scholarly journals Effect of Temperature on Carbon and Electron Flow and on the Archaeal Community in Methanogenic Rice Field Soil

2000 ◽  
Vol 66 (11) ◽  
pp. 4790-4797 ◽  
Author(s):  
Axel Fey ◽  
Ralf Conrad
Keyword(s):  
Steady State ◽  
Rice Field ◽  
Electron Flow ◽  
Rflp Analysis ◽  
Archaeal Community ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Field Soil ◽  
Rice Field Soil ◽  
Different Temperatures

ABSTRACT Temperature is an important factor controlling CH4production in anoxic rice soils. Soil slurries, prepared from Italian rice field soil, were incubated anaerobically in the dark at six temperatures of between 10 to 37°C or in a temperature gradient block covering the same temperature range at intervals of 1°C. Methane production reached quasi-steady state after 60 to 90 days. Steady-state CH4 production rates increased with temperature, with an apparent activation energy of 61 kJ mol−1. Steady-state partial pressures of the methanogenic precursor H2 also increased with increasing temperature from <0.5 to 3.5 Pa, so that the Gibbs free energy change of H2 plus CO2-dependent methanogenesis was kept at −20 to −25 kJ mol of CH4 −1 over the whole temperature range. Steady-state concentrations of the methanogenic precursor acetate, on the other hand, increased with decreasing temperature from <5 to 50 μM. Simultaneously, the relative contribution of H2 as methanogenic precursor decreased, as determined by the conversion of radioactive bicarbonate to 14CH4, so that the carbon and electron flow to CH4 was increasingly dominated by acetate, indicating that psychrotolerant homoacetogenesis was important. The relative composition of the archaeal community was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes (16S rDNA). T-RFLP analysis differentiated the archaeal Methanobacteriaceae,Methanomicrobiaceae, Methanosaetaceae,Methanosarcinaceae, and Rice clusters I, III, IV, V, and VI, which were all present in the rice field soil incubated at different temperatures. The 16S rRNA genes of Rice cluster I andMethanosaetaceae were the most frequent methanogenic groups. The relative abundance of Rice cluster I decreased with temperature. The substrates used by this microbial cluster, and thus its function in the microbial community, are unknown. The relative abundance of acetoclastic methanogens, on the other hand, was consistent with their physiology and the acetate concentrations observed at the different temperatures, i.e., the high-acetate-requiring Methanosarcinaceae decreased and the more modest Methanosaetaceae increased with increasing temperature. Our results demonstrate that temperature not only affected the activity but also changed the structure and the function (carbon and electron flow) of a complex methanogenic system.

scholarly journals Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil

2008 ◽  
Vol 74 (9) ◽  
pp. 2894-2901 ◽  
Author(s):  
Jingjing Peng ◽  
Zhe Lü ◽  
Junpeng Rui ◽  
Yahai Lu
Keyword(s):  
Rice Field ◽  
Dynamic Structure ◽  
Archaeal Community ◽  
Plant Residue ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Plant Residues ◽  
Field Soil ◽  
Rice Field Soil ◽  
Residue Decomposition

ABSTRACT Incorporation of plant residues strongly enhances the methane production and emission from flooded rice fields. Temperature and residue type are important factors that regulate residue decomposition and CH4 production. However, the response of the methanogenic archaeal community to these factors in rice field soil is not well understood. In the present experiment, the structure of the archaeal community was determined during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures (15°C, 30°C, and 45°C). More CH4 was produced in the straw treatment than root treatment. Increasing the temperature from 15°C to 45°C enhanced CH4 production. Terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of 16S rRNA genes showed that Methanosarcinaceae developed early in the incubations, whereas Methanosaetaceae became more abundant in the later stages. Methanosarcinaceae and Methanosaetaceae seemed to be better adapted at 15°C and 30°C, respectively, while the thermophilic Methanobacteriales and rice cluster I methanogens were significantly enhanced at 45°C. Straw residues promoted the growth of Methanosarcinaceae, whereas the root residues favored Methanosaetaceae. In conclusion, our study revealed a highly dynamic structure of the methanogenic archaeal community during plant residue decomposition. The in situ concentration of acetate (and possibly of H2) seems to be the key factor that regulates the shift of methanogenic community.

scholarly journals Effect of Substrate Concentration on Carbon Isotope Fractionation during Acetoclastic Methanogenesis by Methanosarcina barkeri and M. acetivorans and in Rice Field Soil

2009 ◽  
Vol 75 (9) ◽  
pp. 2605-2612 ◽  
Author(s):  
Dennis Goevert ◽  
Ralf Conrad
Keyword(s):  
Substrate Concentration ◽  
Isotope Fractionation ◽  
Rice Field ◽  
Methanosarcina Barkeri ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Field Soil ◽  
Rice Field Soil ◽  
Pure Cultures ◽  
Acetoclastic Methanogenesis

ABSTRACT Methanosarcina is the only acetate-consuming genus of methanogenic archaea other than Methanosaeta and thus is important in methanogenic environments for the formation of the greenhouse gases methane and carbon dioxide. However, little is known about isotopic discrimination during acetoclastic CH4 production. Therefore, we studied two species of the Methanosarcinaceae family, Methanosarcina barkeri and Methanosarcina acetivorans, and a methanogenic rice field soil amended with acetate. The values of the isotope enrichment factor (ε) associated with consumption of total acetate (εac), consumption of acetate-methyl (εac-methyl) and production of CH4 (εCH4) were an εac of −30.5‰, an εac-methyl of −25.6‰, and an εCH4 of −27.4‰ for M. barkeri and an εac of −35.3‰, an εac-methyl of −24.8‰, and an εCH4 of −23.8‰ for M. acetivorans. Terminal restriction fragment length polymorphism of archaeal 16S rRNA genes indicated that acetoclastic methanogenic populations in rice field soil were dominated by Methanosarcina spp. Isotope fractionation determined during acetoclastic methanogenesis in rice field soil resulted in an εac of −18.7‰, an εac-methyl of −16.9‰, and an εCH4 of −20.8‰. However, in rice field soil as well as in the pure cultures, values of εac and εac-methyl decreased as acetate concentrations decreased, eventually approaching zero. Thus, isotope fractionation of acetate carbon was apparently affected by substrate concentration. The ε values determined in pure cultures were consistent with those in rice field soil if the concentration of acetate was taken into account.

scholarly journals Effect of Temperature on Structure and Function of the Methanogenic Archaeal Community in an Anoxic Rice Field Soil

1999 ◽  
Vol 65 (6) ◽  
pp. 2341-2349 ◽  
Author(s):  
Kuk-Jeong Chin ◽  
Thomas Lukow ◽  
Ralf Conrad
Keyword(s):  
Sequence Analysis ◽  
Rice Field ◽  
Incubation Temperature ◽  
Electron Flow ◽  
Temperature Shift ◽  
Archaeal Community ◽  
Rice Soil ◽  
Field Soil ◽  
Soil Slurry ◽  
Rice Field Soil

ABSTRACT Soil temperatures in Italian rice fields typically range between about 15 and 30°C. A change in the incubation temperature of anoxic methanogenic soil slurry from 30°C to 15°C typically resulted in a decrease in the CH4 production rate, a decrease in the steady-state H2 partial pressure, and a transient accumulation of acetate. Previous experiments have shown that these changes were due to an alteration of the carbon and electron flow in the methanogenic degradation pathway of organic matter caused by the temperature shift (K. J. Chin and R. Conrad, FEMS Microbiol. Ecol. 18:85–102, 1995). To investigate how temperature affects the structure of the methanogenic archaeal community, total DNA was extracted from soil slurries incubated at 30 and 15°C. The archaeal small-subunit (SSU) rRNA-encoding genes (rDNA) of these environmental DNA samples were amplified by PCR with an archaeal-specific primer system and used for the generation of clone libraries. Representative rDNA clones (n = 90) were characterized by terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis. T-RFLP analysis produced for the clones terminally labeled fragments with a characteristic length of mostly 185, 284, or 392 bp. Sequence analysis allowed determination of the phylogenetic affiliation of the individual clones with their characteristic T-RFLP fragment lengths and showed that the archaeal community of the anoxic rice soil slurry was dominated by members of the families Methanosarcinaceae(185 bp) and Methanosaetaceae (284 bp), the kingdomCrenarchaeota (185 or 284 bp), and a novel, deeply branching lineage of the (probably methanogenic) kingdomEuryarchaeota (392 bp) that has recently been detected on rice roots (R. Großkopf, S. Stubner, and W. Liesack, Appl. Environ. Microbiol. 64:4983–4989, 1998). The structure of the archaeal community changed when the temperature was shifted from 30°C to 15°C. Before the temperature shift, the clones (n = 30) retrieved from the community were dominated byCrenarchaeota (70%), “novel Euryarchaeota” (23%), and Methanosarcinacaeae (7%). Further incubation at 30°C (n = 30 clones) resulted in a relative increase in members of the Methanosarcinaceae (77%), whereas further incubation at 15°C (n = 30 clones) resulted in a much more diverse community consisting of 33%Methanosarcinaceae, 23% Crenarchaeota, 20%Methanosaetaceae, and 17% novel Euryarchaeota. The appearance of Methanosaetaceae at 15°C was conspicuous. These results demonstrate that the structure of the archaeal community in anoxic rice field soil changed with time and incubation temperature.

Composition of the archaeal community involved in methane production during the decomposition of Microcystis blooms in the laboratory

2012 ◽  
Vol 58 (10) ◽  
pp. 1153-1158 ◽  
Author(s):  
Peng Xing ◽  
Huabing Li ◽  
Qing Liu ◽  
Jiuwen Zheng
Keyword(s):  
Lake Taihu ◽  
Archaeal Community ◽  
Oxygen Depletion ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Methanogenic Community ◽  
Controlled Systems ◽  
Microcystis Blooms ◽  
Different Temperatures

We investigated the microbial processes involved in methane (CH4) production from Microcystis bloom scums at different temperatures. A Microcystis slurry was collected from Lake Taihu and incubated in airtight bottles at 15, 25, and 35 °C. The production of CH4 was monitored, and the emission rate was calculated. The dynamics of the methanogenic community were analyzed by terminal restriction fragment length polymorphism analysis of archaeal 16S rRNA genes. Phylogenetic information for the methanogens was obtained by cloning and sequencing selected samples. Significant CH4 emission from the Microcystis scums was delayed by approximately 12 days by the natural oxygen depletion process, and CH4 production was enhanced at higher temperatures. Phylogenetic analysis indicated that the archaeal community was composed of Methanomicrobiales, Methanobacteriaceae, and a novel cluster of Archaea. An apparent succession of the methanogenic community was demonstrated, with a predominance of Methanobacteriaceae at higher temperatures. Higher temperatures enhanced the methanogenic transformation of the Microcystis biomass and the phylogenetic dominance of hydrogenotrophic methanogens, suggesting that H2 and CO2 might be the primary substrates for CH4 production during Microcystis decomposition without the participation of lake sediment. This work provides insight into the microbial components involved in Microcystis biomass fermentation in controlled systems.

scholarly journals Archaeal Population Dynamics during Sequential Reduction Processes in Rice Field Soil

2000 ◽  
Vol 66 (7) ◽  
pp. 2732-2742 ◽  
Author(s):  
Tillmann Lueders ◽  
Michael Friedrich
Keyword(s):  
Population Dynamics ◽  
Gene Frequency ◽  
Rice Field ◽  
Rflp Analysis ◽  
Ssu Rrna ◽  
Field Soil ◽  
Reduction Processes ◽  
Rice Field Soil ◽  
Restriction Sites ◽  
Over Time

ABSTRACT The population dynamics of Archaea after flooding of an Italian rice field soil were studied over 17 days. Anoxically incubated rice field soil slurries exhibited a typical sequence of reduction processes characterized by reduction of nitrate, Fe3+, and sulfate prior to the initiation of methane production. Archaeal population dynamics were followed using a dual approach involving molecular sequence retrieval and fingerprinting of small-subunit (SSU) rRNA genes. We retrieved archaeal sequences from four clone libraries (30 each) constructed for different time points (days 0, 1, 8, and 17) after flooding of the soil. The clones could be assigned to known methanogens (i.e., Methanosarcinaceae,Methanosaetaceae, Methanomicrobiaceae, andMethanobacteriaceae) and to novel euryarchaeotal (rice clusters I, II, and III) and crenarchaeotal (rice clusters IV and VI) lineages previously detected in anoxic rice field soil and on rice roots (R. Grosskopf, S. Stubner, and W. Liesack, Appl. Environ. Microbiol. 64:4983–4989, 1998). During the initiation of methanogenesis (days 0 to 17), we detected significant changes in the frequency of individual clones, especially of those affiliated with theMethanosaetaceae and Methanobacteriaceae. However, these findings could not be confirmed by terminal restriction fragment length polymorphism (T-RFLP) analysis of SSU rDNA amplicons. Most likely, the fluctuations in sequence composition of clone libraries resulted from cloning bias. Clonal SSU rRNA gene sequences were used to define operational taxonomic units (OTUs) for T-RFLP analysis, which were distinguished by group-specific TaqI restriction sites. Sequence analysis showed a high degree of conservation of TaqI restriction sites within the different archaeal lineages present in Italian rice field soil. Direct T-RFLP analysis of archaeal populations in rice field soil slurries revealed the presence of all archaeal lineages detected by cloning with a predominance of terminal restriction fragments characteristic of rice cluster I (389 bp), Methanosaetaceae (280 bp), andMethanosarcinaceae/rice cluster VI (182 bp). In general, the relative gene frequency of most detected OTUs remained rather constant over time during the first 17 days after flooding of the soil. Most minor OTUs (e.g., Methanomicrobiaceae and rice cluster III) and Methanosaetaceae did not change in relative frequency. Rice cluster I (37 to 30%) and to a lesser extent rice cluster IV as well as Methanobacteriaceae decreased over time. Only the relative abundance of Methanosarcinaceae(182 bp) increased, roughly doubling from 15 to 29% of total archaeal gene frequency within the first 11 days, which was positively correlated to the dynamics of acetate and formate concentrations. Our results indicate that a functionally dynamic ecosystem, a rice field soil after flooding, was linked to a relatively stable archaeal community structure.

Sign in / Sign up

Export Citation Format

Share Document