The genetic origin (abiogenic vs. biogenic, microbial vs. thermogenic), maturity of thermogenic component, compositional change due to migration, and extent of biodegradation of natural hydrocarbon gases in Japan are interpreted using carbon isotope compositions of methane, ethane and propane, and hydrocarbon molecular ratios. Mixing of gases with different origins or different maturities can also be evaluated using gas isotopic and molecular compositions. Abiogenic gas contribution is not detected in the natural gases. Most production gases are classified into thermogenic or mixed microbial/thermogenic except for some water-dissolved type gases of microbial origin. Ethane and propane carbon isotope compositions of thermogenic hydrocarbons are controlled largely by maturity. The gases in the Niigata Basin show generally higher maturity than the gases in the Akita/Yamagata Basin.
Carbon isotope analyses of headspace and/or mud gas can be used to delineate subsurface hydrocarbon reservoirs and to understand gas migration and accumulation processes. Carbon isotope compositions in commingled production could be used to allocate contributions from individual production zones if isotopic differences exist between the gases from the contributing reservoirs. Origin of gas seepage in production sites could be investigated by the gas molecular and isotope compositions if enough reference data exist in the area.

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Stable isotopic compositions of organic matters have been studied to investigate their sources and formation processes for various natural samples including meteorites, sediments and biological materials. In particular, compound-specific isotope analysis is a powerful means to distinguish kinetic and thermodynamic isotope effects for a series of PAH homologues in meteorite and exhaust samples as well as to clarify geochemical cycles of lipid biomarkers and their carbon and hydrogen sources associated with different metabolic pathways in sedimentary and biological samples. The compound-specific multi-isotope analysis will further provide better understanding for origins and occurrence of organic compounds in natural environments.

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Continuous-flow (on-line) system has revolutionized the study of natural stable isotope variations in organic matter and organic compounds. In particular, carbon and nitrogen isotope analysis of bulk samples using elemental analyzer/isotope ratio mass spectrometer (EA/IRMS) has been widely used in various field of studies, which allows a simple and rapid analysis of the isotope ratios for all types of organic and a wide range of inorganic samples, with a small amount of sample materials compared to the traditional off-line Dual-Inlet method. However, stability, accuracy, and precision on the observed isotope ratios strongly reflect various factors associated with continuous-flow system, such as peak intensity (i.e., sample weight), memory effect, and He dilution ratio. Unfortunately, the complete removal of such uncertainties should not be realistic, particularly in routine isotope measurements of a great number of samples. Here, we review the principles of stable isotope analysis on the traditional off-line Dual-Inlet and continuous-flow EA/IRMS methods, and also show an applicable calibration and standardization sequence. We hope that this paper is useful for routine application of EA/IRMS technique to various studies in geochemistry, ecology, biology, food science, and other area of sciences.

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Hydrogen and oxygen isotope analysis has become increasingly important as a potential powerful tool for the reconstruction of climatic conditions, the wildlife forensics and food authenticity. The development of thermal conversion elemental analyzer/isotope ratio mass spectrometer (TCEA/IRMS) facilitates a rapid and routine analysis of hydrogen and oxygen isotope ratios for a great number of samples. Despite a rapidly growing literature on applications of hydrogen and oxygen isotope ratios in geochemistry, ecology and food sciences, the lack of reliable technique to measure hydrogen and oxygen isotope ratios at organic materials is regrettable. In this paper, we review the technical fundamentals (e.g. calibration and standardization) in measurement of hydrogen and oxygen isotope ratios of organic materials. We also address an application to the authenticity of food and chemical materials.

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Herein I introduce "taphonomy" as a new methodology in organic geochemistry. Organogeochemical taphonomy treats analyses of both chemical transformation processes leading precursory biomolecules to fossil molecules as well as analyses of provenances of these fossilized molecules in space and time. As an introductory example, present paper analyzes the former "organic geochemical" taphonomy, focusing in particular on the early transformation reactions of chlorophylls leading to fossil porphyrin preservation. In chloropgments and their derivatives, the carbon atom located in the exocyclic five-membered ring adjacent to the carbonyl group is exceptionally nucleophilic, being a "weak point" of these molecules. This reaction center represents both α-position of the β-carbonyl ester system and benzyl position of the chloron/porphyrin aromatic system; hence its acidic proton is quite amenable to deprotonation in natural environment leading to generation of chlorin/porphyrin enolate anion. This stable enolate anion with delocalized paired electron over the aromatic macrocycle is subjected to extraction of an electron by triplet-state oxygen molecule, leading radical chain oxidation reactions and opening the exocyclic ring. In absence of molecular oxygen and other oxygen radical species, the enolate anion can undergo intramolecular Claissen condensation with electrophilic C-17 alkoxycarbnylethyl or carboxyvinyl functions. The resulted compounds, 13², 17³-cyclopheoforbide a enol and isochlorin e₆ esters, respectively, are conclusive precursors of certain fossil porphyrins that retains carbon skeletons of those rearranged exocyclic rings. Furthermore, demethoxycarbonylation at this reaction center reduces the reactivity of the original exocyclic ring, preventing formation of reactive enolate anion in natural environments. Interestingly, the demethoxycarbonylation is suggested to proceed in fact from chlorine/porphyrin enolate anion. Such transformations divert the fate of chloropigments to be preserved in the sedimentary record; inversely, intactness and rearrangement of the exocyclic ring found in the fossil porphyrins should reflect their process immediately after the death of the phototrophs in the geological timescale, hence possibly retaining environmental conditions or food-web structures in the water-sediment system at the time of sedimentation. Such taphonomical approaches in organic geochemistry should be increasingly important since compound-specific isotopic analyses of molecular fossils have recently been developing rapidly. Understanding of the taphonomy will bring out further potentials of compound-specific isotopic studies as paleoproxies for the past biological processes.

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There are few carbon isotope measurements of acetate in marine sediments, even though acetate could play important roles in biological activity as well as in the carbon cycle in marine sediments. In this study, abundance and carbon isotopic composition of water-soluble acetate are investigated using a surface sediment core (ca. 30cm) from the northwestern Pacific. A large ¹³C-depletion in acetate by up to 14‰ is observed with increasing depth, as the concentration of acetate decreases. The depletion could reflect a kinetic isotope effect during decarboxylation of pyruvate as the sediment becomes anoxic. On the other hand, there is no difference in ¹³C between acetate and total organic carbon (ca. -20.6‰) in the upper 13cm of the core, which suggests that the acetate could be produced by fermentative degradation of organic matter and quantitatively consumed. The carbon isotopic composition of acetate can be useful for better understanding the carbon cycle in marine sediments.

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Recent advances in the application of molecular approaches have emphasized our potentially underestimate of microbial diversity in natural environments and have revealed comprehensive biogeochemical processes. One of the biggest challenges for organic geochemists and/or microbial ecologists is to identify which organisms are carrying out a specific set of metabolic processes. To answer this fundamental question, stable isotope probing (SIP) together with compound-specific isotope analysis (CSIA) is a useful technique to understand the microbial ecology and its biogeochemical cycles. The method relies on the incorporation of a substrate that is highly enriched in a stable isotope such as ¹³C and¹⁵N, and the identification of specific molecular targets through active microorganisms in any environment. However, we have to pay attention about highly SI-enriched contamination problems and co-elution problems during pretreatment of chemical analysis and also in chromatographic procedures, which potentially prevent us from performing precise CSIA. Here, we point out quality control by wet chemical pre-treatment for precise compound-specific isotope analysis by isotope-ratio mass spectrometry coupled to gas chromatography and liquid chromatography. Not only in biogeochemical background but also from a scope of common welfare, CSIA technique is also widely useful tools for validation approaches in food material, anti-doping test, and environmental assessment. For further precise CSIA, we also discuss representative optimized analytical conditions of some model compounds including intact polar lipids (IPLs) with its derivatives, n-alkane, and amino acids.

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Biogeochemical processes involving acetate in sub-seafloor sediments were investigated by examining the stable carbon isotopic relationships of acetate and other relevant carbon-bearing materials (i.e., total organic carbon (TOC) and ΣCO₂) in five piston cores retrieved from the Sea of Okhotsk off Sakhalin Island, Russia. The cores were classified into two types on the basis of SO₄^2- content: (I) those with sulfate-reducing sediments in which the depletion of pore-water SO₄^2- with increasing depth was slight, and (II) those with methanogenic sediments in which SO₄^2- concentrations were less than 2mM more than 3m below the seafloor. Acetate was detected in all cores. The acetate content in methanogenic sediments (2.6-23.0μM) was relatively higher than in the sulfate-reducing sediment (2.8-8.8μM). In the sulfate-reducing sediments, the depth profiles of δ¹³C_acetate approximately parallel those of δ¹³C_TOC, with the δ¹³C_acetate values (-39‰ to -33‰) depleted by about 12‰ relative to δ¹³C_TOC (-24.5‰ to -22.3‰). These approximately parallel depth profiles suggest that the principal acetate production process in the sulfate-reducing sediments is fermentation of dissolved organic compounds. The fermentation products, however, tend to be similar or slightly enriched in ¹³C compared to their substrates. Therefore, the ¹³C depletion of acetate relative to TOC in the sulfate reduction zone suggests that some portion of the acetate was synthesized by acetogenesis in which the synthesized acetate is depleted in ¹³C compared with its precursor. Given the large contribution of land-derived organic matter in the studied sediments, organoautotrophic acetogenesis using the lignin-derived syringate monomer, which originates from land plants, is likely. In the methanogenic sediments, the δ¹³C_acetate values in sediments throughout the cores (-39‰ to -25‰) were depleted compared to δ¹³C_TOC (-25.5‰ to -21.4‰). This suggests some acetogenic contribution to the total acetate production. The depth profiles of δ¹³C_acetate in methanogenic sediments did not parallel those of either δ¹³C_TOC; or δ¹³C_ΣCO2, probably because of the mixed isotopic effect from some production and consumption processes; namely fermentation, acetogenesis, and acetoclastic methanogenesis.

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The traditional two-source linear mixing model, based on distinct ¹³C/¹²C signatures among sources and samples, has been widely used in a number of ecological dietary studies. This model is especially useful in the case that the elemental compositions (i.e. H, C, N, and O) are similar among sources (i.e. diets) and samples (i.e. animals). However, elemental compositions (e.g. C/N ratio) are commonly widely variable, which often leads to large errors in observed results and subsequent interpretations. In this study, we propose a modified mixing model, employing the ¹³C/¹²C ratio combined with the C/N ratio, to better evaluate the dietary properties of animals. As a case study, we investigate the relative contributions of riverine algae and terrestrial plants to the diets of aquatic insects, including five grazers and four filterers, in the Chikuma River, Japan. The traditional mixing model indicates that the algal contribution to aquatic insects ranges from 45% to 92%, whereas the modified mixing model yields values ranging from 64% to 97%. These results are in agreement with the C/N ratios of algae, plants, and aquatic insects (5.4±0.7, 13.4±3.3, and 4.9±0.5, respectively), indicating that the traditional mixing model may underestimate the algal contribution to aquatic insects. We suggest that the modified mixing model, using ¹³C/¹²C in combination with C/N, is better than traditional mixing models in terms of evaluating the contribution of various sources in animals, even in the case that elemental compositions are markedly different between animals and their diets.

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This study demonstrates the stable carbon isotope analysis of individual lignin phenols based on off-line degradation and derivatization by tetramethylammonium hydroxide (TMAH) thermochemolysis, semi-purification by high-performance liquid chromatography (HPLC), compound-specific isotope analysis (CSIA) by gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS), and isotope effect correction by isotope mass balance calculation. In GC/C/IRMS, we obtained the following optimal conditions to accurately and precisely determine the isotopic composition: combustion temperature of 1000℃, He carrier flow rate of 1.6mL min^-1, and injection amount of lignin phenols of 30-140ng. HPLC semi-purification using a normal-phase silica column with a column oven (at 30℃) can achieve baseline-separation of individual lignin phenols on the GC chromatogram without isotopic fractionation. Isotopic fractionation during TMAH derivatization can be corrected by the logarithmic correlation between the isotopic composition of the incorporated carbon during TMAH derivatization and the ratio of relative abundance between lignin phenols and TMAH reagents. By using this method, the carbon isotopic composition of individual lignin phenols can be determined within a standard deviation (1σ) of 0.2‰-0.9‰, making this method suitable for molecular isotope studies in the field of organic geochemistry.

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Bacteriohopanepolyols (BHPs) are pentacyclic triterpenoids synthesized by a diverse range of bacteria as cell membrane lipids. The presence of BHPs in sediments suggests in situ production of bacteria in sediments. If BHPs are more stable than previously thought, sedimentary BHP distributions might be useful for reconstruction of bacterial communities and productivity changes. Further research on BHP stabilities would shed light on the potential of BHP as life marker for deep subsurface bacteria and paleoenvironmental information.

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Anaerobic oxidation of methane (AOM) in the marine environment is meditated by three phylogenically distinct clusters of Archaea called ANME-1, 2 and 3 (Anaerobic Methane-Oxidizing Archaea: ANME). ANME-1 and ANME-2 can be distinguished with biomarker composition. Environmental regulation leading to the dominance of ANME-1 or ANME-2 is not clear.
In this study the author investigated the lipid biomarker composition of ANME at the selected seep sites with high methane flux to find the clues to potential niche occupation by the different type of ANME groups. Samples were collected from (1) Umitaka spur off Joetsu, (2) Ryuyo canyon off Tokai, (3) Kumanonada mud volcano, (4) Sagami bay off Hatsushima and (5) Kuroshima knoll. ANME-1 markers were detected in the samples from (1), (2) and (3). On the other hand, ANME-2 markers were detected in the samples from (4) and (5).
This study will be useful in identifying the environmental factors controlling the ANME community.

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