Mono- and dialkyl glycerol ether lipids in anaerobic bacteria: biosynthetic insights from the mesophilic sulfate reducer Desulfatibacillum alkenivorans PF2803T

Nitrogen and sulfur for phosphorus: Lipidome adaptation of anaerobic sulfate-reducing bacteria in phosphorus-deprived conditions

Understanding how microbial lipidomes adapt to environmental and nutrient stress is crucial for comprehending microbial survival and functionality. Certain anaerobic bacteria can synthesize glycerolipids with ether/ester bonds, yet the complexities of their lipidome remodeling under varying physicochemical and nutritional conditions remain largely unexplored. In this study, we thoroughly examined the lipidome adaptations of Desulfatibacillum alkenivorans strain PF2803T, a mesophilic anaerobic sulfate-reducing bacterium known for its high proportions of alkylglycerol ether lipids in its membrane, under various cultivation conditions including temperature, pH, salinity, and ammonium and phosphorous concentrations. Employing an extensive analytical and computational lipidomic methodology, we identified an assemblage of nearly 400 distinct lipids, including a range of glycerol ether/ester lipids with various polar head groups. Information theory-based analysis revealed that temperature fluctuations and phosphate scarcity profoundly influenced the lipidome's composition, leading to an enhanced diversity and specificity of novel lipids. Notably, phosphorous limitation led to the biosynthesis of novel glucuronosylglycerols and sulfur-containing aminolipids, termed butyramide cysteine glycerols, featuring various ether/ester bonds. This suggests a novel adaptive strategy for anaerobic heterotrophs to thrive under phosphorus-depleted conditions, characterized by a diverse array of nitrogen- and sulfur-containing polar head groups, moving beyond a reliance on conventional nonphospholipid types.

Mono- to tetra-alkyl ether cardiolipins in a mesophilic, sulfate-reducing bacterium identified by UHPLC-HRMSn: a novel class of membrane lipids

The composition of membrane lipids varies in a number of ways as adjustment to growth conditions. Variations in head group composition and carbon skeleton and degree of unsaturation of glycerol-bound acyl or alkyl chains results in a high structural complexity of the lipidome of bacterial cells. We studied the lipidome of the mesophilic, sulfate-reducing bacterium, Desulfatibacillum alkenivorans strain PF2803T by ultra-high-pressure liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMSn). This anaerobic bacterium has been previously shown to produce high amounts of mono-and di-alkyl glycerol ethers as core membrane lipids. Our analyses revealed that these core lipids occur with phosphatidylethanomamine (PE) and phosphatidylglycerol (PG) head groups, representing each approximately one third of the phospholipids. The third class was a novel group of phospholipids, i.e., cardiolipins (CDLs) containing one (monoether/triester) to four (tetraether) ether-linked saturated straight-chain or methyl-branched alkyl chains. Tetraether CDLs have been shown to occur in archaea (with isoprenoid alkyl chains) but have not been previously reported in the bacterial Domain. Structurally related CDLs with one or two alkyl/acyl chains missing, so-called monolyso-and dilyso-CDLs, were also observed. The potential biosynthetic pathway of these novel CDLs was investigated by examining the genome of D. alkenivorans. Three CDL synthases were identified; one catalyzes the condensation of two PGs, the other two are probably involved in the condensation of a PE with a PG. A heterologous gene expression experiment showed the in vivo production of dialkylglycerols upon anaerobic expression of the glycerol ester reductase enzyme of D. alkenivorans in E. coli. Reduction of the ester bonds probably occurs first at the sn-1 and subsequently at the sn-2 position after the formation of PEs and PGs.

Intact polar lipidome and membrane adaptations of microbial communities inhabiting serpentinite-hosted fluids

The generation of hydrogen and reduced carbon compounds during serpentinization provides sustained energy for microorganisms on Earth, and possibly on other extraterrestrial bodies (e.g., Mars, icy satellites). However, the geochemical conditions that arise from water-rock reaction also challenge the known limits of microbial physiology, such as hyperalkaline pH, limited electron acceptors and inorganic carbon. Because cell membranes act as a primary barrier between a cell and its environment, lipids are a vital component in microbial acclimation to challenging physicochemical conditions. To probe the diversity of cell membrane lipids produced in serpentinizing settings and identify membrane adaptations to this environment, we conducted the first comprehensive intact polar lipid (IPL) biomarker survey of microbial communities inhabiting the subsurface at a terrestrial site of serpentinization. We used an expansive, custom environmental lipid database that expands the application of targeted and untargeted lipodomics in the study of microbial and biogeochemical processes. IPLs extracted from serpentinite-hosted fluid communities were comprised of >90% isoprenoidal and non-isoprenoidal diether glycolipids likely produced by archaeal methanogens and sulfate-reducing bacteria. Phospholipids only constituted ~1% of the intact polar lipidome. In addition to abundant diether glycolipids, betaine and trimethylated-ornithine aminolipids and glycosphingolipids were also detected, indicating pervasive membrane modifications in response to phosphate limitation. The carbon oxidation state of IPL backbones was positively correlated with the reduction potential of fluids, which may signify an energy conservation strategy for lipid synthesis. Together, these data suggest microorganisms inhabiting serpentinites possess a unique combination of membrane adaptations that allow for their survival in polyextreme environments. The persistence of IPLs in fluids beyond the presence of their source organisms, as indicated by 16S rRNA genes and transcripts, is promising for the detection of extinct life in serpentinizing settings through lipid biomarker signatures. These data contribute new insights into the complexity of lipid structures generated in actively serpentinizing environments and provide valuable context to aid in the reconstruction of past microbial activity from fossil lipid records of terrestrial serpentinites and the search for biosignatures elsewhere in our solar system.

Tocopherols and associated derivatives track the phytoplanktonic response to evolving pelagic redox conditions spanning Oceanic Anoxic Event 2

Tocopherols serve a critical role as antioxidants inhibiting lipid peroxidation in photosynthetic organisms, yet are seldom used in geobiological investigations. The ubiquity of tocopherols in all photosynthetic lifeforms is often cited as an impediment to any diagnostic paleoenvironmental potential, while the inability to readily analyze these compounds via conventional methods, such as gas chromatography-mass spectrometry, further diminishes the capacity to serve as useful 'biomarkers'. Here, we analyzed an exceptionally preserved black shale sequence from the Demerara Rise that spans Oceanic Anoxic Event 2 (OAE-2) to reexamine the significance of tocopherols and associated derivatives (i.e. tocol derivatives) in ancient sediments. Tocol derivatives were analyzed via liquid chromatography-quadrupole time-of-flight-mass spectrometry and included tocopherols, a methyltrimethyltridecylchroman, and the first reported detection of tocopherol quinones and methylphytylbenzoquinones in the geologic record. Strong correlations between tocol derivatives were observed over the studied interval. Tocol derivative concentrations and ratios, which normalized tocopherols to potential derivatives, revealed absolute and relative increases in tocopherols as exclusive features of OAE-2 that can be explained by two possible mechanisms related to tocopherol production and preservation. The development of photic zone euxinia during OAE-2 likely forced an upward migration of oxygenic photoautotrophs, increasing oxidative stress that elicited heightened tocopherol biosynthesis. However, shoaling euxinic conditions may have simultaneously acted to enhance tocopherol preservation given the relatively high lability of tocopherols in the water column. Both scenarios could produce the observed stratigraphic distribution of tocol derivatives in this study, although the elevated tocopherol concentrations that define OAE-2 at the Demerara Rise are primarily attributed to enhanced tocopherol production by shoaling phytoplanktonic communities. Thus, the occurrence of tocopherols and associated derivatives in sediments and rocks of marine origin is likely indicative of shallow-water anoxia, tracking the phytoplanktonic response to the abiotic stresses associated with vertical fluctuations in pelagic redox.

Synthesis of ether lipids: natural compounds and analogues

Ether lipids are compounds present in many living organisms including humans that feature an ether bond linkage at the sn-1 position of the glycerol. This class of lipids features singular structural roles and biological functions. Alkyl ether lipids and alkenyl ether lipids (also identified as plasmalogens) correspond to the two sub-classes of naturally occurring ether lipids. In 1979 the discovery of the structure of the platelet-activating factor (PAF) that belongs to the alkyl ether class of lipids increased the interest in these bioactive lipids and further promoted the synthesis of non-natural ether lipids that was initiated in the late 60's with the development of edelfosine (an anticancer drug). More recently, ohmline, a glyco glycero ether lipid that modulates selectively SK3 ion channels and reduces in vivo the occurrence of bone metastases, and other glyco glycero ether also identified as GAEL (glycosylated antitumor ether lipids) that exhibit promising anticancer properties renew the interest in this class of compounds. Indeed, ether lipid represent a new and promising class of compounds featuring the capacity to modulate selectively the activity of some membrane proteins or, for other compounds, feature antiproliferative properties via an original mechanism of action. The increasing interest in studying ether lipids for fundamental and applied researches invited to review the methodologies developed to prepare ether lipids. In this review we focus on the synthetic method used for the preparation of alkyl ether lipids either naturally occurring ether lipids (e.g., PAF) or synthetic derivatives that were developed to study their biological properties. The synthesis of neutral or charged ether lipids are reported with the aim to assemble in this review the most frequently used methodologies to prepare this specific class of compounds.

Dominance of mixed ether/ester, intact polar membrane lipids in five species of the order Rubrobacterales: Another group of bacteria not obeying the "lipid divide"

The composition of the core lipids and intact polar lipids (IPLs) of five Rubrobacter species was examined. Methylated (ω-4) fatty acids (FAs) characterized the core lipids of Rubrobacter radiotolerans, R. xylanophilus and R. bracarensis. In contrast, R. calidifluminis and R. naiadicus lacked ω-4 methyl FAs but instead contained abundant (i.e., 34-41 % of the core lipids) ω-cyclohexyl FAs not reported before in the order Rubrobacterales. Their genomes contained an almost complete operon encoding proteins enabling production of cyclohexane carboxylic acid CoA thioester, which acts as a building block for ω-cyclohexyl FAs in other bacteria. Hence, the most plausible explanation for the biosynthesis of these cyclic FAs in R. calidifluminis and R. naiadicus is a recent acquisition of this operon. All strains contained 1-O-alkyl glycerol ether lipids in abundance (up to 46 % of the core lipids), in line with the dominance (>90 %) of mixed ether/ester IPLs with a variety of polar headgroups. The IPL head group distribution of R. calidifluminis and R. naiadicus differed, e.g. they lacked a novel IPL tentatively assigned as phosphothreoninol. The genomes of all five Rubrobacter species contained a putative operon encoding the synthesis of the 1-O-alkyl glycerol phosphate, the presumed building block of mixed ether/ester IPLs, which shows some resemblance with an operon enabling ether lipid production in various other aerobic bacteria but requires more study. The uncommon dominance of mixed ether/ester IPLs in Rubrobacter species exemplifies our recent growing awareness that the lipid divide between archaea and bacteria/eukaryotes is not as clear cut as previously thought.

Disentangling the lipid divide: Identification of key enzymes for the biosynthesis of membrane-spanning and ether lipids in Bacteria

Bacterial membranes are composed of fatty acids (FAs) ester-linked to glycerol-3-phosphate, while archaea have membranes made of isoprenoid chains ether-linked to glycerol-1-phosphate. Many archaeal species organize their membrane as a monolayer of membrane-spanning lipids (MSLs). Exceptions to this "lipid divide" are the production by some bacterial species of (ether-bound) MSLs, formed by tail-to-tail condensation of FAs resulting in the formation of (iso) diabolic acids (DAs), which are the likely precursors of paleoclimatological relevant branched glycerol dialkyl glycerol tetraether molecules. However, the enzymes responsible for their production are unknown. Here, we report the discovery of bacterial enzymes responsible for the condensation reaction of FAs and for ether bond formation and confirm that the building blocks of iso-DA are branched iso-FAs. Phylogenomic analyses of the key biosynthetic genes reveal a much wider diversity of potential MSL (ether)-producing bacteria than previously thought, with importantt implications for our understanding of the evolution of lipid membranes.

Tricky Isomers—The Evolution of Analytical Strategies to Characterize Plasmalogens and Plasmanyl Ether Lipids

Typically, glycerophospholipids are represented with two esterified fatty acids. However, by up to 20%, a significant proportion of this lipid class carries an ether-linked fatty alcohol side chain at the sn-1 position, generally referred to as ether lipids, which shape their specific physicochemical properties. Among those, plasmalogens represent a distinct subgroup characterized by an sn-1 vinyl-ether double bond. The total loss of ether lipids in severe peroxisomal defects such as rhizomelic chondrodysplasia punctata indicates their crucial contribution to diverse cellular functions. An aberrant ether lipid metabolism has also been reported in multifactorial conditions including Alzheimer’s disease. Understanding the underlying pathological implications is hampered by the still unclear exact functional spectrum of ether lipids, especially in regard to the differentiation between the individual contributions of plasmalogens (plasmenyl lipids) and their non-vinyl-ether lipid (plasmanyl) counterparts. A primary reason for this is that exact identification and quantification of plasmalogens and other ether lipids poses a challenging and usually labor-intensive task. Diverse analytical methods for the detection of plasmalogens have been developed. Liquid chromatography–tandem mass spectrometry is increasingly used to resolve complex lipid mixtures, and with optimized parameters and specialized fragmentation strategies, discrimination between ethers and plasmalogens is feasible. In this review, we recapitulate historic and current methodologies for the recognition and quantification of these important lipids and will discuss developments in this field that can contribute to the characterization of plasmalogens in high structural detail.

Bacterial Homologs of Progestin and AdipoQ Receptors (PAQRs) Affect Membrane Energetics Homeostasis but Not Fluidity

Membrane potential homeostasis is essential for cell survival. Defects in membrane potential lead to pleiotropic phenotypes, consistent with the central role of membrane energetics in cell physiology. Homologs of the progestin and AdipoQ receptors (PAQRs) are conserved in multiple phyla of Bacteria and Eukarya. In eukaryotes, PAQRs are proposed to modulate membrane fluidity and fatty acid (FA) metabolism. The role of bacterial homologs has not been elucidated. Here, we use Escherichia coli and Bacillus subtilis to show that bacterial PAQR homologs, which we name “TrhA,” have a role in membrane energetics homeostasis. Using transcriptional fusions, we show that E. coli TrhA (encoded by yqfA) is part of the unsaturated fatty acid biosynthesis regulon. Fatty acid analyses and physiological assays show that a lack of TrhA in both E. coli and B. subtilis (encoded by yplQ) provokes subtle but consistent changes in membrane fatty acid profiles that do not translate to control of membrane fluidity. Instead, membrane proteomics in E. coli suggested a disrupted energy metabolism and dysregulated membrane energetics in the mutant, though it grew similarly to its parent. These changes translated into a disturbed membrane potential in the mutant relative to its parent under various growth conditions. Similar dysregulation of membrane energetics was observed in a different E. coli strain and in the distantly related B. subtilis. Together, our findings are consistent with a role for TrhA in membrane energetics homeostasis, through a mechanism that remains to be elucidated.

IMPORTANCE Eukaryotic homologs of the progestin and AdipoQ receptor family (PAQR) have been shown to regulate membrane fluidity by affecting, through unknown mechanisms, unsaturated fatty acid (FA) metabolism. The bacterial homologs studied here mediate small and consistent changes in unsaturated FA metabolism that do not seem to impact membrane fluidity but, rather, alter membrane energetics homeostasis. Together, the findings here suggest that bacterial and eukaryotic PAQRs share functions in maintaining membrane homeostasis (fluidity in eukaryotes and energetics for bacteria with TrhA homologs).

Acetate Degradation at Low pH by the Moderately Acidophilic Sulfate Reducer Acididesulfobacillus acetoxydans gen. nov. sp. nov

In acid drainage environments, biosulfidogenesis by sulfate-reducing bacteria (SRB) attenuates the extreme conditions by enabling the precipitation of metals as their sulfides, and the neutralization of acidity through proton consumption. So far, only a handful of moderately acidophilic SRB species have been described, most of which are merely acidotolerant. Here, a novel species within a novel genus of moderately acidophilic SRB is described, Acididesulfobacillus acetoxydans gen. nov. sp. nov. strain INE, able to grow at pH 3.8. Bioreactor studies with strain INE at optimum (5.0) and low (3.9) pH for growth showed that strain INE alkalinized its environment, and that this was more pronounced at lower pH. These studies also showed the capacity of strain INE to completely oxidize organic acids to CO₂, which is uncommon among acidophilic SRB. Since organic acids are mainly in their protonated form at low pH, which increases their toxicity, their complete oxidation may be an acid stress resistance mechanism. Comparative proteogenomic and membrane lipid analysis further indicated that the presence of saturated ether-bound lipids in the membrane, and their relative increase at lower pH, was a protection mechanism against acid stress. Interestingly, other canonical acid stress resistance mechanisms, such as a Donnan potential and increased active charge transport, did not appear to be active.

Messinian bottom-grown selenitic gypsum: An archive of microbial life

Primary gypsum deposits, which accumulated in the Mediterranean Basin during the so-called Messinian salinity crisis (5.97-5.33 Ma), represent an excellent archive of microbial life. We investigated the molecular fossil inventory and the corresponding compound-specific δ¹³ C values of bottom-grown gypsum formed during the first stage of the crisis in four marginal basins across the Mediterranean (Nijar, Spain; Vena del Gesso, Italy; Heraklion, Crete; and Psematismenos, Cyprus). All studied gypsum samples contain intricate networks of filamentous microfossils, whose phylogenetic affiliation has been debated for a long time. Petrographic analysis, molecular fossil inventories (hydrocarbons, alcohols, and carboxylic acids), and carbon stable isotope patterns suggest that the mazes of filamentous fossils represent benthic microbial assemblages dominated by chemotrophic sulfide-oxidizing bacteria; in some of the samples, the body fossils are accompanied by lipids produced by sulfate-reducing bacteria. Abundant isoprenoid alcohols including diphytanyl glycerol diethers (DGDs) and glycerol dibiphytanyl glycerol tetraethers (GDGTs), typified by highly variable carbon stable isotope composition with δ¹³ C values spanning from -40 to -14‰, reveal the presence of planktic and benthic archaeal communities dwelling in Messinian paleoenvironments. The compound inventory of archaeal lipids indicates the existence of a stratified water column, with a normal marine to diluted upper water column and more saline deeper waters. This study documents the lipid biomarker inventory of microbial life preserved in ancient gypsum deposits, helping to reconstruct the widely debated conditions under which Messinian gypsum formed.

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

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.

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

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.

Bioactive Ether Lipids: Primordial Modulators of Cellular Signaling

The primacy of lipids as essential components of cellular membranes is conserved across taxonomic domains. In addition to this crucial role as a semi-permeable barrier, lipids are also increasingly recognized as important signaling molecules with diverse functional mechanisms ranging from cell surface receptor binding to the intracellular regulation of enzymatic cascades. In this review, we focus on ether lipids, an ancient family of lipids having ether-linked structures that chemically differ from their more prevalent acyl relatives. In particular, we examine ether lipid biosynthesis in the peroxisome of mammalian cells, the roles of selected glycerolipids and glycerophospholipids in signal transduction in both prokaryotes and eukaryotes, and finally, the potential therapeutic contributions of synthetic ether lipids to the treatment of cancer.

Microbial biomarkers reveal a hydrothermally active landscape at Olduvai Gorge at the dawn of the Acheulean, 1.7 Ma

Landscape-scale reconstructions of ancient environments within the cradle of humanity may reveal insights into the relationship between early hominins and the changing resources around them. Many studies of Olduvai Gorge during Pliocene-Pleistocene times have revealed the presence of precession-driven wet-dry cycles atop a general aridification trend, though may underestimate the impact of local-scale conditions on early hominins, who likely experienced a varied and more dynamic landscape. Fossil lipid biomarkers from ancient plants and microbes encode information about their surroundings via their molecular structures and composition, and thus can shed light on past environments. Here, we employ fossil lipid biomarkers to study the paleolandscape at Olduvai Gorge at the emergence of the Acheulean technology, 1.7 Ma, through the Lower Augitic Sandstones layer. In the context of the expansion of savanna grasslands, our results represent a resource-rich mosaic ecosystem populated by groundwater-fed rivers, aquatic plants, angiosperm shrublands, and edible plants. Evidence of a geothermally active landscape is reported via an unusual biomarker distribution consistent with the presence of hydrothermal features seen today at Yellowstone National Park. The study of hydrothermalism in ancient settings and its impact on hominin evolution has not been addressed before, although the association of thermal springs in the proximity of archaeological sites documented here can also be found at other localities. The hydrothermal features and resources present at Olduvai Gorge may have allowed early hominins to thermally process edible plants and meat, supporting the possibility of a prefire stage of human evolution.

Natranaerofaba carboxydovora gen. nov., sp. nov., an extremely haloalkaliphilic CO-utilizing acetogen from a hypersaline soda lake representing a novel deep phylogenetic lineage in the class 'Natranaerobiia'

An anaerobic enrichment with CO from sediments of hypersaline soda lakes resulted in a methane‐forming binary culture, whereby CO was utilized by a bacterium and not the methanogenic partner. The bacterial isolate ANCO1 forms a deep‐branching phylogenetic lineage at the level of a new family within the class ‘Natranaerobiia’. It is an extreme haloalkaliphilic and moderate thermophilic acetogen utilizing CO, formate, pyruvate and lactate as electron donors and thiosulfate, nitrate (reduced to ammonia) and fumarate as electron acceptors. The genome of ANCO1 encodes a full Wood–Ljungdahl pathway allowing for CO oxidation and acetogenic conversion of pyruvate. A locus encoding Nap nitrate reductase/NrfA ammonifying nitrite reductase is also present. Thiosulfate respiration is encoded by a Phs/Psr‐like operon. The organism obviously relies on Na‐based bioenergetics, since the genome encodes for the Na⁺‐Rnf complex, Na⁺‐F1F0 ATPase and Na⁺‐translocating decarboxylase. Glycine betaine serves as a compatible solute. ANCO1 has an unusual membrane polar lipid composition dominated by diethers, more common among archaea, probably a result of adaptation to multiple extremophilic conditions. Overall, ANCO1 represents a unique example of a triple extremophilic CO‐oxidizing anaerobe and is classified as a novel genus and species Natranaerofaba carboxydovora in a novel family Natranaerofabacea.

Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes

Acidic pit lakes are abandoned open pit mines filled with acid mine drainage (AMD)-highly acidic, metalliferous waters that pose a severe threat to the environment and are rarely properly remediated. Here, we investigated two meromictic, oligotrophic acidic mine pit lakes in the Iberian Pyrite Belt (IPB), Filón Centro (Tharsis) (FC) and La Zarza (LZ). We observed a natural attenuation of acidity and toxic metal concentrations towards the lake bottom, which was more pronounced in FC. The detection of Cu and Zn sulfides in the monimolimnion of FC suggests precipitation of dissolved metals as metal sulfides, pointing to biogenic sulfide formation. This was supported by microbial diversity analysis via 16S rRNA gene amplicon sequencing of samples from the water column, which showed the presence of sulfidogenic microbial taxa in FC and LZ. In the monimolimnion of FC, sequences affiliated with the putative sulfate-reducing genus Desulfomonile were dominant (58%), whereas in the more acidic and metal-enriched LZ, elemental sulfur-reducing Acidianus and Thermoplasma spp., and disproportionating Desulfocapsa spp. were more abundant. Furthermore, the detection of reads classified as methanogens and Desulfosporosinus spp., although at low relative abundance, represents one of the lowest pH values (2.9 in LZ) at which these taxa have been reported, to our knowledge. Analysis of potential biomarker lipids provided evidence that high levels of phosphocholine lipids with mixed acyl/ether glycerol core structures were associated with Desulfomonile, while ceramide lipids were characteristic of Microbacter in these environments. We propose that FC and LZ function as natural bioremediation reactors where metal sulfide precipitation is mediated by biosulfidogenesis starting from elemental sulfur reduction and disproportionation at an early stage (LZ), followed by sulfate reduction at a later stage (FC).

Lipid Biomarker Record of the Serpentinite-Hosted Ecosystem of the Samail Ophiolite, Oman and Implications for the Search for Biosignatures on Mars

Serpentinization is a weathering process in which ultramafic rocks react with water, generating a range of products, including serpentine and other minerals, in addition to H₂ and low-molecular-weight hydrocarbons that are capable of sustaining microbial life. Lipid biomarker analyses of serpentinite-hosted ecosystems hold promise as tools for investigating microbial activity in ancient Earth environments and other terrestrial planets such as Mars because lipids have the potential for longer term preservation relative to DNA, proteins, and other more labile organic molecules. Here, we report the first lipid biomarker record of microbial activity in the mantle section of the Samail Ophiolite, in the Sultanate of Oman, a site undergoing active serpentinization. We detected isoprenoidal (archaeal) and branched (bacterial) glycerol dialkyl glycerol tetraether (GDGT) lipids, including those with 0-3 cyclopentane moieties, and crenarchaeol, an isoprenoidal GDGT containing four cyclopentane and one cyclohexane moieties, as well as monoether lipids and fatty acids indicative of sulfate-reducing bacteria. Comparison of our geochemical data and 16S rRNA data from the Samail Ophiolite with those from other serpentinite-hosted sites identifies the existence of a common core serpentinization microbiome. In light of these findings, we also discuss the preservation potential of serpentinite lipid biomarker assemblages on Earth and Mars. Continuing investigations of the Samail Ophiolite and other terrestrial analogues will enhance our understanding of microbial habitability and diversity in serpentinite-hosted environments on Earth and elsewhere in the Solar System.

Constraining the formation of authigenic carbonates in a seepage-affected cold-water coral mound by lipid biomarkers

Cold-water coral (CWC) mounds are build-ups comprised of coral-dominated intervals alternating with a mixed carbonate-siliciclastic matrix. At some locations, CWC mounds are influenced by methane seepage, but the impact of methane on CWC mounds is poorly understood. To constrain the potential impact of methane on CWC mound growth, lipid biomarker investigations were combined with mineralogical and petrographic analyses to investigate the anaerobic oxidation of methane (AOM) and authigenic carbonate formation in sediment from a seep-affected CWC mound in the Gulf of Cadiz. The occurrence of AOM was confirmed by characteristic lipids found within a semi-lithified zone (SLZ) consisting of authigenic aragonite, high-magnesium calcite and calcium-excess dolomite. The formation of high-Mg calcite is attributed to AOM, acting as a lithifying agent. Aragonite is only a minor phase. Ca-excess dolomite in the SLZ and upper parts may be formed by organoclastic sulphate reduction, favouring precipitation by increased alkalinity. The AOM biomarkers in the SLZ include isoprenoid-based archaeal membrane lipids, such as abundant glycerol dibiphytanyl glycerol tetraethers (GDGTs) dominated by GDGT-2. The δ¹³ C values of GDGT-2, measured as ether-cleaved monocyclic biphytanes, are as low as -100‰ versus V-PDB. Further, bacterial dialkyl glycerol diethers with two anteiso-C₁₅ alkyl chains and δ¹³ C values of -81‰ are interpreted as biomarkers of sulphate-reducing bacteria. The lipid biomarker signatures and mineralogical patterns suggest that anaerobic methane-oxidizing archaea of the ANME-1 group thrived in the subsurface at times of slow and diffusive methane seepage. Petrographic analyses revealed that the SLZ was exhumed at some point (e.g. signs of bioerosion of the semi-lithified sediment), providing a hard substrate for CWC larval settlement. In addition, this work reveals that AOM-induced semi-lithification likely played a role in mound stabilization. Lipid biomarker analysis proves to be a powerful tool to disentangle early diagenetic processes induced by microbial metabolisms.

Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments

Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H₂ and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was ‘Candidatus Syntrophonatronum acetioxidans,’ and a near-complete draft genome of this SAOB was reconstructed. ‘Ca. S. acetioxidans’ has all genes necessary for operating the Wood–Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na⁺-dependent ATP synthase and marker genes for ‘salt-out‘ strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of ‘Ca. S. acetioxidans’ showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to ‘Ca. S. acetioxidans’ with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.

Temperature-Dependent Alkyl Glycerol Ether Lipid Composition of Mesophilic and Thermophilic Sulfate-Reducing Bacteria

The occurrence of non-isoprenoid alkyl glycerol ether lipids in Bacteria and natural environments is increasingly being reported and the specificity and diagenetic stability of these lipids make them powerful biomarkers for biogeochemical and environmental studies. Yet the environmental controls on the biosynthesis of these peculiar membrane lipids remain poorly documented. Here, the lipid content of two mesophilic (Desulfatibacillum aliphaticivorans and Desulfatibacillum alkenivorans) and one thermophilic (Thermodesulfobacterium commune) sulfate-reducing bacteria-whose membranes are mostly composed of ether lipids-was investigated as a function of growth temperature (20-40°C and 54-84°C, respectively). For all strains, the cellular lipid content was lower at sub- or supra-optimal growth temperature, but the relative proportions of dialkyl glycerols, monoalkyl glycerols and fatty acids remained remarkably stable whatever the growth temperature. Rather than changing the proportions of the different lipid classes, the three strains responded to temperature changes by modifying the average structural composition of the alkyl and acyl chains constitutive of their membrane lipids. Major adaptive mechanisms concerned modifications of the level of branching and of the proportions of the different methyl branched lipids. Specifically, an increase in temperature induced mesophilic strains to produce less dimethyl branched dialkyl glycerols and 10-methyl branched lipids relative to linear structures, and the thermophilic strain to decrease the proportion of anteiso relative to iso methyl branched compounds. These modifications were in agreement with a regulation of the membrane fluidity. In one mesophilic and the thermophilic strains, a modification of the growth temperature further induced changes in the relative proportions of sn-2 vs sn-1 monoalkyl glycerols, suggesting an unprecedented mechanism of homeoviscous adaptation in Bacteria. Strong linear correlations observed between different ratios of alkyl glycerols and temperature allow to hypothesize the use of these specific lipids as indicators of temperature changes in the environment.

The anaerobic biosynthesis of plasmalogens

The biosynthesis of plasmalogens in anaerobic bacteria differs fundamentally from that in animal cells. Firstly, the formation of the alk-1'-enyl ether bond in animal cells is oxygen dependent. Secondly, the first step in plasmalogen formation in animal cells is an acylation of dihydroxyacetone phosphate, which has been ruled out as a precursor in anaerobes. In bacteria the alk-1'-enyl ether bond is formed after the fully formed acyl glycerolipids are synthesized. Evidence will be presented for the conversion of the sn-1 acyl-linked chain to an O-alk-1'-enyl ether by an as yet unknown mechanism.

Synthesis of neutral ether lipid monoalkyl-diacylglycerol by lipid acyltransferases

In mammals, ether lipids exert a wide spectrum of signaling and structural functions, such as stimulation of immune responses, anti-tumor activities, and enhancement of sperm functions. Abnormal accumulation of monoalkyl-diacylglycerol (MADAG) was found in Wolman's disease, a human genetic disorder defined by a deficiency in lysosomal acid lipase. In the current study, we found that among the nine recombinant human lipid acyltransferases examined, acyl-CoA:diacylglycerol acyltransferase (DGAT)1, DGAT2, acyl-CoA:monoacylglycerol acyltransferase (MGAT)2, MGAT3, acyl-CoA:wax-alcohol acyltransferase 2/MFAT, and DGAT candidate 3 were able to use 1-monoalkylglycerol (1-MAkG) as an acyl acceptor for the synthesis of monoalkyl-monoacylglycerol (MAMAG). These enzymes demonstrated different enzymatic turnover rates and relative efficiencies for the first and second acylation steps leading to the synthesis of MAMAG and MADAG, respectively. They also exhibited different degrees of substrate preference when presented with 1-monooleoylglycerol versus 1-MAkG. In CHO-K1 cells, treatment with DGAT1 selective inhibitor, XP-620, completely blocked the synthesis of MADAG, indicating that DGAT1 is the predominant enzyme responsible for the intracellular synthesis of MADAG in this model system. The levels of MADAG in the adrenal gland of DGAT1 KO mice were reduced as compared with those of the WT mice, suggesting that DGAT1 is a major enzyme for the synthesis of MADAG in this tissue. Our findings indicate that several of these lipid acyltransferases may be able to synthesize neutral ether lipids in mammals.

Isolation and whole genome sequencing of a Ruminococcus-like bacterium, associated with irritable bowel syndrome

In our previous studies on the intestinal microbiota in irritable bowel syndrome (IBS), we identified a bacterial phylotype with higher abundance in patients suffering from diarrhea than in healthy controls. In the present work, we have isolated in pure culture strain RT94, belonging to this phylotype, determined its whole genome sequence and performed an extensive genomic analysis and phenotypical testing. This revealed strain RT94 to be a strict anaerobe apparently belonging to a novel species with only 94% similarity in the 16S rRNA gene sequence to the closest relatives Ruminococcus torques and Ruminococcus lactaris. The G + C content of strain RT94 is 45.2 mol% and the major long-chain cellular fatty acids are C16:0, C18:0 and C14:0. The isolate is metabolically versatile but not a mucus or cellulose utilizer. It produces acetate, ethanol, succinate, lactate and formate, but very little butyrate, as end products of glucose metabolism. The mechanisms underlying the association of strain RT94 with diarrhea-type IBS are discussed.