Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching

Marecos, Sabrina; Pian, Brooke; Medin, Sean A.; Schmitz, Alexa; Andrade, Melinna; Wu, Mingming; Balta, J. Brian; Gazel, Esteban; Holycross, Megan; Reid, Matthew C.; Barstow, Buz

doi:10.1038/s42003-025-08061-4

Direct genome-scale screening of Gluconobacter oxydans B58 for rare earth element bioleaching

Journal Article · Wed Apr 30 00:00:00 EDT 2025 · Communications Biology

DOI:https://doi.org/10.1038/s42003-025-08061-4· OSTI ID:2563497

; Pian, Brooke; Medin, Sean A.; Schmitz, Alexa; ; ; Balta, J. Brian; ; Holycross, Megan; Reid, Matthew C.;

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% (δ GO_1598 , disruption of the gene encoding the orotate phosphoribosyltransferase enzyme PyrE), and one strain significantly reduced it by 97% (δ GO_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.

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Sponsoring Organization:: USDOE

Grant/Contract Number:: AR0001341

OSTI ID:: 2563497

Journal Information:: Communications Biology, Journal Name: Communications Biology Journal Issue: 1 Vol. 8; ISSN 2399-3642

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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