Physical Pretreatments Applied in Three Commercial Kits for the Extraction of High-Quality DNA from Activated Sewage Sludge
| Primer Autor |
Cid-Alda, Fernanda P.
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| Co-autores |
Vasquez, Claudio
Leyton-Carcaman, Benjamin
Segovia, Inaky
Pinto, Fernanda
Abanto, Michel
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| Título |
Physical Pretreatments Applied in Three Commercial Kits for the Extraction of High-Quality DNA from Activated Sewage Sludge
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| Editorial |
MDPI
|
| Revista |
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
|
| Lenguaje |
en
|
| Resumen |
Obtaining 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.
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| Fecha Publicación |
2023
|
| Tipo de Recurso |
artículo original
|
| doi |
10.3390/ijms242015243
|
| Formato Recurso |
PDF
|
| Palabras Claves |
DNA extraction
complex samples
next-generation sequencing
metagenomics
microbiome
bioreactor
|
| Ubicación del archivo | |
| Categoría OCDE |
Bioquímica y biología molecular
Química
|
| Materias |
Extracción de ADN
muestras complejas
secuenciación de próxima generación
metagenómica
microbioma
biorreactor
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| Identificador del recurso (Mandatado-único) |
artículo original
|
| Versión del recurso (Recomendado-único) |
versión publicada
|
| License |
CC BY 4.0
|
| Condición de la licencia (Recomendado-repetible) |
CC BY 4.0
|
| Derechos de acceso |
acceso abierto
|
| Access Rights |
acceso abierto
|
| Id de Web of Science |
WOS:001095441200001
|
| ISSN |
1661-6596
|
| Tipo de ruta |
verde# dorado
|
| Categoría WOS |
Bioquímica y biología molecular
Química
|
| Referencia del Financiador (Mandatado si es aplicable-repetible) |
ANID-FONDECYT 3210626
ANID-FONDEF ID19I10299
ANID 21210454
ANID 3200728
ANID FONDECYT 3210626
ANID FONDEF ID19I10299
UFRO PIA21-0002
|
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