The distinctive isotopic signature of plant-derived chloromethane: possible application in constraining the atmospheric chloromethane budget

Sources and sinks of chloromethane in a salt marsh ecosystem: constraints from concentration and stable isotope measurements of laboratory incubation experiments

Chloromethane (CH₃Cl) is the most abundant long-lived chlorinated organic compound in the atmosphere and contributes significantly to natural stratospheric ozone depletion. Salt marsh ecosystems including halophyte plants are a known source of atmospheric CH₃Cl but estimates of their total global source strength are highly uncertain and knowledge of the major production and consumption processes in the atmosphere-halophyte-soil system is yet incomplete. In this study we investigated the halophyte plant, Salicornia europaea, and soil samples from a coastal salt marsh site in Sardinia/Italy for their potential to emit and consume CH₃Cl and using flux measurements, stable isotope techniques and Arrhenius plots differentiated between biotic and abiotic processes. Our laboratory approach clearly shows that at least 6 different production and consumption processes are active in controlling atmospheric CH₃Cl fluxes of a salt marsh ecosystem. CH₃Cl release by dried plant and soil material was substantially higher than that from the fresh material at temperatures ranging from 20 to 70 °C. Results of Arrhenius plots helped to distinguish between biotic and abiotic formation processes in plants and soils. Biotic CH₃Cl consumption rates were highest at 30 °C for plants and 50 °C for soils, and microbial uptake was higher in soils with higher organic matter content. Stable isotope techniques helped to distinguish between formation and degradation processes and also provided a deeper insight into potential methyl moiety donor compounds, such as S-adenosyl-l-methionine, S-methylmethionine and pectin, that might be involved in the abiotic and biotic CH₃Cl production processes. Our results clearly indicate that cycling of CH₃Cl in salt marsh ecosystems is a result of several biotic and abiotic processes occurring simultaneously in the atmosphere-plant-soil system. Important precursor compounds for biotic and abiotic CH₃Cl formation might be methionine derivatives and pectin. All formation and degradation processes are temperature dependent and thus environmental changes might affect the strength of each source and sink within salt marsh ecosystems and thus considerably alter total fluxes of CH₃Cl from salt marsh ecosystems to the atmosphere.

Chlorine Isotope Fractionation of the Major Chloromethane Degradation Processes in the Environment

Chloromethane (CH₃Cl) is an important source of chlorine in the stratosphere, but detailed knowledge of the magnitude of its sources and sinks is missing. Here, we measured the stable chlorine isotope fractionation (ε_Cl) associated with the major abiotic and biotic CH₃Cl sinks in the environment, namely, CH₃Cl degradation by hydroxyl (^·OH) and chlorine (^·Cl) radicals in the troposphere and by reference bacteria Methylorubrum extorquens CM4 and Leisingera methylohalidivorans MB2 from terrestrial and marine environments, respectively. No chlorine isotope fractionation was detected for reaction of CH₃Cl with ^·OH and ^·Cl radicals, whereas a large chlorine isotope fractionation (ε_Cl) of -10.9 ± 0.7‰ (n = 3) and -9.4 ± 0.9 (n = 3) was found for CH₃Cl degradation by M. extorquens CM4 and L. methylohalidivorans MB2, respectively. The large difference in chlorine isotope fractionation observed between tropospheric and bacterial degradation of CH₃Cl provides an effective isotopic tool to characterize and distinguish between major abiotic and biotic processes contributing to the CH₃Cl sink in the environment. Our findings demonstrate the potential of emerging triple-element isotopic approaches including chlorine to carbon and hydrogen analysis for the assessment of global cycling of organochlorines.

Chloromethane formation and degradation in the fern phyllosphere

Chloromethane (CH₃Cl) is the most abundant halogenated trace gas in the atmosphere. It plays an important role in natural stratospheric ozone destruction. Current estimates of the global CH₃Cl budget are approximate. The strength of the CH₃Cl global sink by microbial degradation in soils and plants is under discussion. Some plants, particularly ferns, have been identified as substantial emitters of CH₃Cl. Their ability to degrade CH₃Cl remains uncertain. In this study, we investigated the potential of leaves from 3 abundant ferns (Osmunda regalis, Cyathea cooperi, Dryopteris filix-mas) to produce and degrade CH₃Cl by measuring their production and consumption rates and their stable carbon and hydrogen isotope signatures. Investigated ferns are able to degrade CH₃Cl at rates from 2.1 to 17 and 0.3 to 0.9μgg_dw^-1day^-1 for C. cooperi and D. filix-mas respectively, depending on CH₃Cl supplementation and temperature. The stable carbon isotope enrichment factor of remaining CH₃Cl was -39±13‰, whereas negligible isotope fractionation was observed for hydrogen (-8±19‰). In contrast, O. regalis did not consume CH₃Cl, but produced it at rates ranging from 0.6 to 128μgg_dw^-1day^-1, with stable isotope values of -97±8‰ for carbon and -202±10‰ for hydrogen, respectively. Even though the 3 ferns showed clearly different formation and consumption patterns, their leaf-associated bacterial diversity was not notably different. Moreover, we did not detect genes associated with the only known chloromethane utilization pathway "cmu" in the microbial phyllosphere of the investigated ferns. Our study suggests that still unknown CH₃Cl biodegradation processes on plants play an important role in global cycling of atmospheric CH₃Cl.

Methanol consumption drives the bacterial chloromethane sink in a forest soil

Halogenated volatile organic compounds (VOCs) emitted by terrestrial ecosystems, such as chloromethane (CH₃Cl), have pronounced effects on troposphere and stratosphere chemistry and climate. The magnitude of the global CH₃Cl sink is uncertain since it involves a largely uncharacterized microbial sink. CH₃Cl represents a growth substrate for some specialized methylotrophs, while methanol (CH₃OH), formed in much larger amounts in terrestrial environments, may be more widely used by such microorganisms. Direct measurements of CH₃Cl degradation rates in two field campaigns and in microcosms allowed the identification of top soil horizons (i.e., organic plus mineral A horizon) as the major biotic sink in a deciduous forest. Metabolically active members of Alphaproteobacteria and Actinobacteria were identified by taxonomic and functional gene biomarkers following stable isotope labeling (SIP) of microcosms with CH₃Cl and CH₃OH, added alone or together as the [¹³C]-isotopologue. Well-studied reference CH₃Cl degraders, such as Methylobacterium extorquens CM4, were not involved in the sink activity of the studied soil. Nonetheless, only sequences of the cmuA chloromethane dehalogenase gene highly similar to those of known strains were detected, suggesting the relevance of horizontal gene transfer for CH₃Cl degradation in forest soil. Further, CH₃Cl consumption rate increased in the presence of CH₃OH. Members of Alphaproteobacteria and Actinobacteria were also ¹³C-labeled upon [¹³C]-CH₃OH amendment. These findings suggest that key bacterial CH₃Cl degraders in forest soil benefit from CH₃OH as an alternative substrate. For soil CH₃Cl-utilizing methylotrophs, utilization of several one-carbon compounds may represent a competitive advantage over heterotrophs that cannot utilize one-carbon compounds.

Chloromethane Degradation in Soils: A Combined Microbial and Two-Dimensional Stable Isotope Approach

Chloromethane (CHCl, methyl chloride) is the most abundant volatile halocarbon in the atmosphere and involved in stratospheric ozone depletion. The global CHCl budget, and especially the CHCl sink from microbial degradation in soil, still involves large uncertainties. These may potentially be resolved by a combination of stable isotope analysis and bacterial diversity studies. We determined the stable isotope fractionation of CHCl hydrogen and carbon and investigated bacterial diversity during CHCl degradation in three soils with different properties (forest, grassland, and agricultural soils) and at different temperatures and headspace mixing ratios of CHCl. The extent of chloromethane degradation decreased in the order forest > grassland > agricultural soil. Rates ranged from 0.7 to 2.5 μg g dry wt. d for forest soil, from 0.1 to 0.9 μg g dry wt. d for grassland soil, and from 0.1 to 0.4 μg g dry wt. d for agricultural soil and increased with increasing temperature and CHCl supplementation. The measured mean stable hydrogen enrichment factor of CHCl of -50 ± 13‰ was unaffected by temperature, mixing ratio, or soil type. In contrast, the stable carbon enrichment factor depended on CHCl degradation rates and ranged from -38 to -11‰. Bacterial community composition correlated with soil properties was independent from CHCl degradation or isotope enrichment. Nevertheless, increased abundance after CHCl incubation was observed in 21 bacterial operational taxonomical units (OTUs at the 97% 16S RNA sequence identity level). This suggests that some of these bacterial taxa, although not previously associated with CHCl degradation, may play a role in the microbial CHCl sink in soil.

Organic Haze as a Biosignature in Anoxic Earth-like Atmospheres

Early Earth may have hosted a biologically mediated global organic haze during the Archean eon (3.8-2.5 billion years ago). This haze would have significantly impacted multiple aspects of our planet, including its potential for habitability and its spectral appearance. Here, we model worlds with Archean-like levels of carbon dioxide orbiting the ancient Sun and an M4V dwarf (GJ 876) and show that organic haze formation requires methane fluxes consistent with estimated Earth-like biological production rates. On planets with high fluxes of biogenic organic sulfur gases (CS2, OCS, CH3SH, and CH3SCH3), photochemistry involving these gases can drive haze formation at lower CH4/CO2 ratios than methane photochemistry alone. For a planet orbiting the Sun, at 30× the modern organic sulfur gas flux, haze forms at a CH4/CO2 ratio 20% lower than at 1× the modern organic sulfur flux. For a planet orbiting the M4V star, the impact of organic sulfur gases is more pronounced: at 1× the modern Earth organic sulfur flux, a substantial haze forms at CH4/CO2 ∼ 0.2, but at 30× the organic sulfur flux, the CH4/CO2 ratio needed to form haze decreases by a full order of magnitude. Detection of haze at an anomalously low CH4/CO2 ratio could suggest the influence of these biogenic sulfur gases and therefore imply biological activity on an exoplanet. When these organic sulfur gases are not readily detectable in the spectrum of an Earth-like exoplanet, the thick organic haze they can help produce creates a very strong absorption feature at UV-blue wavelengths detectable in reflected light at a spectral resolution as low as 10. In direct imaging, constraining CH4 and CO2 concentrations will require higher spectral resolution, and R > 170 is needed to accurately resolve the structure of the CO2 feature at 1.57 μm, likely the most accessible CO2 feature on an Archean-like exoplanet. Key Words: Organic haze-Organic sulfur gases-Biosignatures-Archean Earth. Astrobiology 18, 311-329.

Chloromethane emissions in human breath

Chloromethane (CH₃Cl), currently the most abundant chlorinated organic compound in the atmosphere at around ~550 parts per trillion by volume (pptv), is considered responsible for approximately 16% of halogen-catalyzed stratospheric ozone destruction. Although emissions of CH₃Cl are known to occur from animals such as cattle, formation and release of CH₃Cl from humans has not yet been reported. In this study a pre-concentration unit coupled with a gas chromatograph directly linked to a mass spectrometer was used to precisely measure concentrations of CH₃Cl at the pptv level in exhaled breath from 31 human subjects with ages ranging from 3 to 87years. We provide analytical evidence that all subjects exhaled CH₃Cl in the range of 2.5 to 33 parts per billion by volume, levels which significantly exceed those of inhaled air by a factor of up to 60. If the mean of these emissions was typical for the world's population, then the global source of atmospheric CH₃Cl from humans would be around 0.66Ggyr^-1 (0.33 to 1.48Ggyr^-1), which is less than 0.03% of the total annual global atmospheric source strength. The observed endogenous formation of a chlorinated methyl group in humans might be of interest to biochemists and medical scientists as CH₃Cl is also known to be a potent methylating agent and thus, could be an important target compound in future medical research diagnostic programs.

Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation

Chloromethane (CH₃Cl) is produced on earth by a variety of abiotic and biological processes. It is the most important halogenated trace gas in the atmosphere, where it contributes to ozone destruction. Current estimates of the global CH₃Cl budget are uncertain and suggest that microorganisms might play a more important role in degrading atmospheric CH₃Cl than previously thought. Its degradation by bacteria has been demonstrated in marine, terrestrial, and phyllospheric environments. Improving our knowledge of these degradation processes and their magnitude is thus highly relevant for a better understanding of the global budget of CH₃Cl. The cmu pathway, for chloromethane utilisation, is the only microbial pathway for CH₃Cl degradation elucidated so far, and was characterized in detail in aerobic methylotrophic Alphaproteobacteria. Here, we reveal the potential of using a two-pronged approach involving a combination of comparative genomics and isotopic fractionation during CH₃Cl degradation to newly address the question of the diversity of chloromethane-degrading bacteria in the environment. Analysis of available bacterial genome sequences reveals that several bacteria not yet known to degrade CH₃Cl contain part or all of the complement of cmu genes required for CH₃Cl degradation. These organisms, unlike bacteria shown to grow with CH₃Cl using the cmu pathway, are obligate anaerobes. On the other hand, analysis of the complete genome of the chloromethane-degrading bacterium Leisingera methylohalidivorans MB2 showed that this bacterium does not contain cmu genes. Isotope fractionation experiments with L. methylohalidivorans MB2 suggest that the unknown pathway used by this bacterium for growth with CH₃Cl can be differentiated from the cmu pathway. This result opens the prospect that contributions from bacteria with the cmu and Leisingera-type pathways to the atmospheric CH₃Cl budget may be teased apart in the future.

Hydrogen and carbon isotope fractionation during degradation of chloromethane by methylotrophic bacteria

Chloromethane (CH3 Cl) is a widely studied volatile halocarbon involved in the destruction of ozone in the stratosphere. Nevertheless, its global budget still remains debated. Stable isotope analysis is a powerful tool to constrain fluxes of chloromethane between various environmental compartments which involve a multiplicity of sources and sinks, and both biotic and abiotic processes. In this study, we measured hydrogen and carbon isotope fractionation of the remaining untransformed chloromethane following its degradation by methylotrophic bacterial strains Methylobacterium extorquens CM4 and Hyphomicrobium sp. MC1, which belong to different genera but both use the cmu pathway, the only pathway for bacterial degradation of chloromethane characterized so far. Hydrogen isotope fractionation for degradation of chloromethane was determined for the first time, and yielded enrichment factors (ε) of -29‰ and -27‰ for strains CM4 and MC1, respectively. In agreement with previous studies, enrichment in (13) C of untransformed CH3 Cl was also observed, and similar isotope enrichment factors (ε) of -41‰ and -38‰ were obtained for degradation of chloromethane by strains CM4 and MC1, respectively. These combined hydrogen and carbon isotopic data for bacterial degradation of chloromethane will contribute to refine models of the global atmospheric budget of chloromethane.

Methyl chloride emissions from halophyte leaf litter: dependence on temperature and chloride content

Methyl chloride (CH(3)Cl) is the most abundant natural chlorine containing compound in the atmosphere, and responsible for a significant fraction of stratospheric ozone destruction. Understanding the global CH(3)Cl budget is therefore of great importance. However, the strength of the individual sources and sinks is still uncertain. Leaf litter is a potentially important source of methyl chloride, but factors controlling the emissions are unclear. This study investigated CH(3)Cl emissions from leaf litter of twelve halophyte species. The emissions were not due to biological activity, and emission rates varied between halophyte species up to two orders of magnitude. For all species, the CH(3)Cl emission rates increased with temperature following the Arrhenius relation. Activation energies were similar for all investigated plant species, indicating that even though emissions vary largely between plant species, their response to changing temperatures is similar. The chloride and methoxyl group contents of the leaf litter samples were determined, but those parameters were not significantly correlated to the CH(3)Cl emission rate.

Arabidopsis HARMLESS TO OZONE LAYER protein methylates a glucosinolate breakdown product and functions in resistance to Pseudomonas syringae pv. maculicola

Almost all of the chlorine-containing gas emitted from natural sources is methyl chloride (CH(3)Cl), which contributes to the destruction of the stratospheric ozone layer. Tropical and subtropical plants emit substantial amounts of CH(3)Cl. A gene involved in CH(3)Cl emission from Arabidopsis was previously identified and designated HARMLESS TO OZONE LAYER (hereafter AtHOL1) based on the mutant phenotype. Our previous studies demonstrated that AtHOL1 and its homologs, AtHOL2 and AtHOL3, have S-adenosyl-l-methionine-dependent methyltransferase activities. However, the physiological functions of AtHOLs have yet to be elucidated. In the present study, our comparative kinetic analyses with possible physiological substrates indicated that all of the AtHOLs have low activities toward chloride. AtHOL1 was highly reactive to thiocyanate (NCS(-)), a pseudohalide, synthesizing methylthiocyanate (CH(3)SCN) with a very high k(cat)/K(m) value. We demonstrated in vivo that substantial amounts of NCS(-) were synthesized upon tissue damage in Arabidopsis and that NCS(-) was largely derived from myrosinase-mediated hydrolysis of glucosinolates. Analyses with the T-DNA insertion Arabidopsis mutants (hol1, hol2, and hol3) revealed that only hol1 showed increased sensitivity to NCS(-) in medium and a concomitant lack of CH(3)SCN synthesis upon tissue damage. Bacterial growth assays indicated that the conversion of NCS(-) into CH(3)SCN dramatically increased antibacterial activities against Arabidopsis pathogens that normally invade the wound site. Furthermore, hol1 seedlings showed an increased susceptibility toward an Arabidopsis pathogen, Pseudomonas syringae pv. maculicola. Here we propose that AtHOL1 is involved in glucosinolate metabolism and defense against phytopathogens. Moreover, CH(3)Cl synthesized by AtHOL1 could be considered a byproduct of NCS(-) metabolism.

Identification of methyl chloride-emitting plants and atmospheric measurements on a subtropical island

A survey of methyl chloride (CH3Cl)-emitting plants was performed at a subtropical island in Japan (Iriomote Island). Among the 187 species of tropical/subtropical plants investigated, 33 species from a variety of families were identified as CH3Cl-emitting plants. The strongest emitters were Osmunda banksiifolia, Cibotium balometz, Angiopteris palmiformis, Vitex rotundifolia, Vitex trifolia, and Excoecaria agalloch, each with CH3Cl emission rates exceeding 1microg (gdrywt)(-1)h(-1). The first three species are ferns, and the last three are halophilous plants. Based on our results, the character of CH3Cl emission is likely to be shared at the genus level but not always at the family level. The atmospheric CH3Cl distribution measured on Iriomote Island showed significant enhancement in forested sites (up to 2750 ppt) and a higher concentration on the downwind shore than on the upwind shore. As previously reported, our findings provide strong evidence for the high emission of CH3Cl from tropical/subtropical forests.

Biosignatures from Earth-like planets around M dwarfs

Coupled one-dimensional photochemical-climate calculations have been performed for hypothetical Earth-like planets around M dwarfs. Visible/near-infrared and thermal-infrared synthetic spectra of these planets were generated to determine which biosignature gases might be observed by a future, space-based telescope. Our star sample included two observed active M dwarfs-AD Leo and GJ 643-and three quiescent model stars. The spectral distribution of these stars in the ultraviolet generates a different photochemistry on these planets. As a result, the biogenic gases CH4, N2O, and CH3Cl have substantially longer lifetimes and higher mixing ratios than on Earth, making them potentially observable by space-based telescopes. On the active M-star planets, an ozone layer similar to Earth's was developed that resulted in a spectroscopic signature comparable to the terrestrial one. The simultaneous detection of O2 (or O3) and a reduced gas in a planet's atmosphere has been suggested as strong evidence for life. Planets circling M stars may be good locations to search for such evidence.

Use of DNA-stable isotope probing and functional gene probes to investigate the diversity of methyl chloride-utilizing bacteria in soil

Enrichment and isolation of methyl chloride-utilizing bacteria from various terrestrial environments, including woodland and forest soils, resulted in the identification of seven methyl chloride-utilizing strains belonging to the genus Hyphomicrobium, an Aminobacter strain TW23 and strain WG1, which grouped closely with the genus Mesorhizobium. Methyl chloride enrichment cultures were dominated by Hyphomicrobium species, indicating that these bacteria were most suited to growth under the enrichment and isolation conditions used. However, the application of culture-independent techniques such as DNA-stable isotope probing and the use of a functional gene probe targeting cmuA, which encodes the methyltransferase catalysing the first step in bacterial methyl chloride metabolism, indicated a greater diversity of methyl chloride-utilizing bacteria in the terrestrial environment, compared with the diversity of soil isolates obtained via the enrichment and isolation procedure. It also revealed the presence of as yet uncultured and potentially novel methyl chloride-degrading bacteria in soil.

Chloromethane-dependent expression of the cmu gene cluster of Hyphomicrobium chloromethanicum

The methylotrophic bacterium Hyphomicrobium chloromethanicum CM2 can utilize chloromethane (CH(3)Cl) as the sole carbon and energy source. Previously genes cmuB, cmuC, cmuA, and folD were shown to be essential for the growth of Methylobacterium chloromethanicum on CH(3)Cl. These CH(3)Cl-specific genes were subsequently detected in H. chloromethanicum. Transposon and marker exchange mutagenesis studies were carried out to identify the genes essential for CH(3)Cl metabolism in H. chloromethanicum. New developments in genetic manipulation of Hyphomicrobium are presented in this study. An electroporation protocol has been optimized and successfully applied for transformation of mutagenesis plasmids into H. chloromethanicum to generate stable CH(3)Cl-negative mutants. Both transposon and marker exchange mutageneses were highly applicable for genetic analysis of Hyphomicrobium. A reliable and reproducible selection procedure for screening of CH(3)Cl utilization-negative mutants has also been developed. Mutational inactivation of cmuB, cmuC, or hutI resulted in strains that were unable to utilize CH(3)Cl or to express the CH(3)Cl-dependent polypeptide CmuA. Reverse transcription-PCR analysis indicated that cmuB, cmuC, cmuA, fmdB, paaE, hutI, and metF formed a single cmuBCA-metF operon and were coregulated and coexpressed in H. chloromethanicum. This finding led to the conclusion that, in cmuB and cmuC mutants, impaired expression of cmuA was likely to be due to a polar effect of the defective gene (cmuB or cmuC) located upstream (5') of cmuA. The detrimental effect of mutation in hutI on the upstream (5')-located cmuA is not clear but indicated that all the genes located within the cmuBCA-metF operon are coordinately expressed. Expression of the cmuBCA-metF transcript was also shown to be strictly CH(3)Cl inducible and was not repressed by the alternative C(1) substrate methanol. Sequence analysis of a transposon mutant (D20) led to the discovery of the previously undetected hutI and metF genes located 3' of the paaE gene in H. chloromethanicum. MetF, a putative methylene-tetrahydrofolate reductase, had 27% identity to MetF from M. chloromethanicum. Mutational and transcriptional analysis data indicated that, in H. chloromethanicum, CH(3)Cl is metabolized via a corrinoid-specific (cmuA) and tetrahydrofolate-dependent (metF, purU, folD) methyltransfer system.