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Mahjoubi M, Cherif H, Aliyu H, Chouchane H, Cappello S, Neifar M, Mapelli F, Souissi Y, Borin S, Cowan DA, Cherif A. Brucella pituitosa strain BU72, a new hydrocarbonoclastic bacterium through exopolysaccharide-based surfactant production. Int Microbiol 2024:10.1007/s10123-024-00540-8. [PMID: 38867105 DOI: 10.1007/s10123-024-00540-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/22/2024] [Accepted: 05/19/2024] [Indexed: 06/14/2024]
Abstract
Hydrocarbon and heavy metal pollution are amongst the most severe and prevalent environmental problems due to their toxicity and persistence. Bioremediation using microorganisms is considered one of the most effective ways to treat polluted sites. In the present study, we unveil the bioremediation potential of Brucella pituitosa strain BU72. Besides its ability to grow on multiple hydrocarbons as the sole carbon source and highly tolerant to several heavy metals, BU72 produces different exopolysaccharide-based surfactants (EBS) when grown with glucose or with crude oil as sole carbon source. These EBS demonstrated particular and specific functional groups as determined by Fourier transform infrared (FTIR) spectral analysis that showed a strong absorption peak at 3250 cm-1 generated by the -OH group for both EBS. The FTIR spectra of the produced EBS revealed major differences in functional groups and protein content. To better understand the EBS production coupled with the degradation of hydrocarbons and heavy metal resistance, the genome of strain BU72 was sequenced. Annotation of the genome revealed multiple genes putatively involved in EBS production pathways coupled with resistance to heavy metals genes such as arsenic tolerance and cobalt-zinc-cadmium resistance. The genome sequence analysis showed the potential of BU72 to synthesise secondary metabolites and the presence of genes involved in plant growth promotion. Here, we describe the physiological, metabolic, and genomic characteristics of Brucella pituitosa strain BU72, indicating its potential as a bioremediation agent.
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Affiliation(s)
- Mouna Mahjoubi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Hanene Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Habibu Aliyu
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | - Habib Chouchane
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Simone Cappello
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (IRBIM)-CNR of Messina., Sp. San Raineri, 86, 98122, Messina, Italy
| | - Mohamed Neifar
- Common Services Unit "Bioreactor Coupled With an Ultrafilter"; APVA‑LR16ES20; ENIS, University of Sfax, Sfax, Tunisia
| | | | - Yasmine Souissi
- Department of Engineering, German University of Technology in Oman, P.O. Box 1816, PC 130, Muscat, Sultanate of Oman
| | - Sara Borin
- Common Services Unit "Bioreactor Coupled With an Ultrafilter"; APVA‑LR16ES20; ENIS, University of Sfax, Sfax, Tunisia
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
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Noirungsee N, Changkhong S, Phinyo K, Suwannajak C, Tanakul N, Inwongwan S. Genome-scale metabolic modelling of extremophiles and its applications in astrobiological environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13231. [PMID: 38192220 PMCID: PMC10866088 DOI: 10.1111/1758-2229.13231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/19/2023] [Indexed: 01/10/2024]
Abstract
Metabolic modelling approaches have become the powerful tools in modern biology. These mathematical models are widely used to predict metabolic phenotypes of the organisms or communities of interest, and to identify metabolic targets in metabolic engineering. Apart from a broad range of industrial applications, the possibility of using metabolic modelling in the contexts of astrobiology are poorly explored. In this mini-review, we consolidated the concepts and related applications of applying metabolic modelling in studying organisms in space-related environments, specifically the extremophilic microbes. We recapitulated the current state of the art in metabolic modelling approaches and their advantages in the astrobiological context. Our review encompassed the applications of metabolic modelling in the theoretical investigation of the origin of life within prebiotic environments, as well as the compilation of existing uses of genome-scale metabolic models of extremophiles. Furthermore, we emphasize the current challenges associated with applying this technique in extreme environments, and conclude this review by discussing the potential implementation of metabolic models to explore theoretically optimal metabolic networks under various space conditions. Through this mini-review, our aim is to highlight the potential of metabolic modelling in advancing the study of astrobiology.
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Affiliation(s)
- Nuttapol Noirungsee
- Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
| | - Sakunthip Changkhong
- Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
- Department of Thoracic SurgeryUniversity Hospital ZurichZurichSwitzerland
| | - Kittiya Phinyo
- Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
- Research group on Earth—Space Ecology (ESE), Faculty of ScienceChiang Mai UniversityChiang MaiThailand
- Office of Research AdministrationChiang Mai UniversityChiang MaiThailand
| | | | - Nahathai Tanakul
- National Astronomical Research Institute of ThailandChiang MaiThailand
| | - Sahutchai Inwongwan
- Department of Biology, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
- Research Center of Microbial Diversity and Sustainable Utilizations, Faculty of ScienceChiang Mai UniversityChiang MaiThailand
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Immanuel A, Yennamalli RM, Ulaganathan V. Targeting the Bottlenecks in Levan Biosynthesis Pathway in Bacillus subtilis and Strain Optimization by Computational Modeling and Omics Integration. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:49-58. [PMID: 38315781 DOI: 10.1089/omi.2023.0277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Levan is a fructan polymer with many industrial applications such as the formulation of hydrogels, drug delivery, and wound healing, among others. To this end, metabolic systems engineering is a valuable method to improve the yield of a specific metabolite in a wide range of bacterial and eukaryotic organisms. In this study, we report a systems biology approach integrating genomics data for the Bacillus subtilis model, wherein the metabolic pathway for levan biosynthesis is unpacked. We analyzed a revised genome-scale enzyme-constrained metabolic model (ecGEM) and performed simulations to increase levan biopolymer production capacity in B. subtilis. We used the model ec_iYO844_lvn to (1) identify the essential genes and bottlenecks in levan production, and (2) specifically design an engineered B. subtilis strain capable of producing higher levan yields. The FBA and FVA analysis showed the maximal growth rate of the organism up to 0.624 hr-1 at 20 mmol gDw-1 hr-1 of sucrose intake. Gene knockout analyses were performed to identify gene knockout targets to increase the levan flux in B. subtilis. Importantly, we found that the pgk and ctaD genes are the two target genes for the knockout. The perturbation of these two genes has flux gains for levan production reactions with 1.3- and 1.4-fold the relative flux span in the mutant strains, respectively, compared to the wild type. In all, this work identifies the bottlenecks in the production of levan and possible ways to overcome them. Our results provide deeper insights on the bacterium's physiology and new avenues for strain engineering.
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Affiliation(s)
- Aruldoss Immanuel
- Molecular Motors Lab, Department of Biotechnology, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Venkatasubramanian Ulaganathan
- Molecular Motors Lab, Department of Biotechnology, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
- Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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Yaşar Yıldız S, Radchenkova N. Exploring Extremophiles from Bulgaria: Biodiversity, Biopolymer Synthesis, Functional Properties, Applications. Polymers (Basel) 2023; 16:69. [PMID: 38201734 PMCID: PMC10780585 DOI: 10.3390/polym16010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/10/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Bulgaria stands out as a country rich in diverse extreme environments, boasting a remarkable abundance of mineral hot waters, which positions it as the second-largest source of such natural resources in Europe. Notably, several thermal and coastal solar salterns within its territory serve as thriving habitats for thermophilic and halophilic microorganisms, which offer promising bioactive compounds, including exopolysaccharides (EPSs). Multiple thermophilic EPS producers were isolated, along with a selection from several saltern environments, revealing an impressive taxonomic and bacterial diversity. Four isolates from three different thermophilic species, Geobacillus tepidamans V264, Aeribacillus pallidus 418, Brevibacillus thermoruber 423, and Brevibacillus thermoruber 438, along with the halophilic strain Chromohalobacter canadensis 28, emerged as promising candidates for further exploration. Optimization of cultivation media and conditions was conducted for each EPS producer. Additionally, investigations into the influence of aeration and stirring in laboratory bioreactors provided valuable insights into growth dynamics and polymer synthesis. The synthesized biopolymers showed excellent emulsifying properties, emulsion stability, and synergistic interaction with other hydrocolloids. Demonstrated biological activities and functional properties pave the way for potential future applications in diverse fields, with particular emphasis on cosmetics and medicine. The remarkable versatility and efficacy of biopolymers offer opportunities for innovation and development in different industrial sectors.
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Affiliation(s)
- Songül Yaşar Yıldız
- Department of Bioengineering, Istanbul Medeniyet University, 34720 Istanbul, Turkey;
| | - Nadja Radchenkova
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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Biopolymer production by bacteria isolated from native stingless bee honey, Scaptotrigona jujuyensis. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Hoang Anh N, Min JE, Kim SJ, Phuoc Long N. Biotherapeutic Products, Cellular Factories, and Multiomics Integration in Metabolic Engineering. ACTA ACUST UNITED AC 2020; 24:621-633. [DOI: 10.1089/omi.2020.0112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nguyen Hoang Anh
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Jung Eun Min
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Sun Jo Kim
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Nguyen Phuoc Long
- Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
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