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.

Japanese "nameko" mushrooms (Pholiota microspora) produced via sawdust-based cultivation exhibit severe genetic bottleneck associated with a single founder.

Pholiota microspora ("nameko" in Japanese) is one of the most common edible mushrooms, especially in Japan, where sawdust-based cultivation is the most dominant method accounting for 99% of the production. The current strains for sawdust cultivation in Japan are considered to have been derived from a single wild strain collected from Fukushima, Japan, implying that commercial nameko mushrooms are derived from a severe genetic bottleneck. We tested this single founder hypothesis by developing 14 microsatellite markers for P. microspora to evaluate the genetic diversity of 50 cultivars and 73 wild strains isolated from across Japan. Microsatellite analysis demonstrated that sawdust-cultivated strains from Japan were significantly less genetically diverse than the wild strains, and the former displayed a significant bottleneck signature. Analyzing the genetic relationships among all genotypes also revealed that the sawdust-cultivated samples clustered into one monophyletic subgroup. Moreover, the sawdust-cultivated samples in Japan were more closely related than full-sibs. These results were consistent with the single founder hypothesis that suggests that all commercial nameko mushrooms produced in Japan are descendants of a single ancestor. Therefore, we conclude that cultivated P. microspora originated from a single domestication event that substantially reduced the diversity of commercial nameko mushrooms in Japan.

Inhibition of Ligand Binding Ability of Three Porphyrins by an Organic Effector.

A stimulus-responsive receptor 1 was designed and prepared to control the ligand-binding ability of three active sites, two zinc tetraphenylporphyrin units (P1) and one zinc diethynyldiphenylporphyrin unit (P2), with one effector molecule 2. Bulky hexarylbenzene units were incorporated as shielding panels in the middle of the flexible side arms of 1. Spectroscopic titrations indicated that a stable supramolecular complex 1⋅2 (K1⋅2 =6.7×106 m-1 ) was produced by the cooperative formation of multiple hydrogen and coordination bonds. As a result, the binding of a ligand to P1 was inhibited by 2 in a competitive manner. Additionally, the formation of 1⋅2 brought about conformational restriction of the side arms to cover both faces of P2 with the shielding panels. The binding constant of 4-phenylpyridine with P2 in 1⋅2 decreased to 8.9 % of that in 1. Namely, the ligand-binding ability of P2 was inhibited according to an allosteric mechanism.

Numerical study of transport pathways of 137Cs from forests to freshwater fish living in mountain streams in Fukushima, Japan.

The accident at the Fukushima Dai-ichi Nuclear Power Plant in 2011 released a large quantity of radiocesium into the surrounding environment. Radiocesium concentrations in some freshwater fish caught in rivers in Fukushima Prefecture in October 2018 were still higher than the Japanese limit of 100 Bq kg-1 for general foodstuffs. To assess the uptake of 137Cs by freshwater fish living in mountain streams in Fukushima Prefecture, we developed a compartment model for the migration of 137Cs on the catchment scale from forests to river water. We modelled a generic forest catchment with Fukushima-like parameters to ascertain the importance of three export pathways of 137Cs from forests to river water for the uptake of 137Cs by freshwater fish. The pathways were direct litter fall into rivers, lateral inflow from the forest litter layer, and lateral transfer from the underlying forest soil. Simulation cases modelling only a single export pathway did not reproduce the actual trend of 137Cs concentrations in river water and freshwater fish in Fukushima Prefecture. Simulations allowing a combined effect of the three pathways reproduced the trends well. In the latter simulations, the decreasing trend of 137Cs in river water and freshwater fish was due to a combination of the decreasing trend in the forest leaves/needles and litter compartments, and the increasing trend in soil. The modelled 137Cs concentrations within the forest compartments were predicted to reach an equilibrium state at around ten years after the fallout due to the equilibration of 137Cs cycling in forests. The model suggests that long term 137Cs concentrations in freshwater fish in mountain streams will be controlled by the transfer of 137Cs to river water from forest organic soils.

Role of filamentous fungi in migration of radioactive cesium in the Fukushima forest soil environment.

The fate of radioactive Cs deposited after the Fukushima nuclear power plant accident and its associated radiological impacts are largely dependent on its mobility from surface soils to forest ecosystems. We measured the accumulation of radioactive Cs in the fruit bodies of wild fungi in a forest at Iitate, Fukushima, Japan. The transfer factors (TFs) of radioactive Cs from soil to the fruit bodies of wild fungi were between 10-2 and 102, a range similar to that reported for the fruit bodies collected in Europe after the Chernobyl accident and in parts of Japan contaminated by the nuclear bomb test fallout. Comparison of the TFs of wild mushroom and those of fungal hyphae of 704 stock strains grown on agar medium containing nutrients and 137Cs showed that the TFs of wild mushroom were lower. The TF was less than 0.1 after the addition of the minerals zeolite, vermiculite, phlogopite, smectite, or illite of 1.0% weight to the agar medium. These results indicate that the presence of minerals decreases Cs uptake by fungi grown on the agar medium, and filamentous fungi still accumulate radioactive Cs even when minerals are present in the medium.

Direct accumulation pathway of radioactive cesium to fruit-bodies of edible mushroom from contaminated wood logs.

This paper presents the accumulation process of radioactive Cs in edible mushrooms. We here first report the direct accumulation pathway of radioactive Cs from contaminated wood logs to the fruit-bodies of shiitake mushrooms through the basal portion of the stipe. In this pathway, radioactive Cs is not transported through the hyphae. This pathway results in a high accumulation of radioactive Cs in the fruit-body, more by the excess accumulation of radioactive Cs from the wood logs than that through the hyphae. We grew the fruit-bodies of Shiitake mushroom from radioactive-Cs-contaminated wood logs. The spatial distributions of radioactive Cs and Prussian blue as a tracer of interstitial water in the cross section of the wood log measured after the harvest of the fruit-body from the inoculated sawdust spawn area indicated that some fraction of the radioactive Cs and Prussian blue were transported directly to the basal portion of the stipe during the growth of the fruit-bodies.

Input and output budgets of radiocesium concerning the forest floor in the mountain forest of Fukushima released from the TEPCO's Fukushima Dai-ichi nuclear power plant accident.

Estimations of radiocesium input and output concerning the forest floor within a mountain forest region have been conducted in the north and central part of the Abukuma Mountains of Fukushima, northeast Japan, after a 2-3 year period following the TEPCO Fukushima Dai-ichi nuclear power plant accident. The radiocesium input and output associated with surface washoff, throughfall, stemflow, and litterfall processes at experimental plots installed on the forest floor of evergreen Japanese cedars and deciduous Konara oaks have been monitored. Despite the high output potential in the mountainous forest of Fukushima, the results at both monitoring locations show the radiocesium input to be 4-50 times higher than the output during the summer monsoon in Fukushima. These results indicate that the radiocesium tends to be preserved in the forest ecosystem due to extremely low output ratios (0.05%-0.19%). Thus, the associated fluxes throughout the circulation process are key issues for the projecting the environmental fate of the radiocesium levels, along with the subsequent reconstruction of life emphasized within the setting.

The transfer of radiocesium from the bark to the stemflow of chestnut trees (Castanea crenata) contaminated by radionuclides from the Fukushima Dai-ichi nuclear power plant accident.

We report on the behavior of radiocesium in tree bark and its transfer into the stemflows of chestnut trees in a forest in the Fukushima Prefecture, Japan. In stems that were present at the time of the accident, the radiocesium concentration of the bark was found to be approximately 10 times that of the wood. The average (137)Cs concentration of the dissolved fraction (<0.45 µm) in the stemflow was measured to be around 10 Bq/L. The (137)Cs concentration ratio [present at the time of the accident (Bq/kg) in the bark/the dissolved fraction in the stemflow (Bq/L)] was approximately 10(3). A strong positive correlation was observed between the radiocesium concentration and the electrical conductivity of the dissolved fraction of the stemflow; this result suggests that radiocesium and electrolytes have the same elution mechanism from the tree. The size fractionation analysis of the <0.45 µm fraction through ultrafiltration revealed that the radiocesium was present as an almost dissolved species. Some of the particles in the particulate fraction (>0.45 µm) of the stemflow were strongly adsorbed radiocesium.

Occurrence and potential activity of denitrifiers and methanogens in groundwater at 140 m depth in Pliocene diatomaceous mudstone of northern Japan.

Anaerobic microbial activity has a major influence on the subsurface environment. We investigated the denitrification and methanogenesis in anoxic groundwater at a depth of 140 m in two boreholes drilled in a sedimentary geological setting, where the redox potential fluctuated. The average maximum potential denitrification rates, measured under anaerobic conditions in the two boreholes using an (15) N tracer, were 0.060 and 0.085 nmol (30) N2  mL(-1)  h(-1) . The deduced NirS amino acid sequences obtained from in situ samples were similar to those of isolates belonging to the α-, ß-, and γ-Proteobacteria, and the Firmicutes (72-100% similarity). Based on the nirS gene, the same operational taxonomic unit dominated incubated samples from each borehole. Methanogenesis candidates were detected by 16S rRNA gene analysis, but no sequence was detected using primers for the functional methanogenesis gene mcrA. Although the stable isotope signatures suggested that some of the dissolved methane was of biogenic origin, no potential for methane production was evident during the incubations. The groundwater at 140 m depth did not contain oxygen, had an Eh ranging from -144 to 6.8 mV, and was found to be a potential field for denitrification.

Generation of mercury-hyperaccumulating plants through transgenic expression of the bacterial mercury membrane transport protein MerC.

The merC gene from Acidithiobacillus ferrooxidans functions as a mercury uptake pump. MerC protein localizes in the cytoplasmic membrane of plant cells. When Arabidopsis thaliana and tobacco plants were transformed with the merC gene under the control of the Cauliflower mosaic virus 35S promoter, the resulting overexpression of merC rendered the host plants hypersensitive to Hg2+ and they accumulated approximately twice as much Hg2+ ion as the wild type plants. Thus, bacterial mercuric ion transporters such as MerC may be useful molecular tools for producing transgenic plants that hyperaccumulate Hg2+ ion.

Functional dissection of a mercuric ion transporter, MerC, from Acidithiobacillus ferrooxidans.

Topological analysis with a phoA gene fusion suggested that Acidithiobacillus ferrooxidans MerC, a mercury transporter, has two periplasmic loops and four transmembrane domains. Cys-23 and Cys-26 of the protein were involved in Hg(2+)-recognition/uptake, but Cys-132 and Cys-137 were not. Escherichia coli cells producing the MerC were hypersensitive to CdCl(2). In this case, mutation of His72 rendered the host cells less CdCl(2) sensitive, whereas none of the Cys residues affected it. E. coli cells expressing the gene encoding a mercuric ion transporter (merC)-deletion mutant, in which the coding-sequence of the carboxy-terminal cytoplasmic region was removed, retained Hg(2+) hypersensitivity and showed about 55% HgCl(2) uptake ability compared to that of the one expressing the intact merC, indicating that the region is not essential for Hg(2+) uptake. Coexpression of A. ferrooxidans the gene encoding mercuric reductase (merA) and the merC deletion mutation conferred HgCl(2) tolerance to E. coli host cells. Under this condition, the merC deletion gene product was exclusively present as a monomer.

Conversion of a typical catalase from Bacillus sp. TE124 to a catalase-peroxidase by directed evolution.

We have converted a typical catalase from Bacillus sp. TE124 to a catalase-peroxidase using DNA shuffling and error-prone PCR. A triple mutant, R47H/R356C/D374N, that showed significantly reduced catalase activity and increased peroxidase activity was identified by screening mutant libraries. When single mutant--R47H, R356C and D374N--were generated by site-directed mutagenesis, conserved Arg-47, located on the distal side of the prosthetic heme group in the superfamily of typical catalases, was found to be responsible for the conversion of catalase to catalase-peroxidase. To further clarify the role of Arg-47, arginine was replaced with different amino acids--alanine, lysine, aspartic acid, glutamic acid, glutamine, phenylalanine, tryptophan and tyrosine--and the mutant enzymes were assayed. All of the arginine mutants had increased peroxidase activity coupled with reduced catalase activity. Among these mutants, R47W exhibited the highest peroxidase activity, while R47E and R47Q not only had increased peroxidase activity but also retained relatively high catalase activity. These results suggest that tryptophan plays a key role in the catalytic mechanism of the peroxidase reaction and that glutamic acid and glutamine facilitate both catalatic and peroxidatic reactions.