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1.  Formation of H2 and CH4 by weathering of olivine at temperatures between 30 and 70°C 
Hydrocarbons such as CH4 are known to be formed through the Fischer-Tropsch or Sabatier type reactions in hydrothermal systems usually at temperatures above 100°C. Weathering of olivine is sometimes suggested to account for abiotic formation of CH4 through its redox lowering and water splitting properties. Knowledge about the CH4 and H2 formation processes at low temperatures is important for the research about the origin and cause of early Earth and Martian CH4 and for CO2 sequestration. We have conducted a series of low temperature, long-term weathering experiments in which we have tested the CH4 and H2 formation potential of forsteritic olivine.
The results show low temperature CH4 production that is probably influenced by chromite and magnetite as catalysts. Extensive analyses of a potential CH4 source trapped in the crystal structure of the olivine showed no signs of incorporated CH4. Also, the available sources of organic carbon were not enough to support the total amount of CH4 detected in our experiments. There was also a linear relationship between silica release into solution and the net CH4 accumulation into the incubation bottle headspaces suggesting that CH4 formation under these conditions could be a qualitative indicator of olivine dissolution.
It is likely that minerals such as magnetite, chromite and other metal-rich minerals found on the olivine surface catalyze the formation of CH4, because of the low temperature of the system. This may expand the range of environments plausible for abiotic CH4 formation both on Earth and on other terrestrial bodies.
doi:10.1186/1467-4866-12-6
PMCID: PMC3157414  PMID: 21707970
2.  Olivine-Respiring Bacteria Isolated from the Rock-Ice Interface in a Lava-Tube Cave, a Mars Analog Environment 
Astrobiology  2012;12(1):9-18.
Abstract
The boundary between ice and basalt on Earth is an analogue for some near-surface environments of Mars. We investigated neutrophilic iron-oxidizing microorganisms from the basalt-ice interface in a lava tube from the Oregon Cascades with perennial ice. One of the isolates (Pseudomonas sp. HerB) can use ferrous iron Fe(II) from the igneous mineral olivine as an electron donor and O2 as an electron acceptor. The optimum growth temperature is ∼12–14°C, but growth also occurs at 5°C. Bicarbonate is a facultative source of carbon. Growth of Pseudomonas sp. HerB as a chemolithotrophic iron oxidizer with olivine as the source of energy is favored in low O2 conditions (e.g., 1.6% O2). Most likely, microbial oxidation of olivine near pH 7 requires low O2 to offset the abiotic oxidation of iron. The metabolic capabilities of this bacterium would allow it to live in near-surface, icy, volcanic environments of Mars in the present or recent geological past and make this type of physiology a prime candidate in the search for life on Mars. Key Words: Extremophiles—Mars—Olivine—Iron-oxidizing bacteria—Redox. Astrobiology 12, 9–18.
doi:10.1089/ast.2011.0639
PMCID: PMC3264960  PMID: 22165996
3.  Electrical conductivity of orthopyroxene: Implications for the water content of the asthenosphere 
Electrical conductivity of minerals is sensitive to water content and hence can be used to infer the water content in the mantle. However, previous studies to infer the water content in the upper mantle were based on pure olivine model of the upper mantle. Influence of other minerals particularly that of orthopyroxene needs to be included to obtain a better estimate of water content in view of the high water solubility in this mineral. Here we report new results of electrical conductivity measurements on orthopyroxene, and apply these results to estimate the water content of the upper mantle of Earth. We found that the electrical conductivity of orthopyroxene is enhanced by the addition of water in a similar way as other minerals such as olivine and pyrope garnet. Using these new results, we calculate the electrical conductivity of pyrolite mantle as a function of water content and temperature incorporating the temperature and water fugacity-dependent hydrogen partitioning. Reported values of asthenosphere conductivity of 4 × 10−2−10−1 S/m corresponds to the water content of 0.01–0.04 wt%, a result in good agreement with the petrological model of the upper mantle.
doi:10.2183/pjab.85.466
PMCID: PMC3621551  PMID: 20009379
electrical conductivity; orthopyroxene; water; asthenosphere
4.  Bacterial Communities Associated with Subsurface Geochemical Processes in Continental Serpentinite Springs 
Applied and Environmental Microbiology  2013;79(13):3906-3916.
Reactions associated with the geochemical process of serpentinization can generate copious quantities of hydrogen and low-molecular-weight organic carbon compounds, which may provide energy and nutrients to sustain subsurface microbial communities independently of the photosynthetically supported surface biosphere. Previous microbial ecology studies have tested this hypothesis in deep sea hydrothermal vents, such as the Lost City hydrothermal field. This study applied similar methods, including molecular fingerprinting and tag sequencing of the 16S rRNA gene, to ultrabasic continental springs emanating from serpentinizing ultramafic rocks. These molecular surveys were linked with geochemical measurements of the fluids in an interdisciplinary approach designed to distinguish potential subsurface organisms from those derived from surface habitats. The betaproteobacterial genus Hydrogenophaga was identified as a likely inhabitant of transition zones where hydrogen-enriched subsurface fluids mix with oxygenated surface water. The Firmicutes genus Erysipelothrix was most strongly correlated with geochemical factors indicative of subsurface fluids and was identified as the most likely inhabitant of a serpentinization-powered subsurface biosphere. Both of these taxa have been identified in multiple hydrogen-enriched subsurface habitats worldwide, and the results of this study contribute to an emerging biogeographic pattern in which Betaproteobacteria occur in near-surface mixing zones and Firmicutes are present in deeper, anoxic subsurface habitats.
doi:10.1128/AEM.00330-13
PMCID: PMC3697581  PMID: 23584766
5.  Microbial activity in the marine deep biosphere: progress and prospects 
The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).
doi:10.3389/fmicb.2013.00189
PMCID: PMC3708129  PMID: 23874326
deep biosphere; IODP; biogeochemistry; sediment; oceanic crust; C-DEBI; subsurface microbiology
6.  Olivine Weathering in Soil, and Its Effects on Growth and Nutrient Uptake in Ryegrass (Lolium perenne L.): A Pot Experiment 
PLoS ONE  2012;7(8):e42098.
Mineral carbonation of basic silicate minerals regulates atmospheric CO2 on geological time scales by locking up carbon. Mining and spreading onto the earth's surface of fast-weathering silicates, such as olivine, has been proposed to speed up this natural CO2 sequestration (‘enhanced weathering’). While agriculture may offer an existing infrastructure, weathering rate and impacts on soil and plant are largely unknown. Our objectives were to assess weathering of olivine in soil, and its effects on plant growth and nutrient uptake. In a pot experiment with perennial ryegrass (Lolium perenne L.), weathering during 32 weeks was inferred from bioavailability of magnesium (Mg) in soil and plant. Olivine doses were equivalent to 1630 (OLIV1), 8150, 40700 and 204000 (OLIV4) kg ha−1. Alternatively, the soluble Mg salt kieserite was applied for reference. Olivine increased plant growth (+15.6%) and plant K concentration (+16.5%) in OLIV4. At all doses, olivine increased bioavailability of Mg and Ni in soil, as well as uptake of Mg, Si and Ni in plants. Olivine suppressed Ca uptake. Weathering estimated from a Mg balance was equivalent to 240 kg ha−1 (14.8% of dose, OLIV1) to 2240 kg ha−1 (1.1%, OLIV4). This corresponds to gross CO2 sequestration of 290 to 2690 kg ha−1 (29 103 to 269 103 kg km−2.) Alternatively, weathering estimated from similarity with kieserite treatments ranged from 13% to 58% for OLIV1. The Olsen model for olivine carbonation predicted 4.0% to 9.0% weathering for our case, independent of olivine dose. Our % values observed at high doses were smaller than this, suggesting negative feedbacks in soil. Yet, weathering appears fast enough to support the ‘enhanced weathering’ concept. In agriculture, olivine doses must remain within limits to avoid imbalances in plant nutrition, notably at low Ca availability; and to avoid Ni accumulation in soil and crop.
doi:10.1371/journal.pone.0042098
PMCID: PMC3415406  PMID: 22912685
7.  Hyperthermophiles in the history of life 
Today, hyperthermophilic (‘superheat-loving’) bacteria and archaea are found within high-temperature environments, representing the upper temperature border of life. They grow optimally above 80°C and exhibit an upper temperature border of growth up to 113°C. Members of the genera, Pyrodictium and Pyrolobus, survive at least 1 h of autoclaving. In their basically anaerobic environments, hyperthermophiles (HT) gain energy by inorganic redox reactions employing compounds like molecular hydrogen, carbon dioxide, sulphur and ferric and ferrous iron. Based on their growth requirements, HT could have existed already on the early Earth about 3.9 Gyr ago. In agreement, within the phylogenetic tree of life, they occupy all the short deep branches closest to the root. The earliest archaeal phylogenetic lineage is represented by the extremely tiny members of the novel kingdom of Nanoarchaeota, which thrive in submarine hot vents. HT are very tough survivors, even in deep-freezing at −140°C. Therefore, during impact ejecta, they could have been successfully transferred to other planets and moons through the coldness of space.
doi:10.1098/rstb.2006.1907
PMCID: PMC1664684  PMID: 17008222
archaea; hyperthermophiles; origin of life
8.  Targeted recovery of novel phylogenetic diversity from next-generation sequence data 
The ISME Journal  2012;6(11):2067-2077.
Next-generation sequencing technologies have led to recognition of a so-called ‘rare biosphere'. These microbial operational taxonomic units (OTUs) are defined by low relative abundance and may be specifically adapted to maintaining low population sizes. We hypothesized that mining of low-abundance next-generation 16S ribosomal RNA (rRNA) gene data would lead to the discovery of novel phylogenetic diversity, reflecting microorganisms not yet discovered by previous sampling efforts. Here, we test this hypothesis by combining molecular and bioinformatic approaches for targeted retrieval of phylogenetic novelty within rare biosphere OTUs. We combined BLASTN network analysis, phylogenetics and targeted primer design to amplify 16S rRNA gene sequences from unique potential bacterial lineages, comprising part of the rare biosphere from a multi-million sequence data set from an Arctic tundra soil sample. Demonstrating the feasibility of the protocol developed here, three of seven recovered phylogenetic lineages represented extremely divergent taxonomic entities. These divergent target sequences correspond to (a) a previously unknown lineage within the BRC1 candidate phylum, (b) a sister group to the early diverging and currently recognized monospecific Cyanobacteria Gloeobacter, a genus containing multiple plesiomorphic traits and (c) a highly divergent lineage phylogenetically resolved within mitochondria. A comparison to twelve next-generation data sets from additional soils suggested persistent low-abundance distributions of these novel 16S rRNA genes. The results demonstrate this sequence analysis and retrieval pipeline as applicable for exploring underrepresented phylogenetic novelty and recovering taxa that may represent significant steps in bacterial evolution.
doi:10.1038/ismej.2012.50
PMCID: PMC3475379  PMID: 22791239
rare biosphere; bioprospecting; molecular ecology; organellar evolution; next-generation sequencing; 16S rRNA
9.  Early anaerobic metabolisms 
Before the advent of oxygenic photosynthesis, the biosphere was driven by anaerobic metabolisms. We catalogue and quantify the source strengths of the most probable electron donors and electron acceptors that would have been available to fuel early-Earth ecosystems. The most active ecosystems were probably driven by the cycling of H2 and Fe2+ through primary production conducted by anoxygenic phototrophs. Interesting and dynamic ecosystems would have also been driven by the microbial cycling of sulphur and nitrogen species, but their activity levels were probably not so great. Despite the diversity of potential early ecosystems, rates of primary production in the early-Earth anaerobic biosphere were probably well below those rates observed in the marine environment. We shift our attention to the Earth environment at 3.8 Gyr ago, where the earliest marine sediments are preserved. We calculate, consistent with the carbon isotope record and other considerations of the carbon cycle, that marine rates of primary production at this time were probably an order of magnitude (or more) less than today. We conclude that the flux of reduced species to the Earth surface at this time may have been sufficient to drive anaerobic ecosystems of sufficient activity to be consistent with the carbon isotope record. Conversely, an ecosystem based on oxygenic photosynthesis was also possible with complete removal of the oxygen by reaction with reduced species from the mantle.
doi:10.1098/rstb.2006.1906
PMCID: PMC1664682  PMID: 17008221
Archaean; evolution; hydrogen; anoxygenic photosynthesis; iron; metabolism
10.  Chloroplast redox imbalance governs phenotypic plasticity: the “grand design of photosynthesis” revisited 
Sunlight, the ultimate energy source for life on our planet, enters the biosphere as a direct consequence of the evolution of photoautotrophy. Photoautotrophs must balance the light energy absorbed and trapped through extremely fast, temperature-insensitive photochemistry with energy consumed through much slower, temperature-dependent biochemistry and metabolism. The attainment of such a balance in cellular energy flow between chloroplasts, mitochondria and the cytosol is called photostasis. Photoautotrophs sense cellular energy imbalances through modulation of excitation pressure which is a measure of the relative redox state of QA, the first stable quinone electron acceptor of photosystem II reaction centers. High excitation pressure constitutes a potential stress condition that can be caused either by exposure to an irradiance that exceeds the capacity of C, N, and S assimilation to utilize the electrons generated from the absorbed energy or by low temperature or any stress that decreases the capacity of the metabolic pathways downstream of photochemistry to utilize photosynthetically generated reductants. The similarities and differences in the phenotypic responses between cyanobacteria, green algae, crop plants, and variegation mutants of Arabidopsis thaliana as a function of cold acclimation and photoacclimation are reconciled in terms of differential responses to excitation pressure and the predisposition of photoautotrophs to maintain photostasis. The various acclimation strategies associated with green algae and cyanobacteria versus winter cereals and A. thaliana are discussed in terms of retrograde regulation and the “grand design of photosynthesis” originally proposed by Arnon (1982).
doi:10.3389/fpls.2012.00255
PMCID: PMC3515967  PMID: 23230444
acclimation; excitation pressure; phenotype; photostasis; plasticity; redox sensing/signaling
11.  Is the Genetic Landscape of the Deep Subsurface Biosphere Affected by Viruses? 
Viruses are powerful manipulators of microbial diversity, biogeochemistry, and evolution in the marine environment. Viruses can directly influence the genetic capabilities and the fitness of their hosts through the use of fitness factors and through horizontal gene transfer. However, the impact of viruses on microbial ecology and evolution is often overlooked in studies of the deep subsurface biosphere. Subsurface habitats connected to hydrothermal vent systems are characterized by constant fluid flux, dynamic environmental variability, and high microbial diversity. In such conditions, high adaptability would be an evolutionary asset, and the potential for frequent host–virus interactions would be high, increasing the likelihood that cellular hosts could acquire novel functions. Here, we review evidence supporting this hypothesis, including data indicating that microbial communities in subsurface hydrothermal fluids are exposed to a high rate of viral infection, as well as viral metagenomic data suggesting that the vent viral assemblage is particularly enriched in genes that facilitate horizontal gene transfer and host adaptability. Therefore, viruses are likely to play a crucial role in facilitating adaptability to the extreme conditions of these regions of the deep subsurface biosphere. We also discuss how these results might apply to other regions of the deep subsurface, where the nature of virus–host interactions would be altered, but possibly no less important, compared to more energetic hydrothermal systems.
doi:10.3389/fmicb.2011.00219
PMCID: PMC3211056  PMID: 22084639
viral ecology; microbial evolution; hydrothermal vents; deep subsurface biosphere
12.  Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment 
Nature Communications  2013;4:2120.
Microorganisms in the subsurface represent a substantial but poorly understood component of the Earth’s biosphere. Subsurface environments are complex and difficult to characterize; thus, their microbiota have remained as a ‘dark matter’ of the carbon and other biogeochemical cycles. Here we deeply sequence two sediment-hosted microbial communities from an aquifer adjacent to the Colorado River, CO, USA. No single organism represents more than ~1% of either community. Remarkably, many bacteria and archaea in these communities are novel at the phylum level or belong to phyla lacking a sequenced representative. The dominant organism in deeper sediment, RBG-1, is a member of a new phylum. On the basis of its reconstructed complete genome, RBG-1 is metabolically versatile. Its wide respiration-based repertoire may enable it to respond to the fluctuating redox environment close to the water table. We document extraordinary microbial novelty and the importance of previously unknown lineages in sediment biogeochemical transformations.
Turnover of sediment organic matter contributes to global carbon cycling, yet the microorganisms involved are largely unknown. Castelle et al. reveal that an aquifer sediment core hosts a ‘zoo’ of organisms, including representatives of a previously undescribed phylum (Zixibacteria).
doi:10.1038/ncomms3120
PMCID: PMC3903129  PMID: 23979677
13.  Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments 
Gram-positive spore-forming sulfate reducers and particularly members of the genus Desulfotomaculum are commonly found in the subsurface biosphere by culture based and molecular approaches. Due to their metabolic versatility and their ability to persist as endospores. Desulfotomaculum spp. are well-adapted for colonizing environments through a slow sedimentation process. Because of their ability to grow autotrophically (H2/CO2) and produce sulfide or acetate, these microorganisms may play key roles in deep lithoautotrophic microbial communities. Available data about Desulfotomaculum spp. and related species from studies carried out from deep freshwater lakes, marine sediments, oligotrophic and organic rich deep geological settings are discussed in this review.
doi:10.3389/fmicb.2013.00362
PMCID: PMC3844878  PMID: 24348471
Desulfotomaculum; deep subsurface; geomicrobiology; sulfate-reduction; lithoautotrophy; sporulation
14.  The rate of metabolism in marine animals: environmental constraints, ecological demands and energetic opportunities 
The rates of metabolism in animals vary tremendously throughout the biosphere. The origins of this variation are a matter of active debate with some scientists highlighting the importance of anatomical or environmental constraints, while others emphasize the diversity of ecological roles that organisms play and the associated energy demands. Here, we analyse metabolic rates in diverse marine taxa, with special emphasis on patterns of metabolic rate across a depth gradient, in an effort to understand the extent and underlying causes of variation. The conclusion from this analysis is that low rates of metabolism, in the deep sea and elsewhere, do not result from resource (e.g. food or oxygen) limitation or from temperature or pressure constraint. While metabolic rates do decline strongly with depth in several important animal groups, for others metabolism in abyssal species proceeds as fast as in ecologically similar shallow-water species at equivalent temperatures. Rather, high metabolic demand follows strong selection for locomotory capacity among visual predators inhabiting well-lit oceanic waters. Relaxation of this selection where visual predation is limited provides an opportunity for reduced energy expenditure. Large-scale metabolic variation in the ocean results from interspecific differences in ecological energy demand.
doi:10.1098/rstb.2007.2101
PMCID: PMC2442854  PMID: 17510016
metabolism; deep sea; scaling; oxygen consumption; locomotion; marine
15.  The early heat loss evolution of Mars and their implications for internal and environmental history 
Scientific Reports  2014;4:4338.
The time around 3.7 Ga ago was an epoch when substantial changes in Mars occurred: a substantial decline in aqueous erosion/degradation of landscape features; a change from abundant phyllosilicate formation to abundant acidic and evaporitic mineralogy; a change from olivine-rich volcanism to olivine-pyroxene volcanism; and maybe the cessation of the martian dynamo. Here I show that Mars also experienced profound changes in its internal dynamics in the same approximate time, including a reduction of heat flow and a drastic increasing of lithosphere strength. The reduction of heat flow indicates a limited cooling (or even a heating-up) of the deep interior for post-3.7 Ga times. The drastic increasing of lithosphere strength indicates a cold lithosphere above the inefficiently cooled (or even heated) interior. All those changes experienced by Mars were most probably linked and suggest the existence of profound interrelations between interior dynamics and environmental evolution of this planet.
doi:10.1038/srep04338
PMCID: PMC3949296  PMID: 24614056
16.  Biotechnological uses of enzymes from psychrophiles 
Microbial biotechnology  2011;4(4):449-460.
Summary
The bulk of the Earth's biosphere is cold (e.g. 90% of the ocean's waters are ≤ 5°C), sustaining a broad diversity of microbial life. The permanently cold environments vary from the deep ocean to alpine reaches and to polar regions. Commensurate with the extent and diversity of the ecosystems that harbour psychrophilic life, the functional capacity of the microorganisms that inhabitat the cold biosphere are equally diverse. As a result, indigenous psychrophilic microorganisms provide an enormous natural resource of enzymes that function effectively in the cold, and these cold‐adapted enzymes have been targeted for their biotechnological potential. In this review we describe the main properties of enzymes from psychrophiles and describe some of their known biotechnological applications and ways to potentially improve their value for biotechnology. The review also covers the use of metagenomics for enzyme screening, the development of psychrophilic gene expression systems and the use of enzymes for cleaning.
doi:10.1111/j.1751-7915.2011.00258.x
PMCID: PMC3815257  PMID: 21733127
17.  Prospects for the Study of Evolution in the Deep Biosphere 
Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org).
doi:10.3389/fmicb.2011.00285
PMCID: PMC3265032  PMID: 22319515
deep biosphere; subsurface; evolution; C-DEBI; adaptation
18.  Assessing “Dangerous Climate Change”: Required Reduction of Carbon Emissions to Protect Young People, Future Generations and Nature 
PLoS ONE  2013;8(12):e81648.
We assess climate impacts of global warming using ongoing observations and paleoclimate data. We use Earth’s measured energy imbalance, paleoclimate data, and simple representations of the global carbon cycle and temperature to define emission reductions needed to stabilize climate and avoid potentially disastrous impacts on today’s young people, future generations, and nature. A cumulative industrial-era limit of ∼500 GtC fossil fuel emissions and 100 GtC storage in the biosphere and soil would keep climate close to the Holocene range to which humanity and other species are adapted. Cumulative emissions of ∼1000 GtC, sometimes associated with 2°C global warming, would spur “slow” feedbacks and eventual warming of 3–4°C with disastrous consequences. Rapid emissions reduction is required to restore Earth’s energy balance and avoid ocean heat uptake that would practically guarantee irreversible effects. Continuation of high fossil fuel emissions, given current knowledge of the consequences, would be an act of extraordinary witting intergenerational injustice. Responsible policymaking requires a rising price on carbon emissions that would preclude emissions from most remaining coal and unconventional fossil fuels and phase down emissions from conventional fossil fuels.
doi:10.1371/journal.pone.0081648
PMCID: PMC3849278  PMID: 24312568
19.  The interaction of hydrogen with the {010} surfaces of Mg and Fe olivine as models for interstellar dust grains: a density functional theory study 
There is no consensus as yet to account for the significant presence of water on the terrestrial planets, but suggested sources include direct hydrogen adsorption from the parent molecular cloud after the planets’ formation, and delivery of hydrous material via comets or asteroids external to the zone of the terrestrial planets. Alternatively, a more recent idea is that water may have directly adsorbed onto the interstellar dust grains involved in planetary formation. In this work, we use electronic structure calculations based on the density functional theory to investigate and compare the bulk and {010} surface structures of the magnesium and iron end-members of the silicate mineral olivine, namely forsterite and fayalite, respectively. We also report our results on the adsorption of atomic hydrogen at the mineral surfaces, where our calculations show that there is no activation barrier to the adsorption of atomic hydrogen at these surfaces. Furthermore, different surface sites activate the atom to form either adsorbed hydride or proton species in the form of hydroxy groups on the same surface, which indicates that these mineral surfaces may have acted as catalytic sites in the immobilization and reaction of hydrogen atoms to form dihydrogen gas or water molecules.
doi:10.1098/rsta.2011.0592
PMCID: PMC3682719  PMID: 23734054
olivine; surfaces; hydrogen; adsorption; density functional theory
20.  Response of Atmospheric Biomarkers to NOx-Induced Photochemistry Generated by Stellar Cosmic Rays for Earth-like Planets in the Habitable Zone of M Dwarf Stars 
Astrobiology  2012;12(12):1109-1122.
Abstract
Understanding whether M dwarf stars may host habitable planets with Earth-like atmospheres and biospheres is a major goal in exoplanet research. If such planets exist, the question remains as to whether they could be identified via spectral signatures of biomarkers. Such planets may be exposed to extreme intensities of cosmic rays that could perturb their atmospheric photochemistry. Here, we consider stellar activity of M dwarfs ranging from quiet up to strong flaring conditions and investigate one particular effect upon biomarkers, namely, the ability of secondary electrons caused by stellar cosmic rays to break up atmospheric molecular nitrogen (N2), which leads to production of nitrogen oxides (NOx) in the planetary atmosphere, hence affecting biomarkers such as ozone (O3). We apply a stationary model, that is, without a time dependence; hence we are calculating the limiting case where the atmospheric chemistry response time of the biomarkers is assumed to be slow and remains constant compared with rapid forcing by the impinging stellar flares. This point should be further explored in future work with time-dependent models. We estimate the NOx production using an air shower approach and evaluate the implications using a climate-chemical model of the planetary atmosphere. O3 formation proceeds via the reaction O+O2+M→O3+M. At high NOx abundances, the O atoms arise mainly from NO2 photolysis, whereas on Earth this occurs via the photolysis of molecular oxygen (O2). For the flaring case, O3 is mainly destroyed via direct titration, NO+O3→NO2+O2, and not via the familiar catalytic cycle photochemistry, which occurs on Earth. For scenarios with low O3, Rayleigh scattering by the main atmospheric gases (O2, N2, and CO2) became more important for shielding the planetary surface from UV radiation. A major result of this work is that the biomarker O3 survived all the stellar-activity scenarios considered except for the strong case, whereas the biomarker nitrous oxide (N2O) could survive in the planetary atmosphere under all conditions of stellar activity considered here, which clearly has important implications for missions that aim to detect spectroscopic biomarkers. Key Words: M dwarf—Atmosphere—Earth-like—Biomarkers—Stellar cosmic rays. Astrobiology 12, 1109–1122.
doi:10.1089/ast.2011.0682
PMCID: PMC3522229  PMID: 23215581
21.  Processes affecting the remediation of chromium-contaminated sites. 
The remediation of chromium-contaminated sites requires knowledge of the processes that control the migration and transformation of chromium. Advection, dispersion, and diffusion are physical processes affecting the rate at which contaminants can migrate in the subsurface. Heterogeneity is an important factor that affects the contribution of each of these mechanisms to the migration of chromium-laden waters. Redox reactions, chemical speciation, adsorption/desorption phenomena, and precipitation/dissolution reactions control the transformation and mobility of chromium. The reduction of CrVI to CrIII can occur in the presence of ferrous iron in solution or in mineral phases, reduced sulfur compounds, or soil organic matter. At neutral to alkaline pH, the CrIII precipitates as amorphous hydroxides or forms complexes with organic matter. CrIII is oxidized by manganese dioxide, a common mineral found in many soils. Solid-phase precipitates of hexavalent chromium such as barium chromate can serve either as sources or sinks for CrVI. Adsorption of CrVI in soils increases with decreasing chromium concentration, making it more difficult to remove the chromium as the concentration decreases during pump-and-treat remediation. Knowledge of these chemical and physical processes is important in developing and selecting effective, cost-efficient remediation designs for chromium-contaminated sites.
PMCID: PMC1519387  PMID: 1935849
22.  Rheological decoupling at the Moho and implication to Venusian tectonics 
Scientific Reports  2014;4:4403.
Plate tectonics is largely responsible for material and heat circulation in Earth, but for unknown reasons it does not exist on Venus. The strength of planetary materials is a key control on plate tectonics because physical properties, such as temperature, pressure, stress, and chemical composition, result in strong rheological layering and convection in planetary interiors. Our deformation experiments show that crustal plagioclase is much weaker than mantle olivine at conditions corresponding to the Moho in Venus. Consequently, this strength contrast may produce a mechanical decoupling between the Venusian crust and interior mantle convection. One-dimensional numerical modeling using our experimental data confirms that this large strength contrast at the Moho impedes the surface motion of the Venusian crust and, as such, is an important factor in explaining the absence of plate tectonics on Venus.
doi:10.1038/srep04403
PMCID: PMC3957145  PMID: 24638113
23.  Modelling global terrestrial vegetation-climate interaction 
By coupling an atmospheric general circulation model asynchronously with an equilibrium vegetation model, manifold equilibrium solutions of the atmosphere-biosphere system have been explored. It is found that under present-day conditions of the Earth's orbital parameters and sea-surface temperatures, two stable equilibria of vegetation patterns are possible: one corresponding to present-day sparse vegetation in the Sahel, the second solution yielding savannah which extends far into the south-western part of the Sahara. A similar picture is obtained for conditions during the last glacial maximum (21 000 years before present (BP)). For the mid-Holocene (6000 years BP), however, the model finds only one solution: the green Sahara. We suggest that this intransitive behaviour of the atmosphere-biosphere is related to a westward shift of the Hadley-Walker circulation. A conceptual model of atmosphere-vegetation dynamics is used to interpret the bifurcation as well as its change in terms of stability theory.
doi:10.1098/rstb.1998.0190
PMCID: PMC1692172
24.  Selective Phylogenetic Analysis Targeting 16S rRNA Genes of Hyperthermophilic Archaea in the Deep-Subsurface Hot Biosphere▿  
International drilling projects for the study of microbial communities in the deep-subsurface hot biosphere have been expanded. Core samples obtained by deep drilling are commonly contaminated with mesophilic microorganisms in the drilling fluid, making it difficult to examine the microbial community by 16S rRNA gene clone library analysis. To eliminate mesophilic organism contamination, we previously developed a new method (selective phylogenetic analysis [SePA]) based on the strong correlation between the guanine-plus-cytosine (G+C) contents of the 16S rRNA genes and the optimal growth temperatures of prokaryotes, and we verified the method's effectiveness (H. Kimura, M. Sugihara, K. Kato, and S. Hanada, Appl. Environ. Microbiol. 72:21-27, 2006). In the present study we ascertained SePA's ability to eliminate contamination by archaeal rRNA genes, using deep-sea hydrothermal fluid (117°C) and surface seawater (29.9°C) as substitutes for deep-subsurface geothermal samples and drilling fluid, respectively. Archaeal 16S rRNA gene fragments, PCR amplified from the surface seawater, were denatured at 82°C and completely digested with exonuclease I (Exo I), while gene fragments from the deep-sea hydrothermal fluid remained intact after denaturation at 84°C because of their high G+C contents. An examination using mixtures of DNAs from the two environmental samples showed that denaturation at 84°C and digestion with Exo I completely eliminated archaeal 16S rRNA genes from the surface seawater. Our method was quite useful for culture-independent community analysis of hyperthermophilic archaea in core samples recovered from deep-subsurface geothermal environments.
doi:10.1128/AEM.02800-06
PMCID: PMC1855651  PMID: 17277228
25.  Ion association in concentrated NaCI brines from ambient to supercritical conditions: results from classical molecular dynamics simulations 
Highly concentrated NaCl brines are important geothermal fluids; chloride complexation of metals in such brines increases the solubility of minerals and plays a fundamental role in the genesis of hydrothermal ore deposits. There is experimental evidence that the molecular nature of the NaCl–water system changes over the pressure–temperature range of the Earth's crust. A transition of concentrated NaCl–H2O brines to a "hydrous molten salt" at high P and T has been argued to stabilize an aqueous fluid phase in the deep crust.
In this work, we have done molecular dynamic simulations using classical potentials to determine the nature of concentrated (0.5–16 m) NaCl–water mixtures under ambient (25°C, 1 bar), hydrothermal (325°C, 1 kbar) and deep crustal (625°C, 15 kbar) conditions. We used the well-established SPCE model for water together with the Smith and Dang Lennard-Jones potentials for the ions (J. Chem. Phys., 1994, 100, 3757). With increasing temperature at 1 kbar, the dielectric constant of water decreases to give extensive ion-association and the formation of polyatomic (NanClm)n-m clusters in addition to simple NaCl ion pairs. Large polyatomic (NanClm)n-m clusters resemble what would be expected in a hydrous NaCl melt in which water and NaCl were completely miscible. Although ion association decreases with pressure, temperatures of 625°C are not enough to overcome pressures of 15 kbar; consequently, there is still enhanced Na–Cl association in brines under deep crustal conditions.
doi:10.1186/1467-4866-3-102
PMCID: PMC1475619

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