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Powell T, Sumner DY, Jungblut AD, Hawes I, Mackey T, Grettenberger C. Metagenome-assembled bacterial genomes from benthic microbial mats in ice-covered Lake Vanda, Antarctica. Microbiol Resour Announc 2024; 13:e0125023. [PMID: 38587419 PMCID: PMC11080526 DOI: 10.1128/mra.01250-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/10/2024] [Indexed: 04/09/2024] Open
Abstract
We recovered 57 bacterial metagenome-assembled genomes (MAGs) from benthic microbial mat pinnacles from Lake Vanda, Antarctica. These MAGs provide access to genomes from polar environments and can assist in culturing and utilizing these Antarctic bacteria.
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Affiliation(s)
- Tyler Powell
- Department of Earth and Planetary Sciences, University of California, Davis, USA
- Microbiology Graduate Group, University of California, Davis, USA
| | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, USA
| | - Anne D. Jungblut
- Department of Sciences, The Natural History Museum, London, United Kingdom
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand
| | - Tyler Mackey
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, New Mexico, USA
| | - Christen Grettenberger
- Department of Earth and Planetary Sciences, University of California, Davis, USA
- Department of Environmental Toxicology, University of California, Davis, USA
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2
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Rawat M, Chauhan M, Pandey A. Extremophiles and their expanding biotechnological applications. Arch Microbiol 2024; 206:247. [PMID: 38713374 DOI: 10.1007/s00203-024-03981-x] [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: 02/22/2024] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024]
Abstract
Microbial life is not restricted to any particular setting. Over the past several decades, it has been evident that microbial populations can exist in a wide range of environments, including those with extremes in temperature, pressure, salinity, and pH. Bacteria and Archaea are the two most reported types of microbes that can sustain in extreme environments, such as hot springs, ice caves, acid drainage, and salt marshes. Some can even grow in toxic waste, organic solvents, and heavy metals. These microbes are called extremophiles. There exist certain microorganisms that are found capable of thriving in two or more extreme physiological conditions simultaneously, and are regarded as polyextremophiles. Extremophiles possess several physiological and molecular adaptations including production of extremolytes, ice nucleating proteins, pigments, extremozymes and exopolysaccharides. These metabolites are used in many biotechnological industries for making biofuels, developing new medicines, food additives, cryoprotective agents etc. Further, the study of extremophiles holds great significance in astrobiology. The current review summarizes the diversity of microorganisms inhabiting challenging environments and the biotechnological and therapeutic applications of the active metabolites obtained as a response to stress conditions. Bioprospection of extremophiles provides a progressive direction with significant enhancement in economy. Moreover, the introduction to omics approach including whole genome sequencing, single cell genomics, proteomics, metagenomics etc., has made it possible to find many unique microbial communities that could be otherwise difficult to cultivate using traditional methods. These findings might be capable enough to state that discovery of extremophiles can bring evolution to biotechnology.
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Affiliation(s)
- Manvi Rawat
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India
| | - Mansi Chauhan
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India.
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3
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Jeilu O, Alexandersson E, Johansson E, Simachew A, Gessesse A. A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation. Sci Rep 2024; 14:10012. [PMID: 38693138 PMCID: PMC11063200 DOI: 10.1038/s41598-024-60645-y] [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: 11/16/2023] [Accepted: 04/25/2024] [Indexed: 05/03/2024] Open
Abstract
Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, β-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a β-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50 °C and pH 8.5. In addition, supplementation of 1 M salt and 300 mM glucose enhanced the β-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the β-glucosidase activity. However, Cu2+ and Mn2+ ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied β-glucosidase enzyme has multiple industrially desirable properties including thermostability, and alkaline, salt, and glucose tolerance.
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Affiliation(s)
- Oliyad Jeilu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden.
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia.
| | - Erik Alexandersson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 23422, Lomma, Sweden
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, P O Box 1176, Addis Ababa, Ethiopia
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
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Gaur S, Kaur M, Kalra R, Rene ER, Goel M. Application of microbial resources in biorefineries: Current trend and future prospects. Heliyon 2024; 10:e28615. [PMID: 38628756 PMCID: PMC11019186 DOI: 10.1016/j.heliyon.2024.e28615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
The recent growing interest in sustainable and alternative sources of energy and bio-based products has driven the paradigm shift to an integrated model termed "biorefinery." Biorefinery framework implements the concepts of novel eco-technologies and eco-efficient processes for the sustainable production of energy and value-added biomolecules. The utilization of microbial resources for the production of various value-added products has been documented in the literatures. However, the appointment of these microbial resources in integrated resource management requires a better understanding of their status. The main of aim of this review is to provide an overview on the defined positioning and overall contribution of the microbial resources, i.e., algae, fungi and bacteria, for various bioprocesses and generation of multiple products from a single biorefinery. By utilizing waste material as a feedstock, biofuels can be generated by microalgae while sequestering environmental carbon and producing value added compounds as by-products. In parallel, fungal biorefineries are prolific producers of lignocellulose degrading enzymes along with pharmaceutically important novel products. Conversely, bacterial biorefineries emerge as a preferred platform for the transformation of standard cells into proficient bio-factories, developing chassis and turbo cells for enhanced target compound production. This comprehensive review is poised to offer an intricate exploration of the current trends, obstacles, and prospective pathways of microbial biorefineries, for the development of future biorefineries.
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Affiliation(s)
- Suchitra Gaur
- Sustainable Agriculture Program, The Energy and Resources Institute, TERI-Gram, Gurugram, 122001, Haryana, India
| | - Mehak Kaur
- Sustainable Agriculture Program, The Energy and Resources Institute, TERI-Gram, Gurugram, 122001, Haryana, India
| | - Rishu Kalra
- Sustainable Agriculture Program, The Energy and Resources Institute, TERI-Gram, Gurugram, 122001, Haryana, India
| | - Eldon R. Rene
- Department of Water Supply, Sanitation and Environmental Engineering, IHE Delft Institute for Water Education, Westvest 7, Delft, 2601DA, the Netherlands
| | - Mayurika Goel
- Sustainable Agriculture Program, The Energy and Resources Institute, TERI-Gram, Gurugram, 122001, Haryana, India
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Allison SD, AdeelaYasid N, Shariff FM, Abdul Rahman N. Molecular Cloning, Characterization, and Application of Organic Solvent-Stable and Detergent-Compatible Thermostable Alkaline Protease from Geobacillus thermoglucosidasius SKF4. J Microbiol Biotechnol 2024; 34:436-456. [PMID: 38044750 PMCID: PMC10940756 DOI: 10.4014/jmb.2306.06050] [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: 06/28/2023] [Revised: 10/12/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Abstract
Several thermostable proteases have been identified, yet only a handful have undergone the processes of cloning, comprehensive characterization, and full exploitation in various industrial applications. Our primary aim in this study was to clone a thermostable alkaline protease from a thermophilic bacterium and assess its potential for use in various industries. The research involved the amplification of the SpSKF4 protease gene, a thermostable alkaline serine protease obtained from the Geobacillus thermoglucosidasius SKF4 bacterium through polymerase chain reaction (PCR). The purified recombinant SpSKF4 protease was characterized, followed by evaluation of its possible industrial applications. The analysis of the gene sequence revealed an open reading frame (ORF) consisting of 1,206 bp, coding for a protein containing 401 amino acids. The cloned gene was expressed in Escherichia coli. The molecular weight of the enzyme was measured at 28 kDa using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The partially purified enzyme has its highest activity at a pH of 10 and a temperature of 80°C. In addition, the enzyme showed a half-life of 15 h at 80°C, and there was a 60% increase in its activity at 10 mM Ca2+ concentration. The activity of the protease was completely inhibited (100%) by phenylmethylsulfonyl fluoride (PMSF); however, the addition of sodium dodecyl sulfate (SDS) resulted in a 20% increase in activity. The enzyme was also stable in various organic solvents and in certain commercial detergents. Furthermore, the enzyme exhibited strong potential for industrial use, particularly as a detergent additive and for facilitating the recovery of silver from X-ray film.
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Affiliation(s)
- Suleiman D Allison
- Department of Food Science and Technology, Faculty of Agriculture and Agricultural Technology, Moddibo Adama University, Yola 640230, Nigeria
| | - Nur AdeelaYasid
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra, Malaysia, 43400 Serdang Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang Selangor, Malaysia
| | - Nor'Aini Abdul Rahman
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra, Malaysia, 43400 Serdang Selangor, Malaysia
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Xu H, Xu D, Liu Y. Molecular Biology Applications of Psychrophilic Enzymes: Adaptations, Advantages, Expression, and Prospective. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04810-5. [PMID: 38183603 DOI: 10.1007/s12010-023-04810-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 01/08/2024]
Abstract
Psychrophilic enzymes are primarily produced by microorganisms from extremely low-temperature environments which are known as psychrophiles. Their high efficiency at low temperatures and easy heat inactivation property have attracted extensive attention from various food and industrial bioprocesses. However, the application of these enzymes in molecular biology is still limited. In a previous review, the applications of psychrophilic enzymes in industries such as the detergent additives, the food additives, the bioremediation, and the pharmaceutical medicine, and cosmetics have been discussed. In this review, we discuss the main cold adaptation characteristics of psychrophiles and psychrophilic enzymes, as well as the relevant information on different psychrophilic enzymes in molecular biology. We summarize the mining and screening methods of psychrophilic enzymes. We finally recap the expression of psychrophilic enzymes. We aim to provide a reference process for the exploration and expression of new generation of psychrophilic enzymes.
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Affiliation(s)
- Hu Xu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Dawei Xu
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Yongqin Liu
- Center for Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China.
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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7
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Ortiz-Cortés LY, Aréchiga-Carvajal ET, Ventura-Canseco LMC, Ruíz-Valdiviezo VM, Gutiérrez-Miceli FA, Alvarez-Gutiérrez PE. Analysis of phenotypic changes in high temperature and low pH extreme conditions of Alicyclobacillus sendaiensis PA2 related with the cell wall and sporulation genes. Arch Microbiol 2024; 206:53. [PMID: 38180563 DOI: 10.1007/s00203-023-03735-1] [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: 09/22/2023] [Revised: 11/01/2023] [Accepted: 11/04/2023] [Indexed: 01/06/2024]
Abstract
The A. sendaiensis PA2 is a polyextremophile bacterium. In this study, we analyze the A. sendaiensis PA2 genome. The genome was assembled and annotated. The A. sendaiensis PA2 genome structure consists of a 2,956,928 bp long chromosome and 62.77% of G + C content. 3056 CDSs were predicted, and 2921 genes were assigned to a putative function. The ANIm and ANIb value resulted in 97.17% and 96.65%, the DDH value was 75.5%, and the value of TETRA (Z-score) was 0.98. Comparative genomic analyses indicated that three systems are enriched in A. sendaiensis PA2. This strain has phenotypic changes in cell wall during batch culture at 65 °C, pH 5.0 and without carbon and nitrogen source. The presence of unique genes of cell wall and sporulation subsystem could be related to the adaptation of A. sendaiensis PA2 to hostile conditions.
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Affiliation(s)
- Lourdes Yaret Ortiz-Cortés
- Tecnológico Nacional de México/IT de Tuxtla Gutiérrez, Carretera Panamericana Km 1080, Col. Terán, 29050, Tuxtla Gutiérrez, Chiapas, México
| | | | | | - Victor Manuel Ruíz-Valdiviezo
- Tecnológico Nacional de México/IT de Tuxtla Gutiérrez, Carretera Panamericana Km 1080, Col. Terán, 29050, Tuxtla Gutiérrez, Chiapas, México
| | - Federico Antonio Gutiérrez-Miceli
- Tecnológico Nacional de México/IT de Tuxtla Gutiérrez, Carretera Panamericana Km 1080, Col. Terán, 29050, Tuxtla Gutiérrez, Chiapas, México
| | - Peggy Elizabeth Alvarez-Gutiérrez
- Tecnológico Nacional de México/IT de Tuxtla Gutiérrez, Carretera Panamericana Km 1080, Col. Terán, 29050, Tuxtla Gutiérrez, Chiapas, México.
- CONAHCYT/IT de Tuxtla Gutiérrez, Carretera Panamericana Km 1080, Col. Terán, 29050, Tuxtla Gutiérrez, Chiapas, México.
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8
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Możejko-Ciesielska J, Ray S, Sankhyan S. Recent Challenges and Trends of Polyhydroxyalkanoate Production by Extremophilic Bacteria Using Renewable Feedstocks. Polymers (Basel) 2023; 15:4385. [PMID: 38006109 PMCID: PMC10674690 DOI: 10.3390/polym15224385] [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: 10/02/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biodegradable polymers with immense potential in addressing the global plastic pollution crisis and advancing sustainable bioplastics production. Among the various microbes known for PHA production, extremophilic bacteria possess unique capabilities to thrive under extreme conditions, making them attractive candidates for PHA synthesis. Furthermore, the utilization of renewable feedstocks for PHA production aligns with the growing demand for sustainable bioplastic alternatives. A diverse range of extremophilic bacteria, especially halophiles and thermophiles, has provided cost-competitive platforms for producing customized PHA polymers. Extremophilic bacteria offer unique advantages over mesophiles due to their contamination resistance, high cell density growth, and unique culture conditions. The current status of Halomonas spp. as a chassis further allows exploration of metabolic engineering approaches to overcome the challenges associated with current industrial biotechnology. This article especially focuses on extremophilic bacteria and explores recent advances in utilizing renewable feedstocks such as lignocellulosic biomass, agro-industrial residues, and waste streams for PHA production. The integration of biorefinery concepts and circular economy principles in PHA manufacturing is also examined. This review is an attempt to provide an understanding of renewable substrates as feedstocks and emerging trends in PHA production by extremophilic bacteria. It underscores the pivotal role of extremophiles and sustainable feedstock sources in advancing the feasibility and eco-friendliness of PHAs as a promising biopolymer alternative.
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Affiliation(s)
- Justyna Możejko-Ciesielska
- Department of Microbiology and Mycology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10719 Olsztyn, Poland
| | - Subhasree Ray
- Department of Life Sciences, School of Basic Science and Research, Sharda University, Greater Noida 201310, India;
| | - Shivangi Sankhyan
- Department of Life Sciences, School of Basic Science and Research, Sharda University, Greater Noida 201310, India;
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Sharma N, Agarwal A, Bijoy A, Pandit S, Sharma RK. Lignocellulolytic extremozymes and their biotechnological applications. Extremophiles 2023; 28:2. [PMID: 37950773 DOI: 10.1007/s00792-023-01314-2] [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: 01/02/2023] [Accepted: 09/26/2023] [Indexed: 11/13/2023]
Abstract
Lignocellulolytic enzymes are used in different industrial and environmental processes. The rigorous operating circumstances of these industries, however, might prevent these enzymes from performing as intended. On the other side, extremozymes are enzymes produced by extremophiles that can function in extremely acidic or basic; hot or cold; under high or low salinity conditions. These severe conditions might denature the normal enzymes that are produced by mesophilic microorganisms. The increased stability of these enzymes has been contributed to a number of conformational modifications in their structures. These modifications may result from a few amino acid substitutions, an improved hydrophobic core, the existence of extra ion pairs and salt bridges, an increase in compactness, or an increase in positively charged amino acids. These enzymes are the best option for industrial and bioremediation activities that must be carried out under difficult conditions due to their improved stability. The review, therefore, discusses lignocellulolytic extremozymes, their structure and mechanisms along with industrial and biotechnological applications.
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Affiliation(s)
- Nikita Sharma
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Aditi Agarwal
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Ananya Bijoy
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Sunidhi Pandit
- Department of Biosciences, Manipal University Jaipur, Jaipur, 303007, Rajasthan, India
| | - Rakesh Kumar Sharma
- Department of Life Sciences, Chhatrapati Shahu Ji Maharaj University, Kanpur, India.
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Arias PM, Butler J, Randhawa GS, Soltysiak MPM, Hill KA, Kari L. Environment and taxonomy shape the genomic signature of prokaryotic extremophiles. Sci Rep 2023; 13:16105. [PMID: 37752120 PMCID: PMC10522608 DOI: 10.1038/s41598-023-42518-y] [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: 06/06/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
This study provides comprehensive quantitative evidence suggesting that adaptations to extreme temperatures and pH imprint a discernible environmental component in the genomic signature of microbial extremophiles. Both supervised and unsupervised machine learning algorithms were used to analyze genomic signatures, each computed as the k-mer frequency vector of a 500 kbp DNA fragment arbitrarily selected to represent a genome. Computational experiments classified/clustered genomic signatures extracted from a curated dataset of [Formula: see text] extremophile (temperature, pH) bacteria and archaea genomes, at multiple scales of analysis, [Formula: see text]. The supervised learning resulted in high accuracies for taxonomic classifications at [Formula: see text], and medium to medium-high accuracies for environment category classifications of the same datasets at [Formula: see text]. For [Formula: see text], our findings were largely consistent with amino acid compositional biases and codon usage patterns in coding regions, previously attributed to extreme environment adaptations. The unsupervised learning of unlabelled sequences identified several exemplars of hyperthermophilic organisms with large similarities in their genomic signatures, in spite of belonging to different domains in the Tree of Life.
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Affiliation(s)
- Pablo Millán Arias
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada.
| | - Joseph Butler
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Gurjit S Randhawa
- School of Mathematical and Computational Sciences, University of Prince Edward Island, Charlottetown, PE, Canada
| | | | - Kathleen A Hill
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Lila Kari
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
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Rekadwad BN, Li WJ, Gonzalez JM, Punchappady Devasya R, Ananthapadmanabha Bhagwath A, Urana R, Parwez K. Extremophiles: the species that evolve and survive under hostile conditions. 3 Biotech 2023; 13:316. [PMID: 37637002 PMCID: PMC10457277 DOI: 10.1007/s13205-023-03733-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/26/2023] [Indexed: 08/29/2023] Open
Abstract
Extremophiles possess unique cellular and molecular mechanisms to assist, tolerate, and sustain their lives in extreme habitats. These habitats are dominated by one or more extreme physical or chemical parameters that shape existing microbial communities and their cellular and genomic features. The diversity of extremophiles reflects a long list of adaptations over millions of years. Growing research on extremophiles has considerably uncovered and increased our understanding of life and its limits on our planet. Many extremophiles have been greatly explored for their application in various industrial processes. In this review, we focused on the characteristics that microorganisms have acquired to optimally thrive in extreme environments. We have discussed cellular and molecular mechanisms involved in stability at respective extreme conditions like thermophiles, psychrophiles, acidophiles, barophiles, etc., which highlight evolutionary aspects and the significance of extremophiles for the benefit of mankind.
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Affiliation(s)
- Bhagwan Narayan Rekadwad
- Present Address: Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018 Karnataka India
- National Centre for Microbial Resource (NCMR), DBT-National Centre for Cell Science (DBT-NCCS), Savitribai Phule Pune University Campus, Ganeshkhind Road, Pune, 411007 Maharashtra India
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University (SPPU), Ganeshkhind Road, Pune, 411007 Maharashtra India
| | - Wen-Jun Li
- 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 People’s Republic of China
| | - Juan M. Gonzalez
- Microbial Diversity and Microbiology of Extreme Environments Research Group, Agencia Estatal Consejo Superior De Investigaciones Científicas, IRNAS-CSIC, Avda. Reina Mercedes, 10, 41012 Seville, Spain
| | - Rekha Punchappady Devasya
- Present Address: Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018 Karnataka India
| | - Arun Ananthapadmanabha Bhagwath
- Present Address: Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018 Karnataka India
- Yenepoya Institute of Arts, Science, Commerce and Management, A Constituent Unit of Yenepoya (Deemed to be University), Yenepoya Complex, Balmatta, Mangalore, 575002 Karnataka India
| | - Ruchi Urana
- Department of Environmental Science and Engineering, Faculty of Environmental and Bio Sciences and Technology, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001 India
| | - Khalid Parwez
- Department of Microbiology, Shree Narayan Medical Institute and Hospital, Saharsa, Bihar 852201 India
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Samal S, Banerjee S, Dey P, Rangarajan V. Production and characterization of a novel poly amino acid from a thermophilic bacterium, and preliminary testing of its coagulating potential for imminent wastewater treatment application. Int J Biol Macromol 2023; 246:125589. [PMID: 37385322 DOI: 10.1016/j.ijbiomac.2023.125589] [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: 04/23/2023] [Revised: 06/15/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023]
Abstract
The increasing demand for biopolymers across diverse fields, such as food, medicine, cosmetics, and environmental applications, has prompted researchers to explore novel molecules with enhanced functionalities that meet these demands. In this study, a thermophilic strain of Bacillus licheniformis was employed to produce a unique polyamino acid. This thermophilic isolate exhibited rapid growth at 50 °C in a sucrose mineral salts medium, resulting in a biopolymer concentration of 7.4 g/L. Interestingly, the biopolymer produced at different temperatures exhibited varying glass-transition temperatures (ranging from 87.86 °C to 104.11 °C) and viscosities (7.5 cP to 16.3 cP), suggesting that the fermentation temperature significantly influenced the degree of polymerization. Furthermore, the biopolymer was characterized using various techniques, including Thin Layer Chromatography (TLC), Fourier Transform Infrared (FTIR) spectroscopy, Liquid Chromatography-Electrospray Ionization-Mass Spectroscopy (LC-ESI MS), Nuclear Magnetic Resonance (NMR), and Differential Scanning Calorimetry-Thermogravimetric Analysis (DSC-TGA). The results revealed that the obtained biopolymer was a poly amino acid, with poly-γ-glutamic acid as the major monomeric component in the polymer backbone with a few appendages of aspartic acid residues in its side chain. Finally, the biopolymer demonstrated significant coagulation potential for water treatment applications, as evidenced by coagulation studies conducted under varying pH conditions using kaolin-clay as a model precipitant.
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Affiliation(s)
- Subhranshu Samal
- Department of Chemical Engineering, Birla Institute of Technology and Science Pilani K.K. Birla Goa Campus, 403726, India
| | - Subhadeep Banerjee
- Department of Chemistry, Birla Institute of Technology and Science Pilani K.K. Birla Goa Campus, 403726, India
| | - Pinaki Dey
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram, Kerala, India
| | - Vivek Rangarajan
- Department of Chemical Engineering, Birla Institute of Technology and Science Pilani K.K. Birla Goa Campus, 403726, India.
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Schultz J, Modolon F, Peixoto RS, Rosado AS. Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles. Front Microbiol 2023; 14:1167718. [PMID: 37333658 PMCID: PMC10272570 DOI: 10.3389/fmicb.2023.1167718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.
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Affiliation(s)
- Júnia Schultz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Flúvio Modolon
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Pham VHT, Kim J, Chang S, Bang D. Investigating Bio-Inspired Degradation of Toxic Dyes Using Potential Multi-Enzyme Producing Extremophiles. Microorganisms 2023; 11:1273. [PMID: 37317247 DOI: 10.3390/microorganisms11051273] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/03/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Biological treatment methods overcome many of the drawbacks of physicochemical strategies and play a significant role in removing dye contamination for environmental sustainability. Numerous microorganisms have been investigated as promising dye-degrading candidates because of their high metabolic potential. However, few can be applied on a large scale because of the extremely harsh conditions in effluents polluted with multiple dyes, such as alkaline pH, high salinity/heavy metals/dye concentration, high temperature, and oxidative stress. Therefore, extremophilic microorganisms offer enormous opportunities for practical biodegradation processes as they are naturally adapted to multi-stress conditions due to the special structure of their cell wall, capsule, S-layer proteins, extracellular polymer substances (EPS), and siderophores structural and functional properties such as poly-enzymes produced. This review provides scientific information for a broader understanding of general dyes, their toxicity, and their harmful effects. The advantages and disadvantages of physicochemical methods are also highlighted and compared to those of microbial strategies. New techniques and methodologies used in recent studies are briefly summarized and discussed. In particular, this study addresses the key adaptation mechanisms, whole-cell, enzymatic degradation, and non-enzymatic pathways in aerobic, anaerobic, and combination conditions of extremophiles in dye degradation and decolorization. Furthermore, they have special metabolic pathways and protein frameworks that contribute significantly to the complete mineralization and decolorization of the dye when all functions are turned on. The high potential efficiency of microbial degradation by unculturable and multi-enzyme-producing extremophiles remains a question that needs to be answered in practical research.
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Affiliation(s)
- Van Hong Thi Pham
- Department of Environmental Energy Engineering, College of Creative Engineering of Kyonggi University, Suwon 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Science of Kyonggi University, Suwon 16227, Republic of Korea
| | - Soonwoong Chang
- Department of Environmental Energy Engineering, College of Creative Engineering of Kyonggi University, Suwon 16227, Republic of Korea
| | - Donggyu Bang
- Department of Environmental Energy Engineering, Graduate School of Kyonggi University, Suwon 16227, Republic of Korea
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15
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Fahmy NM, El-Deeb B. Optimization, partial purification, and characterization of a novel high molecular weight alkaline protease produced by Halobacillus sp. HAL1 using fish wastes as a substrate. J Genet Eng Biotechnol 2023; 21:48. [PMID: 37121925 PMCID: PMC10149429 DOI: 10.1186/s43141-023-00509-6] [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: 05/02/2022] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
Abstract
BACKGROUND Hydrolytic enzymes from halophilic microorganisms have a wide range of industrial applications. Herein, we report the isolation of Halobacillus sp. HAL1, a moderately halophilic bacterium that produces a novel high molecular weight extracellular alkaline protease when grown in fish processing wastes as a substrate. RESULTS Results showed that the isolated strain belonged to the genus Halobacillus, and it was designated as Halobacillus sp. HAL1 with the GenBank accession number OK001470. The strain secreted an extracellular alkaline protease, and the highest yield was obtained when it was grown in a medium with fish wastes substrate as the sole nutritional source (10 g/L) and incubated at 25 °C under shaking conditions. The enzyme was partially purified by Sephadex G-100 column chromatography. Zymographic analysis showed two casein degrading bands of about 190 and 250 KDa. The optimum enzyme activity was at a temperature of 50 °C at pH 8. The proteolytic activity was enhanced in the presence of metal ions (Ca2+, Mg2+, and Mn2+), surfactants (Tween 80, SDS, and Triton-X100), H2O2, and EDTA. CONCLUSION Our study indicates that Haobacillus sp. HAL1 is a moderately halophilic strain and secrets a novel high molecular wight alkaline protease that is suitable for detergent formulation.
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Affiliation(s)
- Nayer M Fahmy
- Marine Microbiology Laboratory, National Institute of Oceanography & Fisheries, Cairo, Egypt.
| | - Bahig El-Deeb
- Faculty of Science, Botany and Microbiology Department, Sohag University, Sohag, Egypt
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16
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Ye JW, Lin YN, Yi XQ, Yu ZX, Liu X, Chen GQ. Synthetic biology of extremophiles: a new wave of biomanufacturing. Trends Biotechnol 2023; 41:342-357. [PMID: 36535816 DOI: 10.1016/j.tibtech.2022.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/12/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Microbial biomanufacturing, powered by the advances of synthetic biology, has attracted growing interest for the production of diverse products. In contrast to conventional microbes, extremophiles have shown better performance for low-cost production owing to their outstanding growth and synthesis capacity under stress conditions, allowing unsterilized fermentation processes. We review increasing numbers of products already manufactured utilizing extremophiles in recent years. In addition, genetic parts, molecular tools, and manipulation approaches for extremophile engineering are also summarized, and challenges and opportunities are predicted for non-conventional chassis. Next-generation industrial biotechnology (NGIB) based on engineered extremophiles promises to simplify biomanufacturing processes and achieve open and continuous fermentation, without sterilization, and utilizing low-cost substrates, making NGIB an attractive green process for sustainable manufacturing.
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Affiliation(s)
- Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yi-Na Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China; Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xue-Qing Yi
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuo-Xuan Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Xu Liu
- PhaBuilder Biotech Company, Shunyi District, Zhaoquan Ying, Beijing 101309, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; Ministry of Education (MOE) Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China.
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17
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Nor FHM, Abdullah S, Ibrahim Z, Nor MHM, Osman MI, Al Farraj DA, AbdelGawwad MR, Kamyab H. Role of extremophilic Bacillus cereus KH1 and its lipopeptide in treatment of organic pollutant in wastewater. Bioprocess Biosyst Eng 2023; 46:381-391. [PMID: 35779113 DOI: 10.1007/s00449-022-02749-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/13/2022] [Indexed: 12/01/2022]
Abstract
An effective biosurfactant producer and extremophiles bacteria, Bacillus cereus KH1, was isolated from textile effluent and the biosurfactant was produced using molasses as the sole carbon source. Growth parameters such as pH, temperature, salinity and concentration of molasses were optimised for decolourising the textile effluent with 24-h incubation. The biosurfactant property of B. cereus KH1 was evaluated based on haemolytic activity, oil displacement technique, drop-collapsing test and emulsification index. The results of the produced biosurfactant showed a positive reaction in haemolytic activity, oil displacement technique, drop-collapsing test and exhibiting a 67% emulsification index. The cell-free broth was stable in 40 °C pH 7, 7% salinity and 7% molasses. Thin-Layer Chromatography and Fourier Transform Infrared Spectroscopy analysis revealed that the biosurfactant was a lipopeptide with a yield 2.98 g L-1. These findings proved the synergistic action of B. cereus KH1 with lipopeptide biosurfactant may accelerated the decolourisation efficiency to 87%.
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Affiliation(s)
- Farhah Husna Mohd Nor
- Department of Physics and Chemistry, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Education Hub, Pagoh, 84600, Muar, Johor, Malaysia
| | - Shakila Abdullah
- Department of Physics and Chemistry, Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Education Hub, Pagoh, 84600, Muar, Johor, Malaysia.
| | - Zaharah Ibrahim
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Muhamad Hanif Md Nor
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Mohd Isa Osman
- Setia Impian Development, Peringgit Centre, Taman Peringgit Jaya, 75400, Melaka, Malaysia
| | - Dunia A Al Farraj
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh, 11451, Saudi Arabia
| | - Mohamed Ragab AbdelGawwad
- Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, 71210, Sarajevo, Bosnia and Herzegovina
| | - Hesam Kamyab
- Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100, Kuala Lumpur, Malaysia
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18
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Liew KJ, Zakaria MR, Hong CWL, Tan MCY, Chong CS. Draft genome sequence of Joostella atrarenae M1-2 T with cellulolytic and hemicellulolytic ability. 3 Biotech 2023; 13:50. [PMID: 36685320 PMCID: PMC9845502 DOI: 10.1007/s13205-023-03472-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
The halophilic genus Joostella is one of the least-studied genera in the family of Flavobacteriaceae. So far, only two species were taxonomically identified with limited genomic analysis in the aspect of application has been reported. Joostella atrarenae M1-2T was previously isolated from a seashore sample and it is the second discovered species of the genus Joostella. In this project, the genome of J. atrarenae M1-2T was sequenced using NovaSeq 6000. The final assembled genome is comprised of 71 contigs, a total of 3,983,942 bp, a GC ratio of 33.2%, and encoded for 3,416 genes. The 16S rRNA gene sequence of J. atrarenae M1-2T shows 97.3% similarity against J. marina DSM 19592T. Genome-genome comparison between the two strains by ANI, dDDH, AAI, and POCP shows values of 80.8%, 23.3%, 83.4%, and 74.1% respectively. Pan-genome analysis shows that strain M1-2T and J. marina DSM 19592T shared a total of 248 core genes. Taken together, strain M-2T and J. marina DSM 19592T belong to the same genus but are two different species. CAZymes analysis revealed that strain M1-2T harbors 109 GHs, 40 GTs, 5 PLs, 9 CEs, and 6 AAs. Among these CAZymes, while 5 genes are related to cellulose degradation, 12 and 24 genes are found to encode for xylanolytic enzymes and other hemicellulases that involve majorly in the side chain removal of the lignocellulose structure, respectively. Furthermore, both the intracellular and extracellular crude extracts of strain M1-2T exhibited enzymatic activities against CMC, xylan, pNPG, and pNPX substrates, which corresponding to endoglucanase, xylanase, β-glucosidase, and β-xylosidase, respectively. Collectively, description of genome coupled with the enzyme assay results demonstrated that J. atrarenae M1-2T has a role in lignocellulosic biomass degradation, and the strain could be useful for lignocellulosic biorefining.
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Affiliation(s)
- Kok Jun Liew
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
| | | | - Clarine Wan Ling Hong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
| | - Melvin Chun Yun Tan
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor Malaysia
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Dias MAM, Nitschke M. Bacterial-derived surfactants: an update on general aspects and forthcoming applications. Braz J Microbiol 2023; 54:103-123. [PMID: 36662441 PMCID: PMC9857925 DOI: 10.1007/s42770-023-00905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 01/10/2023] [Indexed: 01/21/2023] Open
Abstract
The search for sustainable alternatives to the production of chemicals using renewable substrates and natural processes has been widely encouraged. Microbial surfactants or biosurfactants are surface-active compounds synthesized by fungi, yeasts, and bacteria. Due to their great metabolic versatility, bacteria are the most traditional and well-known microbial surfactant producers, being Bacillus and Pseudomonas species their typical representatives. To be successfully applied in industry, surfactants need to maintain stability under the harsh environmental conditions present in manufacturing processes; thus, the prospection of biosurfactants derived from extremophiles is a promising strategy to the discovery of novel and useful molecules. Bacterial surfactants show interesting properties suitable for a range of applications in the oil industry, food, agriculture, pharmaceuticals, cosmetics, bioremediation, and more recently, nanotechnology. In addition, they can be synthesized using renewable resources as substrates, contributing to the circular economy and sustainability. The article presents a general and updated review of bacterial-derived biosurfactants, focusing on the potential of some groups that are still underexploited, as well as, recent trends and contributions of these versatile biomolecules to circular bioeconomy and nanotechnology.
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Affiliation(s)
- Marcos André Moura Dias
- grid.11899.380000 0004 1937 0722Departamento de Físico-Química, Instituto de Química de São Carlos, Universidade de São Paulo-USP, Av Trabalhador São Carlense 400, CP 780, CEP 13560-970 São Carlos, SP Brasil
| | - Marcia Nitschke
- Departamento de Físico-Química, Instituto de Química de São Carlos, Universidade de São Paulo-USP, Av Trabalhador São Carlense 400, CP 780, CEP 13560-970, São Carlos, SP, Brasil.
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20
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Diaz CJ, Douglas KJ, Kang K, Kolarik AL, Malinovski R, Torres-Tiji Y, Molino JV, Badary A, Mayfield SP. Developing algae as a sustainable food source. Front Nutr 2023; 9:1029841. [PMID: 36742010 PMCID: PMC9892066 DOI: 10.3389/fnut.2022.1029841] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/05/2022] [Indexed: 01/20/2023] Open
Abstract
Current agricultural and food production practices are facing extreme stress, posed by climate change and an ever-increasing human population. The pressure to feed nearly 8 billion people while maintaining a minimal impact on the environment has prompted a movement toward new, more sustainable food sources. For thousands of years, both the macro (seaweed and kelp) and micro (unicellular) forms of algae have been cultivated as a food source. Algae have evolved to be highly efficient at resource utilization and have proven to be a viable source of nutritious biomass that could address many of the current food production issues. Particularly for microalgae, studies of their large-scale growth and cultivation come from the biofuel industry; however, this knowledge can be reasonably translated into the production of algae-based food products. The ability of algae to sequester CO2 lends to its sustainability by helping to reduce the carbon footprint of its production. Additionally, algae can be produced on non-arable land using non-potable water (including brackish or seawater), which allows them to complement rather than compete with traditional agriculture. Algae inherently have the desired qualities of a sustainable food source because they produce highly digestible proteins, lipids, and carbohydrates, and are rich in essential fatty acids, vitamins, and minerals. Although algae have yet to be fully domesticated as food sources, a variety of cultivation and breeding tools exist that can be built upon to allow for the increased productivity and enhanced nutritional and organoleptic qualities that will be required to bring algae to mainstream utilization. Here we will focus on microalgae and cyanobacteria to highlight the current advancements that will expand the variety of algae-based nutritional sources, as well as outline various challenges between current biomass production and large-scale economic algae production for the food market.
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Affiliation(s)
- Crisandra J. Diaz
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Kai J. Douglas
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Kalisa Kang
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Ashlynn L. Kolarik
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Rodeon Malinovski
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Yasin Torres-Tiji
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - João V. Molino
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Amr Badary
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Stephen P. Mayfield
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States,California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, United States,*Correspondence: Stephen P. Mayfield,
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21
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Fermentation of Abelmoschus manihot Extract with Halophilic Bacillus licheniformis CP6 Results in Enhanced Anti-Inflammatory Activities. Nutrients 2023; 15:nu15020309. [PMID: 36678181 PMCID: PMC9864326 DOI: 10.3390/nu15020309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Microbial fermentation provides a valorization strategy, through biotransformation, to convert plant-derived raw materials into health-promoting agents. In this study, we have investigated the antioxidative activity of Abelmoschus manihot fermented with various Bacillaceae strains from specific environments and demonstrated the anti-inflammatory effects of Bacillus licheniformis CP6 fermented A. manihot extract (FAME) in lipopolysaccharide (LPS)-stimulated Raw264.7 macrophages. Of 1500 bacteria isolated from various specific environments, 47 extracellular protease- and amylase-producing strains with qualified presumption safety status, belonging to the family Bacillaceae, were selected for A. manihot fermentation. Among them, strain CP6, a halophilic bacterium isolated from Tongyeong seawater in Korea and identified as B. licheniformis, showed the highest antioxidant activity. In particular, FAME exerted anti-inflammatory effects on LPS-stimulated Raw264.7 macrophages. Consequently, FAME had a potent inhibitory effect on nitric oxide (NO) production in LPS-stimulated macrophages, without cytotoxicity. Moreover, FAME downregulated LPS-induced pro-inflammatory mediator and enzyme levels in LPS-induced Raw264.7 cells, including IL-1β, IL-6, TNF-α, iNOS, and COX-2, compared to levels when cells were incubated in A. manihot extract (IAME). Further detailed characterization indicated that FAME suppresses inflammation by blocking NF-κB via IKK phosphorylation inhibition and IκB-α degradation and by downregulating NO production, and inflammatory mediators also decreased NF-κB translocation. Furthermore, FAME inhibited LPS-stimulated activation of MAPKs, including ERK1/2, JNK, and p38, compared to that with either IAME. Therefore, we suggest that FAME could be used for inflammation-related disorders.
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22
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Yousef NMH, Mawad AMM. Characterization of thermo/halo stable cellulase produced from halophilic Virgibacillus salarius BM-02 using non-pretreated biomass. World J Microbiol Biotechnol 2023; 39:22. [PMID: 36422734 PMCID: PMC9691493 DOI: 10.1007/s11274-022-03446-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/21/2022] [Indexed: 11/27/2022]
Abstract
The production of extremozymes from halophilic bacteria has increased significantly due to their stability and efficiency in catalyzing a reaction, as well as their capacity to display optimum activity at various salt concentrations. In the current study, the halophilic bacterium Virgibacillus salarius strain BM-02 could utilize many non-pretreated substrates including cellulose, corn stover, sugarcane bagasse and wheat bran as a sole carbon source. However, wheat bran was the best substrate for achieving optimum saccharification yield (90.1%). The partially purified cellulase was active and stable at a wide range of pH (5-8) with residual activities > 58%. Moreover, it was stable at 5-12% of NaCl. Metal ions have a variable impact on the activity of partially purified cellulase however, Fe+3 exhibited the highest increase in the cellulase activity. The enzyme exhibited a thermal stability at 40, 50 and 60 °C with half-lives of 1049.50, 168.14 and 163.5 min, respectively. The value of Vmax was 22.27 U/mL while Km was 2.1 mM. The activation energy of denaturation Ed 69.81 kJ/mol, the enthalpy values (ΔHd) were positive, and the entropy values (ΔS) were negative. Therefore, V. Salarius is recommended as a novel promising halophilic extremozyme producer and agricultural waste remover in the bio-industrial applications.
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Affiliation(s)
- Naeima M. H. Yousef
- grid.252487.e0000 0000 8632 679XBotany and Microbiology Department, Faculty of Science, Assiut University, Assiut, 71516 Egypt
| | - Asmaa M. M. Mawad
- grid.252487.e0000 0000 8632 679XBotany and Microbiology Department, Faculty of Science, Assiut University, Assiut, 71516 Egypt
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23
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Jeilu O, Gessesse A, Simachew A, Johansson E, Alexandersson E. Prokaryotic and eukaryotic microbial diversity from three soda lakes in the East African Rift Valley determined by amplicon sequencing. Front Microbiol 2022; 13:999876. [PMID: 36569062 PMCID: PMC9772273 DOI: 10.3389/fmicb.2022.999876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Soda lakes are unique poly-extreme environments with high alkalinity and salinity that support diverse microbial communities despite their extreme nature. In this study, prokaryotic and eukaryotic microbial diversity in samples of the three soda lakes, Lake Abijata, Lake Chitu and Lake Shala in the East African Rift Valley, were determined using amplicon sequencing. Culture-independent analysis showed higher diversity of prokaryotic and eukaryotic microbial communities in all three soda lakes than previously reported. A total of 3,603 prokaryotic and 898 eukaryotic operational taxonomic units (OTUs) were found through culture-independent amplicon sequencing, whereas only 134 bacterial OTUs, which correspond to 3%, were obtained by enrichment cultures. This shows that only a fraction of the microorganisms from these habitats can be cultured under laboratory conditions. Of the three soda lakes, samples from Lake Chitu showed the highest prokaryotic diversity, while samples from Lake Shala showed the lowest diversity. Pseudomonadota (Halomonas), Bacillota (Bacillus, Clostridia), Bacteroidota (Bacteroides), Euryarchaeota (Thermoplasmata, Thermococci, Methanomicrobia, Halobacter), and Nanoarchaeota (Woesearchaeia) were the most common prokaryotic microbes in the three soda lakes. A high diversity of eukaryotic organisms were identified, primarily represented by Ascomycota and Basidiomycota. Compared to the other two lakes, a higher number of eukaryotic OTUs were found in Lake Abijata. The present study showed that these unique habitats harbour diverse microbial genetic resources with possible use in biotechnological applications, which should be further investigated by functional metagenomics.
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Affiliation(s)
- Oliyad Jeilu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden,*Correspondence: Oliyad Jeilu,
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
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Jeilu O, Simachew A, Alexandersson E, Johansson E, Gessesse A. Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics. Front Microbiol 2022; 13:1059061. [PMID: 36569080 PMCID: PMC9768486 DOI: 10.3389/fmicb.2022.1059061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.
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Affiliation(s)
- Oliyad Jeilu
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden,*Correspondence: Oliyad Jeilu,
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia,Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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Ali N, Aiman A, Shamsi A, Hassan I, Shahid M, Gaur NA, Islam A. Identification of Thermostable Xylose Reductase from Thermothelomyces thermophilus: A Biochemical Characterization Approach to Meet Biofuel Challenges. ACS OMEGA 2022; 7:44241-44250. [PMID: 36506193 PMCID: PMC9730754 DOI: 10.1021/acsomega.2c05690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
The constant rise in energy demands, costs, and concerns about global warming has created a demand for new renewable alternative fuels that can be produced sustainably. Lignocellulose biomass can act as an excellent energy source and various value-added compounds like xylitol. In this research study, we have explored the xylose reductase that was obtained from the genome of a thermophilic fungus Thermothelomyces thermophilus while searching for an enzyme to convert xylose to xylitol at higher temperatures. The recombinant thermostable TtXR histidine-tagged fusion protein was expressed in Escherichia coli and successfully purified for the first time. Further, it was characterized for its function and novel structure at varying temperatures and pH. The enzyme showed maximal activity at 7.0 pH and favored d-xylose over other pentoses and hexoses. Biophysical approaches such as ultraviolet-visible (UV-visible), fluorescence spectrometry, and far-UV circular dichroism (CD) spectroscopy were used to investigate the structural integrity of pure TtXR. This research highlights the potential application of uncharacterized xylose reductase as an alternate source for the effective utilization of lignocellulose in fermentation industries at elevated temperatures. Moreover, this research would give environment-friendly and long-term value-added products, like xylitol, from lignocellulosic feedstock for both scientific and commercial purposes.
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Affiliation(s)
- Nabeel Ali
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi110025, India
| | - Ayesha Aiman
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi110025, India
| | - Anas Shamsi
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi110025, India
| | - Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi110025, India
| | - Mohammad Shahid
- Department
of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, P.O. Box: 173, Al Kharj11942, Kingdom of Saudi Arabia
| | - Naseem A. Gaur
- International
Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi110067, India
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi110025, India
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Mukti IJ, Sardari RRR, Kristjansdottir T, Hreggvidsson GO, Karlsson EN. Medium development and production of carotenoids and exopolysaccharides by the extremophile Rhodothermus marinus DSM16675 in glucose-based defined media. Microb Cell Fact 2022; 21:220. [PMID: 36274123 PMCID: PMC9590192 DOI: 10.1186/s12934-022-01946-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The marine thermophilic bacterium Rhodothermus marinus can degrade many polysaccharides which makes it interesting as a future cell factory. Progress using this bacterium has, however, been hampered by limited knowledge on media and conditions for biomass production, often resulting in low cell yields and low productivity, highlighting the need to develop conditions that allow studies of the microbe on molecular level. This study presents development of defined conditions that support growth, combined with evaluation of production of carotenoids and exopolysaccharides (EPSs) by R. marinus strain DSM 16675. RESULTS Two defined media were initially prepared: one including a low addition of yeast extract (modified Wolfe's medium) and one based on specific components (defined medium base, DMB) to which two amino acids (N and Q), were added. Cultivation trials of R. marinus DSM 16675 in shake flasks, resulted in maximum cell densities (OD620 nm) of 2.36 ± 0.057, cell dry weight (CDW) 1.2 ± 0.14 mg/L, total carotenoids 0.59 × 10-3 mg/L, and EPSs 1.72 ± 0.03 mg/L using 2 g/L glucose in DMB. In Wolfe's medium (supplemented by 0.05 g/L yeast extract and 2.5 g/L glucose), maximum OD620 nm was 2.07 ± 0.05, CDW 1.05 ± 0.07 mg/L, total carotenoids 0.39 × 10-3 mg/L, and EPSs 1.74 ± 0.2 mg/L. Growth trials at 5 g/L glucose in these media either failed or resulted in incomplete substrate utilization. To improve reproducibility and increase substrate utilization, a screening of macroelements (e.g. phosphate) in DMB, was combined with use of trace elements and vitamins of the modified Wolfe's medium. The resulting defined minimal R. marinus medium, (DRM), allowed reproducible cultivations to a final OD620nm of 6.6 ± 0.05, CDW 2.85 ± 0.07 mg/L, a maximum specific growth rate (µmax) of 0.26 h-1, total carotenoids 0.77 × 10-3 mg/L and EPSs 3.4 ± 0.17 mg/L in cultivations supplemented with up to 5 g/L glucose. CONCLUSION A minimal defined medium (DRM) was designed that resulted in reproducible growth and an almost doubled formation of both total carotenoids and EPSs. Such defined conditions, are necessary for systematic studies of metabolic pathways, to determine the specific requirements for growth and fully characterize metabolite production.
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Affiliation(s)
- Israt Jahan Mukti
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden
| | - Roya R R Sardari
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden.
| | - Thordis Kristjansdottir
- Matis Ohf, Vinlandsleid 12, 113, Reykjavik, Iceland.,Department of Biology, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102, Reykjavik, Iceland
| | - Gudmundur O Hreggvidsson
- Matis Ohf, Vinlandsleid 12, 113, Reykjavik, Iceland.,Department of Biology, School of Engineering and Natural Sciences, University of Iceland, Sturlugata 7, 102, Reykjavik, Iceland
| | - Eva Nordberg Karlsson
- Division of Biotechnology, Department of Chemistry, Lund University, Naturvetarvägen 14, 22100, Lund, Sweden
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Chen J, Liu Y, Diep P, Mahadevan R. Genetic engineering of extremely acidophilic Acidithiobacillus species for biomining: Progress and perspectives. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129456. [PMID: 35777147 DOI: 10.1016/j.jhazmat.2022.129456] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
With global demands for mineral resources increasing and ore grades decreasing, microorganisms have been increasingly deployed in biomining applications to recover valuable metals particularly from normally considered waste, such as low-grade ores and used consumer electronics. Acidithiobacillus are a genus of chemolithoautotrophic extreme acidophiles that are commonly found in mining process waters and acid mine drainage, which have been reported in several studies to aid in metal recovery from bioremediation of metal-contaminated sites. Compared to conventional mineral processing technologies, biomining is often cited as a more sustainable and environmentally friendly process, but long leaching cycles and low extraction efficiency are main disadvantages that have hampered its industrial applications. Genetic engineering is a powerful technology that can be used to enhance the performance of microorganisms, such as Acidithiobacillus species. In this review, we compile existing data on Acidithiobacillus species' physiological traits and genomic characteristics, progresses in developing genetic tools to engineer them: plasmids, shutter vectors, transformation methods, selection markers, promoters and reporter systems developed, and genome editing techniques. We further propose genetic engineering strategies for enhancing biomining efficiency of Acidithiobacillus species and provide our perspectives on their future applications.
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Affiliation(s)
- Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, Canada.
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Valorization of Biomasses from Energy Crops for the Discovery of Novel Thermophilic Glycoside Hydrolases through Metagenomic Analysis. Int J Mol Sci 2022; 23:ijms231810505. [PMID: 36142415 PMCID: PMC9505709 DOI: 10.3390/ijms231810505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
The increasing interest for environmentally friendly technologies is driving the transition from fossil-based economy to bioeconomy. A key enabler for circular bioeconomy is to valorize renewable biomasses as feedstock to extract high value-added chemicals. Within this transition the discovery and the use of robust biocatalysts to replace toxic chemical catalysts play a significant role as technology drivers. To meet both the demands, we performed microbial enrichments on two energy crops, used as low-cost feed for extremophilic consortia. A culture-dependent approach coupled to metagenomic analysis led to the discovery of more than 300 glycoside hydrolases and to characterize a new α-glucosidase from an unknown hyperthermophilic archaeon. Aglu1 demonstrated to be the most active archaeal GH31 on 4Np-α-Glc and it showed unexpected specificity vs. kojibiose, revealing to be a promising candidate for biotechnological applications such as the liquefaction/saccharification of starch.
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29
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Molecular identification and phylogenetic analysis of Pseudomonas sp. and Aeromonas sp. isolated from mine drainage water in Slovinky and Markušovce (Slovakia). Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01170-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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30
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Rammala B, Zhou N. Looking into the world's largest elephant population in search of ligninolytic microorganisms for biorefineries: a mini-review. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:64. [PMID: 35689287 PMCID: PMC9188235 DOI: 10.1186/s13068-022-02159-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/12/2022] [Indexed: 11/24/2022]
Abstract
Gastrointestinal tracts (GIT) of herbivores are lignin-rich environments with the potential to find ligninolytic microorganisms. The occurrence of the microorganisms in herbivore GIT is a well-documented mutualistic relationship where the former benefits from the provision of nutrients and the latter benefits from the microorganism-assisted digestion of their recalcitrant lignin diets. Elephants are one of the largest herbivores that rely on the microbial anaerobic fermentation of their bulky recalcitrant low-quality forage lignocellulosic diet given their inability to break down major components of plant cells. Tapping the potential of these mutualistic associations in the biggest population of elephants in the whole world found in Botswana is attractive in the valorisation of the bulky recalcitrant lignin waste stream generated from the pulp and paper, biofuel, and agro-industries. Despite the massive potential as a feedstock for industrial fermentations, few microorganisms have been commercialised. This review focuses on the potential of microbiota from the gastrointestinal tract and excreta of the worlds' largest population of elephants of Botswana as a potential source of extremophilic ligninolytic microorganisms. The review further discusses the recalcitrance of lignin, achievements, limitations, and challenges with its biological depolymerisation. Methods of isolation of microorganisms from elephant dung and their improvement as industrial strains are further highlighted.
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Affiliation(s)
- Bame Rammala
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
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31
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Sponge–Microbial Symbiosis and Marine Extremozymes: Current Issues and Prospects. SUSTAINABILITY 2022. [DOI: 10.3390/su14126984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Marine microorganisms have great potential for producing extremozymes. They enter useful relationships like many other organisms in the marine habitat. Sponge–microbial symbiosis enables both sponges and microorganisms to mutually benefit each other while performing their activities within the ecosystem. Sponges, because of their nature as marine cosmopolitan benthic epifaunas and filter feeders, serve as a host for many extremophilic marine microorganisms. Potential extremozymes from microbial symbionts are largely dependent on their successful relationship. Extremozymes have found relevance in food processing, bioremediation, detergent, and drug production. Species diversity approach, industrial-scale bioremediation, integrative bioremediation software, government and industrial support are considered. The high cost of sampling, limited research outcomes, low species growth in synthetic media, laborious nature of metagenomics projects, difficulty in the development of synthetic medium, limited number of available experts, and technological knowhow are current challenges. The unique properties of marine extremozymes underpin their application in industry and biotechnological processes. There is therefore an urgent need for the development of cost-effective methods with government and industry support.
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32
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Roy JJ, Rarotra S, Krikstolaityte V, Zhuoran KW, Cindy YDI, Tan XY, Carboni M, Meyer D, Yan Q, Srinivasan M. Green Recycling Methods to Treat Lithium-Ion Batteries E-Waste: A Circular Approach to Sustainability. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2103346. [PMID: 34632652 DOI: 10.1002/adma.202103346] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/14/2021] [Indexed: 06/13/2023]
Abstract
E-waste generated from end-of-life spent lithium-ion batteries (LIBs) is increasing at a rapid rate owing to the increasing consumption of these batteries in portable electronics, electric vehicles, and renewable energy storage worldwide. On the one hand, landfilling and incinerating LIBs e-waste poses environmental and safety concerns owing to their constituent materials. On the other hand, scarcity of metal resources used in manufacturing LIBs and potential value creation through the recovery of these metal resources from spent LIBs has triggered increased interest in recycling spent LIBs from e-waste. State of the art recycling of spent LIBs involving pyrometallurgy and hydrometallurgy processes generates considerable unwanted environmental concerns. Hence, alternative innovative approaches toward the green recycling process of spent LIBs are essential to tackle large volumes of spent LIBs in an environmentally friendly way. Such evolving techniques for spent LIBs recycling based on green approaches, including bioleaching, waste for waste approach, and electrodeposition, are discussed here. Furthermore, the ways to regenerate strategic metals post leaching, efficiently reprocess extracted high-value materials, and reuse them in applications including electrode materials for new LIBs. The concept of "circular economy" is highlighted through closed-loop recycling of spent LIBs achieved through green-sustainable approaches.
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Affiliation(s)
- Joseph Jegan Roy
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
| | - Saptak Rarotra
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
| | - Vida Krikstolaityte
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
| | - Kenny Wu Zhuoran
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
| | - Yang Dja-Ia Cindy
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
| | - Xian Yi Tan
- School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Michael Carboni
- Université de Montpellier, CEA, CNRS, ENSCM; UMR 5257 (ICSM) BP 17171, Bagnols-sur-Cèze Cedex, 30207, France
| | - Daniel Meyer
- Université de Montpellier, CEA, CNRS, ENSCM; UMR 5257 (ICSM) BP 17171, Bagnols-sur-Cèze Cedex, 30207, France
| | - Qingyu Yan
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
- School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Madhavi Srinivasan
- Energy Research Institute @ NTU (ERI@N), SCARCE Laboratory, Nanyang Technological University, Singapore, 637459, Singapore
- School of Materials Science and Engineering, Nanyang Technological University (NTU), 50 Nanyang Avenue, Singapore, 639798, Singapore
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Yunus IS, Lee TS. Applications of targeted proteomics in metabolic engineering: advances and opportunities. Curr Opin Biotechnol 2022; 75:102709. [DOI: 10.1016/j.copbio.2022.102709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/22/2022]
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Zhu D, Qaria MA, Zhu B, Sun J, Yang B. Extremophiles and extremozymes in lignin bioprocessing. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2022; 157:112069. [DOI: 10.1016/j.rser.2021.112069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Kochhar N, I․K K, Shrivastava S, Ghosh A, Rawat VS, Sodhi KK, Kumar M. Perspectives on the microorganism of extreme environments and their applications. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100134. [PMID: 35909612 PMCID: PMC9325743 DOI: 10.1016/j.crmicr.2022.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/21/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
The applications of extremophiles in various fields like biotechnology, biodegradation, bioremediation, biorefinery and astrobiology along with other industries like pharmaceuticals, food, agricultural, cosmetics, and textile. Further research in biodegradation, bioremediation and generation of biofuels using extremophiles is required considering the current climate crisis as it helps in reduction of environmental contamination load. The importance of promoting the use of extremophiles in food and agricultural industries and how extremophiles can be the key to achieving the Sustainable Development Goal of global food security. Keeping in mind the current global scenario with regards to the Covid-19 pandemic, our paper also focuses on the importance of by-products of extremophiles like biosurfactants in the vaccine production process. For advancement of the astrobiology sector, more PFA sites should be located and the extremophiles inhabiting them should be studied.
Extremophiles are organisms that can survive and thrive in conditions termed as “extreme” by human beings. Conventional methods cannot be applied under extreme conditions like temperature and pH fluctuations, high salinity, etc. for a variety of reasons. Extremophiles can function and are adapted to thrive in these environments and are sustainable, cheaper, and efficient, therefore, they serve as better alternatives to the traditional methods. They adapt to these environments with biochemical and physiological changes and produce products like extremolytes, extremozymes, biosurfactants, etc., which are found to be useful in a wide range of industries like sustainable agriculture, food, cosmetics, and pharmaceuticals. These products also play a crucial role in bioremediation, production of biofuels, biorefinery, and astrobiology. This review paper comprehensively lists out the current applications of extremophiles and their products in various industries and explores the prospects of the same. They help us understand the underlying basis of biological mechanisms exploring the boundaries of life and thus help us understand the origin and evolution of life on Earth. This helps us in the research for extra-terrestrial life and space exploration. The structure and biochemical properties of extremophiles along with any possible long-term effects of their applications need to be investigated further.
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Affiliation(s)
- Nikita Kochhar
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
| | - Kavya I․K
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
| | | | - Anshika Ghosh
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
| | | | - Kushneet Kaur Sodhi
- Department of Zoology, Hansraj College, University of Delhi, Delhi-110007, India
- Department of Zoology, University of Delhi, Delhi-110007, India
| | - Mohit Kumar
- Department of Zoology, Hindu College, University of Delhi, Delhi-110007, India
- Department of Zoology, University of Delhi, Delhi-110007, India
- Corresponding author.
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36
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Structural and Biochemical Characterization of Endo-β-1,4-glucanase from Dictyoglomus thermophilum, a Hyperthermostable and Halotolerant Cellulase. Catalysts 2022. [DOI: 10.3390/catal12030302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Enzymatic conversion of polysaccharides in the lignocellulosic biomass is currently the subject of intensive research and will be a key technology in future biorefineries. Using a bioinformatics approach, we previously identified a putative endo-β-1,4-glucanase (DtCel5A) from Dictyoglomus thermophilum, a chemoorganotrophic and thermophilic bacterium. Here, we structurally and functionally characterize DtCel5A and show that it is endowed with remarkable thermal and chemical stability. The structural features of DtCel5A and of its complex with cellobiose have been investigated by combining X-ray crystallography and other biophysical studies. Importantly, biochemical assays show that DtCel5A retains its activity on cellulose at high temperatures and at elevated salt concentrations. These features make DtCel5A an enzyme with interesting biotechnological applications for biomass degradation.
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CRISPR-based metabolic engineering in non-model microorganisms. Curr Opin Biotechnol 2022; 75:102698. [PMID: 35217297 DOI: 10.1016/j.copbio.2022.102698] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/20/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022]
Abstract
Non-model microorganisms possess unique and versatile metabolic characteristics, offering great opportunities as cell factories for biosynthesis of target products. However, lack of efficient genetic tools for pathway engineering represents a big challenge to unlock the full production potential of these microbes. Over the past years, CRISPR systems have been extensively developed and applied to domesticate non-model microorganisms. In this paper, we summarize the current significant advances in designing and constructing CRISPR-mediated genetic modification systems in non-model microorganisms, such as bacteria, fungi and cyanobacteria. We particularly put emphasis on reviewing some successful implementations in metabolic pathway engineering via CRISPR-based genome editing tools. Moreover, the current barriers and future perspectives on improving the editing efficiency of CRISPR systems in non-model microorganisms are also discussed.
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Ahmad A, Rahamtullah, Mishra R. Structural and functional adaptation in extremophilic microbial α-amylases. Biophys Rev 2022; 14:499-515. [PMID: 35528036 PMCID: PMC9043155 DOI: 10.1007/s12551-022-00931-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/12/2022] [Indexed: 01/26/2023] Open
Abstract
Maintaining stable native conformation of a protein under a given ecological condition is the prerequisite for survival of organisms. Extremophilic bacteria and archaea have evolved to adapt under extreme conditions of temperature, pH, salt, and pressure. Molecular adaptations of proteins under these conditions are essential for their survival. These organisms have the capability to maintain stable, native conformations of proteins under extreme conditions. The enzymes produced by the extremophiles are also known as extremozyme, which are used in several industries. Stability and functionality of extremozymes under varying temperature, pH, and solvent conditions are the most desirable requirement of industry. α-Amylase is one of the most important enzymes used in food, pharmaceutical, textile, and detergent industries. This enzyme is produced by diverse microorganisms including various extremophiles. Therefore, understanding its stability is important from fundamental as well as an applied point of view. Each class of extremophiles has a distinctive set of dominant non-covalent interactions which are important for their stability. Static information obtained by comparative analysis of amino acid sequence and atomic resolution structure provides information on the prevalence of particular amino acids or a group of non-covalent interactions. Protein folding studies give the information about thermodynamic and kinetic stability in order to understand dynamic aspect of molecular adaptations. In this review, we have summarized information on amino acid sequence, structure, stability, and adaptability of α-amylases from different classes of extremophiles.
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Affiliation(s)
- Aziz Ahmad
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rahamtullah
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110,067 India
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Gurunathan R, Rathinam AJ, Hwang JS, Dahms HU. Shallow Hydrothermal Vent Bacteria and Their Secondary Metabolites with a Particular Focus on Bacillus. Mar Drugs 2021; 19:681. [PMID: 34940680 PMCID: PMC8704404 DOI: 10.3390/md19120681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/21/2022] Open
Abstract
Extreme environments are hostile for most organisms, but such habitats represent suitable settings to be inhabited by specialized microorganisms. A marine shallow-water hydrothermal vent field is located offshore in northeast Taiwan, near the shallow shore of the southeast of Kueishantao Island (121°55' E, 24°50' N). Research on extremophilic microorganisms makes use of the biotechnological potential associated with such microorganisms and their cellular products. With the notion that extremophiles are capable of surviving in extreme environments, it is assumed that their metabolites are adapted to function optimally under such conditions. As extremophiles, they need specific culture conditions, and only a fraction of species from the original samples are recovered in culture. We used different non-selective and selective media to isolate bacterial species associated with the hydrothermal vent crab Xenograpsus testudinatus and the sediments of its habitat. The highest number of colonies was obtained from Zobell marine agar plates with an overall number of 29 genetically distinct isolates. 16sRNA gene sequencing using the Sanger sequencing method revealed that most of the bacterial species belonged to the phylum Firmicutes and the class Bacilli. The present study indicates that hydrothermal vent bacteria and their secondary metabolites may play an important role for the reconstruction of the evolutionary history of the phylum Procaryota.
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Grants
- MOST 107-2621-M-019-001, MOST 108-2621-M-019-003, MOST 109-2621-M-019-002 and MOST 110-2621-M-019-001 Ministry of Science and Technology, Taiwan.
- 109J13801-51, 110J13801-51 Center of Excellence for Ocean Engineering, NTOU, Taiwan.
- MOST 107-2621-M-037-001, MOST 108-2621-M-037-001, and MOST 109-2621-M-037-001 Ministry of Science and Technology, Taiwan.
- KMU-TC108A01 and KMU-TC108A02 Kaohsiung Medical University Research Center, Taiwan.
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Affiliation(s)
- Revathi Gurunathan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan;
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirapalli 620024, India
| | - Jiang-Shiou Hwang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 20224, Taiwan
- Center of Excellence for Ocean Engineering, National Taiwan Ocean University, Keelung 20224, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Marine Biotechnology and Resources, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
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Iquebal MA, Passari AK, Jagannadham J, Ahmad F, Leo VV, Singh G, Jaiswal S, Rai A, Kumar D, Singh BP. Microbiome of Pukzing Cave in India shows high antimicrobial activity against plant and animal pathogens. Genomics 2021; 113:4098-4108. [PMID: 34699904 DOI: 10.1016/j.ygeno.2021.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
Pukzing cave, the largest cave of Mizoram, India was explored for bacterial diversity. Culture dependent method revealed 235 bacterial isolates using three different treatments. Identity of the microbial species was confirmed by 16S rDNA sequencing. The highest bacterial population was recovered from heat treatment (n = 97;41.2%) followed by normal (n = 79;33.6%) and cold treatment (n = 59;25.1%) indicating dominance of moderate thermophiles. Antimicrobial potential of isolates showed 20.4% isolates having antimicrobial ability against tested pathogens. Amplicon sequencing of PKSI, PKSII and NRP specific genes revealed presence of AMP genes in the microbial population. Six microbial pathogens were selected for screening as they are well known for different disease cause organism in various fields such as agriculture and human health. Cave environment harbors unique microbial flora and hypervariable region V4 is more informative. Higher activity of AMP assay against these microbes indicates that cave microbial communities could be potential source of future genomic resources.
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Affiliation(s)
- M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ajit Kumar Passari
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram, India; Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico 04510, Mexico
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Farzana Ahmad
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram, India
| | | | - Garima Singh
- Department of Botany, Pachhunga University College, Mizoram University, Aizawl 796001, Mizoram, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.
| | - Bhim Pratap Singh
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram, India; Department of Agriculture and Environmental Sciences, National Institute of Food Technology Entrepreneurship and Management (NIFTEM), Kundli, Sonipat 131028, Haryana, India.
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Kumar A, Mukhia S, Kumar R. Industrial applications of cold-adapted enzymes: challenges, innovations and future perspective. 3 Biotech 2021; 11:426. [PMID: 34567931 DOI: 10.1007/s13205-021-02929-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Extreme cold environments are potential reservoirs of microorganisms producing unique and novel enzymes in response to environmental stress conditions. Such cold-adapted enzymes prove to be valuable tools in industrial biotechnology to meet the increasing demand for efficient biocatalysts. The inherent properties like high catalytic activity at low temperature, high specific activity and low activation energy make the cold-adapted enzymes well suited for application in various industries. The interest in this group of enzymes is expanding as they are the preferred alternatives to harsh chemical synthesis owing to their biodegradable and non-toxic nature. Irrespective of the multitude of applications, the use of cold-adapted enzymes at the industrial level is still limited. The current review presents the unique adaptive features and the role of cold-adapted enzymes in major industries like food, detergents, molecular biology and bioremediation. The review highlights the significance of omics technology i.e., metagenomics, metatranscriptomics and metaproteomics in enzyme bioprospection from extreme environments. It further points out the challenges in using cold-adapted enzymes at the industrial level and the innovations associated with novel enzyme prospection strategies. Documentations on cold-adapted enzymes and their applications are abundant; however, reports on the role of omics tools in exploring cold-adapted enzymes are still scarce. So, the review covers the aspect concerning the novel techniques for enzyme discovery from nature.
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Affiliation(s)
- Anil Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201 002 India
| | - Srijana Mukhia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab 143005 India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, Himachal Pradesh 176 061 India
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Biorefinery Gets Hot: Thermophilic Enzymes and Microorganisms for Second-Generation Bioethanol Production. Processes (Basel) 2021. [DOI: 10.3390/pr9091583] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To mitigate the current global energy and the environmental crisis, biofuels such as bioethanol have progressively gained attention from both scientific and industrial perspectives. However, at present, commercialized bioethanol is mainly derived from edible crops, thus raising serious concerns given its competition with feed production. For this reason, lignocellulosic biomasses (LCBs) have been recognized as important alternatives for bioethanol production. Because LCBs supply is sustainable, abundant, widespread, and cheap, LCBs-derived bioethanol currently represents one of the most viable solutions to meet the global demand for liquid fuel. However, the cost-effective conversion of LCBs into ethanol remains a challenge and its implementation has been hampered by several bottlenecks that must still be tackled. Among other factors related to the challenging and variable nature of LCBs, we highlight: (i) energy-demanding pretreatments, (ii) expensive hydrolytic enzyme blends, and (iii) the need for microorganisms that can ferment mixed sugars. In this regard, thermophiles represent valuable tools to overcome some of these limitations. Thus, the aim of this review is to provide an overview of the state-of-the-art technologies involved, such as the use of thermophilic enzymes and microorganisms in industrial-relevant conditions, and to propose possible means to implement thermophiles into second-generation ethanol biorefineries that are already in operation.
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Liczbiński P, Borowski S. Effect of hyperthermophilic pretreatment on methane and hydrogen production from garden waste under mesophilic and thermophilic conditions. BIORESOURCE TECHNOLOGY 2021; 335:125264. [PMID: 34004562 DOI: 10.1016/j.biortech.2021.125264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Anaerobic digestion of garden waste was investigated in a two-stage process consisting of hyperthermophilic pretreatment followed by mesophilic or thermophilic fermentation. The greatest digestion performance was achieved when the substrates were first treated at 70 °C for 3 days with no inoculation, and then mixed with inoculum (anaerobic sludge) and subjected to anaerobic digestion at 55 °C. Under such conditions, the maximum methane and hydrogen yields from grass were 517 NmlCH4/kgVS and 52 NmlH2/kgVS, whereas the corresponding values for leaves were 421 NmlCH4/kgVS and 23 NmlH2/kgVS, and these figure were far greater than the yields obtained in experiments with no hyperthermophilic stage. A metagenomic analysis of hyperthermophilic environments revealed the appearance of thermophilic and hyperthermophilic bacteria showing hydrolytic activity against lignocellulosic materials, including Caldicellulosiruptor, Thermovenabulum, Thermoanaerobacter, Moorella, Tepimicrobium, Geobacillus and Thermobacillus at a genus level. A noticeable methane production in the hyperthermophilic stage could be linked to the presence of Methanothermobacter sp.
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Affiliation(s)
- Przemysław Liczbiński
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland
| | - Sebastian Borowski
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
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Ding N, Zhao B, Ban X, Li C, Venkataram Prasad BV, Gu Z, Li Z. Carbohydrate-Binding Module and Linker Allow Cold Adaptation and Salt Tolerance of Maltopentaose-Forming Amylase From Marine Bacterium Saccharophagus degradans 2-40 T. Front Microbiol 2021; 12:708480. [PMID: 34335544 PMCID: PMC8317173 DOI: 10.3389/fmicb.2021.708480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Marine extremophiles produce cold-adapted and/or salt-tolerant enzymes to survive in harsh conditions. These enzymes are naturally evolved with unique structural features that confer a high level of flexibility, solubility and substrate-binding ability compared to mesophilic and thermostable homologs. Here, we identified and characterized an amylase, SdG5A, from the marine bacterium Saccharophagus degradans 2-40 T . We expressed the protein in Bacillus subtilis and found that the purified SdG5A enabled highly specific production of maltopentaose, an important health-promoting food and nutrition component. Notably, SdG5A exhibited outstanding cold adaptation and salt tolerance, retaining approximately 30 and 70% of its maximum activity at 4°C and in 3 M NaCl, respectively. It converted 68 and 83% of starch into maltooligosaccharides at 4 and 25°C, respectively, within 24 h, with 79% of the yield being the maltopentaose. By analyzing the structure of SdG5A, we found that the C-terminal carbohydrate-binding module (CBM) coupled with an extended linker, displayed a relatively high negative charge density and superior conformational flexibility compared to the whole protein and the catalytic domain. Consistent with our bioinformatics analysis, truncation of the linker-CBM region resulted in a significant loss in activities at low temperature and high salt concentration. This highlights the linker-CBM acting as the critical component for the protein to carry out its activity in biologically unfavorable condition. Together, our study indicated that these unique properties of SdG5A have great potential for both basic research and industrial applications in food, biology, and medical and pharmaceutical fields.
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Affiliation(s)
- Ning Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, China
| | - Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, China
| | - B. V. Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, China
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Sethupathy S, Morales GM, Li Y, Wang Y, Jiang J, Sun J, Zhu D. Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:154. [PMID: 34225772 PMCID: PMC8256616 DOI: 10.1186/s13068-021-02006-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/26/2021] [Indexed: 05/10/2023]
Abstract
The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.
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Affiliation(s)
- Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Gabriel Murillo Morales
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yixuan Li
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yongli Wang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Evaluation of temperature, pH and nutrient conditions in bacterial growth and extracellular hydrolytic activities of two Alicyclobacillus spp. strains. Arch Microbiol 2021; 203:4557-4570. [PMID: 34159433 DOI: 10.1007/s00203-021-02332-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 12/16/2022]
Abstract
Extremophile bacteria have developed the metabolic machinery for living in extreme temperatures, pH, and high-salt content. Two novel bacterium strains Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2, were isolated from crater lake El Chichon in Chiapas, Mexico. Phylogenetic tree analysis based on the 16SrRNA gene sequence revealed that the strain Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2 were closely related to Alicyclobacillus species (98% identity and 94.73% identity, respectively). Both strains were Gram variable, and colonies were circular, smooth and creamy. Electron microscopy showed than Alicyclobacillus sp. PA1 has a daisy-like form and Alicyclobacillus sp. PA2 is a regular rod. Both strains can use diverse carbohydrates and triglycerides as carbon source and they also can use organic and inorganic nitrogen source. But, the two strains can grow without any carbon or nitrogen sources in the culture medium. Temperature, pH and nutrition condition affect bacterial growth. Maximum growth was produced at 65 °C for Alicyclobacillus sp. PA1 (0.732 DO600) at pH 3 and Alicyclobacillus sp. PA2 (0.725 DO600) at pH 5. Inducible extracellular extremozyme activities were determined for β-galactosidase (Alicyclobacillus sp. PA1: 88.07 ± 0.252 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), cellulose (Alicyclobacillus sp. PA1: 141.20 ± 0.585 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), lipase (Alicyclobacillus sp. PA1: 138.25 ± 0.600 U/mg, Alicyclobacillus sp. PA2: 175.75 ± 1.387 U/mg), xylanase (Alicyclobacillus sp. PA1: 174.72 ± 1.746 U/mg, Alicyclobacillus sp. PA2: 172.69 ± 0.855U/mg), and protease (Alicyclobacillus sp. PA1: 15.12 ± 0.121 U/mg, Alicyclobacillus sp. PA2: 15.33 ± 0.284 U/mg). These results provide new insights on extreme enzymatic production on Alicyclobacillus species.
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Chukwuma OB, Rafatullah M, Tajarudin HA, Ismail N. A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:6001. [PMID: 34204975 PMCID: PMC8199887 DOI: 10.3390/ijerph18116001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022]
Abstract
Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.
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Affiliation(s)
| | - Mohd Rafatullah
- Division of Environmental Technology, School of Industrial Technology, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia; (O.B.C.); (H.A.T.); (N.I.)
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Efficient genome editing of an extreme thermophile, Thermus thermophilus, using a thermostable Cas9 variant. Sci Rep 2021; 11:9586. [PMID: 33953310 PMCID: PMC8100143 DOI: 10.1038/s41598-021-89029-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/20/2021] [Indexed: 02/03/2023] Open
Abstract
Thermophilic organisms are extensively studied in industrial biotechnology, for exploration of the limits of life, and in other contexts. Their optimal growth at high temperatures presents a challenge for the development of genetic tools for their genome editing, since genetic markers and selection substrates are often thermolabile. We sought to develop a thermostable CRISPR-Cas9 based system for genome editing of thermophiles. We identified CaldoCas9 and designed an associated guide RNA and showed that the pair have targetable nuclease activity in vitro at temperatures up to 65 °C. We performed a detailed characterization of the protospacer adjacent motif specificity of CaldoCas9, which revealed a preference for 5'-NNNNGNMA. We constructed a plasmid vector for the delivery and use of the CaldoCas9 based genome editing system in the extreme thermophile Thermus thermophilus at 65 °C. Using the vector, we generated gene knock-out mutants of T. thermophilus, targeting genes on the bacterial chromosome and megaplasmid. Mutants were obtained at a frequency of about 90%. We demonstrated that the vector can be cured from mutants for a subsequent round of genome editing. CRISPR-Cas9 based genome editing has not been reported previously in the extreme thermophile T. thermophilus. These results may facilitate development of genome editing tools for other extreme thermophiles and to that end, the vector has been made available via the plasmid repository Addgene.
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Reyes JS, Fuentes-Lemus E, Aspée A, Davies MJ, Monasterio O, López-Alarcón C. M. jannaschii FtsZ, a key protein in bacterial cell division, is inactivated by peroxyl radical-mediated methionine oxidation. Free Radic Biol Med 2021; 166:53-66. [PMID: 33588048 DOI: 10.1016/j.freeradbiomed.2021.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/27/2021] [Accepted: 02/01/2021] [Indexed: 11/17/2022]
Abstract
Oxidation and inactivation of FtsZ is of interest due to the key role of this protein in bacterial cell division. In the present work, we studied peroxyl radical (from AAPH, 2,2'-azobis(2-methylpropionamidine)dihydrochloride) mediated oxidation of the highly stable FtsZ protein (MjFtsZ) from M. jannaschii, a thermophilic microorganism. MjFtsZ contains eleven Met, and single Tyr and Trp residues which would be expected to be susceptible to oxidation. We hypothesized that exposure of MjFtsZ to AAPH-derived radicals would induce Met oxidation, and cross-linking (via di-Tyr and di-Trp formation), with concomitant loss of its functional polymerization and depolymerization (GTPase) activities. Solutions containing MjFtsZ and AAPH (10 or 100 mM) were incubated at 37 °C for 3 h. Polymerization/depolymerization were assessed by light scattering, while changes in mass were analyzed by SDS-PAGE. Amino acid consumption was quantified by HPLC with fluorescence detection, or direct fluorescence (Trp). Oxidation products and modifications at individual Met residues were quantified by UPLC with mass detection. Oxidation inhibited polymerization-depolymerization activity, and yielded low levels of irreversible protein dimers. With 10 mM AAPH only Trp and Met were consumed giving di-alcohols, kynurenine and di-Trp (from Trp) and the sulfoxide (from Met). With 100 mM AAPH low levels of Tyr oxidation (but not di-Tyr formation) were also observed. Correlation with the functional analyses indicates that Met oxidation, and particularly Met164 is the key driver of MjFtsZ inactivation, probably as a result of the position of this residue at the protein-protein interface of longitudinal interactions and in close proximity to the GTP binding site.
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Affiliation(s)
- Juan Sebastián Reyes
- Departamento de Química Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile; Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile
| | - Eduardo Fuentes-Lemus
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Alexis Aspée
- Departamento de Ciencias Del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Denmark
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile.
| | - Camilo López-Alarcón
- Departamento de Química Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Chile.
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Role of extremophiles and their extremozymes in biorefinery process of lignocellulose degradation. Extremophiles 2021; 25:203-219. [PMID: 33768388 DOI: 10.1007/s00792-021-01225-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/10/2021] [Indexed: 12/20/2022]
Abstract
Technological advances in the field of life sciences have led to discovery of organisms that live in harsh environmental conditions referred to as extremophiles. These organisms have adapted themselves to thrive in extreme habitat giving these organisms an advantage over conventional mesophilic organisms in various industrial applications. Extremozymes produced by these extremophiles have high tolerance to inhospitable environmental conditions making them an ideal enzyme system for various industrial processes. A notable application of these extremophiles and extremozymes is their use in the degradation of recalcitrant lignocellulosic biomass and application in biorefineries. For maximum utilization of the trapped carbon source from this obstinate biomass, pretreatment is a necessary step that requires various physiochemical and enzymatic treatments. From search for novel extremophiles and extremozymes to development of various genetic and protein engineering techniques, investigation on extremozymes with enhanced stability and efficiency is been done. Since extremozymes are easily calibrated to work under such conditions, they have become an emerging topic in the research field of biofuel production. The review discusses the various extremozymes that play an important role in lignocellulose degradation along with recent studies on their molecular and genetic evolution for industrial application and production of biofuels and various value-added products.
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