Isomerization of n- and i-butyrate in anaerobic methanogenic systems

Production of a newly discovered PHA family member with an isobutyrate-fed enrichment culture

Abstract

Using microbial enrichment cultures for the production of waste-derived polyhydroxyalkanoates (PHAs) is a promising technology to recover secondary resources. Volatile fatty acids (VFAs) form the preferred substrate for PHA production. Isobutyrate is a VFA appearing in multiple waste valorization routes, such as anaerobic fermentation, chain elongation, and microbial electrosynthesis, but has never been assessed individually on its PHA production potential. This research investigates isobutyrate as sole carbon source for a microbial enrichment culture in comparison to its structural isomer butyrate. The results reveal that the enrichment of isobutyrate has a very distinct character regarding microbial community development, PHA productivity, and even PHA composition. Although butyrate is a superior substrate in almost every aspect, this research shows that isobutyrate-rich waste streams have a noteworthy PHA-producing potential. The main finding is that the dominant microorganism, a Comamonas sp., is linked to the production of a unique PHA family member, poly(3-hydroxyisobutyrate) (PHiB), up to 37% of the cell dry weight. This is the first scientific report identifying microbial PHiB production, demonstrating that mixed microbial communities can be a powerful tool for discovery of new metabolic pathways and new types of polymers.

Key points

• PHiB production is a successful storage strategy in an isobutyrate-fed SBR

• Isomers isobutyrate and butyrate reveal a very distinct PHA production behavior

• Enrichments can be a tool for discovery of new metabolic pathways and polymers

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11742-9.

Hydrogen as a Co-electron Donor for Chain Elongation With Complex Communities

Electron donor scarcity is seen as one of the major issues limiting economic production of medium-chain carboxylates from waste streams. Previous studies suggest that co-fermentation of hydrogen in microbial communities that realize chain elongation relieves this limitation. To better understand how hydrogen co-feeding can support chain elongation, we enriched three different microbial communities from anaerobic reactors (A, B, and C with ascending levels of diversity) for their ability to produce medium-chain carboxylates from conventional electron donors (lactate or ethanol) or from hydrogen. In the presence of abundant acetate and CO₂, the effects of different abiotic parameters (pH values in acidic to neutral range, initial acetate concentration, and presence of chemical methanogenesis inhibitors) were tested along with the enrichment. The presence of hydrogen facilitated production of butyrate by all communities and improved production of i-butyrate and caproate by the two most diverse communities (B and C), accompanied by consumption of acetate, hydrogen, and lactate/ethanol (when available). Under optimal conditions, hydrogen increased the selectivity of conventional electron donors to caproate from 0.23 ± 0.01 mol e^-/mol e^- to 0.67 ± 0.15 mol e^-/mol e^- with a peak caproate concentration of 4.0 g L^-1. As a trade-off, the best-performing communities also showed hydrogenotrophic methanogenesis activity by Methanobacterium even at high concentrations of undissociated acetic acid of 2.9 g L^-1 and at low pH of 4.8. According to 16S rRNA amplicon sequencing, the suspected caproate producers were assigned to the family Anaerovoracaceae (Peptostreptococcales) and the genera Megasphaera (99.8% similarity to M. elsdenii), Caproiciproducens, and Clostridium sensu stricto 12 (97-100% similarity to C. luticellarii). Non-methanogenic hydrogen consumption correlated to the abundance of Clostridium sensu stricto 12 taxa (p < 0.01). If a robust methanogenesis inhibition strategy can be found, hydrogen co-feeding along with conventional electron donors can greatly improve selectivity to caproate in complex communities. The lessons learned can help design continuous hydrogen-aided chain elongation bioprocesses.

Simplified Reactor Design for Mixed Culture-Based Electrofermentation toward Butyric Acid Production

Mixed microbial culture (MMC) electrofermentation (EF) represents a promising tool to drive metabolic pathways toward the production of a specific compound. Here, the MMC-EF process has been exploited to obtain butyric acid in simplified membrane-less reactors operated by applying a difference of potential between two low-cost graphite electrodes. Ten values of voltage difference, from −0.60 V to −1.5 V, have been tested and compared with the experiment under open circuit potential (OCP). In all the tested conditions, an enhancement in the production rate of butyric acid (from a synthetic mixture of glucose, acetate, and ethanol) was observed, ranging from 1.3- to 2.7-fold relative to the OCP. Smaller enhancements in the production rate resulted in higher values of the calculated specific energy consumption. However, at all applied voltages, a low flow of current was detected in the one-chamber reactors, accounting for an average value of approximately −100 µA. These results hold a substantial potential with respect to the scalability of the electrofermentation technology, since they pinpoint the possibility to control MMC-based bioprocesses by simply inserting polarized electrodes into traditional fermenters.

Open microbiome dominated by Clostridium and Eubacterium converts methanol into i-butyrate and n-butyrate

Isobutyrate (i-butyrate) is a versatile platform chemical, whose acid form is used as a precursor of plastic and emulsifier. It can be produced microbially either using genetically engineered organisms or via microbiomes, in the latter case starting from methanol and short-chain carboxylates. This opens the opportunity to produce i-butyrate from non-sterile feedstocks. Little is known on the ecology and process conditions leading to i-butyrate production. In this study, we steered i-butyrate production in a bioreactor fed with methanol and acetate under various conditions, achieving maximum i-butyrate productivity of 5.0 mM day^-1, with a concurrent production of n-butyrate of 7.9 mM day^-1. The production of i-butyrate was reversibly inhibited by methanogenic inhibitor 2-bromoethanesulfonate. The microbial community data revealed the co-dominance of two major OTUs during co-production of i-butyrate and n-butyrate in two distinctive phases throughout a period of 54 days and 28 days, respectively. The cross-comparison of product profile with microbial community composition suggests that the relative abundance of Clostridium sp. over Eubacterium sp. is correlated with i-butyrate productivity over n-butyrate productivity.

Branched Medium Chain Fatty Acids: Iso-Caproate Formation from Iso-Butyrate Broadens the Product Spectrum for Microbial Chain Elongation

Chain elongation fermentation can be used to convert organic residues into biobased chemicals. This research aimed to develop a bioprocess for branched medium chain fatty acids (MCFAs) production. A long-term continuous reactor experiment showed that iso-caproate (4-methyl pentanoate, i-C₆) can be produced via ethanol based chain elongation. The enriched microbiome formed iso-caproate from iso-butyrate at a rate of 44 ± 6 mmol C L^-1 day^-1 during the last phase. This amounted to 20% of all formed compounds based on carbon atoms. The main fermentation product was n-caproate (55% of all carbon), as a result of acetate and subsequent n-butyrate elongation. The microbiome preferred straight-chain elongation over branched-chain elongation. Lowering the acetate concentration in the influent led to an increase of excessive ethanol oxidation (EEO) into electron equivalents (e.g., H₂) and acetate. The formed acetate in turn stimulated straight chain elongation, but the resulting lower net acetate supply rate towards straight chain elongation led to an increased selectivity towards and productivity of i-C₆. The electrons produced via oxidation routes and chain elongation were apparently utilized by hydrogenotrophic methanogens, homoacetogens, and carboxylate-to-alcohol reducing bacteria. Further improvements could be achieved if the acetate-producing EEO was minimized and limitations of ethanol and CO₂ were prevented.

Intrinsic gas production kinetics of selected intermediates in anaerobic filters for demand-orientated energy supply

As a consequence of a growing share of solar and wind power, recent research on biogas production highlighted a need for demand-orientated, flexible gas production to provide grid services and enable a decentralized stabilization of the electricity infrastructure. Two-staged anaerobic digestion is particularly suitable for shifting the methane production into times of higher demand due to the spatio-temporal separation of hydrolysis and methanogenesis. To provide a basis for predicting gas production in an anaerobic filter, kinetic parameters of gas production have been determined experimentally in this study. A new methodology is used, enabling their determination during continuous operation. An order in methane production rate could be established by comparing the half lives of methane production. The order was beginning with the fastest: acetic acid>ethanol>butyric acid>iso-butyric acid>valeric acid>propionic acid>1,2propanediol>lactic acid. However, the mixture of a natural hydrolysate from the acidification tank appeared to produce methane faster than all single components tested.

Phase separation and microbial distribution in the hyperthermophilic-mesophilic-type temperature-phased anaerobic digestion (TPAD) of waste activated sludge (WAS)

In order to investigate the phase separation and microbial distribution in the TPAD, the conventional thermophilic-mesophilic type (TM-TPAD) and the hyperthermophilic-mesophilic type (HM-TPAD) were operated with a single-stage mesophilic anaerobic digestion (MAD) as control. HM-TPAD accomplished the volatile solids destruction 14.5% higher than MAD. Calculating conversion efficiencies distinguished the separation of acidogenic and methanogenic phases in HM-TPAD, which was not found in TM-TPAD. The differences on microbial distributions also reflected the phase separation in HM-TPAD. The protein degraders, Coprothermobacter had higher abundance in the first stage than the second stage of HM-TPAD but it had similar abundance between the two stages of TM-TPAD. Also, the archaeal communities from the two stages of HM-TPAD shared the least similarity but those from the two stages of TM-TPAD were closely similar.

Control of hydrogen partial pressures on the rates of syntrophic microbial metabolisms: a kinetic model for butyrate fermentation

A new model describing the rate of syntrophic butyrate fermentation is constructed based on a thermodynamically consistent rate law and the metabolic pathway. This model takes into account the mechanism of reverse electron transfer and proposes that the net amount of energy saved by microorganisms as ATP depends on hydrogen partial pressures in the environment. Hydrogen partial pressures thus control not only the energy available in the environment but also the energy conserved by microorganisms. This new model predicts the rates of butyrate fermentation as a product of a kinetic factor and a thermodynamic potential factor: the kinetic factor describes how butyrate concentration controls the rates; the thermodynamic factor accounts for how the thermodynamic driving force controls the rates. Increases in hydrogen partial pressures decrease the energy available, lowering the driving force and fermentation rates. To maintain butyrate fermentation at significant rates, microorganisms decrease the amount of energy conserved, maximizing the driving force. Application of the new model demonstrates that the thermodynamic driving force is a dominant factor in controlling the rates of butyrate fermentation.

Kinetics of thermophilic, anaerobic oxidation of straight and branched chain butyrate and valerate

The degradation kinetics of normal and branched chain butyrate and valerate are important in protein-fed anaerobic systems, as a number of amino acids degrade to these organic acids. Including activated and primary wastewater sludge digesters, the majority of full-scale systems digest feeds with a significant or major fraction of COD as protein. This study assesses the validity of using a common kinetic parameter set and biological catalyst to represent butyrate, n-valerate, and i-valerate degradation in dynamic models. The i-valerate degradation stoichiometry in a continuous, mixed population system is also addressed, extending previous pure-culture and batch studies. A previously published mathematical model was modified to allow competitive uptake of i-valerate, and used to model a thermophilic manure digester operated over 180 days. The digester was periodically pulsed with straight and branched chain butyrate and valerate. Parameters were separately optimized to describe butyrate, i-valerate, and n-valerate degradation, as well as a lumped set optimized for all three substrates, and nonlinear, correlated parameter spaces estimated using an F distribution in the objective function (J). Each parameter set occupied mutually exclusive parameter spaces, indicating that all were statistically different from each other. However, qualitatively, the influence on model outputs was similar, and the lumped set would be reasonable for mixed acid digestion. The main characteristic not represented by Monod kinetics was a delay in i-valerate uptake, and was compensated for by a decreased maximum uptake rate (k(m)). Therefore, the kinetics need modification if fed predominantly i-valerate. Butyrate (i- and n-) and n-valerate could be modeled using stoichiometry consistent with beta-oxidation degradation pathways. However, i-valerate produced acetate only, supporting the stoichiometry of a reaction determined by other researchers in pure culture. Therefore, lumping i-valerate stoichiometry with that of n-valerate will not allow good system representation, especially when the feed consists of proteins high in leucine (which produces i-valerate), and the modified model structure and stoichiometry as proposed here should be used. This requires no additional kinetic parameters and one additional dynamic concentration state variable (i-valerate) in addition to the variables in the base model.

Perspectives for anaerobic digestion

The modern society generates large amounts of waste that represent a tremendous threat to the environment and human and animal health. To prevent and control this, a range of different waste treatment and disposal methods are used. The choice of method must always be based on maximum safety, minimum environmental impact and, as far as possible, on valorization of the waste and final recycling of the end products. One of the main trends of today's waste management policies is to reduce the stream of waste going to landfills and to recycle the organic material and the plant nutrients back to the soil. Anaerobic digestion (AD) is one way of achieving this goal and it will furthermore, reduce energy consumption or may even be net energy producing. This chapter aims at provide a basic understanding of the world in which anaerobic digestion is operating today. The newest process developments as well as future perspectives will be discussed.

Monitoring and control of anaerobic reactors

The current status in monitoring and control of anaerobic reactors is reviewed. The influence of reactor design and waste composition on the possible monitoring and control schemes is examined. After defining the overall control structure, and possible control objectives, the possible process measurements are reviewed in detail. In the sequel, possible manipulated variables, such as the hydraulic retention time, the organic loading rate, the sludge retention time, temperature, pH and alkalinity are evaluated with respect to the two main reactor types: high-rate and low-rate. Finally, the different control approaches that have been used are comprehensively described. These include simple and adaptive controllers, as well as more recent developments such as fuzzy controllers, knowledge-based controllers and controllers based on neural networks.

Scale-up of anaerobic digestion of the biowaste fraction from domestic wastes

In the City of Karlsruhe/Germany anaerobic digestion of 7200 ta(-1) of separately collected biowaste has proven its feasibility at an organic loading rate (OLR) of up to 8.5 kg CODm(-3)d(-1). An extension of biowaste collection over the whole city area would increase the amount of biowaste to 12,000 ta(-1), leading to an OLR of the existing anaerobic reactor of up to 15 kg CODm(-3)d(-1). To test, whether the increased amount of biowaste could be stabilized in the existing plant, biowaste suspensions were digested in a laboratory reactor at a maximum OLR, that exceeded the future OLR of the full-scale plant. The laboratory reactor was started with effluent of the full-scale biowaste digester. Like in full-scale, biowaste suspension from the hydropulper was added in a fed-batch mode. The elimination of organic material (measured as COD, chemical oxygen demand) and the volumetric gas production were linearly increasing with the OLR from 4.3 to 19 kg CODm(-3)d(-1). Thus, safe operation of the full-scale plant at an OLR of 15 kg CODm(-3)d(-1) should be possible, leaving still some reserve capacity. To determine the metabolic reserves for fatty acid degradation during digestion at an OLR of 10 kg CODm(-3)d(-1), digester effluent was supplemented with either 40 mmoll(-1) acetate, propionate, i-butyrate or n-butyrate. Results of these batch assays indicated a rapid degradation of all fatty acids and fatty acid conversion rates, that would allow a stable anaerobic fermentation at 15 kg CODm(-3)d(-1)OLR. On the basis of the laboratory results the OLR of the full-scale methane reactor was increased to 15 kg CODm(-3)d(-1). After 7 months, results of full-scale digestion were still consistent with the previously obtained laboratory results.