著者

Shinsuke Kawagucci Sanae Sakai Eiji Tasumi Miho Hirai Yoshihiro Takaki Takuro Nunoura Masafumi Saitoh Yuichiro Ueno Naohiro Yoshida Takazo Shibuya James Clifford Sample Tomoyo Okumura Ken Takai

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.38, no.2, pp.ME22108, 2023 (Released:2023-06-16)

参考文献数

114

被引用文献数

1

---

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 mole­cular hydrogen (H2) was low throughout core samples, but markedly increased at specific depths that were close to potential faults predicted by logging-while-drilling ana­lyses. 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.

著者

Motoko Igisu Masayuki Miyazaki Sanae Sakai Satoshi Nakagawa Hiroyuki D. Sakai Ken Takai

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.38, no.4, pp.ME23052, 2023 (Released:2023-10-18)

参考文献数

29

---

Infrared spectroscopy is used for the chemical characterization of prokaryotes. However, its application has been limited to cell aggregates and lipid extracts because of the relatively low spatial resolution of diffraction. We herein report optical photothermal infrared (O-PTIR) spectroscopy of prokaryotes for a domain-level diagnosis at the single-cell level. The technique provided infrared spectra of individual bacterial as well as archaeal cells, and the resulting aliphatic CH3/CH2 intensity ratios showed domain-specific signatures, which may reflect distinctive cellular lipid compositions; however, there was interference by other cellular components. These results suggest the potential of O-PTIR for a domain-level diagnosis of single prokaryotic cells in natural environments.

著者

Ken Takai

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.31, no.4, pp.367-368, 2016 (Released:2016-12-23)

参考文献数

39

被引用文献数

3 3

著者

Ken Takai

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.34, no.3, pp.223-225, 2019 (Released:2019-09-25)

参考文献数

26

被引用文献数

11 26

著者

Takuro Nunoura Manabu Nishizawa Miho Hirai Shigeru Shimamura Phurt Harnvoravongchai Osamu Koide Yuki Morono Toshiaki Fukui Fumio Inagaki Junichi Miyazaki Yoshihiro Takaki Ken Takai

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.33, no.2, pp.186-194, 2018 (Released:2018-07-04)

参考文献数

72

被引用文献数

67

---

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 lineages), Bacteroidetes, Planctomycetes, “Ca. Marinimicrobia” (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and “Ca. Woesearchaeota” (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.

著者

Ken Takai

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.34, no.4, pp.345-346, 2019 (Released:2019-12-27)

参考文献数

28

被引用文献数

3

著者

Kentaro Nakamura Shinsuke Kawagucci Kazuya Kitada Hidenori Kumagai Ken Takai Kyoko Okino

出版者

GEOCHEMICAL SOCIETY OF JAPAN

雑誌

GEOCHEMICAL JOURNAL (ISSN:00167002)

巻号頁・発行日

vol.49, no.6, pp.579-596, 2015-11-26 (Released:2015-12-05)

参考文献数

40

被引用文献数

37 61

---

Polymetallic sulfides deposited in seafloor hydrothermal vents have recently attracted attention as potential deep-sea mineral resources for base, rare, and precious metals such as Cu, Zn, Pb, In, Ga, Ge, Au, and Ag. For future exploitation of this type of deep-sea mineral resources, development of effective methods for exploring seafloor hydrothermal activity is a key to provide the most promising list of fields. However, conventional exploration methods are likely laborious and time-consuming, and a more efficient methods for exploration of seafloor hydrothermal vents are to be further developed. In the last decade, water column observation using multibeam echo souder (MBES) systems have become successfully applied to exploration of seafloor hydrothermal vents. In 2013 and 2014, we conducted extensive water column surveys using MBES systems in the mid-Okinawa Trough. During the surveys, we detected 10 hydrothermal vent sites, including previously known sites, belonging to four relatively large hydrothermal vent fields, located at the Izena Hole, Iheya North Knoll, Iheya Small Ridge, and a seamount 15 km northwest of the Izena Hole. All of the hydrothermal vent sites are in groups of 2–3 vent sites belonging to a hydrothermal field. Morphological features of the acoustic water column anomalies (rising vertically up to ~1000 m from the seafloor without a significant change of width) implied that the acoustic water column anomalies were not caused directly by hydrothermal vent fluid flows. The depth of the top of the acoustic water column anomalies (~500 m) corresponded rather well to the depth of the CO2 phase transition from liquid/clathrate-hydrate to vapor. This suggests that the acoustic water column anomalies are attributed to water mass including dense liquid CO2 droplets with clathrate-hydrate crusts, which are originally derived from the seafloor hydrothermal fluid discharges.

著者

Hisashi Muto Yoshihiro Takaki Miho Hirai Sayaka Mino Shigeki Sawayama Ken Takai Satoshi Nakagawa

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.32, no.4, pp.330-335, 2017 (Released:2017-12-27)

参考文献数

55

被引用文献数

10

---

RNA-based microbiological analyses, e.g., transcriptome and reverse transcription-quantitative PCR, require a relatively large amount of high quality RNA. RNA-based analyses on microbial communities in deep-sea hydrothermal environments often encounter methodological difficulties with RNA extraction due to the presence of unique minerals in and the low biomass of samples. In the present study, we assessed RNA extraction methods for deep-sea vent chimneys that had complex mineral compositions. Mineral-RNA adsorption experiments were conducted using mock chimney minerals and Escherichia coli total RNA solution, and showed that detectable RNA significantly decreased possibly due to adsorption onto minerals. This decrease in RNA was prevented by the addition of sodium tripolyphosphate (STPP), deoxynucleotide triphosphates (dNTPs), salmon sperm DNA, and NaOH. The addition of STPP was also effective for RNA extraction from the mixture of E. coli cells and mock chimney minerals when TRIzol reagent and the RNeasy column were used, but not when the RNeasy PowerSoil total RNA kit was used. A combination of STPP, TRIzol reagent, the RNeasy column, and sonication resulted in the highest RNA yield from a natural chimney. This indirect extraction procedure is simple, rapid, inexpensive, and may be used for large-scale RNA extraction.

著者

JUN-ICHIRO ISHIBASHI TAKUROH NOGUCHI TOMOHIRO TOKI SHUNSUKE MIYABE SHOSEI YAMAGAMI YUJI ONISHI TOSHIRO YAMANAKA YUKA YOKOYAMA ERIKO OMORI YOSHIO TAKAHASHI KENTA HATADA YUZURU NAKAGUCHI MOTOKO YOSHIZAKI UTA KONNO TAKAZO SHIBUYA KEN TAKAI FUMIO INAGAKI SHINSUKE KAWAGUCCI

出版者

GEOCHEMICAL SOCIETY OF JAPAN

雑誌

GEOCHEMICAL JOURNAL (ISSN:00167002)

巻号頁・発行日

vol.48, no.4, pp.357-369, 2014-07-20 (Released:2014-07-31)

参考文献数

48

被引用文献数

23 67

---

Two active hydrothermal fields, Jade and Hakurei fields have been discovered within the Izena Hole, a rectangular 6 km × 3 km shape depression located in the middle Okinawa Trough back arc basin. In both fields, intense hydrothermal activity is represented by venting of high-temperature fluid (>300°C) and occurrence of sulfide/sulfate ore deposits. We collected hydrothermal fluids during dive expeditions of ROV Hyper Dolphin conducted in 2003, 2010 and 2011, in order to analyze both elemental and gas species. The geochemistry of high temperature hydrothermal fluids collected from the Jade and Hakurei fields is very similar to each other with exceptions in minor gas composition. Little temporal variation was observed in geochemistry of the high-temperature hydrothermal fluid of the Jade field over two decades, since a previous study carried out in 1989. These results suggest that these fluids are derived from a common fluid reservoir where fluid chemistry is basically controlled by fluid-mineral equilibria and gas species are dominantly contributed from the same magma. Venting of low temperature fluid (about 104°C) was discovered in the distal part of the Jade field, which was named as the Biwako vent. Chemical composition of the Biwako vent fluid was distinctive from that of the high temperature fluid in the proximal part of the Jade field, and could not be explained by simple dilution or cooling. This intra-field chemical diversity could be caused by phase separation and segregation during fluid upwelling, based on relationships in concentrations of Cl and major cations. On the other hand, the chemical diversity recognized in minor gas composition between the Jade and Hakurei fields is in accordance with results from previous plume survey. Difference in concentrations of minor gases such as H2 is attributed to contribution from thermal degradation of organic matter in the sediment, during fluid upwelling.

著者

Tomo-o Watsuji Kaori Motoki Emi Hada Yukiko Nagai Yoshihiro Takaki Asami Yamamoto Kenji Ueda Takashi Toyofuku Hiroyuki Yamamoto Ken Takai

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.33, no.4, pp.348-356, 2018 (Released:2018-12-28)

参考文献数

46

被引用文献数

2 8

---

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 metabolic function of the epibiont community were investigated using S. crosnieri individuals, which were reared for one year in a tank fed with methane as the energy and carbon source. The results obtained indicated that indigenous predominant thioautotrophic populations, such as Sulfurovum and Thiotrichaceae members, became absent, possibly due to the lack of an energy source, and epibiotic communities were dominated by indigenous Methylococcaceae and betaproteobacterial methylotrophic members that adapted to the conditions present during rearing for 12 months with a supply of methane. Furthermore, the overall phylogenetic composition of the epibiotic community markedly changed from a composition dominated by chemolithotrophs to one enriched with cross-feeding heterotrophs in addition to methanotrophs and methylotrophs. Thus, the composition and function of the S. crosnieri epibiotic bacterial community were strongly affected by the balance between the energy and carbon sources supplied for chemosynthetic production as well as that between the production and consumption of organic compounds.

著者

Hisashi Muto Junichi Miyazaki Shigeki Sawayama Ken Takai Satoshi Nakagawa

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

vol.38, no.6, pp.ME23072, 2023 (Released:2023-12-16)

参考文献数

45

---

Strictly hydrogen- and sulfur-oxidizing chemolithoautotrophic bacteria, particularly members of the phyla Campylobacterota and Aquificota, have a cosmopolitan distribution in deep-sea hydrothermal fields. The successful cultivation of these microorganisms in liquid media has provided insights into their physiological, evolutionary, and ecological characteristics. Notably, recent population genetic studies on Sulfurimonas (Campylobacterota) and Persephonella (Aquificota) revealed geographic separation in their populations. Advances in this field of research are largely dependent on the availability of pure cultures, which demand labor-intensive liquid cultivation procedures, such as dilution-to-extinction, given the longstanding assumption that many strictly or facultatively anaerobic chemolithoautotrophs cannot easily form colonies on solid media. We herein describe a simple and cost-effective approach for cultivating these chemolithoautotrophs on solid media. The results obtained suggest that not only the choice of gelling agent, but also the gas phase composition significantly affect the colony-forming ratio of diverse laboratory strains. The use of gellan gum as a gelling agent combined with high concentrations of H2 and CO2 in a pouch bag promoted the formation of colonies. This contrasted with the absence of colony formation on an agar-solidified medium, in which thiosulfate served as an electron donor, nitrate as an electron acceptor, and bicarbonate as a carbon source, placed in anaerobic jars under an N2 atmosphere. Our method efficiently isolated chemolithoautotrophs from a deep-sea vent sample, underscoring its potential value in research requiring pure cultures of hydrogen- and sulfur-oxidizing chemolithoautotrophs.

著者

UTA KONNO KEN TAKAI SHINSUKE KAWAGUCCI

出版者

GEOCHEMICAL SOCIETY OF JAPAN

雑誌

GEOCHEMICAL JOURNAL (ISSN:00167002)

巻号頁・発行日

vol.47, no.4, pp.469-473, 2013-08-20 (Released:2013-11-26)

参考文献数

10

被引用文献数

1 2

---

An analytical system using continuous-flow isotope ratio mass spectrometry (CF-IRMS) was developed to determine the stable chlorine isotope ratios (δ37Cl) for CH3Cl. By using appropriate devices for sample processing prior to introduction into the spectrometer, the newly developed system successfully reduces sample requirements (>0.6 nmol-CH3Cl) to less than one hundredth of that required by the previous CF-IRMS systems while maintaining comparable precision in the δ37Cl determination (±0.1‰, 1σ). This system is also able to determine carbon isotope ratio for CH3Cl with comparable precision (±0.3‰, 1σ, >0.3 nmol-CH3Cl) to the previous study. δ37ClSMOC and δ13CVPDB values of CH3Cl in commercial tank were determined to be -6.8 ± 0.1‰ and -46.9 ± 0.3‰, respectively.

著者

Takuro Nunoura Manabu Nishizawa Miho Hirai Shigeru Shimamura Phurt Harnvoravongchai Osamu Koide Yuki Morono Toshiaki Fukui Fumio Inagaki Junichi Miyazaki Yoshihiro Takaki Ken Takai

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME17194, (Released:2018-05-25)

被引用文献数

67

---

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 lineages), Bacteroidetes, Planctomycetes, “Ca. Marinimicrobia” (SAR406), and Gemmatimonadetes and by the archaeal α subgroup of MGI Thaumarchaeota and “Ca. Woesearchaeota” (Deep-sea Hydrothermal Vent Euryarchaeotic Group 6). The SSU rRNA gene sequencing analysis indicated that the dominant populations of the thaumarchaeal α group in hadal water and sediments were similar to each other at the species or genus level. In addition, the co-occurrence of nitrification and denitrification was revealed by the combination of pore water geochemical analyses and quantitative PCR for nitrifiers.

著者

Shingo Kato Sanae Sakai Miho Hirai Eiji Tasumi Manabu Nishizawa Katsuhiko Suzuki Ken Takai

出版者

日本微生物生態学会・日本土壌微生物学会

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME17165, (Released:2018-02-16)

被引用文献数

31

---

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, and reconstructed the whole genome of the maintained populations using metagenomics. Some metagenome-assembled genomes (MAGs), affiliated into phylum-level bacterial and archaeal clades without cultivated representatives, contained genes involved in nitrogen metabolism including nitrification and denitrification. Our results show genetic components and their potential interactions for the biogeochemical nitrogen cycle in a subsurface geothermal environment.