Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station.

A major incident occurred at the Fukushima Daiichi Nuclear Power Station following the tsunami triggered by the Tohoku-Pacific Ocean Earthquake in March 2011, whereby seawater entered the torus room in the basement of the reactor building. Here, we identify and analyze the bacterial communities in the torus room water and several environmental samples. Samples of the torus room water (1 × 109 Bq137Cs/L) were collected by the Tokyo Electric Power Company Holdings from two sampling points between 30 cm and 1 m from the bottom of the room (TW1) and the bottom layer (TW2). A structural analysis of the bacterial communities based on 16S rRNA amplicon sequencing revealed that the predominant bacterial genera in TW1 and TW2 were similar. TW1 primarily contained the genus Limnobacter, a thiosulfate-oxidizing bacterium. γ-Irradiation tests on Limnobacter thiooxidans, the most closely related phylogenetically found in TW1, indicated that its radiation resistance was similar to ordinary bacteria. TW2 predominantly contained the genus Brevirhabdus, a manganese-oxidizing bacterium. Although bacterial diversity in the torus room water was lower than seawater near Fukushima, ~70% of identified genera were associated with metal corrosion. Latent environment allocation-an analytical technique that estimates habitat distributions and co-detection analyses-revealed that the microbial communities in the torus room water originated from a distinct blend of natural marine microbial and artificial bacterial communities typical of biofilms, sludge, and wastewater. Understanding the specific bacteria linked to metal corrosion in damaged plants is important for advancing decommissioning efforts. IMPORTANCE: In the context of nuclear power station decommissioning, the proliferation of microorganisms within the reactor and piping systems constitutes a formidable challenge. Therefore, the identification of microbial communities in such environments is of paramount importance. In the aftermath of the Fukushima Daiichi Nuclear Power Station accident, microbial community analysis was conducted on environmental samples collected mainly outside the site. However, analyses using samples from on-site areas, including adjacent soil and seawater, were not performed. This study represents the first comprehensive analysis of microbial communities, utilizing meta 16S amplicon sequencing, with a focus on environmental samples collected from the radioactive element-containing water in the torus room, including the surrounding environments. Some of the identified microbial genera are shared with those previously identified in spent nuclear fuel pools in countries such as France and Brazil. Moreover, our discussion in this paper elucidates the correlation of many of these bacteria with metal corrosion.

The Birthplace of Proto-Life: Role of Secondary Minerals in Forming Metallo-Proteins through Water-Rock Interaction of Hadean Rocks.

The surface of Hadean Earth was mainly covered with three types of rocks-komatiite, KREEP basalt and anorthosite-which were remarkably different from those on the modern Earth. The water-rock interaction between these rocks and water provided a highly reducing environment and formed secondary minerals on the surface of the rocks that are important for producing metallo-enzymes for the emergence of primordial life. Previous studies suggested a correlation between the active site of metallo-enzymes and sulfide minerals based on the affinity of their structures, but they did not discuss the origin of metallic elements contained in these minerals which is critical to understanding where life began. We investigated secondary minerals formed through water-rock interactions of komatiite in a subaerial geyser system, then discussed the relationship between the active site of metallo-enzymes and secondary minerals. Instead of komatiite, we used serpentinite collected from the Hakuba Happo area, Nagano Prefecture in central-north Japan, which is thought to be a modern analog for the Hadean environment. We found several minor minerals, such as magnetite, chromite, pyrite and pentlandite in addition to serpentine minerals. Pentlandite has not been mentioned in previous studies as one of the candidates that could supply important metallic elements to build metallo-enzymes. It has been shown to be a catalyst for hydrogen generation possibly, because of structural similarity to the active site of hydrogenases. We consider the possibility that nickel-iron sulfide, pentlandite, could be important minerals for the origin of life. In addition, we estimated what kinds of minor minerals would be obtained from the water-rock interaction of these rocks using thermodynamic calculations. KREEP basalt contains a large amount of iron and it could be useful for producing metallo-enzymes, especially ferredoxins-electron transfer enzymes, which may have assisted in the emergence of life.

Metagenomic Thermometer.

Various microorganisms exist in environments, and each of them has its optimal growth temperature (OGT). The relationship between genomic information and OGT of each species has long been studied, and one such study revealed that OGT of prokaryotes can be accurately predicted based on the fraction of seven amino acids (IVYWREL) among all encoded amino-acid sequences in its genome. Extending this discovery, we developed a 'Metagenomic Thermometer' as a means of predicting environmental temperature based on metagenomic sequences. Temperature prediction of diverse environments using publicly available metagenomic data revealed that the Metagenomic Thermometer can predict environmental temperatures with small temperature changes and little influx of microorganisms from other environments. The accuracy of the Metagenomic Thermometer was also confirmed by a demonstration experiment using an artificial hot water canal. The Metagenomic Thermometer was also applied to human gut metagenomic samples, yielding a reasonably accurate value for human body temperature. The result further suggests that deep body temperature determines the dominant lineage of the gut community. Metagenomic Thermometer provides a new insight into temperature-driven community assembly based on amino-acid composition rather than microbial taxa.

Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era.

Methanogenic microbes may be one of the most primitive organisms, although it is uncertain when methanogens first appeared on Earth. During the Archaean era (before 2.5 Gyr ago), methanogens may have been important in regulating climate, because they could have provided sufficient amounts of the greenhouse gas methane to mitigate a severely frozen condition that could have resulted from lower solar luminosity during these times. Nevertheless, no direct geological evidence has hitherto been available in support of the existence of methanogens in the Archaean period, although circumstantial evidence is available in the form of approximately 2.8-Gyr-old carbon-isotope-depleted kerogen. Here we report crushing extraction and carbon isotope analysis of methane-bearing fluid inclusions in approximately 3.5-Gyr-old hydrothermal precipitates from Pilbara craton, Australia. Our results indicate that the extracted fluids contain microbial methane with carbon isotopic compositions of less than -56 per thousand included within original precipitates. This provides the oldest evidence of methanogen (> 3.46 Gyr ago), pre-dating previous geochemical evidence by about 700 million years.

Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals.

As a consequence of recent developments in molecular phylogenomics, all extant orders of placental mammals have been grouped into 3 lineages: Afrotheria, Xenarthra, and Boreotheria, which originated in Africa, South America, and Laurasia, respectively. Despite this advancement, the order of divergence of these 3 lineages remains unresolved. Here, we performed extensive retroposon analysis with mammalian genomic data. Surprisingly, we identified a similar number of informative retroposon loci that support each of 3 possible phylogenetic hypotheses: the basal position for Afrotheria (22 loci), Xenarthra (25 loci), and Boreotheria (21 loci). This result indicates that the divergence of the placental common ancestor into the 3 lineages occurred nearly simultaneously. Thus, we examined whether these molecular data could be integrated into the geological context by incorporating recent geological data. We obtained firm evidence that complete separation of Gondwana into Africa and South America occurred 120 +/- 10 Ma. Accordingly, the previous reported time frame (division of Pangea into Gondwana and Laurasia at 148-138 Ma and division of Gondwana at 105 Ma) cannot be used to validate mammalian divergence order. Instead, we use our retroposon results and the recent geological data to propose that near-simultaneous divisions of continents leading to isolated Africa, South America, and Laurasia caused nearly concomitant divergence of the ancient placental ancestor into 3 lineages, Afrotheria, Xenarthra, and Boreotheria, approximately 120 Ma.

Micro-scale (1.5 microm) sulphur isotope analysis of contemporary and early Archean pyrite.

We present a method for in situ sulphur (S) isotopic analysis of significantly small areas (1.5 microm in diameter) in pyrite using secondary ion mass spectrometry (NanoSIMS) to interpret microbial sulphur metabolism in the early earth. We evaluated the precision and accuracy of S isotopic ratios obtained by this method using hydrothermal pyrite samples with homogeneous S isotopic ratios. The internal precision of the delta(34)S value was 1.5 per thousand at the level of 1 sigma of standard error (named 1SE) for a single spot, while the external reproducibility was estimated to be 1.6 per thousand at the level of 1 sigma of standard deviation (named 1SD, n = 25). For each separate sample, the average delta(34)S value was comparable with that measured by a conventional method, and the accuracy was better than 2.3 per thousand. Consequently, the in situ method is sufficiently accurate and precise to detect the S isotopic variations of small sample of the pyrite (less than 20 microm) that occurs ubiquitously in ancient sedimentary rocks. This method was applied to measure the S isotopic distribution of pyrite within black chert fragments in early Archean sandstone. The pyrite had isotopic zoning with a (34)S-depleted core and (34)S-enriched rim, suggesting isotopic evolution of the source H(2)S from -15 to -5 per thousand. Production of H(2)S by microbial sulphate reduction (MSR) in a closed system provides a possible explanation for both the (34)S-depleted initial H(2)S and the progressive increase in the delta(34)S(H2S) value. Although more extensive data are necessary to strengthen the explanation for the origin of the MSR, the results show that the S isotopic distribution within pyrite crystals may be a key tracer for MSR activity in the early earth.

The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan.

Diverse microorganisms specifically inhabit extreme environments, such as hot springs and deep-sea hydrothermal vents. To test the hypothesis that the microbial community structure is predictable based on environmental factors characteristic of such extreme environments, we conducted correlation analyses of microbial taxa/functions and environmental factors using metagenomic and 61 types of physicochemical data of water samples from nine hot springs in the Kirishima area (Kyusyu, Japan), where hot springs with diverse chemical properties are distributed in a relatively narrow area. Our metagenomic analysis revealed that the samples can be classified into two major types dominated by either phylum Crenarchaeota or phylum Aquificae. The correlation analysis showed that Crenarchaeota dominated in nutrient-rich environments with high concentrations of ions and total carbons, whereas Aquificae dominated in nutrient-poor environments with low ion concentrations. These environmental factors were also important explanatory variables in the generalized linear models constructed to predict the abundances of Crenarchaeota or Aquificae. Functional enrichment analysis of genes also revealed that the separation of the two major types is primarily attributable to genes involved in autotrophic carbon fixation, sulfate metabolism and nitrate reduction. Our results suggested that Aquificae and Crenarchaeota play a vital role in the Kirishima hot spring water ecosystem through their metabolic pathways adapted to each environment. Our findings provide a basis to predict microbial community structures in hot springs from environmental parameters, and also provide clues for the exploration of biological resources in extreme environments.

Changes of aliphatic C-H bonds in cyanobacteria during experimental thermal maturation in the presence or absence of silica as evaluated by FTIR microspectroscopy.

Aliphatic C-H bonds are one of the major organic signatures detected in Proterozoic organic microfossils, and their origin is a topic of interest. To investigate the influence of the presence of silica on the thermal alteration of aliphatic C-H bonds in prokaryotic cells during diagenesis, cyanobacteria Synechocystis sp. PCC6803 were heated at temperatures of 250-450°C. Changes in the infrared (IR) signals were monitored by micro-Fourier transform infrared (FTIR) spectroscopy. Micro-FTIR shows that absorbances at 2,925 cm-1 band (aliphatic CH2 ) and 2,960 cm-1 band (aliphatic CH3 ) decrease during heating, indicating loss of the C-H bonds, which was delayed by the presence of silica. A theoretical approach using solid-state kinetics indicates that the most probable process for the aliphatic C-H decrease is three-dimensional diffusion of alteration products under both non-embedded and silica-embedded conditions. The extrapolation of the experimental results obtained at 250-450°C to lower temperatures implies that the rate constant for CH3 (kCH3 ) is similar to or lower than that for CH2 (kCH2 ; i.e., CH3 decreases at a similar rate or more slowly than CH2 ). The peak height ratio of 2,960 cm-1 band (CH3 )/2,925 cm-1 band (CH2 ; R3/2 values) either increased or remained constant during the heating. These results reveal that the presence of silica does affect the decreasing rate of the aliphatic C-H bonds in cyanobacteria during thermal maturation, but that it does not significantly decrease the R3/2 values. Meanwhile, studies of microfossils suggest that the R3/2 values of Proterozoic prokaryotic fossils from the Bitter Springs Group and Gunflint Formation have decreased during fossilization, which is inconsistent with the prediction from our experimental results that R3/2 values did not decrease after silicification. Some process other than thermal degradation, possibly preservation of specific classes of biomolecules with low R3/2 values, might have occurred during fossilization.

Ar-Ar dating for hydrothermal quartz from the 2.4 Ga Ongeluk Formation, South Africa: implications for seafloor hydrothermal circulation.

Fluid inclusions in hydrothermal quartz in the 2.4 Ga Ongeluk Formation, South Africa, are expected to partially retain a component of the ancient seawater. To constrain the origin of the fluid and the quartz precipitation age, we conducted Ar-Ar dating for the quartz via a stepwise crushing method. The obtained argon isotopes show two or three endmembers with one or two binary mixing lines as the crushing proceeds, suggesting that the isotopic compositions of these endmembers correspond to fluid inclusions of each generation, earlier generated smaller 40Ar- and K-rich inclusions, moderate 40Ar- and 38ArCl (neutron-induced 38Ar from Cl)-rich inclusions and later generated larger atmospheric-rich inclusions. The K-rich inclusions show significantly different 40Ar/38ArCl values compared to the 38ArCl-rich inclusions, indicating that it is difficult to constrain the quartz formation age using only fluid inclusions containing excess 40Ar. The highest obtained 40Ar/36Ar value from the fluid inclusions is consistent with an expected value of the Ongeluk plume source, suggesting that the quartz precipitation was driven by Ongeluk volcanism. Considering the fluid inclusion generations and their compositions, the hydrothermal system was composed of crustal fluid and magmatic fluid without seawater before the beginning of a small amount of seawater input to the hydrothermal system.

In situ infrared microspectroscopy of approximately 850 million-year-old prokaryotic fossils.

In situ infrared (IR) and Raman microspectroscopy have been conducted on Neoproterozoic, organic-walled microfossils (prokaryotic fossils) in doubly polished, petrographic thin sections in order to detect their spectral signatures. The microfossils are very well preserved and occur in black chert from the approximately 850 million-year-old Bitter Springs Formation, Northern Territory, Australia. Raman microspectroscopy on two species of microfossils, one a filament and the other a coccoid, shows disordered peaks (D peak, 1340 cm(-1)) and graphite peaks (G peak, 1600 cm(-1)), indicating that they consist of disordered carbonaceous materials. IR micro-mapping results of the filament reveal that the distributions of peak heights at 2920 cm(-1) (aliphatic CH(2)), 1585 cm(-1) (aromatic C-C), and 1370 cm(-1) (aliphatic CH(3)) match the shape of the filamentous microfossil. These results suggest that IR microspectroscopy can be used for in situ characterization of organic polar signatures that morphologically indicate microfossils embedded in chert by using doubly-polished rock (petrographic) thin section samples. Further, these methods can be applied to controversial microfossil-like structures to test their biogenic nature.

The Argyre Region as a Prime Target for in situ Astrobiological Exploration of Mars.

At the time before ∼3.5 Ga that life originated and began to spread on Earth, Mars was a wetter and more geologically dynamic planet than it is today. The Argyre basin, in the southern cratered highlands of Mars, formed from a giant impact at ∼3.93 Ga, which generated an enormous basin approximately 1800 km in diameter. The early post-impact environment of the Argyre basin possibly contained many of the ingredients that are thought to be necessary for life: abundant and long-lived liquid water, biogenic elements, and energy sources, all of which would have supported a regional environment favorable for the origin and the persistence of life. We discuss the astrobiological significance of some landscape features and terrain types in the Argyre region that are promising and accessible sites for astrobiological exploration. These include (i) deposits related to the hydrothermal activity associated with the Argyre impact event, subsequent impacts, and those associated with the migration of heated water along Argyre-induced basement structures; (ii) constructs along the floor of the basin that could mark venting of volatiles, possibly related to the development of mud volcanoes; (iii) features interpreted as ice-cored mounds (open-system pingos), whose origin and development could be the result of deeply seated groundwater upwelling to the surface; (iv) sedimentary deposits related to the formation of glaciers along the basin's margins, such as evidenced by the ridges interpreted to be eskers on the basin floor; (v) sedimentary deposits related to the formation of lakes in both the primary Argyre basin and other smaller impact-derived basins along the margin, including those in the highly degraded rim materials; and (vi) crater-wall gullies, whose morphology points to a structural origin and discharge of (wet) flows.

Domain-level identification and quantification of relative prokaryotic cell abundance in microbial communities by Micro-FTIR spectroscopy.

Domain-level identification of microbial cells or cell-like structures is crucial for investigating natural microbial communities and their ecological significance. By using micro-Fourier transform infrared (micro-FTIR) spectroscopy, we established a technical basis for the domain-level diagnosis and quantification of prokaryotic cell abundance in natural microbial communities. Various prokaryotic cultures (12 species of bacteria and 10 of archaea) were examined using micro-FTIR spectroscopic analysis. The aliphatic CH3 /CH2 absorbance ratios (R3/2 ) showed domain-specific signatures, possibly reflecting distinctive cellular lipid compositions. The signatures were preserved even after chemical cell fixation (formaldehyde) and nucleic acid staining (DAPI) processes - techniques that are essential in studying microbial ecology. The micro-FTIR technique was successfully applied for quantification of the bacteria/archaea abundance ratio in an active microbial mat community in a subsurface hot aquifer stream. We conclude that the micro-FTIR R3/2 measurement is both fast and effective for domain-level diagnosis and quantification of first-order prokaryotic community structures.