Microbial life in marine sediment contributes substantially to global biomass and is a crucial component of the Earth system. Subseafloor sediment includes both aerobic and anaerobic microbial ...ecosystems, which persist on very low fluxes of bioavailable energy over geologic time. However, the taxonomic diversity of the marine sedimentary microbial biome and the spatial distribution of that diversity have been poorly constrained on a global scale. We investigated 299 globally distributed sediment core samples from 40 different sites at depths of 0.1 to 678 m below the seafloor. We obtained ~47 million 16S ribosomal RNA (rRNA) gene sequences using consistent clean subsampling and experimental procedures, which enabled accurate and unbiased comparison of all samples. Statistical analysis reveals significant correlations between taxonomic composition, sedimentary organic carbon concentration, and presence or absence of dissolved oxygen. Extrapolation with two fitted species–area relationship models indicates taxonomic richness in marine sediment to be 7.85 × 10³ to 6.10 × 10⁵ and 3.28 × 10⁴ to 2.46 × 10⁶ amplicon sequence variants for Archaea and Bacteria, respectively. This richness is comparable to the richness in topsoil and the richness in seawater, indicating that Bacteria are more diverse than Archaea in Earth’s global biosphere.
Ferromanganese minerals are widely distributed in subseafloor sediments and on the seafloor in oceanic abyssal plains. Assessing their input, formation and preservation is important for understanding ...the global marine manganese cycle and associated trace elements. However, the extent of ferromanganese minerals buried in subseafloor sediments remains unclear. Here we show that abundant (10
-10
particles cm
) micrometer-scale ferromanganese mineral particles (Mn-microparticles) are found in the oxic pelagic clays of the South Pacific Gyre (SPG) from the seafloor to the ~100 million-year-old sediments above the basement. Three-dimensional micro-texture, and major and trace element compositional analyses revealed that these Mn-microparticles consist of poorly crystalline ferromanganese oxides precipitating from bottom water. Based on our findings, we extrapolate that 1.5-8.8 × 10
Mn-microparticles, accounting for 1.28-7.62 Tt of manganese, are globally present in oxic subseafloor sediments. This estimate is at least two orders of magnitude larger than the manganese budget for nodules and crusts on the seafloor. Subseafloor Mn-microparticles thus contribute significantly to the global manganese budget.
To reconstruct the interaction between Antarctic Bottom Water (AABW) and global climate change, extracting information about past AABW formation from the sedimentary record is crucial. The Prydz Bay ...region, East Antarctica, has high glacier outflow and is a region of vigorous formation of AABW associated with sea ice formation. The Cape Darnley Bottom Water (CDBW), a primary AABW precursor, flows into Wild Canyon west of Prydz Bay. Thus, the sedimentary record of Wild Canyon can serve as an archive for CDBW flow. In this study, to identify the sedimentary processes and mineral compositions characteristic of CDBW flow, we evaluate deep-sea camera imagery, X-ray computed tomography images, grain-size data, and optical and chemical mineralogical analyses. Heavy minerals in the surface sediments are characterized by pyrope-rich almandine garnets (up to 80% of the heavy-mineral assemblage, 0.2%–3.7% of the dry bulk sediment by weight) typical of nearshore sediment derived from Mac. Robertson Land. In addition, ripples on the channel floor indicate sediment transport occurred as tractional bedload, whereas settling of suspended sediment prevailed on the canyon levee. We propose that modern CDBW flow is the dominant process of sediment reworking through sustained high flow velocities, distinctly different from turbidity currents triggered by ice sheet expansion and rapid retreat. Our results further suggest that fine-grained sediments are transported to the canyon levee as CDBW flows through the submarine canyon. These findings will be a key for reconstructing past AABW formation, which is crucial for understanding the response of AABW to future climate change.
•Ripples formed by Cape Darnley Bottom Water are identified in Wild Canyon.•Antarctic Bottom Water flow triggers the reworking of pre-existing sediments.•Sedimentary processes are different during AABW active/inactive periods.
•An improved method to identify organic matter located within aggregate structure was developed.•Samples were prepared using liquid-state osmium-thiocarbohydrazide-osmium staining and resin-embedding ...techniques.•SEM/EDS analysis showed plant detritus that was enriched in Os and C.•Dual energy scanning by μCT identified Os-rich spots of roughly 5−50μm in size.•Advantages and cautions associated with current method were discussed.
Organic matter (OM) in surface soil is largely present within porous mineral-dominant clusters called aggregates. Recent studies have shown the localization of OM within large macroaggregate structure based on synchrotron X-ray micro-computed tomography (μCT) coupled with a vapor-phase, osmium (Os)-staining pretreatment. Here we developed a new approach to identify OM locations within submillimeter-sized aggregates at higher spatial resolution and assessed its applicability using a well-characterized surface volcanic soil, an allophanic Andisol, under no-tillage with leaf compost addition. Water-stable aggregates (500–800 μm in diameter) were embedded in agarose, chemically fixed, and repeatedly stained by osmium tetroxide and thiocarbohydrazide, followed by gradual dehydration with ethanol and resin fixation. Scanning electron microscopy and μCT observation showed no signs of physical alteration during sample preparation. Energy-dispersive X-ray spectroscopy analysis of the microtome-cut surface of the aggregate identified plant detritus highly enriched in Os and much smaller amorphous OM (<10 μm) that were high in Fe, Al, and Si as well as Os. Synchrotron μCT imaging by photon energies above and below Os L3 X-ray absorption edge (10.87 keV) and subsequent image calculation showed the distribution of Os-stained voxels down to micrometer scale. The improved resolution compared to previous studies was partly attributable to liquid-state staining and thiocarbohydrazide bridging. Other advantages and some cautions of the proposed method were discussed.
Marine sediments host an unexpectedly large microbial biosphere, suggesting unique microbial mechanisms for surviving burial and slow metabolic turnover. Although dormancy is generally considered an ...important survival strategy, its specific role in subsurface sediments remains unclear. We quantified dormant bacterial endospores in 331 marine sediment samples from diverse depositional types and geographical origins. The abundance of endospores relative to vegetative cells increased with burial depth and endospores became dominant below 25 m, with an estimated population of 2.5 × 10
to 1.9 × 10
endospores in the uppermost kilometer of sediment and a corresponding biomass carbon of 4.6 to 35 Pg surpassing that of vegetative cells. Our data further identify distinct endospore subgroups with divergent resistance to burial and aging. Endospores may shape the deep biosphere by providing a core population for colonization of new habitats and/or through low-frequency germination to sustain slow growth in this environment.
Human-made structures and shaped stones on the seafloor near coasts, possibly submerged by tsunami waves, coseismic subsidence, or flooding during typhoons, can often be linked to folk traditions of ...ancient natural disasters. Stone pillars that appear to have been artificially shaped are submerged in shallow waters inshore Tosashimizu city, southeast Japan, an area subject to repeated Nankai Trough earthquakes. We performed geophysical and geochemical analyses of samples from these pillars, building stones in use in villages in the Tsumajiro area, and nearby natural rock outcrops. In porosity and grain density, the pillars are similar to sandstone from the Tatsukushi Formation and to foundation stones used in the villages; this similarity was confirmed by a principal component analysis of chemical composition data. The shape and surface morphology of the pillars are also similar to those of the foundation stones and stone steps at nearby temples. Therefore, we inferred that the submerged stone pillars were made from Tatsukushi sandstone and had been utilized as building stones for structures such as steps and foundations in Tsumajiro village possibly >100 years ago. Because radiocarbon ages obtained on calcareous fragments adhering to the pillars were inconclusive, when, and by what process, the stone pillars were transported from the land and submerged in the sea is still uncertain.
A stone pillar inshore Tsumajiro beach and a foundation stone in Tsumajiro village. Principal component analysis (PCA) results for the chemical components using pXRF spectrometer suggested the submerged stone pillars are made from Tatsukushi sandstone and had been utilized as building stones in Tsumajiro village. Display omitted
•Stone pillars are submerged in shallow water off Tosashimizu city, Japan.•PCA method using pXRF was very useful for provenance study.•X-CT images identified cutting marks on the surface of stone pillars.•The submerged stone pillars were made from Tatsukushi sandstone.•The pillars had been utilized as local old building stones for steps and foundations.
Marine sediments are composed of various mineral species and are characterized by micro‐scale grain fabric. The arrangements and interactions of component particles place critical constraints on the ...physical, chemical, and biological processes that occur in subseafloor environments. However, the observation of nearly intact microstructures is difficult, especially in soft, muddy sediments because of their high water content and the presence of organic molecules. In this study, a modified version of the resin‐embedding method generally used for biological samples was applied to marine sediment sample preparation. The new method was compared with the conventional t‐butyl alcohol freeze‐drying method using microfocus X‐ray computed tomography (µXCT) and scanning electron microscopy (SEM). The µXCT and SEM results showed that all t‐butyl alcohol freeze‐dried sediment samples contained microstructural disturbances (e.g., cracks). In contrast, no cracks were observed in the samples prepared using the new resin‐embedding method, and the microstructural arrangement of the sediment particles were clearly visible. In addition, the porosity visible from SEM images of the resin‐embedded samples was similar to that measured using the moisture and density method, providing additional evidence that the microstructures of the resin‐embedded samples were well preserved. The resin‐embedding method allowed observation of the limited contact of the fine particles in clayey sediments, the clay microaggregates throughout the continental margin to pelagic sediments, and the presence of organic materials in environmental sediments. This modified biological resin‐embedding method is suitable for the detailed observation and characterization of fine‐grained marine sediment microstructure.
The Chikyu Shallow Core Program (SCORE) has been started to provide
more opportunities for the scientific ocean drilling of shallow boreholes
(up to 100 m) during a short-term expedition. The ...proposal flow is a
simplified version of that of the International Ocean Discovery Program (IODP).
Although there are several limitations for a SCORE project, the opportunity
to retrieve 100 m of continuous core samples will be of great interest for
the scientific ocean drilling community in multiple disciplines. The first
expedition of the SCORE program was implemented off Cape Erimo, Hokkaido,
northern Japan. The target of the drilling was to investigate the impact of
submarine mass transport on the subseafloor sedimentary biosphere. In the
preliminary observation of the core samples, including X-ray computed tomography (CT) scan image
analysis, chaotic and inclined beds were found and interpreted as mass
transport deposit (MTD) units.
Tosa-suzuri inkstone of Gendani, a traditional craft product of Kochi Prefecture, Japan, has been produced in Mihara Village, Hata District, using the Miharaishi slate that occurs in the Shimanto ...Belt. The slate-bearing sequence was thought to be Cretaceous in age. The slate is known for its fine texture that is ideal for grinding inksticks, and contains a copper-colored powder called “golden stars” that enhances the beauty of the inkstone. However, the geological characteristics of the slate have received little scientific attention. Based on a literature survey, the slate-bearing sequence is estimated to be middle Eocene-early Miocene in age. X-ray diffraction analyses show that the main minerals in the slate are muscovite and quartz, and X-ray spectroscopy identified pyrite as the main mineral in the golden stars. Microtomographic and electron microscopic observations show step-like microstructures on the surface of the inkstone, particularly at the edges of clay minerals, that may be favorable structures for grinding inksticks. The geological characteristics of the Miharaishi slate are similar to those of the source rocks of high-quality inkstones in other areas of Japan and China.
Geological CO2 sequestration in unmineable subsurface oil/gas fields and coal formations has been proposed as a means of reducing anthropogenic greenhouse gasses in the atmosphere. However, the ...feasibility of injecting CO2 into subsurface depends upon a variety of geological and economic conditions, and the ecological consequences are largely unpredictable. In this study, we developed a new flow-through-type reactor system to examine potential geophysical, geochemical and microbiological impacts associated with CO2 injection by simulating in-situ pressure (0-100 MPa) and temperature (0-70°C) conditions. Using the reactor system, anaerobic artificial fluid and CO2 (flow rate: 0.002 and 0.00001 ml/min, respectively) were continuously supplemented into a column comprised of bituminous coal and sand under a pore pressure of 40 MPa (confined pressure: 41 MPa) at 40°C for 56 days. 16S rRNA gene analysis of the bacterial components showed distinct spatial separation of the predominant taxa in the coal and sand over the course of the experiment. Cultivation experiments using sub-sampled fluids revealed that some microbes survived, or were metabolically active, under CO2-rich conditions. However, no methanogens were activated during the experiment, even though hydrogenotrophic and methylotrophic methanogens were obtained from conventional batch-type cultivation at 20°C. During the reactor experiment, the acetate and methanol concentration in the fluids increased while the δ(13)Cacetate, H2 and CO2 concentrations decreased, indicating the occurrence of homo-acetogenesis. 16S rRNA genes of homo-acetogenic spore-forming bacteria related to the genus Sporomusa were consistently detected from the sandstone after the reactor experiment. Our results suggest that the injection of CO2 into a natural coal-sand formation preferentially stimulates homo-acetogenesis rather than methanogenesis, and that this process is accompanied by biogenic CO2 conversion to acetate.
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