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Archaeal membrane lipids known as glycerol dibiphytanyl glycerol tetraethers (GDGTs) are the basis of the TEX86 paleotemperature proxy. Because GDGTs preserved in marine sediments are thought to originate mainly from planktonic, ammonia-oxidizing Thaumarchaeota, the basis of the correlation between TEX86 and sea surface temperature (SST) remains unresolved: How does TEX86 predict surface temperatures, when maximum thaumarchaeal activity occurs below the surface mixed layer and TEX86 does not covary with in situ growth temperatures? Here we used isothermal studies of the model thaumarchaeon Nitrosopumilus maritimus SCM1 to investigate how GDGT composition changes in response to ammonia oxidation rate. We used continuous culture methods to avoid potential confounding variables that can be associated with experiments in batch cultures. The results show that the ring index scales inversely (R(2) = 0.82) with ammonia oxidation rate (ϕ), indicating that GDGT cyclization depends on available reducing power. Correspondingly, the TEX86 ratio decreases by an equivalent of 5.4 °C of calculated temperature over a 5.5 fmol·cell(-1)·d(-1) increase in ϕ. This finding reconciles other recent experiments that have identified growth stage and oxygen availability as variables affecting TEX86 Depth profiles from the marine water column show minimum TEX86 values at the depth of maximum nitrification rates, consistent with our chemostat results. Our findings suggest that the TEX86 signal exported from the water column is influenced by the dynamics of ammonia oxidation. Thus, the global TEX86-SST calibration potentially represents a composite of regional correlations based on nutrient dynamics and global correlations based on archaeal community composition and temperature.

Long-chain diols are biomarkers commonly used in the marine realm to reconstruct several environmental parameters such as sea surface temperature and salinity. However, they are also produced in lacustrine and slow-flowing river environments, a characteristic that has proved to be useful to trace past riverine inputs in coastal sedimentary records. So far, their use in lacustrine settings is sparse as their controls are not well-known. Previous studies in two lakes have shown that long-chain diol distribution is linked to changes in temperature (in a small Spanish alpine lake), but also to water column stratification (in a large deep Swiss lake). To understand the controls on i) the presence of long-chain diols in lakes, and ii) the distribution of long-chain diol isomers, surface sediments from 52 Swiss lakes were studied. Long-chain diols are present in 57% of the lakes, and machine learning (i.e., random forest model) showed that their presence is mainly controlled by mean annual air temperature, sodium and potassium concentrations and area of the lakes. Long-chain diol isomer relative distribution seems to react to temperature, nutrient (here nitrate) and oxygen concentrations in the lakes. This new insight was tested on a short sedimentary core from Lake Zurich, and compared with other biomarker proxies (based on branched and isoprenoid glycerol dialkyl glycerol tetraethers), as well as with historical record of nutrient contents and temperature. Variations in the long-chain diol index (LDI) mirror measured temperature, but also reacted to changes in nutrients and oxygenation in the lake. This study highlights the potential of long-chain diols as a proxy to trace both nutrients and temperature in lakes, potentially on geological timescales. [ABSTRACT FROM AUTHOR]

The sole unifying feature of the incredibly diverse Archaea is their isoprenoid‐based ether‐linked lipid membranes. Unique lipid membrane composition, including an abundance of membrane‐spanning tetraether lipids, impart resistance to extreme conditions. Many questions remain, however, regarding the synthesis and modification of tetraether lipids and how dynamic changes to archaeal lipid membrane composition support hyperthermophily. Tetraether membranes, termed glycerol dibiphytanyl glycerol tetraethers (GDGTs), are generated by tetraether synthase (Tes) by joining the tails of two bilayer lipids known as archaeol. GDGTs are often further specialized through the addition of cyclopentane rings by GDGT ring synthase (Grs). A positive correlation between relative GDGT abundance and entry into stationary phase growth has been observed, but the physiological impact of inhibiting GDGT synthesis has not previously been reported. Here, we demonstrate that the model hyperthermophile Thermococcus kodakarensis remains viable when Tes (TK2145) or Grs (TK0167) are deleted, permitting phenotypic and lipid analyses at different temperatures. The absence of cyclopentane rings in GDGTs does not impact growth in T. kodakarensis, but an overabundance of rings due to ectopic Grs expression is highly fitness negative at supra‐optimal temperatures. In contrast, deletion of Tes resulted in the loss of all GDGTs, cyclization of archaeol, and loss of viability upon transition to the stationary phase in this model archaea. These results demonstrate the critical roles of highly specialized, dynamic, isoprenoid‐based lipid membranes for archaeal survival at high temperatures. Plain Language Summary: The preponderance of tetraether membrane‐spanning lipids in many archaeal clades indicates the fitness advantage of unique membranes for archaeal survival. The inability to rationally control the synthesis of tetraether and cyclized tetraether‐lipids has limited investigations into how dynamic shifts in lipid composition support archaeal growth and phase transitions. Employing the facile genetic system of the model hyperthermophilic archaeon Thermococcus kodakarensis that naturally synthesizes abundant tetraether lipids, we identified and targeted the genes necessary for tetraether lipid synthesis and derivatization. While impairing tetraether lipid biosynthesis is possible, the lack of specialized lipids dramatically impairs long‐term survival, supporting a critical role for dynamic lipidome changes in supporting archaeal life in the extremes. [ABSTRACT FROM AUTHOR]

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are membrane-spanning lipids produced by bacteria that are ubiquitous in natural sedimentary archives and preserved over geologic timescales. The main influence on their distributions in the environment appears to be temperature, thus making them a potentially powerful proxy for paleotemperature reconstruction. Application of recent lacustrine brGDGT-based temperature calibration models to specific regions results in inaccurate reconstructed temperatures suggesting that regional or site-specific temperature calibration models may be necessary. Using an extended data set of 692 lake sediment samples from across the globe we determined whether brGDGT distributions in samples from the same regions or sites are significantly different from one another via hierarchical agglomerative clustering analysis (HAC). Results of HAC analysis showed four significant clusters with varying geographic distributions. Cluster 1 samples are mainly located at high latitudes (Mean Annual Air Temperature; MAAT = 3.10 ± 5.91 °C). Cluster 2 samples are concentrated in the Tibetan Plateau (MAAT = 1.54 ± 5.91 °C). Cluster 3 samples span temperate-tropical latitudes (MAAT = 17.26 ± 8.16 °C). Cluster 4 samples are mainly located in Central and South America (MAAT = 24.56 ± 4.01 °C). The clustering led us to develop random forest regression models to predict temperature (MAAT and Months Above Freezing, MAF, air temperature) based on samples within each cluster (cluster-specific temperature models). Model performance was the highest for Cluster 3 (MAF: R2 = 0.78, RMSE = 2.85 °C, n = 261; MAAT: R2 = 0.76, RMSE = 4.07 °C, n = 270), followed by Cluster 1 (MAF: R2 = 0.54, RMSE = 1.67 °C; n = 219; MAAT: R2 = 0.62, RMSE = 3.62 °C, n = 226) and Cluster 4 (MAF: R2 = 0.58, RMSE = 2.46, n = 67; MAAT: R2 = 0.59, RMSE = 2.52 °C, n = 67). The Cluster 2 model had the lowest model performance (MAF: R2 = 0.42, RMSE = 4.51, n = 38; MAAT: R2 = 0.51, RMSE = 1.74 °C, n = 129). We also developed a random forest classification model to predict the cluster assignment for new samples (cluster prediction model with an overall accuracy of 95%), which informs the user as to which cluster-specific temperature model(s) to apply to their samples. Finally, we applied our approach (i.e., cluster assignment followed by cluster-specific temperature reconstruction) to seven published lacustrine (paleo)records and illustrate pitfalls among the temperature reconstructions from brGDGT-based temperature calibration models. Overall, our study defines broad geographic relationships among lacustrine brGDGT distributions and air temperature while underscoring model limitations for paleotemperature reconstruction and subsequent interpretation. [ABSTRACT FROM AUTHOR]

The Younger Dryas (YD, 12.9–11.7 ka) is the most recent, near‐global interval of abrupt climate change with rates similar to modern global warming. Understanding the causes and biodiversity effects of YD climate changes requires determining the spatial fingerprints of past temperature changes. Here we build pollen‐based and branched glycerol dialkyl glycerol tetraether‐based temperature reconstructions in eastern North America (ENA) to better understand deglacial temperature evolution. YD cooling was pronounced in the northeastern United States and muted in the north central United States. Florida sites warmed during the YD, while other southeastern sites maintained a relatively stable climate. This fingerprint is consistent with an intensified subtropical high during the YD and demonstrates that interhemispheric responses were more complex spatially in ENA than predicted by the bipolar seesaw model. Reduced‐amplitude or antiphased millennial‐scale temperature variability in the southeastern United States may support regional hotspots of biodiversity and endemism. Plain Language Summary: The Younger Dryas, circa 12,900 to 11,700 years ago, is a hemispheric abrupt climate change event that occurred at rates similar to those projected by the 21st century. Its cause has been linked to a reduction in northward oceanic heat transport in the Atlantic that led to Northern Hemispheric cooling and Southern Hemispheric warming. Here we present detailed reconstructions of Younger Dryas temperature variations in eastern North America that suggest a more complex spatial fingerprint than predicted by the standard global model. New England, Maritime Canada, and the Great Lakes Region all cooled, like Greenland and elsewhere in the Northern Hemisphere. However, regions south of Virginia experienced little temperature change and Florida warmed slightly. Possible mechanisms include atmospheric processes that enhanced advection from the subtropics and oceanic processes that transported heat northward from the equatorial Atlantic. These reconstructions also help explain the hotspot of biodiversity and endemic species in the southeastern United States, by showing that this region was buffered from past abrupt millennial‐scale climate reversals. Key Points: The spatial fingerprint of Younger Dryas (YD) temperature changes is reconstructed in eastern North America from brGDGTs and fossil pollenReconstructions demonstrate higher YD temperatures in Florida, no change south of 40°N, and cooling north of 40°NThese patterns are consistent with intensified subtropical highs during the YD and help explain high regional biodiversity [ABSTRACT FROM AUTHOR]

Highlights • Selective sn 2 ether cleavage reveals the glycerol configurations of GDGTs. • GDGTs in marine sediment have a predominantly parallel glycerol configuration. • Both crenarchaeol and its regioisomer possess the parallel glycerol configuration. • Branched GDGTs in the Messel shale and marine sediment are mainly antiparallel. Abstract The glycerol configurations of glycerol dialkyl glycerol tetraethers (GDGTs) in environmental samples were investigated using a selective sn 2 ether cleavage protocol. Using this procedure, GDGTs with a parallel glycerol configuration afford two types of derivatives, diols and diallylethers, whereas only one kind, monoallylethers, originate from their antiparallel isomers. Isoprenoidal GDGTs from a marine sediment are shown to be predominately parallel based on the distributions of these ether cleavage products. Crenarchaeol and its so-called regioisomer both have parallel configurations with the cyclohexane ring located on the sn 3,3 ether bonded tricyclic biphytanyl moiety. A Messel shale sample containing isoprenoidal GDGTs contributed mainly by methanogenic archaea has a substantial portion with the antiparallel configuration. Branched (non-isoprenoidal) GDGTs in both the Messel shale and the marine sediment are mainly antiparallel. This selective sn 2 ether cleavage approach provides a potentially powerful analytical tool to investigate not only the exact molecular structures of GDGT constitutional isomers and their biosynthetic pathways but also the heterogeneous inputs of sedimentary GDGT and their isotopic signatures, if different source species synthesize GDGTs with unique glycerol configurations. Further analyses of this type will reveal the glycerol configurations of the GDGTs of a broad range of microbial cultures and environmental samples. [ABSTRACT FROM AUTHOR]

Isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGTs) of archaeal origin and branched (br)GDGTs of bacterial origin occur in a diverse range of lacustrine sedimentary environments. They have attracted attention as potential temperature proxies, providing high resolution (palaeo)environmental reconstruction from continental interiors. For this study, the distribution of GDGTs in, and application of GDGT-based proxies to, surface samples from Chaka Salt Lake (China), as well as soils and in-flow river sediments, were investigated to assess whether GDGT-based proxies were applicable to this hypersaline lake system. We show that iso- and brGDGTs were present in all sediments and soils from the Chaka Salt Lake system. GDGT-0 and crenarchaeol were generally the two most abundant isoGDGTs, suggesting Thaumarchaeota as a major biological source of isoGDGTs. The low ratio of crenarchaeol/crenarchaeol regioisomer suggests that Thaumarchaeota of the lake sediments is likely Thaumarchaeota group I.1b derived from the surrounding alkaline soils, arguing against the use of the TEX 86 proxy in this system. Because alkaline soils generally have high isoGDGT concentrations, it is likely that a large allochthonous input of isoGDGTs would be a pervasive challenge to palaeoclimate applications in such settings. On the other hand, the brGDGT distributions in the lake and river sediments differed markedly from those in the surrounding soils, suggesting that, instead of deriving from the surrounding soils, at least part of the brGDGTs is synthesized in situ or delivered from more distal upland soils. Taken together, our results indicate that the mixed sources of GDGTs in Chaka Salt Lake complicate the application of GDGT-based proxies, and it will be challenging to use such proxies in this system. [ABSTRACT FROM AUTHOR]

The spatial and temporal distributions of the glycerol dialkyl glycerol tetraether (GDGT) concentrations in suspended materials were investigated to determine whether the GDGT-based TEX 86 can be used as a proxy for annual mean sea surface temperature in the northern East China Sea (ECS). Seawater samples were collected seasonally at three-month intervals from the surface and subsurface of the northern ECS. GDGT in the surface seawater was detected consistently across all seasons. However, the TEX 86 temperatures of the surface seawater samples differed significantly from the in situ temperatures over the entire study area; in particular, TEX 86 temperatures were higher (4–7 °C) than in situ temperatures in winter, and lower (9–12 °C) than in situ temperatures in summer. The occurrence of a high concentration of GDGTs near the bottom, with marked differences between TEX 86 and in situ temperatures in the shallow water (~30 m) supports the possibility of sediment resuspension near the bottom in the western part and subsequent transportation eastward. GDGTs may have been resuspended owing to vertical mixing by strong winds, such as those from the monsoon (winter) and typhoons (summer), and increased turbulence near the bottom caused by tides across all seasons in the shallow waters (30–50 m). In contrast, the vertical distribution of GDGT concentration in the eastern part of the study area deeper than 100 m indicated that maximum GDGT concentrations occurred at depths of between 20 m and 50 m in all seasons. The TEX 86 temperatures of the subsurface samples were similar to or warmer than in situ temperatures between 20 m and 50 m, suggesting that the main depth at which GDGT was produced in the eastern area could be the subsurface in that same depth range. A new local calibration equation was established based on the subsurface samples from the east. Our results indicate that sediment resuspension and subsurface production of GDGTs can have a significant impact on the use of GDGT-based TEX 86 as a SST proxy in continental shelf area. • TEX 86 temperatures of surface seawater samples differed from in situ temperatures. • Sediment resuspension and vertical mixing affect TEX 86 temperatures in shallow water. • GDGT production depth was between 20 m and 50 m in area deeper than 100 m. • A new local calibration equation was established at sites deeper than 100 m. [ABSTRACT FROM AUTHOR]

Four representatives of methanogenic Euryarchaeota ( Methanosarcina mazei strain Gö1, Methanosphaera stadtmanae , Methanobrevibacter smithii and Methanosaeta thermophila ), the hyperthermophilic euryarchaeon Thermococcus kodakarensis and the halophilic euryarchaeon Haloferax volcanii were studied for their glycerol ether lipid composition. The predominant core membrane lipid in all of them was archaeol, which was accompanied by variable quantities of sn -2-hydroxyarchaeol in the methanogens M. mazei (Methanosarcinales) and M. stadtmanae (Methanobacteriales). All methanogenic and hyperthermophilic Euryarchaeota also contained comparatively high abundances of the glycerol dialkyl glycerol tetraether without a cyclopentane moiety (GDGT-0). The methanoarchaeon M. stadtmanae , in addition to GDGT-0, contained GDGT core lipid structures with 1–4 cyclopentane moieties (GDGTs 1–4). We also found minor amounts of a glycerol trialkyl glycerol tetraether (GTGT) and a glycerol dialkanol diether (GDD), both of which did not contain cyclopentane moieties, as well as methylated and dimethylated GDGT-0 in all the archaea with the exception of H. volcanii . Like its GDGT distribution, M. stadtmanae showed an extended range of GDD structures with up to two cyclopentane ring systems. Our results thus indicate that both methanogenic and hyperthermophilic Euryarchaeota may represent source organisms of GTGT-0, GDDs and methylated-GDGTs in natural environments. All the latter components have recently been reported to be ubiquitously distributed in marine sediments but their biological origin is largely unknown. Moreover, a suite of unsaturated GDGTs without a cyclopentane moiety and up to four double bonds in the hyperthermophile T. kodakarensis was tentatively assigned. [ABSTRACT FROM AUTHOR]

Liquid chromatography–mass spectrometry (LC–MS) analysis of glycerol dialkyl glycerol tetraethers (GDGTs) from sediment and soil samples has become a widely adopted approach for reconstructing past ocean and continental climate variables such as temperature and pH. The LC–MS data used for constructing these GDGT climate proxies are taken directly from the peak area values of individual GDGT [M+H] + ions, often determined from manual peak integration due to unreliable computer integrators in commercial software, particularly in cases of complex baselines, asymmetric peak shapes and peak coelution. Manual integration is not only time consuming, but also prone to user induced inconsistency when individuals utilize different criteria for peak/baseline definition. To overcome these problems, we have developed a user friendly, graphical user interface (GUI) programmed in the MATLAB environment, allowing users to efficiently and reproducibly perform batch processing and peak integration of LC–MS data. The program, “TEXPRESS” v1.0 (“tetraether index express”), incorporates modern chemometric based techniques for baseline definition and deconvolution of complex chromatographic peaks and we show that LC–MS data processed using the TEXPRESS toolbox are in strong agreement with results obtained from manual peak integration. We provide a general overview of the concepts and architecture of the TEXPRESS toolbox and discuss the advantages of chemometric based peak integration methods for processing branched and isoprenoid GDGT LC–MS data. [ABSTRACT FROM AUTHOR]

Mounting evidence suggests that ammonia-oxidizing archaea (AOA) may play important roles in nitrogen cycling in geothermal environments. In this study, the diversity, distribution and ecological significance of AOA in terrestrial hot springs in Kamchatka (Far East Russia) were explored using amoA genes complemented by analysis of glycerol dialkyl glycerol tetraethers (GDGTs) of archaea. PCR amplification of functional genes (amoA) from AOA and ammonia-oxidizing bacteria (AOB) was performed on microbial mats/streamers and sediments collected from three hot springs (42°C to 87°C and pH 5.5-7.0). No amoA genes of AOB were detected. The amoA genes of AOA formed three distinct phylogenetic clusters with Cluster 3 representing the majority (∼59%) of OTUs. Some of the sequences from Cluster 3 were closely related to those from acidic soil environments, which is consistent with the predominance of low pH (<7.0) in these hot springs. Species richness (estimated by Chao1) was more frequently higher at temperatures below 75°C than above it, indicating that AOA may be favored in the moderately high temperature environments. Quantitative PCR of 16S rRNA genes showed that crenarchaeota counted for up to 80% of total archaea. S-LIBSHUFF separated all samples into two phylogenetic groups. The profiles of GDGTs were well separated among the studied springs, suggesting a spatial patterning of archaeal lipid biomarkers. However, this patterning did not correlate significantly with variation in archaeal amoA, suggesting that AOA are not the predominant archaeal group in these springs producing the observed GDGTs. [ABSTRACT FROM AUTHOR]

• Five GDGT-based calibrations were tested against reanalysis temperatures. • The best fit was obtained using with a quadratic calibration. • The GDGT-based sea surface temperature (SST) represented the Oct-Nov-Dec season. • Organic matter input was controlled mainly by SST, precipitation and glacier retreat. Isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs) are archaeal biomarkers. In many settings, the degree of cyclization of isoGDGTs is correlated with temperature, forming the basis of the TEX 86 paleothermometer that is widely used to reconstruct sea surface temperature (SST) across a range of time scales. However, the application of TEX 86 to the polar regions is relatively limited and there is currently no consensus on which calibration is best suited for polar environments. In addition, application of TEX 86 to the polar regions is complicated by uncertainty regarding the source of organic matter input in coastal polar environments. We tested five different calibrations for TEX 86 in marine sediments from the Antarctic coastal region of Admiralty Bay near King George Island, using four short cores that span the second half of the 20th century. We also explored the possible sources of organic matter in these cores using sterol biomarkers. Best results for TEX 86 were obtained using a quadratic calibration. The TEX 86 signal presented a strong seasonal signal and best matched reanalysis temperatures of the austral spring season (Oct-Nov-Dec). The most abundant compounds observed in the sediments were the sterols cholest-5-en-3β-ol and 24-ethylcholest-5-en-3β-ol, the fatty alcohols C 16 and phytol, and isoGDGT-0, indicating a dominant marine origin of the organic matter. Differences in their vertical distributions suggests that some compounds (such as cholest-5-en-3β-ol and phytol) may have had different sources over the evaluated period. Together our results indicate that TEX 86 can be used to reconstruct SSTs in the Antarctic coastal region. [ABSTRACT FROM AUTHOR]