Effect of a salinity gradient on methane emissions in paddy rice: a mesocosm experiment

Rice is a crucial crop for food security, but it is also a significant source of anthropogenic greenhouse gas emissions, particularly methane (CH₄). Projected sea level rise caused by climate change will impact on rice yield through increased salinity. On the other hand, increased salinity potentially mitigates CH₄ emissions by inhibiting methanogenesis mediated by the dominance of sulphate-reducing bacteria. To investigate this dual effect, we conducted a mesocosm experiment creating a water salinity gradient with four levels: 2 ppm (control), 4 ppm, 6 ppm and 35 ppm (seawater). CH₄ emissions, abundance and gene expression of microbial populations and grain yield were assessed.

The experiment took place in year 2022 at IRTA facilities (Spain) using a variety of japonica rice (Oryza sativa L.). Rice was grown following the standard practices, notably permanent flooding, and crop residue incorporation into the soil after the harvest. CH₄ emissions were weekly assessed throughout the rice growing season (May to September) and the post-harvest (October to December). Gas samples were collected using gas chambers and analysed through gas chromatography. Yield and aboveground biomass were measured at harvest. Thereafter, crop residues in each mesocosm, where present, were incorporated into the soil. Soil samples for microbial analyses were taken twice during post-harvest:  6 days before the harvest and 28 days after straw incorporation.  The microbial community diversity was assessed based on 16S/ITS-metataxonomy of total (DNA) and metabolically active (cDNA) bacteria, archaea, and fungi, as well as the quantification of total bacteria (16S rRNA gene), methanogenic archaea (mcrA gene ), and sulphate-reducing bacteria (aprA gene) by qPCR.  The activity of methanogenic archaea and sulphate reducing populations were assessed by quantifying gene transcripts of mcrA and aprA by RT-qPCR.

Rice grain yield decreased by 30% with increasing salinity from 2 ppm to 4 ppm, while there was no yield above 6 ppm. The biomass of straw produced and then added into the soil declined along the salinity gradient: 72.9 ± 12.4 g and 49.8 ± 6.1 g at 2 ppm and 4 ppm treatments, respectively, and zero in the remainder. The results confirmed that salinity significantly reduces CH₄ emissions, but the sensitivity of this response differed between the growing and post-harvest seasons. During the growing season, CH₄ declined with increasing salinity, ranging from 8.0 ± 1.7 to 0.05 ± 0.02 mg CH4 m^-2 h^-1. However, in the post-harvest, no CH₄ emissions were detected at water salinities above 4 ppm, in contrast to 14.8 ± 0.75 mg CH4 m^-2 h^-1 found at 2 ppm. In regard to the microbial processes, the abundance of methanogenic archaea declined with increased salinity and the gene expression was highly inhibited at salinities larger than 6 ppm. By contrast, the abundance of sulphate-reducing bacteria was preserved over the salinity gradient while gene expression remained active, though slightly reduced from 6 ppm, probably due to the lower availability of organic carbon at the highest salinities.

Acknowledgments: The study has been carried out within the framework of the MIC-RICE project PID2019-111572RB-I00 funded by AEI/10.13039/501100011033