scholarly journals Relatedness of Chromosomal and Plasmid DNAs of Erwinia pyrifoliae and Erwinia amylovora

2002 ◽  
Vol 68 (12) ◽  
pp. 6182-6192 ◽  
Author(s):  
Gayle C. McGhee ◽  
Elise L. Schnabel ◽  
Kimberly Maxson-Stein ◽  
Beatrix Jones ◽  
Verlyn K. Stromberg ◽  
...  
Keyword(s):  
Erwinia Amylovora ◽  
Bacterial Species ◽  
Its Region ◽  
Nucleotide Composition ◽  
Molecular Properties ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Probe ◽  
Separate Species ◽  
Hybridization Data

ABSTRACT The plant pathogen Erwinia pyrifoliae has been classified as a separate species from Erwinia amylovora based in part on differences in molecular properties. In this study, these and other molecular properties were examined for E. pyrifoliae and for additional strains of E. amylovora, including strains from brambles (Rubus spp.). The nucleotide composition of the internal transcribed spacer (ITS) region was determined for six of the seven 16S-23S rRNA operons detected in these species with a 16S rRNA gene probe. Each species contained four operons with a tRNAGlu gene and two with tRNAIle and tRNAAla genes, and analysis of the operons from five strains of E. amylovora indicated a high degree of ITS variability among them. One tRNAGlu-containing operon from E. pyrifoliae Ep1/96 was identical to one in E. amylovora Ea110, but three tRNAGlu operons and two tRNAIle and tRNAAla operons from E. pyrifoliae contained unique nucleotide changes. When groEL sequences were used for species-specific identification, E. pyrifoliae and E. amylovora were the closest phylogenetic relatives among a set of 12 bacterial species. The placement of E. pyrifoliae distinct from E. amylovora corroborated molecular hybridization data indicating low DNA-DNA similarity between them. Determination of the nucleotide sequence of plasmid pEP36 from E. pyrifoliae Ep1/96 revealed a number of presumptive genes that matched genes previously found in pEA29 from E. amylovora and similar organization for the genes and origins of replication. Also, pEP36 and pEA29 were incompatible with clones containing the reciprocal origin regions. Finally, the ColE1-like plasmid pEP2.6 from strain Ep1/96 contained sequences found in small plasmids in E. amylovora strains IL-5 and IH3-1.

Characterization of root-associated bacterial species of Leklek variety of common bean (Phaseolus sp.)

2021 ◽  
Vol 26 (5) ◽  
pp. 3008-3013
Author(s):  
DİLEK TEKDAL ◽  
◽  
İLKNUR AKÇA ◽  
ASLI KÜÇÜKRECEP ◽  
SELİM ÇETİNER ◽  
...  
Keyword(s):  
Common Bean ◽  
Ribosomal Rna ◽  
Root Nodules ◽  
Bacterial Species ◽  
Its Region ◽  
23S Rrna ◽  
Nodule Formation ◽  
Rrna Gene ◽  
Microbacterium Paraoxydans ◽  
23S Ribosomal Rna

The common bean is a valuable food source in the human diet. Leklek is a local variety of common bean (Phaseolus sp.) widely grown in Mersin's Gülnar district, but little is known about this variety. In the present study, bacterial species from root nodules of this common bean variety were identified by PCR-amplified 16S ribosomal RNA (rRNA) gene and 16S-23S ribosomal RNA (rRNA) Internal Transcribed Spacer (ITS) region and sequencing. The partial 16S rRNA gene and 16S-23S rRNA ITS region sequences were submitted to the NCBI database (accession numbers MT967369, MT968518, respectively). Amplified sequences were used to construct a phylogenetic tree. Phylogenetic analysis based on the identified sequences showed that the isolate belonged to the genus Microbacterium and was closely related to Microbacterium paraoxydans. The findings presented here will provide a clue for understanding this bacterium's role in nodule formation in Phaseolus sp. (variety Leklek).

scholarly journals Mobile Elements in a Single-Filament Orange Guaymas Basin Beggiatoa (“Candidatus Maribeggiatoa”) sp. Draft Genome: Evidence for Genetic Exchange with Cyanobacteria

2013 ◽  
Vol 79 (13) ◽  
pp. 3974-3985 ◽  
Author(s):  
Barbara J. MacGregor ◽  
Jennifer F. Biddle ◽  
Andreas Teske
Keyword(s):  
Gulf Of California ◽  
Bacterial Species ◽  
Draft Genome ◽  
Genetic Exchange ◽  
23S Rrna ◽  
Rrna Gene ◽  
Homing Endonucleases ◽  
Guaymas Basin ◽  
Content Type ◽  
Group I

ABSTRACTThe draft genome sequence of a single orangeBeggiatoa(“CandidatusMaribeggiatoa”) filament collected from a microbial mat at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) shows evidence of extensive genetic exchange with cyanobacteria, in particular for sensory and signal transduction genes. A putative homing endonuclease gene and group I intron within the 23S rRNA gene; several group II catalytic introns; GyrB and DnaE inteins, also encoding homing endonucleases; multiple copies of sequences similar to thefdxNexcision elements XisH and XisI (required for heterocyst differentiation in some cyanobacteria); and multiple sequences related to an open reading frame (ORF) (00024_0693) of unknown function all have close non-Beggiatoaceaematches with cyanobacterial sequences. Sequences similar to the uncharacterized ORF and Xis elements are found in otherBeggiatoaceaegenomes, a variety of cyanobacteria, and a few phylogenetically dispersed pleiomorphic or filamentous bacteria. We speculate that elements shared among filamentous bacterial species may have been exchanged in microbial mats and that some of them may be involved in cell differentiation.

scholarly journals Comparison of Genospecies and Antimicrobial Resistance Profiles of Isolates in the Acinetobacter calcoaceticus-Acinetobacter baumannii Complex from Various Clinical Specimens

2012 ◽  
Vol 56 (12) ◽  
pp. 6267-6271 ◽  
Author(s):  
Ni Tien ◽  
Bang-Jau You ◽  
Hui-Lan Chang ◽  
Hsiu-Shen Lin ◽  
Chin-Yi Lee ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Acinetobacter Baumannii ◽  
Restriction Analysis ◽  
Acinetobacter Calcoaceticus ◽  
Its Region ◽  
Clinical Isolates ◽  
23S Rrna ◽  
Rrna Gene ◽  
Genotype 3 ◽  
Content Type

ABSTRACTThis study was conducted to compare the prevalences of antimicrobial resistance profiles of clinical isolates in theAcinetobacter calcoaceticus-Acinetobacter baumanniicomplex from sterile and nonsterile sites and to further study the relationship of antimicrobial resistance profiles and genospecies by amplified rRNA gene restriction analysis (ARDRA). A total of 1,381 isolates were tested with 12 different antibiotics to show their antimicrobial susceptibility profiles. A total of 205 clinical isolates were further analyzed by ARDRA of the intergenic spacer (ITS) region of the 16S-23S rRNA gene. It was found that the overall percentage of isolates from nonsterile sites (urine, sputum, pus, or catheter tip) that were resistant to the 12 antibiotics tested was significantly higher than that of isolates from sterile sites (cerebrospinal fluid [CSF], ascites fluid, and bloodstream) (46% versus 22%;P< 0.05). After ARDRA, it was found that 97% of the 62 isolates resistant to all antibiotics tested were theA. baumanniigenospecies, which was identified in only 31% of the isolates susceptible to all antibiotics tested. More genospecies diversity was identified in the isolates susceptible to all antibiotics tested, including genospecies of 13TU (34%), genotype 3 (29%), andA. calcoaceticus(5%). Furthermore, as 91% (10/11) of the isolates from CSF were susceptible to all antibiotics tested, theA. calcoaceticus-A. baumanniicomplex isolates with multidrug resistance could be less invasive than the more susceptible isolates. This study also indicated current emergence of carbapenem-, fluoroquinolone-, aminoglycoside-, and cephalosporin-resistantA. calcoaceticus-A. baumanniicomplex isolates in Taiwan.

Variations in the 16S–23S rRNA internal transcribed spacer of fibrolytic Butyrivibrio isolates from the reindeer rumen

2011 ◽  
Vol 57 (7) ◽  
pp. 617-622 ◽  
Author(s):  
Kirsti E. Præsteng ◽  
Roderick I. Mackie ◽  
Isaac K.O. Cann ◽  
Svein D. Mathiesen ◽  
Monica A. Sundset
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rangifer Tarandus ◽  
Its Region ◽  
16S Rrna Gene Sequencing ◽  
23S Rrna ◽  
Rrna Gene ◽  
Its Sequence ◽  
Neighbor Joining ◽  
Phylogenetic Neighbor

Strains of Butyrivibrio are principal cellulytic bacteria in the rumen of the High Arctic Svalbard reindeer ( Rangifer tarandus platyrhynchus ). According to phylogenetic analysis based on 16S rRNA gene sequencing, Butyrivibrio can be divided into three subgroups within the Clostridia class of the phylum Firmicutes, but the current phenotypic and genotypic differentiation within the family Lachnospiraceae is insufficient. This current study describes the sequence diversity of the 16S–23S rRNA intergenic transcribed spacer (ITS) region of Butyrivibrio isolates from reindeer. A total of 17 different ITS sequences with sizes between 449 and 784 nt were obtained. Genes encoding tRNAIle and tRNAAla were identified in four of the sequences. Phylogenetic neighbor-joining trees were constructed based on the ITS sequence and compared with a phylogenetic neighbor-joining tree based on 16S rRNA gene sequences previously obtained for the same isolates. These comparisons indicated a better differentiation between strains in the ITS sequence than the 16S rRNA gene based tree. Through this study, a better means for identifying and tracking fibrolytic and potentially probiotic Butyrivibrio strains in reindeer and other ruminants has been provided.

scholarly journals Motilimonas cestriensis sp. nov., isolated from an inland brine spring in Northern England

2021 ◽  
Author(s):  
Matthew Kelbrick ◽  
Raeid M. M. Abed ◽  
André Antunes
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Separate Species ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Hybridization Data ◽  
Physiological And Biochemical Characteristics ◽  
Brine Sample

A novel slightly halophilic Gram-stain-negative bacterial strain (MKS20T) was isolated from a brine sample collected from one of the Anderton brine springs in the Cheshire salt district, located in Northern England. Phylogenetic analysis of the 16S rRNA gene sequence revealed a close proximity to Motilimonas eburnea (98.30 %), followed by Motilimonas pumila (96.62 %), the two currently described species within the genus Motilimonas . Strain MKS20T forms white-beige-pigmented colonies and grows optimally at 28–30 °C, in 1–3 % (w/v) NaCl and at pH 7–7.5. The strain was facultatively anaerobic and showed a broader range of carbohydrate use than other species in the genus Motilimonas . Q-8 was the sole respiratory quinone and the major fatty acids (>10 %) were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and C16 : 0. The polar lipid profile included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyglycerol and several unidentified lipids. The G+C content of the genomic DNA was 44.2 mol%. Average nucleotide identity and DNA–DNA hybridization data were consistent with assignment to a separate species. Based on the phylogenetic and genomic-based analyses, as well as physiological and biochemical characteristics, we propose that strain MKS20T (=DSM 109936T, MCCC 1K04071T) represents a new species of the genus Motilimonas , with the name Motilimonas cestriensis sp. nov.

scholarly journals Effect of Incubation Temperature on the Detection of Thermophilic Campylobacter Species from Freshwater Beaches, Nearby Wastewater Effluents, and Bird Fecal Droppings

2013 ◽  
Vol 79 (24) ◽  
pp. 7639-7645 ◽  
Author(s):  
Izhar U. H. Khan ◽  
Stephen Hill ◽  
Eva Nowak ◽  
Thomas A. Edge
Keyword(s):  
Surface Water ◽  
Large Scale ◽  
Incubation Temperature ◽  
Its Region ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
C 32 ◽  
Species Specific ◽  
Incubation Temperatures

ABSTRACTThis large-scale study compared incubation temperatures (37°C versus 42°C) to study the detection of thermophilicCampylobacterspecies, includingCampylobacter jejuni,C. coli, andC. lari, in various surface water samples and bird fecal droppings around Hamilton Harbor, Lake Ontario. The putative culture isolates obtained from incubation temperatures of 37 and 42°C were confirmed byCampylobactergenus- and species-specific triplex PCR assays targeting the 16S rRNA gene and the 16S-23S rRNA gene internal transcribed spacer (ITS) region. A total of 759 water, wastewater, and bird fecal dropping samples were tested. Positive amplification reactions for the genusCampylobacterwere found for 454 (60%) samples incubated at 37°C, compared to 258 (34%) samples incubated at 42°C.C. jejuni(16%) andC. lari(12%) were detected significantly more frequently at the 42°C incubation temperature than at 37°C (8% and 5%, respectively). In contrast, significantly higher rates ofC. coli(14%) and otherCampylobacterspp. (36%) were detected at the 37°C incubation temperature than at 42°C (8% and 7%, respectively). These results were consistent across surface water, wastewater, and bird fecal dropping samples. At times,Campylobacterspp. were recovered and detected at 37°C (3% forC. jejuni, 10% forC. coli, and 3% forC. lari) when the same samples incubated at 42°C were negative. A significantly higher rate of otherCampylobacterspp. was detected only at 37°C (32%) than only at 42°C (3%). These results indicate that incubation temperature can significantly influence the culturability and detection of thermophilic and other fastidiousCampylobacterspp. and that a comprehensive characterization of theCampylobacterspp. in surface water, wastewaters, or bird fecal droppings will require incubation at both 37 and 42°C.

scholarly journals Isolates of ‘Candidatus Nostocoida limicola’ Blackall et al. 2000 should be described as three novel species of the genus Tetrasphaera, as Tetrasphaera jenkinsii sp. nov., Tetrasphaera vanveenii sp. nov. and Tetrasphaera veronensis sp. nov.

2006 ◽  
Vol 56 (10) ◽  
pp. 2279-2290 ◽  
Author(s):  
C. M. McKenzie ◽  
E. M. Seviour ◽  
P. Schumann ◽  
A. M. Maszenan ◽  
J.-R. Liu ◽  
...  
Keyword(s):  
Type Strain ◽  
Sequence Data ◽  
23S Rrna ◽  
Phenotypic Characterization ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Intergenic Regions ◽  
Single Genus ◽  
Additional Support

Despite differences in their morphologies, comparative analyses of 16S rRNA gene sequences revealed high levels of similarity (>94 %) between strains of the filamentous bacterium ‘Candidatus Nostocoida limicola’ and the cocci Tetrasphaera australiensis and Tetrasphaera japonica and the rod Tetrasphaera elongata, all isolated from activated sludge. These sequence data and their chemotaxonomic characters, including cell wall, menaquinone and lipid compositions and fingerprints of their 16S–23S rRNA intergenic regions, support the proposition that these isolates should be combined into a single genus containing six species, in the family Intrasporangiaceae in the Actinobacteria. This suggestion receives additional support from DNA–DNA hybridization data and when partial sequences of the rpoC1 gene are compared between these strains. Even though few phenotypic characterization data were obtained for these slowly growing isolates, it is proposed, on the basis of the extensive chemotaxonomic and molecular evidence presented here, that ‘Candidatus N. limicola’ strains Ben 17, Ben 18, Ben 67, Ben 68 and Ben 74 all be placed into the species Tetrasphaera jenkinsii sp. nov. (type strain Ben 74T=DSM 17519T=NCIMB 14128T), ‘Candidatus N. limicola’ strain Ben 70 into Tetrasphaera vanveenii sp. nov. (type strain Ben 70T=DSM 17518T=NCIMB 14127T) and ‘Candidatus N. limicola’ strains Ver 1 and Ver 2 into Tetrasphaera veronensis sp. nov. (type strain Ver 1T=DSM 17520T=NCIMB 14129T).

scholarly journals Species-Specific PCR for Identification of Common Contaminant Mollicutes in Cell Culture

2001 ◽  
Vol 67 (7) ◽  
pp. 3195-3200 ◽  
Author(s):  
Fanrong Kong ◽  
Gregory James ◽  
Susanna Gordon ◽  
Anna Zelynski ◽  
Gwendolyn L. Gilbert
Keyword(s):  
16S Rrna ◽  
Cell Cultures ◽  
Bacterial Species ◽  
Intergenic Spacer ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Species Specific

ABSTRACT Mycoplasma arginini, M. fermentans, M. hyorhinis, M. orale, and Acholeplasma laidlawii are the members of the class Mollicutes most commonly found in contaminated cell cultures. Previous studies have shown that the published PCR primer pairs designed to detect mollicutes in cell cultures are not entirely specific. The 16S rRNA gene, the 16S-23S rRNA intergenic spacer region, and the 5′ end of the 23S rRNA gene, as a whole, are promising targets for design of mollicute species-specific primer pairs. We analyzed the 16S rRNA genes, the 16S-23S rRNA intergenic spacer regions, and the 5′ end of the 23S rRNA genes of these mollicutes and developed PCR methods for species identification based on these regions. Using high melting temperatures, we developed a rapid-cycle PCR for detection and identification of contaminant mollicutes. Previously published, putative mollicute-specific primers amplified DNA from 73 contaminated cell lines, but the presence of mollicutes was confirmed by species-specific PCR in only 60. Sequences of the remaining 13 amplicons were identified as those of gram-positive bacterial species. Species-specific PCR primers are needed to confirm the presence of mollicutes in specimens and for identification, if required.

scholarly journals Mycobacterium colombiense sp. nov., a novel member of the Mycobacterium avium complex and description of MAC-X as a new ITS genetic variant

2006 ◽  
Vol 56 (9) ◽  
pp. 2049-2054 ◽  
Author(s):  
Martha I. Murcia ◽  
Enrico Tortoli ◽  
M. Carmen Menendez ◽  
Elia Palenque ◽  
Maria J. Garcia
Keyword(s):  
Mycobacterium Avium ◽  
Gene Sequence ◽  
Restriction Analysis ◽  
Mycolic Acid ◽  
23S Rrna ◽  
Rrna Gene ◽  
The Novel ◽  
Separate Species ◽  
Molecular Approaches ◽  
Species Specific

Forty-five mycobacterial strains isolated from 23 Colombian HIV-positive patients were identified as members of the Mycobacterium avium complex (MAC) and were characterized using different molecular approaches. Seven of the isolates showed characteristic features that allowed them to be differentiated from other members of the complex. The isolates had a novel 16S–23S rRNA internal transcribed spacer (ITS 1) gene sequence which is described as a new sequevar, MAC-X. All of the seven novel isolates gave a positive result with the MAC-specific AccuProbe (Gen-Probe), but tested negative for Mycobacterium avium and Mycobacterium intracellulare species-specific probes (64 and 100 % of the isolates, respectively). The novel isolates could be differentiated phenotypically from other members of the MAC on the basis of the production of urease and by a consistent mycolic acid pattern. The novel isolates shared some characteristics with M. avium, such as the avium variant I (av-I) pattern of the hsp65 gene as determined by PCR restriction analysis and a positive PCR result for the mig (macrophage-induced) gene. However, the novel isolates showed a unique 16S rRNA gene sequence. DNA–DNA relatedness values, from 24 to 44 %, confirmed the distinction of the novel isolates from other members of the MAC at the genetic level and their status as members of a separate species. The novel isolates are proposed as representatives of a novel species, Mycobacterium colombiense sp. nov., that is closely related to M. avium within the MAC. The type strain is 10BT (=CIP 108962T=CECT 3035T).

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