The membrane lipids of Thaumarchaeota are composed of glycerol dialkyl glycerol tetraethers (GDGTs) which contain 0-3 cyclopentane moieties, whereas crenarchaeol, the characteristic GDGT, contains four cyclopentane moieties and a single cyclohexane moiety. Thaumarchaeota also synthesise a regio-isomer of crenarchaeol. The cyclohexane and cyclopentane rings, formed by internal cyclisation of one of the biphytane chains, have a pronounced effect on the thermal transition points of the Thaumarchaeotal cell membrane. Mesocosm studies demonstrate that the degree of cyclisation is generally governed by growth temperature 
Based upon the relative distribution of isoprenoidal GDGTs, Schouten et al. (2002) proposed the tetraether index of 86 carbon atoms (TEX86) as a proxy for sea surface temperature (SST). GDGT-0 is excluded from the calibration as it can have multiple sources  while GDGT-4 is omitted as it exhibits no correlation with SST and is often an order of magnitude more abundant that its isomer and the other GDGTs. The most recent TEX86 calibration invokes two separate indices and calibrations: TEX86H uses the same combination of GDGTs as in the original TEX86 relationship:
GDGT ratio-2 is correlated to SST using the calibration equation: TEX86H = 68.4*log(GDGT ratio-2) + 38.6). TEX86H has a calibration error of ±2.5°C and is based upon 255 core-top sediments.
TEX86L employs a combination of GDGTs that is different from TEX86H, removing GDGT-3 from the numerator and excluding GDGT-4’ entirely:
GDGT ratio-1 is correlated to SST using the calibration equation:(TEX86L=67.5*log(GDGT ratio-1)+46.9). TEX86Lhas a calibration error of ±4°C and is based upon 396 core-top sediment samples.
Depth of production
Thaumarchaeotal production is not limited to the sea surface (0-30m). Karner et al. (2001) conducted a year-long study of Thaumarchaeota and Euryarchaeota abundance at the Hawai’i Ocean Time-series and demonstrated that both groups thrive throughout the water column (i.e. over 30m). Other studies also provide evidence for epi- and meso-pelagic archaeal communities (Turich et al., 2007). Work by Taylor et al. (2013) shows that the offset between TEX86H and TEX86L (ΔH–L) is a function of the GDGT-2/GDGT-3 ratio (/ratio), and that this can be used to separate low- and high-latitude GDGT distributions in the modern core-top dataset: a range of / ratios and ΔH–L values occur in polar regions, whereas / ratios are high and ΔH–L values are small at lower latitude sites where SSTs are ≥ 15°C. However, in Paleogene datasets, a wide range of / ratios are observed, even for SST estimates ≥ 15°C. Crucially, they found that water depth is a better discriminator of ΔH–L values and / ratios than SST when considering a combined dataset of modern and Paleogene GDGT distributions: ΔH–L values are low (≤ 3.0 °C) and / ratios are high ( ≥ 5.0) where water depth is ≥ 1000 m. Modern water column studies show that the / ratios of GDGTs (both core lipids and in-tact polar lipids) in suspended particulate matter (SPM) increase with depth, suggesting that high / ratios reflect a contribution from archaea living in the deeper water column. This suggests that export dynamics may well influence GDGT-derived SST estimates.
The branched vs isoprenoidal tetratether (BIT) index can used to measure the relative fluvial input of terrestrial organic matter (TOM) into the marine realm (Hopmans et al., 2004). The BIT index is based upon the premise that GDGT-4 (also known as crenarchaeol) is derived from marine-dwelling Thaumarchaeota and branched GDGTs are derived from terrestrial soil bacteria. When BIT values exceed 0.4, a deviation of >2°C is incorporated into TEX86 SST estimates. However, isoprenoidal GDGTs can be synthesised in the terrestrial environment and can render BIT values unreliable (Weijers et al., 2006; Sluijs et al., 2007; Xie et al., 2012). A strong co-variation between GDGT-4 and branched GDGTs in modern marine and freshwater environments also suggests a common or mixed source for isoprenoidal and branched GDGTs (Fietz et al., 2012).
Anaerobic Oxidation of Methane
The Methane Index (MI) was proposed to help distinguish the relative input of methanotrophic Euryarchaeota vs. ammonia-oxidising Thaumarchaeota in settings characterised by diffuse methane flux and anaerobic oxidation of methane (AOM) (Zhang et al., 2011). These sites are characterised by a distinct GDGT distribution, namely the predominance of GDGT-1. -2 and -3. High MI values (>0.5) reflect high rates of gas-hydrate-related AOM and low values (<0.3) suggest normal sedimentary conditions (i.e. no appreciable AOM input).
Thermal maturity is only thought to affect GDGTs when temperature exceed 240°C. This can be tested using a ratio of specific hopane isomers. Oxic degradation, which is a selective process and degrades compounds at different rates, has been shown to affect TEX86 values and can bias SST values by up to 6°C.
The oldest TEX86 record is from the middle Jurassic (~160Ma) and indicates relatively warm sea surface temperatures. TEX86 has been used to reconstruct temperature throughout the Cenozoic era (65-0Ma) and is useful when other SST proxies are diagenetically altered (e.g. planktonic foraminifera) or absent (e.g. alkenones)
TEX86 has been extensively used to reconstruct Eocene (55-34Ma) SST. During the early Eocene, TEX86 values indicate warm high southern hemisphere latitude SSTs(20-25°C) in agreement with other, independently derived proxies (e.g. alkenones, CLAMP, Mg/Ca). Only one low-latitude SST record exists and suggests warm conditions (~35°C) during this period. During the middle and late Eocene, high southern latitude sites cooled while the tropics remained stable and warm. Possible reasons for this cooling include long-term changes in carbon dioxide and/or changes in gateway reorganisation (e.g. tasman gateway, drake passage). TEX86 values from a single northern hemisphere site indicate warm subtropical conditions in the high Arctic during the early and middle Eocene.
- Schouten, S., Hopmans, E.C., Schefus, E., and Sinninghe Damste. (2002) Distributional variation in marine crenarchaeotal membrane lipids: a new tool for reconstructing ancient sea water temperatures?. Earth and Planetary Science Letters, 204, 265.
- Kim, J.-H., S. Schouten, E. C. Hopmans, B. Donner, J. S. Sinninghe Damsté. (2008) Global sediment core-top calibration of the TEX86 paleothermometer in the ocean. Geochimica et Cosmochimica Acta, 72, 1154.
- Schouten, S., Hopmans, E. C., and Sinninghe Damsté, J. S., 2013, The organic geochemistry of glycerol dialkyl glycerol tetraether lipids: A review: Organic Geochemistry, v. 54, no. 0, p. 19-61.
- Wuchter, C., Schouten, S., Coolen, M. J. L., and Sinninghe Damsté, J. S., 2004, Temperature-dependent variation in the distribution of tetraether membrane lipids of marine Crenarchaeota: Implications for TEX86 paleothermometry: Paleoceanography, v. 19, no. 4, p. PA4028
- Koga, Y., Nishihara, M., Morii, H., and Akagawa-Matsushita, M., 1993, Ether polar lipids of methanogenic bacteria: structures, comparative aspects, and biosyntheses: Microbiological Reviews, v. 57, no. 1, p. 164-182
- Kim, J.-H., van der Meer, J., Schouten, S., Helmke, P., Willmott, V., Sangiorgi, F., Koç, N., Hopmans, E. C., and Damsté, J. S. S., 2010, New indices and calibrations derived from the distribution of crenarchaeal isoprenoid tetraether lipids: Implications for past sea surface temperature reconstructions: Geochimica et Cosmochimica Acta, v. 74, no. 16, p. 4639-4654.
- Liu, Z., Pagani, M., Zinniker, D., DeConto, R., Huber, M., Brinkhuis, H., Shah, S. R., Leckie, R. M., and Pearson, A., 2009, Global Cooling During the Eocene-Oligocene Climate Transition: Science, v. 323, no. 5918, p. 1187-1190
- Sluijs, A., Schouten, S., Pagani, M., Woltering, M., Brinkhuis, H., Damsté, J. S. S., Dickens, G. R., Huber, M., Reichart, G.-J., Stein, R., Matthiessen, J., Lourens, L. J., Pedentchouk, N., Backman, J., Moran, K., and the Expedition, S., 2006, Subtropical Arctic Ocean temperatures during the Palaeocene/Eocene thermal maximum: Nature, v. 441, no. 7093, p. 610-613.
- Hollis, C. J., Taylor, K. W. R., Handley, L., Pancost, R. D., Huber, M., Creech, J. B., Hines, B. R., Crouch, E. M., Morgans, H. E. G., Crampton, J. S., Gibbs, S., Pearson, P. N., and Zachos, J. C., 2012, Early Paleogene temperature history of the Southwest Pacific Ocean: Reconciling proxies and models: Earth and Planetary Science Letters, v. 349–350, no. 0, p. 53-66.
- Taylor, K. W. R., Hollis, C. J., Huber, M., Hernandez-Sanchez, M. T., and Pancost, R. D., 2013, Re-evaluating modern and Paleogene GDGT distributions: Implications for SST reconstructions, Global and Planetary Change , v. 108, p. 158-174
- Jenkyns, H., Schouten-Huibers, L., Schouten S. and Sinninghe-Damste, J.S., 2012, Warm Middle Jurassic-early Cretaceous high-latitude sea surface temperature from the Southern Ocean. Climate of the Past, v. 8, p.215-226
- Sluijs, A., Schouten, S., Donders, T. H., Schoon, P. L., Rohl, U., Reichart, G.-J., Sangiorgi, F., Kim, J.-H., Sinninghe Damste, J. S., and Brinkhuis, H., 2009, Warm and wet conditions in the Arctic region during Eocene Thermal Maximum 2: Nature Geosci, v. 2, no. 11, p. 777-780.
- Zachos, J. C., Schouten, S., Bohaty, S., Quattlebaum, T., Sluijs, A., Brinkhuis, H., Gibbs, S. J., and Bralower, T. J., 2006, Extreme warming of mid-latitude coastal ocean during the Paleocene-Eocene Thermal Maximum: Inferences from TEX86 and isotope data: Geology, v. 34, no. 9, p. 737-740.
- Pearson, P. N., van Dongen, B. E., Nicholas, C. J., Pancost, R. D., Schouten, S., Singano, J. M., and Wade, B. S., 2007, Stable warm tropical climate through the Eocene Epoch: Geology, v. 35, no. 3, p. 211-214.
- Bijl, P. K., Schouten, S., Sluijs, A., Reichart, G.-J., Zachos, J. C., and Brinkhuis, H., 2009, Early Palaeogene temperature evolution of the southwest Pacific Ocean: Nature, v. 461, no. 7265, p. 776-779.