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Purohit A, Pawar L, Yadav SK. Structural and functional insights of a cold-adaptive β-glucosidase with very high glucose tolerance from Microbacterium sp. CIAB417. Enzyme Microb Technol 2023; 169:110284. [PMID: 37406591 DOI: 10.1016/j.enzmictec.2023.110284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/07/2023]
Abstract
A gene glu1 (WP_243232135.1) coding for β-glucosidase from the genome of Microbacterium sp. CIAB417 was characterized for its cold adaptive nature and tolerance to high levels of glucose and ethanol. The phylogenetic analysis suggested the close association of glu1 with a similar gene from a mesophilic bacterium Microbacterium indicum. The purified recombinant GLU1 displayed its optimal activity and stability at pH 5 and temperature 30ᴼC. Additionally, the presence of L3 loop in GLU1 suggested its cold adaptive nature. The glucose tolerant Gate keeper residues (Leu 174 & Trp 169) with a distance of ∼ 6.953 Å between them was also predicted in GLU1. The GLU1 enzyme showed ≥ 95% and ≥ 40% relative activity in the presence of 5 M glucose and 20% ethanol. The Vmax, Km, and Kcat values of GLU1 for cellobiose substrate were observed to be 45.22 U/mg, 3.5 mM, and 41.0157 s-1, respectively. The GLU1 was found to be highly efficient in hydrolysis of celloologosaccharides (C2-C5), lactose and safranal picrocrocin into glucose. Hence, cold adaptive GLU1 with very high glucose and ethanol tolerance could be very useful in bio-refinery, dairy, and flavor industries.
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Affiliation(s)
- Anjali Purohit
- Biotechnology and Synthetic Biology, Center of Innovative and Applied Bioprocessing (CIAB), Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Lata Pawar
- Biotechnology and Synthetic Biology, Center of Innovative and Applied Bioprocessing (CIAB), Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Sudesh Kumar Yadav
- Biotechnology and Synthetic Biology, Center of Innovative and Applied Bioprocessing (CIAB), Knowledge City, Sector-81, Mohali 140306, Punjab, India; Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur 176061, India.
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2
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Xylan Deconstruction by Thermophilic Thermoanaerobacterium bryantii Hemicellulases Is Stimulated by Two Oxidoreductases. Catalysts 2022. [DOI: 10.3390/catal12020182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Thermoanaerobacterium bryantii strain mel9T is a thermophilic bacterium isolated from a waste pile of a corn-canning factory. The genome of T. bryantii mel9T was sequenced and a hemicellulase gene cluster was identified. The cluster encodes seven putative enzymes, which are likely an endoxylanase, an α-glucuronidase, two oxidoreductases, two β-xylosidases, and one acetyl xylan esterase. These genes were designated tbxyn10A, tbagu67A, tbheoA, tbheoB, tbxyl52A, tbxyl39A, and tbaxe1A, respectively. Only TbXyn10A released reducing sugars from birchwood xylan, as shown by thin-layer chromatography analysis. The five components of the hemicellulase cluster (TbXyn10A, TbXyl39A, TbXyl52A, TbAgu67A, and TbAxe1A) functioned in synergy to hydrolyze birchwood xylan. Surprisingly, the two putative oxidoreductases increased the enzymatic activities of the gene products from the xylanolytic gene cluster in the presence of NADH and manganese ions. The two oxidoreductases were therefore named Hemicellulase-Enhancing Oxidoreductases (HEOs). All seven enzymes were thermophilic and acted in synergy to degrade xylans at 60 °C. Except for TbXyn10A, the other enzymes encoded by the gene cluster were conserved with high amino acid identities (85–100%) in three other Thermoanaerobacterium species. The conservation of the gene cluster is, therefore, suggestive of an important role of these enzymes in xylan degradation by these bacteria. The mechanism for enhancement of hemicellulose degradation by the HEOs is under investigation. It is anticipated, however, that the discovery of these new actors in hemicellulose deconstruction will have a significant impact on plant cell wall deconstruction in the biofuel industry.
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Bing RG, Sulis DB, Wang JP, Adams MW, Kelly RM. Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:272-293. [PMID: 33684253 PMCID: PMC10519370 DOI: 10.1111/1758-2229.12943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The potential to convert renewable plant biomasses into fuels and chemicals by microbial processes presents an attractive, less environmentally intense alternative to conventional routes based on fossil fuels. This would best be done with microbes that natively deconstruct lignocellulose and concomitantly form industrially relevant products, but these two physiological and metabolic features are rarely and simultaneously observed in nature. Genetic modification of both plant feedstocks and microbes can be used to increase lignocellulose deconstruction capability and generate industrially relevant products. Separate efforts on plants and microbes are ongoing, but these studies lack a focus on optimal, complementary combinations of these disparate biological systems to obtain a convergent technology. Improving genetic tools for plants have given rise to the generation of low-lignin lines that are more readily solubilized by microorganisms. Most focus on the microbiological front has involved thermophilic bacteria from the genera Caldicellulosiruptor and Clostridium, given their capacity to degrade lignocellulose and to form bio-products through metabolic engineering strategies enabled by ever-improving molecular genetics tools. Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Daniel B. Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Michael W.W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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Abdalla M, Hassanin HA, Yao X, Iqbal MW, Karrar E, Jiang B. Genetic and biochemical characterization of thermophilic β-cyclodextrin glucanotransferase from Gracilibacillus alcaliphilus SK51.001. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:3308-3318. [PMID: 33222223 DOI: 10.1002/jsfa.10960] [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: 02/28/2020] [Revised: 10/27/2020] [Accepted: 11/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Gracilibacillus alcaliphilus SK51.001, a strain that produces β-CGTase (β-cyclodextrin glucanotransferase) (EC 2.4.1.19), was screened and isolated from Sudanese soil. The objective of this study was to sequence and characterize the β-CGTase gene from G. alcaliphilus SK51.001. RESULTS According to 16S rRNA analysis of the strain and its morphological shape, it was identified as G. alcaliphilus. The β-CGTase gene was successfully cloned, sequenced, and expressed in Escherichia coli BL21. This gene showed 706 amino acid residues including 33 amino acids as a signal peptide. The active site residues of G. alcaliphilus SK51.001CGTase were described using enzyme modeling and docking with the products. The estimated molecular mass of G. alcaliphilus SK51.001CGTase was approximately 74 kDa as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and the evaluation of the gel filtration showed approximately 85 kDa, which means G. alcaliphilus SK51.001CGTase is a monomer. The optimum temperature and pH of G. alcaliphilus SK51.001CGTase were 60 °C and 7.0 respectively. Gracilibacillus alcaliphilus SK51.001CGTase was comparatively stable at a pH levels between 6.0 and 9.0 and temperatures of 30-50 °C. The activity of G. alcaliphilus SK51.001CGTase was increased by Ni2+ , and Co2+ but inhibited by Al3+ and Fe3+ . The kinetic parameters of Km and Vmax were 2068.52 μg mL-1 and 0.13 μmol mL-1 min-1 , respectively. CONCLUSION Gracilibacillus alcaliphilus SK51.001CGTase could hydrolyze soluble starch into α-, β-, and γ-cyclodextrin in a ratio of 2: 83: 15% respectively. This high ratio production of β-CD could allow the enzyme to be used in β-CD production. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Mohammed Abdalla
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory of Food Science and Safety, Jiangnan University, Wuxi, China
- Department of Food Processing, Faculty of Engineering, University of El Imam El Mahadi, Kosti, Sudan
| | - Hinawi Am Hassanin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory of Food Science and Safety, Jiangnan University, Wuxi, China
| | - Xiaolin Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory of Food Science and Safety, Jiangnan University, Wuxi, China
| | - Muhammad W Iqbal
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory of Food Science and Safety, Jiangnan University, Wuxi, China
| | - Emad Karrar
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory of Food Science and Safety, Jiangnan University, Wuxi, China
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory of Food Science and Safety, Jiangnan University, Wuxi, China
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Mohapatra S, Jena S, Jena PK, Badhai J, Acharya AN, Thatoi H. Partial consolidated bioprocessing of pretreated Pennisetum sp. by anaerobic thermophiles for enhanced bioethanol production. CHEMOSPHERE 2020; 256:127126. [PMID: 32470736 DOI: 10.1016/j.chemosphere.2020.127126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 05/26/2023]
Abstract
Rapid industrialization and consumption of fossil fuels have led to considerable progress in the production of renewable biofuels like bioethanol. Lignocellulosic biomass such as grasses serves as cheap feedstocks for the production of bioethanol. However, the process involved in lignocellulosic bioethanol production is expensive which restricts its industrial production. The present study thus attempted to investigate a partially consolidated bioprocessing (PCB) approach using two isolated anaerobic thermophiles i.e. Bacillus paranthracis and Bacillus nitratireducens for direct conversion of ultra-sonication assisted sodium hydroxide (UA-NaOH) pretreated Denannath grass to bioethanol in co-culture consortium batch fermentation experiments. The process parameters for the PCB approach were optimized using the Box-Behnken design of Response Surface Methodology (RSM). The parameters that were considered were substrate concentration (5-10 g), incubation time (30-66 h), inoculum volume [1:1 to 3:3 (% v/v) and temperature (50-65 °C). The maximum ethanol concentration of 8.46 mM (0.39 g/L from 7.5 g/L of substrate loading) and ethanol yield (Yp/s) of 0.55 g/g of reducing sugar was obtained at 57.5 °C. In the same conditions the cellulase and xylanase activities were 0.8 U/mL and 11.53 U/mL respectively, while the lactate and acetate concentrations were 0.2 mM (0.009 g/L) and 2.9 mM (0.13 g/L) correspondingly. An increase in the substrate loadings to 250 g/L in a batch fermenter (3 L) resulted in the production of 373.35 mM (17.1 g/L) of ethanol concentration and Yp/s of 0.16 g/g of reducing sugar.
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Affiliation(s)
- Sonali Mohapatra
- Department of Biotechnology, College of Engineering & Technology, Ghatika, Bhubaneswar, 751003, India.
| | - Swarnamanjuri Jena
- Department of Biotechnology, College of Engineering & Technology, Ghatika, Bhubaneswar, 751003, India
| | - Pradip Kumar Jena
- Department of Chemistry, Odisha University of Agricultural Technology, Bhubaneswar, 751003, India
| | | | - Achyuta Nanda Acharya
- Department of Chemistry, College of Engineering & Technology, Ghatika, Bhubaneswar, 751003, India
| | - Hrudayanath Thatoi
- Department of Biotechnology North Odisha University, Baripada, 757003, India
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Mahmood S, Iqbal MW, Riaz T, Zhang W, Mu W. Characterization of recombinant L-ribose isomerase acquired from Cryobacterium sp. N21 with potential application in L-ribulose production. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Development of a thermophilic coculture for corn fiber conversion to ethanol. Nat Commun 2020; 11:1937. [PMID: 32321909 PMCID: PMC7176698 DOI: 10.1038/s41467-020-15704-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/25/2020] [Indexed: 12/27/2022] Open
Abstract
The fiber in corn kernels, currently unutilized in the corn to ethanol process, represents an opportunity for introduction of cellulose conversion technology. We report here that Clostridium thermocellum can solubilize over 90% of the carbohydrate in autoclaved corn fiber, including its hemicellulose component glucuronoarabinoxylan (GAX). However, Thermoanaerobacterium thermosaccharolyticum or several other described hemicellulose-fermenting thermophilic bacteria can only partially utilize this GAX. We describe the isolation of a previously undescribed organism, Herbinix spp. strain LL1355, from a thermophilic microbiome that can consume 85% of the recalcitrant GAX. We sequence its genome, and based on structural analysis of the GAX, identify six enzymes that hydrolyze GAX linkages. Combinations of up to four enzymes are successfully expressed in T. thermosaccharolyticum. Supplementation with these enzymes allows T. thermosaccharolyticum to consume 78% of the GAX compared to 53% by the parent strain and increases ethanol yield from corn fiber by 24%. Corn fiber is a difficult feedstock to utilize due to its recalcitrant hemicellulose. Here, the authors characterize the recalcitrant structures, isolate a new bacterium to consume the hemicellulose, identify its enzymes, and show the benefit with increased conversion of corn fiber to ethanol.
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8
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Mahmood S, Iqbal MW, Riaz T, Hassanin HA, Zhu Y, Ni D, Mu W. Characterization of a recombinant l-ribose isomerase from Mycetocola miduiensis and its application for the production of l-ribulose. Enzyme Microb Technol 2020; 135:109510. [DOI: 10.1016/j.enzmictec.2020.109510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/08/2020] [Accepted: 01/12/2020] [Indexed: 11/30/2022]
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9
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A Staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis. Nat Commun 2020; 11:1539. [PMID: 32210242 PMCID: PMC7093394 DOI: 10.1038/s41467-020-15344-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 03/03/2020] [Indexed: 11/08/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic and fatal disease of unknown etiology; however, apoptosis of lung alveolar epithelial cells plays a role in disease progression. This intractable disease is associated with increased abundance of Staphylococcus and Streptococcus in the lungs, yet their roles in disease pathogenesis remain elusive. Here, we report that Staphylococcus nepalensis releases corisin, a peptide conserved in diverse staphylococci, to induce apoptosis of lung epithelial cells. The disease in mice exhibits acute exacerbation after intrapulmonary instillation of corisin or after lung infection with corisin-harboring S. nepalensis compared to untreated mice or mice infected with bacteria lacking corisin. Correspondingly, the lung corisin levels are significantly increased in human IPF patients with acute exacerbation compared to patients without disease exacerbation. Our results suggest that bacteria shedding corisin are involved in acute exacerbation of IPF, yielding insights to the molecular basis for the elevation of staphylococci in pulmonary fibrosis.
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Cann I, Pereira GV, Abdel-Hamid AM, Kim H, Wefers D, Kayang BB, Kanai T, Sato T, Bernardi RC, Atomi H, Mackie RI. Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products. Appl Environ Microbiol 2020; 86:e02296-19. [PMID: 31980431 PMCID: PMC7082577 DOI: 10.1128/aem.02296-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Renewable fuels have gained importance as the world moves toward diversifying its energy portfolio. A critical step in the biomass-to-bioenergy initiative is deconstruction of plant cell wall polysaccharides to their unit sugars for subsequent fermentation to fuels. To acquire carbon and energy for their metabolic processes, diverse microorganisms have evolved genes encoding enzymes that depolymerize polysaccharides to their carbon/energy-rich building blocks. The microbial enzymes mostly target the energy present in cellulose, hemicellulose, and pectin, three major forms of energy storage in plants. In the effort to develop bioenergy as an alternative to fossil fuel, a common strategy is to harness microbial enzymes to hydrolyze cellulose to glucose for fermentation to fuels. However, the conversion of plant biomass to renewable fuels will require both cellulose and hemicellulose, the two largest components of the plant cell wall, as feedstock to improve economic feasibility. Here, we explore the enzymes and strategies evolved by two well-studied bacteria to depolymerize the hemicelluloses xylan/arabinoxylan and mannan. The sets of enzymes, in addition to their applications in biofuels and value-added chemical production, have utility in animal feed enzymes, a rapidly developing industry with potential to minimize adverse impacts of animal agriculture on the environment.
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Affiliation(s)
- Isaac Cann
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
| | - Gabriel V Pereira
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ahmed M Abdel-Hamid
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Daniel Wefers
- Karlsruhe Institute of Technology, Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe, Germany
| | - Boniface B Kayang
- Department of Animal Science, School of Agriculture, University of Ghana, Legon, Ghana
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
| | - Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
- JST, CREST, Tokyo, Japan
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
- JST, CREST, Tokyo, Japan
| | - Roderick I Mackie
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Waheed Iqbal M, Riaz T, Hassanin HA, Zhang W, Saeed M, Mahmood S, Abdalla M, Mu W. Biochemical characterization of recombinant L-fucose isomerase from Caldanaerobius polysaccharolyticus for L-fuculose production. Int J Biol Macromol 2020; 146:965-975. [DOI: 10.1016/j.ijbiomac.2019.09.221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/24/2019] [Accepted: 09/20/2019] [Indexed: 01/22/2023]
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12
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Khomyakova MA, Merkel AY, Kopitsyn DS, Bonch-Osmolovskaya EA, Slobodkin AI. Calorimonas adulescens gen. nov., sp. nov., an anaerobic thermophilic bacterium utilizing methoxylated benzoates. Int J Syst Evol Microbiol 2020; 70:2066-2071. [DOI: 10.1099/ijsem.0.004019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, thermophilic bacterium (strain A05 MBT) was isolated from Daginsky thermal springs (Sakhalin, Russia) on 2-methoxybenzoate as a substrate. Cells of the strain were motile long rods, 3.0–5.0 µm in length and 0.5–0.6 µm in diameter. The temperature range for growth was 47–68 °C, with an optimum at 60 °C. The pH range for growth was 4.5–8.0, with an optimum at pH 5.5–6.0. Strain A05 MBTdid not require NaCl for growth. The strain utilized methoxylated aromatic compounds (2-methoxybenzoate and 3,4-dimethoxybenzoate), a number of carbohydrates (glucose, fructose, mannose, trehalose, xylose, sucrose, galactose, ribose, maltose, raffinose, lactose, cellobiose and dextrin) and proteinaceous substrates (yeast extract, beef extract, peptone and tryptone). The end products of glucose fermentation were acetate, ethanol and CO2. The DNA G+C content of strain A05 MBTwas 40.2 mol% (whole-genome analysis). 16S rRNA gene sequence analysis revealed that strain A05MBTbelongs to the orderThermoanaerobacterales(phylumFirmicutes). The closest relative of strain A05 MBTwasCaloribacterium cisternae(94.3 % 16S rRNA gene sequence similarity). Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain A05 MBTis considered to represent a novel species of a new genus, for which the nameCalorimonas adulescensgen. nov., sp. nov. is proposed. The type strain ofCalorimonas adulescensis A05 MBT(=KCTC 15839T=VKM B-3388T).
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Affiliation(s)
- M. A. Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Russia
| | - A. Y. Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Russia
| | - D. S. Kopitsyn
- Gubkin University, Leninskiy Prospect, 65/1, 119991, Moscow, Russia
| | - E. A. Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Russia
| | - A. I. Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Russia
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Lackner N, Wagner AO, Markt R, Illmer P. pH and Phosphate Induced Shifts in Carbon Flow and Microbial Community during Thermophilic Anaerobic Digestion. Microorganisms 2020; 8:E286. [PMID: 32093251 PMCID: PMC7074938 DOI: 10.3390/microorganisms8020286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 01/11/2023] Open
Abstract
pH is a central environmental factor influencing CH4 production from organic substrates, as every member of the complex microbial community has specific pH requirements. Here, we show how varying pH conditions (5.0-8.5, phosphate buffered) and the application of a phosphate buffer per se induce shifts in the microbial community composition and the carbon flow during nine weeks of thermophilic batch digestion. Beside monitoring the methane production as well as volatile fatty acid concentrations, amplicon sequencing of the 16S rRNA gene was conducted. The presence of 100 mM phosphate resulted in reduced CH4 production during the initial phase of the incubation, which was characterized by a shift in the dominant methanogenic genera from a mixed Methanosarcina and Methanoculleus to a pure Methanoculleus system. In buffered samples, acetate strongly accumulated in the beginning of the batch digestion and subsequently served as a substrate for methanogens. Methanogenesis was permanently inhibited at pH values ≤5.5, with the maximum CH4 production occurring at pH 7.5. Adaptations of the microbial community to the pH variations included shifts in the archaeal and bacterial composition, as less competitive organisms with a broad pH range were able to occupy metabolic niches at unfavorable pH conditions.
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Affiliation(s)
- Nina Lackner
- Department of Microbiology, Universität Innsbruck, 6020 Innsbruck, Austria; (A.O.W.); (R.M.); (P.I.)
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Characterization of a novel d-arabinose isomerase from Thermanaeromonas toyohensis and its application for the production of d-ribulose and l-fuculose. Enzyme Microb Technol 2019; 131:109427. [DOI: 10.1016/j.enzmictec.2019.109427] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/09/2019] [Accepted: 09/10/2019] [Indexed: 12/18/2022]
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15
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Enzymatic Mechanism for Arabinan Degradation and Transport in the Thermophilic Bacterium Caldanaerobius polysaccharolyticus. Appl Environ Microbiol 2017; 83:AEM.00794-17. [PMID: 28710263 DOI: 10.1128/aem.00794-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/05/2017] [Indexed: 12/21/2022] Open
Abstract
The plant cell wall polysaccharide arabinan provides an important supply of arabinose, and unraveling arabinan-degrading strategies by microbes is important for understanding its use as a source of energy. Here, we explored the arabinan-degrading enzymes in the thermophilic bacterium Caldanaerobius polysaccharolyticus and identified a gene cluster encoding two glycoside hydrolase (GH) family 51 α-l-arabinofuranosidases (CpAbf51A, CpAbf51B), a GH43 endoarabinanase (CpAbn43A), a GH27 β-l-arabinopyranosidase (CpAbp27A), and two GH127 β-l-arabinofuranosidases (CpAbf127A, CpAbf127B). The genes were expressed as recombinant proteins, and the functions of the purified proteins were determined with para-nitrophenyl (pNP)-linked sugars and naturally occurring pectin structural elements as the substrates. The results demonstrated that CpAbn43A is an endoarabinanase while CpAbf51A and CpAbf51B are α-l-arabinofuranosidases that exhibit diverse substrate specificities, cleaving α-1,2, α-1,3, and α-1,5 linkages of purified arabinan-oligosaccharides. Furthermore, both CpAbf127A and CpAbf127B cleaved β-arabinofuranose residues in complex arabinan side chains, thus providing evidence of the function of this family of enzymes on such polysaccharides. The optimal temperatures of the enzymes ranged between 60°C and 75°C, and CpAbf43A and CpAbf51A worked synergistically to release arabinose from branched and debranched arabinan. Furthermore, the hydrolytic activity on branched arabinan oligosaccharides and degradation of pectic substrates by the endoarabinanase and l-arabinofuranosidases suggested a microbe equipped with diverse activities to degrade complex arabinan in the environment. Based on our functional analyses of the genes in the arabinan degradation cluster and the substrate-binding studies on a component of the cognate transporter system, we propose a model for arabinan degradation and transport by C. polysaccharolyticusIMPORTANCE Genomic DNA sequencing and bioinformatic analysis allowed the identification of a gene cluster encoding several proteins predicted to function in arabinan degradation and transport in C. polysaccharolyticus The analysis of the recombinant proteins yielded detailed insights into the putative arabinan metabolism of this thermophilic bacterium. The use of various branched arabinan oligosaccharides provided a detailed understanding of the substrate specificities of the enzymes and allowed assignment of two new GH127 polypeptides as β-l-arabinofuranosidases able to degrade pectic substrates, thus expanding our knowledge of this rare group of glycoside hydrolases. In addition, the enzymes showed synergistic effects for the degradation of arabinans at elevated temperatures. The enzymes characterized from the gene cluster are, therefore, of utility for arabinose production in both the biofuel and food industries.
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O-Thong S, Khongkliang P, Mamimin C, Singkhala A, Prasertsan P, Birkeland NK. Draft genome sequence of Thermoanaerobacterium sp. strain PSU-2 isolated from thermophilic hydrogen producing reactor. GENOMICS DATA 2017; 12:49-51. [PMID: 28337413 PMCID: PMC5347514 DOI: 10.1016/j.gdata.2017.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 02/24/2017] [Indexed: 11/17/2022]
Abstract
Thermoanaerobacterium sp. strain PSU-2 was isolated from thermophilic hydrogen producing reactor and subjected to draft genome sequencing on 454 pyrosequencing and annotated on RAST. The draft genome sequence of strain PSU-2 contains 2,552,497 bases with an estimated G + C content of 35.2%, 2555 CDS, 8 rRNAs and 57 tRNAs. The strain had a number of genes responsible for carbohydrates metabolic, amino acids and derivatives, and protein metabolism of 17.7%, 14.39% and 9.81%, respectively. Strain PSU-2 also had gene responsible for hydrogen biosynthesis as well as the genes related to Ni-Fe hydrogenase. Comparative genomic analysis indicates strain PSU-2 shares about 94% genome sequence similarity with Thermoanaerobacterium xylanolyticum LX-11. The nucleotide sequence of this draft genome was deposited into DDBJ/ENA/GenBank under the accession MSQD00000000.
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Affiliation(s)
- Sompong O-Thong
- Research Center in Energy and Environment, Faculty of Science, Thaksin University, Phatthalung 93210, Thailand; Biotechnology Program, Department of Biology, Faculty of Science, Thaksin University, Phatthalung 93210, Thailand
| | - Peerawat Khongkliang
- Biotechnology Program, Department of Biology, Faculty of Science, Thaksin University, Phatthalung 93210, Thailand
| | - Chonticha Mamimin
- Biotechnology Program, Department of Biology, Faculty of Science, Thaksin University, Phatthalung 93210, Thailand
| | - Apinya Singkhala
- Biotechnology Program, Department of Biology, Faculty of Science, Thaksin University, Phatthalung 93210, Thailand
| | - Poonsuk Prasertsan
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Songkhla 90112, Thailand
| | - Nils-Kåre Birkeland
- Department of Biology and Centre for Geobiology, University of Bergen, P.O. Box 7800, N-5020 Bergen, Norway
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Description of a new anaerobic thermophilic bacterium, Thermoanaerobacterium butyriciformans sp. nov. Syst Appl Microbiol 2017; 40:86-91. [PMID: 28057375 DOI: 10.1016/j.syapm.2016.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 11/23/2016] [Accepted: 11/25/2016] [Indexed: 11/22/2022]
Abstract
Strain USBA-019T, an anaerobic and thermophilic strain, was identified as a new member of the genus Thermoanaerobacterium. USBA-019T cells are gram-positive, strictly anaerobic, thermophilic, chemoorganotrophic, moderately acidophilic, non-motile, endospore-forming, slightly curved, and rod-shaped. Cells measure 0.4×3.0-7.0μm. Optimal growth occurs at 50-55°C (35-65°C). Optimum pH is 5.0-5.5 (4.0-8.5). Thiosulfate, elemental sulfur and nitrate were utilized as electron acceptors. Fermentation of glucose, lactose, cellobiose, galactose, arabinose, xylose, starch and xylan primarily produced acetate and butyrate. Xylan, starch and cellobiose produced ethanol and starch, cellobiose, galactose, arabinose and mannose produced lactic acid. Phylogenetic analyses based on 16S rRNA gene sequence comparison and genomic relatedness indices show the close relation of USBA-019T to Thermoanaerobacterium thermostercoris and Thermoanaerobacterium aotearoense (similarity value: 99%). Hybridization of USBA-019T, Th. thermostercoris DSM22141T and Th. aotearoense DMS10170T found DNA-DNA relatedness of 33.2% and 18.2%, respectively. Based on phenotypic, chemotaxonomic and phylogenetic evidence, along with low identity at whole genome level, USBA-019T is a novel species of the genus Thermoanaerobacterium which we propose to name Thermoanaerobacterium butyriciformans sp. nov. The type strain is USBA-019T (=CMPUJ U-019T=DSM 101588T).
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Abstract
The deconstruction of biomass is a pivotal process for the manufacture of target products using microbial cells and their enzymes. But the enzymes that possess a significant role in the breakdown of biomass remain relatively unexplored. Thermophilic microorganisms are of special interest as a source of novel thermostable enzymes. Many thermophilic microorganisms possess properties suitable for biotechnological and commercial use. There is, indeed, a considerable demand for a new generation of stable enzymes that are able to withstand severe conditions in industrial processes by replacing or supplementing traditional chemical processes. This manuscript reviews the pertinent role of thermophilic microorganisms as a source for production of thermostable enzymes, factors afftecting them, recent patents on thermophiles and moreso their wide spectrum applications for commercial and biotechnological use.
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Effect of pH on Thermoanaerobacterium thermosaccharolyticum DSM 571 growth, spore heat resistance and recovery. Food Microbiol 2016; 55:64-72. [DOI: 10.1016/j.fm.2015.11.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/03/2015] [Accepted: 11/25/2015] [Indexed: 11/19/2022]
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Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters. Appl Environ Microbiol 2015; 82:1519-1529. [PMID: 26712547 DOI: 10.1128/aem.03360-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/18/2015] [Indexed: 01/03/2023] Open
Abstract
Cellulose and xylan are two major components of lignocellulosic biomass, which represents a potentially important energy source, as it is abundant and can be converted to methane by microbial action. However, it is recalcitrant to hydrolysis, and the establishment of a complete anaerobic digestion system requires a specific repertoire of microbial functions. In this study, we maintained 2-year enrichment cultures of anaerobic digestion sludge amended with cellulose or xylan to investigate whether a cellulose- or xylan-digesting microbial system could be assembled from sludge previously used to treat neither of them. While efficient methane-producing communities developed under mesophilic (35°C) incubation, they did not under thermophilic (55°C) conditions. Illumina amplicon sequencing results of the archaeal and bacterial 16S rRNA genes revealed that the mature cultures were much lower in richness than the inocula and were dominated by single archaeal (genus Methanobacterium) and bacterial (order Clostridiales) groups, although at finer taxonomic levels the bacteria were differentiated by substrates. Methanogenesis was primarily via the hydrogenotrophic pathway under all conditions, although the identity and growth requirements of syntrophic acetate-oxidizing bacteria were unclear. Incubation conditions (substrate and temperature) had a much greater effect than inoculum source in shaping the mature microbial community, although analysis based on unweighted UniFrac distance found that the inoculum still determined the pool from which microbes could be enriched. Overall, this study confirmed that anaerobic digestion sludge treating nonlignocellulosic material is a potential source of microbial cellulose- and xylan-digesting functions given appropriate enrichment conditions.
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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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22
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Recent Advances in Second Generation Ethanol Production by Thermophilic Bacteria. ENERGIES 2014. [DOI: 10.3390/en8010001] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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23
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Chekan JR, Kwon IH, Agarwal V, Dodd D, Revindran V, Mackie RI, Cann I, Nair SK. Structural and biochemical basis for mannan utilization by Caldanaerobius polysaccharolyticus strain ATCC BAA-17. J Biol Chem 2014; 289:34965-77. [PMID: 25342756 DOI: 10.1074/jbc.m114.579904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hemicelluloses, the polysaccharide component of plant cell walls, represent one of the most abundant biopolymers in nature. The most common hemicellulosic constituents of softwoods, such as conifers and cycads, are mannans consisting of a 1,4-linked β-mannopyranosyl main chain with branch decorations. Efforts toward the utilization of hemicellulose for bioconversion into cellulosic biofuels have resulted in the identification of several families of glycoside hydrolases that can degrade mannan. However, effective biofermentation of manno-oligosaccharides is limited by a lack of appropriate uptake route in ethanologenic organisms. Here, we used transcriptome sequencing to gain insights into mannan degradation by the thermophilic anaerobic bacterium Caldanaerobius polysaccharolyticus. The most highly up-regulated genes during mannan fermentation occur in a cluster containing several genes encoding enzymes for efficient mannan hydrolysis as well as a solute-binding protein (CpMnBP1) that exhibits specificity for short mannose polymers but exhibited the flexibility to accommodate branched polysaccharide decorations. Co-crystal structures of CpMnBP1 in complex with mannobiose (1.4-Å resolution) and mannotriose (2.2-Å resolution) revealed the molecular rationale for chain length and oligosaccharide specificity. Calorimetric analysis of several active site variants confirmed the roles of residues critical to the function of CpMnBP1. This work represents the first biochemical characterization of a mannose-specific solute-binding protein and provides a framework for engineering mannan utilization capabilities for microbial fermentation.
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Affiliation(s)
| | | | | | - Dylan Dodd
- Institute for Genomic Biology, Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801 Microbiology
| | - Vanessa Revindran
- Institute for Genomic Biology, Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
| | - Roderick I Mackie
- Institute for Genomic Biology, Animal Sciences, and Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801
| | - Isaac Cann
- Institute for Genomic Biology, Animal Sciences, and Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801 Microbiology,
| | - Satish K Nair
- From the Departments of Biochemistry, Institute for Genomic Biology, Center for Biophysics and Computational Biology, and
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24
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Kallistova AY, Goel G, Nozhevnikova AN. Microbial diversity of methanogenic communities in the systems for anaerobic treatment of organic waste. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714050142] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Cao GL, Zhao L, Wang AJ, Wang ZY, Ren NQ. Single-step bioconversion of lignocellulose to hydrogen using novel moderately thermophilic bacteria. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:82. [PMID: 24920960 PMCID: PMC4052809 DOI: 10.1186/1754-6834-7-82] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/16/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Consolidated bioprocessing (CBP) of lignocellulosic biomass to hydrogen offers great potential for lower cost and higher efficiency compared to processes featuring dedicated cellulase production. Current studies on CBP-based hydrogen production mainly focus on using the thermophilic cellulolytic bacterium Clostridium thermocellum and the extremely thermophilic cellulolytic bacterium Caldicellulosiruptor saccharolyticus. However, no studies have demonstrated that the strains in the genus Thermoanaerobacterium could be used as the sole microorganism to accomplish both cellulose degradation and H2 generation. RESULTS We have specifically screened for moderately thermophilic cellulolytic bacteria enabling to produce hydrogen directly from conversion of lignocellulosic materials. Three new strains of thermophilic cellulolytic bacteria in the genus Thermoanaerobacterium growing at a temperature of 60°C were isolated. All of them grew well on various plant polymers including microcrystalline cellulose, filter paper, xylan, glucose, and xylose. In particular, the isolated bacterium, designated as Thermoanaerobacterium thermosaccharolyticum M18, showed high cellulolytic activity and a high yield of H2. When it was grown in 0.5% microcrystalline cellulose, approximately 82% cellulose was consumed, and the H2 yield and maximum production rate reached 10.86 mmol/g Avicel and 2.05 mmol/L/h, respectively. Natural lignocellulosic materials without any physicochemical or biological pretreatment also supported appreciable growth of strain M18, which resulted in 56.07% to 62.71% of insoluble cellulose and hemicellulose polymer degradation in corn cob, corn stalk, and wheat straw with a yield of 3.23 to 3.48 mmol H2/g substrate and an average production rate of 0.10 to 0.13 mmol H2/L/h. CONCLUSIONS The newly isolated strain T. thermosaccharolyticum M18 displayed effective degradation of lignocellulose and produced large amounts of hydrogen. This is the first report of a Thermoanaerobacterium species presenting cellulolytic characteristics, and this species thus represents a novel cellulolytic bacterium distinguished from all other known cellulolytic bacteria. In comparison, the extraordinary yield and specific rate of hydrogen for strain M18 obtained from lignocellulose make it more attractive in monoculture fermentation. T. thermosaccharolyticum M18 is thus a potential candidate for rapid conversion of lignocellulose to biohydrogen in a single step.
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Affiliation(s)
- Guang-Li Cao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150090, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhen-Yu Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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Oyama T, Schmitz GE, Dodd D, Han Y, Burnett A, Nagasawa N, Mackie RI, Nakamura H, Morikawa K, Cann I. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases. PLoS One 2013; 8:e80448. [PMID: 24278284 PMCID: PMC3835425 DOI: 10.1371/journal.pone.0080448] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/03/2013] [Indexed: 11/30/2022] Open
Abstract
CpMan5B is a glycoside hydrolase (GH) family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196) in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.
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Affiliation(s)
- Takuji Oyama
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - George E. Schmitz
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Dylan Dodd
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Yejun Han
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Alanna Burnett
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Naoko Nagasawa
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Kosuke Morikawa
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Isaac Cann
- Institute for Protein Research, Osaka University, Osaka, Japan
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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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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Penislus Shiyan S, Krishnaveni M. Hydrogen production by Pseudomonas stutzeri JX442762 isolated from thermal soil at Mettur power station, Salem district, Tamil Nadu, India. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.jopr.2012.11.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Rittmann S, Herwig C. A comprehensive and quantitative review of dark fermentative biohydrogen production. Microb Cell Fact 2012; 11:115. [PMID: 22925149 PMCID: PMC3443015 DOI: 10.1186/1475-2859-11-115] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 08/03/2012] [Indexed: 01/25/2023] Open
Abstract
Biohydrogen production (BHP) can be achieved by direct or indirect biophotolysis, photo-fermentation and dark fermentation, whereof only the latter does not require the input of light energy. Our motivation to compile this review was to quantify and comprehensively report strains and process performance of dark fermentative BHP. This review summarizes the work done on pure and defined co-culture dark fermentative BHP since the year 1901. Qualitative growth characteristics and quantitative normalized results of H2 production for more than 2000 conditions are presented in a normalized and therefore comparable format to the scientific community.Statistically based evidence shows that thermophilic strains comprise high substrate conversion efficiency, but mesophilic strains achieve high volumetric productivity. Moreover, microbes of Thermoanaerobacterales (Family III) have to be preferred when aiming to achieve high substrate conversion efficiency in comparison to the families Clostridiaceae and Enterobacteriaceae. The limited number of results available on dark fermentative BHP from fed-batch cultivations indicates the yet underestimated potential of this bioprocessing application. A Design of Experiments strategy should be preferred for efficient bioprocess development and optimization of BHP aiming at improving medium, cultivation conditions and revealing inhibitory effects. This will enable comparing and optimizing strains and processes independent of initial conditions and scale.
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Affiliation(s)
- Simon Rittmann
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorferstraße 1a, Vienna University of Technology, Vienna, 1060, Austria
| | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Gumpendorferstraße 1a, Vienna University of Technology, Vienna, 1060, Austria
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Han Y, Agarwal V, Dodd D, Kim J, Bae B, Mackie RI, Nair SK, Cann IKO. Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus. J Biol Chem 2012; 287:34946-34960. [PMID: 22918832 DOI: 10.1074/jbc.m112.391532] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.
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Affiliation(s)
- Yejun Han
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801
| | - Vinayak Agarwal
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801; Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Dylan Dodd
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Microbiology, University of Illinois, Urbana, Illinois 61801
| | - Jason Kim
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801
| | - Brian Bae
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Roderick I Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801
| | - Satish K Nair
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801; Department of Biochemistry, University of Illinois, Urbana, Illinois 61801.
| | - Isaac K O Cann
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois 61801; Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801; Department of Microbiology, University of Illinois, Urbana, Illinois 61801; Department of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801; Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801.
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Burgess EA, Unrine JM, Mills GL, Romanek CS, Wiegel J. Comparative geochemical and microbiological characterization of two thermal pools in the Uzon Caldera, Kamchatka, Russia. MICROBIAL ECOLOGY 2012; 63:471-489. [PMID: 22124570 DOI: 10.1007/s00248-011-9979-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 11/02/2011] [Indexed: 05/31/2023]
Abstract
Arkashin Schurf (Arkashin) and Zavarzin Spring (Zavarzin), two active thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied for geochemical and microbiological characterization. Arkashin, the smaller of the two pools, had broader temperature and pH ranges, and the sediments had higher concentrations of total As (4,250 mg/kg) relative to Zavarzin (48.9 mg/kg). Glycerol dialkyl glycerol tetraether profiles represented distinct archaeal communities in each pool and agreed well with previous studies of these pools. Although no archaeal 16S rRNA sequences were recovered from Arkashin, sequences recovered from Zavarzin were mostly representatives of the Crenarchaeota and "Korarchaeota," and 13% of the sequences were unclassifiable. The bacterial community in Arkashin was dominated by uncultured "Bacteroidetes," Hydrogenobaculum of the Aquificales and Variovorax of the Betaproteobacteria, and 19% of the sequences remained unclassified. These results were consistent with other studies of As-rich features. The most abundant members of the Zavarzin bacterial community included the Chloroflexi, as well as members of the classes Deltaproteobacteria and Clostridia. In addition, 24% of the sequences were unclassified and at least 5% of those represent new groups among the established Bacterial phyla. Ecological structure in each pool was inferred from taxonomic classifications and bulk stable isotope δ values of C, N, and S. Hydrogenobaculum was responsible for primary production in Arkashin. However, in Zavarzin, the carbon source appeared to be allochthonous to the identified bacterial community members. Additionally, sequences related to organisms expected to participate in N and S cycles were identified from both pools.
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Affiliation(s)
- Elizabeth A Burgess
- Savannah River Ecology Laboratory, University of Georgia, P.O. Drawer E, Aiken, SC 29802, USA.
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Slobodkina GB, Kolganova TV, Kostrikina NA, Bonch-Osmolovskaya EA, Slobodkin AI. Caloribacterium cisternae gen. nov., sp. nov., an anaerobic thermophilic bacterium from an underground gas storage reservoir. Int J Syst Evol Microbiol 2011; 62:1543-1547. [PMID: 21856985 DOI: 10.1099/ijs.0.033076-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anaerobic, moderately thermophilic bacterium (strain SGL43(T)) was isolated from Severo-Stavropolskoye underground gas storage reservoir (Russia). Cells of strain SGL43(T) were motile straight rods, 0.4 µm in diameter and 2.0-3.0 µm in length. The temperature range for growth was 28-65 °C, with optimum growth at 50 °C. The pH range for growth was 5.5-8.0, with optimum growth at pH 7.0-7.5. Growth of strain SGL43(T) was observed at NaCl concentrations of 0-4.0% (w/v) with optimum growth at 1.0% (w/v) NaCl. Substrates utilized by strain SGL43(T) included peptone, yeast extract, glucose, fructose, maltose, galactose, pyruvate and citrate. Products of glucose or citrate fermentation were acetate, hydrogen and CO(2). Thiosulfate was reduced to sulfide. The DNA G+C content of strain SGL43(T) was 43.1 mol%. 16S rRNA gene sequence analysis revealed that strain SGL43(T) belongs to the order Thermoanaerobacterales (phylum 'Firmicutes'). The closest relative of strain SGL43(T) was Thermoanaerobacterium saccharolyticum (86.2% 16S rRNA gene sequence similarity with the type strain). Based on the data presented here, strain SGL43(T) is considered to represent a novel species of a new genus, for which the name Caloribacterium cisternae gen. nov., sp. nov. is proposed. The type strain of Caloribacterium cisternae, the type species of the genus, is SGL43(T) (=DSM 23830(T)=VKM B-2670(T)).
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Affiliation(s)
- G B Slobodkina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - T V Kolganova
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - N A Kostrikina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - E A Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312 Moscow, Russia
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Comparative analyses of two thermophilic enzymes exhibiting both beta-1,4 mannosidic and beta-1,4 glucosidic cleavage activities from Caldanaerobius polysaccharolyticus. J Bacteriol 2010; 192:4111-21. [PMID: 20562312 DOI: 10.1128/jb.00257-10] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hydrolysis of polysaccharides containing mannan requires endo-1,4-beta-mannanase and 1,4-beta-mannosidase activities. In the current report, the biochemical properties of two endo-beta-1,4-mannanases (Man5A and Man5B) from Caldanaerobius polysaccharolyticus were studied. Man5A is composed of an N-terminal signal peptide (SP), a catalytic domain, two carbohydrate-binding modules (CBMs), and three surface layer homology (SLH) repeats, whereas Man5B lacks the SP, CBMs, and SLH repeats. To gain insights into how the two glycoside hydrolase family 5 (GH5) enzymes may aid the bacterium in energy acquisition and also the potential application of the two enzymes in the biofuel industry, two derivatives of Man5A (Man5A-TM1 [TM1 stands for truncational mutant 1], which lacks the SP and SLH repeats, and Man5A-TM2, which lacks the SP, CBMs, and SLH repeats) and the wild-type Man5B were biochemically analyzed. The Man5A derivatives displayed endo-1,4-beta-mannanase and endo-1,4-beta-glucanase activities and hydrolyzed oligosaccharides with a degree of polymerization (DP) of 4 or higher. Man5B exhibited endo-1,4-beta-mannanase activity and little endo-1,4-beta-glucanase activity; however, this enzyme also exhibited 1,4-beta-mannosidase and cellodextrinase activities. Man5A-TM1, compared to either Man5A-TM2 or Man5B, had higher catalytic activity with soluble and insoluble polysaccharides, indicating that the CBMs enhance catalysis of Man5A. Furthermore, Man5A-TM1 acted synergistically with Man5B in the hydrolysis of beta-mannan and carboxymethyl cellulose. The versatility of the two enzymes, therefore, makes them a resource for depolymerization of mannan-containing polysaccharides in the biofuel industry. Furthermore, on the basis of the biochemical and genomic data, a molecular mechanism for utilization of mannan-containing nutrients by C. polysaccharolyticus is proposed.
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Romano I, Dipasquale L, Orlando P, Lama L, d’Ippolito G, Pascual J, Gambacorta A. Thermoanaerobacterium thermostercus sp. nov., a new anaerobic thermophilic hydrogen-producing bacterium from buffalo-dung. Extremophiles 2010; 14:233-40. [DOI: 10.1007/s00792-010-0303-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 01/27/2010] [Indexed: 11/28/2022]
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Nelson DM, Glawe AJ, Labeda DP, Cann IKO, Mackie RI. Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundra. Int J Syst Evol Microbiol 2009; 59:1708-14. [DOI: 10.1099/ijs.0.004572-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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van Groenestijn JW, Geelhoed JS, Goorissen HP, Meesters KPM, Stams AJM, Claassen PAM. Performance and population analysis of a non-sterile trickle bed reactor inoculated with Caldicellulosiruptor saccharolyticus, a thermophilic hydrogen producer. Biotechnol Bioeng 2009; 102:1361-7. [PMID: 19016484 DOI: 10.1002/bit.22185] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Non-axenic operation of a 400 L trickle bed reactor inoculated with the thermophile Caldicellulosiruptor saccharolyticus, yielded 2.8 mol H2/mol hexose converted. The reactor was fed with a complex medium with sucrose as the main substrate, continuously flushed with nitrogen gas, and operated at 73 degrees C. The volumetric productivity was 22 mmol H2/(L filterbed h). Acetic acid and lactic acid were the main by-products in the liquid phase. Production of lactic acid occurred when hydrogen partial pressure was elevated above 2% and during suboptimal fermentation conditions that also resulted in the presence of mono- and disaccharides in the effluent. Methane production was negligible. The microbial community was analyzed at two different time points during operation. Initially, other species related to members of the genera Thermoanaerobacterium and Caldicellulosiruptor were present in the reactor. However, these were out-competed by C. saccharolyticus during a period when sucrose was completely used and no saccharides were discharged with the effluent. In general, the use of pure cultures in non-sterile industrial applications is known to be less useful because of contamination. However, our results show that the applied fermentation conditions resulted in a culture of a single dominant organism with excellent hydrogen production characteristics.
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Lee M, Hidaka T, Hagiwara W, Tsuno H. Comparative performance and microbial diversity of hyperthermophilic and thermophilic co-digestion of kitchen garbage and excess sludge. BIORESOURCE TECHNOLOGY 2009; 100:578-585. [PMID: 18752938 DOI: 10.1016/j.biortech.2008.06.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 06/26/2008] [Accepted: 06/26/2008] [Indexed: 05/26/2023]
Abstract
The objective of this study was to evaluate the performance characteristics of a hyperthermophilic digester system that consists of an acidogenic reactor operated at hyperthermophilic (70 degrees C) conditions in series with a methane reactor operated at mesophilic (35 degrees C), thermophilic (55 degrees C), and hyperthermophilic (65 degrees C) conditions. Lab-scale reactors were operated continuously, and were fed with co-substrates composed of artificial kitchen garbage (TS 9.8%) and excess sludge (TS 0.5%) at the volumetric ratio of 20:80. In the acidification step, COD solubilization was in the range of 22-46% at 70 degrees C, while it was 21-29% at 55 degrees C. The average protein solubilization was 44% at 70 degrees C. The double bond fatty acid removal ratio at 70 degrees C was much higher than at 55 degrees C. These results suggested that the optimal operation conditions for the acidogenic fermenter were about 3.1 days of HRT and 4 days of SRT at 70 degrees C. Methane conversion efficiency and the VS removal percentage in the methanogenic step following acidification was around 65% and 64% on average at 55 degrees C, respectively. The optimal operational conditions for this system are acidogenesis performed at 70 degrees C and methanogenesis at 55 degrees C. The key microbes determined in the hyperthermophilic acidification step were Anaerobic thermophile IC-BH at 6.4 days of HRT and Thermoanaerobacter thermohydrosulfuricus DSM 567 at 2.4 days of HRT. These results indicated that the hyperthermophilic system provides considerable advantages in treating co-substrates containing high concentrations of proteins, lipids, and nonbiodegradable solid matter.
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Affiliation(s)
- Myungyeol Lee
- Department of Urban and Environmental Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8540, Japan
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O-Thong S, Prasertsan P, Birkeland NK. Evaluation of methods for preparing hydrogen-producing seed inocula under thermophilic condition by process performance and microbial community analysis. BIORESOURCE TECHNOLOGY 2009; 100:909-18. [PMID: 18768309 DOI: 10.1016/j.biortech.2008.07.036] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Revised: 07/17/2008] [Accepted: 07/19/2008] [Indexed: 05/08/2023]
Abstract
Five methods for preparation of hydrogen-producing seeds (base, acid, 2-bromoethanesulfonic acid (BESA), load-shock and heat shock treatments) as well as an untreated anaerobic digested sludge were compared for their hydrogen production performance and responsible microbial community structures under thermophilic condition (60 degrees C). The results showed that the load-shock treatment method was the best for enriching thermophilic hydrogen-producing seeds from mixed anaerobic cultures as it completely repressed methanogenic activity and gave the a maximum hydrogen production yield of 1.96 mol H(2) mol(-1) hexose with an hydrogen production rate of 11.2 mmol H(2) l(-1)h(-1). Load-shock and heat-shock treatments resulted in a dominance of Thermoanaerobacterium thermosaccharolyticum with acetic acid and butyric acid type of fermentation while base- and acid-treated seeds were dominated by Clostridium sp. and BESA-treated seeds were dominated by Bacillus sp. The comparative experimental results from hydrogen production performance and microbial community analysis showed that the load-shock treatment method was better than the other four methods for enriching thermophilic hydrogen-producing seeds from anaerobic digested sludge. Load-shock treated sludge was implemented in palm oil mill effluent (POME) fermentation and was found to give maximum hydrogen production rates of 13.34 mmol H(2) l(-1)h(-1) and resulted in a dominance of Thermoanaerobacterium spp. Load-shock treatment is an easy and practical method for enriching thermophilic hydrogen-producing bacteria from anaerobic digested sludge.
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Affiliation(s)
- Sompong O-Thong
- Department of Biology, Faculty of Science, Thaksin University, Patthalung 93110, Thailand
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Abstract
Thermophilic anaerobes are Archaea and Bacteria that grow optimally at temperatures of 50 degrees C or higher and do not require the use of O(2) as a terminal electron acceptor for growth. The prokaryotes with this type of physiology are studied for a variety of reasons, including (a) to understand how life can thrive under extreme conditions, (b) for their biotechnological potential, and (c) because anaerobic thermophiles are thought to share characteristics with the early evolutionary life forms on Earth. Over 300 species of thermophilic anaerobes have been described; most have been isolated from thermal environments, but some are from mesobiotic environments, and others are from environments with temperatures below 0 degrees C. In this overview, the authors outline the phylogenetic and physiological diversity of thermophilic anaerobes as currently known. The purpose of this overview is to convey the incredible diversity and breadth of metabolism within this subset of anaerobic microorganisms.
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Affiliation(s)
- Isaac D Wagner
- 212 Biological Sciences Building, 1000 Cedar Street, University of Georgia, Athens, GA 30602-2605, USA
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Koskinen PE, Beck SR, Örlygsson J, Puhakka JA. Ethanol and hydrogen production by two thermophilic, anaerobic bacteria isolated from Icelandic geothermal areas. Biotechnol Bioeng 2008; 101:679-90. [DOI: 10.1002/bit.21942] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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41
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Lee YJ, Mackie RI, Cann IKO, Wiegel J. Description of Caldanaerobius fijiensis gen. nov., sp. nov., an inulin-degrading, ethanol-producing, thermophilic bacterium from a Fijian hot spring sediment, and reclassification of Thermoanaerobacterium polysaccharolyticum and Thermoanaerobacterium zeae as Caldanaerobius polysaccharolyticus comb. nov. and Caldanaerobius zeae comb. nov. Int J Syst Evol Microbiol 2008; 58:666-70. [DOI: 10.1099/ijs.0.65329-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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O-Thong S, Prasertsan P, Intrasungkha N, Dhamwichukorn S, Birkeland NK. Improvement of biohydrogen production and treatment efficiency on palm oil mill effluent with nutrient supplementation at thermophilic condition using an anaerobic sequencing batch reactor. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.05.002] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lee YJ, Dashti M, Prange A, Rainey FA, Rohde M, Whitman WB, Wiegel J. Thermoanaerobacter sulfurigignens sp. nov., an anaerobic thermophilic bacterium that reduces 1 M thiosulfate to elemental sulfur and tolerates 90 mM sulfite. Int J Syst Evol Microbiol 2007; 57:1429-1434. [PMID: 17625170 DOI: 10.1099/ijs.0.64748-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two anaerobic thermophilic bacteria, designated strains JW/SL824 and JW/SL-NZ826(T), were isolated from an acidic volcanic steam outlet on White Island, New Zealand. Cells were rod-shaped, spore-forming, motile and Gram-stain negative, but contained Gram-type positive cell wall. Strain JW/SL-NZ826(T) utilized various carbohydrates including xylose and glucose. The fermentation end products produced from glucose in the absence of thiosulfate were lactate, ethanol, acetate, CO(2) and H(2). The temperature range for growth was 34-72 degrees C, with an optimum at 63-67 degrees C. The pH(60 degrees C) range for growth was 4.0-8.0, with an optimum at 5.0-6.5. The doubling time of strain JW/SL-NZ826(T) under optimal growth conditions was 2.4 h. The DNA G+C content was 34-35 mol% (HPLC). The two strains reduced up to 1 M thiosulfate to elemental sulfur without sulfide formation, which is a trend typically observed among species belonging to the genus Thermoanaerobacterium. Sulfur globules containing short and long sulfur chains but no S(8)-ring sulfur were produced inside and outside the cells. Up to 90 mM sulfite was tolerated. This tolerance is assumed to be an adaptation to the geochemistry of the environment of White Island. The 16S rRNA gene sequence analysis, however, indicated that the two strains belonged to the genus Thermoanaerobacter, with similarities in the range 95.6-92.7 %. Therefore, strains JW/SL-NZ824 and JW/SL-NZ826(T) represent a novel taxon, for which the name Thermoanaerobacter sulfurigignens sp. nov. is proposed, with strain JW/SL-NZ826(T) (=ATCC 700320(T)=DSM 17917(T)) as the type strain. Based on this and previous studies, an emended description of the genus Thermoanaerobacter is given.
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MESH Headings
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fermentation
- Genes, rRNA
- Glucose/metabolism
- Hydrogen-Ion Concentration
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- New Zealand
- Oxidation-Reduction
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
- Sulfites/metabolism
- Sulfur/metabolism
- Temperature
- Thermoanaerobacter/classification
- Thermoanaerobacter/genetics
- Thermoanaerobacter/isolation & purification
- Thermoanaerobacter/metabolism
- Thiosulfates/metabolism
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Affiliation(s)
- Yong-Jin Lee
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Mona Dashti
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Alexander Prange
- Center for Advanced Microstructures and Devices (CAMD), Louisiana State University, Baton Rouge, LA 70806, USA
- Hochschule Niederrhein, FB Oecotrophologie, 41065 Mönchengladbach, Germany
| | - Fred A Rainey
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Manfred Rohde
- Department of Microbial Pathogenicity, Helmholtz Center for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Juergen Wiegel
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Kublanov IV, Prokofeva MI, Kostrikina NA, Kolganova TV, Tourova TP, Wiegel J, Bonch-Osmolovskaya EA. Thermoanaerobacterium aciditolerans sp. nov., a moderate thermoacidophile from a Kamchatka hot spring. Int J Syst Evol Microbiol 2007; 57:260-264. [PMID: 17267961 DOI: 10.1099/ijs.0.64633-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An anaerobic, moderately thermoacidophilic bacterium, strain 761-119T, was isolated from an acidic hot spring in the Orange Field of the Uzon Caldera (Kamchatka, far-eastern Russia). Cells were spore-forming, Gram-positive rods, possessing one polar flagellum. Growth of strain 761-119Twas observed between 37 and 68 °C and in the pH20 °Crange 3.2–7.1. No growth was observed within 5 days of incubation at or below 35 °C and at or above 70 °C, as well as at or below pH20 °C2.8 and at or above pH20 °C7.5. The optimal temperature and pH20 °Cfor growth were 55 °C and pH20 °C5.7, respectively. A wide range of carbohydrates and polysaccharides were fermented, as well as peptides and proteinaceous substrates. The main products of glucose fermentation were acetate, ethanol, lactate, H2and CO2. The DNA G+C content was 34 (±0.5) mol%. 16S rRNA gene sequence analysis indicated that strain 761-119Tbelonged to the genusThermoanaerobacterium. The level of 16S rRNA gene sequence similarity with otherThermoanaerobacteriumspecies was 86.5–97.8 %, with the only moderately acidophilic member of this genus,Thermoanaerobacterium aotearoense, being one of its closest relatives. DNA–DNA hybridization withT. aotearoenseshowed 33 % relatedness. Thus, morphological (one polar flagellum) and physiological characteristics (lower pH limit of growth at pH20 °C3.2 compared withT. aotearoense) and 16S rRNA gene sequence analyses revealed that strain 761-119Trepresents a novel species in the genusThermoanaerobacterium, for which the nameThermoanaerobacterium aciditoleranssp. nov. is proposed, with the type strain 761-119T(=DSM 16487T=VKM B-2363T).
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Affiliation(s)
- I V Kublanov
- Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - M I Prokofeva
- Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - N A Kostrikina
- Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - T V Kolganova
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - T P Tourova
- Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - J Wiegel
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - E A Bonch-Osmolovskaya
- Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
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Prokofeva MI, Kublanov IV, Nercessian O, Tourova TP, Kolganova TV, Lebedinsky AV, Bonch-Osmolovskaya EA, Spring S, Jeanthon C. Cultivated anaerobic acidophilic/acidotolerant thermophiles from terrestrial and deep-sea hydrothermal habitats. Extremophiles 2005; 9:437-48. [PMID: 15970992 DOI: 10.1007/s00792-005-0461-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Accepted: 05/25/2005] [Indexed: 11/27/2022]
Abstract
Metabolic and phylogenetic diversity of cultivated anaerobic microorganisms from acidic continental hot springs and deep-sea hydrothermal vents was studied by molecular and microbiological methods. Anaerobic organotrophic enrichment cultures growing at pH 3.5-4.0 and 60 or 85 degrees C with organic energy sources were obtained from samples of acidic hot springs of Kamchatka Peninsula (Pauzhetka, Moutnovski Volcano, Uzon Caldera) and Kunashir Island (South Kurils) as well as from the samples of chimneys of East Pacific Rise (13 degrees N). The analyses of clone libraries obtained from terrestrial enrichment cultures growing at 60 degrees C revealed the presence of archaea of genus Thermoplasma and bacteria of genus Thermoanaerobacter. Bacterial isolates from these enrichments were shown to belong to genera Thermoanaerobacter and Thermoanaerobacterium, being acidotolerant with the pH optimum for growth at 5.5-6.0 and the pH minimum at 3.0. At 85 degrees C, domination of thermoacidophilic archaea of genus Acidilobus in terrestrial enrichments was found by both molecular and microbiological methods. Five isolates belonging to this genus possessed some phenotypic features that were new for this genus, such as flagellation or the ability to grow on monosaccharides or disaccharides. Analyses of clone libraries from the deep-sea thermoacidophilic enrichment cultures showed that the representatives of the genus Thermococcus were present at both 60 and 85 degrees C. From the 60 degrees C deep-sea enrichment, a strain belonging to Thermoanaerobacter siderophilus was isolated. It grew optimally at pH 6.0 with the minimum pH for growth at 3.0 and with salinity optimum at 0-2.5% NaCl and the maximum at 7%, thus differing significantly from the type strain. These data show that fermentative degradation of organic matter may occur at low pH and wide temperature range in both terrestrial and deep-sea habitats and can be performed by acidophilic or acidotolerant thermophilic prokaryotes.
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Affiliation(s)
- Maria I Prokofeva
- Institute of Microbiology, Russian Academy of Sciences, Prospect 60-Letya Oktyabrya 7/2, 117312 Moscow, Russia.
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Hosoya R, Hamana K, Niitsu M, Itoh T. Polyamine analysis for chemotaxonomy of thermophilic eubacteria: Polyamine distribution profiles within the orders Aquificales, Thermotogales, Thermodesulfobacteriales, Thermales, Thermoanaerobacteriales, Clostridiales and Bacillales. J GEN APPL MICROBIOL 2005; 50:271-87. [PMID: 15747232 DOI: 10.2323/jgam.50.271] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Cellular polyamines of 45 thermophilic and 8 related mesophilic eubacteria were investigated by HPLC and GC analyses for the thermophilic and chemotaxonomic significance of polyamine distribution profiles. Spermidine and a quaternary branched penta-amine, N4-bis(aminopropyl)norspermidine, were the major polyamine in Thermocrinis, Hydrogenobacter, Hydrogenobaculum, Aquifex, Persephonella, Sulfurihydrogenibium, Hydrogenothermus, Balnearium and Thermovibrio, located in the order Aquificales. Thermodesulfobacterium and Thermodesulfatator belonging to the order Thermodesulfobacteriales contained another quaternary penta-amine, N4-bis(aminopropyl)spermidine. In the order Thermotogales, Thermotoga contained spermidine, norspermidine, caldopentamine and homocaldopentamine. The latter two linear penta-amines were not found in Marinitoga and Petrotoga. In the order Thermales, Thermus and Marinithermus contained homospermidine, norspermine and the linear penta-amines. Meiothermus lacked penta-amines. Vulcanithermus contained linear penta-amines and hexa-amines but not homospermidine. Oceanithermus contained spermine alone. Within the order Thermoanaerobacteriales, the two quaternary branched penta-amines were found in Thermanaeromonas and Thermoanaerobacter. Caldanaerobacter contained N4-bis(aminopropyl)spermidine. Thermoanaerobacterium lacked penta-amines. Thermaerobacter of the order Clostridiales contained N4-bis(aminopropyl)spermidine and agmatine. Thermosyntropha, Thermanaerovibrio, Thermobrachium ( the order Clostridiales), Sulfobacillus, Alicyclobacillus, Anoxybacillus, Ureibacillus, Thermicanus ( the order Bacillales), Desulfotomaculum, Desulfitobacterium and Pelotomaculum (the family Peptococcaceae) ubiquitously contained spermine. Some thermophiles of Bacillales added linear and branched penta-amines.
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Affiliation(s)
- Ryuichi Hosoya
- Gunma University School of Health Sciences, Maebashi, Gunma 371-8514, Japan
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Zhang T, Liu H, Fang HHP. Biohydrogen production from starch in wastewater under thermophilic condition. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2003; 69:149-156. [PMID: 14550657 DOI: 10.1016/s0301-4797(03)00141-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Batch experiments were conducted to convert starch in wastewater into hydrogen at 55 degrees C at various wastewater pH (4.0-9.0) and starch concentrations (9.2-36.6 g/l). The maximum hydrogen yield of 92 ml/g of starch added (17% of the theoretical value) was found at wastewater pH 6.0, and the maximum specific hydrogen production rate of 365 ml/(g-VSS.d) was at wastewater pH 7.0. The methane-free biogas contained up to 60% of hydrogen. The mixed liquor was composed mostly of acetate (40.2-53.4%) and butyrate (26.0-40.9%). Phylogenetic analysis based on 16S rDNA sequences of the 72 clones developed from the sludge at pH 6.0 shows that 85.7% of the clones were closely affiliated with genus Thermoanaerobacterium in family Thermoanaerobacteriaceae; the remaining 14.3% were with an uncultured Saccharococcus sp. clone ETV-T2.
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Affiliation(s)
- Tong Zhang
- Department of Civil Engineering, Centre for Environmental Engineering Research, University of Hong Kong, Pokulam Road, Hong Kong, China
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Cann IK, Kocherginskaya S, King MR, White BA, Mackie RI. Molecular cloning, sequencing, and expression of a novel multidomain mannanase gene from Thermoanaerobacterium polysaccharolyticum. J Bacteriol 1999; 181:1643-51. [PMID: 10049399 PMCID: PMC93557 DOI: 10.1128/jb.181.5.1643-1651.1999] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The manA gene of Thermoanaerobacterium polysaccharolyticum was cloned in Escherichia coli. The open reading frame of manA is composed of 3,291 bases and codes for a preprotein of 1,097 amino acids with an estimated molecular mass of 119,627 Da. The start codon is preceded by a strong putative ribosome binding site (TAAGGCGGTG) and a putative -35 (TTCGC) and -10 (TAAAAT) promoter sequence. The ManA of T. polysaccharolyticum is a modular protein. Sequence comparison and biochemical analyses demonstrate the presence of an N-terminal leader peptide, and three other domains in the following order: a putative mannanase-cellulase catalytic domain, cellulose binding domains 1 (CBD1) and CBD2, and a surface-layer-like protein region (SLH-1, SLH-2, and SLH-3). The CBD domains show no sequence homology to any cellulose binding domain yet reported, hence suggesting a novel CBD. The duplicated CBDs, which lack a disulfide bridge, exhibit 69% identity, and their deletion resulted in both failure to bind to cellulose and an apparent loss of carboxymethyl cellulase and mannanase activities. At the C-terminal region of the gene are three repeats of 59, 67, and 56 amino acids which are homologous to conserved sequences found in the S-layer-associated regions within the xylanases and cellulases of thermophilic members of the Bacillus-Clostridium cluster. The ManA of T. polysaccharolyticum, besides being an extremely active enzyme, is the only mannanase gene cloned which shows this domain structure.
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Affiliation(s)
- I K Cann
- Department of Animal Sciences, University of Illinois at Urbana-Champaign Urbana, IL 61801, USA
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