Microbial communities in cores obtained from methane hydrate-bearing deep marine sediments (down to more than 300 m below the seafloor) in the forearc basin of the Nankai Trough near Japan were characterized with cultivation-dependent and -independent techniques. Acridine orange direct count data indicated that cell numbers generally decreased with sediment depth. Lipid biomarker analyses indicated the presence of viable biomass at concentrations greater than previously reported for terrestrial subsurface environments at similar depths. Archaeal lipids were more abundant than bacterial lipids. Methane was produced from both acetate and hydrogen in enrichments inoculated with sediment from all depths evaluated, at both 10 and 35°C. Characterization of 16S rRNA genes amplified from the sediments indicated that archaeal clones could be discretely grouped within the Euryarchaeota and Crenarchaeota domains. The bacterial clones exhibited greater overall diversity than the archaeal clones, with sequences related to the Bacteroidetes, Planctomycetes, Actinobacteria, Proteobacteria, and green nonsulfur groups. The majority of the bacterial clones were either members of a novel lineage or most closely related to uncultured clones. The results of these analyses suggest that the microbial community in this environment is distinct from those in previously characterized methane hydrate-bearing sediments.

Lanmodulin (LanM) is a recently discovered protein that undergoes a large conformational change in response to rareearth elements (REEs). Here, we use multiple physicochemical methods to demonstrate that LanM is the most selective macromolecule for REEs characterized to date and even outperforms many synthetic chelators. Moreover, LanM exhibits metal-binding properties and structural stability unseen in most other metalloproteins. LanM retains REE binding down to pH ≈ 2.5, and LanM-REE complexes withstand high temperature (up to 95 °C), repeated acid treatments, and up to molar amounts of competing non-REE metal ions (including Mg, Ca, Zn, and Cu), allowing the protein's use in harsh chemical processes. LanM's unrivaled properties were applied to metal extraction from two distinct REE-containing industrial feedstocks covering a broad range of REE and non-REE concentrations, namely, precombustion coal and electronic waste leachates. After only a single all-aqueous step, quantitative and selective recovery of the REEs from all non-REEs initially present (Li, Na, Mg, Ca, Sr, Al, Si, Mn, Fe, Co, Ni, Cu, Zn, and U) was achieved, demonstrating the universal selectivity of LanM for REEs against non-REEs and its potential application even for industrial low-grade sources, which are currently underutilized. Our work indicates that biosourced macromolecules such as LanM may offer a new paradigm for extractive metallurgy and other applications involving felements.

With the increasing demand for rare earth elements (REEs) in many emerging clean energy technologies, there is an urgent need for the development of new approaches for efficient REE extraction and recovery. As a step towards this goal, we genetically engineered the aerobic bacterium Caulobacter crescentus for REE adsorption through high-density cell surface display of lanthanide binding tags (LBTs) on its S-layer. The LBT-displayed strains exhibited enhanced adsorption of REEs compared to cells lacking LBT, high specificity for REEs, and an adsorption preference for REEs with small atomic radii. Adsorbed Tb3+ could be effectively recovered using citrate, consistent with thermodynamic speciation calculations that predicted strong complexation of Tb3+ by citrate. No reduction in Tb3+ adsorption capacity was observed following citrate elution, enabling consecutive adsorption/desorption cycles. The LBT-displayed strain was effective for extracting REEs from the acid leachate of core samples collected at a prospective rare earth mine. Our collective results demonstrate a rapid, efficient and reversible process for REE adsorption with potential industrial application for REE enrichment and separation.

Microbial cultures were evaluated for organic acid production and their potential utility for leaching of rare earth elements (REE) from retorted phosphor powder (RPP) and spent fluid catalytic cracking (FCC) catalyst. Two bacterial and one fungal strain were isolated from environmental and industrial materials known to contain REE and compared to the industrially important bacterium Gluconobacter oxydans. Gluconic acid was the predominant organic acid product identified in all of the cultures. Maximum REE leaching (49% of the total REE) from the FCC material was observed using cell-free culture supernatants of G. oxydans, with preferential recovery of lanthanum over cerium. The phosphor powder was more difficult to leach; only about 2% of the total REE was leached with G. oxydans. Leaching experiments with the RPP material indicated that the extent of REE solubilization was similar whether whole cell cultures or cell-free supernatants were used. Abiotic control experiments showed that increasing gluconic acid concentrations increased leaching efficiency; for example, total REE leaching from FCC catalyst increased from 24% to 45% when gluconic acid was increased from 10 mM to 90 mM. However, G. oxydans cell-free culture supernatants containing 10-15 mM gluconic acid were more effective than abiotically prepared leaching solutions with higher gluconic acid concentrations, suggesting that other exudate components were important too. Our results indicate that microorganisms producing gluconic and other organic acids can induce effective leaching of REE from waste materials, and that increasing organic acid production will improve recovery.

The use of biomass for adsorption of rare earth elements (REEs) has been the subject of many recent investigations. However, REE adsorption by bioengineered systems has been scarcely documented, and rarely tested with complex natural feedstocks. Herein, we engineered E. coli cells for enhanced cell surface-mediated extraction of REEs by functionalizing the OmpA protein with 16 copies of a lanthanide binding tag (LBT). Through biosorption experiments conducted with leachates from metal-mine tailings and rare earth deposits, we show that functionalization of the cell surface with LBT yielded several notable advantages over the nonengineered control. First, the efficiency of REE adsorption from all leachates was enhanced as indicated by a 2-10-fold increase in distribution coefficients for individual REEs. Second, the relative affinity of the cell surface for REEs was increased over all non-REEs except Cu. Third, LBT-display systematically enhanced the affinity of the cell surface for REEs as a function of decreasing atomic radius, providing a means to separate high value heavy REEs from more common light REEs. Together, our results demonstrate that REE biosorption of high efficiency and selectivity from low-grade feedstocks can be achieved by engineering the native bacterial surface.