Lecture 4
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| What are pieces of information content found in biomarkers and are species specific? | Carbon skeleton, type and positions of functional groups, stereochemistry and isotope content (13C, 14C, 2H, 15N, 34S, etc.) |
| Species-specific biosynthesis relys on the principle that: | Same amount of C’s and H’s but different structure, functional groups or d13C can tell us about the species specific biosynthesis/pathway of synthesizing the lipid/environment |
| Diagenesis and catagenesis ... | Increase loss of information during the increasing burial and time |
| Over time the carbon skeleton may survive,, but the functional groups may get lost, this causes ... | It to become more difficult to recognize the original biomarker and thus the source organism |
| Over time dinosterol may turn into... (dia/catagenesis) | Dinosterene (loss of OH, substituted by double bond) and dinosterane (loss of double bonds, replaced by H's?) |
| What kind of organisms make dinosterol? | Eukaryotes (sterol! 3 cyclohexane, 1 cyclopentane) - specifically dinoflagellates |
| Prokaryotes | Are organisms whose cells lack a nucleus and other organelles. Prokaryotes are divided into two distinct groups: the bacteria and the archaea. Most prokaryotes are small, single-celled organisms that have a relatively simple structure. |
| Eukaryotes | Are organisms whose cells contain a nucleus and other membrane-bound organelles. There is a wide range of eukaryotic organisms, including all animals, plants, fungi, and protists, as well as most algae. Eukaryotes may be either single-celled or multicellular. |
| Ribosomes | The cell’s protein-synthesising factories, are composed of structural RNA and various proteins. Ribosomes are present in ALL cells and the sequence of the gene encoding for 16S or 18S ribosomal RNA is used for molecular phylogeny of all organisms. |
| Chlorophyll a = present in almost all phytoplankton species, a good biomarker for this is ? | Phytol (acyclic diterpene alcohol) is a good biomarker for algae! Due to diagenesis this may turn into phytane (no OH group) -> diterpene alcohol |
| A good biomarker for algae is polyunsaturated fatty acids, what is their disadvantage ? | Due to unsaturation they are quite unstable |
| IPL are the basic building blocks of cell membranes. They contain at least one .... headgroup. They are very good biomarkers because ? | Hydrophilic - Large structural variety in the fatty acid tails, types of bonds and also in the headgroups |
| Sterols occur generally in eukaryotes but are only directly biosynthesized by photosynthetic eukaryotes (algae and higher plants) and are used as membrane modifiers. What are these sterols?Look at the methyls and double bonds! | Dinosterol (dinoflagellates), "diatom"sterol, d7 sterol (double bond at 7), occur abundantly in green algae |
| Why are sterols not the best biomarkers? | They are not really exclusive to certain groups |
| Who make these | Occurs specifically in Chrysophyte algae (‘brown algae’) |
| Who make these | Occurs in Porifera (“sponges”) (but also a bit in Chrysophytes, brown algae) |
| Who makes this 27-nor? | Kareniadinoflagellate algae (but also occur in other dinoflagellates as minor compounds) |
| Proboscia (diatom) lipids ar long chain diols - C28 & C30 1,14-diols (saturated or mono-unsaturated at C6), what are they related to/which environement are they most abundant | Upwelling an dnutreint-rich wates - upwelling zones |
| Occurrence of highly branched isoprenoid (HBI) alkenes are produced by...? | A small number of marine diatoms (C25 and C30, with some double bonds)(specific genera: Rhizosolenia, Haslea, Pleurosigma, Navicula) |
| HBIs are found in two seperate diatom clusters, how could this be? | Convergent evolution |
| IP25 is a .... biomarker for .... | Highly branched isoprenoid (HBI) specific to arctic sea ice diatoms (seasonal! not permanent cover, need light!) |
| IPSO25 is a ... biomarker for ... . And what does its name stand for? | Highly branched isoprenoid (HBI) is specific for melting antarctic ice & Ice Proxy for the Southern Ocean with 25 carbon atoms |
| Long-chain alkenones (O double bond at second C-atom) are biomarkers for .... | Abundant haptophytes |
| There are 3 subgroups of haptophytes (for example: coccolithophores) that synthesise long chain alkenones, freshwater, alternating salinity and marine. Each sub group makes a different sort of alkenone. What are the differences | Clusters differ in chain length (C37/C38/C39/C40) and double bond position and isomer |
| Botryococcus braunii is a sometimes abundant freshwater algae that contains extraordinary high amounts of hydrocarbons, what is the unique biomarker (hint in figure), if you find this, what can you say about the deposition? | When you find botryococcene you know it is not marine but lacustrine (easier to get oil!) |
| The composition of membrane lipids of ciliates is determined by their diet and represent the oxic/anoxic state of the watercolumn. If they switch from making making sterols to tetrahymanol (triperpenoid), what happened? | Watercolumn switched from oxic to anoxic and the ciliated switched from eating algae (eukaryotes) to bacteria (bactiverous ciliates) |
| Odd-carbon long chain n-alkanes are a biomarker for? what baout odd and short? | Higher plants vs marine plants |
| Who makes these abietic acids/simonellite | Gymnosperms (nakedseeds) |
| Who makes these b-amyrins/tetra-aromatic triterpanes | Angiosperms (enclosed seed/flowering plants) |
| Who is making the oleanane biomarker (triterpenoid) and what do they originate from | Diagnostic biomarker of angiosperms- tetra-aromatic triterpanes /b-amyrin but lost double bonds |
| What is this and who made it? | Hopane - bacteria |
| What is this and who made it? | Sterane (see sterol structure) - eukaryotes |
| What is this and who made it? | Tetrahymanol (cyclic triterpenoid + alcohol group) - bactivirous ciliates |
| What is this and who made it? | Oleanane (cyclic triterpenoid) - angiosperms |
| What is this and who made it ? | Taraxerol - mangroves (cyclic triterpenoid, alcohol group (-ol), 1 double bond) |
| Lignin phenols trace .... | Vegetation input |
| Levoglucose traces .. | Terrestrial biomass burning |
| Who make sterols in their membrane lipids? | Eukaryotes (sterol = 3-cyclohexane, 1-cyclopentane & OH-group) |
| 3-Methyl hopanoids are found in .... and also in ancient methane seep sediments with 13C-depleted values | (mostly) aerobic methanotrophic bacteria |
| What types of lipids & bonds are specific to archaea ? | Isoprenoid ether lipids - so ether bonded |
| Some archaea form ... for their membranes instead of bilayers | Monolayers (2 polar heads with 1 polar tail in between) |
| What is the type of molecule that makes of a monolayer called? | Tetraether lipid / GDGT (4 ether bonds) |
| What is the type of molecule called that makes up a bilayer in archaea | Diether lipid / archaeol |
| Crenarchaeol (GDGT with a cyclohexane ring) is specific for ... ? | Ammonium oxidizing thaumarchaeota |
| Isoprenoid ether lipids with low 13C contents are specific for ... | Methanotrophic archaea |
| Dietherlipid with a C25 isoprenoid chain may be specific for ... | Halophilic (salt loving) archaea |
| Crenarchaeota are ... and make ... | Hyperthermophyles - cyclopentane rings in their monolayer lipids (tetraether GDGTs-n) |
| Euryarcheaota are for example .... and .... . How are their membranes structured? | Halophiles and methanogens . They have bilayers of archaeol or monolayers of GDGTs |
| How do we analyse tetraetherlipids? | Take off the head groups leaving the carbon skeleton and its rings to be analysed with GC-MS. LC-MS nowadays more suitable for larger molecules if soluble. |
| Ether bonds of archaea are very... | Strong and resitant to acids compared to ester bond |
| Covalently bonded monolayers are.. | Stronger than bilayers |
| Non extremophiles can for example be found in... | Soils, lakes and peats |
| Thaumarchaeota are the ones making ... | Crenarchaeol - GDGT with 4 cyclopentanes and 1 cyclohexane |
| What is crenarchaeol a biomarker for? | Thaumarchaeota - ammonia oxidizing archaea (and so ammonia oxidation) |
| Ammonium oxidation by thaumarcheaota uses ... and releases ... | Ammonia (NH3) to nitrite (NO2 -) (increases when thaumarchaeota bloom) |
| Crenarcheol hate.. . And why does this matter? | Free sulphite, causes them not to occur that much anymore at great depth (2000m) |
| Crenarcheol don't show 13C depletion of methane because | They are in the nitrogen cycle not in methane cycle |
| Occurrence in archae of GDGTs. | Yeh no question, just loook at it for a second |
| Irregylar acyclic isoprenoids - characteristic for ? and because? | Methanogens & anaerobic oxidation of methane - depletion in 13C due to methane cycle - so archae involved in methane cycle |
| The membrane lipids of bacteria are bound by | Ester bonds |
| (Tetra- and di-) ether lipids also occur in bacteria but ... | With straight chain or branched chains and mostly no cyclopentanes |
| “branched” GDGTs are biomarkers for | Acidobacteria Likely Acidobacteria. |
| Isorenieratene is a characteristic pigment for ... | Photosynthetic anaerobic green sulphur bacteria - and biomarker for euxinia |
| Okenone is a characteristic pigment for | Photosynthetic anaerobic purple sulphur bacteria (anoxia high in photic zone!) |
| Iso- and anteiso fatty acids often in ... | Anaerobic bacteria /sulphate reducers |
| .... are biomarkers for bacteria but only a few are specific for classes of bacteria | Hopanoids (e.g. 3-methyl hopanoids in combination with 13C-depletion for methanotrophic bacteria) |
| Annamox process = | Ammionium + nitrite and releases nitrogen gas (harmless) - used to treating wastewaters! But slow and anoxic |
| Heterocyst glycolipids are biomarkers for | N2-fixing heterocyst cyanobacteria (blue algae), need oxygen! |
| What is heterocyst? | Special cell compartment, this is where N2 fixing takes place for N2 fixing cyanobacteria |
| Ladderane lipids (staircase structure) are biomarkers for ... | Anaerobic ammonium oxidizing "annamox" bacteria --> anoxia and ammonium oxidation |
| Bacteria capable of anammox are for example... & the biomarker for anammox by bacteria is? | Planctomycetes - ladderane lipids |
| Are biomarkers specific for microbial groups or biosynthetic pathways? | Through biosynthetic pathways – these pathways can go extinct, and through these microbial groups as well |
| Why do “Early-branching” groups of thermophilic bacteria look to have “unusual” membrane lipids? | They look archaea like, producing non-isoprenoid ether lipids or a mix of ester and ether lipids and form membrane spanning monolayers. |
| Bacterial membrane lipids are always | Non-isoprenoid but rather straight or branched (archaea are isoprenoid) |
| Bacterial branched GDGT are found in | Peats and soils, not much in marine |
| Branched GDGTs are abundant in | Anoxic parts of peat bogs -> anaerobic bacteria (preservation bias?) - made by acidobacteria (peats are acidic - making is diabolic acid) |
| Hopanoids, in contrast to steroids, are not restricted to ... . | Aerobic bacteria, but can also be found in anaerobic bacteria (anammox, iron-reducing, sulfate reducing, etc.) |
| Bacteriohopanepolyol - what is the functional role of hopanoids | Mainly bacterial membrane rigidifiers, but also not completely sure what their unique property is. Polar side chain 9blue) is most unique and indicative part. But also greatd iversity in ringsystem methylations |
| Who has these hopanoids? | Methanotrophs! |
| Cyanobacteria make saturated hydrocarbons, but some cyanobacteria make | Branched alkanes/hydrocarbons |
| Marine symbiotic heterocyst cyanobacteria make glycolipids with .... sugars rather than ...sugars in freshwater free living cyanobacteria | C5 rather than C6 |
| Why do in marine environments heterocyst cyanobacteria mainly occur as symbionts in certain diatom species | Diatom uses the ammonium released from nitrogen fixation |