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Yu T, Fu L, Wang Y, Dong Y, Chen Y, Wegener G, Cheng L, Wang F. Thermophilic Hadarchaeota grow on long-chain alkanes in syntrophy with methanogens. Nat Commun 2024; 15:6560. [PMID: 39095478 PMCID: PMC11297162 DOI: 10.1038/s41467-024-50883-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Methanogenic hydrocarbon degradation can be carried out by archaea that couple alkane oxidation directly to methanogenesis, or by syntrophic associations of bacteria with methanogenic archaea. However, metagenomic analyses of methanogenic environments have revealed other archaea with potential for alkane degradation but apparent inability to form methane, suggesting the existence of other modes of syntrophic hydrocarbon degradation. Here, we provide experimental evidence supporting the existence of a third mode of methanogenic degradation of hydrocarbons, mediated by syntrophic cooperation between archaeal partners. We collected sediment samples from a hot spring sediment in Tengchong, China, and enriched Hadarchaeota under methanogenic conditions at 60 °C, using hexadecane as substrate. We named the enriched archaeon Candidatus Melinoarchaeum fermentans DL9YTT1. We used 13C-substrate incubations, metagenomic, metatranscriptomic and metabolomic analyses to show that Ca. Melinoarchaeum uses alkyl-coenzyme M reductases (ACRs) to activate hexadecane via alkyl-CoM formation. Ca. Melinoarchaeum likely degrades alkanes to carbon dioxide, hydrogen and acetate, which can be used as substrates by hydrogenotrophic and acetoclastic methanogens such as Methanothermobacter and Methanothrix.
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Affiliation(s)
- Tiantian Yu
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; and School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Lin Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yijing Dong
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | - Yifan Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China.
| | - Fengping Wang
- Key Laboratory of Polar Ecosystem and Climate Change, Ministry of Education; and School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China.
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2
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Wu K, Zhou L, Tahon G, Liu L, Li J, Zhang J, Zheng F, Deng C, Han W, Bai L, Fu L, Dong X, Zhang C, Ettema TJG, Sousa DZ, Cheng L. Isolation of a methyl-reducing methanogen outside the Euryarchaeota. Nature 2024; 632:1124-1130. [PMID: 39048829 DOI: 10.1038/s41586-024-07728-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
Methanogenic archaea are main contributors to methane emissions, and have a crucial role in carbon cycling and global warming. Until recently, methanogens were confined to Euryarchaeota, but metagenomic studies revealed the presence of genes encoding the methyl coenzyme M reductase complex in other archaeal clades1-4, thereby opening up the premise that methanogenesis is taxonomically more widespread. Nevertheless, laboratory cultivation of these non-euryarchaeal methanogens was lacking to corroborate their potential methanogenic ability and physiology. Here we report the isolation of a thermophilic archaeon LWZ-6 from an oil field. This archaeon belongs to the class Methanosuratincolia (originally affiliated with 'Candidatus Verstraetearchaeota') in the phylum Thermoproteota. Methanosuratincola petrocarbonis LWZ-6 is a strict hydrogen-dependent methylotrophic methanogen. Although previous metagenomic studies speculated on the fermentative potential of Methanosuratincolia members, strain LWZ-6 does not ferment sugars, peptides or amino acids. Its energy metabolism is linked only to methanogenesis, with methanol and monomethylamine as electron acceptors and hydrogen as an electron donor. Comparative (meta)genome analysis confirmed that hydrogen-dependent methylotrophic methanogenesis is a widespread trait among Methanosuratincolia. Our findings confirm that the diversity of methanogens expands beyond the classical Euryarchaeota and imply the importance of hydrogen-dependent methylotrophic methanogenesis in global methane emissions and carbon cycle.
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Affiliation(s)
- Kejia Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Lei Zhou
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Guillaume Tahon
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Laiyan Liu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Jianchao Zhang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Fengfeng Zheng
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China
| | - Chengpeng Deng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Wenhao Han
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Liping Bai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Lin Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China.
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3
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Guo ZC, Cui MH, Yang CX, Dai HL, Yang TY, Zhai LZ, Chen Y, Liu WZ, Wang AJ. Electrical stress and acid orange 7 synergistically clear the blockage of electron flow in the methanogenesis of low-strength wastewater. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 20:100410. [PMID: 38572083 PMCID: PMC10987894 DOI: 10.1016/j.ese.2024.100410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
Energy recovery from low-strength wastewater through anaerobic methanogenesis is constrained by limited substrate availability. The development of efficient methanogenic communities is critical but challenging. Here we develop a strategy to acclimate methanogenic communities using conductive carrier (CC), electrical stress (ES), and Acid Orange 7 (AO7) in a modified biofilter. The synergistic integration of CC, ES, and AO7 precipitated a remarkable 72-fold surge in methane production rate compared to the baseline. This increase was attributed to an altered methanogenic community function, independent of the continuous presence of AO7 and ES. AO7 acted as an external electron acceptor, accelerating acetogenesis from fermentation intermediates, restructuring the bacterial community, and enriching electroactive bacteria (EAB). Meanwhile, CC and ES orchestrated the assembly of the archaeal community and promoted electrotrophic methanogens, enhancing acetotrophic methanogenesis electron flow via a mechanism distinct from direct electrochemical interactions. The collective application of CC, ES, and AO7 effectively mitigated electron flow impediments in low-strength wastewater methanogenesis, achieving an additional 34% electron recovery from the substrate. This study proposes a new method of amending anaerobic digestion systems with conductive materials to advance wastewater treatment, sustainability, and energy self-sufficiency.
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Affiliation(s)
- Ze-Chong Guo
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Min-Hua Cui
- Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Chun-Xue Yang
- School of Geography and Tourism, Harbin University, Harbin, 150001, China
| | - Hong-Liang Dai
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Tong-Yi Yang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Lin-Zhi Zhai
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Yong Chen
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wen-Zong Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
- School of Civil and Environmental Engineering, Harbin Institute of Technology, Shenzhen, 518055, China
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Yi Y, Dolfing J, Jin G, Fang X, Han W, Liu L, Tang Y, Cheng L. Thermodynamic restrictions determine ammonia tolerance of methanogenic pathways in Methanosarcina barkeri. WATER RESEARCH 2023; 232:119664. [PMID: 36775717 DOI: 10.1016/j.watres.2023.119664] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Ammonia is a ubiquitous potential inhibitor of anaerobic digestion processes, mainly exhibiting inhibition towards methanogenic activity. However, knowledge as to how ammonia affects the methanogens is still limited. In this study, we cultured a multitrophic methanogen, Methanosarcina barkeri DSM 800, with acetate, H2/CO2, and methanol to evaluate the influence of ammonia on different methanogenic pathways. Aceticlastic methanogenesis was more sensitive to increased ammonia concentrations than hydrogenotrophic and methylotrophic methanogenesis. Theoretical maximum NH3 tolerances of M. barkeri fed with acetate, H2/CO2, and methanol were calculated to be 39.1 ± 9.0, 104.3 ± 7.4, and 85.7 ± 1.0 mg/L, respectively. The order of the ΔG range of M. barkeri under three methanogenic pathways reflected the order of ammonia tolerance of M. barkeri. Our results provide insights into the role of the thermodynamic potential of methanogenesis on the tolerance of ammonia stress; and shed light on the mechanism of ammonia inhibition on anaerobic digestion.
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Affiliation(s)
- Yue Yi
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China; College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Wynne Jones 2.11, Ellison Place, Newcastle-upon-Tyne NE1 8QH, UK
| | - Ge Jin
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - XiaoYu Fang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - WenHao Han
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - LaiYan Liu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - YueQin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China.
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China.
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5
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Wei YF, Wang L, Xia ZY, Gou M, Sun ZY, Lv WF, Tang YQ. Microbial communities in crude oil phase and filter-graded aqueous phase from a Daqing oilfield after polymer flooding. J Appl Microbiol 2022; 133:842-856. [PMID: 35490352 DOI: 10.1111/jam.15603] [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: 02/08/2022] [Revised: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 12/01/2022]
Abstract
AIMS The aim was to characterize indigenous microorganisms in oil reservoirs after polymer flooding (RAPF). METHODS The microbial communities in the crude oil phase (Oil) and in the filter-graded aqueous phases Aqu0.22 (>0.22 μm) and Aqu0.1 (0.1~0.22 μm) were investigated by 16S rRNA gene high-throughput sequencing. RESULTS Indigenous microorganisms related to hydrocarbon degradation prevailed in the three phases of each well. However, obvious differences of bacterial compositions were observed among the three phases of the same well and among the same phase of different wells. The crude oil and Aqu0.22 shared many dominant bacteria. Aqu0.1 contained a unique bacterial community in each well. Most bacteria in Aqu0.1 were affiliated to culturable genera, suggesting that they may adapt to the oil reservoir environment by reduction of cell size. Contrary to the bacterial genera, archaeal genera were similar in the three phases but varied in relative abundances. The observed microbial differences may be driven by specific environmental factors in each oil well. CONCLUSIONS The results suggest an application potential of microbial enhanced oil recovery (MEOR) technology in RAPF. The crude oil and Aqu0.1 contain many different functional microorganisms related to hydrocarbon degradation. Both should not be overlooked when investing and exploring the indigenous microorganisms for MEOR. SIGNIFICANCE AND IMPACT OF THE STUDY This work facilitates the understanding of microbial community structures in RAPF and provides information for microbial control in oil fields.
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Affiliation(s)
- Yan-Feng Wei
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Lu Wang
- State Key Laboratory of Enhanced Oil Recovery, Research Institute of Petroleum Exploration and Development, CNPC, Beijing 100083, China
| | - Zi-Yuan Xia
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Wei-Feng Lv
- State Key Laboratory of Enhanced Oil Recovery, Research Institute of Petroleum Exploration and Development, CNPC, Beijing 100083, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
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Shlimon A, Mansurbeg H, Othman R, Head I, Kjeldsen KU, Finster K. Identity and hydrocarbon degradation activity of enriched microorganisms from natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI). Biodegradation 2021; 32:251-271. [PMID: 33782778 DOI: 10.1007/s10532-021-09931-4] [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: 05/26/2020] [Accepted: 02/19/2021] [Indexed: 10/21/2022]
Abstract
A previous cultivation-independent investigation of the microbial community structure of natural oil and asphalt seeps in the Kurdistan Region of Iraq (KRI) revealed the dominance of uncultured bacterial taxa belonging to the phyla Deferribacterota and Coprothermobacterota and the orders Thermodesulfobacteriales, Thermales, and Burkholderiales. Here we report on a cultivation-dependent approach to identify members of these groups involved in hydrocarbon degradation in the KRI oil and asphalt seeps. For this purpose, we set up anoxic crude oil-degrading enrichment cultures based on cultivation media known to support the growth of members of the above-mentioned taxonomic groups. During 100-200 days incubation periods, nitrate-reducing and fermentative enrichments showed up to 90% degradation of C8-C17 alkanes and up to 28% degradation of C18-C33 alkanes along with aromatic hydrocarbons. Community profiling of the enrichment cultures showed that they were dominated by diverse bacterial taxa, which were rare in situ community members in the investigated seeps. Groups initially targeted by our approach were not enriched, possibly because their members are slow-growing and involved in the degradation of recalcitrant hydrocarbons. Nevertheless, the enriched taxa were taxonomically related to phylotypes recovered from hydrocarbon-impacted environments as well as to characterized bacterial isolates not previously known to be involved in hydrocarbon degradation. Marker genes (assA and bssA), diagnostic for fumarate addition-based anaerobic hydrocarbon degradation, were not detectable in the enrichment cultures by PCR. We conclude that hydrocarbon biodegradation in our enrichments occurred via unknown pathways and synergistic interactions among the enriched taxa. We suggest, that although not representing abundant populations in situ, studies of the cultured close relatives of these taxa will reveal an unrecognized potential for anaerobic hydrocarbon degradation, possibly involving poorly characterized mechanisms.
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Affiliation(s)
- Adris Shlimon
- Department of Biology, Soran University, Soran, Iraq. .,Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark.
| | - Howri Mansurbeg
- Department of Petroleum Geoscience, Soran University, Soran, Iraq.,Department of Earth and Environmental Sciences, University of Windsor, Windsor, ON, Canada
| | - Rushdy Othman
- Department of Petroleum Geoscience, Soran University, Soran, Iraq
| | - Ian Head
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Kasper U Kjeldsen
- Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark
| | - Kai Finster
- Section of Microbiology, Department of Biology, Aarhus University, Ny Munkegade 116, 8000, Aarhus, Denmark
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7
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Cai C, Li L, Hua Y, Liu H, Dai X. Ferroferric oxide promotes metabolism in Anaerolineae other than microbial syntrophy in anaerobic methanogenesis of antibiotic fermentation residue. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143601. [PMID: 33261864 DOI: 10.1016/j.scitotenv.2020.143601] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/28/2020] [Accepted: 10/31/2020] [Indexed: 06/12/2023]
Abstract
Antibiotic fermentation residue (AFR) is a kind of protein-rich biosolids that would be utilized as valuable substrates for biogas production. However, the effectiveness of conductive material supplementation and its effect on the microbiome in anaerobic digestion of AFR have not been fully elucidated. The objective of this study is to access the impact of Fe3O4 addition on anaerobic digestion of AFR and reveal its microbial mechanism. By adding Fe3O4 at concentration of 150 mg/gTS to two typical AFRs, the methane yield was decreased while the methane production rate was significantly enhanced by 48% and 21%, respectively. Genomic analyses revealed that the Fe3O4 addition altered the microbial community by selecting the unknown genus of Anaerolineae with the metabolic capacity of carbohydrate hydrolysis and proteolysis. Meanwhile, the hydrogenotrophic methanogenesis was the dominant pathway in the AFR digestion system, which was mostly contributed by the Methanoculleus and Methanolinea. More interestingly, Methanoculleus might possess fermentative capability involved in the versatile hydrolysis pathway. Although the genes related to electrically conductive pili were detected, the induction of direct interspecies electron transfer by Fe3O4 supplementation was not confirmed in this study. In summary, except the accelerated methane production rate, Fe3O4 addition functioned as biostimulator for Anaerolineae other than electron conduit in anaerobic methanogenesis in the AFR digestion system.
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Affiliation(s)
- Chen Cai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Lei Li
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yu Hua
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Huiling Liu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
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Tüccar T, Ilhan-Sungur E, Muyzer G. Bacterial Community Composition in Produced Water of Diyarbakır Oil Fields in Turkey : Bacterial communities in produced waters of south-eastern Turkey reported in detail for the first time. JOHNSON MATTHEY TECHNOLOGY REVIEW 2020. [DOI: 10.1595/205651320x15911723486216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Oil fields harbour a wide variety of microorganisms with different metabolic capabilities. To examine the microbial ecology of petroleum reservoirs, a molecular-based approach was used to assess the composition of bacterial communities in produced water of Diyarbakır oil fields
in Turkey. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments was performed to characterise the bacterial community structure of produced water samples and to identify predominant community members after sequencing of separated
DGGE bands. The majority of bacterial sequences retrieved from DGGE analysis of produced water samples belonged to unclassified bacteria (50%). Among the classified bacteria, Proteobacteria (29.2%), Firmicutes (8.3%), Bacteroidetes (8.3%) and Actinobacteria (4.2%)
groups were identified. Pseudomonas was the dominant genus detected in the produced water samples. The results of this research provide, for the first time, insight into the complexity of microbial communities in the Diyarbakır oil reservoirs and their dominant constituents.
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Affiliation(s)
- Tuğçe Tüccar
- Department of Biology, Institute of Graduate Studies in Sciences, Istanbul University 34134, Vezneciler Istanbul, Turkey
| | - Esra Ilhan-Sungur
- Department of Biology, Faculty of Science, Istanbul University 34134, Vezneciler Istanbul, Turkey
| | - Gerard Muyzer
- Department of Biotechnology, Delft University of Technology van der Maasweg 9, 2629 HZ Delft The Netherlands
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9
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Sierra-Garcia IN, Belgini DRB, Torres-Ballesteros A, Paez-Espino D, Capilla R, Santos Neto EV, Gray N, de Oliveira VM. In depth metagenomic analysis in contrasting oil wells reveals syntrophic bacterial and archaeal associations for oil biodegradation in petroleum reservoirs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136646. [PMID: 32014760 DOI: 10.1016/j.scitotenv.2020.136646] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
Microbial biodegradation of hydrocarbons in petroleum reservoirs has major consequences in the petroleum value and quality. The identification of microorganisms capable of in-situ degradation of hydrocarbons under the reservoir conditions is crucial to understand microbial roles in hydrocarbon transformation and the impact of oil exploration and production on energy resources. The aim of this study was to profile the metagenome of microbial communities in crude oils and associated formation water from two high temperature and relatively saline oil-production wells, where one has been subjected to water flooding (BA-2) and the other one is considered pristine (BA-1). The microbiome was studied in the fluids using shotgun metagenome sequencing. Distinct microbial compositions were revealed when comparing pristine and water flooded oil wells in contrast to the similar community structures observed between the aqueous and oil fluids from the same well (BA-2). The equal proportion of archaea and bacteria together with the greater anaerobic hydrocarbon degradation potential in the BA-1 pristine but degraded reservoir contrasted with the predominance of bacteria over archaea, aerobic pathways and lower frequency of anaerobic degradation genes in the BA-2 water flooded undegraded well. Our results suggest that Syntrophus, Syntrophomonas, candidatus Atribacteria and Synergistia, in association with mainly acetoclastic methanogenic archaea of the genus Methanothrix, were collectively responsible for the oil biodegradation observed in the pristine petroleum well BA-1. Conversely, the microbial composition of the water flooded oil well BA-2 was mainly dominated by the fast-growing and putatively aerobic opportunists Marinobacter and Marinobacterium. This presumable allochthonous community introduced a greater metabolic versatility, although oil biodegradation has not been detected hitherto perhaps due to in-reservoir unfavorable physicochemical conditions. These findings provide a better understanding of the petroleum reservoir microbiomes and their potential roles in biogeochemical processes occurring in environments with different geological and oil recovery histories.
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Affiliation(s)
- Isabel Natalia Sierra-Garcia
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil; Institute of Biology, University of Campinas - UNICAMP, Campinas, Brazil.
| | - Daiane R B Belgini
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil; Institute of Biology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Adriana Torres-Ballesteros
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | | | | | | | - Neil Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Valeria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Campinas, Brazil
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10
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Wu B, Wang J, Hu Z, Yuan S, Wang W. Anaerobic biotransformation and potential impact of quinoline in an anaerobic methanogenic reactor treating synthetic coal gasification wastewater and response of microbial community. JOURNAL OF HAZARDOUS MATERIALS 2020; 384:121404. [PMID: 31628062 DOI: 10.1016/j.jhazmat.2019.121404] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/22/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Phenolic and quinoline compounds are the most primary organic pollutants in coal gasification wastewater (CGW), but the biotransformation of quinoline compounds under methanogenic condition and their potential impacts on treatment performance of CGW are still unclear. Anaerobic biotransformation pathways of quinoline in an upflow anaerobic sludge blanket reactor treating synthetic CGW and response of microbial community were firstly investigated. The result indicated that the degradation of 2(1 H)-quinolinone was the rate-limiting step for the complete conversion of quinoline under methanogenic condition. The reactor performed stably at total phenols concentration of 1000 mg L-1 with a gradual increase of quinoline concentration from 100 to 600 mg L-1. However, the reactor performance was rapidly deteriorated from 98% of COD removal to about 80% at quinoline concentration of 1200 mg L-1 resulting from the accumulation of 2(1 H)-quinolinone. Correspondingly, phenol utilization rate of sludge was significantly reduced by 61% while quinoline utilization rate of sludge was increased by 132%. As phenol degraders, Syntrophorhabdus gradually predominated along with the increase of quinoline concentration, but Syntrophus declined inversely. Compared with syntrophs, acetotrophic methanogens could quickly adapt to quinoline toxicity and tolerate higher quinoline stress. Therefore, anaerobic digestion is an effective method for eliminating quinoline and phenol in CGW.
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Affiliation(s)
- Benteng Wu
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Jing Wang
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Zhenhu Hu
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Shoujun Yuan
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Wei Wang
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China.
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11
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Tarnovetskii IY, Merkel AY, Pimenov NV. Analysis of Cultured Methanogenic Archaea from the Tarkhankut Peninsula Coastal Methane Seeps. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261719060183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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12
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Methanogenic Degradation of Long n-Alkanes Requires Fumarate-Dependent Activation. Appl Environ Microbiol 2019; 85:AEM.00985-19. [PMID: 31175186 DOI: 10.1128/aem.00985-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/29/2019] [Indexed: 11/20/2022] Open
Abstract
Methanogenic degradation of n-alkanes is prevalent in n-alkane-impacted anoxic oil reservoirs and oil-polluted sites. However, little is known about the initial activation mechanism of the substrate, especially n-alkanes with a chain length above C16 Here, a methanogenic C16 to C20 n-alkane-degrading enrichment culture was established from production water of a low-temperature oil reservoir. At the end of the incubation (364 days), C16 to C20 (1-methylalkyl)succinates were detected in the n-alkane-amended enrichment culture, suggesting that fumarate addition had occurred in the degradation process. This evidence is supported further by the positive amplification of the assA gene encoding the alpha subunit of alkylsuccinate synthase. A phylogenetic analysis shows these assA amplicons to be affiliated with Smithella and Desulfatibacillum clades. Together with the high abundance of these clades in the bacterial community, these two species are postulated to be the key players in the degradation of C16 to C20 n-alkanes in the present study. Our results provide evidence that long n-alkanes are activated via a fumarate addition mechanism under methanogenic conditions.IMPORTANCE Methanogenic hydrocarbon degradation is the major process for oil degradation in subsurface oil reservoirs and is blamed for the formation of heavy oil and oil sands. Addition of n-alkanes to fumarate yielding alkyl-substituted succinates is a well-characterized anaerobic activation mechanism for hydrocarbons and is the most common activation mechanism in the anaerobic biodegradation of n-alkanes with chain lengths less than C16 However, the activation mechanism involved in the methanogenic biodegradation of n-alkanes longer than C16 is still uncertain. In this study, we analyzed a methanogenic enrichment culture amended with a mixture of C16 to C20 n-alkanes. These n-alkanes can be activated via fumarate addition by mixed cultures containing Smithella and Desulfatibacillum species under methanogenic conditions. These observations provide a fundamental understanding of long-n-alkane metabolism under methanogenic conditions and have important applications for the remediation of oil-contaminated sites and for energy recovery from oil reservoirs.
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13
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Poirier S, Déjean S, Chapleur O. Support media can steer methanogenesis in the presence of phenol through biotic and abiotic effects. WATER RESEARCH 2018; 140:24-33. [PMID: 29684699 DOI: 10.1016/j.watres.2018.04.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 06/08/2023]
Abstract
A wide variety of inhibitors can induce anaerobic digester disruption. To avoid performance losses, support media can be used to mitigate inhibitions. However, distinguishing the physico-chemical from the biological mechanisms of such strategies remains delicate. In this framework, the impact of 10 g/L of different types of zeolites and activated carbons (AC) on microbial community dynamics during anaerobic digestion of biowaste in the presence of 1.3 g/L of phenol was evaluated with 16 S rRNA gene sequencing. In the presence of AC, methanogenesis inhibition was rapidly removed due to a decrease of phenol concentration. This abiotic effect related to the physico-chemical properties of AC led to increased final CH4 and CO2 productions by 29-31% compared to digesters incubated without support. Interestingly, although zeolite did not adsorb phenol, final CH4 and CO2 production reached comparable levels as with AC. Nevertheless, compared to digesters incubated without support, methanogenesis lag phase duration was less reduced in the presence of zeolites (5 ± 1 days) than in the presence of activated carbons (12 ± 2 days). Both types of support induced biotic effects. AC and zeolite both allowed the preservation of the major representative archaeal genus of the non-inhibited ecosystem, Methanosarcina. By contrast, they distinctly shaped bacterial populations. OTUs belonging to class W5 became dominant at the expense of OTUs assigned to orders Clostridiales, Bacteroidales and Anaerolinales in the presence of AC. Zeolite enhanced the implantation of OTUs assigned to bacterial phylum Cloacimonetes. This study highlighted that supports can induce biotic and abiotic effects within digesters inhibited with phenol, showing potentialities to enhance anaerobic digestion stability under disrupting conditions.
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Affiliation(s)
- Simon Poirier
- Hydrosystems and Bioprocesses Research Unit, Irstea, France.
| | - Sébastien Déjean
- Toulouse Mathematics Institute, UMR 5219 CNRS, Toulouse University, Toulouse, France.
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14
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Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture. Microorganisms 2018; 6:microorganisms6030065. [PMID: 29996505 PMCID: PMC6164631 DOI: 10.3390/microorganisms6030065] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/02/2018] [Accepted: 07/08/2018] [Indexed: 11/23/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses. 16S rRNA gene sequencing of fractionated DNA pinpointed an unclassified Clostridiaceae species as a putative naphthalene degrader after two months of SIP incubation. This finding was supported by metabolite and metagenomic evidence of genes predicted to encode for enzymes facilitating naphthalene carboxylic acid CoA-thioesterification and degradation of an unknown arylcarboxyl-CoA structure. Our findings also suggest a possible but unknown role for Desulfuromonadales in naphthalene degradation. This is the first reported functional evidence of PAH biodegradation by a methanogenic consortium, and we envision that this approach could be used to assess carbon flow through other slow growing enrichment cultures and environmental samples.
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15
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Li Y, Sun Y, Li L, Yuan Z. Acclimation of acid-tolerant methanogenic propionate-utilizing culture and microbial community dissecting. BIORESOURCE TECHNOLOGY 2018; 250:117-123. [PMID: 29161570 DOI: 10.1016/j.biortech.2017.11.034] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 05/28/2023]
Abstract
The acid-tolerant methanogenic propionate degradation culture was acclimated in a propionate-fed semi-continuous bioreactor by daily adjusting the digestate pH. The performance of propionate fermentation, the respond of microbial community structure to the acidic environment, and the microbial network for propionate degradation in the acid-tolerant culture was investigated. The results demonstrated that after long term of acclimation to low pH, the digester could produce methane from propionate at pH 4.8-5.5 with 0.3-0.4 L g-1 propionic acid (HPr) d-1 of the volatile solids (VS) methane production. The predominant methanogens shifted from acetoclastic methanogens (∼87%) to hydrogenotrophic methanogens (∼67%) in the bioreactor with the dropping pH, indicating that hydrogenotrophic methanogens were more acid-tolerant than acetoclastic methanogens. Smithella (∼11%), Syntrophobacter (∼7%) and Pelotomaculum (∼3%) were the main propionate oxidizers in the acid-tolerant propionate-utilizing culture. Methanothrix dominant acetoclastic methanogens, while Methanolinea and Methanospirillum were the major H2 scavengers to support Syntrophobacter and Pelotomaculum syntrophic propionate degradation.
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Affiliation(s)
- Ying Li
- Laboratory of Biomass Bio-chemical Conversion, GuangZhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Yongming Sun
- Laboratory of Biomass Bio-chemical Conversion, GuangZhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, PR China; Key Laboratory of Renewable Energy, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Lianhua Li
- Laboratory of Biomass Bio-chemical Conversion, GuangZhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, PR China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, PR China.
| | - Zhenhong Yuan
- Laboratory of Biomass Bio-chemical Conversion, GuangZhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, PR China; Key Laboratory of Renewable Energy, Chinese Academy of Sciences, Guangzhou 510640, PR China; Guangdong Provincial Key Laboratory of New and Renewable Energy Research and Development, Guangzhou 510640, PR China
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16
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Xia Y, Yang C, Zhang T. Microbial effects of part-stream low-frequency ultrasonic pretreatment on sludge anaerobic digestion as revealed by high-throughput sequencing-based metagenomics and metatranscriptomics. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:47. [PMID: 29483940 PMCID: PMC5820786 DOI: 10.1186/s13068-018-1042-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 02/05/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Part-stream low-frequency ultrasound (LFUS) was one of the common practices for sludge disintegration in full-scale anaerobic digestion (AD) facilities. However, the effectiveness of part-stream LFUS treatment and its effect on AD microbiome have not been fully elucidated. METHODS Here we testified the effectiveness of part-stream LFUS pretreatment by treating only a fraction of feed sludge (23% and 33% total solid of the feed sludge) with 20 Hz LFUS for 70 s. State-of-the-art metagenomic and metatranscriptomic analysis was used to investigate the microbial process underpinning the enhanced AD performance by part-stream LFUS pretreatment. RESULTS By pretreating 33% total solid of the feed sludge, methane yield was increased by 36.5%, while the volatile solid reduction ratio remained unchanged. RNA-seq of the microbiome at stable stage showed that the continuous dosage of easy-degradable LFUS-pretreated feed sludge had gradually altered the microbial community by selecting Bacteroidales hydrolyzer with greater metabolic capability to hydrolyze cellulosic biomass without substrate attachment. Meanwhile, Thermotogales with excellent cell mobility for nutrient capturing was highly active within the community. Foremost proportion of the methanogenesis was contributed by the dominant Methanomicrobiales via carbon dioxide reduction. More interestingly, a perceivable proportion of the reverse electron flow of the community was input from Methanoculleus species other than syntrophic acetate-oxidizing bacteria. In addition, metagenomic binning retrieved several interesting novel metagenomic-assembled genomes (MAGs): MAG-bin6 of Alistipes shahii showed exceptional transcriptional activities towards protein degradation and MAG-bin11 of Candidatus Cloacimonetes with active cellulolytic GH74 gene detected. CONCLUSIONS In summary, despite the unchanged sludge digestibility, the applied part-stream LFUS pretreatment strategy was robust in adjusting the microbial pathways towards more effective substrate conversion enabled by free-living hydrolyser and beta-oxidation-capable methanogens.
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Affiliation(s)
- Yu Xia
- School of Environmental Science and Engineering, Southern University of Science and Technology, No. 1008 Xueyuan Blvd, Nanshan, Shenzhen, China
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
| | - Chao Yang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Tong Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, No. 1008 Xueyuan Blvd, Nanshan, Shenzhen, China
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong
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17
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Oberding LK, Gieg LM. Methanogenic Paraffin Biodegradation: Alkylsuccinate Synthase Gene Quantification and Dicarboxylic Acid Production. Appl Environ Microbiol 2018; 84:e01773-17. [PMID: 29030441 PMCID: PMC5734044 DOI: 10.1128/aem.01773-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/09/2017] [Indexed: 11/20/2022] Open
Abstract
Paraffinic n-alkanes (>C17) that are solid at ambient temperature comprise a large fraction of many crude oils. The comparatively low water solubility and reactivity of these long-chain alkanes can lead to their persistence in the environment following fuel spills and pose serious problems for crude oil recovery operations by clogging oil production wells. However, the degradation of waxy paraffins under the anoxic conditions characterizing contaminated groundwater environments and deep subsurface energy reservoirs is poorly understood. Here, we assessed the ability of a methanogenic culture enriched from freshwater fuel-contaminated aquifer sediments to biodegrade the model paraffin n-octacosane (C28H58). Compared with that in controls, the consumption of n-octacosane was coupled to methane production, demonstrating its biodegradation under these conditions. Smithella was postulated to be an important C28H58 degrader in the culture on the basis of its high relative abundance as determined by 16S rRNA gene sequencing. An identified assA gene (known to encode the α subunit of alkylsuccinate synthase) aligned most closely with those from other Smithella organisms. Quantitative PCR (qPCR) and reverse transcription qPCR assays for assA demonstrated significant increases in the abundance and expression of this gene in C28H58-degrading cultures compared with that in controls, suggesting n-octacosane activation by fumarate addition. A metabolite analysis revealed the presence of several long-chain α,ω-dicarboxylic acids only in the C28H58-degrading cultures, a novel observation providing clues as to how methanogenic consortia access waxy hydrocarbons. The results of this study broaden our understanding of how waxy paraffins can be biodegraded in anoxic environments with an application toward bioremediation and improved oil recovery.IMPORTANCE Understanding the methanogenic biodegradation of different classes of hydrocarbons has important applications for effective fuel-contaminated site remediation and for improved recovery from oil reservoirs. Previous studies have clearly demonstrated that short-chain alkanes (C17) that comprise many fuel mixtures. Using an enrichment culture derived from a freshwater fuel-contaminated site, we demonstrate that the model waxy alkane n-octacosane can be biodegraded under methanogenic conditions by a presumed Smithella phylotype. Compared with that of controls, we show an increased abundance and expression of the assA gene, which is known to be important for anaerobic n-alkane metabolism. Metabolite analyses revealed the presence of a range of α,ω-dicarboxylic acids found only in n-octacosane-degrading cultures, a novel finding that lends insight as to how anaerobic communities may access waxes as growth substrates in anoxic environments.
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Affiliation(s)
- Lisa K Oberding
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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18
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Michas A, Vestergaard G, Trautwein K, Avramidis P, Hatzinikolaou DG, Vorgias CE, Wilkes H, Rabus R, Schloter M, Schöler A. More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis. MICROBIOME 2017; 5:118. [PMID: 28893308 PMCID: PMC5594585 DOI: 10.1186/s40168-017-0337-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/03/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Natural oil seeps offer the opportunity to study the adaptation of ecosystems and the associated microbiota to long-term oil exposure. In the current study, we investigated a land-to-sea transition ecosystem called "Keri Lake" in Zakynthos Island, Greece. This ecosystem is unique due to asphalt oil springs found at several sites, a phenomenon already reported 2500 years ago. Sediment microbiomes at Keri Lake were studied, and their structure and functional potential were compared to other ecosystems with oil exposure histories of various time periods. RESULTS Replicate sediment cores (up to 3-m depth) were retrieved from one site exposed to oil as well as a non-exposed control site. Samples from three different depths were subjected to chemical analysis and metagenomic shotgun sequencing. At the oil-exposed site, we observed high amounts of asphalt oil compounds and a depletion of sulfate compared to the non-exposed control site. The numbers of reads assigned to genes involved in the anaerobic degradation of hydrocarbons were similar between the two sites. The numbers of denitrifiers and sulfate reducers were clearly lower in the samples from the oil-exposed site, while a higher abundance of methanogens was detected compared to the non-exposed site. Higher abundances of the genes of methanogenesis were also observed in the metagenomes from other ecosystems with a long history of oil exposure, compared to short-term exposed environments. CONCLUSIONS The analysis of Keri Lake metagenomes revealed that microbiomes in the oil-exposed sediment have a higher potential for methanogenesis over denitrification/sulfate reduction, compared to those in the non-exposed site. Comparison with metagenomes from various oil-impacted environments suggests that syntrophic interactions of hydrocarbon degraders with methanogens are favored in the ecosystems with a long-term presence of oil.
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Affiliation(s)
- Antonios Michas
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Kathleen Trautwein
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Pavlos Avramidis
- Department of Geology, University of Patras, Panepistimioupoli Patron, 26504 Rio-Patras, Greece
| | - Dimitris G. Hatzinikolaou
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Constantinos E. Vorgias
- Department of Biology, National and Kapodistrian University of Athens, Zografou University Campus, 15784 Athens, Greece
| | - Heinz Wilkes
- Organic Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
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19
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Ma TT, Liu LY, Rui JP, Yuan Q, Feng DS, Zhou Z, Dai LR, Zeng WQ, Zhang H, Cheng L. Coexistence and competition of sulfate-reducing and methanogenic populations in an anaerobic hexadecane-degrading culture. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:207. [PMID: 28878822 PMCID: PMC5584521 DOI: 10.1186/s13068-017-0895-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Over three-fifths of the world's known crude oil cannot be recovered using state-of-the-art techniques, but microbial conversion of petroleum hydrocarbons trapped in oil reservoirs to methane is one promising path to increase the recovery of fossil fuels. The process requires cooperation between syntrophic bacteria and methanogenic archaea, which can be affected by sulfate-reducing prokaryotes (SRPs). However, the effects of sulfate on hydrocarbon degradation and methane production remain elusive, and the microbial communities involved are not well understood. RESULTS In this study, a methanogenic hexadecane-degrading enrichment culture was treated with six different concentrations of sulfate ranging from 0.5 to 25 mM. Methane production and maximum specific methane production rate gradually decreased to 44 and 56% with sulfate concentrations up to 25 mM, respectively. There was a significant positive linear correlation between the sulfate reduction/methane production ratio and initial sulfate concentration, which remained constant during the methane production phase. The apparent methanogenesis fractionation factor (αapp) gradually increased during the methane production phase in each treatment, the αapp for the treatments with lower sulfate (0.5-4 mM) eventually plateaued at ~1.047, but that for the treatment with 10-25 mM sulfate only reached ~1.029. The relative abundance levels of Smithella and Methanoculleus increased almost in parallel with the increasing sulfate concentrations. Furthermore, the predominant sulfate reducer communities shifted from Desulfobacteraceae in the low-sulfate cultures to Desulfomonile in the high-sulfate cultures. CONCLUSION The distribution of hexadecane carbon between methane-producing and sulfate-reducing populations is dependent on the initial sulfate added, and not affected during the methane production period. There was a relative increase in hydrogenotrophic methanogenesis activity over time for all sulfate treatments, whereas the total activity was inhibited by sulfate addition. Both Smithella and Methanoculleus, the key alkane degraders and methane producers, can adapt to sulfate stress. Specifically, different SRP populations were stimulated at various sulfate concentrations. These results could help to evaluate interactions between sulfate-reducing and methanogenic populations during anaerobic hydrocarbon degradation in oil reservoirs.
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Affiliation(s)
- Ting-Ting Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Lai-Yan Liu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Jun-Peng Rui
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology of Chinese Academy of Sciences, Section 4-9, Renmin South Road, Chengdu, 610041 People's Republic of China
- Environmental Microbiology Key Laboratory of Sichuan Province, Section 4-9, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Quan Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 99 Lincheng West Road, Guanshanhu District, Guiyang, 550081 People's Republic of China
| | - Ding-Shan Feng
- Anhui Normal University, 1 Beijing East Road, Wuhu, 241000 People's Republic of China
| | - Zheng Zhou
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Li-Rong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Wan-Qiu Zeng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041 People's Republic of China
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Qin QS, Feng DS, Liu PF, He Q, Li X, Liu AM, Zhang H, Hu GQ, Cheng L. Metagenomic Characterization of Candidatus Smithella cisternae Strain M82_1, a Syntrophic Alkane-Degrading Bacteria, Enriched from the Shengli Oil Field. Microbes Environ 2017; 32:234-243. [PMID: 28781346 PMCID: PMC5606693 DOI: 10.1264/jsme2.me17022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The methanogenic degradation of hydrocarbons plays an important role in hydrocarbon-contaminated environments in the absence of an external electron acceptor. Members of Syntrophaceae sublineages were previously reported to be responsible for syntrophic alkane degradation. However, limited information is currently available on their physiological capabilities in nature because it is very challenging to cultivate these as-yet uncultured microbes. We herein performed metagenomic sequencing of the methanogenic hexadecane-degrading culture M82 and recovered a nearly complete genome (2.75 Mb, estimated completeness ≥97%) belonging to Syntrophaceae sublineage II. The assembly genome was tentatively named “Candidatus Smithella cisternae strain M82_1”. Genes encoding alkylsuccinate synthase for alkane activation were identified, suggesting that this organism is capable of oxidizing alkanes through fumarate addition. This capability was further supported by the detection of methyl pentadecyl succinic acid and methyl tetradecyl succinic acid in cultures amended with hexadecane and pentadecane, respectively. Genes encoding enzymes for the β-oxidation of long-chain fatty acids and butyrate were also identified. The electron transfer flavoprotein/DUF224 complex is presumed to link electron flow from acyl-CoA dehydrogenase to a membrane hydrogenase or formate dehydrogenase. Although no indications of Rnf complexes were detected, genes encoding electron-confurcating hydrogenase and formate dehydrogenase were proposed to couple the thermodynamically favorable oxidation of ferredoxin to generate H2 and formate from NADH. Strain M82_1 synthesized ATP from acetyl-CoA by substrate-level phosphorylation or F1F0-ATP synthases. These results provide an insight into the potential metabolic traits and ecophysiological roles of the syntrophic alkane degrader Syntrophaceae.
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Affiliation(s)
- Qian-Shan Qin
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture
| | | | - Peng-Fei Liu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture
| | - Qiao He
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture
| | - Xia Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture
| | | | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture
| | - Guo-Quan Hu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture
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21
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Stagars MH, Mishra S, Treude T, Amann R, Knittel K. Microbial Community Response to Simulated Petroleum Seepage in Caspian Sea Sediments. Front Microbiol 2017; 8:764. [PMID: 28503173 PMCID: PMC5409227 DOI: 10.3389/fmicb.2017.00764] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 04/12/2017] [Indexed: 11/17/2022] Open
Abstract
Anaerobic microbial hydrocarbon degradation is a major biogeochemical process at marine seeps. Here we studied the response of the microbial community to petroleum seepage simulated for 190 days in a sediment core from the Caspian Sea using a sediment-oil-flow-through (SOFT) system. Untreated (without simulated petroleum seepage) and SOFT sediment microbial communities shared 43% bacterial genus-level 16S rRNA-based operational taxonomic units (OTU0.945) but shared only 23% archaeal OTU0.945. The community differed significantly between sediment layers. The detection of fourfold higher deltaproteobacterial cell numbers in SOFT than in untreated sediment at depths characterized by highest sulfate reduction rates and strongest decrease of gaseous and mid-chain alkane concentrations indicated a specific response of hydrocarbon-degrading Deltaproteobacteria. Based on an increase in specific CARD-FISH cell numbers, we suggest the following groups of sulfate-reducing bacteria to be likely responsible for the observed decrease in aliphatic and aromatic hydrocarbon concentration in SOFT sediments: clade SCA1 for propane and butane degradation, clade LCA2 for mid- to long-chain alkane degradation, clade Cyhx for cycloalkanes, pentane and hexane degradation, and relatives of Desulfobacula for toluene degradation. Highest numbers of archaea of the genus Methanosarcina were found in the methanogenic zone of the SOFT core where we detected preferential degradation of long-chain hydrocarbons. Sequencing of masD, a marker gene for alkane degradation encoding (1-methylalkyl)succinate synthase, revealed a low diversity in SOFT sediment with two abundant species-level MasD OTU0.96.
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Affiliation(s)
- Marion H Stagars
- Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Sonakshi Mishra
- Department of Marine Biogeochemistry, GEOMAR - Helmholtz Centre for Ocean Research KielKiel, Germany
| | - Tina Treude
- Department of Marine Biogeochemistry, GEOMAR - Helmholtz Centre for Ocean Research KielKiel, Germany.,Department of Earth, Planetary and Space Sciences, University of California, Los Angeles, Los AngelesCA, USA.,Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, Los AngelesCA, USA
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany
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22
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Dai X, Chen C, Yan G, Chen Y, Guo S. A comprehensive evaluation of re-circulated bio-filter as a pretreatment process for petroleum refinery wastewater. J Environ Sci (China) 2016; 50:49-55. [PMID: 28034430 DOI: 10.1016/j.jes.2016.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 06/06/2023]
Abstract
Conventional biological treatment process is not very efficient for the treatment of petroleum refinery wastewater (PRW) that contains high-concentration of organic contaminants. Prior to biological treatment, an additional pretreatment process for PRW is required for the effluent to meet the discharge standards. While re-circulated bio-filter (RBF) has been applied as a pretreatment process in several PRW treatment plants, its effects have not been comprehensively evaluated. In this study, the parameters of operation, the changes in pollution indexes and contaminant composition in an engineered RBF have been investigated. We found that mainly highly active de-carbonization bacteria were present in the RBF, while no nitrification bacteria were found in the RBF. This indicated the absence of nitrification in this process. The biodegradable organic contaminants were susceptible to degradation by RBF, which decreased the Biological Oxygen Demand (BOD5) by 83.64% and the Chemical Oxygen Demand (CODCr) by 54.63%. Consequently, the alkalinity and pH value of RBF effluent significantly increased, which was unfavorable for the control of operating parameters in subsequent biological treatment. Along with the decrease of CODCr, the RBF effluent exhibited a reduction in biodegradability. 834 kinds of recalcitrant polar organic contaminants remained in the effluent; most of the contaminant molecules having complex structures of aromatic, polycyclic and heterocyclic rings. The results of this study showed that RBF could efficiently treat PRW for biodegradable organic contaminants removal; however, it is difficult to treat bio-refractory organic contaminants, which was unfavorable for the subsequent biological treatment process operation. An improved process might provide overall guarantees for the PRW treatment.
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Affiliation(s)
- Xiaoli Dai
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum, Beijing 102249, China.
| | - Chunmao Chen
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum, Beijing 102249, China
| | - Guangxu Yan
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum, Beijing 102249, China
| | - Yu Chen
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum, Beijing 102249, China
| | - Shaohui Guo
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, China University of Petroleum, Beijing 102249, China.
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23
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Poirier S, Bize A, Bureau C, Bouchez T, Chapleur O. Community shifts within anaerobic digestion microbiota facing phenol inhibition: Towards early warning microbial indicators? WATER RESEARCH 2016; 100:296-305. [PMID: 27208731 DOI: 10.1016/j.watres.2016.05.041] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 06/05/2023]
Abstract
Performance stability is a key operational issue for anaerobic digestion (AD) and phenolic compounds are regularly mentioned as a major cause of digester failures. To get more insights into AD microbiota response to a wide range of inhibition levels, anaerobic batch toxicity assays were conducted with ten phenol concentrations up to 5.00 g/L. Final AD performance was not impaired up to 1.00 g/L. However, progressive shifts in microbial community structure were detected from 0.50 g/L. The methanogenic function was maintained along with increasing initial phenol concentrations up to 2.00 g/L thanks to the emergence of genus Methanoculleus at the expense of Methanosarcina. Within syntrophic populations, family Syntrophomonadaceae proportion was gradually reduced by phenol while Synergistaceae gained in importance in the microbiome. Moreover, at 2.00 g/L, the relative abundance of families belonging to order Clostridiales dropped, leading to the predominance of populations assigned to order Bacteroidales even though it did not prevent final AD performance deterioration. It illustrates the high level of adaptability of archaeal and bacterial communities and suggests the possibility of determining early warning microbial indicators associated with phenol inhibition.
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Affiliation(s)
- Simon Poirier
- Irstea, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, F-92761 Antony, France.
| | - Ariane Bize
- Irstea, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, F-92761 Antony, France.
| | - Chrystelle Bureau
- Irstea, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, F-92761 Antony, France.
| | - Théodore Bouchez
- Irstea, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, F-92761 Antony, France.
| | - Olivier Chapleur
- Irstea, Hydrosystems and Bioprocesses Research Unit, 1 rue Pierre-Gilles de Gennes, F-92761 Antony, France.
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24
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Yuan M, Zhu J, Wang C, Wu M, Sun F, Han X, He Y, Wu W. Latitudinal distribution of microbial communities in anaerobic biological stabilization ponds: effect of the mean annual temperature. Microb Biotechnol 2016; 9:834-845. [PMID: 27562316 PMCID: PMC5072199 DOI: 10.1111/1751-7915.12407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 06/28/2016] [Accepted: 08/01/2016] [Indexed: 11/30/2022] Open
Abstract
Considering wide utilization and high methane fluxes from anaerobic biological stabilization ponds (ABSPs), understanding the methanogenesis in ABSPs is of fundamental importance. Here we investigated the variation and impact factors of methanogenesis in seven ABSPs that spanned from the north to the south of China. Results showed that methanogen abundance (7.7 × 109 -8.7 × 1010 copies g-1 dry sediment) and methanogenic activities (2.2-21.2 μmol CH4 g-1 dry sediment h-1 ) were considerable for all sediments. Statistical analysis demonstrated that compared with other factors (ammonium, pH, COD and TOC), mean annual temperature (MAT) showed the lowest P value and thus was the most important influencing factor for the methanogenic process. Besides, with the increasing MAT, methanogenic activity was enhanced mainly due to the shift of the dominant methanogenic pathway from acetoclastic (49.8-70.7%) in low MAT areas to hydrogenotrophic (42.0-54.6%) in high MAT areas. This shift of methanogenic pathway was also paralleled with changes in composition of bacterial communities. These results suggested that future global warming may reshape the composition of methanogen communities and lead to an increasing methane emission from ABSPs. Therefore, further research is urgently needed to globally estimate methane emissions from ABSPs and re-examine the role of ABSPs in wastewater treatment.
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Affiliation(s)
- Mengdong Yuan
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Jing Zhu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Cheng Wang
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Mengxiong Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Faqian Sun
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Xingguo Han
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Yangyang He
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Weixiang Wu
- Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, 310058, China.
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25
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Wawrik B, Marks CR, Davidova IA, McInerney MJ, Pruitt S, Duncan KE, Suflita JM, Callaghan AV. Methanogenic paraffin degradation proceeds via alkane addition to fumarate by 'Smithella' spp. mediated by a syntrophic coupling with hydrogenotrophic methanogens. Environ Microbiol 2016; 18:2604-19. [PMID: 27198766 DOI: 10.1111/1462-2920.13374] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anaerobic microbial biodegradation of recalcitrant, water-insoluble substrates, such as paraffins, presents unique metabolic challenges. To elucidate this process, a methanogenic consortium capable of mineralizing long-chain n-paraffins (C28 -C50 ) was enriched from San Diego Bay sediment. Analysis of 16S rRNA genes indicated the dominance of Syntrophobacterales (43%) and Methanomicrobiales (26%). Metagenomic sequencing allowed draft genome assembly of dominant uncultivated community members belonging to the bacterial genus Smithella and the archaeal genera Methanoculleus and Methanosaeta. Five contigs encoding homologs of the catalytic subunit of alkylsuccinate synthase (assA) were detected. Additionally, mRNA transcripts for these genes, including a homolog binned within the 'Smithella' sp. SDB genome scaffold, were detected via RT-PCR, implying that paraffins are activated via 'fumarate addition'. Metabolic reconstruction and comparison with genome scaffolds of uncultivated n-alkane degrading 'Smithella' spp. are consistent with the hypothesis that syntrophically growing 'Smithella' spp. may achieve reverse electron transfer by coupling the reoxidation of ETFred to a membrane-bound FeS oxidoreductase functioning as an ETF:menaquinone oxidoreductase. Subsequent electron transfer could proceed via a periplasmic formate dehydrogenase and/or hydrogenase, allowing energetic coupling to hydrogenotrophic methanogens such as Methanoculleus. Ultimately, these data provide fundamental insight into the energy conservation mechanisms that dictate interspecies interactions salient to methanogenic alkane mineralization.
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Affiliation(s)
- Boris Wawrik
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK, 73019, USA
| | - Christopher R Marks
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK, 73019, USA.,Institute for Energy and the Environment, University of Oklahoma, 100 East Boyd Street, Norman, OK, 73019, USA
| | - Irene A Davidova
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK, 73019, USA.,Institute for Energy and the Environment, University of Oklahoma, 100 East Boyd Street, Norman, OK, 73019, USA
| | - Michael J McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK, 73019, USA
| | - Shane Pruitt
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK, 73019, USA.,Development and Alumni Relations, Oglethorpe University, 4484 Peachtree Road, NE, Atlanta, GA, 30319, USA
| | - Kathleen E Duncan
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK, 73019, USA.,Institute for Energy and the Environment, University of Oklahoma, 100 East Boyd Street, Norman, OK, 73019, USA
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK, 73019, USA.,Institute for Energy and the Environment, University of Oklahoma, 100 East Boyd Street, Norman, OK, 73019, USA
| | - Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK, 73019, USA
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26
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Stagars MH, Ruff SE, Amann R, Knittel K. High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes. Front Microbiol 2016; 6:1511. [PMID: 26779166 PMCID: PMC4703814 DOI: 10.3389/fmicb.2015.01511] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/14/2015] [Indexed: 11/13/2022] Open
Abstract
Alkanes comprise a substantial fraction of crude oil and are prevalent at marine seeps. These environments are typically anoxic and host diverse microbial communities that grow on alkanes. The most widely distributed mechanism of anaerobic alkane activation is the addition of alkanes to fumarate by (1-methylalkyl)succinate synthase (Mas). Here we studied the diversity of MasD, the catalytic subunit of the enzyme, in 12 marine sediments sampled at seven seeps. We aimed to identify cosmopolitan species as well as to identify factors structuring the alkane-degrading community. Using next generation sequencing we obtained a total of 420 MasD species-level operational taxonomic units (OTU0.96) at 96% amino acid identity. Diversity analysis shows a high richness and evenness of alkane-degrading bacteria. Sites with similar hydrocarbon composition harbored similar alkane-degrading communities based on MasD genes; the MasD community structure is clearly driven by the hydrocarbon source available at the various seeps. Two of the detected OTU0.96 were cosmopolitan and abundant while 75% were locally restricted, suggesting the presence of few abundant and globally distributed alkane degraders as well as specialized variants that have developed under specific conditions at the diverse seep environments. Of the three MasD clades identified, the most diverse was affiliated with Deltaproteobacteria. A second clade was affiliated with both Deltaproteobacteria and Firmicutes likely indicating lateral gene transfer events. The third clade was only distantly related to known alkane-degrading organisms and comprises new divergent lineages of MasD homologs, which might belong to an overlooked phylum of alkane-degrading bacteria. In addition, masD geneFISH allowed for the in situ identification and quantification of the target guild in alkane-degrading enrichment cultures. Altogether, these findings suggest an unexpectedly high number of yet unknown groups of anaerobic alkane degraders and underline the need for comprehensive surveys of microbial diversity based on metabolic genes in addition to ribosomal genes.
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Affiliation(s)
- Marion H Stagars
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - S Emil Ruff
- Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany; HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
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27
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Liang B, Wang LY, Mbadinga SM, Liu JF, Yang SZ, Gu JD, Mu BZ. Anaerolineaceae and Methanosaeta turned to be the dominant microorganisms in alkanes-dependent methanogenic culture after long-term of incubation. AMB Express 2015; 5:117. [PMID: 26080793 PMCID: PMC4469597 DOI: 10.1186/s13568-015-0117-4] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/18/2015] [Indexed: 11/30/2022] Open
Abstract
The methanogenic alkanes-degrading enrichment culture which had been incubated for over 1,300 days amended with n-alkanes (C15–C20) was investigated through clone libraries of bacteria, archaea and assA, mcrA functional genes. These enrichment cultures were obtained from oily sludge after an initial incubation of the oily sludge without any carbon source and then an enrichment transfer with n-alkanes (C15–C20) for acclimation. Activation of alkanes, methane precursor generation and methanogenic pathways are considered as three pivotal stages for the continuous methanogenesis from degradation of alkanes. The presence of functional genes encoding the alkylsuccinate synthase α-subunit indicated that fumarate addition is most likely the one of initial activation step for degradation of n-alkanes. Degradation intermediates of n-alkanes were octadecanoate, hexadecanoate, butyrate, isobutyrate, acetate and propionate, which could provide the appropriate substrates for acetate formation. Both methyl coenzyme M reductase gene and 16S rRNA gene analysis showed that microorganisms of Methanoseata were the most dominant methanogens, capable of using acetate as the electron donor to produce methane. Bacterial clone libraries showed organisms of Anaerolineaceae (within the phylum of Chloroflexi) were predominant (45.5%), indicating syntrophically cooperation with Methanosaeta archaea was likely involved in the process of methanogenic degradation of alkanes. Alkanes may initially be activated via fumarate addition and degraded to fatty acids, then converted to acetate, which was further converted to methane and carbon dioxide by methanogens.
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28
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Xu S, He C, Luo L, Lü F, He P, Cui L. Comparing activated carbon of different particle sizes on enhancing methane generation in upflow anaerobic digester. BIORESOURCE TECHNOLOGY 2015; 196:606-12. [PMID: 26298405 DOI: 10.1016/j.biortech.2015.08.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/03/2015] [Accepted: 08/08/2015] [Indexed: 05/28/2023]
Abstract
Two sizes of conductive particles, i.e. 10-20 mesh granulated activated carbon (GAC) and 80-100 mesh powdered activated carbon (PAC) were added into lab-scale upflow anaerobic sludge blanket reactors, respectively, to testify their enhancement on the syntrophic metabolism of alcohols and volatile fatty acids (VFAs) in 95days operation. When OLR increased to more than 5.8gCOD/L/d, the differences between GAC/PAC supplemented reactors and the control reactor became more significant. The introduction of activated carbon could facilitate the enrichment of methanogens and accelerate the startup of methanogenesis, as indicated by enhanced methane yield and substrate degradation. High-throughput pyrosequencing analysis showed that syntrophic bacteria and Methanosarcina sp. with versatile metabolic capability increased in the tightly absorbed fraction on the PAC surface, leading to the promoted syntrophic associations. Thus PAC prevails over than GAC for methanogenic reactor with heavy load.
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Affiliation(s)
- Suyun Xu
- Department of Environment & Low-Carbon Science, School of Environment and Architecture, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Chuanqiu He
- Department of Environment & Low-Carbon Science, School of Environment and Architecture, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Liwen Luo
- Department of Environment & Low-Carbon Science, School of Environment and Architecture, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Pinjing He
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Lifeng Cui
- Department of Environment & Low-Carbon Science, School of Environment and Architecture, University of Shanghai for Science and Technology, Shanghai 200093, China
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29
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Ding C, Ma T, Hu A, Dai L, He Q, Cheng L, Zhang H. Enrichment and Characterization of a Psychrotolerant Consortium Degrading Crude Oil Alkanes Under Methanogenic Conditions. MICROBIAL ECOLOGY 2015; 70:433-444. [PMID: 25783218 DOI: 10.1007/s00248-015-0590-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 02/26/2015] [Indexed: 06/04/2023]
Abstract
Anaerobic alkane degradation via methanogenesis has been intensively studied under mesophilic and thermophilic conditions. While there is a paucity of information on the ability and composition of anaerobic alkane-degrading microbial communities under low temperature conditions. In this study, we investigated the ability of consortium Y15, enriched from Shengli oilfield, to degrade hydrocarbons under different temperature conditions (5-35 °C). The consortium could use hexadecane over a low temperature range (15-30 °C). No growth was detected below 10 °C and above 35 °C, indicating the presence of cold-tolerant species capable of alkane degradation. The preferential degradation of short chain n-alkanes from crude oil was observed by this consortium. The structure and dynamics of the microbial communities were examined using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and Sanger sequencing of 16S rRNA genes. The core archaeal communities were mainly composed of aceticlastic Methanosaeta spp. Syntrophaceae-related microorganisms were always detected during consecutive transfers and dominated the bacterial communities, sharing 94-96 % sequence similarity with Smithella propionica strain LYP(T). Phylogenetic analysis of Syntrophaceae-related clones in diverse methanogenic alkane-degrading cultures revealed that most of them were clustered into three sublineages. Syntrophaceae clones retrieved from this study were mainly clustered into sublineage I, which may represent psychrotolerant, syntrophic alkane degraders. These results indicate the wide geographic distribution and ecological function of syntrophic alkane degraders.
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Affiliation(s)
- Chen Ding
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041, People's Republic of China
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30
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Johnson JM, Wawrik B, Isom C, Boling WB, Callaghan AV. Interrogation of Chesapeake Bay sediment microbial communities for intrinsic alkane-utilizing potential under anaerobic conditions. FEMS Microbiol Ecol 2015; 91:1-14. [DOI: 10.1093/femsec/fiu035] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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31
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Cheng L, Shi S, Li Q, Chen J, Zhang H, Lu Y. Progressive degradation of crude oil n-alkanes coupled to methane production under mesophilic and thermophilic conditions. PLoS One 2014; 9:e113253. [PMID: 25409013 PMCID: PMC4237390 DOI: 10.1371/journal.pone.0113253] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 10/23/2014] [Indexed: 02/01/2023] Open
Abstract
Although methanogenic degradation of hydrocarbons has become a well-known process, little is known about which crude oil tend to be degraded at different temperatures and how the microbial community is responded. In this study, we assessed the methanogenic crude oil degradation capacity of oily sludge microbes enriched from the Shengli oilfield under mesophilic and thermophilic conditions. The microbial communities were investigated by terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes combined with cloning and sequencing. Enrichment incubation demonstrated the microbial oxidation of crude oil coupled to methane production at 35 and 55°C, which generated 3.7±0.3 and 2.8±0.3 mmol of methane per gram oil, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that crude oil n-alkanes were obviously degraded, and high molecular weight n-alkanes were preferentially removed over relatively shorter-chain n-alkanes. Phylogenetic analysis revealed the concurrence of acetoclastic Methanosaeta and hydrogenotrophic methanogens but different methanogenic community structures under the two temperature conditions. Candidate divisions of JS1 and WWE 1, Proteobacteria (mainly consisting of Syntrophaceae, Desulfobacteraceae and Syntrophorhabdus) and Firmicutes (mainly consisting of Desulfotomaculum) were supposed to be involved with n-alkane degradation in the mesophilic conditions. By contrast, the different bacterial phylotypes affiliated with Caldisericales, “Shengli Cluster” and Synergistetes dominated the thermophilic consortium, which was most likely to be associated with thermophilic crude oil degradation. This study revealed that the oily sludge in Shengli oilfield harbors diverse uncultured microbes with great potential in methanogenic crude oil degradation over a wide temperature range, which extend our previous understanding of methanogenic degradation of crude oil alkanes.
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Affiliation(s)
- Lei Cheng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu, 610041, China
| | - Shengbao Shi
- State Key Laboratory of Petroleum Resources and Prospecting, China University of Petroleum (Beijing), Beijing, 102200, China
| | - Qiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu, 610041, China
| | - Jianfa Chen
- State Key Laboratory of Petroleum Resources and Prospecting, China University of Petroleum (Beijing), Beijing, 102200, China
| | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu, 610041, China
| | - Yahai Lu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
- * E-mail:
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32
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Head IM, Gray ND, Larter SR. Life in the slow lane; biogeochemistry of biodegraded petroleum containing reservoirs and implications for energy recovery and carbon management. Front Microbiol 2014; 5:566. [PMID: 25426105 PMCID: PMC4227522 DOI: 10.3389/fmicb.2014.00566] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/08/2014] [Indexed: 11/15/2022] Open
Abstract
Our understanding of the processes underlying the formation of heavy oil has been transformed in the last decade. The process was once thought to be driven by oxygen delivered to deep petroleum reservoirs by meteoric water. This paradigm has been replaced by a view that the process is anaerobic and frequently associated with methanogenic hydrocarbon degradation. The thermal history of a reservoir exerts a fundamental control on the occurrence of biodegraded petroleum, and microbial activity is focused at the base of the oil column in the oil water transition zone, that represents a hotspot in the petroleum reservoir biome. Here we present a synthesis of new and existing microbiological, geochemical, and biogeochemical data that expands our view of the processes that regulate deep life in petroleum reservoir ecosystems and highlights interactions of a range of biotic and abiotic factors that determine whether petroleum is likely to be biodegraded in situ, with important consequences for oil exploration and production. Specifically we propose that the salinity of reservoir formation waters exerts a key control on the occurrence of biodegraded heavy oil reservoirs and introduce the concept of palaeopickling. We also evaluate the interaction between temperature and salinity to explain the occurrence of non-degraded oil in reservoirs where the temperature has not reached the 80-90°C required for palaeopasteurization. In addition we evaluate several hypotheses that might explain the occurrence of organisms conventionally considered to be aerobic, in nominally anoxic petroleum reservoir habitats. Finally we discuss the role of microbial processes for energy recovery as we make the transition from fossil fuel reliance, and how these fit within the broader socioeconomic landscape of energy futures.
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Affiliation(s)
- Ian M. Head
- School of Civil Engineering and Geosciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Neil D. Gray
- School of Civil Engineering and Geosciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Stephen R. Larter
- School of Civil Engineering and Geosciences, Newcastle UniversityNewcastle upon Tyne, UK
- Petroleum Reservoir Group, Department of Geoscience, University of CalgaryCalgary, AB, Canada
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Gieg LM, Fowler SJ, Berdugo-Clavijo C. Syntrophic biodegradation of hydrocarbon contaminants. Curr Opin Biotechnol 2014; 27:21-9. [DOI: 10.1016/j.copbio.2013.09.002] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 11/30/2022]
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Primers: Functional Genes for Anaerobic Hydrocarbon Degrading Microbes. SPRINGER PROTOCOLS HANDBOOKS 2014. [DOI: 10.1007/8623_2014_44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Rosenkranz F, Cabrol L, Carballa M, Donoso-Bravo A, Cruz L, Ruiz-Filippi G, Chamy R, Lema JM. Relationship between phenol degradation efficiency and microbial community structure in an anaerobic SBR. WATER RESEARCH 2013; 47:6739-49. [PMID: 24083853 DOI: 10.1016/j.watres.2013.09.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 08/21/2013] [Accepted: 09/02/2013] [Indexed: 05/04/2023]
Abstract
Phenol is a common wastewater contaminant from various industrial processes, including petrochemical refineries and chemical compounds production. Due to its toxicity to microbial activity, it can affect the efficiency of biological wastewater treatment processes. In this study, the efficiency of an Anaerobic Sequencing Batch Reactor (ASBR) fed with increasing phenol concentrations (from 120 to 1200 mg L(-1)) was assessed and the relationship between phenol degradation capacity and the microbial community structure was evaluated. Up to a feeding concentration of 800 mg L(-1), the initial degradation rate steadily increased with phenol concentration (up to 180 mg L(-1) d(-1)) and the elimination capacity remained relatively constant around 27 mg phenol removed∙gVSS(-1) d(-1). Operation at higher concentrations (1200 mg L(-1)) resulted in a still efficient but slower process: the elimination capacity and the initial degradation rate decreased to, respectively, 11 mg phenol removed∙gVSS(-1) d(-1) and 154 mg L(-1) d(-1). As revealed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis, the increase of phenol concentration induced level-dependent structural modifications of the community composition which suggest an adaptation process. The increase of phenol concentration from 120 to 800 mg L(-1) had little effect on the community structure, while it involved drastic structural changes when increasing from 800 to 1200 mg L(-1), including a strong community structure shift, suggesting the specialization of the community through the emergence and selection of most adapted phylotypes. The thresholds of structural and functional disturbances were similar, suggesting the correlation of degradation performance and community structure. The Canonical Correspondence Analysis (CCA) confirmed that the ASBR functional performance was essentially driven by specific community traits. Under the highest feeding concentration, the most abundant ribotype probably involved in successful phenol degradation at 1200 mg L(-1) was affiliated to the Anaerolineaceae family.
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Affiliation(s)
- F Rosenkranz
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, General Cruz 34, Valparaíso, Chile; Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, E-15782 Santiago de Compostela, Spain; Fraunhofer Chile Research, Mariano Sánchez Fontecilla 310, Las Condes, Santiago, Chile.
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DNA-SIP reveals that Syntrophaceae play an important role in methanogenic hexadecane degradation. PLoS One 2013; 8:e66784. [PMID: 23840866 PMCID: PMC3698093 DOI: 10.1371/journal.pone.0066784] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 05/11/2013] [Indexed: 02/01/2023] Open
Abstract
The methanogenic degradation of linear alkanes is a common process in oil-impacted environments. However, little is known about the key players involved in this process. Here, the hexadecane-degrading organisms in a methanogenic, hexadecane-degrading consortium designated M82 obtained from Shengli oilfield and maintained at 35°C for over 4 years, were identified by DNA-stable isotope probing with UL-13C-hexadecane, followed by density-resolved terminal restriction fragment length polymorphism (T-RFLP) analysis, cloning and phylogenetic analysis of 16S rRNA gene fragments. Compared to the fractions of the 12C treatment, the relative abundance of two phylotypes significantly increased in the heavy fractions of the 13C-hexadecane incubated microcosm. One belongs to a uncultured member of the bacterial family Syntrophaceae, which show 95–97% rRNA sequence identity with Smithella propionica, and the other is affiliated with Methanoculleus receptaculi (>99% sequence identity). The results of the present study prove the significant role of uncultured Syntrophaceae in degradation of hexadecane, probably through syntrophic interactions with hydrogenotrophic methanogens.
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Agrawal A, Gieg LM. In situ detection of anaerobic alkane metabolites in subsurface environments. Front Microbiol 2013; 4:140. [PMID: 23761789 PMCID: PMC3671572 DOI: 10.3389/fmicb.2013.00140] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 05/17/2013] [Indexed: 11/13/2022] Open
Abstract
Alkanes comprise a substantial fraction of crude oil and refined fuels. As such, they are prevalent within deep subsurface fossil fuel deposits and in shallow subsurface environments such as aquifers that are contaminated with hydrocarbons. These environments are typically anaerobic, and host diverse microbial communities that can potentially use alkanes as substrates. Anaerobic alkane biodegradation has been reported to occur under nitrate-reducing, sulfate-reducing, and methanogenic conditions. Elucidating the pathways of anaerobic alkane metabolism has been of interest in order to understand how microbes can be used to remediate contaminated sites. Alkane activation primarily occurs by addition to fumarate, yielding alkylsuccinates, unique anaerobic metabolites that can be used to indicate in situ anaerobic alkane metabolism. These metabolites have been detected in hydrocarbon-contaminated shallow aquifers, offering strong evidence for intrinsic anaerobic bioremediation. Recently, studies have also revealed that alkylsuccinates are present in oil and coal seam production waters, indicating that anaerobic microbial communities can utilize alkanes in these deeper subsurface environments. In many crude oil reservoirs, the in situ anaerobic metabolism of hydrocarbons such as alkanes may be contributing to modern-day detrimental effects such as oilfield souring, or may lead to more beneficial technologies such as enhanced energy recovery from mature oilfields. In this review, we briefly describe the key metabolic pathways for anaerobic alkane (including n-alkanes, isoalkanes, and cyclic alkanes) metabolism and highlight several field reports wherein alkylsuccinates have provided evidence for anaerobic in situ alkane metabolism in shallow and deep subsurface environments.
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Affiliation(s)
- Akhil Agrawal
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
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Tan B, Dong X, Sensen CW, Foght J. Metagenomic analysis of an anaerobic alkane-degrading microbial culture: potential hydrocarbon-activating pathways and inferred roles of community members. Genome 2013; 56:599-611. [PMID: 24237341 DOI: 10.1139/gen-2013-0069] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A microbial community (short-chain alkane-degrading culture, SCADC) enriched from an oil sands tailings pond was shown to degrade C6-C10 alkanes under methanogenic conditions. Total genomic DNA from SCADC was subjected to 454 pyrosequencing, Illumina paired-end sequencing, and 16S rRNA amplicon pyrotag sequencing; the latter revealed 320 operational taxonomic units at 5% distance. Metagenomic sequences were subjected to in-house quality control and co-assembly, yielding 984 086 contigs, and annotation using MG-Rast and IMG. Substantial nucleotide and protein recruitment to Methanosaeta concilii, Syntrophus aciditrophicus, and Desulfobulbus propionicus reference genomes suggested the presence of closely related strains in SCADC; other genomes were not well mapped, reflecting the paucity of suitable reference sequences for such communities. Nonetheless, we detected numerous homologues of putative hydrocarbon succinate synthase genes (e.g., assA, bssA, and nmsA) implicated in anaerobic hydrocarbon degradation, suggesting the ability of the SCADC microbial community to initiate methanogenic alkane degradation by addition to fumarate. Annotation of a large contig revealed analogues of the ass operon 1 in the alkane-degrading sulphate-reducing bacterium Desulfatibacillum alkenivorans AK-01. Despite being enriched under methanogenic-fermentative conditions, additional metabolic functions inferred by COG profiling indicated multiple CO(2) fixation pathways, organic acid utilization, hydrogenase activity, and sulphate reduction.
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Affiliation(s)
- Boonfei Tan
- a Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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Cheng L, He Q, Ding C, Dai LR, Li Q, Zhang H. Novel bacterial groups dominate in a thermophilic methanogenic hexadecane-degrading consortium. FEMS Microbiol Ecol 2013; 85:568-77. [DOI: 10.1111/1574-6941.12141] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 04/17/2013] [Accepted: 04/24/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy; Biogas Institute of Ministry of Agriculture; Chengdu China
| | - Qiao He
- Key Laboratory of Development and Application of Rural Renewable Energy; Biogas Institute of Ministry of Agriculture; Chengdu China
| | - Chen Ding
- Key Laboratory of Development and Application of Rural Renewable Energy; Biogas Institute of Ministry of Agriculture; Chengdu China
| | - Li-rong Dai
- Key Laboratory of Development and Application of Rural Renewable Energy; Biogas Institute of Ministry of Agriculture; Chengdu China
| | - Qiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy; Biogas Institute of Ministry of Agriculture; Chengdu China
| | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy; Biogas Institute of Ministry of Agriculture; Chengdu China
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Callaghan AV. Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins. Front Microbiol 2013; 4:89. [PMID: 23717304 PMCID: PMC3653055 DOI: 10.3389/fmicb.2013.00089] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 03/31/2013] [Indexed: 11/13/2022] Open
Abstract
Anaerobic microorganisms play key roles in the biogeochemical cycling of methane and non-methane alkanes. To date, there appear to be at least three proposed mechanisms of anaerobic methane oxidation (AOM). The first pathway is mediated by consortia of archaeal anaerobic methane oxidizers and sulfate-reducing bacteria (SRB) via “reverse methanogenesis” and is catalyzed by a homolog of methyl-coenzyme M reductase. The second pathway is also mediated by anaerobic methane oxidizers and SRB, wherein the archaeal members catalyze both methane oxidation and sulfate reduction and zero-valent sulfur is a key intermediate. The third AOM mechanism is a nitrite-dependent, “intra-aerobic” pathway described for the denitrifying bacterium, ‘Candidatus Methylomirabilis oxyfera.’ It is hypothesized that AOM proceeds via reduction of nitrite to nitric oxide, followed by the conversion of two nitric oxide molecules to dinitrogen and molecular oxygen. The latter can be used to functionalize the methane via a particulate methane monooxygenase. With respect to non-methane alkanes, there also appear to be novel mechanisms of activation. The most well-described pathway is the addition of non-methane alkanes across the double bond of fumarate to form alkyl-substituted succinates via the putative glycyl radical enzyme, alkylsuccinate synthase (also known as methylalkylsuccinate synthase). Other proposed mechanisms include anaerobic hydroxylation via ethylbenzene dehydrogenase-like enzymes and an “intra-aerobic” denitrification pathway similar to that described for ‘Methylomirabilis oxyfera.’
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Affiliation(s)
- Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
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