Methanol consumption drives the bacterial chloromethane sink in a forest soil

Abstract

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.