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

Background Chloromethane (CH 3 Cl) is the most abundant halogenated organic compound in the atmosphere and substantially responsible for the destruction of the stratospheric ozone layer. Since anthropogenic CH 3 Cl 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. CH 3 Cl-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 CH 3 Cl sink with the identity of active microorganisms and their biochemical pathways for CH 3 Cl degradation in a deciduous forest soil. When tested in laboratory microcosms, biological CH 3 Cl consumption occurred in leaf litter, senescent leaves, and organic and mineral soil horizons. Highest consumption rates, around 2 mmol CH 3 Cl g −1 dry weight h −1 , were measured in organic soil and senescent leaves, suggesting that top soil layers are active (micro-)biological CH 3 Cl degradation compartments of forest ecosystems. The DNA of these [ 13 C]-CH 3 Cl-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. [ 13 C]-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 CH 3 Cl degradation, via the methyltransferase system encoded by the CH 3 Cl utilisation genes ( cmu ), were undetected in the DNA-SIP metagenome data, suggesting that biological CH 3 Cl sink in this deciduous forest soil operates by a cmu -independent metabolism.