Molecular differentiation of bacteria by PCR amplification of the 16S–23S rRNA spacer

Scheinert, P; Krausse, Rea; Ullmann, U.; Söller, Rainer; Krupp, Guido

doi:10.1016/0167-7012(96)00901-3

Cited by 58 publications

(30 citation statements)

References 34 publications

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“…This measures the length of the gap between the 16S and 23S rRNA genes, which can vary from 150 to 1550 bp (Scheinert et al, 1996;Maron et al, 2005). By amplifying the region in all or a specific group of bacteria in a sample then separating the products by electrophoresis a profile of peaks will be generated.…”

Section: Terminal Restriction Fragment Length Polymorphisms (T-rflp) mentioning

confidence: 99%

Microbiology and atmospheric processes: biological, physical and chemical characterization of aerosol particles

et al. 2009

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Abstract. The interest in bioaerosols has traditionally been linked to health hazards for humans, animals and plants. However, several components of bioaerosols exhibit physical properties of great significance for cloud processes, such as ice nucleation and cloud condensation. To gain a better understanding of their influence on climate, it is therefore important to determine the composition, concentration, seasonal fluctuation, regional diversity and evolution of bioaerosols. In this paper, we will review briefly the existing techniques for detection, quantification, physical and chemical analysis of biological particles, attempting to bridge physical, chemical and biological methods for analysis of biological particles and integrate them with aerosol sampling techniques. We will also explore some emerging spectroscopy techniques for bulk and single-particle analysis that have potential for in-situ physical and chemical analysis. Lastly, we will outline open questions and further desired capabilities (e.g., in-situ, sensitive, both broad and selective, on-line, time-resolved, rapid, versatile, cost-effective techniques) required prior to comprehensive understanding of chemical and physical characterization of bioaerosols.

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Section: Terminal Restriction Fragment Length Polymorphisms (T-rflp) mentioning

confidence: 99%

Microbiology and atmospheric processes: biological, physical and chemical characterization of aerosol particles

et al. 2009

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“…Based on ARDRA of 16S rDNA, nearly all the soybeannodulating bacteria could be grouped into two separate large clusters comprising either the Java or the Sumatra isolates. ARDRA of 16S-23S rDNA spacer fragments was successfully used for subclassification of bacteria (Jensen et al 1993;Masol-Deya et al 1995;Gurtler and Stanisich, 1996;Scheinert et al 1996), because this region exhibits a high degree of sequence and size variation at the level of the genus and species. The sequence variation of the 16S-23S rDNA spacer region of the soybean-nodulating bacteria confirmed the clustering of most Sumatra isolates, and allowed a further classification of the Java isolates into two large distinct clusters.…”

Section: Discussionmentioning

confidence: 99%

Characterisation of Soybean Rhizobial Strains From Java and Sumatra

Waluyo

Lie

Mannetje

et al. 2013

Indones. J. Agric. Sci.

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To get insight in the structure of soybean rhizobial population native to Indonesian soils, a thorough survey of the occurrence of the soybean rhizobia were conducted in several locations in Java and Sumatra. A total of 51 different isolates of rhizobial strains were characterised phenotypically based on their symbiotic properties, and genetically using amplified ribosomal DNA restriction analysis (ARDRA). Based on their nodulation capacity on both soybean and the native legume mungbean, these rhizobial strains could be divided into a group of 16 strains specific for soybean only and another group of 35 promiscuous strains that nodulated both leguminous plants. Based on ARDRA of PCRamplified 16S rDNA and 16S-23S rDNA spacer fragments, the rhizobial strains isolated from Java differed with those from Sumatra. Six Java isolates and only one Sumatra isolate were classified as Bradyrhizobium japonicum and these similar to that of B. japonicum strain USDA 110. All these B. japonicum strains were highly specific for soybean. One isolate from Java showed a rather unique position. The remaining strains from Java (20), which were symbiotically promiscuous strains, were clustered in another group. This group and another group containing most Sumatra isolates were distinct from B. japonicum USDA 110 and therefore it is tempting to speculate that these represent indigenous soybean rhizobial bacteria. Application of agricultural practices, such as enhancement of rhizobial population, to increase soybean production is still essential and noteworthy in Sumatra.

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“…Amplification of the ITS was performed according to Scheinert et al (1996) in a reaction volume of 50 µl, which contained 150-250 ng genomic DNA, 50 pmol each of primers 5h-AAGTCGTAACAAGGTARC-3h (region 3 on the basis of the criteria given by Gu$ rtler & Stanisich, 1996 ; positions 1492-1509 of 16S rDNA) and 5h-GGTTBCCCCATTCRG-3h (region 6 ; Gu$ rtler & Stanisich, 1996 ;positions 115-130 of 23S rDNA), 0n2 mM each of dATP, dCTP, dGTP and dTTP (Boehringer Mannheim), 1 U Taq polymerase (Appligene) and the recommended PCR buffer (10i concentrated, Appligene). The reaction mixture was covered with 40 µl Chill out wax (MJ Research).…”

Section: Methodsmentioning

confidence: 99%

Differentiation of newly described antarctic bacterial isolates related to Roseobacter species based on 16S-23S rDNA internal transcribed spacer sequences.

Söller¹,

Hirsch²,

Blohm³

et al. 2000

International Journal of Systematic and Evolutionary Microbiology

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The 16S-23S rDNA internal transcribed spacer (ITS) of Roseobacter denitrificans, Roseobacter litoralis, Ruegeria algicola and strains of the recently described species Antarctobacter heliothermus and Roseovarius tolerans were analysed in order to examine DNA sequence variations and to draw conclusions about inter-and intraspecific relationships. A. heliothermus included four strains with an ITS fragment length of 1092 bp. Roseovarius tolerans was described on the basis of eight strains. Five of these harboured two ITS fragments of different lengths (959 and about 1100 bp), while the others had one fragment of either 1083 bp (two strains) or 1165 bp (one strain). ITS lengths of the related species Roseobacter denitrificans, Roseobacter litoralis and Ruegeria algicola were found to be 980, 984 and 1158 bp, respectively. Phylogenetic analyses of the DNA sequences allowed species affiliation of strains with sequence length differences of S200 bp and recognition of relationships based on a well-supported ITS tree. The strains of A. heliothermus and Roseovarius tolerans each formed a monophyletic branch and they were separated from each other by Ruegeria algicola. This species was now clearly separated from Roseobacter denitrificans and Roseobacter litoralis, which corresponded to the new genus affiliation of Ruegeria algicola. These data were additionally supported by analyses of the structure, relative position and order of genes for tRNA Ile and tRNA Ala found within the ITS of each strain. Comparative DNA sequence analyses of ITS and 16S rDNA revealed limitations, on species and strain levels, with respect to the phylogenetic resolution of the 16S rDNA due to the limited number of informative (variable) sites, while ITS sequence analyses provided more variable and sufficiently conserved positions to discriminate between strains and to reconstruct their taxonomic relationships.

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Molecular differentiation of bacteria by PCR amplification of the 16S–23S rRNA spacer

Cited by 58 publications

References 34 publications

Microbiology and atmospheric processes: biological, physical and chemical characterization of aerosol particles

Microbiology and atmospheric processes: biological, physical and chemical characterization of aerosol particles

Characterisation of Soybean Rhizobial Strains From Java and Sumatra

Differentiation of newly described antarctic bacterial isolates related to Roseobacter species based on 16S-23S rDNA internal transcribed spacer sequences.

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