Syntrophic microbiomes associated with methane-suppressive irrigation in rice

ABSTRACT Rice, a staple crop of nearly half of the world population, is grown predominantly in flooded paddies which are one of the largest contributors to methane emissions. An effective approach is to minimise the anaerobic flooded conditions that favour the growth of methanogenic archaea. Empirical measurements showed that controlled irrigation regime reduces methane emissions by 70% to 90%. The soil microbiomes of both flood and drip irrigated soil were characterised using whole-genome shotgun metagenomics. Controlled irrigation was shown to suppress methanogens and lower methane emissions. While emissions are correlated with mcrA gene abundance, empty flooded fields exhibited relatively high mcrA levels above baseline despite undetectable methane emissions. Rice cultivar genotype had no significant effect on the soil microbiomes. Co-occurrence network analysis indicates that soil microbial communities stratify according to their oxygen preferences along a gradient. Methanogens were increased in flooded paddies, and methane production attributed to the microorganisms involved in the anaerobic decay of organic matter. Controlled irrigation altered the microbiome by raising the soil redox potential by enhancing aeration and promoting ammonia oxidation and nitrification pathways. IMPORTANCE The temporal dynamics of microbial communities in drip-irrigated rice fields remain poorly characterized to-date. Empirical measurements demonstrate that controlled drip irrigation effectively suppresses methanogens and lowers methane emissions by up to 90%. Statistical analysis further revealed a moderate correlation between methane emissions and the mcrA gene with R = 0.6 and p -value = 2.9e-05. The correlation plot showed that the outliers corresponded to samples from empty flooded fields, where high mcrA gene abundance was observed despite low methane emissions. Methane produced in the soil is likely released into the atmosphere via transport through the aerenchyma of rice plants. Controlled irrigation is shown to be climate friendly as it reduces methane emissions by improving soil aeration and increasing the soil redox potential.