Metal-ion-induced expression of gene fragments from subseafloor micro-organisms in the Kumano forearc basin, Nankai Trough.

Aims: Using substrate-induced gene-expression (SIGEX) screening on subseafloor sediment samples from the Nankai Trough, Japan, we identified gene fragments showing an induction response to metal ions.

Methods And Results: Environmental DNA libraries in Escherichia coli host cells were tested by the addition of metal ions (Ni , Co , Ga or Mo ), followed by cell sorting of clones exhibiting green fluorescence upon co-expression of green fluorescence protein downstream of the inserted gene fragments. One clone displayed Ni -specific induction, three clones displayed Ga -specific induction and three clones displayed an induction response to multiple metal ions.

Comparative metatranscriptomics reveals extracellular electron transfer pathways conferring microbial adaptivity to surface redox potential changes.

Some microbes can capture energy through redox reactions with electron flow to solid-phase electron acceptors, such as metal-oxides or poised electrodes, via extracellular electron transfer (EET). While diverse oxide minerals, exhibiting different surface redox potentials, are widely distributed on Earth, little is known about how microbes sense and use the minerals. Here we show electrochemical, metabolic, and transcriptional responses of EET-active microbial communities established on poised electrodes to changes in the surface redox potentials (as electron acceptors) and surrounding substrates (as electron donors).

Assessment of Capacity to Capture DNA Aerosols by Clean Filters for Molecular Biology Experiments.

Experimental contamination by exogenous DNA is a major issue in molecular biological studies for data quality and its management. We herein assessed DNA aerosols for the risk of contamination and tested the capacity of clean air filters to trap and remove DNA aerosols. DNA aerosols were generated by atomizing a DNA solution and introduced into a laminar flow clean air unit.

A Rapid and Precise Determination of Boron Isotope Ratio in Water and Carbonate Samples by Multiple Collector ICP-MS.

We developed a method for rapid and precise determination of B isotope ratios by MC-ICP-MS through an optimization of washout method, mass-discrimination correction and chemical separation. Resultant reproducibility of δB values was ±0.4‰ (2 × SD) when a simple standard-sample bracketing technique was used, and it was improved to be better than ±0.

D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin.

We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (<74°C) and from one cold station (<9°C). Cell abundance at the two hydrothermal stations dropped from 10 to 10 cells cm within ∼5 m of sediment depth resulting in a 100-fold lower cell number at this depth than at the cold site where numbers remained constant at 10 cells cm throughout the recovered sediment.

Rapid recovery of life at ground zero of the end-Cretaceous mass extinction.

The Cretaceous/Palaeogene mass extinction eradicated 76% of species on Earth. It was caused by the impact of an asteroid on the Yucatán carbonate platform in the southern Gulf of Mexico 66 million years ago , forming the Chicxulub impact crater. After the mass extinction, the recovery of the global marine ecosystem-measured as primary productivity-was geographically heterogeneous ; export production in the Gulf of Mexico and North Atlantic-western Tethys was slower than in most other regions, taking 300 thousand years (kyr) to return to levels similar to those of the Late Cretaceous period.

Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench.

The Challenger Deep is the deepest ocean on Earth. The present study investigated microbial community structures and geochemical cycles associated with the trench bottom sediments of the Challenger Deep, the Mariana Trench. The SSU rRNA gene communities found in trench bottom sediments were dominated by the bacteria Chloroflexi (SAR202 and other lineages), Bacteroidetes, Planctomycetes, "Ca.

Discovery of moganite in a lunar meteorite as a trace of HO ice in the Moon's regolith.

Moganite, a monoclinic SiO phase, has been discovered in a lunar meteorite. Silica micrograins occur as nanocrystalline aggregates of mostly moganite and occasionally coesite and stishovite in the KREEP (high potassium, rare-earth element, and phosphorus)-like gabbroic-basaltic breccia NWA 2727, although these grains are seemingly absent in other lunar meteorites. We interpret the origin of these grains as follows: alkaline water delivery to the Moon via carbonaceous chondrite collisions, fluid capture during impact-induced brecciation, moganite precipitation from the captured HO at pH 9.

Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago.

Recent studies have shown that environmental DNA is found almost everywhere. Flower petal surfaces are an attractive tissue to use for investigation of the dispersal of environmental DNA in nature as they are isolated from the external environment until the bud opens and only then can the petal surface accumulate environmental DNA. Here, we performed a crowdsourced experiment, the "Ohanami Project", to obtain environmental DNA samples from petal surfaces of Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago during spring 2015.

Continuous depth profile of the rock strength in the Nankai accretionary prism based on drilling performance parameters.

A new method for evaluating the in situ rock strength beneath the seafloor is proposed and applied to the Nankai Trough accretionary prism. The depth-continuous in situ rock strength is a critical parameter for numerous studies in earth science, particularly for seismology and tectonics at plate convergence zones; yet, measurements are limited owing to a lack of drilled cores. Here, we propose a new indicator of strength, the equivalent strength (EST), which is determined only by drilling performance parameters such as drill string rotational torque, bit depth, and string rotational speed.

Organic matter in extraterrestrial water-bearing salt crystals.

Direct evidence of complex prebiotic chemistry from a water-rich world in the outer solar system is provided by the 4.5-billion-year-old halite crystals hosted in the Zag and Monahans (1998) meteorites. This study offers the first comprehensive organic analysis of the soluble and insoluble organic compounds found in the millimeter-sized halite crystals containing brine inclusions and sheds light on the nature and activity of aqueous fluids on a primitive parent body.

Aerobic and Anaerobic Methanotrophic Communities Associated with Methane Hydrates Exposed on the Seafloor: A High-Pressure Sampling and Stable Isotope-Incubation Experiment.

High-pressure (HP) environments represent the largest volumetric majority of habitable space for microorganisms on the planet, including the deep-sea and subsurface biosphere. However, the importance of pressure as an environmental variable affecting deep microbial life and their biogeochemical functions in carbon cycling still remains poorly understood. Here, we designed a new high-volume HP-sediment core sampler that is deployable on the payload of a remotely operated vehicle and can maintain HP conditions throughout multi-month enrichment incubations including daily amendments with liquid media and gases and daily effluent sampling for geochemical or microbiological analysis.

A new high-pressure form of MgSiO highlighting diffusionless phase transitions of olivine.

High-pressure polymorphism of olivine (α-phase of MgSiO) is of particular interest for geophysicists aiming to understand the structure and dynamics of the Earth's interior because of olivine's prominent abundance in the upper mantle. Therefore, natural and synthetic olivine polymorphs have been actively studied in the past half century. Here, we report a new high-pressure polymorph, the ε*-phase, which was discovered in a heavily shocked meteorite.

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds.

The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be "hot spots" for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C).

Cyanobacterial exopolymer properties differentiate microbial carbonate fabrics.

Although environmental changes and evolution of life are potentially recorded via microbial carbonates, including laminated stromatolites and clotted thrombolites, factors controlling their fabric are still a matter of controversy. Herein, we report that the exopolymer properties of different cyanobacterial taxa primarily control the microbial carbonates fabrics in modern examples. This study shows that the calcite encrustation of filamentous Phormidium sp.

Stress buildup and drop in inland shallow crust caused by the 2011 Tohoku-oki earthquake events.

To examine the change in stress between before and after the Tohoku-oki Mw9.0 earthquake, we performed stress measurements after the earthquake in the Kamaishi mine in Iwate prefecture in northern Japan, located near the northern termination of the mainshock rupture, following previous measurements before the earthquake in the same mine. The results showed that the magnitudes of the three-dimensional principal stresses and the vertical stress drastically increased after the mainshock and, at 1 year after the earthquake, were more than double those before the earthquake.

Archaeal MutS5 tightly binds to Holliday junction similarly to eukaryotic MutSγ.

Archaeal DNA recombination mechanism and the related proteins are similar to those in eukaryotes. However, no functional homolog of eukaryotic MutSγ, which recognizes Holliday junction to promote homologous recombination, has been identified in archaea. Hence, the whole molecular mechanism of archaeal homologous recombination has not yet been revealed.

Rapid decline in pH of coral calcification fluid due to incorporation of anthropogenic CO.

Marine calcifying organisms, such as stony corals, are under threat by rapid ocean acidification (OA) arising from the oceanic uptake of anthropogenic CO. To better understand how organisms and ecosystems will adapt to or be damaged by the resulting environmental changes, field observations are crucial. Here, we show clear evidence, based on boron isotopic ratio (δB) measurements, that OA is affecting the pH of the calcification fluid (pH) in Porites corals within the western North Pacific Subtropical Gyre at two separate locations, Chichijima Island (Ogasawara Archipelago) and Kikaijima Island.

Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars.

Water from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (E<-550 mV) conditions with low ionic concentrations. These conditions make the springs exceptionally challenging for life. Here, we report the metagenomic data and recovered draft genomes from two different springs, GPS1 and BS5.

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.

Stress state measured at ~7 km depth in the Tarim Basin, NW China.

The in-situ stress state in the Tarim Basin, Northwest China, down to 7 km depth is constrained using the anelastic strain recovery (ASR) method and wellbore failure analysis. Results are consistent between the two methods, and indicate that the maximum principal stresses (σ) are close to vertical and the intermediate and minimum principal stresses (σ and σ) are approximately horizontal. The states of stress at the studied wellbore is in the normal faulting stress regime within the Tarim Basin rather than in the compressional tectonic stress regime as in the periphery of the Tarim Basin, which explains the presence of the normal faults interpreted in 3-D seismic profiles collected from adjacent areas.

Population dynamics of electrogenic microbial communities in microbial fuel cells started with three different inoculum sources.

Microbial fuel cells (MFCs) are one of the bioelectrochemical systems that exploit microorganisms as biocatalysts to degrade organic matters and recover energy as electric power. Here, we explored how the established electrogenic microbial communities were influenced by three different inoculum sources; anaerobic sludge of the wastewater plant, rice paddy field soil, and coastal lagoon sediment. We periodically characterized both electricity generation with sucrose consumption and 16S rRNA-basis microbial community composition.

Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment.

The factors controlling the relative abundances of Archaea and Bacteria in marine sediments are poorly understood. We determined depth distributions of archaeal and bacterial 16S rRNA genes by quantitative PCR at eight stations in Aarhus Bay, Denmark. Bacterial outnumber archaeal genes 10-60-fold in uppermost sediments that are irrigated and mixed by macrofauna.

Extreme hydrothermal conditions at an active plate-bounding fault.

Temperature and fluid pressure conditions control rock deformation and mineralization on geological faults, and hence the distribution of earthquakes. Typical intraplate continental crust has hydrostatic fluid pressure and a near-surface thermal gradient of 31 ± 15 degrees Celsius per kilometre. At temperatures above 300-450 degrees Celsius, usually found at depths greater than 10-15 kilometres, the intra-crystalline plasticity of quartz and feldspar relieves stress by aseismic creep and earthquakes are infrequent.