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Karnachuk OV, Panova IA, Panov VL, Ikkert OP, Kadnikov VV, Rusanov II, Avakyan MR, Glukhova LB, Lukina AP, Rakitin AV, Begmatov S, Beletsky AV, Pimenov NV, Ravin NV. Active Sulfate-Reducing Bacterial Community in the Camel Gut. Microorganisms 2023; 11:microorganisms11020401. [PMID: 36838366 PMCID: PMC9963290 DOI: 10.3390/microorganisms11020401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/18/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
The diversity and activity of sulfate-reducing bacteria (SRB) in the camel gut remains largely unexplored. An abundant SRB community has been previously revealed in the feces of Bactrian camels (Camelus bactrianus). This study aims to combine the 16S rRNA gene profiling, sulfate reduction rate (SRR) measurement with a radioactive tracer, and targeted cultivation to shed light on SRB activity in the camel gut. Fresh feces of 55 domestic Bactrian camels grazing freely on semi-arid mountain pastures in the Kosh-Agach district of the Russian Altai area were analyzed. Feces were sampled in early winter at an ambient temperature of -15 °C, which prevented possible contamination. SRR values measured with a radioactive tracer in feces were relatively high and ranged from 0.018 to 0.168 nmol S cm-3 day-1. The 16S rRNA gene profiles revealed the presence of Gram-negative Desulfovibrionaceae and spore-forming Desulfotomaculaceae. Targeted isolation allowed us to obtain four pure culture isolates belonging to Desulfovibrio and Desulforamulus. An active SRB community may affect the iron and copper availability in the camel intestine due to metal ions precipitation in the form of sparingly soluble sulfides. The copper-iron sulfide, chalcopyrite (CuFeS2), was detected by X-ray diffraction in 36 out of 55 analyzed camel feces. In semi-arid areas, gypsum, like other evaporite sulfates, can be used as a solid-phase electron acceptor for sulfate reduction in the camel gastrointestinal tract.
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Affiliation(s)
- Olga V. Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
- Correspondence:
| | - Inna A. Panova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Vasilii L. Panov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Olga P. Ikkert
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, Russia
| | - Igor I. Rusanov
- Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Marat R. Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Lubov B. Glukhova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Anastasia P. Lukina
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Anatolii V. Rakitin
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, Russia
| | - Nikolai V. Pimenov
- Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, bld. 33-2, 119071 Moscow, Russia
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Park MJ, Kim YJ, Park M, Yu J, Namirimu T, Roh YR, Kwon KK. Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov. Front Microbiol 2022; 13:738205. [PMID: 35694308 PMCID: PMC9174804 DOI: 10.3389/fmicb.2022.738205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 04/11/2022] [Indexed: 01/14/2023] Open
Abstract
Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera (Alkalidesulfovibrio and Salidesulfovibrio) and one former invalid genus (“Psychrodesulfovibrio”) were officially proposed. Further, by applying the 95–96% average nucleotide identity (ANI) standard and the 70% digital DNA–DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes via in silico analysis, it was confirmed that most strains display metal tolerance.
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Affiliation(s)
- Mi-Jeong Park
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yun Jae Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | - Myeongkyu Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Jihyun Yu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Teddy Namirimu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yoo-Rim Roh
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
- *Correspondence: Kae Kyoung Kwon,
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Functional Interrelationships of Microorganisms in Iron-Based Anaerobic Wastewater Treatment. Microorganisms 2021; 9:microorganisms9051039. [PMID: 34065964 PMCID: PMC8151836 DOI: 10.3390/microorganisms9051039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
This study explicated the functional activities of microorganisms and their interrelationships under four previously reported iron reducing conditions to identify critical factors that governed the performance of these novel iron-dosed anaerobic biological wastewater treatment processes. Various iron-reducing bacteria (FeRB) and sulfate reducing bacteria (SRB) were identified as the predominant species that concurrently facilitated organics oxidation and the main contributors to removal of organics. The high organic contents of wastewater provided sufficient electron donors for active growth of both FeRB and SRB. In addition to the organic content, Fe (III) and sulfate concentrations (expressed by Fe/S ratio) were found to play a significant role in regulating the microbial abundance and functional activities. Various fermentative bacteria contributed to this FeRB-SRB synergy by fermenting larger organic compounds to smaller compounds, which were subsequently used by FeRB and SRB. Feammox (ferric reduction coupled to ammonium oxidation) bacterium was identified in the bioreactor fed with wastewater containing ammonium. Organic substrate level was a critical factor that regulated the competitive relationship between heterotrophic FeRB and Feammox bacteria. There were evidences that suggested a synergistic relationship between FeRB and nitrogen-fixing bacteria (NFB), where ferric iron and organics concentrations both promoted microbial activities of FeRB and NFB. A concept model was developed to illustrate the identified functional interrelationships and their governing factors for further development of the iron-based wastewater treatment systems.
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Sim MS, Skennerton CT, Orphan VJ. Physiological, genomic, and sulfur isotopic characterization of methanol metabolism by Desulfovibrio carbinolicus. PLoS One 2021; 16:e0245069. [PMID: 33444327 PMCID: PMC7808614 DOI: 10.1371/journal.pone.0245069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/21/2020] [Indexed: 11/25/2022] Open
Abstract
Methanol is often considered as a non-competitive substrate for methanogenic archaea, but an increasing number of sulfate-reducing microorganisms (SRMs) have been reported to be capable of respiring with methanol as an electron donor. A better understanding of the fate of methanol in natural or artificial anaerobic systems thus requires knowledge of the methanol dissimilation by SRMs. In this study, we describe the growth kinetics and sulfur isotope effects of Desulfovibrio carbinolicus, a methanol-oxidizing sulfate-reducing deltaproteobacterium, together with its genome sequence and annotation. D. carbinolicus can grow with a series of alcohols from methanol to butanol. Compared to longer-chain alcohols, however, specific growth and respiration rates decrease by several fold with methanol as an electron donor. Larger sulfur isotope fractionation accompanies slowed growth kinetics, indicating low chemical potential at terminal reductive steps of respiration. In a medium containing both ethanol and methanol, D. carbinolicus does not consume methanol even after the cessation of growth on ethanol. Among the two known methanol dissimilatory systems, the genome of D. carbinolicus contains the genes coding for alcohol dehydrogenase but lacks enzymes analogous to methanol methyltransferase. We analyzed the genomes of 52 additional species of sulfate-reducing bacteria that have been tested for methanol oxidation. There is no apparent relationship between phylogeny and methanol metabolizing capacity, but most gram-negative methanol oxidizers grow poorly, and none carry homologs for methyltransferase (mtaB). Although the amount of available data is limited, it is notable that more than half of the known gram-positive methanol oxidizers have both enzymatic systems, showing enhanced growth relative to the SRMs containing only alcohol dehydrogenase genes. Thus, physiological, genomic, and sulfur isotopic results suggest that D. carbinolicus and close relatives have the ability to metabolize methanol but likely play a limited role in methanol degradation in most natural environments.
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Affiliation(s)
- Min Sub Sim
- School of Earth and Environmental Sciences, Seoul National University, Seoul, South Korea
- * E-mail:
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
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Baffert C, Kpebe A, Avilan L, Brugna M. Hydrogenases and H 2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus. Adv Microb Physiol 2019; 74:143-189. [PMID: 31126530 DOI: 10.1016/bs.ampbs.2019.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
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Affiliation(s)
- Carole Baffert
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Arlette Kpebe
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Luisana Avilan
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Myriam Brugna
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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6
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The diversity of sulfate-reducing bacteria in the seven bioreactors. Arch Microbiol 2018; 200:945-950. [PMID: 29610938 DOI: 10.1007/s00203-018-1510-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Anaerobic technology has a wide scope of application in different areas such as manufacturing, food industry, and agriculture. Nowadays, it is mainly used to produce electrical and thermal energy from crop processing, solid waste treatment or wastewater treatment. More intensively, trend nowadays is usage of this technology biodegradable and biomass waste processing and biomethane or hydrogen production. In this paper, the diversities of sulfate-reducing bacteria (SRB) under different imputed raw material to the bioreactors were characterized. These diversities at the beginning of sampling and after cultivation were compared. Desulfovibrio, Desulfobulbus, and Desulfomicrobium genus as dominant among sulfate reducers in the bioreactors were detected. The Desulfobulbus species were dominant among other SRB genera before cultivation, but these bacteria were detected only in three out of the seven bioreactors after cultivation dominant.
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8
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Teng W, Liu G, Luo H, Zhang R, Xiang Y. Simultaneous sulfate and zinc removal from acid wastewater using an acidophilic and autotrophic biocathode. JOURNAL OF HAZARDOUS MATERIALS 2016; 304:159-165. [PMID: 26561748 DOI: 10.1016/j.jhazmat.2015.10.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/21/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
The aim of this study was to develop microbial electrolysis cell (MEC) with a novel acidophilic and autotrophic biocathode for treatment of acid wastewater. A biocathode was developed using acidophilic sulfate-reducing bacteria as the catalyst. Artificial wastewater with 200mgL(-1) sulfate and different Zn concentrations (0, 15, 25, and 40 mg L(-1)) was used as the MEC catholyte. The acidophilic biocathode dominated by Desulfovibrio sp. with an abundance of 66% (with 82% of Desulfovibrio sequences similar to Desulfovibrio simplex) and achieved a considerable sulfate reductive rate of 32 gm(-3)d(-1). With 15 mg L(-1) Zn added, the sulfate reductive rate of MEC improved by 16%. The formation of ZnS alleviated the inhibition from sulfide and sped the sulfate reduction. With 15 and 25 mgL(-1) Zn added, more than 99% of Zn was removed from the wastewater. Dissolved Zn ions in the catholyte were converted into insoluble Zn compounds, such as zinc sulfide and zinc hydroxide, due to the sulfide and elevated pH produced by sulfate reduction. The MEC with acidophilic and autotrophic biocathode can be used as an alternative to simultaneously remove sulfate and metals from acid wastewaters, such as acid mine drainage.
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Affiliation(s)
- Wenkai Teng
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Guangli Liu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Haiping Luo
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
| | - Renduo Zhang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Yinbo Xiang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
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Tarasov AL, Borzenkov IA. Sulfate-reducing bacteria of the genus Desulfovibrio from south vietnam seacoast. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715040165] [Citation(s) in RCA: 7] [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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10
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Sim MS, Bosak T, Ono S. Large Sulfur Isotope Fractionation Does Not Require Disproportionation. Science 2011; 333:74-7. [DOI: 10.1126/science.1205103] [Citation(s) in RCA: 420] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Peeters J, Vertommen J, Langhans I. Rate Constants of the Reactions of CF3O2, i-C3H7O2 and t-C4H9O2 with NO. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19920960339] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Unusual starch degradation pathway via cyclodextrins in the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain 7324. J Bacteriol 2007; 189:8901-13. [PMID: 17921308 DOI: 10.1128/jb.01136-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hyperthermophilic archaeon Archaeoglobus fulgidus strain 7324 has been shown to grow on starch and sulfate and thus represents the first sulfate reducer able to degrade polymeric sugars. The enzymes involved in starch degradation to glucose 6-phosphate were studied. In extracts of starch-grown cells the activities of the classical starch degradation enzymes, alpha-amylase and amylopullulanase, could not be detected. Instead, evidence is presented here that A. fulgidus utilizes an unusual pathway of starch degradation involving cyclodextrins as intermediates. The pathway comprises the combined action of an extracellular cyclodextrin glucanotransferase (CGTase) converting starch to cyclodextrins and the intracellular conversion of cyclodextrins to glucose 6-phosphate via cyclodextrinase (CDase), maltodextrin phosphorylase (Mal-P), and phosphoglucomutase (PGM). These enzymes, which are all induced after growth on starch, were characterized. CGTase catalyzed the conversion of starch to mainly beta-cyclodextrin. The gene encoding CGTase was cloned and sequenced and showed highest similarity to a glucanotransferase from Thermococcus litoralis. After transport of the cyclodextrins into the cell by a transport system to be defined, these molecules are linearized via a CDase, catalyzing exclusively the ring opening of the cyclodextrins to the respective maltooligodextrins. These are degraded by a Mal-P to glucose 1-phosphate. Finally, PGM catalyzes the conversion of glucose 1-phosphate to glucose 6-phosphate, which is further degraded to pyruvate via the modified Embden-Meyerhof pathway.
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Vandieken V, Knoblauch C, Jørgensen BB. Desulfovibrio frigidus sp. nov. and Desulfovibrio ferrireducens sp. nov., psychrotolerant bacteria isolated from Arctic fjord sediments (Svalbard) with the ability to reduce Fe(III). Int J Syst Evol Microbiol 2006; 56:681-685. [PMID: 16585676 DOI: 10.1099/ijs.0.64057-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strains 18T, 61T and 77 were isolated from two permanently cold fjord sediments on the west coast of Svalbard. The three psychrotolerant strains, with temperature optima at 20-23 degrees C, were able to grow at the freezing point of sea water, -2 degrees C. The strains oxidized important fermentation products such as hydrogen, formate and lactate with sulfate as the electron acceptor. Sulfate could be replaced by sulfite, thiosulfate or elemental sulfur. Poorly crystalline and soluble Fe(III) compounds were reduced in sulfate-free medium, but no growth occurred under these conditions. In the absence of electron acceptors, fermentative growth was possible. The pH optimum for the strains was around 7.1. The DNA G+C contents were 43.3 and 42.0 mol% for strains 18T and 61T, respectively. Strains 18T, 61T and 77 were most closely related to Desulfovibrio hydrothermalis (95.0-95.7 % 16S rRNA gene sequence similarity). Strains 18T and 77, exhibiting 99.9 % sequence similarity, represent a novel species for which the name Desulfovibrio frigidus sp. nov. is proposed. The type strain is strain 18T (=DSM 17176T = JCM 12924T). Strain 61T was closely related to strains 18T and 77 (97.6 and 97.5 % 16S rRNA gene sequence similarity), but on the basis of DNA-DNA hybridization strain 61T represents a novel species for which the name Desulfovibrio ferrireducens sp. nov. is proposed. The type strain is strain 61T (=DSM 16995T = JCM 12925T).
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Affiliation(s)
- Verona Vandieken
- Max-Planck-Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
| | - Christian Knoblauch
- University of Hamburg, Institute of Soil Science, Allende-Platz 2, 20146 Hamburg, Germany
| | - Bo Barker Jørgensen
- Max-Planck-Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
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López-Cortés A, Fardeau ML, Fauque G, Joulian C, Ollivier B. Reclassification of the sulfate- and nitrate-reducing bacterium Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov. Int J Syst Evol Microbiol 2006; 56:1495-1499. [PMID: 16825618 DOI: 10.1099/ijs.0.64074-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Desulfovibrio vulgaris subsp. oxamicus (type strain, DSM 1925(T)) was found to use nitrate as a terminal electron acceptor, the latter being reduced to ammonium. Phylogenetic studies indicated that strain DSM 1925(T) was distantly related to the type strain of Desulfovibrio vulgaris (95.4 % similarity of the small-subunit rRNA gene) and had as its closest phylogenetic relatives two other nitrate- and sulfate-reducing bacteria, namely Desulfovibrio termitidis (99.4 % similarity) and Desulfovibrio longreachensis (98.4 % similarity). Additional experiments were conducted to characterize better strain DSM 1925(T). This strain incompletely oxidized lactate and ethanol to acetate. It also oxidized butanol, pyruvate and citrate, but not glucose, fructose, acetate, propionate, butyrate, methanol, glycerol or peptone. The optimum temperature for growth was 37 degrees C (range 16-50 degrees C) and the optimum NaCl concentration for growth was 0.1 % (range 0-5 %). Because of significant genotypic and phenotypic differences from Desulfovibrio termitidis and Desulfovibrio longreachensis, reclassification of Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov., is proposed. The type strain is strain Monticello 2(T) (=DSM 1925(T)=NCIMB 9442(T)=ATCC 33405(T)).
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MESH Headings
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Desulfovibrio/classification
- Desulfovibrio/genetics
- Desulfovibrio/metabolism
- Desulfovibrio/physiology
- Desulfovibrio vulgaris/classification
- Desulfovibrio vulgaris/genetics
- Desulfovibrio vulgaris/metabolism
- Desulfovibrio vulgaris/physiology
- Genes, rRNA/genetics
- Growth Inhibitors/pharmacology
- Molecular Sequence Data
- Nitrates/metabolism
- Oxidation-Reduction
- Peptones/metabolism
- Phylogeny
- Quaternary Ammonium Compounds/metabolism
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/pharmacology
- Sulfates/metabolism
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Affiliation(s)
- Alejandro López-Cortés
- Laboratorio de Ecología Microbiana Molecular, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Mar Bermejo 195, Playa Palo Santa Rita, La Paz, Baja California Sur, 23090, Mexico
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie IRD, Universités de Provence et de la Méditerranée, 163 avenue de Luminy, ESIL-GBMA, Case 925, 13288 Marseille Cedex 9, France
| | - Guy Fauque
- Laboratoire de Microbiologie, Géochimie et Ecologie Marines, UMR CNRS 6117, Campus de Luminy, Case 901, 13288 Marseille Cedex 9, France
- Laboratoire de Microbiologie IRD, Universités de Provence et de la Méditerranée, 163 avenue de Luminy, ESIL-GBMA, Case 925, 13288 Marseille Cedex 9, France
| | - Catherine Joulian
- BRGM, Environment and Process Division, Biotechnology Unit, 2, avenue Claude Guillemin, 45060 Orléans Cedex 2, France
| | - Bernard Ollivier
- Laboratoire de Microbiologie IRD, Universités de Provence et de la Méditerranée, 163 avenue de Luminy, ESIL-GBMA, Case 925, 13288 Marseille Cedex 9, France
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Daële V, Ray A, Vassalli I, Poulet G, Bras GL. Kinetic study of reactions of C2H5O2with NO at 298 K and 0.55 - 2 torr. INT J CHEM KINET 2004. [DOI: 10.1002/kin.550271109] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Kitamura M, Takayama Y, Kojima S, Kohno K, Ogata H, Higuchi Y, Inoue H. Cloning and expression of the enolase gene from Desulfovibrio vulgaris (Miyazaki F). ACTA ACUST UNITED AC 2004; 1676:172-81. [PMID: 14746912 DOI: 10.1016/j.bbaexp.2003.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The gene encoding an enolase from Desulfovibrio vulgaris (Miyazaki F) was cloned and overexpressed in Escherichia coli. A 2.1-kb DNA fragment, isolated from D. vulgaris (Miyazaki F) by double digestion with PstI and BamHI, contained an enolase gene (eno) and part of the methylenetetrahydrofolate dehydrogenase gene (folD). The nucleotide sequence of eno indicates that the protein monomer is composed of 434 amino acids. An expression system for eno under control of the T7 promoter was constructed in E. coli. The purified His-tagged enolase formed a homooctamer and was active in the formation of phosphoenolpyruvate (PEP) as well as in the reverse reaction, the formation of D-(+)-2-phosphoglyceric acid (2-PGA). The pH dependence and kinetic properties of the recombinant enolase from the sulfate-reducing bacterium were also studied. The amounts of eno mRNA when the bacterium was grown on glycerol or glucose were compared to that when D. vulgaris was grown on lactate.
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Affiliation(s)
- Masaya Kitamura
- Department of Applied and Bioapplied Chemistry, Graduate School of Engineering, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan.
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Fareleira P, Legall J, Xavier AV, Santos H. Pathways for utilization of carbon reserves in Desulfovibrio gigas under fermentative and respiratory conditions. J Bacteriol 1997; 179:3972-80. [PMID: 9190814 PMCID: PMC179207 DOI: 10.1128/jb.179.12.3972-3980.1997] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The sulfate-reducing bacterium Desulfovibrio gigas accumulates large amounts of polyglucose as an endogenous carbon and energy reserve. In the absence of exogenous substrates, the intracellular polysaccharide was utilized, and energy was conserved in the process (H. Santos, P. Fareleira, A. V. Xavier, L. Chen, M.-Y. Liu, and J. LeGall, Biochem. Biophys. Res. Commun. 195:551-557, 1993). When an external electron acceptor was not provided, degradation of polyglucose by cell suspensions of D. gigas yielded acetate, glycerol, hydrogen, and ethanol. A detailed investigation of the metabolic pathways involved in the formation of these end products was carried out, based on measurements of the activities of glycolytic enzymes in cell extracts, by either spectrophotometric or nuclear magnetic resonance (NMR) assays. All of the enzyme activities associated with the glycogen cleavage and the Embden-Meyerhof pathway were determined as well as those involved in the formation of glycerol from dihydroxyacetone phosphate (glycerol-3-phosphate dehydrogenase and glycerol phosphatase) and the enzymes that catalyze the reactions leading to the production of ethanol (pyruvate decarboxylase and ethanol dehydrogenase). The key enzymes of the Entner-Doudoroff pathway were not detected. The methylglyoxal bypass was identified as a second glycolytic branch operating simultaneously with the Embden-Meyerhof pathway. The relative contribution of these two pathways for polyglucose degradation was 2:3. 13C-labeling experiments with cell extracts using isotopically enriched glucose and 13C-NMR analysis supported the proposed pathways. The information on the metabolic pathways involved in polyglucose catabolism combined with analyses of the end products formed from polyglucose under fermentative conditions provided some insight into the role of NADH in D. gigas. In the presence of electron acceptors, NADH resulting from polyglucose degradation was utilized for the reduction of sulfate, thiosulfate, or nitrite, leading to the formation of acetate as the only carbon end product besides CO2. Evidence supporting the role of NADH as a source of reducing equivalents for the production of hydrogen is also presented.
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Affiliation(s)
- P Fareleira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Hard BC, Friedrich S, Babel W. Bioremediation of acid mine water using facultatively methylotrophic metal-tolerant sulfate-reducing bacteria. Microbiol Res 1997. [DOI: 10.1016/s0944-5013(97)80025-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Niel EW, Pedro Gomes TM, Willems A, Collins MD, Prins RA, Gottschal JC. The role of polyglucose in oxygen-dependent respiration by a new strain of Desulfovibrio salexigens. FEMS Microbiol Ecol 1996. [DOI: 10.1111/j.1574-6941.1996.tb00121.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Parekh M, Drake HL, Daniel SL. Bidirectional transformation of aromatic aldehydes by Desulfovibrio desulfuricans under nitrate-dissimilating conditions. Lett Appl Microbiol 1996; 22:115-20. [PMID: 8936370 DOI: 10.1111/j.1472-765x.1996.tb01122.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Desulfovibrio desulfuricans ATCC 27774 was screened for reactivity against aromatic compounds during lactate-dependent, nitrate-dissimilating growth. Only aromatic aldehydes (benzaldehyde, 2-hydroxybenzaldehyde, 3-hydroxybenzaldehyde, 4-hydroxybenzaldehyde, vanillin, iso-vanillin and o-vanillin) were reactive and, with the exception of 2-hydroxybenzaldehyde, were stimulatory to lactate-dependent growth. Aromatic aldehydes were transformed to their corresponding benzoate and benzyl alcohol derivatives, with the ratio of benzoate-to-benzyl alcohol derivatives being dependent upon lactate availability. In presence of lactate, aromatic aldehydes were primarily reduced to their corresponding benzyl alcohol derivatives; in the absence of lactate, aromatic aldehydes were mainly oxidized to their corresponding benzoate derivatives. In the absence of nitrate, 3-hydroxybenzaldehyde was neither reduced nor oxidized. These results indicate that D. desulfuricans is competent in the bidirectional transformation of aromatic aldehydes under nitrate-dissimilating conditions and that the direction of transformation (i.e. reduction or oxidation) is regulated by reductant availability.
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Affiliation(s)
- M Parekh
- Department of Biology, University of Mississippi, University, USA
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21
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Hard BC, Babel W. Characterization of a methanol-utilizing sulfate-reducing bacterium isolated from a wastewater pond. J Basic Microbiol 1995. [DOI: 10.1002/jobm.3620350605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Barata BA, LeGall J, Moura JJ. Aldehyde oxidoreductase activity in Desulfovibrio gigas: in vitro reconstitution of an electron-transfer chain from aldehydes to the production of molecular hydrogen. Biochemistry 1993; 32:11559-68. [PMID: 8218223 DOI: 10.1021/bi00094a012] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The molybdenum [iron-sulfur] protein, first isolated from Desulfovibrio gigas by Moura et al. [Moura, J. J. G., Xavier, A. V., Bruschi, M., Le Gall, J., Hall, D. O., & Cammack, R. (1976) Biochem. Biophys. Res. Commun. 72, 782-789], was later shown to mediate the electronic flow from salicylaldehyde to a suitable electron acceptor, 2,6-dichlorophenolindophenol (DCPIP) [Turner, N., Barata, B., Bray, R. C., Deistung, J., LeGall, J., & Moura, J. J. G. (1987) Biochem. J. 243, 755-761]. The DCPIP-dependent aldehyde oxidoreductase activity was studied in detail using a wide range of aldehydes and analogues. Steady-state kinetic analysis (KM and Vmax) was performed for acetaldehyde, propionaldehyde, benzaldehyde, and salicylaldehyde in excess DCPIP concentration, and a simple Michaelis-Menten model was shown to be applicable as a first kinetic approach. Xanthine, purine, allopurinol, and N1-methylnicotinamide (NMN) could not be utilized as enzyme substrates. DCPIP and ferricyanide were shown to be capable of cycling the electronic flow, whereas other cation and anion dyes [O2 and NAD(P)+] were not active in this process. The enzyme showed an optimal pH activity profile around 7.8. This molybdenum hydroxylase was shown to be part of an electron-transfer chain comprising four different soluble proteins from D. gigas, with a total of 11 discrete redox centers, which is capable of linking the oxidation of aldehydes to the reduction of protons.
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Affiliation(s)
- B A Barata
- Departamento de Química, Faculdade de Ciências da Universidade de Lisboa, Oeiras, Portugal
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Vainshtein M, Hippe H, Kroppenstedt RM. Cellular Fatty Acid Composition of Desulfovibrio Species and Its Use in Classification of Sulfate-reducing Bacteria. Syst Appl Microbiol 1992. [DOI: 10.1016/s0723-2020(11)80115-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Gibson GR. Physiology and ecology of the sulphate-reducing bacteria. THE JOURNAL OF APPLIED BACTERIOLOGY 1990; 69:769-97. [PMID: 2286579 DOI: 10.1111/j.1365-2672.1990.tb01575.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- G R Gibson
- Medical Research Council, Dunn Clinical Nutrition Centre, Cambridge, UK
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25
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Winter J, Zellner G. Thermophilic anaerobic degradation of carbohydrates - metabolic properties of microorganisms from the different phases. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb04091.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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