Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching
Abstract The transition to a sustainable energy economy will require an enormous increase in the supply of rare earth elements (REEs). Bioleaching offers a promising alternative to conventional hydrometallurgical methods for REE extraction from low-grade ores. However, exploiting this potential rema...
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Nature Portfolio
2025-04-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08061-4 |
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| author | Sabrina Marecos Brooke Pian Sean A. Medin Alexa Schmitz Melinna Andrade Mingming Wu J. Brian Balta Esteban Gazel Megan Holycross Matthew C. Reid Buz Barstow |
| author_facet | Sabrina Marecos Brooke Pian Sean A. Medin Alexa Schmitz Melinna Andrade Mingming Wu J. Brian Balta Esteban Gazel Megan Holycross Matthew C. Reid Buz Barstow |
| author_sort | Sabrina Marecos |
| collection | DOAJ |
| description | Abstract The transition to a sustainable energy economy will require an enormous increase in the supply of rare earth elements (REEs). Bioleaching offers a promising alternative to conventional hydrometallurgical methods for REE extraction from low-grade ores. However, exploiting this potential remains challenging due to large gaps in our understanding of the genetics involved, and inadequate biological tools to address them. We generated a highly non-redundant whole-genome knockout collection for the bioleaching microbe Gluconobacter oxydans B58, reducing redundancy by 85% compared to the previous best collection. This new collection was directly screened for bioleaching neodymium from a synthetic monazite powder, identifying 89 genes important for bioleaching, 68 of which have not previously been associated with this mechanism. We conducted bench-scale experiments to validate the extraction efficiency of promising strains: 8 demonstrated significant increases in extraction by up to 111% (δGO_1598, disruption of the gene encoding the orotate phosphoribosyltransferase enzyme PyrE), and one strain significantly reduced it by 97% (δGO_1096, disruption of the gene encoding the GTP-binding protein TypA). Notable changes in pH were only observed for 3 strains, suggesting an important role for non-acid mechanisms in bioleaching. These findings provide valuable insights into further enhancing REE-bioleaching by G. oxydans through genetic engineering. |
| format | Article |
| id | doaj-art-e8ab854e46e8420fb56bc9afd31802db |
| institution | OA Journals |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
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| series | Communications Biology |
| spelling | doaj-art-e8ab854e46e8420fb56bc9afd31802db2025-08-20T02:10:56ZengNature PortfolioCommunications Biology2399-36422025-04-018111210.1038/s42003-025-08061-4Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleachingSabrina Marecos0Brooke Pian1Sean A. Medin2Alexa Schmitz3Melinna Andrade4Mingming Wu5J. Brian Balta6Esteban Gazel7Megan Holycross8Matthew C. Reid9Buz Barstow10Department of Biological and Environmental Engineering, Cornell UniversityDepartment of Biological and Environmental Engineering, Cornell UniversityDepartment of Biological and Environmental Engineering, Cornell UniversityDepartment of Biological and Environmental Engineering, Cornell UniversityDepartment of Biological and Environmental Engineering, Cornell UniversityDepartment of Biological and Environmental Engineering, Cornell UniversityDepartment of Earth and Atmospheric Sciences, Cornell UniversityDepartment of Earth and Atmospheric Sciences, Cornell UniversityDepartment of Earth and Atmospheric Sciences, Cornell UniversitySchool of Civil and Environmental Engineering, Cornell UniversityDepartment of Biological and Environmental Engineering, Cornell UniversityAbstract The transition to a sustainable energy economy will require an enormous increase in the supply of rare earth elements (REEs). Bioleaching offers a promising alternative to conventional hydrometallurgical methods for REE extraction from low-grade ores. However, exploiting this potential remains challenging due to large gaps in our understanding of the genetics involved, and inadequate biological tools to address them. We generated a highly non-redundant whole-genome knockout collection for the bioleaching microbe Gluconobacter oxydans B58, reducing redundancy by 85% compared to the previous best collection. This new collection was directly screened for bioleaching neodymium from a synthetic monazite powder, identifying 89 genes important for bioleaching, 68 of which have not previously been associated with this mechanism. We conducted bench-scale experiments to validate the extraction efficiency of promising strains: 8 demonstrated significant increases in extraction by up to 111% (δGO_1598, disruption of the gene encoding the orotate phosphoribosyltransferase enzyme PyrE), and one strain significantly reduced it by 97% (δGO_1096, disruption of the gene encoding the GTP-binding protein TypA). Notable changes in pH were only observed for 3 strains, suggesting an important role for non-acid mechanisms in bioleaching. These findings provide valuable insights into further enhancing REE-bioleaching by G. oxydans through genetic engineering.https://doi.org/10.1038/s42003-025-08061-4 |
| spellingShingle | Sabrina Marecos Brooke Pian Sean A. Medin Alexa Schmitz Melinna Andrade Mingming Wu J. Brian Balta Esteban Gazel Megan Holycross Matthew C. Reid Buz Barstow Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching Communications Biology |
| title | Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching |
| title_full | Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching |
| title_fullStr | Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching |
| title_full_unstemmed | Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching |
| title_short | Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching |
| title_sort | direct genome scale screening of gluconobacter oxydans b58 for rare earth element bioleaching |
| url | https://doi.org/10.1038/s42003-025-08061-4 |
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