Simple Analysis of Primary and Secondary Bile Salt Hydrolysis in Mouse and Human Gut Microbiome Samples by Using Fluorogenic Substrates.

Animals produce bile to act as an antibacterial agent and to maximize the absorption of lipophilic nutrients in the gut. The physical properties of bile are largely dictated by amphipathic bile salt molecules, which also participate in signaling pathways by modulating physiological processes upon binding host receptors. Upon excretion of bile salts from the gall bladder into the intestine, the gut microbiota can create metabolites with modified signaling capabilities. The category and magnitude of bile salt metabolism can have positive or negative effects on the host. A key modification is bile salt hydrolysis, which is a prerequisite for all additional microbial transformations. We have synthesized five different fluorogenic bile salts for simple and continuous reporting of hydrolysis in both murine and human fecal samples. Our data demonstrate that most gut microbiomes have the highest capacity for hydrolysis of host-produced primary bile salts, but some microbially modified secondary bile salts also display significant turnover.

(99)Tc(VII) Retardation, Reduction, and Redox Rate Scaling in Naturally Reduced Sediments.

An experimental and modeling study was conducted to investigate pertechnetate (Tc(VII)O4(-)) retardation, reduction, and rate scaling in three sediments from Ringold formation at U.S. Department of Energy's Hanford site, where (99)Tc is a major contaminant in groundwater. Tc(VII) was reduced in all the sediments in both batch reactors and diffusion columns, with a faster rate in a sediment containing a higher concentration of HCl-extractable Fe(II). Tc(VII) migration in the diffusion columns was reductively retarded with retardation degrees correlated with Tc(VII) reduction rates. The reduction rates were faster in the diffusion columns than those in the batch reactors, apparently influenced by the spatial distribution of redox-reactive minerals along transport paths that supplied Tc(VII). X-ray computed tomography and autoradiography were performed to identify the spatial locations of Tc(VII) reduction and transport paths in the sediments, and results generally confirmed the newly found behavior of reaction rate changes from batch to column. The results from this study implied that Tc(VII) migration can be reductively retarded at Hanford site with a retardation degree dependent on reactive Fe(II) content and its distribution in sediments. This study also demonstrated that an effective reaction rate may be faster in transport systems than that in well-mixed reactors.

Environmental controls on the activity of aquifer microbial communities in the 300 area of the Hanford site.

Aquifer microbes in the 300 Area of the Hanford Site in southeastern Washington State, USA, are located in an oligotrophic environment and are periodically exposed to U(VI) concentrations that can range up to 10 µM in small sediment fractures. Assays of (3)H-leucine incorporation indicated that both sediment-associated and planktonic microbes were metabolically active, and that organic C was growth-limiting in the sediments. Although bacteria suspended in native groundwater retained high activity when exposed to 100 µM U(VI), they were inhibited by U(VI) <1 µM in synthetic groundwater that lacked added bicarbonate. Chemical speciation modeling suggested that positively charged species and particularly (UO2)3(OH)5 (+) rose in concentration as more U(VI) was added to synthetic groundwater, but that carbonate complexes dominated U(VI) speciation in natural groundwater. U toxicity was relieved when increasing amounts of bicarbonate were added to synthetic groundwater containing 4.5 µM U(VI). Pertechnetate, an oxyanion that is another contaminant of concern at the Hanford Site, was not toxic to groundwater microbes at concentrations up to 125 µM.

Biotic and abiotic reduction and solubilization of Pu(IV)O2•xH2O(am) as affected by anthraquinone-2,6-disulfonate (AQDS) and ethylenediaminetetraacetate (EDTA).

This study measured reductive solubilization of plutonium(IV) hydrous oxide (Pu(IV)O(2)·xH(2)O((am))) with hydrogen (H(2)) as electron donor, in the presence or absence of dissimilatory metal-reducing bacteria (DMRB), anthraquinone-2,6-disulfonate (AQDS), and ethylenediaminetetraacetate (EDTA). In PIPES buffer at pH 7 with excess H(2), Shewanella oneidensis and Geobacter sulfurreducens both solubilized <0.001% of 0.5 mM Pu(IV)O(2)·xH(2)O((am)) over 8 days, with or without AQDS. However, Pu((aq)) increased by an order of magnitude in some treatments, and increases in solubility were associated with production of Pu(III)((aq)). The solid phase of these treatments contained Pu(III)(OH)(3(am)), with more in the DMRB treatments compared with abiotic controls. In the presence of EDTA and AQDS, PuO(2)·xH(2)O((am)) was completely solubilized by S. oneidensis and G. sulfurreducens in ∼24 h. Without AQDS, bioreductive solubilization was slower (∼22 days) and less extensive (∼83-94%). In the absence of DMRB, EDTA facilitated reductive solubilization of 89% (without AQDS) to 98% (with AQDS) of the added PuO(2)·xH(2)O((am)) over 418 days. An in vitro assay demonstrated electron transfer to PuO(2)·xH(2)O((am)) from the S. oneidensis outer-membrane c-type cytochrome MtrC. Our results (1) suggest that PuO(2)·xH(2)O((am)) reductive solubilization may be important in reducing environments, especially in the presence of complexing ligands and electron shuttles, (2) highlight the environmental importance of polynuclear, colloidal Pu, (3) provide additional evidence that Pu(III)-EDTA is a more likely mobile form of Pu than Pu(IV)-EDTA, and (4) provide another example of outer-membrane cytochromes and electron-shuttling compounds facilitating bioreduction of insoluble electron acceptors in geologic environments.

Purification and characterization of the [NiFe]-hydrogenase of Shewanella oneidensis MR-1.

Shewanella oneidensis MR-1 possesses a periplasmic [NiFe]-hydrogenase (MR-1 [NiFe]-H(2)ase) that has been implicated in H(2) production and oxidation as well as technetium [Tc(VII)] reduction. To characterize the roles of MR-1 [NiFe]-H(2)ase in these proposed reactions, the genes encoding both subunits of MR-1 [NiFe]-H(2)ase were cloned and then expressed in an MR-1 mutant without hyaB and hydA genes. Expression of recombinant MR-1 [NiFe]-H(2)ase in trans restored the mutant's ability to produce H(2) at 37% of that for the wild type. Following purification, MR-1 [NiFe]-H(2)ase coupled H(2) oxidation to reduction of Tc(VII)O(4)(-) and methyl viologen. Change of the buffers used affected MR-1 [NiFe]-H(2)ase-mediated reduction of Tc(VII)O(4)(-) but not methyl viologen. Under the conditions tested, all Tc(VII)O(4)(-) used was reduced in Tris buffer, while in HEPES buffer, only 20% of Tc(VII)O(4)(-) was reduced. The reduced products were soluble in Tris buffer but insoluble in HEPES buffer. Transmission electron microscopy analysis revealed that Tc precipitates reduced in HEPES buffer were aggregates of crystallites with diameters of ∼5 nm. Measurements with X-ray absorption near-edge spectroscopy revealed that the reduction products were a mixture of Tc(IV) and Tc(V) in Tris buffer but only Tc(IV) in HEPES buffer. Measurements with extended X-ray adsorption fine structure showed that while the Tc bonding environment in Tris buffer could not be determined, the Tc(IV) product in HEPES buffer was very similar to Tc(IV)O(2)·nH(2)O, which was also the product of Tc(VII)O(4)(-) reduction by MR-1 cells. These results shows for the first time that MR-1 [NiFe]-H(2)ase catalyzes Tc(VII)O(4)(-) reduction directly by coupling to H(2) oxidation.

Competitive reduction of pertechnetate (99TcO4-) by dissimilatory metal reducing bacteria and biogenic Fe(II).

The fate of pertechnetate ((99)Tc(VII)O(4)(-)) during bioreduction was investigated in the presence of 2-line ferrihydrite (Fh) and various dissimilatory metal reducing bacteria (DMRB) (Geobacter, Anaeromyxobacter, Shewanella) in comparison with TcO(4)(-) bioreduction in the absence of Fh. In the presence of Fh, Tc was present primarily as a fine-grained Tc(IV)/Fe precipitate that was distinct from the Tc(IV)O(2)·nH(2)O solids produced by direct biological Tc(VII) reduction. Aqueous Tc concentrations (<0.2 µm) in the bioreduced Fh suspensions (1.7 to 3.2 × 10(-9) mol L(-1)) were over 1 order of magnitude lower than when TcO(4)(-) was biologically reduced in the absence of Fh (4.0 × 10(-8) to 1.0 × 10(-7) mol L(-1)). EXAFS analyses of the bioreduced Fh-Tc products were consistent with variable chain length Tc-O octahedra bonded to Fe-O octahedra associated with the surface of the residual or secondary Fe(III) oxide. In contrast, biogenic TcO(2)·nH(2)O had significantly more Tc-Tc second neighbors and a distinct long-range order consistent with small particle polymers of TcO(2). In Fe-rich subsurface sediments, the reduction of Tc(VII) by Fe(II) may predominate over direct microbial pathways, potentially leading to lower concentrations of aqueous (99)Tc(IV).

Evaluation of materials for iodine and technetium immobilization through sorption and redox-driven processes.

Radioactive iodine-129 (129I) and technetium-99 (99Tc) pose a risk to groundwater due to their long half-lives, toxicity, and high environmental mobility. Based on literature reviewed in Moore et al. (2019) and Pearce et al. (2019), natural and engineered materials, including iron oxides, low-solubility sulfides, tin-based materials, bismuth-based materials, organoclays, and metal organic frameworks, were tested for potential use as a deployed technology for the treatment of 129I and 99Tc to reduce environmental mobility. Materials were evaluated with metrics including capacity for IO3- and TcO4- uptake, selectivity and long-term immobilization potential. Batch testing was used to determine IO3- and TcO4- sorption under aerobic conditions for each material in synthetic groundwater at different solution to solid ratios. Material association with IO3- and TcO4- was spatially resolved using scanning electron microscopy and X-ray microprobe mapping. The potential for redox reactions was assessed using X-ray absorption near edge structure spectroscopy. Of the materials tested, bismuth oxy(hydroxide) and ferrihydrite performed the best for IO3-. The commercial Purolite A530E anion-exchange resin outperformed all materials in its sorption capacity for TcO4-. Tin-based materials had high capacity for TcO4-, but immobilized TcO4- via reductive precipitation. Bismuth-based materials had high capacity for TcO4-, though slightly lower than the tin-based materials, but did not immobilize TcO4- by a redox-drive process, mitigating potential negative re-oxidation effects over longer time periods under oxic conditions. Cationic metal organic frameworks and polymer networks had high Tc removal capacity, with TcO4- trapped within the framework of the sorbent material. Although organoclays did not have the highest capacity for IO3- and TcO4- removal in batch experiments, they are available commercially in large quantities, are relatively low cost and have low environmental impact, so were investigated in column experiments, demonstrating scale-up and removal of IO3- and TcO4- via sorption, and reductive immobilization with iron- and sulfur-based species.

Electron donor-dependent radionuclide reduction and nanoparticle formation by Anaeromyxobacter dehalogenans strain 2CP-C.

Anaeromyxobacter dehalogenans strain 2CP-C reduces U(VI) and Tc(VII) to U(IV)O(2(s)) (uraninite) and Tc(IV)O(2(S)) respectively. Kinetic studies with resting cells revealed that U(VI) or Tc(VII) reduction rates using H(2) as electron donor exceeded those observed in acetate-amended incubations. The reduction of U(VI) by A. dehalogenans 2CP-C resulted in extracellular accumulation of approximately 5 nm uraninite nanoparticles in association with a lectin-binding extracellular polymeric substance (EPS). The electron donor did not affect UO(2(S)) nanoparticle size or association with EPS, but the utilization of acetate as the source of reducing equivalents resulted in distinct UO(2(S)) nanoparticle aggregates that were approximately 50 nm in diameter. In contrast, reduction of Tc(VII) by A. dehalogenans 2CP-C cell suspensions produced dense clusters of TcO(2) particles, which were localized within the cell periplasm and on the outside of the outer membrane. In addition to direct reduction, A. dehalogenans 2CP-C cell suspensions reduced Tc(VII) indirectly via an Fe(II)-mediated mechanism. Fe(II) produced by strain 2CP-C from either ferrihydrite or Hanford Site sediment rapidly removed (99)Tc(VII)O(4)(-) from solution. These findings expand our knowledge of the radionuclide reduction processes catalysed by Anaeromyxobacter spp. that may influence the fate and transport of radionuclide contaminants in the subsurface.

On Modeling Ensemble Transport of Metal Reducing Motile Bacteria.

Many metal reducing bacteria are motile with their run-and-tumble behavior exhibiting series of flights and waiting-time spanning multiple orders of magnitude. While several models of bacterial processes do not consider their ensemble motion, some models treat motility using an advection diffusion equation (ADE). In this study, Geobacter and Pelosinus, two metal reducing species, are used in micromodel experiments for study of their motility characteristics. Trajectories of individual cells on the order of several seconds to few minutes in duration are analyzed to provide information on (1) the length of runs, and (2) time needed to complete a run (waiting or residence time). A Continuous Time Random Walk (CTRW) model to predict ensemble breakthrough plots is developed based on the motility statistics. The results of the CTRW model and an ADE model are compared with the real breakthrough plots obtained directly from the trajectories. The ADE model is shown to be insufficient, whereas a coupled CTRW model is found to be good at predicting breakthroughs at short distances and at early times, but not at late time and long distances. The inadequacies of the simple CTRW model can possibly be improved by accounting for correlation in run length and waiting time.

Hydrogenase- and outer membrane c-type cytochrome-facilitated reduction of technetium(VII) by Shewanella oneidensis MR-1.

Pertechnetate, (99)Tc(VII)O(4)(-), is a highly mobile radionuclide contaminant at US Department of Energy sites that can be enzymatically reduced by a range of anaerobic and facultatively anaerobic microorganisms, including Shewanella oneidensis MR-1, to poorly soluble Tc(IV)O(2(s)). In other microorganisms, Tc(VII)O(4)(-) reduction is generally considered to be catalysed by hydrogenase. Here, we provide evidence that although the NiFe hydrogenase of MR-1 was involved in the H(2)-driven reduction of Tc(VII)O(4)(-)[presumably through a direct coupling of H(2) oxidation and Tc(VII) reduction], the deletion of both hydrogenase genes did not completely eliminate the ability of MR-1 to reduce Tc(VII). With lactate as the electron donor, mutants lacking the outer membrane c-type cytochromes MtrC and OmcA or the proteins required for the maturation of c-type cytochromes were defective in reducing Tc(VII) to nanoparticulate TcO(2) x nH(2)O((s)) relative to MR-1 or a NiFe hydrogenase mutant. In addition, reduced MtrC and OmcA were oxidized by Tc(VII)O(4)(-), confirming the capacity for direct electron transfer from these OMCs to TcO(4)(-). c-Type cytochrome-catalysed Tc(VII) reduction could be a potentially important mechanism in environments where organic electron donor concentrations are sufficient to allow this reaction to dominate.

Multimodal microfluidic platform for controlled culture and analysis of unicellular organisms.

Modern live-cell imaging approaches permit real-time visualization of biological processes, yet limitations exist for unicellular organism isolation, culturing, and long-term imaging that preclude fully understanding how cells sense and respond to environmental perturbations and the link between single-cell variability and whole-population dynamics. Here, we present a microfluidic platform that provides fine control over the local environment with the capacity to replace media components at any experimental time point, and provides both perfused and compartmentalized cultivation conditions depending on the valve configuration. The functionality and flexibility of the platform were validated using both bacteria and yeast having different sizes, motility, and growth media. The demonstrated ability to track the growth and dynamics of both motile and non-motile prokaryotic and eukaryotic organisms emphasizes the versatility of the devices, which should enable studies in bioenergy and environmental research.

Live Cell Discovery of Microbial Vitamin Transport and Enzyme-Cofactor Interactions.

The rapid completion of microbial genomes is inducing a conundrum in functional gene discovery. Novel methods are needed to shorten the gap between characterizing a microbial genome and experimentally validating bioinformatically predicted functions. Of particular importance are transport mechanisms, which shuttle nutrients such as B vitamins and metabolites across cell membranes and are required for the survival of microbes ranging from members of environmental microbial communities to pathogens. Methods to accurately assign function and specificity for a wide range of experimentally unidentified and/or predicted membrane-embedded transport proteins, along with characterization of intracellular enzyme-cofactor associations, are needed to enable a significantly improved understanding of microbial biochemistry and physiology, microbial interactions, and microbial responses to perturbations. Chemical probes derived from B vitamins B1, B2, and B7 have allowed us to experimentally address the aforementioned needs by identifying B vitamin transporters and intracellular enzyme-cofactor associations through live cell labeling of the filamentous anoxygenic photoheterotroph, Chloroflexus aurantiacus J-10-fl, known to employ mechanisms for both B vitamin biosynthesis and environmental salvage. Our probes provide a unique opportunity to directly link cellular activity and protein function back to ecosystem and/or host dynamics by identifying B vitamin transport and cofactor-dependent interactions required for survival.

Genomic distribution of B-vitamin auxotrophy and uptake transporters in environmental bacteria from the Chloroflexi phylum.

Bacteria from the Chloroflexi phylum are dominant members of phototrophic microbial mat communities in terrestrial thermal environments. Vitamins of B group are key intermediates (precursors) in the biosynthesis of indispensable enzyme cofactors driving numerous metabolic processes in all forms of life. A genomics-based reconstruction and comparative analysis of respective biosynthetic and salvage pathways and riboswitch regulons in over 20 representative Chloroflexi genomes revealed a widespread auxotrophy for some of the vitamins. The most prominent predicted phenotypic signature, auxotrophy for vitamins B1 and B7 was experimentally confirmed for the best studied model organism Chloroflexus aurantiacus. These observations along with identified candidate genes for the respective uptake transporters pointed to B vitamin cross-feeding as an important aspect of syntrophic metabolism in microbial communities. Inferred specificities of homologous substrate-binding components of ABC transporters for vitamins B1 (ThiY) and B2 (RibY) were verified by thermofluorescent shift approach. A functional activity of the thiamine-specific transporter ThiXYZ from C. aurantiacus was experimentally verified by genetic complementation in E. coli. Expanding the integrative approach, which was applied here for a comprehensive analysis of B-vitamin metabolism in Chloroflexi would allow reconstruction of metabolic interdependencies in microbial communities.

An autotrophic H2 -oxidizing, nitrate-respiring, Tc(VII)-reducing Acidovorax sp. isolated from a subsurface oxic-anoxic transition zone.

Increasing concentrations of H2 with depth were observed across a geologic unconformity and associated redox transition zone in the subsurface at the Hanford Site in south-central Washington, USA. An opposing gradient characterized by decreasing O2 and nitrate concentrations was consistent with microbial-catalysed biogeochemical processes. Sterile sand was incubated in situ within a multilevel sampler placed across the redox transition zone to evaluate the potential for Tc(VII) reduction and for enrichment of H2 -oxidizing denitrifiers capable of reducing Tc(VII). H2 -driven TcO4 (-) reduction was detected in sand incubated at all depths but was strongest in material from a depth of 17.1 m. Acidovorax spp. were isolated from H2 -nitrate enrichments from colonized sand from 15.1 m, with one representative, strain JHL-9, subsequently characterized. JHL-9 grew on acetate with either O2 or nitrate as electron acceptor (data not shown) and on medium with bicarbonate, H2 and nitrate. JHL-9 also reduced pertechnetate (TcO4 (-) ) under denitrifying conditions with H2 as the electron donor. H2 -oxidizing Acidovorax spp. in the subsurface at Hanford and other locations may contribute to the maintenance of subsurface redox gradients and offer the potential for Tc(VII) reduction.

CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough.

Geologic carbon dioxide (CO2) sequestration drives physical and geochemical changes in deep subsurface environments that impact indigenous microbial activities. The combined effects of pressurized CO2 on a model sulfate-reducing microorganism, Desulfovibrio vulgaris, have been assessed using a suite of genomic and kinetic measurements. Novel high-pressure NMR time-series measurements using (13)C-lactate were used to track D. vulgaris metabolism. We identified cessation of respiration at CO2 pressures of 10 bar, 25 bar, 50 bar, and 80 bar. Concurrent experiments using N2 as the pressurizing phase had no negative effect on microbial respiration, as inferred from reduction of sulfate to sulfide. Complementary pressurized batch incubations and fluorescence microscopy measurements supported NMR observations, and indicated that non-respiring cells were mostly viable at 50 bar CO2 for at least 4 h, and at 80 bar CO2 for 2 h. The fraction of dead cells increased rapidly after 4 h at 80 bar CO2. Transcriptomic (RNA-Seq) measurements on mRNA transcripts from CO2-incubated biomass indicated that cells up-regulated the production of certain amino acids (leucine, isoleucine) following CO2 exposure at elevated pressures, likely as part of a general stress response. Evidence for other poorly understood stress responses were also identified within RNA-Seq data, suggesting that while pressurized CO2 severely limits the growth and respiration of D. vulgaris cells, biomass retains intact cell membranes at pressures up to 80 bar CO2. Together, these data show that geologic sequestration of CO2 may have significant impacts on rates of sulfate reduction in many deep subsurface environments where this metabolism is a key respiratory process.

Inhibition of bacterial U(VI) reduction by calcium.

The rapid kinetics of bacterial U(VI) reduction and low solubility of uraninite (UO2,cr) make this process an attractive option for removing uranium from groundwater. Nevertheless, conditions that may promote or inhibit U(VI) reduction are not well-defined. Recent descriptions of Ca-UO2-CO3 complexes indicate that these species may dominate the aqueous speciation of U(VI) in many environments. We monitored the bacterial reduction of U(VI) in bicarbonate-buffered solution in the presence and absence of Ca. XAFS measurements confirmed the presence of a Ca-U(VI)-C03 complex in the initial solutions containing calcium. Calcium, at millimolar concentrations (0.45-5 mM), caused a significant decrease in the rate and extent of bacterial U(VI) reduction. Both facultative (Shewanella putrefaciens strain CN32) and obligate (Desulfovibrio desulfuricans, Geobacter sulfurreducens) anaerobic bacteria were affected by the presence of calcium. Reduction of U(VI) ceased when the calculated system Eh reached -0.046 +/- 0.001 V, based on the Ca2UO2(CO3)3 --> UO2,cr couple. The results are consistent with the hypothesis that U is a less energetically favorable electron acceptor when the Ca-UO2-CO3 complexes are present. The results do not support Ca inhibition caused by direct interactions with the cells or with the electron donor as the reduction of fumarate or Tc(VII)O4- under identical conditions was unaffected by the presence of Ca.