Application of a novel Paenibacillus-specific PCR-DGGE method and sequence analysis to assess the diversity of Paenibacillus spp. in the maize rhizosphere

Journal of Microbiological Methods
Katia Regina Araújo da SilvaJan Dirk van Elsas

Abstract

In this study, a Paenibacillus-specific PCR system, based on the specific primer PAEN515F in combination with bacterial primer R1401, was tested and used to amplify specific fragments of the 16S rRNA gene from rhizosphere DNA. The amplicons were used in a second (semi-nested) PCR for DGGE, in which bacterial primers F968GC and R1401 were used. The resulting products were separated into community fingerprints by DGGE. To assess the reliability of the method, the diversity of Paenibacillus species was evaluated on the basis of DNA extracted directly from the rhizospheres of four different cultivars of maize (Zea mays), i.e. CMS04, CMS11, CMS22 and CMS36, sown in two Brazilian field soils (Cerrado and Várzea). In addition, a clone library was generated from the PCR-generated 16S rDNA fragments, and selected clones were sequenced. The results of the bacterial community analyses showed, at the level of clone libraries, that considerable diversity among Paenibacillus spp. was present. The most dominantly found sequences clustered into 12 groups, each one potentially representing a species complex. Sequences closely affiliated with the P. macerans and P. azotofixans complexes were found in all samples, whereas other sequences were sca...Continue Reading

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Citations

Nov 29, 2007·The ISME Journal·Xiaoyan PangLiping Zhao
Jul 9, 2004·Applied and Environmental Microbiology·Joana Falcão SallesJan Dirk van Elsas
May 18, 2007·Annual Review of Microbiology·Harold L Drake, Marcus A Horn
Jan 6, 2016·Plant Molecular Biology·Andrew LareenPatrick Schäfer
May 9, 2016·Journal of Environmental Sciences (China)·Mehdi HassanshahianMichail Yakimov
Jul 15, 2005·Journal of Microbiological Methods·Valéria Maia de OliveiraJan Dirk van Elsas
Dec 1, 2011·Molecular Ecology·Marie-Lara BouffaudYvan Moënne-Loccoz
Sep 8, 2019·Environmental Science and Pollution Research International·Palist JarujareetOramas Suttinun
Mar 6, 2021·International Microbiology : the Official Journal of the Spanish Society for Microbiology·Ayomide Emmanuel FadijiOlubukola Oluranti Babalola
Jun 25, 2015·Microbiology Spectrum·Ines Mandic-MulecJan Dirk van Elsas

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