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The Paleocene‐Eocene Thermal Maximum (PETM) and early Eocene hyperthermal events were characterized by a Hothouse climate state. Our understanding of the climatic impact of these hyperthermals is currently biased toward marine settings and the mid‐latitudes. Here we present organic geochemical data from Stenkul Fiord, Ellesmere Island, Arctic Canada. This organic rich formation was deposited in a high northern latitude wetland setting during the late Paleocene to early Eocene, spanning the PETM and subsequent ETM‐2 hyperthermals. Biomarker data (e.g., diterpenoids), combined with published palynological data from the site, indicate Cupressaceae‐dominated vegetation. Biomarkers suggest that land plant composition remained fairly unchanged across the two hyperthermal events. Increases in abundance and 13C‐depletion of hopanoid biomarkers (minima <−50‰ (VPDB)) highlight periods of enhanced bacterial methane consumption, particularly during the PETM. However, periods of low hopanoid δ13C values were also found outside the hyperthermal intervals. Relatively low δ2H values of higher plant n‐alkanes (average δ2H values of n‐C25, n‐C27, n‐C29 ∼ −230 to −270‰ (SMOW)) indicate that deposition formed during times with enhanced precipitation. The wettest intervals, as identified by the lowest δ2H n‐alkane values, contain high abundances of hopenes, indicating enhanced bacterial turnover. At Stenkul Fiord, high temperatures and CO2 concentrations likely fostered the growth of widespread wetland forests that became a CO2 sink and may have played an important role in carbon drawdown during the Early Paleogene. Key Points: First detailed biomarker study on high‐latitude terrestrial PETM settingBiomarkers and stable isotope signatures demonstrate cypress plant dominated setting with high methane cycling during hyperthermalsSwamp environment suggested and intense bacterial methane consumption not restricted to hyperthermals [ABSTRACT FROM AUTHOR]

ABSTRACTThe symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote Bradyrhizobium symbioses with tropical legumes. To characterize hopanoids in Bradyrhizobium symbiosis with soybean, we validated a recently published cumate-inducible hopanoid mutant of Bradyrhizobium diazoefficiens USDA110, Pcu-shc::∆shc. GC-MS analysis showed that this strain does not produce hopanoids without cumate induction, and under this condition, is impaired in growth in rich medium and under osmotic, temperature, and pH stress. In planta, Pcu-shc::∆shc is an inefficient soybean symbiont with significantly lower rates of nitrogen fixation and low survival within the host tissue. RNA-seq revealed that hopanoid loss reduces the expression of flagellar motility and chemotaxis-related genes, further confirmed by swim plate assays, and enhances the expression of genes related to nitrogen metabolism and protein secretion. These results suggest that hopanoids provide a significant fitness advantage to B. diazoefficiens in legume hosts and provide a foundation for future mechanistic studies of hopanoid function in protein secretion and motility.IMPORTANCEA major problem for global sustainability is feeding our exponentially growing human population while available arable land decreases. Harnessing the power of plant-beneficial microbes is a potential solution, including increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis between Bradyrhizobium diazoefficiens USDA110, an important commercial inoculant strain, and its economically significant host soybean. Our research extends our knowledge of the functions of bacterial lipids in symbiosis to an agricultural context, which may one day help improve the practical applications of plant-beneficial microbes in agriculture.

Carotenoids are isoprenoid lipids found across the tree of life with important implications in oxidative stress adaptations, photosynthetic metabolisms, as well as in membrane dynamics. The canonical view is that C40 carotenoids are synthesized from phytoene and C30 carotenoids from diapophytoene. Squalene is mostly associated with the biosynthesis of polycyclic triterpenes, although there have been suggestions that it could also be involved in the biosynthesis of C30 carotenoids. However, demonstration of the existence of this pathway in nature is lacking. Here, we demonstrate that C30 carotenoids are synthesized from squalene in the Planctomycetes bacteria and that this squalene route to C30 carotenoids is the most widespread in prokaryotes. Using the evolutionary history of carotenoid and squalene amino oxidases, we propose an evolutionary scenario to explain the origin and diversification of the different carotenoid and squalene-related pathways. We show that carotenoid biosynthetic pathways have been constantly transferred and neofunctionalized during prokaryotic evolution. One possible origin of the squalene pathway connects it with the one of C40 carotenoid synthesis of Cyanobacteria. The widespread occurrence of the squalene route to C30 carotenoids in Bacteria increases the functional repertoire of squalene, establishing it as a general hub of carotenoids and polycyclic triterpenes synthesis. [ABSTRACT FROM AUTHOR]

Peats formed widespread early after the Last Glacial Maximum around the coast of the Dogger Bank, the central high of the now flooded "Doggerland" (central North Sea). Here we present biomarker and gas geochemical insights into near-surface peat cored at 43 m water depth. Based on their probable age of ~10 ka before present (BP), the peats are likely part of the so-called basal Holocene peats. Pore waters in the samples document slight methane enrichments in peat layers (up to 250 nM methane vs 60 nM above the peat layer) and δ13C-values of methane ranging between ca. −46‰ and −60‰ PDB. Ethane, propane, and n -butane were also found and may either document upward migration of thermogenic hydrocarbons in the past or, more likely, peat-specific gases, which is indicated by accompanying abundant unsaturated analogs (i.e. ethene and propene). High concentrations of elemental sulfur (up to 19 wt.%) and sulfur-specific transformation products of plant triterpenoids (Des-A-triterpenoids) point to microbial generation during and/or slightly after peat-formation as hydrocarbon source. Biomarkers indicated that peats were formed in a variable environment with high contributions from higher plant wax material. However, a C20 highly branched isoprenoid (HBI) likely records abundant diatoms typical of an oligotrophic lake environment. In addition, all samples contained a suite of bacterial hopenes and fernenes (hop-17(21)-ene, diploptene, fern-7(8)-ene). A strongly fluctuating methane-flux and/or -turnover during peat formation is recorded in partially high 13C-depletions of <−60‰ PDB of these biomarkers. This underlines the importance of peat layers for methane generation and consumption on "Doggerland" during the Holocene. [ABSTRACT FROM AUTHOR]

In this study, alkali/acid treatment and ion exchange post-synthesis modification methods to modify the pore diameter and structure of molecular sieve 13X (MS13X) were applied to obtain products, which could then be implemented to improve the enrichment recovery of hopanoids in petroleum. The modification products were analyzed by SEM with EDS, XRD and nitrogen physisorption. The results indicated that the product which had been prepared in the oxalic acid ethanol solution formed some mesopores, and also retained the initial framework of crystal. It was revealed that this product was able to remarkably increase the recovery rate of hopanoids in petroleum without leading to a significant isotope fractionation phenomenon. It is thus shown that this modification method of non-aqueous oxalic acid solution for MS13X can be used as an effective pretreatment tool in the application of compound-specific isotope analysis of hopanes with low concentration.

Hopanoid lipids, bacteriohopanols and bacteriohopanepolyols, are membrane components exclusive to bacteria. Together with their diagenetic derivatives, they are commonly used as biomarkers for specific bacterial groups or biogeochemical processes in the geologic record. However, the sources of hopanoids to marine and freshwater environments remain inadequately constrained. Recent marker gene studies suggest a widespread potential for hopanoid biosynthesis in marine bacterioplankton, including nitrifying (i.e., ammonia‐ and nitrite‐oxidizing) bacteria. To explore their hopanoid biosynthetic capacities, we studied the distribution of hopanoid biosynthetic genes in the genomes of cultivated and uncultivated ammonia‐oxidizing (AOB), nitrite‐oxidizing (NOB), and complete ammonia‐oxidizing (comammox) bacteria, finding that biosynthesis of diverse hopanoids is common among seven of the nine presently cultivated clades of nitrifying bacteria. Hopanoid biosynthesis genes are also conserved among the diverse lineages of bacterial nitrifiers detected in environmental metagenomes. We selected seven representative NOB isolated from marine, freshwater, and engineered environments for phenotypic characterization. All tested NOB produced diverse types of hopanoids, with some NOB producing primarily diploptene and others producing primarily bacteriohopanepolyols. Relative and absolute abundances of hopanoids were distinct among the cultures and dependent on growth conditions, such as oxygen and nitrite limitation. Several novel nitrogen‐containing bacteriohopanepolyols were tentatively identified, of which the so called BHP‐743.6 was present in all NOB. Distinct carbon isotopic signatures of biomass, hopanoids, and fatty acids in four tested NOB suggest operation of the reverse tricarboxylic acid cycle in Nitrospira spp. and Nitrospina gracilis and of the Calvin–Benson–Bassham cycle for carbon fixation in Nitrobacter vulgaris and Nitrococcus mobilis. We suggest that the contribution of hopanoids by NOB to environmental samples could be estimated by their carbon isotopic compositions. The ubiquity of nitrifying bacteria in the ocean today and the antiquity of this metabolic process suggest the potential for significant contributions to the geologic record of hopanoids. [ABSTRACT FROM AUTHOR]

Komagataeibacter is the dominant taxon and cellulose-producing bacteria in the Kombucha Microbial Community (KMC). This is the first study to isolate the K. oboediens genome from a reactivated space-exposed KMC sample and comprehensively characterize it. The space-exposed genome was compared with the Earth-based reference genome to understand the genome stability of K. oboediens under extraterrestrial conditions during a long time. Our results suggest that the genomes of K. oboediens IMBG180 (ground sample) and K. oboediens IMBG185 (space-exposed) are remarkably similar in topology, genomic islands, transposases, prion-like proteins, and number of plasmids and CRISPR-Cas cassettes. Nonetheless, there was a difference in the length of plasmids and the location of cas genes. A small difference was observed in the number of protein coding genes. Despite these differences, they do not affect any genetic metabolic profile of the cellulose synthesis, nitrogen-fixation, hopanoid lipids biosynthesis, and stress-related pathways. Minor changes are only observed in central carbohydrate and energy metabolism pathways gene numbers or sequence completeness. Altogether, these findings suggest that K. oboediens maintains its genome stability and functionality in KMC exposed to the space environment most probably due to the protective role of the KMC biofilm. Furthermore, due to its unaffected metabolic pathways, this bacterial species may also retain some promising potential for space applications. [ABSTRACT FROM AUTHOR]

The glycerol dialkyl glycerol tetraether (GDGT) lipids of archaea and bacteria have been extensively studied in both modern and ancient wetlands, but their specific biological sources and biogeochemical significance in such settings remain unclear. The stable carbon isotopic composition of GDGTs, and associated tetraether lipids such as butanetriol - DGTs (BDGTs), can help reveal aspects of the carbon metabolism of their source organism. Here we present an in-depth compound-specific analyses of archaeal (isoGDGTs and BDGT-0) and bacterial (brGDGTs) tetraether lipid δ13C values from the Florida Everglades wetland, supplemented by 16S rRNA gene profiling of the archaeal community. We interpret this alongside GDGT δ13C analyses from three additional freshwater wetland sediments, and two ancient wetland deposits (lignites) from the Miocene. Our data suggests that isoGDGT-0 δ13C values, which range from –22.5‰ to −36.5‰ across our wetland sites, could to some degree reflect the relative importance of the acetotrophic and CO 2 -reducing hydrogenotrophic methanogenic pathways, though definitively delineating between the two is challenging due to (a) potential incorporation of dissolved inorganic carbon (DIC) by CO 2 reducers, and (b) the diluting effect of GDGTs derived from seemingly heterotrophic/fermentative Bathyarchaeia, the most abundant archaeal class in the Everglades. In the Everglades, which harbours abundant Methanomassiliicoccales, BDGT-0 is significantly more 13C-depleted than all other lipids, with a δ13C signature at certain depths (∼−40.0 to −45.0‰) that is consistent with an important source from these (likely) methylotrophic methanogens. This adds to a growing body of evidence on the underappreciated role of methylotrophic methanogenesis, largely driven by Methanomassiliicoccales , in the freshwater methane cycle. However, slightly more 13C-enriched values (∼−35.0‰) at certain depths in the same site provide evidence for additional, possibly heterotrophic sources under certain conditions, and BDGT-0 δ13C values in the Miocene lignite (≈ δ13C of TOC) are consistent with a solely heterotrophic source. Where available for measurement, δ13C values of isoGDGTs-1 to -3, averaging –32.7 ± 2.3‰, were significantly more 13C-depleted than isoGDGT-0, suggesting a different mixture of sources, likely including an autotrophic/mixotrophic component derived from archaea belonging to the Crenarchaeota, Nitrososphaeria (formerly Thaumarchaeota) and/or MBG-D/DHVEG-1. Finally, brGDGT δ13C values are generally consistent with their proposed bacterial heterotrophic origin and biosynthetic effects, averaging out at around 4‰ depleted relative to total organic carbon (TOC). Importantly, we find no significant variation between the δ13C values of different brGDGTs across our wetland types. This highlights that spatial and temporal changes in commonly applied brGDGT-based proxies likely do not co-occur with changes in the heterotrophic lifestyle of their producer(s), discounting a possible confounding factor in brGDGT palaeothermometry. Taken together, our results yield insights into wetland archaeal communities and the lipids they produce, and underline the applicability of tetraether δ13C analyses in probing aspects of microbial carbon cycling in modern and ancient wetland sediments. [ABSTRACT FROM AUTHOR]

Omics are the most promising approaches to investigate microbes for which no genetic tools exist such as the nitrogen-fixing symbiotic Frankia. A proteogenomic analysis of symbiotic Frankia alni was done by comparing those proteins more and less abundant in Alnus glutinosa nodules relative to N2-fixing pure cultures with propionate as the carbon source. There were 250 proteins that were significantly overabundant in nodules at a fold change (FC) ≥ 2 threshold, and 1429 with the same characteristics in in vitro nitrogen-fixing pure culture. Nitrogenase, SuF (Fe–Su biogenesis) and hopanoid lipids synthesis determinants were the most overabundant proteins in symbiosis. Nitrogenase was found to constitute 3% of all Frankia proteins in nodules. Sod (superoxide dismutase) was overabundant, indicating a continued oxidative stress, while Kats (catalase) were not. Several transporters were overabundant including one for dicarboxylates and one for branched amino acids. The present results confirm the centrality of nitrogenase in the actinorhizal symbiosis. [ABSTRACT FROM AUTHOR]

Komagataeibacter is the dominant taxon and cellulose-producing bacteria in the Kombucha Microbial Community (KMC). This is the first study to isolate the K. oboediens genome from a reactivated space-exposed KMC sample and comprehensively characterize it. The space-exposed genome was compared with the Earth-based reference genome to understand the genome stability of K. oboediens under extraterrestrial conditions during a long time. Our results suggest that the genomes of K. oboediens IMBG180 (ground sample) and K. oboediens IMBG185 (space-exposed) are remarkably similar in topology, genomic islands, transposases, prion-like proteins, and number of plasmids and CRISPR-Cas cassettes. Nonetheless, there was a difference in the length of plasmids and the location of cas genes. A small difference was observed in the number of protein coding genes. Despite these differences, they do not affect any genetic metabolic profile of the cellulose synthesis, nitrogen-fixation, hopanoid lipids biosynthesis, and stress-related pathways. Minor changes are only observed in central carbohydrate and energy metabolism pathways gene numbers or sequence completeness. Altogether, these findings suggest that K. oboediens maintains its genome stability and functionality in KMC exposed to the space environment most probably due to the protective role of the KMC biofilm. Furthermore, due to its unaffected metabolic pathways, this bacterial species may also retain some promising potential for space applications.

The 2‐methylhopanes (2‐MeHops) are molecular fossils of 2‐methylbacteriohopanepolyols (2‐MeBHPs) and among the oldest biomarkers on Earth. However, these biomarkers' specific sources are currently unexplained, including whether they reflect an expansion of marine cyanobacteria. Here, we study the occurrence of 2‐MeBHPs and the genes involved in their synthesis in modern bacteria and explore the occurrence of 2‐MeHops in the geological record. We find that the gene responsible for 2‐MeBHP synthesis (hpnP) is widespread in cyano‐ and ⍺‐proteobacteria, but absent or very limited in other classes/phyla of bacteria. This result is consistent with the dominance of 2‐MeBHP in cyano‐ and ⍺‐proteobacterial cultures. The review of their geological occurrence indicates that 2‐MeHops are found from the Paleoproterozoic onwards, although some Precambrian samples might be biased by drilling contamination. During the Phanerozoic, high 2‐MeHops' relative abundances (index >15%) are associated with climatic and biogeochemical perturbations such as the Permo/Triassic boundary and the Oceanic Anoxic Events. We analyzed the modern habitat of all hpnP‐containing bacteria and find that the only one species coming from an undisputed open marine habitat is an ⍺‐proteobacterium acting upon the marine nitrogen cycle. Although organisms can change their habitat in response to environmental stress and evolutionary pressure, we speculate that the high sedimentary 2‐MeHops' occurrence observed during the Phanerozoic reflect ⍺‐proteobacteria expansion and marine N‐cycle perturbations in response to climatic and environmental change. [ABSTRACT FROM AUTHOR]

Bacterial lipids are well-preserved in ancient rocks and certain ones have been used as indicators of specific bacterial metabolisms or environmental conditions existing at the time of rock deposition. Here we show that an anaerobic bacterium produces 3-methylhopanoids, pentacyclic lipids previously detected only in aerobic bacteria and widely used as biomarkers for methane-oxidizing bacteria. Both Rhodopila globiformis, a phototrophic purple nonsulfur bacterium isolated from an acidic warm spring in Yellowstone, and a newly isolated Rhodopila species from a geochemically similar spring in Lassen Volcanic National Park (USA), synthesized 3-methylhopanoids and a suite of related hopanoids and contained the genes encoding the necessary biosynthetic enzymes. Our results show that 3-methylhopanoids can be produced under anoxic conditions and challenges the use of 3-methylhopanoids as biomarkers of oxic conditions in ancient rocks and as prima facie evidence that methanotrophic bacteria were active when the rocks were deposited. [ABSTRACT FROM AUTHOR]

Sterols play an essential role in modulating bilayer structure and dynamics. Coarse-grained molecular dynamics parameters for cholesterol and related molecules are available for the Martini force field and have been successfully used in multiple lipid bilayer studies. In this work, we focus on the use of virtual sites as a means of increasing the stability of cholesterol and cholesterol-like structures. We improve and extend the Martini parameterization of sterols in four different ways: 1--the cholesterol parameters were adapted to make use of virtual interaction sites, which markedly improves numerical stability; 2--cholesterol parameters were also modified to address reported shortcomings in reproducing correct lipid phase behavior in mixed membranes; 3--parameters for ergosterol were created and adapted from cholesterols; and 4--parameters for the hopanoid class of bacterial polycyclic molecules were created, namely, for hopane, diploptene, bacteriohopanetetrol, and for their polycyclic base structure. [ABSTRACT FROM AUTHOR]

Hopanoids and carotenoids are two of the major isoprenoid‐derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as sterols. Methylobacterium extorquens contains hopanoids and carotenoids in their outer membrane, making them an ideal system to investigate the role of isoprenoid lipids in surface membrane function and cellular fitness. By genetically knocking out hpnE and crtB we disrupted the production of squalene and phytoene in M. extorquens PA1, which are the presumed precursors for hopanoids and carotenoids respectively. Deletion of hpnE revealed that carotenoid biosynthesis utilizes squalene as a precursor resulting in pigmentation with a C30 backbone, rather than the previously predicted canonical C40 phytoene‐derived pathway. Phylogenetic analysis suggested that M. extorquens may have acquired the C30 pathway through lateral gene transfer from Planctomycetes. Surprisingly, disruption of carotenoid synthesis did not generate any major growth or membrane biophysical phenotypes, but slightly increased sensitivity to oxidative stress. We further demonstrated that hopanoids but not carotenoids are essential for growth at higher temperatures, membrane permeability and tolerance of low divalent cation concentrations. These observations show that hopanoids and carotenoids serve diverse roles in the outer membrane of M. extorquens PA1. [ABSTRACT FROM AUTHOR]

Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requiresmolecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization of squalene by a squalene-tetrahymanol cyclase, acts as a sterol surrogate. This study confirms an early report [C. J. E. A. Bulder, Antonie Van Leeuwenhoek, 37, 353-358 (1971)] that Schizosaccharomyces japonicus is exceptional among yeasts in growing anaerobically on synthetic media lacking sterols and unsaturated fatty acids. Mass spectrometry of lipid fractions of anaerobically grown Sch. japonicus showed the presence of hopanoids, a class of cyclic triterpenoids not previously detected in yeasts, including hop-22(29)-ene, hop-17(21)-ene, hop-21(22)-ene, and hopan-22-ol. A putative gene in Sch. japonicus showed high similarity to bacterial squalene-hopene cyclase (SHC) genes and in particular to those of Acetobacter species. No orthologs of the putative Sch. japonicus SHC were found in other yeast species. Expression of the Sch. japonicus SHC gene (Sjshc1) in Saccharomyces cerevisiae enabled hopanoid synthesis and stimulated anaerobic growth in sterol-free media, thus indicating that one or more of the hopanoids produced by SjShc1 could at least partially replace sterols. Use of hopanoids as sterol surrogates represents a previously unknown adaptation of eukaryotic cells to anaerobic growth. The fast anaerobic growth of Sch. japonicus in sterol-free media is an interesting trait for developing robust fungal cell factories for application in anaerobic industrial processes. [ABSTRACT FROM AUTHOR]

Omics are the most promising approaches to investigate microbes for which no genetic tools exist such as the nitrogen-fixing symbiotic Frankia. A proteogenomic analysis of symbiotic Frankia alni was done by comparing those proteins more and less abundant in Alnus glutinosa nodules relative to N-replete pure cultures with propionate as the carbon source and ammonium as the nitrogen-source. There were 250 proteins that were significantly overabundant in nodules at a fold change (FC) ≥ 2 threshold, and 1429 with the same characteristics in in vitro nitrogen-replete pure culture. Nitrogenase, SuF (Fe–Su biogenesis) and hopanoid lipids synthesis determinants were the most overabundant proteins in symbiosis. Nitrogenase was found to constitute 3% of all Frankia proteins in nodules. Sod (superoxide dismutase) was overabundant, indicating a continued oxidative stress, while Kats (catalase) were not. Several transporters were overabundant including one for dicarboxylates and one for branched amino acids. The present results confirm the centrality of nitrogenase in the actinorhizal symbiosis.

The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote Bradyrhizobium symbioses with tropical legumes. To characterize hopanoids in Bradyrhizobium symbiosis with soybean, we validated a recently published cumate-inducible hopanoid mutant of Bradyrhizobium diazoefficiens USDA110, Pcu- shc ::∆ shc . GC-MS analysis showed that this strain does not produce hopanoids without cumate induction, and under this condition, is impaired in growth in rich medium and under osmotic, temperature, and pH stress. In planta , Pcu- shc ::∆ shc is an inefficient soybean symbiont with significantly lower rates of nitrogen fixation and low survival within the host tissue. RNA-seq revealed that hopanoid loss reduces the expression of flagellar motility and chemotaxis-related genes, further confirmed by swim plate assays, and enhances the expression of genes related to nitrogen metabolism and protein secretion. These results suggest that hopanoids provide a significant fitness advantage to B. diazoefficiens in legume hosts and provide a foundation for future mechanistic studies of hopanoid function in protein secretion and motility., A major problem for global sustainability is feeding our exponentially growing human population while available arable land decreases. Harnessing the power of plant-beneficial microbes is a potential solution, including increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis between Bradyrhizobium diazoefficiens USDA110, an important commercial inoculant strain, and its economically significant host soybean. Our research extends our knowledge of the functions of bacterial lipids in symbiosis to an agricultural context, which may one day help improve the practical applications of plant-beneficial microbes in agriculture., Competing Interests: The authors declare no conflict of interest.

The cohabitation of lipids and proteins in the plasma membrane of mammalian cells is controlled by specific biochemical and biophysical rules. Lipids may be either constitutively tightly bound to cell-surface receptors (non-annular lipids) or less tightly attached to the external surface of the protein (annular lipids). The latter are exchangeable with surrounding bulk membrane lipids on a faster time scale than that of non-annular lipids. Not only do non-annular lipids bind to membrane proteins through stereoselective mechanisms, they can also help membrane receptors acquire (or maintain) a functional 3D structure. Cholesterol is the prototype of membrane lipids that finely controls the 3D structure and function of receptors. However, several other lipids such as sphingolipids may also modulate the function of membrane proteins though conformational adjustments. All these concepts are discussed in this review in the light of representative examples taken from the literature.

We present results of study of the molecular composition of organic matter (OM) in the bottom sediments of the Laptev Sea by gas chromatography-mass spectrometry, isotope gas chromatography-mass spectrometry, and Rock-Eval pyrolytic analysis. The OM of all collected sediment samples shows a significant terrigenous contribution. Compounds that are biomarkersof methanotrophic microorganisms are also found. A positive correlation between the contents of the studied biomarkers and the contents of pelite and total organic carbon is observed at the sites with documented intense methane bubbling. For example, the average content of C30 hopenes at the "methane" stations is twice higher than that at the "background" ones. The average content of C32 aß-hopanes in sediment samples from the methane seepage area is 1.5 times higher than that at the background stations. We suggest that the increased C30 aß-hopane content (~1.5 times higher within the methane seepage area) and the decreased moretane index relative to the C31 hopane index are due to the inflow of OM of petroleum origin. The presence of biphenyl in sediments indicates its petroleum origin, which supports our assumption of the migratory nature of petroleum hydrocarbons in the methane seepage area. Triterpenoids found in the sediment OM indicate diagenetic bacterial transformation of OM in the methane seepage areas, which shows that methane has been released for a long time. We assume the intense activity of the consortium of methanotrophs and sulfate reducers in the methane seepage areas. [ABSTRACT FROM AUTHOR]

Background: Hopanoids modify plasma membrane properties in bacteria and are often compared to sterols that modulate membrane fluidity in eukaryotes. In some microorganisms, they can also allow adaptations to extreme environments. Methods: Hopanoids were identified by liquid chromatography–mass spectrometry in fourteen strains of thermophilic bacteria belonging to five genera, i.e., Alicyclobacillus, Brevibacillus, Geobacillus, Meiothermus, and Thermus. The bacteria were cultivated at temperatures from 42 to 70 °C. Results: Regardless of the source of origin, the strains have the same tendency to adapt the hopanoid content depending on the cultivation temperature. In the case of aminopentol, its content increases; aminotetrol does not show a significant change; and in the case of aminotriol the content decreases by almost a third. The content of bacteriohopanetetrol and bacteriohopanetetrol glycoside decreases with increasing temperature, while in the case of adenosylhopane the opposite trend was found. Conclusions: Changes in hopanoid content can be explained by increased biosynthesis, where adenosylhopane is the first intermediate in the biosynthesis of the hopanoid side chain.

Abstract Biomarker-based climate proxies enable climate and environmental reconstructions for regions where other paleoclimatic approaches are unsuitable. The Antarctic Cenozoic record consists of widely varying lithologies, deposited in rapidly changing depositional settings, with large lateral variations. Previous sedimentological and microfossil studies indicate that the incorporation of reworked older material frequently occurs in these sediments, highlighting the need for an assessment of biomarker distribution across a range of depositional settings and ages to assess the role reworking may have on biomarker-based reconstructions. Here, we compare sedimentary facies with the distribution of n -alkanes and hopanoids within a terrestrial outcrop, two glaciomarine cores and a deep sea core, spanning the Late Oligocene to Miocene in the Ross Sea. Comparisons are also made with n -alkane distributions in Eocene glacial erratics and Mesozoic Beacon Supergroup sediments, which are both potential sources of reworked material. The dominant n -alkane chain length shifts from n -C 29 to n -C 27 between the Late Eocene and the Oligocene. This shift is likely due to changing plant community composition and the plastic response of n -alkanes to climate cooling. Samples from glaciofluvial environments onshore, and subglacial and ice-proximal environments offshore are more likely to display reworked n -alkane distributions, whereas, samples from lower-energy, lacustrine and ice-distal marine environments predominantly yield immature/contemporaneous n -alkanes. These findings emphasise that careful comparisons with sedimentological and paleontological indicators are essential when applying and interpreting n -alkane-based and other biomarker-based proxies in glacially-influenced settings. Highlights • n -Alkanes and hopanoids are characterised in Eocene-Miocene sediments in Antarctica. • A shift in dominant n -alkane chain length occurs between the Eocene and Oligocene. • Contemporaneous and reworked material contributes to biomarker distributions. • Fluvial, subglacial and ice-proximal environments often contain reworked biomarkers. • Lacustrine and ice-distal environments mainly contain contemporaneous biomarkers. [ABSTRACT FROM AUTHOR]

Abstract Oryctes rhinoceros Linn. is one of the most serious pests of coconuts and other palms. Following bioassay guided method, a larvicidal compound, 22-hydroxyhopane has been isolated for the first time from methanol extract of leaves of Adiantum latifolium Lam. against the pest (LC 50 value 20.81 μg/g). It is a hopanoid triterpene with molecular mass of 442.42 g/mol. The compound exhibited antibacterial activity against symbiotic gut bacteria, caused histolysis of midgut tissues and inhibited secretion of digestive enzymes such as protease, amylase and trehalase resulting in weight loss of larvae. Enzyme immunoassay showed an elevation of 20-hydroxyecdysone level in haemolymph causing disruption of metamorphosis of larvae. Graphical abstract Unlabelled Image Highlights • The triterpenoid 22-hydroxyhopane is isolated from methanol extract of leaves of the fern Adiantum latifolium. • The compound has revealed larvicidal efficacy against the larvae of the coconut pest Oryctes rhinoceros. • Mode of action include histolysis of gut tissue and inhibition of digestive enzyme production. • The compound showed antibacterial activity against gut bacteria. • 22-hydroxyhopane caused an elevation of 20-hydroxyecdysone level in haemolymph disrupting metamorphosis. [ABSTRACT FROM AUTHOR]

Vitrinite and resinite are important macerals within the coal. To understand their chemical compositions and structures is of great significance for the evaluation of hydrocarbon potential. The combination of optical microscope and modified laser micropyrolysis GC-MS technique was employed to analyze the vitrinite and resinite within a Paleogene coal of Honghe region of Yunnan Province. The pyrolyzates have shown to have the ubiquitous mono and diaromatic hydrocarbons, diterpenoids as well as n-alkene/ane doublets for both of vitrinite and resinite, among which, the similar distribution of aromatic hydrocarbons and diterpenoids were obvious, and abundant norpimarane and phyllocladane were derived from gymnospermae, especially contributed by conifer resins. However, the distributions of aliphatic hydrocarbons and hopanoids in the pyrolyzates were distinct. The successful application of laser micropyrolysis indicates it is a micrometer scale method to recognize hydrocarbon generation characteristics of various macerals within a single sam-ple, and thus make it possible to identify effective hydrocarbon-generation macerals. In addition, compared with conventional geochemical techniques, the superiority of laser micropyrolysis GC-MS technique was discussed as well. [ABSTRACT FROM AUTHOR]

The Herman Pit, once a mercury mine, is an impoundment located in an active geothermal area. Its acidic waters are permeated by hundreds of gas seeps. One seep was sampled and found to be composed of mostly CO2 with some CH4 present. The δ13CH4 value suggested a complex origin for the methane: i.e., a thermogenic component plus a biological methanogenic portion. The relatively 12C-enriched CO2 suggested a reworking of the ebullitive methane by methanotrophic bacteria. Therefore, we tested bottom sediments for their ability to consume methane by conducting aerobic incubations of slurried materials. Methane was removed from the headspace of live slurries, and subsequent additions of methane resulted in faster removal rates. This activity could be transferred to an artificial, acidic medium, indicating the presence of acidophilic or acid-tolerant methanotrophs, the latter reinforced by the observation of maximum activity at pH = 4.5 with incubated slurries. A successful extraction of sterol and hopanoid lipids characteristic of methanotrophs was achieved, and their abundances greatly increased with increased sediment methane consumption. DNA extracted from methane-oxidizing enrichment cultures was amplified and sequenced for pmoA genes that aligned with methanotrophic members of the Gammaproteobacteria. An enrichment culture was established that grew in an acidic (pH 4.5) medium via methane oxidation.

Abstract Saline and freshwater lacustrine oils from the Dongpu Depression (Bohai Bay Basin) were characterized by negative-ion electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). ESI-FT-ICR MS detected a large range of nitrogen and oxygen compounds in the oils, mostly comprising N 1 , O 1 , O 2 and N 1 O 1 species. The low mature oils are dominated by O 1 species with double bond equivalent of 4 (DBE = 4; mainly alkylphenols), O 2 species with DBE = 5–6 (i.e., hopanoid, secohopanoic and steroid acids) and DBE = 1 (i.e., fatty acids), indicating a genetic relationship between oxygen compounds and their precursors. The nitrogen and oxygen compounds were significantly influenced by maturity, with the lower maturity oils analyzed enriched in O 2 species, particularly fatty acids and 4–5 ring naphthenes with biologically sourced hydrocarbon skeletons: ratios of O 2 /N 1 > 0.7; C 20–30 /C 15–45 -DBE 1 -O 2 > 0.4; and DBE 5–6 /DBE 12–22 -O 2 > 6.0 may be useful indicators of low maturity. With increasing maturity, the condensation degree of the compounds increased and the carbon number decreased. The relative abundances of N 1 and O 1 species with the following specific DBE carbon number ranges were particularly sensitive to maturity: DBE 9–12 /DBE 15–18 -N 1 , C 20–28 /C 29–40 -DBE 12 -N 1 , C 20–30 /C 31–50 -DBE 15 -N 1 , DBE 9–12 /DBE 4–20 -O 1 and C 20–30 /C 31–50 -DBE 8 -O 1. In some instances the FT-ICR MS proxies provided a more reliable indication of high maturity levels than traditional sterane based maturity parameters. However, several of these species were also responsive to other influences, namely C 20–28 /C 29–40 -DBE 12 -N 1 and C 20–30 /C 31–50 -DBE 15 -N 1 ratios reflected an organofacies control and DBE 9–12 /DBE 4–20 -O 1 and C 20–30 /C 31–50 -DBE 8 -O 1 ratios changed with thermochemical sulfate reduction (TSR)– confirmed by δ34S variances of OSCs. In light of the multiple controls on the nitrogen and oxygen compounds, DBE 9–12 /DBE 15–18 -N 1 ratio seems unaffected by organofacies or TSR and was considered the most reliable maturity proxy displaying a similar or better maturity relationship than Ts/(Ts + Tm). Aside from secondary alteration effects, the freshwater samples showed several compositional differences to the saline samples, albeit from a limited data set, including generally higher O 2 and N 1 (particularly low MW) product abundances, lower abundances and quite different distribution of O 1 products. These distinctions suggest ESI FT-ICR MS analysis has potential for distinguishing these sample types. Highlights • Heteroatom compounds in saline lacustrine oils were detected. • Abundant O and N compounds were identified in low mature oils. • Parameters of N and O compounds indicating maturity were proposed. • NSO compounds in several saline lacustrine oils were probably impacted by TSR. [ABSTRACT FROM AUTHOR]

Road dust resuspension is one of the main sources of particulate matter with impacts on air quality, health and climate. With the aim of characterising the thoracic fraction, a portable resuspension chamber was used to collect road dust from five main roads in Oporto and an urban tunnel in Braga, north of Portugal. The PM 10 samples were analysed for: i) carbonates by acidification and quantification of the evolved CO 2 , ii) carbonaceous content (OC and EC) by a thermo-optical technique, iii) elemental composition by ICP-MS and ICP-AES after acid digestion, and iv) organic speciation by GC–MS. Dust loadings of 0.48 ± 0.39 mg PM 10 m −2 were obtained for asphalt paved roads. A much higher mean value was achieved in a cobbled pavement (50 mg PM 10 m −2 ). In general, carbonates were not detected in PM 10 . OC and EC accounted for PM 10 mass fractions up to 11% and 5%, respectively. Metal oxides accounted for 29 ± 7.5% of the PM 10 mass from the asphalt paved roads and 73% in samples from the cobbled street. Crustal and anthropogenic elements, associated with tyre and brake wear, dominated the inorganic fraction. PM 10 comprised hundreds of organic constituents, including hopanoids, n -alkanes and other aliphatics, polycyclic aromatic hydrocarbons (PAH), alcohols, sterols, various types of acids, glycerol derivatives, lactones, sugars and derivatives, phenolic compounds and plasticizers. In samples from the cobbled street, these organic classes represented only 439 μg g −1 PM 10 , while for other pavements mass fractions up to 65 mg g −1 PM 10 were obtained. Except for the cobbled street, on average, about 40% of the analysed organic fraction was composed of plasticizers. Although the risk via inhalation of PAH was found to be insignificant, the PM 10 from some roads can contribute to an estimated excess of 332 to 2183 per million new cancer cases in adults exposed via ingestion and dermal contact. [ABSTRACT FROM AUTHOR]

We present a novel method to measure the 13 C/ 12 C isotope ratio (reported as δ 13 C) of individual, intact bacteriohopanepolyols (BHPs) using semi-preparative ultrahigh pressure liquid chromatography (UPLC) followed by high temperature gas chromatography–isotope ratio mass spectrometry (HT-GC–IRMS). The method is reproducible, as indicated by the precision of δ 13 C values for bacteriohopanetetrol (BHT) extracted from R. palustris biomass and analyzed across an order-of-magnitude range of IRMS peak areas (δ 13 C = −33.4 ± 0.6‰ VPDB, n  = 94, ±1σ). To show that this method successfully separates individual BHPs from complex environmental matrices, we report δ 13 C values for BHT and the BHT stereoisomer (BHT-II) from a ca. 2.9 Ma, organic-rich Mediterranean Sea sediment sample. These analyses suggest that intact BHP δ 13 C measurements can greatly improve the interpretation of environmental signals by alleviating the need for side-chain cleavage which reduces BHP source-specificity. [ABSTRACT FROM AUTHOR]

Comprehensive two-dimensional gas chromatography (GC × GC) has become accepted as one of the most powerful separation techniques in several application areas. In forensic investigations, however, it has not yet been entirely established due to limitations regarding standardized methodology, data interpretation and consistency of results. Nevertheless, GC × GC allows for target analysis, compound class analysis and chemical fingerprinting of samples and is therefore increasingly applied in forensic analytics. In this review, recent and significant advances in GC × GC for application to forensic studies including human scent, arson investigations, security-relevant substances and environmental forensics are discussed. The discussion includes a brief overview of the latest trends and evolutions with regard to the various forensic applications and data evaluation as well as limitations. This leads to the conclusion that the full potential of the comprehensive data sets can only be achieved by implementing standardized analysis and data processing methods. [ABSTRACT FROM AUTHOR]

Three marine sponges-Halichondria glabrata, Sigmadocia petrosioides and Pseudosuberitus andrewsi were collected for isolation of sponge-associated bacteria from Mumbai coastal regions. Among 110 isolates, six strains were selected and studied for its antibacterial activity by disc-diffusion assay. TLC-Bioautography studies were performed. GSA10 isolate from Halichondria glabrata was selected for showing good antagonistic activity for E. coli MTCC-1687, P. aeruginosa MTCC-1688, B. subtilis MTCC-441 and S. aureus MTCC - 737. Various biochemical tests and 16S ribosomal RNA sequencing were performed for GSA10 for its identification which confirmed it to be a Bacillus species. To decipher the activity of GSA10 bacteria, we aligned the 16S rRNA sequence in NCBI database. It represented close relationship with pG1 Bacillus amyloliquefaciens and hypothetical protein ATP synthase from Staphylococcus aureus. TLC direct bioautography was developed and results were found positive for a specific band at Rf 6.8. This bioactive compound was isolated by preparative TLC and characterized by UV, FT-IR, and LC-MS. It was further evaluated for antioxidant activity. It showed good antioxidant activity in DPPH scavenging (99%) and TRAP assay (91%). The purified compound was characterized as a C-30 hopanoid from a marinesponge associated bacteria. [ABSTRACT FROM AUTHOR]

Hopanoids, including the extended side chain-containing bacteriohopanepolyols, are bacterial lipids found abundantly in the geological record and across Earth's surface environments. However, the physiological roles of this biomarker remain uncertain, limiting interpretation of their presence in current and past environments. Recent work investigating the diversity and distribution of hopanoid producers in the marine environment implicated low-oxygen regions as important loci of hopanoid production, and data from marine oxygen minimum zones suggested that the dominant hopanoid producers in these environments are nitrite-utilizing organisms, revealing a potential connection between hopanoid production and the marine nitrogen cycle. Here, we use metagenomic data from the Red Sea to investigate the ecology of hopanoid producers in an environmental setting that is biogeochemically distinct from those investigated previously. The distributions of hopanoid production and nitrite oxidation genes in the Red Sea are closely correlated, and the majority of hopanoid producers are taxonomically affiliated with the major marine nitrite oxidizers, Nitrospinae and Nitrospirae. These results suggest that the relationship between hopanoid production and nitrite oxidation is conserved across varying biogeochemical conditions in dark ocean microbial ecosystems. [ABSTRACT FROM AUTHOR]

Hopanoids are pentacyclic triterpenoids produced by a wide range of bacteria. Within modern settings, hopanoids mostly occur in the biological 17β,21β(H) configuration. However, in some modern peatlands, the C 31 hopane is present as the ‘thermally-mature’ 17α,21β(H) stereoisomer. This has traditionally been ascribed to isomerisation at the C-17 position catalysed by the acidic environment. However, recent work has argued that temperature and/or hydrology also exert a control upon hopane isomerisation. Such findings complicate the application of geohopanoids as palaeoenvironmental proxies. However, due to the small number of peats that have been studied, as well as the lack of peatland diversity sampled, the environmental controls regulating geohopanoid isomerisation remain poorly constrained. Here, we undertake a global approach to investigate the occurrence, distribution and diagenesis of geohopanoids within peat, combining previously published and newly generated data (n = 395) from peatlands with a wide temperature (−1 to 27 °C) and pH (3–8) range. Our results indicate that peats are characterised by a wide range of geohopanoids. However, the C 31 hopane and C 32 hopanoic acid (and occasionally the C 32 hopanol) typically dominate. C 32 hopanoic acids occur as αβ- and ββ-stereoisomers, with the ββ-isomer typically dominating. In contrast, C 31 hopanes occur predominantly as the αβ-stereoisomer. These two observations collectively suggest that isomerisation is not inherited from an original biological precursor (i.e. biohopanoids). Using geohopanoid ββ/(αβ + ββ) indices, we demonstrate that the abundance of αβ-hopanoids is strongly influenced by the acidic environment, and we observe a significant positive correlation between C 31 hopane isomerisation and pH ( n  = 94, r 2  = 0.64, p < 0.001). Crucially, there is no correlation between C 31 hopane isomerisation and temperature. We therefore conclude that within peats, αβ-hopanoids are acid-catalysed diagenetic products and their occurrence at shallow depths indicates that this isomerisation is rapid. This shows that geohopanoid ββ/(αβ + ββ) indices can be used to reconstruct pH within modern and ancient peat-forming environments. However, we only recommend using ββ/(αβ + ββ) indices to interrogate large amplitude (>1 pH unit) and longer-term (>1 kyr) variation. Overall, our findings demonstrate the potential of geohopanoids to provide unique new insights into understanding depositional environments and interpreting terrestrial organic matter sources in the geological record. [ABSTRACT FROM AUTHOR]

The cohabitation of lipids and proteins in the plasma membrane of mammalian cells is controlled by specific biochemical and biophysical rules. Lipids may be either constitutively tightly bound to cell-surface receptors (non-annular lipids) or less tightly attached to the external surface of the protein (annular lipids). The latter are exchangeable with surrounding bulk membrane lipids on a faster time scale than that of non-annular lipids. Not only do non-annular lipids bind to membrane proteins through stereoselective mechanisms, they can also help membrane receptors acquire (or maintain) a functional 3D structure. Cholesterol is the prototype of membrane lipids that finely controls the 3D structure and function of receptors. However, several other lipids such as sphingolipids may also modulate the function of membrane proteins though conformational adjustments. All these concepts are discussed in this review in the light of representative examples taken from the literature. [ABSTRACT FROM AUTHOR]

High molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) are persistent organic pollutants which due to their limited biodegradability accumulate in soils where their increased presence can lead to the impoverishment of the decomposer organisms. As very hydrophobic PAHs easily penetrate cellular membranes of soil bacteria and can be incorporated therein, changing the membrane fluidity and other functions which in consequence can lead to the death of the organism. The structure and size of PAH molecule can be crucial for its membrane activity; however the correlation between PAH structure and its interaction with phospholipids have not been investigated so far. In our studies we applied phospholipid Langmuir monolayers as model bacterial membranes and investigated how the incorporation of six structurally different PAH molecules change the membrane texture and physical properties. In our studies we registered surface pressure and surface potential isotherms upon the monolayer compression, visualized the monolayer texture with the application of Brewster angle microscopy and searched the ordering of the film-forming molecules with molecular resolution with the application of grazing incidence X-ray diffraction (GIXD) method. It turned out that the phospholipid-PAH interactions are strictly structure dependent. Four and five-ring PAHs of the angular or cluster geometry can be incorporated into the model membranes changing profoundly their textures and fluidity; whereas linear or large cluster PAHs cannot be incorporated and separate from the lipid matrix. The observed phenomena were explained based on structural similarities of the applied PAHs with membrane steroids and hopanoids. [ABSTRACT FROM AUTHOR]

Analyses of trimethylsilyl-derivatized neutral lipids by gas chromatography coupled to mass spectrometry afford a wealth of information contained in the marine sediments. This information is useful for unraveling the processes associated with past climate changes such as those from glacial and interglacial periods. Studies of samples from the Iberian Margin deposited about 1,300,000-1,400,000 years ago afforded the qualitative identification and quantification of n-alkanes, n-alkan-1-ols, isoprenoids, triterpenoids, sterols, hopanols, alkenones, alkenols, and polycyclic aromatic hydrocarbons. Using this information, the lipidomic approach has allowed to identifying differences in sea surface temperatures, marine productivity, microbial degradation processes, and inputs from continental plants between these periods. Differences in predominant higher plant species related to climate changes have also been observed. [ABSTRACT FROM AUTHOR]