Unraveling underlying mechanisms and responsible microbes of organic residue-stimulated atmospheric methane uptake in agricultural soils

It has been reported that compost amendment improves atmospheric CH4 uptake of agricultural soils. However, microbes involved as well as the underlying mechanisms responsible for the observed effect remain unclear. Here we identified active MOB at (circum-) atmospheric CH4 concentrations in agricultural soils amended with green compost, and investigated three complementary hypotheses: (i) atmospheric CH4 consumption is driven by highly activated, flush-feeding MOB; (ii) stimulation of internal CH4 production which fuels flush-feeding methanotrophic activity; and (iii) increased availability of H2 that can serve as additional energy source for mixotrophic methanotrophy. First, we showed that MOB previously activated by exposure to high CH4 concentrations can subsequently oxidize atmospheric CH4 via the flush-feeding lifestyle. Second, no internal CH4 production in soil was observed following compost amendment, likely due to lack of suitable substrates for methanogenesis. Third, provision of elevated H2 concentrations did not affect the concurrent atmospheric CH4 oxidation. Phospholipid fatty acid-stable isotope probing (PLFA-SIP) revealed that four distinct MOB groups were active at (circum-) atmospheric CH4 concentrations in agricultural soils and green compost: Methylocaldum sp., Methylosinus sporium, Methylocystis sp./Methylosinus trichosporium, and USCα. These findings enhance our understanding of methanotroph ecology and can be used to craft more effective strategies of creating "climate-smart" soils.