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Abstract
In nature, selenium is actively cycled between oxic and anoxic habitats, and this cycle plays an important role in carbon and nitrogen mineralization through bacterial anaerobic respiration. Selenium-respiring bacteria (SeRB) are found in geographically diverse, pristine or contaminated environments and play a pivotal role in the selenium cycle. Unlike its structural analogues oxygen and sulfur, the chalcogen selenium and its microbial cycling have received much less attention by the scientific community. This review focuses on microorganisms that use selenate and selenite as terminal electron acceptors, in parallel to the well-studied sulfate-reducing bacteria. It overviews the significant advancements made in recent years on the role of SeRB in the biological selenium cycle and their ecological role, phylogenetic characterization, and metabolism, as well as selenium biomineralization mechanisms and environmental biotechnological applications.
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Affiliation(s)
- Y V Nancharaiah
- Environmental Engineering and Water Technology Department, UNESCO-IHE Institute for Water Education, Delft, The Netherlands Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre, Kalpakkam, Tamil Nadu, India
| | - P N L Lens
- Environmental Engineering and Water Technology Department, UNESCO-IHE Institute for Water Education, Delft, The Netherlands
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52
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53
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Kato S, Yoshida R, Yamaguchi T, Sato T, Yumoto I, Kamagata Y. The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium. Front Microbiol 2014; 5:575. [PMID: 25400628 PMCID: PMC4214200 DOI: 10.3389/fmicb.2014.00575] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/13/2014] [Indexed: 11/13/2022] Open
Abstract
Investigation of microbial interspecies interactions is essential for elucidating the function and stability of microbial ecosystems. However, community-based analyses including molecular-fingerprinting methods have limitations for precise understanding of interspecies interactions. Construction of model microbial consortia consisting of defined mixed cultures of isolated microorganisms is an excellent method for research on interspecies interactions. In this study, a model microbial consortium consisting of microorganisms that convert acetate into methane directly (Methanosaeta thermophila) and syntrophically (Thermacetogenium phaeum and Methanothermobacter thermautotrophicus) was constructed and the effects of elevated CO2 concentrations on intermicrobial competition were investigated. Analyses on the community dynamics by quantitative RT-PCR and fluorescent in situ hybridization targeting their 16S rRNAs revealed that high concentrations of CO2 have suppressive effects on the syntrophic microorganisms, but not on the aceticlastic methanogen. The pathways were further characterized by determining the Gibbs free energy changes (ΔG) of the metabolic reactions conducted by each microorganism under different CO2 concentrations. The ΔG value of the acetate oxidation reaction (T. phaeum) under high CO2 conditions became significantly higher than -20 kJ per mol of acetate, which is the borderline level for sustaining microbial growth. These results suggest that high concentrations of CO2 undermine energy acquisition of T. phaeum, resulting in dominance of the aceticlastic methanogen. This study demonstrates that investigation on model microbial consortia is useful for untangling microbial interspecies interactions, including competition among microorganisms occupying the same trophic niche in complex microbial ecosystems.
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Affiliation(s)
- Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
- Research Center for Advanced Science and Technology, The University of TokyoTokyo, Japan
| | - Rina Yoshida
- Department of Civil and Environmental Engineering, Nagaoka University of TechnologyNagaoka, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of TechnologyNagaoka, Japan
| | - Tomoyuki Sato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
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54
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Zhao Z, Zhang Y, Chen S, Quan X, Yu Q. Bioelectrochemical enhancement of anaerobic methanogenesis for high organic load rate wastewater treatment in a up-flow anaerobic sludge blanket (UASB) reactor. Sci Rep 2014; 4:6658. [PMID: 25322701 PMCID: PMC4200407 DOI: 10.1038/srep06658] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/26/2014] [Indexed: 11/09/2022] Open
Abstract
A coupling process of anaerobic methanogenesis and electromethanogenesis was proposed to treat high organic load rate (OLR) wastewater. During the start-up stage, acetate removal efficiency of the electric-biological reactor (R1) reached the maximization about 19 percentage points higher than that of the control anaerobic reactor without electrodes (R2), and CH4 production rate of R1 also increased about 24.9% at the same time, while additional electric input was 1/1.17 of the extra obtained energy from methane. Coulombic efficiency and current recorded showed that anodic oxidation contributed a dominant part in degrading acetate when the metabolism of methanogens was low during the start-up stage. Along with prolonging operating time, aceticlastic methanogenesis gradually replaced anodic oxidation to become the main pathway of degrading acetate. When the methanogens were inhibited under the acidic conditions, anodic oxidation began to become the main pathway of acetate decomposition again, which ensured the reactor to maintain a stable performance. FISH analysis confirmed that the electric field imposed could enrich the H2/H(+)-utilizing methanogens around the cathode to help for reducing the acidity. This study demonstrated that an anaerobic digester with a pair of electrodes inserted to form a coupling system could enhance methanogenesis and reduce adverse impacts.
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Affiliation(s)
- Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Shuo Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xie Quan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qilin Yu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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Kato S, Sasaki K, Watanabe K, Yumoto I, Kamagata Y. Physiological and transcriptomic analyses of the thermophilic, aceticlastic methanogen Methanosaeta thermophila responding to ammonia stress. Microbes Environ 2014; 29:162-7. [PMID: 24920170 PMCID: PMC4103522 DOI: 10.1264/jsme2.me14021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 03/17/2014] [Indexed: 11/12/2022] Open
Abstract
The inhibitory effects of ammonia on two different degradation pathways of methanogenic acetate were evaluated using a pure culture (Methanosaeta thermophila strain PT) and defined co-culture (Methanothermobacter thermautotrophicus strain TM and Thermacetogenium phaeum strain PB), which represented aceticlastic and syntrophic methanogenesis, respectively. Growth experiments with high concentrations of ammonia clearly demonstrated that sensitivity to ammonia stress was markedly higher in M. thermophila PT than in the syntrophic co-culture. M. thermophila PT also exhibited higher sensitivity to high pH stress, which indicated that an inability to maintain pH homeostasis is an underlying cause of ammonia inhibition. Methanogenesis was inhibited in the resting cells of M. thermophila PT with moderate concentrations of ammonia, suggesting that the inhibition of enzymes involved in methanogenesis may be one of the major factors responsible for ammonia toxicity. Transcriptomic analysis revealed a broad range of disturbances in M. thermophila PT cells under ammonia stress conditions, including protein denaturation, oxidative stress, and intracellular cation imbalances. The results of the present study clearly demonstrated that syntrophic acetate degradation dominated over aceticlastic methanogenesis under ammonia stress conditions, which is consistent with the findings of previous studies on complex microbial community systems. Our results also imply that the co-existence of multiple metabolic pathways and their different sensitivities to stress factors confer resiliency on methanogenic processes.
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Affiliation(s)
- Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062–8517, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060–8589, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4–6–1 Komaba, Meguro-ku, Tokyo 153–8904, Japan
| | - Konomi Sasaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062–8517, Japan
- Hokkaido High-Technology College, 2–12–1 Megumino-kita, Eniwa, Hokkaido 061–1374, Japan
| | - Kazuya Watanabe
- Research Center for Advanced Science and Technology, The University of Tokyo, 4–6–1 Komaba, Meguro-ku, Tokyo 153–8904, Japan
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432–1 Horinouchi, Hachioji, Tokyo 192–0392, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062–8517, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062–8517, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido 060–8589, Japan
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56
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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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Das R, Kazy SK. Microbial diversity, community composition and metabolic potential in hydrocarbon contaminated oily sludge: prospects for in situ bioremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:7369-89. [PMID: 24682711 DOI: 10.1007/s11356-014-2640-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 02/10/2014] [Indexed: 05/20/2023]
Abstract
Microbial community composition and metabolic potential have been explored in petroleum-hydrocarbon-contaminated sludge of an oil storage facility. Culture-independent clone library-based 16S rRNA gene analyses revealed that the bacterial community within the sludge was dominated by the members of β-Proteobacteria (35%), followed by Firmicutes (13%), δ-Proteobacteria (11%), Bacteroidetes (10%), Acidobacteria (6%), α-Proteobacteria (3%), Lentisphaerae (2%), Spirochaetes (2%), and unclassified bacteria (5%), whereas the archaeal community was composed of Thermoprotei (54%), Methanocellales (33%), Methanosarcinales/Methanosaeta (8%) and Methanoculleus (1%) members. Methyl coenzyme M reductase A (mcrA) gene (a functional biomarker) analyses also revealed predominance of hydrogenotrophic, methanogenic Archaea (Methanocellales, Methanobacteriales and Methanoculleus members) over acetoclastic methanogens (Methanosarcinales members). In order to explore the cultivable bacterial population, a total of 28 resident strains were identified and characterized in terms of their physiological and metabolic capabilities. Most of these could be taxonomically affiliated to the members of the genera Bacillus, Paenibacillus, Micrococcus, Brachybacterium, Aerococcus, and Zimmermannella, while two strains were identified as Pseudomonas and Pseudoxanthomonas. Metabolic profiling exhibited that majority of these isolates were capable of growing in presence of a variety of petroleum hydrocarbons as sole source of carbon, tolerating different heavy metals at higher concentrations (≥1 mM) and producing biosurfactant during growth. Many strains could grow under a wide range of pH, temperature, or salinity as well as under anaerobic conditions in the presence of different electron acceptors and donors in the growth medium. Correlation between the isolates and their metabolic properties was estimated by the unweighted pair group method with arithmetic mean (UPGMA) analysis. Overall observation indicated the presence of diverse groups of microorganisms including hydrocarbonoclastic, nitrate reducing, sulphate reducing, fermentative, syntrophic, methanogenic and methane-oxidizing bacteria and Archaea within the sludge community, which can be exploited for in situ bioremediation of the oily sludge.
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Affiliation(s)
- Ranjit Das
- Department of Biotechnology, National Institute of Technology, Durgapur, Mahatma Gandhi Avenue, Durgapur, 713 209, West Bengal, India
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Liang R, Grizzle RS, Duncan KE, McInerney MJ, Suflita JM. Roles of thermophilic thiosulfate-reducing bacteria and methanogenic archaea in the biocorrosion of oil pipelines. Front Microbiol 2014; 5:89. [PMID: 24639674 PMCID: PMC3944610 DOI: 10.3389/fmicb.2014.00089] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 02/18/2014] [Indexed: 11/13/2022] Open
Abstract
Thermophilic sulfide-producing microorganisms from an oil pipeline network were enumerated with different sulfur oxyanions as electron acceptors at 55°C. Most-probable number (MPN) analysis showed that thiosulfate-reducing bacteria were the most numerous sulfidogenic microorganisms in pipeline inspection gauge (PIG) scrapings. Thiosulfate-reducing and methanogenic enrichments were obtained from the MPN cultures that were able to use yeast extract as the electron donor. Molecular analysis revealed that both enrichments harbored the same dominant bacterium, which belonged to the genus Anaerobaculum. The dominant archaeon in the methanogenic enrichment was affiliated with the genus Methanothermobacter. With yeast extract as the electron donor, the general corrosion rate by the thiosulfate-reducing enrichment (8.43 ± 1.40 milli-inch per year, abbreviated as mpy) was about 5.5 times greater than the abiotic control (1.49 ± 0.15 mpy), while the comparable measures for the methanogenic culture were 2.03 ± 0.49 mpy and 0.62 ± 0.07 mpy, respectively. Total iron analysis in the cultures largely accounted for the mass loss of iron measured in the weight loss determinations. Profilometry analysis of polished steel coupons incubated in the presence of the thiosulfate-reducing enrichment revealed 59 pits over an area of 71.16 mm(2), while only 6 pits were evident in the corresponding methanogenic incubations. The results show the importance of thiosulfate-utilizing, sulfide-producing fermentative bacteria such as Anaerobaculum sp. in the corrosion of carbon steel, but also suggest that Anaerobaculum sp. are of far less concern when growing syntrophically with methanogens.
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Affiliation(s)
| | | | | | | | - Joseph M. Suflita
- Department of Microbiology and Plant Biology, OU Biocorrosion Center, University of OklahomaNorman, OK, USA
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59
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Lenhart TR, Duncan KE, Beech IB, Sunner JA, Smith W, Bonifay V, Biri B, Suflita JM. Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces. BIOFOULING 2014; 30:823-835. [PMID: 25115517 DOI: 10.1080/08927014.2014.931379] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Microbially influenced corrosion (MIC) has long been implicated in the deterioration of carbon steel in oil and gas pipeline systems. The authors sought to identify and characterize sessile biofilm communities within a high-temperature oil production pipeline, and to compare the profiles of the biofilm community with those of the previously analyzed planktonic communities. Eubacterial and archaeal 16S rRNA sequences of DNA recovered from extracted pipeline pieces, termed 'cookies,' revealed the presence of thermophilic sulfidogenic anaerobes, as well as mesophilic aerobes. Electron microscopy and elemental analysis of cookies confirmed the presence of sessile cells and chemical constituents consistent with corrosive biofilms. Mass spectrometry of cookie acid washes identified putative hydrocarbon metabolites, while surface profiling revealed pitting and general corrosion damage. The results suggest that in an established closed system, the biofilm taxa are representative of the planktonic eubacterial and archaeal community, and that sampling and monitoring of the planktonic bacterial population can offer insight into biocorrosion activity. Additionally, hydrocarbon biodegradation is likely to sustain these communities. The importance of appropriate sample handling and storage procedures to oilfield MIC diagnostics is highlighted.
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Affiliation(s)
- Tiffany R Lenhart
- a Department of Microbiology and Plant Biology , OU Biocorrosion Center, University of Oklahoma , Norman , OK , USA
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60
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Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs. Nat Commun 2013; 4:1998. [PMID: 23759740 PMCID: PMC3709511 DOI: 10.1038/ncomms2998] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/09/2013] [Indexed: 11/09/2022] Open
Abstract
Deep subsurface formations (for example, high-temperature oil reservoirs) are candidate sites for carbon capture and storage technology. However, very little is known about how the subsurface microbial community would respond to an increase in CO2 pressure resulting from carbon capture and storage. Here we construct microcosms mimicking reservoir conditions (55 °C, 5 MPa) using high-temperature oil reservoir samples. Methanogenesis occurs under both high and low CO2 conditions in the microcosms. However, the increase in CO2 pressure accelerates the rate of methanogenesis to more than twice than that under low CO2 conditions. Isotope tracer and molecular analyses show that high CO2 conditions invoke acetoclastic methanogenesis in place of syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis that typically occurs in this environment (low CO2 conditions). Our results present a possibility of carbon capture and storage for enhanced microbial energy production in deep subsurface environments that can mitigate global warming and energy depletion. Deep subsurface formations are potential sites for carbon capture and storage but how subsurface microbial communities may respond to this is not clear. Here, Mayumi et al. construct microcosms and show that increasing CO2 partial pressure via carbon capture and storage more than doubles the rate of methanogenesis.
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61
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Meslé M, Dromart G, Oger P. Microbial methanogenesis in subsurface oil and coal. Res Microbiol 2013; 164:959-72. [DOI: 10.1016/j.resmic.2013.07.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 07/02/2013] [Indexed: 11/17/2022]
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Zhou F, Mbadinga SM, Liu JF, Gu JD, Mu BZ. Evaluation of microbial community composition in thermophilic methane-producing incubation of production water from a high-temperature oil reservoir. ENVIRONMENTAL TECHNOLOGY 2013; 34:2681-2689. [PMID: 24527630 DOI: 10.1080/09593330.2013.786135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Investigation of petroleum microbes is fundamental for the development and utilization of oil reservoirs' microbial resources, and also provides great opportunities for research and development of bio-energy. Production water from a high-temperature oil reservoir was incubated anaerobically at 55 degrees C for more than 400 days without amendment of any nutrients. Over the time of incubation, about 1.6 mmol of methane and up to 107 micromol of hydrogen (H2) were detected in the headspace. Methane formation indicated that methanogenesis was likely the predominant process in spite of the presence of 23.4 mM SO4(2-) in the production water. Microbial community composition of the incubation was characterized by means of 16S rRNA gene clone libraries construction. Bacterial composition changed from Pseudomonales as the dominant population initially to Hydrogenophilales-related microorganisms affiliated to Petrobacter spp. closely. After 400 days of incubation, other bacterial members detected were related to Anareolineales, beta-, gamma-, and delta-Proteobacteria. The archaeal composition of the original production water was essentially composed of obligate acetoclastic methanogens of the genus Methanosaeta, but the incubation was predominantly composed of CO2-reducing methanogens of the genus Methanothermobacter and Crenarchaeotes-related microorganisms. Our results suggest that methanogenesis could be more active than expected in oil reservoir environments and methane formation from CO2-reduction played a significant role in the methanogenic community. This conclusion is consistent with the predominant role played by H2-oxidizing methanogens in the methanogenic conversion of organic matter in high-temperature petroleum reservoirs.
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Affiliation(s)
- Fang Zhou
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, PR China
| | - Serge Maurice Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, PR China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, PR China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, PR China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, PR China
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Acetate production from oil under sulfate-reducing conditions in bioreactors injected with sulfate and nitrate. Appl Environ Microbiol 2013; 79:5059-68. [PMID: 23770914 DOI: 10.1128/aem.01251-13] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Oil production by water injection can cause souring in which sulfate in the injection water is reduced to sulfide by resident sulfate-reducing bacteria (SRB). Sulfate (2 mM) in medium injected at a rate of 1 pore volume per day into upflow bioreactors containing residual heavy oil from the Medicine Hat Glauconitic C field was nearly completely reduced to sulfide, and this was associated with the generation of 3 to 4 mM acetate. Inclusion of 4 mM nitrate inhibited souring for 60 days, after which complete sulfate reduction and associated acetate production were once again observed. Sulfate reduction was permanently inhibited when 100 mM nitrate was injected by the nitrite formed under these conditions. Pulsed injection of 4 or 100 mM nitrate inhibited sulfate reduction temporarily. Sulfate reduction resumed once nitrate injection was stopped and was associated with the production of acetate in all cases. The stoichiometry of acetate formation (3 to 4 mM formed per 2 mM sulfate reduced) is consistent with a mechanism in which oil alkanes and water are metabolized to acetate and hydrogen by fermentative and syntrophic bacteria (K. Zengler et al., Nature 401:266-269, 1999), with the hydrogen being used by SRB to reduce sulfate to sulfide. In support of this model, microbial community analyses by pyrosequencing indicated SRB of the genus Desulfovibrio, which use hydrogen but not acetate as an electron donor for sulfate reduction, to be a major community component. The model explains the high concentrations of acetate that are sometimes found in waters produced from water-injected oil fields.
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64
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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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65
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Nakamura K, Takahashi A, Mori C, Tamaki H, Mochimaru H, Nakamura K, Takamizawa K, Kamagata Y. Methanothermobacter
tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field. Int J Syst Evol Microbiol 2013; 63:715-722. [DOI: 10.1099/ijs.0.041681-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic and hydrogenotrophic methanogen, strain RMAST, was isolated from gas-associated formation water of a gas-producing well in a natural gas field in Japan. Strain RMAST grew solely on H2/CO2 but required Casamino acids, tryptone, yeast extract or vitamins for growth. Growth of strain RMAST was stimulated by acetate. Cells were non-motile, straight rods (0.5×3.5–10.5 µm) and occurred singly or in pairs. Bundles of fimbriae occurred at both poles of cells and the cell wall was thick (approximately 21 nm, as revealed by ultrathin section electron microscopy). Strain RMAST grew at 45–80 °C (optimum, 70 °C), at pH 5.8–8.7 (optimum, pH 6.9–7.7) and with 0.001–20 g NaCl l−1 (optimum, 2.5 g NaCl l−1). Phylogenetic analysis revealed that
Methanothermobacter thermautotrophicus
ΔHT was most closely related to the isolate (95.7 % 16S rRNA gene sequence similarity). On the basis of morphological, phenotypic and phylogenetic characteristics, it is clear that strain RMAST represents a novel species of the genus
Methanothermobacter
, for which we propose the name
Methanothermobacter
tenebrarum sp. nov. The type strain is RMAST ( = DSM 23052T = JCM 16532T = NBRC 106236T).
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Affiliation(s)
- Kohei Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
- Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Azumi Takahashi
- Graduate School of Applied Biological Sciences, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Chikahiro Mori
- Graduate School of Applied Biological Sciences, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Hanako Mochimaru
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Kazunori Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Kazuhiro Takamizawa
- Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan
- Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
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Wentzel A, Lewin A, Cervantes FJ, Valla S, Kotlar HK. Deep Subsurface Oil Reservoirs as Poly-extreme Habitats for Microbial Life. A Current Review. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Starting Up Microbial Enhanced Oil Recovery. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 142:1-94. [DOI: 10.1007/10_2013_256] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Zhou L, Li KP, Mbadinga SM, Yang SZ, Gu JD, Mu BZ. Analyses of n-alkanes degrading community dynamics of a high-temperature methanogenic consortium enriched from production water of a petroleum reservoir by a combination of molecular techniques. ECOTOXICOLOGY (LONDON, ENGLAND) 2012; 21:1680-1691. [PMID: 22688358 DOI: 10.1007/s10646-012-0949-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/24/2012] [Indexed: 06/01/2023]
Abstract
Despite the knowledge on anaerobic degradation of hydrocarbons and signature metabolites in the oil reservoirs, little is known about the functioning microbes and the related biochemical pathways involved, especially about the methanogenic communities. In the present study, a methanogenic consortium enriched from high-temperature oil reservoir production water and incubated at 55 °C with a mixture of long chain n-alkanes (C(15)-C(20)) as the sole carbon and energy sources was characterized. Biodegradation of n-alkanes was observed as methane production in the alkanes-amended methanogenic enrichment reached 141.47 μmol above the controls after 749 days of incubation, corresponding to 17 % of the theoretical total. GC-MS analysis confirmed the presence of putative downstream metabolites probably from the anaerobic biodegradation of n-alkanes and indicating an incomplete conversion of the n-alkanes to methane. Enrichment cultures taken at different incubation times were subjected to microbial community analysis. Both 16S rRNA gene clone libraries and DGGE profiles showed that alkanes-degrading community was dynamic during incubation. The dominant bacterial species in the enrichment cultures were affiliated with Firmicutes members clustering with thermophilic syntrophic bacteria of the genera Moorella sp. and Gelria sp. Other represented within the bacterial community were members of the Leptospiraceae, Thermodesulfobiaceae, Thermotogaceae, Chloroflexi, Bacteroidetes and Candidate Division OP1. The archaeal community was predominantly represented by members of the phyla Crenarchaeota and Euryarchaeota. Corresponding sequences within the Euryarchaeota were associated with methanogens clustering with orders Methanomicrobiales, Methanosarcinales and Methanobacteriales. On the other hand, PCR amplification for detection of functional genes encoding the alkylsuccinate synthase α-subunit (assA) was positive in the enrichment cultures. Moreover, the appearance of a new assA gene sequence identified in day 749 supported the establishment of a functioning microbial species in the enrichment. Our results indicate that n-alkanes are converted to methane slowly by a microbial community enriched from oilfield production water and fumarate addition is most likely the initial activation step of n-alkanes degradation under thermophilic methanogenic conditions.
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MESH Headings
- Alkanes/metabolism
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/isolation & purification
- Bacteria, Anaerobic/metabolism
- Biodegradation, Environmental
- Cloning, Molecular
- Cluster Analysis
- Crenarchaeota/classification
- Crenarchaeota/genetics
- Crenarchaeota/isolation & purification
- Crenarchaeota/metabolism
- Deltaproteobacteria/classification
- Deltaproteobacteria/genetics
- Deltaproteobacteria/isolation & purification
- Deltaproteobacteria/metabolism
- Euryarchaeota/classification
- Euryarchaeota/genetics
- Euryarchaeota/isolation & purification
- Euryarchaeota/metabolism
- Genes, Bacterial
- Hot Temperature
- Methanomicrobiales/classification
- Methanomicrobiales/genetics
- Methanomicrobiales/isolation & purification
- Methanomicrobiales/metabolism
- Methanosarcinales/classification
- Methanosarcinales/genetics
- Methanosarcinales/isolation & purification
- Methanosarcinales/metabolism
- Microbial Consortia
- Molecular Probe Techniques
- Oil and Gas Fields/chemistry
- Oil and Gas Fields/microbiology
- Petroleum/metabolism
- Phylogeny
- RNA, Ribosomal, 16S
- Sequence Analysis, DNA
- Water/chemistry
- Water Microbiology
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Affiliation(s)
- Lei Zhou
- State Key Laboratory of Bioreactor Engineering, Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, People's Republic of China
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Sieber JR, McInerney MJ, Gunsalus RP. Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation. Annu Rev Microbiol 2012; 66:429-52. [PMID: 22803797 DOI: 10.1146/annurev-micro-090110-102844] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Syntrophy is a tightly coupled mutualistic interaction between hydrogen-/formate-producing and hydrogen-/formate-using microorganisms that occurs throughout the microbial world. Syntrophy is essential for global carbon cycling, waste decomposition, and biofuel production. Reverse electron transfer, e.g., the input of energy to drive critical redox reactions, is a defining feature of syntrophy. Genomic analyses indicate multiple systems for reverse electron transfer, including ion-translocating ferredoxin:NAD(+) oxidoreductase and hydrogenases, two types of electron transfer flavoprotein:quinone oxidoreductases, and other quinone reactive complexes. Confurcating hydrogenases that couple the favorable production of hydrogen from reduced ferredoxin with the unfavorable production of hydrogen from NADH are present in almost all syntrophic metabolizers, implicating their critical role in syntrophy. Transcriptomic analysis shows upregulation of many genes without assigned functions in the syntrophic lifestyle. High-throughput technologies provide insight into the mechanisms used to establish and maintain syntrophic consortia and conserve energy from reactions that operate close to thermodynamic equilibrium.
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Affiliation(s)
- Jessica R Sieber
- Department of Botany and Microbiology, University of Oklahoma, Norman, 73019, USA.
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71
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Morris BEL, Herbst FA, Bastida F, Seifert J, von Bergen M, Richnow HH, Suflita JM. Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:297-306. [PMID: 23760793 DOI: 10.1111/j.1758-2229.2012.00333.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Carbon flow in a model methanogenic consortium capable of hydrocarbon degradation was investigated using a combination of stable isotope fractionation, protein-based stable isotope probing, and metaproteomics. Overall δ(13) C enrichment for methane and CO2 in the presence and absence of oil suggests that complex microbial interactions occur during methanogenic hydrocarbon mineralization. Specifically, the Δδ(13) C of CO2 was statistically identical in all incubations irrespective of oil presence, but the Δδ(13) C for methane was greater in the presence of oil compared with fatty acids alone. In addition, carbon from uniformly ((13) C) labelled n-fatty acids was distributed evenly among consortium members in the presence of oil, but used by relatively few community members when provided alone. In all incubations, aceticlastic and hydrogenotrophic methanogens were labelled to an equal extent, suggesting that no pathway is overwhelmingly dominant during methane production by the model consortium. Protein-based stable isotope probing identified key enzymes responsible for methanogenesis from CO2 and acetate labelled with 78.0 ± 4.4% and 73.3 ± 1.0% (13) C respectively. Results suggest that acetate was used directly by methanogens in the presence of n-fatty acids alone, and that methanogenesis from CO2 was a secondary process. Proteins capable of catalysing hydrocarbon activation by addition to fumarate were not found. Collectively, this study demonstrates that significant microbial cooperation is required to recover hydrocarbons as methane.
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Affiliation(s)
- Brandon E L Morris
- Department of Botany & Microbiology, Institute for Energy & the Environment, The University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019, USADepartments of Isotope Biogeochemistry Proteomics Metabolomics, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany Department of Soil and Water Conservation, CEBAS-CSIC, Campus Universitario de Espinardo, 30100, Espinardo, Murcia, Spain
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Phylogenetic diversity of microbial communities associated with the crude-oil, large-insoluble-particle and formation-water components of the reservoir fluid from a non-flooded high-temperature petroleum reservoir. J Biosci Bioeng 2012; 113:204-10. [DOI: 10.1016/j.jbiosc.2011.09.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 09/21/2011] [Accepted: 09/23/2011] [Indexed: 11/20/2022]
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Analysis of alkane-dependent methanogenic community derived from production water of a high-temperature petroleum reservoir. Appl Microbiol Biotechnol 2012; 96:531-42. [DOI: 10.1007/s00253-011-3828-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Revised: 12/05/2011] [Accepted: 12/07/2011] [Indexed: 10/14/2022]
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Kobayashi H, Kawaguchi H, Endo K, Mayumi D, Sakata S, Ikarashi M, Miyagawa Y, Maeda H, Sato K. Analysis of methane production by microorganisms indigenous to a depleted oil reservoir for application in Microbial Enhanced Oil Recovery. J Biosci Bioeng 2012; 113:84-7. [DOI: 10.1016/j.jbiosc.2011.09.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 08/17/2011] [Accepted: 09/12/2011] [Indexed: 10/16/2022]
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Isolation and characterization of Methanothermobacter crinale sp. nov., a novel hydrogenotrophic methanogen from the Shengli oil field. Appl Environ Microbiol 2011; 77:5212-9. [PMID: 21705537 DOI: 10.1128/aem.00210-11] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis is an alternative methanogenic pathway in certain thermophilic anaerobic environments such as high-temperature oil reservoirs and thermophilic biogas reactors. In these environments, the dominant thermophilic methanogens were generally related to uncultured organisms of the genus Methanothermobacter. Here we isolated two representative strains, Tm2(T) and HMD, from the oil sands and oil production water in the Shengli oil field in the People's Republic of China. The type strain, Tm2(T), was nonmotile and stained Gram positive. The cells were straight to slightly curved rods (0.3 μm in width and 2.2 to 5.9 μm in length), but some of them possessed a coccal shape connecting with the rods at the ends. Strain Tm2(T) grew with H(2)-CO(2), but acetate is required. Optimum growth of strain Tm2(T) occurred in the presence of 0.025 g/liter NaCl at pH 6.9 and a temperature of 65°C. The G+C content of the genomic DNA was 40.1 mol% ± 1.3 mol% (by the thermal denaturation method) or 41.1 mol% (by high-performance liquid chromatography). Analysis of the 16S rRNA gene sequence indicated that Tm2(T) was most closely related to Methanothermobacter thermautotrophicus ΔH(T) and Methanothermobacter wolfeii VKM B-1829(T) (both with a sequence similarity of 96.4%). Based on these phenotypic and phylogenic characteristics, a novel species was proposed and named Methanothermobacter crinale sp. nov. The type strain is Tm2(T) (ACCC 00699(T) = JCM 17393(T)).
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