Lipidomic chemotaxonomy aligned with phylogeny of Halobacteria

Abstract

Archaea play an important role in global biogeochemical cycles and are considered ancestral to eukaryotes. The unique lipid composition of archaea, characterized by isoprenoid alkyl chains and ether linkage to glycerol-1-phosphate, offers valuable insights into archaeal phylogeny and evolution. However, comprehensive studies focusing on archaeal lipidomes, especially at the intact polar lipid level, are currently limited. Here, we built an in-house library of archaeal lipids by using high-performance liquid chromatography coupled with mass-spectrometry, which was integrated with bioinformatics and molecular network analyses. Seven halobacterial strains, representing three distinct orders, were cultured under identical conditions to investigate their lipidomes. A total of 162 features were identified, corresponding to 107 lipids that could be assigned to different strains. Clustering analyses of both core lipids and total lipids matched the phylogeny of Halobacteria at the order level. Notably, lipids such as triglycosyl diether-phosphatidyl acid and bis-sulfate glycosyl lipids were specific to particular groups and could serve as diagnostic intact lipid biomarkers for Halobacteria. Furthermore, the analysis of network-coordinated features facilitated the linkage of unknown lipid compounds to phylogeny, which promotes a lipidome to phylogeny matchup among three Haloferax strains, thereby expanding the knowledge of the halobacterial lipidome. Our study provides a comprehensive view of the lipidomes of the seven strains of Halobacteria and highlights the potential of lipidomics for studying archaeal phylogeny.

Selective lipid recruitment by an archaeal DPANN symbiont from its host

“…Lipidome annotation remains a challenge in lipidomic studies, as public spectral databases are inadequately populated. Nevertheless, by comparison with literature 30 – 37 , as well as tentative identification, we were able to annotate 246 likely archaeal lipids (Supplementary Fig. 6 ).…”

Selective lipid recruitment by an archaeal DPANN symbiont from its host

“…In terms of natural differences, unlike the other reported host archaea which primarily consist of monolayer membrane tetraether lipids, mostly glycerol dialkyl glycerol tetraethers (GDGTs) 46 , the cellular membranes of Hrr. lacusprofundi are exclusively formed by bilayer AR lipids 30,31,37 . The composition of bilayer-forming intact polar lipids in Halobacteriales stands as one of the most extreme instance of negatively charged membranes across the tree of life and is considered to be an adaptation to the high cationic environment 31 .…”

“…Lipidome annotation remains a challenge in lipidomic studies, as public spectral databases are inadequately populated. Nevertheless, by comparison with literature 30,31,32,33,34,35,36,37 , as well as tentative identification, we were able to annotate 246 likely archaeal lipids (Supplementary Fig. 6).…”

Proposed minimal standards for description of new taxa of the class Halobacteria

“…The polar lipids of members of the Halobacteria class account for about 90 % of total lipids and consist of 2,3-diphytanyl-sn-glycerol analogues of phospholipids and glycolipids [40][41][42]. The phospholipids mainly consist of C 20 C 20 (diphytanyl), C 20 C 25 (phytanylsesterterpanyl), or C 25 C 25 (disesterterpanyl) diether analogues of phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), and phosphatidylglycerol sulfate (PGS) [43,44].…”

“…PA, PG, and PGP-Me are present in all known taxa, while PGS is found in many, but not in all genera and species. Different glycolipids are found in different genera, including mannosyl glucosyl diether (DGD-1), another diglycosyl diether (DGD-2), sulfated mannosyl glucosyl diethers (S-DGD-1, S-DGD-3, S-DGD-5), disulfated mannosyl glucosyl diether (S 2 -DGD), galactosyl mannosyl glycosyl diether (TGD-l), glycosyl mannosyl glucosyl diether (TGD-2), sulfated galactosyl mannosyl glucosyl diether (S-TGD-1), and sulfated galactosyl mannosyl galactofuranosyl glucosyl diether (S-TeGD) [12,[40][41][42][43][44]. Alkaliphilic species often lack glycolipids.…”