Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench)
Date
2015Author
Maropola, Mapula Kgomotso Annah
Ramond, Jean-Baptiste
Trindade, Marla
Metadata
Show full item recordAbstract
Culture-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.