Ken Takai

Japan Agency for Marine-Earth Science Technology | JAMSTEC · SUGAR Program

A novel bacterium, strain MOT50T, was isolated from the chimney structure at the Iheya North field in the Mid-Okinawa Trough. The cells were motile short rods with a single polar flagellum. Growth was observed between 40 and 65 ℃ (optimum, 52 ℃), at pH values between 5.0 and 7.1 (optimum, pH 6.1) and in the presence of 2.0–4.0% NaCl (optimum, 2.5%)...

In deep-sea hydrothermal environments, inorganic sulfur compounds are important energy substrates for sulfur-oxidizing, -reducing, and -disproportionating microorganisms. Among these, sulfur-disproportionating bacteria have been poorly understood in terms of ecophysiology and phylogenetic diversity. Here, we isolated and characterized a novel mesop...

The genus Nitratiruptor represents one of the most numerically abundant chemolithoautotrophic Campylobacterota populations in the mixing zones of habitats between hydrothermal fluids and ambient seawater in deep-sea hydrothermal environments. We isolated and characterized four novel temperate phages (NrS-2, NrS-3, NrS-4, and NrS-5) having a siphovi...

Prebiotic chemical evolution and the emergence of life in the seafloor hydrothermal systems of Hadean Earth is among the most plausible and popular hypotheses for the origin of earthly life. In contrast, many studies pointed out that this hypothesis intrinsically harbors a critical unsolved problem called the “water paradox”: Abundant water limits...

Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was obs...

In microbiology, cultivation is a central approach for uncovering novel physiology, ecology, and evolution of microorganisms, but conventional methods have left many microorganisms found in nature uncultured. To overcome the limitations of traditional methods and culture indigenous microorganisms, we applied a two-stage approach: enrichment/activat...

Carbonaceous matter (CM) in silica veins contained in the ~3.5 billion-year-old (Ga) Dresser Formation, Western Australia, can offer insights into biological activity in Earth’s oldest seafloor hydrothermal deposits, although a biological origin for this material remains debated. Herein, CM from Dresser hydrothermal vein deposits was analyzed using...

The hadal amphipod Hirondellea gigas is an emblematic animal of the Pacific trenches, and has a number of special adaptations to thrive in this ‘extreme’ environment, which includes the deepest part of the Earth’s ocean. One such adaptation that has been suggested is the presence of an ‘aluminum gel shield’ on the surface of its body in order to pr...

Raman and Fourier-transform infrared (FTIR) microspectroscopic analyses were performed to examine the chemical signatures and their spatial distribution of organic-walled microfossils together with organic matter (OM) in a black chert nodule from the Ediacaran (635–551 Ma) Doushantuo Formation in China. Raman spectral parameters (I-1350/1600 values...

Organisms use various forms and orientations of chitin nanofibres to make structures with a wide range of functions, from insect wings to mussel shells. Lophotrochozoan animals such as snails and annelid worms possess an ancient ‘biomineralization toolkit’, enabling them to flexibly and rapidly evolve unique hard parts. The scaly-foot snail is a ga...

The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields...

The Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough is characterized by abundant methane derived from organic-rich sediments and diverse chemosynthetic animal species, including those harboring methanotrophic bacterial symbionts, such as bathymodiolin mussels Bathymodiolus japonicus and “ Bathymodiolus ” platifrons and a galatheoi...

A novel mesophilic, strictly anaerobic, chemolithoautotrophic sulphate-reducing bacterium, designated strain KT2 T , was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc. Strain KT2 T grew at 25–40 °C (optimum 35 °C) and pH 5.5–7.0 (optimum 6.6) in the presence of 25–45 g l ⁻¹ NaCl (optimum 30 g l ⁻¹ )....

Geological processes at subduction zones control seismicity, plutonism and volcanism, and geochemical cycling between the oceans, crust, and mantle. The down-going plate experiences metamorphism, and the associated dehydration and fluid flow alters the physical properties of the plate interface and mantle wedge, as well as controlling the compositi...

Abiotic fixation of atmospheric dinitrogen to ammonia is important in prebiotic chemistry and biological evolution in the Hadean and Archean oceans. Though it is widely accepted that nitrate (NO3−) was generated in the early atmospheres, the stable pathways of ammonia production from nitrate deposited in the early oceans remain unknown. This paper...

A prevailing scenario of the origin of life postulates thioesters as key intermediates in protometabolism, but there is no experimental support for the prebiotic CO2 fixation routes to thioesters. Here we demonstrate that, under a simulated geoelectrochemical condition in primordial ocean hydrothermal systems (–0.6 to –1.0 V versus the standard hyd...

A novel thermophilic bacterium, strain SSM-sur55T, was isolated from a chimney structure at the Urashima site on the Southern Mariana Trough in the Pacific Ocean. Growth was observed at temperatures between 25 and 60 °C (optimum, 55 °C; 180 min doubling time), at pH values between 5.3 and 7.2 (optimum, pH 5.9) and in the presence of between 1.6 and...

Seafloor cratering is an important process that records the impact history of the Earth, affects projectile survivability, and determines the mass of ejecta from benthic rock that is transported to the atmosphere. We report experimental hypervelocity impacts of chondrite and other projectiles (olivine, stainless‐steel, polycarbonate) on a water‐cov...

A mannan-degrading halophilic archaeal strain, MD130-1 T , was isolated from a commercial salt sample. Cells were motile, rod-shaped, and stained Gram-negative. Colonies were pink pigmented. Strain MD130-1 T was able to grow at 1.5–4.6 M NaCl (optimum, 3.6 M) at pH 6.0–8.0 (optimum, pH 7.0) and at 25–50 °C (optimum, 40 °C). The DNA G+C content was...

Deep-sea hydrothermal vent ecosystems remain mysterious. To depict in detail the enigmatic life of chemosynthetic microbes, which are key primary producers in these ecosystems, metatranscriptomic analysis is expected to be a promising approach. However, this has been hindered by substantial perturbation (e.g., RNA degradation) during time-consuming...

Thioester synthesis by CO dehydrogenase/acetyl-CoA synthase is among the most ancient autotrophic metabolisms. Although the preceding prebiotic CO2 fixation routes to thioesters are often suggested, none has any experimentally supported evidence. Here we demonstrate that, under an electrochemical condition realizable in early ocean hydrothermal sys...

Nitrous oxide (N2O) is a potent greenhouse gas and has significantly increased in the atmosphere. Deep-sea hydrothermal fields are representative environments dominated by mesophilic to thermophilic members of the class Campylobacteria that possess clade II nosZ encoding nitrous oxide reductase. Here, we report a strain HRV44T representing the firs...

NDP-forming type acyl-CoA synthetase superfamily proteins are known to have six essential subdomains (1, 2, 3, a, b, c) of which partition and order are varied, suggesting yet-to-be-defined subdomain rearrangement happened in its evolution. Comparison in physicochemical and biochemical characteristics between the recombinant proteins which we made...

The Scaly-foot Snail, Chrysomallon squamiferum, presents a combination of biomineralised features, reminiscent of enigmatic early fossil taxa with complex shells and sclerites such as sachtids, but in a recently-diverged living species which even has iron-infused hard parts. Thus the Scaly-foot Snail is an ideal model to study the genomic mechanism...

The subduction of seamounts and ridge features at convergent plate boundaries plays an important role in the deformation of the overriding plate and influences geochemical cycling and associated biological processes. Active serpentinization of forearc mantle and serpentinite mud volcanism on the Mariana forearc (between the trench and active volcan...

Some deep-sea chemosynthetic invertebrates and their symbiotic bacteria can use molecular hydrogen (H2) as their energy source. However, how much the chemosynthetic holobiont (endosymbiont-host association) physiologically depends on H2 oxidation has not yet been determined. Here, we demonstrate that the Campylobacterota endosymbionts of the gastro...

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 a...

Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explore...

Chemical evolution is an abiotic reaction process in which complex organic molecules arise from a combination of simple inorganic and organic chemical compounds. To assess the possible ongoing chemical evolution in the subsurface ocean of Saturn’s icy satellite Enceladus, we explored the water-rock aqueous reactions and the peptide formation capabi...

Significance Highly adapted to deep-sea hot vents, the scaly-foot gastropod Chrysomallon squamiferum is unique among living and extinct animals in possessing an imbricating scale-armor reinforced by iron sulfide nanoparticles. Mechanisms behind its biogenic sulfide synthesis are expected to revolutionize industrial production of metal chalcogenide...

Hadal trench bottom (>6,000 m below sea level) sediments harbor higher microbial cell abundance compared to adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been explored yet....

The origin of eukaryotes remains enigmatic. Current data suggests that eukaryotes may have risen from an archaeal lineage known as "Asgard archaea". Despite the eukaryote-like genomic features found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear due to the lack of cultured representatives and corresponding...

Serpentinitic systems are potential habitats for microbial life due to frequently high concentrations of microbial energy substrates, such as hydrogen (H2), methane (CH4), and short-chain organic acids (SCOAs). Yet, many serpentinitic systems are also physiologically challenging environments due to highly alkaline conditions (pH > 10) and elevated...

Conventional and synchrotron radiation‐based (SR) Fourier transform infrared microspectroscopies (micro‐FTIR) were applied to four types of ~ 810 Ma organic‐walled microfossils together with diffuse organic matter (OM) and one irregularly shaped structure from the Fifteenmile Group, in Yukon, Canada, for their chemical characterization. The microfo...

Viruses are the most abundant biological entities on Earth and perform essential ecological functions in aquatic environments by mediating biogeochemical cycling and lateral gene transfer. Cellular life as well as viruses have been found in deep subseafloor sediment. However, the study of deep sediment viruses has been hampered by the complexities...

A novel hydrogenotrophic methanogen, strain HHBT, was isolated from a deep-sea hydrothermal vent chimney sample collected from Beebe Vent Field at the Mid-Cayman Spreading Center, Caribbean Sea. The cells were non-motile regular to irregular cocci possessing several flagella. The novel isolate grew at 60-80 °C, pH 5.0-7.4 and with 1-4 % of NaCl (w/...

Recent explorations of scientific ocean drilling have revealed the presence of microbial communities persisting in sediments down to ~2.5 km below the ocean floor. However, our knowledge of these microbial populations in the deep subseafloor sedimentary biosphere remains limited. Here, we present a cultivation experiment of 2-km-deep subseafloor mi...

A novel slow-growing, facultatively anaerobic, filamentous bacterium, strain MO-CFX2T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediment collected off the Shimokita Peninsula of Japan. Cells were multicellular filamentous, non-motile and Gram-stain-negative. The filam...

Serpentinite-hosting mud volcanoes, located in the Marianna forearc subduction zone, were drilled during IODP Expedition 366. Recovered samples from Asùt Tesoru seamount provide new insights on the generation of organic matter in deep environments. Short-chain alcohols, volatile fatty acids and light hydrocarbons are produced within hyperalkaline p...

Abstract South Chamorro Seamount (SCS) is a blueschist-bearing serpentinite mud volcano in the Mariana forearc. Previous scientific drilling conducted at SCS revealed highly alkaline, sulfate-rich formation fluids resulting from slab-derived fluid upwelling combined with serpentinization both beneath and within the seamount. In the present study, a...

Carbonaceous matter in ~ 3.5 Ga hydrothermal vein deposits from the Dresser Formation, Western Australia, was analyzed using Fourier transform infrared (FTIR) microspectroscopy. Based on the spectroscopy, the carbonaceous matter was mainly composed of disordered aromatic structures, with minor aliphatic C–H functional groups. Spatially resolved ana...

Studying the diversity of extant metabolisms and enzymes, especially those involved in the biosynthesis of primary metabolites including amino acids, is important to shed light on the evolution of life. Many organisms synthesize serine from phosphoserine via a reaction catalyzed by phosphoserine phosphatase (PSP). Two types of PSPs, belonging to di...

Pelolinea submarina strain MO-CFX1T (=JCM 17238T, =KCTC 5975T) is an anaerobic chemoorganotrophic bacterium isolated from subseafloor sediments collected off the Shimokita Peninsula of Japan, north-western Pacific Ocean. This strain was the first isolate belonging to the phylum Chloroflexi from deep-sea sedimentary environment. Here, we report the...

Nitrous oxide (N2O) is a greenhouse gas and also leads to stratospheric ozone depletion. In natural environments, only a single N2O sink process is the microbial reduction of N2O to N2, which is mediated by nitrous oxide reductase (NosZ) encoded by nosZ gene. The nosZ phylogeny has two distinct clades, clade I and formerly overlooked clade II. In d...

The hydrothermal vent squat lobster Shinkaia crosnieri Baba & Williams harbors an epibiotic bacterial community, which is numerically and functionally dominated by methanotrophs affiliated with Methylococcaceae and thioautotrophs affiliated with Sulfurovum and Thiotrichaceae. In the present study, shifts in the phylogenetic composition and metaboli...

The study of extracellular DNA viral particles in the ocean is currently one of the most advanced fields of research in viral metagenomic analysis. However, even though the intracellular viruses of marine microorganisms might be the major source of extracellular virus particles in the ocean, the diversity of these intracellular viruses is not well...

Microbial life inhabiting subseafloor sediments plays an important role in Earth’s carbon cycle. However, the impact of geodynamic processes on the distributions and carbon-cycling activities of subseafloor life remains poorly constrained. We explore a submarine mud volcano of the Nankai accretionary complex by drilling down to 200 m below the summ...

The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other li...

Deep‐sea hydrothermal vents are hot springs on the seafloor. In recent years, electricity generation in deep‐sea hydrothermal vents has been reported. Electricity can be generated through the sulfide minerals that form in seafloor hydrothermal deposits, and these minerals can convert the redox and heat energy between hydrothermal fluids and seawate...

Phylogeography of animals provides clues to processes governing their evolution and diversification. The Indian Ocean has been hypothesized as a ‘dispersal corridor’ connecting hydrothermal vent fauna of Atlantic and Pacific oceans. Stalked barnacles of the family Eolepadidae are common associates of deep-sea vents in Southern, Pacific and Indian o...

A stable d-lactate electrochemical sensing system was developed using a dye-linked d-lactate dehydrogenase (Dye-DLDH) from an uncultivated thermophilic archaeon, Candidatus Caldiarchaeum subterraneum. To develop the system, the putative gene encoding the Dye-DLDH from Ca. Caldiarchaeum subterraneum was overexpressed in Escherichia coli, and the exp...

Many thermophiles thriving in a natural high-temperature environment remain uncultivated, and their ecophysiological functions in the biogeochemical cycle remain unclear. In the present study, we performed long-term continuous cultivation at 65°C and 70°C using a microbial mat sample, collected from a subsurface geothermal stream, as the inoculum,...