Syntrophic propionate-oxidizing bacteria in methanogenic systems

The mutual nutritional cooperation underpinning syntrophic propionate degradation provides a scant amount of energy for the microorganisms involved, so propionate degradation often acts as a bottleneck in methanogenic systems. Understanding the ecology, physiology, and metabolic capacities of syntrophic propionate-oxidizing bacteria is of interest in both engineered and natural ecosystems, as it offers prospects to guide further development of technologies for biogas production and biomass-derived chemicals, and is important in forecasting contributions by biogenic methane emissions to climate change. Syntrophic propionate-oxidizing bacteria are distributed across different phyla. They can exhibit broad metabolic capabilities in addition to syntrophy (e.g. fermentative, sulfidogenic, and acetogenic metabolism) and demonstrate variations in interplay with cooperating partners, indicating nuances in their syntrophic lifestyle. In this review, we discuss distinctions in gene repertoire and organization for the methylmalonyl-CoA pathway, hydrogenases and formate dehydrogenases, and emerging facets of (formate/hydrogen/direct) electron transfer mechanisms. We also use information from cultivations, thermodynamic calculations, and omic analyses as the basis for identifying environmental conditions governing propionate oxidation in various ecosystems. Overall, this review improves basic and applied understanding of syntrophic propionate-oxidizing bacteria and highlights knowledge gaps, hopefully encouraging future research and engineering on propionate metabolism in biotechnological processes.

1-13C-propionate breath testing as a surrogate endpoint to assess efficacy of liver-directed therapies in methylmalonic acidemia (MMA)

Purpose To develop a safe and noninvasive in vivo assay of hepatic propionate oxidative capacity. Methods A modified 1-13C-propionate breath test was administered to 57 methylmalonic acidemia (MMA) subjects, including 19 transplant recipients, and 16 healthy volunteers. Isotopomer enrichment (13CO2/12CO2) was measured in exhaled breath after an enteral bolus of sodium-1-13C-propionate, and normalized for CO2 production. 1-13C-propionate oxidation was then correlated with clinical, laboratory, and imaging parameters collected via a dedicated natural history protocol. Results Lower propionate oxidation was observed in patients with the severe mut0 and cblB subtypes of MMA, but was near normal in those with the cblA and mut− forms of the disorder. Liver transplant recipients demonstrated complete restoration of 1-13C-propionate oxidation to control levels. 1-13C-propionate oxidation correlated with cognitive test result, growth indices, bone mineral density, renal function, and serum biomarkers. Test repeatability was robust in controls and in MMA subjects (mean coefficient of variation 6.9% and 12.8%, respectively), despite widely variable serum methylmalonic acid concentrations in the patients. Conclusion Propionate oxidative capacity, as measured with 1-13C-propionate breath testing, predicts disease severity and clinical outcomes, and could be used to assess the therapeutic effects of liver-targeted genomic therapies for MMA and related disorders of propionate metabolism. TRIAL REGISTRATION This clinical study is registered in www.clinicaltrials.gov with the ID: NCT00078078. Study URL: http://clinicaltrials.gov/ct2/show/NCT00078078

Comprehensive Bioenergetic Evaluation of Microbial Pathway Variants in Syntrophic Propionate Oxidation

ABSTRACT In this work, a systematic methodology was developed (based on known biochemistry, physiology, and bioenergetics) for the automated feasibility evaluation and net ATP yield quantification of large sets of pathway variants. Possible pathway variants differ in their intermediate metabolites, in which electron carriers are involved, in which steps are consuming/producing ATP, and in which steps are coupled to (and to how many) proton (or its equivalent) translocations. A pathway variant is deemed feasible, under a given set of physiological and environmental conditions, only if all pathway reaction steps have nonpositive Gibbs energy changes and if all the metabolite concentrations remain within an acceptable physiological range (10−6 to 10−2 M). The complete understanding of syntrophic propionate oxidation remains elusive due to uncertainties in pathways and the mechanisms for interspecies electron transfer (IET). Several million combinations of pathway variants and parameters/conditions were evaluated for propionate oxidation, providing unprecedented mechanistic insight into its biochemical and bioenergetic landscape. Our results show that, under a scenario of optimum environmental conditions for propionate oxidation, the Smithella pathway yields the most ATP and the methylmalonyl-coenzyme A (CoA) pathways can generate sufficient ATP for growth only under a cyclical pathway configuration with pyruvate. The results under conditions typical of methanogenic environments show that propionate oxidation via the lactate and via the hydroxypropionyl-CoA pathways yield the most ATP. IET between propionate oxidizers and methanogens can proceed either by dissolved hydrogen via the Smithella pathway or by different mechanisms (e.g., formate or direct IET) if other pathways are used. IMPORTANCE In this work, an original methodology was developed that quantifies bioenergetically and physiologically feasible net ATP yields for large numbers of microbial metabolic pathways and their variants under different conditions. All variants are evaluated, which ensures global optimality in finding the pathway variant(s) leading to the highest ATP yield. The methodology is designed to be especially relevant to hypothesize on which microbial pathway variants should be most favored in microbial ecosystems under high selective pressure for efficient metabolic energy conservation. Syntrophic microbial oxidation of propionate to acetate has an extremely small quantity of available energy and requires an extremely high metabolic efficiency to sustain life. Our results bring mechanistic insights into the optimum pathway variants, other metabolic bottlenecks, and the impact of environmental conditions on the ATP yields. Additionally, our results conclude that, as previously reported, under specific conditions, IET mechanisms other than hydrogen must exist to simultaneously sustain the growth of both propionate oxidizers and hydrogenotrophic methanogens.

Optimal microbial pathway variants can be determined by large-scale bioenergetic evaluation in syntrophic propionate oxidation

The complete understanding of microbial propionate oxidation in syntrophy with hydrogenotrophic methanogenesis remains elusive due to uncertainties in pathways and mechanisms for interspecies electron transfer (IET). Possible pathway variants differ in their intermediate metabolites, on which electron carriers are involved and in which steps are coupled to (and to how many) proton translocations. In this work, a systematic methodology was developed (based on sound biochemical, physiological and bioenergetic principles) to evaluate the feasibility and net ATP yield of large sets of pathway variants under different physiological and environmental conditions. A pathway variant is deemed feasible under given conditions only if all pathway reaction steps have non-positive Gibbs energy change and if all the metabolite concentrations remain within an acceptable physiological range (10−6 to 10−2 M). Several million combinations of pathway variants and parameters/conditions were evaluated for propionate oxidation, providing an unprecedented mechanistic insight into its biochemical and bioenergetic landscape. Propionate oxidation via lactate appeared as the most ATP yielding pathway under most of the conditions evaluated. Results under typical methanogenic conditions indicate that syntrophic propionate oxidation can sustain life only at hydrogen partial pressures within the range of 1.2 to 4 Pa. These extremely low concentrations constitute a kinetic impossibility and strongly suggest for IET mechanisms other than dissolved hydrogen.ImportanceIn this work an original methodology was developed that quantifies the bioenergetically and physiologically feasible net ATP yields for large numbers of microbial metabolic pathways and their variants under different conditions. This ensures global optimality in finding the pathway variant(s) leading to the highest ATP yield. The methodology is especially relevant to hypothesise which microbial pathway variants are most likely to prevail in microbial ecosystems under high selective pressure for efficient metabolic energy conservation.Syntrophic microbial oxidation of propionate to acetate has extremely low energy available and requires very high metabolic efficiency in order to sustain life. Our results bring mechanistic insights into the optimum pathway variants and the impact of environmental conditions on the ATP yields and other metabolic bottlenecks. Additionally, our results conclude that IET mechanisms other than hydrogen must exist to simultaneously sustain the growth of both propionate oxidisers and hydrogenotrophic methanogens.

Integration of bioenergetics in the ADM1 and its impact on model predictions

In this work, the integration of dynamic bioenergetic calculations in the IWA Anaerobic Digestion Model No. 1 (ADM1) is presented. The impact of bioenergetics on kinetics was addressed via two different approaches: a thermodynamic-based inhibition function and variable microbial growth yields based on dynamic Gibbs free energy calculations. The dynamic bioenergetic calculations indicate that the standard ADM1 predicts positive reaction rates under thermodynamically unfeasible conditions. The dissolved hydrogen inhibition approach used in ADM1 is, however, deemed as adequate, offering the trade-off of not requiring dynamic bioenergetics computation despite the need of hydrogen inhibition parameters. Simulations of the model with bioenergetics showed the low amount of energy available in butyrate and propionate oxidation, suggesting that microbial growth on these substrates must be very limited or occur via alternative mechanisms rather than dissolved hydrogen.