Physical Pretreatments Applied in Three Commercial Kits for the Extraction of High-Quality DNA from Activated Sewage Sludge

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dc.contributor.authorVasquez, Claudio
dc.contributor.authorLeyton Carcaman, Benjamin
dc.contributor.authorCid Alda, Fernanda P.
dc.contributor.authorSegovia, Inaky
dc.contributor.authorPinto, Fernanda
dc.contributor.authorAbanto, Michel
dc.date2023
dc.date.accessioned2024-05-27T18:27:51Z
dc.date.available2024-05-27T18:27:51Z
dc.description.abstractObtaining sufficient and high-quality genomic DNA from sludge samples is a fundamental issue of feasibility and comparability in genomic studies of microbial diversity. Commercial kits for soil are often used for the extraction of gDNA from sludge samples due to the lack of specific kits. However, the evaluation of the performance of commercial kits for sludge DNA extraction is scarce and optimization of these methods to obtain a high quantity and quality of DNA is necessary, especially for downstream genomic sequencing. Sequential batch reactors (SBRs) loaded with lignocellulosic biomass are used for the synthesis of renewable resources such as levulinic acid (LA), adipic acid (AA), and polyhydroxyalkanoates (PHAs), and the biochemical synthesis of these compounds is conducted through the inoculation of microbes present in the residual activated sludge (AS) obtained from a municipal wastewater treatment plant. To characterize these microbes, the extraction of DNA from residual sewage sludge was conducted with three different commercial kits: Nucleospin (R) Soil from Macherey-Nagel, DNEasy (R) PowerSoil (R) from Qiagen, and E.Z.N.A.(R) Plant DNA Kit from Omega BIO-TEK. Nevertheless, to obtain the highest load and quality of DNA for next-generation sequencing (NGS) analysis, different pretreatments and different combinations of these pretreatments were used. The pretreatments considered were an ultrasonic bath and a temperature of 80 degrees C, together and separately with different incubation time periods of 30, 60, and 90 min. The results obtained suggest a significant improvement in the efficiency and quality of DNA extraction with the three commercial extraction kits when used together with the ultrasonic bath and 80 degrees C for 60 min. Here, we were able to prove that physical pretreatments are a viable alternative to chemical lysis for DNA extraction from complex samples such as sludge.
dc.identifier.citationINTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,Vol.24,2023
dc.identifier.doi10.3390/ijms242015243
dc.identifier.urihttps://repositoriodigital.uct.cl/handle/10925/5883
dc.language.isoen
dc.publisherMDPI
dc.sourceINTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
dc.subject.englishDNA extraction
dc.subject.englishcomplex samples
dc.subject.englishnext-generation sequencing
dc.subject.englishmetagenomics
dc.subject.englishmicrobiome
dc.subject.englishbioreactor
dc.titlePhysical Pretreatments Applied in Three Commercial Kits for the Extraction of High-Quality DNA from Activated Sewage Sludge
dc.typeArticle
uct.indizacionSCI
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