A modified isooctane‐based DNA extraction method from crude oil
Abstract Microbes from oil reservoirs shape petroleum composition through processes such as biodegradation or souring. Such processes are considered economically detrimental and might pose health and safety hazards. It is therefore crucial to understand the composition of a reservoir's microbia...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-09-01
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| Series: | mLife |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/mlf2.12081 |
| _version_ | 1797671741602922496 |
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| author | Armando Alibrandi Rolando diPrimio Alexander Bartholomäus Jens Kallmeyer |
| author_facet | Armando Alibrandi Rolando diPrimio Alexander Bartholomäus Jens Kallmeyer |
| author_sort | Armando Alibrandi |
| collection | DOAJ |
| description | Abstract Microbes from oil reservoirs shape petroleum composition through processes such as biodegradation or souring. Such processes are considered economically detrimental and might pose health and safety hazards. It is therefore crucial to understand the composition of a reservoir's microbial community and its metabolic capabilities. However, such analyses are hindered by difficulties in extracting DNA from such complex fluids as crude oil. Here, we present a novel DNA extraction method from oils with a wide American Petroleum Institute (API) gravity (density) range. We investigated the ability to extract cells from oils with different solvents and surfactants, the latter both nonionic and ionic. Furthermore, we evaluated three DNA extraction methods. Overall, the best DNA yields and the highest number of 16S rRNA reads were achieved with isooctane as a solvent, followed by an ionic surfactant treatment using sodium dodecyl sulfate and DNA extraction using the PowerSoil Pro Kit (Qiagen). The final method was then applied to various oils from oil reservoirs collected in aseptic conditions. Despite the expected low cell density of 101–103 cells/ml, the new method yielded reliable results, with average 16S rRNA sequencing reads in the order of 41431 (±8860) per sample. Thermophilic, halophilic, and anaerobic taxa, which are most likely to be indigenous to the oil reservoir, were found in all samples. API gravity and DNA yield, despite the sufficient DNA obtained, did not show a correlation. |
| first_indexed | 2024-03-11T21:19:57Z |
| format | Article |
| id | doaj.art-6829a71c617747e6932a9b44b060317f |
| institution | Directory Open Access Journal |
| issn | 2770-100X |
| language | English |
| last_indexed | 2024-03-11T21:19:57Z |
| publishDate | 2023-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | mLife |
| spelling | doaj.art-6829a71c617747e6932a9b44b060317f2023-09-28T10:25:53ZengWileymLife2770-100X2023-09-012332833810.1002/mlf2.12081A modified isooctane‐based DNA extraction method from crude oilArmando Alibrandi0Rolando diPrimio1Alexander Bartholomäus2Jens Kallmeyer3GFZ German Research Centre for Geoscience, Section Geomicrobiology Potsdam GermanyAker BP Lysaker NorwayGFZ German Research Centre for Geoscience, Section Geomicrobiology Potsdam GermanyGFZ German Research Centre for Geoscience, Section Geomicrobiology Potsdam GermanyAbstract Microbes from oil reservoirs shape petroleum composition through processes such as biodegradation or souring. Such processes are considered economically detrimental and might pose health and safety hazards. It is therefore crucial to understand the composition of a reservoir's microbial community and its metabolic capabilities. However, such analyses are hindered by difficulties in extracting DNA from such complex fluids as crude oil. Here, we present a novel DNA extraction method from oils with a wide American Petroleum Institute (API) gravity (density) range. We investigated the ability to extract cells from oils with different solvents and surfactants, the latter both nonionic and ionic. Furthermore, we evaluated three DNA extraction methods. Overall, the best DNA yields and the highest number of 16S rRNA reads were achieved with isooctane as a solvent, followed by an ionic surfactant treatment using sodium dodecyl sulfate and DNA extraction using the PowerSoil Pro Kit (Qiagen). The final method was then applied to various oils from oil reservoirs collected in aseptic conditions. Despite the expected low cell density of 101–103 cells/ml, the new method yielded reliable results, with average 16S rRNA sequencing reads in the order of 41431 (±8860) per sample. Thermophilic, halophilic, and anaerobic taxa, which are most likely to be indigenous to the oil reservoir, were found in all samples. API gravity and DNA yield, despite the sufficient DNA obtained, did not show a correlation.https://doi.org/10.1002/mlf2.12081crude oilDNA extraction methodoil reservoir microbiome |
| spellingShingle | Armando Alibrandi Rolando diPrimio Alexander Bartholomäus Jens Kallmeyer A modified isooctane‐based DNA extraction method from crude oil mLife crude oil DNA extraction method oil reservoir microbiome |
| title | A modified isooctane‐based DNA extraction method from crude oil |
| title_full | A modified isooctane‐based DNA extraction method from crude oil |
| title_fullStr | A modified isooctane‐based DNA extraction method from crude oil |
| title_full_unstemmed | A modified isooctane‐based DNA extraction method from crude oil |
| title_short | A modified isooctane‐based DNA extraction method from crude oil |
| title_sort | modified isooctane based dna extraction method from crude oil |
| topic | crude oil DNA extraction method oil reservoir microbiome |
| url | https://doi.org/10.1002/mlf2.12081 |
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