Drip irrigation suppresses methane emissions by reshaping the rhizosphere microbiomes in rice

The rhizosphere microbiomes of rice plants consist of a complex consortium of methanogens, methanotrophs, nitrogen- and/or sulphur-assimilating microorganisms. Controlled irrigation has been purported to be the cultivation method of choice over continuous flooding as it reduces water usage and aerates the soil to minimize the emission of the potent greenhouse gases. However, a systemic understanding of the assembly and function of microbiota in the rhizosphere under drip and flood irrigation remains unclear. Here, we report a significant reduction in methane emissions in drip irrigation compared to flooded paddies. Genotypic or varietal differences did not influence such increased methane emissions from flooded soil cultivation of rice. Using metagenomic sequencing and computational analyses, we provide a deeper understanding of how drip irrigation or continuous flooding affect the root-associated microbiomes in rice. Rhizosphere soil from two different rice varieties, Huanghuazhan and Temasek rice, grown under drip or flood conditions in a greenhouse was collected 2 months post-transplantation for metagenomic analysis. Our results reveal that drip irrigation favours microbes involved in the nitrifying-denitrifying processes while continuous flooding enriches for methanotrophs and methanogenic archaea. Syntrophic microbial clusters associated with methanogenesis were significantly reduced in drip irrigation. We identified several keystone taxa in the co-occurrence network models related to methanogenic and methanotrophic activities, as well as beneficial microbes from the soil rhizosphere, andActinomycetesfrom floodwater. Lastly, oxygen availability and redox potential were identified as key drivers that reshape rhizosphere microbiota leading to the functional differences observed between the two irrigation regimes.