Special methods for the analysis of ether lipid structure and metabolism in archaea

Selective chemical degradation of silica sinters of the Taupo Volcanic Zone (New Zealand). Implications for early Earth and Astrobiology

Most organic matter (OM) on Earth occurs as kerogen-like materials, that is naturally formed macromolecules insoluble with standard organic solvents. The formation of this insoluble organic matter (IOM) is a topic of much interest, especially when it limits the detection of compounds of geomicrobiological interest. For example, studies that search for biomarker evidence of life on early Earth or other planets usually use solvent-based extractions. This leaves behind a pool of OM as unexplored post-extraction residues, potentially containing diagnostic biomarkers. Since the IOM has an enhanced potential for preservation compared to soluble OM, analysing IOM-released biomarkers can also provide even deeper insights into the ecology of ancient settings, with implications for early Earth and Astrobiology investigations. Here, we analyse the prokaryotic lipid biosignature within soluble and IOM of the Taupo Volcanic Zone (TVZ) silica sinters, which are key analogues in the search for life. We apply sequential solvent extractions and a selective chemical degradation upon the post-solvent extraction residue. Moreover, we compare the IOM from TVZ sinters to analogous studies on peat and marine sediments to assess patterns in OM insolubilisation across the geosphere. Consistent with previous work, we find significant but variable proportions-1%-45% of the total prokaryotic lipids recovered-associated with IOM fractions. This occurs even in recently formed silica sinters, likely indicating inherent cell insolubility. Moreover, archaeal lipids seem more prone to insolubilisation as compared to the bacterial analogues, which might enhance their preservation and also bias overall biomarkers interpretation. These observations are similar to those observed in other settings, confirming that even in a setting where the OM derives predominantly from prokaryotic sources, patterns of IOM formation/occurrence are conserved. Differences with other settings, however, such as the occurrence of archaeol in IOM fractions, could be indicative of different mechanisms for IOM formation that merit further exploration.

Identification of CDP-archaeol synthase, a missing link of ether lipid biosynthesis in Archaea

Archaeal membrane lipid composition is distinct from Bacteria and Eukarya, consisting of isoprenoid chains etherified to the glycerol carbons. Biosynthesis of these lipids is poorly understood. Here we identify and characterize the archaeal membrane protein CDP-archaeol synthase (CarS) that catalyzes the transfer of the nucleotide to its specific archaeal lipid substrate, leading to the formation of a CDP-activated precursor (CDP-archaeol) to which polar head groups are attached. The discovery of CarS enabled reconstitution of the entire archaeal lipid biosynthesis pathway in vitro, starting from simple isoprenoid building blocks and using a set of five purified enzymes. The cell free synthetic strategy for archaeal lipids we describe opens opportunity for studies of archaeal lipid biochemistry. Additionally, insights into archaeal lipid biosynthesis reported here allow addressing the evolutionary hypothesis of the lipid divide between Archaea and Bacteria.

Ubiquitous distribution of phosphatidylinositol phosphate synthase and archaetidylinositol phosphate synthase in Bacteria and Archaea, which contain inositol phospholipid

In Eukarya, phosphatidylinositol (PI) is biosynthesized from CDP-diacylglycerol (CDP-DAG) and inositol. In Archaea and Bacteria, on the other hand, we found a novel inositol phospholipid biosynthetic pathway. The precursors, inositol 1-phosphate, CDP-archaeol (CDP-ArOH), and CDP-DAG, form archaetidylinositol phosphate (AIP) and phosphatidylinositol phosphate (PIP) as intermediates. These intermediates are dephosphorylated to synthesize archaetidylinositol (AI) and PI. To date, the activities of the key enzymes (AIP synthase, PIP synthase) have been confirmed in only three genera (two archaeal genera, Methanothermobacter and Pyrococcus, and one bacterial genus, Mycobacterium). In the present study, we demonstrated that this novel biosynthetic pathway is universal in both Archaea and Bacteria, which contain inositol phospholipid, and elucidate the specificity of PIP synthase and AIP synthase for lipid substrates. PIP and AIP synthase activity were confirmed in all recombinant cells transformed with the respective gene constructs for four bacterial species (Streptomyces avermitilis, Propionibacterium acnes, Corynebacterium glutamicum, and Rhodococcus equi) and two archaeal species (Aeropyrum pernix and Sulfolobus solfataricus). Inositol was not incorporated. CDP-ArOH was used as the substrate for PIP synthase in Bacteria, and CDP-DAG was used as the substrate for AIP synthase in Archaea, despite their fundamentally different structures. PI synthase activity was observed in two eukaryotic species, Saccharomyces cerevisiae and Homo sapiens; however, inositol 1-phosphate was not incorporated. In Eukarya, the only pathway converts free inositol and CDP-DAG directly into PI. Phylogenic analysis of PIP synthase, AIP synthase, and PI synthase revealed that they are closely related enzymes.

Bacterial abundance and composition in marine sediments beneath the Ross Ice Shelf, Antarctica

Marine sediments of the Ross Sea, Antarctica, harbor microbial communities that play a significant role in the decomposition, mineralization, and recycling of organic carbon (OC). In this study, the cell densities within a 153-cm sediment core from the Ross Sea were estimated based on microbial phospholipid fatty acid (PLFA) concentrations and acridine orange direct cell counts. The resulting densities were as high as 1.7 × 10⁷ cells mL⁻¹ in the top ten centimeters of sediments. These densities are lower than those calculated for most near-shore sites but consistent with deep-sea locations with comparable sedimentation rates. The δ¹³C measurements of PLFAs and sedimentary and dissolved carbon sources, in combination with ribosomal RNA (SSU rRNA) gene pyrosequencing, were used to infer microbial metabolic pathways. The δ¹³C values of dissolved inorganic carbon (DIC) in porewaters ranged downcore from -2.5‰ to -3.7‰, while δ¹³C values for the corresponding sedimentary particulate OC (POC) varied from -26.2‰ to -23.1‰. The δ¹³C values of PLFAs ranged between -29‰ and -35‰ throughout the sediment core, consistent with a microbial community dominated by heterotrophs. The SSU rRNA gene pyrosequencing revealed that members of this microbial community were dominated by β-, δ-, and γ-Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Among the sequenced organisms, many appear to be related to known heterotrophs that utilize OC sources such as amino acids, oligosaccharides, and lactose, consistent with our interpretation from δ¹³CPLFA analysis. Integrating phospholipids analyses with porewater chemistry, δ¹³CDIC and δ¹³CPOC values and SSU rRNA gene sequences provides a more comprehensive understanding of microbial communities and carbon cycling in marine sediments, including those of this unique ice shelf environment.

The relative contribution of methanotrophs to microbial communities and carbon cycling in soil overlying a coal-bed methane seep

Seepage of coal-bed methane (CBM) through soils is a potential source of atmospheric CH4 and also a likely source of ancient (i.e. (14) C-dead) carbon to soil microbial communities. Natural abundance (13) C and (14) C compositions of bacterial membrane phospholipid fatty acids (PLFAs) and soil gas CO2 and CH4 were used to assess the incorporation of CBM-derived carbon into methanotrophs and other members of the soil microbial community. Concentrations of type I and type II methanotroph PLFA biomarkers (16:1ω8c and 18:1ω8c, respectively) were elevated in CBM-impacted soils compared with a control site. Comparison of PLFA and 16s rDNA data suggested type I and II methanotroph populations were well estimated and overestimated by their PLFA biomarkers, respectively. The δ(13) C values of PLFAs common in type I and II methanotrophs were as negative as -67‰ and consistent with the assimilation of CBM. PLFAs more indicative of nonmethanotrophic bacteria had δ(13) C values that were intermediate indicating assimilation of both plant- and CBM-derived carbon. Δ(14) C values of select PLFAs (-351 to -936‰) indicated similar patterns of CBM assimilation by methanotrophs and nonmethanotrophs and were used to estimate that 35-91% of carbon assimilated by nonmethanotrophs was derived from CBM depending on time of sampling and soil depth.

Archaeol: an indicator of methanogenesis in water-saturated soils

Oxic soils typically are a sink for methane due to the presence of high-affinity methanotrophic Bacteria capable of oxidising methane. However, soils experiencing water saturation are able to host significant methanogenic archaeal communities, potentially affecting the capacity of the soil to act as a methane sink. In order to provide insight into methanogenic populations in such soils, the distribution of archaeol in free and conjugated forms was investigated as an indicator of fossilised and living methanogenic biomass using gas chromatography-mass spectrometry with selected ion monitoring. Of three soils studied, only one organic matter-rich site contained archaeol in quantifiable amounts. Assessment of the subsurface profile revealed a dominance of archaeol bound by glycosidic headgroups over phospholipids implying derivation from fossilised biomass. Moisture content, through control of organic carbon and anoxia, seemed to govern trends in methanogen biomass. Archaeol and crenarchaeol profiles differed, implying the former was not of thaumarcheotal origin. Based on these results, we propose the use of intact archaeol as a useful biomarker for methanogen biomass in soil and to track changes in moisture status and aeration related to climate change.

Thermal adaptation of the archaeal and bacterial lipid membranes

The physiological characteristics that distinguish archaeal and bacterial lipids, as well as those that define thermophilic lipids, are discussed from three points of view that (1) the role of the chemical stability of lipids in the heat tolerance of thermophilic organisms: (2) the relevance of the increase in the proportion of certain lipids as the growth temperature increases: (3) the lipid bilayer membrane properties that enable membranes to function at high temperatures. It is concluded that no single, chemically stable lipid by itself was responsible for the adaptation of surviving at high temperatures. Lipid membranes that function effectively require the two properties of a high permeability barrier and a liquid crystalline state. Archaeal membranes realize these two properties throughout the whole biological temperature range by means of their isoprenoid chains. Bacterial membranes meet these requirements only at or just above the phase-transition temperature, and therefore their fatty acid composition must be elaborately regulated. A recent hypothesis sketched a scenario of the evolution of lipids in which the “lipid divide” emerged concomitantly with the differentiation of archaea and bacteria. The two modes of thermal adaptation were established concurrently with the “lipid divide.”

The major lipid cores of the archaeon Ignisphaera aggregans: implications for the phylogeny and biosynthesis of glycerol monoalkyl glycerol tetraether isoprenoid lipids

The lipid cores from Ignisphaera aggregans, a hyperthermophilic Crenarchaeon recently isolated from New Zealand hot springs, have been profiled by liquid chromatography-tandem mass spectrometry. The distribution revealed includes relatively high proportions of monoalkyl (also known as H-shaped) tetraether cores which have previously been implicated as kingdom-specific biomarkers for the Euryarchaeota. Such high expression of monoalkyl tetraether lipids is unusual in the archaeal domain and may indicate that formation of these components is an adaptive mechanism that allows I. aggregans to regulate membrane behaviour at high temperatures. The observed dialkyl tetraether and monoalkyl tetraether lipid distributions are similar but not fully concordant, showing differences in the average number of incorporated rings. The similarity supports a biosynthetic route to the ring-containing dialkyl and monoalkyl tetraether lipids via a dialkyl tetraether core containing zero rings, or a closely related structural relative, as an intermediate. Currently, however, the precise nature of the biosynthetic route to these lipids cannot be deduced.

Early evolution of membrane lipids: how did the lipid divide occur?

The ubiquitous distribution, homology over three domains, and key role in the membrane formation of the enzymes of the CDP-alcohol phosphatidyltransferase family, as well as phylogenetic analyses of lipid synthesizing enzymes suggest that the membranes of Wächtershäuser's hypothetical pre-cells (universal common ancestor) [Mol Microbiol 47:13-22 (2003)] comprised a lipid bilayer with four types of core lipids [G-1-P-isoprenoid ether (Ai), G-3-P-fatty acyl ester (Bf), G-1-P-fatty acyl ester (Af) and G-3-P-isoprenoid ether (Bi)]. Here, a complementary hypothesis is presented to explain the difference between archaeal and bacterial lipids (lipid divide). The main driving force of lipid segregation is assumed to be glycerophosphate (GP) enantiomers, as Wächtershäuser proposed, but in the present study the hydrocarbon chains bound to each backbone are also hypothesized to affect lipid segregation. It is assumed that segregation was stimulated by different hydrocarbon chains bound to different GP backbones (Ai:Bf or Af:Bi). Because Ai and Bi are diastereomers and Af and Bf are enantiomers, Ai:Bf and Af:Bi are not equivalent. G-1-P-isoprenoid ether is provisionally assumed to segregate more easily from Bf than Bi does from Af. G-1-P-isoprenoid ether and Bf could more easily achieve the more stable homochiral membranes that are the ancestors of Archaea and Bacteria. This can explain why the extant archaeal and bacterial membrane lipids are mainly composed by Ai and Bf lipids, respectively. Because polar head groups were localized in the cytoplasmic compartment of pre-cells, they were equally carried over to Archaea and Bacteria during differentiation. Consequently, the both descendants shared the main head groups of membrane phospholipids.

Rapid discrimination of archaeal tetraether lipid cores by liquid chromatography-tandem mass spectrometry

Atmospheric pressure chemical ionization liquid chromatography-tandem mass spectrometry (APCI LC-MS/MS) of tetraether lipid cores of archaeal origin reveals distinct dissociation pathways for three classes of core lipid extracted from Methanobacter thermautotrophicus. Within these classes, two isobaric tetraether lipids, one a scarcely reported lipid constituent of M. thermautotrophicus and the other an artefact formed during extraction from cultured cells, were identified and distinguished via their MS(2) spectra. APCI LC-MS/MS discriminates different tetraether core lipid types and isobaric species and reveals the mass of the constituent biphytanyl chains within the tetraether cores, albeit without full elucidation of their structures. Furthermore, the method allows direct estimation of the relative proportions of tetraether core lipids from chromatographic peak area measurement, allowing rapid profiling of these compounds in microbiological and environmental extracts.

Lipid biomarker and phylogenetic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment

This study has utilized the tools of lipid biomarker chemistry and molecular phylogenetic analyses to assess the archaeal contribution to diversity and abundance within a microbial mat and underlying sediment from a hypersaline lagoon in Baja California. Based on abundance of ether-linked isoprenoids, archaea made up from 1 to 4% of the cell numbers throughout the upper 100 mm of mat and sediment core. Below this depth archaeal lipid was two times more abundant than bacterial. Archaeol was the primary archaeal lipid in all layers. Relatively small amounts of caldarchaeol (dibiphytanyl glyceroltetraether) were present at most depths with phytanyl to biphytanyl molar ratios lowest (approximately 10 : 1) in the 4-17 mm and 100-130 mm horizons, and highest (132 : 1) in the surface 0-2 mm. Lipids with cyclic biphytanyl cores were only detected below 100 mm. A novel polar lipid containing a C(30) isoprenoid (squalane) moiety was isolated from the upper anoxic portion of the core and partially characterized. Hydrocarbon biomarker lipids included pentamethylicosane (2-10 mm) and crocetane (primarily below 10 mm). Archaeal molecular diversity varied somewhat with depth. With the exception of samples at 0-2 mm and 35-65 mm, Thermoplasmatales of marine benthic group D dominated clone libraries. A significant number of phylotypes representing the Crenarchaeota from marine benthic group B were generally present below 17 mm and dominated the 35-65 mm sample. Halobacteriaceae family made up 80% of the clone library of the surface 2 mm, and consisted primarily of sequences affiliated with the haloalkaliphilic Natronomonas pharaonis.

Subsurface microbial diversity in deep-granitic-fracture water in Colorado

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This "Henderson candidate division" dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems.

Immunostimulatory colloidal delivery systems for cancer vaccines

Cancer vaccine delivery is a multidisciplinary scientific field that is currently undergoing rapid development. An important component of cancer vaccines is the development of novel vaccine delivery strategies, such as colloidal immunostimulatory delivery systems. The importance of formulation strategies for cancer vaccines can be explained by the poor immunogenicity of tumour antigens. Colloidal vaccine delivery systems modify the kinetics, body distribution, uptake and release of the vaccine. This review explores recent research that is directed towards more targeted treatments of cancer through to colloidal vaccine delivery systems. Widely investigated carrier systems include polymeric micro- and nanoparticles, liposomes, archaeal lipid liposomes (archaeosomes), immune-stimulating complexes and virus-like particles. These systems are evaluated in terms of their formulation techniques, immunological mechanisms of action as well as the potential and limitations of such colloidal systems in the field of cancer vaccines.