Article

Responses of Methanogen mcrA Genes and Their Transcripts to an 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: 3.67). 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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    • "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). "
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    ABSTRACT: Intermittent drainage is one of the most promising approaches to mitigate methane (CH4) emission from paddy fields. Irrigated rice fields in Uruguay are temporarily established on soils used as cattle pastures. We studied soil from the pasture-rice rotation (UR) as well as soil from a permanent cattle pasture (UT) hypothesizing that activity and structure of the bacterial and archaeal communities involved in production of CH4 change systematically with intermittent drainage. Methane production started after 7 days and 16 days of anoxic incubation in UR and UT soil, respectively. Then, production rates of CH4 were higher in UT than UR soil. Intermittent drainage significantly decreased the rates of CH4 production. Analysis of δ13C indicated that CH4 was mainly produced from acetate both in UR (73–98%) and UT (51–80%) soil. Intermittent drainage did not change the pathway of CH4 production. Quantitative PCR showed that methanogenic archaeal gene copy numbers (16S rRNA, mcrA) were much lower in UT than UR soil, but increased upon incubation under anoxic conditions. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing of bacterial and archaeal 16S rRNA genes showed that the communities were clearly different between UR and UT soil. The bacterial community consisted of 9 phyla with relative abundance of >1% in both soils. Whereas the archaeal community in UR soil was dominated by Methanocellales and Methanosarcinaceae, that in UT soil was dominated by Crenarchaeota. Anoxic incubation affected the composition of the bacterial and archaeal communities in UT soil, but not so much in UR soil. In UT soil, the relative abundance of Clostridiales increased to 19%, and the archaeal community changed to dominance by Methanosarcinaceae and Methanobacteriales. Subsequent drainage and re-flooding, however, had comparatively little effect on the composition, although it decreased the rates of CH4 production in both soils. Difference in previous soil management and in the structures of the microbial communities apparently only affected their dynamics and functioning after the first flooding but not upon subsequent drainage and re-flooding.
    No preview · Article · Oct 2015 · Soil Biology and Biochemistry
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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). "

    Full-text · Article · Oct 2015 · Soil Biology and Biochemistry
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    • "T-RFLPwasperformedasdescribedpreviously(LiuandConrad, 2011).T-RFLPanalysisofrDNAandrRNAwerefromtriplicate DNAandRNAextractionsforeachsample.Bacterial/archaeal communitiesT-RFLPanalysiswereperformedusingprimers Ba27f/Ba907randAr109f/Ar915rwithBa27fandAr915rwere labeledatthe5′endand3′endwith6-carboxyfluorescein (FAM),respectively.Briefly,tominimizethePCRartifacts,the PCRamplificationprocedurewasmodified:20ngoftemplate DNA,doubledconcentrationofprimerand25amplification cyclesofPCRwereusedasdescribedpreviouslyindetail (Zhangetal.,2005).FluorescentlylabeledPCRproductswere purifiedanddigestedusingMspI(Fermentas)forbacteriaand TaqI(Fermentas)forarchaea,respectively,andsubsequently analyzedusinganautomatedsequencerABIPRISM3730XL (AppliedBiosystems).T-RFLPpatternsofeachsamplewere evaluatedbypeakheightintegrationofthedifferentterminal restrictionfragments(T-RFs)usingGeneMapper4.1analysis software(AppliedBiosystems).TherelativeabundanceofT-RFs wascalculatedasdescribedpreviously(Maetal.,2012)asthe percentageofonedistinctT-RFinthesumofallpeakheightsin anindividualT-RFLPprofile.Statisticalanalyseswereperformed usingSigmaPlotforWindowsVersion11.0(systatsoftware,Inc., USA). "
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    ABSTRACT: Methanosaeta harundinacea and Methanosarcina barkeri, known as classic acetoclastic methanogens, are capable of directly accepting electrons from Geobacter metallireducens for the reduction of carbon dioxide to methane, having been revealed as direct interspecies electron transfer (DIET) in the laboratory co-cultures. However, whether their co-occurrences are ubiquitous in the iron (III)-reducing environments and the other species of acetoclastic methanogens such as Methanosarcina mazei are capable of DIET are still unknown. Instead of initiating the co-cultures with pure cultures, two-step cultivation was employed to selectively enrich iron (III)-reducing microorganisms in a coastal gold mining river, Jiehe River, with rich iron content in the sediments. First, iron (III) reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III) oxides as electron acceptor and acetate as electron donor. High-throughput Illumina sequencing, terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures actively contained the bacteria belong to Geobacteraceae and Bacilli, exclusively dominated by the archaea belong to Methanosarcinaceae. Second, the enrichment cultures including methanogens and Geobacteraceae were transferred with ethanol as alternative electron donor. Remarkably, aggregates were successively formed in the enrichments after three transfers. The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Furthermore, the aggregates, as close physical contact, formed in the enrichment culture, indicate that DIET could be a possible option for interspecies electron transfer in the aggregates.
    Full-text · Article · Sep 2015 · Frontiers in Microbiology
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