Molecular fossil record of elevated methane levels in late Pleistocene coastal waters

Methane fueled lake pelagic food webs in a Cretaceous greenhouse world

Methane (CH4) is a potent greenhouse gas but also an important carbon and energy substrate for some lake food webs. Understanding how CH4 incorporates into food webs is, therefore, crucial for unraveling CH4 cycling and its impacts on climate and ecosystems. However, CH4-fueled lake food webs from pre-Holocene intervals, particularly during greenhouse climates in Earth history, have received relatively little attention. Here, we present a long-term record of CH4-fueled pelagic food webs across the Cretaceous Oceanic Anoxic Event 1a (~120 Mya) that serves as a geological analog to future warming. We show an exceptionally strong expansion of both methanogens and CH4-oxidizing bacteria (up to 87% of hopanoid-producing bacteria) during this Event. Grazing on CH4-oxidizing bacteria by zooplankton (up to 47% of ciliate diets) within the chemocline transferred substantial CH4-derived carbon to the higher trophic levels, representing an important CH4 sink in the water column. Our findings suggest that as Earth warms, microbial CH4 cycling could restructure food webs and fundamentally alter carbon and energy flows and trophic pathways in lake ecosystems.

Lipidomic diversity and proxy implications of archaea from cold seep sediments of the South China Sea

Cold seeps on the continental margins are characterized by intense microbial activities that consume a large portion of methane by anaerobic methanotrophic archaea (ANME) through anaerobic oxidation of methane (AOM). Although ANMEs are known to contain unique ether lipids that may have an important function in marine carbon cycling, their full lipidomic profiles and functional distribution in particular cold-seep settings are still poorly characterized. Here, we combined the 16S rRNA gene sequencing and lipidomic approaches to analyze archaeal communities and their lipids in cold seep sediments with distinct methane supplies from the South China Sea. The archaeal community was dominated by ANME-1 in the moderate seepage area with strong methane emission. Low seepage area presented higher archaeal diversity covering Lokiarchaeia, Bathyarchaeia, and Thermoplasmata. A total of 55 core lipids (CLs) and intact polar lipids (IPLs) of archaea were identified, which included glycerol dialkyl glycerol tetraethers (GDGTs), hydroxy-GDGTs (OH-GDGTs), archaeol (AR), hydroxyarchaeol (OH-AR), and dihydroxyarchaeol (2OH-AR). Diverse polar headgroups constituted the archaeal IPLs. High concentrations of dissolved inorganic carbon (DIC) with depleted δ13CDIC and high methane index (MI) values based on both CLs (MICL) and IPLs (MIIPL) indicate that ANMEs were active in the moderate seepage area. The ANME-2 and ANME-3 clades were characterized by enhanced glycosidic and phosphoric diether lipids production, indicating their potential role in coupling carbon and phosphurus cycling in cold seep ecosystems. ANME-1, though representing a smaller proportion of total archaea than ANME-2 and ANME-3 in the low seepage area, showed a positive correlation with MIIPL, indicating a different mechanism contributing to the IPL-GDGT pool. This also suggests that MIIPL could be a sensitive index to trace AOM activities performed by ANME-1. Overall, our study expands the understanding of the archaeal lipid composition in the cold seep and improves the application of MI using intact polar lipids that potentially link to extent ANME activities.

Coupled Simulation of Hydrate-Bearing and Overburden Sedimentary Layers to Study Hydrate Dissociation and Methane Leakage

Methane leakage during natural gas hydrate (NGH) exploitation is one of the important challenges restricting its safe development, which necessitates further investigation. However, only a few experimental studies have been conducted to characterize the relationship between methane (CH4) leakage and NGH exploitation. The CH4 leakage mechanism and controlling factors in the hydrate dissociation process are still unclear. A coupled simulator has been developed to study the CH4 hydrate exploitation and the possible leakage of CH4. The new system overcomes the difficulty of constructing hydrate-free overlying strata and seawater in previous studies and can simulate the in situ natural environment containing hydrate reservoirs, overlying strata and overlying seawater as well. In addition, the simulator integrates the spatial distribution of temperature, pressure and electric resistance in hydrate reservoir systems, and allows for the visual monitoring of the overlying strata and the sampling of overburden gas and liquids. The effectiveness of the coupled simulations was verified through experimental testing. The coupled simulations allowed for the characterization of the CH4 leakage mechanism and can be used to develop safe strategies for NGH exploitation.

Deep-Sea Sediment and Water Simulator for Investigation of Methane Seeping and Hydrate Formation

The ubiquitous methane seeping process in the deep-sea environment could significantly influence the global methane cycle and carbon budget. Hydrate formation on the methane bubble during the seeping process is an important way for sequestrating methane during bubble migration. Uncovering the complete methane leakage process needs to reveal the methane leakage pathway and hydrate conversion mechanism. Hence, we built a deep-sea sediment and water simulator to investigate the methane seeping and hydrate formation. The simulator can mimic the deep-sea sediment and water environment with a lower sediment chamber and an upper seawater chamber. The monitoring of the bubble migration path and hydrate transformation and aggregation in the sediment chamber is realized mainly through the spatial distribution of electric resistance and temperature variations. The seawater chamber is equipped with a built-in movable camera and four external windows to observe the rising and morphological evolution of gas and hydrate bubbles. The quantitative storage and escape of CH4 gas could be realized through the measurement of multiple gas/liquid collection ports and cumulative incoming/outgoing gas volume. In addition, a movable biological liquid injection port was designed in the seawater chamber for the coupling CH4 conversion of hydrate formation and microorganism-mediated oxidation. Through the experimental test on each function of the system, the effectiveness of the device was proved. The development of this device has pioneering significance for the experimental simulation of the methane seeping process in a simulated submarine cold spring area.

Unique Authigenic Mineral Assemblages and Planktonic Foraminifera Reveal Dynamic Cold Seepage in the Southern South China Sea

Many cold seeps and gas hydrate areas have not been discovered beside the Beikan basin in the southern South China Sea (SCS), and their characteristics and histories also remain poorly known. Here we describe authigenic minerals and the carbon and oxygen isotopic composition of planktonic foraminifera Globigerinoides ruber from sediment core 2PC, recovered from the gas hydrate zone of the Nansha Trough, southern SCS, to elucidate its history of dynamic cold seepage. We infer that the occurrence of authigenic gypsum crystals and pyrite concretions, and anomalously negative δ13C values of Globigerinoides ruber, reflect paleo-methane seepage. Two major methane release events were identified, based on remarkable excursions in foraminifera δ13C at depths of 150–250 cm and 350–370 cm. Euhedral gypsum crystals and tubular pyrite concretions co-occur with extremely negative planktonic foraminifera δ13C values, indicating a shift in the sulfate methane transition zone and a change in the methane flux. Our data suggest that authigenic mineral assemblages and δ13C values of planktonic foraminifera provide a valuable tool in elucidating the characteristics of dynamic methane seepage in a marine environment.

Life on the edge: active microbial communities in the Kryos MgCl2-brine basin at very low water activity

The Kryos Basin is a deep-sea hypersaline anoxic basin (DHAB) located in the Eastern Mediterranean Sea (34.98°N 22.04°E). It is filled with brine of re-dissolved Messinian evaporites and is nearly saturated with MgCl₂-equivalents, which makes this habitat extremely challenging for life. The strong density difference between the anoxic brine and the overlying oxic Mediterranean seawater impedes mixing, giving rise to a narrow chemocline. Here, we investigate the microbial community structure and activities across the seawater-brine interface using a combined biogeochemical, next-generation sequencing, and lipid biomarker approach. Within the interface, we detected fatty acids that were distinctly ¹³C-enriched when compared to other fatty acids. These likely originated from sulfide-oxidizing bacteria that fix carbon via the reverse tricarboxylic acid cycle. In the lower part of the interface, we also measured elevated rates of methane oxidation, probably mediated by aerobic methanotrophs under micro-oxic conditions. Sulfate reduction rates increased across the interface and were highest within the brine, providing first evidence that sulfate reducers (likely Desulfovermiculus and Desulfobacula) thrive in the Kryos Basin at a water activity of only ~0.4 A_w. Our results demonstrate that a highly specialized microbial community in the Kryos Basin has adapted to the poly-extreme conditions of a DHAB with nearly saturated MgCl₂ brine, extending the known environmental range where microbial life can persist.

Assessment of sediment hydrocarbon contamination from the 2009 Montara oil blow out in the Timor Sea

In August 2009, a blowout of the Montara H1 well 260 km off the northwest coast of Australia resulted in the uncontrolled release of about 4.7 M L of light crude oil and gaseous hydrocarbons into the Timor Sea. Over the 74 day period of the spill, the oil remained offshore and did not result in shoreline incidents on the Australia mainland. At various times slicks were sighted over a 90,000 km(2) area, forming a layer of oil which was tracked by airplanes and satellites but the slicks typically remained within 35 km of the well head platform and were treated with 183,000 L of dispersants. The shelf area where the spill occurred is shallow (100-200 m) and includes off shore emergent reefs and cays and submerged banks and shoals. This study describes the increased inputs of oil to the system and assesses the environmental impact. Concentrations of hydrocarbon in the sediment at the time of survey were very low (total aromatic hydrocarbons (PAHs) ranged from 0.04 to 31 ng g(-1)) and were orders of magnitude lower than concentrations at which biological effects would be expected.

Structures, Stabilities, and Spectra Properties of Fused CH4 Endohedral Water Cage (CH4)m(H2O)n Clusters from DFT-D Methods

In order to understand the cage fusion behavior during the nucleation processes of methane hydrate (MH), methane-encapsulated double-cage clusters (CH4)2(H2O)n (n = 30-43) and several multicage structures with three or more cages were studied employing DFT-D methods. We find that almost all the lowest-energy double-cage structures can be constructed by merging the most stable structures of the monocage clusters CH4(H2O)n (n = 18-24). Double-cage structures can achieve higher stability through sharing a hexagon than a pentagon, which may be applicable to larger fused cage clusters. The preference of hexagons during cage fusion should be favorable for the appearance of the cages including hexagons such as the 5(12)6(2), 5(12)6(4) cages during the MH nucleation process. The symmetric C-H stretching modes of methane molecules in the double-cage structures show a clear trend of red shift with increasing size of the composing monocages. Compared with the case of monocages, the stretching frequencies of methane molecules in double-cage structures shift slightly, indicating variation of monocage configuration when cage fusion occurs. The larger multicage structures are found to possess higher fusion energies through sharing more polygons. Their thermodynamic stabilities do not simply increase with the number of fused monocages and are affected by the spatial arrangement of the building cages.

Recent advances in hopanoids analysis: Quantification protocols overview, main research targets and selected problems of complex data exploration

Pentacyclic triterpenoids, particularly hopanoids, are organism-specific compounds and are generally considered as useful biomarkers that allow fingerprinting and classification of biological, environmental and geological samples. Simultaneous quantification of various hopanoids together with battery of related non-polar and low-molecular mass compounds may provide principal information for geochemical and environmental research focusing on both modern and ancient investigations. Target compounds can be derived from microbial biomass, water columns, sediments, coals, crude fossils or rocks. This create number of analytical problems due to different composition of the analytical matrix and interfering compounds and therefore, proper optimization of quantification protocols for such biomarkers is still the challenge. In this work we summarizing typical analytical protocols that were recently applied for quantification of hopanoids like compounds from different samples. Main steps including components of interest extraction, pre-purification, fractionation, derivatization and quantification involving gas (1D and 2D) as well as liquid separation techniques (liquid-liquid extraction, solid-phase extraction, planar and low resolution column chromatography, high-performance liquid chromatography) are described and discussed from practical point of view, mainly based on the experimental papers that were published within last two years, where significant increase in hopanoids research was noticed. The second aim of this review is to describe the latest research trends concerning determination of hopanoids and related low-molecular mass lipids analyzed in various samples including sediments, rocks, coals, crude oils and plant fossils as well as stromatolites and microbial biomass cultivated under different conditions. It has been found that majority of the most recent papers are based on uni- or bivariate approach for complex data analysis. Data interpretation involves number of physicochemical parameters and hopanoids quantities or given biomarkers mass ratios derived from high-throughput separation and detection systems, typically GC-MS and HPLC-MS. Based on quantitative data reported in recently published experimental works it has been demonstrated that multivariate data analysis using e.g. principal components computations may significantly extend our knowledge concerning proper biomarkers selection and samples classification by means of hopanoids and related non-polar compounds.

Ultra-high-resolution paleoenvironmental records via direct laser-based analysis of lipid biomarkers in sediment core samples

Marine microorganisms adapt to their habitat by structural modification of their membrane lipids. This concept is the basis of numerous molecular proxies used for paleoenvironmental reconstruction. Archaeal tetraether lipids from ubiquitous marine planktonic archaea are particularly abundant, well preserved in the sedimentary record and used in several molecular proxies. We here introduce the direct, extraction-free analysis of these compounds in intact sediment core sections using laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). LDI FTICR-MS can detect the target lipids in single submillimeter-sized spots on sediment sections, equivalent to a sample mass in the nanogram range, and could thus pave the way for biomarker-based reconstruction of past environments and ecosystems at subannual to decadal resolution. We demonstrate that ratios of selected archaeal tetraethers acquired by LDI FTICR-MS are highly correlated with values obtained by conventional liquid chromatography/MS protocols. The ratio of the major archaeal lipids, caldarchaeol and crenarchaeol, analyzed in a 6.2-cm intact section of Mediterranean sapropel S1 at 250-µm resolution (∼ 4-y temporal resolution), provides an unprecedented view of the fine-scale patchiness of sedimentary biomarker distributions and the processes involved in proxy signal formation. Temporal variations of this lipid ratio indicate a strong influence of the ∼ 200-y de Vries solar cycle on reconstructed sea surface temperatures with possible amplitudes of several degrees, and suggest signal amplification by a complex interplay of ecological and environmental factors. Laser-based biomarker analysis of geological samples has the potential to revolutionize molecular stratigraphic studies of paleoenvironments.

Microbial community in a sediment-hosted CO2 lake of the southern Okinawa Trough hydrothermal system

Increasing levels of CO2 in the atmosphere are expected to cause climatic change with negative effects on the earth's ecosystems and human society. Consequently, a variety of CO2 disposal options are discussed, including injection into the deep ocean. Because the dissolution of CO2 in seawater will decrease ambient pH considerably, negative consequences for deep-water ecosystems have been predicted. Hence, ecosystems associated with natural CO2 reservoirs in the deep sea, and the dynamics of gaseous, liquid, and solid CO2 in such environments, are of great interest to science and society. We report here a biogeochemical and microbiological characterization of a microbial community inhabiting deep-sea sediments overlying a natural CO2 lake at the Yonaguni Knoll IV hydrothermal field, southern Okinawa Trough. We found high abundances (>10(9) cm(-3)) of microbial cells in sediment pavements above the CO2 lake, decreasing to strikingly low cell numbers (10(7) cm(-3)) at the liquid CO2/CO2-hydrate interface. The key groups in these sediments were as follows: (i) the anaerobic methanotrophic archaea ANME-2c and the Eel-2 group of Deltaproteobacteria and (ii) sulfur-metabolizing chemolithotrophs within the Gamma- and Epsilonproteobacteria. The detection of functional genes related to one-carbon assimilation and the presence of highly 13C-depleted archaeal and bacterial lipid biomarkers suggest that microorganisms assimilating CO2 and/or CH4 dominate the liquid CO2 and CO2-hydrate-bearing sediments. Clearly, the Yonaguni Knoll is an exceptional natural laboratory for the study of consequences of CO2 disposal as well as of natural CO2 reservoirs as potential microbial habitats on early Earth and other celestial bodies.

Microbiological investigation of methane- and hydrocarbon-discharging mud volcanoes in the Carpathian Mountains, Romania

Paclele Mici is a terrestrial mud volcano field located in the Carpathian Mountains (Romania), where thermal alteration of sedimentary organic compounds leads to methane, higher hydrocarbons and other petroleum compounds that are continuously released into the environment. The hydrocarbons represent potential substrates for microorganisms. We studied lipid biomarkers, stable isotope ratios, the effect of substrate (methane, other organic compounds) addition and 16S rRNA genes to gain insights into the hitherto unknown microbial community at this site. Quantitative real-time polymerase chain reaction analysis demonstrated that bacteria were much more abundant than archaea. Phylogenetic analyses of 16S rDNA clone sequences indicated the presence of bacterial and archaeal lineages generally associated with the methane cycle (methanogens, aerobic and anaerobic methanotrophs), the sulfur cycle (sulfate reducers), and groups linked to the anaerobic degradation of alkanes or aromatic hydrocarbons. The presence of sulfate reducers, methanogens and methanotrophs in this habitat was also confirmed by concurrent surveys of lipid biomarkers and their isotopic signatures. Incubation experiments with several common and complex substrates revealed the potential of the indigenous microbial community for sulfate reduction, methanogenesis and aerobic methanotrophy. Additionally, consistently to the detection of methane-oxidizing archaea (ANME) and 13C-depleted archaeal lipids, a weak but significant activity of anaerobic methane oxidation was measured by radiotracer techniques and in vitro. This survey is the first to report the presence and activity of ANME in a terrestrial environment.

Evidence for large methane releases to the atmosphere from deep-sea gas-hydrate dissociation during the last glacial episode

Past atmospheric methane-concentration oscillations recorded in polar ice cores vary together with rapid global climatic changes during the last glacial episode. In the "clathrate gun hypothesis," massive releases of deep-sea methane from marine gas-hydrate dissociation led to these well known, global, abrupt warmings in the past. If evidence for such releases in the water column exists, however, the mechanism and eventual transfer to the atmosphere has not yet been documented clearly. Here we describe a high-resolution marine-sediment record of stable carbon isotopic changes from the Papua Gulf, off Papua New Guinea, which exhibits two extremely depleted excursions (down to -9 per thousand ) at approximately 39,000 and approximately 55,000 years. Morphological, isotopic, and trace metal evidence dismisses authigenic calcite as the main source of depleted carbon. Massive methane release associated with deep-sea gas-hydrate dissociation is the most likely cause for such large depletions of delta(13)C. The absence of a delta(13)C gradient in the water column during these events implies that the methane rose through the entire water column, reaching the sea-air interface and thus the atmosphere. Foraminiferal delta(18)O composition suggests that the rise of the methane in the water column created an upwelling flow. These inferred emission events suggest that during the last glacial episode, this process was likely widespread, including tropical regions. Thus, the release of methane from the ocean floor into the atmosphere cannot be dismissed as a strong positive feedback in climate dynamics processes.

Evidence for rapid climate change in the Mesozoic-Palaeogene greenhouse world

The best-documented example of rapid climate change that characterized the so-called 'greenhouse world' took place at the time of the Palaeocene-Eocene boundary: introduction of isotopically light carbon into the ocean-atmosphere system, accompanied by global warming of 5-8 degrees C across a range of latitudes, took place over a few thousand years. Dissociation, release and oxidation of gas hydrates from continental-margin sites and the consequent rapid global warming from the input of greenhouses gases are generally credited with causing the abrupt negative excursions in carbon- and oxygen-isotope ratios. The isotopic anomalies, as recorded in foraminifera, propagated downwards from the shallowest levels of the ocean, implying that considerable quantities of methane survived upward transit through the water column to oxidize in the atmosphere. In the Mesozoic Era, a number of similar events have been recognized, of which those at the Triassic-Jurassic boundary, in the early Toarcian (Jurassic) and in the early Aptian (Cretaceous) currently carry the best documentation for dramatic rises in temperature. In these three examples, and in other less well-documented cases, the lack of a definitive time-scale for the intervals in question hinders calculation of the rate of environmental change. However, comparison with the Palaeocene-Eocene thermal maximum (PETM) suggests that these older examples could have been similarly rapid. In both the early Toarcian and early Aptian cases, the negative carbon-isotope excursion precedes global excess carbon burial across a range of marine environments, a phenomenon that defines these intervals as oceanic anoxic events (OAEs). Osmium-isotope ratios ((187)Os/(188)Os) for both the early Toarcian OAE and the PETM show an excursion to more radiogenic values, demonstrating an increase in weathering and erosion of continental crust consonant with elevated temperatures. The more highly buffered strontium-isotope system ((87)Sr/(86)Sr) also shows relatively more radiogenic signatures during the early Toarcian OAE, but the early Aptian and Cenomanian-Turonian OAEs show the reverse effect, implying that increased rates of sea-floor spreading and hydrothermal activity dominated over continental weathering in governing sea-water chemistry. The Cretaceous climatic optimum (late Cenomanian to mid Turonian) also shows evidence for abrupt cooling episodes characterized by episodic invasion of boreal faunas into temperate and subtropical regions and changes in terrestrial vegetation; drawdown of CO(2) related to massive marine carbon burial (OAE) may be implicated here. The absence of a pronounced negative carbon-isotope excursion preceding the Cenomanian-Turonian OAE indicates that methane release is not necessarily connected to global deposition of marine organic carbon, but relative thermal maxima are common to all OAEs. 'Cold snaps' have also been identified from the Mesozoic record but their duration, causes and effects are poorly documented.