Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797 SZ 't Horntje, Texel, The Netherlands.
Department of Earth Sciences, Faculty of Geosciences, Utrecht University, 3584 CS Utrecht, The Netherlands.
ISME J. 2024 Jan 8;18(1). doi: 10.1093/ismejo/wrae153.
Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply metalipidomics combined with metagenomics in the Black Sea, classifying and tentatively identifying 1623 lipid-like species across 18 lipid classes. We discovered over 200 novel, abundant, and structurally diverse sphingolipids in euxinic waters, including unique 1-deoxysphingolipids with long-chain fatty acids and sulfur-containing groups. Sphingolipids were thought to be rare in bacteria and their molecular and ecological functions in bacterial membranes remain elusive. However, genomic analysis focused on sphingolipid biosynthesis genes revealed that members of 38 bacterial phyla in the Black Sea can synthesize sphingolipids, representing a 4-fold increase from previously known capabilities and accounting for up to 25% of the microbial community. These sphingolipids appear to be involved in oxidative stress response, cell wall remodeling, and are associated with the metabolism of nitrogen-containing molecules. Our findings underscore the effectiveness of multi-omics approaches in exploring microbial chemical ecology.
微生物脂质可用作分类标志物和生理指标，主要通过培养进行研究。然而，由于环境微生物培养物的稀缺性，这种方法受到限制，从而限制了对脂质多样性及其生态作用的深入了解。为了解决这一限制，我们在这里将金属组学与宏基因组学结合应用于黑海，对 18 个脂质类别的 1623 种脂质类似物进行分类和初步鉴定。我们在缺氧水域中发现了 200 多种新型、丰富且结构多样的神经酰胺，包括具有长链脂肪酸和含硫基团的独特 1-去氧神经酰胺。神经酰胺被认为在细菌中很少见，其在细菌膜中的分子和生态功能仍不清楚。然而，专注于神经酰胺生物合成基因的基因组分析表明，黑海 38 个细菌门的成员可以合成神经酰胺，这比以前已知的能力增加了 4 倍，占微生物群落的比例高达 25%。这些神经酰胺似乎参与了氧化应激反应、细胞壁重塑，并与含氮分子的代谢有关。我们的研究结果强调了多组学方法在探索微生物化学生态学方面的有效性。
