Nitrogen K-edge X-ray adsorption near-edge structure spectroscopy of chemically adsorbed ammonia gas on clay minerals and the 15N/14N-nitrogen isotopic fractionation.

Ammonia (NH3) is a simple and essential nitrogen carrier in the universe. Its adsorption on mineral surfaces is an important step in the synthesis of nitrogenous organic molecules in extraterrestrial environments. The nitrogen isotopic ratios provide a useful tool for understanding the formation processes of N-bearing molecules. In this study, adsorption experiments were conducted using gaseous NH3 and representative clay minerals. The strongly adsorbed NH3 was 15N-enriched in a state of chemical equilibrium between the adsorption and desorption on the siliceous host surface. The nitrogen K-edge X-ray adsorption near-edge structure spectroscopy study revealed that these initial ammonia gases were chemically adsorbed as ammonium ions (NH4+) on clay minerals.

Polycyclic aromatic hydrocarbons in samples of Ryugu formed in the interstellar medium.

Polycyclic aromatic hydrocarbons (PAHs) contain ≲20% of the carbon in the interstellar medium. They are potentially produced in circumstellar environments (at temperatures ≳1000 kelvin), by reactions within cold (~10 kelvin) interstellar clouds, or by processing of carbon-rich dust grains. We report isotopic properties of PAHs extracted from samples of the asteroid Ryugu and the meteorite Murchison. The doubly-13C substituted compositions (Δ2×13C values) of the PAHs naphthalene, fluoranthene, and pyrene are 9 to 51‰ higher than values expected for a stochastic distribution of isotopes. The Δ2×13C values are higher than expected if the PAHs formed in a circumstellar environment, but consistent with formation in the interstellar medium. By contrast, the PAHs phenanthrene and anthracene in Ryugu samples have Δ2×13C values consistent with formation by higher-temperature reactions.

Chemical evolution of primordial salts and organic sulfur molecules in the asteroid 162173 Ryugu.

Samples from the carbonaceous asteroid (162173) Ryugu provide information on the chemical evolution of organic molecules in the early solar system. Here we show the element partitioning of the major component ions by sequential extractions of salts, carbonates, and phyllosilicate-bearing fractions to reveal primordial brine composition of the primitive asteroid. Sodium is the dominant electrolyte of the salt fraction extract. Anions and NH4+ are more abundant in the salt fraction than in the carbonate and phyllosilicate fractions, with molar concentrations in the order SO42- > Cl- > S2O32- > NO3- > NH4+. The salt fraction extracts contain anionic soluble sulfur-bearing species such as Sn-polythionic acids (n < 6), Cn-alkylsulfonates, alkylthiosulfonates, hydroxyalkylsulfonates, and hydroxyalkylthiosulfonates (n < 7). The sulfur-bearing soluble compounds may have driven the molecular evolution of prebiotic organic material transforming simple organic molecules into hydrophilic, amphiphilic, and refractory S allotropes.

Application of a porous graphitic carbon column to carbon and nitrogen isotope analysis of underivatized individual amino acids using high-performance liquid chromatography coupled with elemental analyzer/isotope ratio mass spectrometry.

RATIONALE: Isolation of underivatized amino acids (AAs) using high-performance liquid chromatography (HPLC) is becoming a popular method for carbon (δ13 C) and nitrogen isotope (δ15 N) analyses of AAs because of the high analytical precision and for performing dual-isotope analysis. However, some AAs in natural samples, especially small, hydrophilic AAs, are not suitably separated using reversed-phase columns (e.g., C18) and ion-exchange columns (e.g., Primesep A). METHODS: We developed a new method for HPLC using a porous graphitic carbon column for the separation of nine hydrophilic AAs. After purification, δ13 C and δ15 N values of AAs were determined using elemental analyzer/isotope ratio mass spectrometry (EA/IRMS). We demonstrated the application of this method by determining δ13 C and δ15 N values of individual hydrophilic AAs in a biological sample, the muscle of blue mackerel (Scomber australasicus). RESULTS: Chromatographically, the baseline separation of hydrophilic AAs was achieved in both the standard mixture and the biological sample. We confirmed that δ13 C and δ15 N values of AA standards remained unchanged during the whole experimental procedure. The δ13 C values of AAs in mackerel muscle are also in good agreement with the values obtained using another verified method for δ13 C analysis. CONCLUSIONS: The good separation performance of hydrophilic AAs and the reliability of δ13 C and δ15 N analyses of individual AAs using the porous graphite column offer a significant advantage over conventional settings. We suggest that, in the future, the HPLC × EA/IRMS method can be used for reliable δ13 C and δ15 N analyses of AAs in natural samples.

mTORC1 regulates phagosome digestion of symbiotic bacteria for intracellular nutritional symbiosis in a deep-sea mussel.

Phagocytosis is one of the methods used to acquire symbiotic bacteria to establish intracellular symbiosis. A deep-sea mussel, Bathymodiolus japonicus, acquires its symbiont from the environment by phagocytosis of gill epithelial cells and receives nutrients from them. However, the manner by which mussels retain the symbiont without phagosome digestion remains unknown. Here, we show that controlling the mechanistic target of rapamycin complex 1 (mTORC1) in mussels leads to retaining symbionts in gill cells. The symbiont is essential for the host mussel nutrition; however, depleting the symbiont's energy source triggers the phagosome digestion of symbionts. Meanwhile, the inhibition of mTORC1 by rapamycin prevented the digestion of the resident symbionts and of the engulfed exogenous dead symbionts in gill cells. This indicates that mTORC1 promotes phagosome digestion of symbionts under reduced nutrient supply from the symbiont. The regulation mechanism of phagosome digestion by mTORC1 through nutrient signaling with symbionts is key for maintaining animal-microbe intracellular nutritional symbiosis.

A new era of isotope ecology: Nitrogen isotope ratio of amino acids as an approach for unraveling modern and ancient food web.

Food web research is rapidly expanding through study of natural fractional abundance of 15N in individual amino acids. This paper overviews the principles of this isotope approach, and from my perspective, reanalyzes applications, and further extends the discussion. It applies kinetic isotope effects that enriches 15N in certain amino acids associated with the metabolic processes, which was clearly demonstrated by observations of both natural ecosystem and laboratory experiments. In trophic processes 'trophic amino acids' such as glutamic acid that significantly enrich 15N, whereas 'source amino acids' such as phenylalanine and methionine show little 15N enrichment. Through various applications conducted over the years, the principles of the method have shown to operate well and disentangle complex food webs and relevant problems. Applications include food chain length estimate, nitrogen resource assessment, tracking fish migration, and reconstruction of paleodiet. With this approach, considerations of a wide range of classical issues have been reinvigorated, while in the same time, new challenging frontiers are emerging.

Chitin nanofiber-coated biodegradable polymer microparticles via one-pot aqueous process.

Tailoring the surface of biodegradable microparticles is important for various applications in the fields of cosmetics, biotechnology, and drug delivery. Chitin nanofibers (ChNFs) are one of the promising materials for surface tailoring owing to its functionality, such as biocompatibility and antibiotic properties. Here, we show biodegradable polymer microparticles densely coated with ChNFs. Cellulose acetate (CA) was used as the core material in this study, and ChNF coating was successfully carried out via a one-pot aqueous process. The average particle size of the ChNF-coated CA microparticles was approximately 6 µm, and the coating procedure had little effect on the size or shape of the original CA microparticles. The ChNF-coated CA microparticles comprised 0.2-0.4 wt% of the thin surface ChNF layers. Owing to the surface cationic ChNFs, the ζ-potential value of the ChNF-coated microparticles was +27.4 mV. The surface ChNF layer efficiently adsorbed anionic dye molecules, and repeatable adsorption/desorption behavior was exhibited owing to the coating stability of the surface ChNFs. The ChNF coating in this study was a facile aqueous process and was applicable to CA-based materials of various sizes and shapes. This versatility will open new possibilities for future biodegradable polymer materials that satisfy the increasing demand for sustainable development.

Uracil in the carbonaceous asteroid (162173) Ryugu.

The pristine sample from the near-Earth carbonaceous asteroid (162173) Ryugu collected by the Hayabusa2 spacecraft enabled us to analyze the pristine extraterrestrial material without uncontrolled exposure to the Earth's atmosphere and biosphere. The initial analysis team for the soluble organic matter reported the detection of wide variety of organic molecules including racemic amino acids in the Ryugu samples. Here we report the detection of uracil, one of the four nucleobases in ribonucleic acid, in aqueous extracts from Ryugu samples. In addition, nicotinic acid (niacin, a B3 vitamer), its derivatives, and imidazoles were detected in search for nitrogen heterocyclic molecules. The observed difference in the concentration of uracil between A0106 and C0107 may be related to the possible differences in the degree of alteration induced by energetic particles such as ultraviolet photons and cosmic rays. The present study strongly suggests that such molecules of prebiotic interest commonly formed in carbonaceous asteroids including Ryugu and were delivered to the early Earth.

Soluble organic molecules in samples of the carbonaceous asteroid (162173) Ryugu.

The Hayabusa2 spacecraft collected samples from the surface of the carbonaceous near-Earth asteroid (162173) Ryugu and brought them to Earth. The samples were expected to contain organic molecules, which record processes that occurred in the early Solar System. We analyzed organic molecules extracted from the Ryugu surface samples. We identified a variety of molecules containing the atoms CHNOS, formed by methylation, hydration, hydroxylation, and sulfurization reactions. Amino acids, aliphatic amines, carboxylic acids, polycyclic aromatic hydrocarbons, and nitrogen-heterocyclic compounds were detected, which had properties consistent with an abiotic origin. These compounds likely arose from an aqueous reaction on Ryugu's parent body and are similar to the organics in Ivuna-type meteorites. These molecules can survive on the surfaces of asteroids and be transported throughout the Solar System.

Insights into the Methanogenic Population and Potential in Subsurface Marine Sediments Based on Coenzyme F430 as a Function-Specific Biomarker.

Coenzyme F430, the prosthetic group of methyl coenzyme M reductase (MCR), is a key compound in methane metabolism. We applied coenzyme F430 as a function-specific biomarker of methanogenesis to subsurface marine sediments collected below the sulfate reduction zone to investigate the distribution and activity of methanogens. In addition, we examined the kinetics of the epimerization of coenzyme F430, which is the first stage of the degradation process after cell death, at various temperatures (4, 15, 34, 60 °C) and pH (5, 7, 9) conditions, which cover in situ conditions of drilled sediments used in this study. The degradation experiments revealed that the kinetics of the epimerization well follow the thermodynamic laws, and the half-life of coenzyme F430 is decreasing from 304 days to 11 h with increasing the in situ temperature. It indicates that the native F430 detected in the sediments is derived from living methanogens, because the abiotic degradation of F430 is much faster than the sedimentation rate and will not be fossilized. Based on coenzyme F430 analysis and degradation experiments, the native form of F430 detected in subseafloor sediments off the Shimokita Peninsula originates from living methanogen cells, which is protected from degradation in cells but disappears soon after cell death. The biomass of methanogens calculated from in situ F430 concentration and F430 contents in cultivable methanogen species decreases by 2 orders of magnitude up to a sediment depth of 2.5 km, with a maximum value at ∼70 m below the seafloor (mbsf), while the proportion of methanogens to the total prokaryotic cell abundance increases with the depth, which is 1 to 2 orders of magnitude higher than expected previously. Our results indicate the presence of undetectable methanogens using conventional techniques.

In situ experimental evidences for responses of abyssal benthic biota to shifts in phytodetritus compositions linked to global climate change.

Abyssal plains cover more than half of Earth's surface, and the main food source in these ecosystems is phytodetritus, mainly originating from primary producers in the euphotic zone of the ocean. Global climate change is influencing phytoplankton abundance, productivity, and distribution. Increasing importance of picoplankton over diatom as primary producers in surface oceans (especially projected for higher latitudes) is projected and hence altering the quantity of organic carbon supplied to the abyssal seafloor as phytodetritus, consequences of which remain largely unknown. Here, we investigated the in situ responses of abyssal biota from viruses to megafauna to different types of phytoplankton input (diatoms or cyanobacteria which were labeled with stable isotopes) at equatorial (oligotrophic) and temperate (eutrophic) benthic sites in the Pacific Ocean (1°N at 4277 m water depth and 39°N at 5260 m water depth, respectively). Our results show that meiofauna and macrofauna generally preferred diatoms as a food source and played a relatively larger role in the consumption of phytodetritus at higher latitudes (39°N). Contrarily, prokaryotes and viruses showed similar or even stronger responses to cyanobacterial than to diatom supply. Moreover, the response of prokaryotes and viruses was very rapid (within 1-2 days) at both 1°N and 39°N, with quickest responses reported in the case of cyanobacterial supply at higher latitudes. Overall, our results suggest that benthic deep-sea eukaryotes will be negatively affected by the predicted decrease in diatoms in surface oceans, especially at higher latitudes, where benthic prokaryotes and viruses will otherwise likely increase their quantitative role and organic carbon cycling rates. In turn, such changes can contribute to decrease carbon transfer from phytodetritus to higher trophic levels, with strong potential to affect oceanic food webs, their biodiversity and consequently carbon sequestration capacity at the global scale.

Carbon and nitrogen stable isotopic offsets between diet and hair/feces in captive orangutans.

Estimating stable isotopic offset values is crucial for dietary reconstructions. Although research into stable isotope ecology of wild nonhuman primates is increasing overall, only a minority of studies involve laboratory experiments. This study is the first to report the carbon and nitrogen stable isotopic offset values in hair and feces of orangutans. During an experiment lasting 1 week, the weight of each consumed food item was recorded for each of six captive Bornean orangutan (Pongo pygmaeus) individuals. The food, hair, and fecal samples were collected for a few days, and their stable carbon and nitrogen isotope ratios were measured using an elemental analyzer/isotope ratio mass spectrometer. Subsamples of feces were treated with ethanol during the preservation process. Monte Carlo analyses showed that the 95% confidence intervals (CIs) of the carbon and nitrogen offset values between hair and diet were +0.9‰ to +3.9‰ and +2.3‰ to +4.5‰, respectively. The 95% CIs of the carbon and nitrogen offset values between feces and diet were -3.7‰ to -0.9‰ and +0.3‰ to +2.7‰, respectively. The effect of ethanol treatment on the stable isotope ratios of feces was unclear and inconclusive. The computed offset values of hair in captive orangutans are similar to those reported in other nonhuman primates, although those of feces showed greater interspecies variations. The offset values estimated in this study contribute to isotopic studies into the feeding ecology of free-ranging orangutans who are critically endangered in most wild settings.

Discovery of a colossal slickhead (Alepocephaliformes: Alepocephalidae): an active-swimming top predator in the deep waters of Suruga Bay, Japan.

A novel species of the family Alepocephalidae (slickheads), Narcetes shonanmaruae, is described based on four specimens collected at depths greater than 2171 m in Suruga Bay, Japan. Compared to other alepocephalids, this species is colossal (reaching ca. 140 cm in total length and 25 kg in body weight) and possesses a unique combination of morphological characters comprising anal fin entirely behind the dorsal fin, multiserial teeth on jaws, more scale rows than congeners, precaudal vertebrae less than 30, seven branchiostegal rays, two epurals, and head smaller than those of relatives. Mitogenomic analyses also support the novelty of this large deep-sea slickhead. Although most slickheads are benthopelagic or mesopelagic feeders of gelatinous zooplankton, behavioural observations and dietary analyses indicate that the new species is piscivorous. In addition, a stable nitrogen isotope analysis of specific amino acids showed that N. shonanmaruae occupies one of the highest trophic positions reported from marine environments to date. Video footage recorded using a baited camera deployed at a depth of 2572 m in Suruga Bay revealed the active swimming behaviour of this slickhead. The scavenging ability and broad gape of N. shonanmaruae might be correlated with its colossal body size and relatively high trophic position.

A method for stable carbon isotope measurement of underivatized individual amino acids by multi-dimensional high-performance liquid chromatography and elemental analyzer/isotope ratio mass spectrometry.

RATIONALE: To achieve better precision and accuracy for δ13 C analysis of individual amino acids (AAs), we have developed a new analytical method based on multi-dimensional high-performance liquid chromatography (HPLC) and elemental analyzer/isotope ratio mass spectrometry (EA/IRMS). Unlike conventional methods using gas chromatography, this approach omits pre-column chemical derivatization, thus reducing systematic errors associated with the isotopic measurement. METHODS: The separation and isolation of individual AAs in a standard mixture containing 15 AAs and a biological sample, spear squid (Heterololigo bleekeri) were performed. AAs were isolated using an HPLC system equipped with a reversed-phase column and a mixed-mode column and collected using a fraction collector. After the chromatographic separation and further post-HPLC purification, the δ13 C values of AAs were measured by EA/IRMS. RESULTS: The complete isolation of all 15 AAs in the standard mixture was achieved. The δ13 C values of these AAs before and after the experiment were in good agreement. Also, 15 AAs in the biological sample, H. bleekeri, were successfully measured. The δ13 C values of AAs in H. bleekeri varied by as much as 30‰ with glycine being most enriched in13 C. CONCLUSIONS: The consistency between the δ13 C values of reference and processed AAs demonstrates that the experimental procedure generates accurate δ13 C values unaffected by fractionation effects and contamination. This method is therefore suitable for δ13 C analysis of biological samples with higher precision than conventional approaches. We propose this new method as a tool to measure δ13 C values of AAs in biological, ecological and biogeochemical studies.

Quantification and Carbon and Nitrogen Isotopic Measurements of Heme B in Environmental Samples.

Heme B is an iron-coordinated tetrapyrrole molecule that acts as a cofactor in hemoproteins. It is expected to be ubiquitous in the environment, as b-type hemoproteins catalyze a variety of essential biochemical reactions. In this study, we developed an analytical method to quantify heme B in biological and environmental samples using high-performance liquid chromatography (HPLC) coupled to a photodiode array detector. The applicability of our method was further extended by the use of liquid chromatography/mass spectrometry (LC/MS; detection limit: ∼1 fmol), which enabled the quantification of a trace amount of dissolved heme B in filtered seawater and sedimentary heme B coexisting with an abundant interfering organic matrix. For compound-specific carbon and nitrogen isotopic measurements, heme B was successfully isolated and purified from biological and environmental samples by a combination of anion-exchange column chromatography, methyl esterification, and dual-step HPLC. While carbon and nitrogen isotopic compositions of heme B in phototrophs were mostly comparable to those of chlorophyll a, heme B in suspended particulate materials in coastal water and an intertidal sediment was 13C-depleted and 15N-enriched relative to chlorophyll a, suggesting that nonphototrophic microorganisms are also a significant source of heme B in natural environments.

Marine Os isotopic evidence for multiple volcanic episodes during Cretaceous Oceanic Anoxic Event 1b.

The Aptian-Albian boundary is marked by one of the major oceanic perturbations during the Cretaceous, called Oceanic Anoxic Event (OAE) 1b. Extensive volcanic episodes at the Southern Kerguelen Plateau has been suggested as the trigger of OAE1b, but compelling evidence remains lacking. Here, we reconstructed the temporal variations of marine Os isotopic ratios across the Aptian-Albian boundary in the Tethyan and Pacific pelagic sedimentary records to elucidate the causal links between OAE1b, the biotic turnover, and volcanic episodes. Our new Os isotopic records show two negative spikes that correlate with a period of planktonic foraminiferal turnover across the Aptian-Albian boundary during OAE1b and suggest multiple submarine volcanic events. By comparing our Os isotopic profile with carbon isotopic compositions of carbonate, CaCO3 content, and the relative abundances of agglutinated foraminifera, we conclude that ocean acidification caused by the massive release of CO2 through extensive volcanic episodes could have promoted the major planktonic foraminiferal turnover during OAE1b.

Tracking long-distance migration of marine fishes using compound-specific stable isotope analysis of amino acids.

The long-distance migrations by marine fishes are difficult to track by field observation. Here, we propose a new method to track such migrations using stable nitrogen isotopic composition at the base of the food web (δ15 NBase ), which can be estimated by using compound-specific isotope analysis. δ15 NBase exclusively reflects the δ15 N of nitrate in the ocean at a regional scale and is not affected by the trophic position of sampled organisms. In other words, δ15 NBase allows for direct comparison of isotope ratios between proxy organisms of the isoscape and the target migratory animal. We initially constructed a δ15 NBase isoscape in the northern North Pacific by bulk and compound-specific isotope analyses of copepods (n = 360 and 24, respectively), and then we determined retrospective δ15 NBase values of spawning chum salmon (Oncorhynchus keta) from their vertebral centra (10 sections from each of two salmon). We then estimated the migration routes of chum salmon during their skeletal growth by using a state-space model. Our isotope tracking method successfully reproduced a known chum salmon migration route between the Okhotsk and Bering seas, and our findings suggest the presence of a new migration route to the Bering Sea Shelf during a later growth stage.

Evaluation of δ13C and δ15N Uncertainties Associated with the Compound-Specific Isotope Analysis of Geoporphyrins.

Compound-specific isotope analyses of geoporphyrins, which are derivatives of chloropigments possessed by phototrophs, provide essential records of the biogeochemical cycle of past aquatic environments. Here, we evaluated uncertainties in carbon and nitrogen isotopic compositions (δ13C and δ15N) associated with high-performance liquid chromatography (HPLC) purification and isotopic measurements of geoporphyrins. Evaluation of total blank carbon and nitrogen for the HPLC and our sensitivity-improved elemental analyzer/isotope ratio mass spectrometer (nano-EA/IRMS) analysis confirmed that blank carbon can be corrected and that blank nitrogen is negligible compared to the mass of geoporphyrins required for the isotopic measurement. While geoporphyrins exhibited substantial in-peak carbon and nitrogen isotopic fractionations, no systematic changes in δ13C and δ15N values were observed during reversed- and normal-phase HPLC isolation of Ni- and VO-porphyrin standards, with the changes in δ13C and δ15N values being within ±0.6‰ and ±1.2‰ (2σ), respectively. These values are comparable to the instrumental precision of the nano-EA/IRMS system (±1.3‰ for 0.70 µgC and ±1.1‰ for 0.08 µgN, 2σ), confirming that no substantial artifact in the δ13C and δ15N values would be expected during the reversed- and normal-phase HPLC purification. The sensitivity and precision of our method enable us to determine δ13C and δ15N values of both major and minor geoporphyrins found in ancient sediments, which would provide detailed information on the photosynthetic primary producers and the carbon and nitrogen cycles in the past.

Extraterrestrial ribose and other sugars in primitive meteorites.

Sugars are essential molecules for all terrestrial biota working in many biological processes. Ribose is particularly essential as a building block of RNA, which could have both stored information and catalyzed reactions in primitive life on Earth. Meteorites contain a number of organic compounds including key building blocks of life, i.e., amino acids, nucleobases, and phosphate. An amino acid has also been identified in a cometary sample. However, the presence of extraterrestrial bioimportant sugars remains unclear. We analyzed sugars in 3 carbonaceous chondrites and show evidence of extraterrestrial ribose and other bioessential sugars in primitive meteorites. The 13C-enriched stable carbon isotope compositions (δ13C vs.VPDB) of the detected sugars show that the sugars are of extraterrestrial origin. We also conducted a laboratory simulation experiment of a potential sugar formation reaction in space. The compositions of pentoses in meteorites and the composition of the products of the laboratory simulation suggest that meteoritic sugars were formed by formose-like processes. The mineral compositions of these meteorites further suggest the formation of these sugars both before and after the accretion of their parent asteroids. Meteorites were carriers of prebiotic organic molecules to the early Earth; thus, the detection of extraterrestrial sugars in meteorites establishes the existence of natural geological routes to make and preserve them as well as raising the possibility that extraterrestrial sugars contributed to forming functional biopolymers like RNA on the early Earth or other primitive worlds.