surgery (IJOHNS) , 2012, DOI: 10.4236/ijohns.2012.13015
Abstract: Background: The aim of the study was to analyze the performance of PCR-DGGE based assay and its applicability as a tool for the identification of bacteria in the middle ear of children with otitis media with effusion (OME). Methods: The middle ear effusions from 20 children with OME were analyzed both by bacterial culture and by 16S rDNA-gene-targeted PCR assay, DGGE fingerprinting and sequencing analysis. Results: In bacterial culture assay, only three middle ear effusions (15%) showed bacterial growth. None of the samples were positive for anaerobic culture. The PCR assay with 16S rDNA-gene-targeted universal primers was positive in 10 (50%) cases. The subsequent DGGE fingerprinting and 16S rDNA sequencing analysis revealed that the most commonly encountered bacteria in the middle ear effusions of children with OME are Haemophilus influenzae, Alloiococcus otitidis and Bacteroides spp. Conclusions: The present study demonstrated the applicability of PCR-DGGE based assay and 16S rDNA sequencing for analyzing of bacterial diversity in the middle ear effusion of children OME. The results of our study may contribute to a better understanding of the etiology of OME.
Application of PCR primer sets for detection of Pseudomonas sp. functional genes in the plant rhizosphere  [PDF]
Jong-Shik Kim, Pauline M. Mele, David E. Crowley
Journal of Agricultural Chemistry and Environment (JACEN) , 2013, DOI: 10.4236/jacen.2013.21002
Abstract: Plant growth promoting pseudomonads play an important role in disease suppression and there is considerable interest in development of bio-marker genes that can be used to monitor these bacteria in agricultural soils. Here, we report the application ofa PCR primer sets targeting genes encoding the main antibiotic groups. Distribution of the genes was variably distributed across type strains of 28 species with no phylogenetic groupingfor the detected antibioticsgenes, phlD for 2,4-diacetylphloroglucinol (2,4-DAPG) and phzCD for phenazine-1-carboxylic acid or hcnBC for hydrogen cyanide production. Analysis of field soils showed that primer sets for phlD and phzCD detected these genes in a fallowed neutral pH soil following wheat production, but that the copy numbers were below the detection limits in bulk soils having an acidic pH. In contrast, PCR products for the phzCD, pltc and hcnBc genes were detectable in mature root zones following plantingwith wheat. The ability to rapidly characterize populations of antibiotics producers using specific primer sets will improve our ability to assess the impacts of management practices on the functional traits of Pseudomonas spp. populations in agricultural soils.
Bacterial Biofilm in Water Bodies of Cherrapunjee: The Rainiest Place on Planet Earth  [PDF]
Subhro Banerjee, Sudha Rai, Barnali Sarma, Santa Ram Joshi
Advances in Microbiology (AiM) , 2012, DOI: 10.4236/aim.2012.24060
Abstract: Bacterial attachment is influenced by the cell surface, attachment media and other environmental factors. Bacterial community composition involved in biofilm formation in extremely high rainfall areas like Cherrapunjee has not been reported. The present study was undertaken to characterize bacteria involved in biofilm formation on different substrata in water bodies of Cherrapunjee, the highest rainfall receiving place on planet earth and to assess if the continuous rainfall has an effect on nature and colonization of biofilm bacteria. We developed the biofilm bacteria on stainless steel and glass surfaces immersed in water bodies of the study sites. Isolation of biofilm bacteria were performed on different culture media followed by estimation of protein and carbohydrate content of bacterial exopolysaccharides. 16S rRNA gene sequences were amplified for molecular characterization. The results showed that the biofilm bacterial diversity in water bodies of Cherrapunjee was influenced by substratum and was observed more in stainless steel than glass surface. Scanning electron microscopy images revealed that biofilm microstructure may represent a key determinant of biofilm growth and physiology of associated bacteria. The overall protein content of the extracted EPS of all the isolates were relatively higher than the carbohydrate content. Diverse bacteria proliferated on the substrata regardless of each other's presence, with more diverse bacteria colonizing the substrata on 7th day compared to 15th day of incubation. The biofilm bacteria compositions in the highest rainfall receiving habitat were not distinctly different from reports available, hence not unique from other water bodies.
The use of 16s rDNA methods in soil microbial ecology
Macrae, Andrew;
Brazilian Journal of Microbiology , 2000, DOI: 10.1590/S1517-83822000000200002
Abstract: new and exciting molecular methods, many using the 16s small sub-unit ribosomal nucleic acid molecule, are opening the microbial "black box" in soil. these studies have added much to our knowledge of microbial diversity in soils, and are beginning to advance our understanding of the relationship between this diversity and its function in soil processes. over the next few years, the knowledge gained from molecular studies will, we hope, lead to improvements in sustainable land management and sustainable exploitation of soil genetic resources. as we enter the third millenium, it is appropriate to review the application of 16s rdna methods to soil microbiology. this review examines 16s ribosomal dna (rdna) methods and their application to soil. it mentions their limits and suggests how they may be applied in the future.
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