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Ratios of glycerol dialkyl glycerol tetraethers (GDGT), which are membrane lipids of bacteria and archaea, are at the base of several paleoenvironmental proxies. They are frequently applied to soils as well as lake‐ and marine sediments to generate records of past temperature and soil pH. To derive meaningful environmental information from these reconstructions, high analytical reproducibility is required. Based on submitted results by 39 laboratories from across the world, which employ a diverse range of analytical and quantification methods, we explored the reproducibility of brGDGT‐based proxies (MBT′5ME, IR, and #ringstetra) measured on four soil samples and four soil lipid extracts. Correct identification and integration of 5‐ and 6‐methyl brGDGTs is a prerequisite for the robust calculation of proxy values, but this can be challenging as indicated by the large inter‐interlaboratory variation. The exclusion of statistical outliers improves the reproducibility, where the remaining uncertainty translates into a temperature offset from median proxy values of 0.3–0.9°C and a pH offset of 0.05–0.3. There is no apparent systematic impact of the extraction method and sample preparation steps on the brGDGT ratios. Although reported GDGT concentrations are generally consistent within laboratories, they vary greatly between laboratories. This large variability in brGDGT quantification may relate to variations in ionization efficiency or specific mass spectrometer settings possibly impacting the response of brGDGTs masses relative to that of the internal standard used. While ratio values of GDGT are generally comparable, quantities can currently not be compared between laboratories. Key Points: 39 laboratories participated in a round robin to determine the reproducibility of glycerol dialkyl glycerol tetraethers (GDGT) proxy values and quantitiesPeak selection impacts the ratio values and there is no apparent systematic impact of the extraction method and sample preparation stepsQuantification of GDGTs remains a problem, and comparison of GDGT concentrations between laboratories requires further method development [ABSTRACT FROM AUTHOR]

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]

The enzymology of the key steps in the archaeal phospholipid biosynthetic pathway has been elucidated in recent years. In contrast, the complete biosynthetic pathways for proposed membrane regulators consisting of polyterpenes, such as carotenoids, respiratory quinones, and polyprenols remain unknown. Notably, the multiplicity of geranylgeranyl reductases (GGRs) in archaeal genomes has been correlated with the saturation of polyterpenes. Although GGRs, which are responsible for saturation of the isoprene chains of phospholipids, have been identified and studied in detail, there is little information regarding the structure and function of the paralogs. Here, we discuss the diversity of archaeal membrane-associated polyterpenes which is correlated with the genomic loci, structural and sequence-based analyses of GGR paralogs. [ABSTRACT FROM AUTHOR]

Ancient lake deposits in the Mojave Desert indicate that the water cycle in this currently dry place was radically different under past climates. Here we revisit a 700 m core drilled 55 years ago from Searles Valley, California, that recovered evidence for a lacustrine phase during the late Pliocene. We update the paleomagnetic age model and extract new biomarker evidence for climatic conditions from lacustrine deposits (3.373–2.706 Ma). The MBT′5Me temperature proxy detects present‐day conditions (21 ± 3°C, n = 2) initially, followed by warmer‐than‐present conditions (25 ± 3°C, n = 17) starting at 3.268 and ending at 2.734 Ma. Bacterial and archeal biomarkers reveal lake salinity increased after 3.268 Ma likely reflecting increased evaporation in response to higher temperatures. The δ13C values of plant waxes (−30.7 ± 1.4‰, n = 28) are consistent with local C3 taxa, likely expanded conifer woodlands during the pluvial with less C4 than the Pleistocene. δD values (−174 ± 5‰, n = 25) of plant waxes indicate precipitation δD values (−89 ± 5‰, n = 25) in the late Pliocene are within the same range as the late Pleistocene precipitation δD. Microbial biomarkers identify a deep, freshwater lake and a cooling that corresponds to the onset of major Northern Hemisphere glaciation at marine isotope stage marine isotope stages M2 (3.3 Ma). A more saline lake persisted for ∼0.6 Ma across the subsequent warmth of the late Pliocene (3.268–2.734 Ma) before the lake desiccated at the Pleistocene intensification of Northern Hemisphere Glaciation. Plain Language Summary: During a generally warm period 3 million years ago, there were large lakes in the Mojave Desert, California. We measured organic matter preserved in ancient lake mud below today's salt flat in Searles Valley to investigate the climate changes that sustained these 3‐million‐year‐old lakes. We compiled evidence for a freshwater lake, increased rainfall, and woody plants around the lake during a cooler interval, with similar‐to‐modern temperatures, that interrupted what was generally a warm period between 5 and 3 million years ago. Today the valley contains a saltpan, the evaporated remains of the former lake, surrounded by open desert shrubland. We compare the evidence from the lake with other climate reconstructions and find the wetter conditions coincided with cooling both locally and at higher latitudes. Key Points: Lacustrine sediments in Mojave Desert sediment core span 3.373–2.706 MaMicrobial biomarkers record deep, fresh lake during cool period 3.373–3.268 MaLake salinity increases after 3.268 Ma, associated with warming [ABSTRACT FROM AUTHOR]

Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors such as temperature, pH, and energy availability shifts. However, archaeal expression patterns that correspond with changes in GDGT composition are less understood. Here we characterize the acid and cold stress responses of the thermoacidophilic crenarchaeon Saccharolobus islandicus REY15A using growth rates, core GDGT lipid profiles, transcriptomics and proteomics. We show that both stressors result in impaired growth, lower average GDGT cyclization, and differences in gene and protein expression. Transcription data revealed differential expression of the GDGT ring synthase grsB in response to both acid stress and cold stress. Although the GDGT ring synthase encoded by grsB forms highly cyclized GDGTs with =5 ring moieties, S. islandicus grsB upregulation under acidic pH conditions did not correspond with increased abundances of highly cyclized GDGTs. Our observations highlight the inability to predict GDGT changes from transcription data alone. Broader analysis of transcriptomic data revealed that S. islandicus differentially expresses many of the same transcripts in response to both acid and cold stress. These included upregulation of several biosynthetic pathways and downregulation of oxidative phosphorylation and motility. Transcript responses specific to either of the two stressors tested here included upregulation of genes related to proton pumping and molecular turnover in acid stress conditions and upregulation of transposases in cold stress conditions. Overall, our study provides a comprehensive understanding of the GDGT modifications and differential expression characteristic of the acid stress and cold stress responses in S. islandicus. [ABSTRACT FROM AUTHOR]

The TEX86 paleothermometer has been extensively used to reconstruct past sea water temperatures, but it remains unclear which export depths the proxy represents. Here we used a novel approach to better constrain the proxy recording depths by investigating paleotemperature proxies (TEX86, U37K′ ${\mathrm{U}}_{37}^{{\mathrm{K}}^{\prime }}$, RI−OH and RI−OH′) from two pairs of proximal (<12 km apart) cores from Chilean and Angola margins, respectively. These cores are from steep continental slopes and lower shelves, which leads to a substantial difference in water depth between them despite being closely located. Surprisingly, the deep and the shallow U37K′ ${\mathrm{U}}_{37}^{{\mathrm{K}}^{\prime }}$ records at the Chilean margin show dissimilarities, in contrast to the similar records from the Angola margin, which may be due to post‐depositional alteration at the former sites. In contrast, the TEX86 records were statistically indistinguishable between the sites at both the locations, even though the GDGT [2]/[3] ratio suggests GDGTs derived from potentially different archaeal communities residing at different depths. A short‐lived difference between the TEX86 records is observed during the last glacial period at the Angola margin, possibly due to a contribution of Antarctic Intermediate Waters to the deep site. Modelling suggests that the TEX86 source signal at our core sites reaches its peak abundance at water depths shallower than 350 m. The RI−OH and RI−OH′ records show similar variability as the TEX86 records, although regional differences in their absolute temperature estimates exist. Our approach using proximal sediment cores at steep slopes appears useful to constrain the export depth of organic proxy signals for paleo‐reconstructions. Key Points: Source signal of TEX86 proxy is likely derived from depths shallower than 350 m at Chilean and Angola marginsOH‐GDGT based proxies show similar variability as TEX86 records, but show regional differences in their absolute temperature estimatesU37K′ ${\mathrm{U}}_{37}^{{\mathrm{K}}^{\prime }}$ proxy signal may be impacted by post‐depositional changes or lateral transport even for closely located cores [ABSTRACT FROM AUTHOR]

Great Salt Lake (GSL), Utah, is a hypersaline terminal lake in the Great Basin, and the remnant of the late glacial Lake Bonneville. Holocene hydroclimate variations cannot be interpreted from the shoreline record, but instead can be investigated by proxies archived in the sediments. GLAD1‐GSL00‐1B was cored in 2000 and recently dated by radiocarbon for the Holocene section with the top 11 m representing ∼7 ka to present. Sediment samples every 30 cm (∼220 years) were studied for the full suite of microbial membrane lipids, including those responsive to temperature and salinity. The Archaeol and Caldarchaeol Ecometric (ACE) index detects the increase in lipids of halophilic archaea, relative to generalists, as salinity increases. We find Holocene ACE values ranged from 81 to 98, which suggests persistent hypersalinity with <50 g/L variability across 7.2 ka. The temperature proxy, MBTʹ5Me, yields values similar to modern mean annual air temperature for months above freezing (MAF = 15.7°C) over the last 5.5 ka. Several glycerol dialkyl glycerol tetraether metrics show a step shift in microbial communities and limnology at 5.5 ka. Extended archaeol detects elevated salinity during the regional mid‐Holocene drought, not readily detected in the ACE record that is often near the upper limit of the index. We infer that the mid‐Holocene GSL was shallower and saltier than the late Holocene. The current drying may be returning the lake to conditions not seen since the mid‐Holocene. Plain Language Summary: Great Salt Lake (GSL) in Utah is the remnant of a once much larger lake and is currently at a historically low level. We study a lake sediment core, collected in 2000 from the floor of GSL, and recently dated. We take new samples from the core and measure them for molecules made by microbes, whether living in the lake or washed in from the surrounding soils. We reconstruct lake conditions during the last 7,200 years and assess whether lake level fluctuated during that time. Over the past 7,200 years, we find evidence that the lake was shallower from 7,200 to 5,500 years ago but has been relatively stable until the modifications of the lake in the 20th century and the current drying trend. Key Points: Glycerol dialkyl glycerol tetraethers produced by bacteria and archaea detect Holocene limnological changes at Great Salt Lake (GSL)The Archaeol and Caldarchaeol Ecometric salinity index remains near its upper limit in GSL from 7.2 ka to presentA 5.5 ka step shift in microbial lipids suggests limnological change coeval with the end of a regional dry spell in the mid‐Holocene [ABSTRACT FROM AUTHOR]

Cellular membranes are essential for compartmentalization, maintenance of permeability, and fluidity in all three domains of life. Archaea belong to the third domain of life and have a distinct phospholipid composition. Membrane lipids of archaea are ether-linked molecules, specifically bilayer-forming dialkyl glycerol diethers (DGDs) and monolayer-forming glycerol dialkyl glycerol tetraethers (GDGTs). The antifungal allylamine terbinafine has been proposed as an inhibitor of GDGT biosynthesis in archaea based on radiolabel incorporation studies. The exact target(s) and mechanism of action of terbinafine in archaea remain elusive. Sulfolobus acidocaldarius is a strictly aerobic crenarchaeon thriving in a thermoacidophilic environment, and its membrane is dominated by GDGTs. Here, we comprehensively analyzed the lipidome and transcriptome of S. acidocaldarius in the presence of terbinafine. Depletion of GDGTs and the accompanying accumulation of DGDs upon treatment with terbinafine were growth phase-dependent. Additionally, a major shift in the saturation of caldariellaquinones was observed, which resulted in the accumulation of unsaturated molecules. Transcriptomic data indicated that terbinafine has a multitude of effects, including significant differential expression of genes in the respiratory complex, motility, cell envelope, fatty acid metabolism, and GDGT cyclization. Combined, these findings suggest that the response of S. acidocaldarius to terbinafine inhibition involves respiratory stress and the differential expression of genes involved in isoprenoid biosynthesis and saturation. [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]

Tropical peatlands are an important carbon store and source of greenhouse gases, but the microbial component, particularly community structure, remains poorly understood. While microbial communities vary between tropical peatland land uses, and with biogeochemical gradients, it is unclear if their structure varies at smaller spatial scales as has been established for a variety of peat properties. We assessed the abundances of PLFAs and GDGTs, two membrane spanning lipid biomarkers in bacteria and fungi, and bacteria and archaea, respectively, to characterise peat microbial communities under two dominant and contrasting plant species, Campnosperma panamensis (a broadleaved evergreen tree), and Raphia taedigera (a canopy palm), in a Panamanian tropical peatland. The plant communities supported similar microbial communities dominated by Gram negative bacteria (38.9–39.8%), with smaller but significant fungal and archaeal communities. The abundance of specific microbial groups, as well as the ratio of caldarchaeol:crenarchaeol, isoGDGT: brGDGTs and fungi:bacteria were linearly related to gravimetric moisture content, redox potential, pH and organic matter content indicating their role in regulating microbial community structure. These results suggest that tropical peatlands can exhibit significant variability in microbial community abundance even at small spatial scales, driven by both peat botanical origin and localised differences in specific peat properties. [ABSTRACT FROM AUTHOR]

Archaea play an important role in marine biogeochemical cycle; however, their phylogenetic distribution and lipid composition in the hadal zone (6–11 km water depth) are poorly known. Here, we analyzed archaeal membrane lipids and 16S rRNA gene sequences in sediments from Mariana Trench (MT), Massau Trench (MS), and New Britain Trench (NBT), varying from 1,560 to 10,840 m depth. Forty‐two intact polar lipids (IPLs) were identified, including glycerol dialkyl glycerol tetraethers (GDGTs), OH‐GDGTs, glycerol dialkyl diethers (GDDs), and archaeol (AR) with polar headgroups of monohexose (1G), dihexose (2G), trihexose (3G), and hexose‐phosphohexose (HPH). Compositional and spatial distribution patterns of archaeal lipids suggest benthic Thaumarchaeota as a major source for IPLs, consistent with the predominance of Thaumarchaeota genes (>80%). The redundancy analysis (RDA) based on lipid and 16S rRNA data separates samples into three groups: extremely deep water (MT), significant terrestrial influence (NBT 1, 4, and 6), and predominant marine influence (MS, NBT 2, 3, 7, and 10). 1G‐GDDs and 1G‐AR positively correlate with water depth, likely reflecting the adaptation of benthic archaea to elevated hydrostatic pressure or variation of archaeal community in trench sediments. Bathyarchaeota are more abundant in sediments receiving terrestrial input; this pattern was attributed to their capability of utilizing terrestrial organic matter as an energy source. Our study highlights important environmental influences (e.g., pressure and organic matter quality and quantity) on benthic archaeal community and archaeal IPL compositions, which should be considered when IPLs and core lipids are applied as chemotaxonomic markers and paleo‐proxies. Key Points: Benthic archaea are a major source for IPLs in trench sedimentsSome IPLs positively correlate with water depth, reflecting adaption of archaea to hydrostatic pressure or changes of archaeal communityBathyarchaeota are more abundant in sediments receiving terrestrial input, attributed to utilization of terrestrial organic matter Plain Language Summary: This work is the first report on intact polar lipids (IPLs) of archaea in the hadal trenches, the deepest ocean realm with water depth exceeding 6,000 m. We have investigated in IPL biomarker 16S rRNA gene sequences and biogeochemical parameters in 19 sediments from the Mariana Trench, Massau Trench, and New Britain Trench. These samples are characterized by different water depth (1,560 to 10,840 m), net primary productivity (48 to 123 C m−2 year−1), and terrestrial influence. By comparing biomarker, gene data, and bulk geochemical parameters, we have achieved three key findings: (1) Benthic Thaumarchaeota are a major source for IPLs in hadal sediments; (2) Some IPLs positively correlate with water depth, likely reflecting an adaption mechanism of benthic archaea to elevated hydrostatic pressure or variation of archaeal community in different environments; and (3) Bathyarchaeota are more abundant in sediments receiving terrestrial input (New Britain Trench); this pattern is attributed to their capability of utilizing terrestrial organic matter as an energy source. Our findings provide important information toward understanding of the distribution and adaptation of hadal microbes to extremely high pressure, dark, and food‐depleted environments. [ABSTRACT FROM AUTHOR]

Glycerol dibiphytanyl glycerol tetraethers (GDGTs) are distinctive archaeal membrane-spanning lipids with up to eight cyclopentane rings and/or one cyclohexane ring. The number of rings added to the GDGT core structure can vary as a function of environmental conditions, such as changes in growth temperature. This physiological response enables cyclic GDGTs preserved in sediments to be employed as proxies for reconstructing past global and regional temperatures and to provide fundamental insights into ancient climate variability. Yet, confidence in GDGT-based paleotemperature proxies is hindered by uncertainty concerning the archaeal communities contributing to GDGT pools in modern environments and ambiguity in the environmental and physiological factors that affect GDGT cyclization in extant archaea. To properly constrain these uncertainties, a comprehensive understanding of GDGT biosynthesis is required. Here, we identify 2 GDGT ring synthases, GrsA and GrsB, essential for GDGT ring formation in Sulfolobus acidocaldarius. Both proteins are radical S-adenosylmethionine proteins, indicating that GDGT cyclization occurs through a free radical mechanism. In addition, we demonstrate that GrsA introduces rings specifically at the C-7 position of the core GDGT lipid, while GrsB cyclizes at the C-3 position, suggesting that cyclization patterns are differentially controlled by 2 separate enzymes and potentially influenced by distinct environmental factors. Finally, phylogenetic analyses of the Grs proteins reveal that marine Thaumarchaeota, and not Euryarchaeota, are the dominant source of cyclized GDGTs in open ocean settings, addressing a major source of uncertainty in GDGT-based paleotemperature proxy applications. [ABSTRACT FROM AUTHOR]

This study evaluates the application of biomarkerbased temperature proxy data (alkenone with its resultant U 37 K ′ index and glycerol dialkyl glycerol tetraether (GDGT) with its resultant TEX86and TEX index) in the Ulleung Basin of the East Sea. Based U 37 K ′ on the and TEX86 indices from particles trapped for 10 days in December, 2015 and core-top sediment as well as the comparison of these indices to in situ seawater temperature data (from 2012 to 2016) from the Korea Oceanographic Data Center, this study confirms that the U 37 K ′ index of core-top sediment indicates the annual mean SST of the surface water. This study also suggests that TEX86 data of core-top sediment may represent the annual mean temperature of the subsurface water. However, a reliable calibration equation for GDGT will be required in this regional environment for the proper application of GDGT-based paleotemperature reconstruction. [ABSTRACT FROM AUTHOR]

Archaea are ubiquitous in the modern ocean where they are involved in the carbon and nitrogen biogeochemical cycles. However, the majority of Archaea remain uncultured. Archaeal specific membrane intact polar lipids (IPLs) are biomarkers of the presence and abundance of living cells. They comprise archaeol and glycerol dibiphytanyl glycerol tetraethers (GDGTs) attached to various polar headgroups. However, little is known of the IPLs of uncultured marine Archaea, complicating their use as biomarkers. Here, we analyzed suspended particulate matter (SPM) obtained in high depth resolution from a coastal and open ocean site in the eastern tropical South Pacific (ETSP) oxygen deficient zone (ODZ) with the aim of determining possible biological sources of archaeal IPL by comparing their composition by Ultra High Pressure Liquid Chromatography coupled to high resolution mass spectrometry with the archaeal diversity by 16S rRNA gene amplicon sequencing and their abundance by quantitative PCR. Thaumarchaeotal Marine Group I (MGI) closely related to Ca. Nitrosopelagicus and Nitrosopumilus dominated the oxic surface and upper ODZ water together with Marine Euryarchaeota Group II (MGII). High relative abundance of hexose phosphohexose- (HPH) crenarchaeol, the specific biomarker for living Thaumarchaeota, and HPH-GDGT-0, dihexose- (DH) GDGT-3 and -4 were detected in these water masses. Within the ODZ, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaea) of the Woesearchaeota DHVE-6 group and Marine Euryarchaeota Group III (MGIII) were present together with a higher proportion of archaeol-based IPLs, which were likely made by MGIII, since DPANN archaea are supposedly unable to synthesize their own IPLs and possibly have a symbiotic or parasitic partnership with MGIII. Finally, in deep suboxic/oxic waters a different MGI population occurred with HPH-GDGT-1, -2 and DH-GDGT-0 and -crenarchaeol, indicating that here MGI synthesize membranes with IPLs in a different relative abundance which could be attributed to the different detected population or to an environmental adaptation. Our study sheds light on the complex archaeal community of one of the most prominent ODZs and on the IPL biomarkers they potentially synthesize. [ABSTRACT FROM AUTHOR]

Archaea have many unique physiological features of which the lipid composition of their cellular membranes is the most striking. Archaeal ether-linked isoprenoidal membranes can occur as bilayers or monolayers, possess diverse polar head groups, and a multiplicity of ring structures in the isoprenoidal cores. These lipid structures are proposed to provide protection from the extreme temperature, pH, salinity, and nutrient-starved conditions that many archaea inhabit. However, many questions remain regarding the synthesis and physiological role of some of the more complex archaeal lipids. In this study, we identify a radical S-adenosylmethionine (SAM) protein in Sulfolobus acidocaldarius required for the synthesis of a unique cyclopentyl head group, known as calditol. Calditollinked glycerol dibiphytanyl glycerol tetraethers (GDGTs) are membrane spanning lipids in which calditol is ether bonded to the glycerol backbone and whose production is restricted to a subset of thermoacidophilic archaea of the Sulfolobales order within the Crenarchaeota phylum. Several studies have focused on the enzymatic mechanism for the synthesis of the calditol moiety, but to date no protein that catalyzes this reaction has been discovered. Phylogenetic analyses of this putative calditol synthase (Cds) reveal the genetic potential for calditol-GDGT synthesis in phyla other than the Crenarchaeota, including the Korarchaeota and Marsarchaeota. In addition, we identify Cds homologs in metagenomes predominantly from acidic ecosystems. Finally, we demonstrate that deletion of calditol synthesis renders S. acidocaldarius sensitive to extremely low pH, indicating that calditol plays a critical role in protecting archaeal cells from acidic stress. [ABSTRACT FROM AUTHOR]

The TEX86 proxy, based on the distribution of isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) from planktonic Thaumarchaeota, is widely used to reconstruct sea surface temperature (SST). Recent observations of species‐specific and regionally dependent TEX86‐SST relationships in cultures and the modern ocean raise the question of whether nonthermal factors may have impacted TEX86 paleorecords. Here we evaluate the effects of ecological changes on TEX86 using one Pliocene and two Pleistocene sapropels from the Mediterranean Sea. We find that TEX86‐derived SSTs deviate from U37K'‐derived SSTs before, during, and after each sapropel event. U37K'‐derived SSTs vary by less than 6 °C, while TEX86‐derived SSTs vary by up to 15 °C within a single record. Compound‐specific carbon isotope compositions indicate minimal confounding influence on TEX86 from exogenous sources. Some of the variation can be accounted for by changes in nitrogen cycling intensity affecting thaumarchaeal iGDGT biosynthesis, as demonstrated by an inverse relationship between TEX86 and δ15NTN. TEX86‐derived SSTs also consistently show warm anomalies in the Pleistocene, while the Pliocene samples exhibit both warmer and cooler relative offsets. These anomalies result from systematic differences between Plio‐Pleistocene iGDGT distributions and both modern Mediterranean and modern, globally distributed core top samples. Through characteristic GDGT distributions, we suggest the existence of three distinct endemic populations of Thaumarchaeota in the Pliocene, Pleistocene, and modern Mediterranean Sea, respectively. Importantly, these communities prevailed during both sapropel and oligotrophic conditions. Our results demonstrate that ecological and community‐specific effects must be considered when applying the TEX86 proxy to paleorecords. Key Points: Mediterranean Pliocene‐Pleistocene sapropels were investigated for TEX86, archaeal lipid carbon isotopic compositions, and UK'37Nontemperature effects on TEX86 ocean temperature reconstructions are observed in all sapropels and surrounding marlsDistinct archaeal lipid distributions could be indicative of changing thaumarchaeal communities through time [ABSTRACT FROM AUTHOR]

Terrestrial paleoclimate archives such as lake sediments are essential for our understanding of the continental climate system and for the modeling of future climate scenarios. However, quantitative proxies for the determination of paleotemperatures are sparse. The relative abundances of certain bacterial lipids, i.e., branched glycerol dialkyl glycerol tetraethers (brGDGTs), respond to changes in environmental temperature, and thus have great potential for climate reconstruction. Their application to lake deposits, however, is hampered by the lack of fundamental knowledge on the ecology of brGDGT-producing microbes in lakes. Here, we show that brGDGTs are synthesized by multiple groups of bacteria thriving under contrasting redox regimes in a deep meromictic Swiss lake (Lake Lugano). This niche partitioning is evidenced by highly distinct brGDGT inventories in oxic vs. anoxic watermasses, and corresponding vertical patterns in bacterial 16S rRNA gene abundances, implying that sedimentary brGDGT records are affected by temperatureindependent changes in the community composition of their microbial producers. Furthermore, the stable carbon isotope composition (δ13C) of brGDGTs in Lake Lugano and 34 other (peri-)Alpine lakes attests to the widespread heterotrophic incorporation of 13C-depleted, methane-derived biomass at the redox transition zone of mesotrophic to eutrophic lake systems. The brGDGTs produced under such hypoxic/ methanotrophic conditions reflect near-bottom water temperatures, and are characterized by comparatively low δ13C values. Depending on climate zone and water depth, lake sediment archives predominated by deeper water/low-13C brGDGTsmay providemore reliable records of climate variability than those where brGDGTs derive from terrestrial and/or aquatic sources with distinct temperature imprints. [ABSTRACT FROM AUTHOR]

The abundance and composition of glycerol dibiphytanyl glycerol tetraether (GDGT) and glycerol tribiphytanyl glycerol tetraether (GTGT) lipids were determined as a function of growth phase as a proxy for nutrient availability, the pH of growth medium, and incubation temperature in cultures of the thermoacidophile Picrophilus torridus. Regardless of the cultivation condition, the abundance of GDGTs and GTGTs was greater in the polar than core fraction, with a marked decrease in core GDGTs in cultures harvested during log phase growth. These data are consistent with previous suggestions indicating that core GDGTs are re-functionalized during polar lipid synthesis. Under all conditions examined, polar lipids were enriched in a GDGT with 2 cyclopentyl rings (GDGT-2), indicating GDGT-2 is the preferred lipid in this taxon. However, lag or stationary phase grown cells or cells subjected to pH or thermal stress were enriched in GDGTs with 4, 5, or 6 rings and depleted in GDGTs with 1, 2, 3, rings relative to log phase cells grown under optimal conditions. Variation in the composition of polar GDGT lipids in cells harvested during various growth phases tended to be greater than in cells cultivated over a pH range of 0.3-1.1 and a temperature range of 53-63°C. These results suggest that the growth phase, the pH of growth medium, and incubation temperature are all important factors that shape the composition of tetraether lipids in Picrophilus. The similarity in enrichment of GDGTs with more rings in cultures undergoing nutrient, pH, and thermal stress points to GDGT cyclization as a generalized physiological response to stress in this taxon. [ABSTRACT FROM AUTHOR]

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 (R2 = 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. [ABSTRACT FROM AUTHOR]

Higher homologues of widely reported C86 isoprenoid diglycerol tetraether lipid cores, containing 0-6 cyclopentyl rings, have been identified in (hyper)thermophilic archaea, representing up to 21% of total tetraether lipids in the cells. Liquid chromatography-tandem mass spectrometry confirms that the additional carbon atoms in the C87-88 homologues are located in the etherified chains. Structures identified include dialkyl and monoalkyl ('H-shaped') tetraethers containing C40-42 or C81-82 hydrocarbons, respectively,many representing novel compounds. Gas chromatography-mass spectrometric analysis of hydrocarbons released from the lipid cores by ether cleavage suggests that the C40 chains are biphytanes and the C41 chains 13-methylbiphytanes. Multiple isomers, having different chain combinations, were recognised among the dialkyl lipids. Methylated tetraethers are produced by Methanothermobacter thermautotrophicus in varying proportions depending on growth conditions, suggesting that methylation may be an adaptive mechanism to regulate cellular function. The detection of methylated lipids in Pyrobaculum sp. AQ1.S2 and Sulfolobus acidocaldarius represents the first reported occurrences in Crenarchaeota. Soils and aquatic sediments fromgeographically distinct mesotemperate environments that were screened for homologues contained monomethylated tetraethers, with di- and trimethylated structures being detected occasionally. The structural diversity and range of occurrences of the C87-89 tetraethers highlight their potential as complementary biomarkers for archaea in natural environments. [ABSTRACT FROM AUTHOR]

Marine ammonia-oxidizing archaea (AOA) are among the most abundant of marine microorganisms, spanning nearly the entire water column of diverse oceanic provinces. Historical patterns of abundance are preserved in sediments in the form of their distinctive glycerol dibiphytanyl glycerol tetraether (GDGT) membrane lipids. The correlation between the composition of GDGTs in surface sediment and the overlying annual average sea surface temperature forms the basis for a paleotemperature proxy (TEX86) that is used to reconstruct surface ocean temperature as far back as the Middle Jurassic. However, mounting evidence suggests that factors other than temperature could also play an important role in determining GDGT distributions. We here use a study set of four marine AOA isolates to demonstrate that these closely related strains generate different TEX86--temperature relationships and that oxygen (O2) concentration is at least as important as temperature in controlling TEX86 values in culture. All of the four strains characterized showed a unique membrane compositional response to temperature, with TEX86-inferred temperatures varying as much as 12 °C from the incubation temperatures. In addition, both linear and nonlinear TEX86-- temperature relationships were characteristic of individual strains. Increasing relative abundance of GDGT-2 and GDGT-3 with increasing O2 limitation, at the expense of GDGT-1, led to significant elevations in TEX86-derived temperature. Although the adaptive significance of GDGT compositional changes in response to both temperature and O2 is unclear, this observation necessitates a reassessment of archaeal lipid-based paleotemperature proxies, particularly in records that span low-oxygen events or underlie oxygen minimum zones. [ABSTRACT FROM AUTHOR]

We investigated microbial life preserved in a hydrothermally inactive silica-barite chimney in comparison with an active barite chimney and sediment from the Loki's Castle low-temperature venting area at the Arctic Mid-Ocean Ridge (AMOR) using lipid biomarkers. Carbon and sulfur isotopes were used to constrain possible metabolic pathways. Multiple sulfur (δS, ∆S) isotopes on barite over a cross section of the extinct chimney range between 21.1 and 22.5 ‰ in δS, and between 0.020 and 0.034 ‰ in ΔS, indicating direct precipitation from seawater. Biomarker distributions within two discrete zones of this silica-barite chimney indicate a considerable difference in abundance and diversity of microorganisms from the chimney exterior to the interior. Lipids in the active and inactive chimney barite and sediment were dominated by a range of C-depleted unsaturated and branched fatty acids with δC values between −39.7 and −26.7 ‰, indicating the presence of sulfur-oxidizing and sulfate-reducing bacteria. The majority of lipids (99.5 %) in the extinct chimney interior that experienced high temperatures were of archaeal origin. Unusual glycerol monoalkyl glycerol tetraethers (GMGT) with 0-4 rings were the dominant compounds suggesting the presence of mainly (hyper-) thermophilic archaea. Isoprenoid hydrocarbons with δC values as low as −46 ‰ also indicated the presence of methanogens and possibly methanotrophs. [ABSTRACT FROM AUTHOR]

We investigated the spatial distribution of glycerol dialkyl glycerol tetraethers (GDGTs), alkenones, and polyunsaturated fatty acids in particulate organic matter collected at four sites along a depth transect from the continental shelf to the Okinawa Trough in the East China Sea during the spring bloom in 2008. The maximum alkenone concentration appeared in the top 25 m at all sites and the $$ U_{37}^{{{\text{K}}'}} $$ values were consistent with in situ water temperatures in the depth interval, suggesting that the alkenones were produced mainly in surface water. At the slope and shelf sites, GDGTs in the water column showed a concentration maximum at 74-99 m depth, and the $$ {\text{TEX}}_{86}^{\text{H}} $$ agreed with in situ water temperatures, suggesting the in situ production of GDGTs in the depth interval. The low-salinity surface water above 20 m depth was characterized by low GDGT concentrations and low $$ {\text{TEX}}_{86}^{\text{L}} $$-based temperatures, suggesting either the production of GDGTs in winter season or the lateral advection of GDGTs by an eastward current. At the slope and Okinawa Trough sites, TEX-based temperatures were nearly constant in the water column deeper than 300 m and corresponded to temperatures at the surface and near-surface waters rather than in situ temperatures. This observation is consistent with a hypothesis that Thaumarchaeota cells produced in surface waters are delivered to deeper water and also indicates that the residence time of suspended GDGTs in the deep-water column is large enough to mix the GDGTs produced in different seasons. [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]

Cyclization in glycerol dibiphytanyl glycerol tetraethers (GDGTs) results in internal cyclopentane moieties which are believed to confer thermal stability to crenarchaeal membranes. While the average number of rings per GDGT lipid (ring index) is positively correlated with temperature in many temperate environments, poor correlations are often observed in geothermal environments, suggesting that additional parameters may influence GDGT core lipid composition in these systems. However, the physical and chemical parameters likely to influence GDGT cyclization which are often difficult to decouple in geothermal systems, making it challenging to assess their influence on lipid composition. In the present study, the influence of temperature (range 65-81°C), pH (range 3.0-5.0), and ionic strength (range 10.1-55.7 mM) on GDGT core lipid composition was examined in the hyperthermoacidophile Acidilobus sulfurireducens, a crenarchaeon originally isolated from a geothermal spring in Yellowstone National Park, Wyoming. When cultivated under defined laboratory conditions, the composition of individual and total GDGTs varied significantly with temperature and to a lesser extent with the pH of the growth medium. Ionic strength over the range of values tested did not influence GDGT composition. The GDGT core lipid ring index was positively correlated with temperature and negatively correlated with pH, suggesting that A. sulfurireducens responds to increasing temperature and acidity by increasing the number of cyclopentyl rings in GDGT core membrane lipids. [ABSTRACT FROM AUTHOR]