scholarly journals Identification of Acetate-Assimilating Microorganisms under Methanogenic Conditions in Anoxic Rice Field Soil by Comparative Stable Isotope Probing of RNA

2006 ◽  
Vol 73 (1) ◽  
pp. 101-109 ◽  
Author(s):  
Tomoyuki Hori ◽  
Matthias Noll ◽  
Yasuo Igarashi ◽  
Michael W. Friedrich ◽  
Ralf Conrad
Keyword(s):  
Stable Isotope ◽  
Rice Field ◽  
Ferric Iron ◽  
Stable Isotope Probing ◽  
Polymorphism Analysis ◽  
Field Soil ◽  
Bacterial Populations ◽  
Density Fractions ◽  
Reverse Transcription Pcr ◽  
Rice Field Soil

ABSTRACT Acetate is the most abundant intermediate of organic matter degradation in anoxic rice field soil and is converted to CH4 and/or CO2. Aceticlastic methanogens are the primary microorganisms dissimilating acetate in the absence of sulfate and reducible ferric iron. In contrast, very little is known about bacteria capable of assimilating acetate under methanogenic conditions. Here, we identified active acetate-assimilating microorganisms by using a combined approach of frequent label application at a low concentration and comparative RNA-stable isotope probing with 13C-labeled and unlabeled acetate. Rice field soil was incubated anaerobically at 25°C for 12 days, during which 13C-labeled acetate was added at a concentration of 500 μM every 3 days. 13C-labeled CH4 and CO2 were produced from the beginning of the incubation and accounted for about 60% of the supplied acetate 13C. RNA was extracted from the cells in each sample taken and separated by isopycnic centrifugation according to molecular weight. Bacterial and archaeal populations in each density fraction were screened by reverse transcription-PCR-mediated terminal restriction fragment polymorphism analysis. No differences in the bacterial populations were observed throughout the density fractions of the unlabeled treatment. However, in the heavy fractions of the 13C treatment, terminal restriction fragments (T-RFs) of 161 bp and 129 bp in length predominated. These T-RFs were identified by cloning and sequencing of 16S rRNA as from a Geobacter sp. and an Anaeromyxobacter sp., respectively. Apparently these bacteria, which are known as dissimilatory iron reducers, were able to assimilate acetate under methanogenic conditions, i.e., when CO2 was the predominant electron acceptor. We hypothesize that ferric iron minerals with low bioavailability might have served as electron acceptors for Geobacter spp. and Anaeromyxobacter spp. under these conditions.

scholarly journals Incorporation of plant residue-derived carbon into the microeukaryotic community in a rice field soil revealed by DNA stable-isotope probing

2011 ◽  
Vol 79 (2) ◽  
pp. 371-379 ◽  
Author(s):  
Jun Murase ◽  
Manami Shibata ◽  
Chol Gyu Lee ◽  
Takeshi Watanabe ◽  
Susumu Asakawa ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Rice Field ◽  
Stable Isotope Probing ◽  
Plant Residue ◽  
Field Soil ◽  
Rice Field Soil

scholarly journals Syntrophic Oxidation of Propionate in Rice Field Soil at 15 and 30°C under Methanogenic Conditions

2012 ◽  
Vol 78 (14) ◽  
pp. 4923-4932 ◽  
Author(s):  
Yanlu Gan ◽  
Qiongfen Qiu ◽  
Pengfei Liu ◽  
Junpeng Rui ◽  
Yahai Lu
Keyword(s):  
Organic Matter ◽  
Rice Field ◽  
Stable Isotope Probing ◽  
Field Soil ◽  
Content Type ◽  
Rice Field Soil ◽  
Decomposition Of Organic Matter ◽  
Syntrophic Oxidation ◽  
Propionate Oxidation ◽  
Syntrophic Interaction

ABSTRACTPropionate is one of the major intermediary products in the anaerobic decomposition of organic matter in wetlands and paddy fields. Under methanogenic conditions, propionate is decomposed through syntrophic interaction between proton-reducing and propionate-oxidizing bacteria and H2-consuming methanogens. Temperature is an important environmental regulator; yet its effect on syntrophic propionate oxidation has been poorly understood. In the present study, we investigated the syntrophic oxidation of propionate in a rice field soil at 15°C and 30°C. [U-13C]propionate (99 atom%) was applied to anoxic soil slurries, and the bacteria and archaea assimilating13C were traced by DNA-based stable isotope probing.Syntrophobacterspp.,Pelotomaculumspp., andSmithellaspp. were found significantly incorporating13C into their nucleic acids after [13C]propionate incubation at 30°C. The activity ofSmithellaspp. increased in the later stage, and concurrently that ofSyntrophomonasspp. increased. AceticlasticMethanosaetaceaeand hydrogenotrophicMethanomicrobialesandMethanocellalesacted as methanogenic partners at 30°C. Syntrophic oxidation of propionate also occurred actively at 15°C.Syntrophobacterspp. were significantly labeled with13C, whereasPelotomaculumspp. were less active at this temperature. In addition,Methanomicrobiales,Methanocellales, andMethanosarcinaceaedominated the methanogenic community, whileMethanosaetaceaedecreased. Collectively, temperature markedly influenced the activity and community structure of syntrophic guilds degrading propionate in the rice field soil. Interestingly,Geobacterspp. and some other anaerobic organisms likeRhodocyclaceae,Acidobacteria,Actinobacteria, andThermomicrobiaprobably also assimilated propionate-derived13C. The mechanisms for the involvement of these organisms remain unclear.

scholarly journals Effects of Amendment with Ferrihydrite and Gypsum on the Structure and Activity of Methanogenic Populations in Rice Field Soil

2002 ◽  
Vol 68 (5) ◽  
pp. 2484-2494 ◽  
Author(s):  
Tillmann Lueders ◽  
Michael W. Friedrich
Keyword(s):  
Rice Field ◽  
Small Subunit ◽  
Strong Increase ◽  
Polymorphism Analysis ◽  
Ssu Rrna ◽  
The Novel ◽  
Field Soil ◽  
Sulfate Reducing ◽  
Rice Field Soil ◽  
Reducing Bacteria

ABSTRACT Methane emission from paddy fields may be reduced by the addition of electron acceptors to stimulate microbial populations competitive to methanogens. We have studied the effects of ferrihydrite and gypsum (CaSO4 · 2H2O) amendment on methanogenesis and population dynamics of methanogens after flooding of Italian rice field soil slurries. Changes in methanogen community structure were followed by archaeal small subunit (SSU) ribosomal DNA (rDNA)- and rRNA-based terminal restriction fragment length polymorphism analysis and by quantitative SSU rRNA hybridization probing. Under ferrihydrite amendment, acetate was consumed efficiently (<60 μM) and a rapid but incomplete inhibition of methanogenesis occurred after 3 days. In contrast to unamended controls, the dynamics of Methanosarcina populations were largely suppressed as indicated by rDNA and rRNA analysis. However, the low acetate availability was still sufficient for activation of Methanosaeta spp., as indicated by a strong increase of SSU rRNA but not of relative rDNA frequencies. Unexpectedly, rRNA amounts of the novel rice cluster I (RC-I) methanogens increased significantly, while methanogenesis was low, which may be indicative of transient energy conservation coupled to Fe(III) reduction by these methanogens. Under gypsum addition, hydrogen was rapidly consumed to low levels (∼0.4 Pa), indicating the presence of a competitive population of hydrogenotrophic sulfate-reducing bacteria (SRB). This was paralleled by a suppressed activity of the hydrogenotrophic RC-I methanogens as indicated by the lowest SSU rRNA quantities detected in all experiments. Full inhibition of methanogenesis only became apparent when acetate was depleted to nonpermissive thresholds (<5 μM) after 10 days. Apparently, a competitive, acetotrophic population of SRB was not present initially, and hence, acetotrophic methanosarcinal populations were less suppressed than under ferrihydrite amendment. In conclusion, although methane production was inhibited effectively under both mitigation regimens, different methanogenic populations were either suppressed or stimulated, which demonstrates that functionally similar disturbances of an ecosystem may result in distinct responses of the populations involved.

scholarly journals Responses of MethanogenmcrAGenes and Their Transcripts to an Alternate Dry/Wet Cycle of Paddy Field Soil

2011 ◽  
Vol 78 (2) ◽  
pp. 445-454 ◽  
Author(s):  
Ke Ma ◽  
Ralf Conrad ◽  
Yahai Lu
Keyword(s):  
Methane Production ◽  
Paddy Field ◽  
Ferric Iron ◽  
Pcr Analysis ◽  
Polymorphism Analysis ◽  
Field Soil ◽  
Soil Redox ◽  
Rice Field Soil ◽  
Paddy Field Soil ◽  
Intermittent Drainage

ABSTRACTIntermittent 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 methanogenmcrAgenes (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 bothmcrAgene copies andmcrAtranscripts significantly decreased after dry/wet alternation compared to continuous flooding. Correlation and regression analyses showed that the abundance ofmcrAgenes 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 ofmcrAgenes was reduced to a greater extent than the abundance ofmcrAgenes, resulting in very lowmcrAtranscript/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 ofmcrAtranscripts than ofmcrAgenes in rice field soil.

scholarly journals Succession of Bacterial Populations during Plant Residue Decomposition in Rice Field Soil

2009 ◽  
Vol 75 (14) ◽  
pp. 4879-4886 ◽  
Author(s):  
Junpeng Rui ◽  
Jingjing Peng ◽  
Yahai Lu
Keyword(s):  
Rice Field ◽  
Short Chain Fatty Acids ◽  
Decomposition Temperature ◽  
Plant Residue ◽  
Plant Residues ◽  
Field Soil ◽  
Bacterial Populations ◽  
Rice Field Soil ◽  
Residue Decomposition ◽  
Decomposition Processes

ABSTRACT The incorporation of rice residues into paddy fields strongly enhances methane production and emissions. Although the decomposition processes of plant residues in rice field soil has been documented, the structure and dynamics of the microbial communities involved are poorly understood. The purpose of the present study was to determine the dynamics of short-chain fatty acids and the structure of bacterial communities during residue decomposition in a rice field soil. The soil was anaerobically incubated with the incorporation of rice root or straw residues for 90 days at three temperatures (15, 30, and 45°C). The dynamics of fatty acid intermediates showed an initial cumulative phase followed by a rapid consumption phase and a low-concentration quasi-steady state. Correspondingly, the bacterial populations displayed distinct successions during residue decomposition. Temperature showed a strong effect on the dynamics of bacterial populations. Members of Clostridium (clusters I and III) were most dominant in the incubations, particularly in the early successions. Bacteroidetes and Chlorobi were abundant in the later successions at 15 and 30°C, while Acidobacteria were selected at 45°C. We suggest that the early successional groups are responsible for the decomposition of the easily degradable fraction of residues, while the late successional groups become more important in decomposing the less-degradable or resistant fraction of plant residues. The bacterial succession probably is related to resource availability during residue decomposition. The fast-growing organisms are favored at the beginning, while the slow-growing bacteria are better adapted in the later stages, when substrate availability is limiting.

scholarly journals Temporal shifts of nitrite reducing communities in a rice field soil in Ibague (Colombia)

2016 ◽  
Vol 34 (1) ◽  
pp. 82-91 ◽  
Author(s):  
Maribeb Castro-González ◽  
Amanda Lima
Keyword(s):  
Community Composition ◽  
Rice Field ◽  
Agricultural Soils ◽  
Polymorphism Analysis ◽  
Field Soil ◽  
Operational Taxonomic Units ◽  
Rice Field Soil ◽  
Uncultivated Soil ◽  
Abundance And Diversity ◽  
Key Steps

Denitrification and nitrification are microbial processes that regulate the cycle of nitrogen and nitrous oxide, which is considered an important greenhouse gas. Rice field soils have been known to have strong denitrifying activities; however, the microorganism structure that is responsible for denitrification and the temporal variation of these communities in the agricultural soils of Ibague (Colombia) is not well known. In this study, the denitrifying community composition was compared between a rice field soil and an uncultivated soil at three different times during the year using a terminal restriction fragment length polymorphism analysis of the nirS functional gene, which codes the enzyme that reduces nitrite, one of the key steps in the denitrification process. The results showed changes in the richness, relative abundance and diversity of the operational taxonomic units between the soils and sampling times. The canonical correspondence analysis indicated that the moisture and the pH were the environmental factors that explained the observed changes in the nirS-type denitrifiers' community composition in the studied soils.

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