Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients

There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator

Geological characterization of a lower Cambrian marine shale: implications for shale gas potential in North-Western Hunan, South China

We have investigated the geologic features of the lower Cambrian-aged Niutitang Shale in the northwestern Hunan province of South China. Our results indicate that the Niutitang Shale has abundant and highly mature algal kerogen with total organic carbon (TOC) content ranging from 0.6% to 18.2%. The equivalent vitrinite reflectance (equal-Ro) value is between 2.5% and 4.3%. Mineral constituents are dominated by quartz and clay. The average quartz content (62.8%) is much higher than that of clay minerals (26.1%), and this suggests a high brittleness index. Organic-matter pores, interparticle pores, intraparticle pores, interlaminated fractures, and structural fractures are all well developed. The porosity ranges from 0.6% to 8.8%, with an average of 4.8%, whereas the permeability varies from 0.0018 to [Formula: see text] (microdarcy) (averaging [Formula: see text]). The porosity of TOC- and clay-rich shale samples is generally higher than that of quartz-rich shale samples. The gas adsorption capacity of the Niutitang Shale varies from 2.26 to [Formula: see text], with a mean value of [Formula: see text]. The TOC content appears to significantly influence gas adsorption capacity. In general, TOC-rich samples exhibit a much higher adsorption capacity than TOC-poor samples. </jats:p

Organic matter provenance and depositional environment of marine-to-continental mudstones and coals in eastern Ordos Basin, China—Evidence from molecular geochemistry and petrology

Cyclothems, composed of interbedded mudstone, coal and sandstone layers, make up the Taiyuan and Shanxi Formations in the Late Carboniferous to Early Permian in North China under a marine-to-continental depositional environment. The cyclothems act as important fossil energy hosts, such as coalbeds, hydrocarbon source rocks and unconventional natural gas reservoirs. Organic geochemistry and petrology of mudstones and coals in the Taiyuan and Shanxi Formations in the eastern Ordos Basin were studied to reveal the organic matter sources and paleoenvironments. Total organic carbon (TOC) contents vary from 1.1 wt% (mudstone) to 72.6 wt% (coal). The samples are mainly within the oil window, with the Tmax values ranging from 433 to 469 °C. Organic petrology and source biomarkers indicate that the mudstones were sourced from a mixed organic matter input, and terrigenous organic matter predominates over aquatic organic matter. The coals are mostly sourced by terrigenous organic matter inputs. High concentrations of hopanes argue for a strong bacterial input. Some m/z 217 mass chromatograms have peaks at the hopanes' retention times as a result of high hopane to sterane ratios. These hopane-derived peaks do not interfere the identification of the steranes because the hopanes and the steranes have different retention times. Maturity-dependent biomarkers demonstrate that the samples have been thermally mature, which agree with the Tmax values. Anomalously low C29 20S/(20S + 20R) and C29 ββ/(ββ + αα) sterane ratios are present in all the samples, and are interpreted as due to the terrigenous organic matter input or the coal-related depositional environment. In addition, biomarkers and iron sulfide morphology indicate that the organic matter of the mudstones deposited in a proximal setting with shallow, brackish/fresh water bodies. With consideration of preservation of organic matter, the redox conditions are dysoxic. Redox oscillations resulted in the records of oxic conditions in some samples. Finally, the coals and the mudstones mainly generate gas and have poor oil generative potential

Effect of Water Saturation on Gas-Accessible Effective Pore Space in Gas Shales

AbstractThe existence and content of water will certainly affect the effective pore space of shales and therefore is a key point for the evaluation of in-situ gas content and gas flow capacity of shale reservoirs. In order to reasonably evaluate the gas storage and flow capacities of water-bearing shale reservoirs, the effect of water on the effective pore space of shales needs to be understood. In this study, the Upper Permian Longtan shale in the southeastern Sichuan Basin, China, was selected as an example to conduct nuclear magnetic resonance cryoporometry (NMRC) measurements under different water saturation levels. The gas-accessible effective pore spaces in shales under different water saturation levels were quantified, and the effect of water saturation on gas-accessible effective pore space in shales was investigated. The results show that water plays an important role in the gas-accessible effective pore space of shales. When the Longtan shale increases from a dry state to a water saturation of 65%, 75%, and 90%, the gas-accessible effective pore volume decreases by 35%-60% (average 46.3%), 50%-70% (average 58.8%), and 65%-82% (average 75.8%), respectively. Water has an effect on the gas-accessible effective pore space regardless of pore size, and the effect is the strongest in the 4-100 nm range, which may be mainly due to the high content of clay minerals in the Longtan shale. Our studies are of important theoretical significance and application prospects for accurately evaluating the gas-accessible effective pore space of gas shales under actual geological conditions

The Msx1 Homeoprotein Recruits G9a Methyltransferase to Repressed Target Genes in Myoblast Cells

Although the significance of lysine modifications of core histones for regulating gene expression is widely appreciated, the mechanisms by which these modifications are incorporated at specific regulatory elements during cellular differentiation remains largely unknown. In our previous studies, we have shown that in developing myoblasts the Msx1 homeoprotein represses gene expression by influencing the modification status of chromatin at its target genes. We now show that genomic binding by Msx1 promotes enrichment of the H3K9me2 mark on repressed target genes via recruitment of G9a histone methyltransferase, the enzyme responsible for catalyzing this histone mark. Interaction of Msx1 with G9a is mediated via the homeodomain and is required for transcriptional repression and regulation of cellular differentiation, as well as enrichment of the H3K9me2 mark in proximity to Msx1 binding sites on repressed target genes in myoblast cells as well as the developing limb. We propose that regulation of chromatin status by Msx1 recruitment of G9a and other histone modifying enzymes to regulatory regions of target genes represents an important means of regulating the gene expression during development

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Schiefergaspotenzial der wichtigen marinen Schieferformationen in der Oberen Yangtze Plattform im Süden Chinas

Die Schieferformationen des Ediacarium (Oberes Sinian), Unterkambrium und Untersilur der Oberen Yangtze Plattform (OYP) im Süden Chinas sind vielversprechende Schiefergasvorkommen. Die hier vorgelegte Arbeit, in Form einer Dissertation, beabsichtigt es den Gasvorrat und die sogenannte frackability dieser Schieferformationen zu evaluieren. Angefangen mit einer detaillierten Untersuchung der geologischen Gegebenheiten und dem Sedimentationsverlauf, wurde eine umfassende Studie mit Fokus auf organochemische, Petroleum-physikalische, petrophysikalische und felsmechanische Attribute, Methan-Sorptionsvermögen, mineralogische Komponenten und Lithofazies der Schiefer durchgeführt. Der gemessene gesamtorganische Kohlenstoff (TOC) betrug meistens über 2%, durchschnittlich 5%. Das Kerogen hat die Metagenese-Phase bereits erreicht, demnach sind die Pyrolysate geprägt durch leichte Kohlenwasserstoffe. Vermutlich besteht das ursprüngliche organische Material überdurschnittlich aus wasserstoffreichem Kerogen und wurde unter marinen Bedingungen mit selektiver Ansammlung von Algen abgelagert. Dies bedeutet, dass die OYP-Schiefer ursprünglich exzellentes Kohlenwasserstoffgenerationspotenzial basaßen. Der errechnete Beginn (Umwandlungsrate TR=10%) und das errechnete Ende (TR=90%) der Gesamtkohlenwasserstoffgenese liegen jeweils bei 120°C und 165°C bei einer geologischen Heizrate von 1.5°C/Ma. Die Position des Schieferreservoirs innerhalb des Sedimentbeckens weist darauf hin, dass der Sättigungsdruck stets unterhalb des Reservoirdrucks war und dass Fluide im Schieferreservoir nur als einzelne, untersättigte Phase während der gesamten Maturitätsentwicklung existierten. Ergebnisse von Hochdruck- (bis zu 25 MPa) Methan-Sorptions-Isothermen deuten darauf hin, dass die maximale Methan-Überschuss-Sorption der Proben zwischen 0.036 und 0.210 mmol/g Gestein schwankt. Die Lanmuir-Sorptionskapazität reicht von 0.077 bis 0.310 mmol/g Gestein. Die Form der Sorptionsisothermen und damit auch die Methansorptionskapazität variieren von Probe zu Probe. Dies könnte durch TOC-Gehalt, thermische Reife, Tonminerale, Feuchtegehalt, Poreneigenschaften, Partikelgröße, sowie angewandte Temperaturen und Drücke beeinflusst worden sein. Die Gesamtmineralogie aller drei Formationen ist kennzeichnet durch einen hohen Quarz-, niedrigen Ton- und sehr niedrigen bis nichtvorhandenen Karbonatgehalt. Lithologisch gesehen dominieren laminierte und nicht-laminierte kieselige Mudstones mit eher geringerfrequenten Zuschaltungen anderer Lithotypen. Poren weisen generell Nanometer- bis Mikrometer-Größen auf, wobei das organische Material reichliche Porenräume aufweist. Die meisten der gemessenen Proben haben Porositäten von weniger als 4%. Trotzdem gibt es einige Proben mit Porositäten über 10%. Die Permeabilität ist extrem niedrig und Helium-Permeabilitätskoeffizienten (Klinkenberg korrigierter Permeabilitätskoeffizient) sind kleiner als 20.2 nD (nano-Darcy, ~2×10-20 m2). Die felsmechanischen Eigenschaften der Proben sind gekennzeichnet durch hoch-brüchiges Verhalten. Dies geht mit hohen Druck- und Zugfestigkeiten, sowie elastischen Merkmalen einher. Der Unterkambrische Schiefer ist im Allgemeinen brüchiger als der untersilurische Schiefer. Dennoch hängen die felsmechanischen Eigenschaften der gemessenen Proben insgesamt von der Mineralzusammensetzung und von physikalischen Merkmalen ab.The Ediacaran (Upper Sinian), Lower Cambrian, and Lower Silurian marine shale formations in the Upper Yangtze Platform, south China are promising shale gas plays. The work presented in this dissertation aims to evaluate their gas-in-place and fraccability. Beginning with a detailed investigation on the geological setting and sedimentary history, a comprehensive study was then conducted focusing on the organic geochemical characteristics, petroleum physical properties, methane sorptive capacity, mineralogical constituents, lithofacies, petrophysical features, and rock mechanical properties of the shales. Measured total organic carbon (TOC) is mainly higher than 2%, and averages 5%. The kerogen has evolved into the metagenesis stage, and thus pyrolysates are dominated by light hydrocarbons. The original organic matter is presumably dominated by hydrogen-rich kerogen deposited under marine conditions via selective accumulation of algal material, which implies a massive original hydrocarbon potential. The onset (transformation ratio TR=10%) and end (TR=90%) of bulk hydrocarbon generation was calculated to take place at 120°C and 165°C respectively for an assumed average geological heating rate of 1.5°C/Ma. The shale reservoir position within the sedimentary basin indicates that the bubble point pressure was always below the reservoir pressure, and fluids in the shale reservoir occurred only as a single, undersaturated phase throughout maturation history. Results of the high pressure (up to 25 MPa) methane sorption isotherms indicate that the maximum methane excess sorption is between 0.036 and 0.210 mmol/g rock, while the Langmuir sorption capacity ranges from 0.077 to 0.310 mmol/g rock. The shape of sorption isotherms and thus methane sorption capacity vary from sample to sample, which can be affected by the TOC content, thermal maturity, clay mineral, moisture content, pore properties, particle size, as well as the applied temperature and pressure. The bulk mineralogy of all three formations is dominated by a high proportion of quartz, low content of clay, and rare or non-existent content of carbonates. Lithologically, laminated and non-laminated siliceous mudstones predominate, with minor contributions of other lithotypes. Pores generally have diameters in the nanometer to micrometer range, and abundant pores are found within organic matter. Most of the measured samples have porosities less than 4%, although a few samples show porosity in excess of 10%. Permeability is extremely low, and helium permeability coefficients are less than 20.2 nD (nano-Darcy, ~2×10-20 m2). The rock mechanical properties of the samples are characterised by a highly brittle behaviour, which coincides with their high compressive and tensile strengths and elastic properties. The Lower Cambrian shale is generally more brittle than the Lower Silurian shales. The rock mechanical properties of the measured samples, however, depend on the overall mineral compositions and physical properties

Application of waveform stacking methods for seismic location at multiple scales

Seismic source location specifies the spatial and temporal coordinates of seismic sources and lays the foundation for advanced seismic monitoring at all scales. In this work, we firstly introduce the principles of diffraction stacking (DS) and cross-correlation stacking (CCS) for seismic location. The DS method utilizes the travel time from the source to receivers, while the CCS method considers the differential travel time from pairwise receivers to the source. Then, applications with three field datasets ranging from small-scale microseismicity to regional-scale induced seismicity are presented to investigate the feasibility, imaging resolution, and location reliability of the two stacking operators. Both of the two methods can focus the source energy by stacking the waveforms of the selected events. Multiscale examples demonstrate that the imaging resolution is not only determined by the inherent property of the stacking operator but also highly dependent on the acquisition geometry. By comparing to location results from other methods, we show that the location bias is consistent with the scale size, as well as the frequency contents of the seismograms and grid spacing values