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Detecting Active Methanogenic Populations On Rice Roots Using Stable Isotope Probing.

Y. Lu, T. Lueders, M. Friedrich, R. Conrad
Published 2005 · Biology, Medicine
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Methane is formed on rice roots mainly by CO2 reduction. The present study aimed to identify the active methanogenic populations responsible for this process. Soil-free rice roots were incubated anaerobically under an atmosphere of H2/(13CO2) or N2/(13CO2) with phosphate or carbonate (marble) as buffer medium. Nucleic acids were extracted and fractionated by caesium trifluoroacetate equilibrium density gradient centrifugation after 16-day incubation. Community analyses were performed for gradient fractions using terminal restriction fragment polymorphism analysis (T-RFLP) and sequencing of the 16S rRNA genes. In addition, rRNA was extracted and analysed at different time points to trace the community change during the 16-day incubation. The Methanosarcinaceae and the yet-uncultured archaeal lineage Rice Cluster-I (RC-I) were predominant in the root incubations when carbonate buffer and N2 headspace were used. The analysis of [13C]DNA showed that the relative 16S rRNA gene abundance of RC-I increased whereas that of the Methanosarcinaceae decreased with increasing DNA buoyant density, indicating that members of RC-I were more active than the Methanosarcinaceae. However, an unexpected finding was that RC-I was suppressed in the presence of high H2 concentrations (80%, v/v), which during the early incubation period caused a lower CH4 production compared with that with N2 in the headspace. Eventually, however, CH4 production increased, probably because of the activity of Methanosarcinaceae, which became prevalent. Phosphate buffer appeared to inhibit the activity of the Methanosarcinaceae, resulting in lower CH4 production as compared with carbonate buffer. Under these conditions, Methanobacteriaceae were the prevalent methanogens. Our study suggests that the active methanogenic populations on rice roots change in correspondence to the presence of H2 (80%, v/v) and the type of buffer used in the system.



This paper is referenced by
10.1038/srep27065
Carbon isotope fractionation reveals distinct process of CH4 emission from different compartments of paddy ecosystem
Guangbin Zhang (2016)
10.1128/AEM.01259-14
Response of a Rice Paddy Soil Methanogen to Syntrophic Growth as Revealed by Transcriptional Analyses
P. Liu (2014)
10.3389/fmicb.2017.00932
Methanogenic Community Was Stable in Two Contrasting Freshwater Marshes Exposed to Elevated Atmospheric CO2
Yongxin Lin (2017)
10.1111/gcb.14750
Long-term nitrogen addition modifies microbial composition and functions for slow carbon cycling and increased sequestration in tropical forest soil.
Jing Tian (2019)
10.1371/journal.pone.0073982
Methanogenic Pathway and Fraction of CH4 Oxidized in Paddy Fields: Seasonal Variation and Effect of Water Management in Winter Fallow Season
Guangbin Zhang (2013)
10.1128/AEM.00969-14
Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants
Zhihua Bao (2014)
10.1016/J.GEODERMA.2010.03.009
Biogeochemistry of paddy soils
I. Kögel-Knabner (2010)
10.1128/AEM.00688-12
Syntrophic Oxidation of Propionate in Rice Field Soil at 15 and 30°C under Methanogenic Conditions
Y. Gan (2012)
10.1111/1462-2920.12576
Direct interspecies electron transfer accelerates syntrophic oxidation of butyrate in paddy soil enrichments.
H. Li (2015)
10.3389/fmicb.2018.01551
Concerted Metabolic Shifts Give New Insights Into the Syntrophic Mechanism Between Propionate-Fermenting Pelotomaculum thermopropionicum and Hydrogenotrophic Methanocella conradii
P. Liu (2018)
10.1128/9781555816896.CH10
Trophic Interactions in Microbial Communities and Food Webs Traced by Stable Isotope Probing of Nucleic Acids
Michael W Friedrich (2011)
10.1007/s00253-017-8349-7
The response of archaeal species to seasonal variables in a subtropical aerated soil: insight into the low abundant methanogens
Wei Xie (2017)
10.1007/s00248-007-9287-1
Endophytic Bacterial Diversity in Rice (Oryza sativa L.) Roots Estimated by 16S rDNA Sequence Analysis
L. Sun (2007)
10.1128/AEM.00190-11
Syntrophomonadaceae-Affiliated Species as Active Butyrate-Utilizing Syntrophs in Paddy Field Soil†
P. Liu (2011)
10.1128/JB.00207-12
Complete genome sequence of a thermophilic methanogen, Methanocella conradii HZ254, isolated from Chinese rice field soil.
Zhe Lü (2012)
10.1007/s00253-014-5705-8
Applications and impacts of stable isotope probing for analysis of microbial interactions
Wolf-Rainer Abraham (2014)
10.1038/ismej.2008.66
Seasonality of rDNA- and rRNA-derived archaeal communities and methanogenic potential in a boreal mire
H. Juottonen (2008)
10.1016/j.resmic.2011.06.004
Production and consumption of methane in freshwater lake ecosystems.
Guillaume Borrel (2011)
10.1007/8623_2015_138
Primers: Functional Genes and 16S rRNA Genes for Methanogens
Takashi Narihiro (2015)
10.1101/2020.03.08.982587
Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon
Marie E. Kroeger (2020)
10.1111/1574-6941.12261
¹³C pulse-chase labeling comparative assessment of the active methanogenic archaeal community composition in the transgenic and nontransgenic parental rice rhizospheres.
Weijing Zhu (2014)
10.1128/AEM.02835-08
Cultivation of Methanogens under Low-Hydrogen Conditions by Using the Coculture Method
Sanae Sakai (2009)
10.1016/j.anaerobe.2014.11.009
Methanogenic archaea diversity in hyporheic sediments of a small lowland stream.
Lenka Brablcová (2015)
10.1196/annals.1419.019
Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea.
Y. Liu (2008)
fractionation in a straw incorporated rice field
G. Zhang (2012)
10.1371/journal.pone.0066784
DNA-SIP Reveals That Syntrophaceae Play an Important Role in Methanogenic Hexadecane Degradation
L. Cheng (2013)
10.1080/01490451.2012.737091
Intra-habitat Differences in the Composition of the Methanogenic Archaeal Community between the Microcystis-Dominated and the Macrophyte-Dominated Bays in Taihu Lake
Xianfang Fan (2014)
10.4018/978-1-5225-2325-3.CH005
Microbiological Carbon Sequestration: A Novel Solution for Atmospheric Carbon – Carbon Sequestration through Biological Approach
Mohammad Oves (2017)
10.1007/s12237-012-9496-9
Anaerobic Metabolism in Tidal Freshwater Wetlands: II. Effects of Plant Removal on Archaeal Microbial Communities
David Todd Emerson (2012)
Decomposition in an Anoxic Rice Field Soil Community during Plant Residue Dynamics of the Methanogenic Archaeal
Jingjing Peng (2014)
10.1007/978-3-319-53114-4_5-1
Diversity and Taxonomy of Methanogens
Zhe Lyu (2018)
10.1016/j.wasman.2018.09.042
Effect of inoculum and substrate/inoculum ratio on the performance and methanogenic archaeal community structure in solid state anaerobic co-digestion of tomato residues with dairy manure and corn stover.
Y. Y. Li (2018)
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