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

Effects of methyl halide flux characteristics following Spartina alterniflora invasion in a seaward direction in a temperate salt marsh, China

In this study, we explored the source-sink characteristics of methyl halide (CH₃X; X = Cl, Br, I) in coastal wetlands located in temperate regions, and identified key factors affecting the spatio-temporal variation of CH₃X during the invasion of Spartina alterniflora. We used static chamber-gas chromatography to monitor CH₃X fluxes in the S. alterniflora area and bare flat area of the Jiaozhou Bay salt marsh for a long time from August 2015 to May 2017. Our results indicated that CH₃X emissions showed obvious seasonal and diurnal variations. The S. alterniflora area was a source of CH₃X, with higher fluxes in the spring and autumn seasons. CH₃X fluxes were higher during the daytime than at night, and the diurnal difference in CH₃Br was the most significant (4.51 times). The bare flat area was mainly a sink for CH₃X, and the maximum absorption flux occurred in summer. At this time, the microbial activity was greater, and the consumption rate during the day was higher than that at night. Extreme linear correlations existed between the fluxes of CH₃Cl, CH₃Br, and CH₃I (P < 0.01), indicating that the production and consumption of the three gases were likely to have similar mechanisms and were affected by the same factors. S. alterniflora invasion increased CH₃X emissions and shifted the original bare flat area from a sink to a source of CH₃X. The biomass of S. alterniflora, especially the leaf, significantly affects CH₃X fluxes. Additionally, S. alterniflora increased the content of total organic carbon, total sulfur, available sulfur, and iron (III) in the soil, which were the main factors promoting the source-sink transformation of CH₃X. Based on the current invasive area of S. alterniflora in China, we estimated that the annual emissions of CH₃Cl, CH₃Br, and CH₃I from S. alterniflora into the troposphere were 9.04 × 10⁶, 2.42 × 10⁵ and 2.06 × 10⁵ mol, respectively.

A putatively new family of alphaproteobacterial chloromethane degraders from a deciduous forest soil revealed by stable isotope probing and metagenomics

BACKGROUND

Chloromethane (CH₃Cl) is the most abundant halogenated organic compound in the atmosphere and substantially responsible for the destruction of the stratospheric ozone layer. Since anthropogenic CH₃Cl sources have become negligible with the application of the Montreal Protocol (1987), natural sources, such as vegetation and soils, have increased proportionally in the global budget. CH₃Cl-degrading methylotrophs occurring in soils might be an important and overlooked sink.

RESULTS AND CONCLUSIONS

The objective of our study was to link the biotic CH₃Cl sink with the identity of active microorganisms and their biochemical pathways for CH₃Cl degradation in a deciduous forest soil. When tested in laboratory microcosms, biological CH₃Cl consumption occurred in leaf litter, senescent leaves, and organic and mineral soil horizons. Highest consumption rates, around 2 mmol CH₃Cl g^-1 dry weight h^-1, were measured in organic soil and senescent leaves, suggesting that top soil layers are active (micro-)biological CH₃Cl degradation compartments of forest ecosystems. The DNA of these [¹³C]-CH₃Cl-degrading microbial communities was labelled using stable isotope probing (SIP), and the corresponding taxa and their metabolic pathways studied using high-throughput metagenomics sequencing analysis. [¹³C]-labelled Metagenome-Assembled Genome closely related to the family Beijerinckiaceae may represent a new methylotroph family of Alphaproteobacteria, which is found in metagenome databases of forest soils samples worldwide. Gene markers of the only known pathway for aerobic CH₃Cl degradation, via the methyltransferase system encoded by the CH₃Cl utilisation genes (cmu), were undetected in the DNA-SIP metagenome data, suggesting that biological CH₃Cl sink in this deciduous forest soil operates by a cmu-independent metabolism.

13 C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern

Chloromethane (CH₃ Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH₃ Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH₃ Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH₃ Cl-degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with ¹³ C-labelled CH₃ Cl combined with metagenomics. Metagenome-assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH₃ Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH₃ Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH₃ Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA-independent pathway may drive CH₃ Cl degradation in the investigated tree ferns.

Methyl Chloride and Methyl Bromide Production and Consumption in Coastal Antarctic Tundra Soils Subject to Sea Animal Activities

Methyl chloride (CH₃Cl) and methyl bromide (CH₃Br) are the predominant carriers of natural chlorine and bromine from the troposphere to the stratosphere, which can catalyze the destruction of stratospheric ozone. Here, penguin colony soils (PCS) and the adjacent tundra soils (i.e., penguin-lacking colony soils, PLS), seal colony soils (SCS), tundra marsh soils (TMS), and normal upland tundra soils (UTS) in coastal Antarctica were collected and incubated for the first time to confirm that these soils were CH₃Cl and CH₃Br sources or sinks. Overall, tundra soil acted as a net sink for CH₃Cl and CH₃Br with potential flux ranges from -18.1 to -2.8 pmol g^-1 d^-1 and -1.32 to -0.24 pmol g^-1 d^-1, respectively. The deposition of penguin guano or seal excrement into tundra soils facilitated the simultaneous production of CH₃Cl and CH₃Br and resulted in a smaller sink in PCS, SCS, and PLS. Laboratory-based thermal treatments and anaerobic incubation experiments suggested that the consumption of CH₃Cl and CH₃Br was predominantly mediated by microbes while the production was abiotic and O₂ independent. Temperature gradient incubations revealed that increasing soil temperature promoted the consumption of CH₃Cl and CH₃Br in UTS, suggesting that the regional sink may increase with Antarctic warming, depending on changes in soil moisture and abiotic production rates.

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.

Isotopic Characterization (2H, 13C, 37Cl, 81Br) of Abiotic Degradation of Methyl Bromide and Methyl Chloride in Water and Implications for Future Studies

Methyl bromide (CH₃Br) and methyl chloride (CH₃Cl) significantly contribute to stratospheric ozone depletion. The atmospheric budgets of both compounds are unbalanced with known degradation processes outweighing known emissions. Stable isotope analysis may be capable to identify and quantify emissions and to achieve a balanced budget. Degradation processes do, however, cause isotope fractionation in methyl halides after emission and hence knowledge about these processes is a crucial prerequisite for any isotopic mass balance approach. In the current study, triple-element isotope analysis (²H, ¹³C, ³⁷Cl/⁸¹Br) was applied to investigate the two main abiotic degradation processes of methyl halides (CH₃X) in fresh and seawater: hydrolysis and halide exchange. For CH₃Br, nucleophilic attack by both H₂O and Cl^- caused significant primary carbon and bromine isotope effects accompanied by a secondary inverse hydrogen isotope effect. For CH₃Cl only nucleophilic substitution by H₂O was observed at significant rates causing large primary carbon and chlorine isotope effects and a secondary inverse hydrogen isotope effect. Observed dual-element isotope ratios differed slightly from literature values for microbial degradation in water and hugely from radical reactions in the troposphere. This bodes well for successfully distinguishing and quantifying degradation processes in atmospheric methyl halides using triple-element isotope analysis.

Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds

Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.

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.