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Mashzhan A, Kistaubayeva A, Javier-López R, Bissenbay A, Birkeland NK. Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov., a Novel Feather-Degrading Anaerobic Thermophile. Microorganisms 2024; 12:1277. [PMID: 39065046 PMCID: PMC11278675 DOI: 10.3390/microorganisms12071277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Caldanaerobacter subterraneus subsp. keratinolyticus subsp. nov. strain KAk was isolated from a geothermal hot spring located in Kazakhstan. Growth occurred at temperatures ranging from 50 to 80 °C, with approximately 70 °C as optimum. It also thrived in pH conditions ranging from 4.0 to 9.0, with the best growth occurring at 6.8. Under optimal conditions in a glucose-containing medium, the cells were predominantly observed singly, in pairs, or less frequently in chains, and did not form endospores. However, under conditions involving growth with merino wool or feathers, or under suboptimal conditions, the cells of strain KAk exhibited a notably elongated and thinner morphology, with lengths ranging from 5 to 8 µm, and spores were observed. The KAk strain exhibited efficient degradation of feather keratin and merino wool at temperatures ranging from 65 to 70 °C. Analysis of the 16S rRNA gene sequence placed KAk within the genus Caldanaerobacter, family Thermoanaerobacteraceae, with the highest similarity to C. subterraneus subsp. tengcongensis MB4T (98.84% sequence identity). Furthermore, our analysis of the draft genome sequence indicated a genome size of 2.4 Mbp, accompanied by a G+C value of 37.6 mol%. This study elucidated the physiological and genomic characteristics of strain KAk, highlighting its keratinolytic capabilities and distinctiveness compared to other members of the genus Caldanaerobacter.
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Affiliation(s)
- Akzhigit Mashzhan
- Department of Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan; (A.K.); (A.B.)
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway;
- Science Research Institute of Biology and Biotechnology Peoblem, Al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan
- Almaty Branch of National Center for Biotechnology in Central Reference Laboratory (CRL), Zhahanger St. 14, 050054 Almaty, Kazakhstan
- Department of Botany, E.A. Buketov Karaganda State University, Universitet St. 28, 100028 Karaganda, Kazakhstan
| | - Aida Kistaubayeva
- Department of Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan; (A.K.); (A.B.)
- Science Research Institute of Biology and Biotechnology Peoblem, Al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan
| | - Rubén Javier-López
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway;
| | - Akerke Bissenbay
- Department of Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Av. 71, 050040 Almaty, Kazakhstan; (A.K.); (A.B.)
- Almaty Branch of National Center for Biotechnology in Central Reference Laboratory (CRL), Zhahanger St. 14, 050054 Almaty, Kazakhstan
| | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway;
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Yao J, Wang ZN, Liu H, Jin H, Zhang Y. Survey of Acetylation for Thermoanaerobacter tengcongensis. Appl Biochem Biotechnol 2023; 195:6081-6097. [PMID: 36809429 DOI: 10.1007/s12010-023-04361-9] [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] [Accepted: 01/10/2023] [Indexed: 02/23/2023]
Abstract
Non-histone protein acetylation is involved in key cellular processes both in eukaryotes and prokaryotes. Acetylation in bacteria is used to modify proteins involved in metabolism and allow the bacteria to adapt to their environment. TTE (Thermoanaerobacter tengcongensis) is an anaerobic, thermophilic saccharolytic bacterium that grows at extreme temperature range between 50 and 80 ℃. The annotated TTE proteome contains less than 3000 proteins. We analyzed the proteome and acetylome of TTE using 2DLC-MS/MS (2-dimensional liquid chromatography mass spectrum). We evaluated the ability of mass spectrometry technology to cover a relatively small proteome as much as possible. And we also observed wide spread of acetylation in TTE, which changed under different temperatures. A total of 2082 proteins were identified, which accounts for about 82% of the database. A total of 2050 (~ 98%) proteins were quantified in at least one culture condition and 1818 proteins were quantified in all 4 conditions. The result also consisted 3457 acetylation sites corresponding to 827 distinct proteins, which covered 40% of the proteins identified. Bioinformatics analysis reported that proteins related to replication, recombination, repair, and extracellular structure cell wall biogenesis had more than half members acetylated, while energy production, carbohydrate transport, and metabolism related proteins were least acetylated. Our result suggested that acetylation affects the ATP-related energy metabolism and energy-dependent biosynthesis process. Comparing the enzymes related with lysine acetylation and acetyl-CoA (acetyl-coenzyme A) metabolism, we suggested that the acetylation of TTE took a non-enzymatic mechanism and affected by abundance of acetyl-CoA.
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Affiliation(s)
- Jun Yao
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Ze-Ning Wang
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Hang Liu
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Jin
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
| | - Yang Zhang
- Department of Chemistry, Shanghai Stomatological Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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Yoo BK, Kruglik SG, Lambry JC, Lamarre I, Raman CS, Nioche P, Negrerie M. The H-NOX protein structure adapts to different mechanisms in sensors interacting with nitric oxide. Chem Sci 2023; 14:8408-8420. [PMID: 37564404 PMCID: PMC10411614 DOI: 10.1039/d3sc01685d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
Some classes of bacteria within phyla possess protein sensors identified as homologous to the heme domain of soluble guanylate cyclase, the mammalian NO-receptor. Named H-NOX domain (Heme-Nitric Oxide or OXygen-binding), their heme binds nitric oxide (NO) and O2 for some of them. The signaling pathways where these proteins act as NO or O2 sensors appear various and are fully established for only some species. Here, we investigated the reactivity of H-NOX from bacterial species toward NO with a mechanistic point of view using time-resolved spectroscopy. The present data show that H-NOXs modulate the dynamics of NO as a function of temperature, but in different ranges, changing its affinity by changing the probability of NO rebinding after dissociation in the picosecond time scale. This fundamental mechanism provides a means to adapt the heme structural response to the environment. In one particular H-NOX sensor the heme distortion induced by NO binding is relaxed in an ultrafast manner (∼15 ps) after NO dissociation, contrarily to other H-NOX proteins, providing another sensing mechanism through the H-NOX domain. Overall, our study links molecular dynamics with functional mechanism and adaptation.
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Affiliation(s)
- Byung-Kuk Yoo
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Sergei G Kruglik
- Laboratoire Jean Perrin, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS 75005 Paris France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - Isabelle Lamarre
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
| | - C S Raman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore Maryland 21201 USA
| | - Pierre Nioche
- Environmental Toxicity, Therapeutic Targets, Cellular Signaling and Biomarkers, UMR S1124, Centre Universitaire des Saints-Pères, Université Paris Descartes 75006 Paris France
- Structural and Molecular Analysis Platform, BioMedTech Facilities, INSERM US36-CNRS-UMS2009, Paris Université Paris France
| | - Michel Negrerie
- Laboratoire d'Optique et Biosciences, INSERM U-1182, Ecole Polytechnique 91120 Palaiseau France
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Centeno-Leija S, Espinosa-Barrera L, Velazquez-Cruz B, Cárdenas-Conejo Y, Virgen-Ortíz R, Valencia-Cruz G, Saenz RA, Marín-Tovar Y, Gómez-Manzo S, Hernández-Ochoa B, Rocha-Ramirez LM, Zataraín-Palacios R, Osuna-Castro JA, López-Munguía A, Serrano-Posada H. Mining for novel cyclomaltodextrin glucanotransferases unravels the carbohydrate metabolism pathway via cyclodextrins in Thermoanaerobacterales. Sci Rep 2022; 12:730. [PMID: 35031648 PMCID: PMC8760340 DOI: 10.1038/s41598-021-04569-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/20/2021] [Indexed: 11/21/2022] Open
Abstract
Carbohydrate metabolism via cyclodextrins (CM-CD) is an uncommon starch-converting pathway that thoroughly depends on extracellular cyclomaltodextrin glucanotransferases (CGTases) to transform the surrounding starch substrate to α-(1,4)-linked oligosaccharides and cyclodextrins (CDs). The CM-CD pathway has emerged as a convenient microbial adaptation to thrive under extreme temperatures, as CDs are functional amphipathic toroids with higher heat-resistant values than linear dextrins. Nevertheless, although the CM-CD pathway has been described in a few mesophilic bacteria and archaea, it remains obscure in extremely thermophilic prokaryotes (Topt ≥ 70 °C). Here, a new monophyletic group of CGTases with an exceptional three-domain ABC architecture was detected by (meta)genome mining of extremely thermophilic Thermoanaerobacterales living in a wide variety of hot starch-poor environments on Earth. Functional studies of a representative member, CldA, showed a maximum activity in a thermoacidophilic range (pH 4.0 and 80 °C) with remarkable product diversification that yielded a mixture of α:β:γ-CDs (34:62:4) from soluble starch, as well as G3-G7 linear dextrins and fermentable sugars as the primary products. Together, comparative genomics and predictive functional analysis, combined with data of the functionally characterized key proteins of the gene clusters encoding CGTases, revealed the CM-CD pathway in Thermoanaerobacterales and showed that it is involved in the synthesis, transportation, degradation, and metabolic assimilation of CDs.
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Affiliation(s)
- Sara Centeno-Leija
- Consejo Nacional de Ciencia y Tecnología, Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico.
| | - Laura Espinosa-Barrera
- Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico
| | - Beatriz Velazquez-Cruz
- Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico
| | - Yair Cárdenas-Conejo
- Consejo Nacional de Ciencia y Tecnología, Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico
| | - Raúl Virgen-Ortíz
- Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico
| | - Georgina Valencia-Cruz
- Centro Universitario de Investigaciones Biomédicas, Universidad de Colima, Avenida 25 de julio 965, Colonia Villa de San Sebastián, 28045, Colima, Colima, Mexico
| | - Roberto A Saenz
- Facultad de Ciencias, Universidad de Colima, Bernal Díaz del Castillo 340, 28045, Colima, Colima, Mexico
| | - Yerli Marín-Tovar
- Laboratorio de Bioquímica Estructural, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Mexico
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530, Mexico City, Mexico
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica y Biología Celular, Hospital Infantil de México Federico Gómez, Secretaría de Salud, 06720, Mexico City, Mexico
| | - Luz María Rocha-Ramirez
- Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Dr. Márquez No. 162, Colonia Doctores, 06720, Delegación Cuauhtémoc, Mexico
| | - Rocío Zataraín-Palacios
- Escuela de Medicina General, Universidad José Martí, Bosques del Decán 351, 28089, Colima, Colima, México
| | - Juan A Osuna-Castro
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad de Colima, Autopista Colima-Manzanillo, 28100, Tecomán, Colima, Mexico
| | - Agustín López-Munguía
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Hugo Serrano-Posada
- Consejo Nacional de Ciencia y Tecnología, Laboratorio de Biología Sintética, Estructural y Molecular, Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera Los Limones-Loma de Juárez, 28627, Colima, Colima, Mexico.
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Biological conversion of carbon monoxide and hydrogen by anaerobic culture: Prospect of anaerobic digestion and thermochemical processes combination. Biotechnol Adv 2021; 58:107886. [PMID: 34915147 DOI: 10.1016/j.biotechadv.2021.107886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/26/2021] [Accepted: 12/08/2021] [Indexed: 01/04/2023]
Abstract
Waste biomass is considered a promising renewable energy feedstock that can be converted by anaerobic digestion. However, anaerobic digestion application can be challenging due to the structural complexity of several waste biomass kinds. Therefore, coupling anaerobic digestion with thermochemical processes can offset the limitations and convert the hardly biodegradable waste biomass, including digestate residue, into value-added products: syngas and pyrogas (gaseous mixtures consisting mainly of H2, CO, CO2), bio-oil, and biochar for further valorisation. In this review, the utilisation boundaries and benefits of the aforementioned products by anaerobic culture are discussed. First, thermochemical process parameters for an enhanced yield of desired products are summarised. Particularly, the microbiology of CO and H2 mixture biomethanation and fermentation in anaerobic digestion is presented. Finally, the state-of-the-art biological conversion of syngas and pyrogas to CH4 mediated by anaerobic culture is adequately described. Extensive research shows the successful selective biological conversion of CO and H2 to CH4, acetic acid, and alcohols. The main bottleneck is the gas-liquid mass transfer which can be enhanced appropriately by bioreactors' configurations. A few research groups focus on bio-oil and biochar addition into anaerobic digesters. However, according to the literature review, there has been no research for utilising all value-added products at once in anaerobic digestion published so far. Although synergic effects of such can be expected. In summary, the combination of anaerobic digestion and thermochemical processes is a promising alternative for wide-scale waste biomass utilisation in practice.
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Genomics and simulated laboratory studies reveal Thermococcus sp. 101C5 as a novel hyperthermophilic archaeon possessing a specialized metabolic arsenal for enhanced oil recovery. Antonie van Leeuwenhoek 2021; 115:19-31. [PMID: 34734348 DOI: 10.1007/s10482-021-01667-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/27/2021] [Indexed: 10/19/2022]
Abstract
Laboratory evaluation of hyperthermophiles with the potential for Enhanced Oil Recovery (EOR) is often hampered by the difficulties in replicating the in situ growth conditions in the laboratory. In the present investigation, genome analysis was used to gain insights into the metabolic potential of a hyperthermophile to mobilize the residual oil from depleting high-temperature oil reservoirs. Here, we report the 1.9 Mb draft genome sequence of a hyperthermophilic anaerobic archaeon, Thermococcus sp. 101C5, with a GC content of 44%, isolated from a high-temperature oil reservoir of Gujarat, India. 101C5 possessed the genetic arsenal required for adaptation to harsh oil reservoir conditions, such as various heat shock proteins for thermo-adaptation, Trk potassium uptake system proteins for osmo-adaptation, and superoxide reductases against oxidative stress. Microbial Enhanced Oil Recovery (MEOR) potential of the strain was established by ascertaining the presence of genes encoding enzymes involved in the production of the metabolites such as hydrogen, bio-emulsifier, acetate, exopolysaccharide, etc. Production of these metabolites which pressurize the reservoir, emulsify the crude oil, lower the viscosity and reduce the drag, thus facilitating mobilization of the residual oil was experimentally confirmed. Also, the presence of crude oil degradative genes highlighted the ability of the strain to mobilize heavy residual oil, which was confirmed under simulated conditions in sand-pack studies. The obtained results demonstrated additional oil recoveries of 42.1% and 56.5% at 96 °C and 101 °C, respectively, by the strain 101C5, illustrating its potential for application in high-temperature oil reservoirs. To our best knowledge, this is the first report of genome analysis of any microbe assessed for its suitability for MEOR from the high-temperature oil reservoir.
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Singh NK, Choudhary S. Bacterial and archaeal diversity in oil fields and reservoirs and their potential role in hydrocarbon recovery and bioprospecting. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:58819-58836. [PMID: 33410029 DOI: 10.1007/s11356-020-11705-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
Hydrocarbon is a primary source of energy in the current urbanized society. Considering the increasing demand, worldwide oil productions are declining due to maturity of oil fields and because of difficulty in discovering new oil fields to substitute the exploited ones. To meet current and future energy demands, further exploitation of oil resources is highly required. Microorganisms inhabiting in these areas exhibit highly diverse catabolic activities to degrade, transform, or accumulate various hydrocarbons. Enrichment of hydrocarbon-utilizing bacteria in oil basin is caused by continuous long duration and low molecular weight hydrocarbon microseepage which plays a very important role as an indicator for petroleum prospecting. The important microbial metabolic processes in most of the oil reservoir are sulfate reduction, fermentation, acetogenesis, methanogenesis, NO3- reduction, and Fe (III) and Mn (IV) reduction. The microorganisms residing in these sites have critical control on petroleum composition, recovery, and production methods. Physical characteristics of heavy oil are altered by microbial biotransformation and biosurfactant production. Considering oil to be one of the most vital energy resources, it is important to have a comprehensive understanding of petroleum microbiology. This manuscript reviews the recent research work referring to the diversity of bacteria in oil field and reservoir sites and their applications for enhancing oil transformation in the target reservoir and geomicrobial prospecting scope for petroleum exploration.
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Affiliation(s)
- Nishi Kumari Singh
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan, 304022, India
| | - Sangeeta Choudhary
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan, 304022, India.
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Al-Mur BA, Pugazhendi A, Jamal MT. Application of integrated extremophilic (halo-alkalo-thermophilic) bacterial consortium in the degradation of petroleum hydrocarbons and treatment of petroleum refinery wastewater under extreme condition. JOURNAL OF HAZARDOUS MATERIALS 2021; 413:125351. [PMID: 33930944 DOI: 10.1016/j.jhazmat.2021.125351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/21/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Degradation of petroleum hydrocarbon under extreme conditions such as high salinity, temperature and pH was difficult due to unavailability of potential bacterial strains. The present study details the efficiency of extremophilic bacterial consortium in biodegradation of different petroleum hydrocarbons and treatment of petroleum refinery wastewater under extreme condition. Extreme condition for the degradation of petroleum hydrocarbons was optimized at 8% salinity, pH-10 and temperature-60 °C. The consortium recorded complete degradation of low molecular weight (LMW) petroleum hydrocarbons (200 ppm) such as anthracene, phenanthrene, fluorene and naphthalene in 8 days under optimized extreme condition. High molecular weight (HMW) hydrocarbons such as pyrene (100 ppm), benzo(e)pyrene (20 ppm), benzo(k)fluoranthene (20 ppm) and benzo(a)pyrene (20 ppm), revealed 93%, 60%, 55% and 51% degradation by the extremophilic consortium under optimized extreme condition. The extremophilic consortium mineralized fluorene (61%) at high saline condition up to 24%. Addition of yeast extract potently accelerated the biodegradation under extreme condition. Treatment of petroleum refinery wastewater in continuous stirred tank reactor recorded 92% COD removal with complete removal of LMW hydrocarbons in 16 days and 91% of HMW hydrocarbons in 32 days under extreme condition. The hydrocarbons degrading extremophilic consortium possessed Ochrobactrum, Bacillus, Marinobacter, Pseudomonas, Martelella, Stenotrophomonas and Rhodococcus.
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Affiliation(s)
- Bandar A Al-Mur
- Department of Environmental Science, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Arulazhagan Pugazhendi
- Center of Excellence in Environmental Studies, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Mamdoh T Jamal
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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9
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Rajbongshi A, Gogoi SB. A review on anaerobic microorganisms isolated from oil reservoirs. World J Microbiol Biotechnol 2021; 37:111. [PMID: 34076736 DOI: 10.1007/s11274-021-03080-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022]
Abstract
The Role of microorganisms in the petroleum industry is wide-ranging. To understand the role of microorganisms in hydrocarbon transformation, identification of such microorganisms is vital, especially the ones capable of in situ degradation. Microorganisms play a pivotal role in the degradation of hydrocarbons and remediation of heavy metals. Anaerobic microorganisms such as Sulphate Reducing Bacteria (SRB), responsible for the production of hydrogen sulphide (H2S) within the reservoir, reduces the oil quality by causing reservoir souring and reduction in oil viscosity. This paper reviews the diversity of SRB, methanogens, Nitrogen Reducing Bacteria (NRB), and fermentative bacteria present in oil reservoirs. It also reviews the extensive diversity of these microorganisms, their applications in petroleum industries, characteristics and adaptability to survive in different conditions, the potential to alter the petroleum hydrocarbons properties, the propensity to petroleum hydrocarbon degradation, and remediation of metals.
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Affiliation(s)
- Amarjit Rajbongshi
- Brahmaputra Valley Fertilizer Corporation Limited, Namrup, Assam, India.
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10
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Pinney MM, Mokhtari DA, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, Herschlag D. Parallel molecular mechanisms for enzyme temperature adaptation. Science 2021; 371:371/6533/eaay2784. [PMID: 33674467 DOI: 10.1126/science.aay2784] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/23/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.
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Affiliation(s)
- Margaux M Pinney
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
| | - Daniel A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
| | - David M Sanchez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruibin Liang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Todd J Martinez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
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11
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Ultrafast dynamics of heme distortion in the O 2-sensor of a thermophilic anaerobe bacterium. Commun Chem 2021; 4:31. [PMID: 36697566 PMCID: PMC9814294 DOI: 10.1038/s42004-021-00471-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 02/05/2021] [Indexed: 01/28/2023] Open
Abstract
Heme-Nitric oxide and Oxygen binding protein domains (H-NOX) are found in signaling pathways of both prokaryotes and eukaryotes and share sequence homology with soluble guanylate cyclase, the mammalian NO receptor. In bacteria, H-NOX is associated with kinase or methyl accepting chemotaxis domains. In the O2-sensor of the strict anaerobe Caldanaerobacter tengcongensis (Ct H-NOX) the heme appears highly distorted after O2 binding, but the role of heme distortion in allosteric transitions was not yet evidenced. Here, we measure the dynamics of the heme distortion triggered by the dissociation of diatomics from Ct H-NOX using transient electronic absorption spectroscopy in the picosecond to millisecond time range. We obtained a spectroscopic signature of the heme flattening upon O2 dissociation. The heme distortion is immediately (<1 ps) released after O2 dissociation to produce a relaxed state. This heme conformational change occurs with different proportions depending on diatomics as follows: CO < NO < O2. Our time-resolved data demonstrate that the primary structural event of allostery is the heme distortion in the Ct H-NOX sensor, contrastingly with hemoglobin and the human NO receptor, in which the primary structural events are respectively the motion of the proximal histidine and the rupture of the iron-histidine bond.
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12
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Korzhenkov AA, Toshchakov SV, Podosokorskaya OA, Patrushev MV, Kublanov IV. Data on draft genome sequence of Caldanaerobacter sp. strain 1523vc, a thermophilic bacterium, isolated from a hot spring of Uzon Caldera, (Kamchatka, Russia). Data Brief 2020; 33:106336. [PMID: 33204772 PMCID: PMC7648113 DOI: 10.1016/j.dib.2020.106336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 11/27/2022] Open
Abstract
The draft genome sequence of Caldanaerobacter sp. strain 1523vc, a thermophilic bacterium, isolated from a hot spring of Uzon Caldera, (Kamchatka, Russia) is presented. The complete genome assembly was of 2 713 207 bp with predicted completeness of 99.38%. Genome structural annotation revealed 2674 protein-coding genes, 127 pseudogenes and 77 RNA genes. Pangenome analysis of 7 currently available high quality Caldanaerobacter spp. genomes including 1523vc revealed 4673 gene clusters. Of them, 1130 clusters formed a core genome of genus Caldanaerobacter. Of the rest 3543 Caldanaerobacter pangenome genes, 385 were exclusively represented in 1523vc genome. 101 of 2801 Caldanaerobacter CDS were found to be encoding carbohydrate-active enzymes (CAZymes). The majority of CAZymes were predicted to be involved in degradation of beta-linked polysaccharides as chitin, cellulose and hemicelluloses, reflecting the metabolism of strain 1523vc, isolated on cellulose. 5 of 101 CAZyme genes were found to be unique for the strain 1523vc and belonged to GH23, GT56, GH15 and two CE9 family proteins. The draft genome of strain 1523vc was deposited at DBJ/EMBL/GenBank under the accessions JABEQB000000000, PRJNA629090 and SAMN14766777 for Genome, Bioproject and Biosample, respectively.
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Affiliation(s)
- A A Korzhenkov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - S V Toshchakov
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - O A Podosokorskaya
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Russia, 117312, Moscow, 60-let Oktyabrya prospect 7/2
| | - M V Patrushev
- National Research Center "Kurchatov Institute", Moscow 123182, Russia
| | - I V Kublanov
- Winogradsky Institute of Microbiology of Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Russia, 117312, Moscow, 60-let Oktyabrya prospect 7/2
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Straub CT, Bing RG, Otten JK, Keller LM, Zeldes BM, Adams MWW, Kelly RM. Metabolically engineered Caldicellulosiruptor bescii as a platform for producing acetone and hydrogen from lignocellulose. Biotechnol Bioeng 2020; 117:3799-3808. [PMID: 32770740 DOI: 10.1002/bit.27529] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/12/2020] [Accepted: 08/05/2020] [Indexed: 11/10/2022]
Abstract
The production of volatile industrial chemicals utilizing metabolically engineered extreme thermophiles offers the potential for processes with simultaneous fermentation and product separation. An excellent target chemical for such a process is acetone (Tb = 56°C), ideally produced from lignocellulosic biomass. Caldicellulosiruptor bescii (Topt 78°C), an extremely thermophilic fermentative bacterium naturally capable of deconstructing and fermenting lignocellulose, was metabolically engineered to produce acetone. When the acetone pathway construct was integrated into a parent strain containing the bifunctional alcohol dehydrogenase from Clostridium thermocellum, acetone was produced at 9.1 mM (0.53 g/L), in addition to minimal ethanol 3.3 mM (0.15 g/L), along with net acetate consumption. This demonstrates that C. bescii can be engineered with balanced pathways in which renewable carbohydrate sources are converted to useful metabolites, primarily acetone and H2 , without net production of its native fermentation products, acetate and lactate.
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Affiliation(s)
- Christopher T Straub
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Ryan G Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Jonathan K Otten
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Lisa M Keller
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Benjamin M Zeldes
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
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14
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Modification of the glycolytic pathway in Pyrococcus furiosus and the implications for metabolic engineering. Extremophiles 2020; 24:511-518. [PMID: 32415359 DOI: 10.1007/s00792-020-01172-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/16/2020] [Indexed: 10/24/2022]
Abstract
The key difference in the modified Embden-Meyerhof glycolytic pathway in hyperthermophilic Archaea, such as Pyrococcus furiosus, occurs at the conversion from glyceraldehyde-3-phosphate (GAP) to 3-phosphoglycerate (3-PG) where the typical intermediate 1,3-bisphosphoglycerate (1,3-BPG) is not present. The absence of the ATP-yielding step catalyzed by phosphoglycerate kinase (PGK) alters energy yield, redox energetics, and kinetics of carbohydrate metabolism. Either of the two enzymes, ferredoxin-dependent glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR) or NADP+-dependent non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), responsible for this "bypass" reaction, could be deleted individually without impacting viability, albeit with differences in native fermentation product profiles. Furthermore, P. furiosus was viable in the gluconeogenic direction (growth on pyruvate or peptides plus elemental sulfur) in a ΔgapnΔgapor strain. Ethanol was utilized as a proxy for potential heterologous products (e.g., isopropanol, butanol, fatty acids) that require reducing equivalents (e.g., NAD(P)H, reduced ferredoxin) generated from glycolysis. Insertion of a single gene encoding the thermostable NADPH-dependent primary alcohol dehydrogenase (adhA) (Tte_0696) from Caldanaerobacter subterraneus, resulted in a strain producing ethanol via the previously established aldehyde oxidoreductase (AOR) pathway. This strain demonstrated a high ratio of ethanol over acetate (> 8:1) at 80 °C and enabled ethanol production up to 85 °C, the highest temperature for bio-ethanol production reported to date.
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Abstract
Thermophilic microbes are an attractive bioproduction platform due to their inherently lower contamination risk and their ability to perform thermostable enzymatic processes which may be required for biomass processing and other industrial applications. The engineering of microbes for industrial scale processes requires a suite of genetic engineering tools to optimize existing biological systems as well as to design and incorporate new metabolic pathways within strains. Yet, such tools are often lacking and/or inadequate for novel microbes, especially thermophiles. This chapter focuses on genetic tool development and engineering strategies, in addition to challenges, for thermophilic microbes. We provide detailed instructions and techniques for tool development for an anaerobic thermophile, Caldanaerobacter subterraneus subsp. tengcongensis, including culturing, plasmid construction, transformation, and selection. This establishes a foundation for advanced genetic tool development necessary for the metabolic engineering of this microbe and potentially other thermophilic organisms.
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Omae K, Fukuyama Y, Yasuda H, Mise K, Yoshida T, Sako Y. Diversity and distribution of thermophilic hydrogenogenic carboxydotrophs revealed by microbial community analysis in sediments from multiple hydrothermal environments in Japan. Arch Microbiol 2019; 201:969-982. [PMID: 31030239 PMCID: PMC6687684 DOI: 10.1007/s00203-019-01661-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 03/15/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022]
Abstract
In hydrothermal environments, carbon monoxide (CO) utilisation by thermophilic hydrogenogenic carboxydotrophs may play an important role in microbial ecology by reducing toxic levels of CO and providing H2 for fuelling microbial communities. We evaluated thermophilic hydrogenogenic carboxydotrophs by microbial community analysis. First, we analysed the correlation between carbon monoxide dehydrogenase (CODH)–energy-converting hydrogenase (ECH) gene cluster and taxonomic affiliation by surveying an increasing genomic database. We identified 71 genome-encoded CODH–ECH gene clusters, including 46 whose owners were not reported as hydrogenogenic carboxydotrophs. We identified 13 phylotypes showing > 98.7% identity with these taxa as potential hydrogenogenic carboxydotrophs in hot springs. Of these, Firmicutes phylotypes such as Parageobacillus, Carboxydocella, Caldanaerobacter, and Carboxydothermus were found in different environmental conditions and distinct microbial communities. The relative abundance of the potential thermophilic hydrogenogenic carboxydotrophs was low. Most of them did not show any symbiotic networks with other microbes, implying that their metabolic activities might be low.
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Affiliation(s)
- Kimiho Omae
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8503, Japan
| | - Yuto Fukuyama
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8503, Japan
| | - Hisato Yasuda
- Center for Advanced Marine Core Research, Kochi University, B200 Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Kenta Mise
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8503, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8503, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8503, Japan.
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Sharma N, Lavania M, Kukreti V, Rana DP, Lal B. Laboratory Investigation of Indigenous Consortia TERIJ-188 for Incremental Oil Recovery. Front Microbiol 2018; 9:2357. [PMID: 30356706 PMCID: PMC6189299 DOI: 10.3389/fmicb.2018.02357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/14/2018] [Indexed: 11/13/2022] Open
Abstract
Bacterial Profile modification is an efficient process which brings the alteration in permeability of the porous media of the reservoir by selective plugging which eventually recover the residual oil. It is an advantageous and feasible method for residual oil recovery from high permeability zones of the reservoir. In this study, indigenous bacterial consortia, TERIJ-188 was developed from Gujarat oil fields. TERIJ-188 was identified as Thermoanaerobacter sp., Thermoanaerobacter brockii, Thermoanaerobacter italicus, Thermoanaerobacter mathranii, Thermoanaerobacter thermocopriae. The novelty of consortia was that it produces biomass (850 mg l-1), bio-surfactant (500 mg l-1), and volatile fatty acids (495 mg l-1) at 70°C in the span of 10 days, which are adequate to alter the permeability and sweep efficiency of high permeability zones facilitating the displacement of oil. The biosurfactant was analyzed for its functional group by FTIR and NMR techniques which indicate the presence of C-N bond, aldehydes, triacylglycerols. TERIJ-188 showed an effective reduction in permeability at residual oil saturation from 28.3 to 11.3 mD and 19.2% incremental oil recovery in a core flood assay. Pathogenicity test suggested that TERIJ-188 is non-toxic, non-virulent and safe for field implementation.
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Affiliation(s)
- Neha Sharma
- Microbial Biotechnology, Environmental and Industrial Biotechnology Division, The Energy and Resources Institute, New Delhi, India
| | - Meeta Lavania
- Microbial Biotechnology, Environmental and Industrial Biotechnology Division, The Energy and Resources Institute, New Delhi, India
| | - Vipin Kukreti
- Institute of Reservoir Studies, Oil and Natural Gas Corporation Limited, Ahmadabad, India
| | - Dolly Pal Rana
- Institute of Reservoir Studies, Oil and Natural Gas Corporation Limited, Ahmadabad, India
| | - Banwari Lal
- Microbial Biotechnology, Environmental and Industrial Biotechnology Division, The Energy and Resources Institute, New Delhi, India
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18
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Rathi R, Lavania M, Kukreti V, Lal B. Evaluating the potential of indigenous methanogenic consortium for enhanced oil and gas recovery from high temperature depleted oil reservoir. J Biotechnol 2018; 283:43-50. [DOI: 10.1016/j.jbiotec.2018.06.347] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 06/01/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
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19
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Chades T, Scully SM, Ingvadottir EM, Orlygsson J. Fermentation of Mannitol Extracts From Brown Macro Algae by Thermophilic Clostridia. Front Microbiol 2018; 9:1931. [PMID: 30177924 PMCID: PMC6110305 DOI: 10.3389/fmicb.2018.01931] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/30/2018] [Indexed: 01/30/2023] Open
Abstract
Mannitol-containing macro algae biomass, such as Ascophyllum nodosum and Laminaria digitata, are a potential feedstock for the production of biofuels such as bioethanol. The purpose of this work was to evaluate the ability of thermophilic anaerobes within Class Clostridia to ferment mannitol and mannitol-containing algal extracts. Screening of the type strains of six genera, Caldanaerobius, Caldanaerobacter, Caldicellulosiruptor, Thermoanaerobacter, Thermobrachium, and Thermoanaerobacterium) was conducted on 20 mM mannitol and revealed that 11 of 41 strains could utilize mannitol with ethanol being the dominant end-product. Mannitol utilization seems to be most common within the genus of Thermoanaerobacter (7 of 16 strains) with yields up to 88% of the theoretical yield in the case of Thermoanaerobacter pseudoethanolicus. Six selected mannitol-degrading strains (all Thermoanaerobacter species) were grown on mannitol extracts prepared from A. nodosum and L. digitata. Five of the strains produced similar amounts of ethanol as compared with ethanol yields from mannitol only. Finally, T. pseudoethanolicus was kinetically monitored using mannitol and mannitol extracts made from two macro algae species, A. nodosum and L. digitata for end-product formation.
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Affiliation(s)
- Theo Chades
- Faculty of Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
| | - Sean M Scully
- Faculty of Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
| | - Eva M Ingvadottir
- Faculty of Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
| | - Johann Orlygsson
- Faculty of Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
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20
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Kearney C, Olenginski LT, Hirn TD, Fowler GD, Tariq D, Brewer SH, Phillips-Piro CM. Exploring local solvation environments of a heme protein using the spectroscopic reporter 4-cyano-l-phenylalanine. RSC Adv 2018; 8:13503-13512. [PMID: 29780583 PMCID: PMC5944249 DOI: 10.1039/c8ra02000k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/20/2018] [Indexed: 11/21/2022] Open
Abstract
The vibrational reporter unnatural amino acid (UAA) 4-cyano-l-phenylalanine (pCNF) was genetically incorporated individually at three sites (5, 36, and 78) in the heme protein Caldanaerobacter subterraneus H-NOX to probe local hydration environments. The UAA pCNF was incorporated site-specifically using an engineered, orthogonal tRNA synthetase in E. coli. The ability of all of the pCNF-containing H-NOX proteins to form the ferrous CO, NO, or O2 ligated and unligated states was confirmed with UV-Vis spectroscopy. The solvation state at each site of the three sites of pCNF incorporation was assessed using temperature-dependent infrared spectroscopy. Specifically, the frequency-temperature line slope (FTLS) method was utilized to show that the nitrile group at site 36 was fully solvated and the nitrile group at site 78 was de-solvated (buried) in the heme pocket. The nitrile group at site 5 was found to be partially solvated suggesting that the nitrile group was involved in moderate strength hydrogen bonds. These results were confirmed by the determination of the X-ray crystal structure of the H-NOX protein construct containing pCNF at site 5.
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Affiliation(s)
- Caroline Kearney
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Lukasz T Olenginski
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Trexler D Hirn
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Gwendolyn D Fowler
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Daniyal Tariq
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Scott H Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
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Varjani SJ, Gnansounou E. Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs. BIORESOURCE TECHNOLOGY 2017; 245:1258-1265. [PMID: 28844839 DOI: 10.1016/j.biortech.2017.08.028] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/05/2017] [Accepted: 08/07/2017] [Indexed: 06/07/2023]
Abstract
Petroleum is produced by thermal decay of buried organic material over millions of years. Petroleum oilfield ecosystems represent resource of reduced carbon which favours microbial growth. Therefore, it is obvious that many microorganisms have adapted to harsh environmental conditions of these ecosystems specifically temperature, oxygen availability and pressure. Knowledge of microorganisms present in ecosystems of petroleum oil reservoirs; their physiological and biological properties help in successful exploration of petroleum. Understanding microbiology of petroleum oilfield(s) can be used to enhance oil recovery, as microorganisms in oil reservoirs produce various metabolites viz. gases, acids, solvents, biopolymers and biosurfactants. The aim of this review is to discuss characteristics of petroleum oil reservoirs. This review also provides an updated literature on microbial ecology of these extreme ecosystems including microbial origin as well as various types of microorganisms such as methanogens; iron, nitrate and sulphate reducing bacteria, and fermentative microbes present in petroleum oilfield ecosystems.
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Affiliation(s)
- Sunita J Varjani
- Gujarat Pollution Control Board, Sector-10A, Gandhinagar 382010, Gujarat, India.
| | - Edgard Gnansounou
- Bioenergy and Energy Planning Research Group (BPE), IIC, ENAC, Station 18, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Pugazhendi A, Abbad Wazin H, Qari H, Basahi JMAB, Godon JJ, Dhavamani J. Biodegradation of low and high molecular weight hydrocarbons in petroleum refinery wastewater by a thermophilic bacterial consortium. ENVIRONMENTAL TECHNOLOGY 2017; 38:2381-2391. [PMID: 27852158 DOI: 10.1080/09593330.2016.1262460] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
Clean-up of contaminated wastewater remains to be a major challenge in petroleum refinery. Here, we describe the capacity of a bacterial consortium enriched from crude oil drilling site in Al-Khobar, Saudi Arabia, to utilize polycyclic aromatic hydrocarbons (PAHs) as sole carbon source at 60°C. The consortium reduced low molecular weight (LMW; naphthalene, phenanthrene, fluorene and anthracene) and high molecular weight (HMW; pyrene, benzo(e)pyrene and benzo(k)fluoranthene) PAH loads of up to 1.5 g/L with removal efficiencies of 90% and 80% within 10 days. PAH biodegradation was verified by the presence of PAH metabolites and evolution of carbon dioxide (90 ± 3%). Biodegradation led to a reduction of the surface tension to 34 ± 1 mN/m thus suggesting biosurfactant production by the consortium. Phylogenetic analysis of the consortium revealed the presence of the thermophilic PAH degrader Pseudomonas aeruginosa strain CEES1 (KU664514) and Bacillus thermosaudia (KU664515) strain CEES2. The consortium was further found to treat petroleum wastewater in continuous stirred tank reactor with 96 ± 2% chemical oxygen demand removal and complete PAH degradation in 24 days.
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Affiliation(s)
- Arulazhagan Pugazhendi
- a Center of Excellence in Environmental Studies , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Hadeel Abbad Wazin
- a Center of Excellence in Environmental Studies , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Huda Qari
- a Center of Excellence in Environmental Studies , King Abdulaziz University , Jeddah , Saudi Arabia
| | | | - Jean Jacques Godon
- b Laboratorie de Biotechnologie de l'Environnement , Institut National de la Recherche Agronomique , Narbonne , France
| | - Jeyakumar Dhavamani
- a Center of Excellence in Environmental Studies , King Abdulaziz University , Jeddah , Saudi Arabia
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Mechri S, Ben Elhoul Berrouina M, Omrane Benmrad M, Zaraî Jaouadi N, Rekik H, Moujehed E, Chebbi A, Sayadi S, Chamkha M, Bejar S, Jaouadi B. Characterization of a novel protease from Aeribacillus pallidus strain VP3 with potential biotechnological interest. Int J Biol Macromol 2017; 94:221-232. [DOI: 10.1016/j.ijbiomac.2016.09.112] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 09/16/2016] [Indexed: 12/19/2022]
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24
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Loder AJ, Zeldes BM, Conway JM, Counts JA, Straub CT, Khatibi PA, Lee LL, Vitko NP, Keller MW, Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Adams MW, Kelly RM. Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Andrew J. Loder
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Benjamin M. Zeldes
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Jonathan M. Conway
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - James A. Counts
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Christopher T. Straub
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Piyum A. Khatibi
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Laura L. Lee
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Nicholas P. Vitko
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Matthew W. Keller
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Amanda M. Rhaesa
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gabe M. Rubinstein
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Israel M. Scott
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gina L. Lipscomb
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Michael W.W. Adams
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Robert M. Kelly
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
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25
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Hespen CW, Bruegger JJ, Phillips-Piro CM, Marletta MA. Structural and Functional Evidence Indicates Selective Oxygen Signaling in Caldanaerobacter subterraneus H-NOX. ACS Chem Biol 2016; 11:2337-46. [PMID: 27328180 DOI: 10.1021/acschembio.6b00431] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Acute and specific sensing of diatomic gas molecules is an essential facet of biological signaling. Heme nitric oxide/oxygen binding (H-NOX) proteins are a family of gas sensors found in diverse classes of bacteria and eukaryotes. The most commonly characterized bacterial H-NOX domains are from facultative anaerobes and are activated through a conformational change caused by formation of a 5-coordinate Fe(II)-NO complex. Members of this H-NOX subfamily do not bind O2 and therefore can selectively ligate NO even under aerobic conditions. In contrast, H-NOX domains encoded by obligate anaerobes do form stable 6-coordinate Fe(II)-O2 complexes by utilizing a conserved H-bonding network in the ligand-binding pocket. The biological function of O2-binding H-NOX domains has not been characterized. In this work, the crystal structures of an O2-binding H-NOX domain from the thermophilic obligate anaerobe Caldanaerobacter subterraneus (Cs H-NOX) in the Fe(II)-NO, Fe(II)-CO, and Fe(II)-unliganded states are reported. The Fe(II)-unliganded structure displays a conformational shift distinct from the NO-, CO-, and previously reported O2-coordinated structures. In orthogonal signaling assays using Cs H-NOX and the H-NOX signaling effector histidine kinase from Vibrio cholerae (Vc HnoK), Cs H-NOX regulates Vc HnoK in an O2-dependent manner and requires the H-bonding network to distinguish O2 from other ligands. The crystal structures of Fe(II) unliganded and NO- and CO-bound Cs H-NOX combined with functional assays herein provide the first evidence that H-NOX proteins from obligate anaerobes can serve as O2 sensors.
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Affiliation(s)
- Charles W. Hespen
- Department
of Molecular and Cell Biology, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
| | - Joel J. Bruegger
- QB3
Institute, University of California—Berkeley, 356 Stanley Hall, Berkeley, California, 94720-3220, United States
| | - Christine M. Phillips-Piro
- Department of Chemistry, HAC 416 Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, United States
| | - Michael A. Marletta
- Department
of Molecular and Cell Biology, University of California—Berkeley, 356 Stanley Hall, Berkeley, California 94720-3220, United States
- Department
of Chemistry Department of Molecular and Cell Biology QB3 Institute, University of California—Berkeley, 374B Stanley Hall, Berkeley, California 94720-3220, United States
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26
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Radnagurueva AA, Lavrentieva EV, Budagaeva VG, Barkhutova DD, Dunaevsky YE, Namsaraev BB. Organotrophic bacteria of the Baikal Rift Zone hot springs. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716030103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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27
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Peng T, Pan S, Christopher LP, Sparling R, Levin DB. Growth and metabolic profiling of the novel thermophilic bacterium Thermoanaerobacter sp. strain YS13. Can J Microbiol 2016; 62:762-71. [PMID: 27569998 DOI: 10.1139/cjm-2016-0040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A strictly anaerobic, thermophilic bacterium, designated strain YS13, was isolated from a geothermal hot spring. Phylogenetic analysis using the 16S rRNA genes and cpn60 UT genes suggested strain YS13 as a species of Thermoanaerobacter. Using cellobiose or xylose as carbon source, YS13 was able to grow over a wide range of temperatures (45-70 °C), and pHs (pH 5.0-9.0), with optimum growth at 65 °C and pH 7.0. Metabolic profiling on cellobiose, glucose, or xylose in 1191 medium showed that H2, CO2, ethanol, acetate, and lactate were the major metabolites. Lactate was the predominant end product from glucose or cellobiose fermentations, whereas H2 and acetate were the dominant end products from xylose fermentation. The metabolic balance shifted away from ethanol to H2, acetate, and lactate when YS13 was grown on cellobiose as temperatures increased from 45 to 70 °C. When YS13 was grown on xylose, a metabolic shift from lactate to H2, CO2, and acetate was observed in cultures as the temperature of incubation increased from 45 to 65 °C, whereas a shift from ethanol and CO2 to H2, acetate, and lactate was observed in cultures incubated at 70 °C.
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Affiliation(s)
- Tingting Peng
- a Department of Food Science, Huazhong Agricultural University, Wuhan, China.,d Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 3N3, Canada
| | - Siyi Pan
- a Department of Food Science, Huazhong Agricultural University, Wuhan, China
| | - Lew P Christopher
- b Biorefining Research Institute, Lakehead University, Thunder Bay, ON P7B 5Z5, Canada
| | - Richard Sparling
- c Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 3N3, Canada
| | - David B Levin
- d Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 3N3, Canada
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28
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Diender M, Stams AJM, Sousa DZ. Pathways and Bioenergetics of Anaerobic Carbon Monoxide Fermentation. Front Microbiol 2015; 6:1275. [PMID: 26635746 PMCID: PMC4652020 DOI: 10.3389/fmicb.2015.01275] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/31/2015] [Indexed: 11/29/2022] Open
Abstract
Carbon monoxide can act as a substrate for different modes of fermentative anaerobic metabolism. The trait of utilizing CO is spread among a diverse group of microorganisms, including members of bacteria as well as archaea. Over the last decade this metabolism has gained interest due to the potential of converting CO-rich gas, such as synthesis gas, into bio-based products. Three main types of fermentative CO metabolism can be distinguished: hydrogenogenesis, methanogenesis, and acetogenesis, generating hydrogen, methane and acetate, respectively. Here, we review the current knowledge on these three variants of microbial CO metabolism with an emphasis on the potential enzymatic routes and bio-energetics involved.
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Affiliation(s)
- Martijn Diender
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands ; Centre of Biological Engineering, University of Minho Braga, Portugal
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
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29
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Sant'Anna FH, Lebedinsky AV, Sokolova TG, Robb FT, Gonzalez JM. Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity. BMC Genomics 2015; 16:757. [PMID: 26446804 PMCID: PMC4596419 DOI: 10.1186/s12864-015-1955-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/19/2015] [Indexed: 11/22/2022] Open
Abstract
Background The Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products. In this study, comprehensive analysis of three genomes of C. subterraneus subspecies was carried in order to identify genes encoding key metabolic enzymes and to document the genomic basis for the evolution of these organisms. Methods Average nucleotide identity and in silico DNA relatedness were estimated for the studied C. subterraneus genomes. Genome synteny was evaluated using R2CAT software. Protein conservation was analyzed using mGenome Subtractor. Horizontal gene transfer was predicted through the GOHTAM pipeline (using tetranucleotide composition) and phylogenetic analyses (by maximum likelihood). Hydrolases were identified through the MEROPS and CAZy platforms. Results The three genomes of C. subterraneus showed high similarity, although there are substantial differences in their gene composition and organization. Each subspecies possesses a gene cluster encoding a carbon monoxide dehydrogenase (CODH) and an energy converting hydrogenase (ECH). The CODH gene is associated with an operon that resembles the Escherichia coli hydrogenase hyc/hyf operons, a novel genetic context distinct from that found in archetypical hydrogenogenic carboxydotrophs. Apart from the CODH-associated hydrogenase, these bacteria also contain other hydrogenases, encoded by ech and hyd genes. An Mbx ferredoxin:NADP oxidoreductase homolog similar to that originally described in the archaeon Pyrococcus furiosus was uniquely encoded in the C. subterraneus subsp. yonseiensis genome. Compositional analysis demonstrated that some genes of the CODH-ECH and mbx operons present distinct sequence patterns in relation to the majority of the other genes of each genome. Phylogenetic reconstructions of the genes from these operons and those from the ech operon are incongruent to the species tree. Notably, the cooS gene of C. subterraneus subsp. pacificus and its homologs in C. subterraneus subsp. tengcongensis and C. subterraneus subsp. yonseiensis form distinct clades. The strains have diverse hydrolytic enzymes and they appear to be proteolytic and glycolytic. Divergent glycosidases from 14 families, among them amylases, chitinases, alpha-glucosidases, beta-glucosidases, and cellulases, were identified. Each of the three genomes also contains around 100 proteases from 50 subfamilies, as well about ten different esterases. Conclusions Genomic information suggests that multiple horizontal gene transfers conferred the adaptation of C. subterraneus subspecies to extreme niches throughout the carbon monoxide utilization and hydrogen production. The variety of hydrolases found in their genomes indicate the versatility of the species in obtaining energy and carbon from diverse substrates, therefore these organisms constitute a remarkable resource of enzymes with biotechnological potential. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1955-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- F H Sant'Anna
- Institute of Natural Resources and Agrobiology, Spanish Council for Research, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012, Sevilla, Spain. .,CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, 70040-020, Brazil.
| | - A V Lebedinsky
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312, Moscow, Russia.
| | - T G Sokolova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312, Moscow, Russia.
| | - F T Robb
- Department of Microbiology and Immunology, University of Maryland and Institute of Marine and Environmental Technology, 701 E Pratt Street, Baltimore, MD, 21202, USA.
| | - J M Gonzalez
- Institute of Natural Resources and Agrobiology, Spanish Council for Research, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012, Sevilla, Spain.
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30
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Zuo G, Hao B. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy. GENOMICS, PROTEOMICS & BIOINFORMATICS 2015; 13:321-31. [PMID: 26563468 PMCID: PMC4678791 DOI: 10.1016/j.gpb.2015.08.004] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 08/10/2015] [Indexed: 01/15/2023]
Abstract
A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/ without login requirements.
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Affiliation(s)
- Guanghong Zuo
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China
| | - Bailin Hao
- T-Life Research Center, Department of Physics, Fudan University, Shanghai 200433, China.
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31
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Scully SM, Iloranta P, Myllymaki P, Orlygsson J. Branched-chain alcohol formation by thermophilic bacteria within the genera of Thermoanaerobacter and Caldanaerobacter. Extremophiles 2015; 19:809-18. [PMID: 25997396 DOI: 10.1007/s00792-015-0756-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/10/2015] [Indexed: 11/30/2022]
Abstract
Fifty-six thermophilic strains including members of Caldanaerobacter, Caldicellulosiruptor, Caloramator, Clostridium, Thermoanaerobacter, and Thermoanaerobacterium, were investigated for branched-chain amino acid degradation in the presence of thiosulfate in batch culture. All of the Thermoanaerobacter and Caldanaerobacter strains (24) degraded the branched-chain amino acids (leucine, isoleucine, and valine) to a mixture of their corresponding branched-chain fatty acids and branched-chain alcohols. Only one Caloramator strain degraded the branched-chain amino acids to the corresponding branched-chain fatty acids. The ratio of branched-chain fatty acid production over branched-chain alcohol production for Thermoanaerobacter was 7.15, 6.61, and 11.53 for leucine, isoleucine, and valine, respectively. These values for Caldanaerobacter were 3.49, 4.13, and 7.31, respectively. This indicates that members within Caldanaerobacter produce proportionally more of the alcohols as compared with Thermoanaerobacter. No species within other genera investigated produced branched-chain alcohols from branched-chain amino acids in the presence of thiosulfate.
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Affiliation(s)
- Sean M Scully
- Faculty of Natural Resource Sciences, University of Akureyri, Nordurslod 2, Borgir, 600, Akureyri, Iceland
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32
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Rathi R, Lavania M, Sawale M, Kukreti V, Kumar S, Lal B. Stimulation of an indigenous thermophillic anaerobic bacterial consortium for enhanced oil recovery. RSC Adv 2015. [DOI: 10.1039/c5ra10489k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Production of gases, VFAs, solvents and surfactants was achieved by thermophilic methanogenic consortium TERIL63, showing reduction in surface tension from 69 to 35 dynes cm−1. TERIL63 with an optimized nutrient recipe showed 15.49% EOR at 70 °C in a core flood study.
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Affiliation(s)
- Rohit Rathi
- Microbial Biotechnology
- Environmental and Industrial Biotechnology Division
- The Energy and Resources Institute (TERI)
- New Delhi 110003
- India
| | - Meeta Lavania
- Microbial Biotechnology
- Environmental and Industrial Biotechnology Division
- The Energy and Resources Institute (TERI)
- New Delhi 110003
- India
| | | | - Vipin Kukreti
- Institute of Reservoir Studies
- Oil and Natural Gas Corporation Limited
- Ahmedabad
- India
| | - Subir Kumar
- Institute of Reservoir Studies
- Oil and Natural Gas Corporation Limited
- Ahmedabad
- India
| | - Banwari Lal
- Microbial Biotechnology
- Environmental and Industrial Biotechnology Division
- The Energy and Resources Institute (TERI)
- New Delhi 110003
- India
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33
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Rittmann SKM, Lee HS, Lim JK, Kim TW, Lee JH, Kang SG. One-carbon substrate-based biohydrogen production: Microbes, mechanism, and productivity. Biotechnol Adv 2015; 33:165-177. [DOI: 10.1016/j.biotechadv.2014.11.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/10/2014] [Accepted: 11/11/2014] [Indexed: 11/28/2022]
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34
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Zeng X, Zhang Z, Li X, Zhang X, Cao J, Jebbar M, Alain K, Shao Z. Anoxybacter fermentans gen. nov., sp. nov., a piezophilic, thermophilic, anaerobic, fermentative bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2014; 65:710-715. [PMID: 25505345 DOI: 10.1099/ijs.0.068221-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel piezophilic, thermophilic, anaerobic, fermentative bacterial strain, designated strain DY22613(T), was isolated from a deep-sea hydrothermal sulfide deposit at the East Pacific Rise (GPS position: 102.6° W 3.1° S). Cells of strain DY22613(T) were long, motile rods (10 to 20 µm in length and 0.5 µm in width) with peritrichous flagella and were Gram-stain-negative. Growth was recorded at 44-72 °C (optimum 60-62 °C) and at hydrostatic pressures of 0.1-55 MPa (optimum 20 MPa). The pH range for growth was from pH 5.0 to 9.0 with an optimum at pH 7.0. Growth was observed in the presence of 1 to 8 % (w/v) sea salts and 0.65 to 5.2 % (w/v) NaCl, with optimum salt concentrations at 3.5 % for sea salts and at 2.3 % for NaCl. Under optimal growth conditions, the shortest generation time observed was 27 min (60 °C, 20 MPa). Strain DY22613(T) was heterotrophic, able to utilize complex organic compounds, amino acids, sugars and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamine, methionine, phenylalanine, serine, threonine, fructose, fucose, galactose, gentiobiose, glucose, mannose, melibiose, palatinose, rhamnose, turanose, pyruvate, lactic acid, methyl ester, erythritol, galacturonic acid and glucosaminic acid. Strain DY22613(T) was able to reduce Fe(III) compounds, including Fe(III) oxyhydroxide (pH 7.0), amorphous iron(III) oxide (pH 9.0), goethite (α-FeOOH, pH 12.0), Fe(III) citrate and elementary sulfur. Products of fermentation were butyrate, acetate and hydrogen. Main cellular fatty acids were iso-C15 : 0, iso-C14 : 0 3-OH and C14 : 0. The genomic DNA G+C content of strain DY22613(T) was 36.7 mol%. Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class Clostridia and clusters with the order Haloanaerobiales (86.92 % 16S rRNA gene sequence similarity). The phylogenetic data suggest that the lineage represents at least a novel genus and species, for which the name Anoxybacter fermentans gen. nov., sp. nov. is proposed. The type strain is DY22613(T) ( = JCM 19466(T) = DSM 28033(T) = MCCC 1A06456(T)).
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Affiliation(s)
- Xiang Zeng
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Zhao Zhang
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Xi Li
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Xiaobo Zhang
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
| | - Junwei Cao
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China
| | - Mohamed Jebbar
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Karine Alain
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Zongze Shao
- Xiamen State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, Fujian 361005, PR China.,Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography SOA, Xiamen, Fujian 361005, PR China
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Piceno YM, Reid FC, Tom LM, Conrad ME, Bill M, Hubbard CG, Fouke BW, Graff CJ, Han J, Stringfellow WT, Hanlon JS, Hu P, Hazen TC, Andersen GL. Temperature and injection water source influence microbial community structure in four Alaskan North Slope hydrocarbon reservoirs. Front Microbiol 2014; 5:409. [PMID: 25147549 PMCID: PMC4124708 DOI: 10.3389/fmicb.2014.00409] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 07/18/2014] [Indexed: 11/29/2022] Open
Abstract
A fundamental knowledge of microbial community structure in petroleum reservoirs can improve predictive modeling of these environments. We used hydrocarbon profiles, stable isotopes, and high-density DNA microarray analysis to characterize microbial communities in produced water from four Alaskan North Slope hydrocarbon reservoirs. Produced fluids from Schrader Bluff (24–27°C), Kuparuk (47–70°C), Sag River (80°C), and Ivishak (80–83°C) reservoirs were collected, with paired soured/non-soured wells sampled from Kuparuk and Ivishak. Chemical and stable isotope data suggested Schrader Bluff had substantial biogenic methane, whereas methane was mostly thermogenic in deeper reservoirs. Acetoclastic methanogens (Methanosaeta) were most prominent in Schrader Bluff samples, and the combined δD and δ13C values of methane also indicated acetoclastic methanogenesis could be a primary route for biogenic methane. Conversely, hydrogenotrophic methanogens (e.g., Methanobacteriaceae) and sulfide-producing Archaeoglobus and Thermococcus were more prominent in Kuparuk samples. Sulfide-producing microbes were detected in all reservoirs, uncoupled from souring status (e.g., the non-soured Kuparuk samples had higher relative abundances of many sulfate-reducers compared to the soured sample, suggesting sulfate-reducers may be living fermentatively/syntrophically when sulfate is limited). Sulfate abundance via long-term seawater injection resulted in greater relative abundances of Desulfonauticus, Desulfomicrobium, and Desulfuromonas in the soured Ivishak well compared to the non-soured well. In the non-soured Ivishak sample, several taxa affiliated with Thermoanaerobacter and Halomonas predominated. Archaea were not detected in the deepest reservoirs. Functional group taxa differed in relative abundance among reservoirs, likely reflecting differing thermal and/or geochemical influences.
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Affiliation(s)
- Yvette M Piceno
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Francine C Reid
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Lauren M Tom
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Mark E Conrad
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Markus Bill
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Christopher G Hubbard
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Bruce W Fouke
- Energy Biosciences Institute Berkeley, CA, USA ; Department of Geology, University of Illinois at Urbana-Champaign, Urbana-Champaign IL, USA
| | - Craig J Graff
- Production Chemistry, BP Exploration Anchorage, AK, USA
| | - Jiabin Han
- Production Chemistry, BP Exploration Anchorage, AK, USA
| | - William T Stringfellow
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA ; Ecological Engineering Research Program, University of the Pacific Stockton, CA, USA
| | - Jeremy S Hanlon
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Ecological Engineering Research Program, University of the Pacific Stockton, CA, USA
| | - Ping Hu
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee Knoxville, TN, USA
| | - Gary L Andersen
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Energy Biosciences Institute Berkeley, CA, USA
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Zhang F, Zhang Y, Ding J, Dai K, van Loosdrecht MCM, Zeng RJ. Stable acetate production in extreme-thermophilic (70°C) mixed culture fermentation by selective enrichment of hydrogenotrophic methanogens. Sci Rep 2014; 4:5268. [PMID: 24920064 PMCID: PMC4053707 DOI: 10.1038/srep05268] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/20/2014] [Indexed: 11/09/2022] Open
Abstract
The control of metabolite production is difficult in mixed culture fermentation. This is particularly related to hydrogen inhibition. In this work, hydrogenotrophic methanogens were selectively enriched to reduce the hydrogen partial pressure and to realize efficient acetate production in extreme-thermophilic (70°C) mixed culture fermentation. The continuous stirred tank reactor (CSTR) was stable operated during 100 days, in which acetate accounted for more than 90% of metabolites in liquid solutions. The yields of acetate, methane and biomass in CSTR were 1.5 ± 0.06, 1.0 ± 0.13 and 0.4 ± 0.05 mol/mol glucose, respectively, close to the theoretical expected values. The CSTR effluent was stable and no further conversion occurred when incubated for 14 days in a batch reactor. In fed-batch experiments, acetate could be produced up to 34.4 g/L, significantly higher than observed in common hydrogen producing fermentations. Acetate also accounted for more than 90% of soluble products formed in these fed-batch fermentations. The microbial community analysis revealed hydrogenotrophic methanogens (mainly Methanothermobacter thermautotrophicus and Methanobacterium thermoaggregans) as 98% of Archaea, confirming that high temperature will select hydrogenotrophic methanogens over aceticlastic methanogens effectively. This work demonstrated a potential application to effectively produce acetate as a value chemical and methane as an energy gas together via mixed culture fermentation.
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Affiliation(s)
- Fang Zhang
- 1] Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China [2] Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, People's Republic of China
| | - Yan Zhang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jing Ding
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Kun Dai
- Hebei Key Laboratory of Applied Chemistry, School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, People's Republic of China
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Raymond J Zeng
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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Draft Genome Sequence of an Anaerobic and Extremophilic Bacterium, Caldanaerobacter yonseiensis, Isolated from a Geothermal Hot Stream. GENOME ANNOUNCEMENTS 2013; 1:1/6/e00923-13. [PMID: 24201201 PMCID: PMC3820782 DOI: 10.1128/genomea.00923-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Caldanaerobacter yonseiensis is a strictly anaerobic, thermophilic, spore-forming bacterium, which was isolated from a geothermal hot stream in Indonesia. This bacterium utilizes xylose and produces a variety of proteases. Here, we report the draft genome sequence of C. yonseiensis, which reveals insights into the pentose phosphate pathway and protein degradation metabolism in thermophilic microorganisms.
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Tomás AF, Karakashev D, Angelidaki I. Thermoanaerobacter pentosaceus sp. nov., an anaerobic, extremely thermophilic, high ethanol-yielding bacterium isolated from household waste. Int J Syst Evol Microbiol 2013. [DOI: 10.1099/ijs.0.045211-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extremely thermophilic, xylanolytic, spore-forming and strictly anaerobic bacterium, strain DTU01T, was isolated from a continuously stirred tank reactor fed with xylose and household waste. Cells stained Gram-negative and were rod-shaped (0.5–2 µm in length). Spores were terminal with a diameter of approximately 0.5 µm. Optimal growth occurred at 70 °C and pH 7, with a maximum growth rate of 0.1 h−1. DNA G+C content was 34.2 mol%. Strain DTU01T could ferment arabinose, cellobiose, fructose, galactose, glucose, lactose, mannitol, mannose, melibiose, pectin, starch, sucrose, xylan, yeast extract and xylose, but not cellulose, Avicel, inositol, inulin, glycerol, rhamnose, acetate, lactate, ethanol, butanol or peptone. Ethanol was the major fermentation product and a maximum yield of 1.39 mol ethanol per mol xylose was achieved when sulfite was added to the cultivation medium. Thiosulfate, but not sulfate, nitrate or nitrite, could be used as electron acceptor. On the basis of 16S rRNA gene sequence similarity, strain DTU01T was shown to be closely related to
Thermoanaerobacter mathranii
A3T,
Thermoanaerobacter italicus
Ab9T and
Thermoanaerobacter thermocopriae
JT3-3T, with 98–99 % similarity. Despite this, the physiological and phylogenetic differences (DNA G+C content, substrate utilization, electron acceptors, phylogenetic distance and isolation site) allow for the proposal of strain DTU01T as a representative of a novel species within the genus
Thermoanaerobacter
, for which the name Thermoanaerobacter pentosaceus sp. nov. is proposed, with the type strain DTU01T ( = DSM 25963T = KCTC 4529T = VKM B-2752T = CECT 8142T).
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Affiliation(s)
- Ana Faria Tomás
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej 113, 2800 Kongens Lyngby, Denmark
| | - Dimitar Karakashev
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej 113, 2800 Kongens Lyngby, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Miljoevej 113, 2800 Kongens Lyngby, Denmark
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André S, Zuber F, Remize F. Thermophilic spore-forming bacteria isolated from spoiled canned food and their heat resistance. Results of a French ten-year survey. Int J Food Microbiol 2013; 165:134-43. [DOI: 10.1016/j.ijfoodmicro.2013.04.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 11/25/2022]
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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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Verbeke TJ, Zhang X, Henrissat B, Spicer V, Rydzak T, Krokhin OV, Fristensky B, Levin DB, Sparling R. Genomic evaluation of Thermoanaerobacter spp. for the construction of designer co-cultures to improve lignocellulosic biofuel production. PLoS One 2013; 8:e59362. [PMID: 23555660 PMCID: PMC3608648 DOI: 10.1371/journal.pone.0059362] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/13/2013] [Indexed: 02/07/2023] Open
Abstract
The microbial production of ethanol from lignocellulosic biomass is a multi-component process that involves biomass hydrolysis, carbohydrate transport and utilization, and finally, the production of ethanol. Strains of the genus Thermoanaerobacter have been studied for decades due to their innate abilities to produce comparatively high ethanol yields from hemicellulose constituent sugars. However, their inability to hydrolyze cellulose, limits their usefulness in lignocellulosic biofuel production. As such, co-culturing Thermoanaerobacter spp. with cellulolytic organisms is a plausible approach to improving lignocellulose conversion efficiencies and yields of biofuels. To evaluate native lignocellulosic ethanol production capacities relative to competing fermentative end-products, comparative genomic analysis of 11 sequenced Thermoanaerobacter strains, including a de novo genome, Thermoanaerobacter thermohydrosulfuricus WC1, was conducted. Analysis was specifically focused on the genomic potential for each strain to address all aspects of ethanol production mentioned through a consolidated bioprocessing approach. Whole genome functional annotation analysis identified three distinct clades within the genus. The genomes of Clade 1 strains encode the fewest extracellular carbohydrate active enzymes and also show the least diversity in terms of lignocellulose relevant carbohydrate utilization pathways. However, these same strains reportedly are capable of directing a higher proportion of their total carbon flux towards ethanol, rather than non-biofuel end-products, than other Thermoanaerobacter strains. Strains in Clade 2 show the greatest diversity in terms of lignocellulose hydrolysis and utilization, but proportionately produce more non-ethanol end-products than Clade 1 strains. Strains in Clade 3, in which T. thermohydrosulfuricus WC1 is included, show mid-range potential for lignocellulose hydrolysis and utilization, but also exhibit extensive divergence from both Clade 1 and Clade 2 strains in terms of cellular energetics. The potential implications regarding strain selection and suitability for industrial ethanol production through a consolidated bioprocessing co-culturing approach are examined throughout the manuscript.
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Affiliation(s)
- Tobin J. Verbeke
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Xiangli Zhang
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Bernard Henrissat
- Centre national de la recherche scientifique, Aix-Marseille Université, Marseille, France
| | - Vic Spicer
- Department of Physics & Astronomy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Thomas Rydzak
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Oleg V. Krokhin
- Department of Internal Medicine & Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brian Fristensky
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David B. Levin
- Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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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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Li YL. Hexagonal platelet-like magnetite as a biosignature of thermophilic iron-reducing bacteria and its applications to the exploration of the modern deep, hot biosphere and the emergence of iron-reducing bacteria in early precambrian oceans. ASTROBIOLOGY 2012; 12:1100-8. [PMID: 23145573 PMCID: PMC3522128 DOI: 10.1089/ast.2012.0847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 08/26/2012] [Indexed: 05/19/2023]
Abstract
Dissimilatory iron-reducing bacteria are able to enzymatically reduce ferric iron and couple to the oxidation of organic carbon. This mechanism induces the mineralization of fine magnetite crystals characterized by a wide distribution in size and irregular morphologies that are indistinguishable from authigenic magnetite. Thermoanaerobacter are thermophilic iron-reducing bacteria that predominantly inhabit terrestrial hot springs or deep crusts and have the capacity to transform amorphous ferric iron into magnetite with a size up to 120 nm. In this study, I first characterize the formation of hexagonal platelet-like magnetite of a few hundred nanometers in cultures of Thermoanaerobacter spp. strain TOR39. Biogenic magnetite with such large crystal sizes and unique morphology has never been observed in abiotic or biotic processes and thus can be considered as a potential biosignature for thermophilic iron-reducing bacteria. The unique crystallographic features and strong ferrimagnetic properties of these crystals allow easy and rapid screening for the previous presence of iron-reducing bacteria in deep terrestrial crustal samples that are unsuitable for biological detection methods and, also, the search for biogenic magnetite in banded iron formations that deposited only in the first 2 billion years of Earth with evidence of life.
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Affiliation(s)
- Yi-Liang Li
- Department of Earth Sciences, The University of Hong Kong , Hong Kong.
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Production of ethanol from sugars and lignocellulosic biomass by Thermoanaerobacter J1 isolated from a hot spring in Iceland. J Biomed Biotechnol 2012; 2012:186982. [PMID: 23118498 PMCID: PMC3484324 DOI: 10.1155/2012/186982] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/16/2012] [Accepted: 09/04/2012] [Indexed: 11/17/2022] Open
Abstract
Thermophilic bacteria have gained increased attention as candidates for bioethanol production from lignocellulosic biomass. This study investigated ethanol production by Thermoanaerobacter strain J1 from hydrolysates made from lignocellulosic biomass in batch cultures. The effect of increased initial glucose concentration and the partial pressure of hydrogen on end product formation were examined. The strain showed a broad substrate spectrum, and high ethanol yields were observed on glucose (1.70 mol/mol) and xylose (1.25 mol/mol). Ethanol yields were, however, dramatically lowered by adding thiosulfate or by cocultivating strain J1 with a hydrogenotrophic methanogen with acetate becoming the major end product. Ethanol production from 4.5 g/L of lignocellulosic biomass hydrolysates (grass, hemp stem, wheat straw, newspaper, and cellulose) pretreated with acid or alkali and the enzymes Celluclast and Novozymes 188 was investigated. The highest ethanol yields were obtained on cellulose (7.5 mM·g−1) but the lowest on straw (0.8 mM·g−1). Chemical pretreatment increased ethanol yields substantially from lignocellulosic biomass but not from cellulose. The largest increase was on straw hydrolysates where ethanol production increased from 0.8 mM·g−1 to 3.3 mM·g−1 using alkali-pretreated biomass. The highest ethanol yields on lignocellulosic hydrolysates were observed with hemp hydrolysates pretreated with acid, 4.2 mM·g−1.
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Verbeke TJ, Dumonceaux TJ, Wushke S, Cicek N, Levin DB, Sparling R. Isolates of Thermoanaerobacter thermohydrosulfuricus from decaying wood compost display genetic and phenotypic microdiversity. FEMS Microbiol Ecol 2011; 78:473-87. [PMID: 22066958 DOI: 10.1111/j.1574-6941.2011.01181.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 07/21/2011] [Accepted: 07/24/2011] [Indexed: 11/28/2022] Open
Abstract
In this study, 12 strains of Thermoanaerobacter were isolated from a single decaying wood compost sample and subjected to genetic and phenotypic profiling. The 16S rRNA encoding gene sequences suggested that the isolates were most similar to strains of either Thermoanaerobacter pseudethanolicus or Thermoanaerobacter thermohydrosulfuricus. Examination of the lesser conserved chaperonin-60 (cpn60) universal target showed that some isolates shared the highest sequence identity with T. thermohydrosulfuricus; however, others to Thermoanaerobacter wiegelii and Thermoanaerobacter sp. Rt8.G4 (formerly Thermoanaerobacter brockii Rt8.G4). BOX-PCR fingerprinting profiles identified differences in the banding patterns not only between the isolates and the reference strains, but also among the isolates themselves. To evaluate the extent these genetic differences were manifested phenotypically, the utilization patterns of 30 carbon substrates were examined and the niche overlap indices (NOI) calculated. Despite showing a high NOI (> 0.9), significant differences existed in the substrate utilization capabilities of the isolates suggesting that either a high degree of niche specialization or mechanisms allowing for non-competitive co-existence, were present within this ecological context. Growth studies showed that the isolates were physiologically distinct in both growth rate and the fermentation product ratios. Our data indicate that phenotypic diversity exists within genetically microdiverse Thermoanaerobacter isolates from a common environment.
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Affiliation(s)
- Tobin J Verbeke
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Enzymatic properties and substrate specificity of the trehalose phosphorylase from Caldanaerobacter subterraneus. Appl Environ Microbiol 2011; 77:6939-44. [PMID: 21803886 DOI: 10.1128/aem.05190-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A putative glycoside phosphorylase from Caldanaerobacter subterraneus subsp. pacificus was recombinantly expressed in Escherichia coli, after codon optimization and chemical synthesis of the encoding gene. The enzyme was purified by His tag chromatography and was found to be specifically active toward trehalose, with an optimal temperature of 80°C. In addition, no loss of activity could be detected after 1 h of incubation at 65°C, which means that it is the most stable trehalose phosphorylase reported so far. The substrate specificity was investigated in detail by measuring the relative activity on a range of alternative acceptors, applied in the reverse synthetic reaction, and determining the kinetic parameters for the best acceptors. These results were rationalized based on the enzyme-substrate interactions observed in a homology model with a docked ligand. The specificity for the orientation of the acceptor's hydroxyl groups was found to decrease in the following order: C-3 > C-2 > C-4. This results in a particularly high activity on the monosaccharides d-fucose, d-xylose, l-arabinose, and d-galactose, as well as on l-fucose. However, determination of the kinetic parameters revealed that these acceptors bind less tightly in the active site than the natural acceptor d-glucose, resulting in drastically increased K(m) values. Nevertheless, the enzyme's high thermostability and broad acceptor specificity make it a valuable candidate for industrial disaccharide synthesis.
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Verbeke TJ, Sparling R, Hill JE, Links MG, Levin D, Dumonceaux TJ. Predicting relatedness of bacterial genomes using the chaperonin-60 universal target (cpn60 UT): application to Thermoanaerobacter species. Syst Appl Microbiol 2011; 34:171-9. [PMID: 21392917 DOI: 10.1016/j.syapm.2010.11.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/27/2010] [Accepted: 11/12/2010] [Indexed: 10/18/2022]
Abstract
D.R. Zeigler determined that the sequence identity of bacterial genomes can be predicted accurately using the sequence identities of a corresponding set of genes that meet certain criteria [32]. This three-gene model for comparing bacterial genome pairs requires the determination of the sequence identities for recN, thdF, and rpoA. This involves the generation of approximately 4.2kb of genomic DNA sequence from each organism to be compared, and also normally requires that oligonucleotide primers be designed for amplification and sequencing based on the sequences of closely related organisms. However, we have developed an analogous mathematical model for predicting the sequence identity of whole genomes based on the sequence identity of the 542-567 base pair chaperonin-60 universal target (cpn60 UT). The cpn60 UT is accessible in nearly all bacterial genomes with a single set of universal primers, and its length is such that it can be completely sequenced in one pair of overlapping sequencing reads via di-deoxy sequencing. These mathematical models were applied to a set of Thermoanaerobacter isolates from a wood chip compost pile and it was shown that both the one-gene cpn60 UT-based model and the three-gene model based on recN, rpoA, and thdF predicted that these isolates could be classified as Thermoanaerobacter thermohydrosulfuricus. Furthermore, it was found that the genomic prediction model using cpn60 UT gave similar results to whole-genome sequence alignments over a broad range of taxa, suggesting that this method may have general utility for screening isolates and predicting their taxonomic affiliations.
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Affiliation(s)
- Tobin J Verbeke
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Kozina IV, Kublanov IV, Kolganova TV, Chernyh NA, Bonch-Osmolovskaya EA. Caldanaerobacter uzonensis sp. nov., an anaerobic, thermophilic, heterotrophic bacterium isolated from a hot spring. Int J Syst Evol Microbiol 2010; 60:1372-1375. [DOI: 10.1099/ijs.0.012328-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An anaerobic thermophilic bacterium, strain K67T, was isolated from a terrestrial hot spring of Uzon Caldera, Kamchatka Peninsula. Analysis of the 16S rRNA gene sequence revealed that the novel isolate belongs to the genus Caldanaerobacter, with 95 % 16S rRNA gene sequence similarity to Caldanaerobacter subterraneus subsp. subterraneus SEBR 7858T, suggesting that it represents a novel species of the genus Caldanaerobacter. Strain K67T was characterized as an obligate anaerobe, a thermophile (growth at 50–75 °С; optimum 68–70 °C), a neutrophile (growth at pH25 °C 4.8–8.0; optimum pH25 °C 6.8) and an obligate organotroph (growth by fermentation of various sugars, peptides and polysaccharides). Major fermentation products were acetate, H2 and CO2; ethanol, lactate and l-alanine were formed in smaller amounts. Thiosulfate stimulated growth and was reduced to hydrogen sulfide. Nitrate, sulfate, sulfite and elemental sulfur were not reduced and did not stimulate growth. Thus, according to the strain's phylogenetic position and phenotypic novelties (lower upper limit of temperature range for growth, the ability to grow on arabinose, the inability to reduce elemental sulfur and the formation of alanine as a minor fermentation product), the novel species Caldanaerobacter uzonensis sp. nov. is proposed, with the type strain K67T (=DSM 18923T =VKM В-2408T).
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Affiliation(s)
- Irina V. Kozina
- Winogradsky Institute of Microbiology Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - Tatyana V. Kolganova
- Bioengineering Center, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - Nikolai A. Chernyh
- Winogradsky Institute of Microbiology Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, 117312 Moscow, Russia
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Natural competence in Thermoanaerobacter and Thermoanaerobacterium species. Appl Environ Microbiol 2010; 76:4713-9. [PMID: 20472726 DOI: 10.1128/aem.00402-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Low-G+C thermophilic obligate anaerobes in the class Clostridia are considered among the bacteria most resistant to genetic engineering due to the difficulty of introducing foreign DNA, thus limiting the ability to study and exploit their native hydrolytic and fermentative capabilities. Here, we report evidence of natural genetic competence in 13 Thermoanaerobacter and Thermoanaerobacterium strains previously believed to be difficult to transform or genetically recalcitrant. In Thermoanaerobacterium saccharolyticum JW/SL-YS485, natural competence-mediated DNA incorporation occurs during the exponential growth phase with both replicating plasmid and homologous recombination-based integration, and circular or linear DNA. In T. saccharolyticum, disruptions of genes similar to comEA, comEC, and a type IV pilus (T4P) gene operon result in strains unable to incorporate further DNA, suggesting that natural competence occurs via a conserved Gram-positive mechanism. The relative ease of employing natural competence for gene transfer should foster genetic engineering in these industrially relevant organisms, and understanding the mechanisms underlying natural competence may be useful in increasing the applicability of genetic tools to difficult-to-transform organisms.
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