Dataset Information

Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil.

ABSTRACT: 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.

SUBMITTER: Ma K

PROVIDER: S-EPMC3255761 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil.

Ma Ke K Conrad Ralf R Lu Yahai Y

Applied and environmental microbiology 20111118 2

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 ...[more]

PMID: 22101043

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Project description:The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (using terminal restriction fragment length polymorphism [T-RFLP]), and abundance (using quantitative PCR [qPCR]) of methanotroph pmoA genes (encoding a subunit of particulate methane monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA were relatively low but were significantly stimulated by drainage. In contrast, however, in the rhizosphere and surface soils, potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (and to a lesser extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded conditions. Drainage affected the composition of the methanotrophic community only minimally but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in the abundance, composition, and activity of the various type I and type II methanotrophs on both a seasonal and a spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced the attenuation of methane flux into the atmosphere.

Project description:BackgroundPaddies are an important anthropogenic source of methane emissions to the atmosphere, and they are impacted by heavy metal pollution. Nickel (Ni) and cobalt (Co) pollution might either enhance or mitigate CH4 emission from paddy soils due to the total amounts of metals, bioavailability and functional microbial activity and composition.MethodsAn incubation experiment was conducted, and different Ni and Co concentrations were added to test the effects of trace metals on methane production in paddy soil. The archaea community structure and the abundance of methanogen functional groups in the paddy soil with added Ni and Co were detected using high-throughput sequencing and quantitative PCR based on the 16S rRNA and mcrA (methyl coenzyme M reductase) genes, respectively.ResultsThe highest methane production rate was 561 mg CH4 kg-1 dry soil d-1 with the addition of 50 mg kg-1 Ni and 684 mg CH4 kg-1 dry soil d-1 with the addition of 25 mg kg-1 Co. Accordingly, the mcrA gene was most abundant in the 50 mg kg-1 Ni addition (3.1 × 106 ± 0.5 × 106 copies g-1 dry soil). The lowest mcrA gene abundance was detected in the 500 mg kg-1 Co addition (9.2× 105 ± 0.4 × 105 copies g-1 dry soil). The dominant methanogens were Methanobacterium, Methanosarcina, Methanocella, Methanomassiliicoccus, Bathyarchaeota, and Rice Cluster I (RC-I), and the relative abundances of these groups were higher than 1% in the Ni and Co treatments. Additionally, the archaeal compositions differed significantly in the soils with various Ni and Co additions. The most abundant Methanococcus spp. represented 51.3% of the composition in the 50 mg kg-1 Ni addition, which was significantly higher than that of the control (12.9% to 17.5%).DiscussionOur results indicated that the contamination of soil by Ni and Co significantly affected total methanogens abundance and specific methanogen functional groups. Ni and Co additions to paddy soil promoted methanogenic activity at low concentrations, while they had inhibitory effects at high concentrations. Because paddy soils largely contribute to methane emissions and are increasingly exposed to heavy metal pollution, our results show that future assessments of greenhouse gas flux from paddy soils should take into account the effects of pollution by Ni and Co.

Dataset Information

Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil.

Publications

Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil.

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