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Qiu Y, Zhang J, Tong YW, He Y. Reverse electron transfer: Novel anaerobic methanogenesis pathway regulated through exogenous CO 2 synergized with biochar. BIORESOURCE TECHNOLOGY 2024; 401:130741. [PMID: 38670292 DOI: 10.1016/j.biortech.2024.130741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/25/2024] [Accepted: 04/24/2024] [Indexed: 04/28/2024]
Abstract
Acid accumulation and carbon emission are two major challenges in anaerobic digestion. Syntrophic consortia can employ reverse electron transfer (RET) to facilitate thermodynamically unfavorable redox reactions during acetogenesis. However, the potential mechanisms and regulatory methods of RET remain unclear. This study examines the regulatory mechanisms by which exogenous CO2 affects RET and demonstrates that biochar maximizes CO2 solubility at 25.8 mmol/L to enhance effects further. CO2 synergized with biochar significantly increases cumulative methane production and propionate degradation rate. From the bioenergetic perspective, CO2 decreases energy level to a maximum of -87 kJ/mol, strengthening the thermodynamic viability. The underlying mechanism can be attributed to RET promotion, as indicated by increased formate dehydrogenase and enrichment of H2/formate-producing bacteria with their partner Methanospirillum hungatei. Moreover, the 5 % 13CH4 and methane contribution result show that CO2 accomplishes directed methanogenesis. Overall, this investigation riches the roles of CO2 and biochar in AD surrounding RET.
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Affiliation(s)
- Yang Qiu
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingxin Zhang
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; Energy and Environmental Sustainability Solutions for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore.
| | - Yen Wah Tong
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore; Energy and Environmental Sustainability Solutions for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore, 138602, Singapore
| | - Yiliang He
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 200240, China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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2
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Yeo J, Jeon YW. Impact of Polyethylene-Glycol-Induced Water Potential on Methane Yield and Microbial Consortium Dynamics in the Anaerobic Degradation of Glucose. Bioengineering (Basel) 2024; 11:433. [PMID: 38790299 PMCID: PMC11117670 DOI: 10.3390/bioengineering11050433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
This study investigated the relationship between water potential (Ψ) and the cation-induced inhibition of methane production in anaerobic digesters. The Ψ around methanogens was manipulated using polyethylene glycol (PEG) in a batch anaerobic reactor, ranging from -0.92 to -5.10 MPa. The ultimate methane potential (Bu) decreased significantly from 0.293 to 0.002 Nm3 kg-1-VSadded as Ψ decreased. When Ψ lowered from -0.92 MPa to -1.48 MPa, the community distribution of acetoclastic Methanosarcina decreased from 59.62% to 40.44%, while those of hydrogenotrophic Methanoculleus and Methanobacterium increased from 17.70% and 1.30% to 36.30% and 18.07%, respectively. These results mirrored changes observed in methanogenic communities affected by cation inhibition with KCl. Our findings strongly indicate that the inhibitory effect of cations on methane production may stem more from the water stress induced by cations than from their direct toxic effects. This study highlights the importance of considering Ψ dynamics in understanding cation-mediated inhibition in anaerobic digesters, providing insights into optimizing microbial processes for enhanced methane production from organic substrates.
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Affiliation(s)
- Jin Yeo
- Biogas Research Center, Hankyong National University, Anseong 17579, Republic of Korea;
| | - Yong-Woo Jeon
- Environmental Technology Division, Korea Testing Laboratory, Seoul 08389, Republic of Korea
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3
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Ni S, Lv W, Ji Z, Wang K, Mei Y, Li Y. Progress of Crude Oil Gasification Technology Assisted by Microorganisms in Reservoirs. Microorganisms 2024; 12:702. [PMID: 38674646 PMCID: PMC11051786 DOI: 10.3390/microorganisms12040702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Crude oil gasification bacteria, including fermenting bacteria, hydrocarbon-oxidizing bacteria, reducing bacteria, and methanogenic bacteria, participate in multi-step reactions involving initial activation, intermediate metabolism, and the methanogenesis of crude oil hydrocarbons. These bacteria degrade crude oil into smaller molecules such as hydrogen, carbon dioxide, acetic acid, and formic acid. Ultimately, they convert it into methane, which can be utilized or stored as a strategic resource. However, the current challenges in crude oil gasification include long production cycles and low efficiency. This paper provides a summary of the microbial flora involved in crude oil gasification, the gasification metabolism pathways within reservoirs, and other relevant information. It specifically focuses on analyzing the factors that affect the efficiency of crude oil gasification metabolism and proposes suggestions for improving this efficiency. These studies deepen our understanding of the potential of reservoir ecosystems and provide valuable insights for future reservoir development and management.
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Affiliation(s)
- Shumin Ni
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Weifeng Lv
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
- State Key Laboratory of Enhanced Oil Recovery, Research Institute of Petroleum Exploration and Development, CNPC, Beijing 100083, China
| | - Zemin Ji
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Kai Wang
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Yuhao Mei
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
| | - Yushu Li
- University of Chinese Academy of Sciences, Beijing 100049, China; (S.N.); (K.W.); (Y.M.); (Y.L.)
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China;
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Mbow FT, Akbari A, Dopffel N, Schneider K, Mukherjee S, Meckenstock RU. Insights into the effects of anthropogenic activities on oil reservoir microbiome and metabolic potential. N Biotechnol 2024; 79:30-38. [PMID: 38040289 DOI: 10.1016/j.nbt.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Microbial communities have long been observed in oil reservoirs, where the subsurface conditions are major drivers shaping their structure and functions. Furthermore, anthropogenic activities such as water flooding during oil production can affect microbial activities and community compositions in oil reservoirs through the injection of recycled produced water, often associated with biocides. However, it is still unclear to what extent the introduced chemicals and microbes influence the metabolic potential of the subsurface microbiome. Here we investigated an onshore oilfield in Germany (Field A) that undergoes secondary oil production along with biocide treatment to prevent souring and microbially induced corrosion (MIC). With the integrated approach of 16 S rRNA gene amplicon and shotgun metagenomic sequencing of water-oil samples from 4 production wells and 1 injection well, we found differences in microbial community structure and metabolic functions. In the injection water samples, amplicon sequence variants (ASVs) belonging to families such as Halanaerobiaceae, Ectothiorhodospiraceae, Hydrogenophilaceae, Halobacteroidaceae, Desulfohalobiaceae, and Methanosarcinaceae were dominant, while in the production water samples, ASVs of families such as Thermotogaceae, Nitrospiraceae, Petrotogaceae, Syntrophaceae, Methanobacteriaceae, and Thermoprotei were also dominant. The metagenomic analysis of the injection water sample revealed the presence of C1-metabolism, namely, genes involved in formaldehyde oxidation. Our analysis revealed that the microbial community structure of the production water samples diverged slightly from that of injection water samples. Additionally, a metabolic potential for oxidizing the applied biocide clearly occurred in the injection water samples indicating an adaptation and buildup of degradation capacity or resistance against the added biocide.
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Affiliation(s)
- Fatou T Mbow
- University of Duisburg-Essen - Environmental Microbiology and Biotechnology - Aquatic Microbiology, Universitätsstraße 5, 45141 Essen, Germany
| | - Ali Akbari
- University of Duisburg-Essen - Environmental Microbiology and Biotechnology - Aquatic Microbiology, Universitätsstraße 5, 45141 Essen, Germany
| | - Nicole Dopffel
- BASF SE, Carl-Bosch-Straße 38, 67056 Ludwigshafen am Rhein, Germany
| | | | | | - Rainer U Meckenstock
- University of Duisburg-Essen - Environmental Microbiology and Biotechnology - Aquatic Microbiology, Universitätsstraße 5, 45141 Essen, Germany.
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Xu J, Wang L, Lv W, Song X, Nie Y, Wu XL. Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure conditions. Front Microbiol 2023; 14:1305731. [PMID: 38188585 PMCID: PMC10766756 DOI: 10.3389/fmicb.2023.1305731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/22/2023] [Indexed: 01/09/2024] Open
Abstract
While pressure is a significant characteristic of petroleum reservoirs, it is often overlooked in laboratory studies. To clarify the composition and metabolic properties of microbial communities under high-pressure conditions, we established methanogenic and sulfate-reducing enrichment cultures under high-pressure conditions using production water from the Jilin Oilfield in China. We utilized a metagenomics approach to analyze the microbial community after a 90-day incubation period. Under methanogenic conditions, Firmicutes, Deferribacteres, Ignavibacteriae, Thermotogae, and Nitrospirae, in association with the hydrogenotrophic methanogen Archaeoglobaceae and acetoclastic Methanosaeta, were highly represented. Genomes for Ca. Odinarchaeota and the hydrogen-dependent methylotrophic Ca. Methanosuratus were also recovered from the methanogenic culture. The sulfate-reducing community was dominated by Firmicutes, Thermotogae, Nitrospirae, Archaeoglobus, and several candidate taxa including Ca. Bipolaricaulota, Ca. Aminicenantes, and Candidate division WOR-3. These candidate taxa were key pantothenate producers for other community members. The study expands present knowledge of the metabolic roles of petroleum-degrading microbial communities under high-pressure conditions. Our results also indicate that microbial community interactions were shaped by syntrophic metabolism and the exchange of amino acids and cofactors among members. Furthermore, incubation under in situ pressure conditions has the potential to reveal the roles of microbial dark matter.
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Affiliation(s)
- Jinbo Xu
- School of Earth and Space Sciences, Peking University, Beijing, China
- State Key Laboratory of Enhanced Oil and Gas Recovery, Research Institute of Petroleum Exploration and Development, Beijing, China
| | - Lu Wang
- State Key Laboratory of Enhanced Oil and Gas Recovery, Research Institute of Petroleum Exploration and Development, Beijing, China
| | - Weifeng Lv
- State Key Laboratory of Enhanced Oil and Gas Recovery, Research Institute of Petroleum Exploration and Development, Beijing, China
| | - Xinmin Song
- State Key Laboratory of Enhanced Oil and Gas Recovery, Research Institute of Petroleum Exploration and Development, Beijing, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing, China
- Institute of Ecology, Peking University, Beijing, China
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Microbial Communities in Underground Gas Reservoirs Offer Promising Biotechnological Potential. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8060251] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Securing new sources of renewable energy and achieving national self-sufficiency in natural gas have become increasingly important in recent times. The study described in this paper focuses on three geologically diverse underground gas reservoirs (UGS) that are the natural habitat of methane-producing archaea, as well as other microorganisms with which methanogens have various ecological relationships. The objective of this research was to describe the microbial metabolism of methane in these specific anoxic environments during the year. DNA sequencing analyses revealed the presence of different methanogenic communities and their metabolic potential in all sites studied. Hydrogenotrophic Methanobacterium sp. prevailed in Lobodice UGS, members of the hydrogenotrophic order Methanomicrobiales predominated in Dolní Dunajovice UGS and thermophilic hydrogenotrophic members of the Methanothermobacter sp. were prevalent in Tvrdonice UGS. Gas composition and isotope analyses were performed simultaneously. The results suggest that the biotechnological potential of UGS for biomethane production cannot be neglected.
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The influence of the marine Bacillus cereus over carbon steel, stainless corrosion, and copper coupons. Arch Microbiol 2021; 204:9. [PMID: 34873663 DOI: 10.1007/s00203-021-02607-w] [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: 09/03/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 10/19/2022]
Abstract
The present study evaluated the influence of the marine bacteria Bacillus cereus Mc-1 on the corrosion of 1020 carbon steel, 316L stainless steel, and copper alloy. The Mc-1 strain was grown in a modified ammoniacal citrate culture medium (CFA.ico-), CFA.ico- with sodium nitrate supplementation (NO3-), and CFA.ico- with sodium chloride supplementation (NaCl). The mass loss and corrosion rate were evaluated after the periods of 7, 15, and 30 days. The results showed that in CFA.ico- and CFA.ico- medium added NO3- the corrosion rates of carbon steel and copper alloy were high when compared to the control. Whereas the medium was supplemented with NaCl, despite the rates being above the averages of the control system, they were considerably below the previous results. In general, the corrosion rates induced by Mc-1 on 316L coupons were below the results compared to carbon steel and copper alloy. When analyzing the corrosion rate measurements, regardless of the culture medium, the corrosion levels decreased consistently after 15 days, being below the levels evaluated after 7 days of the experiment. Our analyses suggest that B. cereus Mc-1 has different influences on corrosion in different metals and environmental conditions, such as the presence of NO3- and NaCl. These results can help to better understand the influence of this bacteria genus on the corrosion of metals in marine environments.
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Integrating Hydrogeological and Microbiological Data and Modelling to Characterize the Hydraulic Features and Behaviour of Coastal Carbonate Aquifers: A Case in Western Cuba. WATER 2019. [DOI: 10.3390/w11101989] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Carbonate aquifers are the primary source of freshwater in Cuba. Unfortunately, coastal groundwater is often contaminated by seawater intrusion. The main aim of the present study was to test the efficacy of an experimental modelling approach, ranging from hydrogeology/geomorphology to microbiology, to better characterise both the hydraulic features and behaviour of a coastal carbonate aquifer and acquire useful information to prevent groundwater salinization. The interdisciplinary approach was an effective tool in order to understand (i) the hydraulic role played by some fault zones; (ii) the influence of discontinuous heterogeneities on groundwater flow and saltwater wedge shape; (iii) mixing processes between different water bodies (groundwater, surface water, seawater); (iv) the role of karst conduits in influencing the step-like halocline within the mixing zone between fresh groundwater and seawater.
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9
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Bioconversion Pathway of CO2 in the Presence of Ethanol by Methanogenic Enrichments from Production Water of a High-Temperature Petroleum Reservoir. ENERGIES 2019. [DOI: 10.3390/en12050918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Transformation of CO2 in both carbon capture and storage (CCS) to biogenic methane in petroleum reservoirs is an attractive and promising strategy for not only mitigating the greenhouse impact but also facilitating energy recovery in order to meet societal needs for energy. Available sources of petroleum in the reservoirs reduction play an essential role in the biotransformation of CO2 stored in petroleum reservoirs into clean energy methane. Here, the feasibility and potential on the reduction of CO2 injected into methane as bioenergy by indigenous microorganisms residing in oilfields in the presence of the fermentative metabolite ethanol were assessed in high-temperature petroleum reservoir production water. The bio-methane production from CO2 was achieved in enrichment with ethanol as the hydrogen source by syntrophic cooperation between the fermentative bacterium Synergistetes and CO2-reducing Methanothermobacter via interspecies hydrogen transfer based upon analyses of molecular microbiology and stable carbon isotope labeling. The thermodynamic analysis shows that CO2-reducing methanogenesis and the methanogenic metabolism of ethanol are mutually beneficial at a low concentration of injected CO2 but inhibited by the high partial pressure of CO2. Our results offer a potentially valuable opportunity for clean bioenergy recovery from CCS in oilfields.
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10
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Li XX, Yang T, Mbadinga SM, Liu JF, Yang SZ, Gu JD, Mu BZ. Responses of Microbial Community Composition to Temperature Gradient and Carbon Steel Corrosion in Production Water of Petroleum Reservoir. Front Microbiol 2017; 8:2379. [PMID: 29259586 PMCID: PMC5723327 DOI: 10.3389/fmicb.2017.02379] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/17/2017] [Indexed: 11/13/2022] Open
Abstract
Oil reservoir production systems are usually associated with a temperature gradient and oil production facilities frequently suffer from pipeline corrosion failures. Both bacteria and archaea potentially contribute to biocorrosion of the oil production equipment. Here the response of microbial populations from the petroleum reservoir to temperature gradient and corrosion of carbon steel coupons were investigated under laboratory condition. Carbon steel coupons were exposed to production water from a depth of 1809 m of Jiangsu petroleum reservoir (China) and incubated for periods of 160 and 300 days. The incubation temperatures were set at 37, 55, and 65°C to monitoring mesophilic, thermophilic and hyperthermophilic microorganisms associated with anaerobic carbon steel corrosion. The results showed that corrosion rate at 55°C (0.162 ± 0.013 mm year-1) and 37°C (0.138 ± 0.008 mm year-1) were higher than that at 65°C (0.105 ± 0.007 mm year-1), and a dense biofilm was observed on the surface of coupons under all biotic incubations. The microbial community analysis suggests a high frequency of bacterial taxa associated with families Porphyromonadaceae, Enterobacteriaceae, and Spirochaetaceae at all three temperatures. While the majority of known sulfate-reducing bacteria, in particular Desulfotignum, Desulfobulbus and Desulfovibrio spp., were predominantly observed at 37°C; Desulfotomaculum spp., Thermotoga spp. and Thermanaeromonas spp. as well as archaeal members closely related to Thermococcus and Archaeoglobus spp. were substantially enriched at 65°C. Hydrogenotrophic methanogens of the family Methanobacteriaceae were dominant at both 37 and 55°C; acetoclastic Methanosaeta spp. and methyltrophic Methanolobus spp. were enriched at 37°C. These observations show that temperature changes significantly alter the microbial community structure in production fluids and also affected the biocorrosion of carbon steel under anaerobic conditions.
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Affiliation(s)
- Xiao-Xiao Li
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China
| | - Tao Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China
| | - Serge M Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
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11
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Using Prokaryotes for Carbon Capture Storage. Trends Biotechnol 2017; 35:22-32. [DOI: 10.1016/j.tibtech.2016.06.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 11/20/2022]
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12
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Frank YA, Kadnikov VV, Lukina AP, Banks D, Beletsky AV, Mardanov AV, Sen'kina EI, Avakyan MR, Karnachuk OV, Ravin NV. Characterization and Genome Analysis of the First Facultatively Alkaliphilic Thermodesulfovibrio Isolated from the Deep Terrestrial Subsurface. Front Microbiol 2016; 7:2000. [PMID: 28066337 PMCID: PMC5165239 DOI: 10.3389/fmicb.2016.02000] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 11/29/2016] [Indexed: 11/16/2022] Open
Abstract
Members of the genus Thermodesulfovibrio belong to the Nitrospirae phylum and all isolates characterized to date are neutrophiles. They have been isolated from terrestrial hot springs and thermophilic methanogenic anaerobic sludges. Their molecular signatures have, however, also been detected in deep subsurface. The purpose of this study was to characterize and analyze the genome of a newly isolated, facultatively alkaliphilic Thermodesulfovibrio from a 2 km deep aquifer system in Western Siberia, Russia. The new isolate, designated N1, grows optimally at pH 8.5 and at 65°C. It is able to reduce sulfate, thiosulfate or sulfite with a limited range of electron donors, such as formate, pyruvate, and lactate. Analysis of the 1.93 Mb draft genome of strain N1 revealed that it contains a set of genes for dissimilatory sulfate reduction, including sulfate adenyltransferase, adenosine-5′-phosphosulfate reductase AprAB, membrane-bound electron transfer complex QmoABC, dissimilatory sulfite reductase DsrABC, and sulfite reductase-associated electron transfer complex DsrMKJOP. Hydrogen turnover is enabled by soluble cytoplasmic, membrane-linked, and soluble periplasmic hydrogenases. The use of thiosulfate as an electron acceptor is enabled by a membrane-linked molybdopterin oxidoreductase. The N1 requirement for organic carbon sources corresponds to the lack of the autotrophic C1-fixation pathways. Comparative analysis of the genomes of Thermodesulfovibrio (T. yellowstonii, T. islandicus, T. àggregans, T. thiophilus, and strain N1) revealed a low overall genetic diversity and several adaptive traits. Consistent with an alkaliphilic lifestyle, a multisubunit Na+/H+ antiporter of the Mnh family is encoded in the Thermodesulfovibrio strain N1 genome. Nitrogenase genes were found in T. yellowstonii, T. aggregans, and T. islandicus, nitrate reductase in T. islandicus, and cellulose synthetase in T. aggregans and strain N1. Overall, our results provide genomic insights into metabolism of the Thermodesulfovibrio lineage in microbial communities of the deep subsurface biosphere.
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Affiliation(s)
- Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Anastasia P Lukina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia
| | - David Banks
- Systems, Power and Energy, School of Engineering, Glasgow UniversityGlasgow, UK; Holymoor Consultancy Ltd.Chesterfield, UK
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
| | - Elena I Sen'kina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University Tomsk, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences Moscow, Russia
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