Lipidomics of Environmental Microbial Communities. I: Visualization of Component Distributions Using Untargeted Analysis of High-Resolution Mass Spectrometry Data

Abstract

Lipids, as one of the main building blocks of cells, can provide valuable information on microorganisms in the environment. Traditionally, gas or liquid chromatography coupled to mass spectrometry (MS) has been used to analyze environmental lipids. The resulting spectra were then processed through individual peak identification and comparison with previously published mass spectra. Here, we present an untargeted analysis of MS1 spectral data generated by ultra-high-pressure liquid chromatography coupled with high-resolution mass spectrometry of environmental microbial communities. Rather than attempting to relate each mass spectrum to a specific compound, we have treated each mass spectrum as a component, which can be clustered together with other components based on similarity in their abundance depth profiles through the water column. We present this untargeted data visualization method on lipids of suspended particles from the water column of the Black Sea, which included >14,000 components. These components form clusters that correspond with distinct microbial communities driven by the highly stratified water column. The clusters include both known and unknown compounds, predominantly lipids, demonstrating the value of this rapid approach to visualize component distributions and identify novel lipid biomarkers.

Halapricum desulfuricans sp. nov., carbohydrate-utilizing, sulfur-respiring haloarchaea from hypersaline lakes

“…All steps of the extraction were then repeated, but with a solvent mixture of methanol, DCM and trichloroacetic acid pH 2-3 (2:1:0.8, v:v:v). Finally, the combined extract was dried under a stream of N 2 gas [9]. Before analysis, the extracts were redissolved in MeOH:DCM (9:1, v:v) and filtered through 0.45 lm cellulose syringe filters (4 mm diameter; Grace Alltech, Deerfield, IL, United States).…”

“…Before analysis, the extracts were redissolved in MeOH:DCM (9:1, v:v) and filtered through 0.45 lm cellulose syringe filters (4 mm diameter; Grace Alltech, Deerfield, IL, United States). Analysis of extracts was carried out using an Ultra High-Pressure Liquid Chromatography-High Resolution Mass Spectrometry (UHPLC-HRMS) according to the reversed phase method with modifications of [9,10]. Identification was carried out by comparison of accurate masses and mass spectral fragmentation with published data for IPLs [11] and for quinones [12].…”

Changes in the membrane lipid composition of a Sulfurimonas species depend on the electron acceptor used for sulfur oxidation

“…However, the vast majority of ion components was left unannotated. Lipidome annotation remains a bottleneck in marine microbiology lipidomic studies because public databases in this field are poorly populated [ 35 , 37 ].…”

“…baltica GD2 and S. gotlandica GD1 T ) were collected and freeze dried for lipidome analysis. A detailed description of sample extraction and ultra-high performance liquid chromatography coupled to high-resolution tandem mass spectrometry (UHPLC-HRMS 2 ) analysis and initial data processing is given in Bale, et al [ 35 ]. Briefly, freeze-dried samples were extracted using a modified Bligh-Dyer procedure.…”

Revisiting the precursors of the most abundant natural products on Earth: A look back at 30+ years of bacteriohopanepolyol (BHP) research and ahead to new frontiers

“…Such an untargeted lipidomics approach applied to Black Sea SPM revealed microbial networks and niche partitioning across the oxic and anoxic marine water column (Bale et al, 2021;Ding et al, 2021). This method has the advantage of allowing determination of the diversity of unknown lipids and their importance in specific environmental niches.…”