Shimokita Peninsula Research Articles

Complete genome sequence of the xylan-degrading subseafloor bacterium Microcella alkaliphila JAM-AC0309

Here we report the complete genome sequence of Microcella alkaliphila JAM-AC0309, which was newly isolated from the deep subseafloor core sediment from offshore of the Shimokita Peninsula of Japan. An array of genes related to utilization of xylan in this bacterium was identified by whole genome analysis.

Sedimentibacter acidaminivorans sp. nov., an anaerobic, amino-acid-utilizing bacterium isolated from marine subsurface sediment.

A novel, anaerobic bacterium, strain MO-SEDIT, was isolated from a methanogenic microbial community, which was originally obtained from marine subsurface sediments collected from off the Shimokita Peninsula of Japan. Cells were Gram-stain-negative, non-motile, non-spore-forming rods, 0.4-1.4 μm long by 0.4-0.6 μm wide. The cells also formed long filaments of up to about 11 μm. The strain grew on amino acids (i.e. valine, leucine, isoleucine, methionine, glycine, phenylalanine, tryptophan, lysine and arginine), pyruvate and melezitose in the presence of yeast extract. Growth was observed at 4-37 °C (optimally at 30 °C), at pH 6.0 and 8.5 (optimally at 7.0-7.5) and in 0-60 g l- 1 NaCl (optimally 20 g NaCl l- 1). The G+C content of the DNA was 32.0 mol%. The polar lipids of strain MO-SEDIT were phosphatidylglycerol, phosphatidyl lipids and unknown lipids. The major cellular fatty acids (>10 % of the total) were C14 : 0, C16 : 1ω9 and C16 : 0 dimethyl aldehyde. Comparative sequence analysis of the 16S rRNA gene showed that strain MO-SEDIT was affiliated with the genus Sedimentibacter within the phylum Firmicutes. It was related most closely to the type strain of Sedimentibacter saalensis (94 % sequence similarity). Based on the phenotypic and genetic characteristics, strain MO-SEDIT is considered to represent a novel species of the genus Sedimentibacter, for which the name Sedimentibacter acidaminivorans sp. nov. is proposed. The type strain is MO-SEDIT ( = JCM 17293T = DSM 24004T).

Estimation of methanogenesis by quantification of coenzyme F430 in marine sediments

Coenzyme F430 is the hydrocorphinoid nickel complex which acts as active site in methyl-coenzyme M reductase (MCR). The MCR-F430 complex catalyzes the last step of methanogenesis: reduction of methyl-coenzyme M to methane. Since F430 is a common enzyme for mathanogens, it can be a function-specific biomarker to estimate biomass and activities of methanogens in environmental samples. A recently developed high sensitive method for coenzyme F430 analysis and a further purification step revealed F430 concentrations at 69 and 88 meters below seafloor (mbsf) off Shimokita Peninsula (529 and 31.3 fmol g-wet–1) and at 60 and 275 mbsf at Nankai Trough (31.4 and 26 fmol g-wet–1). Estimated methanogenic biomass and activities based on reported F430 content and activities in methanogens and prokaryotic cell weight, were ranging from 3.9 × 106 to 2.7 × 106 cells g-wet–1 and from 1.7 to 11 μmol d–1 g-wet–1.

Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan.

Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained from the forearc basin off the Shimokita Peninsula. The molecular profiles were combined with data on lithostratigraphy, depositional age, sedimentation rate and pore-water chemistry. The SSU rRNA gene tag structure and diversity changed at around the sulfate-methane transition zone (SMTZ), whereas the profiles varied further with depth below the SMTZ, probably in connection with the variation in pore-water chemistry. The depth profiles of diversity and abundance of dsrA, a key gene for sulfate reduction, suggested the possible niche separations of sulfate-reducing populations, even below the SMTZ. The diversity and abundance patterns of mcrA, a key gene for methanogenesis/anaerobic methanotrophy, suggested a stratified distribution and separation of anaerobic methanotrophy and hydrogenotrophic or methylotrophic methanogensis below the SMTZ. This study provides novel insights into the relationships between the composition and function of microbial communities and the chemical environment in the nutrient-rich continental margin subseafloor sediments, which may result in niche separation and variability in subseafloor microbial populations.

Variability in coal facies as reflected by organic petrological and geochemical data in Cenozoic coal beds offshore Shimokita (Japan) - IODP Exp. 337

This study reports on Cenozoic coal seams recovered at Integrated Ocean Drilling Program (IODP) Site C0020 during Expedition 337. IODP Site C0020 is located in a forearc basin formed by the subduction of the Pacific plate off Shimokita Peninsula (Japan). Hole C0020A penetrated 14 coal layers between 1825 and 2466mbsf. Eleven of them were investigated within the frame of this paper. Investigated seams show a slight maturity increase with depth from lignite to sub-bituminous coal. In order to detect temporal changes in maceral and molecular composition and to relate them to changes in vegetation and depositional environment, macro- and micropetrographic data, bulk geochemical parameters, biomarker analysis, stable isotope geochemistry, and vitrinite reflectance measurements were performed. Results were also compared with palynological data obtained from 9 coal samples.Elevated sulfur contents and high ash yields occur in the upper seams (cores 14R to 18R) whereas low sulfur contents and varying ash yields were determined for the lower coal seams (24R to 30R). The maceral composition and biomarker ratios of the uppermost seams argue for coal formation in a paralic environment and brackish, alkaline water conditions. In contrast, lignite samples from the lower part of unit III point to a limnic-fluviatile deposition. Conifers contributed significantly to peat formation in the uppermost seams (from cores 15R to 22R) and in the lowermost lignite seam. In all other samples, angiosperms are considered as the major peat-forming plants. The pollen and spore floras indicate rich angiosperm vegetation, however significant contributions from Pinaceae and Taxodiaceae are evident for all coals. Sporophytes have no dominant influence on the coal flora. Microbial activity in the peat is suggested for instance by higher concentrations of hop-17(21)-ene with increasing contents of hopanes or by low δ13C values of hop-17(21)-ene. The revealed changes in the environment during coal deposition highlight the importance of combined organic petrography, organic geochemistry and palynology to reconstruct palaeoenvironmental conditions.

Middle to Upper Pleistocene Polycystine Radiolarians from Hole 902-C9001C, Northwestern Pacific

A continuous 740-kyr Quaternary sedimentary sequence containing abundant siliceous microfossils was recovered from Hole C9001C during the D/V Chikyu 2006 Mission off the Shimokita Peninsula, Japan. This region is characterized by mixed water reflecting the influences of one warm current (Tsugaru Current), one cold current (the Oyashio Current), and several intermediate and deep water masses. Polycystine radiolarians (a siliceous microfossil group) are useful for reconstructing paleoceanographic changes in this region during the Quaternary because of their ecological properties in these types of deep-sea sediments. This paper illustrates and reviews the taxonomic features of all the polycystine species encountered during this study. A detailed taxonomy is presented because different taxonomic names have been applied, even to the same morphospecies, in many cases. The taxonomic classification of 104 species belonging to three orders (Collodaria, Spumellaria, and Nassellaria), 16 superfamilies, 33 families, and 66 genera was verified by comparison of the holotypes and the relevant name-bearing specimens in accordance with the International Code of Zoological Nomenclature to the extent possible. The taxonomic classification system was updated with reference to both recent morphological taxonomic schemes and molecular phylogenetic analyses. This paper also provides a detailed synonym list of each previously illustrated species from the northwestern Pacific Ocean in order to standardize applicable taxonomic names for the same morphospecies. In addition, a new family (Amphisphaeridae Suzuki fam. nov.) and a new replacement name (Lithelius haeckelispiralis Matsuzaki and Suzuki, nomen nov. for Lithelius spiralis of Haeckel in 1861 [not Ehrenberg in 1840]) are described, and the diagnoses of the genus Tholomura and the family Lychnocaniidae are emended.

青森県下北地方で採集されたイスカの巣の構造と巣材

We investigated the structure and materials of two nests of the Common Crossbill Loxia curvirostra collected in Shimokita Peninsula, Aomori Prefecture, Japan. The nest bowl was constructed of pine twigs with bark, shredded bark, wood-chips, other twigs, chemical fiber yarns, staple fibers, grasses, pine needles, feathers, rhizomorphs, animal hairs and fishing line. These materials were utilized in different manner in the exterior and interior nest bowl. Pine twigs with bark were used only for the most exterior portion, whereas the middle and interior parts consisted mainly of shredded bark of Cryptomeria japonica. Harder objects, such as twigs, wood chips and flexible fishing line, used for the middle part, served as a framework to produce a space between fibers and strings, creating a spongy layer of air. The area around the interior nest bowl was composed of thinner bark strings than the middle and outer nest bowl. Chemical fiber yarn, feathers and animal hairs were also found around the interior bowl.

下北半島尻屋崎の海成段丘における地中レーダー探査

下北半島尻屋崎の海成段丘における地中レーダー探査

Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta.

An anaerobic, psychrophilic bacterium, strain MO-SPC2(T), was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediments collected from off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. Cells were pleomorphic: spherical, annular, curved rod, helical and coccoid cell morphologies were observed. Motility only occurred in helical cells. Strain MO-SPC2(T) grew at 0-17 °C (optimally at 9 °C), at pH 6.0-8.0 (optimally at pH 6.8-7.2) and in 20-40 g NaCl l(-1) (optimally at 20-30 NaCl l(-1)). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC2(T) were phosphatidylglycolipids, phospholipids and glycolipids. The major cellular fatty acids were C14 : 0, C16 : 0 and C16 : 1ω9. Isoprenoid quinones were not detected. The G+C content of the DNA was 32.3 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-SPC2(T) was affiliated with the genus Sphaerochaeta within the phylum Spirochaetes, and its closest relatives were Sphaerochaeta pleomorpha Grapes(T) (88.4 % sequence identity), Sphaerochaeta globosa Buddy(T) (86.7 %) and Sphaerochaeta coccoides SPN1(T) (85.4 %). Based on phenotypic characteristics and phylogenetic traits, strain MO-SPC2(T) is considered to represent a novel species of the genus Sphaerochaeta, for which the name Sphaerochaeta multiformis sp. nov. is proposed. The type strain is MO-SPC2(T) ( = JCM 17281(T) = DSM 23952(T)). An emended description of the genus Sphaerochaeta is also proposed.

Nutritional Intakes of Obese Elementary School Children Residing in the Shimokita Peninsula of Aomori, Japan

This research examined the lifestyles and eating habits of 42 elementary school fifth graders(20 boys and 22 girls) over a 3-day period; these children resided in theShimokita Peninsula, Aomori prefecture, which has the highest childhood obesityrate in Japan. The children’s nutritionalintakes were recorded via questionnaires and self-documented meal recorddiaries overa 3-day period (1 weekday and the weekend). The meal record diaries recorded which meals the children ate (including snacks) during the 3-day period. A regular feature of these children’s lifestyle was theviewing of at least 3 hours of television per day. Compared with the National Health and Nutrition Survey conductedby the Japanese government, the nutritionaland energy intake levels were the same but when we examined food group intakes,the vegetable intake was lower on weekends in comparison to the weekdays whenthe children were provided school lunches. In addition, salt intake exceededthe recommended standard in more than 80% of the study sample. We suggest thatthe pattern of reduced vegetable intake juxtaposed with high salt intake stemsfrom childhood and is repeated and passed down through generations; therefore, theguardians of these children require nutritional guidance and education.

Archaealβdiversity patterns under the seafloor along geochemical gradients

Recently, deep drilling into the seafloor has revealed that there are vast sedimentary ecosystems of diverse microorganisms, particularly archaea, in subsurface areas. We investigated the β diversity patterns of archaeal communities in sediment layers under the seafloor and their determinants. This study was accomplished by analyzing large environmental samples of 16S ribosomal RNA gene sequences and various geochemical data collected from a sediment core of 365.3 m, obtained by drilling into the seafloor off the east coast of the Shimokita Peninsula. To extract the maximum amount of information from these environmental samples, we first developed a method for measuring β diversity using sequence data by applying probability theory on a set of strings developed by two of the authors in a previous publication. We introduced an index of β diversity between sequence populations from which the sequence data were sampled. We then constructed an estimator of the β diversity index based on the sequence data and demonstrated that it converges to the β diversity index between sequence populations with probability of 1 as the number of sampled sequences increases. Next, we applied this new method to quantify β diversities between archaeal sequence populations under the seafloor and constructed a quantitative model of the estimated β diversity patterns. Nearly 90% of the variation in the archaeal β diversity was explained by a model that included as variables the differences in the abundances of chlorine, iodine, and carbon between the sediment layers.

Nutritional Intakes of Obese Elementary School Children Residing in the Shimokita Peninsula of Aomori, Japan

This research examined the lifestyles and eating habits of 42 elementary school fifth graders(20 boys and 22 girls) over a 3-day period; these children resided in theShimokita Peninsula, Aomori prefecture, which has the highest childhood obesityrate in Japan. The children’s nutritionalintakes were recorded via questionnaires and self-documented meal recorddiaries overa 3-day period (1 weekday and the weekend). The meal record diaries recorded which meals the children ate (including snacks) during the 3-day period. A regular feature of these children’s lifestyle was theviewing of at least 3 hours of television per day. Compared with the National Health and Nutrition Survey conductedby the Japanese government, the nutritionaland energy intake levels were the same but when we examined food group intakes,the vegetable intake was lower on weekends in comparison to the weekdays whenthe children were provided school lunches. In addition, salt intake exceededthe recommended standard in more than 80% of the study sample. We suggest thatthe pattern of reduced vegetable intake juxtaposed with high salt intake stemsfrom childhood and is repeated and passed down through generations; therefore, theguardians of these children require nutritional guidance and education.

Nutritional intakes of obese elementary school children residing in the Shimokita Peninsula of Aomori, Japan

Nutritional intakes of obese elementary school children residing in the Shimokita Peninsula of Aomori, Japan

Low blood cell counts in wild Japanese monkeys after the Fukushima Daiichi nuclear disaster.

In April 2012 we carried out a 1-year hematological study on a population of wild Japanese monkeys inhabiting the forest area of Fukushima City. This area is located 70 km from the Fukushima Daiichi Nuclear Power Plant (NPP), which released a large amount of radioactive material into the environment following the Great East Japan Earthquake of 2011. For comparison, we examined monkeys inhabiting the Shimokita Peninsula in Aomori Prefecture, located approximately 400 km from the NPP. Total muscle cesium concentration in Fukushima monkeys was in the range of 78–1778 Bq/kg, whereas the level of cesium was below the detection limit in all Shimokita monkeys. Compared with Shimokita monkeys, Fukushima monkeys had significantly low white and red blood cell counts, hemoglobin, and hematocrit, and the white blood cell count in immature monkeys showed a significant negative correlation with muscle cesium concentration. These results suggest that the exposure to some form of radioactive material contributed to hematological changes in Fukushima monkeys.

Spirochaeta psychrophila sp. nov., a psychrophilic spirochaete isolated from subseafloor sediment, and emended description of the genus Spirochaeta.

An obligately anaerobic, psychrophilic spirochaete, strain MO-SPC1(T), was isolated from a methanogenic microbial community grown in a continuous-flow bioreactor. Originally, this community was obtained from subseafloor sediments off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. The cells were motile, Gram-stain-negative, helical, 0.25-0.55×3.6-15 µm, with a wavelength of approximately 0.5-0.6 µm. Strain MO-SPC1(T) grew at 0-18 °C (optimally at 15 °C), at pH 6.0-7.5 (optimally at pH 6.8-7.0) and in 20-70 g NaCl l(-1) (optimally at 30-40 NaCl l(-1)). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC1(T) were diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipids and an unknown lipid. The major cellular fatty acids (>5% of the total) were C(14 : 0), C(16 : 0), iso-C(13 : 0), iso-C(14 : 0), iso-C(15 : 0), anteiso-C(13 : 0) and anteiso-C(15 : 0). To the best of our knowledge, this is the first report of the fatty acids iso-C(13 : 0) and anteiso-C(13 : 0) from a species of the genus Spirochaeta. Isoprenoid quinones were not found. The G+C content of the genomic DNA was 39.8 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that strain MO-SPC1(T) was affiliated with the genus Spirochaeta, and its closest relatives were Spirochaeta isovalerica MA-2(T) (95.6% sequence identity) and Spirochaeta litoralis R1(T) (89.4%). Based on its phenotypic characteristics and phylogenetic traits, strain MO-SPC1(T) is placed in a separate taxon at the level of a novel species within the genus Spirochaeta, for which the name Spirochaeta psychrophila sp. nov. is proposed, reflecting its true psychrophilic physiology. The type strain is MO-SPC1(T) ( = JCM 17280(T) = DSM 23951(T)). To our knowledge, this is the first report of an isolate of the phylum Spirochaetes from a deep-sea sedimentary environment, and of an obligately psychrophilic nature.

3D structural analysis of large-scale submarine landslide on a very gentle continental slope off Shimokita Peninsula

3D structural analysis of large-scale submarine landslide on a very gentle continental slope off Shimokita Peninsula

Thermal and transport properties of the sedimentary rocks at Site C0020, IODP Expedition 337 in Sanriku-oki basin off Shimokita Peninsula

Thermal and transport properties of the sedimentary rocks at Site C0020, IODP Expedition 337 in Sanriku-oki basin off Shimokita Peninsula

Reconstruction of the East Asian monsoon fluctuation from a fossil pollen record of the C9001C core, Shimokita Peninsula, for the past 120 kyrs

Reconstruction of the East Asian monsoon fluctuation from a fossil pollen record of the C9001C core, Shimokita Peninsula, for the past 120 kyrs

Paleoenvironmental changes recorded in fossil foraminifera and sediments from Obuchi-numa, Shimokita Peninsula.

Paleoenvironmental changes recorded in fossil foraminifera and sediments from Obuchi-numa, Shimokita Peninsula.

Paleoceanographic history of the Northwest Pacific Ocean over the past 740 kyr, discerned from radiolarian fauna

The Northwest Pacific Ocean is characterized by a strong mixing of water masses, due to the interplay of three distinct currents, i.e., the Kuroshio, the Tsugaru, and the Oyashio. The C9001C drill core site, located east of the Shimokita Peninsula and directly influenced by the Tsugaru warm current and the Oyashio subarctic current was used here to reconstruct the paleoceanographical history of this region, especially focusing on the Mid-Brunhes Event (MBE) and its consequences. This core provides a continuous record from marine isotope stage (MIS) 18 (740ka) to the present. Polycystine radiolarian assemblages were analyzed to highlight paleoceanographic and sea surface temperature changes at this site. Based on the radiolarian fauna, seven time periods are defined, which coincide with changes in the dynamics of the Tsugaru and Oyashio currents, respectively. The oldest time interval covered by our analysis (i.e., VII: 740–621ka) was marked by generally sluggish ocean circulation. The Tsugaru Current influence increased during the following Interval VI (621–478ka) which encompasses interglacials MIS 15 and 13, while the Oyashio Current strengthened during the Interval V (478–337), i.e. from glacials MIS 12 to 10. These latter intervals (VI to V) constitute a long climatic transitional period where Tsugaru Current and Oyashio Current influences are strengthened. In the time period from Interval IV to Interval I (0–337ka), the warming intensity of interglacials (MIS 9, MIS 5) appears to be close to the modern one. However, several unusually warm glacials, associated with a relatively strong Tsugaru Current flow, were identified during this interval (e.g., MIS 8 and MIS 6). Radiolarian productivity data suggest that during Intervals VII to V, deep water masses are rich in nutrient content. However, a high vertical mixing event is recorded after Interval IV, when high nutrient concentrations appear to shift to the surface layer.