Alibrandi Armando, di Primio Rolando, Bartholomäus Alexander, Kallmeyer Jens
GFZ German Research Centre for Geoscience, Section Geomicrobiology Potsdam Germany.
Aker BP Lysaker Norway.
mLife. 2023 Sep 28;2(3):328-338. doi: 10.1002/mlf2.12081. eCollection 2023 Sep.
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 10-10 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.
油藏中的微生物通过生物降解或产酸等过程塑造石油成分。这些过程被认为在经济上具有不利影响，并且可能带来健康和安全风险。因此，了解油藏微生物群落的组成及其代谢能力至关重要。然而，从原油等复杂流体中提取DNA的困难阻碍了此类分析。在此，我们提出了一种从具有广泛美国石油学会（API）重度（密度）范围的油中提取DNA的新方法。我们研究了用不同溶剂和表面活性剂从油中提取细胞的能力，后者包括非离子型和离子型表面活性剂。此外，我们评估了三种DNA提取方法。总体而言，以异辛烷作为溶剂可获得最佳的DNA产量和最多的16S rRNA读数，其次是使用十二烷基硫酸钠进行离子表面活性剂处理以及使用PowerSoil Pro试剂盒（Qiagen）进行DNA提取。然后将最终方法应用于在无菌条件下收集的来自油藏的各种油样。尽管预期细胞密度较低，为10-10个细胞/毫升，但新方法仍产生了可靠的结果，每个样品的平均16S rRNA测序读数约为41431（±8860）。在所有样品中均发现了最有可能是油藏原生的嗜热、嗜盐和厌氧类群。尽管获得了足够的DNA，但API重度与DNA产量之间并未显示出相关性。
