High efficiency rare earth element bioleaching with systems biology guided engineering of Gluconobacter oxydans
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Life Sciences & Biomedicine - Other Topics↗
Engineering topics
Pian, Brooke
Publications and source records attributed to Pian, Brooke.
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 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.
Marecos, Sabrina (ORCID:0000000158529933)↗
Engineered Microorganisms for Enhanced Rare Earth Element Bio-mining and Separations (Final Technical Report)
Rare earth elements (REE) are critical ingredients of sustainable energy technologies, but their extraction from ore and separation from one another pose formidable challenges. To solve the challenge of REE supply, we used advanced genomics, high-throughput screening with synthetic REE minerals, and synthetic biology to engineer two sets of exotic microbes to (1) extract REE from ores, spent cracking catalysts, coal ash and electronic waste with high efficiency and selectivity, and (2) to purify REE into single element batches, all under benign conditions without the need of harsh solvents and high temperatures. This work integrated our expertise in systems and synthetic biology (Buz Barstow); rare-earth geochemistry (Esteban Gazel) and mineral synthesis (Megan Holycross); and microsystems engineering (Mingming Wu) by first elucidating the set of rules that predict an organism’s phenotype and then applying them to solve this critical problem in sustainable energy. These new technologies could help to revitalize the US rare earth industry and provide a new source of these critical elements for future energy technologies. We have already had some big success in tech transfer. Two of our team members (postdoctoral fellow Alexa Schmitz and graduate student Sean Medin) were able to study the supply chain for REE in the United States, and identify an opportunity to commercialize our REE mineral-dissolution technology. Alexa and Sean recently founded REEgen, Inc., an REE biomining company. Dr. Schmitz was recently awarded a fellowship from the Activate Foundation to support the first two years of REEgen. Cornell showed its support for this technology and company, and Dr. Schmitz was awarded the Rising Women Innovator’s award. These two awards unlocked support from Cornell’s Praxis Incubator.
58 GEOSCIENCES↗
Genomic characterization of rare earth binding by Shewanella oneidensis
Abstract Rare earth elements (REE) are essential ingredients of sustainable energy technologies, but separation of individual REE is one of the hardest problems in chemistry today. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for separation of rare earth elements (REE). The REE-biosorption capability of some microorganisms allows for REE separations that, under specialized conditions, are already competitive with solvent extractions, suggesting that genetic engineering could allow it to leapfrog existing technologies. To identify targets for genomic improvement we screened 3,373 mutants from the whole genome knockout collection of the known REE-biosorbing microorganism Shewanella oneidensis MR-1. We found 130 genes that increased biosorption of the middle REE europium, and 112 that reduced it. We verified biosorption changes from the screen for a mixed solution of three REE (La, Eu, Yb) using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) in solution conditions with a range of ionic strengths and REE concentrations. We identified 18 gene ontologies and 13 gene operons that make up key systems that affect biosorption. We found, among other things, that disruptions of a key regulatory component of the arc system ( hptA ), which regulates cellular response to anoxic environments and polysaccharide biosynthesis related genes ( wbpQ , wbnJ , SO_3183 ) consistently increase biosorption across all our solution conditions. Our largest total biosorption change comes from our SO_4685 , a capsular polysaccharide (CPS) synthesis gene, disruption of which results in an up to 79% increase in biosorption; and nusA, a transcriptional termination/anti-termination protein, disruption of which results in an up to 35% decrease in biosorption. Knockouts of glnA , pyrD , and SO_3183 produce small but significant increases (≈ 1%) in relative biosorption affinity for ytterbium over lanthanum in multiple solution conditions tested, while many other genes we explored have more complex binding affinity changes. Modeling suggests that while these changes to lanthanide biosorption selectivity are small, they could already reduce the length of repeated enrichment process by up to 27%. This broad exploratory study begins to elucidate how genetics affect REE-biosorption by S. oneidensis , suggests new areas of investigation for better mechanistic understanding of the membrane chemistry involved in REE binding, and offer potential targets for improving biosorption and separation of REE by genetic engineering.
Medin, Sean↗
Single-cell multimodal imaging uncovers energy conversion pathways in biohybrids
Microbe–semiconductor biohybrids, which integrate microbial enzymatic synthesis with the light-harvesting capabilities of inorganic semiconductors, have emerged as promising solar-to-chemical conversion systems. Improving the electron transport at the nano–bio interface and inside cells is important for boosting conversion efficiencies, yet the underlying mechanism is challenging to study by bulk measurements owing to the heterogeneities of both constituents. Here we develop a generalizable, quantitative multimodal microscopy platform that combines multi-channel optical imaging and photocurrent mapping to probe such biohybrids down to single- to sub-cell/particle levels. We uncover and differentiate the critical roles of different hydrogenases in the lithoautotrophic bacterium Ralstonia eutropha for bioplastic formation, discover this bacterium’s surprisingly large nanoampere-level electron-uptake capability, and dissect the cross-membrane electron-transport pathways. Furthermore, this imaging platform, and the associated analytical framework, can uncover electron-transport mechanisms in various types of biohybrid, and potentially offers a means to use and engineer R. eutropha for efficient chemical production coupled with photocatalytic materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗