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

Journal of Microbiological Methods
Mapula Kgomotso Annah MaropolaMarla Trindade

Abstract

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. The SDS-based protocol enabled access to the highest sorghum endophytic diversities. Therefore, "SDS-extracted" sorghum root and ste...Continue Reading

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Citations

Mar 19, 2016·Journal of Environmental Management·Ying MaHelena Freitas
Oct 8, 2017·Amino Acids·Lanmei YinYulong Yin
Mar 3, 2019·Applied and Environmental Microbiology·Qian LiHongqing Wang
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Feb 7, 2020·Journal of Microbiological Methods·Ayomide Emmanuel Fadiji, Olubukola Oluranti Babalola
Apr 12, 2021·Journal of Microbiological Methods·P PriyaK Harikrishnan
Oct 1, 2021·Plant Signaling & Behavior·Bartholomew Saanu AdelekeOlubukola Oluranti Babalola

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