Intermittent drainage can substantially reduce methane emission from rice fields, but the microbial mechanisms remain poorly understood. In the present study, we determined the rates of methane production and emission, the dynamics of ferric iron and sulfate, and the abundance of methanogen mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase) and their transcripts in response to alternate dry/wet cycles in paddy field soil. We found that intermittent drainage did not affect the growth of rice plants but significantly reduced the rates of both methane production and emission. The dry/wet cycles also resulted in shifts of soil redox conditions, increasing the concentrations of ferric iron and sulfate in the soil. Quantitative PCR analysis revealed that both mcrA gene copies and mcrA transcripts significantly decreased after dry/wet alternation compared to continuous flooding. Correlation and regression analyses showed that the abundance of mcrA genes and transcripts positively correlated with methane production potential and soil water content and negatively correlated with the concentrations of ferric iron and sulfate in the soil. However, the transcription of mcrA genes was reduced to a greater extent than the abundance of mcrA genes, resulting in very low mcrA transcript/gene ratios after intermittent drainage. Furthermore, terminal restriction fragment length polymorphism analysis revealed that the composition of methanogenic community remained stable under dry/ wet cycles, whereas that of metabolically active methanogens strongly changed. Collectively, our study demonstrated a stronger effect of intermittent drainage on the abundance of mcrA transcripts than of mcrA genes in rice field soil.

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.

Soil drainage is one of the most promising approaches to mitigate methane (CH(4) ) emission from paddy fields. The microbial mechanism for the drainage effect on CH(4) emission, however, remains poorly understood. In the present study, we determined the effect of short (four drainages of 5-6 days each) and long drainage cycles (two drainages of 10-11 days each) on CH(4) emission and analyzed the response of the structure and abundance of methanogens and methanotrophs in a Chinese rice field soil at the DNA level. Rice biomass production was similar between drainage and the practice of continuous flooding. The rate of CH(4) emission, however, was reduced by 59% and 85% for the long and short drainage cycles, respectively. Quantitative (real-time) PCR analysis revealed that the total abundance of archaeal populations decreased by 40% after multiple drainages, indicating the inhibitory effects on methanogen growth. The structure of the methanogen community as determined by terminal restriction fragment length polymorphism analysis, however, remained unaffected by drainages, although it varied among rhizosphere, bulk and surface soils. Quantitative PCR analysis of the methanotrophic functional pmoA genes revealed that the total abundance of methanotrophs in rhizosphere soil increased two to three times after soil drainages, indicating a stimulation of methanotroph growth. The CH(4) oxidation potential in the rhizosphere soil also increased significantly. Furthermore, drainages caused a shift of the methanotrophic community, with a significantly increase of type II methanotrophic bacteria in the rhizosphere and surface soil. Thus, both inhibition of methanogens and stimulation of methanotrophs were partly responsible for the reduction of CH(4) emissions. The methanotroph community, however, appeared to react more sensitively to soil drainage compared with the methanogen community.

There is an urgent need to understand the global epidemiological landscape of carbapenem-resistant Escherichia coli (CREC). Here we provide combined genomic and phenotypic characterization of the emergence of a CREC clone from the ST410 lineage. We show that the clone expands with a single plasmid, within which there is frequent switching of the carbapenemase gene type between bla NDM and bla OXA-181 with no impact on plasmid stability or fitness. A search for clone-specific traits identified unique alleles of genes involved in adhesion and iron acquisition, which have been imported via recombination. These recombination-derived allelic switches had no impact on virulence in a simple infection model, but decreased efficiency in binding to abiotic surfaces and greatly enhanced fitness in iron limited conditions. Together our data show a footprint for evolution of a CREC clone, whereby recombination drives new alleles into the clone which provide a competitive advantage in colonizing mammalian hosts.