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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Beta-mannans are insoluble plant polysaccharides with beta-1,4-linked mannose as the backbone. We used three forms of this polysaccharide, namely, pure mannan, glucomannan, and galactomannan, to enrich haloarchaea, which have the ability to utilize mannans for growth. Four mannan-utilizing strains obtained in pure cultures were closely related to each other on the level of the same species. Furthermore, another strain selected from the same habitats with a soluble beta-1,4-glucan (xyloglucan) was also able to grow with mannan. The phylogenomic analysis placed the isolates into a separate lineage of the new genus level within the family Natrialbaceae of the class Halobacteria. The strains are moderate alkaliphiles, extremely halophilic, and aerobic saccharolytics. In addition to the three beta-mannan forms, they can also grow with cellulose, xylan, and xyloglucan. Functional genome analysis of two representative strains demonstrated the presence of several genes coding for extracellular endo- beta-1,4-mannanase from the GH5_7 and 5_8 subfamilies and the GH26 family of glycosyl hydrolases. Furthermore, a large spectrum of genes encoding other glycoside hydrolases that were potentially involved in the hydrolysis of cellulose and xylan were also identified in the genomes. A comparative genomics analysis also showed the presence of similar endo-beta-1,4-mannanase homologs in the cellulotrophic genera Natronobiforma and Halococcoides. Based on the unique physiological properties and the results of phylogenomic analysis, the novel mannan-utilizing halolarchaea are proposed to be classified into a new genus and species Natronoglomus mannanivorans gen. nov., sp. nov. with the type strain AArc-m2/3/4 (=JCM 34861=UQM 41565). [ABSTRACT FROM AUTHOR]

The California current system (CCS) hosts one of the largest oxygen minimum zones (OMZs) in the world: the Eastern North Pacific (ENP) OMZ, which is dissociated into a subtropical and tropical region (i.e., the ESTNP and ETNP). In the modern ENP OMZ, bioavailable nitrogen (N) is lost via denitrification and anaerobic ammonium oxidation (anammox). Even so, paleo-reconstructions of N-loss have focused solely on denitrification. Fluctuations in bulk sedimentary δ15N over glacial-interglacial cycles have been interpreted to reflect variations in denitrification rates in response to ETNP OMZ intensity changes. This δ15N signal is thought to be transported northwards to the ESTNP OMZ. Here, we present the first CCS sedimentary record of ladderane lipids, biomarkers for anammox, located within the ESTNP OMZ (32° N; 118° W). Over the last two glacial terminations (~160 cal ka BP), ladderane concentrations were analysed in combination with the index of ladderanes with five cyclobutane moieties (NL5), short-chain (SC) ladderane degradation products, and productivity proxies. This shows that: 1) ladderanes derived from anammox bacteria living within the ESTNP OMZ water column; 2) ladderanes were continuously present, with relatively high concentrations during both glacial- and interglacial-periods, showcasing the ESTNP OMZ must have retained an anoxic core in which N-loss occurred; and 3) anammox abundance appears to have been driven both by OM-remineralization and advection changes, which regulated nutrient and oxygen levels. Our study shows that anammox was an important feature in the CCS and provides a more holistic picture of N-loss dynamics and the development of the ESTNP OMZ over glacial-interglacial cycles. Lastly, ladderanes were also detected in 160–500 cal ka BP sediments (15.7–37.5 mbsf; analysed at a low temporal resolution), highlighting their potential as anammox biomarkers in relatively deeper buried sediments for future studies. [ABSTRACT FROM AUTHOR]

High-resolution paleoclimate records from tropical continental settings are greatly needed to advance understanding of global climate dynamics. The International Continental Scientific Drilling Program (ICDP) project DeepCHALLA recovered a 214.8-meter long sediment sequence from Lake Chala, a deep and permanently stratified (meromictic) crater lake in equatorial East Africa, covering the past c. 250,000 years (250 kyr) of continuous lacustrine deposition since the earliest phase of lake-basin development. Lipid biomarker analyses on the sediments of this long-lived lake can provide much-needed records of past climate variability from this currently poorly documented region. However, the degree to which climate proxies derived from aquatically produced biomarkers are affected by aspects of lake developmental history is rarely considered, even though it may critically influence their ability to consistently register a particular climate variable through time. Modern-system studies in Lake Chala revealed crucial information about the mechanisms underpinning relationships between proxies based on isoprenoid (iso-) and branched (br-) glycerol dialkyl glycerol tetraethers (GDGTs) and the targeted climate variables, but the persistence of these relationships in the past remains unclear. To assess the reliability of long-term climate signals registered in the sediments of Lake Chala, we compared downcore variations in GDGT distributions with major phases in lake-system evolution as indicated by independent proxies of lake depth, mixing regime and nutrient dynamics: seismic reflection data, lithology and fossil diatom assemblages. Together, these records suggest that during early lake history (before c. 180–200 ka) the distinct mixing-related depth zones with which specific GDGT producers are associated in the modern-day lake were not yet formed, likely due to more open lake hydrology and absence of chemical water-column stratification. Consequently during this early phase the absolute GDGT concentrations are relatively low, proxies sensitive to water-column stratification (e.g., BIT index) display highly irregular temporal variability, and correlations between proxies are dissimilar to expectations based on modern-system understanding. A sequence of lake-system changes between c. 180–200 ka and c. 80 ka first established and then strengthened the chemical density gradient, promoting meromictic conditions despite the overall decrease in lake depth due to sediment accumulation. From c. 180 ka onward some GDGTs and derived proxies (e.g., crenarchaeol concentration, BIT index and IR6Me display strong ~23-kyr periodicity, likely reflecting the predominantly precession-driven insolation forcing of Quaternary climate variability in low-latitude regions. Our results suggest that GDGT-based temperature and moisture-balance proxies in Lake Chala sediments reflect the climate history of eastern equatorial Africa from at least c. 160 ka onwards, i.e., covering the complete last glacial-interglacial cycle and the penultimate glacial maximum. This work confirms the potential of lacustrine GDGTs for elucidating the climate history of tropical regions at Quaternary timescales, provided they are applied to suitably high-quality sediment archives. Additionally, their interpretation should incorporate a broader understanding of the extent to which lake-system evolution limits the extrapolation back in time of proxy-climate relationships established in the modern system. [ABSTRACT FROM AUTHOR]

High-resolution paleoclimate records from tropical continental settings are greatly needed to advance understanding of global climate dynamics. The International Continental Scientific Drilling Program (ICDP) project DeepCHALLA recovered a 214.8-meter long sediment sequence from Lake Chala, a deep and permanently stratified (meromictic) crater lake in equatorial East Africa, covering the past c. 250,000 years (250 kyr) of continuous lacustrine deposition since the earliest phase of lake-basin development. Lipid biomarker analyses on the sediments of this long-lived lake can provide much-needed records 5 of past climate variability from this currently poorly documented region. However, the degree to which climate proxies derived from aquatically produced biomarkers are affected by aspects of lake developmental history is rarely considered, even though it may critically influence their ability to consistently register a particular climate variable through time. Modern-system studies in Lake Chala revealed crucial information about the mechanisms underpinning relationships between proxies based on isoprenoid (iso-) and branched (br-) glycerol dialkyl glycerol tetraethers (GDGTs) and the targeted climate variables, but the 10 persistence of these relationships in the past remains unclear. To assess the reliability of long-term climate signals registered in the sediments of Lake Chala, we compared downcore variations in GDGT distributions with major phases in lake-system evolution as indicated by independent proxies of lake depth, mixing regime and nutrient dynamics: seismic reflection data, lithology and fossil diatom assemblages. Together, these records suggest that during early lake history (before c. 180-200 ka) the distinct mixing-related depth zones with which specific GDGT producers are associated in the modern-day lake were not 15 yet formed, likely due to more open lake hydrology and absence of chemical water-column stratification. Consequently during this early phase the absolute GDGT concentrations are relatively low, proxies sensitive to water-column stratification (e.g., BIT index) display highly irregular temporal variability, and correlations between proxies are dissimilar to expectations based on modern-system understanding. A sequence of lake-system changes between c. 180-200 ka and c. 80 ka first established and then strengthened the chemical density gradient, promoting meromictic conditions despite the overall decrease in lake depth due to sediment accumulation. From c. 180 ka onward some GDGTs and derived proxies (e.g., crenarchaeol concentration, BIT index and IR6Me) display strong 23-kyr periodicity, likely reflecting the predominantly precession-driven insolation forcing of Quaternary climate variability in low-latitude regions. Our results suggest that GDGT-based temperature and moisture-balance proxies in Lake Chala sediments reflect the climate history of eastern equatorial Africa from at least c. 160 ka onwards, i.e., covering the complete last glacial-interglacial cycle and the penultimate glacial maximum. This work confirms the potential of 25 lacustrine GDGTs for elucidating the climate history of tropical regions at Quaternary timescales, provided they are applied to suitably high-quality sediment archives. Additionally, their interpretation should incorporate a broader understanding of the extent to which lake-system evolution limits the extrapolation back in time of proxy-climate relationships established in the modern system. [ABSTRACT FROM AUTHOR]