Incorporating DNA-level microbial constraints helps decipher methane emissions from Chinese water-saving ground cover rice production systems

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• Relating CH 4 fluxes to methanogens and methanotrophs under GCRPS remains unclear. • GCRPS reduced CH 4 emissions and the yield-scaled CH 4 emissions. • GCRPS decreased the abundance of mcrA gene while stimulated that of pmoA gene. • Microbial parameters are useful to better predict CH 4 emissions from rice paddies. While water management has been documented to regulate CH 4 emissions from rice paddies, the mechanisms behind the association between CH 4 emissions and functional microbes remain unclear under water-saving ground cover rice production systems (GCRPS). In GCRPS, the soil is kept aerobic by maintaining 80 %–90 % of the water holding capacity but without standing water over the entire rice-growing season, and the soil surface is covered with rice straw or plastic film to reduce water evaporation. A split-plot field experiment was conducted to examine the effects of various GCRPS-related water-saving regimes on CH 4 emissions by linking to CH 4 -related microbes over the 2015 and 2016 rice growing seasons in a typical Chinese rice field. Methane fluxes and related functional genes [methanogens ( mcrA and methanogenic archaeal 16S rRNA ) and methanotrophs ( pmoA )] abundances were simultaneously measured using the closed chamber method and molecular techniques, respectively. The results showed that relative to the conventional waterlogged control (WRPS), GCRPS-related water-saving practices consistently reduced CH 4 emissions, which was largely attributed to the decreased relative abundance of the methanogenic functional gene mcrA while the methanotrophic functional gene pmoA increased. When averaged over the two rice seasons, the grain yield was 17.38 % and 12.22 % greater under the GCRPS -straw and GCRPS -film water-saving systems relative to WRPS, respectively. Water-saving regimes decreased the yield-scaled CH 4 emissions as compared with the WRPS, especially under GCRPS -film . The CH 4 fluxes showed a positive correlation with the relative abundance of mcrA and its ratio to pmoA , but a negative correlation with the relative abundance of pmoA . The performance of CH 4 -simulated models could be improved by incorporating microbial parameters to predict CH 4 emissions from rice fields. Overall, this study updates our understanding of the microbial mechanisms underlying CH 4 emissions from water-saving GCRPSs. We proposed the GCRPS regime with biodegradable film mulching as a desirable water-saving strategy to reconcile high yields and low CH 4 emissions in rice production.