Effects of graphene oxide on PCR amplification for microbial community survey

Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not bee...

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Bibliographic Details
Published in:BMC microbiology 2020-09, Vol.20 (1), p.278-9, Article 278
Main Authors: Li, Shuzhen, Wang, Zhujun, Wang, Yuanyuan, Song, Maoyong, Lu, Guangxin, Dang, Ning, Yin, Huaqun, Qu, Yuanyuan, Deng, Ye
Format: Article
Language:English
Subjects:
Amplification
Bacteria
Biodiversity
Chimera
Community composition
Deoxyribonucleic acid
DNA
Efficiency
Fungi
Graphene
Microbiomes
Microorganisms
Next-generation sequencing
Oxidized graphene
Polymerase chain reaction
Quantitation
Reagents
RNA
rRNA 16S
Taxonomy
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Summary:Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples. High-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community. Our study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.
ISSN:1471-2180
1471-2180
DOI:10.1186/s12866-020-01965-7