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Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:microorganisms10122355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
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Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
| | - Mohammad J. Taherzadeh
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
- Correspondence:
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Frikha-Dammak D, Ayadi H, Hakim-Rekik I, Belbahri L, Maalej S. Genome analysis of the salt-resistant Paludifilum halophilum DSM 102817 T reveals genes involved in flux-tuning of ectoines and unexplored bioactive secondary metabolites. World J Microbiol Biotechnol 2021; 37:178. [PMID: 34549358 DOI: 10.1007/s11274-021-03147-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Paludifilum halophilum DSM 102817T is the first member of the genus Paludifilum in the Thermoactinomycetaceae family. The thermohalophilic bacterium was isolated from the solar saltern of Sfax, Tunisia and was shown to be able to produce ectoines with a relatively high-yield and to cope with salt stress conditions. In this study, the whole genome of P. halophilum was sequenced and analysed. Analysis revealed 3,789,765 base pairs with an average GC% content of 51.5%. A total of 3775 genes were predicted of which 3616 were protein-coding genes and 73 were RNA genes. The genes encoding key enzymes for ectoines (ectoine and hydroxyectoine) synthesis (ectABCD) were identified from the bacterial genome next to a gene cluster (ehuABCD) encoding a binding-protein-dependent ABC transport system responsible for ectoines mobility through the cell membrane. With the aid of KEGG analysis, we found that the central catabolic network of P. halophilum comprises the pathways of glycolysis, tricarboxylic acid cycle, and pentose phosphate. In addition, anaplerotic pathways replenishing oxaloacetate and glutamate synthesis from central metabolism needed for high ectoines biosynthetic fluxes were identified through several key enzymes. Furthermore, a total of 18 antiSMASH-predicted putative biosynthetic gene clusters for secondary metabolites with high novelty and diversity were identified in P. halophilum genome, including biosynthesis of colabomycine-A, fusaricidin-E, zwittermycin A, streptomycin, mycosubtilin and meilingmycin. Based on these data, P. halophilum emerged as a promising source for ectoines and antimicrobials with the potential to be scaled up for industrial production, which could benefit the pharmaceutical and cosmetic industries.
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Affiliation(s)
- Donyez Frikha-Dammak
- Laboratoire de Biodiversité Marine et Environnement (LR18ES30), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax, Tunisia
| | - Houda Ayadi
- Laboratoire de Biodiversité Marine et Environnement (LR18ES30), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax, Tunisia
| | - Imen Hakim-Rekik
- Unité de Génomique Fonctionnelle et Physiologie des Plantes, Université de Sfax, Institut Supérieur de Biotechnologie de Sfax, BP 1175, 3000, Sfax, Tunisia
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000, Neuchâtel, Switzerland
| | - Sami Maalej
- Laboratoire de Biodiversité Marine et Environnement (LR18ES30), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000, Sfax, Tunisia.
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Ayadi H, Frikha-Dammak D, Fakhfakh J, Chamkha M, Hassairi I, Allouche N, Sayadi S, Maalej S. The saltern-derived Paludifilum halophilum DSM 102817 T is a new high-yield ectoines producer in minimal medium and under salt stress conditions. 3 Biotech 2020; 10:533. [PMID: 33214980 DOI: 10.1007/s13205-020-02512-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
In the present study, the growth conditions and accumulation of ectoines (ectoine and hydroxyectoine) by Paludifilum halophilum DSM 102817T under salt stress conditions have been investigated. The productivity assay of this strain for ectoines revealed that the highest cellular content was reached in the minimal glucose sea water medium (SW-15) within 15% salinity. The addition of 0.1% (w/v) aspartic acid to the medium allowed an average of four times higher biomass production, and a dry mycelial biomass of 1.76 g L-1 was obtained after 6 days of growth in shake flasks at 40 °C and 200 rpm. Among the inorganic cations supplemented to the glucose SW-15 medium, the addition of 1 mM Fe2+ yielded the highest amount of mycelial biomass (3.45 g L-1) and total ectoines content (119 mg g-1), resulting in about 410 mg L-1 of products at the end of exponential growth phase. After 1 h of incubation in an osmotic downshock solution containing 2% NaCl, 70% of this content was released by the mycelium, and recovering cells maintained a high survival, with a maximal growth rate (µ max) of about 93% of the control population exposed to 15% NaCl. During growth at optimal salinity and temperature (15% NaCl and 40 °C), P. halophilum developed a compact and circular pellets that were easy to separate by simple decantation from both fermentation media and after hypoosmotic shock. Overall, the ectoines excreting P. halophilum could be a promising resource for ectoines production in a commercially valuable culture medium and at a large-scale fermentation process.
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Affiliation(s)
- Houda Ayadi
- Laboratoire de Biodiversité Marine et Environment (LR18ES/30), Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Donyez Frikha-Dammak
- Laboratoire de Biodiversité Marine et Environment (LR18ES/30), Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Jawhar Fakhfakh
- Laboratore de Chimie Organique (LR17ES/08), Unité des Substances Naturelles, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Mohamed Chamkha
- Laboratore des Bioprocédés Environnementaux, Centre de Biotechnologie de Sfax, BP 1177, 3018 Sfax, Tunisia
| | - Ilem Hassairi
- Unité de Valorisation des résultats de la Recherche, Centre de Biotechnologie de Sfax, BP 1177, 3018 Sfax, Tunisia
| | - Noureddine Allouche
- Laboratore de Chimie Organique (LR17ES/08), Unité des Substances Naturelles, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Sami Sayadi
- Center for Sustainable Development, College of Arts and Sciences, Qatar University, 2713 Doha, Qatar
| | - Sami Maalej
- Laboratoire de Biodiversité Marine et Environment (LR18ES/30), Université de Sfax, BP 1171, 3000 Sfax, Tunisia
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Enhancement of Antibacterial Activity of Paludifilum halophilum and Identification of N-(1-Carboxy-ethyl)-phthalamic Acid as the Main Bioactive Compound. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4805706. [PMID: 32104693 PMCID: PMC7038168 DOI: 10.1155/2020/4805706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/03/2019] [Accepted: 12/12/2019] [Indexed: 11/17/2022]
Abstract
The aim of this study was to determine the combined effect of fermentation parameters and enhance the production of cellular biomass and antibacterial compounds from Paludifilum halophilum SMBg3 using the response surface methodology (RSM). Eight variables were screened to assess the effects of fermentation parameters on growth and metabolite production by Taguchi experimental design. Among these, the initial pH, temperature, and the percentage of MgSO4·7H2O in the medium were found to be most influential. The Box-Behnken design was applied to derive a statistical model for the optimization of these three fermentation parameters. The optimal parameters were initial pH: 8.3, temperature growth: 44°C, and MgSO4·7H2O: 1.6%, respectively. The maximum yield of biomass and metabolite production were, respectively, 11 mg/mL dry weight and 15.5 mm inhibition zone diameter against Salmonella enterica, which were in agreement with predicted values. The bioactive compounds were separated by the thick-layer chromatography technique and analyzed by GC/MS, NMR (1D and 2D), and Fourier-transform infrared spectroscopy (FT-IR). In addition to several fatty acids, N-(1-carboxy-ethyl)-phthalamic acid was identified as the main antibacterial compound. This element exhibited a potent activity against the ciprofloxacin-resistant Salmonella enterica CIP 8039 and Pseudomonas aeruginosa ATCC 9027 with a minimum inhibitory concentration (MIC) value range of 12.5-25 μg/mL. Results demonstrated that P. halophilum strain SMBg3 is a promising resource for novel antibacterial production due to its high-level yield potential and the capacity for large-scale fermentation.
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Jiang Z, Xiao M, Yang LL, Zhi XY, Li WJ. Genome-based taxonomic classification within the family Thermoactinomycetaceae. Int J Syst Evol Microbiol 2019; 69:2028-2036. [DOI: 10.1099/ijsem.0.003425] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zhao Jiang
- 1Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
- 2School of Medicine, Xizang Minzu University, Xianyang 712082, PR China
| | - Min Xiao
- 3State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- 4Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai 519000, PR China
| | - Ling-Ling Yang
- 1Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Xiao-Yang Zhi
- 1Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, PR China
| | - Wen-Jun Li
- 3State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- 4Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai 519000, PR China
- 5Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Űrűmuqi, 830011, PR China
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Frikha Dammak D, Zarai Z, Najah S, Abdennabi R, Belbahri L, Rateb ME, Mejdoub H, Maalej S. Antagonistic Properties of Some Halophilic Thermoactinomycetes Isolated from Superficial Sediment of a Solar Saltern and Production of Cyclic Antimicrobial Peptides by the Novel Isolate Paludifilum halophilum. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1205258. [PMID: 28819625 PMCID: PMC5551467 DOI: 10.1155/2017/1205258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/18/2017] [Indexed: 02/07/2023]
Abstract
This study has focused on the isolation of twenty-three halophilic actinomycetes from two ponds of different salinity and the evaluation of their ability to exert an antimicrobial activity against both their competitors and several other pathogens. From the 23 isolates, 18 strains showed antagonistic activity, while 19 showed activities against one or more of the seven pathogen strains tested. Six strains exhibited consistent antibacterial activity against Gram-negative and Gram-positive pathogens characterized at the physiological and molecular levels. These strains shared only 94-95% 16S rRNA sequence identity with the closely related species of the Thermoactinomycetaceae family. Among them, the potent strain SMBg3 was further characterized and assigned to a new genus in the family for which the name Paludifilum halophilum (DSM 102817T) is proposed. Sequential extraction of the antimicrobial compounds with ethyl acetate revealed that the crude extract from SMBg3 strain had inhibitory effect on the growth of the plant pathogen Agrobacterium tumefaciens and the human pathogens Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Pseudomonas aeruginosa. Based on the HRESI-MS spectral data, the cyclic lipopeptide Gramicidin S and four cyclic dipeptides (CDPs) named cyclo(L-4-OH-Pro-L-Leu), cyclo(L-Tyr-L-Pro), cyclo(L-Phe-L-Pro), and cyclo(L-Leu-L-Pro) were detected in the fermentation broth of Paludifilum halophilum. To our knowledge, this is the first report on the isolation of these compounds from members of the Thermoactinomycetaceae family.
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Affiliation(s)
- Donyez Frikha Dammak
- Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES/72), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Ziad Zarai
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS, BPW, 1173 Sfax, Tunisia
| | - Soumaya Najah
- Institut de Biologie Integrative, UMR 9198, Université Paris-Sud, Bat 400, 91405 Orsay Cedex, France
| | - Rayed Abdennabi
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000 Neuchatel, Switzerland
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 11 Rue Emile Argand, 2000 Neuchatel, Switzerland
| | - Mostafa E. Rateb
- School of Science & Sport, University of the West of Scotland, Paisley PA1 2BE, UK
| | - Hafedh Mejdoub
- Laboratoire des Biotechnologies Végétales Appliquées à l'Amélioration des Cultures, FSS, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
| | - Sami Maalej
- Unité Biodiversité et Ecosystèmes Aquatiques Environnementaux (UR/11ES/72), Faculté des Sciences de Sfax, Université de Sfax, BP 1171, 3000 Sfax, Tunisia
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