Marine microbes are known to degrade hydrocarbons; however, microbes inhabiting deep-sea sediments remain largely unexplored. Previous studies into the classical pathways of marine microbial metabolism reveal diverse chemistries; however, metabolic profiling of marine microbes cultured with hydrocarbons is limited. In this study, taxonomic (amplicon sequencing) profiles of two environmental deep-sea sediments (>1,200 m deep) were obtained, along with taxonomic and metabolomic (mass spectrometry-based metabolomics) profiles of microbes harbored in deep-sea sediments cultured with hydrocarbons as the sole energy source. Samples were collected from the Gulf of México (GM) and cultured for 28 days using simple (toluene, benzene, hexadecane, and naphthalene) and complex (petroleum API 40) hydrocarbon mixtures as the sole energy sources. The sediment samples harbored diverse microbial communities predominantly classified into Woeseiaceae and Kiloniellaceae families, whereas Pseudomonadaceae and Enterobacteriaceae families prevailed after sediments were cultured with hydrocarbons. Chemical profiling of microbial metabolomes revealed diverse chemical groups belonging primarily to the lipids and lipid-like molecules superclass, as well as the organoheterocyclic compound superclass (ClassyFire annotation). Metabolomic data and prediction of functional profiles indicated an increase in aromatic and alkane degradation in samples cultured with hydrocarbons. Previously unreported metabolites, identified as intermediates in the degradation of hydrocarbons, were annotated as hydroxylated polyunsaturated fatty acids and carboxylated benzene derivatives. In summary, this study used mass spectrometry-based metabolomics coupled to chemoinformatics to demonstrate how microbes from deep-sea sediments could be cultured in the presence of hydrocarbons. This study also highlights how this experimental approach can be used to increase the understanding of hydrocarbon degradation by deep-sea sediment microbes.

中文翻译：

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化学分析为深入了解碳氢化合物降解微生物的代谢机理提供了见解

众所周知，海洋微生物会降解碳氢化合物。然而，居住在深海沉积物中的微生物仍未开发。先前对海洋微生物代谢经典途径的研究揭示了不同的化学性质。但是，用碳氢化合物培养的海洋微生物的代谢谱分析是有限的。在这项研究中，获得了两种环境深海沉积物（> 1,200 m深）的分类学（amplicon测序）图，以及在碳氢化合物培养的深海沉积物中所含微生物的分类学和代谢组学（基于质谱的代谢组学）图谱。作为唯一的能源。从墨西哥湾（GM）收集样品，并使用简单的（甲苯，苯，十六烷和萘）和复杂的（石油API 40）烃混合物作为唯一能源，培养28天。Woeseiaceae和Kiloniellaceae家族，而Pseudomonadaceae和Enterobacteriaceae沉积物用碳氢化合物培养后，这些家庭占了上风。微生物代谢组的化学分析揭示了主要属于脂质和类脂质分子超类以及有机杂环化合物超类的各种化学基团（ClassyFire注解）。代谢组学数据和功能概况的预测表明，用烃培养的样品中芳烃和烷烃降解的增加。以前未被报道的代谢产物被鉴定为烃降解的中间体，被标注为羟基化的多不饱和脂肪酸和羧基化的苯衍生物。总之，这项研究使用了基于质谱的代谢组学和化学信息学，以证明在碳氢化合物存在下如何培养深海沉积物的微生物。