Lipidomics of Environmental Microbial Communities. II: Characterization Using Molecular Networking and Information Theory

Abstract

Structurally diverse, specialized lipids are crucial components of microbial membranes and other organelles and play essential roles in ecological functioning. The detection of such lipids in the environment can reveal not only the occurrence of specific microbes but also the physicochemical conditions to which they are adapted to. Traditionally, liquid chromatography coupled with mass spectrometry allowed for the detection of lipids based on chromatographic separation and individual peak identification, resulting in a limited data acquisition and targeting of certain lipid groups. Here, we explored a comprehensive profiling of microbial lipids throughout the water column of a marine euxinic basin (Black Sea) using ultra high-pressure liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMS/MS). An information theory framework combined with molecular networking based on the similarity of the mass spectra of lipids enabled us to capture lipidomic diversity and specificity in the environment, identify novel lipids, differentiate microbial sources within a lipid group, and discover potential biomarkers for biogeochemical processes. The workflow presented here allows microbial ecologists and biogeochemists to process quickly and efficiently vast amounts of lipidome data to understand microbial lipids characteristics in ecosystems.

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

“…We compare these findings with previous studies, which have examined the lipidome of the Black Sea water column using traditional IPL identification (e.g., Neretin et al, 2007;Wakeham et al, 2007;Schubotz et al, 2009;Sollai et al, 2018). Our rapid visualization method lays a foundation for the study of Ding et al (2021), reported in parallel to this study, which used information theory framework combined with molecular networking to investigate lipid diversity and specificity as well as identify novel lipids.…”

“…At its maxima at 130 mbsl, at the top of the euxinic zone, it is most probably associated with SRB. Three components were 1deoxyceramides and two were sulfono-1-deoxyceramides (as per their assignment in Ding et al, 2021). Also present were two PGs, one with a DAG 33:1 core and one with a 32:0 core.…”

“…Here, we demonstrate this by examining other components in a subcluster containing the sulfate-1-deoxyceramide with m/z 928.8001 (cluster D, associated with the euxinic zone, Table 2). As discussed in Ding et al (2021), this novel 1-deoxysphingolipids may be produced by an as-yet uncultured anaerobic heterotroph related to Bacteroidetes. We examined components with a very similar depth profile, that may be associated with the same microbial producer or with producers that live in the same environmental niche.…”

“…We present here the 10 most abundant components in this subcluster (Dx) (Table 3). All 10 components followed a similar abundance depth profile with a distinct maximum at 130 m. Other than the sulfate-1-deoxyceramide with m/z 928.8001 (Ding et al, 2021), no other components in Dx were in the list of top 10 most abundant components in cluster D.…”

“…Diether lipids have been detected in a limited number of bacteria (e.g., Grossi et al, 2015) but their (core lipid) abundance in the Black Sea water column has been shown to correlate with sulfate reducing bacteria (SRB; Neretin et al, 2007). Two components, tentatively assigned as sulfate-1-deoxyceramides (Ding et al, 2021), were also among most abundant components in cluster D. Ding et al (2021) hypothesize that, as bacterial sphingolipids are mainly produced by Bacteroidetes and selected Proteobacteria (Heaver et al, 2018) and because certain Bacteroidetes from the Black Sea are known to produce capnines (Bale et al, 2020;Yadav et al, 2020), sulfonoanalogs of sphinganine (Godchaux and Leadbetter, 1980), that these novel sulfate-1-deoxyceramides, may also be produced by anaerobic heterotrophs related to Bacteroidetes.…”