Space station biomining experiment demonstrates rare earth element extraction in microgravity and Mars gravity

The study investigates whether microorganisms can bioleach rare earth elements (REEs) from basaltic rock under altered gravity conditions relevant to space exploration. REEs are critical for high-technology applications and may face supply constraints, motivating alternative extraction methods. Microorganisms play essential roles in rock weathering and biomining on Earth, and microbe–mineral interactions are also important for space applications such as in-situ resource utilization. Gravity affects fluid dynamics, nutrient mixing, and microbial physiology, which could alter bioleaching. The authors hypothesized that altered gravity regimens (microgravity, simulated Mars gravity, and simulated Earth gravity) would induce changes in microbial interactions with minerals and thus affect bioleaching efficiency.

Prior research has shown that microbes are integral to geochemical cycling and biomining, enabling extraction of metals like copper and gold and potentially reducing use of toxic reagents. Heterotrophic bacteria and fungi can bioleach under circumneutral to alkaline conditions via pH modulation or release of complexing compounds. REEs, including the lanthanides, scandium, and yttrium, are economically critical and have unique roles in microbial metabolism (e.g., as cofactors in alcohol dehydrogenases), and microbes can mobilize REEs from various mineral matrices. In space contexts, microbe–mineral interactions are relevant for soil formation, dust control, life support, bioenergy, and biocementation. Microgravity and altered gravity can influence microbial growth and metabolism by modifying sedimentation and convection, potentially impacting bioleaching. Previous spaceflight and ground-based studies document microbial growth changes, biofilm formation, and element leaching under different conditions, but systematic evaluation of REE bioleaching in space had been lacking.

Design: The European Space Agency BioRock experiment was performed on the International Space Station (ISS) in 2019 to examine bioleaching of REEs from basalt under three gravity conditions: microgravity, simulated Mars gravity (~0.4 × g), and simulated Earth gravity (1 × g) using a dedicated miniature biomining reactor (Experimental Units within Experiment Containers). Organisms and media: Three bacteria were selected for desiccation tolerance, biofilm potential, rock interaction, and growth in a common medium: Sphingomonas desiccabilis CP1D (DSM 16792), Bacillus subtilis NCIB 3610 (DSM 10), and Cupriavidus metallidurans CH34 (DSM 2839). Cultures were grown in 50% R2A medium (composition provided) at pH 7.2. NOTOXhisto fixative was used to halt metabolism at experiment end. Substrate: Olivine basalt (Iceland, Gufunes near Reykjavik) analogous to lunar and martian basalts. Slides were 1.5 × 1.6 cm, 3 mm thick; sterilized by dry heat (4 h at 250 °C). Basalt REE and bulk compositions were determined by ICP-MS and XRF. Sample preparation: Microbes were applied/desiccated onto basalt slides: S. desiccabilis via overnight culture (OD600 ~0.88), 1 mL inoculum per slide air-dried; B. subtilis spores (10 µL of 1×10^8 spores/mL; 1×10^6 spores per slide) air-dried; C. metallidurans via freeze-drying after immersion in cryoprotectant suspension (~10^9 CFU/mL). Negative controls were sterile slides without cells. Flight hardware and operations: Each Experimental Unit (EU) hosted two independent culture chambers with gas-permeable silicone membranes and reservoirs for 5 mL medium and 1 mL fixative per sample. Chambers were purged with sterile N2. Eighteen flight ECs (36 samples) were launched on SpaceX CRS-18 (July 25, 2019), stored on ISS at 2.1 °C, then incubated in two KUBIK centrifuge incubators at 20 °C from July 30 to August 20, 2019. One KUBIK simulated Earth gravity and the other simulated Mars gravity at the basalt surface; microgravity ECs were placed in static slots. Gravity levels were verified every 10 min by accelerometers with correction for radius. Total run time was 21 days. Fixative was automatically injected on August 20, 2019; ECs were refrigerated until return. Temperature control: EC temperatures remained ≤7.1 °C during storage/transport; 20.16 °C during incubation on ISS. Return occurred Aug 27–29, with 6.6–7.1 °C during transit. Ground control: Six ECs were run at true 1 × g using a KUBIK Interface Simulation Station in a 20 °C incubator, mirroring ISS timelines, with temperatures ~20.62 °C during growth and ~3–4.5 °C during shipment/storage. Sample recovery and contamination handling: From each 6 mL chamber, 3 mL aliquots were acidified (final 4% HNO3) for ion fixation and stored at 4 °C. Four ground chambers failed fixative injection and were manually fixed. Two non-biological control chambers (one ISS microgravity, one ground) showed contamination and were excluded. ICP-MS analyses: Bulk fluids, pellet washes, and cell-associated fractions were quantified by ICP-MS (Agilent 7500ce; specified operating parameters). REEs measured: 139La, 140Ce, 141Pr, 146Nd, 147Sm, 153Eu, 157Gd, 159Tb, 163Dy, 165Ho, 166Er, 169Tm, 172Yb, 175Lu. Calibration used multi-element standards and NIST SRM1640a. Detection limits ranged ~0.001–0.005 ppb depending on element. Basalt REE content was measured by high-resolution ICP-MS (Nu AttoM) after acid digestion. pH measurements: Final pH after fixation was measured for all samples (flight and ground). A separate ground experiment tracked pH at days 0,1,4,7,14,21 in 50% R2A with/without basalt and each organism, including measurements before/after fixative and after cold storage. Statistics: Data were log10-transformed. One- and two-way ANOVAs assessed effects of organism, gravity, and environment (ISS vs ground). Tukey post-hoc tests were applied as appropriate. For specific REEs, two-sample independent two-tailed t-tests compared conditions, acknowledging small sample sizes.

• Across all three organisms and gravity conditions, organism identity significantly affected REE leaching (ANOVA: F(2,369)=87.84, p=0.001). Gravity had no significant effect (ANOVA: F(2,369)=0.202, p=0.818); no significant organism×gravity interaction (F(4,369)=1.75, p=0.138). • Sphingomonas desiccabilis: Enhanced REE concentrations relative to non-biological controls under all gravities; significant vs controls in simulated Mars (ANOVA: F(1,83)=14.14, p<0.0001) and simulated Earth gravity (F(1,83)=24.20, p<0.0001), not significant in microgravity (F(1,69)=2.43, p=0.124). No significant differences between gravity conditions (F(2,123)=1.60, p=0.206). Relative to controls, individual REE enhancements across ISS conditions ranged from 111.9% to 429.2%. Preferential enhancement of heavy REEs (Gd–Lu) was observed; e.g., Er increased by 429.2±92.0% on ISS simulated Earth gravity; ground Yb increased by 767.4±482.4%. Total fraction of REEs released by S. desiccabilis was ~0.024–0.117% of the amounts available in basalt. • Bacillus subtilis: Leached significantly less REEs than controls in microgravity (ANOVA: F(1,69)=13.05, p<0.001) and simulated Mars (F(1,83)=29.55, p<0.0001), marginal in simulated Earth gravity (p=0.055). No significant differences between gravities (F(2,123)=1.45, p=0.240). Per-element tests generally showed lower concentrations vs controls at p<0.05 or p<0.1 for most REEs. • Cupriavidus metallidurans: No significant difference from controls in any gravity (microgravity: F(1,69)=2.25, p=0.138; Mars: F(1,83)=3.47, p=0.066; Earth: F(1,83)=0.265, p=0.608). Few per-element differences detected. For B. subtilis and C. metallidurans, the fraction of elements leached as a percentage of total available ranged ~0.00414–0.0322%. • Controls: Gravity regimen did not significantly affect REE leaching in non-biological controls on ISS (ANOVA: F(2,109)=2.91, p=0.059), though some per-element differences between simulated Mars and Earth controls existed. • Cell-associated REEs: Typically <5% of total REEs in bulk solution; Eu exceeded 5% in several conditions. No evidence that S. desiccabilis had a systematically higher fraction of cell-bound REEs compared with the other organisms. • pH: During growth at 1 × g on ground, bacterial cultures became slightly basic by day 21 (with basalt: S. desiccabilis pH 8.41±0.01; B. subtilis 8.63±0.01; C. metallidurans 8.66±0.01; control 7.35±0.036). Fixative addition lowered pH markedly (~3.6–3.9). Final measured pH in flight/ground samples after fixation ranged 4.16–6.12. • ISS vs ground Earth gravity: For S. desiccabilis, REE leaching was higher in ISS simulated Earth gravity than true ground 1 × g (ANOVA: F(1,82)=8.14, p=0.005). No significant differences for B. subtilis or C. metallidurans. Non-biological controls also showed higher leaching on ISS simulated Earth gravity than ground (F(1,68)=6.90, p=0.011). Potential contributors include centrifugation-induced shear/gradient differences and a small temperature offset.

The findings address the central hypothesis by demonstrating that, while microbial identity strongly determines REE bioleaching outcomes, the final leaching yields were not significantly impacted by gravity regimen within the tested conditions. Sphingomonas desiccabilis effectively enhanced REE extraction from basalt in microgravity and simulated Mars and Earth gravities, supporting the feasibility of biomining across extraterrestrial environments, including asteroids (very low gravity) and Mars. The lack of gravity effect on final yields may reflect sufficient nutrients enabling cultures to reach similar final cell concentrations under all gravities, leading to comparable leaching endpoints. Mechanistically, bulk medium acidification was not responsible; instead, extracellular polymeric substances produced by S. desiccabilis likely facilitated complexation and mobilization, particularly of heavy REEs, consistent with prior observations that biological materials can preferentially bind heavy REEs via phosphate or other moieties. The preference for heavy REEs could also represent a biosignature preserved under altered gravity, with astrobiological implications. In contrast, B. subtilis reduced REE concentrations relative to abiotic controls, potentially via ligand production or other chemical interactions that retard leaching; C. metallidurans had minimal effect. Minimal cell-associated REE fractions and the influence of fixation on pH suggest most REEs remained in solution or associated with extracellular matrices rather than strongly bound to cells. Differences between ISS simulated Earth gravity and true ground 1 × g for S. desiccabilis and controls underscore that centrifugation-based gravity simulation in space is not identical to terrestrial gravity, yet overall biological trends were conserved.

This study demonstrates biological extraction of rare earth elements from basalt in space using a miniature biomining reactor, with Sphingomonas desiccabilis significantly enhancing REE leaching under microgravity and simulated Mars and Earth gravities. Biomining yields did not significantly differ across gravity regimens, indicating the robustness of microbial bioleaching for in-situ resource utilization beyond Earth. The work reveals a preferential enhancement of heavy REEs and validates principles for reactor design for space applications. Future research should: (1) optimize reactor parameters (e.g., crushed feedstock, mixing/stirring) to increase leaching efficiencies; (2) evaluate additional lithologies with higher REE content (e.g., lunar KREEP terrains) and test lunar gravity; (3) extend to other economically relevant materials and asteroid regolith analogs; (4) dissect molecular mechanisms (e.g., EPS composition and binding chemistry) underlying heavy REE preference; and (5) scale up to continuous or semi-continuous biomining operations applicable to ISRU.

• Basalt was used as intact slides rather than crushed rock, likely limiting extraction efficiency (<~0.12% of available REEs), whereas crushed substrates generally yield higher leaching. • Reactors were not stirred to avoid confounding microgravity effects on mixing; industrial systems would employ mixing that could increase yields. • Fixative addition substantially lowered pH and storage at low temperatures could allow continued abiotic leaching, potentially affecting final measurements; however, similar effects occurred in controls and temperatures were minimized. • Only final pH was measured in flight; growth-phase pH dynamics were inferred from ground experiments. • Simulated gravity on ISS via centrifugation differs from true 1 × g (shear forces, gravity gradients due to small rotor radius), and a small temperature offset existed between ISS and ground setups. • Two control samples were contaminated and excluded; small sample sizes reduce power of element-specific tests.