Hideaki Machiyama

Characterization of C1-Metabolizing Prokaryotic Communities in Methane Seep Habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by Analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA Genes

ABSTRACT Samples from three submerged sites (MC, a core obtained in the methane seep area; MR, a reference core obtained at a distance from the methane seep; and HC, a gas-bubbling carbonate sample) at the Kuroshima Knoll in the southern Ryuku arc were analyzed to gain insight into the organisms present and the processes involved in this oxic-anoxic methane seep environment. 16S rRNA gene analyses by quantitative real-time PCR and clone library sequencing revealed that the MC core sediments contained abundant archaea (∼34% of the total prokaryotes), including both mesophilic methanogens related to the genus Methanolobus and ANME-2 members of the Methanosarcinales, as well as members of the δ-Proteobacteria, suggesting that both anaerobic methane oxidation and methanogenesis occurred at this site. In addition, several functional genes connected with methane metabolism were analyzed by quantitative competitive-PCR, including the genes encoding particulate methane monooxygenase (pmoA), soluble methane monooxygenase (mmoX), methanol dehydrogenese (mxaF), and methyl coenzyme M reductase (mcrA). In the MC core sediments, the most abundant gene was mcrA (2.5 × 106 copies/g [wet weight]), while the pmoA gene of the type I methanotrophs (5.9 × 106 copies/g [wet weight]) was most abundant at the surface of the MC core. These results indicate that there is a very complex environment in which methane production, anaerobic methane oxidation, and aerobic methane oxidation all occur in close proximity. The HC carbonate site was rich in γ-Proteobacteria and had a high copy number of mxaF (7.1 × 106 copies/g [wet weight]) and a much lower copy number of the pmoA gene (3.2 × 102 copies/g [wet weight]). The mmoX gene was never detected. In contrast, the reference core contained familiar sequences of marine sedimentary archaeal and bacterial groups but not groups specific to C1 metabolism. Geochemical characterization of the amounts and isotopic composition of pore water methane and sulfate strongly supported the notion that in this zone both aerobic methane oxidation and anaerobic methane oxidation, as well as methanogenesis, occur.

Quaternary bryozoan reef mounds in cool-water, upper slope environments: Great Australian Bight

Bryozoan reef mounds are common features in the geological record, occurring within mid-ramp, slope paleoenvironments, especially in Paleozoic carbonate successions, but until now have not been recorded from the modern ocean. Recent scientific drilling in the Great Australian Bight (Ocean Drilling Program Leg 182) has confirmed the existence of shallow subsurface bryozoan reef mounds in modern water depths of 200–350 m. These structures have as much as 65 m of synoptic relief, and occur both as single mounds and as mound complexes. They are unlithified, have a floatstone texture, and are rich in delicate branching, encrusting and/or nodular-arborescent, flat-robust branching, fenestrate, and articulated zooidal bryozoan growth forms. The muddy matrix is composed of foraminifers, serpulids, fecal pellets, irregular bioclasts, sponge spicules, and calcareous nannofossils. The 14C accelerator mass spectrometry dates of 26.6–35.1 ka indicate that the most recent mounds, the tops of which are 7–10 m below the modern seafloor, flourished during the last glacial lowstand but perished during transgressive sea-level rise. This history reflects changing oceanographic current patterns; strong upwelling during lowstands, and reduced upwelling and lowered trophic resources during highstands. Large specimens of benthic foraminifers restricted to the mounds confirm overall mesotrophic growth conditions. The mounds are similar in geometry, scale, general composition, and paleoenvironments to older structures, but lack obvious microbial influence and extensive synsedimentary cementation. Such differences reflect either short-term local conditions or long-term temporal changes in ocean chemistry and biology.

A marine deep-towed DC resistivity survey in a methane hydrate area, Japan Sea

Abstract We have developed a new deep-towed marine DC resistivity survey system. It was designed to detect the top boundary of the methane hydrate zone, which is not imaged well by seismic reflection surveys. Our system, with a transmitter and a 160-m-long tail with eight source electrodes and a receiver dipole, is towed from a research vessel near the seafloor. Numerical calculations show that our marine DC resistivity survey system can effectively image the top surface of the methane hydrate layer. A survey was carried out off Joetsu, in the Japan Sea, where outcrops of methane hydrate are observed. We successfully obtained DC resistivity data along a profile ~3.5 km long, and detected relatively high apparent resistivity values. Particularly in areas with methane hydrate exposure, anomalously high apparent resistivity was observed, and we interpret these high apparent resistivities to be due to the methane hydrate zone below the seafloor. Marine DC resistivity surveys will be a new tool to image sub-seafloor structures within methane hydrate zones.

Origin of Late Pleistocene Bryozoan Reef Mounds; Great Australian Bight

Bryozoan-rich biogenic mounds grew periodically on the prograding carbonate slope of the central Great Australian Bight throughout Pliocene-Pleistocene time. Cores from three ODP Leg 182 drill sites provide a record of mound growth during the last 300,000 years over a stratigraphic thickness of similar to 150 m. These mounds, the first such structures described from the modern ocean, grew between paleodepths of 100 and 240 m; we infer that the upper limit of growth was established by swell wave base, and the lower boundary was fixed by an oligotrophic water mass. Detailed chronostratigraphy, based on radiometric and U-series dating, benthic foraminifer stable-isotope stratigraphy, and planktonic foraminifer abundance ratios, confirms that buildups flourished during glacial lowstands (even-numbered marine isotope stages) but were largely moribund during interglacial highstands and are not extant today. Mound floatstones are compositionally a mixture of in situ bryozoans comprising 96 genera and characterized by fenestrate, flat robust branching, encrusting, nodular-arborescent, and delicate branching growth forms. The packstone matrix comprises autochthonous and allochthonous sand-size bryozoans, benthic and planktonic foraminifers, serpulids, coralline algae, sponge spicules, peloids, and variable glauconite and quartz grains, together with mud-size ostracods, tunicate spicules, bioeroded sponge chips, and coccoliths. Intermound, allochthonous packstone and local grainstone contain similar particles, but they are conspicuously worn, abraded, blackened, and bioeroded. An integrated model of mound accretion during sea-level lowstands begins with delicate branching bryozoan floatstone that increases in bryozoan abundance and diversity upward over a thickness of 5-10 m, culminating in thin intervals of grainstone characterized by reduced diversity and locally abraded fossils. Mound accumulation was relatively rapid (30-67 cm/ky) and locally punctuated by rudstones and firmgrounds. Intermound highstand deposition was comparatively slow (17-25 cm/ky) and typified by meter-scale, fining-upward packages of packstone and grainstone or burrowed packstone, with local firmgrounds overlain by characteristically abraded particles. Mound growth during glacial periods is interpreted to have resulted from increased nutrient supply and enhanced primary productivity. Such elevated trophic resources were both regional and local, and thought to be focused in this area by cessation of Leeuwin Current flow, together with northward movement of the subtropical convergence and related dynamic mixing.

Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes

Submarine mud volcanoes (SMVs) are formed by muddy sediments and breccias extruded to the seafloor from a source in the deep subseafloor and are characterized by the discharge of methane and other hydrocarbon gasses and deep-sourced fluids into the overlying seawater. Although SMVs act as a natural pipeline connecting the Earth’s surface and subsurface biospheres, the dispersal of deep-biosphere microorganisms and their ecological roles remain largely unknown. In this study, we investigated the microbial communities in sediment and overlying seawater at two SMVs located on the Ryukyu Trench off Tanegashima Island, southern Japan. The microbial communities in mud volcano sediments were generally distinct from those in the overlying seawaters and in the well-stratified Pacific margin sediments collected at the Peru Margin, the Juan de Fuca Ridge flank off Oregon, and offshore of Shimokita Peninsula, northeastern Japan. Nevertheless, in-depth analysis of different taxonomic groups at the sub-species level revealed that the taxon affiliated with Atribacteria, heterotrophic anaerobic bacteria that typically occur in organic-rich anoxic subseafloor sediments, were commonly found not only in SMV sediments but also in the overlying seawater. We designed a new oligonucleotide probe for detecting Atribacteria using the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). CARD-FISH, digital PCR and sequencing analysis of 16S rRNA genes consistently showed that Atribacteria are abundant in the methane plumes of the two SMVs (0.58 and 1.5 × 104 cells/mL, respectively) but not in surrounding waters, suggesting that microbial cells in subseafloor sediments are dispersed as “deep-biosphere seeds” into the ocean. These findings may have important implications for the microbial transmigration between the deep subseafloor biosphere and the hydrosphere.

Regular budding modes in a zooxanthellate dendrophylliid Turbinaria peltata (Scleractinia) revealed by X‐ray CT imaging and three‐dimensional reconstruction

The zooxanthellate dendrophylliid coral, Turbinaria peltata (Scleractinia), exhibit various growth forms that increase the photoreception area through the development of coenosteum skeletons. Because it is difficult to make detailed observations of the internal structures, we visualized inner skeletal structures using nondestructive microfocus X‐ray computed tomography (CT) imaging. After removal of the coenosteum skeletons from the X‐ray CT images, three‐dimensional 3D‐models were reconstructed for individual corallites. Regular budding was observed from the 3D‐model and cross‐sectional images as follows: 1) lateral corallites occurred only near the two primary septa on one side, apart from a directive primary septum with distinct polarity; 2) the budding occurred upward at acute angles; and 3) these regular structures and polarity were repeated throughout growth with every generation. Even in zooxanthellate dendrophylliids, the same budding modes as observed in azooxanthellate equivalents control the colonial growth. These characteristics provide clues for understanding the mechanisms that regulate the shapes of modular marine organisms. J. Morphol. 276:1100–1108, 2015.

Submarine Slope Response to Earthquake Shaking Within Western Sagami Bay, Central Japan

Earthquakes are a major trigger of submarine landslides. Strong ground shaking of the sea floor by an earthquake increases the sediment pore pressure and induces slope failure. As submarine landslides may generate tsunamis, it is important to understand the submarine slope response to earthquake ground shaking. Slope response may change spatially according to the strength of ground shaking and slope characteristics, such as submarine topography, gradient, sea bed materials, and sedimentation rate. For a better understanding of slope response, it is necessary to obtain data on changes to the sea floor following an earthquake. In 1997, 1998, and 2006, the JAMSTEC Hatsushima Deep-Sea Observatory recorded turbidity currents triggered by the Izu-toho-oki earthquake swarm (magnitude ∼6) off Hatsushima Island in western Sagami Bay, Central Japan. In 2004, cores of undisturbed surface sediment were collected using a multiple corer at the foot of the submarine slope near the Observatory. No clear gravity-flow deposits (e.g., turbidites and debrites) were observed near the tops of the cores, indicating that earthquakes of magnitude ∼6 have insufficient energy to generate clearly defined sandy turbidites on this slope. In contrast, several sandy turbidite layers are present in a piston core collected from a nearby site, suggesting that this site is affected by a larger magnitude of ground shaking than that produced by the Izu-toho-oki earthquakes. The most likely origin of this greater ground shaking is the Kanto earthquakes (magnitude ∼8), the epicenter of which is located in the northwestern Sagami Trough.

Acoustical surveys of Methane plumes using the quantitative echo sounder in Japan Sea

R&T/V Umitaka-maru(Tokyo Univ. of Marine Science and Technology) and R/V Natsushima(JAMSTEC) sailed to the methane seep area on a small ridge in the Naoetsu Basin, in the eastern margin of the Sea of Japan in 2004,2005 and 2006 to survey the ocean floor gas hydrate and related acoustic signatures of methane plumes by using a quantitative echo sounder and a multi beam SONER [1]. Detailed bathymetric profiles have revealed a number of mounds, pockmarks and collapse structures within 3 km times 4 km on the ridge at the water depth of 910 m to 980 m. We mapped minutely methane plumes by using a quantitative echo sounder with positioning data from GPS. We also measured averaged echo intensity from the methane plumes and sea bottoms both in every 100 m range and very one minute by the echo integrator. We obtained the following results from the present echo-sounder and SONER surveys. 1) We measured the averaged volume backscattering strength (SV) of each methane plume. The strongest SV, -33dB, of the plumes was stronger than SV of fish school. 2) Averaged SV of each methane plume tend to be related to the water temperature and the water pressure. 3) We recovered several fist-sized chunks of methane hydrate by piston coring at the area where we observed the methane plumes. 4) Using this method, we detected methane bubbles floating up points and revealed that the hydrate bubbles float upward until they reach warm waters at 300 m depth. 5) We revealed the hydrate bubbles in the conic container on the sea bottom. Because of results this acoustical method was effective to know the behaviors of the methane hydrate under water and to monitor the area of the methane seep. As a following up project, we are planning 1) to measure SV of methane hydrate bubbles and methane hydrate floating in water columns in situ, 2) to make a trial calculation of amount of floating methane bubbles and methane hydrates and 3) to study how to sample the acoustical data of methane plumes using the side scanning SONAR, called SeaBat.

Environmental Gamma-Ray Observation in Deep Sea

Deep-Sea in-situ radioactivity measurements were initiated in 1964 for investigation of sunken USN atomic power submarine Thresher by using Geiger counters (Wakelin, 1964). Since then, in-situ radioactivity monitoring utilizing a towed-fish and/or remote sea bottom stations has been carried out in various countries. But they are mainly used for surveys of artificial radio activities to evaluate potential risks around atomic power plants, radioactive waste disposal sites and sunken nuclear objects etc. (Jones et al., 1988). Thus, underwater gamma ray measurement has been rather limitedly performed compared to the sub aerial ones, which has been widely utilized for explorations of uranium or other valuable minerals for mining or much wider environmental analysis (Bristow, 1983), due to very effective shielding by seawater. In underwater environment, Yoshida and Tsukahara (1987) reported environmental gamma ray characteristics around an active cold seepage associating with an active fault in Sagami Bay, southern coast of mainland Japan. Besides that, deep-sea gamma ray surveys for scientific use are intensively carried out by ODP-IODP logging for determination of rock types.

Robust data processing of noisy marine controlled-source electromagnetic data using independent component analysis

Data processing techniques are often used to estimate the noise-free response of marine controlled-source electromagnetic (CSEM) data and magnetotelluric transfer functions. We have implemented a new CSEM data processing scheme that uses a robust method based on independent component analysis (ICA) to extract interpretable datasets from noisy marine CSEM data. We applied the data processing scheme to signals from a new CSEM observation system comprising a remotely operated vehicle (ROV) and an ocean bottom electromagnetometer (OBEM). These datasets were obtained around the Iheya North hydrothermal field, Okinawa Trough, Japan. The observation system allows a small-scale CSEM survey to be conducted in areas of steep topography, such as hydrothermal fields, because the ROV can deploy the OBEM at the exact observation site. The results show that the coherent and environment noise that exists in the raw time series is reduced sufficiently by ICA processing. It makes interpretation of the resulting electric field data possible. The results also show that the processed data has a higher signal-to-noise ratio in the middle-to-high-frequency band than the data without ICA. The normalised spectrum, obtained by normalising the observed data from the hydrothermal area, indicates that a conductive anomaly exists in the near-offset area around the OBEM. We apply 2D inversion to the electric field data and find that a low resistivity body exists beneath the OBEM and 50 m offset from the OBEM. This resistivity structure is consistent with images taken by the ROV that show characteristic organisms in hydrothermal seepage around the OBEM site. We have developed a new controlled-source electromagnetic (CSEM) data processing scheme that uses a robust method based on independent component analysis to extract interpretable datasets from noisy marine CSEM data. The results show that the coherent and environment noise is reduced sufficiently. It makes interpretation of the resulting data possible.