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Berrier DJ, Neubauer SC, Franklin RB. Cooperative microbial interactions mediate community biogeochemical responses to saltwater intrusion in wetland soils. FEMS Microbiol Ecol 2022; 98:6529232. [PMID: 35170736 DOI: 10.1093/femsec/fiac019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 11/12/2022] Open
Abstract
In freshwater wetlands, competitive and cooperative interactions between respiratory, fermentative, and methanogenic microbes mediate the decomposition of organic matter. These interactions may be disrupted by saltwater intrusion disturbances that enhance the activity of sulfate-reducing bacteria (SRB), intensifying their competition with syntrophic bacteria and methanogens for electron donors. We simulated saltwater intrusion into wetland soil microcosms and examined biogeochemical and microbial responses, employing metabolic inhibitors to isolate the activity of various microbial functional groups. Sulfate additions increased total carbon dioxide production but decreased methane production. Butyrate degradation assays showed continued (but lower) levels of syntrophic metabolism despite strong demand by SRB for this key intermediate decomposition product and a shift in the methanogen community toward acetoclastic members. One month after removing SRB competition, total methane production recovered by only ∼50%. Similarly, butyrate assays showed an altered accumulation of products (including less methane), although overall rates of syntrophic butyrate breakdown largely recovered. These effects illustrate that changes in carbon mineralization following saltwater intrusion are driven by more than the oft-cited competition between SRB and methanogens for shared electron donors. Thus, the impacts of disturbances on wetland biogeochemistry are likely to persist until cooperative and competitive microbial metabolic interactions can recover fully.
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Affiliation(s)
- David J Berrier
- Department of Biology, Virginia Commonwealth University, 1000 W Cary Street, Richmond, VA 23284 (USA)
| | - Scott C Neubauer
- Department of Biology, Virginia Commonwealth University, 1000 W Cary Street, Richmond, VA 23284 (USA)
| | - Rima B Franklin
- Department of Biology, Virginia Commonwealth University, 1000 W Cary Street, Richmond, VA 23284 (USA)
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Effect of Dissimilatory Iron Reduction on the Reduction of CH 4Production in Landfill Conditions. J CHEM-NY 2019. [DOI: 10.1155/2019/5163132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A high solid anaerobic incubation system was used to study the effect of dissimilatory iron reduction on the inhibition of methanogenesis in a landfill. Different iron sources including FeC6H5O7, Fe2(SO4)3, Fe2O3, and Fe0were studied. The different iron sources significantly affected the methanogenesis process in the simulated landfill system. FeC6H5O7and Fe2(SO4)3inhibited methanogenesis but Fe0and Fe2O3increased it. The dissimilatory iron reduction with FeC6H5O7as the iron source demonstrates an anaerobic mineralization process, which enhances the biodegradation but inhibits methanogenesis. The highest rate of reduction of CH4production (51.9%) was obtained at a dosage rate of 16,000 mg·kg−1, which corresponded to a reduction of 0.86 g of CH4per kg of organic matrix. Active inhibition by methanogens using both the hydrogenotrophic and acetoclastic pathways is considered to be the main mechanism underlying the reduction of CH4production by dissimilatory iron reduction with FeC6H5O7as the iron source. This is the first report on the effect of different iron forms on the reduction of CH4production during landfilling with organic solid waste.
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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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Li L, Qu Z, Jia R, Wang B, Wang Y, Qu D. Excessive input of phosphorus significantly affects microbial Fe(III) reduction in flooded paddy soils by changing the abundances and community structures of Clostridium and Geobacteraceae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:982-991. [PMID: 28724230 DOI: 10.1016/j.scitotenv.2017.07.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/27/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
Microbial Fe(III) reduction can make an excellent contribution to the bioremediation of contaminated environments and potentially reduce methanogenesis. Excessive input of phosphorus (P) by P fertilizer application and eutrophied irrigation water might have a substantial influence on the process of microbial Fe(III) reduction in flooded paddy soils. To evaluate the effect of P application on microbial Fe(III) reduction, the responses of Clostridium and Geobacteraceae communities to different concentrations of P addition (CK: 0mmolPkg-1 soil; P1: 3.3mmolPkg-1 soil; P2: 20mmolPkg-1 soil) were investigated in anaerobically incubated paddy slurries. P addition significantly inhibited Fe(III) reduction during the early stage of incubation (from days 0 to 20). Compared with the CK treatment, the maximum Fe(III) reduction rate (Vmax) in treatments P1 and P2 remarkably decreased by 0.281 and 0.439mg·g-1·d-1, respectively. However, the addition of P had no significant effect on Fe(III) reduction during the later stage of incubation (after 20days). The abundances of Clostridium and Geobacteraceae were suppressed by P addition, and the suppression effect was more obvious with higher P concentration. P addition significantly changed the community structures of Clostridium and Geobacteraceae during the entire incubation. The communities of Clostridium and Geobacteraceae were closely correlated with the process of Fe(III) reduction. In conclusion, P addition could inhibit the microbial reduction of Fe(III) during the early stage of incubation by reducing the abundances and altering the community structures of Clostridium and Geobacteraceae, however, the inhibition could be eliminated with increased incubation time. This study demonstrates that soil microbial communities are sensitive to excessive P application, which can jointly impact relevant biogeochemical processes in flooded paddy soils.
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Affiliation(s)
- Lina Li
- College of Natural Resources and Environment, Northwest A&F University, No. 3 Taicheng Road, Yangling 712100, China
| | - Zhi Qu
- College of Natural Resources and Environment, Northwest A&F University, No. 3 Taicheng Road, Yangling 712100, China
| | - Rong Jia
- College of Natural Resources and Environment, Northwest A&F University, No. 3 Taicheng Road, Yangling 712100, China
| | - Baoli Wang
- College of Life Sciences, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, China
| | - Yuanyuan Wang
- College of Life Sciences, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, China
| | - Dong Qu
- College of Natural Resources and Environment, Northwest A&F University, No. 3 Taicheng Road, Yangling 712100, China.
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Popovic J, Finneran KT. Electron shuttling to ferrihydrite selects for fermentative rather than Fe 3+ -reducing biomass in xylose-fed batch reactors derived from three different inoculum sources. Biotechnol Bioeng 2017; 115:577-585. [PMID: 29131314 DOI: 10.1002/bit.26494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/08/2017] [Indexed: 11/08/2022]
Abstract
Reports suggest that ferric iron and electron shuttling molecules will select for Fe3+ -reducer dominated microbial biomass. We investigated the influence of the redox mediators anthraquinone-2,6-disulfonate (AQDS) and riboflavin using xylose as the sole fermentation substrate, with or without ferric iron. Electron shuttling to insoluble ferrihydrite enhanced solventogenesis, acidogenesis, hydrogen production, and xylose consumption, relative to the cells plus xylose controls in fermentations inoculated with woodland marsh sediment, wetwood disease, or raw septic liquid, over multiple transfers in 15-day batch fermentations. 16S rRNA gene based community analyses indicated that ferrihydrite alone, and AQDS/riboflavin plus ferrihydrite, immediately shifted native heterogeneous communities to those predominantly belonging to the Clostdridiales, rather than stimulating Fe3+ respiring populations. Data were similar irrespective of the inoculum source, suggesting that Fe3+ and/or electron shuttling compounds select for rapid proliferation of fermentative genera when fermentable substrates are present, and increases the extent of xylose consumption and solvent production.
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Affiliation(s)
- Jovan Popovic
- BioTechnology Institute, University of Minnesota, Minneapolis, Minnesota
| | - Kevin T Finneran
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, South Carolina
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Wörner S, Zecchin S, Dan J, Todorova NH, Loy A, Conrad R, Pester M. Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic composition of the total bacterial community. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:413-423. [PMID: 27085098 DOI: 10.1111/1758-2229.12413] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Rice paddies are indispensable for human food supply but emit large amounts of the greenhouse gas methane. Sulfur cycling occurs at high rates in these water-submerged soils and controls methane production, an effect that is increased by sulfate-containing fertilizers or soil amendments. We grew rice plants until their late vegetative phase with and without gypsum (CaSO4 ·2H2 O) amendment and identified responsive bacteria by 16S rRNA gene amplicon sequencing. Gypsum amendment decreased methane emissions by up to 99% but had no major impact on the general phylogenetic composition of the bacterial community. It rather selectively stimulated or repressed a small number of 129 and 27 species-level operational taxonomic units (OTUs) (out of 1883-2287 observed) in the rhizosphere and bulk soil, respectively. Gypsum-stimulated OTUs were affiliated with several potential sulfate-reducing (Syntrophobacter, Desulfovibrio, unclassified Desulfobulbaceae, unclassified Desulfobacteraceae) and sulfur-oxidizing taxa (Thiobacillus, unclassified Rhodocyclaceae), while gypsum-repressed OTUs were dominated by aerobic methanotrophs (Methylococcaceae). Abundance correlation networks suggested that two abundant (>1%) OTUs (Desulfobulbaceae, Rhodocyclaceae) were central to the reductive and oxidative parts of the sulfur cycle.
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Affiliation(s)
- Susanne Wörner
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sarah Zecchin
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Jianguo Dan
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- College of Environment and Plant Protection, Hainan University, Haikou City, China
| | - Nadezhda Hristova Todorova
- Department of Aquatic Ecosystems, Institute of Biodiversity and Ecosystem Research, BAS, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Ralf Conrad
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Konstanz, Germany
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Ozuolmez D, Na H, Lever MA, Kjeldsen KU, Jørgensen BB, Plugge CM. Methanogenic archaea and sulfate reducing bacteria co-cultured on acetate: teamwork or coexistence? Front Microbiol 2015; 6:492. [PMID: 26074892 PMCID: PMC4445324 DOI: 10.3389/fmicb.2015.00492] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/04/2015] [Indexed: 11/28/2022] Open
Abstract
Acetate is a major product of fermentation processes and an important substrate for sulfate reducing bacteria and methanogenic archaea. Most studies on acetate catabolism by sulfate reducers and methanogens have used pure cultures. Less is known about acetate conversion by mixed pure cultures and the interactions between both groups. We tested interspecies hydrogen transfer and coexistence between marine methanogens and sulfate reducers using mixed pure cultures of two types of microorganisms. First, Desulfovibrio vulgaris subsp. vulgaris (DSM 1744), a hydrogenotrophic sulfate reducer, was cocultured together with the obligate aceticlastic methanogen Methanosaeta concilii using acetate as carbon and energy source. Next, Methanococcus maripaludis S2, an obligate H2- and formate-utilizing methanogen, was used as a partner organism to M. concilii in the presence of acetate. Finally, we performed a coexistence experiment between M. concilii and an acetotrophic sulfate reducer Desulfobacter latus AcSR2. Our results showed that D. vulgaris was able to reduce sulfate and grow from hydrogen leaked by M. concilii. In the other coculture, M. maripaludis was sustained by hydrogen leaked by M. concilii as revealed by qPCR. The growth of the two aceticlastic microbes indicated co-existence rather than competition. Altogether, our results indicate that H2 leaking from M. concilii could be used by efficient H2-scavengers. This metabolic trait, revealed from coculture studies, brings new insight to the metabolic flexibility of methanogens and sulfate reducers residing in marine environments in response to changing environmental conditions and community compositions. Using dedicated physiological studies we were able to unravel the occurrence of less obvious interactions between marine methanogens and sulfate-reducing bacteria.
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Affiliation(s)
- Derya Ozuolmez
- Agrotechnology and Food Sciences, Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Hyunsoo Na
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Mark A Lever
- Department of Environmental Sciences, Institute of Biogeochemistry and Pollutant Dynamics, Eidgenössische Technische Hochschule Zurich Zürich, Switzerland
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University Aarhus, Denmark
| | - Caroline M Plugge
- Agrotechnology and Food Sciences, Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
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8
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Liu Y, Zhang Y, Ni BJ. Evaluating enhanced sulfate reduction and optimized volatile fatty acids (VFA) composition in anaerobic reactor by Fe (III) addition. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:2123-2131. [PMID: 25606811 DOI: 10.1021/es504200j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Anaerobic reactors with ferric iron addition have been experimentally demonstrated to be able to simultaneously improve sulfate reduction and organic matter degradation during sulfate-containing wastewater treatment. In this work, a mathematical model is developed to evaluate the impact of ferric iron addition on sulfate reduction and organic carbon removal as well as the volatile fatty acids (VFA) composition in anaerobic reactor. The model is successfully calibrated and validated using independent long-term experimental data sets from the anaerobic reactor with Fe (III) addition under different operational conditions. The model satisfactorily describes the sulfate reduction, organic carbon removal and VFA production. Results show Fe (III) addition induces the microbial reduction of Fe (III) by iron reducing bacteria (IRB), which significantly enhances sulfate reduction by sulfate reducing bacteria (SRB) and subsequently changes the VFA composition to acetate-dominating effluent. Simultaneously, the produced Fe (II) from IRB can alleviate the inhibition of undissociated H2S on microorganisms through iron sulfide precipitation, resulting in further improvement of the performance. In addition, the enhancement on reactor performance by Fe (III) is found to be more significantly favored at relatively low organic carbon/SO4(2-) ratio (e.g., 1.0) than at high organic carbon/SO4(2-) ratio (e.g., 4.5). The Fe (III)-based process of this work can be easily integrated with a commonly used strategy for phosphorus recovery, with the produced sulfide being recovered and then deposited into conventional chemical phosphorus removal sludge (FePO4) to achieve FeS precipitation for phosphorus recovery while the required Fe (III) being acquired from the waste ferric sludge of drinking water treatment process, to enable maximum resource recovery/reuse while achieving high-rate sulfate removal.
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Affiliation(s)
- Yiwen Liu
- Advanced Water Management Centre, The University of Queensland , St. Lucia, Queensland 4072, Australia
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9
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Microbial community analysis in rice paddy soils irrigated by acid mine drainage contaminated water. Appl Microbiol Biotechnol 2014; 99:2911-22. [DOI: 10.1007/s00253-014-6194-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/23/2014] [Accepted: 10/25/2014] [Indexed: 11/26/2022]
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10
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Rothenberg SE, Windham-Myers L, Creswell JE. Rice methylmercury exposure and mitigation: a comprehensive review. ENVIRONMENTAL RESEARCH 2014; 133:407-23. [PMID: 24972509 PMCID: PMC4119557 DOI: 10.1016/j.envres.2014.03.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 01/25/2014] [Accepted: 03/01/2014] [Indexed: 05/20/2023]
Abstract
Rice cultivation practices from field preparation to post-harvest transform rice paddies into hot spots for microbial mercury methylation, converting less-toxic inorganic mercury to more-toxic methylmercury, which is likely translocated to rice grain. This review includes 51 studies reporting rice total mercury and/or methylmercury concentrations, based on rice (Orzya sativa) cultivated or purchased in 15 countries. Not surprisingly, both rice total mercury and methylmercury levels were significantly higher in polluted sites compared to non-polluted sites (Wilcoxon rank sum, p<0.001). However, rice percent methylmercury (of total mercury) did not differ statistically between polluted and non-polluted sites (Wilcoxon rank sum, p=0.35), suggesting comparable mercury methylation rates in paddy soil across these sites and/or similar accumulation of mercury species for these rice cultivars. Studies characterizing the effects of rice cultivation under more aerobic conditions were reviewed to determine the mitigation potential of this practice. Rice management practices utilizing alternating wetting and drying (instead of continuous flooding) caused soil methylmercury levels to spike, resulting in a strong methylmercury pulse after fields were dried and reflooded; however, it is uncertain whether this led to increased translocation of methylmercury from paddy soil to rice grain. Due to the potential health risks, it is advisable to investigate this issue further, and to develop separate water management strategies for mercury polluted and non-polluted sites, in order to minimize methylmercury exposure through rice ingestion.
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Affiliation(s)
- Sarah E Rothenberg
- University of South Carolina, Arnold School of Public Health, Department of Environmental Health Sciences, 921 Assembly Street, Room 401, Columbia, SC 29208, USA.
| | | | - Joel E Creswell
- Brooks Rand Instruments, 4415 6th Ave NW, Seattle, WA 98107, USA.
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Šimek M, Virtanen S, Simojoki A, Chroňáková A, Elhottová D, Krištůfek V, Yli-Halla M. The microbial communities and potential greenhouse gas production in boreal acid sulphate, non-acid sulphate, and reedy sulphidic soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 466-467:663-672. [PMID: 23962436 DOI: 10.1016/j.scitotenv.2013.07.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/30/2013] [Accepted: 07/24/2013] [Indexed: 06/02/2023]
Abstract
Acid sulphate (AS) soils along the Baltic coasts contain significant amounts of organic carbon and nitrogen in their subsoils. The abundance, composition, and activity of microbial communities throughout the AS soil profile were analysed. The data from a drained AS soil were compared with those from a drained non-AS soil and a pristine wetland soil from the same region. Moreover, the potential production of methane, carbon dioxide, and nitrous oxide from the soils was determined under laboratory conditions. Direct microscopic counting, glucose-induced respiration (GIR), whole cell hybridisation, and extended phospholipid fatty acid (PLFA) analysis confirmed the presence of abundant microbial communities in the topsoil and also in the deepest Cg2 horizon of the AS soil. The patterns of microbial counts, biomass and activity in the profile of the AS soil and partly also in the non-AS soil therefore differed from the general tendency of gradual decreases in soil profiles. High respiration in the deepest Cg2 horizon of the AS soil (5.66 μg Cg(-1)h(-1), as compared to 2.71 μg Cg(-1)h(-1) in a top Ap horizon) is unusual but reasonable given the large amount of organic carbon in this horizon. Nitrous oxide production peaked in the BCgc horizon of the AS and in the BC horizon of the non-AS soil, but the peak value was ten-fold higher in the AS soil than in the non-AS soil (82.3 vs. 8.6 ng Ng(-1)d(-1)). The data suggest that boreal AS soils on the Baltic coast contain high microbial abundance and activity. This, together with the abundant carbon and total and mineral nitrogen in the deep layers of AS soils, may result in substantial gas production. Consequently, high GHG emissions could occur, for example, when the generally high water table is lowered because of arable farming.
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Affiliation(s)
- Miloslav Šimek
- Biology Centre AS CR, v. v. i., Institute of Soil Biology, 370 05 České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, 370 05 České Budějovice, Czech Republic.
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12
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Vandieken V, Finke N, Thamdrup B. Hydrogen, acetate, and lactate as electron donors for microbial manganese reduction in a manganese-rich coastal marine sediment. FEMS Microbiol Ecol 2013; 87:733-45. [DOI: 10.1111/1574-6941.12259] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/20/2013] [Accepted: 11/17/2013] [Indexed: 11/26/2022] Open
Affiliation(s)
- Verona Vandieken
- Department of Biology; Nordic Center for Earth Evolution; University of Southern Denmark; Odense M Denmark
- Institute for Chemistry and Biology of the Marine Environment; University of Oldenburg; Oldenburg Germany
| | - Niko Finke
- Department of Biology; Nordic Center for Earth Evolution; University of Southern Denmark; Odense M Denmark
| | - Bo Thamdrup
- Department of Biology; Nordic Center for Earth Evolution; University of Southern Denmark; Odense M Denmark
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13
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Bertram S, Blumenberg M, Michaelis W, Siegert M, Krüger M, Seifert R. Methanogenic capabilities of ANME-archaea deduced from13C-labelling approaches. Environ Microbiol 2013; 15:2384-93. [DOI: 10.1111/1462-2920.12112] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/20/2012] [Accepted: 02/16/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Sebastian Bertram
- Institute for Biogeochemistry and Marine Chemistry; University of Hamburg; Bundesstr. 55; 20146; Hamburg; Germany
| | - Martin Blumenberg
- Geobiology Group, Geoscience Centre; Georg-August-University Göttingen; Goldschmidtstr. 3; 37077; Göttingen; Germany
| | - Walter Michaelis
- Institute for Biogeochemistry and Marine Chemistry; University of Hamburg; Bundesstr. 55; 20146; Hamburg; Germany
| | - Michael Siegert
- Pennsylvania State University; 127 Sackett Building; University Park; PA; 16802; USA
| | - Martin Krüger
- Federal Institute for Geosciences and Natural Resources; Section Geomicrobiology; Stilleweg 2; 30655; Hannover; Germany
| | - Richard Seifert
- Institute for Biogeochemistry and Marine Chemistry; University of Hamburg; Bundesstr. 55; 20146; Hamburg; Germany
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14
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Maignien L, Parkes RJ, Cragg B, Niemann H, Knittel K, Coulon S, Akhmetzhanov A, Boon N. Anaerobic oxidation of methane in hypersaline cold seep sediments. FEMS Microbiol Ecol 2012; 83:214-31. [PMID: 22882187 DOI: 10.1111/j.1574-6941.2012.01466.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/28/2012] [Accepted: 08/01/2012] [Indexed: 11/30/2022] Open
Abstract
Life in hypersaline environments is typically limited by bioenergetic constraints. Microbial activity at the thermodynamic edge, such as the anaerobic oxidation of methane (AOM) coupled to sulphate reduction (SR), is thus unlikely to thrive in these environments. In this study, carbon and sulphur cycling was investigated in the extremely hypersaline cold seep sediments of Mercator mud volcano. AOM activity was partially inhibited but still present at salinity levels of 292 g L(-1) (c. eightfold sea water concentration) with rates of 2.3 nmol cm(-3) day(-1) and was even detectable under saturated conditions. Methane and evaporite-derived sulphate comigrated in the ascending geofluids, which, in combination with a partial activity inhibition, resulted in AOM activity being spread over unusually wide depth intervals. Up to 79% of total cells in the AOM zone were identified by fluorescence in situ hybridization (FISH) as anaerobic methanotrophs of the ANME-1. Most ANME-1 cells formed monospecific chains without any attached partner. At all sites, AOM activity co-occurred with SR activity and sometimes significantly exceeded it. Possible causes of these unexpected results are discussed. This study demonstrates that in spite of a very low energy yield of AOM, microorganisms carrying this reaction can thrive in salinity up to halite saturation.
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Affiliation(s)
- Loïs Maignien
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Ghent, Belgium.
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15
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Liu S, Zhang L, Liu Q, Zou J. Fe(III) fertilization mitigating net global warming potential and greenhouse gas intensity in paddy rice-wheat rotation systems in China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2012; 164:73-80. [PMID: 22343523 DOI: 10.1016/j.envpol.2012.01.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Revised: 01/16/2012] [Accepted: 01/20/2012] [Indexed: 05/31/2023]
Abstract
A complete accounting of net greenhouse gas balance (NGHGB) and greenhouse gas intensity (GHGI) affected by Fe(III) fertilizer application was examined in typical annual paddy rice-winter wheat rotation cropping systems in southeast China. Annual fluxes of soil carbon dioxide (CO(2)), methane (CH(4)) and nitrous oxide (N(2)O) were measured using static chamber method, and the net ecosystem exchange of CO(2) (NEE) was determined by the difference between soil CO(2) emissions (R(H)) and net primary production (NPP). Fe(III) fertilizer application significantly decreased R(H) without adverse effects on NPP of rice and winter wheat. Fe(III) fertilizer application decreased seasonal CH(4) by 27-44%, but increased annual N(2)O by 65-100%. Overall, Fe(III) fertilizer application decreased the annual NGHGB and GHGI by 35-47% and 30-36%, respectively. High grain yield and low greenhouse gas intensity can be reconciled by Fe(III) fertilizer applied at the local recommendation rate in rice-based cropping systems.
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Affiliation(s)
- Shuwei Liu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, Nanjing Agricultural University, Nanjing 210095, China
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16
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Hori T, Müller A, Igarashi Y, Conrad R, Friedrich MW. Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing. ISME JOURNAL 2009; 4:267-78. [PMID: 19776769 DOI: 10.1038/ismej.2009.100] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In anoxic rice field soil, ferric iron reduction is one of the most important terminal electron accepting processes, yet little is known about the identity of iron-reducing microorganisms. Here, we identified acetate-metabolizing bacteria by RNA-based stable isotope probing in the presence of iron(III) oxides as electron acceptors. After reduction of endogenous iron(III) for 21 days, isotope probing with (13)C-labeled acetate (2 mM) and added ferric iron oxides (ferrihydrite or goethite) was performed in rice field soil slurries for 48 and 72 h. Ferrihydrite reduction coincided with a strong suppression of methanogenesis (77%). Extracted RNA from each treatment was density resolved by isopycnic centrifugation, and analyzed by terminal restriction fragment length polymorphism, followed by cloning and sequencing of 16S rRNA of bacterial and archaeal populations. In heavy, isotopically labeled RNAs of the ferrihydrite treatment, predominant (13)C-assimilating populations were identified as Geobacter spp. (approximately 85% of all clones). In the goethite treatment, iron(II) formation was not detectable. However, Geobacter spp. (approximately 30%), the delta-proteobacterial Anaeromyxobacter spp. (approximately 30%), and novel beta-Proteobacteria were predominant in heavy rRNA fractions indicating that (13)C-acetate had been assimilated in the presence of goethite, whereas none were detected in the control heavy RNA. For the first time, active acetate-oxidizing iron(III)-reducing bacteria, including novel hitherto unrecognized populations, were identified as a functional guild in anoxic paddy soil.
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Affiliation(s)
- Tomoyuki Hori
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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17
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Dodla SK, Wang JJ, Delaune RD, Breitenbeck G. Carbon gas production under different electron acceptors in a freshwater marsh soil. CHEMOSPHERE 2009; 76:517-522. [PMID: 19349060 DOI: 10.1016/j.chemosphere.2009.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/04/2009] [Accepted: 03/05/2009] [Indexed: 05/27/2023]
Abstract
Dynamics of carbon (C) gas emission from wetlands influence global C cycling. In many freshwater systems such as Louisiana freshwater marsh, soil contents of NO3(-) and SO4(2-) have increased due to nutrient loading and saltwater intrusion. This could affect C mineralization and the emission of the major greenhouse gases carbon dioxide (CO2) and methane (CH4). In this investigation, a laboratory microcosm study was carried out to elucidate the effects of NO(3)(-) and SO4(2-) on CO2 and CH4 production from a freshwater marsh soil located in the Barataria Basin of Louisiana coast, which has been subjected to the Mississippi River diversion and seawater intrusion. Composite soil samples were collected from top 50 cm marsh profile, treated with different levels of NO3(-) (0, 3.2 and 5mM) or SO4(2-) (0, 2, and 5mM) concentrations, and incubated for 214d under anaerobic conditions. The results showed that the presence of NO3(-) (especially at 3.2mM) significantly decreased CO2 productions whereas SO4(2-) did not. On the other hand, both NO(3)(-) and SO4(2-) treatments decreased CH4 production but the NO3(-) almost completely inhibited CH4 production (>99%) whereas the SO4(2-) treatments reduced CH4 production by 78-90%. The overall C mineralization rate constant under the NO3(-) presence was also low. In addition, the results revealed that a large proportion (95%) of anaerobic carbon mineralization in the untreated freshwater soil was unexplained by the reduction of any of the measured major electron acceptors.
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Affiliation(s)
- Syam K Dodla
- School of Plant, Environmental and Soil Sciences, Louisiana State Univ. Agricultural Center, 104 Sturgis Hall-LSU, Baton Rouge, LA 70803, United States
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18
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Bagi Z, Acs N, Bálint B, Horváth L, Dobó K, Perei KR, Rákhely G, Kovács KL. Biotechnological intensification of biogas production. Appl Microbiol Biotechnol 2007; 76:473-82. [PMID: 17503035 DOI: 10.1007/s00253-007-1009-6] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 04/18/2007] [Accepted: 04/19/2007] [Indexed: 11/28/2022]
Abstract
The importance of syntrophic relationships among microorganisms participating in biogas formation has been emphasized, and the regulatory role of in situ hydrogen production has been recognized. It was assumed that the availability of hydrogen may be a limiting factor for hydrogenotrophic methanogens. This hypothesis was tested under laboratory and field conditions by adding a mesophilic (Enterobacter cloacae) or thermophilic hydrogen-producing (Caldicellulosyruptor saccharolyticus) strain to natural biogas-producing consortia. The substrates were waste water sludge, dried plant biomass from Jerusalem artichoke, and pig manure. In all cases, a significant intensification of biogas production was observed. The composition of the generated biogas did not noticeably change. In addition to being a good hydrogen producer, C. saccharolyticus has cellulolytic activity; hence, it is particularly suitable when cellulose-containing biomass is fermented. The process was tested in a 5-m(3) thermophilic biogas digester using pig manure slurry as a substrate. Biogas formation increased at least 160-170% upon addition of the hydrogen-producing bacteria as compared to the biogas production of the spontaneously formed microbial consortium. Using the hydrogenase-minus control strain provided evidence that the observed enhancement was due to interspecies hydrogen transfer. The on-going presence of C. saccharolyticus was demonstrated after several months of semicontinuous operation.
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Affiliation(s)
- Zoltán Bagi
- Department of Biotechnology, University of Szeged, Temesvári krt. 62, 6726 Szeged, Hungary
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19
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Finke N, Hoehler TM, Jørgensen BB. Hydrogen 'leakage' during methanogenesis from methanol and methylamine: implications for anaerobic carbon degradation pathways in aquatic sediments. Environ Microbiol 2007; 9:1060-71. [PMID: 17359276 DOI: 10.1111/j.1462-2920.2007.01248.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The effect of variations in H2 concentrations on methanogenesis from the non-competitive substrates methanol and methylamine (used by methanogens but not by sulfate reducers) was investigated in methanogenic marine sediments. Imposed variations in sulfate concentration and temperature were used to drive systematic variations in pore water H2 concentrations. Specifically, increasing sulfate concentrations and decreasing temperatures both resulted in decreasing H2 concentrations. The ratio of CO2 and CH4 produced from 14C-labelled methylamine and methanol showed a direct correlation with the H2 concentration, independent of the treatment, with lower H2 concentrations resulting in a shift towards CO2. We conclude that this correlation is driven by production of H2 by methylotrophic methanogens, followed by loss to the environment with a magnitude dependent on the extracellular H2 concentrations maintained by hydrogenotrophic methanogens (in the case of the temperature experiment) or sulfate reducers (in the case of the sulfate experiment). Under sulfate-free conditions, the loss of reducing power as H2 flux out of the cell represents a loss of energy for the methylotrophic methanogens while, in the presence of sulfate, it results in a favourable free energy yield. Thus, hydrogen leakage might conceivably be beneficial for methanogens in marine sediments dominated by sulfate reduction. In low-sulfate systems such as methanogenic marine or freshwater sediments it is clearly detrimental--an adverse consequence of possessing a hydrogenase that is subject to externally imposed control by pore water H2 concentrations. H2 leakage in methanogens may explain the apparent exclusion of acetoclastic methanogenesis in sediments dominated by sulfate reduction.
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Affiliation(s)
- Niko Finke
- Department of Biogeochemistry, Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.
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20
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Jaisi DP, Dong H, Liu C. Kinetic analysis of microbial reduction of Fe(III) in nontronite. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:2437-44. [PMID: 17438797 DOI: 10.1021/es0619399] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Microbial reduction of structural Fe(III) in nontronite (NAu-2) was studied in batch cultures under non-growth condition using Shewanella putrefaciens strain CN32. The rate and extent of structural Fe(III) reduction was examined as a function of electron acceptor [Fe(III)] and bacterial concentration. Fe(ll) sorption onto NAu-2 and CN32 surfaces was independently measured and described by the Langmuir expression with the affinity constant (log K) of 3.21 and 3.30 for NAu-2 and bacteria, respectively. The Fe(II) sorption capacity of NAu-2 decreased with increasing NAu-2 concentration, suggesting a particle aggregation effect. An empirical equation for maximum sorption capacity was derived from the sorption isotherms as a function of NAu-2 concentration. The total reactive surface concentration of Fe(III) was proposed as a proxy for the "effective" or bioaccessible Fe(III) concentration. The initial rate of microbial reduction was first-order with respect to the effective Fe-(III) concentration. A kinetic biogeochemical model was assembled that incorporated the first-order rate expression with respect to the effective Fe(III) concentration, Fe(II) sorption to cell and NAu-2 surfaces, and the empirical equation for maximum sorption capacity. The model successfully described the experimental results with variable NAu-2 concentration. The initial rate of microbial reduction of Fe(III) in NAu-2 increased with increasing cell concentration from 10(2) up to approximately 10(8) cells/mL, and then leveled off with further increase. A saturation-type kinetics with respect to cell concentration was required to describe microbial reduction of Fe(III) in NAu-2 as a function of cell concentration. Overall, our results indicated that the kinetics of microbial reduction of Fe(III) in NAu-2 can be modeled at variable concentration of key variables (clay and cell concentration) by considering the surface saturation, Fe(II) production, and its sorption to NAu-2 and cell surfaces.
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Affiliation(s)
- Deb P Jaisi
- Department of Geology, Miami University, Oxford, Ohio 45056, USA
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21
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Schnurr-Pütz S, Bååth E, Guggenberger G, Drake HL, Küsel K. Compaction of forest soil by logging machinery favours occurrence of prokaryotes. FEMS Microbiol Ecol 2006; 58:503-16. [PMID: 17117992 DOI: 10.1111/j.1574-6941.2006.00175.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Soil compaction caused by passage of logging machinery reduces the soil air capacity. Changed abiotic factors might induce a change in the soil microbial community and favour organisms capable of tolerating anoxic conditions. The goals of this study were to resolve differences between soil microbial communities obtained from wheel-tracks (i.e. compacted) and their adjacent undisturbed sites, and to evaluate differences in potential anaerobic microbial activities of these contrasting soils. Soil samples obtained from compacted soil had a greater bulk density and a higher pH than uncompacted soil. Analyses of phospholipid fatty acids demonstrated that the eukaryotic/prokaryotic ratio in compacted soils was lower than that of uncompacted soils, suggesting that fungi were not favoured by the in situ conditions produced by compaction. Indeed, most-probable-number (MPN) estimates of nitrous oxide-producing denitrifiers, acetate- and lactate-utilizing iron and sulfate reducers, and methanogens were higher in compacted than in uncompacted soils obtained from one site that had large differences in bulk density. Compacted soils from this site yielded higher iron-reducing, sulfate-reducing and methanogenic potentials than did uncompacted soils. MPN estimates of H2-utilizing acetogens in compacted and uncompacted soils were similar. These results indicate that compaction of forest soil alters the structure and function of the soil microbial community and favours occurrence of prokaryotes.
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Affiliation(s)
- Silvia Schnurr-Pütz
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
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22
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Heimann AC, Batstone DJ, Jakobsen R. Methanosarcina spp. drive vinyl chloride dechlorination via interspecies hydrogen transfer. Appl Environ Microbiol 2006; 72:2942-9. [PMID: 16598001 PMCID: PMC1449020 DOI: 10.1128/aem.72.4.2942-2949.2006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two highly enriched cultures containing Dehalococcoides spp. were used to study the effect of aceticlastic methanogens on reductive vinyl chloride (VC) dechlorination. In terms of aceticlastic methanogens, one culture was dominated by Methanosaeta, while the other culture was dominated by Methanosarcina, as determined by fluorescence in situ hybridization. Cultures amended with 2-bromoethanesulfonate (BES), an efficient inhibitor of methanogens, exhibited slow VC dechlorination when grown on acetate and VC. Methanogenic cultures dominated by Methanosaeta had no impact on dechlorination rates, compared to BES-amended controls. In contrast, methanogenic cultures dominated by Methanosarcina displayed up to sevenfold-higher rates of VC dechlorination than their BES-amended counterparts. Methanosarcina-dominated cultures converted a higher percentage of [2-(14)C]acetate to (14)CO(2) when concomitant VC dechlorination took place, compared to nondechlorinating controls. Respiratory indices increased from 0.12 in nondechlorinating cultures to 0.51 in actively dechlorinating cultures. During VC dechlorination, aqueous hydrogen (H(2)) concentrations dropped to 0.3 to 0.5 nM. However, upon complete VC consumption, H(2) levels increased by a factor of 10 to 100, indicating active hydrogen production from acetate oxidation. This process was thermodynamically favorable by means of the extremely low H(2) levels during dechlorination. VC degradation in nonmethanogenic cultures was not inhibited by BES but was limited by the availability of H(2) as electron donor, in cultures both with and without BES. These findings all indicate that Methanosarcina (but not Methanosaeta), while cleaving acetate to methane, simultaneously oxidizes acetate to CO(2) plus H(2), driving hydrogenotrophic dehalorespiration of VC to ethene by Dehalococcoides.
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Affiliation(s)
- Axel C Heimann
- Institute of Environment & Resources, Bygningstorvet, Building 115, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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23
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Metje M, Frenzel P. Effect of temperature on anaerobic ethanol oxidation and methanogenesis in acidic peat from a northern wetland. Appl Environ Microbiol 2006; 71:8191-200. [PMID: 16332802 PMCID: PMC1317349 DOI: 10.1128/aem.71.12.8191-8200.2005] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effects of temperature on rates and pathways of CH4 production and on the abundance and structure of the archaeal community were investigated in acidic peat from a mire in northern Scandinavia (68 degrees N). We monitored the production of CH4 and CO2 over time and measured the turnover of Fe(II), ethanol, and organic acids. All experiments were performed with and without specific inhibitors (2-bromoethanesulfonate [BES] for methanogenesis and CH3F for acetoclastic methanogenesis). The optimum temperature for methanogenesis was 25 degrees C (2.3 micromol CH4.g [dry weight](-1) . day(-1)), but the activity was relatively high even at 4 degrees C (0.25 micromol CH4. g [dry weight](-1) . day(-1)). The theoretical lower limit for methanogenesis was calculated to be at -5 degrees C. The optimum temperature for growth as revealed by real-time PCR was 25 degrees C for both archaea and bacteria. The population structure of archaea was studied by terminal restriction fragment length polymorphism analysis and remained constant over a wide temperature range. Hydrogenotrophic methanogenesis accounted for about 80% of the total methanogenesis. Most 16S rRNA gene sequences that were affiliated with methanogens and all McrA sequences clustered with the exclusively hydrogenotrophic order Methanobacteriales, correlating with the prevalence of hydrogenotrophic methanogenesis. Fe reduction occurred parallel to methanogenesis and was inhibited by BES, suggesting that methanogens were involved in Fe reduction. Based upon the observed balance of substrates and thermodynamic calculations, we concluded that the ethanol pool was oxidized to acetate by the following two processes: syntrophic oxidation with methanogenesis (i) as an H2 sink and (ii) as a reductant for Fe(III). Acetate accumulated, but a considerable fraction was converted to butyrate, making volatile fatty acids important end products of anaerobic metabolism.
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Affiliation(s)
- Martina Metje
- Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Str., D-35043 Marburg, Germany
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24
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Petrie L, North NN, Dollhopf SL, Balkwill DL, Kostka JE. Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI). Appl Environ Microbiol 2004; 69:7467-79. [PMID: 14660400 PMCID: PMC310038 DOI: 10.1128/aem.69.12.7467-7479.2003] [Citation(s) in RCA: 188] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Iron(III)-reducing bacteria have been demonstrated to rapidly catalyze the reduction and immobilization of uranium(VI) from contaminated subsurface sediments. Thus, these organisms may aid in the development of bioremediation strategies for uranium contamination, which is prevalent in acidic subsurface sediments at U.S. government facilities. Iron(III)-reducing enrichment cultures were initiated from pristine and contaminated (high in uranium, nitrate; low pH) subsurface sediments at pH 7 and pH 4 to 5. Enumeration of Fe(III)-reducing bacteria yielded cell counts of up to 240 cells ml(-1) for the contaminated and background sediments at both pHs with a range of different carbon sources (glycerol, acetate, lactate, and glucose). In enrichments where nitrate contamination was removed from the sediment by washing, MPN counts of Fe(III)-reducing bacteria increased substantially. Sediments of lower pH typically yielded lower counts of Fe(III)-reducing bacteria in lactate- and acetate-amended enrichments, but higher counts were observed when glucose was used as an electron donor in acidic enrichments. Phylogenetic analysis of 16S rRNA gene sequences extracted from the highest positive MPN dilutions revealed that the predominant members of Fe(III)-reducing consortia from background sediments were closely related to members of the Geobacteraceae family, whereas a recently characterized Fe(III) reducer (Anaeromyxobacter sp.) and organisms not previously shown to reduce Fe(III) (Paenibacillus and Brevibacillus spp.) predominated in the Fe(III)-reducing consortia of contaminated sediments. Analysis of enrichment cultures by terminal restriction fragment length polymorphism (T-RFLP) strongly supported the cloning and sequencing results. Dominant members of the Fe(III)-reducing consortia were observed to be stable over several enrichment culture transfers by T-RFLP in conjunction with measurements of Fe(III) reduction activity and carbon substrate utilization. Enrichment cultures from contaminated sites were also shown to rapidly reduce millimolar amounts of U(VI) in comparison to killed controls. With DNA extracted directly from subsurface sediments, quantitative analysis of 16S rRNA gene sequences with MPN-PCR indicated that Geobacteraceae sequences were more abundant in pristine compared to contaminated environments,whereas Anaeromyxobacter sequences were more abundant in contaminated sediments. Thus, results from a combination of cultivation-based and cultivation-independent approaches indicate that the abundance/community composition of Fe(III)-reducing consortia in subsurface sediments is dependent upon geochemical parameters (pH, nitrate concentration) and that microorganisms capable of producing spores (gram positive) or spore-like bodies (Anaeromyxobacter) were representative of acidic subsurface environments.
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Affiliation(s)
- Lainie Petrie
- Department of Oceanography, College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
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25
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Liou RM, Huang SN, Lin CW. Methane emission from fields with differences in nitrogen fertilizers and rice varieties in Taiwan paddy soils. CHEMOSPHERE 2003; 50:237-246. [PMID: 12653295 DOI: 10.1016/s0045-6535(02)00158-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Flooded rice fields are one of the major biogenic methane sources. In this study, methane emission rates were measured after transplanting in paddy fields with application of two kinds of nitrogen fertilizers (ammonium sulfate, NH4+-N and potassium nitrate, NO3(-)-N) and with two kinds of rice varieties (Japonica and Indica). The experiment was conducted in fields located at Tainan District Agricultural Improvement Station in Chia-Yi county (23 degrees 25'08"N, 120 degrees 16'26"E) of southern Taiwan throughout the first and the second crop seasons in 1999. The seasonal methane flux in the first crop season with NH4+-N and NO3(-)-N ranged from 2.48 to 2.78 and from 8.65 to 9.22 g CH4 m(-2); and the values ranged 24.6-34.2 and 36.4-52.6 g CH4 m(-2) in the second crop season, respectively. In the first crop season, there were significantly increased 3.1-3.7-fold in methane emission fluxes due to plantation of Indica rice. In comparison of two rice varieties, the Indica rice variety showed a tendency for larger methane emission than the Japonica rice variety in the second crop season. Moreover, ammonium sulfate treatment significantly reduced CH4 emissions by 37-85% emissions compared to potassium nitrate plots. It was concluded that the CH4 emission was markedly dependent on the type of nitrogen fertilizer and rice variety in Taiwan paddy soils.
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Affiliation(s)
- Rey-May Liou
- Department of Environmental Engineering and Health, Chia-Nan University of Pharmacy and Science, Tainan 717, Taiwan, ROC.
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26
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Kostka JE, Dalton DD, Skelton H, Dollhopf S, Stucki JW. Growth of iron(III)-reducing bacteria on clay minerals as the sole electron acceptor and comparison of growth yields on a variety of oxidized iron forms. Appl Environ Microbiol 2002; 68:6256-62. [PMID: 12450850 PMCID: PMC134413 DOI: 10.1128/aem.68.12.6256-6262.2002] [Citation(s) in RCA: 170] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Smectite clay minerals are abundant in soils and sediments worldwide and are typically rich in Fe. While recent investigations have shown that the structural Fe(III) bound in clay minerals is reduced by microorganisms, previous studies have not tested growth with clay minerals as the sole electron acceptor. Here we have demonstrated that a pure culture of Shewanella oneidensis strain MR-1 as well as enrichment cultures of Fe(III)-reducing bacteria from rice paddy soil and subsurface sediments are capable of conserving energy for growth with the structural Fe(III) bound in smectite clay as the sole electron acceptor. Pure cultures of S. oneidensis were used for more detailed growth rate and yield experiments on various solid- and soluble-phase electron acceptors [smectite, Fe(III) oxyhydroxide FeOOH, Fe(III) citrate, and oxygen] in the same minimal medium. Growth was assessed as direct cell counts or as an increase in cell carbon (measured as particulate organic carbon). Cell counts showed that similar growth of S. oneidensis (10(8) cells ml(-1)) occurred with smectitic Fe(III) and on other Fe forms [amorphous Fe(III) oxyhydroxide, and Fe citrate] or oxygen as the electron acceptor. In contrast, cell yields of S. oneidensis measured as the increase in cell carbon were similar on all Fe forms tested while yields on oxygen were five times higher, in agreement with thermodynamic predictions. Over a range of particle loadings (0.5 to 4 g liter(-1)), the increase in cell number was highly correlated to the amount of structural Fe in smectite reduced. From phylogenetic analysis of the complete 16S rRNA gene sequences, a predominance of clones retrieved from the clay mineral-reducing enrichment cultures were most closely related to the low-G+C gram-positive members of the Bacteria (Clostridium and Desulfitobacterium) and the delta-Proteobacteria (members of the Geobacteraceae). Results indicate that growth with smectitic Fe(III) is similar in magnitude to that with Fe(III) oxide minerals and is dependent upon the mineral surface area available. Iron(III) bound in clay minerals should be considered an important electron acceptor supporting the growth of bacteria in soils or sedimentary environments.
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Affiliation(s)
- Joel E Kostka
- Department of Oceanography, Florida State University, Tallahassee 32306, USA.
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27
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Lueders T, Friedrich MW. Effects of amendment with ferrihydrite and gypsum on the structure and activity of methanogenic populations in rice field soil. Appl Environ Microbiol 2002; 68:2484-94. [PMID: 11976125 PMCID: PMC127547 DOI: 10.1128/aem.68.5.2484-2494.2002] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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 (CaSO(4). 2H(2)O) 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 microM) 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 ( approximately 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 microM) 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.
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Affiliation(s)
- Tillmann Lueders
- Max-Planck-Institut für Terrestrische Mikrobiologie, D-35043 Marburg, Germany
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28
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van Bodegom P, Stams F, Mollema L, Boeke S, Leffelaar P. Methane oxidation and the competition for oxygen in the rice rhizosphere. Appl Environ Microbiol 2001; 67:3586-97. [PMID: 11472935 PMCID: PMC93059 DOI: 10.1128/aem.67.8.3586-3597.2001] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A mechanistic approach is presented to describe oxidation of the greenhouse gas methane in the rice rhizosphere of flooded paddies by obligate methanotrophic bacteria. In flooded rice paddies these methanotrophs compete for available O(2) with other types of bacteria. Soil incubation studies and most-probable-number (MPN) counts of oxygen consumers show that microbial oxygen consumption rates were dominated by heterotrophic and methanotrophic respiration. MPN counts of methanotrophs showed large spatial and temporal variability. The most abundant methanotrophs (a Methylocystis sp.) and heterotrophs (a Pseudomonas sp. and a Rhodococcus sp.) were isolated and characterized. Growth dynamics of these bacteria under carbon and oxygen limitations are presented. Theoretical calculations based on measured growth dynamics show that methanotrophs were only able to outcompete heterotrophs at low oxygen concentrations (frequently < 5 microM). The oxygen concentration at which methanotrophs won the competition from heterotrophs did not depend on methane concentration, but it was highly affected by organic carbon concentrations in the paddy soil. Methane oxidation was severely inhibited at high acetate concentrations. This is in accordance with competition experiments between Pseudomonas spp. and Methylocystis spp. carried out at different oxygen and carbon concentrations. Likely, methane oxidation mainly occurs at microaerophilic and low-acetate conditions and thus not directly at the root surface. Acetate and oxygen concentrations in the rice rhizosphere are in the critical range for methane oxidation, and a high variability in methane oxidation rates is thus expected.
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Affiliation(s)
- P van Bodegom
- Laboratory of Theoretical Production Ecology, Wageningen University, 6700 AK Wageningen, The Netherlands.
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Scheid D, Stubner S. Structure and diversity of Gram-negative sulfate-reducing bacteria on rice roots. FEMS Microbiol Ecol 2001; 36:175-183. [PMID: 11451522 DOI: 10.1111/j.1574-6941.2001.tb00838.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Specific PCR assays were used to amplify the 16S rRNA genes of the Desulfobacteriaceae and the Desulfovibrionaceae from extracted environmental DNA from rice roots. 16S rDNA-based community patterns of the Desulfobacteriaceae were generated via terminal restriction fragment length polymorphism analysis from rice roots and compared with bulk soil. The molecular fingerprints showed no significant difference between rice roots and bulk soil, but changes during the vegetation period. 16S rDNA clone libraries and sequencing showed that the predominant terminal restriction fragments represented distinct phylogenetic groups. The 16S rDNA clone sequences of the Desulfobacteriaceae fell in the phylogenetic radiation of Desulfonema and Desulfosarcina or grouped within the Desulforhabdus-Syntrophobacter assemblage. Three of the latter sequences were closely affiliated with the MPN isolate EZ-2C2 from rice roots. All Desulfovibrionaceae 16S rDNA clone sequences, with one exception, were affiliated with the MPN isolate F1-7b from rice roots. The clustering of the clone sequences and the close phylogenetic affiliation with isolates from MPN enrichments from the same habitat in two cases indicated that these sequence clusters may represent predominant Gram-negative sulfate reducers on rice roots. Quantification of the bacterial abundances was accomplished by rRNA dot blot hybridization. In total the Gram-negative sulfate reducers accounted for approximately 2-3% of the total rRNA content. The relative rRNA abundance of the Desulfobacteriaceae was, at 1.4%, higher than that of the Desulfovibrionaceae (0.5%).
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Affiliation(s)
- D Scheid
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043, Marburg, Germany
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Stubner S, Meuser K. Detection of Desulfotomaculum in an Italian rice paddy soil by 16S ribosomal nucleic acid analyses. FEMS Microbiol Ecol 2000; 34:73-80. [PMID: 11053738 DOI: 10.1111/j.1574-6941.2000.tb00756.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Two specific primers were developed for the amplification of 16S rRNA genes of Desulfotomaculum lineage 1 to detect members of the genus Desulfotomaculum in rice field soil. The combination of both primers in PCR allowed the specific amplification and cloning of ten 16S rDNA sequences of this group from rice paddy soil DNA extracts. The phylogenetic analysis showed that these sequences formed a deeply branching cluster within Desulfotomaculum lineage 1, together with two sequences from the database and two sequences from a hydrocarbon-contaminated aquifer. Dissimilarity values to validly described species, including recently isolated strains of Desulfotomaculum from rice paddy microcosms, were higher than 12%. Within the new cluster the cloned sequences formed three separate groups which were each represented by at least two sequences with identities of >/=99% while one sequence represented an additional group. The sequences should represent sulfate-reducing organisms because they clearly fell into the physiologically coherent group of Gram-positive sulfate reducers. The relative abundance of bacteria of the Desulfotomaculum lineage 1 in rice paddy soil and root samples was estimated with rRNA dot blot hybridizations of extracted RNA. The relative RNA content of Desulfotomaculum lineage 1 was 0.55% in the bulk soil and 1% in the rice root samples, respectively, of the total 16S rRNA content (probe Eub338). Hybridization of rRNA with a probe targeting the new cluster represented by the cloned sequences confirmed the high abundance of 16S rRNA sequences from this cluster in the rice paddy field samples. Another hybridization probe detecting Desulfotomaculum acetoxidans and two closely related Desulfotomaculum isolates from rice paddy soil indicated that these bacteria were less abundant.
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Affiliation(s)
- S Stubner
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße, D-35043, Marburg, Germany
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Scholten JC, Conrad R, Stams AJ. Effect of 2-bromo-ethane sulfonate, molybdate and chloroform on acetate consumption by methanogenic and sulfate-reducing populations in freshwater sediment. FEMS Microbiol Ecol 2000; 32:35-42. [PMID: 10779617 DOI: 10.1111/j.1574-6941.2000.tb00696.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The relative importance of methanogenesis and sulfate reduction in freshwater sediment supplemented with acetate was investigated. Addition of acetate stimulated both methane formation and sulfate reduction, indicating that an active aceticlastic population of methanogens and sulfate reducers was present in the sediment. Sulfate reducers were most important in the consumption of acetate. However, when sulfate reducers were inhibited, acetate was metabolised at a similar rate by methanogens. Acetate, propionate and valerate accumulated only when both processes were inhibited by the combined addition of 2-bromo-ethane sulfonate and molybdate. The relative amounts of acetate, propionate and valerate were 93, 6 and 1 mol%, respectively. These results demonstrate the role of acetate as a key intermediate in the terminal step of organic matter mineralisation in the sediment. Addition of chloroform inhibited both methanogenesis and sulfate reduction. We studied the inhibitory effect of CHCl(3) on homoacetogenic bacteria, sulfate-reducing bacteria and methanogens. The results showed that inhibition by CHCl(3) correlates with microorganisms, which operate the acetyl-CoA cleavage pathway. We propose that chloroform can be used to elucidate the role of different metabolic types of sulfate reducers to sulfate reduction in natural environments.
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Affiliation(s)
- JC Scholten
- Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Str., D-35043, Marburg, Germany
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Chidthaisong A, Conrad R. Turnover of glucose and acetate coupled to reduction of nitrate, ferric iron and sulfate and to methanogenesis in anoxic rice field soil. FEMS Microbiol Ecol 2000; 31:73-86. [PMID: 10620721 DOI: 10.1111/j.1574-6941.2000.tb00673.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Turnover of glucose and acetate in the presence of active reduction of nitrate, ferric iron and sulfate was investigated in anoxic rice field soil by using [U-(14)C]glucose and [2-(14)C]acetate. The turnover of glucose was not much affected by addition of ferrihydrite or sulfate, but was partially inhibited (60%) by addition of nitrate. Nitrate addition also strongly reduced acetate production from glucose while ferrihydrite and sulfate addition did not. These results demonstrate that ferric iron and sulfate reducers did not outcompete fermenting bacteria for glucose at endogenous concentrations. Nitrate reducers may have done so, but glucose fermentation may also have been inhibited by accumulation of toxic denitrification intermediates (nitrite, NO, N(2)O). Addition of nitrate resulted in complete inhibition of CH(4) production from [U-(14)C]glucose and [2-(14)C]acetate. However, addition of ferrihydrite or sulfate decreased the production of (14)CH(4) from [U-(14)C]glucose by only 70 and 65%, respectively. None of the electron acceptors significantly increased the production of (14)CO(2) from [U-(14)C]glucose, but all increased the production of (14)CO(2) from [2-(14)C]acetate. Uptake of acetate was faster in the presence of either nitrate, ferrihydrite or sulfate than in the unamended control. Addition of ferrihydrite and sulfate reduced (14)CH(4) production from [2-(14)C]acetate by 83 and 92%, respectively. Chloroform completely inhibited the methanogenic consumption of acetate. It also inhibited the oxidation of acetate, completely in the presence of sulfate, but not in the presence of nitrate or ferrihydrite. Our results show that, besides the possible toxic effect of products of nitrate reduction (NO, NO(2)(-) and N(2)O) on methanogens, nitrate reducers, ferric iron reducers and sulfate reducers were active enough to outcompete methanogens for acetate and channeling the flow of electrons away from CH(4) towards CO(2) production.
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Affiliation(s)
- A Chidthaisong
- Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse, D-35043, Marburg, Germany
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Measurement of monosaccharides and conversion of glucose to acetate in anoxic rice field soil. Appl Environ Microbiol 1999; 65:2350-5. [PMID: 10347012 PMCID: PMC91347 DOI: 10.1128/aem.65.6.2350-2355.1999] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Degradation of glucose has been implicated in acetate production in rice field soil, but the abundance of glucose, the temporal change of glucose turnover, and the relationship between glucose and acetate catabolism are not well understood. We therefore measured the pool sizes of glucose and acetate in rice field soil and investigated the turnover of [U-14C]glucose and [2-14C]acetate. Acetate accumulated up to about 2 mM during days 5 to 10 after flooding of the soil. Subsequently, methanogenesis started and the acetate concentration decreased to about 100 to 200 &mgr;M. Glucose always made up >50% of the total monosaccharides detected. Glucose concentrations decreased during the first 10 days from 90 &mgr;M initially to about 3 &mgr;M after 40 days of incubation. With the exception at day 0 when glucose consumption was slow, the glucose turnover time was in the range of minutes, while the acetate turnover time was in the range of hours. Anaerobic degradation of [U-14C]glucose released [14C]acetate and 14CO2 as the main products, with [14C]acetate being released faster than 14CO2. The products of [2-14C]acetate metabolism, on the other hand, were 14CO2 during the reduction phase of soil incubation (days 0 to 15) and 14CH4 during the methanogenic phase (after day 15). Except during the accumulation period of acetate (days 5 to 10), approximately 50 to 80% of the acetate consumed was produced from glucose catabolism. However, during the accumulation period of acetate, the rate of acetate production from glucose greatly exceeded that of acetate consumption. Under steady-state conditions, up to 67% of the CH4 was produced from acetate, of which up to 56% was produced from glucose degradation.
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Conrad R. Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS Microbiol Ecol 1999. [DOI: 10.1111/j.1574-6941.1999.tb00575.x] [Citation(s) in RCA: 552] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Roy RÃ, Conrad R. Effect of methanogenic precursors (acetate, hydrogen, propionate) on the suppression of methane production by nitrate in anoxic rice field soil. FEMS Microbiol Ecol 1999. [DOI: 10.1111/j.1574-6941.1999.tb00560.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Krylova NI, Conrad R. Thermodynamics of propionate degradation in methanogenic paddy soil. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00512.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Grosskopf R, Janssen PH, Liesack W. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl Environ Microbiol 1998; 64:960-9. [PMID: 9501436 PMCID: PMC106352 DOI: 10.1128/aem.64.3.960-969.1998] [Citation(s) in RCA: 429] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/1997] [Accepted: 12/17/1997] [Indexed: 02/06/2023] Open
Abstract
A dual approach consisting of cultivation and molecular retrieval of partial archaeal 16S rRNA genes was carried out to characterize the diversity and structure of the methanogenic community inhabiting the anoxic bulk soil of flooded rice microcosms. The molecular approach identified four groups of known methanogens. Three environmental sequences clustered with Methanobacterium bryantii and Methanobacterium formicicum, six were closely related but not identical to those of strains of Methanosaeta concilii, two grouped with members of the genus Methanosarcina, and two were related to the methanogenic endosymbiont of Plagiopyla nasuta. The cultivation approach via most-probable-number counts with a subsample of the same soil as an inoculum yielded cell numbers of up to 10(7) per g of dry soil for the H2-CO2-utilizing methanogens and of up to 10(6) for the acetate-utilizing methanogens. Strain VeH52, isolated from the terminal positive dilution on H2-CO2, grouped within the phylogenetic radiation characterized by M. bryantii and M. formicicum and the environmental sequences of the Methanobacterium-like group. A consortium of two distinct methanogens grew in the terminal positive culture on acetate. These two organisms showed absolute 16S rRNA gene identities with environmental sequences of the novel Methanosaeta-like group and the Methanobacterium-like group. Methanosarcina spp. were identified only in the less-dilute levels of the same dilution series on acetate. These data correlate well with acetate concentrations of about 11 microM in the pore water of this rice paddy soil. These concentrations are too low for the growth of known Methanosarcina spp. but are at the acetate utilization threshold of Methanosaeta spp. Thus, our data indicated Methanosaeta spp. and Methanobacterium spp. to be the dominant methanogenic groups in the anoxic rice soil, whereas Methanosarcina spp. appeared to be less abundant.
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Affiliation(s)
- R Grosskopf
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany
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Klüber H, Conrad R. Effects of nitrate, nitrite, NO and N2O on methanogenesis and other redox processes in anoxic rice field soil. FEMS Microbiol Ecol 1998. [DOI: 10.1111/j.1574-6941.1998.tb00482.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Abstract
Considerable progress has been made towards enhancing our understanding of the phylogeny, ecology and biogeochemical role of dissimilatory iron-reducing bacteria. The known phylogenetic range of iron-reducing bacteria has expanded considerably, as has the known range of iron minerals that serve as a source of Fe(III) for anaerobic respiration. In addition, the number of biotechnological applications of iron-reducing bacteria, including remediation of soils and sediments contaminated with metals, radionuclides and organics, is rapidly expanding.
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Affiliation(s)
- J K Fredrickson
- Pacific Northwest National Laboratory, Washington 99352, USA.
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Wind T, Conrad R. Sulfur compounds, potential turnover of sulfate and thiosulfate, and numbers of sulfate-reducing bacteria in planted and unplanted paddy soil. FEMS Microbiol Ecol 1995. [DOI: 10.1111/j.1574-6941.1995.tb00182.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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