Springs In Japan Research Articles

Sulfuriferula thiophila sp. nov., a chemolithoautotrophic sulfur-oxidizing bacterium, and correction of the name Sulfuriferula plumbophilusWatanabe, Kojima and Fukui 2015 to Sulfuriferula plumbiphila corrig.

A novel sulfur-oxidizing bacterium designated strain mst6T was isolated from spring water of Masutomi hot spring in Japan. The cells were rod-shaped (1.2-4.0 × 0.5-0.7 μm) and Gram-stain-negative. The G+C content of genomic DNA was around 52.6 mol%. The isolate possessed summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0 as major cellular fatty acids. Strain mst6T grew by inorganic carbon fixation and oxidation of inorganic sulfur compounds with oxygen as an electron acceptor. The isolate grew over a temperature range of 5-34 °C, a NaCl concentration range of 0-110 mM and a pH range of 4.6-8.1. Optimum growth occurred at 32 °C, in the absence of NaCl and at pH 5.9-6.2. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain mst6T belongs to the family Sulfuricellaceae in the class Betaproteobacteria. The closest cultured relative was Sulfuriferula multivorans TTNT with a 16S rRNA gene sequence similarity of 97.0 %. On the basis of the data obtained in this study, strain mst6T represents a novel species of the genus Sulfuriferula, for which the name Sulfuriferula thiophila sp. nov. is proposed. The type strain is mst6T ( = NBRC 111150T = DSM 101871T). In addition, we propose correcting the name Sulfuriferula plumbophilus Watanabe, Kojima and Fukui 2015 to Sulfuriferula plumbiphila corrig. based on Rule 12c, Rule 61 and Appendix 9 of the International Code of Nomenclature of Prokaryotes.

Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage φOH3 Which Infects Thermus thermophilus HB8.

A filamentous bacteriophage, φOH3, was isolated from hot spring sediment in Obama hot spring in Japan with the hyperthermophilic bacterium Thermus thermophilus HB8 as its host. Phage φOH3, which was classified into the Inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φOH3 was stable at temperatures ranging from 70 to 90°C and at pHs ranging from 6 to 9. A one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, followed by intracellular virus particle production during the subsequent 40 min. The released virion number of φOH3 was 109. During the latent period, both single stranded DNA (ssDNA) and the replicative form (RF) of phage DNA were multiplied from min 40 onward. During the release period, the copy numbers of both ssDNA and RF DNA increased sharply. The size of the φOH3 genome is 5688 bp, and eight putative open reading frames (ORFs) were annotated. These ORFs were encoded on the plus strand of RF DNA and showed no significant homology with any known phage genes, except ORF 5, which showed 60% identity with the gene VIII product of the Thermus filamentous phage PH75. All the ORFs were similar to predicted genes annotated in the Thermus aquaticus Y51MC23 and Meiothermus timidus DSM 17022 genomes at the amino acid sequence level. This is the first report of the whole genome structure and DNA multiplication of a filamentous T. thermophilus phage within its host cell.

Caldimicrobium thiodismutans sp. nov., a sulfur-disproportionating bacterium isolated from a hot spring, and emended description of the genus Caldimicrobium.

A novel autotrophic, thermophilic bacterium, strain TF1T, was isolated from a hot spring in Japan. Cells of strain TF1T were motile, Gram-stain-negative, rod-shaped, 1.0-2.0 μm in length and 0.5-0.6 μm in width. Major components in the cellular fatty acid profile were C16:0, C18:0 and anteiso-C17:0. The temperature range for growth was 40-77 °C, and optimum temperature was 75 °C. The pH range for growth was 5.9-9.5, and the optimum pH was 7.5-8.8. Strain TF1T grew chemolithoautotrophically by disproportionation of sulfur, thiosulfate and sulfite. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the family Thermodesulfobacteriaceae. The closest cultivated relative was Caldimicrobium rimae DST, with highest 16S rRNA gene sequence similarity of 96%. The genome of strain TF1T consists of one circular chromosome, with a size of 1.8 Mbp and G+C content of 38.30 mol%. On the basis of its phylogenetic and phenotypic properties, strain TF1T (=DSM 29380T=NBRC 110713T) is proposed as the type strain of a novel species, Caldimicrobium thiodismutans sp. nov.

Draft Genome Sequence of High-Temperature-Adapted Protochlamydia sp. HS-T3, an Amoebal Endosymbiotic Bacterium Found in Acanthamoeba Isolated from a Hot Spring in Japan

Here, we report the draft genome sequence of high-temperature-adapted Protochlamydia sp. strain HS-T3, an environmental chlamydia. This bacterium is an amoebal endosymbiont, found in Acanthamoeba isolated from a hot spring in Japan. Strain HS-T3 readily grew in mammalian cells at 37°C, a characteristic not previously reported for environmental chlamydiae.

Secreted protease mediates interspecies interaction and promotes cell aggregation of the photosynthetic bacterium Chloroflexus aggregans.

Interspecies interactions were studied in hot spring microbial mats where diverse species of bacterial cells are densely packed. The anoxygenic photosynthetic bacterium, Chloroflexus aggregans, has been widely found in the microbial mats as a major component in terrestrial hot springs in Japan at the temperature from 50 to 70°C. C. aggregans shows cellular motility to form a microbial mat-like dense cell aggregate. The aggregating ability of C. aggregans was affected by another bacterial species, strain BL55a (related to Bacillus licheniformis) isolated from the microbial mats containing C. aggregans. Cell aggregation rate of C. aggregans was promoted by the addition of culture supernatants of strain BL55a. Similar effects were also detected from other bacterial isolates, specifically Geobacillus sp. and Aeribacillus sp. Protease activity was detected from the culture supernatants from all of these isolates. The promoting effect of strain BL55a was suppressed by a serine protease inhibitor, phenylmethylsulfonyl fluoride. A purified serine protease, subtilisin obtained from B. licheniformis, showed a promoting effect on the cell aggregation. These results suggest that an extracellular protease, secreted from co-existing bacterial species promoted the aggregating motility of C. aggregans. This is the first report that exogenous protease affects bacterial cellular motility.

3-3．温泉に関連した資格制度

3-3．温泉に関連した資格制度

Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs

Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06(T) and AZM44c09(T), were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06(T) were 60 °C, pH 7.4 and 0% additional NaCl, and those for strain AZM44c09(T) were 70 °C, pH 7.4 and 0% additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06(T)) and 2.01 Mbp (AZM44c09(T)). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga. The closest relatives of strains AZM34c06(T) and AZM44c09(T) were the type strains of Thermotoga lettingae (96.0% similarity based on the 16S rRNA gene and 84.1% similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7% similarity), respectively. Using blast, the average nucleotide identity was 70.4-70.5% when comparing strain AZM34c06(T) and T. lettingae TMO(T) and 76.6% when comparing strain AZM44c09(T) and T. hypogea NBRC 106472(T). Both values are far below the 95% threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06(T) = NBRC 106115(T) = DSM 23275(T)) and Thermotoga caldifontis sp. nov. (type strain AZM44c09(T) = NBRC 106116(T) = DSM 23272(T)).

Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4.

Rubrobacter radiotolerans strain RSPS-4 is a slightly thermophilic member of the phylum “Actinobacteria” isolated from a hot spring in São Pedro do Sul, Portugal. This aerobic and halotolerant bacterium is also extremely resistant to gamma and UV radiation, which are the main reasons for the interest in sequencing its genome. Here, we present the complete genome sequence of strain RSPS-4 as well as its assembly and annotation. We also compare the gene sequence of this organism with that of the type strain of the species R. radiotolerans isolated from a hot spring in Japan. The genome of strain RSPS-4 comprises one circular chromosome of 2,875,491 bp with a G+C content of 66.91%, and 3 circular plasmids of 190,889 bp, 149,806 bp and 51,047 bp, harboring 3,214 predicted protein coding genes, 46 tRNA genes and a single rRNA operon.

過去26年間のスギ花粉飛散パターンのクラスター分析

Pollinosis caused by the pollen of Sugi (Cryptopmeria japonica) trees is the most significant allergic disease occurring in the spring in Japan. For pollinosis patients and medical staff, it is important to know when the pollen dispersion would reach maximum or when the pollen count would decrease as well as knowing what would the total density of pollen grains be. These sorts of information could be useful for the purpose of disease prevention and deciding on the therapeutic regimen. In this study, we presented the sugi-dispersal patterns and cited several examples of the dispersal pattern. Airborne pollen grains were collected using a Durham sampler. Total annual pollen counts/cm2 were examined. The sugi-dispersal patterns were classified into several groups by cluster analysis using variables of ten days pollen counts distribution from February to April for the past 26 years. (1987-2012). The annual pollen count revealed an alternate rhythm consisting of an "on" year (high pollen count) and an "off" year (low pollen count). The results of the cluster analysis showed eleven off-years classified as one group (group 1), and fifteen on-years classified into three groups (groups 2A, 2B, and 2C). The dispersal pattern in group 1 was almost symmetrical with the pollen count rapidly decreasing until late-March. On the other hand, the patterns in group 2 were asymmetrical. In group 2A and 2B a high rate of dispersion was indicated after maximum dispersion, whereas in group 2C the high rate of dispersion was indicated before maximum dispersion. In group 2A, a major dispersion of almost 3000 grains was noted in late-March, and immediately proceeded to the cypress (Chamaecyparis) pollen season without any decrease seen in pollen dispersion. The periods of dispersion of over 10 pollen grains/cm2 per day were 38, 47, 47 and 51 days in groups 1, 2A, 2B and 2C, respectively. That in group 2 was significantly longer than that in group 1, but there was no significant differences between groups 2A, 2B and 2C. In conclusion, in the dispersal pattern whereby a major dispersion was seen in late-March and proceeded to the cypress pollen season such as in group 2A, patients' symptoms might be prolonged or be more serious. This new concept of dispersal pattern could very well be useful for clinical management of pollinosis.

Draft Genome Sequence of a Thermophilic Member of the Bacillaceae , Anoxybacillus flavithermus Strain Kn10, Isolated from the Kan-nawa Hot Spring in Japan

Here, we report the draft genome sequence of the Anoxybacillus flavithermus Kn10 strain (NBRC 109594), isolated from a water drain of the Kan-nawa Hot Spring in Japan. The draft genome sequence is composed of 90 contigs for 2,772,624 bp with 41.6% G+C content and contains 2,883 protein-coding genes and 80 tRNA genes.

Changes in quantity of Cry j1, a major cedar pollinosis allergen, in Cryptomeria japonica pollen during spring in Japan

The changes in quantity of Cry j1 in Cryptomeria japonica pollen were assessed during the course of spring in Japan. C. japonica pollen was collected from the same trees in Hiroshima and Yamanashi Prefectures, and Cry j1 was quantified by enzyme-linked immunosorbent assay. The quantities of Cry j1 were found to gradually decrease, and this trend was similar in both Hiroshima and Yamanashi Prefectures. In Yamanashi Prefecture, no significant differences in the quantities of Cry j1 between the upper and lower parts of the tree were observed in samples collected from March 1 to 14. Furthermore, the quantities of Cry j1 on March 1, 5, 10 and 14 were significantly lower than those on February 1. These results suggest that expression of C. japonica pollen levels in terms of particle numbers is not sufficient and that quantities of Cry j1 vary throughout the course of spring.

Mn(II)-Oxidizing Activity of <i>Pseudomonas</i> sp. Strain MM1 is Involved in the Formation of Massive Mn Sediments around Sambe Hot Springs in Japan

There has been an increasing interest in the application of Mn(II) oxidizing microbes for Mn(II) containing waste water treatment, as well as biogenic Mn oxides for remediation of a number of toxic metals. Sambe hot spring in Shimane Prefecture, Japan is known for its Mn-rich spring water, and Mn oxide sediments are widely distributed over an area of 60m © 80m of this region. With an aim to find out Mn(II) oxidizing bacteria involved in this massive Mn(II) oxide deposit formation, culture enrichment was undertaken. Pseudomonas sp. strain MM1 was isolated as dominant Mn(II) oxidizing bacterium from the site. Biogenic Mn oxide formed by strain MM1 was shown to be poorly-crystalline birnessite, having the large specific surface area of 90m 2 ·g ¹1 . Mn(II) was readily oxidized by strain MM1 during the stationary phase and initial Mn(II) concentrations of up to 1.0mmol·dm ¹3 (55mg·dm ¹3 ) went well below the effluent standard of dissolved manganese (10mg·dm ¹3 ; set by Japanese Ministry of Environment). Strain MM1 grew heterotrophically and Mn(II) did not serve as the sole electron donor. Nano-sized (30­ 50nm) Mn oxide particles were produced by strain MM1, which later chained or aggregated to form larger Mn oxide minerals. Cells were observed eventually encrusted inside the Mn oxides. This study showed the important role of strain MM1 in the production of massive Mn oxide deposits at Sambe hot spring. The Mn(II) oxidizing ability of this strain is potentially applied for bioremediation of toxic metals. [doi:10.2320/matertrans.M-M2013825]

日本最強アルカリ温泉(pH10.1)に出現した環境開拓者としての珪藻群集

日本最強アルカリ温泉(pH10.1)に出現した環境開拓者としての珪藻群集

Complete genome sequence of Pyrobaculum oguniense

Pyrobaculum oguniense TE7 is an aerobic hyperthermophilic crenarchaeon isolated from a hot spring in Japan. Here we describe its main chromosome of 2,436,033 bp, with three large-scale inversions and an extra-chromosomal element of 16,887 bp. We have annotated 2,800 protein-coding genes and 145 RNA genes in this genome, including nine H/ACA-like small RNA, 83 predicted C/D box small RNA, and 47 transfer RNA genes. Comparative analyses with the closest known relative, the anaerobe Pyrobaculum arsenaticum from Italy, reveals unexpectedly high synteny and nucleotide identity between these two geographically distant species. Deep sequencing of a mixture of genomic DNA from multiple cells has illuminated some of the genome dynamics potentially shared with other species in this genus.

Production and consumption of hydrogen in hot spring microbial mats dominated by a filamentous anoxygenic photosynthetic bacterium.

Microbial mats containing the filamentous anoxygenic photosynthetic bacterium Chloroflexus aggregans develop at Nakabusa hot spring in Japan. Under anaerobic conditions in these mats, interspecies interaction between sulfate-reducing bacteria as sulfide producers and C. aggregans as a sulfide consumer has been proposed to constitute a sulfur cycle; however, the electron donor utilized for microbial sulfide production at Nakabusa remains to be identified. In order to determine this electron donor and its source, ex situ experimental incubation of mats was explored. In the presence of molybdate, which inhibits biological sulfate reduction, hydrogen gas was released from mat samples, indicating that this hydrogen is normally consumed as an electron donor by sulfate-reducing bacteria. Hydrogen production decreased under illumination, indicating that C. aggregans also functions as a hydrogen consumer. Small amounts of hydrogen may have also been consumed for sulfur reduction. Clone library analysis of 16S rRNA genes amplified from the mats indicated the existence of several species of hydrogen-producing fermentative bacteria. Among them, the most dominant fermenter, Fervidobacterium sp., was successfully isolated. This isolate produced hydrogen through the fermentation of organic carbon. Dispersion of microbial cells in the mats resulted in hydrogen production without the addition of molybdate, suggesting that simultaneous production and consumption of hydrogen in the mats requires dense packing of cells. We propose a cyclic electron flow within the microbial mats, i.e., electron flow occurs through three elements: S (elemental sulfur, sulfide, sulfate), C (carbon dioxide, organic carbon) and H (di-hydrogen, protons).

Oxidative Trapping of Unstable Gaseous Arsines by Hydrogen Peroxide

Hydrogen peroxide was employed as an oxidizing agent for a new method for trapping unstable gaseous arsines. Resin cartridges wetted with hydrogen peroxide trapped over 90% of the gaseous arsines (arsine, methylarsine, dimethylarsine, and trimethylarsine) from laboratory samples. The oxidized products (arsenic acid, methylarsonic acid, dimethylarsinic acid, and trimethylarsine oxide) are relatively stable in Milli-Q water, so they could be extracted from the cartridges and analyzed by liquid chromatography-inductively coupled plasma-mass spectrometry at nanogram per milliliter concentrations. We also used our new method to determine arsine concentrations in field samples from Nishinomaki mine and Tamagawa hot spring in Japan. Inorganic arsine was detected at the highest concentration for each sampling point, and trimethylarsine was observed in the Nishinomaki mine and at one sampling site of the Tamagawa hot spring. This trimethylarsine may have been produced by a variety of microorganisms. Supplementary materials are available for this article. Go to the publisher's online edition of Analytical Letters for the following free supplemental resource(s): tables.

Characterization of Moderately Thermophilic Bacteria Isolated from Saline Hot Spring in Japan

Twelve strains of moderately thermophilic bacteria were isolated from saline hot springs (55°C, pH 8.3) located in Odaito, Hokkaido, Japan. Based on their 16S rRNA gene sequences, all the strains were closely related phylogenetically each other, indicating that the strains belong to a single species. However, maximal growth temperature and enzymatic characteristics of individual strains were slightly different each other. Some of them grew well at 55°C but others did not. The β-galactosidase activity was also different among the strains. Therefore, the representative strains BEK6 and BEK11 were chosen from individual phenotype groups, and were used for further characterization. The nucleotide sequence of full-length 16S rRNA genes of the representative strains showed 96.6% similarity with Bacillus alveayuensis indicating that the strains belong to a novel species of the genus Bacillus . The cells were Gram positive, and showed both catalase and oxidase activities. The optimal growth temperature and pH of strain BEK6 and BEK11 were around 50°C and 7-8, respectively. They were able to grow in the medium containing 10% NaCl in contrast to B. alveayuensis which can grow in the medium with up to 4% NaCl. The strain BEK11 showed relatively strong protease and amylase activities implying the potential industrial uses of these enzymes under the saline condition.

Bacterial symbiosis forming laminated iron‐rich deposits in Okuoku‐hachikurou hot spring, Akita Prefecture, Japan

AbstractBanded iron formations are the most characteristic of Archean–Paleoproterozoic sediment records. Laminated textures resembling banded iron formations can be observed in modern hot‐spring environments. Using sedimentological and microbiological techniques, we investigated the processes of laminar formation and considered the origin of lamination textures. An iron‐rich deposit at the Okuoku‐hachikurou hot spring in Japan exhibits sub‐millimeter laminations consisting of bacteria‐induced ferrihydrite and aragonite. The ferrihydrite particles are spherical and exhibit fine lamination, up to 100 µm thick in ferrihydrite‐rich parts. In aragonite‐rich parts, ferrihydrite particles form filamentous textures with diameters of 10–30 µm, but not laminations. Textural analysis using scanning electron microscopy and phylotype analysis using 16S rRNA indicated the bacterial contribution to ferrihydrite precipitation. A sheath‐like fabric showing a meshwork of nanometer‐order organic filaments, and sheath‐forming bacteria were observed in the deposit specimen etched by citric acid. Phylotype analysis detected in the iron‐rich deposits some bacterial types related to cyanobacteria, purple bacteria, and iron‐oxidizing bacteria. Iron‐oxidizing bacteria probably were responsible for precipitation of the ferrihydrite. Chemolithoautotrophic iron‐oxidizing bacteria are microaerophilic and thrive on Fe(II) in a redox gradient, but dissolved oxygen was not detected in the Okuoku‐hachikurou hot spring. Thus, a certain supply of oxygen is needed for metabolism of the microaerophilic iron‐oxidizing bacteria. The distribution of photosynthetic pigments in the iron‐rich parts indicates that the most likely source of oxygen is photosynthesis by cyanobacteria. This symbiotic relationship between cyanobacteria and iron‐oxidizing bacteria can explain the laminated texture of iron‐rich deposits in the Okuoku‐hachikurou hot spring. These laminations may reflect changes in photosynthetic intensity. There is presently some debate about the bacterial groups that may have played roles in precipitation of banded iron formations. This study presents a new bacterial model for iron precipitation and may provide a mechanism for sub‐millimeter laminations in banded iron formations deposited in shallow water.

Morphological and genetic diversity of the thermophilic cyanobacterium, Mastigocladus laminosus (Stigonematales, Cyanobacteria) from Japan and Myanmar

SUMMARYThe morphology and phylogeny of 13 strains of a thermophilic cyanobacterium, Mastigocladus laminosus Cohn, isolated from hot springs in Japan and Myanmar were analyzed to determine taxonomy and biogeography. From the morphological observations of cell size, there were significant differences among strains. Phylogenetic analyses based on 16S rRNA gene sequences revealed two lineages: Lineages I and II. Lineage I consisted of strains collected in Japan and reference strains from a previous study (CCMEE 5329 and 5331, Hakone, Japan); Lineage II included all of the Myanmar strains and one Japanese strain, and was a novel lineage in phylogeographic studies on M. laminosus. Since strains in the Lineage II tended to have larger cells than those in the Lineage I, the morphological and phylogenetic lineages corresponded well with each other.

A tertiary-branched tetra-amine, N4-aminopropylspermidine is a major cellular polyamine in an anaerobic thermophile, Caldisericum exile belonging to a new bacterial phylum, Caldiserica

Acid-extractable cellular polyamines of thermophilic Caldisericum exile belonging to a new bacterial phylum, Caldiserica were analyzed by HPLC and GC. The coexistence of an unusual tertiary brancehed tetra-amine, N4-aminopropylspermidine with spermine, a linear tetra-amine, as the major polyamines in addition to putrescine and spermidine, is first reported in the moderate thermophile isolated from a terrestrial hot spring in Japan. Linear and branched penta-amines were not detected. The novel cellular polyamine profile found in the moderate thermophile has never been observed within various bacteria and archaea previously analyzed.