Microbial mechanism for rice variety control on methane emission from rice field soil

Abstract

Rice variety is one of the key factors regulating methane (CH 4 ) production and emission from the paddy fields. However, the relationships between rice varieties and populations of microorganisms involved in CH 4 dynamics are poorly understood. Here we investigated CH 4 dynamics and the composition and abundance of CH 4 -producing archaea and CH 4 -oxidizing bacteria in a Chinese rice field soil planted with three types of rice. Hybrid rice produced 50-60% more of shoot biomass than Indica and Japonica cultivars. However, the emission rate of CH 4 was similar to Japonica and lower than Indica. Furthermore, the dissolved CH 4 concentration in the rhizosphere of hybrid rice was markedly lower than Indica and Japonica cultivars. The rhizosphere soil of hybrid rice showed a similar CH 4 production potential but a higher CH 4 oxidation potential compared with the conventional varieties. Terminal restriction fragment length polymorphism analysis of the archaeal 16S rRNA genes showed that the hydrogenotrophic methanogens dominated in the rhizosphere whereas acetoclastic methanogens mainly inhabited the bulk soil. The abundance of total archaea as determined by quantitative (real-time) PCR increased in the later stage of rice growth. However, rice variety did not significantly influence the structure and abundance of methanogenic archaea. The analysis of pmoA gene fragments (encoding the a-subunit of particulate methane monooxygenase) revealed that rice variety also did not influence the structure of methanotrophic proteobacteria, though variable effects of soil layer and sampling time were observed. However, the total copy number of pmoA genes in the rhizosphere of hybrid rice was approximately one order of magnitude greater than the two conventional cultivars. The results suggest that hybrid rice stimulates the growth of methanotrophs in the rice rhizosphere, and hence enhances CH 4 oxidation which attenuates CH 4 emissions from the paddy soil. Hybrid rice is becoming more and more popular in Asian countries. The present study demonstrated that planting of hybrid rice will not enhance CH 4 emissions albeit a higher grain production than the conventional varieties.

Dry/Wet Cycles Change the Activity and Population Dynamics of Methanotrophs in Rice Field Soil

“…All known bacterial methanotrophs except Methylocella and Methyloferula possess a pMMO (7,8). The pmoA gene that encodes the subunit of membrane-bound MMO is highly conserved in proteobacterial methanotrophs and has been widely used as phylogenetic marker for ecological studies (9)(10)(11)(12)(13)(14).…”

Metagenomics analysis of methane metabolisms in manure fertilized paddy soil

“…On the other hand, methylotrophic bacteria including methanotrophs also increase where methane is available as a substrate. Growth of these methanotrophic and methylotrophic bacteria also depend on rice variety (Ma et al, 2010;Bao et al, 2014b), types of fertilizers (Mohanty et al, 2006;Zheng et al, 2014), and number of co-existing methanogens (Edwards et al, 2015). These studies suggest that methane emission system under rice paddy is very complicated, involving various microbial species and environmental factors.…”

“…Most abundant and ubiquitous methanogens in soil environments are acetoclastic methanogens that use acetic acid as a substrate to produce methane (Ma et al, 2010;Das et al, 2011;Das and Adhya, 2012;Datta et al, 2013). On the other hand, there exist some rice paddy specific methanogens, referred to as "Rice cluster I", members of which also contribute substantial amount of methane emission from rice .…”

Methane Emissions among Hybrid Rice Cultivars in the MidSouthern United States

“…Similarly, Simmonds et al [31] observed a reduction in CH 4 emissions from the hybrid CLXL745 relative to the pure-line cultivar, Francis, following heading, while no differences in emissions were observed prior to heading. Although examining cultivars not typically grown in the US, in China, Ma et al [29] observed reduced dissolved CH 4 concentrations in the rhizosphere of hybrid rice as well as a 67% increase in CH 4 oxidation potential relative to pure-line cultivars, while no differences in CH 4 production potential were observed. This indicates a potential for increased CH 4 oxidation with hybrid cultivars, possibly due to greater methanotrophic activity in the rhizosphere of hybrid rice relative to pure-line cultivars.…”

“…Studies have indicated that about 90% of CH 4 emissions from rice fields occur by plant-mediated transport through the aerenchyma tissues of rice plants [16,19,23,24]. Due to the strong influence of rice plants themselves on CH 4 emissions from the system, innate physiological differences between cultivars may lead to differences in CH 4 transport capacities [23], differences in biomass accumulation [25] and root exudation [26,27,28], or differences in microbial populations in the rhizpsphere [29]. Many studies throughout rice-growing countries have reported differences in CH 4 emissions among rice cultivars; however, the complexity of the system and processes involved have led to differing results and, at this point, no single parameter has been identified to consistently explain differences in CH 4 emissions among cultivars.…”