Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill.
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元基因组，荟萃分析组和单细胞测序揭示了对深水地平线溢油的微生物反应。
DOI：
10.1038/ismej.2012.59
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发表时间：
2012-09
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影响因子：
--
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中科院分区：
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--
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墨西哥湾的“深水地平线”石油泄漏造成深海碳氢化合物羽流，导致本地微生物群落组成发生变化，生态后果未知。在泄漏历史的早期，未培养的，因此没有特征的，Oceanoacellellales成员的水华以前被检测到，但他们在石油处置中的作用是未知的。在这里，我们的目标是确定的功能作用的Oceanoacillales和其他活跃的土著微生物群落的成员使用社区DNA和RNA的深度测序，以及单细胞基因组学。鸟枪宏基因组和元转录组测序结果显示，与从羽流深度收集的未污染海水相比，烃羽流样品中的运动性、趋化性和脂肪烃降解基因显著富集和表达。相比之下，尽管在宏基因组中鉴定了编码降解更多柠檬酸化合物（如苯、甲苯、二甲苯、总二甲苯和多环芳烃）的基因，但基于对元转录组的分析，它们以低水平表达，或者根本不表达。分离和测序的两个海洋藻类单细胞显示，这两个细胞具有编码正烷烃和环烷烃降解的基因。具体而言，在海洋藻类单细胞中环己烷氧化的接近完整的途径得到了宏基因组和元转录组数据的阐明和支持。基因组草图还包括趋化性、运动性和营养获取策略的基因，这些基因也在宏基因组和元转录组中被发现。这些数据表明，Oceanoacillales的成员对深海中的脂肪烃有快速反应。
The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.
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