Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)

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dc.contributor.authorMaropola, Mapula Kgomotso Annah
dc.contributor.authorRamond, Jean-Baptiste
dc.contributor.authorTrindade, Marla
dc.date.accessioned2023-06-28T08:45:04Z
dc.date.available2023-06-28T08:45:04Z
dc.date.issued2015
dc.description.abstractCulture-independent studies rely on the quantity and quality of the extracted environmental metagenomic DNA (mDNA). To fully access the plant tissue microbiome, the extracted plant mDNA should allow optimal PCR applications and the genetic content must be representative of the total microbial diversity. In this study, we evaluated the endophytic bacterial diversity retrieved using different mDNA extraction procedures. Metagenomic DNA from sorghum (Sorghum bicolor L. Moench) stem and root tissues were extracted using two classical DNA extraction protocols (CTAB- and SDS-based) and five commercial kits. The mDNA yields and quality as well as the reproducibility were compared. 16S rRNA gene terminal restriction fragment length polymorphism (t-RFLP) was used to assess the impact on endophytic bacterial community structures observed. Generally, the classical protocols obtained high mDNA yields from sorghum tissues; however, they were less reproducible than the commercial kits. Commercial kits retrieved higher quality mDNA, but with lower endophytic bacterial diversities compared to classical protocols.en_US
dc.identifier.citationMaropola, M. K. A. et al. (2015). Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench). Journal of Microbiological Methods, 112, 104-117. https://doi.org/10.1016/j.mimet.2015.03.012en_US
dc.identifier.issn1872-8359
dc.identifier.urihttps://doi.org/10.1016/j.mimet.2015.03.012
dc.identifier.urihttp://hdl.handle.net/10566/9170
dc.language.isoenen_US
dc.publisherElsevieren_US
dc.subjectBiotechnologyen_US
dc.subjectDiversityen_US
dc.subjectPyrosequencingen_US
dc.subjectEndophytic bacteriaen_US
dc.titleImpact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)en_US
dc.typeArticleen_US

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