Determination of the carbon-bound electron composition of microbial cells and metabolites by dichromate oxidation

Strain and model development for auto- and heterotrophic 2,3-butanediol production using Cupriavidus necator H16

The production of platform chemicals from renewable energy sources is a crucial step towards a post-fossil economy. This study reports on the production of acetoin and 2,3-butanediol heterotrophically with fructose as substrate and autotrophically from CO2 as carbon source, H2 as electron donor and O2 as electron acceptor with Cupriavidus necator. In a previous study, the strain was developed for the production of acetoin with high carbon efficiency. Acetoin can serve as a precursor for the synthesis of 2,3-butanediol by the integration of a butanediol dehydrogenase. In this study, different plasmid backbones and butanediol dehydrogenases were evaluated regarding efficiency for CO2-based 2,3-butanediol production. The developed strain utilizes the pBBR1 plasmid bearing a 2,3-butanediol dehydrogenase from Enterobacter cloacae and is characterized by 2,3-butanediol as the main product and a heterotrophic total product yield of 88.11%, an autotrophic volumetric productivity of 39.45 mg L-1 h-1, a total product carbon yield of 81.6%, an H2 efficiency of 33.46%, and a specific productivity of 0.016 g product per gram of biomass per hour. In addition, a mathematical model was developed to simulate the processes under these conditions. With this model, it was possible to calculate productivities and substrate usage at distinct time points of the production processes and calculate productivities and substrate usage with high resolution which will be useful in future applications.

Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum

Clostridium thermocellum rapidly deconstructs cellulose and ferments resulting hydrolysis products into ethanol and other products, and is thus a promising platform organism for the development of cellulosic biofuel production via consolidated bioprocessing. While recent metabolic engineering strategies have targeted eliminating canonical fermentation products (acetate, lactate, formate, and H₂), C. thermocellum also secretes amino acids, which has limited ethanol yields in engineered strains to approximately 70% of the theoretical maximum. To investigate approaches to decrease amino acid secretion, we attempted to reduce ammonium assimilation by deleting the Type I glutamine synthetase (glnA) in an essentially wild type strain of C. thermocellum. Deletion of glnA reduced levels of secreted valine and total amino acids by 53% and 44% respectively, and increased ethanol yields by 53%. RNA-seq analysis revealed that genes encoding the RNF-complex were more highly expressed in ΔglnA and may have a role in improving NADH-availability for ethanol production. While a significant up-regulation of genes involved in nitrogen assimilation and urea uptake suggested that deletion of glnA induces a nitrogen starvation response, metabolomic analysis showed an increase in intracellular glutamine levels indicative of nitrogen-rich conditions. We propose that deletion of glnA causes deregulation of nitrogen metabolism, leading to overexpression of nitrogen metabolism genes and, in turn, elevated glutamine levels. Here we demonstrate that perturbation of nitrogen assimilation is a promising strategy to redirect flux from the production of nitrogenous compounds toward biofuels in C. thermocellum.

Elimination of formate production in Clostridium thermocellum

The ability of Clostridium thermocellum to rapidly degrade cellulose and ferment resulting hydrolysis products into ethanol makes it a promising platform organism for cellulosic biofuel production via consolidated bioprocessing. Currently, however, ethanol yield is far below theoretical maximum due to branched product pathways that divert carbon and electrons towards formate, H₂, lactate, acetate, and secreted amino acids. To redirect carbon and electron flux away from formate, genes encoding pyruvate:formate lyase (pflB) and PFL-activating enzyme (pflA) were deleted. Formate production in the resulting Δpfl strain was eliminated and acetate production decreased by 50 % on both complex and defined medium. The growth rate of the Δpfl strain decreased by 2.9-fold on defined medium and biphasic growth was observed on complex medium. Supplementation of defined medium with 2 mM formate restored Δpfl growth rate to 80 % of the parent strain. The role of pfl in metabolic engineering strategies and C₁ metabolism is discussed.

Nitrogen and sulfur requirements for Clostridium thermocellum and Caldicellulosiruptor bescii on cellulosic substrates in minimal nutrient media

Growth media for cellulolytic Clostridium thermocellum ATCC 27405 and Caldicellulosiruptor bescii bacteria usually contain excess nutrients that would increase costs for consolidated bioprocessing for biofuel production and create a waste stream with nitrogen, sulfur and phosphate. C. thermocellum was grown on crystalline cellulose with varying concentrations of nitrogen and sulfur compounds, and growth rate and ethanol production response curves were determined. Both bacteria assimilated sulfate in the presence of ascorbate reductant, increasing the ratio of oxidized to reduced fermentation products. From these results, a low ionic strength, defined minimal nutrient medium with decreased nitrogen, sulfur, phosphate and vitamin supplements was developed for the fermentation of cellobiose, cellulose and acid-pretreated Populus. Carbon and electron balance calculations indicate the unidentified residual fermentation products must include highly reduced molecules. Both bacterial populations were maintained in co-cultures with substrates containing cellulose and xylan in defined medium with sulfate and basal vitamin supplements.

Microbial ecophysiology of whey biomethanation: characterization of bacterial trophic populations and prevalent species in continuous culture

The organization and species composition of bacterial trophic groups associated with lactose biomethanation were investigated in a whey-processing chemostat by enumeration, isolation, and general characterization studies. The bacteria were spatially organized as free-living forms and as self-immobilized forms appearing in flocs. Three dominant bacterial trophic group populations were present (in most probable number per milliliter) whose species numbers varied with the substrate consumed: hydrolytic, 10; acetogenic, 10 to 10; and methanogenic, 10 to 10. The three prevalent species utilizing lactose were identified as Leuconostoc mesenteroides, Klebsiella oxytoca, and Clostridium butyricum. Clostridium propionicum and Desulfovibrio vulgaris were the dominant lactate-consuming, hydrogen-producing acetogenic bacteria, while D. vulgaris was the only significant ethanol-degrading species. Methanosarcina barkeri and Methanothrix soehngenii were identified as the dominant acetate-utilizing methanogens, and Methanobacterium formicicum was the prevalent hydrogen-utilizing methanogen. A microbial food chain is proposed for lactose biomethanation that comprises multiple species in three different groups, with the major hydrogen-producing acetogen being a sulfate-reducing species, D. vulgaris, which functioned in the absence of significant levels of environmental sulfate.

Microbial ecophysiology of whey biomethanation: intermediary metabolism of lactose degradation in continuous culture

The intermediary carbon and electron flow routes for lactose degradation during whey biomethanation were studied in continuous culture. The chemostat was operated under lactose-limited conditions with a 100-h retention time. The carbon balance observed for lactose degradation was 4.65 mmol of CH(4), 4.36 mmol of CO(2) and 1.15 mmol of cellular carbon per mmol of lactose consumed, with other intermediary metabolites (i.e., acetate, lactate, etc.) accounting for less than 2% of the lactose consumed. The carbon and electron recoveries for this biomethanation were 87 and 90%, respectively. C tracer studies demonstrated that lactose biomethanation occurred in three distinct but simultaneous phases. Lactose was metabolized primarily into lactate, ethanol, acetate, formate, and carbon dioxide. During this hydrolytic phase, 82% of the lactose was transformed into lactate. These metabolites were transformed into acetate and H(2)-CO(2) in a second, acetogenic, phase. Finally, the direct methane precursors were transformed during the methanogenic phase, with acetate accounting for 81% of the methane formed. A general scheme is proposed for the exact carbon and electron flow route during lactose biomethanation, which predicts the prevalent microbial populations in this ecosystem.

Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

Background

Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors.

Results

qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited.

Conclusions

The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.

Anaerobic digestion of microalgae as a necessary step to make microalgal biodiesel sustainable

The potential of microalgae as a source of biofuels and as a technological solution for CO2 fixation is subject to intense academic and industrial research. In the perspective of setting up massive cultures, the management of large quantities of residual biomass and the high amounts of fertilizers must be considered. Anaerobic digestion is a key process that can solve this waste issue as well as the economical and energetic balance of such a promising technology. Indeed, the conversion of algal biomass after lipid extraction into methane is a process that can recover more energy than the energy from the cell lipids. Three main bottlenecks are identified to digest microalgae. First, the biodegradability of microalgae can be low depending on both the biochemical composition and the nature of the cell wall. Then, the high cellular protein content results in ammonia release which can lead to potential toxicity. Finally, the presence of sodium for marine species can also affect the digester performance. Physico-chemical pretreatment, co-digestion, or control of gross composition are strategies that can significantly and efficiently increase the conversion yield of the algal organic matter into methane. When the cell lipid content does not exceed 40%, anaerobic digestion of the whole biomass appears to be the optimal strategy on an energy balance basis, for the energetic recovery of cell biomass. Lastly, the ability of these CO2 consuming microalgae to purify biogas and concentrate methane is discussed.

Extracellular iron reduction is mediated in part by neutral red and hydrogenase in Escherichia coli

Both microbial iron reduction and microbial reduction of anodes in fuel cells can occur by way of soluble electron mediators. To test whether neutral red (NR) mediates iron reduction, as it does anode reduction, by Escherichia coli, ferrous iron levels were monitored in anaerobic cultures grown with amorphous iron oxide. Ferrous iron levels were 19.4 times higher in cultures fermenting pyruvate in the presence of NR than in the absence of NR. NR did not stimulate iron reduction in cultures respiring with nitrate. To explore the mechanism of NR-mediated iron reduction, cell extracts of E. coli were used. Cell extract-NADH-NR mixtures had an enzymatic iron reduction rate almost 15-fold higher than the chemical NR-mediated iron reduction rate observed in controls with no cell extract. Hydrogen was consumed during stationary phase (in which iron reduction was detectable) especially in cultures containing both NR and iron oxide. An E. coli hypE mutant, with no hydrogenase activity, was also impaired in NR-mediated iron reduction activity. NR-mediated iron reduction rates by cell extracts were 1.5 to 2 times higher with hydrogen or formate as the electron source than with NADH. Our findings suggest that hydrogenase donates electrons to NR for extracellular iron reduction. This process appears to be analogous to those of iron reduction by bacteria that use soluble electron mediators (e.g., humic acids and 2,6-anthraquinone disulfonate) and of anode reduction by bacteria using soluble mediators (e.g., NR and thionin) in microbial fuel cells.

Growth kinetics of Acetobacterium sp. on methanol-formate in continuous culture

The fermentative metabolism of Acetobacterium sp. grown on methanol-formate in continuous culture is described. The reaction stoichiometry of methanol-formate, including cells, were as follows: CH3OH + 1.13HCOOH --> 0.87CH3COOH + 0.47 cell C. Formate enhanced growth yields by approximately 60% compared with methanol-CO2-grown cultures. Comparison of yields on methanol-formate allowed calculation of an energy yield of 1.3 mol ATP per mol acetate formed during homoacetate fermentation. The magnitudes of YEG,the theoretical maximum yield of YE, and m, the maintenance coefficient, were determined by growing the organism in methanol-formate and resulted in 16.5 g cell (mol methanol catabolized)-1 and 0.674 mmol methanol catabolized (g cell)-1 h-1, respectively. It is concluded that formate might replace CO2 as a source of carboxyl donor.

Degradation of refinery products and oils from polluted sites by the autochthonous microorganisms of contaminated and pristine soils

The degradation of five refinery products with different boiling ranges and four mineral oils extracted from long-term contaminated soils was monitored by measuring oxygen consumption and the concentration of the total hydrocarbons. Degradation was catalyzed by the isolated communities of the microorganisms from contaminated and pristine soils in an aqueous medium, and partly also directly in the soils. Degradation exceeding 95% was achieved for diesel fuel and spindle oil. The higher-boiling raffinates and the extracts of long-term contaminated soils were degraded by 40-60%. The extracted oils have higher boiling ranges and are therefore more difficult to degrade. Moreover, the progressive enrichment of persistent (including lower-boiling) hydrocarbons decreases the degree of degradation attainable of such aged oils. Whereas in the medium term the autochthonous microorganisms of the contaminated soils showed better degradation efficiency, in the long term the populations of the natural soils caught up with them. This may be due to a sociological adaptation process.

Comparison between geochemical and biological estimates of subsurface microbial activities

Geochemical and biological estimates of in situ microbial activities were compared from the aerobic and microaerophilic sediments of the Atlantic Coastal Plain. Radioisotope time-course experiments suggested oxidation rates greater than millimolar quantities per year for acetate and glucose. Geochemical analyses assessing oxygen consumption, soluble organic carbon utilization, sulfate reduction, and carbon dioxide production suggested organic oxidation rates of nano- to micromolar quantities per year. Radiotracer timecourse experiments appeared to overestimate rates of organic carbon oxidation, sulfate reduction, and biomass production by a factor of 10(3)-10(6) greater than estimates calculated from groundwater analyses. Based on the geochemical evidence, in situ microbial metabolism was estimated to be in the nano- to micromolar range per year, and the average doubling time for the microbial community was estimated to be centuries.

Biochemical and physiological characterization of the efrotomycin fermentation

An efrotomycin fermentation was characterized through physical, chemical and biochemical studies. Growth of the actinomycete, Nocardia lactamdurans occurred during the first 50 h of the fermentation cycle at the expense of glucose, protein, and triglycerides. The initiation of efrotomycin biosynthesis was observed when glucose dropped to a low concentration. Upon glucose depletion, cell growth ceased and a switch in the respiratory quotient occurred. Efrotomycin biosynthesis was supported by the utilization of soybean oil and starch. Analysis of triglyceride metabolism showed that no diglycerides or monoglycerides accumulated during the fermentation. The activity of extracellular enzymes (lipase, protease, and amylase) increased during the cell growth phase and decreased significantly after 150 h. The concentrations of DNA, tetrahydro-vitamin K2 (a membrane component), and free amino acids in the supernatant increased dramatically late in the fermentation cycle (225 h), indicating massive cell lysis. During this same time period, a reduction in cellular respiratory activity and efrotomycin biosynthesis were observed.

Carbon monoxide metabolism of the methylotrophic acidogen Butyribacterium methylotrophicum

The Marburg strain of Butyribacterium methylotrophicum did not grow on CO alone but did consume CO during growth on a variety of substrates in the presence of a 100% CO gas phase. We selected a strain (the CO strain) that grew vigorously on CO alone. The ability of the CO strain to grow on CO was stable through multiple transfers in the absence of CO. CO dehydrogenase activity was lower in the CO strain grown on CO (13.3 micromol/min per mg of protein) than in the Marburg strain grown on methanol-acetate (47.2 mumol/min per mg of protein); thus, the levels of this enzyme did not explain the growth on CO. CO was dissimilated to acetate and CO2 with the following stoichiometry: 4 CO leads to 2.17 CO2 + 0.74 acetate. We observed a growth rate of 0.05 h-1, a final optical density at 660 nm of 0.8, and a cell yield of 3.0 g of cells per mol of CO during growth of the CO strain. Growing cultures of the CO strain displayed a Ks for CO of 28 to 56 microM. The apparent thermodynamic efficiency of cell synthesis from CO was 57%. Energetic and biochemical aspects of CO metabolism are described.