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Hsu D, Flynn JR, Schuler CJ, Santelli CM, Toner BM, Bond DR, Gralnick JA. Isolation and genomic analysis of " Metallumcola ferriviriculae" MK1, a Gram-positive, Fe(III)-reducing bacterium from the Soudan Underground Mine, an iron-rich Martian analog site. Appl Environ Microbiol 2024; 90:e0004424. [PMID: 39007603 PMCID: PMC11337815 DOI: 10.1128/aem.00044-24] [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: 01/10/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
The Soudan Underground Mine State Park, found in the Vermilion Iron Range in northern Minnesota, provides access to a ~ 2.7 billion-year-old banded iron formation. Exploratory boreholes drilled between 1958 and 1962 on the 27th level (713 m underground) of the mine intersect calcium and iron-rich brines that have recently been subject to metagenomic analysis and microbial enrichments. Using concentrated brine samples pumped from a borehole depth of up to 55 m, a novel Gram-positive bacterium was enriched under anaerobic, acetate-oxidizing, and Fe(III) citrate-reducing conditions. The isolated bacterium, designated strain MK1, is non-motile, rod-shaped, spore-forming, anaerobic, and mesophilic, with a growth range between 24°C and 30°C. The complete circular MK1 genome was found to be 3,720,236 bp and encodes 25 putative multiheme cytochromes, including homologs to inner membrane cytochromes in the Gram-negative bacterium Geobacter sulfurreducens and cytoplasmic membrane and periplasmic cytochromes in the Gram-positive bacterium Thermincola potens. However, MK1 does not encode homologs of the peptidoglycan (CwcA) and cell surface-associated (OcwA) multiheme cytochromes proposed to be required by T. potens to perform extracellular electron transfer. The 16S rRNA gene sequence of MK1 indicates that its closest related isolate is Desulfitibacter alkalitolerans strain sk.kt5 (91% sequence identity), which places MK1 in a novel genus within the Desulfitibacteraceae family and Moorellales order. Within the Moorellales order, only Calderihabitans maritimus strain KKC1 has been reported to reduce Fe(III), and only D. alkalitolerans can also grow in temperatures below 40°C. Thus, MK1 represents a novel species within a novel genus, for which we propose the name "Metallumcola ferriviriculae" strain MK1, and provides a unique opportunity to study a cytochrome-rich, mesophilic, Gram-positive, spore-forming Fe(III)-reducing bacterium.IMPORTANCEThe Soudan Underground Mine State Park gives access to understudied regions of the deep terrestrial subsurface that potentially predate the Great Oxidation Event. Studying organisms that have been relatively unperturbed by surface conditions for as long as 2.7 billion years may give us a window into ancient life before oxygen dominated the planet. Additionally, studying microbes from anoxic and iron-rich environments can help us better understand the requirements of life in analogous environments, such as on Mars. The isolation and characterization of "Metallumcola ferriviriculae" strain MK1 give us insights into a novel genus and species that is distinct both from its closest related isolates and from iron reducers characterized to date. "M. ferriviriculae" strain MK1 may also act as a model organism to study how the processes of sporulation and germination are affected by insoluble extracellular acceptors, as well as the impact of spores in the deep terrestrial biosphere.
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Affiliation(s)
- David Hsu
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Jack R. Flynn
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Christopher J. Schuler
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | - Cara M. Santelli
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | - Brandy M. Toner
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Department of Soil, Water, and Climate, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Daniel R. Bond
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Jeffrey A. Gralnick
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
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Zhang JZ, Li YZ, Xi ZN, Gao HP, Zhang Q, Liu LC, Li FL, Ma XQ. Engineered acetogenic bacteria as microbial cell factory for diversified biochemicals. Front Bioeng Biotechnol 2024; 12:1395540. [PMID: 39055341 PMCID: PMC11269201 DOI: 10.3389/fbioe.2024.1395540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024] Open
Abstract
Acetogenic bacteria (acetogens) are a class of microorganisms with conserved Wood-Ljungdahl pathway that can utilize CO and CO2/H2 as carbon source for autotrophic growth and convert these substrates to acetate and ethanol. Acetogens have great potential for the sustainable production of biofuels and bulk biochemicals using C1 gases (CO and CO2) from industrial syngas and waste gases, which play an important role in achieving carbon neutrality. In recent years, with the development and improvement of gene editing methods, the metabolic engineering of acetogens is making rapid progress. With introduction of heterogeneous metabolic pathways, acetogens can improve the production capacity of native products or obtain the ability to synthesize non-native products. This paper reviews the recent application of metabolic engineering in acetogens. In addition, the challenges of metabolic engineering in acetogens are indicated, and strategies to address these challenges are also discussed.
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Affiliation(s)
- Jun-Zhe Zhang
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Zhen Li
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-Ning Xi
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Hui-Peng Gao
- Sinopec Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, Dalian, China
| | - Quan Zhang
- Sinopec Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, Dalian, China
| | - Li-Cheng Liu
- Key Laboratory of Marine Chemistry Theory and Technology (Ministry of Education), College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Fu-Li Li
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Xiao-Qing Ma
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
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Bellini R, Vasile NS, Bassani I, Vizzarro A, Coti C, Barbieri D, Scapolo M, Pirri CF, Verga F, Menin B. Investigating the activity of indigenous microbial communities from Italian depleted gas reservoirs and their possible impact on underground hydrogen storage. Front Microbiol 2024; 15:1392410. [PMID: 38725680 PMCID: PMC11079786 DOI: 10.3389/fmicb.2024.1392410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/09/2024] [Indexed: 05/12/2024] Open
Abstract
H2 produced from renewable energies will play a central role in both greenhouse gas reduction and decarbonization by 2050. Nonetheless, to improve H2 diffusion and utilization as a fuel, large storage capacity systems are needed. Underground storage of natural gas in depleted reservoirs, aquifers and salt caverns is a well-established technology. However, new challenges arise when it comes to storing hydrogen due to the occurrence and activity of indigenous microbial populations in deep geological formations. In a previous study, four Italian natural gas reservoirs were characterized both from a hydro-chemical and microbiological point of view, and predictive functional analyses were carried out with the perspective of underground hydrogen storage (UHS). In the present work, formation waters from the same reservoirs were used as inoculant during batch cultivation tests to characterize microbial activity and its effects on different gas mixtures. Results evidence a predominant acidogenic/acetogenic activity, whilst methanogenic and sulfate reducing activity were only marginal for all tested inoculants. Furthermore, the microbial activation of tested samples is strongly influenced by nutrient availability. Obtained results were fitted and screened in a computational model which would allow deep insights in the study of microbial activity in the context of UHS.
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Affiliation(s)
- Ruggero Bellini
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Nicolò Santi Vasile
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Ilaria Bassani
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Arianna Vizzarro
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | | | | | | | - Candido Fabrizio Pirri
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Francesca Verga
- Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Barbara Menin
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- National Research Council, Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Milan, Italy
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Benito-Vaquerizo S, Nouse N, Schaap PJ, Hugenholtz J, Brul S, López-Contreras AM, Martins dos Santos VAP, Suarez-Diez M. Model-driven approach for the production of butyrate from CO 2/H 2 by a novel co-culture of C. autoethanogenum and C. beijerinckii. Front Microbiol 2022; 13:1064013. [PMID: 36620068 PMCID: PMC9815533 DOI: 10.3389/fmicb.2022.1064013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
One-carbon (C1) compounds are promising feedstocks for the sustainable production of commodity chemicals. CO2 is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted into valuable products while reducing its atmospheric levels. Acetogens are microorganisms that can grow on CO2/H2 gas mixtures and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with other microbial species that can further process such products, can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone-butanol-ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of an acetogen and a solventogen in a consortium provides a potential platform to produce valuable chemicals from CO2. In this study, metabolic modeling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO2/H2 mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation of Clostridium beijerinckii on these substrates in batch serum bottles and subsequently in pH-controlled bioreactors. Community modeling also suggested that a novel microbial consortium consisting of the acetogen Clostridium autoethanogenum, and the solventogen C. beijerinckii would be feasible and stable. On the basis of this prediction, a co-culture was experimentally established. C. autoethanogenum grew on CO2/H2 producing acetate and traces of ethanol. Acetate was in turn, consumed by C. beijerinckii together with lactate, producing butyrate. These results show that community modeling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable resources.
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Affiliation(s)
- Sara Benito-Vaquerizo
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Niels Nouse
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Peter J. Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,UNLOCK Large Scale Infrastructure for Microbial Communities, Wageningen University and Research and Delft University of Technology, Wageningen, Netherlands
| | - Jeroen Hugenholtz
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, University of Amsterdam, Amsterdam, Netherlands
| | - Ana M. López-Contreras
- Wageningen Food and Biobased Research, Wageningen University and Research, Wageningen, Netherlands
| | | | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands,*Correspondence: Maria Suarez-Diez ✉
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5
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Shi C, Ma J, Wu H, Luo J, Liu Y, Li K, Zhou Y, Wang K. Evaluation of pH regulation in carbohydrate-type municipal waste anaerobic co-fermentation: Roles of pH at acidic, neutral and alkaline conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158327. [PMID: 36037891 DOI: 10.1016/j.scitotenv.2022.158327] [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: 04/11/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
This study investigated and evaluated the roles of acidic (pH 4.0), neutral (pH 7.0) and alkaline (pH 10.0) in anaerobic co-fermentation of sewage sludge and carbohydrate-type municipal waste. CO2, CH4 and H2 are produced in acidic, neutral and alkaline fermentation, respectively. The neutral co-fermentation contained the vast number of aqueous metabolites as total of 22.12 g/L, with the advantage of over 50 % biodegradable components in extracellular polymeric substance and over 80 % hydrolysis rate. Acidic and alkaline pH facilitated ammonia release, with the max concentration of 0.46 g/L and 0.44 g/L, respectively. Microbial analysis indicated that pH is the key parameter to impact microbial activity and drive microbial community transition. The high abundance of Lactobacillus, Bifidobacterium and Clostridium was associated with harvest of ethanol, lactic acid and acetate in acidic, neutral and alkaline fermentation. Meanwhile, the floc feature showed better dewaterability (zeta potential -8.48 mV) and poor nutrient convey (distribution spread index 1.03) in acidic fermentation. In summary, acidic and alkaline fermentation were prioritised for targeted spectrum. Neutral fermentation was prioritised for high production. This study presented an upgraded understanding of the pH role in fermentation performance, microbial structure and sludge behaviour, which benefits the development of fermentation processing unit.
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Affiliation(s)
- Chuan Shi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing 100012, PR China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Jinyuan Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Houkai Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Juan Luo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Yue Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Kun Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Yuexi Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environment Sciences, Beijing 100012, PR China; Research Center of Environmental Pollution Control Engineering Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Kaijun Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
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Pan X, Zhao L, Li C, Angelidaki I, Lv N, Ning J, Cai G, Zhu G. Deep insights into the network of acetate metabolism in anaerobic digestion: focusing on syntrophic acetate oxidation and homoacetogenesis. WATER RESEARCH 2021; 190:116774. [PMID: 33387947 DOI: 10.1016/j.watres.2020.116774] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Acetate is a pivotal intermediate product during anaerobic decomposition of organic matter. Its generation and consumption network is quite complex, which almost covers the most steps in anaerobic digestion (AD) process. Besides acidogenesis, acetogenesis and methanogenesis, syntrophic acetate oxidation (SAO) replaced acetoclastic methanogenesis to release the inhibition of AD at some special conditions, and the importance of considering homoacetogenesis had also been proved when analysing anaerobic fermentations. Syntrophic acetate-oxidizing bacteria (SAOB), with function of SAO, can survive under high temperature and ammonia/ volatile fatty acids (VFAs) concentrations, while, homoacetogens, performed homoacetogenesis, are more active under acidic, alkaline and low temperature (10°C-20°C) conditions, This review summarized the roles of SAO and homoacetogenesis in AD process, which contains the biochemical reactions, metabolism pathways, physiological characteristics and energy conservation of functional bacteria. The specific roles of these two processes in the subprocess of AD (i.e., acidogenesis, acetogenesis and methanogenesis) were also analyzed in detail. A two phases anaerobic digester is proposed for protein-rich waste(water) treatment by enhancing the functions of homoacetogens and SAOB compared to the traditional two-phases anaerobic digesters, in which the first phase is fermentation phase including acidogens and homoacetogens for acetate production, and second phase is a mixed culture coupling syntrophic fatty acids bacteria, SAOB and hydrogenotrophic methanogens for methane production. This review provides a new insight into the network on production and consumption of acetate in AD process.
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Affiliation(s)
- Xiaofang Pan
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Lixin Zhao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, Beijing100081, China
| | - Chunxing Li
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Nan Lv
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Jing Ning
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Guanjing Cai
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Gefu Zhu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China.
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Lv XM, Yang M, Dai LR, Tu B, Chang C, Huang Y, Deng Y, Lawson PA, Zhang H, Cheng L, Tang YQ. Zhaonella formicivorans gen. nov., sp. nov., an anaerobic formate-utilizing bacterium isolated from Shengli oilfield, and proposal of four novel families and Moorellales ord. nov. in the phylum Firmicutes. Int J Syst Evol Microbiol 2020; 70:3361-3373. [DOI: 10.1099/ijsem.0.004178] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A novel obligately anaerobic, thermophilic and formate-utilizing bacterium K32T was isolated from Shengli oilfield of China. Cells were straight rods (0.4–0.8 µm × 2.5–8.0 µm), Gram-stain-positive, non-spore-forming and slightly motile. Optimum growth occurred with pH of 7 and 0.5 g l–1 NaCl under temperature of 55–60 °C. Nitrate could be reduced into nitrite, syntrophic formate oxidation to methane and carbon dioxide occurred when co-culturing strain K32T and
Methanothermobacter thermautotrophicus
ΔH. The main cellular fatty acids were iso-C15 : 0 (24.0 %), anteiso-C15 : 0 (21.7 %), C16 : 0 (12.7 %) and C14 : 0 (10.8 %), and the main polar lipid was phosphatidylglycerol. The G+C content of the genomic DNA was 46.3 mol%. The 16S rRNA gene sequence of K32T shared ≤90.4 % of sequence similarity to closest type strains of
Desulfitibacter alkalitolerans
,
Calderihabitans maritimus
and members of the genus
Moorella
. Based on the phenotypic, biochemical and genotypic characterization, Zhaonella formicivorans gen. nov., sp. nov. is proposed with K32T (=CCAM 584T =DSM 107278T=CGMCC1.5297T) as the type strain, which is the first representative of Zhaonellaceae fam. nov. In addition, the order Thermoanaerobacterales and family
Peptococcaceae
were reclassified, and three novel families in the novel order of Moorellales ord. nov. were also proposed.
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Affiliation(s)
- Xiao-meng Lv
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
| | - Min Yang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
| | - Li-rong Dai
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Bo Tu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Chen Chang
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yan Huang
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yu Deng
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Paul A. Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Hui Zhang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
- China Collection of Anaerobic microorganisms, Chengdu 610041, PR China
| | - Yue-qin Tang
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, 610065, PR China
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Nissen LS, Basen M. The emerging role of aldehyde:ferredoxin oxidoreductases in microbially-catalyzed alcohol production. J Biotechnol 2019; 306:105-117. [DOI: 10.1016/j.jbiotec.2019.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022]
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Ethanol yield and sugar usability in thermophilic ethanol production from lignocellulose hydrolysate by genetically engineered Moorella thermoacetica. J Biosci Bioeng 2019; 129:160-164. [PMID: 31506242 DOI: 10.1016/j.jbiosc.2019.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/29/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023]
Abstract
Bioconversion from inexpensive renewable resource, such as biomass, to liquid fuel is one of the promising technologies to reduce the use of petroleum. We previously reported the genetically engineered Moorella thermoacetica could produce ethanol from the lignocellulosic feedstock. However, it was still unclear which carbon source in the substrate was preferentially consumed to produce ethanol. To identify the hierarchy of the sugar utilization during ethanol fermentation of this strain, we analyzed the sugar composition of lignocellulosic feedstock, and consumption rate of sugars during the fermentation process. The hydrolysates after acid pretreatment and enzymatic saccharification contained glucose, xylose, galactose, arabinose, and mannose. Time course data suggested that xylose was the most preferred carbon source among those sugars during ethanol fermentation. Ethanol yield was 0.40 ± 0.06 and 0.40 ± 0.12 g/g-total sugar, from lignocellulosic hydrolysates of Japanese cedar (Cryptomeria japonica) and rice straw (Oryza sativa), respectively. The results demonstrated that the genetically engineered M. thermoacetica is a promising candidate for thermophilic ethanol fermentation of lignocellulosic feedstocks, especially hemicellulosic sugars.
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Luo K, Pang Y, Yang Q, Wang D, Li X, Lei M, Huang Q. A critical review of volatile fatty acids produced from waste activated sludge: enhanced strategies and its applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:13984-13998. [PMID: 30900121 DOI: 10.1007/s11356-019-04798-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
This paper reviews the recent achievements in the enhanced production of volatile fatty acids (VFAs) from waste activated sludge (WAS). The enhanced strategies are divided into two approaches. The first strategy focuses on the regulation of carbon-to-nitrogen (C/N) ratio by co-digestion of WAS with carbon-rich substrates, including municipal solid wastes (MSW), marine algae, agricultural residues, and animal manures. The other strategy is to enhance the solubilization and hydrolysis of WAS or inhibit the methanogenesis by applying various pretreatments, such as mechanical, chemical, enzymatic, and thermal pretreatment. Finally, the applications of WAS-derived VFAs are discussed. The future researches in enhancing VFAs production and wide application of the VFAs from both technical and economic perspectives are proposed.
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Affiliation(s)
- Kun Luo
- College of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, People's Republic of China
| | - Ya Pang
- College of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, People's Republic of China.
| | - Qi Yang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China.
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Xue Li
- College of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, People's Republic of China
| | - Min Lei
- College of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, People's Republic of China
| | - Qi Huang
- College of Bioengineering and Environmental Science, Changsha University, Changsha, 410003, People's Republic of China
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Merlino G, Barozzi A, Michoud G, Ngugi DK, Daffonchio D. Microbial ecology of deep-sea hypersaline anoxic basins. FEMS Microbiol Ecol 2018; 94:4995905. [DOI: 10.1093/femsec/fiy085] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/09/2018] [Indexed: 01/12/2023] Open
Affiliation(s)
- Giuseppe Merlino
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Alan Barozzi
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Grégoire Michoud
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - David Kamanda Ngugi
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
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12
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Thermophilic Moorella thermoautotrophica -immobilized cathode enhanced microbial electrosynthesis of acetate and formate from CO 2. Bioelectrochemistry 2017; 117:23-28. [DOI: 10.1016/j.bioelechem.2017.05.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 11/20/2022]
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13
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Breitkopf R, Uhlig R, Drenckhan T, Fischer RJ. Two propanediol utilization-like proteins of Moorella thermoacetica with phosphotransacetylase activity. Extremophiles 2016; 20:653-61. [PMID: 27338272 DOI: 10.1007/s00792-016-0854-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/14/2016] [Indexed: 12/16/2022]
Abstract
Moorella thermoacetica is one of the model acetogenic bacteria for the resolution of the Wood-Ljungdahl (acetyl-CoA) pathway in which CO2 is autotrophically assimilated yielding acetyl-CoA as central intermediate. Its further conversion into acetate relies on subsequent phosphotransacetylase (PTA) and acetate kinase reactions. However, the genome of M. thermoacetica contains no pta homologous gene. It has been speculated that the moth_0864 and moth_1181 gene products sharing similarities with an evolutionarily distinct phosphotransacylase involved in 1,2-propanediol utilization (PDUL) of Salmonella enterica act as PTAs in M. thermoacetica. Here, we demonstrate specific PTA activities with acetyl-CoA as substrate of 9.05 and 2.03 U/mg for the recombinant enzymes PDUL1 (Moth_1181) and PDUL2 (Moth_0864), respectively. Both showed maximal activity at 65 °C and pH 7.6. Native proteins (90 kDa) are homotetramers composed of four subunits with apparent molecular masses of about 23 kDa. Thus, one or both PDULs of M. thermoacetica might act as PTAs in vivo catalyzing the penultimate step of the Wood-Ljungdahl pathway toward the formation of acetate. In silico analysis underlined that up to now beside of M. thermoacetica, only Sporomusa ovata contains only PDUL like class(III)-PTAs but no other phosphotransacetylases or phosphotransbutyrylases (PTBs).
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Affiliation(s)
- Ronja Breitkopf
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Ronny Uhlig
- Abteilung Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Tina Drenckhan
- Abteilung Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Ralf-Jörg Fischer
- Abteilung Mikrobiologie, Institut für Biowissenschaften, Universität Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany.
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Schmitt E, Bura R, Gustafson R, Ehsanipour M. Kinetic modeling of Moorella thermoacetica growth on single and dual-substrate systems. Bioprocess Biosyst Eng 2016; 39:1567-75. [DOI: 10.1007/s00449-016-1631-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
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15
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Fermentation of lignocellulosic sugars to acetic acid by Moorella thermoacetica. ACTA ACUST UNITED AC 2016; 43:807-16. [DOI: 10.1007/s10295-016-1756-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
Abstract
Abstract
A systematic study of bioconversion of lignocellulosic sugars to acetic acid by Moorella thermoacetica (strain ATCC 39073) was conducted. Four different water-soluble fractions (hydrolysates) obtained after steam pretreatment of lignocellulosic biomass were selected and fermented to acetic acid in batch fermentations. M. thermoacetica can effectively ferment xylose and glucose in hydrolysates from wheat straw, forest residues, switchgrass, and sugarcane straw to acetic acid. Xylose and glucose were completely utilized, with xylose being consumed first. M. thermoacetica consumed up to 62 % of arabinose, 49 % galactose and 66 % of mannose within 72 h of fermentation in the mixture of lignocellulosic sugars. The highest acetic acid yield was obtained from sugarcane straw hydrolysate, with 71 % of theoretical yield based on total sugars (17 g/L acetic acid from 24 g/L total sugars). The lowest acetic acid yield was observed in forest residues hydrolysate, with 39 % of theoretical yield based on total sugars (18 g/L acetic acid from 49 g/L total sugars). Process derived compounds from steam explosion pretreatment, including 5-hydroxymethylfurfural (0.4 g/L), furfural (0.1 g/L) and total phenolics (3 g/L), did not inhibit microbial growth and acetic acid production yield. This research identified two major factors that adversely affected acetic acid yield in all hydrolysates, especially in forest residues: (i) glucose to xylose ratio and (ii) incomplete consumption of arabinose, galactose and mannose. For efficient bioconversion of lignocellulosic sugars to acetic acid, it is imperative to have an appropriate balance of sugars in a hydrolysate. Hence, the choice of lignocellulosic biomass and steam pretreatment design are fundamental steps for the industrial application of this process.
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16
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Metabolic response of Clostridium ljungdahlii to oxygen exposure. Appl Environ Microbiol 2015; 81:8379-91. [PMID: 26431975 DOI: 10.1128/aem.02491-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022] Open
Abstract
Clostridium ljungdahlii is an important synthesis gas-fermenting bacterium used in the biofuels industry, and a preliminary investigation showed that it has some tolerance to oxygen when cultured in rich mixotrophic medium. Batch cultures not only continue to grow and consume H2, CO, and fructose after 8% O2 exposure, but fermentation product analysis revealed an increase in ethanol concentration and decreased acetate concentration compared to non-oxygen-exposed cultures. In this study, the mechanisms for higher ethanol production and oxygen/reactive oxygen species (ROS) detoxification were identified using a combination of fermentation, transcriptome sequencing (RNA-seq) differential expression, and enzyme activity analyses. The results indicate that the higher ethanol and lower acetate concentrations were due to the carboxylic acid reductase activity of a more highly expressed predicted aldehyde oxidoreductase (CLJU_c24130) and that C. ljungdahlii's primary defense upon oxygen exposure is a predicted rubrerythrin (CLJU_c39340). The metabolic responses of higher ethanol production and oxygen/ROS detoxification were found to be linked by cofactor management and substrate and energy metabolism. This study contributes new insights into the physiology and metabolism of C. ljungdahlii and provides new genetic targets to generate C. ljungdahlii strains that produce more ethanol and are more tolerant to syngas contaminants.
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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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18
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Tsukahara K, Kita A, Nakashimada Y, Hoshino T, Murakami K. Genome-guided analysis of transformation efficiency and carbon dioxide assimilation by Moorella thermoacetica Y72. Gene 2013; 535:150-5. [PMID: 24316126 DOI: 10.1016/j.gene.2013.11.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 09/10/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022]
Abstract
We determined a draft genome sequence for Moorella thermoacetica strain Y72, a syngas-assimilating bacterium with high transformation efficiency. This strain was confirmed to be M. thermoacetica because its overall genome sequence characteristics were similar to those of M. thermoacetica strain ATCC39073. Y72 was confirmed to carry all the genes encoding the enzymes in the reductive acetyl-CoA pathway, with very high similarities to those of ATCC39073. In addition, it was confirmed to assimilate carbon dioxide using this pathway. However, although both Y72 and ATCC39073 carried common genes encoding several enzymes related to the reductive tricarboxylic acid (TCA) cycle, their gene sets were different. Our results suggested that the reason for higher transformation efficiency in Y72 than that in ATCC39073, a reference strain of M. thermoacetica, may be that Y72 possesses only 2 sets of genes considered to be involved in a restriction-modification system, which was half of those found in ATCC39073.
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Affiliation(s)
- Kenichiro Tsukahara
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Akihisa Kita
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Yutaka Nakashimada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Tamotsu Hoshino
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Katsuji Murakami
- Biomass Refinery Research Center, National Institute of Advanced Industrial Science and Technology, 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.
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19
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Hu P, Rismani-Yazdi H, Stephanopoulos G. Anaerobic CO2fixation by the acetogenic bacteriumMoorella thermoacetica. AIChE J 2013. [DOI: 10.1002/aic.14127] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Peng Hu
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge; MA; 02139
| | - Hamid Rismani-Yazdi
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge; MA; 02139
| | - Gregory Stephanopoulos
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge; MA; 02139
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20
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Yoneda Y, Yoshida T, Yasuda H, Imada C, Sako Y. A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera. Int J Syst Evol Microbiol 2013; 63:3602-3608. [PMID: 23606483 DOI: 10.1099/ijs.0.050468-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1(T), was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0-3.0 µm straight rods, often observed with round endospores. Strain KKC1(T) grew at 55-68 °C, pH 5.2-9.2 and 0.8-14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0-7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1(T) grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1(T) was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1(T) ( = DSM 26464(T) = NBRC 109353(T)).
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Affiliation(s)
- Yasuko Yoneda
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hisato Yasuda
- Center for Advance Marine Core Research, Kochi University, Kochi 783-8502, Japan
| | - Chiaki Imada
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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21
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Kita A, Iwasaki Y, Sakai S, Okuto S, Takaoka K, Suzuki T, Yano S, Sawayama S, Tajima T, Kato J, Nishio N, Murakami K, Nakashimada Y. Development of genetic transformation and heterologous expression system in carboxydotrophic thermophilic acetogen Moorella thermoacetica. J Biosci Bioeng 2013. [DOI: 10.1016/j.jbiosc.2012.10.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Isolation of thermophilic acetogens and transformation of them with the pyrF and kan(r) genes. Biosci Biotechnol Biochem 2013; 77:301-6. [PMID: 23391907 DOI: 10.1271/bbb.120720] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The application of microbial catalysts to syngas from the gasification of lignocellulosic biomass is gaining interest. Acetogens, a group of anaerobic bacteria, can grow autotrophically on gaseous substrates such as hydrogen and carbon dioxide or syngas and produce acetate via the acetyl-CoA pathway. Here, we report the isolation from a soil sample of two thermophilic acetogen strains, Y72 and Y73, that are closely related to Moorella sp. HUC22-1 and M. thermoacetica ATCC39073. The optimal growth temperature and pH for the strains were 60 °C and 6.0-6.5. Uracil auxotrophy was induced in them by replacing the orotate monophosphate decarboxylase gene (pyrF) with the kanamycin resistant marker (kan(r)). The transformants were isolated by supplementation of the basal medium with 300 mg/L of kanamycin. The transformation efficiency of strains Y72 and Y73 was 20-fold higher than that of strain ATCC39073. Hence these strains are considered possible hosts for thermophilic syngas fermentation.
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Abstract
Extracellular electron transfer has, in one decade, emerged from an environmental phenomenon to an industrial process driver. On the one hand, electron transfer towards anodes leads to production of power or chemicals such as hydrogen, caustic soda and hydrogen peroxide. On the other hand, electron transfer from cathodes enables bioremediation and bioproduction. Although the microbiology of extracellular electron transfer is increasingly being understood, bringing the processes to application requires a number of considerations that are both operational and technical. In the present paper, we investigate the key applied aspects related to electricity-driven bioproduction, including biofilm development, reactor and electrode design, substrate fluxes, surface chemistry, hydrodynamics and electrochemistry, and finally end-product removal/toxicity. Each of these aspects will be critical for the full exploitation of the intriguing physiological feat that extracellular electron transfer is today.
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Tracy BP, Jones SW, Fast AG, Indurthi DC, Papoutsakis ET. Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Curr Opin Biotechnol 2012; 23:364-81. [DOI: 10.1016/j.copbio.2011.10.008] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 10/06/2011] [Accepted: 10/20/2011] [Indexed: 12/19/2022]
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Song J, Kim Y, Lim M, Lee H, Lee JI, Shin W. Microbes as electrochemical CO2 conversion catalysts. CHEMSUSCHEM 2011; 4:587-90. [PMID: 21538918 DOI: 10.1002/cssc.201100107] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Indexed: 05/23/2023]
Affiliation(s)
- Jieun Song
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Korea
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26
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Kato S, Watanabe K. Ecological and Evolutionary Interactions in Syntrophic Methanogenic Consortia. Microbes Environ 2010; 25:145-51. [DOI: 10.1264/jsme2.me10122] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Kazuya Watanabe
- Hashimoto Light Energy Conversion Project, ERATO, JST
- Research Center for Advanced Science and Technology, University of Tokyo
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27
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Sokolova TG, Henstra AM, Sipma J, Parshina SN, Stams AJM, Lebedinsky AV. Diversity and ecophysiological features of thermophilic carboxydotrophic anaerobes. FEMS Microbiol Ecol 2009; 68:131-41. [PMID: 19573196 DOI: 10.1111/j.1574-6941.2009.00663.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Both natural and anthropogenic hot environments contain appreciable levels of carbon monoxide (CO). Anaerobic microbial communities play an important role in CO conversion in such environments. CO is involved in a number of redox reactions. It is biotransformed by thermophilic methanogens, acetogens, hydrogenogens, sulfate reducers, and ferric iron reducers. Most thermophilic CO-oxidizing anaerobes have diverse metabolic capacities, but two hydrogenogenic species are obligate carboxydotrophs. Among known thermophilic carboxydotrophic anaerobes, hydrogenogens are most numerous, and based on available data they are most important in CO biotransformation in hot environments.
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Affiliation(s)
- Tatyana G Sokolova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60 Let Oktyabrya 7/2, Moscow, Russia.
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28
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Jetten MSM, Niftrik LV, Strous M, Kartal B, Keltjens JT, Op den Camp HJM. Biochemistry and molecular biology of anammox bacteria. Crit Rev Biochem Mol Biol 2009; 44:65-84. [DOI: 10.1080/10409230902722783] [Citation(s) in RCA: 310] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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29
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Calli B, Chung LC, Arslan D, Vanbroekhoven K. H2 production potential in thermophilic mixed fermentation. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2009; 44:78-86. [PMID: 19085598 DOI: 10.1080/10934520802515418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The effect of pH on dark fermentative H(2) production at 55 degrees C was studied using three different inocula namely windrow yard waste compost (G), anaerobic organic waste compost (H) and activated sludge (A) and 2 g/L glucose as substrate. The sequential batch experiments were performed by controlling the pH at 5, 5.5 and 6. The highest molar H(2) yields were found to be 1.7 at pH 5 for G and H and 1.6 at pH 5.5 for A, while severe drops in the subsequent runs were associated with lactate fermentation. At pH 5.5 in G, despite the butyrate formation ceased, lower but more stable H(2) yields of about 1.1 were obtained through acetate-ethanol fermentation. Besides, the clostridial thermopiles prevalent at pH 5 were substituted by Thermoanaerobacterium-related species at pH 5.5 and 6. The findings suggested that for a stable H(2) yield through acetate-butyrate fermentation at 55 degrees C with compost inoculum G or H, the pH has to be controlled between pH 5 and 5.5. This is one of the few papers discussing the effects of pH on H(2) production through thermophilic mixed fermentation of glucose by using three different natural mixed culture inocula.
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Affiliation(s)
- Baris Calli
- Environmental Engineering Department, Faculty of Engineering, Marmara University, Goztepe, Istanbul, Turkey.
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30
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Sipma J, Henstra AM, Parshina SM, Lens PN, Lettinga G, Stams AJM. Microbial CO conversions with applications in synthesis gas purification and bio-desulfurization. Crit Rev Biotechnol 2006; 26:41-65. [PMID: 16594524 DOI: 10.1080/07388550500513974] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Recent advances in the field of microbial physiology demonstrate that carbon monoxide is a readily used substrate by a wide variety of anaerobic micro-organisms, and may be employed in novel biotechnological processes for production of bulk and fine chemicals or in biological treatment of waste streams. Synthesis gas produced from fossil fuels or biomass is rich in hydrogen and carbon monoxide. Conversion of carbon monoxide to hydrogen allows use of synthesis gas in existing hydrogen utilizing processes and is interesting in view of a transition from hydrogen production from fossil fuels to sustainable (CO2-neutral) biomass. The conversion of CO with H2O to CO2 and H2 is catalyzed by a rapidly increasing group of micro-organisms. Hydrogen is a preferred electron donor in biotechnological desulfurization ofwastewaters and flue gases. Additionally, CO is a good alternative electron donor considering the recent isolation of a CO oxidizing, sulfate reducing bacterium. Here we review CO utilization by various anaerobic micro-organisms and their possible role in biotechnological processes, with a focus on hydrogen production and bio-desulfurization.
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Affiliation(s)
- Jan Sipma
- Sub-department of Environmental Technology, Wageningen University, Wageningen, The Netherlands
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31
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Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MSM, Wagner M, Le Paslier D. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 2006; 440:790-4. [PMID: 16598256 DOI: 10.1038/nature04647] [Citation(s) in RCA: 709] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 02/15/2006] [Indexed: 11/09/2022]
Abstract
Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism, the biosynthesis of ladderane lipids and the role of cytoplasm differentiation are unique in biology. Here we use environmental genomics--the reconstruction of genomic data directly from the environment--to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.
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Affiliation(s)
- Marc Strous
- Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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Paarup M, Friedrich MW, Tindall BJ, Finster K. Characterization of the psychrotolerant acetogen strain SyrA5 and the emended description of the species Acetobacterium carbinolicum. Antonie van Leeuwenhoek 2005; 89:55-69. [PMID: 16344912 DOI: 10.1007/s10482-005-9009-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Accepted: 08/16/2005] [Indexed: 11/26/2022]
Abstract
A psychrotolerant, obligate anaerobic, acetogenic bacterium designated strain SyrA5 was isolated from black anoxic sediment of a brackish fjord. Cells were Gram-positive, non-sporeforming rods. The isolate utilized H(2)/CO(2), CO, fructose, glucose, ethanol, ethylene glycol, glycerol, pyruvate, lactate, betaine and the methyl-groups of several methoxylated benzoic derivatives such as syringate, trimethoxybenzoate and vallinate. The optimum temperature for growth was 29 degrees C, whilst slow growth occurred at 2 degrees C. The strain grew optimally with NaCl concentrations below 2.7% (w/v), but growth occurred up to 4.3% (w/v) NaCl. Growth was observed in the range from pH 5.9 to 8.5, optimum at pH 8. The G+C content was 44.1 mol%. Based upon 16S rRNA gene sequence analysis and DNA-DNA reassociation studies, the organism was classified in the genus Acetobacterium. Strain SyrA5 shared a 16S rRNA sequence similarity with A. carbinolicum of 100%, a fthfs gene (which codes for the N5,N10 tetrahydrofolate synthetase) sequence identity of 98.5-98.7% (amino acid sequence similarities were 99.4-100%) and a RNA-DNA hybridization homology of 64-68%. Despite a number of phenotypic differences between strain SyrA5 and A. carbinolicum we propose including strain SyrA5 as a subspecies of A. carbinolicum for which we propose the name Acetobacterium carbinolicum subspecies kysingense. The type strain is SyrA5 (=DSM 16427(T), ATCC BAA-990).
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Affiliation(s)
- Maiken Paarup
- Department of Microbiology, Institute of Biological Sciences, University of Aarhus, Dk-8000, Aarhus C, Denmark
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