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Conrad R. Complexity of temperature dependence in methanogenic microbial environments. Front Microbiol 2023; 14:1232946. [PMID: 37485527 PMCID: PMC10359720 DOI: 10.3389/fmicb.2023.1232946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH4, an important greenhouse gas. Microbial CH4 production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO2 and CH4. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH4 production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H2/CO2 as immediate CH4 precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH4 production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (Ea). Interestingly, CH4 release from defined microbial cultures, from environmental samples and from wetland field sites all show similar Ea values around 100 kJ mol-1 indicating that CH4 production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.
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Li Y, Guo L, Kolton M, Yang R, Zhang M, Qi F, Soleimani M, Sun X, Li B, Gao W, Yan G, Xu R, Sun W. Chemolithotrophic Biological Nitrogen Fixation Fueled by Antimonite Oxidation May Be Widespread in Sb-Contaminated Habitats. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:231-243. [PMID: 36525577 DOI: 10.1021/acs.est.2c06424] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Nitrogen (N) deficiency in mining-contaminated habitats usually hinders plant growth and thus hampers tailing revegetation. Biological N fixation (BNF) is an essential biogeochemical process that contributes to the initial accumulation of N in oligotrophic mining-contaminated regions. Previous studies reported that chemolithotrophic rather than heterotrophic diazotrophs frequently dominated in the mining-contaminated regions. Chemolithotrophic diazotrophs may utilize elements abundant in such habitats (e.g., sulfur (S), arsenic (As), and antimony (Sb)) as electron donors to fix N2. BNF fueled by the oxidation of S and As has been detected in previous studies. However, BNF fueled by Sb(III) oxidation (Sb-dependent BNF) has never been reported. The current study observed the presence of Sb-dependent BNF in slurries inoculated from Sb-contaminated habitats across the South China Sb belt, suggesting that Sb-dependent BNF may be widespread in this region. DNA-stable isotope probing identified bacteria associated with Rhodocyclaceae and Rhizobiaceae as putative microorganisms responsible for Sb-dependent BNF. Furthermore, metagenomic-binning demonstrated that Rhodocyclaceae and Rhizobiaceae contained essential genes involved in Sb(III) oxidation, N2 fixation, and carbon fixation, suggesting their genetic potential for Sb-dependent BNF. In addition, meta-analysis indicated that these bacteria are widespread among Sb-contaminated habitats with different niche preferences: Rhodocyclaceae was enriched in river sediments and tailings, while Rhizobiaceae was enriched only in soils. This study may broaden our fundamental understanding of N fixation in Sb-mining regions.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Lifang Guo
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Rui Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Fangjie Qi
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Mohsen Soleimani
- Department of Natural Resources, Isfahan University of Technology, Isfahan 83111-84156, Iran
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Wenlong Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- Hainan Key Laboratory of Tropical Eco-Circular Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou 571737, China
| | - Geng Yan
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Yuan Z, Liu Q, Pang Z, Fallah N, Liu Y, Hu C, Lin W. Sugarcane Rhizosphere Bacteria Community Migration Correlates with Growth Stages and Soil Nutrient. Int J Mol Sci 2022; 23:ijms231810303. [PMID: 36142216 PMCID: PMC9499485 DOI: 10.3390/ijms231810303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Plants and rhizosphere bacterial microbiota have intimate relationships. As neighbors of the plant root system, rhizosphere microorganisms have a crucial impact on plant growth and health. In this study, we sampled rhizosphere soil of sugarcane in May (seedling), July (tillering), September (elongation) and November (maturity), respectively. We employ 16S rRNA amplicon sequencing to investigate seasonal variations in rhizosphere bacteria community structure and abundance, as well as their association with soil edaphic factors. The results demonstrate that soil pH, total nitrogen (TN) and available nitrogen (AN) decrease substantially with time. Rhizosphere bacteria diversity (Shannon) and the total enriched OTUs are also significantly higher in July relative to other months. Bacteria OTUs and functional composition exhibit a strong and significant correlation with soil temperature (Tem), suggesting that Tem was the potential determinant controlling rhizosphere bacteria diversity, enriched OTUs as well as functional composition. Redundancy analysis (RDA) point toward soil total potassium (TK), pH, TN, Tem and AN as principal determinant altering shifting bacteria community structure. Variation partitioning analysis (VPA) analysis further validate that a substantial proportion of variation (70.79%) detected in the rhizosphere bacteria community structure was attributed to edaphic factors. Mfuzz analysis classified the bacterial genera into four distinct clusters, with cluster two exhibiting a distinct and dramatic increase in July, predominantly occupied by Allocatelliglobosispora. The stochastic forest model found the key characteristic bacterial populations that can distinguish the four key growth periods of sugarcane. It may help us to answer some pending questions about the interaction of rhizosphere microorganisms with plants in the future.
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Affiliation(s)
- Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugar Industry, Nanning 530000, China
- Correspondence:
| | - Qiang Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yueming Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chaohua Hu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Karekar S, Stefanini R, Ahring B. Homo-Acetogens: Their Metabolism and Competitive Relationship with Hydrogenotrophic Methanogens. Microorganisms 2022; 10:microorganisms10020397. [PMID: 35208852 PMCID: PMC8875654 DOI: 10.3390/microorganisms10020397] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Homo-acetogens are microbes that have the ability to grow on gaseous substrates such as H2/CO2/CO and produce acetic acid as the main product of their metabolism through a metabolic process called reductive acetogenesis. These acetogens are dispersed in nature and are found to grow in various biotopes on land, water and sediments. They are also commonly found in the gastro-intestinal track of herbivores that rely on a symbiotic relationship with microbes in order to breakdown lignocellulosic biomass to provide the animal with nutrients and energy. For this motive, the fermentation scheme that occurs in the rumen has been described equivalent to a consolidated bioprocessing fermentation for the production of bioproducts derived from livestock. This paper reviews current knowledge of homo-acetogenesis and its potential to improve efficiency in the rumen for production of bioproducts by replacing methanogens, the principal H2-scavengers in the rumen, thus serving as a form of carbon sink by deviating the formation of methane into bioproducts. In this review, we discuss the main strategies employed by the livestock industry to achieve methanogenesis inhibition, and also explore homo-acetogenic microorganisms and evaluate the members for potential traits and characteristics that may favor competitive advantage over methanogenesis, making them prospective candidates for competing with methanogens in ruminant animals.
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Affiliation(s)
- Supriya Karekar
- Bioproducts Science and Engineering Laboratory, Washington State University Tri-Cities, 2720 Crimson Way, Richland, WA 99354, USA; (S.K.); (R.S.)
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99163, USA
| | - Renan Stefanini
- Bioproducts Science and Engineering Laboratory, Washington State University Tri-Cities, 2720 Crimson Way, Richland, WA 99354, USA; (S.K.); (R.S.)
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99163, USA
| | - Birgitte Ahring
- Bioproducts Science and Engineering Laboratory, Washington State University Tri-Cities, 2720 Crimson Way, Richland, WA 99354, USA; (S.K.); (R.S.)
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99163, USA
- The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99163, USA
- Correspondence:
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Singh A, Müller B, Schnürer A. Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP. Sci Rep 2021; 11:13298. [PMID: 34168213 PMCID: PMC8225771 DOI: 10.1038/s41598-021-92658-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Acetogens play a key role in anaerobic degradation of organic material and in maintaining biogas process efficiency. Profiling this community and its temporal changes can help evaluate process stability and function, especially under disturbance/stress conditions, and avoid complete process failure. The formyltetrahydrofolate synthetase (FTHFS) gene can be used as a marker for acetogenic community profiling in diverse environments. In this study, we developed a new high-throughput FTHFS gene sequencing method for acetogenic community profiling and compared it with conventional terminal restriction fragment length polymorphism of the FTHFS gene, 16S rRNA gene-based profiling of the whole bacterial community, and indirect analysis via 16S rRNA profiling of the FTHFS gene-harbouring community. Analyses and method comparisons were made using samples from two laboratory-scale biogas processes, one operated under stable control and one exposed to controlled overloading disturbance. Comparative analysis revealed satisfactory detection of the bacterial community and its changes for all methods, but with some differences in resolution and taxonomic identification. FTHFS gene sequencing was found to be the most suitable and reliable method to study acetogenic communities. These results pave the way for community profiling in various biogas processes and in other environments where the dynamics of acetogenic bacteria have not been well studied.
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Affiliation(s)
- Abhijeet Singh
- grid.6341.00000 0000 8578 2742Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7025, 750 07 Uppsala, Sweden
| | - Bettina Müller
- grid.6341.00000 0000 8578 2742Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7025, 750 07 Uppsala, Sweden
| | - Anna Schnürer
- grid.6341.00000 0000 8578 2742Anaerobic Microbiology and Biotechnology Group, Department of Molecular Sciences, Swedish University of Agricultural Sciences, Almas Allé 5, Box 7025, 750 07 Uppsala, Sweden
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Yue Y, Wang J, Wu X, Zhang J, Chen Z, Kang X, Lv Z. The fate of anaerobic syntrophy in anaerobic digestion facing propionate and acetate accumulation. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 124:128-135. [PMID: 33611157 DOI: 10.1016/j.wasman.2021.01.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/30/2020] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
How the acetate and propionate accumulation impact anaerobic syntrophy during methane formation is not well understood. To investigate such effect, continuous acetate (35 g/L), propionate (11.25 g/L) and bicarbonate (30 g/L) supplementation were used during mesophilic anaerobic digestion. The high throughput sequencing (16S rRNA and mcrA), Real-Time quantitative PCR, and stable carbon isotope fingerprinting were applied to investigate the structure and activity of microbial community members. The results demonstrated that the abundance of syntrophic acetate oxidizing bacteria exhibited a gradual decrease coupled with heavier stable carbon isotopic signature of methane (δ 13CH4) in the three reagents impacted reactors. The increased acetate and propionate concentrations exerted negative influence on biogas production but the relatively stable hydrogenotrophic methanogens together with syntrophic acetate/propionate oxidizing bacteria kept the stable methane formation facing acetate and propionate accumulation. The functional genes copy number of the hydrogenotrophic Methanocellaceae and Methanomicrobiaceae correlated significantly with δ 13CH4 (R2 > 0.74), but only the abundance of Methanocellaceae fitted well with δ 13CH4 (p < 0.05). The δ 13CH4 signatures can predict methanogenesis, as it directly reflects the main methanogenic pathway; yet, further investigation of isotope fractionation in acetate/propionate coupled with δ 13CH4 is needed. Collectively, these results provide deep insight into anaerobic syntrophy and reveal changes of synergistic relationships, both of which may contribute to the stability of biogas reactors.
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Affiliation(s)
- Yanan Yue
- School of Life, Jiangsu Normal University, Shanghai Road 101, 221116 Xuzhou, China
| | - Junyu Wang
- School of Life, Jiangsu Normal University, Shanghai Road 101, 221116 Xuzhou, China
| | - Xiayuan Wu
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Jianfeng Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhongbing Chen
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic.
| | - Xuejing Kang
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic
| | - Zuopeng Lv
- School of Life, Jiangsu Normal University, Shanghai Road 101, 221116 Xuzhou, China.
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Pan X, Zhao L, Li C, Angelidaki I, Lv N, Ning J, Cai G, Zhu G. Deep insights into the network of acetate metabolism in anaerobic digestion: focusing on syntrophic acetate oxidation and homoacetogenesis. WATER RESEARCH 2021; 190:116774. [PMID: 33387947 DOI: 10.1016/j.watres.2020.116774] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Acetate is a pivotal intermediate product during anaerobic decomposition of organic matter. Its generation and consumption network is quite complex, which almost covers the most steps in anaerobic digestion (AD) process. Besides acidogenesis, acetogenesis and methanogenesis, syntrophic acetate oxidation (SAO) replaced acetoclastic methanogenesis to release the inhibition of AD at some special conditions, and the importance of considering homoacetogenesis had also been proved when analysing anaerobic fermentations. Syntrophic acetate-oxidizing bacteria (SAOB), with function of SAO, can survive under high temperature and ammonia/ volatile fatty acids (VFAs) concentrations, while, homoacetogens, performed homoacetogenesis, are more active under acidic, alkaline and low temperature (10°C-20°C) conditions, This review summarized the roles of SAO and homoacetogenesis in AD process, which contains the biochemical reactions, metabolism pathways, physiological characteristics and energy conservation of functional bacteria. The specific roles of these two processes in the subprocess of AD (i.e., acidogenesis, acetogenesis and methanogenesis) were also analyzed in detail. A two phases anaerobic digester is proposed for protein-rich waste(water) treatment by enhancing the functions of homoacetogens and SAOB compared to the traditional two-phases anaerobic digesters, in which the first phase is fermentation phase including acidogens and homoacetogens for acetate production, and second phase is a mixed culture coupling syntrophic fatty acids bacteria, SAOB and hydrogenotrophic methanogens for methane production. This review provides a new insight into the network on production and consumption of acetate in AD process.
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Affiliation(s)
- Xiaofang Pan
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Lixin Zhao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, Beijing100081, China
| | - Chunxing Li
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Nan Lv
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Jing Ning
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Guanjing Cai
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Gefu Zhu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China.
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Fu B, Jin X, Conrad R, Liu H, Liu H. Competition Between Chemolithotrophic Acetogenesis and Hydrogenotrophic Methanogenesis for Exogenous H 2/CO 2 in Anaerobically Digested Sludge: Impact of Temperature. Front Microbiol 2019; 10:2418. [PMID: 31749772 PMCID: PMC6842956 DOI: 10.3389/fmicb.2019.02418] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/07/2019] [Indexed: 11/13/2022] Open
Abstract
Anaerobic digestion is a widely applied technology for sewage sludge treatment. Hydrogen and CO2 are important degradation products, which serve as substrates for both hydrogenotrophic methanogenesis and chemolithotrophic acetogenesis. In order to understand the competition between these processes for H2/CO2, sludge samples were incubated under H2/CO2 headspace at different temperatures, and analyzed with respect to turnover of H2, CO2, CH4 and acetate including their δ13C values. At 15°C, 13C-depleted acetate (δ13C of -41 to -43‰) and transient acetate accumulation were observed under H2/CO2, and CH4 accumulated with δ13C values increasing from -53 to -33‰. The copy numbers of the fhs gene, which is characteristic for acetogenic bacteria, were at 15°C one order of magnitude higher in the H2/CO2 incubations than the N2 control. At 30°C, however, acetate did not accumulate in the H2/CO2 incubation and the δ13C of CH4 was very low (-100 to -77‰). At 50°C, isotopically enriched acetate was transiently formed and subsequently consumed followed by the production of 13C-depleted CH4. Collectively, the results indicate a high contribution of chemolithotrophic acetogenesis to H2/CO2 utilization at 15°C and 50°C, while H2/CO2 was mainly consumed by hydrogenotrophic methanogenesis at 30°C. Fermentative production and methanogenic consumption of acetate were active at 50°C.
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Affiliation(s)
- Bo Fu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China.,Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou, China
| | - Xin Jin
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China
| | - Ralf Conrad
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hongbo Liu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China.,Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou, China
| | - He Liu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China.,Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou, China
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Fazi S, Ungaro F, Venturi S, Vimercati L, Cruz Viggi C, Baronti S, Ugolini F, Calzolari C, Tassi F, Vaselli O, Raschi A, Aulenta F. Microbiomes in Soils Exposed to Naturally High Concentrations of CO 2 (Bossoleto Mofette Tuscany, Italy). Front Microbiol 2019; 10:2238. [PMID: 31681186 PMCID: PMC6797827 DOI: 10.3389/fmicb.2019.02238] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/12/2019] [Indexed: 01/05/2023] Open
Abstract
Direct and indirect effects of extremely high geogenic CO2 levels, commonly occurring in volcanic and hydrothermal environments, on biogeochemical processes in soil are poorly understood. This study investigated a sinkhole in Italy where long-term emissions of thermometamorphic-derived CO2 are associated with accumulation of carbon in the topsoil and removal of inorganic carbon in low pH environments at the bottom of the sinkhole. The comparison between interstitial soil gasses and those collected in an adjacent bubbling pool and the analysis of the carbon isotopic composition of CO2 and CH4 clearly indicated the occurrence of CH4 oxidation and negligible methanogenesis in soils at the bottom of the sinkhole. Extremely high CO2 concentrations resulted in higher microbial abundance (up to 4 × 109 cell g-1 DW) and a lower microbial diversity by favoring bacteria already reported to be involved in acetogenesis in mofette soils (i.e., Firmicutes, Chloroflexi, and Acidobacteria). Laboratory incubations to test the acetogenic and methanogenic potential clearly showed that all the mofette soil supplied with hydrogen gas displayed a remarkable CO2 fixation potential, primarily due to the activity of acetogenic microorganisms. By contrast, negligible production of acetate occurred in control tests incubated with the same soils, under identical conditions, without the addition of hydrogen. In this study, we report how changes in diversity and functions of the soil microbial community - induced by high CO2 concentration - create peculiar biogeochemical profile. CO2 emission affects carbon cycling through: (i) inhibition of the decomposition of the organic carbon and (ii) promotion of CO2-fixation via the acetyl-CoA pathway. Sites naturally exposed to extremely high CO2 levels could potentially represent an untapped source of microorganisms with unique capabilities to catalytically convert CO2 into valuable organic chemicals and fuels.
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Affiliation(s)
- Stefano Fazi
- Water Research Institute, National Research Council (IRSA-CNR), Rome, Italy
| | - Fabrizio Ungaro
- Institute of BioEconomy - National Research Council (IBE-CNR), Florence, Italy
| | - Stefania Venturi
- Institute of Geosciences and Earth Resources, National Research Council (IGG-CNR), Florence, Italy.,Department of Earth Sciences, University of Florence, Florence, Italy
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | | | - Silvia Baronti
- Institute of BioEconomy - National Research Council (IBE-CNR), Florence, Italy
| | - Francesca Ugolini
- Institute of BioEconomy - National Research Council (IBE-CNR), Florence, Italy
| | - Costanza Calzolari
- Institute of BioEconomy - National Research Council (IBE-CNR), Florence, Italy
| | - Franco Tassi
- Institute of Geosciences and Earth Resources, National Research Council (IGG-CNR), Florence, Italy.,Department of Earth Sciences, University of Florence, Florence, Italy
| | - Orlando Vaselli
- Institute of Geosciences and Earth Resources, National Research Council (IGG-CNR), Florence, Italy.,Department of Earth Sciences, University of Florence, Florence, Italy
| | - Antonio Raschi
- Institute of BioEconomy - National Research Council (IBE-CNR), Florence, Italy
| | - Federico Aulenta
- Water Research Institute, National Research Council (IRSA-CNR), Rome, Italy
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10
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Fu B, Jin X, Conrad R, Liu H, Liu H. Competition Between Chemolithotrophic Acetogenesis and Hydrogenotrophic Methanogenesis for Exogenous H 2/CO 2 in Anaerobically Digested Sludge: Impact of Temperature. Front Microbiol 2019; 10:2418. [PMID: 31749772 DOI: 10.3389/fmicb.2019.02418/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/07/2019] [Indexed: 05/21/2023] Open
Abstract
Anaerobic digestion is a widely applied technology for sewage sludge treatment. Hydrogen and CO2 are important degradation products, which serve as substrates for both hydrogenotrophic methanogenesis and chemolithotrophic acetogenesis. In order to understand the competition between these processes for H2/CO2, sludge samples were incubated under H2/CO2 headspace at different temperatures, and analyzed with respect to turnover of H2, CO2, CH4 and acetate including their δ13C values. At 15°C, 13C-depleted acetate (δ13C of -41 to -43‰) and transient acetate accumulation were observed under H2/CO2, and CH4 accumulated with δ13C values increasing from -53 to -33‰. The copy numbers of the fhs gene, which is characteristic for acetogenic bacteria, were at 15°C one order of magnitude higher in the H2/CO2 incubations than the N2 control. At 30°C, however, acetate did not accumulate in the H2/CO2 incubation and the δ13C of CH4 was very low (-100 to -77‰). At 50°C, isotopically enriched acetate was transiently formed and subsequently consumed followed by the production of 13C-depleted CH4. Collectively, the results indicate a high contribution of chemolithotrophic acetogenesis to H2/CO2 utilization at 15°C and 50°C, while H2/CO2 was mainly consumed by hydrogenotrophic methanogenesis at 30°C. Fermentative production and methanogenic consumption of acetate were active at 50°C.
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Affiliation(s)
- Bo Fu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou, China
| | - Xin Jin
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China
| | - Ralf Conrad
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hongbo Liu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou, China
| | - He Liu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environmental and Civil Engineering, Jiangnan University, Wuxi, China
- Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou, China
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11
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Tsavkelova E, Prokudina L, Egorova M, Leontieva M, Malakhova D, Netrusov A. The structure of the anaerobic thermophilic microbial community for the bioconversion of the cellulose-containing substrates into biogas. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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12
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Pal DS, Tripathee R, Reid MC, Schäfer KVR, Jaffé PR. Simultaneous measurements of dissolved CH 4 and H 2 in wetland soils. ENVIRONMENTAL MONITORING AND ASSESSMENT 2018; 190:176. [PMID: 29484491 DOI: 10.1007/s10661-018-6552-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Biogeochemical processes in wetland soils are complex and are driven by a microbiological community that competes for resources and affects the soil chemistry. Depending on the availability of various electron acceptors, the high carbon input to wetland soils can make them important sources of methane production and emissions. There are two significant pathways for methanogenesis: acetoclastic and hydrogenotrophic methanogenesis. The hydrogenotrophic pathway is dependent on the availability of dissolved hydrogen gas (H2), and there is significant competition for available H2. This study presents simultaneous measurements of dissolved methane and H2 over a 2-year period at three tidal marshes in the New Jersey Meadowlands. Methane reservoirs show a significant correlation with dissolved organic carbon, temperature, and methane emissions, whereas the H2 concentrations measured with dialysis samplers do not show significant relationships with these field variables. Data presented in this study show that increased dissolved H2 reservoirs in wetland soils correlate with decreased methane reservoirs, which is consistent with studies that have shown that elevated levels of H2 inhibit methane production by inhibiting propionate fermentation, resulting in less acetate production and hence decreasing the contribution of acetoclastic methanogenesis to the overall production of methane.
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Affiliation(s)
- David S Pal
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, USA
| | - Rajan Tripathee
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Matthew C Reid
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | | | - Peter R Jaffé
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, USA.
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13
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Zheng S, Wang B, Li Y, Liu F, Wang O. Electrochemically active iron (III)-reducing bacteria in coastal riverine sediments. J Basic Microbiol 2017; 57:1045-1054. [DOI: 10.1002/jobm.201700322] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/30/2017] [Accepted: 09/01/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Shiling Zheng
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai China
| | - Bingchen Wang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai China
- University of Chinese Academy of Sciences; Beijing China
| | - Ying Li
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai China
- University of Chinese Academy of Sciences; Beijing China
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research; Chinese Academy of Sciences; Yantai China
| | - Oumei Wang
- Binzhou Medical University; Yantai China
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14
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Herrmann E, Young W, Rosendale D, Conrad R, Riedel CU, Egert M. Determination of Resistant Starch Assimilating Bacteria in Fecal Samples of Mice by In vitro RNA-Based Stable Isotope Probing. Front Microbiol 2017; 8:1331. [PMID: 28790981 PMCID: PMC5522855 DOI: 10.3389/fmicb.2017.01331] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/30/2017] [Indexed: 01/01/2023] Open
Abstract
The impact of the intestinal microbiota on human health is becoming increasingly appreciated in recent years. In consequence, and fueled by major technological advances, the composition of the intestinal microbiota in health and disease has been intensively studied by high throughput sequencing approaches. Observations linking dysbiosis of the intestinal microbiota with a number of serious medical conditions including chronic inflammatory disorders and allergic diseases suggest that restoration of the composition and activity of the intestinal microbiota may be a treatment option at least for some of these diseases. One possibility to shape the intestinal microbiota is the administration of prebiotic carbohydrates such as resistant starch (RS). In the present study, we aim at establishing RNA-based stable isotope probing (RNA-SIP) to identify bacterial populations that are involved in the assimilation of RS using anaerobic in vitro fermentation of murine fecal material with stable [U13C] isotope-labeled potato starch. Total RNA from these incubations was extracted, processed by gradient ultracentrifugation and fractionated by density. 16S rRNA gene sequences were amplified from reverse transcribed RNA of high and low density fractions suspected to contain labeled and unlabeled RNA, respectively. Phylogenetic analysis of the obtained sequences revealed a distinct subset of the intestinal microbiota involved in starch metabolism. The results suggest Bacteroidetes, in particular genera affiliated with Prevotellaceae, as well as members of the Ruminococcacea family to be primary assimilators of resistant starch due to a significantly higher relative abundance in higher density fractions in RNA samples isolated after 2 h of incubation. Using high performance liquid chromatography coupled to isotope ratio mass spectrometry (HPLC-IRMS) analysis, some stable isotope label was recovered from acetate, propionate and butyrate. Here, we demonstrate the suitability of RNA-SIP to link specific groups of microorganisms with fermentation of a specific substrate. The application of RNA-SIP in future in vivo studies will help to better understand the mechanisms behind functionality of a prebiotic carbohydrate and its impact on an intestinal ecosystem with potential implications for human health.
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Affiliation(s)
- Elena Herrmann
- Faculty of Medical & Life Sciences, Institute of Precision Medicine, Furtwangen UniversityVillingen-Schwenningen, Germany
| | - Wayne Young
- AgResearch Ltd., Food Nutrition and Health Team, Grasslands Research CentrePalmerston North, New Zealand
| | - Douglas Rosendale
- The New Zealand Institute for Plant & Food Research Ltd.Palmerston North, New Zealand
| | - Ralf Conrad
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Christian U Riedel
- Institute of Microbiology and Biotechnology, University of UlmUlm, Germany
| | - Markus Egert
- Faculty of Medical & Life Sciences, Institute of Precision Medicine, Furtwangen UniversityVillingen-Schwenningen, Germany
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15
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RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1829685. [PMID: 28299315 PMCID: PMC5337319 DOI: 10.1155/2017/1829685] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 11/17/2022]
Abstract
RNA-based stable isotope probing (RNA-SIP) and metabolic profiling were used to detect actively glucose-consuming bacteria in a complex microbial community obtained from a murine model system. A faeces-derived microbiota was incubated under anaerobic conditions for 0, 2, and 4 h with 40 mM [U13C]glucose. Isopycnic density gradient ultracentrifugation and fractionation of isolated RNA into labeled and unlabeled fractions followed by 16S rRNA sequencing showed a quick adaptation of the bacterial community in response to the added sugar, which was dominated by unclassified Lachnospiraceae species. Inspection of distinct fractions of isotope-labeled RNA revealed Allobaculum spp. as particularly active glucose utilizers in the system, as the corresponding RNA showed significantly higher proportions among the labeled RNA. With time, the labeled sugar was used by a wider spectrum of faecal bacteria. Metabolic profiling indicated rapid fermentation of [U13C]glucose, with lactate, acetate, and propionate being the principal 13C-labeled fermentation products, and suggested that "cross-feeding" occurred in the system. RNA-SIP combined with metabolic profiling of 13C-labeled products allowed insights into the microbial assimilation of a general model substrate, demonstrating the appropriateness of this technology to study assimilation processes of nutritionally more relevant substrates, for example, prebiotic carbohydrates, in the gut microbiota of mice as a model system.
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16
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Malyan SK, Bhatia A, Kumar A, Gupta DK, Singh R, Kumar SS, Tomer R, Kumar O, Jain N. Methane production, oxidation and mitigation: A mechanistic understanding and comprehensive evaluation of influencing factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 572:874-896. [PMID: 27575427 DOI: 10.1016/j.scitotenv.2016.07.182] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/02/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Methane is one of the critical greenhouse gases, which absorb long wavelength radiation, affects the chemistry of atmosphere and contributes to global climate change. Rice ecosystem is one of the major anthropogenic sources of methane. The anaerobic waterlogged soil in rice field provides an ideal environment to methanogens for methanogenesis. However, the rate of methanogenesis differs according to rice cultivation regions due to a number of biological, environmental and physical factors like carbon sources, pH, Eh, temperature etc. The interplay between the different conditions and factors may also convert the rice fields into sink from source temporarily. Mechanistic understanding and comprehensive evaluation of these variations and responsible factors are urgently required for designing new mitigation options and evaluation of reported option in different climatic conditions. The objective of this review paper is to develop conclusive understanding on the methane production, oxidation, and emission and methane measurement techniques from rice field along with its mitigation/abatement mechanism to explore the possible reduction techniques from rice ecosystem.
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Affiliation(s)
- Sandeep K Malyan
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Arti Bhatia
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Amit Kumar
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Dipak Kumar Gupta
- ICAR-Central Arid Zone Research Institute, Regional Research Station, Pali-Marwar, Rajasthan 342003, India
| | - Renu Singh
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Smita S Kumar
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India
| | - Ritu Tomer
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Om Kumar
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Niveta Jain
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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17
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Güllert S, Fischer MA, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A, Streit WR. Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:121. [PMID: 27279900 PMCID: PMC4897800 DOI: 10.1186/s13068-016-0534-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/26/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND The diverse microbial communities in agricultural biogas fermenters are assumed to be well adapted for the anaerobic transformation of plant biomass to methane. Compared to natural systems, biogas reactors are limited in their hydrolytic potential. The reasons for this are not understood. RESULTS In this paper, we show that a typical industrial biogas reactor fed with maize silage, cow manure, and chicken manure has relatively lower hydrolysis rates compared to feces samples from herbivores. We provide evidence that on average, 2.5 genes encoding cellulolytic GHs/Mbp were identified in the biogas fermenter compared to 3.8 in the elephant feces and 3.2 in the cow rumen data sets. The ratio of genes coding for cellulolytic GH enzymes affiliated with the Firmicutes versus the Bacteroidetes was 2.8:1 in the biogas fermenter compared to 1:1 in the elephant feces and 1.4:1 in the cow rumen sample. Furthermore, RNA-Seq data indicated that highly transcribed cellulases in the biogas fermenter were four times more often affiliated with the Firmicutes compared to the Bacteroidetes, while an equal distribution of these enzymes was observed in the elephant feces sample. CONCLUSIONS Our data indicate that a relatively lower abundance of bacteria affiliated with the phylum of Bacteroidetes and, to some extent, Fibrobacteres is associated with a decreased richness of predicted lignocellulolytic enzymes in biogas fermenters. This difference can be attributed to a partial lack of genes coding for cellulolytic GH enzymes derived from bacteria which are affiliated with the Fibrobacteres and, especially, the Bacteroidetes. The partial deficiency of these genes implies a potentially important limitation in the biogas fermenter with regard to the initial hydrolysis of biomass. Based on these findings, we speculate that increasing the members of Bacteroidetes and Fibrobacteres in biogas fermenters will most likely result in an increased hydrolytic performance.
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Affiliation(s)
- Simon Güllert
- />Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Martin A. Fischer
- />Institute for General Microbiology, Christian Albrecht University Kiel, Kiel, Germany
| | - Dmitrij Turaev
- />CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria
| | - Britta Noebauer
- />CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria
| | - Nele Ilmberger
- />Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Bernd Wemheuer
- />Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, Germany
| | - Malik Alawi
- />Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Martinistr. 52, Hamburg, Germany
- />Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, Hamburg, Germany
| | - Thomas Rattei
- />CUBE-Division for Computational Systems Biology, Dept. of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, Vienna, Austria
| | - Rolf Daniel
- />Institute of Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, Germany
| | - Ruth A. Schmitz
- />Institute for General Microbiology, Christian Albrecht University Kiel, Kiel, Germany
| | - Adam Grundhoff
- />Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistr. 52, Hamburg, Germany
| | - Wolfgang R. Streit
- />Department of Microbiology and Biotechnology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
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18
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Zheng S, Zhang H, Li Y, Zhang H, Wang O, Zhang J, Liu F. Co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Front Microbiol 2015; 6:941. [PMID: 26441876 PMCID: PMC4562271 DOI: 10.3389/fmicb.2015.00941] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 08/24/2015] [Indexed: 01/06/2023] Open
Abstract
Methanosaeta harundinacea and Methanosarcina barkeri, known as classic acetoclastic methanogens, are capable of directly accepting electrons from Geobacter metallireducens for the reduction of carbon dioxide to methane, having been revealed as direct interspecies electron transfer (DIET) in the laboratory co-cultures. However, whether their co-occurrences are ubiquitous in the iron (III)-reducing environments and the other species of acetoclastic methanogens such as Methanosarcina mazei are capable of DIET are still unknown. Instead of initiating the co-cultures with pure cultures, two-step cultivation was employed to selectively enrich iron (III)-reducing microorganisms in a coastal gold mining river, Jiehe River, with rich iron content in the sediments. First, iron (III) reducers including Geobacteraceae were successfully enriched by 3-months successive culture on amorphous Fe(III) oxides as electron acceptor and acetate as electron donor. High-throughput Illumina sequencing, terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures actively contained the bacteria belong to Geobacteraceae and Bacilli, exclusively dominated by the archaea belong to Methanosarcinaceae. Second, the enrichment cultures including methanogens and Geobacteraceae were transferred with ethanol as alternative electron donor. Remarkably, aggregates were successively formed in the enrichments after three transfers. The results revealed by RNA-based analysis demonstrate that the co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (III)-reducing enrichment culture. Furthermore, the aggregates, as close physical contact, formed in the enrichment culture, indicate that DIET could be a possible option for interspecies electron transfer in the aggregates.
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Affiliation(s)
- Shiling Zheng
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Hongxia Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; University of Chinese Academy of Sciences Beijing, China
| | - Ying Li
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; University of Chinese Academy of Sciences Beijing, China
| | - Hua Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
| | - Oumei Wang
- Key Laboratory for Genetic Hearing Disorders in Shandong, Binzhou Medical University Yantai, China
| | - Jun Zhang
- The College of Life Sciences, Northwest University Xi'an, China
| | - Fanghua Liu
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China ; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences Yantai, China
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19
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Isolation of acetogenic bacteria that induce biocorrosion by utilizing metallic iron as the sole electron donor. Appl Environ Microbiol 2014; 81:67-73. [PMID: 25304512 DOI: 10.1128/aem.02767-14] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corrosion of iron occurring under anoxic conditions, which is termed microbiologically influenced corrosion (MIC) or biocorrosion, is mostly caused by microbial activities. Microbial activity that enhances corrosion via uptake of electrons from metallic iron [Fe(0)] has been regarded as one of the major causative factors. In addition to sulfate-reducing bacteria and methanogenic archaea in marine environments, acetogenic bacteria in freshwater environments have recently been suggested to cause MIC under anoxic conditions. However, no microorganisms that perform acetogenesis-dependent MIC have been isolated or had their MIC-inducing mechanisms characterized. Here, we enriched and isolated acetogenic bacteria that induce iron corrosion by utilizing Fe(0) as the sole electron donor under freshwater, sulfate-free, and anoxic conditions. The enriched communities produced significantly larger amounts of Fe(II) than the abiotic controls and produced acetate coupled with Fe(0) oxidation prior to CH4 production. Microbial community analysis revealed that Sporomusa sp. and Desulfovibrio sp. dominated in the enrichments. Strain GT1, which is closely related to the acetogen Sporomusa sphaeroides, was eventually isolated from the enrichment. Strain GT1 grew acetogenetically with Fe(0) as the sole electron donor and enhanced iron corrosion, which is the first demonstration of MIC mediated by a pure culture of an acetogen. Other well-known acetogenic bacteria, including Sporomusa ovata and Acetobacterium spp., did not grow well on Fe(0). These results indicate that very few species of acetogens have specific mechanisms to efficiently utilize cathodic electrons derived from Fe(0) oxidation and induce iron corrosion.
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20
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Montoya L, Celis LB, Razo-Flores E, Alpuche-Solís ÁG. Distribution of CO2 fixation and acetate mineralization pathways in microorganisms from extremophilic anaerobic biotopes. Extremophiles 2012; 16:805-17. [DOI: 10.1007/s00792-012-0487-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 09/27/2012] [Indexed: 11/28/2022]
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21
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Lever MA. Acetogenesis in the energy-starved deep biosphere - a paradox? Front Microbiol 2012; 2:284. [PMID: 22347874 PMCID: PMC3276360 DOI: 10.3389/fmicb.2011.00284] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 12/31/2011] [Indexed: 12/01/2022] Open
Abstract
Under anoxic conditions in sediments, acetogens are often thought to be outcompeted by microorganisms performing energetically more favorable metabolic pathways, such as sulfate reduction or methanogenesis. Recent evidence from deep subseafloor sediments suggesting acetogenesis in the presence of sulfate reduction and methanogenesis has called this notion into question, however. Here I argue that acetogens can successfully coexist with sulfate reducers and methanogens for multiple reasons. These include (1) substantial energy yields from most acetogenesis reactions across the wide range of conditions encountered in the subseafloor, (2) wide substrate spectra that enable niche differentiation by use of different substrates and/or pooling of energy from a broad range of energy substrates, (3) reduced energetic cost of biosynthesis among acetogens due to use of the reductive acetyl CoA pathway for both energy production and biosynthesis coupled with the ability to use many organic precursors to produce the key intermediate acetyl CoA. This leads to the general conclusion that, beside Gibbs free energy yields, variables such as metabolic strategy and energetic cost of biosynthesis need to be taken into account to understand microbial survival in the energy-depleted deep biosphere.
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Affiliation(s)
- Mark Alexander Lever
- Department of Bioscience, Center for Geomicrobiology, Aarhus UniversityAarhus, Denmark
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