Formation of Carbon-Carbon Bonds in the Photochemical Alkylation of Polycyclic Aromatic Hydrocarbons

The reaction of polycyclic aromatic hydrocarbons (PAHs) withalkanes was examined in the presence of ultraviolet (UV) lightunder model prebiotic Earth and interstellar medium (ISM)conditions. We observed the formation of alkylated PAHs from avariety of PAHs and alkanes, which was caused by the absorptionof UV light by the PAH molecule. Photoalkylation occurred inPAHs and alkanes in solution, in thin films in contact withsimulated ocean water, and in matrices simulating ISMconditions. Photoalkylation occurred readily, with significantproduct yields within 5 h of irradiation. Because alkanes andPAHs are presumed to be part of the organic inventory in the ISMand on the early Earth, we propose that this photoalkylation reactionis a plausible pathway for the formation of carbon-carbon bondsin both these environments.     

Formation of proteinoid microspheres under simulated prebiotic atmospheres and individual gases.

The formation of microspheres from acidic and basic proteinoids was attempted under simulated prebiotic atmospheres and constituent gases thereof. Both types of proteinoid yielded microspheres under carbon dioxide, carbon monoxide, methane, hydrogen sulfide, hydrogen, nitrogen, and oxygen (tested separately) and also under nitrogen-carbon dioxide atmospheres; higher proportions of carbon dioxide resulted in fewer spheres from basic proteinoid. Neither type of proteinoid formed spheres on 10-minute exposure to ammonia or methane-hydrogen-ammonia atmospheres. (Brief exposure resulted in spheres from basic proteinoid.) The effects, both qualitative and quantitative, were indicated by control experiments to be due to pH, rather than to the specific gas (or ion). The results suggest that the proteinoid microsphere model for protocells is applicable under a variety of possible prebiotic atmospheres, with some restrictions imposed by pH.     

CHEMICAL EVOLUTION ON TITAN: COMPARISONS TO THE PREBIOTIC EARTH

Models for the origin of Titan's atmosphere, the processing of the atmosphere and surface and its exobiological role are reviewed. Titan has gained widespread acceptance in the origin of life field as a model for the types of evolutionary processes that could have occurred on prebiotic Earth. Both Titan and Earth possess significant atmospheres ( 1 atm) composed mainly of molecular nitrogen with smaller amounts of more reactive species. Both of these atmospheres are processed primarily by solar ultraviolet light with high energy particles interactions contributing to a lesser extent. The products of these reactions condense or are dissolved in other atmospheric species (aerosols/clouds) and fall to the surface. There these products may have been further processed on Titan and the primitive Earth by impacting comets and meteorites. While the low temperatures on Titan ( 72–180 K) preclude the presence of permanent liquid water on the surface, it has been suggested that tectonic activity or impacts by meteors and comets could produce liquid water pools on the surface for thousands of years. Hydrolysis and oligomerization reactions in these pools might form chemicals of prebiological significance. Other direct comparisons between the conditions on present day Titan and those proposed for prebiotic Earth are also presented.     

PAH Degradation and Bioaugmentation by a Marine Methanotrophic Enrichment

Methanotrophic bacteria were enriched from marine sediments and screened for their ability to biotransform polycyclic aromatic hydrocarbons (PAHs). Characterization of the methanotrophic enrichment showed that it was dominated by a Type I methanotroph, although significant amounts of 18:1 fatty acids were detected, suggesting the presence of Type II methanotrophs in marine systems. The methanotrophic enrichment degraded phenanthrene, anthracene, and fluorene to below detectable levels in 15 days. Partial transformation of fluoranthene occurred over 15 days, but pyrene was not transformed. Radiolabeled phenanthrene was oxidized to carbon dioxide with significant production of polar intermediates. The oxidation was inhibited by acetylene, an inhibitor of methane monooxygenase. The addition of the methanotrophic enrichment to a marine culture grown on PAHs as the sole carbon sources increased the transformation rate of phenanthrene, anthracene, and fluorene. The highest removal rates were obtained with a mixture containing 90% methanotroph enrichment and 10% PAH-degrading enrichment (by biomass). Fluoranthene and pyrene degradation rates by the PAH-degrading enrichment were not significantly increased by the addition of the methanotrophic enrichment. A possible mechanism for the increased transformation rate was the rapid oxidation of PAHs by methane monooxygenase, forming an intermediate that is more bioavailable for utilization by the PAH-degraders.     

The origin of the polycyclic aromatic hydrocarbons in meteorites

Polycyclic aromatic hydrocarbons (PAHs) in C1 and C2 Carbonaceous Chondrites appear to be the product of a high-temperature synthesis. This observation counters a prevailing view that PAHs in meteorites are a thermal alternation product of preexisting aliphatic compounds, which in turn required the presence of low-temperature mineral phases such as magnetite and hydrated phyllosilicates for their formation. Such a process would necessarily lead to a more low-temperature assemblage of PAHs, as many low-temperature minerals and compounds are extant in meteorites.Ivuna, a C1 carbonaceous chondrite, has been shown to contain abundant amounts of the three-ring PAHs phenanthrene/anthracene, but no detectable levels of the two- and four-ring PAHs naphthalene and pyrene/fluoranthene. Ivuna and other C1 carbonaceous chondrites are known to have been extensively altered by water. The aqueous solubities of PAHs indicate that some PAHs would have been mobilized during the aqueous alteration phase in meteorite parent bodies. Model geochromatography experiments using crushed serpentine or beach sand as the solid phase and water for elution suggest that the complete separation of two, three, and four-ring PAHs could be expected to occur in the parent body of C1 carbonaceous chondrites. It is proposed that aqueous fluids driven by heat in the parent body of Ivuna migrated from the interior to the surface, in the process transporting, separating and concentrating PAHs at various zones in the parent body.The presence of indigenous PAHs and absence of indigenous amino acids in the H4 ordinary chondrite Forest Vale provides support for the contention that different processes and environments contributed to the synthesis of the organic matter in the solar system.     

A single aromatic core mutation converts a designed “primitive” protein from halophile to mesophile folding

The halophile environment has a number of compelling aspects with regard to the origin of structured polypeptides (i.e., proteogenesis) and, instead of a curious niche that living systems adapted into, the halophile environment is emerging as a candidate “cradle” for proteogenesis. In this viewpoint, a subsequent halophile‐to‐mesophile transition was a key step in early evolution. Several lines of evidence indicate that aromatic amino acids were a late addition to the codon table and not part of the original “prebiotic” set comprising the earliest polypeptides. We test the hypothesis that the availability of aromatic amino acids could facilitate a halophile‐to‐mesophile transition by hydrophobic core‐packing enhancement. The effects of aromatic amino acid substitutions were evaluated in the core of a “primitive” designed protein enriched for the 10 prebiotic amino acids (A,D,E,G,I,L,P,S,T,V)—having an exclusively prebiotic core and requiring halophilic conditions for folding. The results indicate that a single aromatic amino acid substitution is capable of eliminating the requirement of halophile conditions for folding of a “primitive” polypeptide. Thus, the availability of aromatic amino acids could have facilitated a critical halophile‐to‐mesophile protein folding adaptation—identifying a selective advantage for the incorporation of aromatic amino acids into the codon table.     

Thermal polymerization of amino acids under various atmospheres or at low pressures

The kinds and proportions of amino acids formed in two simulated prebiotic experiments or detected in hydrolyzed extracts of three extraterrestrial samples were found to polymerize thermally under various atmospheres or at low pressures. Yields, tested properties, and amino acid compositions of the polymers were not influenced by the type of enveloping atmosphere, including two simulated prebiotic atmospheres and five pure gases. However, polyamino acids prepared at low pressure (0.02, 10^?4 atm) were obtained in appreciably greater yield than those synthesized at 1 atm; amino acid composition was somewhat influenced by low pressure. The results indicate that polyamino acids could have been formed thermally under a variety of possible prebiotic atmospheres and on planetary bodies of low atmospheric pressure.     

The acetylene reduction technique as an assay for nitrogenase activity in the methane oxidizing bacterium Methylococcus capsulatus strain bath

The use of acetylene as a convenient assay substrate for nitrogenase in methane oxidising bacteria is complicated by the observation that it is a potent inhibitor of the methane monooxygenase enzyme in both whole cells and cell-free extracts. If the cells were provided with alternative oxidisable carbon substrates other than methane then nitrogen fixing cells would reduce acetylene to ethylene. Hydrogen gas also served as an oxidisable substrate in the assay. Nitrous oxide, which is reduced by nitrogenase to N₂ and H₂O, was not an inhibitor of methane monooxygenase function and could be used as a convenient assay substrate for nitrogenase. Reduction of both substrates by whole cells showed similar response to oxygen in the assay system and in this respect Methylococcus resembles other free living nitrogen fixing aerobes.     

Enhanced Synthesis of Alkyl Amino Acids in Miller’s 1958 H<Subscript>2</Subscript>S Experiment

Stanley Miller’s 1958 H₂S-containing experiment, which included a simulated prebiotic atmosphere of methane (CH₄), ammonia (NH₃), carbon dioxide (CO₂), and hydrogen sulfide (H₂S) produced several alkyl amino acids, including the α-, β-, and γ-isomers of aminobutyric acid (ABA) in greater relative yields than had previously been reported from his spark discharge experiments. In the presence of H₂S, aspartic and glutamic acids could yield alkyl amino acids via the formation of thioimide intermediates. Radical chemistry initiated by passing H₂S through a spark discharge could have also enhanced alkyl amino acid synthesis by generating alkyl radicals that can help form the aldehyde and ketone precursors to these amino acids. We propose mechanisms that may have influenced the synthesis of certain amino acids in localized environments rich in H₂S and lightning discharges, similar to conditions near volcanic systems on the early Earth, thus contributing to the prebiotic chemical inventory of the primordial Earth.     

Ebullitive methane emissions from oxygenated wetland streams

Stream and river carbon dioxide emissions are an important component of the global carbon cycle. Methane emissions from streams could also contribute to regional or global greenhouse gas cycling, but there are relatively few data regarding stream and river methane emissions. Furthermore, the available data do not typically include the ebullitive (bubble‐mediated) pathway, instead focusing on emission of dissolved methane by diffusion or convection. Here, we show the importance of ebullitive methane emissions from small streams in the regional greenhouse gas balance of a lake and wetland‐dominated landscape in temperate North America and identify the origin of the methane emitted from these well‐oxygenated streams. Stream methane flux densities from this landscape tended to exceed those of nearby wetland diffusive fluxes as well as average global wetland ebullitive fluxes. Total stream ebullitive methane flux at the regional scale (103 Mg C yr^?1; over 6400 km²) was of the same magnitude as diffusive methane flux previously documented at the same scale. Organic‐rich stream sediments had the highest rates of bubble release and higher enrichment of methane in bubbles, but glacial sand sediments also exhibited high bubble emissions relative to other studied environments. Our results from a database of groundwater chemistry support the hypothesis that methane in bubbles is produced in anoxic near‐stream sediment porewaters, and not in deeper, oxygenated groundwaters. Methane interacts with other key elemental cycles such as nitrogen, oxygen, and sulfur, which has implications for ecosystem changes such as drought and increased nutrient loading. Our results support the contention that streams, particularly those draining wetland landscapes of the northern hemisphere, are an important component of the global methane cycle.     

Nitrogen fixation by a marine non‐heterocystous cyanobacterium requires a heterotrophic bacterial consort

Cultures of the non‐heterocystous cyanobacterium, Leptolyngbya nodulosa, could be grown indefinitely in media devoid of combined nitrogen. Acetylene reduction assays showed that these cultures fixed nitrogen in the dark period of a diurnal cycle under micro‐oxygenic or anaerobic conditions. Addition of DCMU to cultures induced much higher rates of nitrogenase activity, most of which occurred in the light. Measurements of activity in the presence of chloramphenicol indicated that nitrogenase is synthesized in darkness and probably destroyed in the subsequent light period. Neither the dark‐mediated nitrogenase in the absence of DCMU nor light‐mediated activity in the presence of DCMU could be sustained for more than 3 days without a photoperiodic light/dark cycle. Axenic cultures could not be grown in the absence of combined nitrogen and did not demonstrate any acetylene reduction activity. An identical nifH gene sequence was found in axenic and non‐axenic cultures of L. nodulosa. RT‐PCR demonstrated that this gene was expressed only in non‐axenic cultures. Western blotting showed that the Fe‐protein of nitrogenase is absent in cultures that are incapable of acetylene reduction, indicating that the lack of nitrogenase activity is likely due to the absence of the enzyme. These observations strongly indicate that L. nodulosa contains a functional nitrogenase which is not expressed in the absence of heterotrophic bacteria.     

Degradation of PAHs by ligninolytic enzymes of <Emphasis Type="Italic">Irpex lacteus</Emphasis>

The ligninolytic fungus Irpex lacteus was shown as an efficient degrader of oligocyclic aromatic hydrocarbons (PAHs; 'polycyclic aromatic hydrocarbons') possessing 3-6 aromatic rings in complex liquid media. The strain produced mainly Mn-dependent peroxidase in media without pollutants. Activity of ligninolytic enzymes was higher in a N-limited medium. However, after contamination with PAHs (especially pyrene) the values increased and significant activity of Mn-independent peroxidase appeared in the complex medium. Other factors (such as the increase in nitrogen concentration or the presence of solvent(s) for dissolution of PAHs) had no effect. Cytochrome P-450 was detected in the microsomal fraction of biomass grown in the complex medium. The rate of PAH degradation was also affected by the presence of various combinations of PAHs. However, independently of the enzyme activities, anthracene was shown to have a positive influence on degradation of pyrene and fluoranthene.     

Prebiotic Microreactors: A Synthesis of Purines and Dihydroxy Compounds in Aqueous Aerosol

We report the synthesis of purine bases and other heterocycles and the formation of amino acids, hydroxy acids and dihydroxy compounds by the spark activation of an atmosphere of methane, nitrogen and hydrogen, in the presence of an aqueous aerosol. With the aid of the interface air–water, the organic material obtained shows greater amounts and diversity of molecules with biological interest than the products obtained in the absence of an aerosol. Our results support the suggestion that aerosols may have played a significant role in the prebiotic origin of molecular diversity and evolution.     

Duration of Hydrogen Formation by Anabaena cylindrica B629 in Atmospheres of Argon, Air, and Nitrogen

The time course of hydrogen formation by Anabaena cylindrica was followed beneath an argon atmosphere alone and also beneath atmospheres of argon, nitrogen, and air in the presence of carbon monoxide (0.2%) and acetylene (5%). Hydrogen production beneath argon alone was comparable in rate and duration (7 to 12 days) to that which occurred beneath air in the presence of carbon monoxide (0.2%) and acetylene (5%). However, much greater longevity (16 to 26 days) and improved rates of hydrogen formation were obtained when algae were incubated beneath argon and particularly nitrogen, each supplemented with carbon monoxide and acetylene. The total hydrogen produced by these cultures was up to three times as much as that released by cultures incubated beneath argon alone. Hydrogen-oxygen ratios for argon cultures either with or without carbon monoxide and acetylene were initially 1:5 but approximated 1:2 when measured over the entire incubation period. In each case oxygen production and nitrogenase activity (acetylene reduction) continued at reduced rates after hydrogen evolution had ceased. The effects of methionine sulfoximine (2 μM), ammonium ions (0.5 mM), or both on oxygen production were generally negligible, while effects on hydrogen production were variable depending on the atmosphere used; in most cases, eventual destabilization of the system occurred. A brief comparison was made of the time courses of anaerobic and aerobic hydrogen formation by the marine cyanobacterium Calothrix membranacea. It was found that shaking of cultures was beneficial for hydrogen production but not strictly necessary. It is concluded that hydrogen production by A. cylindrica in air and particularly nitrogen in the presence of carbon monoxide and acetylene offers the best potential of the atmospheres considered on the basis of four criteria: rates and longevity of hydrogen formation, practicality of the atmosphere used, and tolerance of hydrogen evolution to slight changes in composition of the atmosphere.     

The Diffuse Interstellar Bands: A Tracer For Organics In The Diffuse Interstellar Medium?

The diffuse interstellar bands (DIBs) are absorption bands seen in the spectra of stars obscured by interstellar dust. DIBs are recognized as a tracer for free, organic molecules in the diffuse interstellar medium (ISM). The potential molecular carriers for the DIBs are discussed with an emphasis on neutral and ionized polycyclic aromatic hydrocarbons (PAHs) for which the most focused effort has been made to date. From the combined astronomical, laboratory and theoretical study, it is concluded that a distribution of free neutral and ionized complex organics (PAHs, fullerenes, unsaturated hydrocarbons) represents the most promising class of candidates to account for the DIBs. The case for aromatic hydrocarbons appears particularly strong. The implied widespread distribution of complex organics in the diffuse ISM bears profound implications for our understanding of the chemical complexity of the ISM, the evolution of prebiotic molecules and its impact on the origin and the evolution of life on early Earth through the exogenous delivery (cometary encounters and metoritic bombardments) of prebiotic organics.     

Microspherules from Sugars in the Absence of Nitrogen

Reactions of short sugars under mild, plausibly prebiotic conditions yield organic microspherules that may have played a role in prebiotic chemistry as primitive reaction vessels. It has been widely thought that nitrogen chemistry, in particular Amadori rearrangement, is central to this process, Here we show that microspherules form in the absence of any nitrogen compounds if the pH is sufficiently low. In particular, while the microspherule formation induced by ammonium acetate (pH 7) is not reproduced by ammonium chloride (pH 5), it is reproduced by oxalic acid and by hydrochloric acid (pH 1). The formation of microspherules in the presence of oxalic acid is similar to that in the presence of ammonium acetate: aqueous reactions of D-erythrose, D-ribose, 2-deoxy-D-ribose and D-fructose in the presence of oxalic acid produce microspherules ranging in size from approximately 1–5 μm after eight weeks incubation at 65°C, while the aldohexoses D-glucose, D-galactose and D-mannose do not. This pattern correlates with the occurrence of furanose forms in these sugars.     

Denitrification potential of epilithic communities in a lotic environment

Denitrification potentials of epilithic microbial populations were assessed using the acetylene inhibition method, in which acetylene is used to block the reduction of nitrous oxide (N₂O) to nitrogen (N₂). Samples of the epilithic community were incubated in filtered river water containing modified Bushnell-Haas salts, glycerol, and yeast extract—under aerobic (0.2 atm O₂) and anaerobic (0.2 atm He) acetylene atmospheres. N₂O was produced under both atmospheres only if exogenous nitrate of nitrite was added. Denitrification potentials were typically higher when nitrite was the added electron acceptor. The rates of denitrification were temperature-and carbon-dependent and the maximum rate, 8.53 g N₂O–N per cm² per day occurred at 23°C when nitrite was the electron acceptor.     

Molecular biology approaches for understanding microbial polycyclic aromatic hydrocarbons (PAHs) degradation

The known or suspected hazards of polycyclic aromatic hydrocarbons (PAHs) have provoked enormous concentration and endeavours to relieve or eliminate these precarious compounds from miscellaneous environments including soil, water and air. Among various interventions, biodegradation is an appealing approach for its comparative high efficiency and preferable safety. Microorganisms played crucial role in biodegradation of PAHs. Traditional access mainly including culture-dependent procedures has discovered and isolated PAHs-degrading microorganisms which could be subsequently applied to specific contaminated locus. Although certain progress has been achieved owing to traditional methods, much details in PAHs bioremedation leave pending because of the complexity nature of this process. As the rapid development of biology, molecular techniques such as PCR, fingerprinting technique (mainly DGGE), DNA hybridization technique and gene reporters technique have been intensively applied to gain further insight into the mechanism of PAHs degradation. These techniques not only proved the existence and role of uncultivable microorganisms in the whole population of PAHs degrading related microbials, but also made it possible to revealed the otherwise undetectable complex relationships between multi-microorganism concerned in PAHs biodegradation. Application of such techniques in the field of PAHs biodegradation were reviewed in this article.     

Molecular biology approaches for understanding microbial polycyclic aromatic hydrocarbons (PAHs) degradation

The known or suspected hazards of polycyclic aromatic hydrocarbons (PAHs) have provoked enormous concentration and endeavours to relieve or eliminate these precarious compounds from miscellaneous environments including soil, water and air. Among various interventions, biodegradation is an appealing approach for its comparative high efficiency and preferable safety. Microorganisms played crucial role in biodegradation of PAHs. Traditional access mainly including culture-dependent procedures has discovered and isolated PAHs-degrading microorganisms which could be subsequently applied to specific contaminated locus. Although certain progress has been achieved owing to traditional methods, much details in PAHs bioremedation leave pending because of the complexity nature of this process. As the rapid development of biology, molecular techniques such as PCR, fingerprinting technique (mainly DGGE), DNA hybridization technique and gene reporters technique have been intensively applied to gain further insight into the mechanism of PAHs degradation. These techniques not only proved the existence and role of uncultivable microorganisms in the whole population of PAHs degrading related microbials, but also made it possible to revealed the otherwise undetectable complex relationships between multi-microorganism concerned in PAHs biodegradation. Application of such techniques in the field of PAHs biodegradation were reviewed in this article.     

The loss of mass-independent fractionation in sulfur due to a Palaeoproterozoic collapse of atmospheric methane

We use a 1‐D numerical model to study the atmospheric photochemistry of oxygen, methane, and sulfur after the advent of oxygenic photosynthesis. We assume that mass‐independent fractionation (MIF) of sulfur isotopes – characteristic of the Archean – was best preserved in sediments when insoluble elemental sulfur (S₈) was an important product of atmospheric photochemistry. Efficient S₈ production requires three things: (i) very low levels of tropospheric O₂; (ii) a source of sulfur gases to the atmosphere at least as large as the volcanic SO₂ source today; and (iii) a sufficiently high abundance of methane or other reduced gas. All three requirements must be met. We suggest that the disappearance of a strong MIF sulfur signature at the beginning of the Proterozoic is better explained by the collapse of atmospheric methane, rather than by a failure of volcanism or the rise of oxygen. The photochemical models are consistent in demanding that methane decline before O₂ can rise (although they are silent as to how quickly), and the collapse of a methane greenhouse effect is consistent with the onset of major ice ages immediately following the disappearance of MIF sulfur. We attribute the decline of methane to the growth of the oceanic sulfate pool as indicated by the widening envelope of mass‐dependent sulfur fractionation through the Archean. We find that a given level of biological forcing can support either oxic or anoxic atmospheres, and that the transition between the anoxic state and the oxic state is inhibited by high levels of atmospheric methane. Transition from an oxygen‐poor to an oxygen‐rich atmosphere occurs most easily when methane levels are low, which suggests that the collapse of methane not only caused the end of MIF S and major ice ages, but it may also have enabled the rise of O₂. In this story the early Proterozoic ice ages were ended by the establishment of a stable oxic atmosphere, which protected a renewed methane greenhouse with an ozone shield.