Isolation of an archaeon at the prokaryote-eukaryote interface.

The origin of eukaryotes remains unclear1-4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as 'Asgard' archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon-'Candidatus Prometheoarchaeum syntrophicum' strain MK-D1-is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle-engulf-endogenize (also known as E3) model.

The DESTINY+ Dust Analyser - a dust telescope for analysing cosmic dust dynamics and composition.

The DESTINY+(Demonstration and Experiment of Space Technology for INterplanetary voYage with Phaethon fLyby and dUst Science) Dust Analyser (DDA) is a state-of-the-art dust telescope for the in situ analysis of cosmic dust particles. As the primary scientific payload of the DESTINY+ mission, it serves the purpose of characterizing the dust environment within the Earth-Moon system, investigating interplanetary and interstellar dust populations at 1 AU from the Sun and studying the dust cloud enveloping the asteroid (3200) Phaethon. DDA features a two-axis pointing platform for increasing the accessible fraction of the sky. The instrument combines a trajectory sensor with an impact ionization time-of-flight mass spectrometer, enabling the correlation of dynamical, physical and compositional properties for individual dust grains. For each dust measurement, a set of nine signals provides the surface charge, particle size, velocity vector, as well as the atomic, molecular and isotopic composition of the dust grain. With its capabilities, DDA is a key asset in advancing our understanding of the cosmic dust populations present along the orbit of DESTINY+. In addition to providing the scientific context, we are presenting an overview of the instrument's design and functionality, showing first laboratory measurements and giving insights into the observation planning. This article is part of a theme issue 'Dust in the Solar System and beyond'.

Carbon and nitrogen assimilation in deep subseafloor microbial cells.

Remarkable numbers of microbial cells have been observed in global shallow to deep subseafloor sediments. Accumulating evidence indicates that deep and ancient sediments harbor living microbial life, where the flux of nutrients and energy are extremely low. However, their physiology and energy requirements remain largely unknown. We used stable isotope tracer incubation and nanometer-scale secondary ion MS to investigate the dynamics of carbon and nitrogen assimilation activities in individual microbial cells from 219-m-deep lower Pleistocene (460,000 y old) sediments from the northwestern Pacific off the Shimokita Peninsula of Japan. Sediment samples were incubated in vitro with (13)C- and/or (15)N-labeled glucose, pyruvate, acetate, bicarbonate, methane, ammonium, and amino acids. Significant incorporation of (13)C and/or (15)N and growth occurred in response to glucose, pyruvate, and amino acids (∼76% of total cells), whereas acetate and bicarbonate were incorporated without fostering growth. Among those substrates, a maximum substrate assimilation rate was observed at 67 × 10(-18) mol/cell per d with bicarbonate. Neither carbon assimilation nor growth was evident in response to methane. The atomic ratios between nitrogen incorporated from ammonium and the total cellular nitrogen consistently exceeded the ratios of carbon, suggesting that subseafloor microbes preferentially require nitrogen assimilation for the recovery in vitro. Our results showed that the most deeply buried subseafloor sedimentary microbes maintain potentials for metabolic activities and that growth is generally limited by energy but not by the availability of C and N compounds.

Microbial anabolic and catabolic utilization of hydrocarbons in deep subseafloor sediments of Guaymas Basin.

Guaymas Basin, located in the Gulf of California, is a hydrothermally active marginal basin. Due to steep geothermal gradients and localized heating by sill intrusions, microbial substrates like short-chain fatty acids and hydrocarbons are abiotically produced from sedimentary organic matter at comparatively shallow depths. We analyzed the effect of hydrocarbons on uptake of hydrocarbons by microorganisms via nano-scale secondary ion mass spectrometry (NanoSIMS) and microbial sulfate reduction rates (SRR), using samples from two drill sites sampled by IODP Expedition 385 (U1545C and U1546D). These sites are in close proximity of each other (ca. 1 km) and have very similar sedimentology. Site U1546D experienced the intrusion of a sill that has since then thermally equilibrated with the surrounding sediment. Both sites currently have an identical geothermal gradient, despite their different thermal history. The localized heating by the sill led to thermal cracking of sedimentary organic matter and formation of potentially bioavailable organic substrates. There were low levels of hydrocarbon and nitrogen uptake in some samples from both sites, mostly in surficial samples. Hydrocarbon and methane additions stimulated SRR in near-seafloor samples from Site U1545C, while samples from Site U1546D reacted positively only on methane. Our data indicate the potential of microorganisms to metabolize hydrocarbons even in the deep subsurface of Guaymas Basin.

A primordial noble gas component discovered in the Ryugu asteroid and its implications.

Ryugu is the C-type asteroid from which material was brought to Earth by the Hayabusa2 mission. A number of individual grains and fine-grained samples analysed so far for noble gases have indicated that solar wind and planetary (known as P1) noble gases are present in Ryugu samples with concentrations higher than those observed in CIs, suggesting the former to be more primitive compared to the latter. Here we present results of analyses of three fine-grained samples from Ryugu, in one of which Xe concentration is an order of magnitude higher than determined so far in other samples from Ryugu. Isotopically, this Xe resembles P1, but with a much stronger isotopic fractionation relative to solar wind and significantly lower 36Ar/132Xe ratio than in P1. This previously unknown primordial noble gas component (here termed P7) provides clues to constrain how the solar composition was fractionated to form the planetary components.

Distributions of CHN compounds in meteorites record organic syntheses in the early solar system.

Carbonaceous meteorites contain diverse soluble organic compounds. These compounds formed in the early solar system from volatiles accreted on tiny dust particles. However, the difference in the organic synthesis on respective dust particles in the early solar system remains unclear. We found micrometer-scale heterogeneous distributions of diverse CHN1-2 and CHN1-2O compounds in two primitive meteorites: the Murchison and NWA 801, using a surface-assisted laser desorption/ionization system connected to a high mass resolution mass spectrometer. These compounds contained mutual relationships of ± H2, ± CH2, ± H2O, and ± CH2O and showed highly similar distributions, indicating that they are the products of series reactions. The heterogeneity was caused by the micro-scale difference in the abundance of these compounds and the extent of the series reactions, indicating that these compounds formed on respective dust particles before asteroid accretion. The results of the present study provide evidence of heterogeneous volatile compositions and the extent of organic reactions among the dust particles that formed carbonaceous asteroids. The compositions of diverse small organic compounds associated with respective dust particles in meteorites are useful to understand different histories of volatile evolution in the early solar system.

Samples returned from the asteroid Ryugu are similar to Ivuna-type carbonaceous meteorites.

Carbonaceous meteorites are thought to be fragments of C-type (carbonaceous) asteroids. Samples of the C-type asteroid (162173) Ryugu were retrieved by the Hayabusa2 spacecraft. We measured the mineralogy and bulk chemical and isotopic compositions of Ryugu samples. The samples are mainly composed of materials similar to those of carbonaceous chondrite meteorites, particularly the CI (Ivuna-type) group. The samples consist predominantly of minerals formed in aqueous fluid on a parent planetesimal. The primary minerals were altered by fluids at a temperature of 37° ± 10°C, about [Formula: see text] million (statistical) or [Formula: see text] million (systematic) years after the formation of the first solids in the Solar System. After aqueous alteration, the Ryugu samples were likely never heated above ~100°C. The samples have a chemical composition that more closely resembles that of the Sun's photosphere than other natural samples do.

Copper-Nanocoated Ultra-Small Cells in Grain Boundaries Inside an Extinct Vent Chimney.

Chemosynthetic organisms flourish around deep-sea hydrothermal vents where energy-rich fluids are emitted from metal sulfide chimneys. However, microbial life hosted in mineral assemblages in extinct chimneys lacking fluid venting remains largely unknown. The interior of extinct chimneys remains anoxic where the percolation of oxygenated seawater is limited within tightly packed metal sulfide grains. Given the scarcity of photosynthetic organics in deep seawater, anaerobic microbes might inhabit the grain boundaries energetically depending on substrates derived from rock-water interactions. In this study, we reported ultra-small cells directly visualized in grain boundaries of CuFeS2 inside an extinct metal sulfide chimney from the southern Mariana Trough. Nanoscale solid analyses reveal that ultra-small cells are coated with Cu2O nanocrystals in grain boundaries enriched with C, N, and P. In situ spectroscopic and spectrometric characterizations demonstrate the distribution of organics with amide groups and a large molecular organic compound in the grain boundaries. We inferred that the ultra-small cells are anaerobes because of the fast dissolution of Cu2O nanocrystals in oxygenated solution. This Cu2O property also excludes the possibility of microbial contamination from ambient seawater during sampling. It is shown by 16S rRNA gene sequence analysis that the chimney interior is dominated by Pacearchaeota known to have anaerobic metabolisms and ultra-small cells. Our results support the potential existence of photosynthesis-independent microbial ecosystems in grain boundaries in submarine metal sulfides deposits on the early Earth.

Ryugu's nucleosynthetic heritage from the outskirts of the Solar System.

Little is known about the origin of the spectral diversity of asteroids and what it says about conditions in the protoplanetary disk. Here, we show that samples returned from Cb-type asteroid Ryugu have Fe isotopic anomalies indistinguishable from Ivuna-type (CI) chondrites, which are distinct from all other carbonaceous chondrites. Iron isotopes, therefore, demonstrate that Ryugu and CI chondrites formed in a reservoir that was different from the source regions of other carbonaceous asteroids. Growth and migration of the giant planets destabilized nearby planetesimals and ejected some inward to be implanted into the Main Belt. In this framework, most carbonaceous chondrites may have originated from regions around the birthplaces of Jupiter and Saturn, while the distinct isotopic composition of CI chondrites and Ryugu may reflect their formation further away in the disk, owing their presence in the inner Solar System to excitation by Uranus and Neptune.

Oxygen isotopes of anhydrous primary minerals show kinship between asteroid Ryugu and comet 81P/Wild2.

The extraterrestrial materials returned from asteroid (162173) Ryugu consist predominantly of low-temperature aqueously formed secondary minerals and are chemically and mineralogically similar to CI (Ivuna-type) carbonaceous chondrites. Here, we show that high-temperature anhydrous primary minerals in Ryugu and CI chondrites exhibit a bimodal distribution of oxygen isotopic compositions: 16O-rich (associated with refractory inclusions) and 16O-poor (associated with chondrules). Both the 16O-rich and 16O-poor minerals probably formed in the inner solar protoplanetary disk and were subsequently transported outward. The abundance ratios of the 16O-rich to 16O-poor minerals in Ryugu and CI chondrites are higher than in other carbonaceous chondrite groups but are similar to that of comet 81P/Wild2, suggesting that Ryugu and CI chondrites accreted in the outer Solar System closer to the accretion region of comets.

Microscopic analyses of weathered granite in ion-adsorption rare earth deposit of Jianxi Province, China.

Weathered granite of ion-adsorption rare earth elements (REEs) ore collected at Jiangxi Province, China was investigated to identify the minerals abundant in REEs. The analyses of scanning electron microscopy (SEM)-energy dispersive spectrometry (EDS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) for individual mineral particles of the weathered granite showed that kaolinitic particles formed by K-feldspar weathering contained large amounts of REEs. Scanning transmission electron microscopy (STEM)-EDS analyses revealed that the kaolinitic particles were mainly composed of kaolinite, illite and hematite. The elemental maps by Nano-SIMS for the kaolinitic particle clarified that La and Y are particularly concentrated in illite. The presence of illite presumably contributes to the formation of the REE accumulation zone in weathered granite. Furthermore, in the in-situ desorption experiment, nearly half the REEs (45.5%) remained in the kaolinitic particle after the treatment with 0.5 M ammonium sulfate solution. The desorption ratio of heavy REEs (HREEs: Gd-Lu) (60.4%) was lower than that of light REEs (LREEs: La-Eu) apart from Ce (69.0%). These results suggest that REEs form inner-sphere complexes on the kaolinitic particle. It can be assumed that the inner-sphere complexation suppresses the extraction ratio of REEs from the ores by ion-exchange treatment.

Aerobic microbial life persists in oxic marine sediment as old as 101.5 million years.

Sparse microbial populations persist from seafloor to basement in the slowly accumulating oxic sediment of the oligotrophic South Pacific Gyre (SPG). The physiological status of these communities, including their substrate metabolism, is previously unconstrained. Here we show that diverse aerobic members of communities in SPG sediments (4.3‒101.5 Ma) are capable of readily incorporating carbon and nitrogen substrates and dividing. Most of the 6986 individual cells analyzed with nanometer-scale secondary ion mass spectrometry (NanoSIMS) actively incorporated isotope-labeled substrates. Many cells responded rapidly to incubation conditions, increasing total numbers by 4 orders of magnitude and taking up labeled carbon and nitrogen within 68 days after incubation. The response was generally faster (on average, 3.09 times) for nitrogen incorporation than for carbon incorporation. In contrast, anaerobic microbes were only minimally revived from this oxic sediment. Our results suggest that microbial communities widely distributed in organic-poor abyssal sediment consist mainly of aerobes that retain their metabolic potential under extremely low-energy conditions for up to 101.5 Ma.

Deep microbial proliferation at the basalt interface in 33.5-104 million-year-old oceanic crust.

The upper oceanic crust is mainly composed of basaltic lava that constitutes one of the largest habitable zones on Earth. However, the nature of deep microbial life in oceanic crust remains poorly understood, especially where old cold basaltic rock interacts with seawater beneath sediment. Here we show that microbial cells are densely concentrated in Fe-rich smectite on fracture surfaces and veins in 33.5- and 104-million-year-old (Ma) subseafloor basaltic rock. The Fe-rich smectite is locally enriched in organic carbon. Nanoscale solid characterizations reveal the organic carbon to be microbial cells within the Fe-rich smectite, with cell densities locally exceeding 1010 cells/cm3. Dominance of heterotrophic bacteria indicated by analyses of DNA sequences and lipids supports the importance of organic matter as carbon and energy sources in subseafloor basalt. Given the prominence of basaltic lava on Earth and Mars, microbial life could be habitable where subsurface basaltic rocks interact with liquid water.

Development of a sample holder for synchrotron radiation-based computed tomography and diffraction analysis of extraterrestrial materials.

A sample holder for a suite of synchrotron radiation measurements on extraterrestrial materials, which are fragile and irregularly shaped, was developed using carbon nanotubes and polyimide. The holder enables investigation of such samples with multiple analytical instruments, which means that we can reduce the number of sample transfers between holders. The holder developed in our study also enables investigation of such samples without exposure to the terrestrial atmosphere, which contains abundant contaminants, such as water vapor and organic substances. The stability of the samples in the holder during the measurements and disturbance of the analysis result by the holder were evaluated, which showed that sample drift motion and image disturbance due to x-ray attenuation and scattering of the holder materials are insignificant.

Tiny droplets of ocean island basalts unveil Earth's deep chlorine cycle.

Fully characterising the exchange of volatile elements between the Earth's interior and surface layers has been a longstanding challenge. Volatiles scavenged from seawater by hydrothermally altered oceanic crust have been transferred to the upper mantle during subduction of the oceanic crust, but whether these volatiles are carried deeper into the lower mantle is poorly understood. Here we present evidence of the deep-mantle Cl cycle recorded in melt inclusions in olivine crystals in ocean island basalts sourced from the lower mantle. We show that Cl-rich melt inclusions are associated with radiogenic Pb isotopes, indicating ancient subducted oceanic crust in basalt sources, together with lithophile elements characteristic of melts from a carbonated source. These signatures collectively indicate that seawater-altered and carbonated oceanic crust conveyed surface Cl downward to the lower mantle, forming a Cl-rich reservoir that accounts for 13-26% or an even greater proportion of the total Cl in the mantle.

A novel organic-rich meteoritic clast from the outer solar system.

The Zag meteorite which is a thermally-metamorphosed H ordinary chondrite contains a primitive xenolithic clast that was accreted to the parent asteroid after metamorphism. The cm-sized clast contains abundant large organic grains or aggregates up to 20 µm in phyllosilicate-rich matrix. Here we report organic and isotope analyses of a large (~10 µm) OM aggregate in the Zag clast. The X-ray micro-spectroscopic technique revealed that the OM aggregate has sp2 dominated hydrocarbon networks with a lower abundance of heteroatoms than in IOM from primitive (CI,CM,CR) carbonaceous chondrites, and thus it is distinguished from most of the OM in carbonaceous meteorites. The OM aggregate has high D/H and 15N/14N ratios (δD = 2,370 ± 74‰ and δ15N = 696 ± 100‰), suggesting that it originated in a very cold environment such as the interstellar medium or outer region of the solar nebula, while the OM is embedded in carbonate-bearing matrix resulting from aqueous activities. Thus, the high D/H ratio must have been preserved during the extensive late-stage aqueous processing. It indicates that both the OM precursors and the water had high D/H ratios. Combined with 16O-poor nature of the clast, the OM aggregate and the clast are unique among known chondrite groups. We further propose that the clast possibly originated from D/P type asteroids or trans-Neptunian Objects.

Microbial Metabolism and Community Dynamics in Hydraulic Fracturing Fluids Recovered From Deep Hydrocarbon-Rich Shale.

Hydraulic fracturing is a prominent method of natural gas production that uses injected, high-pressure fluids to fracture low permeability, hydrocarbon rich strata such as shale. Upon completion of a well, the fluid returns to the surface (produced water) and contains natural gas, subsurface constituents, and microorganisms (Barbot et al., 2013; Daly et al., 2016). While the microbial community of the produced fluids has been studied in multiple gas wells, the activity of these microorganisms and their relation to biogeochemical activity is not well understood. In this experiment, we supplemented produced fluid with 13C-labeled carbon sources (glucose, acetate, bicarbonate, methanol, or methane), and 15N-labeled ammonium chloride in order to isotopically trace microbial activity over multiple day in anoxic incubations. Nanoscale secondary ion mass spectrometry (NanoSIMS) was used to generate isotopic images of 13C and 15N incorporation in individual cells, while isotope ratio monitoring-gas chromatography-mass spectrometry (IRM-GC-MS) was used to measure 13CO2, and 13CH4 as metabolic byproducts. Glucose, acetate, and methanol were all assimilated by microorganisms under anoxic conditions. 13CO2 production was only observed with glucose as a substrate indicating that catabolic activity was limited to this condition. The microbial communities observed at 0, 19, and 32 days of incubation did not vary between different carbon sources, were low in diversity, and composed primarily of the class Clostridia. The primary genera detected in the incubations, Halanaerobium and Fusibacter, are known to be adapted to harsh physical and chemical conditions consistent with those that occur in the hydrofracturing environment. This study provides evidence that microorganisms in produced fluid are revivable in laboratory incubations and retained the ability to metabolize added carbon and nitrogen substrates.

Discovery of fossil asteroidal ice in primitive meteorite Acfer 094.

Carbonaceous chondrites are meteorites believed to preserve our planet's source materials, but the precise nature of these materials still remains uncertain. To uncover pristine planetary materials, we performed synchrotron radiation-based x-ray computed nanotomography of a primitive carbonaceous chondrite, Acfer 094, and found ultraporous lithology (UPL) widely distributed in a fine-grained matrix. UPLs are porous aggregates of amorphous and crystalline silicates, Fe─Ni sulfides, and organics. The porous texture must have been formed by removal of ice previously filling pore spaces, suggesting that UPLs represent fossils of primordial ice. The ice-bearing UPLs formed through sintering of fluffy icy dust aggregates around the H2O snow line in the solar nebula and were incorporated into the Acfer 094 parent body, providing new insight into asteroid formation by dust agglomeration.

Organic matter in extraterrestrial water-bearing salt crystals.

Direct evidence of complex prebiotic chemistry from a water-rich world in the outer solar system is provided by the 4.5-billion-year-old halite crystals hosted in the Zag and Monahans (1998) meteorites. This study offers the first comprehensive organic analysis of the soluble and insoluble organic compounds found in the millimeter-sized halite crystals containing brine inclusions and sheds light on the nature and activity of aqueous fluids on a primitive parent body. Associated with these trapped brines are organic compounds exhibiting wide chemical variations representing organic precursors, intermediates, and reaction products that make up life's precursor molecules such as amino acids. The organic compounds also contain a mixture of C-, O-, and N-bearing macromolecular carbon materials exhibiting a wide range of structural order, as well as aromatic, ketone, imine, and/or imidazole compounds. The enrichment in 15N is comparable to the organic matter in pristine Renazzo-type carbonaceous chondrites, which reflects the sources of interstellar 15N, such as ammonia and amino acids. The amino acid content of the Zag halite deviates from the meteorite matrix, supporting an exogenic origin of the halite, and therefore, the Zag meteorite contains organics synthesized on two distinct parent bodies. Our study suggests that the asteroidal parent body where the halite precipitated, potentially asteroid 1 Ceres, shows evidence for a complex combination of biologically and prebiologically relevant molecules.

The search for and analysis of direct samples of early Solar System aqueous fluids.

We describe the current state of the search for direct, surviving samples of early, inner Solar System fluids-fluid inclusions in meteorites. Meteoritic aqueous fluid inclusions are not rare, but they are very tiny and their characterization is at the state of the art for most analytical techniques. Meteoritic fluid inclusions offer us a unique opportunity to study early Solar System brines in the laboratory. Inclusion-by-inclusion analyses of the trapped fluids in carefully selected samples will, in the immediate future, provide us detailed information on the evolution of fluids as they interacted with anhydrous solid materials. Thus, real data can replace calculated fluid compositions in thermochemical calculations of the evolution of water and aqueous reactions in comets, asteroids, moons and the terrestrial planets.This article is part of the themed issue 'The origin, history and role of water in the evolution of the inner Solar System'.