Microbial lipid cycling in the oceans: an integrated 'omics' approach

含有碳、氮、磷和硫的脂类是所有活细胞的主要成分，由于细胞程序性死亡、病毒感染和浮游动物觅食，脂类不断释放到海洋中。目前的估计表明，类脂可以占海洋中总溶解有机物(DOC)的10%左右。然而，我们对海洋中微生物脂肪转化的了解非常有限。无论是所涉及的微生物的身份，还是脂肪被降解的机制，都还没有被很好地理解。理解微生物脂循环的一个主要障碍是难以表征和量化海洋样品中的众多脂类。海洋生态系统中常见的脂类包括磷脂、糖脂和含氨基酸的脂类。最近技术的进步，如LC-ESI-MS(LC-ESI-MS)，使得能够高通量地识别和定量数千种细胞脂分子物种(Shevchenko，2010)，这使得现在能够定性和定量地表征脂质。事实上，脂质组学开始补充基因组学、元基因组学、转录组学和蛋白质组学方面取得的快速进展。在这个项目中，我们将结合实验室和现场的方法来全面揭示海水中的脂质循环。因此，这个项目的目的有两个，首先，我们的目标是建立一个高通量的工作流程，使用我们的内部高效液相色谱-质谱仪平台(见上图1)，同时测定海洋表面水域中的常见脂类。这将包括检查来自西英吉利海峡的样本，这些样本是通过海洋生物协会的研究船Sepia收集的。其次，我们的目标是利用集成组学方法，如16S/18S rRNA高通量测序、元基因组学、元基因组学和脂类组学，确定海洋表层水域和沿海海洋沉积物中具有代表性的脂类循环中关键微生物种群的身份和活性。微生物脂类鉴定将通过LC-ESI-MS进行。脂肪降解途径中的营养物质和关键中间体将通过成熟的层析技术进行分析，例如离子交换层析和气相层析，并在我们之前对实验室菌株进行广泛特征描述的指导下进行分析。微生物群落分析将使用16S rRNA基因的扩增序列、后转录组学和元基因组学进行。

Lipids, containing carbon, nitrogen, phosphorus and sulfur, are a major component of all living cells and are constantly released into the oceans due to programmed cell death, viral infections and zooplankton grazing. Current estimates suggest that lipids can account for ~10% of total dissolved organic matter (DOC) in the oceans. However, our knowledge on microbial lipid transformation in the oceans is very limited. Neither the identities of the microbes involved, nor the mechanisms by which lipids are degraded, have been well understood. A major hurdle in understanding the microbial lipid cycle lies in the difficulty in characterizing and quantifying numerous lipid classes in marine samples. Commonly observed lipids in marine ecosystems include phospholipids, glycolipids and amino acid-containing lipids. Recent advances in technologies such as liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS) has enabled high throughput identification and quantification of thousands of cellular lipid molecular species (Shevchenko, 2010), which now enables lipid characterization both qualitatively and quantitatively. Indeed, lipidomics is starting to complement the rapid progress made in genomics, metagenomics, transcriptomics and proteomics. Here in this project, we will combine laboratory and filed based methodologies to fully uncover the lipid cycle in marine waters. The aim of this project is thus twofold, Firstly, we aim to establish a high throughput workflow for simultaneous determination of common lipids species in marine surface waters using our in house HPLC MS platform (see above figure 1). This will involve examining samples from the Western English Channel, collected via the Marine Biological Association research vessel, Sepia. Secondly, we aim to determine the identity and activity of key microbial populations in the recycling of representative lipids in marine surface waters and coastal marine sediment using integrated omics approach, e.g. high throughput sequencing of 16S/18S rRNA, metagenomics, metagenomics and lipidomics. Microbial lipids identification will be carried out by liquid chromatography-mass spectrometry (LC-ESI-MS). Nutrients and key intermediates in lipid degradation pathways will be analysed by established chromatography techniques, such as ion-exchange chromatography and gas chromatography, and analysis guided by our previous extensive characterisation of laboratory strains. Microbial community analyses will be carried out using amplicon sequencing of 16S rRNA genes, metatranscriptomics and metagenomics.