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1.  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
2.  Sulfur and iron accumulation in three marine-archaeological shipwrecks in the Baltic Sea: The Ghost, the Crown and the Sword 
Scientific Reports  2014;4:4222.
Sulfur and iron concentrations in wood from three 17th century shipwrecks in the Baltic Sea, the Ghost wreck, the Crown and the Sword, were obtained by X-ray fluorescence (XRF) scanning. In near anaerobic environments symbiotic microorganisms degrade waterlogged wood, reduce sulfate and promote accumulation of low-valent sulfur compounds, as previously found for the famous wrecks of the Vasa and Mary Rose. Sulfur K-edge X-ray absorption near-edge structure (XANES) analyses of Ghost wreck wood show that organic thiols and disulfides dominate, together with elemental sulfur probably generated by sulfur-oxidizing Beggiatoa bacteria. Iron sulfides were not detected, consistent with the relatively low iron concentration in the wood. In a museum climate with high atmospheric humidity oxidation processes, especially of iron sulfides formed in the presence of corroding iron, may induce post-conservation wood degradation. Subject to more general confirmation by further analyses no severe conservation concerns are expected for the Ghost wreck wood.
PMCID: PMC3936213  PMID: 24573214
3.  Emission Characteristics and Factors of Selected Odorous Compounds at a Wastewater Treatment Plant 
Sensors (Basel, Switzerland)  2009;9(1):311-326.
This study was initiated to explore the emission characteristics of Reduced Sulfur Compounds (RSCs: hydrogen sulfide, methyl mercaptan, dimethyl sulfide, dimethyl disulfide), ammonia and trimethylamine from a Wastewater Treatment Plant (WWTP) located at Sun-Cheon, Chonlanam-Do in South Korea. The study also evaluates flux profiles of the six selected odorous compounds and their flux rates (μg/m2/min) and compares their emission characteristics. A Dynamic Flux Chamber DFC was used to measure fluxes of pollutants from the treatment plant. Quality control of odor samples using a non-reactive sulfur dioxide gas determined the time taken for DFC concentration to reach equilibrium. The reduced sulfur compounds were analyzed by interfacing gas chromatography with a Pulsed Flame Photometric Detector (PFPD). Air samples were collected in the morning and afternoon on one day during summer (August) and two days in winter (December and January). Their emission rates were determined and it was observed that during summer relatively higher amounts of the selected odorous compounds were emitted compared to winter. Air samples from primary settling basin, aeration basin, and final settling basin were tested and the total amount of selected odorous compounds emitted per wastewater ton was found to be 1344 μg/m3 from the selected treatment processes. It was also observed that, in this study, the dominant odor intensity contribution was caused by dimethyl disulfide (69.1%).
PMCID: PMC3280747  PMID: 22389601
Odorous compounds; emission characteristics; Dynamic Flux Chamber (DFC)
4.  Widespread occurrence of bacterial thiol methyltransferases and the biogenic emission of methylated sulfur gases. 
A majority of heterotrophic bacteria isolated from soil, water, sediment, vegetation, and marine algae cultures methylated sulfide, producing methanethiol. This was demonstrated with intact cells by measuring the emission of methanethiol with a sulfur-selective chemiluminescence detector, and in cell extracts by detection of sulfide-dependent thiol methyltransferase activity. Extracts of two Pseudomonas isolates were fractionated by gel-filtration and ion-exchange chromatography, and with sulfide as the substrate a single peak of thiol methyltransferase activity was seen in each case. Extracts of several bacterial strains also contained thiol methyltransferase activity with organic thiols as substrates. Thus, S-adenosylmethionine-dependent thiol methyltransferase activities are widespread in bacteria and may contribute to biogenic emissions of methylated sulfur gases and to the production of methyl thioethers.
PMCID: PMC203921  PMID: 3662509
5.  Ecophysiological Evidence that Achromatium oxaliferum Is Responsible for the Oxidation of Reduced Sulfur Species to Sulfate in a Freshwater Sediment 
Achromatium oxaliferum is a large, morphologically conspicuous, sediment-dwelling bacterium. The organism has yet to be cultured in the laboratory, and very little is known about its physiology. The presence of intracellular inclusions of calcite and sulfur have given rise to speculation that the bacterium is involved in the carbon and sulfur cycles in the sediments where it is found. Depth profiles of oxygen concentration and A. oxaliferum cell numbers in a freshwater sediment revealed that the A. oxaliferum population spanned the oxic-anoxic boundary in the top 3 to 4 cm of sediments. Some of the A. oxaliferum cells resided at depths where no oxygen was detectable, suggesting that these cells may be capable of anaerobic metabolism. The distributions of solid-phase and dissolved inorganic sulfur species in the sediment revealed that A. oxaliferum was most abundant where sulfur cycling was most intense. The sediment was characterized by low concentrations of free sulfide. However, a comparison of sulfate reduction rates in sediment cores incubated with either oxic or anoxic overlying water indicated that the oxidative and reductive components of the sulfur cycle were tightly coupled in the A. oxaliferum-bearing sediment. A positive correlation between pore water sulfate concentration and A. oxaliferum numbers was observed in field data collected over an 18-month period, suggesting a possible link between A. oxaliferum numbers and the oxidation of reduced sulfur species to sulfate. The field data were supported by laboratory incubation experiments in which sodium molybdate-treated sediment cores were augmented with highly purified suspensions of A. oxaliferum cells. Under oxic conditions, rates of sulfate production in the presence of sodium molybdate were found to correlate strongly with the number of cells added to sediment cores, providing further evidence for a role for A. oxaliferum in the oxidation of reduced sulfur.
PMCID: PMC1389159  PMID: 16535604
6.  Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. 
The vertical distribution of major and intermediate electron acceptors and donors was measured in a shallow stratified fjord. Peaks of zero valence sulfur, Mn(IV), and Fe(III) were observed in the chemocline separating oxic surface waters from sulfidic and anoxic bottom waters. The vertical fluxes of electron acceptors and donors (principally O2 and H2S) balanced within 5%; however, the zones of oxygen reduction and sulfide oxidation were clearly separated. The pathway of electron transfer between O2 and H2S was not apparent from the distribution of sulfur, nitrogen, or metal compounds investigated. The chemical zonation was related to bacterial populations as detected by ethidium bromide (EtBr) staining and by in situ hybridization with fluorescent oligonucleotide probes of increasing specificity. About half of all EtBr-stained cells were detectable with a general oligonucleotide probe for all eubacteria when digital image analysis algorithms were used to improve sensitivity. Both EtBr staining and hybridization indicated a surprisingly uniform distribution of bacteria throughout the water column. However, the average cell size and staining intensity as well as the abundance of different morphotypes changed markedly within the chemocline. The constant overall cell counts thus concealed pronounced population shifts within the water column. Cells stained with a delta 385 probe (presumably sulfate-reducing bacteria) were detected at the chemocline at about 5 x 10(4) cells per ml, and this concentration increased to 2 x 10(5) cells per ml beneath the chemocline. A long slim rod-shaped bacterium was found in large numbers in the oxic part of the chemocline, whereas large ellipsoid cells dominated at greater depth. Application of selective probes for known genera of sulfate-reducing bacteria gave only low cell counts, and thus it was not possible to identify the dominant morphotypes of the sulfate-reducing community.
PMCID: PMC167906  PMID: 8919801
7.  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.
PMCID: PMC3253548  PMID: 22291687
Beggiatoa; sulfur reduction; gradient cultivation; microelectrodes; migration
8.  Methylated sulfur compounds in microbial mats: in situ concentrations and metabolism by a colorless sulfur bacterium. 
The concentrations of the volatile organic sulfur compounds methanethiol, dimethyl disulfide, and dimethyl sulfide (DMS) and the viable population capable of DMS utilization in laminated microbial ecosystems were evaluated. Significant levels of DMS and dimethyl disulfide (maximum concentrations of 220 and 24 nmol cm3 of sediment-1, respectively) could be detected only at the top 20 mm of the microbial mat, whereas methanethiol was found only at depth horizons from 20 to 50 mm (maximum concentration of 42 nmol cm3 of sediment-1). DMS concentrations in the surface layer doubled after cold hydrolysis of its precursor, dimethylsulfoniopropionate. Most-probable-number counts revealed 2.2 x 10(5) cells cm3 of sediment-1, in the 0- to 5-mm depth horizon, capable of growth on DMS as the sole source of energy. An obligately chemolithoautotrophic bacillus designated strain T5 was isolated from the top layer of the marine sediment. Continuous culture studies in which DMS was the growth-limiting substrate revealed a maximum specific growth rate of 0.10 h-1 and a saturation constant of 90 mumol liter-1 for aerobic growth on this substrate.
PMCID: PMC183464  PMID: 1872604
9.  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.
PMCID: PMC1692168
10.  Impact of dissolved inorganic carbon concentrations and pH on growth of the chemolithoautotrophic epsilonproteobacterium Sulfurimonas gotlandica GD1T 
MicrobiologyOpen  2013;3(1):80-88.
Epsilonproteobacteria have been found globally distributed in marine anoxic/sulfidic areas mediating relevant transformations within the sulfur and nitrogen cycles. In the Baltic Sea redox zones, chemoautotrophic epsilonproteobacteria mainly belong to the Sulfurimonas gotlandica GD17 cluster for which recently a representative strain, S. gotlandica GD1T, could be established as a model organism. In this study, the potential effects of changes in dissolved inorganic carbon (DIC) and pH on S. gotlandica GD1T were examined. Bacterial cell abundance within a broad range of DIC concentrations and pH values were monitored and substrate utilization was determined. The results showed that the DIC saturation concentration for achieving maximal cell numbers was already reached at 800 μmol L−1, which is well below in situ DIC levels. The pH optimum was between 6.6 and 8.0. Within a pH range of 6.6–7.1 there was no significant difference in substrate utilization; however, at lower pH values maximum cell abundance decreased sharply and cell-specific substrate consumption increased.
PMCID: PMC3937731  PMID: 24376054
Chemolithoautotrophy; DIC saturation; epsilonproteobacterium; ocean acidification; pelagic redox zones; pH; sulfurimonas
11.  Motility of Marichromatium gracile in Response to Light, Oxygen, and Sulfide 
Applied and Environmental Microbiology  2001;67(12):5410-5419.
The motility of the purple sulfur bacterium Marichromatium gracile was investigated under different light regimes in a gradient capillary setup with opposing oxygen and sulfide gradients. The gradients were quantified with microsensors, while the behavior of swimming cells was studied by video microscopy in combination with a computerized cell tracking system. M. gracile exhibited photokinesis, photophobic responses, and phobic responses toward oxygen and sulfide. The observed migration patterns could be explained solely by the various phobic responses. In the dark, M. gracile formed an ∼500-μm-thick band at the oxic-anoxic interface, with a sharp border toward the oxic zone always positioned at ∼10 μM O2. Flux calculations yielded a molar conversion ratio Stot/O2 of 2.03:1 (Stot = [H2S] + [HS−] + [S2−]) for the sulfide oxidation within the band, indicating that in darkness the bacteria oxidized sulfide incompletely to sulfur stored in intracellular sulfur globules. In the light, M. gracile spread into the anoxic zone while still avoiding regions with >10 μM O2. The cells also preferred low sulfide concentrations if the oxygen was replaced by nitrogen. A light-dark transition experiment demonstrated a dynamic interaction between the chemical gradients and the cell's metabolism. In darkness and anoxia, M. gracile lost its motility after ca. 1 h. In contrast, at oxygen concentrations of >100 μM with no sulfide present the cells remained viable and motile for ca. 3 days both in light and darkness. Oxygen was respired also in the light, but respiration rates were lower than in the dark. Observed aggregation patterns are interpreted as effective protection strategies against high oxygen concentrations and might represent first stages of biofilm formation.
PMCID: PMC93323  PMID: 11722886
12.  Identification of Major Planktonic Sulfur Oxidizers in Stratified Freshwater Lake 
PLoS ONE  2014;9(4):e93877.
Planktonic sulfur oxidizers are important constituents of ecosystems in stratified water bodies, and contribute to sulfide detoxification. In contrast to marine environments, taxonomic identities of major planktonic sulfur oxidizers in freshwater lakes still remain largely unknown. Bacterioplankton community structure was analyzed in a stratified freshwater lake, Lake Mizugaki in Japan. In the clone libraries of 16S rRNA gene, clones very closely related to a sulfur oxidizer isolated from this lake, Sulfuritalea hydrogenivorans, were detected in deep anoxic water, and occupied up to 12.5% in each library of different water depth. Assemblages of planktonic sulfur oxidizers were specifically analyzed by constructing clone libraries of genes involved in sulfur oxidation, aprA, dsrA, soxB and sqr. In the libraries, clones related to betaproteobacteria were detected with high frequencies, including the close relatives of Sulfuritalea hydrogenivorans.
PMCID: PMC3973623  PMID: 24695535
13.  Spectral Fingerprints of Earth-like Planets Around FGK Stars 
Astrobiology  2013;13(3):251-269.
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.
PMCID: PMC3612284  PMID: 23537136
14.  Subfossil 16S rRNA Gene Sequences of Green Sulfur Bacteria in the Black Sea and Their Implications for Past Photic Zone Anoxia▿  
The Black Sea is the largest extant anoxic water body on Earth. Its oxic-anoxic boundary is located at a depth of 100 m and is populated by a single phylotype of marine green sulfur bacteria. This organism, Chlorobium sp. strain BS-1, is extraordinarily low light adapted and can therefore serve as an indicator of deep photic zone anoxia (A. K. Manske, J. Glaeser, M. M. M. Kuypers, and J. Overmann, Appl. Environ. Microbiol. 71:8049-8060, 2005). In the present study, two sediment cores were retrieved from the bottom of the Black Sea at depths of 2,006 and 2,162 m and were analyzed for the presence of subfossil DNA sequences of BS-1 using ancient-DNA methodology. Using optimized cultivation media, viable cells of the BS-1 phylotype were detected only at the sediment surface and not in deeper layers. In contrast, green sulfur bacterial 16S rRNA gene fragments were amplified from all the sediment layers investigated, including turbidites. After separation by denaturing gradient gel electrophoresis and sequencing, 14 different sequence types were distinguished. The sequence of BS-1 represented only a minor fraction of the amplification products and was found in 6 of 22 and 4 of 26 samples from the 2,006- and 2,162-m stations, respectively. Besides the sequences of BS-1, three additional phylotypes of the marine clade of green sulfur bacteria were detected. However, the majority of sequences clustered with groups from freshwater habitats. Our results suggest that a considerable fraction of green sulfur bacterial chemofossils did not originate in a low-light marine chemocline environment and therefore were likely to have an allochthonous origin. Thus, analysis of subfossil DNA sequences permits a more differentiated interpretation and reconstruction of past environmental conditions if specific chemofossils of stenoec species, like Chlorobium sp. strain BS-1, are employed.
PMCID: PMC2227738  PMID: 18039829
15.  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.
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.
PMCID: PMC3103837  PMID: 20879863
16.  Sulfur Production by Obligately Chemolithoautotrophic Thiobacillus Species 
Transient-state experiments with the obligately autotrophic Thiobacillus sp. strain W5 revealed that sulfide oxidation proceeds in two physiological phases, (i) the sulfate-producing phase and (ii) the sulfur- and sulfate-producing phase, after which sulfide toxicity occurs. Specific sulfur-producing characteristics were independent of the growth rate. Sulfur formation was shown to occur when the maximum oxidative capacity of the culture was approached. In order to be able to oxidize increasing amounts of sulfide, the organism has to convert part of the sulfide to sulfur (HS(sup-)(symbl)S(sup0) + H(sup+) + 2e(sup-)) instead of sulfate (HS(sup-) + 4H(inf2)O(symbl)SO(inf4)(sup2-) + 9 H(sup+) + 8e(sup-)), thereby keeping the electron flux constant. Measurements of the in vivo degree of reduction of the cytochrome pool as a function of increasing sulfide supply suggested a redox-related down-regulation of the sulfur oxidation rate. Comparison of the sulfur-producing properties of Thiobacillus sp. strain W5 and Thiobacillus neapolitanus showed that the former has twice the maximum specific sulfide-oxidizing capacity of the latter (3.6 versus 1.9 (mu)mol/mg of protein/min). Their maximum specific oxygen uptake rates were very similar. Significant mechanistic differences in sulfur production between the high-sulfur-producing Thiobacillus sp. strain W5 and the moderate-sulfur-producing species T. neapolitanus were not observed. The limited sulfide-oxidizing capacity of T. neapolitanus appears to be the reason that it can convert only 50% of the incoming sulfide to elemental sulfur.
PMCID: PMC1389182  PMID: 16535627
17.  Using Dimers to Measure Biosignatures and Atmospheric Pressure for Terrestrial Exoplanets 
Astrobiology  2014;14(2):67-86.
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.
PMCID: PMC3928785  PMID: 24432758
18.  Stimulation of Autotrophic Denitrification by Intrusions of the Bosporus Plume into the Anoxic Black Sea 
Autotrophic denitrification was measured in the southwestern coastal Black Sea, where the Bosporus Plume injects oxidized chemical species (especially O2 and NO3−) into the oxic, suboxic, and anoxic layers. Prominent oxygen intrusions caused an overlap of NOx− and sulfide at the same station where autotrophic denitrification activity was detected with incubation experiments. Several bacteria that have been proposed to oxidize sulfide in other low oxygen environments were found in the Black Sea including SUP05, Sulfurimonas, Arcobacter, and BS-GSO2. Comparison of TRFLP profiles from this mixing zone station and the Western Gyre (a station not affected by the Bosporus Plume) indicate the greatest relative abundance of Sulfurimonas and Arcobacter at the appropriate depths at the mixing zone station. The autotrophic gammaproteobacterium BS-GSO2 correlated with ammonium fluxes rather than with sulfide fluxes and the maximum in SUP05 peak height was shallower than the depths where autotrophic denitrification was detected. Notably, anammox activity was not detected at the mixing zone station, though low levels of DNA from the anammox bacteria Candidatus Scalindua were present. These results provide evidence for a modified ecosystem with different N2 production pathways in the southwest coastal region compared to that found in the rest of the Black Sea. Moreover, the same Sulfurimonas phylotype (BS139) was previously detected on >30 μm particles in the suboxic zone of the Western Gyre along with DNA of potential sulfate reducers, so it is possible that particle-attached autotrophic denitrification may be an overlooked N2 production pathway in the central Black Sea as well.
PMCID: PMC3399223  PMID: 22826706
Black Sea; autotrophic denitrification; Sulfurimonas; Bosporus Plume; anammox
19.  Impact of Biogenic Emission Uncertainties on the Simulated Response of Ozone and Fine Particulate Matter to Anthropogenic Emission Reductions 
The role of emissions of volatile organic compounds and nitric oxide from biogenic sources is becoming increasingly important in regulatory air quality modeling as levels of anthropogenic emissions continue to decrease and stricter health-based air quality standards are being adopted. However, considerable uncertainties still exist in the current estimation methodologies for biogenic emissions. The impact of these uncertainties on ozone and fine particulate matter (PM2.5) levels for the eastern United States was studied, focusing on biogenic emissions estimates from two commonly used biogenic emission models, the Model of Emissions of Gases and Aerosols from Nature (MEGAN) and the Biogenic Emissions Inventory System (BEIS). Photochemical grid modeling simulations were performed for two scenarios: one reflecting present day conditions and the other reflecting a hypothetical future year with reductions in emissions of anthropogenic oxides of nitrogen (NOx). For ozone, the use of MEGAN emissions resulted in a higher ozone response to hypothetical anthropogenic NOx emission reductions compared with BEIS. Applying the current U.S. Environmental Protection Agency guidance on regulatory air quality modeling in conjunction with typical maximum ozone concentrations, the differences in estimated future year ozone design values (DVF) stemming from differences in biogenic emissions estimates were on the order of 4 parts per billion (ppb), corresponding to approximately 5% of the daily maximum 8-hr ozone National Ambient Air Quality Standard (NAAQS) of 75 ppb. For PM2.5, the differences were 0.1–0.25 μg/m3 in the summer total organic mass component of DVFs, corresponding to approximately 1–2% of the value of the annual PM2.5 NAAQS of 15 μg/m3. Spatial variations in the ozone and PM2.5 differences also reveal that the impacts of different biogenic emission estimates on ozone and PM2.5 levels are dependent on ambient levels of anthropogenic emissions.
PMCID: PMC3079461  PMID: 21305893
20.  Metabolic Flexibility of Sulfate-Reducing Bacteria 
Dissimilatory sulfate-reducing prokaryotes (SRB) are a very diverse group of anaerobic bacteria that are omnipresent in nature and play an imperative role in the global cycling of carbon and sulfur. In anoxic marine sediments sulfate reduction accounts for up to 50% of the entire organic mineralization in coastal and shelf ecosystems where sulfate diffuses several meters deep into the sediment. As a consequence, SRB would be expected in the sulfate-containing upper sediment layers, whereas methanogenic archaea would be expected to succeed in the deeper sulfate-depleted layers of the sediment. Where sediments are high in organic matter, sulfate is depleted at shallow sediment depths, and biogenic methane production will occur. In the absence of sulfate, many SRB ferment organic acids and alcohols, producing hydrogen, acetate, and carbon dioxide, and may even rely on hydrogen- and acetate-scavenging methanogens to convert organic compounds to methane. SRB can establish two different life styles, and these can be termed as sulfidogenic and acetogenic, hydrogenogenic metabolism. The advantage of having different metabolic capabilities is that it raises the chance of survival in environments when electron acceptors become depleted. In marine sediments, SRB and methanogens do not compete but rather complement each other in the degradation of organic matter. Also in freshwater ecosystems with sulfate concentrations of only 10–200 μM, sulfate is consumed efficiently within the top several cm of the sediments. Here, many of the δ-Proteobacteria present have the genetic machinery to perform dissimilatory sulfate reduction, yet they have an acetogenic, hydrogenogenic way of life. In this review we evaluate the physiology and metabolic mode of SRB in relation with their environment.
PMCID: PMC3119409  PMID: 21734907
sulfate-reducing bacteria; metabolic flexibility; syntrophy; metabolic interactions
21.  Associations among hair loss, oral sulfur-containing gases, and gastrointestinal and metabolic linked diseases in Japanese elderly men: pilot study 
BMC Public Health  2009;9:82.
Male pattern baldness (MPB), an observable trait, has been reported to be associated with various diseases, such as prostate cancer and cardiovascular disease. Oral sulfur-containing gases have also been suggested to be useful as markers of systemic health condition. However, there are no known reports regarding the associations among MPB, and oral sulfur-containing gases, and systemic health conditions in males.
We studied 170 male subjects aged either 60 or 65 years old. The degree of MPB was assessed using the Norwood-Hamilton Baldness scale. Oral sulfur-containing gases were measured using a compact-designed device. All subjects completed physical and laboratory blood examinations, a face-to-face medical questionnaire, and an oral examination.
There were significant differences between the levels of CH3SCH3 and baldness patterns, independent of age. When we analyzed whether the association was linked to systemic health condition, a strong significant association was observed between the level of CH3SCH3 and severe MPB in subjects with gastrointestinal diseases, hypertension, and hypercholesterolemia.
These results suggest that MPB is associated with the level of CH3SCH3, a sulfur-containing gas that causes oral malodor, in elderly Japanese males. Further, the association was intensified by the existence of gastrointestinal tract and metabolic disorders.
PMCID: PMC2666723  PMID: 19284665
22.  Evaluation of Single Column Trapping/Separation and Chemiluminescence Detection for Measurement of Methanethiol and Dimethyl Sulfide from Pig Production 
Reduced sulfur compounds are considered to be important odorants from pig production due to their low odor threshold values and low solubility in slurry. The objective of the present study was to investigate the use of a portable method with a single silica gel column for trapping/separation coupled with chemiluminescence detection (SCTS-CL) for measurement of methanethiol and dimethyl sulfide in sample air from pig production. Proton-transfer-reaction mass spectrometry (PTR-MS) was used to evaluate the trapping/separation. The silica gel column used for the SCTS-CL efficiently collected hydrogen sulfide, methanethiol and dimethyl sulfide. The measurement of methanethiol by SCTS-CL was clearly interfered by the high concentration of hydrogen sulfide found in pig production, and a removal of hydrogen sulfide was necessary to obtain reliable results. Air samples taken from a facility with growing-finishing pigs were analyzed by SCTS-CL, PTR-MS, and a gas chromatograph with sulfur chemiluminescence detection (GC-SCD) to evaluate the SCTS-CL. The difference between the concentrations of methanethiol and dimethyl sulfide measured with SCTS-CL, PTR-MS, and GC-SCD was below 10%. In conclusion, the SCTS-CL is a portable and low-cost alternative to the commercial methods that can be used to measure methanethiol and dimethyl sulfide in sample air from pig production.
PMCID: PMC3444860  PMID: 22997603
23.  Detection of Greenhouse Gas Precursors from Diesel Engines Using Electrochemical and Photoacoustic Sensors 
Sensors (Basel, Switzerland)  2010;10(11):9726-9741.
Atmospheric pollution is one of the worst threats to modern society. The consequences derived from different forms of atmospheric pollution vary from the local to the global scale, with deep impacts on climate, environment and human health. Several gaseous pollutants, even when present in trace concentrations, play a fundamental role in important processes that occur in atmosphere. Phenomena such as global warming, photochemical smog formation, acid rain and the depletion of the stratospheric ozone layer are strongly related to the increased concentration of certain gaseous species in the atmosphere. The transport sector significantly produces atmospheric pollution, mainly when diesel oil is used as fuel. Therefore, new methodologies based on selective and sensitive gas detection schemes must be developed in order to detect and monitor pollutant gases from this source. In this work, CO2 Laser Photoacoustic Spectroscopy was used to evaluate ethylene emissions and electrochemical analyzers were used to evaluate the emissions of CO, NOx and SO2 from the exhaust of diesel powered vehicles (rural diesel with 5% of biodiesel, in this paper called only diesel) at different engine rotation speeds. Concentrations in the range 6 to 45 ppmV for ethylene, 109 to 1,231 ppmV for carbon monoxide, 75 to 868 ppmV for nitrogen oxides and 3 to 354 ppmV for sulfur dioxide were obtained. The results indicate that the detection techniques used were sufficiently selective and sensitive to detect the gaseous species mentioned above in the ppmV range.
PMCID: PMC3230984  PMID: 22163437
diesel engines; electrochemical sensors; photoacoustic sensors
24.  Sulfur metabolism in Beggiatoa alba. 
Journal of Bacteriology  1987;169(12):5466-5472.
The metabolism of sulfide, sulfur, and acetate by Beggiatoa alba was investigated under oxic and anoxic conditions. B. alba oxidized acetate to carbon dioxide with the stoichiometric reduction of oxygen to water. In vivo acetate oxidation was suppressed by sulfide and by several classic respiratory inhibitors, including dibromothymoquinone, an inhibitor specific for ubiquinones. B. alba also carried out an oxygen-dependent conversion of sulfide to sulfur, a reaction that was inhibited by several electron transport inhibitors but not by dibromothymoquinone, indicating that the electrons released from sulfide oxidation were shuttled to oxygen without the involvement of ubiquinones. Intracellular sulfur stored by B. alba was not oxidized to sulfate or converted to an external soluble form under aerobic conditions. On the other hand, sulfur stored by filaments of Thiothrix nivea was oxidized to extracellular soluble oxidation products, including sulfate. Sulfur stored by filaments of B. alba, however, was reduced to sulfide under short-term anoxic conditions. This anaerobic reduction of sulfur was linked to the endogenous oxidation of stored carbon and to hydrogen oxidation.
PMCID: PMC213973  PMID: 3316186
25.  Biological and Abiological Sulfur Reduction at High Temperatures † 
Reduction of elemental sulfur was studied in the presence and absencè of thermophilic sulfur-reducing bacteria, at temperatures ranging from 65 to 110°C, in anoxic artificial seawater media. Above 80°C, significant amounts of sulfide were produced abiologically at linear rates, presumably by the disproportionation of sulfur. These rates increased with increasing temperature and pH and were enhanced by yeast extract. In the same medium, the sulfur respiration of two recent thermophilic isolates, a eubacterium and an archaebacterium, resulted in sulfide production at exponential rates. Although not essential for growth, sulfur increased the cell yield in both strains up to fourfold. It is suggested that sulfur respiration is favored at high temperatures and that this process is not limited to archaebacteria, but is shared by other extreme thermophiles.
PMCID: PMC238504  PMID: 16346781

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