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Lu Y, Liu Q, Fu L, Hu Y, Zhong L, Zhang S, Liu Q, Xie Q. The effect of modified biochar on methane emission and succession of methanogenic archaeal community in paddy soil. CHEMOSPHERE 2022; 304:135288. [PMID: 35691388 DOI: 10.1016/j.chemosphere.2022.135288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Modified biochars have been widely applied in ameliorating environmental problems. However, the effect of modified biochar on suppressing CH4 emission in rice paddy soil is not fully understood. In order to further study CH4 regulation in paddy soil via the modification of biochar and explore its influence on key archaeal communities, two modified biochars were generated with the pre-treatment of nitric acid (NBC) and hydrogen peroxide (OBC), respectively, and a control group was setup with water-washed biochar (WBC). Results showed that NBC significantly suppressed CH4 emission, followed by OBC and WBC, while NBC promoted the CO2 emission. Besides, the addition of biochars inhibited the accumulation of acetate and H2 in rice paddy soil, especially in the NBC treatment. 16S rRNA gene sequencing revealed that biochars amendment increased α-diversity of archaeal community and the modified biochars could mitigate the loss of α-diversity in the early stage of anaerobic incubation. Additionally, NBC amendment largely declined the relative abundance of methanogens (especially Methanosarcina) in archaeal community, while OBC and NBC promoted the relative abundance of Candidatus_Methanoperedens. Via Spearman's correlation coefficient analysis, NBC had positive correlations with Methanosaeta, and OBC showed a negative correlation with Methanocella. Overall, this study provided a practical way to regulate the CH4 emission and associated methanogenic archaea via the amendment of different modified biochars in rice paddy soil.
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Affiliation(s)
- Yue Lu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China.
| | - Qian Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Leiling Fu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Yingju Hu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Shoujuan Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Qi Liu
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
| | - Qingqing Xie
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, Hunan, China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, 410082, Hunan, China
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2
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Hao X, Jiao S, Lu Y. Geographical pattern of methanogenesis in paddy and wetland soils across eastern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:281-290. [PMID: 30243161 DOI: 10.1016/j.scitotenv.2018.09.167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/08/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Large variation of CH4 emissions from paddy and wetland ecosystems exists across different geographical locations in China. To obtain mechanistic understanding of this variation, we investigated the dynamics of methanogenesis over the course of glucose degradation in fourteen paddy field soils and five wetland soils collected from different regions of China. The results revealed that the maximal rate (2-3 mM per day) and the total amount (25-30 mM) of CH4 produced were similar across soil samples. The lag phase of methanogenesis, however, differed substantially with the shortest lag phase of 4 days in a paddy soil from north China and the longest of 32 days in a soil from south China, and this difference reflected a general geographical trend among all soils tested. Nitrate was reduced completely within 4 days in all soils. The reduction of Fe(III) and sulfate was completed after 21 days and 29 days, respectively. The depletion time of Fe(III) and sulfate were positively correlated with the lag phase of methanogenesis. Competition for common substrates between methanogens and iron and sulfate reducers, however, does not explain this coincidence because a slow production of CH4 was detected at the very beginning. It appears that the geographical variations in methanogenesis and the reduction of ferric iron and sulfate are related to the variation in soil pH but not to temperature, soil organic C and nutrient conditions in paddy and wetland soils across eastern China.
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Affiliation(s)
- Xin Hao
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Shuo Jiao
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China.
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3
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Fu L, Song T, Zhang W, Zhang J, Lu Y. Stimulatory Effect of Magnetite Nanoparticles on a Highly Enriched Butyrate-Oxidizing Consortium. Front Microbiol 2018; 9:1480. [PMID: 30026737 PMCID: PMC6041394 DOI: 10.3389/fmicb.2018.01480] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 11/13/2022] Open
Abstract
Syntrophic oxidation of butyrate is catabolized by a few bacteria specialists in the presence of methanogens. In the present study, a highly enriched butyrate-oxidizing consortium was obtained from a wetland sediment in Tibetan Plateau. During continuous transfers of the enrichment, the addition of magnetite nanoparticles (nanoFe3O4) consistently enhanced butyrate oxidation and CH4 production. Molecular analysis revealed that all bacterial sequences from the consortium belonged to Syntrophomonas with the closest relative of Syntrophomonas wolfei and 96% of the archaeal sequences were related to Methanobacteria with the remaining sequences to Methanocella. Addition of graphite and carbon nanotubes for a replacement of nanoFe3O4 caused the similar stimulatory effect. Silica coating of nanoFe3O4 surface, however, completely eliminated the stimulatory effect. The control experiment with axenic cultivation of a Syntrophomonas strain and two methanogen strains showed no effect by nanoFe3O4. Together, the results in the present study support that syntrophic oxidation of butyrate is likely facilitated by direct interspecies electron transfer in the presence of conductive nanomaterials.
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Affiliation(s)
- Li Fu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tianze Song
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Wei Zhang
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Jie Zhang
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
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Alpana S, Vishwakarma P, Adhya TK, Inubushi K, Dubey SK. Molecular ecological perspective of methanogenic archaeal community in rice agroecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 596-597:136-146. [PMID: 28431358 DOI: 10.1016/j.scitotenv.2017.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/02/2017] [Accepted: 04/02/2017] [Indexed: 06/07/2023]
Abstract
Methane leads to global warming owing to its warming potential higher than carbon dioxide (CO2). Rice fields represent the major source of methane (CH4) emission as the recent estimates range from 34 to 112 Tg CH4 per year. Biogenic methane is produced by anaerobic methanogenic archaea. Advances in high-throughput sequencing technologies and isolation methodologies enabled investigators to decipher methanogens to be unexpectedly diverse in phylogeny and ecology. Exploring the link between biogeochemical methane cycling and methanogen community dynamics can, therefore, provide a more effective mechanistic understanding of CH4 emission from rice fields. In this review, we summarize the current knowledge on the diversity and activity of methanogens, factors controlling their ecology, possible interactions between rice plants and methanogens, and their potential involvement in the source relationship of greenhouse gas emissions from rice fields.
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Affiliation(s)
- Singh Alpana
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - P Vishwakarma
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - T K Adhya
- School of Biotechnology, KIIT University, Bhubaneshwar 751024, India
| | - K Inubushi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 2718510, Japan
| | - S K Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil. Appl Microbiol Biotechnol 2016; 100:5989-98. [PMID: 26923143 DOI: 10.1007/s00253-016-7377-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 01/31/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
Abstract
Nitrogen fertilization and returning straw to paddy soil are important factors that regulate CH4 production. To evaluate the effect of rice straw and/or nitrate amendment on methanogens, a paddy soil was anaerobically incubated for 40 days. The results indicated that while straw addition increased CH4 production and the abundances of mcrA genes and their transcripts, nitrate amendment showed inhibitory effects on them. The terminal restriction fragment length polymorphism (T-RFLP) analysis based on mcrA gene revealed that straw addition obviously changed methanogenic community structure. Based on mcrA gene level, straw-alone addition stimulated Methanosarcinaceaes at the early stage of incubation (first 11 days), but nitrate showed inhibitory effect. The relative abundance of Methanobacteriaceae was also stimulated by straw addition during the first 11 days. Furthermore, Methanosaetaceae were enriched by nitrate-alone addition after 11 days, while Methanocellaceae were enriched by nitrate addition especially within the first 5 days. The transcriptional methanogenic community indicated more dynamic and complicated responses to straw and/or nitrate addition. Based on mcrA transcript level, nitrate addition alone resulted in the increase of Methanocellaceae and the shift from Methanosarcinaceae to Methanosaetaceae during the first 5 days of incubation. Straw treatments increased the relative abundance of Methanobacteriaceae after 11 days. These results demonstrate that nitrate addition influences methanogens which are transcriptionally and functionally active and can alleviate CH4 production associated with straw amendment in paddy soil incubations, presumably through competition for common substrates between nitrate-utilizing organisms and methanogens.
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Response of a rice paddy soil methanogen to syntrophic growth as revealed by transcriptional analyses. Appl Environ Microbiol 2015; 80:4668-76. [PMID: 24837392 DOI: 10.1128/aem.01259-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of Methanocellales are widespread in paddy field soils and play the key role in methane production. These methanogens feature largely in these organisms’ adaptation to low H2 and syntrophic growth with anaerobic fatty acid oxidizers. The adaptive mechanisms, however, remain unknown. In the present study, we determined the transcripts of 21 genes involved in the key steps of methanogenesis and acetate assimilation of Methanocella conradii HZ254, a strain recently isolated from paddy field soil. M. conradii was grown in monoculture and syntrophically with Pelotomaculum thermopropionicum (a propionate syntroph) or Syntrophothermus lipocalidus (a butyrate syntroph). Comparison of the relative transcript abundances showed that three hydrogenase-encoding genes and all methanogenesis-related genes tested were upregulated in cocultures relative to monoculture. The genes encoding formylmethanofuran dehydrogenase (Fwd), heterodisulfide reductase (Hdr), and the membrane-bound energy-converting hydrogenase (Ech) were the most upregulated among the evaluated genes. The expression of the formate dehydrogenase (Fdh)-encoding gene also was significantly upregulated. In contrast, an acetate assimilation gene was downregulated in cocultures. The genes coding for Fwd, Hdr, and the D subunit of F420-nonreducing hydrogenase (Mvh) form a large predicted transcription unit; therefore, the Mvh/Hdr/Fwd complex, capable of mediating the electron bifurcation and connecting the first and last steps of methanogenesis, was predicted to be formed in M. conradii. We propose that Methanocella methanogens cope with low H2 and syntrophic growth by (i) stabilizing the Mvh/Hdr/Fwd complex and (ii) activating formatedependent methanogenesis.
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Fu L, Song T, Lu Y. Snapshot of methanogen sensitivity to temperature in Zoige wetland from Tibetan plateau. Front Microbiol 2015; 6:131. [PMID: 25745422 PMCID: PMC4333864 DOI: 10.3389/fmicb.2015.00131] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 02/04/2015] [Indexed: 12/02/2022] Open
Abstract
Zoige wetland in Tibetan plateau represents a cold environment at high altitude where significant methane emission has been observed. However, it remains unknown how the production and emission of CH4 from Zoige wetland will respond to a warming climate. Here we investigated the temperature sensitivity of methanogen community in a Zoige wetland soil under the laboratory incubation conditions. One soil sample was collected and the temperature sensitivity of the methanogenic activity, the structure of methanogen community and the methanogenic pathways were determined. We found that the response of methanogenesis to temperature could be separated into two phases, a high sensitivity in the low temperature range and a modest sensitivity under mesophilic conditions, respectively. The aceticlastic methanogens Methanosarcinaceae were the main methanogens at low temperatures, while hydrogenotrophic Methanobacteriales, Methanomicrobiales, and Methanocellales were more abundant at higher temperatures. The total abundance of mcrA genes increased with temperature indicating that the growth of methanogens was stimulated. The growth of hydrogenotrophic methanogens, however, was faster than aceticlastic ones resulting in the shift of methanogen community. Determination of carbon isotopic signatures indicated that methanogenic pathway was also shifted from mainly aceticlastic methanogenesis to a mixture of hydrogenotrophic and aceticlastic methanogenesis with the increase of temperature. Collectively, the shift of temperature responses of methanogenesis was in accordance with the changes in methanogen composition and methanogenic pathway in this wetland sample. It appears that the aceticlastic methanogenesis dominating at low temperatures is more sensitive than the hydrogenotrophic one at higher temperatures.
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Affiliation(s)
- Li Fu
- College of Resources and Environmental Sciences, China Agricultural University Beijing, China
| | - Tianze Song
- School of Life Science, Fudan University Shanghai, China ; College of Urban and Environmental Sciences, Peking University Beijing, China
| | - Yahai Lu
- College of Resources and Environmental Sciences, China Agricultural University Beijing, China ; College of Urban and Environmental Sciences, Peking University Beijing, China
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Bao QL, Xiao KQ, Chen Z, Yao HY, Zhu YG. Methane production and methanogenic archaeal communities in two types of paddy soil amended with different amounts of rice straw. FEMS Microbiol Ecol 2014; 88:372-85. [DOI: 10.1111/1574-6941.12305] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/11/2014] [Accepted: 02/12/2014] [Indexed: 11/25/2022] Open
Affiliation(s)
- Qiong-Li Bao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Ke-Qing Xiao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Zheng Chen
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Huai-Ying Yao
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
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9
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Zhang C, Yuan Q, Lu Y. Inhibitory effects of ammonia on methanogenmcrAtranscripts in anaerobic digester sludge. FEMS Microbiol Ecol 2013; 87:368-77. [DOI: 10.1111/1574-6941.12229] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/10/2013] [Accepted: 09/18/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Chen Zhang
- College of Resources and Environmental Sciences; China Agricultural University; Beijing China
| | - Quan Yuan
- College of Resources and Environmental Sciences; China Agricultural University; Beijing China
- Max-Planck Institute for Terrestrial Microbiology; Marburg Germany
| | - Yahai Lu
- College of Resources and Environmental Sciences; China Agricultural University; Beijing China
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Xu Y, Ma K, Huang S, Liu L, Lu Y. Diel cycle of methanogen mcrA transcripts in rice rhizosphere. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:655-663. [PMID: 23760937 DOI: 10.1111/j.1758-2229.2012.00392.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/01/2012] [Indexed: 06/02/2023]
Abstract
Methanogens are known to inhabit not only the anaerobic bulk soil but also the rhizosphere of rice plants. The release of root exudates, a major carbon source for CH4 production in the rhizosphere, is closely coupled to plant photosynthesis. In the present study we hypothesized that the diel cycle of plant photosynthetic activity may shape the structure and function of methanogens in the rhizosphere of rice. We performed a field experiment to determine the diel dynamics of methanogen mcrA and their transcripts in the rhizosphere and bulk soil. The chemistry of NH4 (+) , NO3 (-) , SO4 (2-) and Fe(II) in the rice rhizosphere remained constant over a diel sampling. The mcrA copy number and their transcripts were greater in the rice rhizosphere compared with the bulk soil, indicating the enhanced activity of methanogens in the rhizosphere. The hydrogenotrophic Methanomicrobiales in particular increased in the rhizosphere whereas Methanosarcinaceae were more abundant in the bulk soil. Both the phylogenetic affiliation and copy numbers of methanogen mcrA in the rice rhizosphere did not display diel dynamics. The mcrA transcripts, however, significantly increased in the night compared with the daytime. The diel pattern of physical factors like temperature appeared not to affect the methanogen dynamics. The response of mcrA transcripts is probably due to the plant attributes, which release less O2 from roots in the night and hence stimulate the methanogen gene transcription and activity compared with the daytime.
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Affiliation(s)
- Yuan Xu
- College of Resources and Environmental Sciences, China Agricultural University, 100193, Beijing, China
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Syntrophic oxidation of propionate in rice field soil at 15 and 30°C under methanogenic conditions. Appl Environ Microbiol 2012; 78:4923-32. [PMID: 22582054 DOI: 10.1128/aem.00688-12] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Propionate 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 H(2)-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-(13)C]propionate (99 atom%) was applied to anoxic soil slurries, and the bacteria and archaea assimilating (13)C were traced by DNA-based stable isotope probing. Syntrophobacter spp., Pelotomaculum spp., and Smithella spp. were found significantly incorporating (13)C into their nucleic acids after [(13)C]propionate incubation at 30°C. The activity of Smithella spp. increased in the later stage, and concurrently that of Syntrophomonas spp. increased. Aceticlastic Methanosaetaceae and hydrogenotrophic Methanomicrobiales and Methanocellales acted as methanogenic partners at 30°C. Syntrophic oxidation of propionate also occurred actively at 15°C. Syntrophobacter spp. were significantly labeled with (13)C, whereas Pelotomaculum spp. were less active at this temperature. In addition, Methanomicrobiales, Methanocellales, and Methanosarcinaceae dominated the methanogenic community, while Methanosaetaceae decreased. Collectively, temperature markedly influenced the activity and community structure of syntrophic guilds degrading propionate in the rice field soil. Interestingly, Geobacter spp. and some other anaerobic organisms like Rhodocyclaceae, Acidobacteria, Actinobacteria, and Thermomicrobia probably also assimilated propionate-derived (13)C. The mechanisms for the involvement of these organisms remain unclear.
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Lü Z, Lu Y. Methanocella conradii sp. nov., a thermophilic, obligate hydrogenotrophic methanogen, isolated from Chinese rice field soil. PLoS One 2012; 7:e35279. [PMID: 22530002 PMCID: PMC3328440 DOI: 10.1371/journal.pone.0035279] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/15/2012] [Indexed: 11/18/2022] Open
Abstract
Background Methanocellales contributes significantly to anthropogenic methane emissions that cause global warming, but few pure cultures for Methanocellales are available to permit subsequent laboratory studies (physiology, biochemistry, etc.). Methodology/Principal Findings By combining anaerobic culture and molecular techniques, a novel thermophilic methanogen, strain HZ254T was isolated from a Chinese rice field soil located in Hangzhou, China. The phylogenetic analyses of both the 16S rRNA gene and mcrA gene (encoding the α subunit of methyl-coenzyme M reductase) confirmed its affiliation with Methanocellales, and Methanocella paludicola SANAET was the most closely related species. Cells were non-motile rods, albeit with a flagellum, 1.4–2.8 µm long and by 0.2–0.3 µm in width. They grew at 37–60°C (optimally at 55°C) and salinity of 0–5 g NaCl l−1 (optimally at 0–1 g NaCl l−1). The pH range for growth was 6.4–7.2 (optimum 6.8). Under the optimum growth condition, the doubling time was 6.5–7.8 h, which is the shortest ever observed in Methanocellales. Strain HZ254T utilized H2/CO2 but not formate for growth and methane production. The DNA G+C content of this organism was 52.7 mol%. The sequence identities of 16S rRNA gene and mcrA gene between strain HZ254T and SANAET were 95.0 and 87.5% respectively, and the genome based Average Nucleotide Identity value between them was 74.8%. These two strains differed in phenotypic features with regard to substrate utilization, possession of a flagellum, doubling time (under optimal conditions), NaCl and temperature ranges. Taking account of the phenotypic and phylogenetic characteristics, we propose strain HZ254T as a representative of a novel species, Methanocella conradii sp. nov. The type strain is HZ254T ( = CGMCC 1.5162T = JCM 17849T = DSM 24694T). Conclusions/Significance Strain HZ254T could potentially serve as an excellent laboratory model for studying Methanocellales due to its fast growth and consistent cultivability.
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Affiliation(s)
- Zhe Lü
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Yahai Lu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
- * E-mail:
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Yuan Q, Liu P, Lu Y. Differential responses of nirK- and nirS-carrying bacteria to denitrifying conditions in the anoxic rice field soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:113-122. [PMID: 23757237 DOI: 10.1111/j.1758-2229.2011.00311.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Denitrification occurs actively in rice field soils. In the present study, the responses of nirK and nirS denitrifier communities to nitrate addition in the anoxic rice soil were determined through molecular analyses of nitrite reductase genes nirK and nirS and 16S rRNA genes. Denitrification occurred rapidly when nitrate was added at the beginning of anoxic incubation (experiment I). The structure of nirK-type denitrifiers did not change; but their abundance as determined by quantitative (real-time) PCR increased in nitrate treatments compared with control. Both the structure and abundance of nirS denitrifiers remained unaffected in experiment I. The rate of denitrification was slowed down when nitrate was added 20 days after the onset of anoxic incubation (experiment II). The structure and abundance of nirK-type denitrifier community did not respond to nitrate addition; but the nirS community changed substantially in this experiment. The copy number of nirS genes increased by an order of magnitude in the treatments of 5 mM and 10 mM nitrate compared with control. The terminal restriction fragment length polymorphism (T-RFLP) analysis of nirS genes revealed that the 100 bp T-RF substantially increased in the nitrate treatments. Cloning and sequence analysis indicated that this T-RF had similarity of up to 90% with Herbaspirillum sp. T-RFLP profiles of the bacterial 16S rRNA genes also showed that Herbaspirillum sp. increased after nitrate amendments. Collectively, the nirK-type denitrifiers were probably active at the beginning of anaerobic incubation, while the nirS denitrifiers, especially those related with Herbaspirillum sp. probably were more active when anaerobic condition was fully developed.
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Affiliation(s)
- Quan Yuan
- College of Resources and Environmental Sciences, China Agricultural University, 100193 Beijing, China
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14
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Liu P, Qiu Q, Lu Y. Syntrophomonadaceae-affiliated species as active butyrate-utilizing syntrophs in paddy field soil. Appl Environ Microbiol 2011; 77:3884-7. [PMID: 21460111 PMCID: PMC3127591 DOI: 10.1128/aem.00190-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 03/23/2011] [Indexed: 11/20/2022] Open
Abstract
DNA-based stable-isotope probing was applied to identify the active microorganisms involved in syntrophic butyrate oxidation in paddy field soil. After 14 and 21 days of incubation with [U-(13)C]butyrate, the bacterial Syntrophomonadaceae and the archaeal Methanosarcinaceae and Methanocellales incorporated substantial amounts of (13)C label into their nucleic acids. Unexpectedly, members of the Planctomycetes and Chloroflexi were also labeled with (13)C by yet-unclear mechanisms.
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MESH Headings
- Butyrates/metabolism
- Carbon Isotopes/metabolism
- Chloroflexi/growth & development
- Chloroflexi/metabolism
- Cluster Analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Euryarchaeota/growth & development
- Euryarchaeota/metabolism
- Genes, rRNA
- Gram-Positive Bacteria/growth & development
- Gram-Positive Bacteria/isolation & purification
- Gram-Positive Bacteria/metabolism
- Gram-Positive Bacteria/physiology
- Isotope Labeling
- Molecular Sequence Data
- Phylogeny
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Symbiosis
- Uridine/metabolism
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Affiliation(s)
- Pengfei Liu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Qiongfen Qiu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Yahai Lu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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Rui J, Qiu Q, Lu Y. Syntrophic acetate oxidation under thermophilic methanogenic condition in Chinese paddy field soil. FEMS Microbiol Ecol 2011; 77:264-73. [PMID: 21470253 DOI: 10.1111/j.1574-6941.2011.01104.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The aim of the present work was to determine and compare the degradation of acetate in a Chinese rice field soil at 25°C and 50°C, respectively, and to identify specifically the active organisms involved in syntrophic acetate oxidation. Soil was preincubated anaerobically for 30 days to reduce alternative electron acceptors other than CO(2). The [2-(13)C] acetate (99% (13)C) was added twice: 0 day and 19 days after preincubation. Addition of [2-(13)C] acetate resulted in an immediate increase of (13)C labeled CH(4) but non-labeling of CO(2) at 25°C. The methanogen community was dominated by Methanosarcinaceae and Methanocellales at 25°C. In contrast, the addition of [2-(13)C] acetate at 50°C resulted in a rapid increase of (13)CO(2). The (13)C labeling of CH(4) gradually increased and reached a similar value to CO(2) (13% (13)C) at the end of incubation (40 days). Nearly all archaeal 16S rRNA genes detected at 50°C belonged to hydrogenotrophic Methanocellales. DNA-based stable isotope probing analysis revealed that the organisms related to Thermacetogenium lineage and the unclassified Thermoanaerobacteraceae group were intensively labeled with (13)C in the incubations at 50°C. Thus, acetate was converted to CH(4) and CO(2) through aceticlastic methanogenesis at 25°C, while syntrophic acetate oxidation occurred at 50°C.
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Affiliation(s)
- Junpeng Rui
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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