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Ortega-de la Rosa ND, Romero-Borbón E, Rodríguez JA, Camacho-Ruiz A, Córdova J. Cloning, Expression, Characterization and Immobilization of a Recombinant Carboxylesterase from the Halophilic Archaeon, Halobacterium salinarum NCR-1. Biomolecules 2024; 14:534. [PMID: 38785941 PMCID: PMC11118615 DOI: 10.3390/biom14050534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Only a few halophilic archaea producing carboxylesterases have been reported. The limited research on biocatalytic characteristics of archaeal esterases is primarily due to their very low production in native organisms. A gene encoding carboxylesterase from Halobacterium salinarum NRC-1 was cloned and successfully expressed in Haloferax volcanii. The recombinant carboxylesterase (rHsEst) was purified by affinity chromatography with a yield of 81%, and its molecular weight was estimated by SDS-PAGE (33 kDa). The best kinetic parameters of rHsEst were achieved using p-nitrophenyl valerate as substrate (KM = 78 µM, kcat = 0.67 s-1). rHsEst exhibited great stability to most metal ions tested and some solvents (diethyl ether, n-hexane, n-heptane). Purified rHsEst was effectively immobilized using Celite 545. Esterase activities of rHsEst were confirmed by substrate specificity studies. The presence of a serine residue in rHsEst active site was revealed through inhibition with PMSF. The pH for optimal activity of free rHsEst was 8, while for immobilized rHsEst, maximal activity was at a pH range between 8 to 10. Immobilization of rHsEst increased its thermostability, halophilicity and protection against inhibitors such as EDTA, BME and PMSF. Remarkably, immobilized rHsEst was stable and active in NaCl concentrations as high as 5M. These biochemical characteristics of immobilized rHsEst reveal its potential as a biocatalyst for industrial applications.
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Affiliation(s)
- Nestor David Ortega-de la Rosa
- Centro Universitario de Tlajomulco, Departamento de Ingeniería Biología, Sintética y de Materiales, Universidad de Guadalajara, Carretera Tlajomulco-Santa Fé Km. 3.5 No.595, Lomas de Tejeda, Tlajomulco de Zúñiga 45641, Mexico;
| | - Evelyn Romero-Borbón
- Centro Universitario de Ciencias Exactas e Ingenierías, Departamento de Química, Universidad de Guadalajara, Blvd. Gral. Marcelino García Barragán 1421, Col. Olímpica, Guadalajara 44430, Mexico;
| | - Jorge Alberto Rodríguez
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A. C., Camino el Arenero 1227, El Bajío del arenal, Zapopan 45019, Mexico;
| | - Angeles Camacho-Ruiz
- Centro Universitario del Norte, Departamento de Fundamentos del Conocimiento, Universidad de Guadalajara, Carretera Federal Km. 191 No. 23, Col. Santiago Tlaltelolco, Colotlán 46200, Mexico;
| | - Jesús Córdova
- Centro Universitario de Ciencias Exactas e Ingenierías, Departamento de Química, Universidad de Guadalajara, Blvd. Gral. Marcelino García Barragán 1421, Col. Olímpica, Guadalajara 44430, Mexico;
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2
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Aparici-Carratalá D, Esclapez J, Bautista V, Bonete MJ, Camacho M. Archaea: current and potential biotechnological applications. Res Microbiol 2023; 174:104080. [PMID: 37196775 DOI: 10.1016/j.resmic.2023.104080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Archaea are microorganisms with great ability to colonize some of the most inhospitable environments in nature, managing to survive in places with extreme characteristics for most microorganisms. Its proteins and enzymes are stable and can act under extreme conditions in which other proteins and enzymes would degrade. These attributes make them ideal candidates for use in a wide range of biotechnological applications. This review describes the most important applications, both current and potential, that archaea present in Biotechnology, classifying them according to the sector to which the application is directed. It also analyzes the advantages and disadvantages of its use.
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Affiliation(s)
- David Aparici-Carratalá
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain.
| | - Julia Esclapez
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain.
| | - Vanesa Bautista
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain.
| | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain.
| | - Mónica Camacho
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Carretera de San Vicente del Raspeig s/n, San Vicente del Raspeig, Alicante, 03690, Spain.
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3
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Gebhard LJ, Duggin IG, Erdmann S. Improving the genetic system for Halorubrum lacusprofundi to allow in-frame deletions. Front Microbiol 2023; 14:1095621. [PMID: 37065119 PMCID: PMC10102395 DOI: 10.3389/fmicb.2023.1095621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Halorubrum lacusprofundi is a cold-adapted halophilic archaeon isolated from Deep Lake, Antarctica. Hrr. lacusprofundi is commonly used to study adaptation to cold environments and thereby a potential source for biotechnological products. Additionally, in contrast to other haloarchaeal model organisms, Hrr. lacusprofundi is also susceptible to a range of different viruses and virus-like elements, making it a great model to study virus-host interactions in a cold-adapted organism. A genetic system has previously been reported for Hrr. lacusprofundi; however, it does not allow in-frame deletions and multiple gene knockouts. Here, we report the successful generation of uracil auxotrophic (pyrE2) mutants of two strains of Hrr. lacusprofundi. Subsequently, we attempted to generate knockout mutants using the auxotrophic marker for selection. However, surprisingly, only the combination of the auxotrophic marker and antibiotic selection allowed the timely and clean in-frame deletion of a target gene. Finally, we show that vectors established for the model organism Haloferax volcanii are deployable for genetic manipulation of Hrr. lacusprofundi, allowing the use of the portfolio of genetic tools available for H. volcanii in Hrr. lacusprofundi.
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Affiliation(s)
- L. Johanna Gebhard
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Iain G. Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Susanne Erdmann
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen, Germany
- *Correspondence: Susanne Erdmann,
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4
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Ma YC, Gao MR, Yang H, Jiang JY, Xie W, Su WP, Zhang B, Yeong YS, Guo WY, Sui LY. Optimization of C 50 Carotenoids Production by Open Fermentation of Halorubrum sp. HRM-150. Appl Biochem Biotechnol 2023; 195:3628-3640. [PMID: 36648604 DOI: 10.1007/s12010-023-04319-x] [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] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
C50 carotenoids, as unique bioactive molecules, have many biological properties, including antioxidant, anticancer, and antibacterial activity, and have a wide range of potential uses in the food, cosmetic, and biomedical industries. The majority of C50 carotenoids are produced by the sterile fermentation of halophilic archaea. This study aims to look at more cost-effective and manageable ways of producing C50 carotenoids. The basic medium, carbon source supplementation, and optimal culture conditions for Halorubrum sp. HRM-150 C50 carotenoids production by open fermentation were examined in this work. The results indicated that Halorubrum sp. HRM-150 grown in natural brine medium grew faster than artificial brine medium. The addition of glucose, sucrose, and lactose (10 g/L) enhanced both biomass and carotenoids productivity, with the highest level reaching 4.53 ± 0.32 μg/mL when glucose was added. According to the findings of orthogonal studies based on the OD600 and carotenoids productivity, the best conditions for open fermentation were salinity 20-25%, rotation speed 150-200 rpm, and pH 7.0-8.2. The up-scaled open fermentation was carried out in a 7 L medium under optimum culture conditions. At 96 h, the OD600 and carotenoids productivity were 9.86 ± 0.51 (dry weight 10.40 ± 1.27 g/L) and 7.31 ± 0.65 μg/mL (701.40 ± 21.51 μg/g dry weight, respectively). When amplified with both universal bacterial primer and archaeal primer in the open fermentation, Halorubrum remained the dominating species, indicating that contamination was kept within an acceptable level. To summarize, open fermentation of Halorubrum is a promising method for producing C50 carotenoids.
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Affiliation(s)
- Ying-Chao Ma
- Key Laboratory of Marine Resource Chemistry and Food Technology (TUST), Ministry of Education, Tianjin, China.,Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China.,Tianjin Key Laboratory of Early Druggability Evaluation of Innovative Drugs, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, China
| | - Mei-Rong Gao
- Key Laboratory of Marine Resource Chemistry and Food Technology (TUST), Ministry of Education, Tianjin, China.,Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Huan Yang
- Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jun-Yao Jiang
- Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Wei Xie
- Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Wan-Ping Su
- Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Bo Zhang
- Tianjin Key Laboratory of Early Druggability Evaluation of Innovative Drugs, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, China
| | - Yik-Sung Yeong
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Wu-Yan Guo
- Tianjin Key Laboratory of Early Druggability Evaluation of Innovative Drugs, Tianjin International Joint Academy of Biomedicine, Tianjin, 300457, China
| | - Li-Ying Sui
- Key Laboratory of Marine Resource Chemistry and Food Technology (TUST), Ministry of Education, Tianjin, China. .,Asian Regional Artemia Reference Center, College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, 300457, China.
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5
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Thompson TP, Megaw J, Kelly SA, Hopps J, Gilmore BF. Microbial communities of halite deposits and other hypersaline environments. ADVANCES IN APPLIED MICROBIOLOGY 2022; 120:1-32. [PMID: 36243451 DOI: 10.1016/bs.aambs.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Large regions of Earth's surface are underlain by salt deposits that evaporated from ancient oceans and are populated by extreme halophilic microbes. While the microbiology of ancient evaporites has been well studied, the ecology of halite deposits and more recently formed NaCl "salticle" stalactite structures (speleothems) in a Triassic halite mine are less well characterized. The microbiome of Kilroot Salt Mine was profiled using conventional and enhanced culturing techniques. From this, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained. Culture-independent metagenomic approaches also revealed that culturing techniques were inadvertently biased toward specific taxa, and the need for optimized isolation procedures are required to enhance cultivation diversity. Speleothems formed from saturated brines are unique structures that have the potential to entomb haloarchaea cells for thousands of years within fluid inclusions. The presence of such fluid inclusions, alongside the high abundance of genes related to glycerol metabolism, biofilm formation, and persister cell formation is highly suggestive of an environmental niche that could promote longevity and survivability. Finally, previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be an untapped source of chemical diversity with high biodiscovery potential.
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Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom.
| | - Julianne Megaw
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Stephen A Kelly
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom
| | - Jason Hopps
- Irish Salt Mining & Exploration Company Ltd., Carrickfergus, United Kingdom
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Medical Biology Centre, Belfast, United Kingdom
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6
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Sala cibi gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt. J Microbiol 2022; 60:899-904. [DOI: 10.1007/s12275-022-2137-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/02/2022] [Accepted: 06/09/2022] [Indexed: 10/17/2022]
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7
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Liu BB, Govindan R, Muthuchamy M, Cheng S, Li X, Ye L, Wang LY, Guo SX, Li WJ, Alharbi NS, M Khaled J, Kadaikunnan S. Halophilic archaea and their extracellular polymeric compounds in the treatment of high salt wastewater containing phenol. CHEMOSPHERE 2022; 294:133732. [PMID: 35101434 DOI: 10.1016/j.chemosphere.2022.133732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Phenol is one of the major organic pollutants in high salt industrial wastewaters. The biological treatment of such waste using microorganisms is considered to be a cost-effective and eco-friendly method. However, in this process, salt tolerance of microorganisms is one of the main limiting factors. Halophilic microorganisms, especially halophilic archaea are thought to be appropriate for such treatment. To develop a novel effective biological method for high salt phenol wastewater treatment, the influence of phenol in high salt phenol wastewater on halophilic archaea and their extracellular polymeric substances (EPS) should be investigated. In the present study, using phenol enrichment method, 75 halophilic archaeal strains were isolated from Wuyongbulake salt lake sediment sample. The majority of the identified strains were phenol-tolerant. Six strains with high phenol tolerance were chosen, and the phenol scavenging effect was observed in the microbial suspension, supernatant, and EPS. It was noticed that the phenol degradation rate of suspensions of both strains 869-1, and 121-1 in salt water exhibited the highest rates of 83.7%, while the supernatant of strain 869-1 reached the highest rate of 78.2%. When combined with the comprehensive analysis of the artificial wastewater simulation experiment, it was discovered that in the artificial wastewater containing phenol, the phenol degradation rate of suspension of strain A387 exhibited the highest rates of 55.74% both, and supernatant of strain 630-3 reached the highest rate of 62.3%. The EPS produced by strains A00135, 558-1, 869-1, 121-1 and A387 removed 100% phenol within 96 h, and the phenol removal efficiency of EPS produced by 869-1 reached 56.1% under an artificial wastewater simulation experiment with high salt (15%NaCl) condition. The present study suggests that halophilic archaea and their EPS play an important role in phenol degradation. This approach could be potentially used for industrial high-salt wastewater treatment.
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Affiliation(s)
- Bing-Bing Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Rajivgandhi Govindan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Maruthupandy Muthuchamy
- Lab of Toxicology, Department of Health Sciences, The Graduate School of Dong-A University, 37, Nakdong-Dearo 550 Beon-Gil, Saha-Gu Busan, 49315, South Korea
| | - Shuang Cheng
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Xuebin Li
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Lijing Ye
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Lai-You Wang
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Shu-Xian Guo
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China.
| | - Wen-Jun Li
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, PR China.
| | - Naiyf S Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Jamal M Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Shine Kadaikunnan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
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8
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Macías-Pérez LA, Levard C, Barakat M, Angeletti B, Borschneck D, Poizat L, Achouak W, Auffan M. Contrasted microbial community colonization of a bauxite residue deposit marked by a complex geochemical context. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127470. [PMID: 34687997 DOI: 10.1016/j.jhazmat.2021.127470] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Bauxite residue is the alkaline byproduct generated during alumina extraction and is commonly landfilled in open-air deposits. The growth in global alumina production have raised environmental concerns about these deposits since no large-scale reuses exist to date. Microbial-driven techniques including bioremediation and critical metal bio-recovery are now considered sustainable and cost-effective methods to revalorize bauxite residues. However, the establishment of microbial communities and their active role in these strategies are still poorly understood. We thus determined the geochemical composition of different bauxite residues produced in southern France and explored the development of bacterial and fungal communities using Illumina high-throughput sequencing. Physicochemical parameters were influenced differently by the deposit age and the bauxite origin. Taxonomical analysis revealed an early-stage microbial community dominated by haloalkaliphilic microorganisms and strongly influenced by chemical gradients. Microbial richness, diversity and network complexity increased significantly with the deposit age, reaching an equilibrium community composition similar to typical soils after decades of natural weathering. Our results suggested that salinity, pH, and toxic metals affected the bacterial community structure, while fungal community composition showed no clear correlations with chemical variations.
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Affiliation(s)
- Luis Alberto Macías-Pérez
- Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, CEREGE, Technopôle de l'Arbois-Méditerranée, BP80, 13545 Aix-en-Provence, France; Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France.
| | - Clément Levard
- Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, CEREGE, Technopôle de l'Arbois-Méditerranée, BP80, 13545 Aix-en-Provence, France.
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France.
| | - Bernard Angeletti
- Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, CEREGE, Technopôle de l'Arbois-Méditerranée, BP80, 13545 Aix-en-Provence, France.
| | - Daniel Borschneck
- Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, CEREGE, Technopôle de l'Arbois-Méditerranée, BP80, 13545 Aix-en-Provence, France.
| | | | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, Laboratory of Microbial Ecology of the Rhizosphere, ECCOREV FR 3098, F-13108 St-Paul-lez-Durance, France.
| | - Mélanie Auffan
- Aix Marseille Université, CNRS, IRD, INRAE, Collège de France, CEREGE, Technopôle de l'Arbois-Méditerranée, BP80, 13545 Aix-en-Provence, France; Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA.
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9
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Arya PS, Yagnik SM, Rajput KN, Panchal RR, Raval VH. Understanding the Basis of Occurrence, Biosynthesis, and Implications of Thermostable Alkaline Proteases. Appl Biochem Biotechnol 2021; 193:4113-4150. [PMID: 34648116 DOI: 10.1007/s12010-021-03701-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/04/2021] [Indexed: 12/29/2022]
Abstract
The group of hydrolytic enzymes synonymously known as proteases is predominantly most favored for the class of industrial enzymes. The present work focuses on the thermostable nature of these proteolytic enzymes that occur naturally among mesophilic and thermophilic microbes. The broad thermo-active feature (40-80 °C), ease of cultivation, maintenance, and bulk production are the key features associated with these enzymes. Detailing of contemporary production technologies, and controllable operational parameters including the purification strategies, are the key features that justify their industrial dominance as biocatalysts. In addition, the rigorous research inputs by protein engineering and enzyme immobilization studies add up to the thermo-catalytic features and application capabilities of these enzymes. The work summarizes key features of microbial proteases that make them numero-uno for laundry, biomaterials, waste management, food and feed, tannery, and medical as well as pharmaceutical industries. The quest for novel and/or designed and engineered thermostable protease from unexplored sources is highly stimulating and will address the ever-increasing industrial demands.
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Affiliation(s)
- Prashant S Arya
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Shivani M Yagnik
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Kiransinh N Rajput
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Rakeshkumar R Panchal
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India
| | - Vikram H Raval
- Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India.
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10
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Cui HL, Dyall-Smith ML. Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:243-251. [PMID: 37073340 PMCID: PMC10077297 DOI: 10.1007/s42995-020-00087-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/25/2020] [Indexed: 05/03/2023]
Abstract
As a group, the halophilic archaea (class Halobacteria) are the most salt-requiring and salt-resistant microorganisms within the domain Archaea. Halophilic archaea flourish in thalassohaline and athalassohaline environments and require over 100-150 g/L NaCl for growth and structural stability. Natural hypersaline environments vary in salt concentration, chemical composition and pH, and occur in climates ranging from tropical to polar and even under-sea. Accordingly, their resident haloarchaeal species vary enormously, as do their individual population compositions and community structures. These diverse halophilic archaeal strains are precious resources for theoretical and applied research but assessing their taxonomic and metabolic novelty and diversity in natural environments has been technically difficult up until recently. Environmental DNA-based high-throughput sequencing technology has now matured sufficiently to allow inexpensive recovery of massive amounts of sequence data, revealing the distribution and community composition of halophilic archaea in different hypersaline environments. While cultivation of haloarchaea is slow and tedious, and only recovers a fraction of the natural diversity, it is the conventional means of describing new species, and provides strains for detailed study. As of the end of May 2020, the class Halobacteria contains 71 genera and 275 species, 49.8% of which were first isolated from the marine salt environment and 50.2% from the inland salt environment, indicating that both thalassohaline and athalassohaline environments contain diverse halophilic archaea. However, there remain taxa that have not yet been isolated in pure culture, such as the nanohaloarchaea, which are widespread in the salt environment and may be one of the hot spots in the field of halophilic archaea research in the future. In this review, we focus on the cultivation strategies that have been used to isolate extremely halophilic archaea and point out some of the pitfalls and challenges. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00087-3.
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Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013 China
| | - Mike L. Dyall-Smith
- Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, 3010 Australia
- Computational Biology Group, Max-Planck-Institute of Biochemistry, 82152 Martinsried, Germany
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11
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Kasirajan L, Maupin-Furlow JA. Halophilic archaea and their potential to generate renewable fuels and chemicals. Biotechnol Bioeng 2020; 118:1066-1090. [PMID: 33241850 DOI: 10.1002/bit.27639] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/27/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
Lignocellulosic biofuels and chemicals have great potential to reduce our dependence on fossil fuels and mitigate air pollution by cutting down on greenhouse gas emissions. Chemical, thermal, and enzymatic processes are used to release the sugars from the lignocellulosic biomass for conversion to biofuels. These processes often operate at extreme pH conditions, high salt concentrations, and/or high temperature. These harsh treatments add to the cost of the biofuels, as most known biocatalysts do not operate under these conditions. To increase the economic feasibility of biofuel production, microorganisms that thrive in extreme conditions are considered as ideal resources to generate biofuels and value-added products. Halophilic archaea (haloarchaea) are isolated from hypersaline ecosystems with high salt concentrations approaching saturation (1.5-5 M salt concentration) including environments with extremes in pH and/or temperature. The unique traits of haloarchaea and their enzymes that enable them to sustain catalytic activity in these environments make them attractive resources for use in bioconversion processes that must occur across a wide range of industrial conditions. Biocatalysts (enzymes) derived from haloarchaea occupy a unique niche in organic solvent, salt-based, and detergent industries. This review focuses on the use of haloarchaea and their enzymes to develop and improve biofuel production. The review also highlights how haloarchaea produce value-added products, such as antibiotics, carotenoids, and bioplastic precursors, and can do so using feedstocks considered "too salty" for most microbial processes including wastes from the olive-mill, shell fish, and biodiesel industries.
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Affiliation(s)
- Lakshmi Kasirajan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Coimbatore, India
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Genetics Institute, University of Florida, Gainesville, Florida, USA
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12
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Fongaro G, Maia GA, Rogovski P, Cadamuro RD, Lopes JC, Moreira RS, Camargo AF, Scapini T, Stefanski FS, Bonatto C, Marques Souza DS, Stoco PH, Duarte RTD, Cabral da Cruz AC, Wagner G, Treichel H. Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools. Curr Genomics 2020; 21:240-252. [PMID: 33071618 PMCID: PMC7521039 DOI: 10.2174/1389202921999200601144137] [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: 01/10/2020] [Revised: 02/02/2020] [Accepted: 04/20/2020] [Indexed: 12/03/2022] Open
Abstract
Abstract: Genomic and proteomic advances in extremophile microorganism studies are increasingly demonstrating their ability to produce a variety of enzymes capable of converting biomass into bioenergy. Such microorganisms are found in environments with nutritional restrictions, anaerobic environments, high salinity, varying pH conditions and extreme natural environments such as hydrothermal vents, soda lakes, and Antarctic sediments. As extremophile microorganisms and their enzymes are found in widely disparate locations, they generate new possibilities and opportunities to explore biotechnological prospecting, including biofuels (biogas, hydrogen and ethanol) with an aim toward using multi-omics tools that shed light on biotechnological breakthroughs.
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Affiliation(s)
- Gislaine Fongaro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Guilherme Augusto Maia
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Paula Rogovski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rafael Dorighello Cadamuro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Joana Camila Lopes
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Renato Simões Moreira
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Aline Frumi Camargo
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Thamarys Scapini
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Fábio Spitza Stefanski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Charline Bonatto
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Doris Sobral Marques Souza
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Patrícia Hermes Stoco
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Tadeu Delgado Duarte
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Ariadne Cristiane Cabral da Cruz
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Glauber Wagner
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Helen Treichel
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
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Gómez-Villegas P, Vigara J, Vila M, Varela J, Barreira L, Léon R. Antioxidant, Antimicrobial, and Bioactive Potential of Two New Haloarchaeal Strains Isolated from Odiel Salterns (Southwest Spain). BIOLOGY 2020; 9:biology9090298. [PMID: 32962162 PMCID: PMC7564620 DOI: 10.3390/biology9090298] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 12/23/2022]
Abstract
Simple Summary Halophilic archaea are microorganisms that inhabit in extreme environments for life, under salt saturation, high temperature and elevated UV radiation. The interest in these microorganisms lies on the properties of their molecules, that present high salt and temperature tolerance, as well as, antioxidant power, being an excellent source of compounds for several biotechnological applications. However, the bioactive properties from haloarcahaea remain scarcely studied compared to other groups as plants or algae, usually reported as good health promoters. In this work we describe the isolation and the molecular identification of two new haloarchaeal strains from Odiel salterns (SW Spain), and the antioxidant, antimicrobial and bioactive potential of their extracts. The results revealed that the extracts obtained with acetone presented the highest activities in the antioxidant, antimicrobial and anti-inflammatory assays, becoming a promising source of metabolites with applied interest in pharmacy, cosmetics and food industry. Abstract The need to survive in extreme environments has furnished haloarchaea with a series of components specially adapted to work in such conditions. The possible application of these molecules in the pharmaceutical and industrial fields has received increasing attention; however, many potential bioactivities of haloarchaea are still poorly explored. In this paper, we describe the isolation and identification of two new haloarchaeal strains from the saltern ponds located in the marshlands of the Odiel River, in the southwest of Spain, as well as the in vitro assessment of their antioxidant, antimicrobial, and bioactive properties. The acetone extract obtained from the new isolated Haloarcula strain exhibited the highest antioxidant activity, while the acetone extracts from both isolated strains demonstrated a strong antimicrobial activity, especially against other halophilic microorganisms. Moreover, these extracts showed a remarkable ability to inhibit the enzyme cyclooxygenase-2 and to activate the melanogenic enzyme tyrosinase, indicating their potential against chronic inflammation and skin pigmentation disorders. Finally, the aqueous protein-rich extracts obtained from both haloarchaea exhibited an important inhibitory effect on the activity of the acetylcholinesterase enzyme, involved in the hydrolysis of cholinergic neurotransmitters and related to several neurological diseases.
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Affiliation(s)
- Patricia Gómez-Villegas
- Laboratory of Biochemistry, Department of Chemistry, University of Huelva, Avda. de las Fuerzas Armadas s/n, 21071 Huelva, Spain; (P.G.-V.); (J.V.); (M.V.)
| | - Javier Vigara
- Laboratory of Biochemistry, Department of Chemistry, University of Huelva, Avda. de las Fuerzas Armadas s/n, 21071 Huelva, Spain; (P.G.-V.); (J.V.); (M.V.)
| | - Marta Vila
- Laboratory of Biochemistry, Department of Chemistry, University of Huelva, Avda. de las Fuerzas Armadas s/n, 21071 Huelva, Spain; (P.G.-V.); (J.V.); (M.V.)
| | - João Varela
- Centre of Marine Sciences, University of Algarve, Campus of Gambelas, 8005-139 Faro, Portugal; (J.V.); (L.B.)
| | - Luísa Barreira
- Centre of Marine Sciences, University of Algarve, Campus of Gambelas, 8005-139 Faro, Portugal; (J.V.); (L.B.)
| | - Rosa Léon
- Laboratory of Biochemistry, Department of Chemistry, University of Huelva, Avda. de las Fuerzas Armadas s/n, 21071 Huelva, Spain; (P.G.-V.); (J.V.); (M.V.)
- Correspondence: ; Tel.: +34-95-921-9951
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14
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Kaur R, Tiwari SK. Identification and characterization of a halocin-producing haloarchaeon isolated from Pachpadra salt lake. Lett Appl Microbiol 2020; 71:620-626. [PMID: 32844475 DOI: 10.1111/lam.13377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/15/2020] [Accepted: 08/15/2020] [Indexed: 01/06/2023]
Abstract
Haloarchaea are known to produce antimicrobial proteins, halocins which are generally stable at extreme conditions suggesting their potential biotechnological applications. Here, we report a halocin-producing haloarchaeon isolated from salt lake and identified as Haloferax larsenii HA4 using partial 16S rDNA sequence and biochemical properties. Whole-cell methanolysate showed ether-linked lipids, which is a characteristic feature of haloarchaea. Strain HA4 was able to grow at pH 6·0-10·0 and 15-30% NaCl. The growth response was normal but antimicrobial activity was detected only during the log-phase. Crude halocin HA4 was active in the pH range of pH 2·0-10·0 with stability up to 100°C. Cell-free supernatant (CFS) was also stable in different organic solvents and detergents tested. However, halocin activity was reduced after treatment with proteinase K suggesting the proteinaceous nature of the active compound. Concentrated CFS showed the presence of several proteins from 6·5-66 kDa but bioassay suggested ~14 kDa protein as halocin. Crude halocin preparation showed cytocidal activity against indicator strain, H. larsenii HA10 and inhibited the growth of other related strains such as H. larsenii HA3, HA8, HA9 and HA10.
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Affiliation(s)
- R Kaur
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, India
| | - S K Tiwari
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, India
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15
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Genomic analysis of facultatively oligotrophic haloarchaea of the genera Halarchaeum, Halorubrum, and Halolamina, isolated from solar salt. Arch Microbiol 2020; 203:261-268. [PMID: 32918097 DOI: 10.1007/s00203-020-02027-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 08/19/2020] [Accepted: 09/02/2020] [Indexed: 11/27/2022]
Abstract
Extremely halophilic archaea (haloarchaea) belonging to the phylum Euryarchaeota have been found in high-salinity environments. In this study, Halarchaeum sp. CBA1220, Halorubrum sp. CBA1229, and Halolamina sp. CBA1230, which are facultatively oligotrophic haloarchaea, were isolated from solar salt by culture under oligotrophic culture conditions. The complete genomes of strains CBA1220, CBA1229, and CBA1230 were sequenced and were found to contain 3,175,875, 3,582,278, and 3,465,332 bp, with a G + C content of 68.25, 67.66, and 66.75 mol %, respectively. In total, 60, 36, and 33 carbohydrate-active enzyme genes were determined in the respective strains. The strains harbored various genes encoding stress-tolerance proteins, including universal stress proteins, cold-shock proteins, and rubrerythrin and rubrerythrin-related proteins. The genome data produced in this study will facilitate further research to improve our understanding of other halophilic strains and promote their industrial application.
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16
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A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy). Microorganisms 2020; 8:microorganisms8060936. [PMID: 32580393 PMCID: PMC7356649 DOI: 10.3390/microorganisms8060936] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 02/06/2023] Open
Abstract
Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.
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Jin M, Gai Y, Guo X, Hou Y, Zeng R. Properties and Applications of Extremozymes from Deep-Sea Extremophilic Microorganisms: A Mini Review. Mar Drugs 2019; 17:md17120656. [PMID: 31766541 PMCID: PMC6950199 DOI: 10.3390/md17120656] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 01/09/2023] Open
Abstract
The deep sea, which is defined as sea water below a depth of 1000 m, is one of the largest biomes on the Earth, and is recognised as an extreme environment due to its range of challenging physical parameters, such as pressure, salinity, temperature, chemicals and metals (such as hydrogen sulphide, copper and arsenic). For surviving in such extreme conditions, deep-sea extremophilic microorganisms employ a variety of adaptive strategies, such as the production of extremozymes, which exhibit outstanding thermal or cold adaptability, salt tolerance and/or pressure tolerance. Owing to their great stability, deep-sea extremozymes have numerous potential applications in a wide range of industries, such as the agricultural, food, chemical, pharmaceutical and biotechnological sectors. This enormous economic potential combined with recent advances in sampling and molecular and omics technologies has led to the emergence of research regarding deep-sea extremozymes and their primary applications in recent decades. In the present review, we introduced recent advances in research regarding deep-sea extremophiles and the enzymes they produce and discussed their potential industrial applications, with special emphasis on thermophilic, psychrophilic, halophilic and piezophilic enzymes.
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Affiliation(s)
- Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Yingbao Gai
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
| | - Xun Guo
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
| | - Yanping Hou
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Correspondence: ; Tel.: +86-592-2195323
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Expression, Folding, and Activation of Halophilic Alkaline Phosphatase in Non-Halophilic Brevibacillus choshinensis. Protein J 2019; 39:46-53. [DOI: 10.1007/s10930-019-09874-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Qian H, Ju P, Zhang D, Ma L, Hu Y, Li Z, Huang L, Lou Y, Du C. Effect of Dissolved Oxygen Concentration on the Microbiologically Influenced Corrosion of Q235 Carbon Steel by Halophilic Archaeon Natronorubrum tibetense. Front Microbiol 2019; 10:844. [PMID: 31073296 PMCID: PMC6495067 DOI: 10.3389/fmicb.2019.00844] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
The influence of dissolved oxygen concentration (DOC) on the microbiologically influenced corrosion (MIC) of Q235 carbon steel in the culture medium of halophilic archaeon Natronorubrum tibetense was investigated. The increase of DOC from 0.0 to 3.0 ppm was found to strengthen the oxygen concentration cell by promoting cathodic reaction. Meanwhile, the increased DOC also promoted archaeal cell growth, which could consume more metallic iron as energy source and aggravated the localized corrosion. When the DOC further increased to 5.0 ppm, the uniform corrosion was dominant as the biofilms became uniformly presented on the steel surface. Combined with the stronger inhibition effect of oxygen diffusion by the increased biofilm coverage, the MIC of carbon steel in the 5.0 ppm medium was weaker than that in the 3.0 ppm medium. From weight loss and electrochemical tests, the results all demonstrated that the carbon steel in the 3.0 ppm medium had the largest corrosion rate.
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Affiliation(s)
- Hongchang Qian
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
| | - Pengfei Ju
- Shanghai Aerospace Equipment Manufacturer, Shanghai, China
| | - Dawei Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
| | - Lingwei Ma
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
| | - Yuting Hu
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
| | - Ziyu Li
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
| | - Luyao Huang
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
| | - Yuntian Lou
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
| | - Cuiwei Du
- Beijing Advanced Innovation Center for Materials Genome Engineering, Institute for Advanced Materials and Technology, University of Science and Technology Beijing, Beijing, China
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20
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Increased production of polyhydroxyalkanoates with controllable composition and consistent material properties by fed-batch fermentation. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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21
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Gómez-Villegas P, Vigara J, León R. Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain). Mar Drugs 2018; 16:md16090332. [PMID: 30213145 PMCID: PMC6164061 DOI: 10.3390/md16090332] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/28/2018] [Accepted: 09/08/2018] [Indexed: 12/11/2022] Open
Abstract
The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown.
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Affiliation(s)
- Patricia Gómez-Villegas
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, 21071 Huelva, Spain.
| | - Javier Vigara
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, 21071 Huelva, Spain.
| | - Rosa León
- Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, 21071 Huelva, Spain.
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Cerletti M, Giménez MI, Tröetschel C, D' Alessandro C, Poetsch A, De Castro RE, Paggi RA. Proteomic Study of the Exponential-Stationary Growth Phase Transition in the Haloarchaea Natrialba magadii and Haloferax volcanii. Proteomics 2018; 18:e1800116. [PMID: 29888524 DOI: 10.1002/pmic.201800116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/09/2018] [Indexed: 11/12/2022]
Abstract
The dynamic changes that take place along the phases of microbial growth (lag, exponential, stationary, and death) have been widely studied in bacteria at the molecular and cellular levels, but little is known for archaea. In this study, a high-throughput approach was used to analyze and compare the proteomes of two haloarchaea during exponential and stationary growth: the neutrophilic Haloferax volcanii and the alkaliphilic Natrialba magadii. Almost 2000 proteins were identified in each species (≈50% of the predicted proteome). Among them, 532 and 432 were found to be differential between growth phases in H. volcanii and N. magadii, respectively. Changes upon entrance into stationary phase included an overall increase in proteins involved in the transport of small molecules and ions, stress response, and fatty acid catabolism. Proteins related to genetic processes and cell division showed a notorious decrease in amount. The data reported in this study not only contributes to our understanding of the exponential-stationary growth phase transition in extremophilic archaea but also provides the first comprehensive analysis of the proteome composition of N. magadii. The MS proteomics data have been deposited in the ProteomeXchange Consortium with the dataset identifier JPST000395.
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Affiliation(s)
- Micaela Cerletti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Mar del Plata, 7600, Argentina
| | - María Ines Giménez
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Mar del Plata, 7600, Argentina
| | | | - Celeste D' Alessandro
- Laboratório de Patologia e Controle Microbiano de Insetos, ESALQ-USP, Piracicaba-SP, 13418-900, Brazil
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, 44801, Germany.,School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, PL4 8AA, United Kingdom
| | - Rosana Ester De Castro
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Mar del Plata, 7600, Argentina
| | - Roberto A Paggi
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Mar del Plata, 7600, Argentina
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Erkorkmaz BA, Kırtel O, Ateş Duru Ö, Toksoy Öner E. Development of a cost-effective production process for Halomonas levan. Bioprocess Biosyst Eng 2018; 41:1247-1259. [DOI: 10.1007/s00449-018-1952-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/06/2018] [Indexed: 12/20/2022]
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24
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Menasria T, Aguilera M, Hocine H, Benammar L, Ayachi A, Si Bachir A, Dekak A, Monteoliva-Sánchez M. Diversity and bioprospecting of extremely halophilic archaea isolated from Algerian arid and semi-arid wetland ecosystems for halophilic-active hydrolytic enzymes. Microbiol Res 2018; 207:289-298. [PMID: 29458865 DOI: 10.1016/j.micres.2017.12.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/15/2017] [Accepted: 12/23/2017] [Indexed: 11/19/2022]
Abstract
The diversity of haloarchaea associated with different dry salt lakes in northeastern Algeria was investigated together with their potential of hydrolytic enzyme production. A total of 68 aerobic halophilic archaea were isolated from saline sediments. Based on the 16S rRNA gene sequencing, the isolates were assigned to seven phylotypes within the class Halobacteria, namely Haloarcula, Halococcus, Haloferax, Halogeometricum, Haloterrigena, Natrialba, and Natrinema. The results showed that Haloferax group was found to be dominant in all samples (30 isolates) (44%) with high diversity, followed by Halococcus spp. (13%) (9 isolates). All phylotypes are extreme halophiles and thermotolerant with the ability to grow at temperatures up to 48 °C. In addition, the screening for extracellular halophilic enzymes showed that 89.7% of the isolates were able to produce at least two types of the screened enzymes. The strains producing esterase, gelatinase, inulinase, cellulase and protease activities were the most diverse functional group. These data showed an abundant and diverse haloarchaeal community, detected in Algerian wetland ecosystems, presenting a promising source of molecules with important biotechnological applications.
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Affiliation(s)
- Taha Menasria
- Department of Microbiology and Biochemistry, Faculty of Natural and Life Sciences University of Batna 2, Batna 05078, Algeria; Department of Microbiology, School of Pharmacy, University of Granada, Granada, Spain; Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Tebessa, Tebessa 12002, Algeria.
| | - Margarita Aguilera
- Department of Microbiology, School of Pharmacy, University of Granada, Granada, Spain.
| | - Hacene Hocine
- Cellular and Molecular Biology Laboratory, University of Sciences and Technology Houari Boumediene, Bp 32, El Alia, 16111 Bab Ezzouar, Algiers, Algeria
| | - Leyla Benammar
- Department of Microbiology and Biochemistry, Faculty of Natural and Life Sciences University of Batna 2, Batna 05078, Algeria
| | - Ammar Ayachi
- Veterinary and Agricultural Sciences Institute, Department of Veterinary Sciences, University of Batna 1, Batna 05000, Algeria
| | - Abdelkrim Si Bachir
- Department of Ecology and Environment, Faculty of Natural and Life Sciences, University of Batna 2, Batna 05078, Algeria
| | - Ahmed Dekak
- Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Tebessa, Tebessa 12002, Algeria
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25
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Amoozegar MA, Siroosi M, Atashgahi S, Smidt H, Ventosa A. Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. MICROBIOLOGY-SGM 2017; 163:623-645. [PMID: 28548036 DOI: 10.1099/mic.0.000463] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Halophilic archaea, also referred to as haloarchaea, dominate hypersaline environments. To survive under such extreme conditions, haloarchaea and their enzymes have evolved to function optimally in environments with high salt concentrations and, sometimes, with extreme pH and temperatures. These features make haloarchaea attractive sources of a wide variety of biotechnological products, such as hydrolytic enzymes, with numerous potential applications in biotechnology. The unique trait of haloarchaeal enzymes, haloenzymes, to sustain activity under hypersaline conditions has extended the range of already-available biocatalysts and industrial processes in which high salt concentrations inhibit the activity of regular enzymes. In addition to their halostable properties, haloenzymes can also withstand other conditions such as extreme pH and temperature. In spite of these benefits, the industrial potential of these natural catalysts remains largely unexplored, with only a few characterized extracellular hydrolases. Because of the applied impact of haloarchaea and their specific ability to live in the presence of high salt concentrations, studies on their systematics have intensified in recent years, identifying many new genera and species. This review summarizes the current status of the haloarchaeal genera and species, and discusses the properties of haloenzymes and their potential industrial applications.
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Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Siroosi
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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26
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Xu JQ, Xu WM, Li Y, Zhou Y, Lü ZZ, Hou J, Zhu L, Cui HL. Halorussus salinus sp. nov., isolated from a marine solar saltern. Arch Microbiol 2016; 198:957-961. [PMID: 27290647 DOI: 10.1007/s00203-016-1253-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 05/31/2016] [Accepted: 06/02/2016] [Indexed: 01/23/2023]
Abstract
A halophilic archaeal strain YJ-37-HT was isolated from Yangjiang marine solar saltern, China. Cells were pleomorphic rods, stained Gram negative and formed red-pigmented colonies on agar plate. Strain YJ-37-HT was able to grow at 20-50 °C (optimum 37 °C), at 0.9-4.8 M NaCl (optimum 2.6 M NaCl), at 0-1.0 M MgCl2 (optimum 0.3 MgCl2) and at pH 6.5-9.0 (optimum pH 7.0). The cells lysed in distilled water, and the minimal NaCl concentration to prevent cell lysis was found to be 5 % (w/v). The 16S rRNA gene and rpoB' gene of strain YJ-37-HT were phylogenetically related to the corresponding genes of Halorussus members (93.2-95.8 % and 90.1-93.9 % similarities, respectively). The major polar lipids of the strain were phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS) and five glycolipids, sulfated galactosyl mannosyl glucosyl diether (S-TGD-1), galactosyl mannosyl glucosyl diether (TGD-1), sulfated mannosyl glucosyl diether (S-DGD-1), mannosyl glucosyl diether (DGD-1) and diglycosyl diether (DGD-2). The DNA G+C content of strain YJ-37-HT was 64.9 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain YJ-37-HT (=CGMCC 1.12571T = JCM 30032T) represents a new species of Halorussus, for which the name Halorussus salinus sp. nov. is proposed.
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Affiliation(s)
- Jia-Qi Xu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Wen-Mei Xu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Yang Li
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Yao Zhou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Zhen-Zhen Lü
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Lin Zhu
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, People's Republic of China.
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Hao Z, Dong H, Li Z, Lin H. Analysis of physicochemical properties during the processing of Yiluxian, a traditional chinese low-salt fish product. Int J Food Sci Technol 2016. [DOI: 10.1111/ijfs.13171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zina Hao
- Lab of Food Safety; College of Food Science and Engineering; Ocean University of China; Qingdao 266003 Shandong China
| | - Hao Dong
- Lab of Food Safety; College of Food Science and Engineering; Ocean University of China; Qingdao 266003 Shandong China
| | - Zhenxing Li
- Lab of Food Safety; College of Food Science and Engineering; Ocean University of China; Qingdao 266003 Shandong China
| | - Hong Lin
- Lab of Food Safety; College of Food Science and Engineering; Ocean University of China; Qingdao 266003 Shandong China
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28
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Characterization and antimicrobial potential of extremely halophilic archaea isolated from hypersaline environments of the Algerian Sahara. Microbiol Res 2016; 186-187:119-31. [PMID: 27242149 DOI: 10.1016/j.micres.2016.04.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 01/20/2023]
Abstract
Halophilic archaea were isolated from different chotts and sebkha, dry salt lakes and salt flat respectively, of the Algerian Sahara and characterized using phenotypic and phylogenetic approaches. From 102 extremely halophilic strains isolated, forty three were selected and studied. These strains were also screened for their antagonistic potential and the production of hydrolytic enzymes. Sequencing of the 16S rRNA genes and phylogenetic analysis allowed the identification of 10 archaeal genera within the class Halobacteria: Natrinema (13 strains), Natrialba (12 strains), Haloarcula (4 strains), Halopiger (4 strains), Haloterrigena (3 strains), Halorubrum (2 strains), Halostagnicola (2 strains), Natronococcus, Halogeometricum and Haloferax (1 strain each). The most common producers of antimicrobial compounds belong to the genus Natrinema while the most hydrolytic isolates, with combined production of several enzymes, belong to the genus Natrialba. The strain affiliated to Halopiger djelfamassilliensis was found to produce some substances of interest (halocins, anti-Candida, enzymes). After partial purification and characterization of one of the strains Natrinema gari QI1, we found similarities between the antimicrobial compound and the halocin C8. Therefore, the gene encoding halocin C8 was amplified and sequenced.
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29
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Chuprom J, Bovornreungroj P, Ahmad M, Kantachote D, Dueramae S. Approach toward enhancement of halophilic protease production by Halobacterium sp. strain LBU50301 using statistical design response surface methodology. ACTA ACUST UNITED AC 2016; 10:17-28. [PMID: 28352520 PMCID: PMC5040864 DOI: 10.1016/j.btre.2016.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 01/15/2023]
Abstract
Halophilic protease producing Halobacterium sp. strain LBU50301 was isolated. RSM optimized the fermentation conditions to enhance halophilic protease yield. Optimized conditions used in bioreactor resulted about 13-fold enhancement.
A new potent halophilic protease producer, Halobacterium sp. strain LBU50301 was isolated from salt-fermented fish samples (budu) and identified by phenotypic analysis, and 16S rDNA gene sequencing. Thereafter, sequential statistical strategy was used to optimize halophilic protease production from Halobacterium sp. strain LBU50301 by shake-flask fermentation. The classical one-factor-at-a-time (OFAT) approach determined gelatin was the best nitrogen source. Based on Plackett–Burman (PB) experimental design; gelatin, MgSO4·7H2O, NaCl and pH significantly influenced the halophilic protease production. Central composite design (CCD) determined the optimum level of medium components. Subsequently, an 8.78-fold increase in corresponding halophilic protease yield (156.22 U/mL) was obtained, compared with that produced in the original medium (17.80 U/mL). Validation experiments proved the adequacy and accuracy of model, and the results showed the predicted value agreed well with the experimental values. An overall 13-fold increase in halophilic protease yield was achieved using a 3 L laboratory fermenter and optimized medium (231.33 U/mL).
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Affiliation(s)
- Julalak Chuprom
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Preeyanuch Bovornreungroj
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Mehraj Ahmad
- Institute of Nutrition (INMU), Mahidol University, 999 Phutthamonthon 4 Rd., Salaya, Nakhon Pathom 73170, Thailand
| | - Duangporn Kantachote
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Sawitree Dueramae
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
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30
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Sánchez-Nieves R, Facciotti M, Saavedra-Collado S, Dávila-Santiago L, Rodríguez-Carrero R, Montalvo-Rodríguez R. Draft genome of Haloarcula rubripromontorii strain SL3, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico. GENOMICS DATA 2016; 7:287-9. [PMID: 26981428 PMCID: PMC4778667 DOI: 10.1016/j.gdata.2016.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 11/30/2022]
Abstract
The genus Haloarcula belongs to the family Halobacteriaceae which currently has 10 valid species. Here we report the draft genome sequence of strain SL3, a new species within this genus, isolated from the Solar Salterns of Cabo Rojo, Puerto Rico. Genome assembly performed using NGEN Assembler resulted in 18 contigs (N50 = 601,911 bp), the largest of which contains 1,023,775 bp. The genome consists of 3.97 MB and has a GC content of 61.97%. Like all species of Haloarcula, the genome encodes heterogeneous copies of the small subunit ribosomal RNA. In addition, the genome includes 6 rRNAs, 48 tRNAs, and 3797 protein coding sequences. Several carbohydrate-active enzymes genes were found, as well as enzymes involved in the dihydroxyacetone processing pathway which are not found in other Haloarcula species. The NCBI accession number for this genome is LIUF00000000 and the strain deposit number is CECT9001.
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Affiliation(s)
- Rubén Sánchez-Nieves
- Biology Department, University of Puerto Rico, Mayaguez, Box 9000, 00681-9000, Puerto Rico
| | - Marc Facciotti
- Biomedical Engineering and Genome Center, 451 Health Sciences Drive, Davis, CA, 95618, United States
| | - Sofía Saavedra-Collado
- Biology Department, University of Puerto Rico, Mayaguez, Box 9000, 00681-9000, Puerto Rico
| | | | - Roy Rodríguez-Carrero
- Biology Department, University of Puerto Rico, Mayaguez, Box 9000, 00681-9000, Puerto Rico
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31
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Dammak DF, Smaoui SM, Ghanmi F, Boujelben I, Maalej S. Characterization of halo-alkaline and thermostable protease from Halorubrum ezzemoulense
strain ETR14 isolated from Sfax solar saltern in Tunisia. J Basic Microbiol 2016; 56:337-46. [DOI: 10.1002/jobm.201500475] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/11/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Donyez Frikha Dammak
- Faculté des Sciences de Sfax; Université de Sfax; Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES72) Sfax; Tunisia
| | - Salma Masmoudi Smaoui
- Faculté des Sciences de Sfax; Université de Sfax; Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES72) Sfax; Tunisia
| | - Fadoua Ghanmi
- Faculté des Sciences de Sfax; Université de Sfax; Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES72) Sfax; Tunisia
| | - Ines Boujelben
- Faculté des Sciences de Sfax; Université de Sfax; Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES72) Sfax; Tunisia
| | - Sami Maalej
- Faculté des Sciences de Sfax; Université de Sfax; Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES72) Sfax; Tunisia
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32
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Kumar S, Grewal J, Sadaf A, Hemamalini R, K. Khare S. Halophiles as a source of polyextremophilic α-amylase for industrial applications. AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.1.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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33
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Extremophilic Proteases: Developments of Their Special Functions, Potential Resources and Biotechnological Applications. BIOTECHNOLOGY OF EXTREMOPHILES: 2016. [DOI: 10.1007/978-3-319-13521-2_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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34
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Derntl C, Selb R, Klein R, Alte B, Witte A. Genomic manipulations in alkaliphilic haloarchaea demonstrated by a gene disruption in Natrialba magadii. FEMS Microbiol Lett 2015; 362:fnv179. [PMID: 26424765 DOI: 10.1093/femsle/fnv179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2015] [Indexed: 11/14/2022] Open
Abstract
Alkaliphilic haloarchaea, a distinct physiological group from the closely related neutrophilic haloarchaea, represent an underutilized resource for basic research and industrial applications. In contrast to the neutrophilic haloarchaea, no reports on genomic manipulations in haloalkaliphiles have been published until now. Genomic manipulations via homologous recombination are useful for basic research. In this study, we demonstrate the possibility for this strategy in alkaliphilic haloarchaea for the first time. In a previous study, we developed a PEG-mediated transformation technique for alkaliphilic haloarchaea that was deployed in this study to deliver a gene disruption cassette into the model organism Natrialba magadii. The gene encoding for the well-studied Natrialba extracellular protease was successfully disrupted by a recombination marker gene, demonstrating a proof of principle for the usability of homologous recombination for genomic manipulations in alkaliphilic haloarchaea. Since halo(alkali)philic Archaea are polyploid, a selection process was applied in order to obtain a mutant strain containing exclusively disrupted genes. The resulting strain exhibited no proteolytic activity measurable by an azo-casein assay. Complementation was able to restore proteolytic activity. The expression pattern of the Natrialba extracellular protease was different in the complemented strain.
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Affiliation(s)
- Christian Derntl
- Department of Microbiology, Immunobiology and Genetics, MFPL Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Regina Selb
- Department of Microbiology, Immunobiology and Genetics, MFPL Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Reinhard Klein
- IMC FH Krems, University of Applied Sciences, Piaristengasse 1, 3500 Krems, Austria
| | - Beatrix Alte
- Department of Microbiology, Immunobiology and Genetics, MFPL Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Angela Witte
- Department of Microbiology, Immunobiology and Genetics, MFPL Laboratories, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
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35
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Exploring the multiple biotechnological potential of halophilic microorganisms isolated from two Argentinean salterns. Extremophiles 2015; 19:1133-43. [PMID: 26369649 DOI: 10.1007/s00792-015-0785-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/30/2015] [Indexed: 10/23/2022]
Abstract
The biodiversity and biotechnological potential of microbes from central Argentinean halophilic environments have been poorly explored. Salitral Negro and Colorada Grande salterns are neutral hypersaline basins exploded for NaCl extraction. As part of an ecological analysis of these environments, two bacterial and seven archaeal representatives were isolated, identified and examined for their biotechnological potential. The presence of hydrolases (proteases, amylases, lipases, cellulases and nucleases) and bioactive molecules (surfactants and antimicrobial compounds) was screened. While all the isolates exhibited at least one of the tested activities or biocompounds, the species belonging to Haloarcula genus were the most active, also producing antimicrobial compounds against their counterparts. In general, the biosurfactants were more effective against olive oil and aromatic compounds than detergents (SDS or Triton X-100). Our results demonstrate the broad spectrum of activities with biotechnological potential exhibited by the microorganisms inhabiting the Argentinean salterns and reinforce the importance of screening pristine extreme environments to discover interesting/novel bioactive molecules.
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36
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Solid-state fermentation as a potential technique for esterase/lipase production by halophilic archaea. Extremophiles 2015; 19:1121-32. [PMID: 26369647 DOI: 10.1007/s00792-015-0784-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 08/30/2015] [Indexed: 10/23/2022]
Abstract
Halophilic archaea are extremophiles, adapted to high-salt environments, showing a big biotechnological potential as enzyme, lipids and pigments producers. Four inert supports (perlite, vermiculite, polyurethane foam and glass fiber) were employed for solid-state fermentation (SSF) of the halophilic archaeon Natronococcus sp. TC6 to investigate biomass and esterase production. A very low esterase activity and high water activity were observed when perlite, vermiculite and polyurethane were used as supports. When glass fiber was employed, an important moisture loss was observed (8.6%). Moreover, moisture retention was improved by mixing polyurethane and glass fiber, resulting in maximal biomass and esterase production. Three halophilic archaea: Natronococcus sp. TC6, Halobacterium sp. NRC-1 and Haloarcula marismortui were cultured by submerged fermentation (SmF) and by SSF; an improvement of 1.3- to 6.2-fold was observed in the biomass and esterase production when SSF was used. Growth was not homogeneous in the mixture, but was predominant in the glass fiber thus was probably because the glass fiber provides a holder to the cells, while the polyurethane acts as an impregnation medium reservoir. To the best of our knowledge, this work is the first report on haloarchaea cultivation by SSF aiming biomass and esterase/lipase activity production.
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37
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Raddadi N, Cherif A, Daffonchio D, Neifar M, Fava F. Biotechnological applications of extremophiles, extremozymes and extremolytes. Appl Microbiol Biotechnol 2015; 99:7907-13. [PMID: 26272092 DOI: 10.1007/s00253-015-6874-9] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 11/24/2022]
Abstract
In the last decade, attention to extreme environments has increased because of interests to isolate previously unknown extremophilic microorganisms in pure culture and to profile their metabolites. Microorganisms that live in extreme environments produce extremozymes and extremolytes that have the potential to be valuable resources for the development of a bio-based economy through their application to white, red, and grey biotechnologies. Here, we provide an overview of extremophile ecology, and we review the most recent applications of microbial extremophiles and the extremozymes and extremolytes they produce to biotechnology.
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Affiliation(s)
- Noura Raddadi
- Department of Civil, Chemical, Environmental and Materials Engineering (DICAM), University of Bologna, via Terracini 28, 40131, Bologna, Italy,
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Cretoiu MS, Berini F, Kielak AM, Marinelli F, van Elsas JD. A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil. Appl Microbiol Biotechnol 2015; 99:8199-215. [PMID: 26040993 PMCID: PMC4561078 DOI: 10.1007/s00253-015-6639-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/21/2015] [Accepted: 04/24/2015] [Indexed: 12/04/2022]
Abstract
Here, we report on the construction of a metagenomic library from a chitin-amended disease-suppressive agricultural soil and its screening for genes that encode novel chitinolytic enzymes. The library, constructed in fosmids in an Escherichia coli host, comprised 145,000 clones containing inserts of sizes of 21 to 40 kb, yielding a total of approximately 5.8 GB of cloned soil DNA. Using genetic screenings by repeated PCR cycles aimed to detect gene sequences of the bacterial chitinase A-class (hereby named chi A genes), we identified and characterized five fosmids carrying candidate genes for chitinolytic enzymes. The analysis thus allowed access to the genomic (fosmid-borne) context of these genes. Using the chiA-targeted PCR, which is based on degenerate primers, the five fosmids all produced amplicons, of which the sequences were related to predicted chitinolytic enzyme-encoding genes of four different host organisms, including Stenotrophomonas maltophilia. Sequencing and de novo annotation of the fosmid inserts confirmed that each one of these carried one or more open reading frames that were predicted to encode enzymes active on chitin, including one for a chitin deacetylase. Moreover, the genetic contexts in which the putative chitinolytic enzyme-encoding genes were located were unique per fosmid. Specifically, inserts from organisms related to Burkholderia sp., Acidobacterium sp., Aeromonas veronii, and the chloroflexi Nitrolancetus hollandicus and/or Ktedonobacter racemifer were obtained. Remarkably, the S. maltophilia chiA-like gene was found to occur in two different genetic contexts (related to N. hollandicus/K. racemifer), indicating the historical occurrence of genetic reshufflings in this part of the soil microbiota. One fosmid containing the insert composed of DNA from the N. hollandicus-like organism (denoted 53D1) was selected for further work. Using subcloning procedures, its putative gene for a chitinolytic enzyme was successfully brought to expression in an E. coli host. On the basis of purified protein preparations, the produced protein was characterized as a chitobiosidase of 43.6 kDa, with a pI of 4.83. Given its activity spectrum, it can be typified as a halotolerant chitobiosidase.
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Affiliation(s)
- Mariana Silvia Cretoiu
- />Department of Microbial Ecology, CEES, University of Groningen, Groningen, The Netherlands
- />Department of Marine Microbiology, Royal Netherlands Institute for Sea Research, Yerseke, The Netherlands
| | - Francesca Berini
- />Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- />“The Protein Factory” Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, Varese, Italy
| | - Anna Maria Kielak
- />Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO), Wageningen, The Netherlands
| | - Flavia Marinelli
- />Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- />“The Protein Factory” Research Center, Politecnico of Milano, ICRM CNR Milano and University of Insubria, Varese, Italy
| | - Jan Dirk van Elsas
- />Department of Microbial Ecology, CEES, University of Groningen, Groningen, The Netherlands
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Oliveira LCG, Ramos PL, Marem A, Kondo MY, Rocha RCS, Bertolini T, Silveira MAV, da Cruz JB, de Vasconcellos SP, Juliano L, Okamoto DN. Halotolerant bacteria in the São Paulo Zoo composting process and their hydrolases and bioproducts. Braz J Microbiol 2015; 46:347-54. [PMID: 26273248 PMCID: PMC4507525 DOI: 10.1590/s1517-838246220130316] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 08/15/2014] [Indexed: 01/14/2023] Open
Abstract
Halophilic microorganisms are able to grow in the presence of salt and are also
excellent source of enzymes and biotechnological products, such as
exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs). Salt-tolerant
bacteria were screened in the Organic Composting Production Unit (OCPU) of São
Paulo Zoological Park Foundation, which processes 4 ton/day of organic residues
including plant matter from the Atlantic Rain Forest, animal manure and
carcasses and mud from water treatment. Among the screened microorganisms, eight
halotolerant bacteria grew at NaCl concentrations up to 4 M. These cultures were
classified based on phylogenetic characteristics and comparative partial 16S
rRNA gene sequence analysis as belonging to the genera
Staphylococcus, Bacillus and
Brevibacterium. The results of this study describe the
ability of these halotolerant bacteria to produce some classes of hydrolases,
namely, lipases, proteases, amylases and cellulases, and biopolymers. The strain
characterized as of Brevibacterium avium presented cellulase
and amylase activities up to 4 M NaCl and also produced EPSs and PHAs. These
results indicate the biotechnological potential of certain microorganisms
recovered from the composting process, including halotolerant species, which
have the ability to produce enzymes and biopolymers, offering new perspectives
for environmental and industrial applications.
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Affiliation(s)
- Lilian C G Oliveira
- Universidade Federal de São Paulo, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Patricia Locosque Ramos
- Universidade Federal de São Paulo, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil. ; Laboratório de Microbiologia Aplicada, Fundação Parque Zoológico de São Paulo, São Paulo, SP, Brasil, Laboratório de Microbiologia Aplicada, Fundação Parque Zoológico de São Paulo, São Paulo, SP, Brazil
| | - Alyne Marem
- Universidade Federal de São Paulo, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Marcia Y Kondo
- Universidade Federal de São Paulo, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Rafael C S Rocha
- Universidade Federal de São Paulo, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil. ; Koppert Biological Systems, Itapetininga, SP, Brasil, Koppert Biological Systems, Itapetininga, SP, Brazil
| | - Thiago Bertolini
- Universidade Federal de São Paulo, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Marghuel A V Silveira
- Universidade Federal de São Paulo, Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, SP, Brasil, Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - João Batista da Cruz
- Laboratório de Microbiologia Aplicada, Fundação Parque Zoológico de São Paulo, São Paulo, SP, Brasil, Laboratório de Microbiologia Aplicada, Fundação Parque Zoológico de São Paulo, São Paulo, SP, Brazil
| | - Suzan Pantaroto de Vasconcellos
- Universidade Federal de São Paulo, Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, SP, Brasil, Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, SP, Brazil. ; Laboratório de Microbiologia Aplicada, Fundação Parque Zoológico de São Paulo, São Paulo, SP, Brasil, Laboratório de Microbiologia Aplicada, Fundação Parque Zoológico de São Paulo, São Paulo, SP, Brazil
| | - Luiz Juliano
- Universidade Federal de São Paulo, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil. ; Laboratório de Microbiologia Aplicada, Fundação Parque Zoológico de São Paulo, São Paulo, SP, Brasil, Laboratório de Microbiologia Aplicada, Fundação Parque Zoológico de São Paulo, São Paulo, SP, Brazil
| | - Debora N Okamoto
- Universidade Federal de São Paulo, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil, Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
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Shapcott A, Forster PI, Guymer GP, McDonald WJF, Faith DP, Erickson D, Kress WJ. Mapping biodiversity and setting conservation priorities for SE Queensland's rainforests using DNA barcoding. PLoS One 2015. [PMID: 25803607 DOI: 10.1371/journal.pone.o122164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
Australian rainforests have been fragmented due to past climatic changes and more recently landscape change as a result of clearing for agriculture and urban spread. The subtropical rainforests of South Eastern Queensland are significantly more fragmented than the tropical World Heritage listed northern rainforests and are subject to much greater human population pressures. The Australian rainforest flora is relatively taxonomically rich at the family level, but less so at the species level. Current methods to assess biodiversity based on species numbers fail to adequately capture this richness at higher taxonomic levels. We developed a DNA barcode library for the SE Queensland rainforest flora to support a methodology for biodiversity assessment that incorporates both taxonomic diversity and phylogenetic relationships. We placed our SE Queensland phylogeny based on a three marker DNA barcode within a larger international rainforest barcode library and used this to calculate phylogenetic diversity (PD). We compared phylo- diversity measures, species composition and richness and ecosystem diversity of the SE Queensland rainforest estate to identify which bio subregions contain the greatest rainforest biodiversity, subregion relationships and their level of protection. We identified areas of highest conservation priority. Diversity was not correlated with rainforest area in SE Queensland subregions but PD was correlated with both the percent of the subregion occupied by rainforest and the diversity of regional ecosystems (RE) present. The patterns of species diversity and phylogenetic diversity suggest a strong influence of historical biogeography. Some subregions contain significantly more PD than expected by chance, consistent with the concept of refugia, while others were significantly phylogenetically clustered, consistent with recent range expansions.
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Affiliation(s)
- Alison Shapcott
- Genecology Research Center, Faculty of Science, Health, Education, and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Paul I Forster
- Queensland Herbarium, Queensland Department of Science, Information Technology, Innovation and the Arts, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| | - Gordon P Guymer
- Queensland Herbarium, Queensland Department of Science, Information Technology, Innovation and the Arts, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| | - William J F McDonald
- Queensland Herbarium, Queensland Department of Science, Information Technology, Innovation and the Arts, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| | | | - David Erickson
- National Museum of Natural History, Smithsonian Institution Washington D.C., United States of America
| | - W John Kress
- National Museum of Natural History, Smithsonian Institution Washington D.C., United States of America
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Lorentzen G, Wesmajervi Breiland MS, Østli J, Wang-Andersen J, Olsen RL. Growth of halophilic microorganisms and histamine content in dried salt-cured cod (Gadus morhua L.) stored at elevated temperature. Lebensm Wiss Technol 2015. [DOI: 10.1016/j.lwt.2014.08.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Lee MH, Lee HW, Song EJ, Song HS, Yim KJ, Cha IT, Seo MJ, Rhee JK, Choi HJ, Kim D, Kim KN, Roh SW, Nam YD. Draft genome sequence of Halolamina rubra CBA1107(T), an agarolytic haloarchaeon isolated from solar salt. Mar Genomics 2014; 18 Pt B:127-8. [PMID: 25218781 DOI: 10.1016/j.margen.2014.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 09/01/2014] [Accepted: 09/04/2014] [Indexed: 11/30/2022]
Abstract
Halolamina rubra CBA1107(T) (=CECT 8421(T), JCM 19436(T)), an extremely halophilic archaeon, was isolated from non-purified solar salt in the Republic of Korea. H. rubra CBA1107(T) shows agarase activity, and its draft genome contains 2955,064bp with a G+C content of 69.0%. This is the first genome that has been sequenced in the genus Halolamina.
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Affiliation(s)
- Mi-Hwa Lee
- Fermentation Research Center, Korea Food Research Institute, Sungnam 463-746, Republic of Korea
| | - Hae-Won Lee
- World Institute of Kimchi, Gwangju 503-360, Republic of Korea
| | - Eun-Ji Song
- Fermentation Research Center, Korea Food Research Institute, Sungnam 463-746, Republic of Korea; Korea University of Science and Technology, Daejeon 305-350, Republic of Korea
| | - Hye Seon Song
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
| | - Kyung June Yim
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
| | - In-Tae Cha
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea; Division of Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea
| | - Myung-Ji Seo
- Division of Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea
| | - Jin-Kyu Rhee
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
| | - Hak-Jong Choi
- World Institute of Kimchi, Gwangju 503-360, Republic of Korea
| | - Daekyung Kim
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
| | - Kil-Nam Kim
- Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
| | - Seong Woon Roh
- Korea University of Science and Technology, Daejeon 305-350, Republic of Korea; Korea Basic Science Institute, Daejeon 305-806, Republic of Korea.
| | - Young-Do Nam
- Fermentation Research Center, Korea Food Research Institute, Sungnam 463-746, Republic of Korea; Korea University of Science and Technology, Daejeon 305-350, Republic of Korea.
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Characterization of an organic solvent-tolerant lipase from Haloarcula sp. G41 and its application for biodiesel production. Folia Microbiol (Praha) 2014; 59:455-63. [DOI: 10.1007/s12223-014-0320-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
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44
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Biotechnological applications of halophilic lipases and thioesterases. Appl Microbiol Biotechnol 2013; 98:1011-21. [DOI: 10.1007/s00253-013-5417-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/14/2013] [Accepted: 11/16/2013] [Indexed: 12/13/2022]
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45
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A novel esterase from a psychrotrophic bacterium Psychrobacter celer 3Pb1 showed cold-adaptation and salt-tolerance. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.10.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Production of biosurfactant on crude date syrup under saline conditions by entrapped cells of Natrialba sp. strain E21, an extremely halophilic bacterium isolated from a solar saltern (Ain Salah, Algeria). Extremophiles 2013; 17:981-93. [PMID: 24061687 DOI: 10.1007/s00792-013-0580-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
Abstract
A bacterial strain E21 was isolated from a sample of water collected in the salt lake located close to Ain Salah, Algeria. The analysis of 16S rRNA gene sequence had indicated that the strain had 93 % sequence similarity with the genus Natrialba sp. strain E21 (GenBank, FR750525.1) and was considered extremely halophilic. Production of biosurfactant by the strain E21 with free and entrapped cells was investigated using soluble starch in the saline conditions. Biosurfactant synthesis was followed by measuring the surface tension and emulsifying index 9 days under optimal conditions (40 °C, pH 7). Some diffusional limitations in alginate and agar beads affected the kinetics of biosurfactant production when compared to that obtained with free cells culture. The minimum values of surface tension were 27 and 30 mN m(-1) achieved after 9 days with free and immobilized cells, respectively, while the corresponding maximum E24 values were 65.3 and 62.3 %, respectively. The re-use of bacterial cells along with the limited cell losses provided by the immobilized system might lead to significant reduction of the biosurfactant production cost.
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Halostable cellulase with organic solvent tolerance from Haloarcula sp. LLSG7 and its application in bioethanol fermentation using agricultural wastes. J Ind Microbiol Biotechnol 2013; 40:1357-65. [PMID: 24037323 DOI: 10.1007/s10295-013-1340-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/02/2013] [Indexed: 10/26/2022]
Abstract
A haloarchaeal strain LLSG7 with cellulolytic activity was isolated from the saline soil of Yuncheng Salt Lake, China. Biochemical and physiological characterization along with 16S rRNA gene sequence analysis placed the isolate in the genus Haloarcula. Cellulase production was strongly influenced by the salinity of the culture medium with the maximum obtained in the presence of 25 % NaCl. Substrate specificity tests showed that the crude cellulase was a multicomponent enzyme system, and zymogram analysis revealed that five different endoglucanases were secreted by strain LLSG7. Optimal cellulase activity was at 50 °C, pH 8.0, and 20 % NaCl. In addition, it was highly active and stable over broad ranges of temperature (40-80 °C), pH (7.0-11.0), and NaCl concentration (17.5-30 %). The cellulase displayed remarkable stability in the presence of non-polar organic solvents with log P ow ≥ 1.97. The crude cellulase secreted by strain LLSG7 was further applied to hydrolyze alkali-pretreated rice straw and the enzymatic hydrolysate was used as the substrate for bioethanol fermentation by Saccharomyces cerevisiae. The yield of ethanol was 0.177 g per gram of pretreated rice straw, suggesting that it might be potentially useful for bioethanol production.
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Li X, Yu HY. Characterization of a halostable endoglucanase with organic solvent-tolerant property from Haloarcula sp. G10. Int J Biol Macromol 2013; 62:101-6. [PMID: 23999019 DOI: 10.1016/j.ijbiomac.2013.08.047] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 08/25/2013] [Accepted: 08/26/2013] [Indexed: 11/16/2022]
Abstract
A haloarchaeal strain G10 with celluolytic activity was isolated from the saline soil of Yuncheng Salt Lake, China. Biochemical and physiological characterization along with 16S rRNA gene sequence analysis placed the isolate in the genus Haloarcula. The extracellular cellulase was purified to homogeneity with a molecular mass of 36 kDa. Substrate specificity test indicated that it was an endoglucanase for soluble cellulose. Optimal enzyme activity was found to be at 60 °C, pH 9.0 and 17.5% NaCl. Furthermore, high activity and stability over broad ranges of temperature (40-80 °C), pH (7.0-10.0) and NaCl concentration (12.5-27.5%) were observed, showing thermostable, alkali-stable and halostable properties of the cellulase. Significant inhibition by EDTA, phenylmethylsulfonyl fluoride (PMSF) and diethyl pyrocarbonate (DEPC) revealed it was a metalloenzyme with serine and histidine residues essential for enzyme catalysis. The surfactants tested had little effects on the enzyme activity. The endoglucanase showed high activity and stability in the presence of non-polar hydrophobic organic solvents with log Pow≥0.88. Together these results indicated the cellulase from Haloarcula sp. G10 maybe an ideal choice for applications in industrial process under harsh conditions.
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Affiliation(s)
- Xin Li
- Life Science College, Yuncheng University, 1155 Fudan West Street, Yuncheng 044000, China
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Vijayendra SVN, Shamala TR. Film forming microbial biopolymers for commercial applications—A review. Crit Rev Biotechnol 2013; 34:338-57. [DOI: 10.3109/07388551.2013.798254] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Functional expression and characterization of a chitinase from the marine archaeon Halobacterium salinarum CECT 395 in Escherichia coli. Appl Microbiol Biotechnol 2013; 98:2133-43. [PMID: 23893326 DOI: 10.1007/s00253-013-5124-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 07/10/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
The HschiA1 gene of the archaeon Halobacterium salinarum CECT 395 was cloned and overexpressed as an active protein of 66.5 kDa in Escherichia coli. The protein called HsChiA1p has a modular structure consisting of a glycosyl hydrolase family 18 catalytic region, as well as a N-terminal family 5 carbohydrate-binding module and a polycystic kidney domain. The purified recombinant chitinase displayed optimum catalytic activity at pH 7.3 and 40 °C and showed high stability over broad pH (6-8.5) and temperature (25-45 °C) ranges. Protein activity was stimulated by the metal ions Mg(+2), K(+), and Ca(+2) and strongly inhibited by Mn(+2). HsChiA1p is salt-dependent with its highest activity in the presence of 1.5 M of NaCl, but retains 20% of its activity in the absence of salt. The recombinant enzyme hydrolysed p-NP-(GlcNAc)3, p-NP-(GlcNAc), crystalline chitin, and colloidal chitin. From its sequence features and biochemical properties, it can be identified as an exo-acting enzyme with potential interest regarding the biodegradation of chitin waste or its bioconversion into biologically active products.
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