Unexpected role of canonical aerobic methanotrophs in upland agricultural soils

Aerobic oxidation of methane at (circum-)atmospheric concentrations (< 40 ppmv; Singh et al., 2010) has long been assumed to be catalyzed by the putative high-affinity methanotrophs in upland soils, the only known biological methane sink globally. In contrast, genes regulating methane oxidation in a low-affinity (canonical) methanotroph was only induced at > 600 ppmv methane (Baani & Liesack, 2008). These methanotrophs act as a methane bio-filter at oxic-anoxic interfaces in methane-emitting environments (Ho et al., 2013). Here, we show that canonical methanotrophs contributed to (circum-)atmospheric methane uptake in two agricultural soils, revealing as yet unrecognized reservoir of high-affinity methane-oxidizers. We performed a stable-isotope 13C-CH4 labelling incubation in the presence and absence of soil additives (bio-based residues) to track the flow of methane into the soil. Residue amendment transiently stimulated methane uptake rate, and shifted the bacterial community composition as revealed by MiSeq amplicon sequencing of the 16S rRNA gene. The 13C-enriched phospholipid fatty acids (PLFAs) were distinct in both soils, irrespective of amendments, and were unambiguously assigned almost exclusively to canonical alphaproteobacterial methanotrophs. The stable-isotope labelling approach allows a direct link attributing soil methane uptake to canonical methanotrophs not expected to consume (circum-)atmospheric methane. Our findings challenge the presumed role of the putative high-affinity methanotrophs as a methane sink in upland soils.