Carbon Source For Reduction Research Articles

Metabolic niche of a prominent sulfate-reducing human gut bacterium

Sulfate-reducing bacteria (SRB) colonize the guts of ∼50% of humans. We used genome-wide transposon mutagenesis and insertion-site sequencing, RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy US adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. piger and fed diets with different levels and types of carbohydrates and sulfur sources. Diet was a major determinant of functions expressed by this artificial nine-member community and of the genes that impact D. piger fitness; the latter includes high- and low-affinity systems for using ammonia, a limiting resource for D. piger in mice consuming a polysaccharide-rich diet. Although genes involved in hydrogen consumption and sulfate reduction are necessary for its colonization, varying dietary-free sulfate levels did not significantly alter levels of D. piger, which can obtain sulfate from the host in part via cross-feeding mediated by Bacteroides-encoded sulfatases. Chondroitin sulfate, a common dietary supplement, increased D. piger and H2S levels without compromising gut barrier integrity. A chondroitin sulfate-supplemented diet together with D. piger impacted the assemblage's substrate utilization preferences, allowing consumption of more reduced carbon sources and increasing the abundance of the H2-producing Actinobacterium, Collinsella aerofaciens. Our findings provide genetic and metabolic details of how this H2-consuming SRB shapes the responses of a microbiota to diet ingredients and a framework for examining how individuals lacking D. piger differ from those who harbor it.

Fate of lead oxide during thermal treatment with tetrabromobisphenol A

In this paper, the bromination reaction between lead oxide and hydrogen bromide originating from the thermal decomposition of tetrabromobisphenol A (TBBPA), under inert and oxidizing atmospheres, was investigated, using a laboratory-scale furnace. The results obtained under inert conditions indicated that bromination of PbO proceeded simultaneously with debromination of TBBPA, with an average effectiveness of 69% (max. 80%). Volatilization of the formed PbBr2 began at 315°C, intensified at 750°C, and reached 98% at 850°C. The formed organic char served as a source of carbon for reduction of the unreacted lead oxide to metallic lead in the range 315–750°C. Additional experiments conducted at selected temperatures under slightly oxidizing (5vol% O2) and quasi-atmospheric (20vol% O2) conditions showed no significant effects on bromination–evaporation of lead in the studied mixture. However, in isothermal treatment under quasi-atmospheric oxygen levels, complete vaporization of the formed lead bromide was obtained at a temperature of only 650°C.

Enhancement of succinate production by metabolically engineered Escherichia coli with co-expression of nicotinic acid phosphoribosyltransferase and pyruvate carboxylase

Escherichia coli BA002, in which the ldhA and pflB genes are deleted, cannot utilize glucose anaerobically due to the inability to regenerate NAD(+). To restore glucose utilization, overexpression of nicotinic acid phosphoribosyltransferase (NAPRTase) encoded by the pncB gene, a rate-limiting enzyme of NAD(H) synthesis pathway, resulted in a significant increase in cell mass and succinate production under anaerobic conditions. However, a high concentration of pyruvate accumulated. Thus, co-expression of NAPRTase and the heterologous pyruvate carboxylase (PYC) of Lactococcus lactis subsp. cremoris NZ9000 in recombinant E. coli BA016 was investigated. The total concentration of NAD(H) was 9.8-fold higher in BA016 than in BA002, and the NADH/NAD(+) ratio decreased from 0.60 to 0.04. Under anaerobic conditions, BA016 consumed 17.50 g l(-1) glucose and produced 14.08 g l(-1) succinate with a small quantity of pyruvate. Furthermore, when the reducing agent dithiothreitol or reduced carbon source sorbitol was added, the cell growth and carbon source consumption rate of BA016 was reasonably enhanced and succinate productivity increased.

Reduced isotope fractionation by denitrification under conditions relevant to the ocean

Experiments with two well-studied denitrifiers and one recently isolated marine suboxic zone denitrifier show that the cellular-level denitrification N isotope effect (15ε) is typically lower than the canonical value of ∼25‰ under many conditions prevalent in the ocean. Across all three strains, 15ε is 10–15‰ at cellular nitrate reduction rates that are more representative of the environment than the very high rates under which we and previous investigators measure 15ε to be 20–30‰. A sharp decrease in 15ε is also observed in individual nitrate drawdown assays as the extracellular nitrate concentrations approach 2–35μM and nitrate uptake becomes the rate-limiting step. On an apparently strain-specific basis, lower values of 15ε are observed under diverse conditions common in the natural environment: less reduced carbon sources, small inputs of oxygen, nutrient availability, agitation, and age of starter culture (i.e., initiation of assays with cells that had recently depleted a large previous nitrate amendment or were more recently in the exponential growth (“bloom”) phase). A conserved oxygen-to-nitrogen isotope relationship across the experiments for all three denitrifiers (18ε/15ε=0.93±0.06 (1SD)) supports the interpretation that fractionation is imparted solely by the internal respiratory nitrate reductase, with the amplitude of 15ε varying with the proportional importance of cellular nitrate efflux relative to uptake. Aspects of the 15ε variation are unexpected; nevertheless, the occurrence of lower 15ε is robust. It is uncertain if our lower 15ε estimates apply to oceanic water column denitrification because field studies have generally yielded 15εwc between 20–30‰, more similar to previous culture estimates and our estimates at high cell specific nitrate reduction rates. If denitrification in the ocean’s major suboxic zones does have an 15ε of ∼10–15‰, it would remove an apparent imbalance between global ocean N inputs and outputs previously suggested by fixed N isotope budgeting.

IDENTIFICATION AND PHYSIOLOGICAL ASPECTS OF A NOVEL CAROTENOID-ENRICHED, METAL-RESISTANT MICROALGA ISOLATED FROM AN ACIDIC RIVER IN HUELVA (SPAIN)(1).

A heavy-metal-resistant, carotenoid-enriched novel unicellular microalga was isolated from an acidic river in Huelva, Spain. The isolated ribosomal 18S subunit rDNA sequence showed homology with known sequences from green microalgae, the closest sequence (98% homology) belonging to the genus Coccomyxa. The isolated microalga therefore was an up to now uncultured microalga. The microalga was isolated from Tinto River area (Huelva, Spain), an acidic river that exhibits very low pH (1.7-3.1) with high concentrations of sulfuric acid and heavy metals, including Fe, Cu, Mn, Ni, and Al. Electron micrographs show that the microalga contains a large chloroplast with a presence of lipid droplets, an increased number of starch bodies as well as electron-dense deposits and plastoglobules, the last observed only in iron-exposed cells. Unlike other acidophile microalgae, the isolated microalga showed high growth rates when cultivated photoautotrophycally (up to 0.6 d(-1) ) in a suitable culture medium prepared at our laboratory. The growth was shown to be iron dependent. When the microalga is grown in fluidized bed reactors, the high growth rates resulted in unexpectedly high productivities for being a microalga that naturally grows in acidic environments (0.32 g·L(-1) ·d(-1) ). The microalga also grows optimally on reduced carbon sources, including glucose and urea, and at an optimal temperature of 35°C. The alga pigment profile is particularly rich in carotenoids, especially lutein, suggesting that the microalga might have potential for antioxidant production, namely, xanthophylls.

Temperature resistant mutants of Rhodobacter capsulatus generated by a directed evolution approach and effects of temperature resistance on hydrogen production

Abstract Hydrogen (H2) is a promising alternative energy carrier which can be produced biologically. Rhodobacter capsulatus, a non-sulfur purple photosynthetic bacterium, can produce H2 under nitrogen-limited, photoheterotrophic conditions by using reduced carbon sources such as simple organic acids. Outdoor closed photobioreactors; used for biological H2 production are located under direct sunlight, as a result; bioreactors are exposed to temperature fluctuations during day time. In this study to overcome this problem, temperature-resistant mutants (up to 42 °C) of R. capsulatus were generated in this study by a directed evolution approach. Eleven mutant strains of R. capsulatus DSM 1710 were obtained by initial ethyl methane sulfonate (EMS) mutagenesis of the wild-type strain, followed by batch selection at gradually increasing temperatures up to 42 °C under respiratory conditions. The genetic stability of the mutants was tested and eight were genetically stable. Moreover, H2 production of mutant strains was analyzed; five mutants produced higher amounts of H2 when compared to the DSM 1710 wild-type strain and three mutants produced less H2 by volume. The highest H2- producing mutant (B41) produced 24% more H2 compared to wild type, and the mutant with lowest H2-production capacity (A52) generated 7% less H2 compared to the wild type. These results indicated that heat resistance of R. capsulatus can be improved by directed evolution, which is a useful tool to improve industrially important microbial properties. To understand molecular changes that confer high temperature-resistance and high hydrogen production capacity to these mutants, detailed transcriptomic and proteomic analyses would be necessary.

Tree-ring widths and isotopes of artificially defoliated balsam firs: A simulation of spruce budworm outbreaks in Eastern Canada

Defoliation by insects is a major disturbance influencing the forest dynamics in many ecosystems and can affect forest productivity worldwide. The main objective of this research was to further investigate the potential use of tree-ring widths and isotopic compositions to identify different degrees of past spruce budworm defoliation episodes. A secondary objective was to understand the responses of trees to defoliation episodes using carbon isotopes as a proxy to provide insights into subsequent physiological changes. Tree-ring widths, carbon and oxygen isotopic compositions in wood cellulose and gas exchange measurements were compared among 288 balsam fir (Abies balsamea Mill.) seedlings grown in a controlled experiment that involved different intensities of defoliation. Observations were performed over four growing periods. Moderate to heavy-defoliated seedlings showed reduced radial growth and enriched their cellulose carbon isotopic composition probably as a result of mobilized stored carbohydrates enriched in 13C. Less severely defoliated seedlings did not show significant reductions in growth and 13C enrichments. The gas exchange observations and wood cellulose oxygen isotope compositions do not suggest photosynthetic compensation in the remaining needles although a positive trend in the response of both assimilation rate (A) and stomatal conductance (gs) to defoliation was observed in the first growing period. Thus it remains open as to which mechanisms were employed to compensate for the reduced carbon source in the mildly defoliated seedlings. While further investigations are advised, the results of this study still help promote the utilization of tree-ring widths in combination with carbon isotopic compositions for reconstructing severe past defoliation events.

Hydrogen production properties of Rhodobacter capsulatus with genetically modified redox balancing pathways

Rhodobacter capsulatus produces molecular hydrogen under the photoheterotrophic growth condition with reduced carbon sources (organic acids). Under this condition, ubiquinol pool is over reduced and excess reducing equivalents are primarily consumed via the reduction of CO2 through the Calvin–Benson–Bassham (CBB) pathway, the dimethylsulfoxide reductase (DMSOR) system or by the reduction of protons into hydrogen gas with the use of nitrogenase to maintain a balanced intracellular oxidation-reduction potential (redox balance). In order to investigate the effect of redox balancing pathways on nitrogenase-dependent hydrogen production, CO2 fixation was blocked by inactivating the phosphoribulokinase (PRK) of CBB pathway in wild type (MT1131), uptake-hydrogenase deficient strain (YO3), and cyt cbb3 oxidase and uptake-hydrogenase deficient double mutant (YO4) strains. The hydrogen production properties of newly generated strains deficient in the CBB pathway were analyzed and compared with wild type strains. The obtained data indicated that, the total hydrogen production was increased slightly in CBB deficient mutant of YO3 and YO4 (4.7% and 12.5% respectively). Moreover, the maximum hydrogen production rate was increased by 13.3% and 12.7% for CBB deficient mutant of MT1131 and YO3 respectively. It was also observed that under the photoheterotrophic growth condition with ammonium as a nitrogen source, PRK deficient strains gave photoheterotrophically competent ammonium insensitive revertants.

Utilization Of Raw Glycerol From Biodiesel Industry For The Production Of Yeast Biomass and Secondary Metabolites

Raw glycerol is not only the main by product of biodiesel production but also a reduced carbon source that can be utilised for the preparation of fermentation broth and the cultivation of numerous yeast species of biotechnological interest such as Candida, Debariomyces, Kluyveromyces, Phaffia, Pichia, Rhodosporidium, Rhodotorula, Saccharomyces, Sporobolomyces, Torulaspora, Yarrowia . Some of these yeasts are able to produce citric acid (Papanikolaou et al., 2002), Single Cell Oils (Papanikolaou and Aggelis, 2002) Single Cell Proteins, superoxide dismutase (Dellomonaco et al., 2007) and biosurfactants (Morita et al., 2007) when grown on glycerol. However, at present little is known about the productivity of biotechnological processes based on raw glycerol as compared to other carbon sources commonly utilized. In this context, with the aim of increasing the sustainability of biodiesel production through the utilization of its main by product, we are investigating the possibility of utilizing raw glycerol for the industrial production of microbial biomass and secondary metabolites of interest in feed, food and pharmaceutical industries. To do that we are carrying out yeast batch fermentation trials on glycerol containing media under full aerobic condition and evaluating both biomass and secondary metabolites production. The results of the selection of yeast cultures able to efficiently utilize raw glycerol, in terms of biomass and secondary metabolites yields per time unit and per gram of glycerol utilized, and the individuation of the chemical-physical parameters able to enhance microbial growth in view of the maximization of the production will be presented.The present work is financially supported by Ministero delle Politiche Agricole Alimentari e Forestali (MIPAF).

Metabolic engineering to improve ethanol production in Thermoanaerobacter mathranii

Thermoanaerobacter mathranii can produce ethanol from lignocellulosic biomass at high temperatures, but its biotechnological exploitation will require metabolic engineering to increase its ethanol yield. With a cofactor-dependent ethanol production pathway in T. mathranii, it may become crucial to regenerate cofactor to increase the ethanol yield. Feeding the cells with a more reduced carbon source, such as mannitol, was shown to increase ethanol yield beyond that obtained with glucose and xylose. The ldh gene coding for lactate dehydrogenase was previously deleted from T. mathranii to eliminate an NADH oxidation pathway. To further facilitate NADH regeneration used for ethanol formation, a heterologous gene gldA encoding an NAD(+)-dependent glycerol dehydrogenase was expressed in T. mathranii. One of the resulting recombinant strains, T. mathranii BG1G1 (Deltaldh, P(xyl)GldA), showed increased ethanol yield in the presence of glycerol using xylose as a substrate. With an inactivated lactate pathway and expressed glycerol dehydrogenase activity, the metabolism of the cells was shifted toward the production of ethanol over acetate, hence restoring the redox balance. It was also shown that strain BG1G1 acquired the capability to utilize glycerol as an extra carbon source in the presence of xylose, and utilization of the more reduced substrate glycerol resulted in a higher ethanol yield.

Enhanced production of succinic acid by Actinobacillus succinogenes with reductive carbon source

Abstract Carbon sources with different oxidation states were used to investigate the possibility increasing the availability of NADH and the NADH/NAD + ratio and to determine the effect of this manipulation on the distribution of metabolites in Actinobacillus succinogenes NJ113. The sugars glucose, sorbitol and gluconate were each used at an initial concentration of 40 g/L. The yield of succinic acid (0.75) and the ratio of succinic acid to acetic acid (5.06) were both higher for sorbitol than the values obtained with glucose (0.66 and 2.68, respectively). In contrast, with gluconate as the carbon source the yield of succinic acid was 0.54 and the ratio of succinic acid to acetic acid was only 1.70. This work showed that different levels of NADH availability and the NADH/NAD + ratio can be achieved by using carbon sources that have different oxidation states. Highly reduced sorbitol was examined as a possible carbon substrate for maximizing the redox potential during the production of succinic acid.

Existence of periplasmic barriers preventing green fluorescent protein diffusion from cell to cell in the cyanobacterium Anabaena sp. strain PCC 7120

When deprived of combined nitrogen, the filamentous cyanobacterium Anabaena PCC 7120 relies on intercellular cooperation involving two cell types: nitrogen-fixing heterocysts and photosynthetic vegetative cells. Heterocysts send fixed nitrogen to vegetative cells over long distances along the filament, receiving a reduced carbon source from them. These intercellular exchanges might involve a continuous periplasm along the filament or cytoplasm-to-cytoplasm conduits or both. In the present study, the green fluorescent protein (GFP) was fused to a twin-arginine translocation signal sequence, which exported GFP to the periplasm of either a heterocyst using the heterocyst-specific promoters PhepA and PpatB or to the periplasm of vegetative cells using the vegetative cell-specific promoter PrbcL. Using the techniques of FRAP (fluorescence recovery after photobleaching) and FLIP (fluorescence loss in photobleaching), we found no evidence for intercellular diffusion of GFP through the periplasm, either from a heterocyst to vegetative cells or vice versa, or among vegetative cells. GFP could diffuse within the periplasm of the producing cell, but the diffusion stopped at the cell border. GFP diffusion could occur between two dividing cells before septum closure. This study indicates that barriers exist at the periplasmic space to prevent free GFP diffusion across cell border along the filament.

Optimization of the biological component of a bioelectrochemical cell

The efficiency of electron transduction by Shewanella oneidensis MR-1 was investigated both in batch culture and in a dual-chambered electrochemical cell. Aerobically grown bacteria were inoculated into an insoluble FeOOH suspension in an anaerobic environment. As the bacteria reduced Fe(III) to Fe(II) there was a visible color change from red to bluish black; this simple color change assay proved to be a robust method for determining the electrochemical activity of S. oneidensis MR-1. In an effort to improve electricity production by S. oneidensis MR-1, the performance of the electrochemical cell with lactate as a fuel was first optimized with respect to both poised potential and fuel concentration. Ultimately, electricity production proved to be proportional to both the poised potential and to fuel concentration. In particular, higher poised potentials increased charge production. Finally, we attempted to optimize the bacteria themselves for the efficient transduction of reduced carbon sources into electricity. The batch culture underwent a series of serial dilutions; after the 4th dilution the microbe population exhibited a 30% increase in charge production. We are further exploring whether this increase was due to metabolic adaptations or to genetic mutations, and examining additional ways to evolve electrogenic organisms.

Anaerobic fermentation of glycerol byEscherichia coli: A new platform for metabolic engineering

The worldwide surplus of glycerol generated as inevitable byproduct of biodiesel fuel and oleochemical production is resulting in the shutdown of traditional glycerol-producing/refining plants and new applications are needed for this now abundant carbon source. In this article we report our finding that Escherichia coli can ferment glycerol in a pH-dependent manner. We hypothesize that glycerol fermentation is linked to the availability of CO(2), which under acidic conditions is produced by the oxidation of formate by the enzyme formate hydrogen lyase (FHL). In agreement with this hypothesis, glycerol fermentation was severely impaired by blocking the activity of FHL. We demonstrated that, unlike CO(2), hydrogen (the other product of FHL-mediated formate oxidation) had a negative impact on cell growth and glycerol fermentation. In addition, supplementation of the medium with CO(2) partially restored the ability of an FHL-deficient strain to ferment glycerol. High pH resulted in low CO(2) generation (low activity of FHL) and availability (most CO(2) is converted to bicarbonate), and consequently very inefficient fermentation of glycerol. Most of the fermented glycerol was recovered in the reduced compounds ethanol and succinate (93% of the product mixture), which reflects the highly reduced state of glycerol and confirms the fermentative nature of this process. Since glycerol is a cheap, abundant, and highly reduced carbon source, our findings should enable the development of an E. coli-based platform for the anaerobic production of reduced chemicals from glycerol at yields higher than those obtained from common sugars, such as glucose.

Mechanistic Studies of Rhodobacter sphaeroides Me2SO Reductase

Studies of the molybdenum-containing dimethyl sulfoxide reductase from Rhodobacter sphaeroides have yielded new insight into its catalytic mechanism. A series of reductive titrations, performed over the pH range 6-10, reveal that the absorption spectrum of reduced enzyme is highly sensitive to pH. The reaction of reduced enzyme with dimethyl sulfoxide is found to be clearly biphasic throughout the pH range 6-8 with a fast, initial substrate-binding phase and substrate-concentration independent catalytic phase. The intermediate formed at the completion of the fast phase has the characteristic absorption spectrum of the established dimethyl sulfoxide-bound species. Quantitative reductive and oxidative titrations of the enzyme demonstrate that the molybdenum center takes up only two reducing equivalents, implying that the two pyranopterin equivalents of the molybdenum center are not formally redox active. Finally, the visible spectrum associated with the catalytically relevant "high-g split" Mo(V) species has been determined. Spectral deconvolution and EPR quantitation of enzyme-monitored turnover experiments with trimethylamine N-oxide as substrate reveal that no substrate-bound intermediate accumulates and that Mo(V) content remains near unity for the duration of the reaction. Similar experiments with dimethyl sulfoxide show that significant quantities of both the Mo(V) species and the dimethyl sulfoxide-bound complex accumulate during the course of reaction. Accumulation of the substrate-bound complex in the steady-state with dimethyl sulfoxide arises from partial reversal of the physiological reaction in which the accumulating product, dimethyl sulfide, reacts with oxidized enzyme to yield the substrate-bound intermediate, a process that significantly slows turnover.

NapF Is a Cytoplasmic Iron-Sulfur Protein Required for Fe-S Cluster Assembly in the Periplasmic Nitrate Reductase

The periplasmic nitrate reductase (Nap) is wide-spread in proteobacteria. NapA, the nitrate reductase catalytic subunit, contains a Mo-bisMGD cofactor and one [4Fe-4S] cluster. The nap gene clusters in many bacteria, including Rhodobacter sphaeroides DSM158, contain an napF gene, disruption of which drastically decreases both in vitro and in vivo nitrate reductase activities. In spite its importance in the Nap system, NapF has never been characterized biochemically, and its role remains unknown. The NapF protein has four polycysteine clusters that suggest that it is an iron-sulfur-containing protein. In the present study, a His(6)-tagged NapF protein was overproduced in Escherichia coli and purified anaerobically. The purified NapF protein was used to obtain polyclonal antibodies raised in rabbit, and cellular fractionation of R. sphaeroides followed by immunoprobing with anti-NapF antibodies revealed that the native NapF protein is located in the cytoplasm. This contrasts with the periplasmic location of the mature NapA. However, NapA could not be detected in an isogenic napF(-) strain of R. sphaeroides. The His(6)-tagged NapF protein displayed spectral properties indicative of Fe-S clusters, but these features were rapidly lost, suggesting cluster lability. However, reconstitution of the Fe-S centers into the apo-NapF protein was achieved in the presence of Azotobacter vinelandii cysteine desulfurase (NifS), and this allowed the recovery of nitrate reductase activity in NapA protein that had previously been treated with 2,2'-dipyridyl to remove the [4Fe-4S] cluster. This activity was not recovered in the absence of NapF. Taking into account the cytoplasmic localization of NapF, the presence of labile Fe-S clusters in the protein, the napF(-) strain phenotype, and the NapF-dependent reactivation of the 2,2'-dipyridyl-treated NapA, we propose a role for NapF in assembling the [4Fe-4S] center of the catalytic subunit NapA.

Fine root branch orders respond differentially to carbon source-sink manipulations in a longleaf pine forest.

Fine roots are a key component of carbon (C) flow and nitrogen (N) cycling in forest ecosystems. However, the complexity and heterogeneity of the fine root branching system have hampered the assessment and prediction of C and N dynamics at ecosystem scales. We examined how root morphology, biomass, and chemistry differed with root branch orders (1-5 with root tips classified as first order roots) and how different root orders responded to increased C sink strength (via N fertilization) and reduced carbon source strength (via canopy scorching) in a longleaf pine (Pinus palustris L.) ecosystem. With increasing root order, the diameter and length of individual roots increased, whereas the specific root length decreased. Total root biomass on an areal basis was similar among the first four orders but increased for the fifth order roots. Consequently, total root length and total root surface area decreased systematically with increasing root order. Fine root N and lignin concentrations decreased, while total non-structural carbohydrate (TNC) and cellulose concentrations increased with increasing root order. N addition and canopy disturbance did not alter root morphology, but they did influence root chemistry. N fertilization increased fine root N concentration and content per unit area in all five orders, while canopy scorching decreased root N concentration. Moreover, TNC concentration and content in fifth order roots were also reduced by canopy scorching. Our results indicate that the small, fragile, and more easily overlooked first and second order roots may be disproportionately important in ecosystem scale C and N fluxes due to their large proportions of fine root biomass, high N concentrations, relatively short lifespans, and potentially high decomposition rates.

Bacterial Growth Dynamics, Limiting Factors, and Community Diversity in a Proposed Geological Nuclear Waste Repository Environment

Microbiological growth parameters, including limiting factors, kinetics, and minimal cell densities were assessed for subsurface microbiological communities collected with rock from an area proposed for a nuclear waste repository at Yucca Mountain, Nevada. Phospholipid fatty acid analysis revealed that approximately 104–105 viable cells per gram of dry rock are extant, and water availability was shown to be the primary factor limiting microbial growth in situ. Phosphate and carbon limitation, however, also suppress final cell densities by at least one order of magnitude under saturated conditions. Despite these limiting factors, significant growth of aerobic chemoheterotrophic microorganisms was shown to occur in unconcentrated simulated groundwater with or without addition of a reduced carbon source (7 × 107 and 8 × 106 planktonic cells/mL, respectively), indicating that when water becomes available in the repository environment, microbial growth will ensue. Organisms that were isolated from stationary cultures grown from Yucca Mountain rock in concentrated and unconcentrated simulated groundwaters showed significant 16S rDNA sequence divergence from reference organisms. Different (but related) organisms were isolated from concentrated and unconcentrated groundwater-grown cultures. Generally, as experimental conditions approached those expected to be encountered in situ, the organisms isolated were more divergent from reference organisms. Organisms that were isolated have metabolic properties that could allow them to be active and grow within the repository environment if water availability is sufficient.

The effect of carbon sources and lactate dehydrogenase deletion on 1,2-propanediol production in Escherichia coli.

In previous studies, we showed that cofactor manipulations can potentially be used as a tool in metabolic engineering. In this study, sugars similar to glucose, that can feed into glycolysis and pyruvate production, but with different oxidation states, were used as substrates. This provided a simple way of testing the effect of manipulating the NADH/NAD+ ratio or the availability of NADH on the metabolic patterns of Escherichia coli under anaerobic conditions and on the production of 1,2-propanediol (1,2-PD), which requires NADH for its synthesis. Production of 1,2-PD was achieved by overexpressing the two enzymes methylglyoxal synthase from Clostridium acetobutylicum and glycerol dehydrogenase from E. coli. In addition, the effect of eliminating a pathway competing for NADH by using a ldh(-) strain (without lactate dehydrogenase activity) on the production of 1,2-PD was investigated. The oxidation state of the carbon source significantly affected the yield of metabolites, such as ethanol, acetate and lactate. However, feeding a more reduced carbon source did not increase the yield of 1,2-PD. The production of 1,2-PD with glucose as the carbon source was improved by the incorporation of a ldh(-) mutation. The results of these experiments indicate that our current 1,2-PD production system is not limited by NADH, but rather by the pathways following the formation of methylglyoxal.

Control of periplasmic nitrate reductase gene expression (napEDABC) from Paracoccus pantotrophus in response to oxygen and carbon substrates.

The napEDABC operon of Paracoccus pantotrophus encodes a periplasmic nitrate reductase (NAP), together with electron-transfer components and proteins required for the synthesis of a fully functional enzyme. Previously, it had been shown that high NAP activity was observed when P. pantotrophus was grown aerobically on highly reduced carbon sources such as butyrate or caproate, but not when cultured on more oxidized substrates such as succinate or malate. The enzyme is not present to any extent when the organism is grown anaerobically under denitrifying conditions, regardless of the carbon source. Transcriptional analyses of the nap operon have now identified two initiation sites which were differentially regulated in response to the carbon source, with expression being maximal when cells were grown aerobically with butyrate. Analysis of a P. pantotrophus mutant (M6) deregulated for NAP activity identified a single C-->A transversion in a heptameric inverted-repeat sequence that partially overlapped the proximal promoter. Transcription analysis of this mutant revealed that expression of nap was completely derepressed under all growth conditions examined. Taken together, these findings indicate that nap transcription is negatively regulated during anaerobiosis, such that expression is restricted to aerobic growth, but only when the carbon source is highly reduced.