A rice gene for microbial symbiosis, Oryza sativa CCaMK, reduces CH₄ flux in a paddy field with low nitrogen input

Plants have mutualistic symbiotic relationships with rhizobia and fungi by the common symbiosis pathway, of which Ca²⁺/calmodulin- dependent protein kinase (encoded by CCaMK) is a central component. Although Oryza sativa CCaMK (OsCCaMK) is required for fungal accommodation in rice roots, little is known about the role of OsCCaMK in rice symbiosis with bacteria. Here, we report the effect of a Tos17-induced OsCCaMK mutant (NE1115) on CH₄ flux in low-nitrogen (LN) and standard-nitrogen (SN) paddy fields compared with wild-type (WT) Nipponbare. The growth of NE1115 was significantly decreased compared with that of the WT, especially in the LN field. The CH₄ flux of NE1115 in the LN field was significantly greater (156 to 407% in 2011 and 170 to 816% in 2012) than that of the WT, although no difference was observed in the SN field. The copy number of pmoA (encodes methane monooxygenase in methanotrophs) was significantly higher in the roots and rhizosphere soil of the WT than in those of NE1115. However, the mcrA (encodes methyl coenzymeMreductase in methanogens) copy number did not differ between the WT and NE1115. These results were supported by a ¹³C-labeled CH₄-feeding experiment. In addition, the natural abundance of ¹⁵N in WT shoots (3.05‰) was significantly lower than in NE1115 shoots (3.45‰), suggesting greater N₂ fixation in the WT because of dilution with atmospheric N₂ (0.00‰). Thus, CH₄ oxidation and N₂ fixation were simultaneously activated in the root zone of WT rice in the LN field and both processes are likely controlled by OsCCaMK.