Methane emission and dynamics of methanotrophic and methanogenic communities in a flooded rice field ecosystem

Abstract

Methane emissions, along with methanotrophs and methanogens and soil chemical properties, were investigated in a flooded rice ecosystem. Methane emission increased after rice transplantation (from 7.2 to 552 mg day(-1) m(-2) ) and was positively and significantly correlated with transcripts of pmoA and mcrA genes, transcript/gene ratios of mcrA, temperature and total organic carbon. Methane flux was negatively correlated with sulfate concentration. Methanotrophs represented only a small proportion (0.79-1.75%) of the total bacterial 16S rRNA gene reads: Methylocystis (type II methanotroph) decreased rapidly after rice transplantation, while Methylosinus and unclassified Methylocystaceae (type II) were relatively constant throughout rice cultivation. Methylocaldum, Methylobacter, Methylomonas and Methylosarcina (type I) were sparse during the early period, but they increased after 60 days, and their maximum abundances were observed at 90-120 days. Of 33 218 archaeal reads, 68.3-86.6% were classified as methanogens. Methanosaeta, Methanocella, Methanosarcina and Methanobacterium were dominant methanogens, and their maximum abundances were observed at days 60-90. Only four reads were characteristic of anaerobic methanotrophs, suggesting that anaerobic methane metabolism is negligible in this rice paddy system. After completing a multivariate canonical correspondence analysis of our integrated data set, we found normalized mcrA/pmoA transcript ratios to be a promising parameter for predicting net methane fluxes emitted from rice paddy soils.

Aboveground morphological traits do not predict rice variety effects on CH4 emissions

“…Thus, differences in CH 4 emissions among rice varieties should primarily stem from the effect of rice plants on the belowground processes (CH 4 production and/or oxidation in soil). These results are in consistent with the increasing recognition of the importance of belowground processes over methane emissions (Aulakh et al, 2001;Gutierrez et al, 2014;Kerdchoechuen, 2005;Lee et al, 2014). Relative to the indirect effect of aboveground plant traits on the CH 4 emission, rice roots play an important role in all CH 4 -related processes, contributing to the direct impact on the CH 4 emission.…”

Structure, variation, and assembly of the root-associated microbiomes of rice

“…Currently, the model for CH 4 emissions under rice cultivation is that CH 4 is formed in the soil away from the roots and diffuses through the soil to the rice root, where it is expelled via the aerenchyma in the roots (19,32,36). We used our dataset to examine the abundances of taxa related to CH 4 cycling.…”

Effect of Elevated CO₂ Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil

“…Lee et al (20) also showed that the methane-oxidizing bacterial community changed between different rice-growing stages in a flooded paddy field in Korea. A parallel study to the present study demonstrated that the abundance of methane-oxidizing bacteria in rice roots decreased under elevated [CO 2 ], which interacted with elevated soil temperature in the paddy field (31).…”

“…The copy number of the pmoA gene in the upper soil layer correlated with methane emission, whereas no correlation was observed in the lower soil layer at the PI stage (data not shown), indicating the greater contribution of methane-oxidizing bacteria in the upper, than in the lower soil layer to methane emission. Previous studies used the ratio of the mcrA / pmoA genes (14) or mcrA / pmoA transcripts (20) as a parameter to assess methane emission in paddy fields. In the present study, although no correlation was found at the MR stage, possibly due to large variations in methane emission rates (Fig.…”

“…The amount of methane emitted from paddy field represents a balance between methane production and oxidation (8), which indicates that the effects of environmental changes such as elevated [CO 2 ] and elevated soil temperature on methanogenic archaea and methane-oxidizing bacteria need to be simultaneously evaluated with a focus on the specific soil layers/sites in which the microorganisms function. Recent studies have shown that the simultaneous study of methanogenic archaea and methane-oxidizing bacteria is important for understanding methane metabolism in paddy field soil (6, 8, 10, 20). …”