Hydroxyarchaeol

Last updated
hydroxyarchaeol
Hydroxyarchaeol structure.png
Names
IUPAC name
1-(3-hydroxy-2-((3,7,11,15-tetramethylhexadecyl)oxy)propoxy)-3-7-11-15-tetramethylhexadecan-3-ol
Other names
hydroxyarchaeol lipid|3'-hydroxydiether lipid|2-O-(3,7,11,15-tetramethyl)hexadecyl-3-O-(3'-hydroxy-3',7',11',15'-tetramethyl)hexadecyl-sn-glycerol
Identifiers
3D model (JSmol)
PubChem CID
  • InChI=1S/C43H88O4/c1-35(2)17-11-19-37(5)21-13-23-39(7)24-15-26-41(9)28-31-47-42(33-44)34-46-32-30-43(10,45)29-16-27-40(8)25-14-22-38(6)20-12-18-36(3)4/h35-42,44-45H,11-34H2,1-10H3
    Key: WZRFZYVQKWIZEV-UHFFFAOYSA-N
  • CC(C)CCCC(C)CCCC(C)CCCC(C)CCOC(CO)COCCC(C)(CCCC(C)CCCC(C)CCCC(C)C)O
Properties
C43H88O4
Molar mass 699.17 g·mol−1
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
Infobox references
Chemical structure of the two major isomers of hydroxyarchaeol. A) sn-2 hydroxyarchaeol, B) sn-3 hydroxyarchaeol. Chemical structure of the two major forms of hydroxyarchaeol (sn-2 (A) and sn-3 (B)).png
Chemical structure of the two major isomers of hydroxyarchaeol. A) sn-2 hydroxyarchaeol, B) sn-3 hydroxyarchaeol.

Hydroxyarchaeol is a core lipid unique to archaea, similar to archaeol, with a hydroxide functional group at the carbon-3 position of one of its ether side chains. [1] It is found exclusively in certain taxa of methanogenic archaea, [2] and is a common biomarker for methanogenesis and methane-oxidation. Isotopic analysis of hydroxyarchaeol can be informative about the environment and substrates for methanogenesis. [3]

Contents

Discovery

Hydroxyarchaeol was first identified by Dennis G. Sprott and colleagues in 1990 from Methanosaeta concilii by a combination of TLC, NMR and mass spectrometric analysis. [1]

Structure and function

The lipid consists of a glycerol backbone with two C20 phytanyl ether chains attached, one of which has a hydroxyl (-OH) group attached at the C3 carbon. It is one of the major core lipids of methanogenic archaea alongside archaeol, forming the basis of their cell membrane. The two major forms are sn-2- and sn-3-hydroxyarchaeol, depending on if the hydroxyl group is on the sn-2 or sn-3 phytanyl chain of the glycerol backbone. [4]

Methanogen biomarker

Use of hydroxyarchaeol as a biomarker was a primary way to identify methanogens in the environment, though it has become supplementary to metagenomic and 16S rRNA techniques for identifying phylogeny. [2] [4] [5] [3] While hydroxyarchaeol has only been identified in methanogenic archaea, not all methanogens count it among their core lipids. [2] [4] Other methanogens may contain different derivatives of archaeol, including cyclic archaeol and caldarchaeol based on taxonomic differences. [2] Hydroxyarchaeol has been identified in many different taxa, including within the orders Methanococcales, Methanosarcinales, which contains the genus Methanosaeta, and a genus from the order Methanobacteriales. [2] There is evidence that there is a taxonomic preference for the sn-2 vs sn-3 form based on phylogeny, as a mix of the two forms do not tend to appear in the same organism, but the reason for this difference is not well understood. [1] Because of the hydroxyl group, which is prone to degradation over time, hydroxyarchaeol has not been observed in ancient samples, and thus is thought to indicate modern sources of methanogens . [6]

Measurement techniques

Original measurements of hydroxyarchaeol were done using TLC and NMR, but have become dominated by gas-chromatograph/mass spectrometry. For most methods, extraction of the core lipid is typically done using variations of a Bligh-Dyer method, [7] which makes use of the various polarities and miscibility of dichloromethane (DCM), methanol, and water. Acidic conditions using trichloroacetic acid (TCA) during extraction and additional cleanup of samples with polar solvents such as DCM is often needed to better isolate the lipids of interest. [1] [3] [5]

GC-MS

Prior to GC-MS analysis, the intact hydroxyarchaeol lipid is typically hydrolyzed to the core lipid component and derivatized by adding trimethyl silyl (TMS) groups to the free hydroxyl functional groups. [1] [5] [3] This allows for the lipid to volatilize in the GC and reach the MS analyzer. Because hydroxyarchaeol has multiple sites that can be modified after TMS derivatization, the observed mass spectra can be either the mono- or di-TMS derivative, and need to be compared to authentic standards to properly identify and quantify. [8] For identification and quantification, the mass spectrometer typically utilizes a quadrupole mass analyzer, but isotopic analysis uses an isotope-ratio mass spectrometer (IRMS) that has higher mass resolution and sensitivity. [5] [3]

δ13C Isotope ratio analysis

The relative isotopic ratio of carbon (δ13C) found in hydroxyarchaeol is used to identify what the methane-associated organism is using as a carbon source. [3] Carbon sources in the environment will have a measurable δ13C signature that can be matched with the biomarkers found in an organism, which will gain the isotopic signature of its food source. Since archaea that make hydroxyarchaeol can harness a number of carbon sources, including dissolved inorganic carbon (DIC), methanol, trimethylamine, and methane, [2] [3] this is a useful way to determine which is the primary source of energy, or if there is a mixture of use in the environment.

Case Study

Methane-oxidizing archaea in association with sulfate reducing bacteria (ANME-SRB) found at methane-seeps. Red = ANME, green = SRB. [9]

Hydroxyarchaeol has been found in peat bogs [6] and methane seeps in the deep ocean [3] [5] as a marker of both methanogens and methanotrophs. The deep sea sediment hydroxyarchaeol had very depleted δ13C at methane seeps. Both the methane and DIC present also had depleted δ13C values, but not as a perfect match to the identified biomarker. [3] By modeling the isotopic ratio of DIC and methane to the isotopic ratio of the biomarkers, the researchers could estimate the relative contribution to biosynthesis and metabolic pathways that each source had for the organism. The model could predict a relative contribution that matched well with actual measurements, indicating there was mixed metabolism occurring at these sites, with specific biosynthetic pathways using different proportions of carbon derived from each source. [3] This method made use of hydroxyarchaeol in the bulk sample to target the metabolism of a specific group of microbes without need for exhaustive separations of different organisms, making it useful for environmental analysis.

Related Research Articles

Isotope analysis

Isotope analysis is the identification of isotopic signature, the abundance of certain stable isotopes and chemical elements within organic and inorganic compounds. Isotopic analysis can be used to understand the flow of energy through a food web, to reconstruct past environmental and climatic conditions, to investigate human and animal diets in the past, for food authentification, and a variety of other physical, geological, palaeontological and chemical processes. Stable isotope ratios are measured using mass spectrometry, which separates the different isotopes of an element on the basis of their mass-to-charge ratio.

Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domains Archaea and Bacteria. They are common in wetlands, where they are responsible for marsh gas, and in the digestive tracts of animals such as ruminants and many humans, where they are responsible for the methane content of belching in ruminants and flatulence in humans. In marine sediments, the biological production of methane, also termed methanogenesis, is generally confined to where sulfates are depleted, below the top layers. Moreover, methanogenic archaea populations play an indispensable role in anaerobic wastewater treatments. Others are extremophiles, found in environments such as hot springs and submarine hydrothermal vents as well as in the "solid" rock of Earth's crust, kilometers below the surface.

Methanogenesis or biomethanation is the formation of methane by microbes known as methanogens. Organisms capable of producing methane have been identified only from the domain Archaea, a group phylogenetically distinct from both eukaryotes and bacteria, although many live in close association with anaerobic bacteria. The production of methane is an important and widespread form of microbial metabolism. In anoxic environments, it is the final step in the decomposition of biomass. Methanogenesis is responsible for significant amounts of natural gas accumulations, the remainder being thermogenic.

<i>Methanosarcina</i> Genus of archaea

Methanosarcina is a genus of euryarchaeote archaea that produce methane. These single-celled organisms are known as anaerobic methanogens that produce methane using all three metabolic pathways for methanogenesis. They live in diverse environments where they can remain safe from the effects of oxygen, whether on the earth's surface, in groundwater, in deep sea vents, and in animal digestive tracts. Methanosarcina grow in colonies.

Phytane is the isoprenoid alkane formed when phytol, a constituent of chlorophyll, loses its hydroxyl group. When phytol loses one carbon atom, it yields pristane. Other sources of phytane and pristane have also been proposed than phytol.

Methanobacteria Class of archaea

In taxonomy, the Methanobacteria are a class of the Euryarchaeota. Several of the classes of the Euryarchaeota are methanogens and the Methanobacteria are one of these classes.

Methanobrevibacter smithii is the predominant archaeon in the microbiota of the human gut. M. smithii has a coccobacillus shape. It plays an important role in the efficient digestion of polysaccharides by consuming the end products of bacterial fermentation. Methanobrevibacter smithii is a single-celled microorganism from the Archaea domain. M. smithii is a methanogen, and a hydrogenotroph that recycles the hydrogen by combining it with carbon dioxide to methane. The removal of hydrogen by M. smithii is thought to allow an increase in the extraction of energy from nutrients by shifting bacterial fermentation to more oxidized end products.

Archaea Domain of single-celled organisms

Archaea constitute a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

Archaeol is one of the main core membrane lipids of archaea, one of the three domains of life. One of the key features that distinguishes archaea from bacteria and eukarya is their membrane lipids, where archaeol plays an important role. Because of this, archaeol is also broadly used as a biomarker for ancient archaea, especially methanogens, activity.

Methanocaldococcus jannaschii is a thermophilic methanogenic archaean in the class Methanococci. It was the first archaeon to have its complete genome sequenced. The sequencing identified many genes unique to the archaea. Many of the synthesis pathways for methanogenic cofactors were worked out biochemically in this organism, as were several other archaeal-specific metabolic pathways.

CDP-archaeol synthase is an enzyme with systematic name CTP:2,3-bis-O-(geranylgeranyl)-sn-glycero-1-phosphate cytidylyltransferase. This enzyme catalyses the following chemical reaction

Methanococcoides burtonii is a methylotrophic methanogenic archaeon first isolated from Ace Lake, Antarctica. Its type strain is DSM 6242.

<i>Methanohalophilus mahii</i> Species of archaeon

Methanohalophilus mahii is an obligately anaerobic, methylotrophic, methanogenic cocci-shaped archaeon of the genus Methanohalophilus that can be found in high salinity aquatic environments. The name Methanohalophilus is said to be derived from methanum meaning "methane" in Latin; halo meaning "salt" in Greek; and mahii meaning "of Mah" in Latin, after R.A. Mah, who did substantial amounts of research on aerobic and methanogenic microbes. The proper word in ancient Greek for "salt" is however hals (ἅλς). The specific strain type was designated SLP and is currently the only identified strain of this species.

<i>Methanosarcina barkeri</i> Species of archaeon

Methanosarcina barkeri is the most fundamental species of the genus Methanosarcina, and their properties apply generally to the genus Methanosarcina. Methanosarcina barkeri can produce methane anaerobically through different metabolic pathways. M. barkeri can subsume a variety of molecules for ATP production, including methanol, acetate, methylamines, and different forms of hydrogen and carbon dioxide. Although it is a slow developer and is sensitive to change in environmental conditions, M. barkeri is able to grow in a variety of different substrates, adding to its appeal for genetic analysis. Additionally, M. barkeri is the first organism in which the amino acid pyrrolysine was found. Furthermore, two strains of M. barkeri, M. b. Fusaro and M. b. MS have been identified to possess an F-type ATPase along with an A-type ATPase.

Hydrogenotrophs are organisms that are able to metabolize molecular hydrogen as a source of energy.

Hydrogen isotope biogeochemistry is the scientific study of biological, geological, and chemical processes in the environment using the distribution and relative abundance of hydrogen isotopes. There are two stable isotopes of hydrogen, protium 1H and deuterium 2H, which vary in relative abundance on the order of hundreds of permil. The ratio between these two species can be considered the hydrogen isotopic fingerprint of a substance. Understanding isotopic fingerprints and the sources of fractionation that lead to variation between them can be applied to address a diverse array of questions ranging from ecology and hydrology to geochemistry and paleoclimate reconstructions. Since specialized techniques are required to measure natural hydrogen isotope abundance ratios, the field of hydrogen isotope biogeochemistry provides uniquely specialized tools to more traditional fields like ecology and geochemistry.

Methane clumped isotopes are methane molecules that contain two or more rare isotopes. Methane (CH4) contains two elements, carbon and hydrogen, each of which has two stable isotopes. For carbon, 98.9% are in the form of carbon-12 (12C) and 1.1% are carbon-13 (13C); while for hydrogen, 99.99% are in the form of protium (1H) and 0.01% are deuterium (2H or D). Carbon-13 (13C) and deuterium (2H or D) are rare isotopes in methane molecules. The abundance of the clumped isotopes provides information independent from the traditional carbon or hydrogen isotope composition of methane molecules.

The sulfate-methane transition zone (SMTZ) is a zone in oceans, lakes, and rivers found below the sediment surface in which sulfate and methane coexist. The formation of a SMTZ is driven by the diffusion of sulfate down the sediment column and the diffusion of methane up the sediments. At the SMTZ, their diffusion profiles meet and sulfate and methane react with one another, which allows the SMTZ to harbor a unique microbial community whose main form of metabolism is anaerobic oxidation of methane (AOM). The presence of AOM marks the transition from dissimilatory sulfate reduction to methanogenesis as the main metabolism utilized by organisms.

Lycopane Chemical compound

Lycopane (C40H82; 2,6,10,14,19,23,27,31-octamethyldotriacontane), a 40 carbon alkane isoprenoid, is a widely present biomarker that is often found in anoxic settings. It has been identified in anoxically deposited lacustrine sediments (such as the Messel formation and the Condor oil shale deposit). It has been found in sulfidic and anoxic hypersaline environments (such as the Sdom Formation). It has been widely identified in modern marine sediments, including the Peru upwelling zone, the Black Sea, and the Cariaco Trench. It has been found only rarely in crude oils.

Glycerol dialkyl glycerol tetraether lipids (GDGTs) are a class of membrane lipids synthesized by archaea and some bacteria, making them useful biomarkers for these organisms in the geological record. Their presence, structure, and relative abundances in natural materials can be useful as proxies for temperature, terrestrial organic matter input, and soil pH for past periods in Earth history. Some structural forms of GDGT form the basis for the TEX86 paleothermometer. Isoprenoid GDGTs, now known to be synthesized by many archaeal classes, were first discovered in extremophilic archaea cultures. Branched GDGTs, likely synthesized by acidobacteria, were first discovered in a natural Dutch peat sample in 2000.

References

  1. 1 2 3 4 5 Sprott GD, Ekiel I, Dicaire C (August 1990). "Novel, acid-labile, hydroxydiether lipid cores in methanogenic bacteria". The Journal of Biological Chemistry. 265 (23): 13735–40. doi: 10.1016/S0021-9258(18)77411-5 . PMID   2380184.
  2. 1 2 3 4 5 6 Koga Y, Morii H, Akagawa-Matsushita M, Ohga M (January 1998). "Correlation of Polar Lipid Composition with 16S rRNA Phylogeny in Methanogens. Further Analysis of Lipid Component Parts". Bioscience, Biotechnology, and Biochemistry. 62 (2): 230–6. doi:10.1271/bbb.62.230. PMID   27388514.
  3. 1 2 3 4 5 6 7 8 9 10 Bird LR, Dawson KS, Chadwick GL, Fulton JM, Orphan VJ, Freeman KH (November 2019). "Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane-oxidizing archaea". Geobiology. 17 (6): 611–627. doi:10.1111/gbi.12354. PMID   31364272.
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  5. 1 2 3 4 5 Hinrichs KU, Summons RE, Orphan V, Sylva SP, Hayes JM (December 2000). "Molecular and isotopic analysis of anaerobic methane-oxidizing communities in marine sediments". Organic Geochemistry. 31 (12): 1685–1701. doi:10.1016/S0146-6380(00)00106-6.
  6. 1 2 Pancost RD, McClymont EL, Bingham EM, Roberts Z, Charman DJ, Hornibrook ER, et al. (November 2011). "Archaeol as a methanogen biomarker in ombrotrophic bogs". Organic Geochemistry. 42 (10): 1279–1287. doi:10.1016/j.orggeochem.2011.07.003.
  7. Bligh EG, Dyer WJ (August 1959). "A rapid method of total lipid extraction and purification". Canadian Journal of Biochemistry and Physiology. 37 (8): 911–7. doi:10.1139/o59-099. PMID   13671378.
  8. Hinrichs KU, Pancost RD, Summons RE, Sprott GD, Sylva SP, Sinninghe Damsté JS, Hayes JM (May 2000). "Mass spectra of sn-2-hydroxyarchaeol, a polar lipid biomarker for anaerobic methanotrophy". Geochemistry, Geophysics, Geosystems. 1 (5): 1025. Bibcode:2000GGG.....1.1025H. doi: 10.1029/2000GC000042 .
  9. Ruff SE, Arnds J, Knittel K, Amann R, Wegener G, Ramette A, Boetius A (September 2013). "Microbial communities of deep-sea methane seeps at Hikurangi continental margin (New Zealand)". PLOS ONE. 8 (9): e72627. Bibcode:2013PLoSO...872627R. doi: 10.1371/journal.pone.0072627 . PMC   3787109 . PMID   24098632.