Selective ion transport through nanochannels plays a crucial role in osmotic energy conversion in cellular systems. We show that this cell-essential process occurs in a submarine hydrothermal vent (HV) precipitate derived from a serpentine-hosted geological environment. Plate-like layered nanocrystals are aligned on the nano to millimeter scale, forming confined nanochannels in the HV precipitate. The nanochannels with surface charges function as a cation- and anion-selective ion transport membrane, allowing the precipitates to convert ionic gradients of Na+, K+, H+, and Cl- into electrical energy. Our findings suggest that osmotic energy conversion can occur spontaneously and widely through geological processes, offering valuable insights into the establishment of electrochemically coupled ion transport in early life as well as the creation of self-organized structures in engineering fields.

The Asal Rift is a continental rift segment in which the hydrothermal reactions of hot volcanic rocks and seawater-derived groundwater are comparable to the submarine hydrothermal processes. Formation of recent evaporites in the hypersaline Lake Asal and Lake Abhé is superimposed on this seafloor-type hydrothermal activity. From a geological and planetary science perspective, these continental rift lakes are valuable natural calibration fields for constraining the water–rock interaction and elemental cycles. In this study, we report on the chemical composition and stable isotopic fractionation of Mg, Sr, and Li in the hydrothermal fluids and brines of these two hypersaline lakes. The hydrothermal fluids of both Lake Asal and Lake Abhé were characterized by lower Mg isotopic ratios than seawater. This is explained by the removal of 26Mg from the fluids during the hydrothermal fluid–basalt interaction. In contrast, the brine from Lake Asal is indistinguishable from seawater, and no apparent effect of evaporite minerals on δ26Mg was observed. The 87Sr/86Sr and δ88Sr values of the hydrothermal fluid vary within the same range as the basalt, indicating that the effect of Sr leaching from the rock is significant. In contrast, the variation in δ88Sr is mainly caused by the precipitation of carbonates from the lake brine. The correlation between δ7Li and 87Sr/86Sr is clear regardless of the sample type (hydrothermal fluid, brine, or river water) and is thought to reflect the mixing of solutes. The δ7Li values of the hydrothermal end-members can be used as an indicator of the reservoir temperature of fluids.

Cells harvest energy from ionic gradients by selective ion transport across membranes, and the same principle is recently being used for osmotic power generation from salinity gradients at ocean-river interfaces. Common to these ionic gradient conversions is that they require intricate nanoscale structures. Here, we show that natural submarine serpentinite-hosted hydrothermal vent (HV) precipitates are capable of converting ionic gradients into electrochemical energy by selective transport of Na+, K+, H+, and Cl-. Layered hydroxide nanocrystals are aligned radially outwards from the HV fluid channels, constituting confined nanopores that span millimeters in the HV wall. The nanopores change the surface charge depending on adsorbed ions, allowing the mineral to function as a cation- and anion-selective ion transport membrane. Our findings indicate that chemical disequilibria originating from flow and concentration gradients in geologic environments generate confined nanospaces which enable the spontaneous establishment of osmotic energy conversion. Nakamura and colleagues show selective ion transport through mineral nanochannels in submarine hydrothermal vent (HV) precipitates, enabling HVs to convert ionic gradients into electrochemical energy, similar to cellular systems

Background Corallium japonicum, a prized resource in Japan, plays a vital role in traditional arts and fishing industries. Because of diminished stock due to overexploitation, ongoing efforts are focused on restoration through transplantation. This study aimed to enhance our understanding of the reproductive biology of these valuable corals and find more efficient methods for sex determination, which may significantly contribute to conservation initiatives. Methods We used 12 three-month aquarium reared C. japonicum colony fragments, conducted histological analysis for maturity and sex verification, and performed transcriptome analysis via de novo assembly and mapping using the C. rubrum transcriptome to explore gene expression differences between female and male C. japonicum. Results Our histological observations enabled sex identification in 33% of incompletely mature samples. However, the sex of the remaining 67% of samples, classified as immature, could not be identified. RNA-seq yielded approximately 21–31 million short reads from 12 samples. De novo assembly yielded 404,439 highly expressed transcripts. Among them, 855 showed significant differential expression, with 786 differentially expressed transcripts between females and males. Heatmap analysis highlighted 283 female-specific and 525 male-specific upregulated transcripts. Transcriptome assembly mapped to C. rubrum yielded 28,092 contigs, leading to the identification of 190 highly differentially expressed genes, with 113 upregulated exclusively in females and 70 upregulated exclusively in males. Blastp analysis provided putative protein annotations for 83 female and 72 male transcripts. Annotation analysis revealed that female biological processes were related to oocyte proliferation and reproduction, whereas those in males were associated with cell adhesion. Discussion Transcriptome analysis revealed sex-specific gene upregulation in incompletely mature C. japonicum and shared transcripts with C. rubrum, providing insight into its gene expression patterns. This study highlights the importance of using both de novo and reference-based assembly methods. Functional enrichment analysis showed that females exhibited enrichment in cell proliferation and reproduction pathways, while males exhibited enrichment in cell adhesion pathways. To the best of our knowledge, this is the first report on the gene expressions of each sex during the spawning season. Our findings offer valuable insights into the physiological ecology of incompletely mature red Japanese precious corals and suggest a method for identifying sex using various genes expressed in female and male individuals. In the future, techniques such as transplantation, artificial fertilization, and larval rearing may involve sex determination methods based on differences in gene expression to help conserve precious coral resources and ecosystems.

Metatranscriptome sequencing expanded the known diversity of the bacterial RNA virome, suggesting that additional riboviruses infecting bacterial hosts remain to be discovered. Here we employed double-stranded RNA sequencing to recover complete genome sequences of two ribovirus groups from acidic hot springs in Japan. One group, denoted hot spring riboviruses (HsRV), consists of viruses with distinct RNA-directed RNA polymerases (RdRPs) that seem to be intermediates between typical ribovirus RdRPs and viral reverse transcriptases. This group forms a distinct phylum, Artimaviricota , or even kingdom within the realm Riboviria . We identified viruses encoding HsRV-like RdRPs in marine water, river sediments and salt marshes, indicating that this group is widespread beyond extreme ecosystems. The second group, denoted hot spring partiti-like viruses (HsPV), forms a distinct branch within the family Partitiviridae . The genome architectures of HsRV and HsPV and their identification in bacteria-dominated habitats suggest that these viruses infect thermoacidophilic bacteria.

The early growth of Indian squid, Uroteuthis duvaucelii, was examined in specimens with sizes ranging from 41 - 215 mm ML from fisheries catches in coastal waters of Central Philippines. The linear relationship between mantle length and statolith radial length indicates that statolith growth is proportional to body size growth. At 60 days after hatching in different months, growth trajectories revealed high individual growth variability. At this age, monsoons influenced the growth variation and seasonality of U. duvaucelii, revealing the squid's high growth plasticity and adaptability towards changes in environmental conditions. During the first 40 days, the growth of female U. duvaucelii was significantly influenced by ambient temperature and food availability, indicating that these factors play a crucial role in the survival of their young. Hatching occurs continuously throughout the year, with prominent peaks in July and October. The lateral dome of the statolith contains significant amounts of trace elements, including strontium (Sr), uranium (U), magnesium (Mg), barium (Ba), and sodium (Na), which are known to be correlated with environmental conditions, habitat, and physiology of squids.

A seafloor hydrothermal system located at the Iheya Ridge (Okinawa Trough), named CLAM, deposits Mn‑carbonate chimneys that have no analogue found so far on the seafloor. The chimneys are composed of Mn-calcite and Ca-rhodochrosite. The crystallographic differences between these carbonates appear to control the rare earth elements (REE) partitioning between them that results in enrichment of the Ca-rhodochrosite in middle and heavy REE, and enrichment of the Mn-calcite in light REE. Chemistry of the CLAM hydrothermal fluids suggests: (1) low water/rock ratio of the hydrothermal system; (2) phase separation and dominance of low-chlorinity vapor phase; (3) sub-seafloor formation of Na-rich alteration minerals during fluid/rock reactions; (4) removal of some elements from the seawater to the host rocks during the seawater/rock interaction; (5) high Mn/Ca ratio of the basement rocks is responsible for the high Mn concentration in the hydrothermal fluids. C-O-isotope compositions of the CLAM Mn‑carbonates suggest they precipitated through binary mixing of end-member hydrothermal fluid and seawater accompanied by progressive degassing and cooling of the fluid. Mn-calcite precipitated from almost pure end-member hydrothermal fluid, whereas Ca-rhodochrosite precipitated from seawater-dominated vent fluid. Mg-isotope fractionation during Mn‑carbonate precipitation is assumed to depend on carbonate growth conditions and resulting carbonate mineralogy. S-isotope composition of the CLAM Mn‑carbonates suggests that the Ca-rhodochrosite precipitated in oxic conditions through rapid mixing of hydrothermal fluid and seawater, whereas the Mn-calcite precipitated in reduced conditions (thermochemical or microbial sulfate reduction) through slow mixing of hydrothermal fluid and seawater. Sr-isotope composition of the CLAM hydrothermal fluids is close to that of Okinawa Trough deep seawater. In contrast, Sr-isotopes in the CLAM Mn‑carbonates are more variable, indicating that Sr was derived from seawater, local lavas and sediments. Nd-isotope composition of the Mn‑carbonates indicates that Nd was derived from the local lavas and sediments. Pb in the majority of the CLAM Mn‑carbonates is of sedimentary origin (Pb isotope data), but involvement of anthropogenic Pb in the hydrothermal system is inferred for some Mn-calcite samples. Stability phase diagram modeling coupled with C-O-S-Sr-isotope data suggest that in the CLAM vent fluid the rhodochrosite is stable in a narrow Eh-pH range (6 < pH < 10; Eh > 0) and in a wide range of [Mn] and [Ca] activities, whereas calcite precipitates from a close to the end-member hydrothermal fluid in reduced conditions (Eh < 0).

Post-mega-earthquake geochemical and microbiological properties in subseafloor sediments of the Japan Trench accretionary wedge were investigated using core samples from Hole C0019E, which was drilled down to 851‍ ‍m below seafloor (mbsf) at a water depth of 6,890 m. Methane was abundant throughout accretionary prism sediments; however, its concentration decreased close to the plate boundary decollement. Methane isotope systematics indicated a biogenic origin. The content of mole-cular hydrogen (H2) was low throughout core samples, but markedly increased at specific depths that were close to potential faults predicted by logging-while-drilling ana-lyses. Based on isotopic systematics, H2 appeared to have been abundantly produced via a low-temperature interaction between pore water and the fresh surface of crushed rock induced by earthquakes. Subseafloor microbial cell density remained constant at approximately 105‍ ‍cells‍ ‍mL-1. Amplicon sequences revealed that predominant members at the phylum level were common throughout the units tested, which also included members frequently found in anoxic subseafloor sediments. Metabolic potential assays using radioactive isotopes as tracers revealed homoacetogenic activity in H2-enriched core samples collected near the fault. Furthermore, homoacetogenic bacteria, including Acetobacterium carbinolicum, were isolated from similar samples. Therefore, post-earthquake subseafloor microbial communities in the Japan Trench accretionary prism appear to be episodically dominated by homoacetogenic populations and potentially function due to the earthquake-induced low-temperature generation of H2. These post-earthquake microbial communities may eventually return to the steady-state communities dominated by oligotrophic heterotrophs and hydrogenotrophic and methylotrophic methanogens that are dependent on refractory organic matter in the sediment.

Recent massive metatranscriptome mining substantially expanded the diversity of the bacterial RNA virome, suggesting that additional groups of riboviruses infecting bacterial hosts remain to be discovered. We employed full length double-stranded (ds) RNA sequencing for identification of riboviruses associated with microbial consortia dominated by bacteria and archaea in acidic hot springs in Japan. Whole sequences of two groups of multisegmented riboviruses genomes were obtained. One group, which we denoted hot spring riboviruses (HsRV), consists of unusual viruses with distinct RNA-dependent RNA polymerases (RdRPs) that seem to be intermediates between typical ribovirus RdRPs and viral reverse transcriptases. We also identified viruses encoding HsRV-like RdRPs in moderate aquatic environments, including marine water, river sediments and salt marsh, indicating that this previously overlooked ribovirus group is not restricted to the extreme ecosystem. The HsRV-like viruses are candidates for a distinct phylum or even kingdom within the viral realm Riboviria . The second group, denoted hot spring partiti-like viruses (HsPV), is a distinct branch within the family Partitiviridae . All genome segments in both these groups of viruses display the organization typical of bacterial riboviruses, where multiple open reading frames encoding individual proteins are preceded by ribosome-binding sites. Together with the identification in bacteria-dominated habitats, this genome architecture indicates that riboviruses of these distinct groups infect thermoacidophilic bacterial hosts.

The travertine deposits could provide a prospective geomicrobiological snapshot of the early Earth considering its similarity with ancient stromatolites. Herein, we investigated the travertine carbonate deposits in a calcareous and sulfidic hot spring at Sipoholon, Northern Sumatra, Indonesia, with an emphasis on the formation of a laminated texture similar to one observed in the stromatolites. The travertine deposits were associated with microbial mats of different colors that change from yellow, pink, and green, lowering water temperature and H2S concentration along the water passages. A phylotype analysis of the Prokaryotic 16S rRNA gene revealed that chemolithoautotrophic sulfur and hydrogen oxidizing bacteria were abundant in the yellow sediment around vent sites. At the same time, photoheterotrophs, a linage of Anaerolineae, dominated the pink to green sediment at mid- to downstream. Laminated textures are developed in pink and green-colored sediments among these categories. Monitoring water chemical parameters and sediment texture for an Anaerolineae-dominated sample collected from a midstream site revealed that daily lamination was formed due to the daytime biofilm formation under the stable chemical composition of water conditions except for dissolved oxygen concentration. Daily laminations were also formed in other samples by microbial communities with lower Anaerolineae abundance. Further, the results showed that if mineral precipitation and microbial growth rates are appropriately balanced, cyanobacteria were not essential for the lamina development. This indicating that such a geochemical system could occur in early-time stromatolites even before the evolution of cyanobacteria. The microbial-mineral precipitation systems identified in this study provide significant insights into the formation of stromatolites, which can in turn shed light on the history of early Earth.

Two dead specimens of the precious coral Pleurocorallium elatius were obtained from the sea-bottom surface in submarine depressions at ~350 m water depth off Zanpa Cape, Okinawajima Island. Three samples were dated by 14C analysis, and yielded ages of 32,824-31,709 and 33,685-32,911 cal BP for one specimen and 20,480-20,060 cal BP for the other. These ages suggest that there was almost no deposition of sediment for an extended period in the depressions, which are interpreted as obstacle scours on the basis of their acoustic features. The obtained ages are the oldest known for dead precious corals, suggesting that favorable chemical conditions in the sea water facilitated long-term preservation of dead coral.

In the East Asian monsoon area, stalagmites generally record lower and higher oxygen isotope (δ18O) levels during warm humid interglacial and cold dry glacial periods, respectively. Here, we report unusually low stalagmite δ18O from the last glacial period (ca. 32.2–22.3 ka) in Fukugaguchi Cave, Niigata Prefecture, Japan, where a major moisture source is the East Asian winter monsoon (EAWM) that carries vapor from the warm surface of the Japan Sea. The δ18O profile of this stalagmite may imply millennial-scale changes, and high δ18O intervals that are related to Dansgaard–Oeschger (D–O) interstadials. More importantly, the stalagmite exhibits low overall δ18O values; the mean δ18O (− 8.87‰) is distinctly lower than the mid-Holocene mean of another stalagmite from the same cave (4.2–8.2 ka, − 7.64‰). An interpretation assuming a more intense EAWM and greater vapor transportation during the last glacial period, compared with the mid-Holocene, contradicts the limited inflow of the Tsushima Warm Current into the Japan Sea because of lowered sea level. Additionally, our model calculation using δ18O data from meteoric water indicated that the amount effect of winter meteoric water was insignificant (1.2‰/1000 mm). Low stalagmite δ18O for the last glacial period in Fukugaguchi Cave most likely resulted from 18O-depleted surface water, which developed in the isolated Japan Sea. The estimated amplitude of the δ18O decrease in surface water was ~ 3‰ at most, consistent with the abnormally low values for foraminifera (by ~ 2.5‰) in sediment during the last glacial period, shown by samples collected from the Japan Sea. This is the first terrestrial evidence of 18O depletion in Japan Sea surface water during the last glacial period.

ABSTRACT Radiocarbon ( 14 C) dating was performed for various types of precious coral colony fragments collected from the Ashizuri fishing field, around 100–200 m deep, off the southwest coast of Kochi Prefecture, Japan, to understand the historical background of one of the largest precious coral fishing fields in Japan. The 14 C ages of the 55 specimens range from ~7500 years ago to the modern. Most of the measured samples were older than 1871, when fishing activities of precious corals began in Kochi Prefecture. These results suggest that most of the deaths of the precious coral colonies were due to natural causes, such as natural mortality, predation, or various forms of environmental degradation, and not strictly related to destructive fishing practices. Additionally, precious corals started inhabiting the study area at least ~7500 years ago, when the marine condition became similar to that of today after the Last Glacial Period. This study is the first to focus on the age of dead precious coral fragments and has revealed that they might be an important fossil resource that could lengthen the timespan of precious coral fishery. This additional time may enable us to establish reasonable and effective regulations for sustainable fishery.

At the place where the submarine Aden Ridge encroaches on the African continent and interacts with the East African Rift system, two small basins form: Ghoubbet-al-Kharab and Lake Asal. Whereas Ghoubbet-al-Kharab is connected to the open ocean, Lake Asal is a typical example of oceanic "embryo", which is defined as a system that is detached from the ocean, but has features of a marine basin with an oceanic type crust and a seawater-based water body. In order to shed light on the source of water, type of hydrothermal activity and hydrothermal deposits, and controls on the water chemistry in an oceanic "embryo", we undertook a mineralogical-geochemical study of the lake water, hydrothermal fluids and hydrothermal carbonate deposits of Lake Asal. The geochemical analyses of lake water and hydrothermal fluids show that Lake Asal (located in an arid zone with strong evaporation and with no riverine input) is fed by seafloor-type hydrothermal fluids according to the following scenario: percolation of seawater along faults and cracks of extension in the rift, reaction of seawater with the hot basaltic rocks and hydrothermal fluid generation, discharge of the hydrothermal fluid in the Asal depression and accumulation of the Lake Asal water body. The fluid venting at the Lake Asal bottom is a mixture of 97% end-member hydrothermal fluid and 3% lake water. The calculated end-member hydrothermal fluid of this oceanic "embryo" is poorer in metals than the seafloor hydrothermal fluids of an open and evolved ocean. In addition to the seawater/rock interaction, the chemistry of Lake Asal is also controlled by evaporation leading to hyper salinity. In a hyper saline water body a number of hydrothermally supplied metals are stabilized as chloride complexes and accumulate. This results in a metal rich and mildly acidic "embryonic" ocean. Unlike an open and evolved modern ocean, the "embryonic" ocean located in an arid zone has heavy C and O isotope composition and light Zn and Fe isotope composition. Calcium isotope compositions of both types of ocean are similarly heavy. There are two genetically different sources of elements to the Lake Asal that are vertically separated: hydrothermal (lower, or bottom) and aeolian (upper, or surficial). Another important control on the lake water chemistry is the formation of carbonate spires at the lake bottom. Ca‑carbonate precipitation immobilizes substantial amount of hydrothermally supplied Ca and drives up the (Mg/Ca)mol of the lake water. Increasing (Mg/Ca)mol of the evolving lake water leads to changes in the mineralogy of spires: from low-Mg calcite to aragonite. Thus, the spire formation exerts a self-control on its mineralogy. Carbonate spire deposition affects also the Ca, Zn and Fe isotope composition of the lake water through adsorption or/and co-precipitation induced isotope fractionation.

We report here hourly variations of Mg/Ca, Sr/Ca, and Ba/Ca ratios in a Mediterranean mussel shell (Mytilus galloprovincialis) collected at the Otsuchi bay, on the Pacific coast of northeastern Japan. This bivalve was living in the intertidal zone, where such organisms are known to form a daily or bidaily growth line comprised of abundant organic matter. Mg/Ca ratios of the inner surface of the outer shell layer, corresponding to the most recent date, show cyclic changes at 25–90 μm intervals, while no interpretable variations are observed in Sr/Ca and Ba/Ca ratios. High Mg/Ca ratios were probably established by (1) cessation of the external supply of Ca and organic layer forming when the shell is closed at low tide, and (2) the strong binding of Mg to the organic layer, but not of Sr and Ba. Immediately following the great tsunami induced by the 2011 Tohoku earthquake, Mg/Ca enrichment occurred, up to 10 times that of normal low tide, while apparent Ba/Ca enrichment was observed for only a few days following the event, therefore serving a proxy of the past tsunami. Following the tsunami, periodic peaks and troughs in Mg/Ca continued, perhaps due to a biological memory effect as an endogenous clock.

Data used in the manuscript [Identification of paleomagnetic remanence carriers in ca. 3.47 Ga dacite from the Duffer Formation, the Pilbara Craton] by Usui et al., Physics of the Earth and Planetary Interiors.

Relative contribution of microbially mediated and purely abiotic processes during Mn(II) oxidation is evaluated by investigating microbially colonized manganese deposits at the Sambe hot spring in Japan. Microscopic observations and DNA analyses suggest that manganese-oxidizing bacteria are present in the deposits at all of the sites investigated, while thick microbial mats, which consist mainly of phototrophic microorganisms, are developed at only one site. Microelectrode measurements (pH, O-2 concentration, and Mn(II) concentration) near the deposit surface indicate that microbially mediated processes are dominant at all sites. These microbially mediated processes exceed the purely abiotic process by more than 2-24 times. At sites without abundant phototrophs, the major microbially mediated process that is occurring is lightindependent oxidation (e.g., direct/indirect oxidation via manganese-oxidizing bacteria/fungi). In contrast, the site with abundant phototrophs is characterized by the occurrence of light-independent oxidation (mostly indirect oxidation by oxygenic phototrophs), and the contribution of light-independent oxidation is subordinate. Chemical gradients, which are established within a diffusive boundary layer and microbial mat, drive indirect oxidation by oxygenic phototrophs, and the O-2 concentration gradient is particularly important when the concentration of dissolved inorganic carbon is higher than ca. 3 mM. Xray diffraction and X-ray absorption fine-structure spectrometry analyses indicate that microbially mediated processes yield poorly-crystalline birnessite (i.e., vernadite) regardless of their relative contribution. The observations of this study imply that (1) photosynthetic increases in the O-2 concentration drive indirect oxidation by oxygenic phototrophs at high concentrations of dissolved inorganic carbon like the Precambrian ocean, and that (2) the contribution of indirect oxidation by oxygenic phototrophs to ancient manganese oxides can be evaluated via geochemical redox proxies. (C) 2019 Elsevier Ltd. All rights reserved.