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

BACKGROUND

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