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Ru J, Xue J, Sun J, Cova L, Deng L. Unveiling the hidden role of aquatic viruses in hydrocarbon pollution bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132299. [PMID: 37597386 DOI: 10.1016/j.jhazmat.2023.132299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/28/2023] [Accepted: 08/12/2023] [Indexed: 08/21/2023]
Abstract
Hydrocarbon pollution poses substantial environmental risks to water and soil. Bioremediation, which utilizes microorganisms to manage pollutants, offers a cost-effective solution. However, the role of viruses, particularly bacteriophages (phages), in bioremediation remains unexplored. This study examines the diversity and activity of hydrocarbon-degradation genes encoded by environmental viruses, focusing on phages, within public databases. We identified 57 high-quality phage-encoded auxiliary metabolic genes (AMGs) related to hydrocarbon degradation, which we refer to as virus-encoded hydrocarbon degradation genes (vHYDEGs). These genes are encoded by taxonomically diverse aquatic phages and highlight the under-characterized global virosphere. Six protein families involved in the initial alkane hydroxylation steps were identified. Phylogenetic analyses revealed the diverse evolutionary trajectories of vHYDEGs across habitats, revealing previously unknown biodegraders linked evolutionarily with vHYDEGs. Our findings suggest phage AMGs may contribute to alkane and aromatic hydrocarbon degradation, participating in the initial, rate-limiting hydroxylation steps, thereby aiding hydrocarbon pollution bioremediation and promoting their propagation. To support future research, we developed vHyDeg, a database containing identified vHYDEGs with comprehensive annotations, facilitating the screening of hydrocarbon degradation AMGs and encouraging their bioremediation applications.
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Affiliation(s)
- Jinlong Ru
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Jianfeng Sun
- Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Linda Cova
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Freising 85354, Germany.
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Pompa-Monroy DA, Iglesias AL, Dastager SG, Thorat MN, Olivas-Sarabia A, Valdez-Castro R, Hurtado-Ayala LA, Cornejo-Bravo JM, Pérez-González GL, Villarreal-Gómez LJ. Comparative Study of Polycaprolactone Electrospun Fibers and Casting Films Enriched with Carbon and Nitrogen Sources and Their Potential Use in Water Bioremediation. MEMBRANES 2022; 12:327. [PMID: 35323802 PMCID: PMC8951516 DOI: 10.3390/membranes12030327] [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: 12/31/2021] [Revised: 03/04/2022] [Accepted: 03/11/2022] [Indexed: 12/02/2022]
Abstract
Augmenting bacterial growth is of great interest to the biotechnological industry. Hence, the effect of poly (caprolactone) fibrous scaffolds to promote the growth of different bacterial strains of biological and industrial interest was evaluated. Furthermore, different types of carbon (glucose, fructose, lactose and galactose) and nitrogen sources (yeast extract, glycine, peptone and urea) were added to the scaffold to determinate their influence in bacterial growth. Bacterial growth was observed by scanning electron microscopy; thermal characteristics were also evaluated; bacterial cell growth was measured by ultraviolet-visible spectrophotometry at 600-nm. Fibers produced have an average diameter between 313 to 766 nm, with 44% superficial porosity of the scaffolds, a glass transition around ~64 °C and a critical temperature of ~338 °C. The fibrous scaffold increased the cell growth of Escherichia coli by 23% at 72 h, while Pseudomonas aeruginosa and Staphylococcus aureus increased by 36% and 95% respectively at 48 h, when compared to the normal growth of their respective bacterial cultures. However, no significant difference in bacterial growth between the scaffolds and the casted films could be observed. Cell growth depended on a combination of several factors: type of bacteria, carbon or nitrogen sources, casted films or 3D scaffolds. Microscopy showed traces of a biofilm formation around 3 h in culture of P. aeruginosa. Water bioremediation studies showed that P. aeruginosa on poly (caprolactone)/Glucose fibers was effective in removing 87% of chromium in 8 h.
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Affiliation(s)
- Daniella Alejandra Pompa-Monroy
- Facultad de Ciencias de la Ingeniería y Tecnología, Universidad Autónoma de Baja California, Tijuana 21500, Baja California, Mexico; (D.A.P.-M.); (A.L.I.); (G.L.P.-G.)
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Tijuana 22260, Baja California, Mexico; (L.A.H.-A.); (J.M.C.-B.)
| | - Ana Leticia Iglesias
- Facultad de Ciencias de la Ingeniería y Tecnología, Universidad Autónoma de Baja California, Tijuana 21500, Baja California, Mexico; (D.A.P.-M.); (A.L.I.); (G.L.P.-G.)
| | - Syed Gulam Dastager
- National Collection of Industrial Microorganism (NCIM), CSIR-National Chemical Laboratory, Pune 41008, Maharashtra, India; (S.G.D.); (M.N.T.)
| | - Meghana Namdeo Thorat
- National Collection of Industrial Microorganism (NCIM), CSIR-National Chemical Laboratory, Pune 41008, Maharashtra, India; (S.G.D.); (M.N.T.)
| | - Amelia Olivas-Sarabia
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada 22860, Baja California, Mexico; (A.O.-S.); (R.V.-C.)
| | - Ricardo Valdez-Castro
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada 22860, Baja California, Mexico; (A.O.-S.); (R.V.-C.)
| | - Lilia Angélica Hurtado-Ayala
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Tijuana 22260, Baja California, Mexico; (L.A.H.-A.); (J.M.C.-B.)
| | - José Manuel Cornejo-Bravo
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Tijuana 22260, Baja California, Mexico; (L.A.H.-A.); (J.M.C.-B.)
| | - Graciela Lizeth Pérez-González
- Facultad de Ciencias de la Ingeniería y Tecnología, Universidad Autónoma de Baja California, Tijuana 21500, Baja California, Mexico; (D.A.P.-M.); (A.L.I.); (G.L.P.-G.)
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Tijuana 22260, Baja California, Mexico; (L.A.H.-A.); (J.M.C.-B.)
| | - Luis Jesús Villarreal-Gómez
- Facultad de Ciencias de la Ingeniería y Tecnología, Universidad Autónoma de Baja California, Tijuana 21500, Baja California, Mexico; (D.A.P.-M.); (A.L.I.); (G.L.P.-G.)
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Tijuana 22260, Baja California, Mexico; (L.A.H.-A.); (J.M.C.-B.)
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Duran-Bedolla J, Garza-Ramos U, Rodríguez-Medina N, Aguilar Vera A, Barrios-Camacho H. Exploring the environmental traits and applications of Klebsiella variicola. Braz J Microbiol 2021; 52:2233-2245. [PMID: 34626346 DOI: 10.1007/s42770-021-00630-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 10/04/2021] [Indexed: 10/20/2022] Open
Abstract
Klebsiella variicola has been found in various natural niches, alone or in association with other bacteria, and causes diseases in animals and plants with important economic and environmental impacts. K. variicola has the capacity to fix nitrogen in the rhizosphere and soil; produces indole acetic acid, acetoin, and ammonia; and dissolves phosphorus and potassium, which play an important role in plant growth promotion and nutrition. Some members of K. variicola have properties such as halotolerance and alkalotolerance, conferring an evolutionary advantage. In the environmental protection, K. variicola can be used in the wastewater treatment, biodegradation, and bioremediation of polluted soil, either alone or in association with other organisms. In addition, it has the potential to carry out industrial processes in the food and pharmaceutical industries, like the production of maltose and glucose by the catalysis of debranching unmodified oligosaccharides by the pullulanase enzyme. Finally, this bacterium has the ability to transform chemical energy into electrical energy, such as a biocatalyst, which could be useful in the near future. These properties show that K. variicola should be considered an eco-friendly bacterium with hopeful technological promise. In this review, we explore the most significant aspects of K. variicola and highlight its potential applications in environmental and biotechnological processes.
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Affiliation(s)
- Josefina Duran-Bedolla
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Nadia Rodríguez-Medina
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Alejandro Aguilar Vera
- Centro de Ciencias Genómicas, Programa de Genómica Funcional de Procariotes, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Humberto Barrios-Camacho
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico.
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Alown F, Alsharidah A, Shamsah S. Genotypic characterization of soil bacteria in the Umm Al-Namil Island, Kuwait. Saudi J Biol Sci 2021; 28:3847-3854. [PMID: 34220239 PMCID: PMC8241613 DOI: 10.1016/j.sjbs.2021.03.060] [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: 01/04/2021] [Revised: 03/13/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Microflora is an integral part of soil ecosystem, in which bacteria are the largest group of soil microbes. This is a pioneer study for establishing baseline data on the diversity of soil bacteria among different regions in Kuwait. The aim is to understand biodiversity in different settings, how bacteria adapt to different niches in the environment as well as in different hosts. The identification of bacterial 16S rRNA molecules from environmental soil samples was investigated. Genomic Deoxyribonucleic acid DNA was extracted from 25 soil samples derived from five different test regions in the Umm Al-Namil Island, Kuwait. After amplification of bacterial 16S rRNA molecules by the Polymerase chain reaction PCR, the products were characterized and complex band patterns were obtained, indicating high bacterial diversity. A sample of the 16 s rRNA amplicons were sequenced in order to identify the species. The spatial distribution of bacterial taxa in the different soil samples was homogeneous, suggesting a stable and widespread community. Forty-nine isolates from Umm Al-Namil island were identified by comparative analysis of partial 16S rRNA gene sequences. Phylogenetic analysis was carried out in order to study the connection between the isolates to identify species. A large proportion of these isolates represent correspond to known or novel species within the Pseudomonus and Bacillus genera, which are common soil bacteria. Our results provided a reference for future studies to facilitate bacterial identification and ecological research in Kuwait.
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Affiliation(s)
- Fadaa Alown
- Public Authority for Training and Applied Education (PAAET), Department of Science-College of Basic Education, Kuwait
| | - Ahlam Alsharidah
- Public Authority for Training and Applied Education (PAAET), Department of Science-College of Basic Education, Kuwait
| | - Sara Shamsah
- Kuwait University, Department of Medical Laboratory Sciences, Kuwait
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Radwan SS, Al-Mailem DM, Kansour MK. Bioaugmentation failed to enhance oil bioremediation in three soil samples from three different continents. Sci Rep 2019; 9:19508. [PMID: 31862978 PMCID: PMC6925256 DOI: 10.1038/s41598-019-56099-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/30/2019] [Indexed: 11/09/2022] Open
Abstract
Soil samples from Kuwait, Lebanon, Egypt and Germany were polluted with 3% crude oil. Series of samples were left unbioaugmented, others were bioaugmented with Kuwaiti desert soil with a long history of oil pollution and still others with Kuwaiti marine biofouling material. In the samples from Kuwait, Egypt, and Germany, bioaugmentation did not enhance oil removal, whereas it did in the sample from Lebanon. Taxa from the desert-soil bioaugmented batches, but none of those from the biofouling-material bioaugmented ones, succeeded in colonizing the four studied soils. The dynamics of the hydrocarbonoclastic communities during bioremediation were monitored. Those communities differed in composition, not only according to the type of soil, but also for the same soil; at various phases of bioremediation. Although each soil seemed to have its characteristic microflora, they all were similar in harboring lower and higher actinomycetes and pseudomonads in addition to many other taxa. None of the taxa prevailed through all phases of bioremediation. The most powerful isolate in oil-removal; was Rhodococcus erythropolis (Germany), and the weakest was Arthrobacter phenanthrenivorans (Lebanon). The pure hydrocarbonoclastic isolates tolerated unusually high oil concentrations, up to 30%.
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Affiliation(s)
- Samir S Radwan
- Department of Biological Sciences, Faculty of Science, Kuwait University, P O Box 5969, Safat, 13060, Kuwait. .,Von Einem Str. 25, 48159, Münster, Germany.
| | - Dina M Al-Mailem
- Department of Biological Sciences, Faculty of Science, Kuwait University, P O Box 5969, Safat, 13060, Kuwait.
| | - Mayada K Kansour
- Department of Biological Sciences, Faculty of Science, Kuwait University, P O Box 5969, Safat, 13060, Kuwait
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