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Heng S, Sutheeworapong S, Champreda V, Uke A, Kosugi A, Pason P, Waeonukul R, Ceballos RM, Ratanakhanokchai K, Tachaapaikoon C. Genomics and cellulolytic, hemicellulolytic, and amylolytic potential of Iocasia fonsfrigidae strain SP3-1 for polysaccharide degradation. PeerJ 2022; 10:e14211. [PMID: 36281362 PMCID: PMC9587714 DOI: 10.7717/peerj.14211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/19/2022] [Indexed: 01/24/2023] Open
Abstract
Background Cellulolytic, hemicellulolytic, and amylolytic (CHA) enzyme-producing halophiles are understudied. The recently defined taxon Iocasia fonsfrigidae consists of one well-described anaerobic bacterial strain: NS-1T. Prior to characterization of strain NS-1T, an isolate designated Halocella sp. SP3-1 was isolated and its genome was published. Based on physiological and genetic comparisons, it was suggested that Halocella sp. SP3-1 may be another isolate of I. fronsfrigidae. Despite being geographic variants of the same species, data indicate that strain SP3-1 exhibits genetic, genomic, and physiological characteristics that distinguish it from strain NS-1T. In this study, we examine the halophilic and alkaliphilic nature of strain SP3-1 and the genetic substrates underlying phenotypic differences between strains SP3-1 and NS-1T with focus on sugar metabolism and CHA enzyme expression. Methods Standard methods in anaerobic cell culture were used to grow strains SP3-1 as well as other comparator species. Morphological characterization was done via electron microscopy and Schaeffer-Fulton staining. Data for sequence comparisons (e.g., 16S rRNA) were retrieved via BLAST and EzBioCloud. Alignments and phylogenetic trees were generated via CLUTAL_X and neighbor joining functions in MEGA (version 11). Genomes were assembled/annotated via the Prokka annotation pipeline. Clusters of Orthologous Groups (COGs) were defined by eegNOG 4.5. DNA-DNA hybridization calculations were performed by the ANI Calculator web service. Results Cells of strain SP3-1 are rods. SP3-1 cells grow at NaCl concentrations of 5-30% (w/v). Optimal growth occurs at 37 °C, pH 8.0, and 20% NaCl (w/v). Although phylogenetic analysis based on 16S rRNA gene indicates that strain SP3-1 belongs to the genus Iocasia with 99.58% average nucleotide sequence identity to Iocasia fonsfrigida NS-1T, strain SP3-1 is uniquely an extreme haloalkaliphile. Moreover, strain SP3-1 ferments D-glucose to acetate, butyrate, carbon dioxide, hydrogen, ethanol, and butanol and will grow on L-arabinose, D-fructose, D-galactose, D-glucose, D-mannose, D-raffinose, D-xylose, cellobiose, lactose, maltose, sucrose, starch, xylan and phosphoric acid swollen cellulose (PASC). D-rhamnose, alginate, and lignin do not serve as suitable culture substrates for strain SP3-1. Thus, the carbon utilization profile of strain SP3-1 differs from that of I. fronsfrigidae strain NS-1T. Differences between these two strains are also noted in their lipid composition. Genomic data reveal key differences between the genetic profiles of strain SP3-1 and NS-1T that likely account for differences in morphology, sugar metabolism, and CHA-enzyme potential. Important to this study, I. fonsfrigidae SP3-1 produces and extracellularly secretes CHA enzymes at different levels and composition than type strain NS-1T. The high salt tolerance and pH range of SP3-1 makes it an ideal candidate for salt and pH tolerant enzyme discovery.
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Affiliation(s)
- Sobroney Heng
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Ayaka Uke
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Akihiko Kosugi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Ibaraki, Japan
| | - Patthra Pason
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Rattiya Waeonukul
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Ruben Michael Ceballos
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States of America,Arkansas Center for Space & Planetary Sciences, University of Arkansas, Fayetteville, AR, United States of America
| | - Khanok Ratanakhanokchai
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
| | - Chakrit Tachaapaikoon
- School of Bioresources and Technology, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand,Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute, King Mongkut’s Institute of Technology Thonburi, Bangkok, Thailand
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Solchaga JI, Busalmen JP, Nercessian D. Unraveling Anaerobic Metabolisms in a Hypersaline Sediment. Front Microbiol 2022; 13:811432. [PMID: 35369499 PMCID: PMC8966722 DOI: 10.3389/fmicb.2022.811432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The knowledge on the microbial diversity inhabiting hypersaline sediments is still limited. In particular, existing data about anaerobic hypersaline archaea and bacteria are scarce and refer to a limited number of genera. The approach to obtain existing information has been almost exclusively attempting to grow every organism in axenic culture on the selected electron acceptor with a variety of electron donors. Here, a different approach has been used to interrogate the microbial community of submerged hypersaline sediment of Salitral Negro, Argentina, aiming at enriching consortia performing anaerobic respiration of different electron acceptor compounds, in which ecological associations can maximize the possibilities of successful growth. Growth of consortia was demonstrated on all offered electron acceptors, including fumarate, nitrate, sulfate, thiosulfate, dimethyl sulfoxide, and a polarized electrode. Halorubrum and Haloarcula representatives are here shown for the first time growing on lactate, using fumarate or a polarized electrode as the electron acceptor; in addition, they are shown also growing in sulfate-reducing consortia. Halorubrum representatives are for the first time shown to be growing in nitrate-reducing consortia, probably thanks to reduction of N2O produced by other consortium members. Fumarate respiration is indeed shown for the first time supporting growth of Halanaeroarchaeum and Halorhabdus belonging to the archaea, as well as growth of Halanaerobium, Halanaerobaculum, Sporohalobacter, and Acetohalobium belonging to the bacteria. Finally, evidence is presented suggesting growth of nanohaloarchaea in anaerobic conditions.
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Affiliation(s)
- Juan Ignacio Solchaga
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
| | - Juan Pablo Busalmen
- Laboratorio de Bioelectroquímica, INTEMA - CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
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Was the Last Bacterial Common Ancestor a Monoderm after All? Genes (Basel) 2022; 13:genes13020376. [PMID: 35205421 PMCID: PMC8871954 DOI: 10.3390/genes13020376] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection.
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Microbial Lipopeptide-Producing Strains and Their Metabolic Roles under Anaerobic Conditions. Microorganisms 2021; 9:microorganisms9102030. [PMID: 34683351 PMCID: PMC8540375 DOI: 10.3390/microorganisms9102030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
The lipopeptide produced by microorganisms is one of the representative biosurfactants and is characterized as a series of structural analogues of different families. Thirty-four families covering about 300 lipopeptide compounds have been reported in the last decades, and most of the reported lipopeptides produced by microorganisms were under aerobic conditions. The lipopeptide-producing strains under anaerobic conditions have attracted much attention from both the academic and industrial communities, due to the needs and the challenge of their applications in anaerobic environments, such as in oil reservoirs and in microbial enhanced oil recovery (MEOR). In this review, the fifty-eight reported bacterial strains, mostly isolated from oil reservoirs and dominated by the species Bacillus subtilis, producing lipopeptide biosurfactants, and the species Pseudomonas aeruginosa, producing glycolipid biosurfactants under anaerobic conditions were summarized. The metabolic pathway and the non-ribosomal peptide synthetases (NRPSs) of the strain Bacillus subtilis under anaerobic conditions were analyzed, which is expected to better understand the key mechanisms of the growth and production of lipopeptide biosurfactants of such kind of bacteria under anaerobic conditions, and to expand the industrial application of anaerobic biosurfactant-producing bacteria.
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Liu D, Zhang C, Zhang J, Xin X, Liao X. Metagenomics reveals the formation mechanism of flavor metabolites during the spontaneous fermentation of potherb mustard (Brassica juncea var. multiceps). Food Res Int 2021; 148:110622. [PMID: 34507766 DOI: 10.1016/j.foodres.2021.110622] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/23/2021] [Accepted: 07/19/2021] [Indexed: 01/15/2023]
Abstract
Fermented vegetable flavors are closely associated with microbial metabolism. Here, shifts in flavor metabolites and their correlations to the structure and function of fermentative microbial communities were explored during the spontaneous fermentation process of potherb mustard (Brassica juncea var. multiceps), a traditionally fermented vegetable from China. Halophilic bacteria (HAB, i.e., Halomonas, Salinivibrio, and Vibrio) and lactic acid bacteria (LAB, i.e., Lactobacillus-related genera and Weissella) became highly abundant after potherb mustard fermentation. Further, HAB and LAB abundances exhibited significant, positive correlations with metabolites important in fermented potherb mustard flavoring (e.g., organic acids, amino acids, alcohols, aldehydes, and nitriles). Metagenomic analysis indicated that Halomonas, Salinivibrio, Weissella, and Lactobacillus-related genera were likely actively engaged in pyruvate metabolism (ko00620) and citrate cycle (TCA cycle, ko00020), leading to higher lactic and acetic acid concentrations, along with lower pH, which would affect levels of volatile isothiocyanates and nitriles that contribute to flavoring of fermented potherb mustard. Further, HAB and LAB were the primary populations inferred to be responsible for amino acid and fatty acid metabolism in addition to the biosynthesis of numerous volatile flavor compounds. This study highlights the predominance and importance of LAB and HAB during spontaneous fermentation of potherb mustard and provides new insights into their roles in this process.
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Affiliation(s)
- Daqun Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China; Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Chengcheng Zhang
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Jianming Zhang
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Xiaoting Xin
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China.
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Ali M, Elreedy A, Ibrahim MG, Fujii M, Nakatani K, Tawfik A. Regulating acidogenesis and methanogenesis for the separated bio-generation of hydrogen and methane from saline-to-hypersaline industrial wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 250:109546. [PMID: 31545177 DOI: 10.1016/j.jenvman.2019.109546] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/22/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
Given the limitations of acidogens and methanogens activities under saline environments, this work aims to optimize the main operational parameters affecting hydrogen and methane production from saline-to-hypersaline wastewater containing mono-ethylene glycol (MEG). MEG is the main contaminant in several saline industrial effluents. Anaerobic baffled reactor (ABR), as a multi-stage system, was used at different temperatures (i.e., 19-31 °C [ambient] and 35 °C), organic loading rates (OLRs) of 0.6-2.2 gCOD/L/d, and salinity of 5-35 gNaCl/L. Mesophilic conditions of 35 °C substantially promoted MEG biodegradability (92-98%) and hydrogen/methane productivity, even at elevated salinity. Hydrogen yield (HY) and methane yield (MY) peaked to 258 and 140 mL/gCODadd, respectively, at OLR 0.64 gCOD/L/d and salinity up to 20-25 gNaCl/L. An immobilized sludge ABR (ISABR), packed with polyurethane media, was further compared with classical ABR, resulting in 1.8-fold higher MY, at 35 gNaCl/L. Microbial analysis showed that introducing attached growth system (ISABR) substantially promoted methanogens abundance, which was dominated by genus Methanosarcina. Among bacterial genera, Acetobacterium was dominant, particularly in 1st compartment, representing MEG-degrading/salt-tolerant genus. At high salinity up to 35 gNaCl/L, the multi-phase and attached growth configuration can efficiently reduce the induced salt stress, particularly on methanogens, towards balanced and separated acidogenesis/methanogenesis. Overall, producing hydrogen and methane from anaerobic treatment of MEG-based saline wastewater is feasible at optimized parameters and configuration.
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Affiliation(s)
- Manal Ali
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan; Environmental Engineering Department, Egypt-Japan University of Science and Technology, Alexandria, 21934, Egypt; Civil Engineering Department, Aswan University, Aswan, 81511, Egypt
| | - Ahmed Elreedy
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan; Sanitary Engineering Department, Alexandria University, Alexandria, 21544, Egypt.
| | - Mona G Ibrahim
- Environmental Engineering Department, Egypt-Japan University of Science and Technology, Alexandria, 21934, Egypt; Environmental Health Department, High Institute of Public Health, Alexandria University, Alexandria, 21544, Egypt
| | - Manabu Fujii
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan
| | - Kota Nakatani
- Department of Civil and Environmental Engineering, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8552, Japan
| | - Ahmed Tawfik
- Water Pollution Research Department, National Research Centre, Giza, 12622, Egypt
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Taheri E, Amin MM, Fatehizadeh A, Pourzamani H, Bina B, Spanjers H. Biohydrogen production under hyper salinity stress by an anaerobic sequencing batch reactor with mixed culture. JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2018; 16:159-170. [PMID: 30728988 PMCID: PMC6277343 DOI: 10.1007/s40201-018-0304-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/05/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND This study investigated the effect of organic loading rate (OLR) and NaCl concentration on biohydrogen production by preheated anaerobic sludge in a lab scale anaerobic sequencing batch reactor (ASBR) fed with glucose during long time operation. METHODS During ASBR operation, the OLR was increased in steps from 0.5 to 5 g glucose/L.d and NaCl addition started at an OLR of 5 g glucose/L.d, to obtain NaCl concentrations in the reactor in the range of 0.5-30 g/L. RESULTS With an increasing OLR from 0.5 to 5 g glucose/L.d, the biohydrogen yield increased and reached 0.8 ± 0.4 mol H2/mol glucose at an OLR of 5 g glucose/L.d. A NaCl concentration of 0.5 g/L resulted in a higher yield of biohydrogen (1.1 ± 0.2 mol H2/mol glucose). Concentrations above 0.5 g/L NaCl led to decreasing biohydrogen yield and the lowest yield (0.3 ± 0.1 mol H2/mol glucose) was obtained at 30 g/L of NaCl. The mass balance errors for C, H, and O in all constructed stoichiometric reactions were below 5%. CONCLUSIONS The modified Monod model indicated that r (H2)max and Ccrit values were 23.3 mL H2/g VSS/h and 119.9 g/L, respectively. Additionally, ASBR operation at high concentrations of NaCl shifted the metabolic pathway from acidogenic toward solventogenic.
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Affiliation(s)
- Ensiyeh Taheri
- 1Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
- 2Student Research Committee, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
- 3Environment Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Mehdi Amin
- 1Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
- 3Environment Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Fatehizadeh
- 1Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
- 3Environment Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamidreza Pourzamani
- 1Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
- 3Environment Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bijan Bina
- 1Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
- 3Environment Research Center, Research Institute for Primordial Prevention of Non-communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Henri Spanjers
- 4Section Sanitary Engineering, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, The Netherlands
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Seck EH, Diop A, Armstrong N, Delerce J, Fournier PE, Raoult D, Khelaifia S. Microbial culturomics to isolate halophilic bacteria from table salt: genome sequence and description of the moderately halophilic bacterium Bacillus salis sp. nov. New Microbes New Infect 2018; 23:28-38. [PMID: 29707210 PMCID: PMC5917939 DOI: 10.1016/j.nmni.2017.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 11/15/2022] Open
Abstract
Bacillus salis strain ES3T (= CSUR P1478 = DSM 100598) is the type strain of B. salis sp. nov. It is an aerobic, Gram-positive, moderately halophilic, motile and spore-forming bacterium. It was isolated from commercial table salt as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of halophilic bacteria in salty food. Here we describe the phenotypic characteristics of this isolate, its complete genome sequence and annotation, together with a comparison with closely related bacteria. Phylogenetic analysis based on 16S rRNA gene sequences indicated 97.5% similarity with Bacillus aquimaris, the closest species. The 8 329 771 bp long genome (one chromosome, no plasmids) exhibits a G+C content of 39.19%. It is composed of 18 scaffolds with 29 contigs. Of the 8303 predicted genes, 8109 were protein-coding genes and 194 were RNAs. A total of 5778 genes (71.25%) were assigned a putative function.
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Affiliation(s)
- E H Seck
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - A Diop
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - N Armstrong
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - J Delerce
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - P-E Fournier
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - D Raoult
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - S Khelaifia
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
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Gunde-Cimerman N, Plemenitaš A, Oren A. Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations. FEMS Microbiol Rev 2018. [DOI: 10.1093/femsre/fuy009] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Ana Plemenitaš
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 1, SI-1000 Ljubljana, Slovenia
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
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Gao R, Shi T, Liu X, Zhao M, Cui H, Yuan L. Purification and characterisation of a salt-stable protease from the halophilic archaeon Halogranum rubrum. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:1412-1419. [PMID: 27378532 DOI: 10.1002/jsfa.7879] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 05/26/2016] [Accepted: 06/24/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Because proteases play an important role in the fermentation of fish sauce, the purification and characterisation of an extracellular protease from the halophilic archaeon Halogranum rubrum was investigated. RESULTS The molecular mass of the protease was estimated to be approximately 47 kDa based on sodium dodecyl sulfate-polyacrylamide gel electropheresis (SDS-PAGE) and native-PAGE analysis. The optimum conditions for catalytic activity were pH 8.0 and 50°C. The protease showed alkaline stability (pH 7.0-10.0). The protease also exhibited novel catalytic ability over a broad range of salinity (NaCl 0-3 mol L-1 ). Calcium ion enhanced the proteolytic activity of the enzyme. The Km and Vmax values of the purified protease for casein were calculated to be 4.89 mg mL-1 and 1111.11 U mL-1 , respectively. The protease was strongly inhibited by ethylenediamine tetraacetic acid (EDTA) and phenylmethanesulfonyl fluoride (PMSF). Meanwhile, the protease was stable in the presence of Triton X-100, isopropanol, ethanol or dithio-bis-nitrobenzoic (DTNB), but was inhibited by sodium dodecyl sulfate (SDS), dimethyl sulfoxide (DMSO) or methanol. MALDI -TOF/TOF MS analysis revealed that the protease shared some functional traits with protease produced by Halogranum salarium. Furthermore, it exhibited high hydrolytic activity on silver carp myosin protein. CONCLUSION The protease is an alkaline and salt-tolerant enzyme that hydrolyses silver carp myosin with high efficiency. These excellent characteristics make this protease an attractive candidate for industrial use in low-salt fish sauce fermentation. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Ruichang Gao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Tong Shi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Xiangdong Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Mengqin Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Henglin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Li Yuan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, China
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Oren A. Glycerol metabolism in hypersaline environments. Environ Microbiol 2016; 19:851-863. [DOI: 10.1111/1462-2920.13493] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/05/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus; Jerusalem 91904 Israel
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12
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Oren A. Life in Hypersaline Environments. THEIR WORLD: A DIVERSITY OF MICROBIAL ENVIRONMENTS 2016. [DOI: 10.1007/978-3-319-28071-4_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Nolla-Ardèvol V, Strous M, Tegetmeyer HE. Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome. Front Microbiol 2015; 6:597. [PMID: 26157422 PMCID: PMC4475827 DOI: 10.3389/fmicb.2015.00597] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/31/2015] [Indexed: 12/02/2022] Open
Abstract
A haloalkaline anaerobic microbial community obtained from soda lake sediments was used to inoculate anaerobic reactors for the production of methane rich biogas. The microalga Spirulina was successfully digested by the haloalkaline microbial consortium at alkaline conditions (pH 10, 2.0 M Na+). Continuous biogas production was observed and the obtained biogas was rich in methane, up to 96%. Alkaline medium acted as a CO2 scrubber which resulted in low amounts of CO2 and no traces of H2S in the produced biogas. A hydraulic retention time (HRT) of 15 days and 0.25 g Spirulina L−1 day−1 organic loading rate (OLR) were identified as the optimal operational parameters. Metagenomic and metatranscriptomic analysis showed that the hydrolysis of the supplied substrate was mainly carried out by Bacteroidetes of the “ML635J-40 aquatic group” while the hydrogenotrophic pathway was the main producer of methane in a methanogenic community dominated by Methanocalculus.
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Affiliation(s)
- Vímac Nolla-Ardèvol
- Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld Bielefeld, Germany
| | - Marc Strous
- Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld Bielefeld, Germany ; Department of Geoscience, University of Calgary Calgary, AB, Canada ; Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Halina E Tegetmeyer
- Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld Bielefeld, Germany ; Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany ; HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research Bremerhaven, Germany
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14
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García-Maldonado JQ, Bebout BM, Everroad RC, López-Cortés A. Evidence of novel phylogenetic lineages of methanogenic archaea from hypersaline microbial mats. MICROBIAL ECOLOGY 2015; 69:106-117. [PMID: 25108574 DOI: 10.1007/s00248-014-0473-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/25/2014] [Indexed: 06/03/2023]
Abstract
Methanogenesis in hypersaline and high-sulfate environments is typically dominated by methylotrophic methanogens because sulfate reduction is thermodynamically favored over hydrogenotrophic methanogenesis in these environments. We characterized the community composition of methanogenic archaea in both unmanipulated and incubated microbial mats from different hypersaline environments in Baja California Sur, Mexico. Clone libraries of methyl coenzyme-M reductase (mcrA) sequences and DGGE band patterns of 16S rRNA and mcrA sequences showed that the methanogen community in these microbial mats is dominated by methylotrophic methanogens of the genus Methanohalophilus. However, phylogenetic analyses of mcrA sequences from these mats also revealed two new lineages corresponding to putative hydrogenotrophic methanogens related with the strictly hydrogenotrophic order Methanomicrobiales. Stimulated methane production under decreased salinity and sulfate concentrations also suggested the presence of hydrogenotrophic methanogens in these samples. The relative abundance of mcrA gene and transcripts, estimated by SYBR green I qPCR assays, suggested the activity of different phylogenetic groups of methanogens, including the two novel clusters, in unmanipulated samples of hypersaline microbial mats. Using geochemical and molecular approaches, we show that substrate limitation and values of salinity and sulfate higher than 3 % and 25 mM (respectively) are potential environmental constraints for methanogenesis in these environments. Microcosm experiments with modifications of salinity and sulfate concentrations and TMA addition showed that upper salt and sulfate concentrations for occurrence of methylotrophic methanogenesis were 28 % and 263 mM, respectively. This study provides phylogenetic information about uncultivated and undescribed methanogenic archaea from hypersaline environments.
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Affiliation(s)
- José Q García-Maldonado
- Laboratorio de Geomicrobiología y Biotecnología, Centro de Investigaciones Biológicas del Noroeste, La Paz, BCS, Mexico
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15
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Batista-García RA, Balcázar-López E, Miranda-Miranda E, Sánchez-Reyes A, Cuervo-Soto L, Aceves-Zamudio D, Atriztán-Hernández K, Morales-Herrera C, Rodríguez-Hernández R, Folch-Mallol J. Characterization of lignocellulolytic activities from a moderate halophile strain of Aspergillus caesiellus isolated from a sugarcane bagasse fermentation. PLoS One 2014; 9:e105893. [PMID: 25162614 PMCID: PMC4146556 DOI: 10.1371/journal.pone.0105893] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 07/25/2014] [Indexed: 01/31/2023] Open
Abstract
A moderate halophile and thermotolerant fungal strain was isolated from a sugarcane bagasse fermentation in the presence of 2 M NaCl that was set in the laboratory. This strain was identified by polyphasic criteria as Aspergillus caesiellus. The fungus showed an optimal growth rate in media containing 1 M NaCl at 28°C and could grow in media added with up to 2 M NaCl. This strain was able to grow at 37 and 42°C, with or without NaCl. A. caesiellus H1 produced cellulases, xylanases, manganese peroxidase (MnP) and esterases. No laccase activity was detected in the conditions we tested. The cellulase activity was thermostable, halostable, and no differential expression of cellulases was observed in media with different salt concentrations. However, differential band patterns for cellulase and xylanase activities were detected in zymograms when the fungus was grown in different lignocellulosic substrates such as wheat straw, maize stover, agave fibres, sugarcane bagasse and sawdust. Optimal temperature and pH were similar to other cellulases previously described. These results support the potential of this fungus to degrade lignocellulosic materials and its possible use in biotechnological applications.
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Affiliation(s)
- Ramón Alberto Batista-García
- Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Edgar Balcázar-López
- Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Estefan Miranda-Miranda
- Centro Nacional de Investigación Disciplinaria en Parasitología Veterinaria, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Cuernavaca, Morelos, Mexico
| | - Ayixón Sánchez-Reyes
- Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Laura Cuervo-Soto
- Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Denise Aceves-Zamudio
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Karina Atriztán-Hernández
- Facultad de Ciencias Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Catalina Morales-Herrera
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Rocío Rodríguez-Hernández
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Jorge Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
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16
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Effects of temperature on microbial succession and metabolite change during saeu-jeot fermentation. Food Microbiol 2014; 38:16-25. [DOI: 10.1016/j.fm.2013.08.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 06/03/2013] [Accepted: 08/10/2013] [Indexed: 11/18/2022]
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17
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Arakaki RL, Monteiro DA, Boscolo M, Dasilva R, Gomes E. Halotolerance, ligninase production and herbicide degradation ability of basidiomycetes strains. Braz J Microbiol 2014; 44:1207-14. [PMID: 24688513 PMCID: PMC3958189 DOI: 10.1590/s1517-83822014005000014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 04/04/2013] [Indexed: 12/01/2022] Open
Abstract
Fungi have been recently recognized as organisms able to grow in presence of high salt concentration with halophilic and halotolerance properties and their ligninolytic enzyme complex have an unspecific action enabling their use to degradation of a number of xenobiotic compounds. In this work, both the effect of salt and polyols on growth of the basidiomycetes strains, on their ability to produce ligninolytic enzyme and diuron degradation were evaluated. Results showed that the presence of NaCl in the culture medium affected fungal specimens in different ways. Seven out of ten tested strains had growth inhibited by salt while Dacryopinax elegans SXS323, Polyporus sp MCA128 and Datronia stereoides MCA167 fungi exhibited higher biomass production in medium containing 0.5 and 0.6 mol.L−1 of NaCl, suggesting to be halotolerant. Polyols such as glycerol and mannitol added into the culture media improved the biomass and ligninases production by D. elegans but the fungus did not reveal consumption of these polyols from media. This fungus degraded diuron in medium control, in presence of NaCl as well as polyols, produced MnP, LiP and laccase.
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Affiliation(s)
- R L Arakaki
- Laboratório de Bioquímica Aplicada, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
| | - D A Monteiro
- Laboratório de Bioquímica Aplicada, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
| | - M Boscolo
- Laboratório de Bioquímica Aplicada, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
| | - R Dasilva
- Laboratório de Bioquímica Aplicada, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
| | - E Gomes
- Laboratório de Bioquímica Aplicada, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
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Lorantfy B, Seyer B, Herwig C. Stoichiometric and kinetic analysis of extreme halophilic Archaea on various substrates in a corrosion resistant bioreactor. N Biotechnol 2014; 31:80-9. [DOI: 10.1016/j.nbt.2013.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 08/06/2013] [Accepted: 08/07/2013] [Indexed: 11/28/2022]
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19
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Dynamic Experiments for Bioprocess Parameter Optimization with Extreme Halophilic Archaea. Bioengineering (Basel) 2013. [DOI: 10.3390/bioengineering1010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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20
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Oren A. Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes. Front Microbiol 2013; 4:315. [PMID: 24204364 PMCID: PMC3817357 DOI: 10.3389/fmicb.2013.00315] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/06/2013] [Indexed: 11/23/2022] Open
Abstract
Extremely halophilic microorganisms that accumulate KCl for osmotic balance (the Halobacteriaceae, Salinibacter) have a large excess of acidic amino acids in their proteins. This minireview explores the occurrence of acidic proteomes in halophiles of different physiology and phylogenetic affiliation. For fermentative bacteria of the order Halanaerobiales, known to accumulate KCl, an acidic proteome was predicted. However, this is not confirmed by genome analysis. The reported excess of acidic amino acids is due to a high content of Gln and Asn, which yield Glu and Asp upon acid hydrolysis. The closely related Halorhodospira halophila and Halorhodospira halochloris use different strategies to cope with high salt. The first has an acidic proteome and accumulates high KCl concentrations at high salt concentrations; the second does not accumulate KCl and lacks an acidic proteome. Acidic proteomes can be predicted from the genomes of some moderately halophilic aerobes that accumulate organic osmotic solutes (Halomonas elongata, Chromohalobacter salexigens) and some marine bacteria. Based on the information on cultured species it is possible to understand the pI profiles predicted from metagenomic data from hypersaline environments.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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21
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Genome Sequence of Halanaerobium saccharolyticum subsp. saccharolyticum Strain DSM 6643T, a Halophilic Hydrogen-Producing Bacterium. GENOME ANNOUNCEMENTS 2013; 1:1/2/e00187-13. [PMID: 23640197 PMCID: PMC3642252 DOI: 10.1128/genomea.00187-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Halanaerobium saccharolyticum is a halophilic anaerobic fermentative bacterium capable of producing hydrogen, a potential future energy carrier molecule. The high-quality draft genome of H. saccharolyticum subsp. saccharolyticum strain DSM 6643T consists of 24 contigs for 2,873,865 bp with a G+C content of 32.3%.
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22
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Analyses of archaeal communities in Doenjang and Ganjang using a culture-independent manner based on 16S rRNA sequences. Food Sci Biotechnol 2013. [DOI: 10.1007/s10068-013-0100-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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23
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The amino acid composition of proteins from anaerobic halophilic bacteria of the order Halanaerobiales. Extremophiles 2012; 16:567-72. [DOI: 10.1007/s00792-012-0455-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 04/05/2012] [Indexed: 11/25/2022]
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