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

College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.
Applied and Environmental Microbiology (Impact Factor: 3.95). 11/2011; 78(2):445-54. DOI: 10.1128/AEM.06934-11
Source: PubMed

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.

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Available from: Ke Ma, Aug 28, 2015
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    • "The response to environmental conditions seems to be regulated mainly by changes in transcription and enzyme expression (Shrestha et al., 2009; Yuan et al., 2011; Ma et al., 2012). The methanogenic archaeal communities in wetland rice fields are quite diverse, typically containing members of Methanocellales, Methanosarcinaceae, Methanosaetaceae, Methanobacteriales and Methanomicrobiales (Lueders et al., 2001; Conrad, 2007). "
    Soil Biology and Biochemistry 10/2015; 89:238-247. · 4.41 Impact Factor
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    • "In drained soil, where soil Eh values are higher, Fe 3+ or SO 4 2− are produced (Patrick and Jugsujinda 1992). In such soils, methanogenic archaea are outcompeted by iron or sulfate reducers for organic matter after flooding (Ma et al. 2012). Probably, soil layer above 5 cm was more likely to be important for CH 4 control because soil Eh at soil–water interface is higher than that at 5 cm depth during both flooded and drained conditions (Hasebe et al. 1985). "
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    ABSTRACT: Dry-thermophilic anaerobic co-digestion (DTAD) can be used to treat forage rice straw and pig manure and generate biogas as an energy source. Solid residue produced from DTAD process can be used as a fertilizer in forage rice fields, while addition of the residue could increase methane (CH4) and nitrous oxide (N2O) emissions from the soil. We evaluated the effects of adding DTAD residue and water management on CH4 and N2O emissions from a forage rice field. Three treatments were evaluated: (a) 100 kg N · ha−1 chemical fertilizer and continuous flooding (CC); (b) residue addition (300 kg N · ha−1 DTAD residue) with continuous flooding (RC); and (c) residue addition with intermittent irrigation (RI). RC and RI showed higher CH4 fluxes than CC throughout the growing period. After a midsummer drainage, RI showed higher soil Eh values and lower CH4 fluxes (mean, 7.6 mg C · m−2 · h−1) than those in RC (mean, 18.6 mg C · m−2 · h−1). Abundance of mcrA gene copy number was not different between RC and RI, suggesting CH4 flux was reduced by suppression of methanogenic activity by intermittent irrigation. Cumulative CH4 emissions during the cultivation period were 105, 509, and 306 kg C · ha−1 in CC, RC, and RI, respectively. N2O fluxes were within detection limits in all treatments. Our results, to our knowledge, are the first to show greenhouse gas emission from forage rice fields supplemented with DTAD residue and of the effectiveness of water management in CH4 mitigation.
    Water Air and Soil Pollution 08/2014; 225. DOI:10.1007/s11270-014-2118-3 · 1.69 Impact Factor
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    • "influences, such as continuous flooding and wet/dry cycles (Ma et al. 2012) and oxygen exposure (Yuan et al. 2009). This phenomenon could be interpreted as a result of reduced activity of methane metabolizing in both methane oxidizing and producing processes in wet season according to previously results (Ma et al. 2012; Yuan et al. 2009, 2011). It is apparent that the activation of mcrA gene transcripts of ANMEs or methanogens in response to seasonal changes deserves further attention due to the availability of carbon and then the activity of relevant microbial community. "
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    ABSTRACT: Two pairs of PCR primes ANMEallF/R and ANME23F/R were designed by Codehop method based on sequences available to retrieve more anaerobic methanotrophic (ANME) archaea mcrA gene sequences and ANME 2 and 3 subtypes from reedbed in two seasons. Overall, the PCR primers showed slightly favor for ANME group mcrA gene sequences. Due to the predominance of methanogens mainly affiliated to Methanomicrobiales in the samples, a large portion of mcrA gene sequences amplified in the clone libraries belonged to methanogens. Differences in PCR primers and performance affected the mcrA gene-PCR-amplified community composition to a minor extent. PCR primers targeting ANME mcrA group g-h were designed to apply real-time PCR for quantifying more groups of mcrA gene-affiliated ANME archaea and tested with these same samples, and the most abundant group in the whole ANME mcrA community was ANME group g-h. In addition, a stable mcrA gene-harboring archaeal community pattern was detected in the reedbed sediment samples collected from two distinctively different seasons. The PCR and qPCR primers designed in this study can expand our knowledge on the distribution of ANME mcrA genes and community composition in the ecosystem to better understand the carbon cycle.
    Applied Microbiology and Biotechnology 03/2014; DOI:10.1007/s00253-014-5599-5 · 3.81 Impact Factor
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