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1.  Potential Biosignatures in Super-Earth Atmospheres II. Photochemical Responses 
Astrobiology  2013;13(5):415-438.
Abstract
Spectral characterization of super-Earth atmospheres for planets orbiting in the habitable zone of M dwarf stars is a key focus in exoplanet science. A central challenge is to understand and predict the expected spectral signals of atmospheric biosignatures (species associated with life). Our work applies a global-mean radiative-convective-photochemical column model assuming a planet with an Earth-like biomass and planetary development. We investigated planets with gravities of 1g and 3g and a surface pressure of 1 bar around central stars with spectral classes from M0 to M7. The spectral signals of the calculated planetary scenarios have been presented by in an earlier work by Rauer and colleagues. The main motivation of the present work is to perform a deeper analysis of the chemical processes in the planetary atmospheres. We apply a diagnostic tool, the Pathway Analysis Program, to shed light on the photochemical pathways that form and destroy biosignature species. Ozone is a potential biosignature for complex life. An important result of our analysis is a shift in the ozone photochemistry from mainly Chapman production (which dominates in Earth's stratosphere) to smog-dominated ozone production for planets in the habitable zone of cooler (M5–M7)-class dwarf stars. This result is associated with a lower energy flux in the UVB wavelength range from the central star, hence slower planetary atmospheric photolysis of molecular oxygen, which slows the Chapman ozone production. This is important for future atmospheric characterization missions because it provides an indication of different chemical environments that can lead to very different responses of ozone, for example, cosmic rays. Nitrous oxide, a biosignature for simple bacterial life, is favored for low stratospheric UV conditions, that is, on planets orbiting cooler stars. Transport of this species from its surface source to the stratosphere where it is destroyed can also be a key process. Comparing 1g with 3g scenarios, our analysis suggests it is important to include the effects of interactive chemistry. Key Words: Exoplanets—Earth-like—M-dwarf—Photochemistry—Biosignatures. Astrobiology 13, 415–438.
doi:10.1089/ast.2012.0926
PMCID: PMC3941937  PMID: 23683046
2.  Abiotic Production of Methane in Terrestrial Planets 
Astrobiology  2013;13(6):550-559.
Abstract
On Earth, methane is produced mainly by life, and it has been proposed that, under certain conditions, methane detected in an exoplanetary spectrum may be considered a biosignature. Here, we estimate how much methane may be produced in hydrothermal vent systems by serpentinization, its main geological source, using the kinetic properties of the main reactions involved in methane production by serpentinization. Hydrogen production by serpentinization was calculated as a function of the available FeO in the crust, given the current spreading rates. Carbon dioxide is the limiting reactant for methane formation because it is highly depleted in aqueous form in hydrothermal vent systems. We estimated maximum CH4 surface fluxes of 6.8×108 and 1.3×109 molecules cm−2 s−1 for rocky planets with 1 and 5 M⊕, respectively. Using a 1-D photochemical model, we simulated atmospheres with volume mixing ratios of 0.03 and 0.1 CO2 to calculate atmospheric methane concentrations for the maximum production of this compound by serpentinization. The resulting abundances were 2.5 and 2.1 ppmv for 1 M⊕ planets and 4.1 and 3.7 ppmv for 5 M⊕ planets. Therefore, low atmospheric concentrations of methane may be produced by serpentinization. For habitable planets around Sun-like stars with N2-CO2 atmospheres, methane concentrations larger than 10 ppmv may indicate the presence of life. Key Words: Serpentinization—Exoplanets—Biosignatures—Planetary atmospheres. Astrobiology 13, 550–559.
doi:10.1089/ast.2012.0817
PMCID: PMC3689174  PMID: 23742231
3.  Using Dimers to Measure Biosignatures and Atmospheric Pressure for Terrestrial Exoplanets 
Astrobiology  2014;14(2):67-86.
Abstract
We present a new method to probe atmospheric pressure on Earth-like planets using (O2-O2) dimers in the near-infrared. We also show that dimer features could be the most readily detectable biosignatures for Earth-like atmospheres and may even be detectable in transit transmission with the James Webb Space Telescope (JWST). The absorption by dimers changes more rapidly with pressure and density than that of monomers and can therefore provide additional information about atmospheric pressures. By comparing the absorption strengths of rotational and vibrational features to the absorption strengths of dimer features, we show that in some cases it may be possible to estimate the pressure at the reflecting surface of a planet. This method is demonstrated by using the O2 A band and the 1.06 μm dimer feature, either in transmission or reflected spectra. It works best for planets around M dwarfs with atmospheric pressures between 0.1 and 10 bar and for O2 volume mixing ratios above 50% of Earth's present-day level. Furthermore, unlike observations of Rayleigh scattering, this method can be used at wavelengths longer than 0.6 μm and is therefore potentially applicable, although challenging, to near-term planet characterization missions such as JWST. We also performed detectability studies for JWST transit transmission spectroscopy and found that the 1.06 and 1.27 μm dimer features could be detectable (SNR>3) for an Earth analogue orbiting an M5V star at a distance of 5 pc. The detection of these features could provide a constraint on the atmospheric pressure of an exoplanet and serve as biosignatures for oxygenic photosynthesis. We calculated the required signal-to-noise ratios to detect and characterize O2 monomer and dimer features in direct imaging–reflected spectra and found that signal-to-noise ratios greater than 10 at a spectral resolving power of R=100 would be required. Key Words: Remote sensing—Extrasolar terrestrial planets—Habitability—Radiative transfer—Biosignatures. Astrobiology 14, 67–86.
doi:10.1089/ast.2013.0990
PMCID: PMC3928785  PMID: 24432758
4.  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
5.  Spectral Fingerprints of Earth-like Planets Around FGK Stars 
Astrobiology  2013;13(3):251-269.
Abstract
We present model atmospheres for an Earth-like planet orbiting the entire grid of main sequence FGK stars with effective temperatures ranging from Teff=4250 K to Teff=7000 K in 250 K intervals. We have modeled the remotely detectable spectra of Earth-like planets for clear and cloudy atmospheres at the 1 AU equivalent distance from the VIS to IR (0.4 to 20 μm) to compare detectability of features in different wavelength ranges in accordance with the James Webb Space Telescope and future design concepts to characterize exo-Earths. We have also explored the effect of the stellar UV levels as well as spectral energy distribution on a terrestrial atmosphere, concentrating on detectable atmospheric features that indicate habitability on Earth, namely, H2O, O3, CH4, N2O, and CH3Cl.
The increase in UV dominates changes of O3, OH, CH4, N2O, and CH3Cl, whereas the increase in stellar temperature dominates changes in H2O. The overall effect as stellar effective temperatures and corresponding UV increase is a lower surface temperature of the planet due to a bigger part of the stellar flux being reflected at short wavelengths, as well as increased photolysis. Earth-like atmosphere models show more O3 and OH but less stratospheric CH4, N2O, CH3Cl, and tropospheric H2O (but more stratospheric H2O) with increasing effective temperature of main sequence stars. The corresponding detectable spectral features, on the other hand, show different detectability depending on the wavelength observed.
We concentrate on directly imaged planets here as a framework to interpret future light curves, direct imaging, and secondary eclipse measurements of atmospheres of terrestrial planets in the habitable zone at varying orbital positions. Key Words: Habitability—Planetary atmospheres—Extrasolar terrestrial planets—Spectroscopic biosignatures. Astrobiology 13, 251–269.
doi:10.1089/ast.2012.0888
PMCID: PMC3612284  PMID: 23537136
6.  The Effect of Host Star Spectral Energy Distribution and Ice-Albedo Feedback on the Climate of Extrasolar Planets 
Astrobiology  2013;13(8):715-739.
Abstract
Planetary climate can be affected by the interaction of the host star spectral energy distribution with the wavelength-dependent reflectivity of ice and snow. In this study, we explored this effect with a one-dimensional (1-D), line-by-line, radiative transfer model to calculate broadband planetary albedos as input to a seasonally varying, 1-D energy balance climate model. A three-dimensional (3-D) general circulation model was also used to explore the atmosphere's response to changes in incoming stellar radiation, or instellation, and surface albedo. Using this hierarchy of models, we simulated planets covered by ocean, land, and water-ice of varying grain size, with incident radiation from stars of different spectral types. Terrestrial planets orbiting stars with higher near-UV radiation exhibited a stronger ice-albedo feedback. We found that ice extent was much greater on a planet orbiting an F-dwarf star than on a planet orbiting a G-dwarf star at an equivalent flux distance, and that ice-covered conditions occurred on an F-dwarf planet with only a 2% reduction in instellation relative to the present instellation on Earth, assuming fixed CO2 (present atmospheric level on Earth). A similar planet orbiting the Sun at an equivalent flux distance required an 8% reduction in instellation, while a planet orbiting an M-dwarf star required an additional 19% reduction in instellation to become ice-covered, equivalent to 73% of the modern solar constant. The reduction in instellation must be larger for planets orbiting cooler stars due in large part to the stronger absorption of longer-wavelength radiation by icy surfaces on these planets in addition to stronger absorption by water vapor and CO2 in their atmospheres, which provides increased downwelling longwave radiation. Lowering the IR and visible-band surface ice and snow albedos for an M-dwarf planet increased the planet's climate stability against changes in instellation and slowed the descent into global ice coverage. The surface ice-albedo feedback effect becomes less important at the outer edge of the habitable zone, where atmospheric CO2 could be expected to be high such that it maintains clement conditions for surface liquid water. We showed that ∼3–10 bar of CO2 will entirely mask the climatic effect of ice and snow, leaving the outer limits of the habitable zone unaffected by the spectral dependence of water ice and snow albedo. However, less CO2 is needed to maintain open water for a planet orbiting an M-dwarf star than would be the case for hotter main-sequence stars. Key Words: Extrasolar planets—M stars—Habitable zone—Snowball Earth. Astrobiology 13, 715–739.
doi:10.1089/ast.2012.0961
PMCID: PMC3746291  PMID: 23855332
7.  Tidal Venuses: Triggering a Climate Catastrophe via Tidal Heating 
Astrobiology  2013;13(3):225-250.
Abstract
Traditionally, stellar radiation has been the only heat source considered capable of determining global climate on long timescales. Here, we show that terrestrial exoplanets orbiting low-mass stars may be tidally heated at high-enough levels to induce a runaway greenhouse for a long-enough duration for all the hydrogen to escape. Without hydrogen, the planet no longer has water and cannot support life. We call these planets “Tidal Venuses” and the phenomenon a “tidal greenhouse.” Tidal effects also circularize the orbit, which decreases tidal heating. Hence, some planets may form with large eccentricity, with its accompanying large tidal heating, and lose their water, but eventually settle into nearly circular orbits (i.e., with negligible tidal heating) in the habitable zone (HZ). However, these planets are not habitable, as past tidal heating desiccated them, and hence should not be ranked highly for detailed follow-up observations aimed at detecting biosignatures. We simulated the evolution of hypothetical planetary systems in a quasi-continuous parameter distribution and found that we could constrain the history of the system by statistical arguments. Planets orbiting stars with masses<0.3 MSun may be in danger of desiccation via tidal heating. We have applied these concepts to Gl 667C c, a ∼4.5 MEarth planet orbiting a 0.3 MSun star at 0.12 AU. We found that it probably did not lose its water via tidal heating, as orbital stability is unlikely for the high eccentricities required for the tidal greenhouse. As the inner edge of the HZ is defined by the onset of a runaway or moist greenhouse powered by radiation, our results represent a fundamental revision to the HZ for noncircular orbits. In the appendices we review (a) the moist and runaway greenhouses, (b) hydrogen escape, (c) stellar mass-radius and mass-luminosity relations, (d) terrestrial planet mass-radius relations, and (e) linear tidal theories. Key Words: Extrasolar terrestrial planets—Habitability—Habitable zone—Liquid water—Tides. Astrobiology 13, 225–250.
doi:10.1089/ast.2012.0851
PMCID: PMC3612283  PMID: 23537135
8.  Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). 
Microbiological Reviews  1996;60(4):609-640.
Production and consumption processes in soils contribute to the global cycles of many trace gases (CH4, CO, OCS, H2, N2O, and NO) that are relevant for atmospheric chemistry and climate. Soil microbial processes contribute substantially to the budgets of atmospheric trace gases. The flux of trace gases between soil and atmosphere is usually the result of simultaneously operating production and consumption processes in soil: The relevant processes are not yet proven with absolute certainty, but the following are likely for trace gas consumption: H2 oxidation by abiontic soil enzymes; CO cooxidation by the ammonium monooxygenase of nitrifying bacteria; CH4 oxidation by unknown methanotrophic bacteria that utilize CH4 for growth; OCS hydrolysis by bacteria containing carbonic anhydrase; N2O reduction to N2 by denitrifying bacteria; NO consumption by either reduction to N2O in denitrifiers or oxidation to nitrate in heterotrophic bacteria. Wetland soils, in contrast to upland soils are generally anoxic and thus support the production of trace gases (H2, CO, CH4, N2O, and NO) by anaerobic bacteria such as fermenters, methanogens, acetogens, sulfate reducers, and denitrifiers. Methane is the dominant gaseous product of anaerobic degradation of organic matter and is released into the atmosphere, whereas the other trace gases are only intermediates, which are mostly cycled within the anoxic habitat. A significant percentage of the produced methane is oxidized by methanotrophic bacteria at anoxic-oxic interfaces such as the soil surface and the root surface of aquatic plants that serve as conduits for O2 transport into and CH4 transport out of the wetland soils. The dominant production processes in upland soils are different from those in wetland soils and include H2 production by biological N2 fixation, CO production by chemical decomposition of soil organic matter, and NO and N2O production by nitrification and denitrification. The processes responsible for CH4 production in upland soils are completely unclear, as are the OCS production processes in general. A problem for future research is the attribution of trace gas metabolic processes not only to functional groups of microorganisms but also to particular taxa. Thus, it is completely unclear how important microbial diversity is for the control of trace gas flux at the ecosystem level. However, different microbial communities may be part of the reason for differences in trace gas metabolism, e.g., effects of nitrogen fertilizers on CH4 uptake by soil; decrease of CH4 production with decreasing temperature; or different rates and modes of NO and N2O production in different soils and under different conditions.
PMCID: PMC239458  PMID: 8987358
9.  Ecosystem-scale biosphere-atmosphere interactions of a hemiboreal mixed forest stand at Järvselja, Estonia 
Forest ecology and management  2011;262(2):71-81.
During two measurement campaigns, from August to September 2008 and 2009, we quantified the major ecosystem fluxes in a hemiboreal forest ecosystem in Järvselja, Estonia. The main aim of this study was to separate the ecosystem flux components and gain insight into the performance of a multi-species multi-layered tree stand. Carbon dioxide and water vapor fluxes were measured using the eddy covariance method above and below the canopy in conjunction with the microclimate. Leaf and soil contributions were quantified separately by cuvette and chamber measurements, including fluxes of carbon dioxide, water vapor, nitrogen oxides, nitrous oxide, methane, ozone, sulfur dioxide, and biogenic volatile organic compounds (isoprene and monoterpenes). The latter have been as well characterized for monoterpenes in detail. Based on measured atmospheric trace gas concentrations, the flux tower site can be characterized as remote and rural with low anthropogenic disturbances. Our results presented here encourage future experimental efforts to be directed towards year round integrated biosphere-atmosphere measurements and development of process-oriented models of forest-atmosphere exchange taking the special case of a multi-layered and multi-species tree stand into account. As climate change likely leads to spatial extension of hemiboreal forest ecosystems a deep understanding of the processes and interactions therein is needed to foster management and mitigation strategies.
PMCID: PMC3859925  PMID: 24347809
Eddy-covariance; net ecosystem CO2 exchange; monoterpene emission; soil trace gas fluxes; leaf photosynthesis
10.  The Effect of a Strong Stellar Flare on the Atmospheric Chemistry of an Earth-like Planet Orbiting an M Dwarf 
Astrobiology  2010;10(7):751-771.
Abstract
Main sequence M stars pose an interesting problem for astrobiology: their abundance in our galaxy makes them likely targets in the hunt for habitable planets, but their strong chromospheric activity produces high-energy radiation and charged particles that may be detrimental to life. We studied the impact of the 1985 April 12 flare from the M dwarf AD Leonis (AD Leo), simulating the effects from both UV radiation and protons on the atmospheric chemistry of a hypothetical, Earth-like planet located within its habitable zone. Based on observations of solar proton events and the Neupert effect, we estimated a proton flux associated with the flare of 5.9 × 108 protons cm−2 sr−1 s−1 for particles with energies >10 MeV. Then we calculated the abundance of nitrogen oxides produced by the flare by scaling the production of these compounds during a large solar proton event called the Carrington event. The simulations were performed with a 1-D photochemical model coupled to a 1-D radiative/convective model. Our results indicate that the UV radiation emitted during the flare does not produce a significant change in the ozone column depth of the planet. When the action of protons is included, the ozone depletion reaches a maximum of 94% two years after the flare for a planet with no magnetic field. At the peak of the flare, the calculated UV fluxes that reach the surface, in the wavelength ranges that are damaging for life, exceed those received on Earth during less than 100 s. Therefore, flares may not present a direct hazard for life on the surface of an orbiting habitable planet. Given that AD Leo is one of the most magnetically active M dwarfs known, this conclusion should apply to planets around other M dwarfs with lower levels of chromospheric activity. Key Words: M dwarf—Flare—Habitable zone—Planetary atmospheres. Astrobiology 10, 751–771.
doi:10.1089/ast.2009.0376
PMCID: PMC3103837  PMID: 20879863
11.  Exomoon Habitability Constrained by Illumination and Tidal Heating 
Astrobiology  2013;13(1):18-46.
Abstract
The detection of moons orbiting extrasolar planets (“exomoons”) has now become feasible. Once they are discovered in the circumstellar habitable zone, questions about their habitability will emerge. Exomoons are likely to be tidally locked to their planet and hence experience days much shorter than their orbital period around the star and have seasons, all of which works in favor of habitability. These satellites can receive more illumination per area than their host planets, as the planet reflects stellar light and emits thermal photons. On the contrary, eclipses can significantly alter local climates on exomoons by reducing stellar illumination. In addition to radiative heating, tidal heating can be very large on exomoons, possibly even large enough for sterilization. We identify combinations of physical and orbital parameters for which radiative and tidal heating are strong enough to trigger a runaway greenhouse. By analogy with the circumstellar habitable zone, these constraints define a circumplanetary “habitable edge.” We apply our model to hypothetical moons around the recently discovered exoplanet Kepler-22b and the giant planet candidate KOI211.01 and describe, for the first time, the orbits of habitable exomoons. If either planet hosted a satellite at a distance greater than 10 planetary radii, then this could indicate the presence of a habitable moon. Key Words: Astrobiology—Extrasolar planets—Habitability—Habitable zone—Tides. Astrobiology 13, 18–46.
doi:10.1089/ast.2012.0859
PMCID: PMC3549631  PMID: 23305357
12.  Earth as an Extrasolar Planet: Earth Model Validation Using EPOXI Earth Observations 
Astrobiology  2011;11(5):393-408.
Abstract
The EPOXI Discovery Mission of Opportunity reused the Deep Impact flyby spacecraft to obtain spatially and temporally resolved visible photometric and moderate resolution near-infrared (NIR) spectroscopic observations of Earth. These remote observations provide a rigorous validation of whole-disk Earth model simulations used to better understand remotely detectable extrasolar planet characteristics. We have used these data to upgrade, correct, and validate the NASA Astrobiology Institute's Virtual Planetary Laboratory three-dimensional line-by-line, multiple-scattering spectral Earth model. This comprehensive model now includes specular reflectance from the ocean and explicitly includes atmospheric effects such as Rayleigh scattering, gas absorption, and temperature structure. We have used this model to generate spatially and temporally resolved synthetic spectra and images of Earth for the dates of EPOXI observation. Model parameters were varied to yield an optimum fit to the data. We found that a minimum spatial resolution of ∼100 pixels on the visible disk, and four categories of water clouds, which were defined by using observed cloud positions and optical thicknesses, were needed to yield acceptable fits. The validated model provides a simultaneous fit to Earth's lightcurve, absolute brightness, and spectral data, with a root-mean-square (RMS) error of typically less than 3% for the multiwavelength lightcurves and residuals of ∼10% for the absolute brightness throughout the visible and NIR spectral range. We have extended our validation into the mid-infrared by comparing the model to high spectral resolution observations of Earth from the Atmospheric Infrared Sounder, obtaining a fit with residuals of ∼7% and brightness temperature errors of less than 1 K in the atmospheric window. For the purpose of understanding the observable characteristics of the distant Earth at arbitrary viewing geometry and observing cadence, our validated forward model can be used to simulate Earth's time-dependent brightness and spectral properties for wavelengths from the far ultraviolet to the far infrared. Key Words: Astrobiology—Extrasolar terrestrial planets—Habitability—Planetary science—Radiative transfer. Astrobiology 11, 393–408.
doi:10.1089/ast.2011.0642
PMCID: PMC3133830  PMID: 21631250
13.  Ecosystem feedbacks on climate at the landscape scale 
Vegetation controls aspects of climate at all scales. These controls operate through fluxes of mass (water vapour, particulates, trace gases, condensation nuclei, and ice nuclei) and energy (latent and sensible heat, radiative exchanges, and momentum dissipation) between the biosphere and the atmosphere. The role these fluxes play in controlling minimum and maximum temperature, temperature range, rainfall, and precipitation processes are detailed. On the hemispheric scale, the importance of evapotranspiration, vegetation surface roughness, and vegetation albedo in the current generation of atmospheric general circulation models is reviewed. Finally, I assess at the planetary scale the global climate effects of biogenic emissions that are well mixed throughout the troposphere. I show that daily maximum and minimum temperatures are, in part, controlled by the emission of non-methane hydrocarbons and transpired water vapour. In many regions, a substantial fraction of the rainfall arises from upstream evapotranspiration rather than from oceanic evaporation. Biosphere evapotranspiration, surface roughness, and albedo are key controls in the general circulation of the atmosphere: climate models that lack adequate specifications for these biosphere attributes fail. The biosphere modulates climate at all scales.
doi:10.1098/rstb.1998.0186
PMCID: PMC1692168
14.  Formation of Amino Acids and Nucleotide Bases in a Titan Atmosphere Simulation Experiment 
Astrobiology  2012;12(9):809-817.
Abstract
The discovery of large (>100 u) molecules in Titan's upper atmosphere has heightened astrobiological interest in this unique satellite. In particular, complex organic aerosols produced in atmospheres containing C, N, O, and H, like that of Titan, could be a source of prebiotic molecules. In this work, aerosols produced in a Titan atmosphere simulation experiment with enhanced CO (N2/CH4/CO gas mixtures of 96.2%/2.0%/1.8% and 93.2%/5.0%/1.8%) were found to contain 18 molecules with molecular formulae that correspond to biological amino acids and nucleotide bases. Very high-resolution mass spectrometry of isotopically labeled samples confirmed that C4H5N3O, C4H4N2O2, C5H6N2O2, C5H5N5, and C6H9N3O2 are produced by chemistry in the simulation chamber. Gas chromatography–mass spectrometry (GC-MS) analyses of the non-isotopic samples confirmed the presence of cytosine (C4H5N3O), uracil (C5H4N2O2), thymine (C5H6N2O2), guanine (C5H5N5O), glycine (C2H5NO2), and alanine (C3H7NO2). Adenine (C5H5N5) was detected by GC-MS in isotopically labeled samples. The remaining prebiotic molecules were detected in unlabeled samples only and may have been affected by contamination in the chamber. These results demonstrate that prebiotic molecules can be formed by the high-energy chemistry similar to that which occurs in planetary upper atmospheres and therefore identifies a new source of prebiotic material, potentially increasing the range of planets where life could begin. Key Words: Astrochemistry—Planetary atmospheres—Titan—Astrobiology. Astrobiology 12, 809–817.
doi:10.1089/ast.2011.0623
PMCID: PMC3444770  PMID: 22917035
15.  Sulfur Respiration in a Marine Chemolithoautotrophic Beggiatoa Strain 
The chemolithoautotrophic strain Beggiatoa sp. 35Flor shows an unusual migration behavior when cultivated in a gradient medium under high sulfide fluxes. As common for Beggiatoa spp., the filaments form a mat at the oxygen–sulfide interface. However, upon prolonged incubation, a subpopulation migrates actively downward into the anoxic and sulfidic section of the medium, where the filaments become gradually depleted in their sulfur and polyhydroxyalkanoates (PHA) inclusions. This depletion is correlated with the production of hydrogen sulfide. The sulfur- and PHA-depleted filaments return to the oxygen–sulfide interface, where they switch back to depositing sulfur and PHA by aerobic sulfide oxidation. Based on these observations we conclude that internally stored elemental sulfur is respired at the expense of stored PHA under anoxic conditions. Until now, nitrate has always been assumed to be the alternative electron acceptor in chemolithoautotrophic Beggiatoa spp. under anoxic conditions. As the medium and the filaments were free of oxidized nitrogen compounds we can exclude this metabolism. Furthermore, sulfur respiration with PHA under anoxic conditions has so far only been described for heterotrophic Beggiatoa spp., but our medium did not contain accessible organic carbon. Hence the PHA inclusions must originate from atmospheric CO2 fixed by the filaments while at the oxygen–sulfide interface. We propose that the directed migration of filaments into the anoxic section of an oxygen–sulfide gradient system is used as a last resort to preserve cell integrity, which would otherwise be compromised by excessive sulfur deposition occurring in the presence of oxygen and high sulfide fluxes. The regulating mechanism of this migration is still unknown.
doi:10.3389/fmicb.2011.00276
PMCID: PMC3253548  PMID: 22291687
Beggiatoa; sulfur reduction; gradient cultivation; microelectrodes; migration
16.  Distribution and Rate of Methane Oxidation in Sediments of the Florida Everglades † 
Rates of methane emission from intact cores were measured during anoxic dark and oxic light and dark incubations. Rates of methane oxidation were calculated on the basis of oxic incubations by using the anoxic emissions as an estimate of the maximum potential flux. This technique indicated that methane oxidation consumed up to 91% of the maximum potential flux in peat sediments but that oxidation was negligible in marl sediments. Oxygen microprofiles determined for intact cores were comparable to profiles measured in situ. Thus, the laboratory incubations appeared to provide a reasonable approximation of in situ activities. This was further supported by the agreement between measured methane fluxes and fluxes predicted on the basis of methane profiles determined by in situ sampling of pore water. Methane emissions from peat sediments, oxygen concentrations and penetration depths, and methane concentration profiles were all sensitive to light-dark shifts as determined by a combination of field and laboratory analyses. Methane emissions were lower and oxygen concentrations and penetration depths were higher under illuminated than under dark conditions; the profiles of methane concentration changed in correspondence to the changes in oxygen profiles, but the estimated flux of methane into the oxic zone changed negligibly. Sediment-free, root-associated methane oxidation showed a pattern similar to that for methane oxidation in the core analyses: no oxidation was detected for roots growing in marl sediment, even for roots of Cladium jamaicense, which had the highest activity for samples from peat sediments. The magnitude of the root-associated oxidation rates indicated that belowground plant surfaces may not markedly increase the total capacity for methane consumption. However, the data collectively support the notion that the distribution and activity of methane oxidation have a major impact on the magnitude of atmospheric fluxes from the Everglades.
PMCID: PMC184862  PMID: 16348299
17.  Metabolism of Reduced Methylated Sulfur Compounds in Anaerobic Sediments and by a Pure Culture of an Estuarine Methanogen † 
Addition of dimethylsulfide (DMS), dimethyldisulfide (DMDS), or methane thiol (MSH) to a diversity of anoxic aquatic sediments (e.g., fresh water, estuarine, alkaline/hypersaline) stimulated methane production. The yield of methane recovered from DMS was often 52 to 63%, although high concentrations of DMS (as well as MSH and DMDS) inhibited methanogenesis in some types of sediments. Production of methane from these reduced methylated sulfur compounds was blocked by 2-bromoethanesulfonic acid. Sulfate did not influence the metabolism of millimolar levels of DMS, DMDS, or MSH added to sediments. However, when DMS was added at ∼2-μM levels as [14C]DMS, metabolism by sediments resulted in a 14CH4/14CO2 ratio of only 0.06. Addition of molybdate increased the ratio to 1.8, while 2-bromoethanesulfonic acid decreased it to 0, but did not block 14CO2 production. These results indicate the methanogens and sulfate reducers compete for DMS when it is present at low concentrations; however, at high concentrations, DMS is a “noncompetitive” substrate for methanogens. Metabolism of DMS by sediments resulted in the appearance of MSH as a transient intermediate. A pure culture of an obligately methylotrophic estuarine methanogen was isolated which was capable of growth on DMS. Metabolism of DMS by the culture also resulted in the transient appearance of MSH, but the organism could grow on neither MSH nor DMDS. The culture metabolized [14C]-DMS to yield a 14CH4/14CO2 ratio of ∼2.8. Reduced methylated sulfur compounds represent a new class of substrates for methanogens and may be potential precursors of methane in a variety of aquatic habitats.
PMCID: PMC239170  PMID: 16347202
18.  Production and Fate of Methylated Sulfur Compounds from Methionine and Dimethylsulfoniopropionate in Anoxic Salt Marsh Sediments † 
Applied and Environmental Microbiology  1987;53(10):2426-2434.
Anoxic salt marsh sediments were amended with dl-methionine and dimethylsulfoniopropionate (DMSP). Microbial metabolism of methionine yielded methane thiol (MSH) as the major volatile organosulfur product, with the formation of lesser amounts of dimethylsulfide (DMS). Biological transformation of DMSP resulted in the rapid release of DMS and only small amounts of MSH. Experiments with microbial inhibitors indicated that production of MSH from methionine was carried out by procaryotic organisms, probably sulfate-reducing bacteria. Methane-producing bacteria did not metabolize methionine. The involvement of specific groups of organisms in DMSP hydrolysis could not be determined with the inhibitors used, because DMSP was hydrolyzed in all samples except those which were autoclaved. Unamended sediment slurries, prepared from Spartina alterniflora sediments, contained significant (1 to 10 μM) concentrations of DMS. Endogenous methylated sulfur compounds and those produced from added methionine and DMSP were consumed by sediment microbes. Both sulfate-reducing and methane-producing bacteria were involved in DMS and MSH consumption. Methanogenesis was stimulated by the volatile organosulfur compounds released from methionine and DMSP. However, apparent competition for these compounds exists between methanogens and sulfate reducers. At low (1 μM) concentrations of methionine, the terminal S-methyl group was metabolized almost exclusively to CO2 and only small amounts of CH4. At higher (>100 μM) concentrations of methionine, the proportion of the methyl-sulfur group converted to CH4 increased. The results of this study demonstrate that methionine and DMSP are potential precursors of methylated sulfur compounds in anoxic sediments and that the microbial community is capable of metabolizing volatile methylated sulfur compounds.
PMCID: PMC204124  PMID: 16347461
19.  Habitable Planets Around White and Brown Dwarfs: The Perils of a Cooling Primary 
Astrobiology  2013;13(3):279-291.
Abstract
White and brown dwarfs are astrophysical objects that are bright enough to support an insolation habitable zone (IHZ). Unlike hydrogen-burning stars, they cool and become less luminous with time; hence their IHZ moves in with time. The inner edge of the IHZ is defined as the orbital radius at which a planet may enter a moist or runaway greenhouse, phenomena that can remove a planet's surface water forever. Thus, as the IHZ moves in, planets that enter it may no longer have any water and are still uninhabitable. Additionally, the close proximity of the IHZ to the primary leads to concern that tidal heating may also be strong enough to trigger a runaway greenhouse, even for orbital eccentricities as small as 10−6. Water loss occurs due to photolyzation by UV photons in the planetary stratosphere, followed by hydrogen escape. Young white dwarfs emit a large amount of these photons, as their surface temperatures are over 104 K. The situation is less clear for brown dwarfs, as observational data do not constrain their early activity and UV emission very well. Nonetheless, both types of planets are at risk of never achieving habitable conditions, but planets orbiting white dwarfs may be less likely to sustain life than those orbiting brown dwarfs. We consider the future habitability of the planet candidates KOI 55.01 and 55.02 in these terms and find they are unlikely to become habitable. Key Words: Extrasolar terrestrial planets—Habitability—Habitable zone—Tides—Exoplanets. Astrobiology 13, 279–291.
doi:10.1089/ast.2012.0867
PMCID: PMC3612282  PMID: 23537137
20.  ON THE GROWTH AND RESPIRATION OF SULFUR-OXIDIZING BACTERIA 
1. It is shown that Sulfomonas thiooxidans oxidizes elementary sulfur completely to sulfuric acid. Sodium thiosulfate is oxidized by this organism completely to sulfate. Sulfomonas thiooxidans differs, in this respect, from various other sulfur-oxidizing bacilli which either produce elementary sulfur, from the thiosulfate, or convert it into sulfates and persulfates. 2. The organism derives its carbon from the CO2 of the atmosphere, but is incapable of deriving the carbon from carbonates or organic matter. 3. The S:C, or ratio between the amount of sulfur oxidized to sulfate and amount of carbon assimilated chemosynthetically from the CO2 of the atmosphere, is, with elementary sulfur as a source of energy, 31.8, and with thiosulfate 64.2. The higher ratio in the case of the thiosulfate is due to the smaller amount of energy liberated in the oxidation of sulfur compound than in the elementary form. 4. Of the total energy made available in the oxidation of the sulfur to sulfuric acid, only 6.65 per cent is used by the organism for the reduction of atmospheric CO2 and assimilation of carbon. 5. Sulfates do not exert any injurious effect upon sulfur oxidation by Sulfomonas thiooxidans. Any effect obtained is due to the cation rather than the sulfate radical. Nitrates exert a distinctly injurious action both on the growth and respiration of the organism. 6. There is a definite correlation between the amount of sulfur present and velocity of oxidation, very similar to that found in the growth of yeasts and nitrifying bacteria. Oxidation reaches a maximum with about 25 gm. of sulfur added to 100 cc. of medium. However, larger amounts of sulfur have no injurious effect. 7. Dextrose does not exert any appreciable injurious effect in concentrations less than 5 per cent. The injurious effect of peptone sets in at 0.1 per cent concentration and brings sulfur oxidation almost to a standstill in 1 per cent concentration. Dextrose does not exert any appreciable influence upon sulfur oxidation and carbon assimilation from the carbon dioxide of the atmosphere. 8. Sulfomonas thiooxidans can withstand large concentrations of sulfuric acid. The oxidation of sulfur is affected only to a small extent even by 0.25 molar initial concentration of the acid. In 0.5 molar solutions, the injurious effect becomes marked. The organism may produce as much as 1.5 molar acid, without being destroyed. 9. Growth is at an optimum at a hydrogen ion concentration equivalent to pH 2.0 to 5.5, dropping down rapidly on the alkaline side, but not to such an extent on the acid, particularly when a pure culture is employed. 10. Respiration of the sulfur-oxidizing bacteria can be studied by using the filtrate of a vigorously growing culture, to which a definite amount of sulfur is added, and incubating for 12 to 24 hours.
PMCID: PMC2140527  PMID: 19871997
21.  Metabolic stratification driven by surface and subsurface interactions in a terrestrial mud volcano 
The ISME Journal  2012;6(12):2280-2290.
Terrestrial mud volcanism represents the prominent surface geological feature, where fluids and hydrocarbons are discharged along deeply rooted structures in tectonically active regimes. Terrestrial mud volcanoes (MVs) directly emit the major gas phase, methane, into the atmosphere, making them important sources of greenhouse gases over geological time. Quantification of methane emission would require detailed insights into the capacity and efficiency of microbial metabolisms either consuming or producing methane in the subsurface, and establishment of the linkage between these methane-related metabolisms and other microbial or abiotic processes. Here we conducted geochemical, microbiological and genetic analyses of sediments, gases, and pore and surface fluids to characterize fluid processes, community assemblages, functions and activities in a methane-emitting MV of southwestern Taiwan. Multiple lines of evidence suggest that aerobic/anaerobic methane oxidation, sulfate reduction and methanogenesis are active and compartmentalized into discrete, stratified niches, resembling those in marine settings. Surface evaporation and oxidation of sulfide minerals are required to account for the enhanced levels of sulfate that fuels subsurface sulfate reduction and anaerobic methanotrophy. Methane flux generated by in situ methanogenesis appears to alter the isotopic compositions and abundances of thermogenic methane migrating from deep sources, and to exceed the capacity of microbial consumption. This metabolic stratification is sustained by chemical disequilibria induced by the mixing between upward, anoxic, methane-rich fluids and downward, oxic, sulfate-rich fluids.
doi:10.1038/ismej.2012.61
PMCID: PMC3504961  PMID: 22739492
metabolic stratification; terrestrial mud volcano; sulfate-to-methane transition zone; methanogenesis; 16S rRNA gene clone library; metagenome
22.  Attributes of Atmospheric Carbon Monoxide Oxidation by Maine Forest Soils† 
Applied and Environmental Microbiology  1999;65(12):5257-5264.
CO, one of the most important trace gases, regulates tropospheric methane, hydroxyl radical, and ozone contents. Ten to 25% of the estimated global CO flux may be consumed by soils annually. Depth profiles for 14CO oxidation and CO concentration indicated that CO oxidation occurred primarily in surface soils and that photooxidation of soil organic matter did not necessarily contribute significantly to CO fluxes. Kinetic analyses revealed that the apparent Km was about 18 nM (17 ppm) and the Vmax was 6.9 μmol g (fresh weight)−1 h−1; the apparent Km was similar to the apparent Km for atmospheric methane consumption, but the Vmax was more than 100 times higher. Atmospheric CO oxidation responded sensitively to soil water regimes; decreases in water content in initially saturated soils resulted in increased uptake, and optimum uptake occurred at water contents of 30 to 60%. However, extended drying led to decreased uptake and net CO production. Rewetting could restore CO uptake, albeit with a pronounced hysteresis. The responses to changing temperatures indicated that the optimum temperature for net uptake was between 20 and 25°C and that there was a transition to net production at temperatures above 30°C. The responses to methyl fluoride and acetylene indicated that populations other than ammonia oxidizers and methanotrophs must be involved in forest soils. The response to acetylene was notable, since the strong initial inhibition was reversed after 12 h of incubation; in contrast, methyl fluoride did not have an inhibitory effect. Ammonium did not inhibit CO uptake; the level of nitrite inhibition was initially substantial, but nitrite inhibition was reversible over time. Nitrite inhibition appeared to occur through indirect effects based on abiological formation of NO.
PMCID: PMC91714  PMID: 10583974
23.  Formation of Dimethyl Sulfide and Methanethiol in Anoxic Freshwater Sediments 
Applied and Environmental Microbiology  1997;63(12):4741-4747.
Concentrations of volatile organic sulfur compounds (VOSC) were measured in water and sediment columns of ditches in a minerotrophic peatland in The Netherlands. VOSC, with methanethiol (4 to 40 nM) as the major compound, appeared to be mainly of sediment origin. Both VOSC and hydrogen sulfide concentrations decreased dramatically towards the water surface. High methanethiol and high dimethyl sulfide concentrations in the sediment and just above the sediment surface coincided with high concentrations of hydrogen sulfide (correlation factors, r = 0.91 and r = 0.81, respectively). Production and degradation of VOSC were studied in 32 sediment slurries collected from various freshwater systems in The Netherlands. Maximal endogenous methanethiol production rates of the sediments tested (up to 1.44 (mu)mol per liter of sediment slurry (middot) day(sup-1)) were determined after inhibition of methanogenic and sulfate-reducing populations in order to stop VOSC degradation. These experiments showed that the production and degradation of VOSC in sediments are well balanced. Statistical analysis revealed multiple relationships of methanethiol production rates with the combination of methane production rates (indicative of total anaerobic mineralization) and hydrogen sulfide concentrations (r = 0.90) or with the combination of methane production rates and the sulfate/iron ratios in the sediment (r = 0.82). These findings and the observed stimulation of methanethiol formation in sediment slurry incubations in which the hydrogen sulfide concentrations were artificially increased provided strong evidence that the anaerobic methylation of hydrogen sulfide is the main mechanism for VOSC formation in most freshwater systems. Methoxylated aromatic compounds are likely a major source of methyl groups for this methylation of hydrogen sulfide, since they are important degradation products of the abundant biopolymer lignin. Increased sulfate concentrations in several freshwater ecosystems caused by the inflow of water from the river Rhine into these systems result in higher hydrogen sulfide concentrations. As a consequence, higher fluxes of VOSC towards the atmosphere are conceivable.
PMCID: PMC1389307  PMID: 16535751
24.  Microbial Removal of Atmospheric Carbon Tetrachloride in Bulk Aerobic Soils▿ 
Applied and Environmental Microbiology  2011;77(17):5835-5841.
Atmospheric concentrations of carbon tetrachloride (CCl4) were removed by bulk aerobic soils from tropical, subtropical, and boreal environments. Removal was observed in all tested soil types, indicating that the process was widespread. The flux measured in field chamber experiments was 0.24 ± 0.10 nmol CCl4 (m2 day)−1 (average ± standard deviation [SD]; n = 282). Removal of CCl4 and removal of methane (CH4) were compared to explore whether the two processes were linked. Removal of both gases was halted in laboratory samples that were autoclaved, dry heated, or incubated in the presence of mercuric chloride (HgCl2). In marl soils, treatment with antibiotics such as tetracycline and streptomycin caused partial inhibition of CCl4 (50%) and CH4 (76%) removal, but removal was not affected in soils treated with nystatin or myxothiazol. These data indicated that bacteria contributed to the soil removal of CCl4 and that microeukaryotes may not have played a significant role. Amendments of methanol, acetate, and succinate to soil samples enhanced CCl4 removal by 59%, 293%, and 72%, respectively. Additions of a variety of inhibitors and substrates indicated that nitrification, methanogenesis, or biological reduction of nitrate, nitrous oxide, or sulfate (e.g., occurring in possible anoxic microzones) did not play a significant role in the removal of CCl4. Methyl fluoride inhibited removal of CH4 but not CCl4, indicating that CH4 and CCl4 removals were not directly linked. Furthermore, CCl4 removal was not affected in soils amended with copper sulfate or methane, supporting the results with MeF and suggesting that the observed CCl4 removal was not significantly mediated by methanotrophs.
doi:10.1128/AEM.05341-11
PMCID: PMC3165379  PMID: 21724884
25.  Effects of Extreme Obliquity Variations on the Habitability of Exoplanets 
Astrobiology  2014;14(4):277-291.
Abstract
We explore the impact of obliquity variations on planetary habitability in hypothetical systems with high mutual inclination. We show that large-amplitude, high-frequency obliquity oscillations on Earth-like exoplanets can suppress the ice-albedo feedback, increasing the outer edge of the habitable zone. We restricted our exploration to hypothetical systems consisting of a solar-mass star, an Earth-mass planet at 1 AU, and 1 or 2 larger planets. We verified that these systems are stable for 108 years with N-body simulations and calculated the obliquity variations induced by the orbital evolution of the Earth-mass planet and a torque from the host star. We ran a simplified energy balance model on the terrestrial planet to assess surface temperature and ice coverage on the planet's surface, and we calculated differences in the outer edge of the habitable zone for planets with rapid obliquity variations. For each hypothetical system, we calculated the outer edge of habitability for two conditions: (1) the full evolution of the planetary spin and orbit and (2) the eccentricity and obliquity fixed at their average values. We recovered previous results that higher values of fixed obliquity and eccentricity expand the habitable zone, but we also found that obliquity oscillations further expand habitable orbits in all cases. Terrestrial planets near the outer edge of the habitable zone may be more likely to support life in systems that induce rapid obliquity oscillations as opposed to fixed-spin planets. Such planets may be the easiest to directly characterize with space-borne telescopes. Key Words: Exoplanets—Habitable zone—Energy balance models. Astrobiology 14, 277–291.
doi:10.1089/ast.2013.1129
PMCID: PMC3995117  PMID: 24611714

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