Discovering Nature's Fingerprints: Isotope Ratio Analysis on Bioanalytical Mass Spectrometers

For a generation or more, the mass spectrometry that developed at the frontier of molecular biology was worlds apart from isotope ratio mass spectrometry, a label-free approach done on optimized gas-source magnetic sector instruments. Recent studies show that electrospray-ionization Orbitraps and other mass spectrometers widely used in the life sciences can be fine-tuned for high-precision isotope ratio analysis. Since isotope patterns form everywhere in nature based on well-understood principles, intramolecular isotope measurements allow unique insights into a fascinating range of research topics. This Perspective introduces a wider readership to current topics in stable isotope research with the aim of discussing how soft-ionization mass spectrometry coupled with ultrahigh mass resolution can enable long-envisioned progress. We highlight novel prospects of observing isotopes in intact polar compounds and speculate on future directions of this adventure into the overlapping realms of biology, chemistry, and geology.

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.

Reconstructing the diet, trophic level and migration pattern of mysticete whales based on baleen isotopic composition

Baleen from mysticete whales is a well-preserved proteinaceous material that can be used to identify migrations and feeding habits for species whose migration pathways are unknown. Analysis of δ13C and δ15N values from bulk baleen have been used to infer migration patterns for individuals. However, this approach has fallen short of identifying migrations between regions as it is difficult to determine variations in isotopic shifts without temporal sampling of prey items. Here, we apply analysis of δ15N values of amino acids to five baleen plates belonging to three species, revealing novel insights on trophic position, metabolic state and migration between regions. Humpback and minke whales had higher reconstructed trophic levels than fin whales (3.7-3.8 versus 3-3.2, respectively) as expected due to different feeding specialization. Isotopic niche areas between baleen minima and maxima were well separated, indicating regional resource use for individuals during migration that aligned with isotopic gradients in Atlantic Ocean particulate organic matter. Phenylanine δ15N values confirmed regional separation between the niche areas for two fin whales as migrations occurred and elevated glycine and threonine δ15N values suggested physiological changes due to fasting. Simultaneous resolution of trophic level and physiological changes allow for identification of regional migrations in mysticetes.

Negligible Quantities of Particulate Low-Temperature Pyrogenic Carbon Reach the Atlantic Ocean via the Amazon River

Particulate pyrogenic carbon (PyC) transported by rivers and aerosols, and deposited in marine sediments, is an important part of the carbon cycle. The chemical composition of PyC is temperature dependent and levoglucosan is a source-specific burning marker used to trace low-temperature PyC. Levoglucosan associated to particulate material has been shown to be preserved during riverine transport and marine deposition in high- and mid-latitudes, but it is yet unknown if this is also the case for (sub)tropical areas, where 90% of global PyC is produced. Here, we investigate transport and deposition of levoglucosan in suspended and riverbed sediments from the Amazon River system and adjacent marine deposition areas. We show that the Amazon River exports negligible amounts of levoglucosan and that concentrations in sediments from the main Amazon tributaries are not related to long-term mean catchment-wide fire activity. Levoglucosan concentrations in marine sediments offshore the Amazon Estuary are positively correlated to total organic content regardless of terrestrial or marine origin, supporting the notion that association of suspended or dissolved PyC to biogenic particles is critical in the preservation of PyC. We estimate that 0.5-10 × 10⁶ g yr^-1 of levoglucosan is exported by the Amazon River. This represents only 0.5-10 ppm of the total exported PyC and thereby an insignificant fraction, indicating that riverine derived levoglucosan and low-temperature PyC in the tropics are almost completely degraded before deposition. Hence, we suggest caution in using levoglucosan as tracer for past fire activity in tropical settings near rivers.

Lipidomics of Environmental Microbial Communities. I: Visualization of Component Distributions Using Untargeted Analysis of High-Resolution Mass Spectrometry Data

Lipids, as one of the main building blocks of cells, can provide valuable information on microorganisms in the environment. Traditionally, gas or liquid chromatography coupled to mass spectrometry (MS) has been used to analyze environmental lipids. The resulting spectra were then processed through individual peak identification and comparison with previously published mass spectra. Here, we present an untargeted analysis of MS¹ spectral data generated by ultra-high-pressure liquid chromatography coupled with high-resolution mass spectrometry of environmental microbial communities. Rather than attempting to relate each mass spectrum to a specific compound, we have treated each mass spectrum as a component, which can be clustered together with other components based on similarity in their abundance depth profiles through the water column. We present this untargeted data visualization method on lipids of suspended particles from the water column of the Black Sea, which included >14,000 components. These components form clusters that correspond with distinct microbial communities driven by the highly stratified water column. The clusters include both known and unknown compounds, predominantly lipids, demonstrating the value of this rapid approach to visualize component distributions and identify novel lipid biomarkers.

Lipidomics of Environmental Microbial Communities. II: Characterization Using Molecular Networking and Information Theory

Structurally diverse, specialized lipids are crucial components of microbial membranes and other organelles and play essential roles in ecological functioning. The detection of such lipids in the environment can reveal not only the occurrence of specific microbes but also the physicochemical conditions to which they are adapted to. Traditionally, liquid chromatography coupled with mass spectrometry allowed for the detection of lipids based on chromatographic separation and individual peak identification, resulting in a limited data acquisition and targeting of certain lipid groups. Here, we explored a comprehensive profiling of microbial lipids throughout the water column of a marine euxinic basin (Black Sea) using ultra high-pressure liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMS/MS). An information theory framework combined with molecular networking based on the similarity of the mass spectra of lipids enabled us to capture lipidomic diversity and specificity in the environment, identify novel lipids, differentiate microbial sources within a lipid group, and discover potential biomarkers for biogeochemical processes. The workflow presented here allows microbial ecologists and biogeochemists to process quickly and efficiently vast amounts of lipidome data to understand microbial lipids characteristics in ecosystems.

Total Synthesis of the Alleged Structure of Crenarchaeol Enables Structure Revision*

Crenarchaeol is a glycerol dialkyl glycerol tetraether lipid produced exclusively in Archaea of the phylum Thaumarchaeota. This membrane‐spanning lipid is undoubtedly the structurally most sophisticated of all known archaeal lipids and an iconic molecule in organic geochemistry. The 66‐membered macrocycle possesses a unique chemical structure featuring 22 mostly remote stereocenters, and a cyclohexane ring connected by a single bond to a cyclopentane ring. Herein we report the first total synthesis of the proposed structure of crenarchaeol. Comparison with natural crenarchaeol allowed us to propose a revised structure of crenarchaeol, wherein one of the 22 stereocenters is inverted.

A late Pleistocene dataset of Agulhas Current variability

The interocean transfer of thermocline water between the Indian and the Atlantic Oceans known as 'Agulhas leakage' is of global significance as it influences the Atlantic Meridional Overturning Circulation (AMOC) on different time scales. Variability in the Agulhas Current regime is key in shaping hydroclimate on the adjacent coastal areas of the African continent today as well as during past climates. However, the lack of long, continuous records from the proximal Agulhas Current region dating beyond the last glacial cycle prevents elucidation of its role in regional and wider global climate changes. This is the first continuous record of hydrographic variability (SST; δ18Osw) from the Agulhas Current core region spanning the past 270,000 years. The data set is analytical sound and provides a solid age model. As such, it can be used by paleoclimate scientists, archaeologists, and climate modelers to evaluate, for example, linkages between the Agulhas Current system and AMOC dynamics, as well as connections between ocean heat transport and Southern African climate change in the past and its impact on human evolution.

A Warm, Stratified, and Restricted Labrador Sea Across the Middle Eocene and Its Climatic Optimum

Several studies indicate that North Atlantic Deep Water (NADW) formation might have initiated during the globally warm Eocene (56-34 Ma). However, constraints on Eocene surface ocean conditions in source regions presently conducive to deep water formation are sparse. Here we test whether ocean conditions of the middle Eocene Labrador Sea might have allowed for deep water formation by applying (organic) geochemical and palynological techniques, on sediments from Ocean Drilling Program (ODP) Site 647. We reconstruct a long-term sea surface temperature (SST) drop from ~30°C to ~27°C between 41.5 to 38.5 Ma, based on TEX86. Superimposed on this trend, we record ~2°C warming in SST associated with the Middle Eocene Climatic Optimum (MECO; ~40 Ma), which is the northernmost MECO record as yet, and another, likely regional, warming phase at ~41.1 Ma, associated with low-latitude planktic foraminifera and dinoflagellate cyst incursions. Dinoflagellate cyst assemblages together with planktonic foraminiferal stable oxygen isotope ratios overall indicate low surface water salinities and strong stratification. Benthic foraminifer stable carbon and oxygen isotope ratios differ from global deep ocean values by 1-2‰ and 2-4‰, respectively, indicating geographic basin isolation. Our multiproxy reconstructions depict a consistent picture of relatively warm and fresh but also highly variable surface ocean conditions in the middle Eocene Labrador Sea. These conditions were unlikely conducive to deep water formation. This implies either NADW did not yet form during the middle Eocene or it formed in a different source region and subsequently bypassed the southern Labrador Sea.

Practical considerations for improved reliability and precision during determination of δ15 N values in amino acids using a single combined oxidation-reduction reactor

RATIONALE

There has been increased interest in the measurement of δ¹⁵ N values in amino acids (AAs) to gain simultaneous insight into both trophic relationships and the composition of biogeochemical sources used by producers at the base of the food web. A new combustion reactor design in gas chromatography/combustion isotope ratio mass spectrometry (GC/C-irMS) equipment has brought to light variable outcomes in performance, highlighting the need for better information about best practices for new systems.

METHODS

Precision for δ¹⁵ N values in amino acids using the single combined oxidation-reduction reactor is improved across a sequence of analyses if the reactor is oxidized for a substantial period (2 h) and subsequently maintained throughout the sequence with 12-17 s seed oxidation before each run during GC/C-irMS. A five-point calibration curve using amino acids with a range of δ¹⁵ N values from -2.4‰ to +61.5‰ was used in combination with a 13-15 amino acid mixture to consistently normalize measurements to internationally calibrated reference materials.

RESULTS

Combining this oxidation method with normalization techniques using both internal and external standards provided a reliable throughput of ~25 samples per week. It allowed for a reproducible level of precision of <±0.5‰, n = 10 within a derivatized standard mixture across each sequence and an average sample precision of ±0.27‰ n = 3, which is lower than the analytical precision typically associated with δ¹⁵ N values for amino acid analysis (<±1‰).

CONCLUSIONS

A few practical considerations regarding oxidation and conditioning of the combustion reactor allow for increased sequence capacity with the single combined oxidation-reduction reactor. These considerations combined with normalization techniques result in a higher throughput and reduced analytical error during the measurement of δ¹⁵ N values in amino acids.

Anaerobic methanotrophic archaea of the ANME-2d clade feature lipid composition that differs from other ANME archaea

The anaerobic oxidation of methane (AOM) is a microbial process present in marine and freshwater environments. AOM is important for reducing the emission of the second most important greenhouse gas methane. In marine environments anaerobic methanotrophic archaea (ANME) are involved in sulfate-reducing AOM. In contrast, Ca. Methanoperedens of the ANME-2d cluster carries out nitrate AOM in freshwater ecosystems. Despite the importance of those organisms for AOM in non-marine environments little is known about their lipid composition or carbon sources. To close this gap, we analysed the lipid composition of ANME-2d archaea and found that they mainly synthesise archaeol and hydroxyarchaeol as well as different (hydroxy-) glycerol dialkyl glycerol tetraethers, albeit in much lower amounts. Abundant lipid headgroups were dihexose, monomethyl-phosphatidyl ethanolamine and phosphatidyl hexose. Moreover, a monopentose was detected as a lipid headgroup that is rare among microorganisms. Batch incubations with ¹³C labelled bicarbonate and methane showed that methane is the main carbon source of ANME-2d archaea varying from ANME-1 archaea that primarily assimilate dissolved inorganic carbon (DIC). ANME-2d archaea also assimilate DIC, but to a lower extent than methane. The lipid characterisation and analysis of the carbon source of Ca. Methanoperedens facilitates distinction between ANME-2d and other ANMEs.

Factors regulating primary producers' assemblages in Posidonia oceanica (L.) Delile ecosystems over the past 1800 years

Posidonia oceanica (L.) Delile meadows are highly productive coastal marine ecosystems that provide multiple ecosystem services. The seagrass is not always the major contributor to total primary production, however, little is known about long-term changes in the composition of primary producers within seagrass meadows. Understanding compositional shifts within the community of primary producers is crucial to evaluate how climate and anthropogenic change affect the functioning of seagrass ecosystems. Here we analysed marker pigment composition in seagrass cores from two bays of the Cabrera Island (Balearic Islands, Spain) to asses long-term changes in phototrophic community composition and production in seagrass meadows, and identify the environmental factors triggering those changes. The proxy dataset was explored using principal component analyses (PCA): one including the pigment dataset to look for associations between producers' groups, and another one combining the pigment dataset with plausible local and global regulatory factors to assess the environmental drivers of change. Analyses of characteristic pigments and morphological fossils (cysts) showed that the abundance of dinoflagellates increased over the last 150-300 years, coeval with a rise in solar irradiance and air temperature. When compared among embayments, pigments from cyanobacteria predominated in seagrass meadows located at Es Port, a sheltered bay receiving higher terrestrial runoff; whereas pigments from diatoms, seagrasses and rodophytes were more common at Santa Maria, an exposed bay with clearer waters. Water depth also played a role in controlling the phototrophic community composition, with greater abundance of diatoms in the shallowest waters (<5 m). Overall, our results suggested that historical and spatial variation in seagrass meadows' phototrophic community composition was influenced by the interaction between local factors (catchment-bay characteristics) and global climate processes (energy influx). Together these patterns forecast how marine primary producers and seagrass ecosystem structure may respond to future global warming.

The absence of intact polar lipid-derived GDGTs in marine waters dominated by Marine Group II: Implications for lipid biosynthesis in Archaea

The marine pelagic archaeal community is dominated by three major groups, the marine group I (MGI) Thaumarchaeota, and the marine groups II and III (MGII and MGIII) Euryarchaeota. Studies of both MGI cultures and the environment have shown that the MGI core membrane lipids are predominantly composed of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids and the diether lipid archaeol. However, there are no cultured representatives of MGII and III archaea and, therefore, both their membrane lipid composition and potential contribution to the marine archaeal lipid pool remain unknown. Here, we show that GDGTs present in suspended particulate matter of the (sub)surface waters of the North Atlantic Ocean and the coastal North Sea are derived from MGI archaea, and that MGII archaea do not significantly contribute to the pool of GDGTs and archaeol. This implies, in contrast to previous suggestions, that their lipids do not affect the widely used sea surface temperature proxy TEX₈₆. These findings also indicate that MGII archaea are not able to produce any known archaeal lipids, implying that our understanding of the evolution of membrane lipid biosynthesis in Archaea is far from complete.

Human-induced fire regime shifts during 19th century industrialization: A robust fire regime reconstruction using northern Polish lake sediments

Fire regime shifts are driven by climate and natural vegetation changes, but can be strongly affected by human land management. Yet, it is poorly known how humans have influenced fire regimes prior to active wildfire suppression. Among the last 250 years, the human contribution to the global increase in fire occurrence during the mid-19^th century is especially unclear, as data sources are limited. Here, we test the extent to which forest management has driven fire regime shifts in a temperate forest landscape. We combine multiple fire proxies (macroscopic charcoal and fire-related biomarkers) derived from highly resolved lake sediments (i.e., 3–5 years per sample), and apply a new statistical approach to classify source area- and temperature-specific fire regimes (biomass burnt, fire episodes). We compare these records with independent climate and vegetation reconstructions. We find two prominent fire regime shifts during the 19^th and 20^th centuries, driven by an adaptive socio-ecological cycle in human forest management. Although individual fire episodes were triggered mainly by arson (as described in historical documents) during dry summers, the biomass burnt increased unintentionally during the mid-19^th century due to the plantation of flammable, fast-growing pine tree monocultures needed for industrialization. State forest management reacted with active fire management and suppression during the 20^th century. However, pine cover has been increasing since the 1990s and climate projections predict increasingly dry conditions, suggesting a renewed need for adaptations to reduce the increasing fire risk.

Biosynthesis of Long Chain Alkyl Diols and Long Chain Alkenols in Nannochloropsis spp. (Eustigmatophyceae)

We investigated potential biosynthetic pathways of long chain alkenols (LCAs), long chain alkyl diols (LCDs), and long chain hydroxy fatty acids (LCHFAs) in Nannochloropsis oceanica and Nannochloropsis gaditana, by combining culturing experiments with genomic and transcriptomic analyses. Incubation of Nannochloropsis spp. in the dark for 1 week led to significant increases in the cellular concentrations of LCAs and LCDs in both species. Consistently, 13C-labelled substrate experiments confirmed that both LCA and LCD were actively produced in the dark from C14-18 fatty acids by either condensation or elongation/hydroxylation, although no enzymatic evidence was found for the former pathway. Nannochloropsis spp. did, however, contain (i) multiple polyketide synthases (PKSs) including one type (PKS-Clade II) that might catalyze incomplete fatty acid elongations leading to the formation of 3-OH-fatty acids, (ii) 3-hydroxyacyl dehydratases (HADs), which can possibly form Δ2/Δ3 monounsaturated fatty acids, and (iii) fatty acid elongases (FAEs) that could elongate 3-OH-fatty acids and Δ2/Δ3 monounsaturated fatty acids to longer products. The enzymes responsible for reduction of the long chain fatty acids to LCDs and LCAs are, however, unclear. A putative wax ester synthase/acyl coenzyme A (acyl-CoA): diacylglycerol acyltransferase is likely to be involved in the esterification of LCAs and LCDs in the cell wall. Our data thus provide useful insights in predicting the biosynthetic pathways of LCAs and LCDs in phytoplankton suggesting a key role of FAE and PKS enzymes.

Climate- and gateway-driven cooling of Late Eocene to earliest Oligocene sea surface temperatures in the North Sea Basin

During the late Eocene, the Earth’s climate experienced several transient temperature fluctuations including the Vonhof cooling event (C16n.1n; ~35.8 Ma) hitherto known mainly from the southern oceans. Here we reconstruct sea-surface temperatures (SST) and provide δ¹⁸O and δ¹³C foraminiferal records for the late Eocene and earliest Oligocene in the North Sea Basin. Our data reveal two main perturbations: (1), an abrupt brief cooling of ~4.5 °C dated to ~35.8 Ma and synchronous with the Vonhof cooling, which thus may be a global event, and (2) a gradual nearly 10 °C temperature fall starting at 36.1 Ma and culminating near the Eocene-Oligocene transition at ~33.9 Ma. The late Priabonian temperature trend in the North Sea shows some resemblance IODP Site U1404 from the North Atlantic, offshore Newfoundland; and is in contrast to the more abrupt change observed in the deep-sea δ¹⁸O records from the southern oceans. The cooling in the North Sea is large compared to the pattern seen in the North Atlantic record. This difference may be influenced by a late Eocene closure of the warm gateways connecting the North Sea with the Atlantic and Tethys oceans.

Bisnorgammacerane traces predatory pressure and the persistent rise of algal ecosystems after Snowball Earth

Eukaryotic algae rose to ecological relevance after the Neoproterozoic Snowball Earth glaciations, but the causes for this consequential evolutionary transition remain enigmatic. Cap carbonates were globally deposited directly after these glaciations, but they are usually organic barren or thermally overprinted. Here we show that uniquely-preserved cap dolostones of the Araras Group contain exceptional abundances of a newly identified biomarker: 25,28-bisnorgammacerane. Its secular occurrence, carbon isotope systematics and co-occurrence with other demethylated terpenoids suggest a mechanistic connection to extensive microbial degradation of ciliate-derived biomass in bacterially dominated ecosystems. Declining 25,28-bisnorgammacerane concentrations, and a parallel rise of steranes over hopanes, indicate the transition from a bacterial to eukaryotic dominated ecosystem after the Marinoan deglaciation. Nutrient levels already increased during the Cryogenian and were a prerequisite, but not the ultimate driver for the algal rise. Intense predatory pressure by bacterivorous protists may have irrevocably cleared self-sustaining cyanobacterial ecosystems, thereby creating the ecological opportunity that allowed for the persistent rise of eukaryotic algae to global importance.

Early Response of Sulfolobus acidocaldarius to Nutrient Limitation

In natural environments microorganisms encounter extreme changes in temperature, pH, osmolarities and nutrient availability. The stress response of many bacterial species has been described in detail, however, knowledge in Archaea is limited. Here, we describe the cellular response triggered by nutrient limitation in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. We measured changes in gene transcription and protein abundance upon nutrient depletion up to 4 h after initiation of nutrient depletion. Transcript levels of 1118 of 2223 protein coding genes and abundance of approximately 500 proteins with functions in almost all cellular processes were affected by nutrient depletion. Our study reveals a significant rerouting of the metabolism with respect to degradation of internal as well as extracellular-bound organic carbon and degradation of proteins. Moreover, changes in membrane lipid composition were observed in order to access alternative sources of energy and to maintain pH homeostasis. At transcript level, the cellular response to nutrient depletion in S. acidocaldarius seems to be controlled by the general transcription factors TFB2 and TFEβ. In addition, ribosome biogenesis is reduced, while an increased protein degradation is accompanied with a loss of protein quality control. This study provides first insights into the early cellular response of Sulfolobus to organic carbon and organic nitrogen depletion.

Molecular fossils from phytoplankton reveal secular Pco2 trend over the Phanerozoic

Past changes in the atmospheric concentration of carbon dioxide (Pco₂) have had a major impact on earth system dynamics; yet, reconstructing secular trends of past Pco₂ remains a prevalent challenge in paleoclimate studies. The current long-term Pco₂ reconstructions rely largely on the compilation of many different proxies, often with discrepancies among proxies, particularly for periods older than 100 million years (Ma). Here, we reconstructed Phanerozoic Pco₂ from a single proxy: the stable carbon isotopic fractionation associated with photosynthesis (Ɛ_p) that increases as Pco₂ increases. This concept has been widely applied to alkenones, but here, we expand this concept both spatially and temporally by applying it to all marine phytoplankton via a diagenetic product of chlorophyll, phytane. We obtained data from 306 marine sediments and oils, which showed that Ɛ_p ranges from 11 to 24‰, agreeing with the observed range of maximum fractionation of Rubisco (i.e., 25 to 28‰). The observed secular Pco₂ trend derived from phytane-based Ɛ_p mirrors the available compilations of Pco₂ over the past 420 Ma, except for two periods in which our higher estimates agree with the warm climate during those time periods. Our record currently provides the longest secular trend in Pco₂ based on a single marine proxy, covering the past 500 Ma of Earth history.

Vegetation response to exceptional global warmth during Oceanic Anoxic Event 2

The Cenomanian–Turonian Oceanic Anoxic Event (OAE2; ~94.5 million years ago) represents an episode of global-scale marine anoxia and biotic turnover, which corresponds to one of the warmest time intervals in the Phanerozoic. Despite its global significance, information on continental ecosystem response to this greenhouse episode is lacking. Here we present a terrestrial palynological record combined with marine-derived temperature data (TEX₈₆) across an expanded OAE2 section from the Southern Provençal Basin, France. Despite high TEX₈₆-derived temperature estimates reaching up to 38 °C, the continental hinterland did support a diverse vegetation, adapted to persist under elevated temperatures. A transient phase of climatic instability and cooling during OAE2 known as Plenus Cold Event (PCE) is marked by the proliferation of open, savanna-type vegetation rich in angiosperms at the expanse of conifer-dominated forest ecosystems. A rise in early representatives of Normapolles-type pollen during the PCE marks the initial radiation of this important angiosperm group.

The Cretaceous Oceanic Anoxic Event 2 represents one of the warmest episodes in the last 250 million years. Here, the authors present spore-pollen data and temperature estimates (TEX₈₆) across an expanded stratigraphic section illustrating the dynamic response of vegetation during this exceptionally warm interval.

Synchronous tropical and polar temperature evolution in the Eocene

Palaeoclimate reconstructions of periods with warm climates and high atmospheric CO₂ concentrations are crucial for developing better projections of future climate change. Deep-ocean^1,2 and high-latitude³ palaeotemperature proxies demonstrate that the Eocene epoch (56 to 34 million years ago) encompasses the warmest interval of the past 66 million years, followed by cooling towards the eventual establishment of ice caps on Antarctica. Eocene polar warmth is well established, so the main obstacle in quantifying the evolution of key climate parameters, such as global average temperature change and its polar amplification, is the lack of continuous high-quality tropical temperature reconstructions. Here we present a continuous Eocene equatorial sea surface temperature record, based on biomarker palaeothermometry applied on Atlantic Ocean sediments. We combine this record with the sparse existing data^4-6 to construct a 26-million-year multi-proxy, multi-site stack of Eocene tropical climate evolution. We find that tropical and deep-ocean temperatures changed in parallel, under the influence of both long-term climate trends and short-lived events. This is consistent with the hypothesis that greenhouse gas forcing^7,8, rather than changes in ocean circulation^9,10, was the main driver of Eocene climate. Moreover, we observe a strong linear relationship between tropical and deep-ocean temperatures, which implies a constant polar amplification factor throughout the generally ice-free Eocene. Quantitative comparison with fully coupled climate model simulations indicates that global average temperatures were about 29, 26, 23 and 19 degrees Celsius in the early, early middle, late middle and late Eocene, respectively, compared to the preindustrial temperature of 14.4 degrees Celsius. Finally, combining proxy- and model-based temperature estimates with available CO₂ reconstructions⁸ yields estimates of an Eocene Earth system sensitivity of 0.9 to 2.3 kelvin per watt per square metre at 68 per cent probability, consistent with the high end of previous estimates¹¹.

A Comparison of Late Quaternary Organic Proxy-Based Paleotemperature Records of the Central Sea of Okhotsk

The long-chain diol index (LDI) is a new organic sea surface temperature (SST) proxy based on the distribution of long-chain diols. It has been applied in several environments but not yet in subpolar regions. Here we tested the LDI on surface sediments and a sediment core from the Sea of Okhotsk, which is the southernmost seasonal sea ice-covered region in the Northern Hemisphere, and compared it with other organic temperature proxies, that is, U 37 k ' and TEXL 86. In the surface sediments, the LDI is correlated with autumn SST, similar to the U 37 k ' but different from the TEXL 86 that correlates best with summer sea subsurface temperature. Remarkably, the obtained local LDI calibration was significantly different from the global core-top calibration. We used the local LDI calibration to reconstruct past SST changes in the central Sea of Okhotsk. The LDI-SST record shows low glacial (Marine Isotope Stage, MIS 2, 4, and 6) and high interglacial (MIS 1 and MIS 5) temperatures and follows the same pattern as the U 37 k ' -SST and a previously published TEXL 86 temperature record. Similar to the modern situation, the reconstructed temperatures during the interglacials likely reflect different seasons, that is, summer for the TEXL 86 and autumn for U 37 k ' and LDI. During glacials, the reconstructed temperatures of all three proxies are similar to each other, likely reflecting summer temperatures as this was the only season free of sea ice. Our results suggest that the LDI is a suitable proxy to reconstruct subpolar seawater temperatures.

Model for a novel membrane envelope in a filamentous hyperthermophilic virus

Biological membranes create compartments, and are usually formed by lipid bilayers. However, in hyperthermophilic archaea that live optimally at temperatures above 80°C the membranes are monolayers which resemble fused bilayers. Many double-stranded DNA viruses which parasitize such hosts, including the filamentous virus AFV1 of Acidianus hospitalis, are enveloped with a lipid-containing membrane. Using cryo-EM, we show that the membrane in AFV1 is a ~2 nm-thick monolayer, approximately half the expected membrane thickness, formed by host membrane-derived lipids which adopt a U-shaped ‘horseshoe’ conformation. We hypothesize that this unusual viral envelope structure results from the extreme curvature of the viral capsid, as ‘horseshoe’ lipid conformations favor such curvature and host membrane lipids that permit horseshoe conformations are selectively recruited into the viral envelope. The unusual envelope found in AFV1 also has many implications for biotechnology, since this membrane can survive the most aggressive conditions involving extremes of temperature and pH.

DOI:http://dx.doi.org/10.7554/eLife.26268.001

Virtually every environment on the planet is home to some form of life, even places that, at first glance, appear to be too harsh for any organism to survive in. For example, a microscopic organism known as Acidianus hospitalis thrives in highly acidic environments that are hotter than 80°C, conditions that would kill humans and many other species.

Acidianus hospitalis has many adaptations that allow it to survive in its extreme environment. For example, the membrane that surrounds its cells has a different structure to the membranes that surround the cells of most other species. Membranes are made of molecules known as lipids. Generally these lipids assemble into two distinct layers (known as a bilayer) to form the membrane. However, in A. hospitalis the membrane contains only a single layer of lipids that resembles a bilayer in which lipids in opposite layers have fused together to make longer molecules.

A virus known as AFV1 is able to infect A. hospitalis. Like many other viruses, AFV1 steals part of its host cell’s membrane when it leaves the cell in search of new cells to infect. This stolen membrane helps to protect the virus from its surroundings, however, the structure of the membrane surrounding AFV1 was not known.

Kasson et al. combined a technique called cryo-electron microscopy with computer simulations to study the membrane surrounding AFV1. The study shows that this membrane is only half as thick as the membrane that surrounds A. hospitalis. To make this thinner membrane, flexible lipid molecules from the A. hospitalis membrane bend into a U-shape.

These findings reveal a new type of membrane structure not previously seen in the natural world. In the future, this thinner membrane could have many uses in biotechnology, such as to make probes for medical imaging in patients or to deliver drugs to specific sites in the body. Enveloped by this unusual membrane, these structures may be more resistant to the normal processes that degrade and destroy foreign materials in humans and other organisms.

DOI:http://dx.doi.org/10.7554/eLife.26268.002

Miocene flooding events of western Amazonia

There is a considerable controversy about whether western Amazonia was ever covered by marine waters during the Miocene [23 to 5 Ma (million years ago)]. We investigated the possible occurrence of Miocene marine incursions in the Llanos and Amazonas/Solimões basins, using sedimentological and palynological data from two sediment cores taken in eastern Colombia and northwestern Brazil together with seismic information. We observed two distinct marine intervals in the Llanos Basin, an early Miocene that lasted ~0.9 My (million years) (18.1 to 17.2 Ma) and a middle Miocene that lasted ~3.7 My (16.1 to 12.4 Ma). These two marine intervals are also seen in Amazonas/Solimões Basin (northwestern Amazonia) but were much shorter in duration, ~0.2 My (18.0 to 17.8 Ma) and ~0.4 My (14.1 to 13.7 Ma), respectively. Our results indicate that shallow marine waters covered the region at least twice during the Miocene, but the events were short-lived, rather than a continuous full-marine occupancy of Amazonian landscape over millions of years.

Extreme warmth and heat-stressed plankton in the tropics during the Paleocene-Eocene Thermal Maximum

Global ocean temperatures rapidly warmed by ~5°C during the Paleocene-Eocene Thermal Maximum (PETM; ~56 million years ago). Extratropical sea surface temperatures (SSTs) met or exceeded modern subtropical values. With these warm extratropical temperatures, climate models predict tropical SSTs >35°C-near upper physiological temperature limits for many organisms. However, few data are available to test these projected extreme tropical temperatures or their potential lethality. We identify the PETM in a shallow marine sedimentary section deposited in Nigeria. On the basis of planktonic foraminiferal Mg/Ca and oxygen isotope ratios and the molecular proxy [Formula: see text], latest Paleocene equatorial SSTs were ~33°C, and [Formula: see text] indicates that SSTs rose to >36°C during the PETM. This confirms model predictions on the magnitude of polar amplification and refutes the tropical thermostat theory. We attribute a massive drop in dinoflagellate abundance and diversity at peak warmth to thermal stress, showing that the base of tropical food webs is vulnerable to rapid warming.

A progressively wetter climate in southern East Africa over the past 1.3 million years

African climate is generally considered to have evolved towards progressively drier conditions over the past few million years, with increased variability as glacial-interglacial change intensified worldwide. Palaeoclimate records derived mainly from northern Africa exhibit a 100,000-year (eccentricity) cycle overprinted on a pronounced 20,000-year (precession) beat, driven by orbital forcing of summer insolation, global ice volume and long-lived atmospheric greenhouse gases. Here we present a 1.3-million-year-long climate history from the Lake Malawi basin (10°-14° S in eastern Africa), which displays strong 100,000-year (eccentricity) cycles of temperature and rainfall following the Mid-Pleistocene Transition around 900,000 years ago. Interglacial periods were relatively warm and moist, while ice ages were cool and dry. The Malawi record shows limited evidence for precessional variability, which we attribute to the opposing effects of austral summer insolation and the temporal/spatial pattern of sea surface temperature in the Indian Ocean. The temperature history of the Malawi basin, at least for the past 500,000 years, strongly resembles past changes in atmospheric carbon dioxide and terrigenous dust flux in the tropical Pacific Ocean, but not in global ice volume. Climate in this sector of eastern Africa (unlike northern Africa) evolved from a predominantly arid environment with high-frequency variability to generally wetter conditions with more prolonged wet and dry intervals.

Nitrogen and phosphorus uptake rates of different species from a coral reef community after a nutrient pulse

Terrestrial runoff after heavy rainfall can increase nutrient concentrations in waters overlying coral reefs that otherwise experience low nutrient levels. Field measurements during a runoff event showed a sharp increase in nitrate (75-fold), phosphate (31-fold) and ammonium concentrations (3-fold) in waters overlying a fringing reef at the island of Curaçao (Southern Caribbean). To understand how benthic reef organisms make use of such nutrient pulses, we determined ammonium, nitrate and phosphate uptake rates for one abundant coral species, turf algae, six macroalgal and two benthic cyanobacterial species in a series of laboratory experiments. Nutrient uptake rates differed among benthic functional groups. The filamentous macroalga Cladophora spp., turf algae and the benthic cyanobacterium Lyngbya majuscula had the highest uptake rates per unit biomass, whereas the coral Madracis mirabilis had the lowest. Combining nutrient uptake rates with the standing biomass of each functional group on the reef, we estimated that the ammonium and phosphate delivered during runoff events is mostly taken up by turf algae and the two macroalgae Lobophora variegata and Dictyota pulchella. Our results support the often proposed, but rarely tested, assumption that turf algae and opportunistic macroalgae primarily benefit from episodic inputs of nutrients to coral reefs.

Antarctic ice sheet sensitivity to atmospheric CO2 variations in the early to mid-Miocene

Geological records from the Antarctic margin offer direct evidence of environmental variability at high southern latitudes and provide insight regarding ice sheet sensitivity to past climate change. The early to mid-Miocene (23-14 Mya) is a compelling interval to study as global temperatures and atmospheric CO2 concentrations were similar to those projected for coming centuries. Importantly, this time interval includes the Miocene Climatic Optimum, a period of global warmth during which average surface temperatures were 3-4 °C higher than today. Miocene sediments in the ANDRILL-2A drill core from the Western Ross Sea, Antarctica, indicate that the Antarctic ice sheet (AIS) was highly variable through this key time interval. A multiproxy dataset derived from the core identifies four distinct environmental motifs based on changes in sedimentary facies, fossil assemblages, geochemistry, and paleotemperature. Four major disconformities in the drill core coincide with regional seismic discontinuities and reflect transient expansion of grounded ice across the Ross Sea. They correlate with major positive shifts in benthic oxygen isotope records and generally coincide with intervals when atmospheric CO2 concentrations were at or below preindustrial levels (∼280 ppm). Five intervals reflect ice sheet minima and air temperatures warm enough for substantial ice mass loss during episodes of high (∼500 ppm) atmospheric CO2 These new drill core data and associated ice sheet modeling experiments indicate that polar climate and the AIS were highly sensitive to relatively small changes in atmospheric CO2 during the early to mid-Miocene.

Compound-specific stable isotope analysis of nitrogen-containing intact polar lipids

RATIONALE

Compound-specific isotope analysis (CSIA) of nitrogen in amino acids has proven a valuable tool in many fields (e.g. ecology). Several intact polar lipids (IPLs) also contain nitrogen, and their nitrogen isotope ratios have the potential to elucidate food-web interactions or metabolic pathways. Here we have developed novel methodology for the determination of δ(15)N values of nitrogen-containing headgroups of IPLs using gas chromatography coupled with isotope-ratio mass spectrometry.

METHODS

Intact polar lipids with nitrogen-containing headgroups were hydrolyzed and the resulting compounds were derivatized by (1) acetylation with pivaloyl chloride for compounds with amine and hydroxyl groups or (2) esterification using acidified 2-propanol followed by acetylation with pivaloyl chloride for compounds with both carboxyl and amine groups. The δ(15)N values of the derivatives were subsequently determined using gas chromatography/combustion/isotope-ratio mass spectrometry.

RESULTS

Intact polar lipids with ethanolamine and amino acid headgroups, such as phosphatidylethanolamine and phosphatidylserine, were successfully released from the IPLs and derivatized. Using commercially available pure compounds it was established that δ(15)N values of ethanolamine and glycine were not statistically different from the offline-determined values. Application of the technique to microbial cultures and a microbial mat showed that the method works well for the release and derivatization of the headgroup of phosphatidylethanolamine, a common IPL in bacteria.

CONCLUSIONS

A method to enable CSIA of nitrogen of selected IPLs has been developed. The method is suitable for measuring natural stable nitrogen isotope ratios in microbial lipids, in particular phosphatidylethanolamine, and will be especially useful for tracing the fate of nitrogen in deliberate tracer experiments.

Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids

Microorganisms are involved in all elemental cycles and therefore it is important to study their metabolism in the natural environment. A recent technique to investigate this is the hydrogen isotopic composition of microbial fatty acids, i.e., heterotrophic microorganisms produce fatty acids enriched in deuterium (D) while photoautotrophic and chemoautotrophic microorganisms produce fatty acids depleted in D compared to the water in the culture medium (growth water). However, the impact of factors other than metabolism have not been investigated. Here, we evaluate the impact of growth phase compared to metabolism on the hydrogen isotopic composition of fatty acids of different environmentally relevant microorganisms with heterotrophic, photoautotrophic and chemoautotrophic metabolisms. Fatty acids produced by heterotrophs are enriched in D compared to growth water with ε_lipid/water between 82 and 359‰ when grown on glucose or acetate, respectively. Photoautotrophs (ε_lipid/water between −149 and −264‰) and chemoautotrophs (ε_lipid/water between −217 and −275‰) produce fatty acids depleted in D. Fatty acids become, in general, enriched by between 4 and 46‰ with growth phase which is minor compared to the influence of metabolisms. Therefore, the D/H ratio of fatty acids is a promising tool to investigate community metabolisms in nature.

Comparison of the effect of salinity on the D/H ratio of fatty acids of heterotrophic and photoautotrophic microorganisms

The core metabolism of microorganisms has a major influence on the hydrogen isotopic composition of their fatty acids. Heterotrophic microorganisms produce fatty acids with a deuterium to hydrogen (D/H) ratio either slightly depleted or enriched in D compared to the growth water, while photo- and chemoautotrophic microorganisms produce fatty acids which are heavily depleted in D. However, besides metabolism other biochemical and environmental factors (i.e. biosynthetic pathways, growth phase and temperature) have been shown to affect the D/H ratio of fatty acids, and it is necessary to evaluate the magnitude of these effects compared to that of metabolism. Here, we show that the effect of salinity on the D/H ratio of fatty acids depends on the core metabolism of the microorganism. While fatty acids of the photoautotroph Isochrysis galbana become more enriched in D with increasing salinity (enrichment of 30-40‰ over a range of 25 salinity units), no effect of salinity on the D/H ratio of fatty acids of the heterotrophic Pseudomonas str. LFY10 was observed ((ε)lipid/water of the C16:0 fatty acid of ~120‰ over a range of 10 salinity units). This can likely be explained by the relative contributions of different H and nicotinamide adenine dinucleotide phosphate sources during fatty acid biosynthesis.

Asynchronous changes in vegetation, runoff and erosion in the nile river watershed during the holocene

The termination of the African Humid Period in northeastern Africa during the early Holocene was marked by the southward migration of the rain belt and the disappearance of the Green Sahara. This interval of drastic environmental changes was also marked by the initiation of food production by North African hunter-gatherer populations and thus provides critical information on human-environment relationships. However, existing records of regional climatic and environmental changes exhibit large differences in timing and modes of the wet/dry transition at the end of the African Humid Period. Here we present independent records of changes in river runoff, vegetation and erosion in the Nile River watershed during the Holocene obtained from a unique sedimentary sequence on the Nile River fan using organic and inorganic proxy data. This high-resolution reconstruction allows to examine the phase relationship between the changes of these three parameters and provides a detailed picture of the environmental conditions during the Paleolithic/Neolithic transition. The data show that river runoff decreased gradually during the wet/arid transition at the end of the AHP whereas rapid shifts of vegetation and erosion occurred earlier between 8.7 and ∼6 ka BP. These asynchronous changes are compared to other regional records and provide new insights into the threshold responses of the environment to climatic changes. Our record demonstrates that the degradation of the environment in northeastern Africa was more abrupt and occurred earlier than previously thought and may have accelerated the process of domestication in order to secure sustainable food resources for the Neolithic African populations.

Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea)

Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria.

Depth-related distribution of a key gene of the tetraether lipid biosynthetic pathway in marine Thaumarchaeota

The distribution of isoprenoid glycerol dialkyl glycerol tetraethers (GDGT) lipids synthesized by Thaumarchaeota has been shown to be temperature-dependent in world oceans. Depth-related differences in the ammonia monooxygenase (amoA) of Thaumarchaeota have led to the classification of 'shallow' and 'deep water' clusters, potentially affecting GDGT distributions. Here, we investigate if this classification is also reflected in a key gene of the thaumarchaeotal lipid biosynthetic pathway coding for geranylgeranylglyceryl phosphate (GGGP) synthase. We investigated metagenomic databases, suspended particulate matter and surface sediment of the Arabian Sea oxygen minimum zone. These revealed significant differences in amoA and GGGP synthase between 'shallow' and 'deep water' Thaumarchaeota. Intriguingly, amoA and GGGP synthase sequences of benthic Thaumarchaeota clustered with the 'shallow water' rather than with 'deep water' Thaumarchaeota. This suggests that pressure and temperature are unlikely factors that drive the differentiation, and suggests an important role of ammonia concentration that is higher in benthic and 'shallow water' niches. Analysis of the relative abundance of GDGTs in the Arabian Sea and in globally distributed surface sediments showed differences in GDGT distributions from subsurface to deep waters that may be explained by differences in the GGGP synthase, suggesting a genetic control on GDGT distributions.

Fossilization and degradation of archaeal intact polar tetraether lipids in deeply buried marine sediments (Peru Margin)

Glycerol dibiphytanyl glycerol tetraether (GDGT) lipids are part of the cellular membranes of Thaumarchaeota, an archaeal phylum composed of aerobic ammonia oxidizers, and are used in the paleotemperature proxy TEX86 . GDGTs in live cells possess polar head groups and are called intact polar lipids (IPL-GDGTs). Their transformation to core lipids (CL) by cleavage of the head group was assumed to proceed rapidly after cell death, but it has been suggested that some of these IPL-GDGTs can, just like the CL-GDGTs, be preserved over geological timescales. Here, we examined IPL-GDGTs in deeply buried (0.2-186 mbsf, ~2.5 Myr) sediments from the Peru Margin. Direct measurements of the most abundant IPL-GDGT, IPL-crenarchaeol, specific for Thaumarchaeota, revealed depth profiles, which differed per head group. Shallow sediments (<1 mbsf) contained IPL-crenarchaeol with both glycosidic and phosphate head groups, as also observed in thaumarchaeal enrichment cultures, marine suspended particulate matter and marine surface sediments. However, hexose, phosphohexose-crenarchaeol is not detected anymore below 6 mbsf (~7 kyr), suggesting a high lability. In contrast, IPL-crenarchaeol with glycosidic head groups is preserved over timescales of Myr. This agrees with previous analyses of deeply buried (>1 m) marine sediments, which only reported glycosidic and no phosphate-containing IPL-GDGTs. TEX86 values of CL-GDGTs did not markedly change with depth, and the TEX86 of IPL-derived GDGTs decreased only when the proportions of monohexose- to dihexose-GDGTs changed, likely due to the enhanced preservation of the monohexose GDGTs. Our results support the hypothesis that in situ GDGT production and differential IPL degradation in sediments is not substantially affecting TEX86 paleotemperature estimations based on CL-GDGTs and indicates that likely only a small amount of IPL-GDGTs present in deeply buried sediments is part of cell membranes of active archaea. The amount of archaeal biomass in the deep biosphere based on these IPLs may have been substantially overestimated.

Genetic biomarkers of the sterol-biosynthetic pathway in microalgae

Sterols are cyclic isoprenoid lipids present in all eukaryotes. These compounds have been used to determine the composition of algal communities in marine and lake environments, and because of their preservation potential have been used to reconstruct the evolution of eukaryotes. In the last years, there have been major advances in understanding the sterol biosynthetic pathways and the enzymes involved. Here, we have explored the diversity and phylogenetic distribution of the gene coding the cycloartenol synthase (CS), a key enzyme of the phytosterol biosynthetic pathway. We propose a gene-based approach that can be used to assess the sterol-forming potential of algal groups. CS coding gene was annotated in genomes of microalgae using protein homology with previously annotated CS sequences. Primers for the detection of CS gene sequences of diatoms, one of the most dominant groups of microalgae, were designed and evaluated in cultures and environmental samples. A comparison of the phylogeny of the recovered CS sequences in combination with sequence data of the gene rbcL coding for the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) demonstrates the potential of the CS gene as phylogenetic marker, as well as an indicator for the identity of sterol-producing organisms in the environment.

Mesoaciditoga lauensis gen. nov., sp. nov., a moderately thermoacidophilic member of the order Thermotogales from a deep-sea hydrothermal vent

A novel moderately thermophilic, heterotrophic bacterium was isolated from a deep-sea hydrothermal vent deposit from the Mariner field along the Eastern Lau Spreading Center of the south-western Pacific Ocean. Cells were short motile rods (about 0.4×0.8 µm) that occurred singly or in pairs and were surrounded by a sheath-like membrane or 'toga'. The cells grew between 45 and 65 °C (optimum 57-60 °C) and at pH 4.1-6.0 (optimum pH 5.5-5.7) and grew optimally at 3 % (w/v) NaCl. The isolate grew on a range of carbon and proteinaceous substrates and reduced sulfur. The G+C content of the DNA was about 45 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the new isolate as a deeply diverging lineage within the order Thermotogales. Based on the physiological, morphological and phylogenetic data, the isolate represents a novel species of a new genus with the proposed name Mesoaciditoga lauensis gen. nov., sp. nov. The type strain of Mesoaciditoga lauensis is cd-1655R(T) ( = DSM 25116(T) = OCM 1212(T)).

Diversity and distribution of a key sulpholipid biosynthetic gene in marine microbial assemblages

Sulphoquinovosyldiacylglycerols (SQDG) are polar sulphur-containing membrane lipids, whose presence has been related to a microbial strategy to adapt to phosphate deprivation. In this study, we have targeted the sqdB gene coding the uridine 5'-diphosphate-sulphoquinovose (UDP-SQ) synthase involved in the SQDG biosynthetic pathway to assess potential microbial sources of SQDGs in the marine environment. The phylogeny of the sqdB-coding protein reveals two distinct clusters: one including green algae, higher plants and cyanobacteria, and another one comprising mainly non-photosynthetic bacteria, as well as other cyanobacteria and algal groups. Evolutionary analysis suggests that the appearance of UDP-SQ synthase occurred twice in cyanobacterial evolution, and one of those branches led to the diversification of the protein in members of the phylum Proteobacteria. A search of homologues of sqdB-proteins in marine metagenomes strongly suggested the presence of heterotrophic bacteria potential SQDG producers. Application of newly developed sqdB gene primers in the marine environment revealed a high diversity of sequences affiliated to cyanobacteria and Proteobacteria in microbial mats, while in North Sea surface water, most of the detected sqdB genes were attributed to the cyanobacterium Synechococcus sp. Lipid analysis revealed that specific SQDGs were characteristic of microbial mat depth, suggesting that SQDG lipids are associated with specific producers.

Hyperthermophilic archaea produce membrane vesicles that can transfer DNA

Thermococcales are hyperthermophilic archaea found in deep-sea hydrothermal vents. They have been recently reported to produce membrane vesicles (MVs) into their culture medium. Here, we have characterized the mode of production and determined the biochemical composition of MVs from two species of Thermococcales, Thermococcus gammatolerans and Thermococcus kodakaraensis. We observed that MVs are produced by a budding process from the cell membrane reminiscent of ectosome (microparticle) formation in eukaryotes. MVs and cell membranes from the same species have a similar protein and lipid composition, confirming that MVs are produced from cell membranes. The major protein present in cell membranes and MVs of both species is the oligopeptide binding protein OppA. This protein is also abundant in MVs from cells grown in minimal medium, suggesting that OppA could be involved in processes other than peptides scavenging. We have previously shown that MVs from Thermococcales harbour DNA and protect DNA against thermodegradation. Here, we show that T. kodakaraensis cells transformed with the shuttle plasmid pLC70 release MVs harbouring this plasmid. Notably, these MVs can be used to transfer pLC70 into plasmid-free cells, suggesting that MVs could be involved in DNA transfer between cells at high temperature.

Endosymbiotic heterocystous cyanobacteria synthesize different heterocyst glycolipids than free-living heterocystous cyanobacteria

The heterocysts of limnetic nitrogen-fixing filamentous cyanobacteria contain unique glycolipids in their cell wall that create the distinctive gas impermeability of the heterocyst cell wall as well as serve as biomarker lipids for these microbes. It has been assumed that marine free-living and endosymbiotic cyanobacteria synthesize the same glycolipids although they have not been investigated in any detail. Here we report the glycolipid composition of several marine free-living heterocystous cyanobacteria as well as the heterocystous endosymbiont Richelia intracellularis found in the biogeochemically important diatoms Hemiaulus hauckii and Hemiaulus membranaceus. In the marine cyanobacteria Nostoc muscorum and Calothrix sp., we detected the same glycolipids as found in freshwater representatives of these genera. However, we did not detect these glycolipids in the Hemiaulus-Richelia association. Instead, we identified glycolipids which comprised a C₅ sugar, ribose, rather than the C₆ sugars normally encountered in glycolipids of free-living cyanobacteria. In addition, the glycolipids had slightly longer chain lengths (C₃₀ and C₃₂ versus C₂₆ and C₂₈) in the aglycone moiety. The different glycolipid composition of the marine endosymbotic heterocystous cyanobacteria compared to their free-living counterparts may be an adaptation to the high intracellular O₂ concentrations within their host. These glycolipids may provide unique tracers for the presence of these microbes in marine environments and permit exploration of the evolutionary origins of these symbioses.

Comparison of intact polar lipid with microbial community composition of vent deposits of the Rainbow and Lucky Strike hydrothermal fields

The intact polar lipid (IPL) composition of twelve hydrothermal vent deposits from the Rainbow (RHF) and Lucky Strike hydrothermal fields (LSHF) has been investigated in order to assess its utility as a proxy for microbial community composition associated with deep-sea hydrothermal locations. Gene-based culture-independent surveys of the microbial populations of the same vent deposits have shown that microbial populations are different in the two locations and appear to be controlled by the geochemical and geological processes that drive hydrothermal circulation. Large differences in the IPL composition between these two sites are evident. In the ultramafic-hosted RHF, mainly archaeal-IPLs were identified, including those known to be produced by hyperthermophilic Euryarchaeota. More specifically, polyglycosyl derivatives of archaeol and macrocyclic archaeol indicate the presence of hyperthermophilic methanogenic archaea in the vent deposits, which are related to members of the Methanocaldococcaceae or Methanococcaceae. In contrast, bacterial IPLs dominate IPL distributions from LSHF, suggesting that bacteria are more predominant at LSHF than at RHF. Bacterial Diacyl glycerol (DAG) IPLs containing phosphocholine, phosphoethanolamine or phosphoglycerol head groups were identified at both vent fields. In some vent deposits from LSHF ornithine lipids and IPLs containing phosphoaminopentanetetrol head groups were also observed. By comparison with previously characterized bacterial communities at the sites, it is likely the DAG-IPLs observed derive from Epsilon- and Gammaproteobacteria. Variation in the relative amounts of archaeal versus bacterial IPLs appears to indicate differences in the microbial community between vent sites. Overall, IPL distributions appear to be consistent with gene-based surveys.