Low genetic diversity amongFrankiaspp. strains nodulating sympatric populations of actinorhizal species of Rosaceae,Ceanothus(Rhamnaceae) andDatisca glomerata(Datiscaceae) west of the Sierra Nevada (California)

2004 ◽  
Vol 50 (12) ◽  
pp. 989-1000 ◽  
Author(s):  
Brian D Vanden Heuvel ◽  
David R Benson ◽  
Esteban Bortiri ◽  
Daniel Potter
Keyword(s):  
Host Specificity ◽  
Sierra Nevada ◽  
Root Nodules ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
Strain Diversity ◽  
Environmental Selection ◽  
Group 1

Frankia spp. strains typically induce N2-fixing root nodules on actinorhizal plants. The majority of host plant taxa associated with the uncultured Group 1 Frankia strains, i.e., Ceanothus of the Rhamnaceae, Datisca glomerata (Datiscaceae), and all actinorhizal members of the Rosaceae except Dryas, are found in California. A study was conducted to determine the distribution of Frankia strains among root nodules collected from both sympatric and solitary stands of hosts. Three DNA regions were examined, the 5' end of the 16S rRNA gene, the internal transcribed spacer region between the 16S and 23S rRNA genes, and a portion of the glutamine synthetase gene (glnA). The results suggest that a narrow range of Group 1 Frankia spp. strains dominate in root nodules collected over a large area of California west of the Sierra Nevada crest with no apparent host-specificity. Comparisons with Group 2 Frankia strain diversity from Alnus and Myrica within the study range suggest that the observed low diversity is peculiar to Group 1 Frankia strains only. Factors that may account for the observed lack of genetic variability and host specificity include strain dominance over a large geographical area, current environmental selection, and (or) a past evolutionary bottleneck.Key words: actinorhizal Rosaceae, Ceanothus, Frankia, Datisca, strain diversity.

scholarly journals Phylogenetic relationships within the family Halomonadaceae based on comparative 23S and 16S rRNA gene sequence analysis

2010 ◽  
Vol 60 (4) ◽  
pp. 737-748 ◽  
Author(s):  
Rafael R. de la Haba ◽  
David R. Arahal ◽  
M. Carmen Márquez ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The Family ◽  
23S Rrna Gene ◽  
Group 2 ◽  
Group 1

A phylogenetic study of the family Halomonadaceae was carried out based on complete 16S rRNA and 23S rRNA gene sequences. Several 16S rRNA genes of type strains were resequenced, and 28 new sequences of the 23S rRNA gene were obtained. Currently, the family includes nine genera (Carnimonas, Chromohalobacter, Cobetia, Halomonas, Halotalea, Kushneria, Modicisalibacter, Salinicola and Zymobacter). These genera are phylogenetically coherent except Halomonas, which is polyphyletic. This genus comprises two clearly distinguished clusters: group 1 includes Halomonas elongata (the type species) and the species Halomonas eurihalina, H. caseinilytica, H. halmophila, H. sabkhae, H. almeriensis, H. halophila, H. salina, H. organivorans, H. koreensis, H. maura and H. nitroreducens. Group 2 comprises the species Halomonas aquamarina, H. meridiana, H. axialensis, H. magadiensis, H. hydrothermalis, H. alkaliphila, H. venusta, H. boliviensis, H. neptunia, H. variabilis, H. sulfidaeris, H. subterranea, H. janggokensis, H. gomseomensis, H. arcis and H. subglaciescola. Halomonas salaria forms a cluster with Chromohalobacter salarius and the recently described genus Salinicola, and their taxonomic affiliation requires further study. More than 20 Halomonas species are phylogenetically not within the core constituted by the Halomonas sensu stricto cluster (group 1) or group 2 and, since their positions on the different phylogenetic trees are not stable, they cannot be recognized as additional groups either. In general, there is excellent agreement between the phylogenies based on the two rRNA gene sequences, but the 23S rRNA gene showed higher resolution in the differentiation of species of the family Halomonadaceae.

scholarly journals Spontaneous Erythromycin Resistance Mutation in a 23S rRNA Gene, rrlA, of the Extreme Thermophile Thermus thermophilus IB-21

2001 ◽  
Vol 183 (14) ◽  
pp. 4382-4385 ◽  
Author(s):  
Steven T. Gregory ◽  
Jamie H. D. Cate ◽  
Albert E. Dahlberg
Keyword(s):  
Genetic Manipulation ◽  
Thermus Thermophilus ◽  
Resistance Mutation ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Erythromycin Resistance ◽  
23S Rrna Gene ◽  
Resistant Mutants ◽  
23S Rrna Genes

ABSTRACT Spontaneous, erythromycin-resistant mutants of Thermus thermophilus IB-21 were isolated and found to carry the mutation A2058G in one of two 23S rRNA operons. The heterozygosity of these mutants indicates that A2058G confers a dominant or codominant phenotype in this organism. This mutation provides a valuable tool for the genetic manipulation of the 23S rRNA genes ofThermus.

Molecular taxonomic reassessment of the Cloud Forest’s Bolitoglossa salamanders (Caudata: Plethodontidae) from Cordillera de Mérida (Mérida state, Venezuela)

Zootaxa ◽  
2012 ◽  
Vol 3356 (1) ◽  
pp. 47 ◽  
Author(s):  
GUSTAVO FERMIN ◽  
JAVIER GARCÍA-GUTIÉRREZ ◽  
MOISÉS ESCALONA ◽  
ANDRÉS MORA ◽  
AMELIA DÍAZ
Keyword(s):  
16S Rrna ◽  
Sierra Nevada ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Morphological Evidence ◽  
Rrna Gene ◽  
Putative Species ◽  
Salamander Species ◽  
The 16S Rrna Gene ◽  
Tissue Digestion

Salamanders found at different localities nearby Mérida city, Venezuela, are thus far reported as Bolitoglossa orestes or B.spongai. However, morphological ambiguities among individuals from several populations of both putative species, besidestheir reported disparate geographical distributions, prompted us to clarify the specific identity of these bolitoglossines throughthe sequence analysis of their corresponding 16S rRNA genes. Seventeen specimens belonging to the vertebrates collection ofUniversidad de Los Andes (CVULA), collected at separated cloud forests in Sierra La Culata (San Eusebio, Macho Capaz andSan Javier del Valle) and Sierra Nevada de Mérida (La Mucuy), were used to extract DNA upon tissue digestion. Sequenceanalysis of the 16S rRNA gene supports a biogeographical scenario where, so far, there is only one salamander species for eachsierra: B. orestes, which is widely distributed in Sierra La Culata, and a so far undescribed species of a Venezuelan bolitogloss-ine apparently restricted to Sierra Nevada de Mérida. Based on our molecular results and an examination of morphological evidence, B. spongai should be considered a synonym of B. orestes.

scholarly journals Diagnosis of Meningococcal Meningitis by Broad-Range Bacterial PCR with Cerebrospinal Fluid

1998 ◽  
Vol 36 (8) ◽  
pp. 2205-2209 ◽  
Author(s):  
Pirkko Kotilainen ◽  
Jari Jalava ◽  
Olli Meurman ◽  
Olli-Pekka Lehtonen ◽  
Esa Rintala ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Bacterial Meningitis ◽  
Bacterial Culture ◽  
Rrna Genes ◽  
23S Rrna ◽  
Acute Bacterial Meningitis ◽  
Rrna Gene ◽  
Gram Staining ◽  
Negative Findings ◽  
New Research

We used broad-range bacterial PCR combined with DNA sequencing to examine prospectively cerebrospinal fluid (CSF) samples from patients with suspected meningitis. Fifty-six CSF samples from 46 patients were studied during the year 1995. Genes coding for bacterial 16S and/or 23S rRNA genes could be amplified from the CSF samples from five patients with a clinical picture consistent with acute bacterial meningitis. For these patients, the sequenced PCR product shared 98.3 to 100% homology with the Neisseria meningitidis sequence. For one patient, the diagnosis was initially made by PCR alone. Of the remaining 51 CSF samples, for 50 (98.0%) samples the negative PCR findings were in accordance with the negative findings by bacterial culture and Gram staining, as well as with the eventual clinical diagnosis for the patient. However, the PCR test failed to detect the bacterial rRNA gene in one CSF sample, the culture of which yielded Listeria monocytogenes. These results invite new research efforts to be focused on the application of PCR with broad-range bacterial primers to improve the etiologic diagnosis of bacterial meningitis. In a clinical setting, Gram staining and bacterial culture still remain the cornerstones of diagnosis.

scholarly journals Identification of non-fermenting Gram-negative bacteria of clinical importance by an oligonucleotide array

2009 ◽  
Vol 58 (5) ◽  
pp. 596-605 ◽  
Author(s):  
Siou Cing Su ◽  
Mario Vaneechoutte ◽  
Lenie Dijkshoorn ◽  
Yu Fang Wei ◽  
Ya Lei Chen ◽  
...  
Keyword(s):  
Clinical Importance ◽  
Intergenic Spacer ◽  
16S Rrna Genes ◽  
Oligonucleotide Array ◽  
Rrna Genes ◽  
Universal Primers ◽  
23S Rrna ◽  
Rrna Gene ◽  
Nylon Membrane ◽  
Gram Negative

Many species of non-fermenting Gram-negative bacilli (non-fermenters) are important opportunistic and nosocomial pathogens. Identification of most species of non-fermenters by phenotypic characteristics can be difficult. In this study, an oligonucleotide array was developed to identify 38 species of clinically relevant non-fermenters. The method consisted of PCR-based amplification of 16S–23S rRNA gene intergenic spacer (ITS) regions using bacterial universal primers, followed by hybridization of the digoxigenin-labelled PCR products with oligonucleotide probes immobilized on a nylon membrane. A total of 398 strains, comprising 276 target strains (i.e. strains belonging to the 38 species to be identified) and 122 non-target strains (i.e. strains not included in the array), were analysed by the array. Four target strains (three reference strains and one clinical isolate) produced discrepant identification by array hybridization. Three of the four discordant strains were found to be correctly identified by the array, as confirmed by sequencing of the ITS and 16S rRNA genes, with the remaining one being an unidentified species. The sensitivity and specificity of the array for identification of non-fermenters were 100 and 96.7 %, respectively. In summary, the oligonucleotide array described here offers a very reliable method for identification of clinically relevant non-fermenters, with results being available within one working day.

scholarly journals rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira The GenBank accession numbers of the 16S rDNA gene sequences reported in this paper are AY038032–AY038037.

Microbiology ◽  
2002 ◽  
Vol 148 (2) ◽  
pp. 481-496 ◽  
Author(s):  
Isabelle Iteman ◽  
Rosmarie Rippka ◽  
Nicole Tandeau de Marsac ◽  
Michael Herdman
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Genomic Sequence ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Heterocystous Cyanobacteria

The taxonomic coherence and phylogenetic relationships of 11 planktonic heterocystous cyanobacterial isolates were examined by investigating two areas of the rRNA operon, the 16S rRNA gene (rrnS) and the internal transcribed spacer (ITS) located between the 16S rRNA and 23S rRNA genes. The rrnS sequences were determined for five strains, including representatives of Anabaena flos-aquae, Aphanizomenon flos-aquae, Nodularia sp. and two alkaliphilic planktonic members of the genera Anabaenopsis and Cyanospira, whose phylogenetic position was previously unknown. Comparison of the data with those previously published for individual groups of planktonic heterocystous cyanobacteria showed that, with the exception of members assigned to the genus Cylindrospermopsis, all the planktonic strains form a distinct subclade within the monophyletic clade of heterocystous cyanobacteria. Within this subclade five different phylogenetic clusters were distinguished. The phylogenetic groupings of Anabaena and Aphanizomenon strains within three of these clusters were not always consistent with their generic or specific assignments based on classical morphological definitions, and the high degree of sequence similarity between strains of Anabaenopsis and Cyanospira suggests that they may be assignable to a single genus. Ribotyping and additional studies performed on PCR amplicons of the 16S rDNA or the ITS for the 11 planktonic heterocystous strains demonstrated that they all contain multiple rrn operons and ITS regions of variable size. Finally, evidence is provided for intra-genomic sequence heterogeneity of the 16S rRNA genes within most of the individual isolates.

scholarly journals Identification of Mycobacterium kansasiiby Using a DNA Probe (AccuProbe) and Molecular Techniques

1999 ◽  
Vol 37 (4) ◽  
pp. 964-970 ◽  
Author(s):  
Elvira Richter ◽  
Stefan Niemann ◽  
Sabine Rüsch-Gerdes ◽  
Sven Hoffner
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Restriction Pattern ◽  
Molecular Techniques ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Genetic Analyses ◽  
New Formulation ◽  
The 16S Rrna Gene

The newly formulated Mycobacterium kansasii AccuProbe was evaluated, and the results obtained with the new version were compared to the results obtained with the old version of this test by using 116 M. kansasii strains, 1 Mycobacterium gastri strain, and 19 strains of several mycobacterial species. The sensitivity of this new formulation was 97.4% and the specificity was 100%. Still, three M. kansasii strains were missed by this probe. To evaluate the variability within the species, genetic analyses of the hsp65 gene, the spacer sequence between the 16S and 23S rRNA genes, and the 16S rRNA gene of several M. kansasii AccuProbe-positive strains as well as all AccuProbe-negative strains were performed. Genetic analyses of the oneM. gastri strain from the comparative assay and of two further M. gastri strains were included because of the identity of the 16S rRNA gene in M. gastri to that inM. kansasii. The data confirmed the genetic heterogeneity of M. kansasii. Furthermore, a subspecies with an unpublished hsp65 restriction pattern and spacer sequence was described. The genetic data indicate that all M. kansasii strains missed by the AccuProbe test belong to one subspecies, the newly described subspecies VI, as determined by thehsp65 restriction pattern and the spacer sequence. Since the M. kansasii strains that are missed are rare and allM. gastri strains are correctly negative, the new formulated AccuProbe provides a useful tool for the identification ofM. kansasii.

scholarly journals Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese (Anser anser domesticus) with reproductive pathology

2020 ◽  
Vol 70 (4) ◽  
pp. 2369-2381 ◽  
Author(s):  
Dmitriy V. Volokhov ◽  
Dénes Grózner ◽  
Miklós Gyuranecz ◽  
Naola Ferguson-Noel ◽  
Yamei Gao ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S–23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02–99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00–96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma . Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis . Based on the genetic data, we propose a novel species of the genus Mycoplasma , for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.

scholarly journals Reassessment of the phylogenetic relationships of Thiomonas cuprina

2007 ◽  
Vol 57 (11) ◽  
pp. 2720-2724 ◽  
Author(s):  
Donovan P. Kelly ◽  
Yoshihito Uchino ◽  
Harald Huber ◽  
Ricardo Amils ◽  
Ann P. Wood
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Significant Similarity ◽  
23S Rrna Gene ◽  
The 16S Rrna Gene

The published sequence of the 16S rRNA gene of Thiomonas cuprina strain Hö5 (=DSM 5495T) (GenBank accession no. U67162) was found to be erroneous. The 16S rRNA genes from the type strain held by the DSMZ since 1990 (DSM 5495T =NBRC 102145T) and strain Hö5 maintained frozen in the Universität Regensburg for 23 years (=NBRC 102094) were sequenced and found to be identical, but to show no significant similarity to the U67162 sequence. This also casts some doubt on the previously published 5S and 23S rRNA gene sequences (GenBank accession nos U67171 and X75567). The correct 16S rRNA gene sequence showed 99.8 % identity to those from Thiomonas delicata NBRC 14566T and ‘Thiomonas arsenivorans’ DSM 16361. The properties of these three species are re-evaluated, and emended descriptions are provided for the genus Thiomonas and the species Thiomonas cuprina.

scholarly journals Establishment and Assessment of An Amplicon Sequencing Method Targeting The 16S-ITS-23S rRNA Operon For Analysis of The Equine Gut Microbiome

2021 ◽  
Author(s):  
Yuta Kinoshita ◽  
Hidekazu NIWA ◽  
Eri UCHIDA-FUJII ◽  
Toshio NUKADA
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Amplicon Sequencing ◽  
Full Length ◽  
Rrna Operon ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
23S Rrna ◽  
Rrna Gene ◽  
Fecal Samples

Abstract Microbial communities are commonly studied by using amplicon sequencing of part of the 16S rRNA gene. Sequencing of the full-length 16S rRNA gene can provide higher taxonomic resolution and accuracy. To obtain even higher taxonomic resolution, with as few false-positives as possible, we assessed a method using long amplicon sequencing targeting the rRNA operon combined with a CCMetagen pipeline. Taxonomic assignment had >90% accuracy at the species level in a mock sample and at the family level in equine fecal samples, generating similar taxonomic composition as shotgun sequencing. The rRNA operon amplicon sequencing of equine fecal samples underestimated compositional percentages of bacterial strains containing unlinked rRNA genes by a third to almost a half, but unlinked rRNA genes had a limited effect on the overall results. The rRNA operon amplicon sequencing with the A519F + U2428R primer set was able to reflect archaeal genomes, whereas full-length 16S rRNA with 27F + 1492R could not. Therefore, we conclude that amplicon sequencing targeting the rRNA operon captures more detailed variations of bacterial and archaeal microbiota.

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