Journal:

Article Title: A Highly Selective PCR Protocol for Detecting 16S rRNA Genes of the Genus Pseudomonas (Sensu Stricto) in Environmental Samples

doi:

Figure Lengend Snippet: Primer mismatch testing in RDP with the CHECK_PROBE algorithm

Article Snippet: P. syringae pv. syringae Biolog 7350* , A , Psm.A.

Techniques: Bacteria

Journal:

Article Title: A Highly Selective PCR Protocol for Detecting 16S rRNA Genes of the Genus Pseudomonas (Sensu Stricto) in Environmental Samples

doi:

Figure Lengend Snippet: PCR amplification and HaeIII RFLP patterns of pure cultures. PCR amplification (30 cycles) of 16S DNA coding for rRNA of pure cultures was performed either with a universal SSU primer set (a) or with the Ps-PCR primer set (b). (a1 and b1) Amplification products from cultures (lanes 1 to 18) and a negative control (neg) on 1% agarose gels. The molecular weight marker (MW) was λ HindIII. (a2 and b2) HaeIII RFLP patterns on 2% agarose gels. The molecular weight marker (MW) was ΦX174 HaeIII. The 18 cultures were “Pseudomonas” boreopolis (ATCC 3242) (lane 1), Burkholderia andropogonis (ATCC 23061) (lane 2), P. cichorii (ATCC 10857) (lane 3), P. syringae pv. syringae (Biolog 7350) (lane 4), “P.” floridana (ATCC 25616) (lane 5), “Pseudomonas” sp.-like group II (Biolog 1574) (lane 6), P. taetrolens (Biolog 8570) (lane 7), P. putida biotype B (ATCC 17527) (lane 8), P. synxantha (ATCC 9890) (lane 9), P. fragi (ATCC 4973) (lane 10), P. recinovorans (ATCC 14235) (lane 11), P. mendocina (ATCC 25411) (lane 12), P. agarici (ATCC 25941) (lane 13), P. fulva (ATCC 31418) (lane 14), P. stutzeri (ATCC 17588) (lane 15), P. alcaligenes (ATCC 14909) (lane 16), P. fluorescens biotype G (isolate 27cm) (lane 17), and P. marginalis (isolate A5P4C3) (lane 18). The Pseudomonas genus names that are in quotation marks are not Pseudomonas (sensu stricto) cultures.)

Article Snippet: P. syringae pv. syringae Biolog 7350* , A , Psm.A.

Techniques: Amplification, Negative Control, Molecular Weight, Marker

Journal:

Article Title: A Highly Selective PCR Protocol for Detecting 16S rRNA Genes of the Genus Pseudomonas (Sensu Stricto) in Environmental Samples

doi:

Figure Lengend Snippet: PCR amplification and HaeIII RFLP patterns of pure cultures. PCR amplification (30 cycles) of 16S DNA coding for rRNA of pure cultures was performed either with a universal SSU primer set (a) or with the Ps-PCR primer set (b). (a1 and b1) Amplification products from cultures (lanes 1 to 18) and a negative control (neg) on 1% agarose gels. The molecular weight marker (MW) was λ HindIII. (a2 and b2) HaeIII RFLP patterns on 2% agarose gels. The molecular weight marker (MW) was ΦX174 HaeIII. The 18 cultures were “Pseudomonas” boreopolis (ATCC 3242) (lane 1), Burkholderia andropogonis (ATCC 23061) (lane 2), P. cichorii (ATCC 10857) (lane 3), P. syringae pv. syringae (Biolog 7350) (lane 4), “P.” floridana (ATCC 25616) (lane 5), “Pseudomonas” sp.-like group II (Biolog 1574) (lane 6), P. taetrolens (Biolog 8570) (lane 7), P. putida biotype B (ATCC 17527) (lane 8), P. synxantha (ATCC 9890) (lane 9), P. fragi (ATCC 4973) (lane 10), P. recinovorans (ATCC 14235) (lane 11), P. mendocina (ATCC 25411) (lane 12), P. agarici (ATCC 25941) (lane 13), P. fulva (ATCC 31418) (lane 14), P. stutzeri (ATCC 17588) (lane 15), P. alcaligenes (ATCC 14909) (lane 16), P. fluorescens biotype G (isolate 27cm) (lane 17), and P. marginalis (isolate A5P4C3) (lane 18). The Pseudomonas genus names that are in quotation marks are not Pseudomonas (sensu stricto) cultures.)

Article Snippet: In summary, the Ps-PCR protocol was suitable for specific amplification of 16S rRNA Pseudomonas genes, and Hae III RFLP analysis of Ps-PCR products experimentally confirmed the specificity of the Ps-PCR method for target organisms at 100%. table ft1 table-wrap mode="anchored" t5 TABLE 3 caption a7 Culture description a Hae III RFLP pattern Ps-PCR b Universal PCR c Culture collections P. putida type B ATCC 17527* A Psm.A P. putida ATCC 11172 A Psm.A P. aeruginosa ATCC 10145 A Psm.A P. syringae pv. syringae Biolog 7350* A Psm.A P. syringae pv. syringae EPA 22A-93 A Psm.A P. syringae pv. tomato EPA PT-23 A Psm.A P. syringae pv. phaseolica EPA JA-019 A Psm.A P. cichorii ATCC 10857* A Psm.A P. taetrolens Biolog 8570* A Psm.A P. synxantha ATCC 9890* A Psm.A P. fragi ATCC 4973* A Psm.A P. resinovorans ATCC 14235* A Psm.A P. mendocina ATCC 25411* A Psm.A P. agarici ATCC 25941* B Psm.B P. fulva ATCC 31418* A Psm.A P. stutzeri ATCC 17588* A Psm.A P. alcaligenes B ATCC 14909* A Psm.A P. aureofaciens EPA 604 A Psm.A Burkholderia pickettii ATCC 27511 − BuhI.A Burkholderia andropogonis ATCC 23061* − BuhII.A Burkholderia cepacia ATCC 25416 − BuhII.A Comamonas testosteroni ATCC 11996 − Com.A Acidovorax facilis ATCC 11228 − Acv.A Hydrogenophaga flava ATCC 33667 − Hyp.A Brevundimonas vesicularis ATCC 11426 − Brm.A Stenotrophomonas maltophila ATCC 13637 − Stm.A P. floridana ATCC 25616* − “Psm”.A Pseudomonas species-like group II Biolog 1574* − “Psm”.A P. boreopolis ATCC 3242* − “Psm”.B Biolog-identified environmental isolates P. putida A1 isolates E8P3D2, E12P3C1, F2P4B3, and 77ys A Psm.A P. putida B1 isolates F2C1B1, BMD B2, and BMD B7 A Psm.A P. fluorescens type A isolate E2P5B1 A Psm.A P. fluorescens type B isolates 75csr, 137ymr, 182ysr, and 228csr A Psm.A P. fluorescens type C isolate F4C3D3 A Psm.A P. fluorescens type G isolates E2P5A3, F2C1B3, 27cm, 129,ymr, 7A, and 2A A Psm.A P. marginalis isolates A5P4C3 and 18B C Psm.A P. corrugata isolates E8C1D1 and 104ysr A Psm.A P. viridilivida isolates E2P4B3 and E2P4A1 A Psm.A P. aurantiaca isolates RES A5 and FB49H A Psm.A P. viridiflava isolate RES A7 A Psm.A P. fragi isolate 7C A Psm.A P. fuscovaginae isolate 7B A Psm.A Pseudomonas sp. isolate RES A4 A Psm.A Pseudomonas sp. isolate BMD B36 A Psm.A Acinetobacter sp. isolate 78 cs − Acb.A Acinetobacter calcoacitices isolate FA18C − Acb.A Alcaligenes xylosoxidans isolate FA30G − Alc.A Open in a separate window a Fifty Pseudomonas and 14 non- Pseudomonas cultures used to test the specificity of the Ps-PCR protocol.

Techniques: Amplification, Negative Control, Molecular Weight, Marker

Journal:

Article Title: Azospirillum brasilense Produces the Auxin-Like Phenylacetic Acid by Using the Key Enzyme for Indole-3-Acetic Acid Biosynthesis

doi: 10.1128/AEM.71.4.1803-1810.2005

Figure Lengend Snippet: Strains and plasmids

Article Snippet: P. syringae pv. glycinea LMG5066 , Wild-type isolate , Laboratorium voor Microbiologie, Universiteit Gent, Ghent, Belgium.

Techniques: Plasmid Preparation, Isolation, Mutagenesis