Additional file 2: of System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

RP model and gene knockout results. (XLSX 133 kb

Additional file 1: of System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

System-level Analyses of robustness of metabolism to environmental and genetic perturbations. (DOCX 3179 kb

Additional file 3: of System-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris

SBML format of the RP model. (XML 1614 kb

Reduction of Plutonium(VI) to (V) by Hydroxamate Compounds at Environmentally Relevant pH

Natural organic matter is known to influence the mobility of plutonium (Pu) in the environment via complexation and reduction mechanisms. Hydroxamate siderophores have been specifically implicated due to their strong association with Pu. Hydroxamate siderophores can also break down into di and monohydroxamates and may influence the Pu oxidation state, and thereby its mobility. In this study we explored the reactions of Pu­(VI) and Pu­(V) with a monohydroxamate compound (acetohydroxamic acid, AHA) and a trihydroxamate siderophore desferrioxamine B (DFOB) at an environmentally relevant pH (5.5–8.2). Pu­(VI) was instantaneously reduced to Pu­(V) upon reaction with AHA. The presence of hydroxylamine was not observed at these pHs; however, AHA was consumed during the reaction. This suggests that the reduction of Pu­(VI) to Pu­(V) by AHA is facilitated by a direct one electron transfer. Importantly, further reduction to Pu­(IV) or Pu­(III) was not observed, even with excess AHA. We believe that further reduction of Pu­(V) did not occur because Pu­(V) does not form a strong complex with hydroxamate compounds at a circum-neutral pH. Experiments performed using desferrioxamine B (DFOB) yielded similar results. Broadly, this suggests that Pu­(V) reduction to Pu­(IV) in the presence of natural organic matter is not facilitated by hydroxamate functional groups and that other natural organic matter moieties likely play a more prominent role

Self-Biased Solar-Microbial Device for Sustainable Hydrogen Generation

Here we demonstrate the feasibility of continuous, self-sustained hydrogen gas production based solely on solar light and biomass (wastewater) recycling, by coupling solar water splitting and microbial electrohydrogenesis in a photoelectrochemical cell–microbial fuel cell (PEC-MFC) hybrid device. The PEC device is composed of a TiO2 nanowire-arrayed photoanode and a Pt cathode. The MFC is an air cathode dual-chamber device, inoculated with either Shewanella oneidensis MR-1 (batch-fed on artificial growth medium) or natural microbial communities (batch-fed on local municipal wastewater). Under light illumination, the TiO2 photoanode provided a photovoltage of ∼0.7 V that shifted the potential of the MFC bioanode to overcome the potential barrier for microbial electrohydrogenesis. As a result, under light illumination (AM 1.5G, 100 mW/cm2) without external bias, and using wastewater as the energy source, we observed pronounced current generation as well as continuous production of hydrogen gas. The successful demonstration of such a self-biased, sustainable microbial device for hydrogen generation could provide a new solution that can simultaneously address the need of wastewater treatment and the increasing demand for clean energy

Comparison of Kill Switch Toxins in Plant-Beneficial <i>Pseudomonas fluorescens</i> Reveals Drivers of Lethality, Stability, and Escape

Kill switches provide a biocontainment strategy in which unwanted growth of an engineered microorganism is prevented by expression of a toxin gene. A major challenge in kill switch engineering is balancing evolutionary stability with robust cell killing activity in application relevant host strains. Understanding host-specific containment dynamics and modes of failure helps to develop potent yet stable kill switches. To guide the design of robust kill switches in the agriculturally relevant strain Pseudomonas fluorescens SBW25, we present a comparison of lethality, stability, and genetic escape of eight different toxic effectors in the presence of their cognate inactivators (i.e., toxin–antitoxin modules, polymorphic exotoxin–immunity systems, restriction endonuclease–methyltransferase pair). We find that cell killing capacity and evolutionary stability are inversely correlated and dependent on the level of protection provided by the inactivator gene. Decreasing the proteolytic stability of the inactivator protein can increase cell killing capacity, but at the cost of long-term circuit stability. By comparing toxins within the same genetic context, we determine that modes of genetic escape increase with circuit complexity and are driven by toxin activity, the protective capacity of the inactivator, and the presence of mutation-prone sequences within the circuit. Collectively, the results of our study reveal that circuit complexity, toxin choice, inactivator stability, and DNA sequence design are powerful drivers of kill switch stability and valuable targets for optimization of biocontainment systems

Recovery of Rare Earth Elements from Geothermal Fluids through Bacterial Cell Surface Adsorption

The increasing demand for rare earth elements (REEs) in the modern economy motivates the development of novel strategies for cost-effective REE recovery from nontraditional feedstocks. We previously engineered E. coli to express lanthanide binding tags on the cell surface, which increased the REE biosorption capacity and selectivity. Here we examined how REE adsorption by the engineered E. coli is affected by various geochemical factors relevant to geothermal fluids, including total dissolved solids (TDS), temperature, pH, and the presence of specific competing metals. REE biosorption is robust to TDS, with high REE recovery efficiency and selectivity observed with TDS as high as 165,000 ppm. Among several metals tested, U, Al, and Pb were found to be the most competitive, causing >25% reduction in REE biosorption when present at concentrations ∼3- to 11-fold higher than the REEs. Optimal REE biosorption occurred between pH 5–6, and sorption capacity was reduced by ∼65% at pH 2. REE recovery efficiency and selectivity increased as a function of temperature up to ∼70 °C due to the thermodynamic properties of metal complexation on the bacterial surface. Together, these data define the optimal and boundary conditions for biosorption and demonstrate its potential utility for selective REE recovery from geofluids

Shotgun Proteomic Analysis Unveils Survival and Detoxification Strategies by <i>Caulobacter crescentus</i> during Exposure to Uranium, Chromium, and Cadmium

The ubiquitous bacterium <i>Caulobacter crescentus</i> holds promise to be used in bioremediation applications due to its ability to mineralize U­(VI) under aerobic conditions. Here, cell free extracts of <i>C. crescentus</i> grown in the presence of uranyl nitrate [U­(VI)], potassium chromate [Cr­(VI)], or cadmium sulfate [Cd­(II)] were used for label-free proteomic analysis. Proteins involved in two-component signaling and amino acid metabolism were up-regulated in response to all three metals, and proteins involved in aerobic oxidative phosphorylation and chemotaxis were down-regulated under these conditions. Clustering analysis of proteomic enrichment revealed that the three metals also induce distinct patterns of up- or down-regulated expression among different functional classes of proteins. Under U­(VI) exposure, a phytase enzyme and an ABC transporter were up-regulated. Heat shock and outer membrane responses were found associated with Cr­(VI), while efflux pumps and oxidative stress proteins were up-regulated with Cd­(II). Experimental validations were performed on select proteins. We found that a phytase plays a role in U­(VI) and Cr­(VI) resistance and detoxification and that a Cd­(II)-specific transporter confers Cd­(II) resistance. Interestingly, analysis of promoter regions in genes associated with differentially expressed proteins suggests that U­(VI) exposure affects cell cycle progression

Bridging Hydrometallurgy and Biochemistry: A Protein-Based Process for Recovery and Separation of Rare Earth Elements

The extraction and subsequent separation of individual rare earth elements (REEs) from REE-bearing feedstocks represent a challenging yet essential task for the growth and sustainability of renewable energy technologies. As an important step toward overcoming the technical and environmental limitations of current REE processing methods, we demonstrate a biobased, all-aqueous REE extraction and separation scheme using the REE-selective lanmodulin protein. Lanmodulin was conjugated onto porous support materials using thiol-maleimide chemistry to enable tandem REE purification and separation under flow-through conditions. Immobilized lanmodulin maintains the attractive properties of the soluble protein, including remarkable REE selectivity, the ability to bind REEs at low pH, and high stability over numerous low-pH adsorption/desorption cycles. We further demonstrate the ability of immobilized lanmodulin to achieve high-purity separation of the clean-energy-critical REE pair Nd/Dy and to transform a low-grade leachate (0.043 mol % REEs) into separate heavy and light REE fractions (88 mol % purity of total REEs) in a single column run while using ∼90% of the column capacity. This ability to achieve, for the first time, tandem extraction and grouped separation of REEs from very complex aqueous feedstock solutions without requiring organic solvents establishes this lanmodulin-based approach as an important advance for sustainable hydrometallurgy

Microbial Carbonation of Monocalcium Silicate

Biocement formed through microbially induced calcium carbonate precipitation (MICP) is an emerging biotechnology focused on reducing the environmental impact of concrete production. In this system, CO2 species are provided via ureolysis by Sporosarcina pasteurii (S. pasteurii) to carbonate monocalcium silicate for MICP. This is one of the first studies of its kind that uses a solid-state calcium source, while prior work has used highly soluble forms. Our study focuses on microbial physiological, chemical thermodynamic, and kinetic studies of MICP. Monocalcium silicate incongruently dissolves to form soluble calcium, which must be coupled with CO2 release to form calcium carbonate. Chemical kinetic modeling shows that calcium solubility is the rate-limiting step, but the addition of organic acids significantly increases the solubility, enabling extensive carbonation to proceed up to 37 mol %. The microbial urease activity by S. pasteurii is active up to pH 11, 70 °C, and 1 mol L–1 CaCl2, producing calcite as a means of solidification. Cell-free extracts are also effective albeit less robust at extreme pH, producing calcite with different physical properties. Together, these data help determine the chemical, biological, and thermodynamic parameters critical for scaling microbial carbonation of monocalcium silicate to high-density cement and concrete