Functional metagenomic and enrichment metatranscriptomic analysis of marine microbial activities within a marine oil spill area.
Functional metagenomic and enrichment metatranscriptomic analysis of marine microbial activities within a marine oil spill area.
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DOI：
10.1016/j.envpol.2021.116555
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发表时间：
2021-01
影响因子：
8.9
通讯作者：
Bingkui Song;Zhihao Li;Si Li;Zhongzhen Zhang;Qitong Fu;Shijie Wang;Liang Li;Shuting Qi
中科院分区：
文献类型：
--
作者：
Bingkui Song;Zhihao Li;Si Li;Zhongzhen Zhang;Qitong Fu;Shijie Wang;Liang Li;Shuting Qi
微生物可以降解石油烃，具有成本低、对生态系统副作用小等优点。本文采用宏基因组学和元转录组学方法对海洋石油烃的微生物降解机制进行了研究，以期为石油烃的微生物降解提供新的视角。从渤海湾钻井平台附近的一个区域采集了2.8m深的海水样品，并使用宏基因组测序来评估这些海洋微生物群落的功能潜力。元转录组测序，荧光原位杂交实验，流式细胞术也进行了12个不同的培养条件下的样品的微生物群落。数据还经过加权基因共表达网络分析（WGCNA）和共转录数据可视化以评估基因功能的共转录。宏基因组测序表明，存在许多与石油烃代谢相关的基因。此外，多个途径中基因的高度共转录表明基因组协同转录以代谢石油烃。元转录组学还显示，微生物代谢在富集中高度活跃，并且大量原核复制和修复基因的转录显著上调，包括编码VI型分泌系统（T6SS）蛋白、DNA聚合酶I、胸苷磷酸化酶、甲羟戊酸激酶和双组分系统的基因。与此同时，参与翻译的核糖体基因和参与能量代谢的光合作用基因的转录也下调。总的来说，油和氧的存在可以提高石油降解率和相关基因的转录。许多不同的代谢是共同调节，以利用来自石油烃代谢的营养物质。本研究对宏基因组、元转录组和降解数据的分析表明，广泛的基因谱参与了石油降解，基因间的协同作用是非常重要的。
Microorganisms can degrade petroleum hydrocarbons, providing the advantages of low cost and few side effects towards ecosystems. Here, we evaluated the mechanisms of microbial degradation of marine petroleum hydrocarbon using metagenomics and metatranscriptomics approaches in order to provide new insight into microbial degradation of petroleum hydrocarbon. Seawater samples were collected at a depth of ∼8 m from an area near a drilling platform in the Bohai Bay and metagenomic sequencing was used to evaluate the functional potential of these marine microbial communities. Metatranscriptomic sequencing, fluorescence in-situ hybridization experiments, and flow cytometry were also performed on the microbial communities of samples subjected to 12 different culture conditions. The data were also subjected to Weighted Gene Co-expression Network Analysis (WGCNA) and co-transcription data visualization to evaluate co-transcription of gene functions. Metagenomic sequencing indicated the presence of numerous genes that were related to petroleum hydrocarbon metabolism. Further, the high co-transcription of genes in multiple pathways, indicated that groups of genes were synergistically transcribed to metabolize petroleum hydrocarbons. Metatranscriptomics also showed that microbial metabolism was highly active in the enrichments and that the transcription of a large number of prokaryotic replication and repair genes were significantly up-regulated including those encoding for the type VI secretion system (T6SS) protein, DNA polymerase I, thymidine phosphorylase, mevalonate kinase, and two-component systems. Concomitantly, the transcription of ribosomal genes involved in translation and photosynthetic genes involved in energy metabolism were down-regulated. Overall, oil and oxygen presence can increase the oil-degradation rates and related genes’ transcription. Lot different metabolisms are co-regulated to exploit nutrients derived from the metabolism of petroleum hydrocarbons. Our analysis of metagenomic, metatranscriptomic and degradation data in this study show that a widespread gene spectrum involved in oil-degradation and the cooperation among genes is of great importance.