Decreased CH4 emissions associated with methanogenic and methanotrophic communities and their interactions following Fe(III) fertiliser application in rice paddies

Rice paddies are important sources of atmospheric methane (CH4), where CH4 fluxes are determined by the balance of production and oxidation. While the application of Fe(III) fertilizer is a proven effective strategy for mitigating CH4 emissions from rice paddies, little is known about the role of methanogen and methanotroph communities and their interactions. In this study, we measured the CH4 flux in a rice paddy field experiment, where the responses of methanogenic and methanotrophic activities to Fe(III) fertiliser applied at medium (Fe-M) and high (Fe-H) levels were examined using real-time quantitative PCR coupled with co-occurrence network analysis after Illumina MiSeq sequencing of the mcrA and pmoA genes. Relative to the control without Fe(III) fertiliser application, in the Fe-M and Fe-H treatments, seasonal CH4 emissions were significantly decreased by 65% and 62%, respectively. Fe(III) fertilisation significantly decreased the copy numbers and potential activity of methanogens, and had an opposite effect on methanotrophs. We found Methanothrix was the predominant genus more adaptive to grow in Fe-rich environments. Fe(III) fertilisation caused a shift in the methanotrophic community towards a predominance of Type II methanotrophs. Soil total Fe concentration, soil electrical conductivity, and different valences of iron were key factors in the composition of methanogenic and methanotrophic communities. Fe(III) fertilisation led to a less complex community taxonomic structure mostly attributed to fewer nodes and edges in both the co-occurrence and mutual exclusion networks of methanogen and methanotrophs. Our findings suggest that adding Fe(III) fertiliser in rice paddies could mitigate CH4 emissions by regulating both methanogens and methanotrophs.